def main(command_line=True, **kwargs):
"""
NAME
_2g_bin_magic.py
DESCRIPTION
takes the binary 2g format magnetometer files and converts them to magic_measurements, er_samples.txt and er_sites.txt file
SYNTAX
2g_bin_magic.py [command line options]
OPTIONS
-f FILE: specify input 2g (binary) file
-F FILE: specify magic_measurements output file, default is: magic_measurements.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-Fsi FILE: specify output file, default is: er_sites.txt
-ncn NCON: specify naming convention: default is #2 below
-ocn OCON: specify orientation convention, default is #5 below
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-ASC an ASC orientation device was used
SO-MAG orientation with magnetic compass
SO-SUN orientation with sun compass
-loc: location name, default="unknown"
-spc NUM : specify number of characters to designate a specimen, default = 0
-ins INST : specify instsrument name
-a: average replicate measurements
INPUT FORMAT
Input files are horrible mag binary format (who knows why?)
Orientation convention:
[1] Lab arrow azimuth= mag_azimuth; Lab arrow dip=-field_dip
i.e., field_dip is degrees from vertical down - the hade [default]
[2] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = -field_dip
i.e., mag_azimuth is strike and field_dip is hade
[3] Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
i.e., lab arrow same as field arrow, but field_dip was a hade.
[4] lab azimuth and dip are same as mag_azimuth, field_dip
[5] lab azimuth is same as mag_azimuth,lab arrow dip=field_dip-90
[6] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = 90-field_dip
[7] all others you will have to either customize your
self or e-mail [email protected] for help.
Magnetic declination convention:
Az will use supplied declination to correct azimuth
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
OUTPUT
output saved in magic_measurements.txt & er_samples.txt formatted files
will overwrite any existing files
"""
#
# initialize variables
#
mag_file = ''
specnum = 0
ub_file, samp_file, or_con, corr, meas_file = "", "er_samples.txt", "3", "1", "magic_measurements.txt"
pos_file, site_file = "", "er_sites.txt"
noave = 1
args = sys.argv
bed_dip, bed_dip_dir = "", ""
samp_con, Z, average_bedding = "2", 1, "0"
meths = 'FS-FD'
sclass, lithology, _type = "", "", ""
user, inst = "", ""
DecCorr = 0.
location_name = "unknown"
months = [
'Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct',
'Nov', 'Dec'
]
gmeths = ""
#
#
dir_path = '.'
if command_line:
if '-WD' in args:
ind = args.index("-WD")
dir_path = sys.argv[ind + 1]
if "-h" in args:
print(main.__doc__)
return False
if "-f" in args:
ind = args.index("-f")
mag_file = sys.argv[ind + 1]
if "-fpos" in args:
ind = args.index("-fpos")
pos_file = sys.argv[ind + 1]
if "-F" in args:
ind = args.index("-F")
meas_file = sys.argv[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = sys.argv[ind + 1]
if "-Fsi" in args:
ind = args.index("-Fsi")
site_file = sys.argv[ind + 1]
if "-ocn" in args:
ind = args.index("-ocn")
or_con = sys.argv[ind + 1]
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "-mcd" in args:
ind = args.index("-mcd")
gmeths = (sys.argv[ind + 1])
if "-loc" in args:
ind = args.index("-loc")
location_name = (sys.argv[ind + 1])
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if "-ins" in args:
ind = args.index("-ins")
inst = args[ind + 1]
if "-a" in args:
noave = 0
#
ID = False
if '-ID' in args:
ind = args.index('-ID')
ID = args[ind + 1]
#
if not command_line:
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file', '')
pos_file = kwargs.get('pos_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt')
or_con = kwargs.get('or_con', '3')
samp_con = kwargs.get('samp_con', '2')
corr = kwargs.get('corr', '1')
gmeths = kwargs.get('gmeths', '')
location_name = kwargs.get('location_name', '')
specnum = int(kwargs.get('specnum', 0))
inst = kwargs.get('inst', '')
noave = kwargs.get('noave', 1) # default is DO average
ID = kwargs.get('ID', '')
# format and fix variables acquired from command line args or input with **kwargs
if specnum != 0: specnum = -specnum
if ID:
input_dir_path = ID
else:
input_dir_path = dir_path
if samp_con:
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if "6" in samp_con:
try:
Samps, file_type = pmag.magic_read(
os.path.join(input_dir_path, 'er_samples.txt'))
except:
print(
"there is no er_samples.txt file in your input directory - you can't use naming convention #6"
)
return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
if file_type == 'bad_file':
print(
"there is no er_samples.txt file in your input directory - you can't use naming convention #6"
)
return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
if not mag_file:
print("mag file is required input")
return False, "mag file is required input"
output_dir_path = dir_path
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = output_dir_path + '/' + samp_file
site_file = output_dir_path + '/' + site_file
meas_file = output_dir_path + '/' + meas_file
samplist = []
try:
Samps, file_type = pmag.magic_read(samp_file)
for samp in Samps:
if samp['er_sample_name'] not in samplist:
samplist.append(samp['er_sample_name'])
except:
Samps = []
MagRecs = []
try:
f = open(mag_file, 'brU')
input = str(f.read()).strip("b '")
f.close()
except Exception as ex:
print('ex', ex)
print("bad mag file")
return False, "bad mag file"
firstline, date = 1, ""
d = input.split('\\xcd')
for line in d:
rec = line.split('\\x00')
if firstline == 1:
firstline = 0
spec, vol = "", 1
el = 51
while line[el:el + 1] != "\\":
spec = spec + line[el]
el += 1
# check for bad sample name
test = spec.split('.')
date = ""
if len(test) > 1:
spec = test[0]
kk = 24
while line[kk] != '\\x01' and line[kk] != '\\x00':
kk += 1
vcc = line[24:kk]
el = 10
while rec[el].strip() != '':
el += 1
date, comments = rec[el + 7], []
else:
el = 9
while rec[el] != '\\x01':
el += 1
vcc, date, comments = rec[el - 3], rec[el + 7], []
specname = spec.lower()
print('importing ', specname)
el += 8
while rec[el].isdigit() == False:
comments.append(rec[el])
el += 1
while rec[el] == "":
el += 1
az = float(rec[el])
el += 1
while rec[el] == "":
el += 1
pl = float(rec[el])
el += 1
while rec[el] == "":
el += 1
bed_dip_dir = float(rec[el])
el += 1
while rec[el] == "":
el += 1
bed_dip = float(rec[el])
el += 1
while rec[el] == "":
el += 1
if rec[el] == '\\x01':
bed_dip = 180. - bed_dip
el += 1
while rec[el] == "":
el += 1
fold_az = float(rec[el])
el += 1
while rec[el] == "":
el += 1
fold_pl = rec[el]
el += 1
while rec[el] == "":
el += 1
if rec[el] != "" and rec[el] != '\\x02' and rec[el] != '\\x01':
deccorr = float(rec[el])
az += deccorr
bed_dip_dir += deccorr
fold_az += deccorr
if bed_dip_dir >= 360: bed_dip_dir = bed_dip_dir - 360.
if az >= 360.: az = az - 360.
if fold_az >= 360.: fold_az = fold_az - 360.
else:
deccorr = 0
if specnum != 0:
sample = specname[:specnum]
else:
sample = specname
SampRec = {}
SampRec["er_sample_name"] = sample
SampRec["er_location_name"] = location_name
SampRec["er_citation_names"] = "This study"
labaz, labdip = pmag.orient(az, pl,
or_con) # convert to labaz, labpl
#
# parse information common to all orientation methods
#
SampRec["sample_bed_dip"] = '%7.1f' % (bed_dip)
SampRec["sample_bed_dip_direction"] = '%7.1f' % (bed_dip_dir)
SampRec["sample_dip"] = '%7.1f' % (labdip)
SampRec["sample_azimuth"] = '%7.1f' % (labaz)
if vcc.strip() != "":
vol = float(vcc) * 1e-6 # convert to m^3 from cc
SampRec["sample_volume"] = '%10.3e' % (vol) #
SampRec["sample_class"] = sclass
SampRec["sample_lithology"] = lithology
SampRec["sample_type"] = _type
SampRec["sample_declination_correction"] = '%7.1f' % (deccorr)
methods = gmeths.split(':')
if deccorr != "0":
if 'SO-MAG' in methods: del methods[methods.index('SO-MAG')]
methods.append('SO-CMD-NORTH')
meths = ""
for meth in methods:
meths = meths + meth + ":"
meths = meths[:-1]
SampRec["magic_method_codes"] = meths
if int(samp_con) < 6 or int(samp_con) == 7:
site = pmag.parse_site(SampRec["er_sample_name"], samp_con,
Z) # parse out the site name
SampRec["er_site_name"] = site
elif len(Samps) > 1:
site, location = "", ""
for samp in Samps:
if samp["er_sample_name"] == SampRec["er_sample_name"]:
site = samp["er_site_name"]
location = samp["er_location_name"]
break
SampRec["er_location_name"] = samp["er_location_name"]
SampRec["er_site_name"] = samp["er_site_name"]
if sample not in samplist:
samplist.append(sample)
Samps.append(SampRec)
else:
MagRec = {}
MagRec["treatment_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"] = '0'
MagRec["treatment_dc_field"] = '0'
MagRec["treatment_dc_field_phi"] = '0'
MagRec["treatment_dc_field_theta"] = '0'
meas_type = "LT-NO"
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = '1'
MagRec["er_specimen_name"] = specname
MagRec["er_sample_name"] = SampRec['er_sample_name']
MagRec["er_site_name"] = SampRec['er_site_name']
MagRec["er_location_name"] = location_name
el, demag = 1, ''
treat = rec[el]
if treat[-1] == 'C':
demag = 'T'
elif treat != 'NRM':
demag = 'AF'
el += 1
while rec[el] == "":
el += 1
MagRec["measurement_dec"] = rec[el]
cdec = float(rec[el])
el += 1
while rec[el] == "":
el += 1
MagRec["measurement_inc"] = rec[el]
cinc = float(rec[el])
el += 1
while rec[el] == "":
el += 1
gdec = rec[el]
el += 1
while rec[el] == "":
el += 1
ginc = rec[el]
el = skip(2, el, rec) # skip bdec,binc
# el=skip(4,el,rec) # skip gdec,ginc,bdec,binc
# print 'moment emu: ',rec[el]
MagRec["measurement_magn_moment"] = '%10.3e' % (
float(rec[el]) * 1e-3) # moment in Am^2 (from emu)
MagRec["measurement_magn_volume"] = '%10.3e' % (
float(rec[el]) * 1e-3 / vol) # magnetization in A/m
el = skip(2, el, rec) # skip to xsig
MagRec["measurement_sd_x"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el = skip(3, el, rec) # skip to ysig
MagRec["measurement_sd_y"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el = skip(3, el, rec) # skip to zsig
MagRec["measurement_sd_z"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el += 1 # skip to positions
MagRec["measurement_positions"] = rec[el]
# el=skip(5,el,rec) # skip to date
# mm=str(months.index(date[0]))
# if len(mm)==1:
# mm='0'+str(mm)
# else:
# mm=str(mm)
# dstring=date[2]+':'+mm+':'+date[1]+":"+date[3]
# MagRec['measurement_date']=dstring
MagRec["magic_instrument_codes"] = inst
MagRec["er_analyst_mail_names"] = ""
MagRec["er_citation_names"] = "This study"
MagRec["magic_method_codes"] = meas_type
if demag == "AF":
MagRec["treatment_ac_field"] = '%8.3e' % (
float(treat[:-2]) * 1e-3) # peak field in tesla
meas_type = "LT-AF-Z"
MagRec["treatment_dc_field"] = '0'
elif demag == "T":
MagRec["treatment_temp"] = '%8.3e' % (float(treat[:-1]) + 273.
) # temp in kelvin
meas_type = "LT-T-Z"
MagRec['magic_method_codes'] = meas_type
MagRecs.append(MagRec)
MagOuts = pmag.measurements_methods(MagRecs, noave)
MagOuts, keylist = pmag.fillkeys(MagOuts)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print("Measurements put in ", meas_file)
SampsOut, sampkeys = pmag.fillkeys(Samps)
pmag.magic_write(samp_file, SampsOut, "er_samples")
Sites = []
for samp in Samps:
SiteRec = {}
SiteRec['er_site_name'] = samp['er_site_name']
SiteRec['er_location_name'] = samp['er_location_name']
SiteRec['site_definition'] = 's'
SiteRec['er_citation_names'] = 'This study'
if 'sample_class' in list(samp.keys()):
SiteRec['site_class'] = samp['sample_class']
if 'sample_lithology' in list(samp.keys()):
SiteRec['site_lithology'] = samp['sample_lithology']
if 'sample_type' in list(samp.keys()):
SiteRec['site_lithology'] = samp['sample_lithology']
if 'sample_lat' in list(samp.keys()):
SiteRec['site_lat'] = samp['sample_lat']
else:
SiteRec['site_lat'] = "-999"
if 'sample_lon' in list(samp.keys()):
SiteRec['site_lon'] = samp['sample_lon']
else:
SiteRec['site_lon'] = "-999"
if 'sample_height' in list(samp.keys()):
SiteRec['site_height'] = samp['sample_height']
Sites.append(SiteRec)
pmag.magic_write(site_file, Sites, 'er_sites')
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
jr6_jr6_magic.py
DESCRIPTION
converts JR6 .jr6 format files to magic_measurements format files
SYNTAX
jr6_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify sample naming convention (6 and 7 not yet implemented)
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-JR IODP samples measured on the JOIDES RESOLUTION
-v NUM : specify the volume in cc of the sample, default 2.5^3cc
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
JR6 .jr6 format file
"""
# initialize some stuff
noave = 0
#volume=2.5**3 #default volume is a 2.5cm cube
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
inst = ""
samp_con, Z = '1', ""
missing = 1
demag = "N"
er_location_name = "unknown"
citation = 'This study'
args = sys.argv
meth_code = "LP-NO"
specnum = 1
version_num = pmag.get_version()
Samps = [] # keeps track of sample orientations
user = ""
mag_file = ""
dir_path = '.'
MagRecs = []
ErSamps = []
SampOuts = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
tmp_file = "fixed.jr6"
meth_code, JR = "", 0
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
#try:
# open(samp_file,'r')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-A" in args: noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind + 1]
if "-JR" in args:
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
JR = 1
samp_con = '5'
if "-v" in args:
ind = args.index("-v")
volume = float(
args[ind + 1]) * 1e-6 # enter volume in cc, convert to m^3
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
else:
#convert cm^3 to m^3
volume *= 1e-6
JR = kwargs.get('JR', 0)
if JR:
if meth_code == "LP-NO":
meth_code = ""
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
samp_con = '5'
# format variables
mag_file = input_dir_path + "/" + mag_file
meas_file = output_dir_path + "/" + meas_file
samp_file = output_dir_path + "/" + samp_file
tmp_file = output_dir_path + "/" + tmp_file
if specnum != 0:
specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
ErSampRec, ErSiteRec = {}, {}
# parse data
# fix .jr6 file so that there are spaces between all the columns.
pre_data = open(mag_file, 'r')
tmp_data = open(tmp_file, 'w')
line = pre_data.readline()
while line != '':
line = line.replace('-', ' -')
#print "line=", line
tmp_data.write(line)
line = pre_data.readline()
tmp_data.close()
pre_data.close()
data = pd.read_csv(tmp_file, delim_whitespace=True, header=None)
if JR == 0: #
data.columns = [
'er_specimen_name', 'step', 'x', 'y', 'z', 'expon',
'sample_azimuth', 'sample_dip', 'sample_bed_dip_direction',
'sample_bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2',
'param3', 'param4', 'measurement_csd'
]
cart = np.array([data['x'], data['y'], data['z']]).transpose()
else: # measured on the Joides Resolution JR6
data.columns = [
'er_specimen_name', 'step', 'negz', 'y', 'x', 'expon',
'sample_azimuth', 'sample_dip', 'sample_bed_dip_direction',
'sample_bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2',
'param3', 'param4', 'measurement_csd'
]
cart = np.array([data['x'], data['y'], -data['negz']]).transpose()
dir = pmag.cart2dir(cart).transpose()
data['measurement_dec'] = dir[0]
data['measurement_inc'] = dir[1]
data['measurement_magn_moment'] = dir[2] * (
10.0**
data['expon']) * volume # the data are in A/m - this converts to Am^2
data['measurement_magn_volume'] = dir[2] * (10.0**data['expon']
) # A/m - data in A/m
data['sample_dip'] = -data['sample_dip']
DGEOs, IGEOs = [], []
for ind in range(len(data)):
dgeo, igeo = pmag.dogeo(data.iloc[ind]['measurement_dec'],
data.iloc[ind]['measurement_inc'],
data.iloc[ind]['sample_azimuth'],
data.iloc[ind]['sample_dip'])
DGEOs.append(dgeo)
IGEOs.append(igeo)
data['specimen_dec'] = DGEOs
data['specimen_inc'] = IGEOs
data['specimen_tilt'] = '1'
if specnum != 0:
data['er_sample_name'] = data['er_specimen_name'][:specnum]
else:
data['er_sample_name'] = data['er_specimen_name']
if int(samp_con) in [1, 2, 3, 4, 5, 7]:
data['er_site_name'] = pmag.parse_site(data['er_sample_name'],
samp_con, Z)
# else:
# if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampRec['er_site_name']
# if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampRec['er_location_name']
# Configure the er_sample table
for rowNum, row in data.iterrows():
sampleFlag = 0
for sampRec in SampOuts:
if sampRec['er_sample_name'] == row['er_sample_name']:
sampleFlag = 1
break
if sampleFlag == 0:
ErSampRec['er_sample_name'] = row['er_sample_name']
ErSampRec['sample_azimuth'] = str(row['sample_azimuth'])
ErSampRec['sample_dip'] = str(row['sample_dip'])
ErSampRec['magic_method_codes'] = meth_code
ErSampRec['er_location_name'] = er_location_name
ErSampRec['er_site_name'] = row['er_site_name']
ErSampRec['er_citation_names'] = 'This study'
SampOuts.append(ErSampRec.copy())
# Configure the magic_measurements table
for rowNum, row in data.iterrows():
MagRec = {}
# MagRec['measurement_description']='Date: '+date
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = row['er_site_name']
MagRec['er_sample_name'] = row['er_sample_name']
MagRec['magic_software_packages'] = version_num
MagRec["treatment_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = '1'
MagRec["er_specimen_name"] = row['er_specimen_name']
MagRec["treatment_ac_field"] = '0'
if row['step'] == 'NRM':
meas_type = "LT-NO"
elif row['step'][0:2] == 'AD':
meas_type = "LT-AF-Z"
treat = float(row['step'][2:])
MagRec["treatment_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type = "LT-T-Z"
treat = float(row['step'][2:])
MagRec["treatment_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
else: # need to add IRM, and ARM options
print("measurement type unknown", row['step'])
return False, "measurement type unknown"
MagRec["measurement_magn_moment"] = str(row['measurement_magn_moment'])
MagRec["measurement_magn_volume"] = str(row['measurement_magn_volume'])
MagRec["measurement_dec"] = str(row['measurement_dec'])
MagRec["measurement_inc"] = str(row['measurement_inc'])
MagRec['magic_method_codes'] = meas_type
MagRecs.append(MagRec.copy())
pmag.magic_write(samp_file, SampOuts, 'er_samples')
print("sample orientations put in ", samp_file)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print("results put in ", meas_file)
print("exit!")
return True, meas_file
def main():
"""
NAME
huji_sample_magic.py
DESCRIPTION
takes tab delimited Hebrew University sample file and converts to MagIC formatted tables
SYNTAX
huji_sample_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-Fsa FILE: specify sample output file, default is: er_samples.txt
-Fsi FILE: specify site output file, default is: er_sites.txt
-Iso: import sample orientation info - default is to set sample_az/dip to 0,0
-ncn NCON: specify naming convention: default is #1 below
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-ASC an ASC orientation device was used
SO-MAG orientation with magnetic compass
-loc: location name, default="unknown"
INPUT FORMAT
Input files must be tab delimited:
Samp Az Dip Dip_dir Dip
Orientation convention:
Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
e.g. field_dip is degrees from horizontal of drill direction
Magnetic declination convention:
Az is already corrected in file
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
OUTPUT
output saved in er_samples.txt will overwrite any existing files
"""
#
# initialize variables
#
version_num=pmag.get_version()
samp_file,or_con,corr = "er_samples.txt","1","1"
site_file='er_sites.txt'
args=sys.argv
date,lat,lon="","","" # date of sampling, latitude (pos North), longitude (pos East)
bed_dip,bed_dip_dir="",""
participantlist=""
sites=[] # list of site names
Lats,Lons=[],[] # list of latitudes and longitudes
SampRecs,SiteRecs,ImageRecs,imagelist=[],[],[],[] # lists of Sample records and Site records
samp_con,Z,average_bedding="1",1,"0"
newbaseline,newbeddir,newbeddip="","",""
meths='FS-FD:SO-POM:SO-SUN'
delta_u="0"
sclass,lithology,type="","",""
newclass,newlith,newtype='','',''
user=""
or_con='3'
corr=="3"
DecCorr=0.
location_name="unknown"
ignore=1
#
#
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-f" in args:
ind=args.index("-f")
orient_file=sys.argv[ind+1]
else:
"Must have orientation file name"
sys.exit()
if "-Fsa" in args:
ind=args.index("-Fsa")
samp_file=sys.argv[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 3-Z where Z is an integer")
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
print(samp_con, Z)
if "-mcd" in args:
ind=args.index("-mcd")
meths=(sys.argv[ind+1])
if "-loc" in args:
ind=args.index("-loc")
location_name=(sys.argv[ind+1])
if "-Iso" in args: ignore=0
#
# read in file to convert
#
azfile=open(orient_file,'r')
AzDipDat=azfile.readlines()
azfile.close()
SampOut=[]
SiteOut=[]
for line in AzDipDat[1:]:
orec=line.split()
if len(orec)>1:
labaz,labdip=pmag.orient(float(orec[1]),float(orec[2]),or_con)
bed_dip_dir=(orec[3])
bed_dip=(orec[4])
SampRec={}
SiteRec={}
SampRec["er_location_name"]=location_name
SampRec["er_citation_names"]="This study"
SiteRec["er_location_name"]=location_name
SiteRec["er_citation_names"]="This study"
SiteRec["site_class"]=""
SiteRec["site_lithology"]=""
SiteRec["site_type"]=""
SiteRec["site_definition"]="s"
SiteRec["er_citation_names"]="This study"
#
# parse information common to all orientation methods
#
SampRec["er_sample_name"]=orec[0]
SampRec["sample_bed_dip_direction"]=orec[3]
SampRec["sample_bed_dip"]=orec[4]
SiteRec["site_bed_dip_direction"]=orec[3]
SiteRec["site_bed_dip"]=orec[4]
if ignore==0:
SampRec["sample_dip"]='%7.1f'%(labdip)
SampRec["sample_azimuth"]='%7.1f'%(labaz)
else:
SampRec["sample_dip"]='0'
SampRec["sample_azimuth"]='0'
SampRec["sample_lat"]=orec[5]
SampRec["sample_lon"]=orec[6]
SiteRec["site_lat"]=orec[5]
SiteRec["site_lon"]=orec[6]
methods=meths.split(":")
SampRec["magic_method_codes"]=meths
site=pmag.parse_site(orec[0],samp_con,Z) # parse out the site name
SampRec["er_site_name"]=site
SampRec['magic_software_packages']=version_num
SiteRec["er_site_name"]=site
SiteRec['magic_software_packages']=version_num
SampOut.append(SampRec)
SiteOut.append(SiteRec)
pmag.magic_write(samp_file,SampOut,"er_samples")
print("Sample info saved in ", samp_file)
pmag.magic_write(site_file,SiteOut,"er_sites")
print("Site info saved in ", site_file)
def main(command_line=True, **kwargs):
"""
NAME
jr6_txt_magic.py
DESCRIPTION
converts JR6 .txt format files to magic_measurements format files
SYNTAX
jr6_txt_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify sample naming convention (6 and 7 not yet implemented)
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-v NUM : specify the volume of the sample, default 2.5cm^3.
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
JR6 .txt format file
"""
# initialize some stuff
noave=0
volume = 2.5 * 1e-6 # default volume is 2.5 cm^3 (2.5 * 1e-6 meters^3)
inst=""
samp_con,Z='1',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
specnum=-1
MagRecs=[]
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
user=""
mag_file=""
dir_path='.'
ErSamps=[]
SampOuts=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind+1]
#try:
# open(samp_file,'r')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind+1])
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args: noave=1
if "-mcd" in args:
ind=args.index("-mcd")
meth_code=args[ind+1]
if "-v" in args:
ind=args.index("-v")
volume=float(args[ind+1]) * 1e-6
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
else:
#convert cm^3 to m^3
volume *= 1e-6
# format variables
mag_file = input_dir_path+"/" + mag_file
meas_file = output_dir_path+"/" + meas_file
samp_file = output_dir_path+"/" + samp_file
if specnum!=0:
specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
ErSampRec,ErSiteRec={},{}
# parse data
data=open(mag_file,'r')
line=data.readline()
line=data.readline()
line=data.readline()
while line !='':
parsedLine=line.split()
sampleName=parsedLine[0]
demagLevel=parsedLine[2]
date=parsedLine[3]
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
parsedLine=line.split()
specimenAngleDec=parsedLine[1]
specimenAngleInc=parsedLine[2]
while parsedLine[0] != 'MEAN' :
line=data.readline()
parsedLine=line.split()
if len(parsedLine) == 0:
parsedLine=["Hello"]
Mx=parsedLine[1]
My=parsedLine[2]
Mz=parsedLine[3]
line=data.readline()
line=data.readline()
parsedLine=line.split()
splitExp = parsedLine[2].split('A')
intensityVolStr=parsedLine[1] + splitExp[0]
intensityVol = float(intensityVolStr)
# check and see if Prec is too big and messes with the parcing.
precisionStr=''
if len(parsedLine) == 6: #normal line
precisionStr=parsedLine[5][0:-1]
else:
precisionStr=parsedLine[4][0:-1]
precisionPer = float(precisionStr)
precision=intensityVol*precisionPer/100
while parsedLine[0] != 'SPEC.' :
line=data.readline()
parsedLine=line.split()
if len(parsedLine) == 0:
parsedLine=["Hello"]
specimenDec=parsedLine[2]
specimenInc=parsedLine[3]
line=data.readline()
line=data.readline()
parsedLine=line.split()
geographicDec=parsedLine[1]
geographicInc=parsedLine[2]
# Add data to various MagIC data tables.
er_specimen_name = sampleName
if specnum!=0:
er_sample_name=er_specimen_name[:specnum]
else:
er_sample_name=er_specimen_name
if int(samp_con) in [1, 2, 3, 4, 5, 7]:
er_site_name=pmag.parse_site(er_sample_name,samp_con,Z)
else:
print("-W- Using unreognized sample convention option: ", samp_con)
# else:
# if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampRec['er_site_name']
# if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampRec['er_location_name']
# check sample list(SampOuts) to see if sample already exists in list before adding new sample info
sampleFlag=0
for sampRec in SampOuts:
if sampRec['er_sample_name'] == er_sample_name:
sampleFlag=1
break
if sampleFlag == 0:
ErSampRec['er_sample_name']=er_sample_name
ErSampRec['sample_azimuth']=specimenAngleDec
sample_dip=str(float(specimenAngleInc)-90.0) #convert to magic orientation
ErSampRec['sample_dip']=sample_dip
ErSampRec['magic_method_codes']=meth_code
ErSampRec['er_location_name']=er_location_name
ErSampRec['er_site_name']=er_site_name
ErSampRec['er_citation_names']='This study'
SampOuts.append(ErSampRec.copy())
MagRec={}
MagRec['measurement_description']='Date: '+date
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['er_site_name']=er_site_name
MagRec['er_sample_name']=er_sample_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=er_specimen_name
MagRec["treatment_ac_field"]='0'
if demagLevel == 'NRM':
meas_type="LT-NO"
elif demagLevel[0] == 'A':
meas_type="LT-AF-Z"
treat=float(demagLevel[1:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif demagLevel[0] == 'T':
meas_type="LT-T-Z"
treat=float(demagLevel[1:])
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
else:
print("measurement type unknown", demag_level)
return False, "measurement type unknown"
MagRec["measurement_magn_moment"]=str(intensityVol*volume) # Am^2
MagRec["measurement_magn_volume"]=intensityVolStr # A/m
MagRec["measurement_dec"]=specimenDec
MagRec["measurement_inc"]=specimenInc
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec.copy())
#read lines till end of record
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
# read all the rest of the special characters. Some data files not consistantly formatted.
while (len(line) <=3 and line!=''):
line=data.readline()
#end of data while loop
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(samp_file,SampOuts,'er_samples')
print("sample orientations put in ",samp_file)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print("results put in ",meas_file)
return True, meas_file
def convert(**kwargs):
# initialize some stuff
dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0]
inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
tdec=[0,90,0,180,270,0,0,90,0]
tinc=[0,0,90,0,0,-90,0,0,90]
demag="N"
trm=0
irm=0
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # site outfile
magfile = kwargs.get('magfile', '')
labfield = int(kwargs.get('labfield', 0)) *1e-6
phi = int(kwargs.get('phi', 0))
theta = int(kwargs.get('theta', 0))
peakfield = int(kwargs.get('peakfield', 0))*1e-3
specnum = int(kwargs.get('specnum', 0))
location = kwargs.get('location', 'unknown')
noave = kwargs.get('noave', False) # 0 means "do average", is default
samp_con = kwargs.get('samp_con', '1')
codelist = kwargs.get('codelist', '')
coil = kwargs.get('coil', '')
arm_labfield = kwargs.get('arm_labfield', 50e-6)
trm_peakT = kwargs.get('trm_peakT', 600+273)
mv = kwargs.get('mv', 'v')
# format/organize variables
if magfile:
try:
infile=open(os.path.join(input_dir_path,magfile),'r')
except IOError:
print("bad mag file name")
return False, "bad mag file name"
else:
print("mag_file field is required option")
return False, "mag_file field is required option"
if specnum!=0:specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print("naming convention option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("naming convention option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
else: Z=1
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if not labfield: methcode="LT-AF-Z"
if labfield: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if not labfield: methcode="LT-T-Z"
if labfield: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
irmunits="mT"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
# should use arm_labfield and trm_peakT as well, but these values are currently never asked for
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if coil:
methcode="LP-IRM"
irmunits="V"
if coil not in ["1","2","3"]:
print('not a valid coil specification')
return False, 'not a valid coil specification'
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
version_num=pmag.get_version()
# find start of data:
DIspec=[]
Data=infile.readlines()
infile.close()
for k in range(len(Data)):
rec=Data[k].split()
if len(rec)<=2: continue
if rec[0].upper()=="LAT:" and len(rec)>3: lat,lon=rec[1],rec[3]; continue
elif rec[0].upper()=="ID": continue
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
specimen=rec[0]
if specnum!=0:
sample=specimen[:specnum]
else:
sample=specimen
site=pmag.parse_site(sample,samp_con,Z)
if mv=='v':
volume = float(rec[12])
if volume > 0: susc_chi_volume='%10.3e'%(old_div((float(rec[11])*1e-5),volume)) #convert to SI (assume Bartington, 10-5 SI)
else: susc_chi_volume='%10.3e'%(float(rec[11])*1e-5) #convert to SI (assume Bartington, 10-5 SI)
else:
mass = float(rec[12])
if mass > 0: susc_chi_mass='%10.3e'%(old_div((float(rec[11])*1e-5),mass)) #convert to SI (assume Bartington, 10-5 SI)
else: susc_chi_mass='%10.3e'%(float(rec[11])*1e-5) #convert to SI (assume Bartington, 10-5 SI)
print((specimen,sample,site,samp_con,Z))
#fill tables besides measurements
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
if mv=='v':
SpecRec["susc_chi_volume"]=susc_chi_volume
SpecRec["volume"]=volume
else:
SpecRec["susc_chi_mass"]=susc_chi_mass
SpecRec["mass"]=mass
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
#fill measurements
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
meas_type="LT-NO"
MeasRec["quality"]='g'
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
MeasRec["specimen"]=specimen
# if mv=='v': MeasRec["susc_chi_volume"]=susc_chi_volume
# else: MeasRec["susc_chi_mass"]=susc_chi_mass
MeasRec["dir_csd"]=rec[3]
MeasRec["magn_moment"]='%10.3e'% (float(rec[4])*1e-7)
MeasRec["dir_dec"]=rec[5]
MeasRec["dir_inc"]=rec[6]
MeasRec["citations"]="This study"
if demag=="AF":
if methcode != "LP-AN-ARM":
MeasRec["treat_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MeasRec["treat_dc_field"]='0'
else: # AARM experiment
if treat[1][0]=='0':
meas_type="LT-AF-Z"
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
else:
meas_type="LT-AF-I"
ipos=int(treat[0])-1
MeasRec["treat_dc_field_phi"]='%7.1f' %(dec[ipos])
MeasRec["treat_dc_field_theta"]='%7.1f'% (inc[ipos])
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
elif demag=="T":
if rec[1][0]==".":rec[1]="0"+rec[1]
treat=rec[1].split('.')
if len(treat)==1:treat.append('0')
MeasRec["treat_temp"]='%8.3e' % (float(rec[1])+273.) # temp in kelvin
meas_type="LT-T-Z"
MeasRec["treat_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if trm==0: # demag=T and not trmaq
if treat[1][0]=='0':
meas_type="LT-T-Z"
else:
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step
if treat[1][0]=='2':
meas_type="LT-PTRM-I" # pTRM check
pTRM=1
if treat[1][0]=='3':
MeasRec["treat_dc_field"]='0' # this is a zero field step
meas_type="LT-PTRM-MD" # pTRM tail check
else:
meas_type="LT-T-I" # trm acquisition experiment
MeasRec['method_codes']=meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
utrecht_magic.py
DESCRIPTION
converts Utrecht magnetometer data files to magic_measurements files
SYNTAX
utrecht_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-WD: output directory for MagIC files
-ncn: Site Naming Convention
Site to Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2: default] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
-spc: number of characters to remove to generate sample names from specimen names
-dmy: European date format
-loc LOCNAME : specify location/study name
-lat latitude of samples
-lon longitude of samples
-A: don't average replicate measurements
-mcd: [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-dc: B PHI THETA: dc lab field (in microTesla), phi,and theta must be input as a tuple "(DC,PHI,THETA)". If not input user will be asked for values, this is advantagious if there are differing dc fields between steps or specimens. Note: this currently only works with the decimal IZZI naming convetion (XXX.0,1,2,3 where XXX is the treatment temperature and 0 is a zero field step, 1 is in field, and 2 is a pTRM check, 3 is a tail check). All other steps are hardcoded dc_field = 0.
INPUT
Utrecht magnetometer data file
"""
# initialize some stuff
sample_lat = 0.0
sample_lon = 0.0
noave = 0
er_location_name = "unknown"
args = sys.argv
meth_code = "LP-NO"
version_num = pmag.get_version()
site_num = 1
mag_file = ""
dir_path = '.'
MagRecs = []
SpecOuts = []
SampOuts = []
SiteOuts = []
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
meth_code = ""
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=args[ind+1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind+1]
if '-Fsi' in args: # LORI addition
ind=args.index("-Fsi")
site_file=args[ind+1]
#try:
# open(samp_file,'r')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind+1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind+1]
if "-lat" in args:
ind = args.index("-lat")
site_lat = args[ind+1]
if "-lon" in args:
ind = args.index("-lon")
site_lon = args[ind+1]
if "-A" in args:
noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind+1]
#samp_con='5'
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
site_num=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
site_num=samp_con.split("-")[1]
samp_con="7"
else: samp_con="1"
if '-dc' in args:
ind=args.index('-dc')
DC_FIELD,DC_PHI,DC_THETA=list(map(float,args[ind+1].strip('( ) [ ]').split(',')))
DC_FIELD *= 1e-6
yn=''
GET_DC_PARAMS=False
else: DC_FIELD,DC_PHI,DC_THETA=0,0,-90
if '-spc' in args:
ind=args.index("-spc")
specnum=-int(args[ind+1])
else: specnum = 0
if '-dmy' in args:
ind=args.index("-dmy")
dmy_flag=True
else: dmy_flag=False
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file', 'er_specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt') # site outfile
er_location_name = kwargs.get('location_name', '')
site_lat = kwargs.get('site_lat', '')
site_lon = kwargs.get('site_lon', '')
#oave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
specnum = -int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '2')
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
site_num=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
site_num=samp_con.split("-")[1]
samp_con="7"
DC_FIELD,DC_PHI,DC_THETA = list(map(float, kwargs.get('dc_params', (0,0,-90))))
DC_FIELD *= 1e-6
noave = kwargs.get('avg', True)
dmy_flag = kwargs.get('dmy_flag', False)
# format variables
if not mag_file:
return False, 'You must provide a Utrecht formated file'
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
# parse data
# Open up the Utrecht file and read the header information
print('mag_file in utrecht_file', mag_file)
AF_or_T = mag_file.split('.')[-1]
data = open(mag_file, 'r')
line = data.readline()
line_items = line.split(',')
operator=line_items[0]
operator=operator.replace("\"","")
machine=line_items[1]
machine=machine.replace("\"","")
machine=machine.rstrip('\n')
print("operator=", operator)
print("machine=", machine)
#read in measurement data
line = data.readline()
while line != "END" and line != '"END"':
ErSpecRec,ErSampRec,ErSiteRec = {},{},{}
line_items = line.split(',')
spec_name=line_items[0]
spec_name=spec_name.replace("\"","")
print("spec_name=", spec_name)
free_string=line_items[1]
free_string=free_string.replace("\"","")
print("free_string=", free_string)
dec=line_items[2]
print("dec=", dec)
inc=line_items[3]
print("inc=", inc)
volume=float(line_items[4])
volume=volume * 1e-6 # enter volume in cm^3, convert to m^3
print("volume=", volume)
bed_plane=line_items[5]
print("bed_plane=", bed_plane)
bed_tilt=line_items[6]
print("bed_tilt=", bed_tilt)
# Configure et er_ tables
ErSpecRec['er_specimen_name'] = spec_name
if specnum==0: sample_name = spec_name
else: sample_name = spec_name[:specnum]
ErSampRec['er_sample_name'] = sample_name
ErSpecRec['er_sample_name'] = sample_name
er_site_name = pmag.parse_site(sample_name,samp_con,site_num)
ErSpecRec['er_site_name']=er_site_name
ErSpecRec['er_location_name']=er_location_name
ErSampRec['sample_azimuth'] = dec
ErSampRec['sample_dip'] = str(float(inc)-90)
ErSampRec['sample_bed_dip_direction'] = bed_plane
ErSampRec['sample_bed_tilt'] = bed_tilt
ErSiteRec['site_lat'] = site_lat
ErSiteRec['site_lon'] = site_lon
ErSpecRec['magic_method_codes'] = meth_code
ErSampRec['er_location_name'] = er_location_name
ErSiteRec['er_location_name'] = er_location_name
ErSiteRec['er_site_name'] = er_site_name
ErSampRec['er_site_name'] = er_site_name
ErSampRec['er_citation_names'] = 'This study'
SpecOuts.append(ErSpecRec)
SampOuts.append(ErSampRec)
SiteOuts.append(ErSiteRec)
#measurement data
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
while line != '9999':
print(line)
step=items[0]
step=step.split('.')
step_value=step[0]
step_type = ""
if len(step) == 2:
step_type=step[1]
if step_type=='5':
step_value = items[0]
A=float(items[1])
B=float(items[2])
C=float(items[3])
# convert to MagIC coordinates
Z=-A
X=-B
Y=C
cart = np.array([X, Y, Z]).transpose()
direction = pmag.cart2dir(cart).transpose()
measurement_dec = direction[0]
measurement_inc = direction[1]
measurement_magn_moment = direction[2] * 1.0e-12 # the data are in pico-Am^2 - this converts to Am^2
measurement_magn_volume = direction[2] * 1.0e-12 / volume # data volume normalized - converted to A/m
print("measurement_magn_moment=", measurement_magn_moment)
print("measurement_magn_volume=", measurement_magn_volume)
error = items[4]
date=items[5]
date=date.strip('"')
if date.count("-") > 0:
date=date.split("-")
elif date.count("/") > 0:
date=date.split("/")
else: print("date format seperator cannot be identified")
print(date)
time=items[6]
time=time.strip('"')
time=time.split(":")
print(time)
if dmy_flag:
date_time = date[1] + ":" + date[0] + ":" + date[2] + ":" + time[0] + ":" + time[1] + ":" + "0.0"
else:
date_time = date[0] + ":" + date[1] + ":" + date[2] + ":" + time[0] + ":" + time[1] + ":" + "0.0"
print(date_time)
MagRec = {}
MagRec["er_analyst_mail_names"] = operator
MagRec["magic_instrument_codes"] = "Utrecht_" + machine
MagRec["measurement_description"] = "free string = " + free_string
MagRec["measurement_date"] = date_time
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = er_site_name
MagRec['er_sample_name'] = sample_name
MagRec['magic_software_packages'] = version_num
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["magic_experiment_name"] = er_location_name + er_site_name + spec_name
MagRec["measurement_number"] = er_location_name + er_site_name + spec_name + items[0]
MagRec["er_specimen_name"] = spec_name
# MagRec["treatment_ac_field"] = '0'
if AF_or_T.lower() == "th":
MagRec["treatment_temp"] = '%8.3e' % (float(step_value)+273.) # temp in kelvin
MagRec['treatment_ac_field']='0'
meas_type = "LP-DIR-T:LT-T-Z"
else:
MagRec['treatment_temp']='273'
MagRec['treatment_ac_field']='%10.3e'%(float(step_value)*1e-3)
meas_type = "LP-DIR-AF:LT-AF-Z"
MagRec['treatment_dc_field']='0'
if step_value == '0':
meas_type = "LT-NO"
print("step_type=", step_type)
if step_type == '0' and AF_or_T.lower() == 'th':
if meas_type == "":
meas_type = "LT-T-Z"
else:
meas_type = meas_type + ":" + "LT-T-Z"
elif step_type == '1':
if meas_type == "":
meas_type = "LT-T-I"
else:
meas_type = meas_type + ":" + "LT-T-I"
MagRec['treatment_dc_field']='%1.2e'%DC_FIELD
elif step_type == '2':
if meas_type == "":
meas_type = "LT-PTRM-I"
else:
meas_type = meas_type + ":" + "LT-PTRM-I"
MagRec['treatment_dc_field']='%1.2e'%DC_FIELD
elif step_type == '3':
if meas_type == "" :
meas_type = "LT-PTRM-Z"
else:
meas_type = meas_type + ":" + "LT-PTRM-Z"
print("meas_type=", meas_type)
MagRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MagRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
MagRec['magic_method_codes'] = meas_type
MagRec["measurement_magn_moment"] = measurement_magn_moment
MagRec["measurement_magn_volume"] = measurement_magn_volume
MagRec["measurement_dec"] = measurement_dec
MagRec["measurement_inc"] = measurement_inc
MagRec['measurement_csd'] = error
# MagRec['measurement_positions'] = '1'
MagRecs.append(MagRec)
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
# write out the data to MagIC data files
pmag.magic_write(spec_file, SpecOuts, 'er_specimens')
pmag.magic_write(samp_file, SampOuts, 'er_samples')
pmag.magic_write(site_file, SiteOuts, 'er_sites')
# MagOuts = pmag.measurements_methods(MagRecs, noave)
# pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
pmag.magic_write(meas_file, MagRecs, 'magic_measurements')
print("results put in ", meas_file)
print("exit!")
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
jr6_jr6_magic.py
DESCRIPTION
converts JR6 .jr6 format files to magic_measurements format files
SYNTAX
jr6_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify sample naming convention (6 and 7 not yet implemented)
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-JR IODP samples measured on the JOIDES RESOLUTION
-v NUM : specify the volume in cc of the sample, default 2.5^3cc
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
JR6 .jr6 format file
"""
# initialize some stuff
noave=0
#volume=2.5**3 #default volume is a 2.5cm cube
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
inst=""
samp_con,Z='1',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
specnum=1
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
user=""
mag_file=""
dir_path='.'
MagRecs=[]
ErSamps=[]
SampOuts=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
tmp_file= "fixed.jr6"
meth_code,JR="",0
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind+1]
#try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind+1])
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args: noave=1
if "-mcd" in args:
ind=args.index("-mcd")
meth_code=args[ind+1]
if "-JR" in args:
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
JR=1
samp_con='5'
if "-v" in args:
ind=args.index("-v")
volume=float(args[ind+1])*1e-6 # enter volume in cc, convert to m^3
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
else:
#convert cm^3 to m^3
volume *= 1e-6
JR = kwargs.get('JR', 0)
if JR:
if meth_code == "LP-NO":
meth_code = ""
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
samp_con='5'
# format variables
mag_file = input_dir_path+"/" + mag_file
meas_file = output_dir_path+"/" + meas_file
samp_file = output_dir_path+"/" + samp_file
tmp_file = output_dir_path+"/" + tmp_file
if specnum!=0:
specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
ErSampRec,ErSiteRec={},{}
# parse data
# fix .jr6 file so that there are spaces between all the columns.
pre_data=open(mag_file, 'rU')
tmp_data=open(tmp_file, 'w')
line=pre_data.readline()
while line !='':
line=line.replace('-',' -')
#print "line=", line
tmp_data.write(line)
line=pre_data.readline()
tmp_data.close()
pre_data.close()
data=pd.read_csv(tmp_file, delim_whitespace=True,header=None)
if JR==0: #
data.columns=['er_specimen_name','step','x','y','z','expon','sample_azimuth','sample_dip', 'sample_bed_dip_direction','sample_bed_dip','bed_dip_dir2','bed_dip2','param1','param2','param3','param4','measurement_csd']
cart=np.array([data['x'],data['y'],data['z']]).transpose()
else: # measured on the Joides Resolution JR6
data.columns=['er_specimen_name','step','negz','y','x','expon','sample_azimuth','sample_dip', 'sample_bed_dip_direction','sample_bed_dip','bed_dip_dir2','bed_dip2','param1','param2','param3','param4','measurement_csd']
cart=np.array([data['x'],data['y'],-data['negz']]).transpose()
dir= pmag.cart2dir(cart).transpose()
data['measurement_dec']=dir[0]
data['measurement_inc']=dir[1]
data['measurement_magn_moment']=dir[2]*(10.0**data['expon'])*volume # the data are in A/m - this converts to Am^2
data['measurement_magn_volume']=dir[2]*(10.0**data['expon']) # A/m - data in A/m
data['sample_dip']=-data['sample_dip']
DGEOs,IGEOs=[],[]
for ind in range(len(data)):
dgeo,igeo=pmag.dogeo(data.ix[ind]['measurement_dec'],data.ix[ind]['measurement_inc'],data.ix[ind]['sample_azimuth'],data.ix[ind]['sample_dip'])
DGEOs.append(dgeo)
IGEOs.append(igeo)
data['specimen_dec']=DGEOs
data['specimen_inc']=IGEOs
data['specimen_tilt']='1'
if specnum!=0:
data['er_sample_name']=data['er_specimen_name'][:specnum]
else:
data['er_sample_name']=data['er_specimen_name']
if int(samp_con) in [1, 2, 3, 4, 5, 7]:
data['er_site_name']=pmag.parse_site(data['er_sample_name'],samp_con,Z)
# else:
# if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampRec['er_site_name']
# if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampRec['er_location_name']
# Configure the er_sample table
for rowNum, row in data.iterrows():
sampleFlag=0
for sampRec in SampOuts:
if sampRec['er_sample_name'] == row['er_sample_name']:
sampleFlag=1
break
if sampleFlag == 0:
ErSampRec['er_sample_name']=row['er_sample_name']
ErSampRec['sample_azimuth']=str(row['sample_azimuth'])
ErSampRec['sample_dip']=str(row['sample_dip'])
ErSampRec['magic_method_codes']=meth_code
ErSampRec['er_location_name']=er_location_name
ErSampRec['er_site_name']=row['er_site_name']
ErSampRec['er_citation_names']='This study'
SampOuts.append(ErSampRec.copy())
# Configure the magic_measurements table
for rowNum, row in data.iterrows():
MagRec={}
# MagRec['measurement_description']='Date: '+date
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['er_site_name']=row['er_site_name']
MagRec['er_sample_name']=row['er_sample_name']
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=row['er_specimen_name']
MagRec["treatment_ac_field"]='0'
if row['step'] == 'NRM':
meas_type="LT-NO"
elif row['step'][0:2] == 'AD':
meas_type="LT-AF-Z"
treat=float(row['step'][2:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type="LT-T-Z"
treat=float(row['step'][2:])
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
else: # need to add IRM, and ARM options
print "measurement type unknown", row['step']
return False, "measurement type unknown"
MagRec["measurement_magn_moment"]=str(row['measurement_magn_moment'])
MagRec["measurement_magn_volume"]=str(row['measurement_magn_volume'])
MagRec["measurement_dec"]=str(row['measurement_dec'])
MagRec["measurement_inc"]=str(row['measurement_inc'])
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec.copy())
pmag.magic_write(samp_file,SampOuts,'er_samples')
print "sample orientations put in ",samp_file
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
print "exit!"
return True, meas_file
def convert(**kwargs):
"""
"""
#get kwargs
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
lat = kwargs.get('lat', 0)
lon = kwargs.get('lon', 0)
specnum = int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
version_num = pmag.get_version()
if specnum != 0: specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print(
"naming convention option [4] must be in form 4-Z where Z is an integer"
)
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
else:
Z = 1
# format variables
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
# parse data
data = open(mag_file, 'r').readlines() # read in data from file
comment = data[0]
line = data[1].strip()
line = line.replace("=", "= ") # make finding orientations easier
rec = line.split() # read in sample orientation, etc.
specimen = rec[0]
SpecRecs, SampRecs, SiteRecs, LocRecs, MeasRecs = [], [], [], [], []
SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {} # make a sample record
if specnum != 0:
sample = rec[0][:specnum]
else:
sample = rec[0]
if int(samp_con) < 6:
site = pmag.parse_site(sample, samp_con, Z)
else:
if 'site' in list(SampRec.keys()): site = ErSampREc['site']
if 'location' in list(SampRec.keys()): location = ErSampREc['location']
az_ind = rec.index('a=') + 1
SampRec['sample'] = sample
SampRec['description'] = comment
SampRec['azimuth'] = rec[az_ind]
dip_ind = rec.index('b=') + 1
dip = -float(rec[dip_ind])
SampRec['dip'] = '%7.1f' % (dip)
strike_ind = rec.index('s=') + 1
SampRec['bed_dip_direction'] = '%7.1f' % (float(rec[strike_ind]) + 90.)
bd_ind = rec.index('d=') + 1
SampRec['bed_dip'] = rec[bd_ind]
v_ind = rec.index('v=') + 1
vol = rec[v_ind][:-3]
date = rec[-2]
time = rec[-1]
SampRec['method_codes'] = meth_code
SampRec['site'] = site
SampRec['citations'] = 'This study'
SampRec['method_codes'] = 'SO-NO'
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['citations'] = 'This study'
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations'] = 'This study'
SiteRec['lat'] = lat
SiteRec['lon'] = lon
LocRec['location'] = location
LocRec['citations'] = 'This study'
LocRec['lat_n'] = lat
LocRec['lat_s'] = lat
LocRec['lon_e'] = lon
LocRec['lon_w'] = lon
SpecRecs.append(SpecRec)
SampRecs.append(SampRec)
SiteRecs.append(SiteRec)
LocRecs.append(LocRec)
for k in range(3, len(data)): # read in data
line = data[k]
rec = line.split()
if len(rec) > 1: # skip blank lines at bottom
MeasRec = {}
MeasRec['description'] = 'Date: ' + date + ' ' + time
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["specimen"] = specimen
if rec[0] == 'NRM':
meas_type = "LT-NO"
elif rec[0][0] == 'M' or rec[0][0] == 'H':
meas_type = "LT-AF-Z"
elif rec[0][0] == 'T':
meas_type = "LT-T-Z"
else:
print("measurement type unknown")
return False, "measurement type unknown"
X = [float(rec[1]), float(rec[2]), float(rec[3])]
Vec = pmag.cart2dir(X)
MeasRec["magn_moment"] = '%10.3e' % (Vec[2]) # Am^2
MeasRec["magn_volume"] = rec[4] # A/m
MeasRec["dir_dec"] = '%7.1f' % (Vec[0])
MeasRec["dir_inc"] = '%7.1f' % (Vec[1])
MeasRec["treat_ac_field"] = '0'
if meas_type != 'LT-NO':
treat = float(rec[0][1:])
else:
treat = 0
if meas_type == "LT-AF-Z":
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif meas_type == "LT-T-Z":
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
MeasRec['method_codes'] = meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def main():
"""
NAME
umich_magic.py
DESCRIPTION
converts UMICH .mag format files to magic_measurements format files
SYNTAX
umich_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .mag format input file, required
-fsa SAMPFILE : specify er_samples.txt file relating samples, site and locations names,default is none
-F FILE: specify output file, default is magic_measurements.txt
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
Format of UMICH .mag files:
Spec Treat CSD Intensity Declination Inclination metadata string
Spec: specimen name
Treat: treatment step
XXX T in Centigrade
XXX AF in mT
Intensity assumed to be total moment in 10^3 Am^2 (emu)
Declination: Declination in specimen coordinate system
Inclination: Declination in specimen coordinate system
metatdata string: mm/dd/yy;hh:mm;[dC,mT];xx.xx;UNITS;USER;INST;NMEAS
hh in 24 hours.
dC or mT units of treatment XXX (see Treat above) for thermal or AF respectively
xx.xxx DC field
UNITS of DC field (microT, mT)
INST: instrument code, number of axes, number of positions (e.g., G34 is 2G, three axes,
measured in four positions)
NMEAS: number of measurements in a single position (1,3,200...)
"""
# initialize some stuff
dir_path = '.'
infile_type = "mag"
noave = 0
methcode, inst = "", ""
phi, theta, peakfield, labfield = 0, 0, 0, 0
pTRM, MD, samp_con, Z = 0, 0, '1', 1
missing = 1
demag = "N"
er_location_name = ""
citation = 'This study'
args = sys.argv
methcode = "LP-NO"
samp_file, ErSamps = '', []
specnum = 0
#
# get command line arguments
#
meas_file = "magic_measurements.txt"
user = ""
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
meas_file = dir_path + '/' + args[ind + 1]
if '-f' in args:
ind = args.index("-f")
magfile = dir_path + '/' + args[ind + 1]
try:
input = open(magfile, 'r')
except:
print("bad mag file name")
sys.exit()
else:
print("mag_file field is required option")
print(main.__doc__)
sys.exit()
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if specnum != 0: specnum = -specnum
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = dir_path + '/' + args[ind + 1]
Samps, file_type = pmag.magic_read(samp_file)
if "-A" in args: noave = 1
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
samp_con = sys.argv[ind + 1]
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "7"
MagRecs, specs = [], []
version_num = pmag.get_version()
if infile_type == "mag":
for line in input.readlines():
instcode = ""
if len(line) > 2:
MagRec = {}
MagRec['er_location_name'] = er_location_name
MagRec['magic_software_packages'] = version_num
MagRec["treatment_temp"] = '%8.3e' % (273
) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (
273) # room temp in kelvin
MagRec["treatment_ac_field"] = '0'
MagRec["treatment_dc_field"] = '0'
MagRec["treatment_dc_field_phi"] = '0'
MagRec["treatment_dc_field_theta"] = '0'
meas_type = "LT-NO"
rec = line.split()
labfield = 0
code1 = rec[6].split(';')
date = code1[0].split('/') # break date into mon/day/year
yy = int(date[2])
if yy < 90:
yyyy = str(2000 + yy)
else:
yyyy = str(1900 + yy)
mm = int(date[0])
if mm < 10:
mm = "0" + str(mm)
else:
mm = str(mm)
dd = int(date[1])
if dd < 10:
dd = "0" + str(dd)
else:
dd = str(dd)
time = code1[1].split(':')
hh = int(time[0])
if hh < 10:
hh = "0" + str(hh)
else:
hh = str(hh)
min = int(time[1])
if min < 10:
min = "0" + str(min)
else:
min = str(min)
MagRec[
"measurement_date"] = yyyy + ":" + mm + ":" + dd + ":" + hh + ":" + min + ":00.00"
MagRec["measurement_time_zone"] = ''
instcode = ''
if len(code1) > 1:
MagRec["measurement_positions"] = code1[6][2]
else:
MagRec["measurement_positions"] = code1[
7] # takes care of awkward format with bubba and flo being different
if user == "": user = code1[5]
if code1[2][-1] == 'C': demag = "T"
if code1[2] == 'mT': demag = "AF"
treat = rec[1].split('.')
if len(treat) == 1: treat.append('0')
if demag == 'T' and treat != 0:
meas_type = "LT-T-Z"
MagRec["treatment_temp"] = '%8.3e' % (
float(treat[0]) + 273.) # temp in kelvin
if demag == "AF":
meas_type = "LT-AF-Z"
MagRec["treatment_ac_field"] = '%8.3e' % (
float(treat[0]) * 1e-3) # Af field in T
MagRec["treatment_dc_field"] = '0'
MagRec["er_specimen_name"] = rec[0]
if rec[0] not in specs:
specs.append(rec[0]) # get a list of specimen names
experiment = rec[0] + ":"
MagRec["er_site_name"] = ""
if specnum != 0:
MagRec["er_sample_name"] = rec[0][:specnum]
else:
MagRec["er_sample_name"] = rec[0]
if "-fsa" in args:
for samp in Samps:
if samp["er_sample_name"] == MagRec["er_sample_name"]:
MagRec["er_location_name"] = samp[
"er_location_name"]
MagRec["er_site_name"] = samp["er_site_name"]
break
elif int(samp_con) != 6:
site = pmag.parse_site(MagRec['er_sample_name'], samp_con,
Z)
MagRec["er_site_name"] = site
if MagRec['er_site_name'] == "":
print('No site name found for: ',
MagRec['er_specimen_name'], MagRec['er_sample_name'])
if MagRec["er_location_name"] == "":
print('no location name for: ', MagRec["er_specimen_name"])
if rec[1] == ".00": rec[1] = "0.00"
MagRec["measurement_csd"] = rec[2]
MagRec["measurement_magn_moment"] = '%10.3e' % (
float(rec[3]) * 1e-3) # moment in Am^2 (from emu)
MagRec["measurement_dec"] = rec[4]
MagRec["measurement_inc"] = rec[5]
MagRec["magic_instrument_codes"] = instcode
MagRec["er_analyst_mail_names"] = user
MagRec["er_citation_names"] = citation
MagRec["magic_method_codes"] = meas_type
MagRec["measurement_flag"] = 'g'
MagRec["er_specimen_name"] = rec[0]
MagRec["measurement_number"] = '1'
MagRecs.append(MagRec)
MagOuts = []
for spec in specs: # gather all demag types for this specimen
SpecRecs, meths, measnum = [], [], 1
for rec in MagRecs:
if rec['er_specimen_name'] == spec:
rec['measurement_number'] = str(measnum)
measnum += 1
if rec['magic_method_codes'] not in meths:
meths.append(rec['magic_method_codes'])
SpecRecs.append(rec)
expname = spec
if "LT-AF-Z" in meths: expname = expname + ':LP-DIR-AF'
if "LT-T-Z" in meths: expname = expname + ':LP-DIR-T'
for rec in SpecRecs:
rec['magic_experiment_name'] = expname
MagOuts.append(rec)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print("results put in ", meas_file)
def convert(**kwargs):
version_num = pmag.get_version()
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # Loc outfile
mag_file = kwargs.get('mag_file') #required
location = kwargs.get('location', 'unknown')
site = kwargs.get('site', '')
samp_con = kwargs.get('samp_con', '1')
specnum = int(kwargs.get('specnum', 0))
timezone = kwargs.get('timestamp', 'US/Pacific')
noave = kwargs.get('noave', False) # default False means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 0.025**3 #default volume is a 2.5 cm cube, translated to meters cubed
else:
volume *= 1e-6 #convert cm^3 to m^3
if specnum != 0:
specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z = int(samp_con.split("-")[1])
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z = int(samp_con.split("-")[1])
samp_con = "7"
else:
Z = 1
# format variables
if not os.path.isfile(mag_file):
print("%s is not a BGC file" % mag_file)
return False, 'You must provide a BCG format file'
mag_file = os.path.join(input_dir_path, mag_file)
# Open up the BGC file and read the header information
print('mag_file in bgc_magic', mag_file)
pre_data = open(mag_file, 'r')
line = pre_data.readline()
line_items = line.split(' ')
specimen = line_items[2]
specimen = specimen.replace('\n', '')
line = pre_data.readline()
line = pre_data.readline()
line_items = line.split('\t')
azimuth = float(line_items[1])
dip = float(line_items[2])
bed_dip = line_items[3]
sample_bed_azimuth = line_items[4]
lon = line_items[5]
lat = line_items[6]
tmp_volume = line_items[7]
if tmp_volume != 0.0:
volume = float(tmp_volume) * 1e-6
pre_data.close()
data = pd.read_csv(mag_file, sep='\t', header=3, index_col=False)
cart = np.array([data['X'], data['Y'], data['Z']]).transpose()
direction = pmag.cart2dir(cart).transpose()
data['dir_dec'] = direction[0]
data['dir_inc'] = direction[1]
data['magn_moment'] = old_div(
direction[2], 1000) # the data are in EMU - this converts to Am^2
data['magn_volume'] = old_div((old_div(direction[2], 1000)),
volume) # EMU - data converted to A/m
# Configure the magic_measurements table
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
for rowNum, row in data.iterrows():
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
if specnum != 0:
sample = specimen[:specnum]
else:
sample = specimen
if site == '':
site = pmag.parse_site(sample, samp_con, Z)
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['volume'] = volume
SpecRec['analysts'] = user
SpecRec['citations'] = 'This study'
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['azimuth'] = azimuth
SampRec['dip'] = dip
SampRec['bed_dip_direction'] = sample_bed_azimuth
SampRec['bed_dip'] = bed_dip
SampRec['method_codes'] = meth_code
SampRec['analysts'] = user
SampRec['citations'] = 'This study'
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRec['analysts'] = user
SiteRec['citations'] = 'This study'
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['analysts'] = user
LocRec['citations'] = 'This study'
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec['description'] = 'Date: ' + str(row['Date']) + ' Time: ' + str(
row['Time'])
if '.' in row['Date']: datelist = row['Date'].split('.')
elif '/' in row['Date']: datelist = row['Date'].split('/')
elif '-' in row['Date']: datelist = row['Date'].split('-')
else:
print(
"unrecogized date formating on one of the measurement entries for specimen %s"
% specimen)
datelist = ['', '', '']
if ':' in row['Time']: timelist = row['Time'].split(':')
else:
print(
"unrecogized time formating on one of the measurement entries for specimen %s"
% specimen)
timelist = ['', '', '']
datelist[2] = '19' + datelist[2] if len(
datelist[2]) <= 2 else datelist[2]
dt = ":".join([
datelist[1], datelist[0], datelist[2], timelist[0], timelist[1],
timelist[2]
])
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp = utc_dt.strftime("%Y-%m-%dT%H:%M:%S") + "Z"
MeasRec["timestamp"] = timestamp
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = rowNum
MeasRec["specimen"] = specimen
MeasRec["treat_ac_field"] = '0'
if row['DM Val'] == '0':
meas_type = "LT-NO"
elif int(row['DM Type']) > 0.0:
meas_type = "LT-AF-Z"
treat = float(row['DM Val'])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif int(row['DM Type']) == -1:
meas_type = "LT-T-Z"
treat = float(row['DM Val'])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
else:
print("measurement type unknown:", row['DM Type'], " in row ",
rowNum)
MeasRec["magn_moment"] = str(row['magn_moment'])
MeasRec["magn_volume"] = str(row['magn_volume'])
MeasRec["dir_dec"] = str(row['dir_dec'])
MeasRec["dir_inc"] = str(row['dir_inc'])
MeasRec['method_codes'] = meas_type
MeasRec['dir_csd'] = '0.0' # added due to magic.write error
MeasRec['meas_n_orient'] = '1' # added due to magic.write error
MeasRecs.append(MeasRec.copy())
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # Loc outfile
magfile = kwargs.get('magfile', '')
datafile = kwargs.get('datafile', '')
specnum = int(kwargs.get('specnum', 0))
labfield = int(kwargs.get('labfield', 0)) *1e-6
phi = int(kwargs.get('phi', 0))
theta = int(kwargs.get('theta', 0))
peakfield = kwargs.get('peakfield', 0)
if peakfield:
peakfield = float(peakfield)*1e-3
location = kwargs.get('location', '')
samp_con = kwargs.get('samp_con', '1')
codelist = kwargs.get('codelist', '')
CR_cooling_times = kwargs.get('CR_cooling_times', None)
noave = kwargs.get('noave', False)
# format and validate variables
if magfile:
try:
infile=open(os.path.join(input_dir_path,magfile),'r')
except IOError:
print("bad mag file name")
return False, "bad mag file name"
else:
print("mag_file field is required option")
print(__doc__)
return False, "mag_file field is required option"
if specnum!=0:
specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z=int(samp_con.split("-")[1])
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=int(samp_con.split("-")[1])
samp_con="7"
else: Z=1
if codelist:
codes=codelist.split(':')
else:
print("Must select experiment type (-LP option)")
return False, "Must select experiment type (-LP option)"
if "AF" in codes:
demag='AF'
LPcode="LP-DIR-AF"
if "T" in codes:
demag="T"
if not labfield: LPcode="LP-DIR-T"
if labfield: LPcode="LP-PI-TRM"
if "ANI" in codes:
if not labfield:
print("missing lab field option")
return False, "missing lab field option"
LPcode="LP-AN-TRM"
if "TRM" in codes:
demag="T"
LPcode="LP-TRM"
#trm=1
if "CR" in codes:
demag="T"
# dc should be in the code
if not labfield:
print("missing lab field option")
return False, "missing lab field option"
LPcode="LP-CR-TRM" # TRM in different cooling rates
if command_line:
ind=sys.argv.index("-LP")
CR_cooling_times=sys.argv[ind+2].split(",")
version_num=pmag.get_version()
#--------------------------------------
# Read the file
# Assumption:
# 1. different lab protocolsa are in different files
# 2. measurements are in the correct order
#--------------------------------------
Data={}
line_no=0
for line in infile.readlines():
line_no+=1
this_line_data={}
line_no+=1
instcode=""
if len(line)<2:
continue
if line[0]=="#": #HUJI way of marking bad data points
continue
rec=line.strip('\n').split()
specimen=rec[0]
date=rec[2].split("/")
hour=rec[3].split(":")
treatment_type=rec[4]
treatment=rec[5].split(".")
dec_core=rec[6]
inc_core=rec[7]
moment_emu=float(rec[-1])
if specimen not in list(Data.keys()):
Data[specimen]=[]
# check duplicate treatments:
# if yes, delete the first and use the second
if len(Data[specimen])>0:
if treatment==Data[specimen][-1]['treatment']:
del(Data[specimen][-1])
print("-W- Identical treatments in file %s magfile line %i: specimen %s, treatment %s ignoring the first. " %(magfile, line_no, specimen,".".join(treatment)))
this_line_data={}
this_line_data['specimen']=specimen
this_line_data['date']=date
this_line_data['hour']=hour
this_line_data['treatment_type']=treatment_type
this_line_data['treatment']=treatment
this_line_data['dec_core']=dec_core
this_line_data['inc_core']=inc_core
this_line_data['moment_emu']=moment_emu
this_line_data['azimuth']=''
this_line_data['dip']=''
this_line_data['bed_dip_direction']=''
this_line_data['bed_dip']=''
this_line_data['lat']=''
this_line_data['lon']=''
this_line_data['volume']=''
Data[specimen].append(this_line_data)
infile.close()
print("-I- done reading file %s"%magfile)
if datafile:
dinfile = open(datafile)
for line in dinfile.readlines():
data = line.split()
if len(data)<8 or data[0]=='': continue
elif data[0] in list(Data.keys()):
for i in range(len(Data[data[0]])):
Data[data[0]][i]['azimuth'] = data[1]
Data[data[0]][i]['dip'] = data[2]
try: Data[data[0]][i]['bed_dip_direction'] = float(data[3])+90
except ValueError: Data[data[0]][i]['bed_dip_direction'] = ''
Data[data[0]][i]['bed_dip'] = data[4]
Data[data[0]][i]['lat'] = data[5]
Data[data[0]][i]['lon'] = data[6]
Data[data[0]][i]['volume'] = data[7]
else:
print("no specimen %s found in magnetometer data file when reading specimen orientation data file, or data file record for specimen too short"%data[0])
dinfile.close()
#--------------------------------------
# Convert to MagIC
#--------------------------------------
specimens_list=list(Data.keys())
specimens_list.sort()
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
for specimen in specimens_list:
for i in range(len(Data[specimen])):
this_line_data=Data[specimen][i]
methcode=""
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
specimen=this_line_data['specimen']
if specnum!=0:
sample=this_line_data['specimen'][:specnum]
else:
sample=this_line_data['specimen']
site=pmag.parse_site(sample,samp_con,Z)
if not location:
location=site
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['azimuth'] = this_line_data['azimuth']
SampRec['dip'] = this_line_data['dip']
SampRec['bed_dip_direction'] = this_line_data['bed_dip_direction']
SampRec['bed_dip'] = this_line_data['bed_dip']
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = this_line_data['lat']
SiteRec['lon'] = this_line_data['lon']
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['lat_n'] = this_line_data['lat']
LocRec['lon_e'] = this_line_data['lon']
LocRec['lat_s'] = this_line_data['lat']
LocRec['lon_w'] = this_line_data['lon']
LocRecs.append(LocRec)
MeasRec['specimen'] = specimen
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["magn_moment"]='%10.3e'% (float(this_line_data['moment_emu'])*1e-3) # moment in Am^2 (from emu)
MeasRec["dir_dec"]=this_line_data['dec_core']
MeasRec["dir_inc"]=this_line_data['inc_core']
date=this_line_data['date']
hour=this_line_data['hour']
if len(date[2])<4 and float(date[2])>=70:
yyyy="19"+date[2]
elif len(date[2])<4 and float(date[2])<70:
yyyy="20"+date[2]
else: yyyy=date[2]
if len (date[0])==1:
date[0]="0"+date[0]
if len (date[1])==1:
date[1]="0"+date[1]
dt=":".join([date[0],date[1],yyyy,hour[0],hour[1],"0"])
local = pytz.timezone("America/New_York")
naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
MeasRec['analysts']=user
MeasRec["citations"]="This study"
MeasRec["instrument_codes"]="HUJI-2G"
MeasRec["quality"]="g"
MeasRec["meas_n_orient"]="1"
MeasRec["standard"]="u"
MeasRec["description"]=""
#----------------------------------------
# AF demag
# do not support AARM yet
#----------------------------------------
if demag=="AF":
treatment_type=this_line_data['treatment_type']
# demag in zero field
if LPcode != "LP-AN-ARM":
MeasRec["treat_ac_field"]='%8.3e' %(float(this_line_data['treatment'][0])*1e-3) # peak field in tesla
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
if treatment_type=="N":
methcode="LP-DIR-AF:LT-NO"
elif treatment_type=="A":
methcode="LP-DIR-AF:LT-AF-Z"
else:
print("ERROR in treatment field line %i... exiting until you fix the problem" %line_no)
print(this_line_data)
return False, "ERROR in treatment field line %i... exiting until you fix the problem" %line_no
# AARM experiment
else:
print("Dont supprot AARM in HUJI format yet. sorry... do be DONE")
MeasRec["method_codes"]=methcode
MeasRec["experiments"]=specimen+ ":" + LPcode
MeasRec["treat_step_num"]="%i"%i
MeasRec["description"]=""
MeasRecs.append(MeasRec)
#----------------------------------------
# Thermal:
# Thellier experiment: "IZ", "ZI", "IZZI", pTRM checks
# Thermal demag
# Thermal cooling rate experiment
# Thermal NLT
#----------------------------------------
if demag=="T":
treatment=this_line_data['treatment']
treatment_type=this_line_data['treatment_type']
#----------------------------------------
# Thellier experimet
#----------------------------------------
if LPcode == "LP-PI-TRM" : # Thelllier experiment
MeasRec["experiments"]=specimen+ ":" + LPcode
methcode=LPcode
if treatment_type=="N" or ( (treatment[1]=='0' or treatment[1]=='00') and float(treatment[0])==0):
LT_code="LT-NO"
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
MeasRec["treat_dc_field"]='0'
MeasRec["treat_temp"]='273.'
elif treatment[1]=='0' or treatment[1]=='00':
LT_code="LT-T-Z"
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
MeasRec["treat_dc_field"]='%8.3e'%(0)
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
# check if this is ZI or IZ:
# check if the same temperature already measured:
methcode="LP-PI-TRM:LP-PI-TRM-ZI"
for j in range (0,i):
if Data[specimen][j]['treatment'][0] == treatment[0]:
if Data[specimen][j]['treatment'][1] == '1' or Data[specimen][j]['treatment'][1] == '10':
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
else:
methcode="LP-PI-TRM:LP-PI-TRM-ZI"
elif treatment[1]=='1' or treatment[1]=='10':
LT_code="LT-T-I"
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
# check if this is ZI or IZ:
# check if the same temperature already measured:
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
for j in range (0,i):
if Data[specimen][j]['treatment'][0] == treatment[0]:
if Data[specimen][j]['treatment'][1] == '0' or Data[specimen][j]['treatment'][1] == '00':
methcode="LP-PI-TRM:LP-PI-TRM-ZI"
else:
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
elif treatment[1]=='2' or treatment[1]=='20':
LT_code="LT-PTRM-I"
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
else:
print("ERROR in treatment field line %i... exiting until you fix the problem" %line_no)
return False, "ERROR in treatment field line %i... exiting until you fix the problem" %line_no
MeasRec["method_codes"]=LT_code+":"+methcode
MeasRec["treat_step_num"]="%i"%i
MeasRec["description"]=""
MeasRecs.append(MeasRec)
#----------------------------------------
# demag experimet
#----------------------------------------
if LPcode == "LP-DIR-T" :
MeasRec["experiments"]=specimen+ ":" + LPcode
methcode=LPcode
if treatment_type=="N":
LT_code="LT-NO"
else:
LT_code="LT-T-Z"
methcode=LPcode+":"+"LT-T-Z"
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
MeasRec["treat_dc_field"]='%8.3e'%(0)
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MeasRec["method_codes"]=LT_code+":"+methcode
MeasRec["treat_step_num"]="%i"%i
MeasRec["description"]=""
MeasRecs.append(MeasRec)
#continue
#----------------------------------------
# ATRM measurements
# The direction of the magnetization is used to determine the
# direction of the lab field.
#----------------------------------------
if LPcode =="LP-AN-TRM":
MeasRec["experiments"]=specimen+ ":" + LPcode
methcode=LPcode
if float(treatment[1])==0:
MeasRec["method_codes"]="LP-AN-TRM:LT-T-Z"
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MeasRec["treat_dc_field"]='0'
else:
if float(treatment[1])==7:
# alteration check
methcode="LP-AN-TRM:LT-PTRM-I"
MeasRec["treat_step_num"]='7'# -z
else:
MeasRec["method_codes"]="LP-AN-TRM:LT-T-I"
inc=float(MeasRec["dir_inc"]);dec=float(MeasRec["dir_dec"])
if abs(inc)<45 and (dec<45 or dec>315): # +x
tdec,tinc=0,0
MeasRec["treat_step_num"]='1'
if abs(inc)<45 and (dec<135 and dec>45):
tdec,tinc=90,0
MeasRec["treat_step_num"]='2' # +y
if inc>45 :
tdec,tinc=0,90
MeasRec["treat_step_num"]='3' # +z
if abs(inc)<45 and (dec<225 and dec>135):
tdec,tinc=180,0
MeasRec["treat_step_num"]='4' # -x
if abs(inc)<45 and (dec<315 and dec>225):
tdec,tinc=270,0
MeasRec["treat_step_num"]='5'# -y
if inc<-45 :
tdec,tinc=0,-90
MeasRec["treat_step_num"]='6'# -z
MeasRec["treat_dc_field_phi"]='%7.1f' %(tdec)
MeasRec["treat_dc_field_theta"]='%7.1f'% (tinc)
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
MeasRec["description"]=""
MeasRecs.append(MeasRec)
#continue
#----------------------------------------
# NLT measurements
# or TRM acquisistion experiment
#----------------------------------------
if LPcode == "LP-TRM" :
MeasRec["experiments"]=specimen+ ":" + LPcode
MeasRec["method_codes"]="LP-TRM:LT-T-I"
if float(treatment[1])==0:
labfield=0
else:
labfield=float(float(treatment[1]))*1e-6
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MeasRec["treat_step_num"]="%i"%i
MeasRec["description"]=""
MeasRecs.append(MeasRec)
#continue
#----------------------------------------
# Cooling rate experiments
#----------------------------------------
if LPcode =="LP-CR-TRM":
index=int(treatment[1][0])
#print index,"index"
#print CR_cooling_times,"CR_cooling_times"
#print CR_cooling_times[index-1]
#print CR_cooling_times[0:index-1]
if index==7 or index==70: # alteration check as final measurement
meas_type="LT-PTRM-I:LP-CR-TRM"
CR_cooling_time=CR_cooling_times[-1]
else:
meas_type="LT-T-I:LP-CR-TRM"
CR_cooling_time=CR_cooling_times[index-1]
MeasRec["method_codes"]=meas_type
MeasRec["experiments"]=specimen+ ":" + LPcode
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MeasRec["treat_step_num"]="%i"%index
MeasRec["description"]="cooling_rate"+":"+CR_cooling_time+":"+"K/min"
#MeasRec["description"]="%.1f minutes per cooling time"%int(CR_cooling_time)
MeasRecs.append(MeasRec)
#continue
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
# initialize some stuff
citations = 'This study'
units = 'cgs'
meth = "LP-HYS"
version_num = pmag.get_version()
args = sys.argv
Samps, Sites = [], []
noave = 1
# get args
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 0) # measurements outfile
spec_file = kwargs.get('spec_file', 0) # specimen outfile
samp_file = kwargs.get('samp_file', 0) # sample outfile
site_file = kwargs.get('site_file', 0) # site outfile
loc_file = kwargs.get('loc_file', 0) # location outfile
agm_file = kwargs.get('agm_file', '')
specnum = kwargs.get('specnum', 0)
specimen = kwargs.get('specimen', 0)
if not specimen:
# grab the specimen name from the input file name
specimen = agm_file.split('.')[0]
if not meas_file:
meas_file = specimen + '.magic'
if not spec_file:
spec_file = specimen + '_specimens.txt'
if not samp_file:
samp_file = specimen + '_samples.txt'
if not site_file:
site_file = specimen + '_sites.txt'
if not loc_file:
loc_file = specimen + '_locations.txt'
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
site_infile = kwargs.get('site_infile', '')
samp_infile = kwargs.get('samp_infile', '')
spec_infile = kwargs.get('spec_infile', '')
inst = kwargs.get('ins', '')
institution = kwargs.get('institution', '')
syn = kwargs.get('syn', 0)
syntype = kwargs.get('syntype', '')
inst = kwargs.get('ins', '')
bak = kwargs.get('bak', 0)
units = kwargs.get('units', 0)
if bak:
meth = "LP-IRM-DCD"
output = output_dir_path + "/irm.magic"
fmt = kwargs.get('new', 0)
xy = kwargs.get('xy', 0)
if fmt:
fmt = 'new'
if not fmt:
fmt = 'old'
if xy:
fmt = 'xy'
if specnum != 0:
specnum = -specnum
if "4" == samp_con[0]:
if "-" not in samp_con:
print(
"naming convention option [4] must be in form 4-Z where Z is an integer")
print('---------------')
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" == samp_con[0]:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
else:
Z = 0
# read stuff in
if site_infile:
Sites, file_type = pmag.magic_read(site_infile)
if samp_infile:
Samps, file_type = pmag.magic_read(samp_infile)
if spec_infile:
Specs, file_type = pmag.magic_read(spec_infile)
if agm_file:
Data = pmag.open_file(agm_file)
if not Data:
print("you must provide a valid agm_file")
return False, "you must provide a valid agm_file"
if not agm_file:
print(__doc__)
print("agm_file field is required option")
return False, "agm_file field is required option"
if "ASCII" not in Data[0] and fmt != 'xy':
fmt = 'new'
measnum, start, end = 1, 0, 0
if fmt == 'new': # new Micromag formatted file
end = 2
for skip in range(len(Data)):
line = Data[skip]
rec = line.strip('\n').strip('\r').split()
if 'Units' in line:
units = rec[-1]
if "Raw" in rec:
start = skip + 2
if ("Field" in rec) and ("Moment" in rec) and (not start):
start = skip + 2
break
elif fmt == 'old':
start = 2
end = 1
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
version_num = pmag.get_version()
##################################
# parse data
stop = len(Data) - end
for line in Data[start:stop]: # skip header stuff
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
# take care of some paper work
if syn == 0:
MeasRec["specimen"] = specimen
if specnum != 0:
sample = specimen[:specnum]
else:
sample = specimen
if samp_infile and Samps: # if samp_infile was provided AND yielded sample data
samp = pmag.get_dictitem(Samps, 'sample', sample, 'T')
if len(samp) > 0:
site = samp[0]["site"]
else:
site = ''
if site_infile and Sites: # if samp_infile was provided AND yielded sample data
sites = pmag.get_dictitem(Sites, 'sample', sample, 'T')
if len(sites) > 0:
site = sites[0]["site"]
else:
site = ''
else:
site = pmag.parse_site(sample, samp_con, Z)
if location != '' and location not in [x['location'] if 'location' in list(x.keys()) else '' for x in LocRecs]:
LocRec['location'] = location
LocRecs.append(LocRec)
if site != '' and site not in [x['site'] if 'site' in list(x.keys()) else '' for x in SiteRecs]:
SiteRec['location'] = location
SiteRec['site'] = site
SiteRecs.append(SiteRec)
if sample != '' and sample not in [x['sample'] if 'sample' in list(x.keys()) else '' for x in SampRecs]:
SampRec['site'] = site
SampRec['sample'] = sample
SampRecs.append(SampRec)
if specimen != '' and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else '' for x in SpecRecs]:
SpecRec["specimen"] = specimen
SpecRec['sample'] = sample
SpecRecs.append(SpecRec)
else:
SampRec["material_type"] = syntype
MeasRec["specimen"] = specimen
if specnum != 0:
sample = specimen[:specnum]
else:
sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
if location != '' and location not in [x['location'] if 'location' in list(x.keys()) else '' for x in LocRecs]:
LocRec['location'] = location
LocRecs.append(LocRec)
if site != '' and site not in [x['site'] if 'site' in list(x.keys()) else '' for x in SiteRecs]:
SiteRec['location'] = location
SiteRec['site'] = site
SiteRecs.append(SiteRec)
if sample != '' and sample not in [x['sample'] if 'sample' in list(x.keys()) else '' for x in SampRecs]:
SampRec['site'] = site
SampRec['sample'] = sample
SampRecs.append(SampRec)
if specimen != '' and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else '' for x in SpecRecs]:
SpecRec["specimen"] = specimen
SpecRec['sample'] = sample
SpecRecs.append(SpecRec)
MeasRec['instrument_codes'] = inst
MeasRec['institution'] = institution
MeasRec['method_codes'] = meth
MeasRec['experiment'] = specimen + ':' + meth
if fmt == 'xy':
rec = list(line.strip('\n').split())
else:
rec = list(line.strip('\n').strip('\r').split(','))
#print (rec)
if rec[0] != "":
if units == 'cgs':
field = float(rec[0]) * 1e-4 # convert from oe to tesla
else:
field = float(rec[0]) # field in tesla
if meth == "LP-HYS":
MeasRec['meas_field_dc'] = '%10.3e' % (field)
MeasRec['treat_dc_field'] = '0'
else:
MeasRec['meas_field_dc'] = '0'
MeasRec['treat_dc_field'] = '%10.3e' % (field)
if units == 'cgs':
MeasRec['magn_moment'] = '%10.3e' % (
float(rec[1]) * 1e-3) # convert from emu to Am^2
else:
MeasRec['magn_moment'] = '%10.3e' % (float(rec[1])) # Am^2
MeasRec['treat_temp'] = '273' # temp in kelvin
MeasRec['meas_temp'] = '273' # temp in kelvin
MeasRec['quality'] = 'g'
MeasRec['standard'] = 'u'
MeasRec['treat_step_num'] = '%i' % (measnum)
MeasRec['measurement'] = specimen + ":" + meth + '%i' % (measnum)
measnum += 1
MeasRec['software_packages'] = version_num
MeasRec['description'] = ""
MeasRecs.append(MeasRec)
# we have to relabel LP-HYS method codes. initial loop is LP-IMT, minor
# loops are LP-M - do this in measurements_methods function
if meth == 'LP-HYS':
recnum = 0
while float(MeasRecs[recnum]['meas_field_dc']) < float(MeasRecs[recnum + 1]['meas_field_dc']) and recnum + 1 < len(MeasRecs): # this is LP-IMAG
MeasRecs[recnum]['method_codes'] = 'LP-IMAG'
MeasRecs[recnum]['experiment'] = MeasRecs[recnum]['specimen'] + \
":" + 'LP-IMAG'
recnum += 1
#
con = nb.Contribution(output_dir_path, read_tables=[])
# create MagIC tables
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
# MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasRecs)
# write MagIC tables to file
con.write_table_to_file('specimens', custom_name=spec_file)
con.write_table_to_file('samples', custom_name=samp_file)
con.write_table_to_file('sites', custom_name=site_file)
con.write_table_to_file('locations', custom_name=loc_file)
con.write_table_to_file('measurements', custom_name=meas_file)
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
utrecht_magic.py
DESCRIPTION
converts Utrecht magnetometer data files to magic_measurements files
SYNTAX
utrecht_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-WD: output directory for MagIC files
-ncn: Site Naming Convention
Site to Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2: default] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
-spc: number of characters to remove to generate sample names from specimen names
-dmy: European date format
-loc LOCNAME : specify location/study name
-lat latitude of samples
-lon longitude of samples
-A: don't average replicate measurements
-mcd: [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-dc: B PHI THETA: dc lab field (in microTesla), phi,and theta must be input as a tuple "(DC,PHI,THETA)". If not input user will be asked for values, this is advantagious if there are differing dc fields between steps or specimens. Note: this currently only works with the decimal IZZI naming convetion (XXX.0,1,2,3 where XXX is the treatment temperature and 0 is a zero field step, 1 is in field, and 2 is a pTRM check, 3 is a tail check). All other steps are hardcoded dc_field = 0.
INPUT
Utrecht magnetometer data file
"""
# initialize some stuff
sample_lat = 0.0
sample_lon = 0.0
noave = 0
er_location_name = "unknown"
args = sys.argv
meth_code = "LP-NO"
version_num = pmag.get_version()
site_num = 1
mag_file = ""
dir_path = '.'
MagRecs = []
SpecOuts = []
SampOuts = []
SiteOuts = []
meas_file = 'magic_measurements.txt'
spec_file = 'er_specimens.txt'
samp_file = 'er_samples.txt'
site_file = 'er_sites.txt'
meth_code = ""
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsp' in args:
ind = args.index("-Fsp")
spec_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
if '-Fsi' in args: # LORI addition
ind = args.index("-Fsi")
site_file = args[ind + 1]
#try:
# open(samp_file,'r')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-lat" in args:
ind = args.index("-lat")
site_lat = args[ind + 1]
if "-lon" in args:
ind = args.index("-lon")
site_lon = args[ind + 1]
if "-A" in args:
noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind + 1]
#samp_con='5'
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print(
"option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
site_num = samp_con.split("-")[1]
samp_con = "4"
elif "7" in samp_con:
if "-" not in samp_con:
print(
"option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
site_num = samp_con.split("-")[1]
samp_con = "7"
else:
samp_con = "1"
if '-dc' in args:
ind = args.index('-dc')
DC_FIELD, DC_PHI, DC_THETA = list(
map(float, args[ind + 1].strip('( ) [ ]').split(',')))
DC_FIELD *= 1e-6
yn = ''
GET_DC_PARAMS = False
else:
DC_FIELD, DC_PHI, DC_THETA = 0, 0, -90
if '-spc' in args:
ind = args.index("-spc")
specnum = -int(args[ind + 1])
else:
specnum = 0
if '-dmy' in args:
ind = args.index("-dmy")
dmy_flag = True
else:
dmy_flag = False
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file',
'er_specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt') # site outfile
er_location_name = kwargs.get('location_name', '')
site_lat = kwargs.get('site_lat', '')
site_lon = kwargs.get('site_lon', '')
#oave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
specnum = -int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '2')
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
site_num = samp_con.split("-")[1]
samp_con = "4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
site_num = samp_con.split("-")[1]
samp_con = "7"
DC_FIELD, DC_PHI, DC_THETA = list(
map(float, kwargs.get('dc_params', (0, 0, -90))))
DC_FIELD *= 1e-6
noave = kwargs.get('avg', True)
dmy_flag = kwargs.get('dmy_flag', False)
# format variables
if not mag_file:
return False, 'You must provide a Utrecht formated file'
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
# parse data
# Open up the Utrecht file and read the header information
print('mag_file in utrecht_file', mag_file)
AF_or_T = mag_file.split('.')[-1]
data = open(mag_file, 'r')
line = data.readline()
line_items = line.split(',')
operator = line_items[0]
operator = operator.replace("\"", "")
machine = line_items[1]
machine = machine.replace("\"", "")
machine = machine.rstrip('\n')
print("operator=", operator)
print("machine=", machine)
#read in measurement data
line = data.readline()
while line != "END" and line != '"END"':
ErSpecRec, ErSampRec, ErSiteRec = {}, {}, {}
line_items = line.split(',')
spec_name = line_items[0]
spec_name = spec_name.replace("\"", "")
print("spec_name=", spec_name)
free_string = line_items[1]
free_string = free_string.replace("\"", "")
print("free_string=", free_string)
dec = line_items[2]
print("dec=", dec)
inc = line_items[3]
print("inc=", inc)
volume = float(line_items[4])
volume = volume * 1e-6 # enter volume in cm^3, convert to m^3
print("volume=", volume)
bed_plane = line_items[5]
print("bed_plane=", bed_plane)
bed_tilt = line_items[6]
print("bed_tilt=", bed_tilt)
# Configure et er_ tables
ErSpecRec['er_specimen_name'] = spec_name
if specnum == 0: sample_name = spec_name
else: sample_name = spec_name[:specnum]
ErSampRec['er_sample_name'] = sample_name
ErSpecRec['er_sample_name'] = sample_name
er_site_name = pmag.parse_site(sample_name, samp_con, site_num)
ErSpecRec['er_site_name'] = er_site_name
ErSpecRec['er_location_name'] = er_location_name
ErSampRec['sample_azimuth'] = dec
ErSampRec['sample_dip'] = str(float(inc) - 90)
ErSampRec['sample_bed_dip_direction'] = bed_plane
ErSampRec['sample_bed_tilt'] = bed_tilt
ErSiteRec['site_lat'] = site_lat
ErSiteRec['site_lon'] = site_lon
ErSpecRec['magic_method_codes'] = meth_code
ErSampRec['er_location_name'] = er_location_name
ErSiteRec['er_location_name'] = er_location_name
ErSiteRec['er_site_name'] = er_site_name
ErSampRec['er_site_name'] = er_site_name
ErSampRec['er_citation_names'] = 'This study'
SpecOuts.append(ErSpecRec)
SampOuts.append(ErSampRec)
SiteOuts.append(ErSiteRec)
#measurement data
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
while line != '9999':
print(line)
step = items[0]
step = step.split('.')
step_value = step[0]
step_type = ""
if len(step) == 2:
step_type = step[1]
if step_type == '5':
step_value = items[0]
A = float(items[1])
B = float(items[2])
C = float(items[3])
# convert to MagIC coordinates
Z = -A
X = -B
Y = C
cart = np.array([X, Y, Z]).transpose()
direction = pmag.cart2dir(cart).transpose()
measurement_dec = direction[0]
measurement_inc = direction[1]
measurement_magn_moment = direction[
2] * 1.0e-12 # the data are in pico-Am^2 - this converts to Am^2
measurement_magn_volume = direction[
2] * 1.0e-12 / volume # data volume normalized - converted to A/m
print("measurement_magn_moment=", measurement_magn_moment)
print("measurement_magn_volume=", measurement_magn_volume)
error = items[4]
date = items[5]
date = date.strip('"')
if date.count("-") > 0:
date = date.split("-")
elif date.count("/") > 0:
date = date.split("/")
else:
print("date format seperator cannot be identified")
print(date)
time = items[6]
time = time.strip('"')
time = time.split(":")
print(time)
if dmy_flag:
date_time = date[1] + ":" + date[0] + ":" + date[
2] + ":" + time[0] + ":" + time[1] + ":" + "0.0"
else:
date_time = date[0] + ":" + date[1] + ":" + date[
2] + ":" + time[0] + ":" + time[1] + ":" + "0.0"
print(date_time)
MagRec = {}
MagRec["er_analyst_mail_names"] = operator
MagRec["magic_instrument_codes"] = "Utrecht_" + machine
MagRec["measurement_description"] = "free string = " + free_string
MagRec["measurement_date"] = date_time
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = er_site_name
MagRec['er_sample_name'] = sample_name
MagRec['magic_software_packages'] = version_num
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec[
"magic_experiment_name"] = er_location_name + er_site_name + spec_name
MagRec[
"measurement_number"] = er_location_name + er_site_name + spec_name + items[
0]
MagRec["er_specimen_name"] = spec_name
# MagRec["treatment_ac_field"] = '0'
if AF_or_T.lower() == "th":
MagRec["treatment_temp"] = '%8.3e' % (float(step_value) + 273.
) # temp in kelvin
MagRec['treatment_ac_field'] = '0'
meas_type = "LP-DIR-T:LT-T-Z"
else:
MagRec['treatment_temp'] = '273'
MagRec['treatment_ac_field'] = '%10.3e' % (float(step_value) *
1e-3)
meas_type = "LP-DIR-AF:LT-AF-Z"
MagRec['treatment_dc_field'] = '0'
if step_value == '0':
meas_type = "LT-NO"
print("step_type=", step_type)
if step_type == '0' and AF_or_T.lower() == 'th':
if meas_type == "":
meas_type = "LT-T-Z"
else:
meas_type = meas_type + ":" + "LT-T-Z"
elif step_type == '1':
if meas_type == "":
meas_type = "LT-T-I"
else:
meas_type = meas_type + ":" + "LT-T-I"
MagRec['treatment_dc_field'] = '%1.2e' % DC_FIELD
elif step_type == '2':
if meas_type == "":
meas_type = "LT-PTRM-I"
else:
meas_type = meas_type + ":" + "LT-PTRM-I"
MagRec['treatment_dc_field'] = '%1.2e' % DC_FIELD
elif step_type == '3':
if meas_type == "":
meas_type = "LT-PTRM-Z"
else:
meas_type = meas_type + ":" + "LT-PTRM-Z"
print("meas_type=", meas_type)
MagRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MagRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
MagRec['magic_method_codes'] = meas_type
MagRec["measurement_magn_moment"] = measurement_magn_moment
MagRec["measurement_magn_volume"] = measurement_magn_volume
MagRec["measurement_dec"] = measurement_dec
MagRec["measurement_inc"] = measurement_inc
MagRec['measurement_csd'] = error
# MagRec['measurement_positions'] = '1'
MagRecs.append(MagRec)
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
# write out the data to MagIC data files
pmag.magic_write(spec_file, SpecOuts, 'er_specimens')
pmag.magic_write(samp_file, SampOuts, 'er_samples')
pmag.magic_write(site_file, SiteOuts, 'er_sites')
# MagOuts = pmag.measurements_methods(MagRecs, noave)
# pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
pmag.magic_write(meas_file, MagRecs, 'magic_measurements')
print("results put in ", meas_file)
print("exit!")
return True, meas_file
def cit_magic(command_line=True, **kwargs):
"""
NAME
cit_magic.py
DESCRIPTION
converts CIT and .sam format files to magic_measurements format files
SYNTAX
cit_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .sam format input file, required
-fsi SITEFILE : specify file with site names and locations [tab delimited magic file]
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt # LORI
-n [gm,kg,cc,m3]: specify normalization
-A: don't average replicate measurements
-spc NUM : specify number of characters to designate a specimen, default = 0
-ncn NCON: specify naming convention
-loc LOCNAME : specify location/study name, must have either LOCNAME or SITEFILE or be a synthetic
-mcd [FS-FD:SO-MAG,.....] colon delimited list for method codes applied to all specimens in .sam file
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.)
NOTES:
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
"""
#
#initialize variables
norm = 'cc'
samp_con, Z = '3', 1
meas_file = 'magic_measurements.txt'
spec_file = 'er_specimens.txt'
samp_file = 'er_samples.txt'
site_file = 'er_sites.txt'
ErSpecs, ErSamps, ErSites, ErLocs, ErCits = [], [], [], [], []
MeasRecs = []
specnum, units, locname = 0, "1", "unknown"
citation = "This study"
dir_path = '.'
args = sys.argv
if command_line:
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-h" in args:
print main.__doc__
return False
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsp' in args:
ind = args.index("-Fsp")
spec_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
if '-Fsi' in args: # LORI addition
ind = args.index("-Fsi")
site_file = args[ind + 1]
if '-loc' in args:
ind = args.index("-loc")
locname = args[ind + 1]
if '-mcd' in args:
ind = args.index("-mcd")
methods = args[ind + 1]
else:
methods = 'SO-MAG'
if '-spc' in args:
ind = args.index("-spc")
specnum = -int(args[ind + 1])
if '-n' in args:
ind = args.index("-n")
norm = args[ind + 1]
if "-A" in args:
avg = 1
else:
avg = 0
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if '-f' in args:
ind = args.index("-f")
magfile = args[ind + 1]
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
# LJ
# if you are running as a module:
elif not command_line:
dir_path = kwargs.get('dir_path', '.')
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file',
'magic_measurements.txt') # outfile
spec_file = kwargs.get('spec_file',
'er_specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'er_samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'er_sites.txt') # site outfile
locname = kwargs.get('locname', '')
methods = kwargs.get('methods', ['SO-MAG'])
specnum = -int(kwargs.get('specnum', 0))
norm = kwargs.get('norm', 'cc')
avg = kwargs.get('avg', 0) # 0 means do average, 1 means don't
samp_con = kwargs.get('samp_con', '3')
magfile = kwargs.get('magfile', '')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
# done with module-specific stuff
# formatting and checking variables
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
magfile = os.path.join(input_dir_path, magfile)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
meas_file = os.path.join(output_dir_path, meas_file)
try:
file_input = open(magfile, 'r')
except Exception as ex:
print "bad sam file name: ", magfile
return False, "bad sam file name"
File = file_input.readlines()
if len(File) == 1:
File = File[0].split('\r')
File = map(lambda x: x + "\r\n", File)
sids, ln, format = [], 0, 'CIT'
formats = ['CIT', '2G', 'APP', 'JRA']
if File[ln].strip() == 'CIT': ln += 1
ErLocRec = {}
ErLocRec["er_location_name"] = locname
ErLocRec["er_citation_names"] = citation
comment = File[ln]
if comment == 'CIT':
format = comment
ln += 1
comment = File[ln]
#print comment
ln += 1
specimens, samples, sites = [], [], []
if format == 'CIT':
line = File[ln].split()
site_lat = line[0]
site_lon = line[1]
ErLocRec["location_begin_lat"] = site_lat
ErLocRec["location_begin_lon"] = site_lon
ErLocRec["location_end_lat"] = site_lat
ErLocRec["location_end_lon"] = site_lon
ErLocs.append(ErLocRec)
try:
Cdec = float(line[2])
except ValueError:
pdb.set_trace()
for k in range(ln + 1, len(File)):
line = File[k]
rec = line.split()
if rec == []: continue
specimen = rec[0]
specimens.append(specimen)
for specimen in specimens:
ErSpecRec, ErSampRec, ErSiteRec = {}, {}, {}
if specnum != 0:
sample = specimen[:specnum]
else:
sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
ErSpecRec['er_specimen_name'] = specimen
ErSpecRec['er_sample_name'] = sample
ErSpecRec['er_site_name'] = site
ErSpecRec['er_location_name'] = locname
ErSpecRec['er_citation_names'] = citation
ErSampRec['er_sample_name'] = sample
ErSampRec['er_site_name'] = site
ErSampRec['er_location_name'] = locname
ErSampRec['er_citation_names'] = citation
ErSampRec['magic_method_codes'] = methods
ErSampRec['sample_declination_correction'] = '%7.1f' % (Cdec)
ErSiteRec['er_site_name'] = site
ErSiteRec['er_location_name'] = locname
ErSiteRec['er_citation_names'] = citation
ErSiteRec['site_lat'] = site_lat
ErSiteRec['site_lon'] = site_lon
f = open(input_dir_path + '/' + specimen, 'rU')
Lines = f.readlines()
comment = ""
line = Lines[0].split()
if len(line) > 2:
comment = line[2]
info = Lines[1].split()
vol = float(info[-1])
if vol != 1.0:
if norm == 'cc': units = "1"
if norm == 'm3': units = "2"
ErSpecRec['specimen_weight'] = ""
if units == "1" or "":
ErSpecRec['specimen_volume'] = '%10.3e' % (vol * 1e-6)
else:
ErSpecRec['specimen_volume'] = '%10.3e' % (vol)
else:
if norm == 'cc': units = "1"
if norm == 'm3': units = "2"
ErSpecRec['specimen_volume'] = ""
if units == "1" or "":
ErSpecRec['specimen_weight'] = '%10.3e' % (vol * 1e-3)
else:
ErSpecRec['specimen_weight'] = '%10.3e' % (vol)
dip = float(info[-2])
dip_direction = float(info[-3]) + Cdec + 90.
sample_dip = -float(info[-4])
sample_azimuth = float(info[-5]) + Cdec - 90.
if len(info) > 5:
ErSampRec['sample_height'] = info[-6]
else:
ErSampRec['sample_height'] = '0'
ErSampRec['sample_azimuth'] = '%7.1f' % (sample_azimuth)
ErSampRec['sample_dip'] = '%7.1f' % (sample_dip)
ErSampRec['sample_bed_dip'] = '%7.1f' % (dip)
ErSampRec['sample_bed_dip_direction'] = '%7.1f' % (dip_direction)
ErSampRec['sample_class'] = ''
ErSampRec['sample_type'] = ''
ErSampRec['sample_lithology'] = ''
if Cdec != 0 or Cdec != "":
ErSampRec['magic_method_codes'] = 'SO-CMD-NORTH'
else:
ErSampRec['magic_method_codes'] = 'SO-MAG'
for line in Lines[2:len(Lines)]:
#print 'line:', line
MeasRec = ErSpecRec.copy()
# Remove specimen_volume and specimen_weight as they do not exits in the magic_measurement table
del MeasRec["specimen_volume"]
del MeasRec["specimen_weight"]
treat_type = line[0:3]
treat = line[2:6]
try:
float(treat)
except ValueError:
treat = line[3:6]
if treat_type.startswith('NRM'):
MeasRec['magic_method_codes'] = 'LT-NO'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '273'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_ac_field'] = '0'
elif treat_type.startswith('AF'):
MeasRec['magic_method_codes'] = 'LT-AF-Z'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '273'
MeasRec['treatment_dc_field'] = '0'
if treat.strip() == '':
MeasRec['treatment_ac_field'] = '0'
else:
MeasRec['treatment_ac_field'] = '%10.3e' % (float(treat) *
1e-3)
elif treat_type.startswith('ARM'):
MeasRec['magic_method_codes'] = "LP-ARM"
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '273'
MeasRec['treatment_dc_field'] = '0'
if treat.strip() == '':
MeasRec['treatment_ac_field'] = '0'
else:
MeasRec['magic_method_codes'] = "LP-ARM-AFD"
MeasRec['treatment_ac_field'] = '%10.3e' % (float(treat) *
1e-3)
elif treat_type.startswith('TT'):
MeasRec['magic_method_codes'] = 'LT-T-Z'
MeasRec['measurement_temp'] = '273'
if treat.strip() == '':
MeasRec['treatment_temp'] = '273'
else:
MeasRec['treatment_temp'] = '%7.1f' % (float(treat) + 273)
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_ac_field'] = '0'
elif treat_type.startswith('LT') or treat_type.startswith('LN2'):
MeasRec['magic_method_codes'] = 'LT-LT-Z'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '77'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_ac_field'] = '0'
else:
print "trouble with your treatment steps"
MeasRec['measurement_dec'] = line[46:51]
MeasRec['measurement_inc'] = line[52:58]
M = '%8.2e' % (float(line[31:39]) * vol * 1e-3) # convert to Am2
MeasRec['measurement_magn_moment'] = M
MeasRec['measurement_csd'] = '%7.1f' % (eval(line[41:46]))
MeasRec["measurement_positions"] = '1'
MeasRec['measurement_standard'] = 'u'
if len(line) > 60:
MeasRec['magic_instrument_codes'] = line[85:]
MeasRec['measurement_sd_x'] = '%8.2e' % (
float(line[58:67]) * 1e-8) #(convert e-5emu to Am2)
MeasRec['measurement_sd_y'] = '%8.2e' % (float(line[67:76]) *
1e-8)
MeasRec['measurement_sd_z'] = '%8.2e' % (float(line[76:85]) *
1e-8)
MeasRecs.append(MeasRec)
ErSpecs.append(ErSpecRec)
if sample not in samples:
samples.append(sample)
ErSamps.append(ErSampRec)
site = pmag.parse_site(sample, samp_con, Z)
if site not in sites:
sites.append(site)
ErSites.append(ErSiteRec)
er_specs = magic_write(spec_file, ErSpecs, 'er_specimens')
#print 'specimens stored in "er_specs"'
er_samps = magic_write(samp_file, ErSamps, 'er_samples')
#print 'samples stored in "er_samps"'
er_sites = magic_write(site_file, ErSites, 'er_sites')
#print 'sites stored in "er_sites"'
Fixed = pmag.measurements_methods(MeasRecs, avg)
magic_meas = magic_write(meas_file, Fixed, 'magic_measurements')
#print 'data stored in "magic_meas"'
return True, meas_file, str(er_specs), str(er_samps), str(er_sites), str(
magic_meas)
def main():
"""
NAME
mst_magic.py
DESCRIPTION
converts MsT data (T,M) to magic_measurements format files
SYNTAX
mst_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify T,M format input file, required
-fsa SFILE: name with sample, site, location information
-F FILE: specify output file, default is MsT_measurements.txt
-dc H: specify applied field during measurement, default is 0.5 T
-syn : This is a synthetic specimen and has no sample/site/location information
-spn SPEC: specimen name
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-ncn NCON: specify naming convention: default is #1 below
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT files:
T M: T is in Centigrade and M is uncalibrated magnitude
"""
# initialize some stuff
samp_con,Z="1","0"
dir_path='.'
citation='This study'
args=sys.argv
specnum,measnum=0,1
#
# get command line arguments
#
user=""
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
meas_file=dir_path+"/MsT_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
labfield='0.5'
if "-dc" in args:
ind=args.index("-dc")
labfield=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=dir_path+'/'+args[ind+1]
Samps,file_type=pmag.magic_read(samp_file)
if '-f' in args:
ind=args.index("-f")
infile=dir_path+'/'+args[ind+1]
try:
input=open(infile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print main.__doc__
print "-f is required option"
sys.exit()
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
er_location_name,syn,specimen_name='unknown',0,'unknown'
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-spn" in args:
ind=args.index("-spn")
specimen_name=args[ind+1]
else:
print main.__doc__
print "-spn is required option"
sys.exit()
if "-syn" in args: syn=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
samp_con=sys.argv[ind+1]
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
MagRecs,specs=[],[]
version_num=pmag.get_version()
data=input.readlines()
T0=float(data[0].split()[0])
for line in data:
instcode=""
if len(line)>1:
MagRec={}
if syn==0: MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_dc_field"]=labfield
rec=line.split()
T=float(rec[0])
MagRec["measurment_temp"]='%8.3e' % (float(rec[0])+273.) # temp in kelvin
if T>T0:
MagRec["magic_method_codes"]='LP-MW-I'
elif T<T0:
MagRec["magic_method_codes"]='LP-MC-I'
T0=T
else:
print 'skipping repeated temperature step'
MagRec["magic_method_codes"]=''
T0=T
MagRec["measurement_magnitude"]='%10.3e'% (float(rec[1])) # uncalibrated magnitude
if syn==0:
MagRec["er_specimen_name"]=specimen_name
MagRec["er_site_name"]=""
if specnum!=0:
MagRec["er_sample_name"]=specimen_name[:specnum]
else:
MagRec["er_sample_name"]=specimen_name
if "-fsa" in args:
for samp in Samps:
if samp["er_sample_name"] == MagRec["er_sample_name"]:
MagRec["er_location_name"]=samp["er_location_name"]
MagRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6:
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
if MagRec['er_site_name']=="":
print 'No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name']
if MagRec["er_location_name"]=="":
print 'no location name for: ',MagRec["er_specimen_name"]
else:
MagRec["er_synthetic_name"]=specimen_name
MagRec["er_location_name"]=""
MagRec["er_sample_name"]=""
MagRec["er_site_name"]=""
MagRec["er_specimen_name"]=""
MagRec["magic_instrument_codes"]=instcode
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
MagRec["measurement_flag"]='g'
MagRec["measurement_number"]=str(measnum)
measnum+=1
MagRecs.append(MagRec)
for rec in MagRecs: # sort out the measurements by experiment type
rec['magic_experiment_name']=specimen_name
if rec['magic_method_codes']=='LP-MW-I':
rec["magic_experiment_name"]=specimen_name+':LP-MW-I:Curie'
elif rec['magic_method_codes']=='LP-MC-I':
rec["magic_experiment_name"]=specimen_name+':LP-MC-I'
pmag.magic_write(meas_file,MagRecs,'magic_measurements')
print "results put in ",meas_file
def main(command_line=True, **kwargs):
"""
NAME
cit_magic.py
DESCRIPTION
converts CIT and .sam format files to magic_measurements format files
SYNTAX
cit_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .sam format input file, required
-WD Working Directory: output directory where files are going to go
-fsi SITEFILE : specify file with site names and locations [tab delimited magic file]
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt # LORI
-n [gm,kg,cc,m3]: specify normalization
-A: don't average replicate measurements
-spc NUM : specify number of characters to designate a specimen, default = 0
-ncn NCON: specify naming convention
-loc LOCNAME : specify location/study name, must have either LOCNAME or SITEFILE or be a synthetic
-mcd [FS-FD:SO-MAG,.....] colon delimited list for method codes applied to all specimens in .sam file
-dc B PHI THETA: dc lab field (in microTesla), phi,and theta must be input as a tuple "(DC,PHI,THETA)". If not input user will be asked for values, this is advantagious if there are differing dc fields between steps or specimens. Note: this currently only works with the decimal IZZI naming convetion (XXX.0,1,2 where XXX is the treatment temperature and 0 is a zero field step, 1 is in field, and 2 is a pTRM check). All other steps are hardcoded dc_field = 0.
INPUT
Best to put separate experiments in separate files (all AF, thermal, thellier, trm aquisition, Shaw, etc.)
NOTES:
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3: default] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] or [email protected] for help.
"""
#
# NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
# -ac B : peak AF field (in mT) for ARM acquisition, default is none
#
#initialize variables
norm = 'cc'
samp_con, Z = '3', 1
meas_file = 'magic_measurements.txt'
spec_file = 'er_specimens.txt'
samp_file = 'er_samples.txt'
site_file = 'er_sites.txt'
ErSpecs, ErSamps, ErSites, ErLocs, ErCits = [], [], [], [], []
MeasRecs = []
specnum, units, locname = 0, "1", "unknown"
citation = "This study"
dir_path = '.'
args = sys.argv
if command_line:
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-h" in args:
print(main.__doc__)
return False
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsp' in args:
ind = args.index("-Fsp")
spec_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
if '-Fsi' in args: # LORI addition
ind = args.index("-Fsi")
site_file = args[ind + 1]
if '-loc' in args:
ind = args.index("-loc")
locname = args[ind + 1]
if '-mcd' in args:
ind = args.index("-mcd")
methods = args[ind + 1]
else:
methods = 'SO-MAG'
if '-spc' in args:
ind = args.index("-spc")
specnum = -int(args[ind + 1])
if '-n' in args:
ind = args.index("-n")
norm = args[ind + 1]
if "-A" in args:
avg = 1
else:
avg = 0
if '-dc' in args:
ind = args.index('-dc')
DC_FIELD, DC_PHI, DC_THETA = list(
map(float, args[ind + 1].strip('( ) [ ]').split(',')))
DC_FIELD *= 1e-6
yn = ''
GET_DC_PARAMS = False
else:
GET_DC_PARAMS, DC_FIELD, DC_PHI, DC_THETA, yn = True, 0, 0, -90, ''
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print(
"option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
elif "7" in samp_con:
if "-" not in samp_con:
print(
"option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if '-f' in args:
ind = args.index("-f")
magfile = args[ind + 1]
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind + 1]
else:
input_dir_path = os.path.split(magfile)[0]
output_dir_path = dir_path
# LJ
# if you are running as a module:
elif not command_line:
dir_path = kwargs.get('dir_path', '.')
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file',
'magic_measurements.txt') # outfile
spec_file = kwargs.get('spec_file',
'er_specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'er_samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'er_sites.txt') # site outfile
locname = kwargs.get('locname', '')
methods = kwargs.get('methods', ['SO-MAG'])
specnum = -int(kwargs.get('specnum', 0))
norm = kwargs.get('norm', 'cc')
avg = kwargs.get('avg', 0) # 0 means do average, 1 means don't
samp_con = kwargs.get('samp_con', '3')
magfile = kwargs.get('magfile', '')
input_dir_path = kwargs.get('input_dir_path',
os.path.split(magfile)[0])
output_dir_path = dir_path
DC_FIELD, DC_PHI, DC_THETA = list(
map(float, kwargs.get('dc_params', (0, 0, -90))))
DC_FIELD *= 1e-6
yn = ''
if DC_FIELD == 0 and DC_PHI == 0 and DC_THETA == -90:
GET_DC_PARAMS = True
else:
GET_DC_PARAMS = False
# done with module-specific stuff
# formatting and checking variables
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
magfile = os.path.join(input_dir_path, magfile)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
meas_file = os.path.join(output_dir_path, meas_file)
FIRST_GET_DC = True
try:
with open(magfile, 'r') as file_input:
File = file_input.readlines()
except Exception as ex:
print("bad sam file name: ", magfile)
return False, "bad sam file name"
if len(File) == 1:
File = File[0].split('\r')
File = [x + "\r\n" for x in File]
sids, ln, format = [], 0, 'CIT'
formats = ['CIT', '2G', 'APP', 'JRA']
if File[ln].strip() == 'CIT': ln += 1
ErLocRec = {}
ErLocRec["er_location_name"] = locname
ErLocRec["er_citation_names"] = citation
comment = File[ln]
if comment == 'CIT':
format = comment
ln += 1
comment = File[ln]
print(comment)
ln += 1
specimens, samples, sites = [], [], []
if format == 'CIT':
line = File[ln].split()
site_lat = line[0]
site_lon = line[1]
ErLocRec["location_begin_lat"] = site_lat
ErLocRec["location_begin_lon"] = site_lon
ErLocRec["location_end_lat"] = site_lat
ErLocRec["location_end_lon"] = site_lon
ErLocs.append(ErLocRec)
try:
Cdec = float(line[2])
except ValueError:
pdb.set_trace()
for k in range(ln + 1, len(File)):
line = File[k]
rec = line.split()
if rec == []: continue
specimen = rec[0]
specimens.append(specimen)
for specimen in specimens:
ErSpecRec, ErSampRec, ErSiteRec = {}, {}, {}
if specnum != 0:
sample = specimen[:specnum]
else:
sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
ErSpecRec['er_specimen_name'] = specimen
ErSpecRec['er_sample_name'] = sample
ErSpecRec['er_site_name'] = site
ErSpecRec['er_location_name'] = locname
ErSpecRec['er_citation_names'] = citation
ErSampRec['er_sample_name'] = sample
ErSampRec['er_site_name'] = site
ErSampRec['er_location_name'] = locname
ErSampRec['er_citation_names'] = citation
ErSampRec['magic_method_codes'] = methods
ErSampRec['sample_declination_correction'] = '%7.1f' % (Cdec)
ErSiteRec['er_site_name'] = site
ErSiteRec['er_location_name'] = locname
ErSiteRec['er_citation_names'] = citation
ErSiteRec['site_lat'] = site_lat
ErSiteRec['site_lon'] = site_lon
with open(os.path.join(input_dir_path, specimen), 'r') as finput:
Lines = list(finput.readlines())
comment = ""
line = Lines[0].split()
if len(line) > 2:
comment = line[2]
info = Lines[1].split()
vol = float(info[-1])
if vol != 1.0:
if norm == 'cc': units = "1"
if norm == 'm3': units = "2"
ErSpecRec['specimen_weight'] = ""
if units == "1" or "":
ErSpecRec['specimen_volume'] = '%10.3e' % (vol * 1e-6)
else:
ErSpecRec['specimen_volume'] = '%10.3e' % (vol)
else:
if norm == 'cc': units = "1"
if norm == 'm3': units = "2"
ErSpecRec['specimen_volume'] = ""
if units == "1" or "":
ErSpecRec['specimen_weight'] = '%10.3e' % (vol * 1e-3)
else:
ErSpecRec['specimen_weight'] = '%10.3e' % (vol)
dip = float(info[-2])
dip_direction = float(info[-3]) + Cdec + 90.
sample_dip = -float(info[-4])
sample_azimuth = float(info[-5]) + Cdec - 90.
if len(info) > 5:
ErSampRec['sample_height'] = info[-6]
else:
ErSampRec['sample_height'] = '0'
ErSampRec['sample_azimuth'] = '%7.1f' % (sample_azimuth)
ErSampRec['sample_dip'] = '%7.1f' % (sample_dip)
ErSampRec['sample_bed_dip'] = '%7.1f' % (dip)
ErSampRec['sample_bed_dip_direction'] = '%7.1f' % (dip_direction)
ErSampRec['sample_class'] = ''
ErSampRec['sample_type'] = ''
ErSampRec['sample_lithology'] = ''
if Cdec != 0 or Cdec != "":
ErSampRec['magic_method_codes'] = 'SO-CMD-NORTH'
else:
ErSampRec['magic_method_codes'] = 'SO-MAG'
for line in Lines[2:len(Lines)]:
if line == '\n': continue
MeasRec = ErSpecRec.copy()
# Remove specimen_volume and specimen_weight as they do not exits in the magic_measurement table
del MeasRec["specimen_volume"]
del MeasRec["specimen_weight"]
treat_type = line[0:3]
if treat_type[1] == '.':
treat_type = 'NRM'
treat = line[2:6]
try:
float(treat)
except ValueError:
treat = line[3:6]
if treat_type.startswith('NRM'):
MeasRec['magic_method_codes'] = 'LT-NO'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '273'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['treatment_ac_field'] = '0'
elif treat_type.startswith('AF'):
MeasRec['magic_method_codes'] = 'LT-AF-Z'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '273'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
if treat.strip() == '':
MeasRec['treatment_ac_field'] = '0'
else:
MeasRec['treatment_ac_field'] = '%10.3e' % (float(treat) *
1e-3)
elif treat_type.startswith('ARM'):
MeasRec['magic_method_codes'] = "LP-ARM"
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '273'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
if treat.strip() == '':
MeasRec['treatment_ac_field'] = '0'
else:
MeasRec['magic_method_codes'] = "LP-ARM-AFD"
MeasRec['treatment_ac_field'] = '%10.3e' % (float(treat) *
1e-3)
elif treat_type.startswith('TT'):
MeasRec['magic_method_codes'] = 'LT-T-Z'
MeasRec['measurement_temp'] = '273'
if treat.strip() == '':
MeasRec['treatment_temp'] = '273'
else:
MeasRec['treatment_temp'] = '%7.1f' % (float(treat) + 273)
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['treatment_ac_field'] = '0'
elif treat_type.startswith('LT') or treat_type.startswith('LN2'):
MeasRec['magic_method_codes'] = 'LT-LT-Z'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '77'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['treatment_ac_field'] = '0'
elif line[
4] == '0': #assume decimal IZZI format 0 field thus can hardcode the dc fields
MeasRec['magic_method_codes'] = 'LT-T-Z'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = str(int(treat_type) + 273)
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['treatment_ac_field'] = '0'
elif line[4] == '1': #assume decimal IZZI format in constant field
if GET_DC_PARAMS:
GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(
FIRST_GET_DC, specimen, treat_type, yn)
MeasRec['magic_method_codes'] = 'LT-T-I'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = str(int(treat_type) + 273)
MeasRec['treatment_dc_field'] = '%1.2e' % DC_FIELD
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['treatment_ac_field'] = '0'
elif line[4] == '2': #assume decimal IZZI format PTRM step
if GET_DC_PARAMS:
GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(
FIRST_GET_DC, specimen, treat_type, yn)
MeasRec['magic_method_codes'] = 'LT-PTRM-I'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = str(int(treat_type) + 273)
MeasRec['treatment_dc_field'] = '%1.2e' % DC_FIELD
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['treatment_ac_field'] = '0'
else:
print("trouble with your treatment steps")
MeasRec['measurement_dec'] = line[46:51]
MeasRec['measurement_inc'] = line[52:58]
M = '%8.2e' % (float(line[31:39]) * vol * 1e-3) # convert to Am2
MeasRec['measurement_magn_moment'] = M
MeasRec['measurement_csd'] = '%7.1f' % (eval(line[41:46]))
MeasRec["measurement_positions"] = '1'
MeasRec['measurement_standard'] = 'u'
if len(line) > 60:
MeasRec['magic_instrument_codes'] = line[85:]
MeasRec['measurement_sd_x'] = '%8.2e' % (
float(line[58:67]) * 1e-8) #(convert e-5emu to Am2)
MeasRec['measurement_sd_y'] = '%8.2e' % (float(line[67:76]) *
1e-8)
MeasRec['measurement_sd_z'] = '%8.2e' % (float(line[76:85]) *
1e-8)
MeasRecs.append(MeasRec)
ErSpecs.append(ErSpecRec)
if sample not in samples:
samples.append(sample)
ErSamps.append(ErSampRec)
site = pmag.parse_site(sample, samp_con, Z)
if site not in sites:
sites.append(site)
ErSites.append(ErSiteRec)
pmag.magic_write(spec_file, ErSpecs, 'er_specimens')
print('specimens stored in ', spec_file)
pmag.magic_write(samp_file, ErSamps, 'er_samples')
print('samples stored in ', samp_file)
pmag.magic_write(site_file, ErSites, 'er_sites')
print('sites stored in ', site_file)
Fixed = pmag.measurements_methods(MeasRecs, avg)
pmag.magic_write(meas_file, Fixed, 'magic_measurements')
print('data stored in ', meas_file)
return True, meas_file
def convert(**kwargs):
# initialize some stuff
methcode="LP-NO"
phi,theta,peakfield,labfield=0,0,0,0
pTRM,MD=0,0
dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0]
inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
tdec=[0,90,0,180,270,0,0,90,0]
tinc=[0,0,90,0,0,-90,0,0,90]
missing=1
demag="N"
citations='This study'
fmt='old'
Samps=[]
trm=0
irm=0
#get args
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
mag_file = kwargs.get('mag_file', '')
labfield = kwargs.get('labfield', '')
if labfield:
labfield = float(labfield) *1e-6
else:
labfield = 0
phi = kwargs.get('phi', 0)
if phi:
phi = float(phi)
else:
phi = 0
theta = kwargs.get('theta', 0)
if theta:
theta=float(theta)
else:
theta = 0
peakfield = kwargs.get('peakfield', 0)
if peakfield:
peakfield=float(peakfield) *1e-3
else:
peakfield = 0
specnum = kwargs.get('specnum', 0)
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
samp_infile = kwargs.get('samp_infile', '')
syn = kwargs.get('syn', 0)
institution = kwargs.get('institution', '')
syntype = kwargs.get('syntype', '')
inst = kwargs.get('inst', '')
noave = kwargs.get('noave', 0)
codelist = kwargs.get('codelist', '')
coil = kwargs.get('coil', '')
cooling_rates = kwargs.get('cooling_rates', '')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
timezone = kwargs.get('timezone', 'UTC')
# make sure all initial values are correctly set up (whether they come from the command line or a GUI)
if samp_infile:
Samps, file_type = pmag.magic_read(samp_infile)
if coil:
coil = str(coil)
methcode="LP-IRM"
irmunits = "V"
if coil not in ["1","2","3"]:
print(__doc__)
print('not a valid coil specification')
return False, '{} is not a valid coil specification'.format(coil)
if mag_file:
lines = pmag.open_file(mag_file)
if not lines:
print("you must provide a valid mag_file")
return False, "you must provide a valid mag_file"
if not mag_file:
print(__doc__)
print("mag_file field is required option")
return False, "mag_file field is required option"
if specnum!=0:
specnum=-specnum
if "4" == samp_con[0]:
if "-" not in samp_con:
print("naming convention option [4] must be in form 4-Z where Z is an integer")
print('---------------')
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" == samp_con[0]:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
else: Z = 0
if codelist:
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in sys.argv: methcode="LT-AF-Z"
if'-dc' in sys.argv: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in sys.argv: methcode="LT-T-Z"
if '-dc' in sys.argv: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
irmunits="mT"
if "I3d" in codes:
methcode="LT-T-Z:LP-IRM-3D"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if "CR" in codes:
demag="T"
cooling_rate_experiment=1
if command_line:
ind=sys.argv.index("CR")
cooling_rates=sys.argv[ind+1]
cooling_rates_list=cooling_rates.split(',')
else:
cooling_rates_list=str(cooling_rates).split(',')
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="T" and "CR" in codes:
methcode="LP-CR-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
version_num=pmag.get_version()
##################################
for line in lines:
instcode=""
if len(line)>2:
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
MeasRec['software_packages']=version_num
MeasRec["description"]=""
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
meas_type="LT-NO"
rec=line.split()
try: float(rec[0]); print("No specimen name for line #%d in the measurement file"%lines.index(line)); continue
except ValueError: pass
if rec[1]==".00":rec[1]="0.00"
treat=rec[1].split('.')
if methcode=="LP-IRM":
if irmunits=='mT':
labfield=float(treat[0])*1e-3
else:
labfield=pmag.getfield(irmunits,coil,treat[0])
if rec[1][0]!="-":
phi,theta=0.,90.
else:
phi,theta=0.,-90.
meas_type="LT-IRM"
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
if len(rec)>6:
code1=rec[6].split(';') # break e.g., 10/15/02;7:45 indo date and time
if len(code1)==2: # old format with AM/PM
missing=0
code2=code1[0].split('/') # break date into mon/day/year
code3=rec[7].split(';') # break e.g., AM;C34;200 into time;instr/axes/measuring pos;number of measurements
yy=int(code2[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(code2[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(code2[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if code3[0]=="PM":hh=hh+12
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else: min=str(min)
dt=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00"
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(dt, "%Y:%m:%d:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
MeasRec["timestamp"]=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
if inst=="":
if code3[1][0]=='C':instcode='SIO-bubba'
if code3[1][0]=='G':instcode='SIO-flo'
else:
instcode=''
MeasRec["meas_n_orient"]=code3[1][2]
elif len(code1)>2: # newest format (cryo7 or later)
if "LP-AN-ARM" not in methcode:labfield=0
fmt='new'
date=code1[0].split('/') # break date into mon/day/year
yy=int(date[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(date[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(date[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else:
min=str(min)
dt=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00"
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(dt, "%Y:%m:%d:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
MeasRec["timestamp"]=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
if inst=="":
if code1[6][0]=='C':
instcode='SIO-bubba'
if code1[6][0]=='G':
instcode='SIO-flo'
else:
instcode=''
if len(code1)>1:
MeasRec["meas_n_orient"]=code1[6][2]
else:
MeasRec["meas_n_orient"]=code1[7] # takes care of awkward format with bubba and flo being different
if user=="":user=code1[5]
if code1[2][-1]=='C':
demag="T"
if code1[4]=='microT' and float(code1[3])!=0. and "LP-AN-ARM" not in methcode: labfield=float(code1[3])*1e-6
if code1[2]=='mT' and methcode!="LP-IRM":
demag="AF"
if code1[4]=='microT' and float(code1[3])!=0.: labfield=float(code1[3])*1e-6
if code1[4]=='microT' and labfield!=0. and meas_type!="LT-IRM":
phi,theta=0.,-90.
if demag=="T": meas_type="LT-T-I"
if demag=="AF": meas_type="LT-AF-I"
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
if code1[4]=='' or labfield==0. and meas_type!="LT-IRM":
if demag=='T':meas_type="LT-T-Z"
if demag=="AF":meas_type="LT-AF-Z"
MeasRec["treat_dc_field"]='0'
if syn==0:
specimen=rec[0]
MeasRec["specimen"]=specimen
if specnum!=0:
sample=rec[0][:specnum]
else:
sample=rec[0]
if samp_infile and Samps: # if samp_infile was provided AND yielded sample data
samp=pmag.get_dictitem(Samps,'sample',sample,'T')
if len(samp)>0:
location=samp[0]["location"]
site=samp[0]["site"]
else:
location=''
site=''
else:
site=pmag.parse_site(sample,samp_con,Z)
if location!='' and location not in [x['location'] if 'location' in list(x.keys()) else '' for x in LocRecs]:
LocRec['location'] = location
LocRec['lat_n'] = lat
LocRec['lat_s'] = lat
LocRec['lon_e'] = lon
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
if site!='' and site not in [x['site'] if 'site' in list(x.keys()) else '' for x in SiteRecs]:
SiteRec['location'] = location
SiteRec['site'] = site
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if sample!='' and sample not in [x['sample'] if 'sample' in list(x.keys()) else '' for x in SampRecs]:
SampRec['site'] = site
SampRec['sample'] = sample
SampRecs.append(SampRec)
if specimen!='' and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else '' for x in SpecRecs]:
SpecRec["specimen"]=specimen
SpecRec['sample'] = sample
SpecRecs.append(SpecRec)
else:
specimen=rec[0]
MeasRec["specimen"]=specimen
if specnum!=0:
sample=rec[0][:specnum]
else:
sample=rec[0]
site=pmag.parse_site(sample,samp_con,Z)
if location!='' and location not in [x['location'] if 'location' in list(x.keys()) else '' for x in LocRecs]:
LocRec['location'] = location
LocRec['lat_n'] = lat
LocRec['lat_s'] = lat
LocRec['lon_e'] = lon
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
if site!='' and site not in [x['site'] if 'site' in list(x.keys()) else '' for x in SiteRecs]:
SiteRec['location'] = location
SiteRec['site'] = site
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if sample!='' and sample not in [x['sample'] if 'sample' in list(x.keys()) else '' for x in SampRecs]:
SampRec['site'] = site
SampRec['sample'] = sample
SampRecs.append(SampRec)
if specimen!='' and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else '' for x in SpecRecs]:
SpecRec["specimen"]=specimen
SpecRec['sample'] = sample
SpecRecs.append(SpecRec)
SampRec["institution"]=institution
SampRec["material_type"]=syntype
if float(rec[1])==0:
pass
elif demag=="AF":
if methcode != "LP-AN-ARM":
MeasRec["treat_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla
if meas_type=="LT-AF-Z": MeasRec["treat_dc_field"]='0'
else: # AARM experiment
if treat[1][0]=='0':
meas_type="LT-AF-Z:LP-AN-ARM:"
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MeasRec["treat_dc_field"]='%8.3e'%(0)
if labfield!=0 and methcode!="LP-AN-ARM": print("Warning - inconsistency in mag file with lab field - overriding file with 0")
else:
meas_type="LT-AF-I:LP-AN-ARM"
ipos=int(treat[0])-1
MeasRec["treat_dc_field_phi"]='%7.1f' %(dec[ipos])
MeasRec["treat_dc_field_theta"]='%7.1f'% (inc[ipos])
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
elif demag=="T" and methcode == "LP-AN-TRM":
MeasRec["treat_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if treat[1][0]=='0':
meas_type="LT-T-Z:LP-AN-TRM"
MeasRec["treat_dc_field"]='%8.3e'%(0)
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
else:
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
if treat[1][0]=='7': # alteration check as final measurement
meas_type="LT-PTRM-I:LP-AN-TRM"
else:
meas_type="LT-T-I:LP-AN-TRM"
# find the direction of the lab field in two ways:
# (1) using the treatment coding (XX.1=+x, XX.2=+y, XX.3=+z, XX.4=-x, XX.5=-y, XX.6=-z)
ipos_code=int(treat[1][0])-1
# (2) using the magnetization
DEC=float(rec[4])
INC=float(rec[5])
if INC < 45 and INC > -45:
if DEC>315 or DEC<45: ipos_guess=0
if DEC>45 and DEC<135: ipos_guess=1
if DEC>135 and DEC<225: ipos_guess=3
if DEC>225 and DEC<315: ipos_guess=4
else:
if INC >45: ipos_guess=2
if INC <-45: ipos_guess=5
# prefer the guess over the code
ipos=ipos_guess
MeasRec["treat_dc_field_phi"]='%7.1f' %(tdec[ipos])
MeasRec["treat_dc_field_theta"]='%7.1f'% (tinc[ipos])
# check it
if ipos_guess!=ipos_code and treat[1][0]!='7':
print("-E- ERROR: check specimen %s step %s, ATRM measurements, coding does not match the direction of the lab field!"%(rec[0],".".join(list(treat))))
elif demag=="S": # Shaw experiment
if treat[1][1]=='0':
if int(treat[0])!=0:
MeasRec["treat_ac_field"]='%8.3e' % (float(treat[0])*1e-3) # AF field in tesla
MeasRec["treat_dc_field"]='0'
meas_type="LT-AF-Z" # first AF
else:
meas_type="LT-NO"
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='0'
elif treat[1][1]=='1':
if int(treat[0])==0:
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MeasRec["treat_dc_field"]='%8.3e'%(arm_labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
meas_type="LT-AF-I"
else:
MeasRec["treat_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MeasRec["treat_dc_field"]='0'
meas_type="LT-AF-Z"
elif treat[1][1]=='2':
if int(treat[0])==0:
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='%8.3e'%(trm_labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
MeasRec["treat_temp"]='%8.3e' % (trm_peakT)
meas_type="LT-T-I"
else:
MeasRec["treat_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MeasRec["treat_dc_field"]='0'
meas_type="LT-AF-Z"
elif treat[1][1]=='3':
if int(treat[0])==0:
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MeasRec["treat_dc_field"]='%8.3e'%(arm_labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
meas_type="LT-AF-I"
else:
MeasRec["treat_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MeasRec["treat_dc_field"]='0'
meas_type="LT-AF-Z"
# Cooling rate experient # added by rshaar
elif demag=="T" and methcode == "LP-CR-TRM":
MeasRec["treat_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if treat[1][0]=='0':
meas_type="LT-T-Z:LP-CR-TRM"
MeasRec["treat_dc_field"]='%8.3e'%(0)
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
else:
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
if treat[1][0]=='7': # alteration check as final measurement
meas_type="LT-PTRM-I:LP-CR-TRM"
else:
meas_type="LT-T-I:LP-CR-TRM"
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
indx=int(treat[1][0])-1
# alteration check matjed as 0.7 in the measurement file
if indx==6:
cooling_time= cooling_rates_list[-1]
else:
cooling_time=cooling_rates_list[indx]
MeasRec["description"]="cooling_rate"+":"+cooling_time+":"+"K/min"
elif demag!='N':
if len(treat)==1:treat.append('0')
MeasRec["treat_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if trm==0: # demag=T and not trmaq
if treat[1][0]=='0':
meas_type="LT-T-Z"
else:
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step
if treat[1][0]=='2':
meas_type="LT-PTRM-I" # pTRM check
pTRM=1
if treat[1][0]=='3':
MeasRec["treat_dc_field"]='0' # this is a zero field step
meas_type="LT-PTRM-MD" # pTRM tail check
else:
labfield=float(treat[1])*1e-6
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
meas_type="LT-T-I:LP-TRM" # trm acquisition experiment
MeasRec["dir_csd"]=rec[2]
MeasRec["magn_moment"]='%10.3e'% (float(rec[3])*1e-3) # moment in Am^2 (from emu)
MeasRec["dir_dec"]=rec[4]
MeasRec["dir_inc"]=rec[5]
MeasRec["instrument_codes"]=instcode
MeasRec["analysts"]=user
MeasRec["citations"]=citations
if "LP-IRM-3D" in methcode : meas_type=methcode
#MeasRec["method_codes"]=methcode.strip(':')
MeasRec["method_codes"]=meas_type
MeasRec["quality"]='g'
if 'std' in rec[0]:
MeasRec["standard"]='s'
else:
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
#print MeasRec['treat_temp']
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path,read_tables=[])
# create MagIC tables
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
# write MagIC tables to file
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
version_num = pmag.get_version()
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file')
input_dir_path = kwargs.get('input_dir_path', dir_path)
if input_dir_path == dir_path:
mag_file = pmag.resolve_file_name(mag_file, dir_path)
input_dir_path = os.path.split(mag_file)[0]
output_dir_path = dir_path
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 2.5)) * 1e-6
timezone = kwargs.get('timestamp', 'UTC')
# format variables
mag_file = os.path.join(input_dir_path, mag_file)
if specnum != 0: specnum = -int(specnum)
if samp_con.startswith("4"):
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
elif samp_con.startswith("7"):
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
else:
Z = 1
#create data holders
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
data = pmag.open_file(mag_file)
# remove garbage/blank lines
data = [i for i in data if len(i) >= 5]
if not len(data):
print('No data')
return
n = 0
end = False
# loop through records
while not end:
first_line = data[n].split()
sampleName = first_line[0]
demagLevel = first_line[2]
date = first_line[3] + ":0:0:0"
n += 2
third_line = data[n].split()
if not third_line[0].startswith('SPEC.ANGLES'):
print('third line of a block should start with SPEC.ANGLES')
print(third_line)
return
specimenAngleDec = third_line[1]
specimenAngleInc = third_line[2]
n += 4
while not data[n].startswith('MEAN'):
n += 1
mean_line = data[n]
Mx = mean_line[1]
My = mean_line[2]
Mz = mean_line[3]
n += 1
precision_line = data[n].split()
if not precision_line[0].startswith('Modulus'):
print('precision line should start with "Modulus"')
return
splitExp = precision_line[2].split('A')
intensityVolStr = precision_line[1] + splitExp[0]
intensityVol = float(intensityVolStr)
# check and see if Prec is too big and messes with the parcing.
precisionStr = ''
if len(precision_line) == 6: #normal line
precisionStr = precision_line[5][0:-1]
else:
precisionStr = precision_line[4][0:-1]
precisionPer = float(precisionStr)
precision = intensityVol * precisionPer / 100
while not data[n].startswith('SPEC.'):
n += 1
specimen_line = data[n].split()
specimenDec = specimen_line[2]
specimenInc = specimen_line[3]
n += 1
geographic_line = data[n]
if not geographic_line.startswith('GEOGR'):
geographic_dec = ''
geographic_inc = ''
else:
geographic_line = geographic_line.split()
geographicDec = geographic_line[1]
geographicInc = geographic_line[2]
# Add data to various MagIC data tables.
specimen = sampleName
if specnum != 0: sample = specimen[:specnum]
else: sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec["citations"] = "This study"
SpecRec["analysts"] = user
SpecRec['volume'] = volume
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec["citations"] = "This study"
SampRec["analysts"] = user
SampRec['azimuth'] = specimenAngleDec
sample_dip = str(float(specimenAngleInc) -
90.0) #convert to magic orientation
SampRec['dip'] = sample_dip
SampRec['method_codes'] = meth_code
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec["citations"] = "This study"
SiteRec["analysts"] = user
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec["citations"] = "This study"
LocRec["analysts"] = user
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(date, "%m-%d-%Y:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp = utc_dt.strftime("%Y-%m-%dT%H:%M:%S") + "Z"
MeasRec["specimen"] = specimen
MeasRec["timestamp"] = timestamp
MeasRec['description'] = ''
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["treat_ac_field"] = '0'
if demagLevel == 'NRM':
meas_type = "LT-NO"
elif demagLevel[0] == 'A':
if demagLevel[:2] == 'AD':
treat = float(demagLevel[2:])
else:
treat = float(demagLevel[1:])
meas_type = "LT-AF-Z"
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif demagLevel[0] == 'T':
meas_type = "LT-T-Z"
treat = float(demagLevel[1:])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
else:
print("measurement type unknown", demagLevel)
return False, "measurement type unknown"
MeasRec["magn_moment"] = str(intensityVol * volume) # Am^2
MeasRec["magn_volume"] = intensityVolStr # A/m
MeasRec["dir_dec"] = specimenDec
MeasRec["dir_inc"] = specimenInc
MeasRec['method_codes'] = meas_type
MeasRecs.append(MeasRec)
# ignore all the rest of the special characters. Some data files not consistantly formatted.
n += 1
while ((len(data[n]) <= 5 and data[n] != '')
or data[n].startswith('----')):
n += 1
if n >= len(data):
break
if n >= len(data):
# we're done!
end = True
#end of data while loop
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
"""
Converts CIT formated Magnetometer data into MagIC format for Analysis and contribution to the MagIC database
Parameters
-----------
dir_path : directory to output files to (default : current directory)
user : colon delimited list of analysts (default : "")
magfile : magnetometer file (.sam) to convert to MagIC (required)
meas_file : measurement file name to output (default : measurements.txt)
spec_file : specimen file name to output (default : specimens.txt)
samp_file : sample file name to output (default : samples.txt)
site_file : site file name to output (default : site.txt)
loc_file : location file name to output (default : locations.txt)
locname : location name
methods : colon delimited list of sample method codes. full list here (https://www2.earthref.org/MagIC/method-codes) (default : SO-MAG
specnum : number of terminal characters that identify a specimen
norm : is volume or mass normalization using cgs or si units (options : cc,m3,g,kg) (default : cc)
noave : average measurement data or not. False is average, True is don't average. (default : False)
samp_con : sample naming convention options as follows:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in sitename column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
input_dir_path : if you did not supply a full path with magfile you can put the directory the magfile is in here
meas_n_orient : Number of different orientations in measurement (default : 8)
labfield : DC_FIELD in microTesla (default : 0)
phi : DC_PHI in degrees (default : 0)
theta : DC_THETA in degrees (default : 0)
Returns
-----------
type - Tuple : (True or False indicating if conversion was sucessful, meas_file name written)
"""
dir_path = kwargs.get('dir_path', '.')
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
locname = kwargs.get('locname', 'unknown')
sitename = kwargs.get('sitename', '')
methods = kwargs.get('methods', ['SO-MAG'])
specnum = -int(kwargs.get('specnum', 0))
norm = kwargs.get('norm', 'cc')
noave = kwargs.get('noave', False) # False means do average
samp_con = kwargs.get('samp_con', '3')
magfile = kwargs.get('magfile', '')
input_dir_path = kwargs.get('input_dir_path',os.path.split(magfile)[0])
meas_n_orient = kwargs.get('meas_n_orient','8')
output_dir_path = dir_path
try:
DC_FIELD = float(kwargs.get('labfield',0))*1e-6
DC_PHI = float(kwargs.get('phi',0))
DC_THETA = float(kwargs.get('theta',0))
except ValueError: raise ValueError('problem with your dc parameters. please provide a labfield in microTesla and a phi and theta in degrees.')
yn = ''
if DC_FIELD==0 and DC_PHI==0 and DC_THETA==0: GET_DC_PARAMS=True
else: GET_DC_PARAMS=False
if locname=='' or locname==None: locname = 'unknown'
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
else: Z=1
#get file names and open magfile to start reading data
if input_dir_path=='': input_dir_path='.'
magfile = os.path.join(input_dir_path, magfile)
FIRST_GET_DC=True
try:
file_input=open(magfile,'r')
except IOError as ex:
print(("bad sam file name: ", magfile))
return False, "bad sam file name"
File = file_input.readlines()
file_input.close()
if len(File) == 1: File = File[0].split('\r'); File = [x+"\r\n" for x in File]
#define initial variables
SpecRecs,SampRecs,SiteRecs,LocRecs,MeasRecs=[],[],[],[],[]
sids,ln,format,citations=[],0,'CIT',"This study"
formats=['CIT','2G','APP','JRA']
if File[ln].strip()=='CIT': ln+=1
LocRec={}
LocRec["location"]=locname
LocRec["citations"]=citations
LocRec['analysts']=user
comment=File[ln]
if comment=='CIT':
format=comment
ln+=1
comment=File[ln]
print(comment)
ln+=1
specimens,samples,sites=[],[],[]
if format=='CIT':
line=File[ln].split()
site_lat=line[0]
site_lon=line[1]
LocRec["lat_n"]=site_lat
LocRec["lon_e"]=site_lon
LocRec["lat_s"]=site_lat
LocRec["lon_w"]=site_lon
LocRecs.append(LocRec)
Cdec=float(line[2])
for k in range(ln+1,len(File)):
line=File[k]
rec=line.split()
if rec == []: continue
specimen=rec[0]
specimens.append(specimen)
for specimen in specimens:
SpecRec,SampRec,SiteRec={},{},{}
if specnum!=0:
sample=specimen[:specnum]
else: sample=specimen
if sitename: site=sitename
else: site=pmag.parse_site(sample,samp_con,Z)
SpecRec['specimen']=specimen
SpecRec['sample']=sample
SpecRec['citations']=citations
SpecRec['analysts']=user
SampRec['sample']=sample
SampRec['site']=site
SampRec['citations']=citations
SampRec['method_codes']=methods
SampRec['azimuth_dec_correction']='%7.1f'%(Cdec)
SampRec['analysts']=user
SiteRec['site']=site
SiteRec['location']=locname
SiteRec['citations']=citations
SiteRec['lat']=site_lat
SiteRec['lon']=site_lon
SiteRec['analysts']=user
f=open(os.path.join(input_dir_path,specimen),'r')
Lines=f.readlines()
f.close()
comment=""
line=Lines[0].split()
if len(line)>2:
comment=line[2]
info=Lines[1].split()
volmass=float(info[-1])
if volmass==1.0:
print('Warning: Specimen volume set to 1.0.')
print('Warning: If volume/mass really is 1.0, set volume/mass to 1.001')
print('Warning: specimen method code LP-NOMAG set.')
SpecRec['weight']=""
SpecRec['volume']=""
SpecRec['method_codes']='LP-NOMAG'
elif norm=="gm":
SpecRec['volume']=''
SpecRec['weight']='%10.3e'%volmass*1e-3
elif norm=="kg":
SpecRec['volume']=''
SpecRec['weight']='%10.3e'*volmass
elif norm=="cc":
SpecRec['weight']=""
SpecRec['volume']='%10.3e'%(volmass*1e-6)
elif norm=="m3":
SpecRec['weight']=""
SpecRec['volume']='%10.3e'%(volmass)
else:
print('Warning: Unknown normalization unit ', norm, '. Using default of cc')
SpecRec['weight']=""
SpecRec['volume']='%10.3e'%(volmass*1e-6)
dip=float(info[-2])
dip_direction=float(info[-3])+Cdec+90.
sample_dip=-float(info[-4])
sample_azimuth=float(info[-5])+Cdec-90.
if len(info)>5:
SampRec['height']=info[-6]
else:
SampRec['height']='0'
SampRec['azimuth']='%7.1f'%(sample_azimuth)
SampRec['dip']='%7.1f'%(sample_dip)
SampRec['bed_dip']='%7.1f'%(dip)
SampRec['bed_dip_direction']='%7.1f'%(dip_direction)
SampRec['geologic_classes']=''
SampRec['geologic_types']=''
SampRec['lithologies']=''
if Cdec!=0 or Cdec!="":
SampRec['method_codes']='SO-CMD-NORTH'
else:
SampRec['method_codes']='SO-MAG'
for line in Lines[2:len(Lines)]:
if line == '\n': continue
MeasRec=SpecRec.copy()
MeasRec.pop('sample')
MeasRec['analysts']=user
# Remove volume and weight as they do not exits in the magic_measurement table
del MeasRec["volume"]
del MeasRec["weight"]
if line[3:6]==' ' : # USGS files have blank for an AF demag value when measurement is the NRM. njarboe
line = 'NRM' + line[3:]
treat_type=line[0:3]
if treat_type[1] == '.':
treat_type = 'NRM'
treat=line[2:6]
try: float(treat)
except ValueError:
treat=line[3:6]
if treat.split()=='': treat='0'
try: float(treat)
except ValueError: treat = line.split()[1]
if treat_type.startswith('NRM'):
MeasRec['method_codes']='LT-NO'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif treat_type.startswith('LT') or treat_type.upper().startswith('LN2'):
MeasRec['method_codes']='LT-LT-Z'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='77'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif treat_type.startswith('AF') or treat_type.startswith('MAF'):
MeasRec['method_codes']='LT-AF-Z'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
if treat.strip() == '':
MeasRec['treat_ac_field']='0'
else:
try: MeasRec['treat_ac_field']='%10.3e'%(float(treat)*1e-3)
except ValueError as e: print(os.path.join(input_dir_path,specimen)); raise e
elif treat_type.startswith('ARM'):
MeasRec['method_codes']="LP-ARM"
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
if treat.strip() == '':
MeasRec['treat_ac_field']='0'
else:
MeasRec['method_codes']="LP-ARM-AFD"
MeasRec['treat_ac_field']='%10.3e'%(float(treat)*1e-3)
elif treat_type.startswith('IRM'):
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']="LT-IRM"
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif treat_type.startswith('TT'):
MeasRec['method_codes']='LT-T-Z'
MeasRec['meas_temp']='273'
if treat.strip() == '':
MeasRec['treat_temp']='273'
else:
MeasRec['treat_temp']='%7.1f'%(float(treat)+273)
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '0': #assume decimal IZZI format 0 field thus can hardcode the dc fields
MeasRec['method_codes']='LT-T-Z'
MeasRec['meas_temp']='273'
try: MeasRec['treat_temp']=str(int(treat_type) + 273)
except ValueError as e: print(specimen); raise e
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '1': #assume decimal IZZI format in constant field
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']='LT-T-I'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']=str(int(treat_type) + 273)
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '2': #assume decimal IZZI format PTRM step
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']='LT-PTRM-I'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']=str(int(treat_type) + 273)
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '3': #assume decimal IZZI format PTRM tail check
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']='LT-PTRM-Z'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']=str(int(treat_type) + 273)
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
else:
print("trouble with your treatment steps")
MeasRec['dir_dec']=line[46:51]
MeasRec['dir_inc']=line[52:58]
# Some MIT files have and extra digit in the exponent of the magnetude.
# That makes those files not compliant with the cit measurement file spec.
# Not sure if we should just print an error message and exit. For now we accept the file and fix it.
# The first digit of the exponent, which should always be zero, is cut out of the line if column 39 is not ' '
if line[39] != ' ': line = line[0:37] + line[38:]
M='%8.2e'%(float(line[31:39])*volmass*1e-3) # convert to Am2
MeasRec['magn_moment']=M
MeasRec['dir_csd']='%7.1f'%(eval(line[41:46]))
MeasRec["meas_n_orient"]=meas_n_orient
MeasRec['standard']='u'
if len(line)>60:
MeasRec['instrument_codes']=line[85:].strip('\n \r \t "')
MeasRec['magn_x_sigma']='%8.2e'%(float(line[58:67])*1e-8) #(convert e-5emu to Am2)
MeasRec['magn_y_sigma']='%8.2e'%(float(line[67:76])*1e-8)
MeasRec['magn_z_sigma']='%8.2e'%(float(line[76:85])*1e-8)
MeasRecs.append(MeasRec)
SpecRecs.append(SpecRec)
if sample not in samples:
samples.append(sample)
SampRecs.append(SampRec)
if site not in sites:
sites.append(site)
SiteRecs.append(SiteRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # Loc outfile
magfile = kwargs.get('magfile', '')
datafile = kwargs.get('datafile', '')
specnum = int(kwargs.get('specnum', 0))
labfield = int(kwargs.get('labfield', 0)) * 1e-6
phi = int(kwargs.get('phi', 0))
theta = int(kwargs.get('theta', 0))
peakfield = kwargs.get('peakfield', 0)
if peakfield:
peakfield = float(peakfield) * 1e-3
location = kwargs.get('location', '')
samp_con = kwargs.get('samp_con', '1')
codelist = kwargs.get('codelist', '')
CR_cooling_times = kwargs.get('CR_cooling_times', None)
noave = kwargs.get('noave', False)
# format and validate variables
if magfile:
try:
infile = open(os.path.join(input_dir_path, magfile), 'r')
except IOError:
print("bad mag file name")
return False, "bad mag file name"
else:
print("mag_file field is required option")
print(__doc__)
return False, "mag_file field is required option"
if specnum != 0:
specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z = int(samp_con.split("-")[1])
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z = int(samp_con.split("-")[1])
samp_con = "7"
else:
Z = 1
if codelist:
codes = codelist.split(':')
else:
print("Must select experiment type (-LP option)")
return False, "Must select experiment type (-LP option)"
if "AF" in codes:
demag = 'AF'
LPcode = "LP-DIR-AF"
if "T" in codes:
demag = "T"
if not labfield: LPcode = "LP-DIR-T"
if labfield: LPcode = "LP-PI-TRM"
if "ANI" in codes:
if not labfield:
print("missing lab field option")
return False, "missing lab field option"
LPcode = "LP-AN-TRM"
if "TRM" in codes:
demag = "T"
LPcode = "LP-TRM"
#trm=1
if "CR" in codes:
demag = "T"
# dc should be in the code
if not labfield:
print("missing lab field option")
return False, "missing lab field option"
LPcode = "LP-CR-TRM" # TRM in different cooling rates
if command_line:
ind = sys.argv.index("-LP")
CR_cooling_times = sys.argv[ind + 2].split(",")
version_num = pmag.get_version()
#--------------------------------------
# Read the file
# Assumption:
# 1. different lab protocolsa are in different files
# 2. measurements are in the correct order
#--------------------------------------
Data = {}
line_no = 0
for line in infile.readlines():
line_no += 1
this_line_data = {}
line_no += 1
instcode = ""
if len(line) < 2:
continue
if line[0] == "#": #HUJI way of marking bad data points
continue
rec = line.strip('\n').split()
specimen = rec[0]
date = rec[2].split("/")
hour = rec[3].split(":")
treatment_type = rec[4]
treatment = rec[5].split(".")
dec_core = rec[6]
inc_core = rec[7]
moment_emu = float(rec[-1])
if specimen not in list(Data.keys()):
Data[specimen] = []
# check duplicate treatments:
# if yes, delete the first and use the second
if len(Data[specimen]) > 0:
if treatment == Data[specimen][-1]['treatment']:
del (Data[specimen][-1])
print(
"-W- Identical treatments in file %s magfile line %i: specimen %s, treatment %s ignoring the first. "
% (magfile, line_no, specimen, ".".join(treatment)))
this_line_data = {}
this_line_data['specimen'] = specimen
this_line_data['date'] = date
this_line_data['hour'] = hour
this_line_data['treatment_type'] = treatment_type
this_line_data['treatment'] = treatment
this_line_data['dec_core'] = dec_core
this_line_data['inc_core'] = inc_core
this_line_data['moment_emu'] = moment_emu
this_line_data['azimuth'] = ''
this_line_data['dip'] = ''
this_line_data['bed_dip_direction'] = ''
this_line_data['bed_dip'] = ''
this_line_data['lat'] = ''
this_line_data['lon'] = ''
this_line_data['volume'] = ''
Data[specimen].append(this_line_data)
infile.close()
print("-I- done reading file %s" % magfile)
if datafile:
dinfile = open(datafile)
for line in dinfile.readlines():
data = line.split()
if len(data) < 8 or data[0] == '': continue
elif data[0] in list(Data.keys()):
for i in range(len(Data[data[0]])):
Data[data[0]][i]['azimuth'] = data[1]
Data[data[0]][i]['dip'] = data[2]
try:
Data[data[0]][i]['bed_dip_direction'] = float(
data[3]) + 90
except ValueError:
Data[data[0]][i]['bed_dip_direction'] = ''
Data[data[0]][i]['bed_dip'] = data[4]
Data[data[0]][i]['lat'] = data[5]
Data[data[0]][i]['lon'] = data[6]
Data[data[0]][i]['volume'] = data[7]
else:
print(
"no specimen %s found in magnetometer data file when reading specimen orientation data file, or data file record for specimen too short"
% data[0])
dinfile.close()
#--------------------------------------
# Convert to MagIC
#--------------------------------------
specimens_list = list(Data.keys())
specimens_list.sort()
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
for specimen in specimens_list:
for i in range(len(Data[specimen])):
this_line_data = Data[specimen][i]
methcode = ""
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
specimen = this_line_data['specimen']
if specnum != 0:
sample = this_line_data['specimen'][:specnum]
else:
sample = this_line_data['specimen']
site = pmag.parse_site(sample, samp_con, Z)
if not location:
location = site
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['azimuth'] = this_line_data['azimuth']
SampRec['dip'] = this_line_data['dip']
SampRec['bed_dip_direction'] = this_line_data[
'bed_dip_direction']
SampRec['bed_dip'] = this_line_data['bed_dip']
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else ""
for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = this_line_data['lat']
SiteRec['lon'] = this_line_data['lon']
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['lat_n'] = this_line_data['lat']
LocRec['lon_e'] = this_line_data['lon']
LocRec['lat_s'] = this_line_data['lat']
LocRec['lon_w'] = this_line_data['lon']
LocRecs.append(LocRec)
MeasRec['specimen'] = specimen
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["magn_moment"] = '%10.3e' % (
float(this_line_data['moment_emu']) * 1e-3
) # moment in Am^2 (from emu)
MeasRec["dir_dec"] = this_line_data['dec_core']
MeasRec["dir_inc"] = this_line_data['inc_core']
date = this_line_data['date']
hour = this_line_data['hour']
if len(date[2]) < 4 and float(date[2]) >= 70:
yyyy = "19" + date[2]
elif len(date[2]) < 4 and float(date[2]) < 70:
yyyy = "20" + date[2]
else:
yyyy = date[2]
if len(date[0]) == 1:
date[0] = "0" + date[0]
if len(date[1]) == 1:
date[1] = "0" + date[1]
dt = ":".join([date[0], date[1], yyyy, hour[0], hour[1], "0"])
local = pytz.timezone("America/New_York")
naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp = utc_dt.strftime("%Y-%m-%dT%H:%M:%S") + "Z"
MeasRec['analysts'] = user
MeasRec["citations"] = "This study"
MeasRec["instrument_codes"] = "HUJI-2G"
MeasRec["quality"] = "g"
MeasRec["meas_n_orient"] = "1"
MeasRec["standard"] = "u"
MeasRec["description"] = ""
#----------------------------------------
# AF demag
# do not support AARM yet
#----------------------------------------
if demag == "AF":
treatment_type = this_line_data['treatment_type']
# demag in zero field
if LPcode != "LP-AN-ARM":
MeasRec["treat_ac_field"] = '%8.3e' % (
float(this_line_data['treatment'][0]) * 1e-3
) # peak field in tesla
MeasRec["treat_dc_field"] = '0'
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
if treatment_type == "N":
methcode = "LP-DIR-AF:LT-NO"
elif treatment_type == "A":
methcode = "LP-DIR-AF:LT-AF-Z"
else:
print(
"ERROR in treatment field line %i... exiting until you fix the problem"
% line_no)
print(this_line_data)
return False, "ERROR in treatment field line %i... exiting until you fix the problem" % line_no
# AARM experiment
else:
print(
"Dont supprot AARM in HUJI format yet. sorry... do be DONE"
)
MeasRec["method_codes"] = methcode
MeasRec["experiments"] = specimen + ":" + LPcode
MeasRec["treat_step_num"] = "%i" % i
MeasRec["description"] = ""
MeasRecs.append(MeasRec)
#----------------------------------------
# Thermal:
# Thellier experiment: "IZ", "ZI", "IZZI", pTRM checks
# Thermal demag
# Thermal cooling rate experiment
# Thermal NLT
#----------------------------------------
if demag == "T":
treatment = this_line_data['treatment']
treatment_type = this_line_data['treatment_type']
#----------------------------------------
# Thellier experimet
#----------------------------------------
if LPcode == "LP-PI-TRM": # Thelllier experiment
MeasRec["experiments"] = specimen + ":" + LPcode
methcode = LPcode
if treatment_type == "N" or (
(treatment[1] == '0' or treatment[1] == '00')
and float(treatment[0]) == 0):
LT_code = "LT-NO"
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
MeasRec["treat_dc_field"] = '0'
MeasRec["treat_temp"] = '273.'
elif treatment[1] == '0' or treatment[1] == '00':
LT_code = "LT-T-Z"
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
MeasRec["treat_dc_field"] = '%8.3e' % (0)
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
# check if this is ZI or IZ:
# check if the same temperature already measured:
methcode = "LP-PI-TRM:LP-PI-TRM-ZI"
for j in range(0, i):
if Data[specimen][j]['treatment'][0] == treatment[
0]:
if Data[specimen][j]['treatment'][
1] == '1' or Data[specimen][j][
'treatment'][1] == '10':
methcode = "LP-PI-TRM:LP-PI-TRM-IZ"
else:
methcode = "LP-PI-TRM:LP-PI-TRM-ZI"
elif treatment[1] == '1' or treatment[1] == '10':
LT_code = "LT-T-I"
MeasRec["treat_dc_field"] = '%8.3e' % (
labfield
) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"] = '%7.1f' % (
phi) # labfield phi
MeasRec["treat_dc_field_theta"] = '%7.1f' % (
theta) # labfield theta
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
# check if this is ZI or IZ:
# check if the same temperature already measured:
methcode = "LP-PI-TRM:LP-PI-TRM-IZ"
for j in range(0, i):
if Data[specimen][j]['treatment'][0] == treatment[
0]:
if Data[specimen][j]['treatment'][
1] == '0' or Data[specimen][j][
'treatment'][1] == '00':
methcode = "LP-PI-TRM:LP-PI-TRM-ZI"
else:
methcode = "LP-PI-TRM:LP-PI-TRM-IZ"
elif treatment[1] == '2' or treatment[1] == '20':
LT_code = "LT-PTRM-I"
MeasRec["treat_dc_field"] = '%8.3e' % (
labfield
) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"] = '%7.1f' % (
phi) # labfield phi
MeasRec["treat_dc_field_theta"] = '%7.1f' % (
theta) # labfield theta
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
methcode = "LP-PI-TRM:LP-PI-TRM-IZ"
else:
print(
"ERROR in treatment field line %i... exiting until you fix the problem"
% line_no)
return False, "ERROR in treatment field line %i... exiting until you fix the problem" % line_no
MeasRec["method_codes"] = LT_code + ":" + methcode
MeasRec["treat_step_num"] = "%i" % i
MeasRec["description"] = ""
MeasRecs.append(MeasRec)
#----------------------------------------
# demag experimet
#----------------------------------------
if LPcode == "LP-DIR-T":
MeasRec["experiments"] = specimen + ":" + LPcode
methcode = LPcode
if treatment_type == "N":
LT_code = "LT-NO"
else:
LT_code = "LT-T-Z"
methcode = LPcode + ":" + "LT-T-Z"
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
MeasRec["treat_dc_field"] = '%8.3e' % (0)
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
MeasRec["method_codes"] = LT_code + ":" + methcode
MeasRec["treat_step_num"] = "%i" % i
MeasRec["description"] = ""
MeasRecs.append(MeasRec)
#continue
#----------------------------------------
# ATRM measurements
# The direction of the magnetization is used to determine the
# direction of the lab field.
#----------------------------------------
if LPcode == "LP-AN-TRM":
MeasRec["experiments"] = specimen + ":" + LPcode
methcode = LPcode
if float(treatment[1]) == 0:
MeasRec["method_codes"] = "LP-AN-TRM:LT-T-Z"
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
MeasRec["treat_dc_field"] = '0'
else:
if float(treatment[1]) == 7:
# alteration check
methcode = "LP-AN-TRM:LT-PTRM-I"
MeasRec["treat_step_num"] = '7' # -z
else:
MeasRec["method_codes"] = "LP-AN-TRM:LT-T-I"
inc = float(MeasRec["dir_inc"])
dec = float(MeasRec["dir_dec"])
if abs(inc) < 45 and (dec < 45 or dec > 315): # +x
tdec, tinc = 0, 0
MeasRec["treat_step_num"] = '1'
if abs(inc) < 45 and (dec < 135 and dec > 45):
tdec, tinc = 90, 0
MeasRec["treat_step_num"] = '2' # +y
if inc > 45:
tdec, tinc = 0, 90
MeasRec["treat_step_num"] = '3' # +z
if abs(inc) < 45 and (dec < 225 and dec > 135):
tdec, tinc = 180, 0
MeasRec["treat_step_num"] = '4' # -x
if abs(inc) < 45 and (dec < 315 and dec > 225):
tdec, tinc = 270, 0
MeasRec["treat_step_num"] = '5' # -y
if inc < -45:
tdec, tinc = 0, -90
MeasRec["treat_step_num"] = '6' # -z
MeasRec["treat_dc_field_phi"] = '%7.1f' % (tdec)
MeasRec["treat_dc_field_theta"] = '%7.1f' % (tinc)
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
MeasRec["treat_dc_field"] = '%8.3e' % (labfield)
MeasRec["description"] = ""
MeasRecs.append(MeasRec)
#continue
#----------------------------------------
# NLT measurements
# or TRM acquisistion experiment
#----------------------------------------
if LPcode == "LP-TRM":
MeasRec["experiments"] = specimen + ":" + LPcode
MeasRec["method_codes"] = "LP-TRM:LT-T-I"
if float(treatment[1]) == 0:
labfield = 0
else:
labfield = float(float(treatment[1])) * 1e-6
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
MeasRec["treat_dc_field"] = '%8.3e' % (
labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"] = '%7.1f' % (
phi) # labfield phi
MeasRec["treat_dc_field_theta"] = '%7.1f' % (
theta) # labfield theta
MeasRec["treat_step_num"] = "%i" % i
MeasRec["description"] = ""
MeasRecs.append(MeasRec)
#continue
#----------------------------------------
# Cooling rate experiments
#----------------------------------------
if LPcode == "LP-CR-TRM":
index = int(treatment[1][0])
#print index,"index"
#print CR_cooling_times,"CR_cooling_times"
#print CR_cooling_times[index-1]
#print CR_cooling_times[0:index-1]
if index == 7 or index == 70: # alteration check as final measurement
meas_type = "LT-PTRM-I:LP-CR-TRM"
CR_cooling_time = CR_cooling_times[-1]
else:
meas_type = "LT-T-I:LP-CR-TRM"
CR_cooling_time = CR_cooling_times[index - 1]
MeasRec["method_codes"] = meas_type
MeasRec["experiments"] = specimen + ":" + LPcode
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
MeasRec["treat_dc_field"] = '%8.3e' % (
labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"] = '%7.1f' % (
phi) # labfield phi
MeasRec["treat_dc_field_theta"] = '%7.1f' % (
theta) # labfield theta
MeasRec["treat_step_num"] = "%i" % index
MeasRec[
"description"] = "cooling_rate" + ":" + CR_cooling_time + ":" + "K/min"
#MeasRec["description"]="%.1f minutes per cooling time"%int(CR_cooling_time)
MeasRecs.append(MeasRec)
#continue
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
pmd_magic.py
DESCRIPTION
converts PMD (Enkin) format files to magic_measurements format files
SYNTAX
pmd_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify naming convention
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
PMD format files
"""
# initialize some stuff
noave=0
inst=""
samp_con,Z='1',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
specnum=-1
MagRecs=[]
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
DIspec=[]
MagFiles=[]
user=""
mag_file=""
dir_path='.'
ErSamps=[]
SampOuts=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind+1]
#try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind+1])
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args: noave=1
if "-mcd" in args:
ind=args.index("-mcd")
meth_code=args[ind+1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 0)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
print samp_con
# format variables
mag_file = input_dir_path+"/" + mag_file
meas_file = output_dir_path+"/" + meas_file
samp_file = output_dir_path+"/" + samp_file
if specnum!=0:specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print "naming convention option [4] must be in form 4-Z where Z is an integer"
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
# parse data
data=open(mag_file,'rU').readlines() # read in data from file
comment=data[0]
line=data[1].strip()
line=line.replace("=","= ") # make finding orientations easier
rec=line.split() # read in sample orientation, etc.
er_specimen_name=rec[0]
ErSampRec,ErSiteRec={},{} # make a sample record
if specnum!=0:
er_sample_name=rec[0][:specnum]
else:
er_sample_name=rec[0]
if len(ErSamps)>0: # need to copy existing
for samp in ErSamps:
if samp['er_sample_name']==er_sample_name:
ErSampRec=samp # we'll ammend this one
else:
SampOuts.append(samp) # keep all the others
if int(samp_con)<6:
er_site_name=pmag.parse_site(er_sample_name,samp_con,Z)
else:
if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampREc['er_site_name']
if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampREc['er_location_name']
az_ind=rec.index('a=')+1
ErSampRec['er_sample_name']=er_sample_name
ErSampRec['er_sample_description']=comment
ErSampRec['sample_azimuth']=rec[az_ind]
dip_ind=rec.index('b=')+1
dip=-float(rec[dip_ind])
ErSampRec['sample_dip']='%7.1f'%(dip)
strike_ind=rec.index('s=')+1
ErSampRec['sample_bed_dip_direction']='%7.1f'%(float(rec[strike_ind])+90.)
bd_ind=rec.index('d=')+1
ErSampRec['sample_bed_dip']=rec[bd_ind]
v_ind=rec.index('v=')+1
vol=rec[v_ind][:-3]
date=rec[-2]
time=rec[-1]
ErSampRec['magic_method_codes']=meth_code
if 'er_location_name' not in ErSampRec.keys():ErSampRec['er_location_name']=er_location_name
if 'er_site_name' not in ErSampRec.keys():ErSampRec['er_site_name']=er_site_name
if 'er_citation_names' not in ErSampRec.keys():ErSampRec['er_citation_names']='This study'
if 'magic_method_codes' not in ErSampRec.keys():ErSampRec['magic_method_codes']='SO-NO'
SampOuts.append(ErSampRec)
for k in range(3,len(data)): # read in data
line=data[k]
rec=line.split()
if len(rec)>1: # skip blank lines at bottom
MagRec={}
MagRec['measurement_description']='Date: '+date+' '+time
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['er_site_name']=er_site_name
MagRec['er_sample_name']=er_sample_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=er_specimen_name
if rec[0]=='NRM':
meas_type="LT-NO"
elif rec[0][0]=='M' or rec[0][0]=='H':
meas_type="LT-AF-Z"
elif rec[0][0]=='T':
meas_type="LT-T-Z"
else:
print "measurement type unknown"
return False, "measurement type unknown"
X=[float(rec[1]),float(rec[2]),float(rec[3])]
Vec=pmag.cart2dir(X)
MagRec["measurement_magn_moment"]='%10.3e'% (Vec[2]) # Am^2
MagRec["measurement_magn_volume"]=rec[4] # A/m
MagRec["measurement_dec"]='%7.1f'%(Vec[0])
MagRec["measurement_inc"]='%7.1f'%(Vec[1])
MagRec["treatment_ac_field"]='0'
if meas_type!='LT-NO':
treat=float(rec[0][1:])
else:
treat=0
if meas_type=="LT-AF-Z":
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif meas_type=="LT-T-Z":
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
pmag.magic_write(samp_file,SampOuts,'er_samples')
print "sample orientations put in ",samp_file
return True, meas_file
def convert(**kwargs):
# initialize some stuff
dec = [315, 225, 180, 135, 45, 90, 270, 270, 270, 90, 180, 180, 0, 0, 0]
inc = [0, 0, 0, 0, 0, -45, -45, 0, 45, 45, 45, -45, -90, -45, 45]
tdec = [0, 90, 0, 180, 270, 0, 0, 90, 0]
tinc = [0, 0, 90, 0, 0, -90, 0, 0, 90]
demag = "N"
trm = 0
irm = 0
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # site outfile
magfile = kwargs.get('magfile', '')
labfield = int(kwargs.get('labfield', 0)) * 1e-6
phi = int(kwargs.get('phi', 0))
theta = int(kwargs.get('theta', 0))
peakfield = int(kwargs.get('peakfield', 0)) * 1e-3
specnum = int(kwargs.get('specnum', 0))
location = kwargs.get('location', 'unknown')
noave = kwargs.get('noave', False) # 0 means "do average", is default
samp_con = kwargs.get('samp_con', '1')
codelist = kwargs.get('codelist', '')
coil = kwargs.get('coil', '')
arm_labfield = kwargs.get('arm_labfield', 50e-6)
trm_peakT = kwargs.get('trm_peakT', 600 + 273)
mv = kwargs.get('mv', 'v')
# format/organize variables
if magfile:
try:
infile = open(os.path.join(input_dir_path, magfile), 'r')
except IOError:
print("bad mag file name")
return False, "bad mag file name"
else:
print("mag_file field is required option")
return False, "mag_file field is required option"
if specnum != 0: specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print(
"naming convention option [4] must be in form 4-Z where Z is an integer"
)
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
elif "7" in samp_con:
if "-" not in samp_con:
print(
"naming convention option [7] must be in form 7-Z where Z is an integer"
)
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
else:
Z = 1
codes = codelist.split(':')
if "AF" in codes:
demag = 'AF'
if not labfield: methcode = "LT-AF-Z"
if labfield: methcode = "LT-AF-I"
if "T" in codes:
demag = "T"
if not labfield: methcode = "LT-T-Z"
if labfield: methcode = "LT-T-I"
if "I" in codes:
methcode = "LP-IRM"
irmunits = "mT"
if "S" in codes:
demag = "S"
methcode = "LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield = labfield
# should use arm_labfield and trm_peakT as well, but these values are currently never asked for
if "G" in codes: methcode = "LT-AF-G"
if "D" in codes: methcode = "LT-AF-D"
if "TRM" in codes:
demag = "T"
trm = 1
if coil:
methcode = "LP-IRM"
irmunits = "V"
if coil not in ["1", "2", "3"]:
print('not a valid coil specification')
return False, 'not a valid coil specification'
if demag == "T" and "ANI" in codes:
methcode = "LP-AN-TRM"
if demag == "AF" and "ANI" in codes:
methcode = "LP-AN-ARM"
if labfield == 0: labfield = 50e-6
if peakfield == 0: peakfield = .180
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
version_num = pmag.get_version()
# find start of data:
DIspec = []
Data = infile.readlines()
infile.close()
for k in range(len(Data)):
rec = Data[k].split()
if len(rec) <= 2: continue
if rec[0].upper() == "LAT:" and len(rec) > 3:
lat, lon = rec[1], rec[3]
continue
elif rec[0].upper() == "ID":
continue
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
specimen = rec[0]
if specnum != 0:
sample = specimen[:specnum]
else:
sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
if mv == 'v':
volume = float(rec[12])
if volume > 0:
susc_chi_volume = '%10.3e' % (old_div(
(float(rec[11]) * 1e-5),
volume)) #convert to SI (assume Bartington, 10-5 SI)
else:
susc_chi_volume = '%10.3e' % (
float(rec[11]) * 1e-5
) #convert to SI (assume Bartington, 10-5 SI)
else:
mass = float(rec[12])
if mass > 0:
susc_chi_mass = '%10.3e' % (old_div(
(float(rec[11]) * 1e-5),
mass)) #convert to SI (assume Bartington, 10-5 SI)
else:
susc_chi_mass = '%10.3e' % (
float(rec[11]) * 1e-5
) #convert to SI (assume Bartington, 10-5 SI)
print((specimen, sample, site, samp_con, Z))
#fill tables besides measurements
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
if mv == 'v':
SpecRec["susc_chi_volume"] = susc_chi_volume
SpecRec["volume"] = volume
else:
SpecRec["susc_chi_mass"] = susc_chi_mass
SpecRec["mass"] = mass
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
#fill measurements
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"] = '0'
MeasRec["treat_dc_field"] = '0'
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
meas_type = "LT-NO"
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["specimen"] = specimen
# if mv=='v': MeasRec["susc_chi_volume"]=susc_chi_volume
# else: MeasRec["susc_chi_mass"]=susc_chi_mass
MeasRec["dir_csd"] = rec[3]
MeasRec["magn_moment"] = '%10.3e' % (float(rec[4]) * 1e-7)
MeasRec["dir_dec"] = rec[5]
MeasRec["dir_inc"] = rec[6]
MeasRec["citations"] = "This study"
if demag == "AF":
if methcode != "LP-AN-ARM":
MeasRec["treat_ac_field"] = '%8.3e' % (float(rec[1]) * 1e-3
) # peak field in tesla
meas_type = "LT-AF-Z"
MeasRec["treat_dc_field"] = '0'
else: # AARM experiment
if treat[1][0] == '0':
meas_type = "LT-AF-Z"
MeasRec["treat_ac_field"] = '%8.3e' % (
peakfield) # peak field in tesla
else:
meas_type = "LT-AF-I"
ipos = int(treat[0]) - 1
MeasRec["treat_dc_field_phi"] = '%7.1f' % (dec[ipos])
MeasRec["treat_dc_field_theta"] = '%7.1f' % (inc[ipos])
MeasRec["treat_dc_field"] = '%8.3e' % (labfield)
MeasRec["treat_ac_field"] = '%8.3e' % (
peakfield) # peak field in tesla
elif demag == "T":
if rec[1][0] == ".": rec[1] = "0" + rec[1]
treat = rec[1].split('.')
if len(treat) == 1: treat.append('0')
MeasRec["treat_temp"] = '%8.3e' % (float(rec[1]) + 273.
) # temp in kelvin
meas_type = "LT-T-Z"
MeasRec["treat_temp"] = '%8.3e' % (float(treat[0]) + 273.
) # temp in kelvin
if trm == 0: # demag=T and not trmaq
if treat[1][0] == '0':
meas_type = "LT-T-Z"
else:
MeasRec["treat_dc_field"] = '%8.3e' % (
labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"] = '%7.1f' % (
phi) # labfield phi
MeasRec["treat_dc_field_theta"] = '%7.1f' % (
theta) # labfield theta
if treat[1][0] == '1':
meas_type = "LT-T-I" # in-field thermal step
if treat[1][0] == '2':
meas_type = "LT-PTRM-I" # pTRM check
pTRM = 1
if treat[1][0] == '3':
MeasRec[
"treat_dc_field"] = '0' # this is a zero field step
meas_type = "LT-PTRM-MD" # pTRM tail check
else:
meas_type = "LT-T-I" # trm acquisition experiment
MeasRec['method_codes'] = meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
_2g_bin_magic.py
DESCRIPTION
takes the binary 2g format magnetometer files and converts them to magic_measurements, er_samples.txt and er_sites.txt file
SYNTAX
2g_bin_magic.py [command line options]
OPTIONS
-f FILE: specify input 2g (binary) file
-F FILE: specify magic_measurements output file, default is: magic_measurements.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-Fsi FILE: specify output file, default is: er_sites.txt
-ncn NCON: specify naming convention: default is #2 below
-ocn OCON: specify orientation convention, default is #5 below
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-ASC an ASC orientation device was used
SO-MAG orientation with magnetic compass
SO-SUN orientation with sun compass
-loc: location name, default="unknown"
-spc NUM : specify number of characters to designate a specimen, default = 0
-ins INST : specify instsrument name
-a: average replicate measurements
INPUT FORMAT
Input files are horrible mag binary format (who knows why?)
Orientation convention:
[1] Lab arrow azimuth= mag_azimuth; Lab arrow dip=-field_dip
i.e., field_dip is degrees from vertical down - the hade [default]
[2] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = -field_dip
i.e., mag_azimuth is strike and field_dip is hade
[3] Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
i.e., lab arrow same as field arrow, but field_dip was a hade.
[4] lab azimuth and dip are same as mag_azimuth, field_dip
[5] lab azimuth is same as mag_azimuth,lab arrow dip=field_dip-90
[6] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = 90-field_dip
[7] all others you will have to either customize your
self or e-mail [email protected] for help.
Magnetic declination convention:
Az will use supplied declination to correct azimuth
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
OUTPUT
output saved in magic_measurements.txt & er_samples.txt formatted files
will overwrite any existing files
"""
#
# initialize variables
#
mag_file = ''
specnum=0
ub_file,samp_file,or_con,corr,meas_file = "","er_samples.txt","3","1","magic_measurements.txt"
pos_file,site_file="","er_sites.txt"
noave=1
args=sys.argv
bed_dip,bed_dip_dir="",""
samp_con,Z,average_bedding="2",1,"0"
meths='FS-FD'
sclass,lithology,_type="","",""
user,inst="",""
DecCorr=0.
location_name="unknown"
months=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov','Dec']
gmeths=""
#
#
dir_path='.'
if command_line:
if '-WD' in args:
ind=args.index("-WD")
dir_path=sys.argv[ind+1]
if "-h" in args:
print main.__doc__
return False
if "-f" in args:
ind=args.index("-f")
mag_file=sys.argv[ind+1]
if "-fpos" in args:
ind=args.index("-fpos")
pos_file=sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
meas_file=sys.argv[ind+1]
if "-Fsa" in args:
ind=args.index("-Fsa")
samp_file=sys.argv[ind+1]
if "-Fsi" in args:
ind=args.index("-Fsi")
site_file=sys.argv[ind+1]
if "-ocn" in args:
ind=args.index("-ocn")
or_con=sys.argv[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-mcd" in args:
ind=args.index("-mcd")
gmeths=(sys.argv[ind+1])
if "-loc" in args:
ind=args.index("-loc")
location_name=(sys.argv[ind+1])
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-a" in args:
noave=0
#
ID = False
if '-ID' in args:
ind = args.index('-ID')
ID = args[ind+1]
#
if not command_line:
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file', '')
pos_file = kwargs.get('pos_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt')
or_con = kwargs.get('or_con', '3')
samp_con = kwargs.get('samp_con', '2')
corr = kwargs.get('corr', '1')
gmeths = kwargs.get('gmeths', '')
location_name = kwargs.get('location_name', '')
specnum = int(kwargs.get('specnum', 0))
inst = kwargs.get('inst', '')
noave = kwargs.get('noave', 1) # default is DO average
ID = kwargs.get('ID', '')
# format and fix variables acquired from command line args or input with **kwargs
if specnum!=0:specnum=-specnum
if ID:
input_dir_path = ID
else:
input_dir_path = dir_path
if samp_con:
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
if "6" in samp_con:
try:
Samps,file_type=pmag.magic_read(os.path.join(input_dir_path, 'er_samples.txt'))
except:
print "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
if file_type == 'bad_file':
print "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
if not mag_file:
print "mag file is required input"
return False, "mag file is required input"
output_dir_path = dir_path
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = output_dir_path+'/'+samp_file
site_file = output_dir_path+'/'+site_file
meas_file= output_dir_path+'/'+meas_file
samplist=[]
try:
Samps,file_type=pmag.magic_read(samp_file)
for samp in Samps:
if samp['er_sample_name'] not in samplist: samplist.append(samp['er_sample_name'])
except:
Samps=[]
MagRecs=[]
try:
f=open(mag_file,'rU')
input=f.read()
f.close()
except Exception as ex:
print 'ex', ex
print "bad mag file"
return False, "bad mag file"
firstline,date=1,""
d=input.split('\xcd')
for line in d:
rec=line.split('\x00')
if firstline==1:
firstline=0
spec,vol="",1
for c in line[15:23]:
if c!='\x00':spec=spec+c
# check for bad sample name
test=spec.split('.')
date=""
if len(test)>1:
spec=test[0]
kk=24
while line[kk]!='\x01' and line[kk]!='\x00':
kk+=1
vcc=line[24:kk]
el=10
while rec[el].strip()!='':el+=1
date,comments=rec[el+7],[]
else:
el=9
while rec[el]!='\x01':el+=1
vcc,date,comments=rec[el-3],rec[el+7],[]
specname=spec.lower()
print 'importing ',specname
el+=8
while rec[el].isdigit()==False:
comments.append(rec[el])
el+=1
while rec[el]=="":el+=1
az=float(rec[el])
el+=1
while rec[el]=="":el+=1
pl=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip_dir=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip=float(rec[el])
el+=1
while rec[el]=="":el+=1
if rec[el]=='\x01':
bed_dip=180.-bed_dip
el+=1
while rec[el]=="":el+=1
fold_az=float(rec[el])
el+=1
while rec[el]=="":el+=1
fold_pl=rec[el]
el+=1
while rec[el]=="":el+=1
if rec[el]!="" and rec[el]!='\x02' and rec[el]!='\x01':
deccorr=float(rec[el])
az+=deccorr
bed_dip_dir+=deccorr
fold_az+=deccorr
if bed_dip_dir>=360:bed_dip_dir=bed_dip_dir-360.
if az>=360.:az=az-360.
if fold_az>=360.:fold_az=fold_az-360.
else:
deccorr=0
if specnum!=0:
sample=specname[:specnum]
else:
sample=specname
SampRec={}
SampRec["er_sample_name"]=sample
SampRec["er_location_name"]=location_name
SampRec["er_citation_names"]="This study"
labaz,labdip=pmag.orient(az,pl,or_con) # convert to labaz, labpl
#
# parse information common to all orientation methods
#
SampRec["sample_bed_dip"]='%7.1f'%(bed_dip)
SampRec["sample_bed_dip_direction"]='%7.1f'%(bed_dip_dir)
SampRec["sample_dip"]='%7.1f'%(labdip)
SampRec["sample_azimuth"]='%7.1f'%(labaz)
if vcc.strip()!="":vol=float(vcc)*1e-6 # convert to m^3 from cc
SampRec["sample_volume"]='%10.3e'%(vol) #
SampRec["sample_class"]=sclass
SampRec["sample_lithology"]=lithology
SampRec["sample_type"]=_type
SampRec["sample_declination_correction"]='%7.1f'%(deccorr)
methods=gmeths.split(':')
if deccorr!="0":
if 'SO-MAG' in methods:del methods[methods.index('SO-MAG')]
methods.append('SO-CMD-NORTH')
meths=""
for meth in methods:meths=meths+meth+":"
meths=meths[:-1]
SampRec["magic_method_codes"]=meths
if int(samp_con)<6 or int(samp_con) == 7:
site=pmag.parse_site(SampRec["er_sample_name"],samp_con,Z) # parse out the site name
SampRec["er_site_name"]=site
elif len(Samps)>1:
site,location="",""
for samp in Samps:
if samp["er_sample_name"] == SampRec["er_sample_name"]:
site=samp["er_site_name"]
location=samp["er_location_name"]
break
SampRec["er_location_name"]=samp["er_location_name"]
SampRec["er_site_name"]=samp["er_site_name"]
if sample not in samplist:
samplist.append(sample)
Samps.append(SampRec)
else:
MagRec={}
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=specname
MagRec["er_sample_name"]=SampRec['er_sample_name']
MagRec["er_site_name"]=SampRec['er_site_name']
MagRec["er_location_name"]=location_name
el,demag=1,''
treat=rec[el]
if treat[-1]=='C':
demag='T'
elif treat!='NRM':
demag='AF'
el+=1
while rec[el]=="":el+=1
MagRec["measurement_dec"]=rec[el]
cdec=float(rec[el])
el+=1
while rec[el]=="":el+=1
MagRec["measurement_inc"]=rec[el]
cinc=float(rec[el])
el+=1
while rec[el]=="":el+=1
gdec=rec[el]
el+=1
while rec[el]=="":el+=1
ginc=rec[el]
el=skip(2,el,rec) # skip bdec,binc
# el=skip(4,el,rec) # skip gdec,ginc,bdec,binc
# print 'moment emu: ',rec[el]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[el])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_magn_volume"]='%10.3e'% (float(rec[el])*1e-3/vol) # magnetization in A/m
el=skip(2,el,rec) # skip to xsig
MagRec["measurement_sd_x"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to ysig
MagRec["measurement_sd_y"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to zsig
MagRec["measurement_sd_z"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el+=1 # skip to positions
MagRec["measurement_positions"]=rec[el]
# el=skip(5,el,rec) # skip to date
# mm=str(months.index(date[0]))
# if len(mm)==1:
# mm='0'+str(mm)
# else:
# mm=str(mm)
# dstring=date[2]+':'+mm+':'+date[1]+":"+date[3]
# MagRec['measurement_date']=dstring
MagRec["magic_instrument_codes"]=inst
MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"]="This study"
MagRec["magic_method_codes"]=meas_type
if demag=="AF":
MagRec["treatment_ac_field"]='%8.3e' %(float(treat[:-2])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
elif demag=="T":
MagRec["treatment_temp"]='%8.3e' % (float(treat[:-1])+273.) # temp in kelvin
meas_type="LT-T-Z"
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
MagOuts, keylist = pmag.fillkeys(MagOuts)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "Measurements put in ",meas_file
SampsOut,sampkeys=pmag.fillkeys(Samps)
pmag.magic_write(samp_file,SampsOut,"er_samples")
Sites=[]
for samp in Samps:
SiteRec={}
SiteRec['er_site_name']=samp['er_site_name']
SiteRec['er_location_name']=samp['er_location_name']
SiteRec['site_definition']='s'
SiteRec['er_citation_names']='This study'
if 'sample_class' in samp.keys():SiteRec['site_class']=samp['sample_class']
if 'sample_lithology' in samp.keys():SiteRec['site_lithology']=samp['sample_lithology']
if 'sample_type' in samp.keys():SiteRec['site_lithology']=samp['sample_lithology']
if 'sample_lat' in samp.keys():
SiteRec['site_lat']=samp['sample_lat']
else:
SiteRec['site_lat']="-999"
if 'sample_lon' in samp.keys():
SiteRec['site_lon']=samp['sample_lon']
else:
SiteRec['site_lon']="-999"
if 'sample_height' in samp.keys():SiteRec['site_height']=samp['sample_height']
Sites.append(SiteRec)
pmag.magic_write(site_file,Sites,'er_sites')
return True, meas_file
def main():
"""
NAME
mst_magic.py
DESCRIPTION
converts MsT data (T,M) to magic_measurements format files
SYNTAX
mst_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify T,M format input file, required
-fsa SFILE: name with sample, site, location information
-F FILE: specify output file, default is MsT_measurements.txt
-dc H: specify applied field during measurement, default is 0.5 T
-syn : This is a synthetic specimen and has no sample/site/location information
-spn SPEC: specimen name
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-ncn NCON: specify naming convention: default is #1 below
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT files:
T M: T is in Centigrade and M is uncalibrated magnitude
"""
# initialize some stuff
samp_con, Z = "1", "0"
dir_path = '.'
citation = 'This study'
args = sys.argv
specnum, measnum = 0, 1
#
# get command line arguments
#
user = ""
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
meas_file = dir_path + "/MsT_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
labfield = '0.5'
if "-dc" in args:
ind = args.index("-dc")
labfield = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
meas_file = dir_path + '/' + args[ind + 1]
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = dir_path + '/' + args[ind + 1]
Samps, file_type = pmag.magic_read(samp_file)
if '-f' in args:
ind = args.index("-f")
infile = dir_path + '/' + args[ind + 1]
try:
input = open(infile, 'rU')
except:
print "bad mag file name"
sys.exit()
else:
print main.__doc__
print "-f is required option"
sys.exit()
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if specnum != 0: specnum = -specnum
er_location_name, syn, specimen_name = 'unknown', 0, 'unknown'
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-spn" in args:
ind = args.index("-spn")
specimen_name = args[ind + 1]
else:
print main.__doc__
print "-spn is required option"
sys.exit()
if "-syn" in args: syn = 1
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
samp_con = sys.argv[ind + 1]
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "7"
MagRecs, specs = [], []
version_num = pmag.get_version()
data = input.readlines()
T0 = float(data[0].split()[0])
for line in data:
instcode = ""
if len(line) > 1:
MagRec = {}
if syn == 0: MagRec['er_location_name'] = er_location_name
MagRec['magic_software_packages'] = version_num
MagRec["treatment_dc_field"] = labfield
rec = line.split()
T = float(rec[0])
MagRec["measurment_temp"] = '%8.3e' % (float(rec[0]) + 273.
) # temp in kelvin
if T > T0:
MagRec["magic_method_codes"] = 'LP-MW-I'
elif T < T0:
MagRec["magic_method_codes"] = 'LP-MC-I'
T0 = T
else:
print 'skipping repeated temperature step'
MagRec["magic_method_codes"] = ''
T0 = T
MagRec["measurement_magnitude"] = '%10.3e' % (float(
rec[1])) # uncalibrated magnitude
if syn == 0:
MagRec["er_specimen_name"] = specimen_name
MagRec["er_site_name"] = ""
if specnum != 0:
MagRec["er_sample_name"] = specimen_name[:specnum]
else:
MagRec["er_sample_name"] = specimen_name
if "-fsa" in args:
for samp in Samps:
if samp["er_sample_name"] == MagRec["er_sample_name"]:
MagRec["er_location_name"] = samp[
"er_location_name"]
MagRec["er_site_name"] = samp["er_site_name"]
break
elif int(samp_con) != 6:
site = pmag.parse_site(MagRec['er_sample_name'], samp_con,
Z)
MagRec["er_site_name"] = site
if MagRec['er_site_name'] == "":
print 'No site name found for: ', MagRec[
'er_specimen_name'], MagRec['er_sample_name']
if MagRec["er_location_name"] == "":
print 'no location name for: ', MagRec["er_specimen_name"]
else:
MagRec["er_synthetic_name"] = specimen_name
MagRec["er_location_name"] = ""
MagRec["er_sample_name"] = ""
MagRec["er_site_name"] = ""
MagRec["er_specimen_name"] = ""
MagRec["magic_instrument_codes"] = instcode
MagRec["er_analyst_mail_names"] = user
MagRec["er_citation_names"] = citation
MagRec["measurement_flag"] = 'g'
MagRec["measurement_number"] = str(measnum)
measnum += 1
MagRecs.append(MagRec)
for rec in MagRecs: # sort out the measurements by experiment type
rec['magic_experiment_name'] = specimen_name
if rec['magic_method_codes'] == 'LP-MW-I':
rec["magic_experiment_name"] = specimen_name + ':LP-MW-I:Curie'
elif rec['magic_method_codes'] == 'LP-MC-I':
rec["magic_experiment_name"] = specimen_name + ':LP-MC-I'
pmag.magic_write(meas_file, MagRecs, 'magic_measurements')
print "results put in ", meas_file
def main(command_line=True, **kwargs):
"""
NAME
sio_magic.py
DESCRIPTION
converts SIO .mag format files to magic_measurements format files
SYNTAX
sio_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .mag format input file, required
-fsa SAMPFILE : specify er_samples.txt file relating samples, site and locations names,default is none -- values in SAMPFILE will override selections for -loc (location), -spc (designate specimen), and -ncn (sample-site naming convention)
-F FILE: specify output file, default is magic_measurements.txt
-Fsy: specify er_synthetics file, default is er_sythetics.txt
-LP [colon delimited list of protocols, include all that apply]
AF: af demag
T: thermal including thellier but not trm acquisition
S: Shaw method
I: IRM (acquisition)
I3d: 3D IRM experiment
N: NRM only
TRM: trm acquisition
ANI: anisotropy experiment
D: double AF demag
G: triple AF demag (GRM protocol)
CR: cooling rate experiment.
The treatment coding of the measurement file should be: XXX.00,XXX.10, XXX.20 ...XX.70 etc. (XXX.00 is optional)
where XXX in the temperature and .10,.20... are running numbers of the cooling rates steps.
XXX.00 is optional zerofield baseline. XXX.70 is alteration check.
syntax in sio_magic is: -LP CR xxx,yyy,zzz,..... xxx -A
where xxx, yyy, zzz...xxx are cooling time in [K/minutes], seperated by comma, ordered at the same order as XXX.10,XXX.20 ...XX.70
if you use a zerofield step then no need to specify the cooling rate for the zerofield
It is important to add to the command line the -A option so the measurements will not be averaged.
But users need to make sure that there are no duplicate measurements in the file
-V [1,2,3] units of IRM field in volts using ASC coil #1,2 or 3
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-syn INST TYPE: sets these specimens as synthetics created at institution INST and of type TYPE
-ins INST : specify which demag instrument was used (e.g, SIO-Suzy or SIO-Odette),default is ""
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] synthetic - has no site name
[9] ODP naming convention
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in
seperate .mag files (eg. af.mag, thermal.mag, etc.)
Format of SIO .mag files:
Spec Treat CSD Intensity Declination Inclination [optional metadata string]
Spec: specimen name
Treat: treatment step
XXX T in Centigrade
XXX AF in mT
for special experiments:
Thellier:
XXX.0 first zero field step
XXX.1 first in field step [XXX.0 and XXX.1 can be done in any order]
XXX.2 second in-field step at lower temperature (pTRM check)
XXX.3 second zero-field step after infield (pTRM check step)
XXX.3 MUST be done in this order [XXX.0, XXX.1 [optional XXX.2] XXX.3]
AARM:
X.00 baseline step (AF in zero bias field - high peak field)
X.1 ARM step (in field step) where
X is the step number in the 15 position scheme
(see Appendix to Lecture 13 - http://magician.ucsd.edu/Essentials_2)
ATRM:
X.00 optional baseline
X.1 ATRM step (+X)
X.2 ATRM step (+Y)
X.3 ATRM step (+Z)
X.4 ATRM step (-X)
X.5 ATRM step (-Y)
X.6 ATRM step (-Z)
X.7 optional alteration check (+X)
TRM:
XXX.YYY XXX is temperature step of total TRM
YYY is dc field in microtesla
Intensity assumed to be total moment in 10^3 Am^2 (emu)
Declination: Declination in specimen coordinate system
Inclination: Declination in specimen coordinate system
Optional metatdata string: mm/dd/yy;hh:mm;[dC,mT];xx.xx;UNITS;USER;INST;NMEAS
hh in 24 hours.
dC or mT units of treatment XXX (see Treat above) for thermal or AF respectively
xx.xxx DC field
UNITS of DC field (microT, mT)
INST: instrument code, number of axes, number of positions (e.g., G34 is 2G, three axes,
measured in four positions)
NMEAS: number of measurements in a single position (1,3,200...)
"""
# initialize some stuff
mag_file = None
codelist = None
infile_type="mag"
noave=0
methcode,inst="LP-NO",""
phi,theta,peakfield,labfield=0,0,0,0
pTRM,MD,samp_con,Z=0,0,'1',1
dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0]
inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
tdec=[0,90,0,180,270,0,0,90,0]
tinc=[0,0,90,0,0,-90,0,0,90]
missing=1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
fmt='old'
syn=0
synfile='er_synthetics.txt'
samp_infile,Samps='',[]
trm=0
irm=0
specnum=0
coil=""
mag_file=""
#
# get command line arguments
#
meas_file="magic_measurements.txt"
user=""
if not command_line:
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', '')
syn_file = kwargs.get('syn_file', '')
mag_file = kwargs.get('mag_file', '')
labfield = kwargs.get('labfield', '')
if labfield:
labfield = float(labfield) *1e-6
else:
labfield = 0
phi = kwargs.get('phi', 0)
if phi:
phi = float(phi)
else:
phi = 0
theta = kwargs.get('theta', 0)
if theta:
theta=float(theta)
else:
theta = 0
peakfield = kwargs.get('peakfield', 0)
if peakfield:
peakfield=float(peakfield) *1e-3
else:
peakfield = 0
specnum = kwargs.get('specnum', 0)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
samp_infile = kwargs.get('samp_infile', '')
syn = kwargs.get('syn', 0)
institution = kwargs.get('institution', '')
syntype = kwargs.get('syntype', '')
inst = kwargs.get('inst', '')
noave = kwargs.get('noave', 0)
codelist = kwargs.get('codelist', '')
coil = kwargs.get('coil', '')
cooling_rates = kwargs.get('cooling_rates', '')
if command_line:
if "-h" in args:
print(main.__doc__)
return False
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsy' in args:
ind=args.index("-Fsy")
synfile=args[ind+1]
if '-f' in args:
ind=args.index("-f")
mag_file=args[ind+1]
if "-dc" in args:
ind=args.index("-dc")
labfield=float(args[ind+1])*1e-6
phi=float(args[ind+2])
theta=float(args[ind+3])
if "-ac" in args:
ind=args.index("-ac")
peakfield=float(args[ind+1])*1e-3
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
samp_infile = args[ind+1]
if '-syn' in args:
syn=1
ind=args.index("-syn")
institution=args[ind+1]
syntype=args[ind+2]
if '-fsy' in args:
ind=args.index("-fsy")
synfile=args[ind+1]
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-A" in args: noave=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
if "-V" in args:
ind=args.index("-V")
coil=args[ind+1]
# make sure all initial values are correctly set up (whether they come from the command line or a GUI)
if samp_infile:
Samps, file_type = pmag.magic_read(samp_infile)
if coil:
coil = str(coil)
methcode="LP-IRM"
irmunits = "V"
if coil not in ["1","2","3"]:
print(main.__doc__)
print('not a valid coil specification')
return False, '{} is not a valid coil specification'.format(coil)
if mag_file:
try:
#with open(mag_file,'r') as finput:
# lines = finput.readlines()
lines=pmag.open_file(mag_file)
except:
print("bad mag file name")
return False, "bad mag file name"
if not mag_file:
print(main.__doc__)
print("mag_file field is required option")
return False, "mag_file field is required option"
if specnum!=0:
specnum=-specnum
#print 'samp_con:', samp_con
if samp_con:
if "4" == samp_con[0]:
if "-" not in samp_con:
print("naming convention option [4] must be in form 4-Z where Z is an integer")
print('---------------')
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" == samp_con[0]:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
if codelist:
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in args: methcode="LT-AF-Z"
if'-dc' in args: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in args: methcode="LT-T-Z"
if '-dc' in args: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
irmunits="mT"
if "I3d" in codes:
methcode="LT-T-Z:LP-IRM-3D"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if "CR" in codes:
demag="T"
cooling_rate_experiment=1
if command_line:
ind=args.index("CR")
cooling_rates=args[ind+1]
cooling_rates_list=cooling_rates.split(',')
else:
cooling_rates_list=str(cooling_rates).split(',')
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="T" and "CR" in codes:
methcode="LP-CR-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
SynRecs,MagRecs=[],[]
version_num=pmag.get_version()
##################################
if 1:
#if infile_type=="SIO format":
for line in lines:
instcode=""
if len(line)>2:
SynRec={}
MagRec={}
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
rec=line.split()
if rec[1]==".00":rec[1]="0.00"
treat=rec[1].split('.')
if methcode=="LP-IRM":
if irmunits=='mT':
labfield=float(treat[0])*1e-3
else:
labfield=pmag.getfield(irmunits,coil,treat[0])
if rec[1][0]!="-":
phi,theta=0.,90.
else:
phi,theta=0.,-90.
meas_type="LT-IRM"
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
if len(rec)>6:
code1=rec[6].split(';') # break e.g., 10/15/02;7:45 indo date and time
if len(code1)==2: # old format with AM/PM
missing=0
code2=code1[0].split('/') # break date into mon/day/year
code3=rec[7].split(';') # break e.g., AM;C34;200 into time;instr/axes/measuring pos;number of measurements
yy=int(code2[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(code2[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(code2[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if code3[0]=="PM":hh=hh+12
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else: min=str(min)
MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00"
MagRec["measurement_time_zone"]='SAN'
if inst=="":
if code3[1][0]=='C':instcode='SIO-bubba'
if code3[1][0]=='G':instcode='SIO-flo'
else:
instcode=''
MagRec["measurement_positions"]=code3[1][2]
elif len(code1)>2: # newest format (cryo7 or later)
if "LP-AN-ARM" not in methcode:labfield=0
fmt='new'
date=code1[0].split('/') # break date into mon/day/year
yy=int(date[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(date[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(date[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else:
min=str(min)
MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00"
MagRec["measurement_time_zone"]='SAN'
if inst=="":
if code1[6][0]=='C':
instcode='SIO-bubba'
if code1[6][0]=='G':
instcode='SIO-flo'
else:
instcode=''
if len(code1)>1:
MagRec["measurement_positions"]=code1[6][2]
else:
MagRec["measurement_positions"]=code1[7] # takes care of awkward format with bubba and flo being different
if user=="":user=code1[5]
if code1[2][-1]=='C':
demag="T"
if code1[4]=='microT' and float(code1[3])!=0. and "LP-AN-ARM" not in methcode: labfield=float(code1[3])*1e-6
if code1[2]=='mT' and methcode!="LP-IRM":
demag="AF"
if code1[4]=='microT' and float(code1[3])!=0.: labfield=float(code1[3])*1e-6
if code1[4]=='microT' and labfield!=0. and meas_type!="LT-IRM":
phi,theta=0.,-90.
if demag=="T": meas_type="LT-T-I"
if demag=="AF": meas_type="LT-AF-I"
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
if code1[4]=='' or labfield==0. and meas_type!="LT-IRM":
if demag=='T':meas_type="LT-T-Z"
if demag=="AF":meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
if syn==0:
MagRec["er_specimen_name"]=rec[0]
MagRec["er_synthetic_name"]=""
MagRec["er_site_name"]=""
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
if samp_infile and Samps: # if samp_infile was provided AND yielded sample data
samp=pmag.get_dictitem(Samps,'er_sample_name',MagRec['er_sample_name'],'T')
if len(samp)>0:
MagRec["er_location_name"]=samp[0]["er_location_name"]
MagRec["er_site_name"]=samp[0]["er_site_name"]
else:
MagRec['er_location_name']=''
MagRec["er_site_name"]=''
elif int(samp_con)!=6:
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
if MagRec['er_site_name']=="":
print('No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name'])
if MagRec["er_location_name"]=="":
print('no location name for: ',MagRec["er_specimen_name"])
else:
MagRec["er_specimen_name"]=rec[0]
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
MagRec["er_site_name"]=""
MagRec["er_synthetic_name"]=MagRec["er_specimen_name"]
SynRec["er_synthetic_name"]=MagRec["er_specimen_name"]
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
SynRec["synthetic_parent_sample"]=site
SynRec["er_citation_names"]="This study"
SynRec["synthetic_institution"]=institution
SynRec["synthetic_type"]=syntype
SynRecs.append(SynRec)
if float(rec[1])==0:
pass
elif demag=="AF":
if methcode != "LP-AN-ARM":
MagRec["treatment_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla
if meas_type=="LT-AF-Z": MagRec["treatment_dc_field"]='0'
else: # AARM experiment
if treat[1][0]=='0':
meas_type="LT-AF-Z:LP-AN-ARM:"
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e'%(0)
if labfield!=0 and methcode!="LP-AN-ARM": print("Warning - inconsistency in mag file with lab field - overriding file with 0")
else:
meas_type="LT-AF-I:LP-AN-ARM"
ipos=int(treat[0])-1
MagRec["treatment_dc_field_phi"]='%7.1f' %(dec[ipos])
MagRec["treatment_dc_field_theta"]='%7.1f'% (inc[ipos])
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
elif demag=="T" and methcode == "LP-AN-TRM":
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if treat[1][0]=='0':
meas_type="LT-T-Z:LP-AN-TRM"
MagRec["treatment_dc_field"]='%8.3e'%(0)
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
else:
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
if treat[1][0]=='7': # alteration check as final measurement
meas_type="LT-PTRM-I:LP-AN-TRM"
else:
meas_type="LT-T-I:LP-AN-TRM"
# find the direction of the lab field in two ways:
# (1) using the treatment coding (XX.1=+x, XX.2=+y, XX.3=+z, XX.4=-x, XX.5=-y, XX.6=-z)
ipos_code=int(treat[1][0])-1
# (2) using the magnetization
DEC=float(rec[4])
INC=float(rec[5])
if INC < 45 and INC > -45:
if DEC>315 or DEC<45: ipos_guess=0
if DEC>45 and DEC<135: ipos_guess=1
if DEC>135 and DEC<225: ipos_guess=3
if DEC>225 and DEC<315: ipos_guess=4
else:
if INC >45: ipos_guess=2
if INC <-45: ipos_guess=5
# prefer the guess over the code
ipos=ipos_guess
MagRec["treatment_dc_field_phi"]='%7.1f' %(tdec[ipos])
MagRec["treatment_dc_field_theta"]='%7.1f'% (tinc[ipos])
# check it
if ipos_guess!=ipos_code and treat[1][0]!='7':
print("-E- ERROR: check specimen %s step %s, ATRM measurements, coding does not match the direction of the lab field!"%(rec[0],".".join(list(treat))))
elif demag=="S": # Shaw experiment
if treat[1][1]=='0':
if int(treat[0])!=0:
MagRec["treatment_ac_field"]='%8.3e' % (float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z" # first AF
else:
meas_type="LT-NO"
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
elif treat[1][1]=='1':
if int(treat[0])==0:
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e'%(arm_labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
meas_type="LT-AF-I"
else:
MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z"
elif treat[1][1]=='2':
if int(treat[0])==0:
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='%8.3e'%(trm_labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
MagRec["treatment_temp"]='%8.3e' % (trm_peakT)
meas_type="LT-T-I"
else:
MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z"
elif treat[1][1]=='3':
if int(treat[0])==0:
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e'%(arm_labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
meas_type="LT-AF-I"
else:
MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z"
# Cooling rate experient # added by rshaar
elif demag=="T" and methcode == "LP-CR-TRM":
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if treat[1][0]=='0':
meas_type="LT-T-Z:LP-CR-TRM"
MagRec["treatment_dc_field"]='%8.3e'%(0)
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
else:
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
if treat[1][0]=='7': # alteration check as final measurement
meas_type="LT-PTRM-I:LP-CR-TRM"
else:
meas_type="LT-T-I:LP-CR-TRM"
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
indx=int(treat[1][0])-1
# alteration check matjed as 0.7 in the measurement file
if indx==6:
cooling_time= cooling_rates_list[-1]
else:
cooling_time=cooling_rates_list[indx]
MagRec["measurement_description"]="cooling_rate"+":"+cooling_time+":"+"K/min"
elif demag!='N':
if len(treat)==1:treat.append('0')
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if trm==0: # demag=T and not trmaq
if treat[1][0]=='0':
meas_type="LT-T-Z"
else:
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step
if treat[1][0]=='2':
meas_type="LT-PTRM-I" # pTRM check
pTRM=1
if treat[1][0]=='3':
MagRec["treatment_dc_field"]='0' # this is a zero field step
meas_type="LT-PTRM-MD" # pTRM tail check
else:
labfield=float(treat[1])*1e-6
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
meas_type="LT-T-I:LP-TRM" # trm acquisition experiment
MagRec["measurement_csd"]=rec[2]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[3])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_dec"]=rec[4]
MagRec["measurement_inc"]=rec[5]
MagRec["magic_instrument_codes"]=instcode
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
if "LP-IRM-3D" in methcode : meas_type=methcode
#MagRec["magic_method_codes"]=methcode.strip(':')
MagRec["magic_method_codes"]=meas_type
MagRec["measurement_flag"]='g'
MagRec["er_specimen_name"]=rec[0]
if 'std' in rec[0]:
MagRec["measurement_standard"]='s'
else:
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
#print MagRec['treatment_temp']
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print("results put in ",meas_file)
if len(SynRecs)>0:
pmag.magic_write(synfile,SynRecs,'er_synthetics')
print("synthetics put in ",synfile)
return True, meas_file
def convert(**kwargs):
# initialize some stuff
version_num = pmag.get_version()
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs = [],[],[],[],[]
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # site outfile
location = kwargs.get('location', 'unknown')
dmy_flag = kwargs.get('dmy_flag', False)
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
#oave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
specnum = -int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '2')
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
site_num=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
site_num=samp_con.split("-")[1]
samp_con="7"
else: site_num=1
try:
DC_FIELD = float(kwargs.get('labfield',0))*1e-6
DC_PHI = float(kwargs.get('phi',0))
DC_THETA = float(kwargs.get('theta',0))
except ValueError: raise ValueError('problem with your dc parameters. please provide a labfield in microTesla and a phi and theta in degrees.')
noave = kwargs.get('noave', False)
dmy_flag = kwargs.get('dmy_flag', False)
meas_n_orient = kwargs.get('meas_n_orient', '8')
# format variables
if not mag_file:
return False, 'You must provide a Utrecht formated file'
mag_file = os.path.join(input_dir_path, mag_file)
# parse data
# Open up the Utrecht file and read the header information
AF_or_T = mag_file.split('.')[-1]
data = open(mag_file, 'r')
line = data.readline()
line_items = line.split(',')
operator=line_items[0]
operator=operator.replace("\"","")
machine=line_items[1]
machine=machine.replace("\"","")
machine=machine.rstrip('\n')
# print("operator=", operator)
# print("machine=", machine)
#read in measurement data
line = data.readline()
while line != "END" and line != '"END"':
SpecRec,SampRec,SiteRec,LocRec = {},{},{},{}
line_items = line.split(',')
spec_name=line_items[0]
spec_name=spec_name.replace("\"","")
# print("spec_name=", spec_name)
free_string=line_items[1]
free_string=free_string.replace("\"","")
# print("free_string=", free_string)
dec=line_items[2]
# print("dec=", dec)
inc=line_items[3]
# print("inc=", inc)
volume=float(line_items[4])
volume=volume * 1e-6 # enter volume in cm^3, convert to m^3
# print("volume=", volume)
bed_plane=line_items[5]
# print("bed_plane=", bed_plane)
bed_dip=line_items[6]
# print("bed_dip=", bed_dip)
# Configure et er_ tables
if specnum==0: sample_name = spec_name
else: sample_name = spec_name[:specnum]
site = pmag.parse_site(sample_name,samp_con,site_num)
SpecRec['specimen'] = spec_name
SpecRec['sample'] = sample_name
if volume!=0: SpecRec['volume']=volume
SpecRecs.append(SpecRec)
if sample_name!="" and sample_name not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample_name
SampRec['azimuth'] = dec
SampRec['dip'] = str(float(inc)-90)
SampRec['bed_dip_direction'] = bed_plane
SampRec['bed_dip'] = bed_dip
SampRec['method_codes'] = meth_code
SampRec['site'] = site
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
#measurement data
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
while line != '9999':
step=items[0]
step=step.split('.')
step_value=step[0]
step_type = ""
if len(step) == 2:
step_type=step[1]
if step_type=='5':
step_value = items[0]
A=float(items[1])
B=float(items[2])
C=float(items[3])
# convert to MagIC coordinates
Z=-A
X=-B
Y=C
cart = array([X, Y, Z]).transpose()
direction = pmag.cart2dir(cart).transpose()
measurement_dec = direction[0]
measurement_inc = direction[1]
magn_moment = direction[2] * 1.0e-12 # the data are in pico-Am^2 - this converts to Am^2
if volume!=0:
magn_volume = direction[2] * 1.0e-12 / volume # data volume normalized - converted to A/m
# print("magn_moment=", magn_moment)
# print("magn_volume=", magn_volume)
error = items[4]
date=items[5]
date=date.strip('"').replace(' ','')
if date.count("-") > 0:
date=date.split("-")
elif date.count("/") > 0:
date=date.split("/")
else: print("date format seperator cannot be identified")
# print(date)
time=items[6]
time=time.strip('"').replace(' ','')
time=time.split(":")
# print(time)
dt = date[0] + ":" + date[1] + ":" + date[2] + ":" + time[0] + ":" + time[1] + ":" + "0"
local = pytz.timezone("Europe/Amsterdam")
try:
if dmy_flag: naive = datetime.datetime.strptime(dt, "%d:%m:%Y:%H:%M:%S")
else: naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
except ValueError:
naive = datetime.datetime.strptime(dt, "%Y:%m:%d:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
# print(timestamp)
MeasRec = {}
MeasRec["timestamp"]=timestamp
MeasRec["analysts"] = operator
MeasRec["instrument_codes"] = "Utrecht_" + machine
MeasRec["description"] = "free string = " + free_string
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["experiments"] = location + site + spec_name
MeasRec["treat_step_num"] = location + site + spec_name + items[0]
MeasRec["specimen"] = spec_name
# MeasRec["treat_ac_field"] = '0'
if AF_or_T.lower() == "th":
MeasRec["treat_temp"] = '%8.3e' % (float(step_value)+273.) # temp in kelvin
MeasRec['treat_ac_field']='0'
lab_treat_type = "T"
else:
MeasRec['treat_temp']='273'
MeasRec['treat_ac_field']='%10.3e'%(float(step_value)*1e-3)
lab_treat_type = "AF"
MeasRec['treat_dc_field']='0'
if step_value == '0':
meas_type = "LT-NO"
# print("step_type=", step_type)
if step_type == '0' or step_type == '00':
meas_type = "LT-%s-Z"%lab_treat_type
elif step_type == '1' or step_type == '11':
meas_type = "LT-%s-I"%lab_treat_type
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
elif step_type == '2' or step_type == '12':
meas_type = "LT-PTRM-I"
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
elif step_type == '3' or step_type == '13':
meas_type = "LT-PTRM-Z"
# print("meas_type=", meas_type)
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['method_codes'] = meas_type
MeasRec["magn_moment"] = magn_moment
if volume!=0: MeasRec["magn_volume"] = magn_volume
MeasRec["dir_dec"] = measurement_dec
MeasRec["dir_inc"] = measurement_inc
MeasRec['dir_csd'] = error
MeasRec['meas_n_orient'] = meas_n_orient
# print(MeasRec)
MeasRecs.append(MeasRec)
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
data.close()
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave) #figures out method codes for measuremet data
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
cit_magic.py
DESCRIPTION
converts CIT and .sam format files to magic_measurements format files
SYNTAX
cit_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .sam format input file, required
-WD Working Directory: output directory where files are going to go
-fsi SITEFILE : specify file with site names and locations [tab delimited magic file]
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt # LORI
-n [gm,kg,cc,m3]: specify normalization
-A: don't average replicate measurements
-spc NUM : specify number of characters to designate a specimen, default = 0
-ncn NCON: specify naming convention
-loc LOCNAME : specify location/study name, must have either LOCNAME or SITEFILE or be a synthetic
-mcd [FS-FD:SO-MAG,.....] colon delimited list for method codes applied to all specimens in .sam file
-dc B PHI THETA: dc lab field (in microTesla), phi,and theta must be input as a tuple "(DC,PHI,THETA)". If not input user will be asked for values, this is advantagious if there are differing dc fields between steps or specimens. Note: this currently only works with the decimal IZZI naming convetion (XXX.0,1,2 where XXX is the treatment temperature and 0 is a zero field step, 1 is in field, and 2 is a pTRM check). All other steps are hardcoded dc_field = 0.
INPUT
Best to put separate experiments in separate files (all AF, thermal, thellier, trm aquisition, Shaw, etc.)
NOTES:
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3: default] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] or [email protected] for help.
"""
#
# NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
# -ac B : peak AF field (in mT) for ARM acquisition, default is none
#
#initialize variables
norm='cc'
samp_con,Z='3',1
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MeasRecs=[]
specnum,units,locname=0,"1","unknown"
citation="This study"
dir_path='.'
args=sys.argv
if command_line:
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print(main.__doc__)
return False
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
if '-Fsi' in args: # LORI addition
ind=args.index("-Fsi")
site_file=args[ind+1]
if '-loc' in args:
ind=args.index("-loc")
locname=args[ind+1]
if '-mcd' in args:
ind=args.index("-mcd")
methods=args[ind+1]
else:
methods='SO-MAG'
if '-spc' in args:
ind=args.index("-spc")
specnum=-int(args[ind+1])
if '-n' in args:
ind=args.index("-n")
norm=args[ind+1]
if "-A" in args:
avg=1
else:
avg=0
if '-dc' in args:
ind=args.index('-dc')
DC_FIELD,DC_PHI,DC_THETA=list(map(float,args[ind+1].strip('( ) [ ]').split(',')))
DC_FIELD *= 1e-6
yn=''
GET_DC_PARAMS=False
else: GET_DC_PARAMS,DC_FIELD,DC_PHI,DC_THETA,yn=True,0,0,-90,''
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind+1]
else:
input_dir_path = os.path.split(magfile)[0]
output_dir_path = dir_path
# LJ
# if you are running as a module:
elif not command_line:
dir_path = kwargs.get('dir_path', '.')
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'er_specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'er_samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'er_sites.txt') # site outfile
locname = kwargs.get('locname', '')
methods = kwargs.get('methods', ['SO-MAG'])
specnum = -int(kwargs.get('specnum', 0))
norm = kwargs.get('norm', 'cc')
avg = kwargs.get('avg', 0) # 0 means do average, 1 means don't
samp_con = kwargs.get('samp_con', '3')
magfile = kwargs.get('magfile', '')
input_dir_path = kwargs.get('input_dir_path', os.path.split(magfile)[0])
output_dir_path = dir_path
DC_FIELD,DC_PHI,DC_THETA = list(map(float, kwargs.get('dc_params', (0,0,-90))))
DC_FIELD *= 1e-6
yn = ''
if DC_FIELD==0 and DC_PHI==0 and DC_THETA==-90: GET_DC_PARAMS=True
else: GET_DC_PARAMS=False
# done with module-specific stuff
# formatting and checking variables
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
magfile = os.path.join(input_dir_path, magfile)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
meas_file= os.path.join(output_dir_path, meas_file)
FIRST_GET_DC=True
try:
with open(magfile,'r') as file_input:
File = file_input.readlines()
except Exception as ex:
print("bad sam file name: ", magfile)
return False, "bad sam file name"
if len(File) == 1: File = File[0].split('\r'); File = [x+"\r\n" for x in File]
sids,ln,format=[],0,'CIT'
formats=['CIT','2G','APP','JRA']
if File[ln].strip()=='CIT': ln+=1
ErLocRec={}
ErLocRec["er_location_name"]=locname
ErLocRec["er_citation_names"]=citation
comment=File[ln]
if comment=='CIT':
format=comment
ln+=1
comment=File[ln]
print(comment)
ln+=1
specimens,samples,sites=[],[],[]
if format=='CIT':
line=File[ln].split()
site_lat=line[0]
site_lon=line[1]
ErLocRec["location_begin_lat"]=site_lat
ErLocRec["location_begin_lon"]=site_lon
ErLocRec["location_end_lat"]=site_lat
ErLocRec["location_end_lon"]=site_lon
ErLocs.append(ErLocRec)
try: Cdec=float(line[2])
except ValueError: pdb.set_trace()
for k in range(ln+1,len(File)):
line=File[k]
rec=line.split()
if rec == []: continue
specimen=rec[0]
specimens.append(specimen)
for specimen in specimens:
ErSpecRec,ErSampRec,ErSiteRec={},{},{}
if specnum!=0:
sample=specimen[:specnum]
else: sample=specimen
site=pmag.parse_site(sample,samp_con,Z)
ErSpecRec['er_specimen_name']=specimen
ErSpecRec['er_sample_name']=sample
ErSpecRec['er_site_name']=site
ErSpecRec['er_location_name']=locname
ErSpecRec['er_citation_names']=citation
ErSampRec['er_sample_name']=sample
ErSampRec['er_site_name']=site
ErSampRec['er_location_name']=locname
ErSampRec['er_citation_names']=citation
ErSampRec['magic_method_codes']=methods
ErSampRec['sample_declination_correction']='%7.1f'%(Cdec)
ErSiteRec['er_site_name']=site
ErSiteRec['er_location_name']=locname
ErSiteRec['er_citation_names']=citation
ErSiteRec['site_lat']=site_lat
ErSiteRec['site_lon']=site_lon
with open(os.path.join(input_dir_path,specimen),'r') as finput:
Lines = list(finput.readlines())
comment = ""
line=Lines[0].split()
if len(line)>2:
comment=line[2]
info=Lines[1].split()
vol=float(info[-1])
if vol!=1.0:
if norm=='cc':units="1"
if norm=='m3':units="2"
ErSpecRec['specimen_weight']=""
if units=="1" or "":
ErSpecRec['specimen_volume']='%10.3e'%(vol*1e-6)
else:
ErSpecRec['specimen_volume']='%10.3e'%(vol)
else:
if norm=='cc':units="1"
if norm=='m3':units="2"
ErSpecRec['specimen_volume']=""
if units=="1" or "":
ErSpecRec['specimen_weight']='%10.3e'%(vol*1e-3)
else:
ErSpecRec['specimen_weight']='%10.3e'%(vol)
dip=float(info[-2])
dip_direction=float(info[-3])+Cdec+90.
sample_dip=-float(info[-4])
sample_azimuth=float(info[-5])+Cdec-90.
if len(info)>5:
ErSampRec['sample_height']=info[-6]
else:
ErSampRec['sample_height']='0'
ErSampRec['sample_azimuth']='%7.1f'%(sample_azimuth)
ErSampRec['sample_dip']='%7.1f'%(sample_dip)
ErSampRec['sample_bed_dip']='%7.1f'%(dip)
ErSampRec['sample_bed_dip_direction']='%7.1f'%(dip_direction)
ErSampRec['sample_class']=''
ErSampRec['sample_type']=''
ErSampRec['sample_lithology']=''
if Cdec!=0 or Cdec!="":
ErSampRec['magic_method_codes']='SO-CMD-NORTH'
else:
ErSampRec['magic_method_codes']='SO-MAG'
for line in Lines[2:len(Lines)]:
if line == '\n': continue
MeasRec=ErSpecRec.copy()
# Remove specimen_volume and specimen_weight as they do not exits in the magic_measurement table
del MeasRec["specimen_volume"]
del MeasRec["specimen_weight"]
treat_type=line[0:3]
if treat_type[1] == '.':
treat_type = 'NRM'
treat=line[2:6]
try: float(treat)
except ValueError: treat = line[3:6]
if treat_type.startswith('NRM'):
MeasRec['magic_method_codes']='LT-NO'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treatment_ac_field']='0'
elif treat_type.startswith('AF'):
MeasRec['magic_method_codes']='LT-AF-Z'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
if treat.strip() == '':
MeasRec['treatment_ac_field']='0'
else:
MeasRec['treatment_ac_field']='%10.3e'%(float(treat)*1e-3)
elif treat_type.startswith('ARM'):
MeasRec['magic_method_codes']="LP-ARM"
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
if treat.strip() == '':
MeasRec['treatment_ac_field']='0'
else:
MeasRec['magic_method_codes']="LP-ARM-AFD"
MeasRec['treatment_ac_field']='%10.3e'%(float(treat)*1e-3)
elif treat_type.startswith('TT'):
MeasRec['magic_method_codes']='LT-T-Z'
MeasRec['measurement_temp']='273'
if treat.strip() == '':
MeasRec['treatment_temp']='273'
else:
MeasRec['treatment_temp']='%7.1f'%(float(treat)+273)
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treatment_ac_field']='0'
elif treat_type.startswith('LT') or treat_type.startswith('LN2'):
MeasRec['magic_method_codes']='LT-LT-Z'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='77'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treatment_ac_field']='0'
elif line[4] == '0': #assume decimal IZZI format 0 field thus can hardcode the dc fields
MeasRec['magic_method_codes']='LT-T-Z'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']=str(int(treat_type) + 273)
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treatment_ac_field']='0'
elif line[4] == '1': #assume decimal IZZI format in constant field
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['magic_method_codes']='LT-T-I'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']=str(int(treat_type) + 273)
MeasRec['treatment_dc_field']='%1.2e'%DC_FIELD
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treatment_ac_field']='0'
elif line[4] == '2': #assume decimal IZZI format PTRM step
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['magic_method_codes']='LT-PTRM-I'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']=str(int(treat_type) + 273)
MeasRec['treatment_dc_field']='%1.2e'%DC_FIELD
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treatment_ac_field']='0'
else:
print("trouble with your treatment steps")
MeasRec['measurement_dec']=line[46:51]
MeasRec['measurement_inc']=line[52:58]
M='%8.2e'%(float(line[31:39])*vol*1e-3) # convert to Am2
MeasRec['measurement_magn_moment']=M
MeasRec['measurement_csd']='%7.1f'%(eval(line[41:46]))
MeasRec["measurement_positions"]='1'
MeasRec['measurement_standard']='u'
if len(line)>60:
MeasRec['magic_instrument_codes']=line[85:]
MeasRec['measurement_sd_x']='%8.2e'%(float(line[58:67])*1e-8) #(convert e-5emu to Am2)
MeasRec['measurement_sd_y']='%8.2e'%(float(line[67:76])*1e-8)
MeasRec['measurement_sd_z']='%8.2e'%(float(line[76:85])*1e-8)
MeasRecs.append(MeasRec)
ErSpecs.append(ErSpecRec)
if sample not in samples:
samples.append(sample)
ErSamps.append(ErSampRec)
site=pmag.parse_site(sample,samp_con,Z)
if site not in sites:
sites.append(site)
ErSites.append(ErSiteRec)
pmag.magic_write(spec_file,ErSpecs,'er_specimens')
print('specimens stored in ',spec_file)
pmag.magic_write(samp_file,ErSamps,'er_samples')
print('samples stored in ',samp_file)
pmag.magic_write(site_file,ErSites,'er_sites')
print('sites stored in ', site_file)
Fixed=pmag.measurements_methods(MeasRecs,avg)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print('data stored in ',meas_file)
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
ldeo_magic.py
DESCRIPTION
converts LDEO format files to magic_measurements format files
SYNTAX
ldeo_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .ldeo format input file, required
-F FILE: specify output file, default is magic_measurements.txt
-Fsy: specify er_synthetics file, default is er_sythetics.txt
-LP [colon delimited list of protocols, include all that apply]
AF: af demag
T: thermal including thellier but not trm acquisition
S: Shaw method
I: IRM (acquisition)
N: NRM only
TRM: trm acquisition
ANI: anisotropy experiment
D: double AF demag
G: triple AF demag (GRM protocol)
-V [1,2,3] units of IRM field in volts using ASC coil #1,2 or 3
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-syn INST TYPE: sets these specimens as synthetics created at institution INST and of type TYPE
-ins INST : specify which demag instrument was used (e.g, SIO-Suzy or SIO-Odette),default is ""
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-ARM_dc # default value is 50e-6
-ARM_temp # default is 600c
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] synthetic - has no site name
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in
seperate .mag files (eg. af.mag, thermal.mag, etc.)
Format of LDEO files:
isaf2.fix
LAT: .00 LON: .00
ID TREAT I CD J CDECL CINCL GDECL GINCL BDECL BINCL SUSC M/V
________________________________________________________________________________
is031c2 .0 SD 0 461.600 163.9 17.5 337.1 74.5 319.1 74.4 .0 .0
ID: specimen name
TREAT: treatment step
I: Instrument
CD: Circular standard devation
J: intensity. assumed to be total moment in 10^-4 (emu)
CDECL: Declination in specimen coordinate system
CINCL: Declination in specimen coordinate system
GDECL: Declination in geographic coordinate system
GINCL: Declination in geographic coordinate system
BDECL: Declination in bedding adjusted coordinate system
BINCL: Declination in bedding adjusted coordinate system
SUSC: magnetic susceptibility (in micro SI)a
M/V: mass or volume for nomalizing (0 won't normalize)
"""
# initialize some stuff
noave = 0
codelist = ''
methcode, inst = "LP-NO", ""
phi, theta, peakfield, labfield = 0, 0, 0, 0
pTRM, MD, samp_con, Z = 0, 0, '1', 1
dec = [315, 225, 180, 135, 45, 90, 270, 270, 270, 90, 180, 180, 0, 0, 0]
inc = [0, 0, 0, 0, 0, -45, -45, 0, 45, 45, 45, -45, -90, -45, 45]
tdec = [0, 90, 0, 180, 270, 0, 0, 90, 0]
tinc = [0, 0, 90, 0, 0, -90, 0, 0, 90]
missing = 1
demag = "N"
er_location_name = ""
citation = 'This study'
args = sys.argv
fmt = 'old'
syn = 0
synfile = 'er_synthetics.txt'
magfile = ''
trm = 0
irm = 0
specnum = 0
coil = ""
arm_labfield = 50e-6
trm_peakT = 600 + 273
#
# get command line arguments
#
meas_file = "magic_measurements.txt"
user = ""
if command_line:
if "-h" in args:
print(main.__doc__)
return False
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsy' in args:
ind = args.index("-Fsy")
synfile = args[ind + 1]
if '-f' in args:
ind = args.index("-f")
magfile = args[ind + 1]
if "-dc" in args:
ind = args.index("-dc")
labfield = float(args[ind + 1]) * 1e-6
phi = float(args[ind + 2])
theta = float(args[ind + 3])
if "-ac" in args:
ind = args.index("-ac")
peakfield = float(args[ind + 1]) * 1e-3
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if '-syn' in args:
syn = 1
ind = args.index("-syn")
institution = args[ind + 1]
syntype = args[ind + 2]
if '-fsy' in args:
ind = args.index("-fsy")
synfile = args[ind + 1]
if "-ins" in args:
ind = args.index("-ins")
inst = args[ind + 1]
if "-A" in args: noave = 1
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if '-LP' in args:
ind = args.index("-LP")
codelist = args[ind + 1]
if "-V" in args:
ind = args.index("-V")
coil = args[ind + 1]
if '-ARM_dc' in args:
ind = args.index("-ARM_dc")
arm_labfield = args[ind + 1]
if '-ARM_temp' in args:
ind = args.index('-ARM_temp')
trm_peakT = args[ind + 1]
if not command_line:
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
synfile = kwargs.get('synfile', 'er_synthetics.txt')
# rm samp_file = kwargs.get('samp_file', '')
magfile = kwargs.get('magfile', '')
labfield = int(kwargs.get('labfield', 0)) * 1e-6
phi = int(kwargs.get('phi', 0))
theta = int(kwargs.get('theta', 0))
peakfield = int(kwargs.get('peakfield', 0)) * 1e-3
specnum = int(kwargs.get('specnum', 0))
er_location_name = kwargs.get('er_location_name', '')
# rm samp_infile = kwargs.get('samp_infile', '')
syn = kwargs.get('syn', 0)
institution = kwargs.get('institution', '')
syntype = kwargs.get('syntype', '')
inst = kwargs.get('inst', '')
noave = kwargs.get('noave', 0) # 0 means "do average", is default
samp_con = kwargs.get('samp_con', '1')
codelist = kwargs.get('codelist', '')
coil = kwargs.get('coil', '')
arm_labfield = kwargs.get('arm_labfield', 50e-6)
trm_peakT = kwargs.get('trm_peakT', 600 + 273)
# format/organize variables
if magfile:
try:
input = open(magfile, 'r')
except:
print("bad mag file name")
return False, "bad mag file name"
else:
print("mag_file field is required option")
print(main.__doc__)
return False, "mag_file field is required option"
if specnum != 0: specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print(
"naming convention option [4] must be in form 4-Z where Z is an integer"
)
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print(
"naming convention option [7] must be in form 7-Z where Z is an integer"
)
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
codes = codelist.split(':')
if "AF" in codes:
demag = 'AF'
if not labfield: methcode = "LT-AF-Z"
if labfield: methcode = "LT-AF-I"
if "T" in codes:
demag = "T"
if not labfield: methcode = "LT-T-Z"
if labfield: methcode = "LT-T-I"
if "I" in codes:
methcode = "LP-IRM"
irmunits = "mT"
if "S" in codes:
demag = "S"
methcode = "LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield = labfield
# should use arm_labfield and trm_peakT as well, but these values are currently never asked for
if "G" in codes: methcode = "LT-AF-G"
if "D" in codes: methcode = "LT-AF-D"
if "TRM" in codes:
demag = "T"
trm = 1
if coil:
methcode = "LP-IRM"
irmunits = "V"
if coil not in ["1", "2", "3"]:
print(main.__doc__)
print('not a valid coil specification')
return False, 'not a valid coil specification'
if demag == "T" and "ANI" in codes:
methcode = "LP-AN-TRM"
if demag == "AF" and "ANI" in codes:
methcode = "LP-AN-ARM"
if labfield == 0: labfield = 50e-6
if peakfield == 0: peakfield = .180
SynRecs, MagRecs = [], []
version_num = pmag.get_version()
if 1: # ldeo file format
#
# find start of data:
#
DIspec = []
Data, k = input.readlines(), 0
for k in range(len(Data)):
rec = Data[k].split()
if rec[0][0] == "_" or rec[0][0:2] == "!_":
break
start = k + 1
for k in range(start, len(Data)):
rec = Data[k].split()
if len(rec) > 0:
MagRec = {}
MagRec["treatment_temp"] = '%8.3e' % (273
) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (
273) # room temp in kelvin
MagRec["treatment_ac_field"] = '0'
MagRec["treatment_dc_field"] = '0'
MagRec["treatment_dc_field_phi"] = '0'
MagRec["treatment_dc_field_theta"] = '0'
meas_type = "LT-NO"
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = '1'
MagRec["er_specimen_name"] = rec[0]
if specnum != 0:
MagRec["er_sample_name"] = rec[0][:specnum]
else:
MagRec["er_sample_name"] = rec[0]
site = pmag.parse_site(MagRec['er_sample_name'], samp_con, Z)
MagRec["er_site_name"] = site
MagRec["er_location_name"] = er_location_name
MagRec["measurement_csd"] = rec[3]
MagRec["measurement_magn_moment"] = '%10.3e' % (
float(rec[4]) * 1e-7) # moment in Am^2 (from 10^-4 emu)
#
#if samp_file!="" and MagRec["er_sample_name"] not in Samps: # create er_samples.txt file with these data
# cdec,cinc=float(rec[5]),float(rec[6])
# gdec,ginc=float(rec[7]),float(rec[8])
# az,pl=pmag.get_azpl(cdec,cinc,gdec,ginc)
# bdec,binc=float(rec[9]),float(rec[10])
# if rec[7]!=rec[9] and rec[6]!=rec[8]:
# dipdir,dip=pmag.get_tilt(gdec,ginc,bdec,binc)
# else:
# dipdir,dip=0,0
# ErSampRec={}
# ErSampRec['er_location_name']=MagRec['er_location_name']
# ErSampRec['er_sample_name']=MagRec['er_sample_name']
# ErSampRec['er_site_name']=MagRec['er_site_name']
# ErSampRec['sample_azimuth']='%7.1f'%(az)
# ErSampRec['sample_dip']='%7.1f'%(pl)
# ErSampRec['sample_bed_dip_direction']='%7.1f'%(dipdir)
# ErSampRec['sample_bed_dip']='%7.1f'%(dip)
# ErSampRec['sample_description']='az,pl,dip_dir and dip recalculated from [c,g,b][dec,inc] in ldeo file'
# ErSampRec['magic_method_codes']='SO-REC'
# ErSamps.append(ErSampRec)
# Samps.append(ErSampRec['er_sample_name'])
MagRec["measurement_dec"] = rec[5]
MagRec["measurement_inc"] = rec[6]
MagRec["measurement_chi"] = '%10.3e' % (
float(rec[11]) * 1e-5
) #convert to SI (assume Bartington, 10-5 SI)
#MagRec["magic_instrument_codes"]=rec[2]
#MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"] = "This study"
MagRec["magic_method_codes"] = meas_type
if demag == "AF":
if methcode != "LP-AN-ARM":
MagRec["treatment_ac_field"] = '%8.3e' % (
float(rec[1]) * 1e-3) # peak field in tesla
meas_type = "LT-AF-Z"
MagRec["treatment_dc_field"] = '0'
else: # AARM experiment
if treat[1][0] == '0':
meas_type = "LT-AF-Z"
MagRec["treatment_ac_field"] = '%8.3e' % (
peakfield) # peak field in tesla
else:
meas_type = "LT-AF-I"
ipos = int(treat[0]) - 1
MagRec["treatment_dc_field_phi"] = '%7.1f' % (
dec[ipos])
MagRec["treatment_dc_field_theta"] = '%7.1f' % (
inc[ipos])
MagRec["treatment_dc_field"] = '%8.3e' % (labfield)
MagRec["treatment_ac_field"] = '%8.3e' % (
peakfield) # peak field in tesla
elif demag == "T":
if rec[1][0] == ".": rec[1] = "0" + rec[1]
treat = rec[1].split('.')
if len(treat) == 1: treat.append('0')
MagRec["treatment_temp"] = '%8.3e' % (float(rec[1]) + 273.
) # temp in kelvin
meas_type = "LT-T-Z"
MagRec["treatment_temp"] = '%8.3e' % (
float(treat[0]) + 273.) # temp in kelvin
if trm == 0: # demag=T and not trmaq
if treat[1][0] == '0':
meas_type = "LT-T-Z"
else:
MagRec["treatment_dc_field"] = '%8.3e' % (
labfield
) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"] = '%7.1f' % (
phi) # labfield phi
MagRec["treatment_dc_field_theta"] = '%7.1f' % (
theta) # labfield theta
if treat[1][0] == '1':
meas_type = "LT-T-I" # in-field thermal step
if treat[1][0] == '2':
meas_type = "LT-PTRM-I" # pTRM check
pTRM = 1
if treat[1][0] == '3':
MagRec[
"treatment_dc_field"] = '0' # this is a zero field step
meas_type = "LT-PTRM-MD" # pTRM tail check
else:
meas_type = "LT-T-I" # trm acquisition experiment
MagRec['magic_method_codes'] = meas_type
MagRecs.append(MagRec)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print("results put in ", meas_file)
if len(SynRecs) > 0:
pmag.magic_write(synfile, SynRecs, 'er_synthetics')
print("synthetics put in ", synfile)
return True, meas_file
def convert(**kwargs):
#
# initialize variables
#
bed_dip,bed_dip_dir="",""
sclass,lithology,_type="","",""
DecCorr=0.
months=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov','Dec']
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file', '')
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
or_con = kwargs.get('or_con', '3')
samp_con = kwargs.get('samp_con', '2')
corr = kwargs.get('corr', '1')
gmeths = kwargs.get('gmeths', 'FS-FD:SO-POM')
location = kwargs.get('location', 'unknown')
specnum = int(kwargs.get('specnum', 0))
inst = kwargs.get('inst', '')
user = kwargs.get('user', '')
noave = kwargs.get('noave', 0) # default is DO average
ID = kwargs.get('ID', '')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
# format and fix variables acquired from command line sys.argv or input with **kwargs
if specnum!=0:specnum=-specnum
if ID:
input_dir_path = ID
else:
input_dir_path = dir_path
if samp_con:
Z = 1
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
if "6" in samp_con:
print('Naming convention option [6] not currently supported')
return False, 'Naming convention option [6] not currently supported'
#Z=1
#try:
# SampRecs,file_type=pmag.magic_read(os.path.join(input_dir_path, 'er_samples.txt'))
#except:
# print("there is no er_samples.txt file in your input directory - you can't use naming convention #6")
# return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
#if file_type == 'bad_file':
# print("there is no er_samples.txt file in your input directory - you can't use naming convention #6")
# return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
#else: Z=1
if not mag_file:
print("mag file is required input")
return False, "mag file is required input"
output_dir_path = dir_path
mag_file = os.path.join(input_dir_path, mag_file)
samplist=[]
try:
SampRecs,file_type=pmag.magic_read(samp_file)
except:
SampRecs=[]
MeasRecs,SpecRecs,SiteRecs,LocRecs=[],[],[],[]
try:
f=open(mag_file,'br')
input=str(f.read()).strip("b '")
f.close()
except Exception as ex:
print('ex', ex)
print("bad mag file")
return False, "bad mag file"
firstline,date=1,""
d=input.split('\\xcd')
for line in d:
rec=line.split('\\x00')
if firstline==1:
firstline=0
spec,vol="",1
el=51
while line[el:el+1]!="\\": spec=spec+line[el];el+=1
# check for bad sample name
test=spec.split('.')
date=""
if len(test)>1:
spec=test[0]
kk=24
while line[kk]!='\\x01' and line[kk]!='\\x00':
kk+=1
vcc=line[24:kk]
el=10
while rec[el].strip()!='':el+=1
date,comments=rec[el+7],[]
else:
el=9
while rec[el]!='\\x01':el+=1
vcc,date,comments=rec[el-3],rec[el+7],[]
specname=spec.lower()
print('importing ',specname)
el+=8
while rec[el].isdigit()==False:
comments.append(rec[el])
el+=1
while rec[el]=="":el+=1
az=float(rec[el])
el+=1
while rec[el]=="":el+=1
pl=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip_dir=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip=float(rec[el])
el+=1
while rec[el]=="":el+=1
if rec[el]=='\\x01':
bed_dip=180.-bed_dip
el+=1
while rec[el]=="":el+=1
fold_az=float(rec[el])
el+=1
while rec[el]=="":el+=1
fold_pl=rec[el]
el+=1
while rec[el]=="":el+=1
if rec[el]!="" and rec[el]!='\\x02' and rec[el]!='\\x01':
deccorr=float(rec[el])
az+=deccorr
bed_dip_dir+=deccorr
fold_az+=deccorr
if bed_dip_dir>=360:bed_dip_dir=bed_dip_dir-360.
if az>=360.:az=az-360.
if fold_az>=360.:fold_az=fold_az-360.
else:
deccorr=0
if specnum!=0:
sample=specname[:specnum]
else:
sample=specname
methods=gmeths.split(':')
if deccorr!="0":
if 'SO-MAG' in methods:del methods[methods.index('SO-MAG')]
methods.append('SO-CMD-NORTH')
meths = reduce(lambda x,y: x+':'+y, methods)
method_codes=meths
site=pmag.parse_site(sample,samp_con,Z) # parse out the site name
SpecRec,SampRec,SiteRec,LocRec={},{},{},{}
SpecRec["specimen"]=specname
SpecRec["sample"]=sample
if vcc.strip()!="":vol=float(vcc)*1e-6 # convert to m^3 from cc
SpecRec["volumne"]='%10.3e'%(vol) #
SpecRec["geologic_classes"]=sclass
SpecRec["lithologies"]=lithology
SpecRec["geologic_types"]=_type
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec["sample"]=sample
SampRec["site"]=site
labaz,labdip=pmag.orient(az,pl,or_con) # convert to labaz, labpl
SampRec["bed_dip"]='%7.1f'%(bed_dip)
SampRec["bed_dip_direction"]='%7.1f'%(bed_dip_dir)
SampRec["dip"]='%7.1f'%(labdip)
SampRec["azimuth"]='%7.1f'%(labaz)
SampRec["azimuth_dec_correction"]='%7.1f'%(deccorr)
SampRec["geologic_classes"]=sclass
SampRec["lithologies"]=lithology
SampRec["geologic_types"]=_type
SampRec["method_codes"]=method_codes
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRec["geologic_classes"]=sclass
SiteRec["lithologies"]=lithology
SiteRec["geologic_types"]=_type
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRec["geologic_classes"]=sclass
LocRec["lithologies"]=lithology
LocRec["geologic_types"]=_type
LocRecs.append(LocRec)
else:
MeasRec={}
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
meas_type="LT-NO"
MeasRec["quality"]='g'
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
MeasRec["specimen"]=specname
el,demag=1,''
treat=rec[el]
if treat[-1]=='C':
demag='T'
elif treat!='NRM':
demag='AF'
el+=1
while rec[el]=="":el+=1
MeasRec["dir_dec"]=rec[el]
cdec=float(rec[el])
el+=1
while rec[el]=="":el+=1
MeasRec["dir_inc"]=rec[el]
cinc=float(rec[el])
el+=1
while rec[el]=="":el+=1
gdec=rec[el]
el+=1
while rec[el]=="":el+=1
ginc=rec[el]
el=skip(2,el,rec) # skip bdec,binc
# el=skip(4,el,rec) # skip gdec,ginc,bdec,binc
# print 'moment emu: ',rec[el]
MeasRec["magn_moment"]='%10.3e'% (float(rec[el])*1e-3) # moment in Am^2 (from emu)
MeasRec["magn_volume"]='%10.3e'% (float(rec[el])*1e-3/vol) # magnetization in A/m
el=skip(2,el,rec) # skip to xsig
MeasRec["magn_x_sigma"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to ysig
MeasRec["magn_y_sigma"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to zsig
MeasRec["magn_z_sigma"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el+=1 # skip to positions
MeasRec["meas_n_orient"]=rec[el]
# el=skip(5,el,rec) # skip to date
# mm=str(months.index(date[0]))
# if len(mm)==1:
# mm='0'+str(mm)
# else:
# mm=str(mm)
# dstring=date[2]+':'+mm+':'+date[1]+":"+date[3]
# MeasRec['measurement_date']=dstring
MeasRec["instrument_codes"]=inst
MeasRec["analysts"]=user
MeasRec["citations"]="This study"
MeasRec["method_codes"]=meas_type
if demag=="AF":
MeasRec["treat_ac_field"]='%8.3e' %(float(treat[:-2])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MeasRec["treat_dc_field"]='0'
elif demag=="T":
MeasRec["treat_temp"]='%8.3e' % (float(treat[:-1])+273.) # temp in kelvin
meas_type="LT-T-Z"
MeasRec['method_codes']=meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.write_table_to_file('specimens', custom_name=spec_file)
con.write_table_to_file('samples', custom_name=samp_file)
con.write_table_to_file('sites', custom_name=site_file)
con.write_table_to_file('locations', custom_name=loc_file)
con.write_table_to_file('measurements', custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
"""
Converts CIT formated Magnetometer data into MagIC format for Analysis and contribution to the MagIC database
Parameters
-----------
dir_path : directory to output files to (default : current directory)
user : colon delimited list of analysts (default : "")
magfile : magnetometer file (.sam) to convert to MagIC (required)
meas_file : measurement file name to output (default : measurements.txt)
spec_file : specimen file name to output (default : specimens.txt)
samp_file : sample file name to output (default : samples.txt)
site_file : site file name to output (default : site.txt)
loc_file : location file name to output (default : locations.txt)
locname : location name
methods : colon delimited list of sample method codes. full list here (https://www2.earthref.org/MagIC/method-codes) (default : SO-MAG
specnum : number of terminal characters that identify a specimen
norm : is volume or mass normalization using cgs or si units (options : cc,m3,g,kg) (default : cc)
oersted : demag step vales are in Oersted
noave : average measurement data or not. False is average, True is don't average. (default : False)
samp_con : sample naming convention options as follows:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in sitename column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
input_dir_path : if you did not supply a full path with magfile you can put the directory the magfile is in here
meas_n_orient : Number of different orientations in measurement (default : 8)
labfield : DC_FIELD in microTesla (default : 0)
phi : DC_PHI in degrees (default : 0)
theta : DC_THETA in degrees (default : 0)
Returns
-----------
type - Tuple : (True or False indicating if conversion was sucessful, meas_file name written)
"""
dir_path = kwargs.get('dir_path', '.')
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
locname = kwargs.get('locname', 'unknown')
sitename = kwargs.get('sitename', '')
methods = kwargs.get('methods', ['SO-MAG'])
specnum = -int(kwargs.get('specnum', 0))
norm = kwargs.get('norm', 'cc')
oersted = kwargs.get('oersted', False) # mT (oe/10) is the default value
noave = kwargs.get('noave', False) # False means do average
samp_con = kwargs.get('samp_con', '3')
magfile = kwargs.get('magfile', '')
input_dir_path = kwargs.get('input_dir_path',os.path.split(magfile)[0])
meas_n_orient = kwargs.get('meas_n_orient','8')
output_dir_path = dir_path
try:
DC_FIELD = float(kwargs.get('labfield',0))*1e-6
DC_PHI = float(kwargs.get('phi',0))
DC_THETA = float(kwargs.get('theta',0))
except ValueError: raise ValueError('problem with your dc parameters. please provide a labfield in microTesla and a phi and theta in degrees.')
yn = ''
if DC_FIELD==0 and DC_PHI==0 and DC_THETA==0: GET_DC_PARAMS=True
else: GET_DC_PARAMS=False
if locname=='' or locname==None: locname = 'unknown'
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
else: Z=1
#get file names and open magfile to start reading data
if input_dir_path=='': input_dir_path='.'
magfile = os.path.join(input_dir_path, magfile)
FIRST_GET_DC=True
try:
file_input=open(magfile,'r')
except IOError as ex:
print(("bad sam file name: ", magfile))
return False, "bad sam file name"
File = file_input.readlines()
file_input.close()
if len(File) == 1: File = File[0].split('\r'); File = [x+"\r\n" for x in File]
#define initial variables
SpecRecs,SampRecs,SiteRecs,LocRecs,MeasRecs=[],[],[],[],[]
sids,ln,format,citations=[],0,'CIT',"This study"
formats=['CIT','2G','APP','JRA']
if File[ln].strip()=='CIT': ln+=1
LocRec={}
LocRec["location"]=locname
LocRec["citations"]=citations
LocRec['analysts']=user
comment=File[ln]
if comment=='CIT':
format=comment
ln+=1
comment=File[ln]
print(comment)
ln+=1
specimens,samples,sites=[],[],[]
if format=='CIT':
line=File[ln].split()
site_lat=line[0]
site_lon=line[1]
LocRec["lat_n"]=site_lat
LocRec["lon_e"]=site_lon
LocRec["lat_s"]=site_lat
LocRec["lon_w"]=site_lon
LocRecs.append(LocRec)
Cdec=float(line[2])
for k in range(ln+1,len(File)):
line=File[k]
rec=line.split()
if rec == []: continue
specimen=rec[0]
specimens.append(specimen)
for specimen in specimens:
SpecRec,SampRec,SiteRec={},{},{}
if specnum!=0:
sample=specimen[:specnum]
else: sample=specimen
if sitename: site=sitename
else: site=pmag.parse_site(sample,samp_con,Z)
SpecRec['specimen']=specimen
SpecRec['sample']=sample
SpecRec['citations']=citations
SpecRec['analysts']=user
SampRec['sample']=sample
SampRec['site']=site
SampRec['citations']=citations
SampRec['method_codes']=methods
SampRec['azimuth_dec_correction']='%7.1f'%(Cdec)
SampRec['analysts']=user
SiteRec['site']=site
SiteRec['location']=locname
SiteRec['citations']=citations
SiteRec['lat']=site_lat
SiteRec['lon']=site_lon
SiteRec['analysts']=user
f=open(os.path.join(input_dir_path,specimen),'r')
Lines=f.readlines()
f.close()
comment=""
line=Lines[0].split()
if len(line)>2:
comment=line[2]
info=Lines[1].split()
volmass=float(info[-1])
if volmass==1.0:
print('Warning: Specimen volume set to 1.0.')
print('Warning: If volume/mass really is 1.0, set volume/mass to 1.001')
print('Warning: specimen method code LP-NOMAG set.')
SpecRec['weight']=""
SpecRec['volume']=""
SpecRec['method_codes']='LP-NOMAG'
elif norm=="gm":
SpecRec['volume']=''
SpecRec['weight']='%10.3e'%volmass*1e-3
elif norm=="kg":
SpecRec['volume']=''
SpecRec['weight']='%10.3e'*volmass
elif norm=="cc":
SpecRec['weight']=""
SpecRec['volume']='%10.3e'%(volmass*1e-6)
elif norm=="m3":
SpecRec['weight']=""
SpecRec['volume']='%10.3e'%(volmass)
else:
print('Warning: Unknown normalization unit ', norm, '. Using default of cc')
SpecRec['weight']=""
SpecRec['volume']='%10.3e'%(volmass*1e-6)
dip=float(info[-2])
dip_direction=float(info[-3])+Cdec+90.
sample_dip=-float(info[-4])
sample_azimuth=float(info[-5])+Cdec-90.
if len(info)>5:
SampRec['height']=info[-6]
else:
SampRec['height']='0'
SampRec['azimuth']='%7.1f'%(sample_azimuth)
SampRec['dip']='%7.1f'%(sample_dip)
SampRec['bed_dip']='%7.1f'%(dip)
SampRec['bed_dip_direction']='%7.1f'%(dip_direction)
SampRec['geologic_classes']=''
SampRec['geologic_types']=''
SampRec['lithologies']=''
if Cdec!=0 or Cdec!="":
SampRec['method_codes']='SO-CMD-NORTH'
else:
SampRec['method_codes']='SO-MAG'
for line in Lines[2:len(Lines)]:
if line == '\n': continue
MeasRec=SpecRec.copy()
MeasRec.pop('sample')
MeasRec['analysts']=user
# Remove volume and weight as they do not exits in the magic_measurement table
del MeasRec["volume"]
del MeasRec["weight"]
if line[3:6]==' ' : # USGS files have blank for an AF demag value when measurement is the NRM. njarboe
line = 'NRM' + line[3:]
treat_type=line[0:3]
if treat_type[1] == '.':
treat_type = 'NRM'
treat=line[2:6]
try: float(treat)
except ValueError:
treat=line[3:6]
if treat.split()=='': treat='0'
try: float(treat)
except ValueError: treat = line.split()[1]
if treat_type.startswith('NRM'):
MeasRec['method_codes']='LT-NO'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif treat_type.startswith('LT') or treat_type.upper().startswith('LN2'):
MeasRec['method_codes']='LT-LT-Z'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='77'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif treat_type.startswith('AF') or treat_type.startswith('MAF'):
MeasRec['method_codes']='LT-AF-Z'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
if treat.strip() == '':
MeasRec['treat_ac_field']='0'
else:
try: MeasRec['treat_ac_field']='%10.3e'%(float(treat)*1e-3)
except ValueError as e: print(os.path.join(input_dir_path,specimen)); raise e
if MeasRec['treat_ac_field']!='0':
MeasRec['treat_ac_field']='%10.3e'%(float(MeasRec['treat_ac_field'])/10)
elif treat_type.startswith('ARM'):
MeasRec['method_codes']="LP-ARM"
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
if treat.strip() == '':
MeasRec['treat_ac_field']='0'
else:
MeasRec['method_codes']="LP-ARM-AFD"
MeasRec['treat_ac_field']='%10.3e'%(float(treat)*1e-3)
elif treat_type.startswith('IRM'):
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']="LT-IRM"
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif treat_type.startswith('TT'):
MeasRec['method_codes']='LT-T-Z'
MeasRec['meas_temp']='273'
if treat.strip() == '':
MeasRec['treat_temp']='273'
else:
MeasRec['treat_temp']='%7.1f'%(float(treat)+273)
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '0': #assume decimal IZZI format 0 field thus can hardcode the dc fields
MeasRec['method_codes']='LT-T-Z'
MeasRec['meas_temp']='273'
try: MeasRec['treat_temp']=str(int(treat_type) + 273)
except ValueError as e: print(specimen); raise e
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '1': #assume decimal IZZI format in constant field
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']='LT-T-I'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']=str(int(treat_type) + 273)
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '2': #assume decimal IZZI format PTRM step
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']='LT-PTRM-I'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']=str(int(treat_type) + 273)
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '3': #assume decimal IZZI format PTRM tail check
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']='LT-PTRM-Z'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']=str(int(treat_type) + 273)
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
else:
print("trouble with your treatment steps")
MeasRec['dir_dec']=line[46:51]
MeasRec['dir_inc']=line[52:58]
# Some MIT files have and extra digit in the exponent of the magnetude.
# That makes those files not compliant with the cit measurement file spec.
# Not sure if we should just print an error message and exit. For now we accept the file and fix it.
# The first digit of the exponent, which should always be zero, is cut out of the line if column 39 is not ' '
if line[39] != ' ': line = line[0:37] + line[38:]
M='%8.2e'%(float(line[31:39])*volmass*1e-3) # convert to Am2
MeasRec['magn_moment']=M
MeasRec['dir_csd']='%7.1f'%(eval(line[41:46]))
MeasRec["meas_n_orient"]=meas_n_orient
MeasRec['standard']='u'
if len(line)>60:
MeasRec['instrument_codes']=line[85:].strip('\n \r \t "')
MeasRec['magn_x_sigma']='%8.2e'%(float(line[58:67])*1e-8) #(convert e-5emu to Am2)
MeasRec['magn_y_sigma']='%8.2e'%(float(line[67:76])*1e-8)
MeasRec['magn_z_sigma']='%8.2e'%(float(line[76:85])*1e-8)
MeasRecs.append(MeasRec)
SpecRecs.append(SpecRec)
if sample not in samples:
samples.append(sample)
SampRecs.append(SampRec)
if site not in sites:
sites.append(site)
SiteRecs.append(SiteRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def main():
"""
NAME
umich_magic.py
DESCRIPTION
converts UMICH .mag format files to magic_measurements format files
SYNTAX
umich_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .mag format input file, required
-fsa SAMPFILE : specify er_samples.txt file relating samples, site and locations names,default is none
-F FILE: specify output file, default is magic_measurements.txt
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
Format of UMICH .mag files:
Spec Treat CSD Intensity Declination Inclination metadata string
Spec: specimen name
Treat: treatment step
XXX T in Centigrade
XXX AF in mT
Intensity assumed to be total moment in 10^3 Am^2 (emu)
Declination: Declination in specimen coordinate system
Inclination: Declination in specimen coordinate system
metatdata string: mm/dd/yy;hh:mm;[dC,mT];xx.xx;UNITS;USER;INST;NMEAS
hh in 24 hours.
dC or mT units of treatment XXX (see Treat above) for thermal or AF respectively
xx.xxx DC field
UNITS of DC field (microT, mT)
INST: instrument code, number of axes, number of positions (e.g., G34 is 2G, three axes,
measured in four positions)
NMEAS: number of measurements in a single position (1,3,200...)
"""
# initialize some stuff
dir_path='.'
infile_type="mag"
noave=0
methcode,inst="",""
phi,theta,peakfield,labfield=0,0,0,0
pTRM,MD,samp_con,Z=0,0,'1',1
missing=1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
methcode="LP-NO"
samp_file,ErSamps='',[]
specnum=0
#
# get command line arguments
#
meas_file="magic_measurements.txt"
user=""
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if '-f' in args:
ind=args.index("-f")
magfile=dir_path+'/'+args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=dir_path+'/'+args[ind+1]
Samps,file_type=pmag.magic_read(samp_file)
if "-A" in args: noave=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
samp_con=sys.argv[ind+1]
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
MagRecs,specs=[],[]
version_num=pmag.get_version()
if infile_type=="mag":
for line in input.readlines():
instcode=""
if len(line)>2:
MagRec={}
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
rec=line.split()
labfield=0
code1=rec[6].split(';')
date=code1[0].split('/') # break date into mon/day/year
yy=int(date[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(date[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(date[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else: min=str(min)
MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00"
MagRec["measurement_time_zone"]=''
instcode=''
if len(code1)>1:
MagRec["measurement_positions"]=code1[6][2]
else:
MagRec["measurement_positions"]=code1[7] # takes care of awkward format with bubba and flo being different
if user=="":user=code1[5]
if code1[2][-1]=='C': demag="T"
if code1[2]=='mT': demag="AF"
treat=rec[1].split('.')
if len(treat)==1:treat.append('0')
if demag=='T' and treat!=0:
meas_type="LT-T-Z"
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if demag=="AF":
meas_type="LT-AF-Z"
MagRec["treatment_ac_field"]='%8.3e' % (float(treat[0])*1e-3) # Af field in T
MagRec["treatment_dc_field"]='0'
MagRec["er_specimen_name"]=rec[0]
if rec[0] not in specs:specs.append(rec[0]) # get a list of specimen names
experiment=rec[0]+":"
MagRec["er_site_name"]=""
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
if "-fsa" in args:
for samp in Samps:
if samp["er_sample_name"] == MagRec["er_sample_name"]:
MagRec["er_location_name"]=samp["er_location_name"]
MagRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6:
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
if MagRec['er_site_name']=="":
print 'No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name']
if MagRec["er_location_name"]=="":
print 'no location name for: ',MagRec["er_specimen_name"]
if rec[1]==".00":rec[1]="0.00"
MagRec["measurement_csd"]=rec[2]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[3])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_dec"]=rec[4]
MagRec["measurement_inc"]=rec[5]
MagRec["magic_instrument_codes"]=instcode
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
MagRec["magic_method_codes"]=meas_type
MagRec["measurement_flag"]='g'
MagRec["er_specimen_name"]=rec[0]
MagRec["measurement_number"]='1'
MagRecs.append(MagRec)
MagOuts=[]
for spec in specs: # gather all demag types for this specimen
SpecRecs,meths,measnum=[],[],1
for rec in MagRecs:
if rec['er_specimen_name']==spec:
rec['measurement_number']=str(measnum)
measnum+=1
if rec['magic_method_codes'] not in meths:meths.append(rec['magic_method_codes'])
SpecRecs.append(rec)
expname=spec
if "LT-AF-Z" in meths:expname=expname+ ':LP-DIR-AF'
if "LT-T-Z" in meths:expname=expname+ ':LP-DIR-T'
for rec in SpecRecs:
rec['magic_experiment_name']=expname
MagOuts.append(rec)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
def convert(**kwargs):
#
# initialize variables
#
bed_dip, bed_dip_dir = "", ""
sclass, lithology, _type = "", "", ""
DecCorr = 0.
months = [
'Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct',
'Nov', 'Dec'
]
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file', '')
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
or_con = kwargs.get('or_con', '3')
samp_con = kwargs.get('samp_con', '2')
corr = kwargs.get('corr', '1')
gmeths = kwargs.get('gmeths', 'FS-FD:SO-POM')
location = kwargs.get('location', 'unknown')
specnum = int(kwargs.get('specnum', 0))
inst = kwargs.get('inst', '')
user = kwargs.get('user', '')
noave = kwargs.get('noave', 0) # default is DO average
ID = kwargs.get('ID', '')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
# format and fix variables acquired from command line sys.argv or input with **kwargs
if specnum != 0: specnum = -specnum
if ID:
input_dir_path = ID
else:
input_dir_path = dir_path
if samp_con:
Z = 1
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if "6" in samp_con:
print('Naming convention option [6] not currently supported')
return False, 'Naming convention option [6] not currently supported'
#Z=1
#try:
# SampRecs,file_type=pmag.magic_read(os.path.join(input_dir_path, 'er_samples.txt'))
#except:
# print("there is no er_samples.txt file in your input directory - you can't use naming convention #6")
# return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
#if file_type == 'bad_file':
# print("there is no er_samples.txt file in your input directory - you can't use naming convention #6")
# return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
#else: Z=1
if not mag_file:
print("mag file is required input")
return False, "mag file is required input"
output_dir_path = dir_path
mag_file = os.path.join(input_dir_path, mag_file)
samplist = []
try:
SampRecs, file_type = pmag.magic_read(samp_file)
except:
SampRecs = []
MeasRecs, SpecRecs, SiteRecs, LocRecs = [], [], [], []
try:
f = open(mag_file, 'br')
input = str(f.read()).strip("b '")
f.close()
except Exception as ex:
print('ex', ex)
print("bad mag file")
return False, "bad mag file"
firstline, date = 1, ""
d = input.split('\\xcd')
for line in d:
rec = line.split('\\x00')
if firstline == 1:
firstline = 0
spec, vol = "", 1
el = 51
while line[el:el + 1] != "\\":
spec = spec + line[el]
el += 1
# check for bad sample name
test = spec.split('.')
date = ""
if len(test) > 1:
spec = test[0]
kk = 24
while line[kk] != '\\x01' and line[kk] != '\\x00':
kk += 1
vcc = line[24:kk]
el = 10
while rec[el].strip() != '':
el += 1
date, comments = rec[el + 7], []
else:
el = 9
while rec[el] != '\\x01':
el += 1
vcc, date, comments = rec[el - 3], rec[el + 7], []
specname = spec.lower()
print('importing ', specname)
el += 8
while rec[el].isdigit() == False:
comments.append(rec[el])
el += 1
while rec[el] == "":
el += 1
az = float(rec[el])
el += 1
while rec[el] == "":
el += 1
pl = float(rec[el])
el += 1
while rec[el] == "":
el += 1
bed_dip_dir = float(rec[el])
el += 1
while rec[el] == "":
el += 1
bed_dip = float(rec[el])
el += 1
while rec[el] == "":
el += 1
if rec[el] == '\\x01':
bed_dip = 180. - bed_dip
el += 1
while rec[el] == "":
el += 1
fold_az = float(rec[el])
el += 1
while rec[el] == "":
el += 1
fold_pl = rec[el]
el += 1
while rec[el] == "":
el += 1
if rec[el] != "" and rec[el] != '\\x02' and rec[el] != '\\x01':
deccorr = float(rec[el])
az += deccorr
bed_dip_dir += deccorr
fold_az += deccorr
if bed_dip_dir >= 360: bed_dip_dir = bed_dip_dir - 360.
if az >= 360.: az = az - 360.
if fold_az >= 360.: fold_az = fold_az - 360.
else:
deccorr = 0
if specnum != 0:
sample = specname[:specnum]
else:
sample = specname
methods = gmeths.split(':')
if deccorr != "0":
if 'SO-MAG' in methods: del methods[methods.index('SO-MAG')]
methods.append('SO-CMD-NORTH')
meths = reduce(lambda x, y: x + ':' + y, methods)
method_codes = meths
site = pmag.parse_site(sample, samp_con,
Z) # parse out the site name
SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}
SpecRec["specimen"] = specname
SpecRec["sample"] = sample
if vcc.strip() != "":
vol = float(vcc) * 1e-6 # convert to m^3 from cc
SpecRec["volumne"] = '%10.3e' % (vol) #
SpecRec["geologic_classes"] = sclass
SpecRec["lithologies"] = lithology
SpecRec["geologic_types"] = _type
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec["sample"] = sample
SampRec["site"] = site
labaz, labdip = pmag.orient(az, pl,
or_con) # convert to labaz, labpl
SampRec["bed_dip"] = '%7.1f' % (bed_dip)
SampRec["bed_dip_direction"] = '%7.1f' % (bed_dip_dir)
SampRec["dip"] = '%7.1f' % (labdip)
SampRec["azimuth"] = '%7.1f' % (labaz)
SampRec["azimuth_dec_correction"] = '%7.1f' % (deccorr)
SampRec["geologic_classes"] = sclass
SampRec["lithologies"] = lithology
SampRec["geologic_types"] = _type
SampRec["method_codes"] = method_codes
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else ""
for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRec["geologic_classes"] = sclass
SiteRec["lithologies"] = lithology
SiteRec["geologic_types"] = _type
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRec["geologic_classes"] = sclass
LocRec["lithologies"] = lithology
LocRec["geologic_types"] = _type
LocRecs.append(LocRec)
else:
MeasRec = {}
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"] = '0'
MeasRec["treat_dc_field"] = '0'
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
meas_type = "LT-NO"
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["specimen"] = specname
el, demag = 1, ''
treat = rec[el]
if treat[-1] == 'C':
demag = 'T'
elif treat != 'NRM':
demag = 'AF'
el += 1
while rec[el] == "":
el += 1
MeasRec["dir_dec"] = rec[el]
cdec = float(rec[el])
el += 1
while rec[el] == "":
el += 1
MeasRec["dir_inc"] = rec[el]
cinc = float(rec[el])
el += 1
while rec[el] == "":
el += 1
gdec = rec[el]
el += 1
while rec[el] == "":
el += 1
ginc = rec[el]
el = skip(2, el, rec) # skip bdec,binc
# el=skip(4,el,rec) # skip gdec,ginc,bdec,binc
# print 'moment emu: ',rec[el]
MeasRec["magn_moment"] = '%10.3e' % (float(rec[el]) * 1e-3
) # moment in Am^2 (from emu)
MeasRec["magn_volume"] = '%10.3e' % (float(rec[el]) * 1e-3 / vol
) # magnetization in A/m
el = skip(2, el, rec) # skip to xsig
MeasRec["magn_x_sigma"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el = skip(3, el, rec) # skip to ysig
MeasRec["magn_y_sigma"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el = skip(3, el, rec) # skip to zsig
MeasRec["magn_z_sigma"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el += 1 # skip to positions
MeasRec["meas_n_orient"] = rec[el]
# el=skip(5,el,rec) # skip to date
# mm=str(months.index(date[0]))
# if len(mm)==1:
# mm='0'+str(mm)
# else:
# mm=str(mm)
# dstring=date[2]+':'+mm+':'+date[1]+":"+date[3]
# MeasRec['measurement_date']=dstring
MeasRec["instrument_codes"] = inst
MeasRec["analysts"] = user
MeasRec["citations"] = "This study"
MeasRec["method_codes"] = meas_type
if demag == "AF":
MeasRec["treat_ac_field"] = '%8.3e' % (float(treat[:-2]) * 1e-3
) # peak field in tesla
meas_type = "LT-AF-Z"
MeasRec["treat_dc_field"] = '0'
elif demag == "T":
MeasRec["treat_temp"] = '%8.3e' % (float(treat[:-1]) + 273.
) # temp in kelvin
meas_type = "LT-T-Z"
MeasRec['method_codes'] = meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.write_table_to_file('specimens', custom_name=spec_file)
con.write_table_to_file('samples', custom_name=samp_file)
con.write_table_to_file('sites', custom_name=site_file)
con.write_table_to_file('locations', custom_name=loc_file)
con.write_table_to_file('measurements', custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
version_num = pmag.get_version()
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
mag_file = kwargs.get('mag_file')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 2.5)) * 1e-6
timezone = kwargs.get('timestamp', 'UTC')
# format variables
mag_file = os.path.join(input_dir_path, mag_file)
if specnum != 0: specnum = -int(specnum)
if samp_con.startswith("4"):
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
elif samp_con.startswith("7"):
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
else:
Z = 1
#create data holders
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
# parse data
data = open(mag_file, 'r')
line = data.readline()
line = data.readline()
line = data.readline()
while line != '':
parsedLine = line.split()
if len(parsedLine) >= 4:
sampleName = parsedLine[0]
demagLevel = parsedLine[2]
date = parsedLine[3] + ":0:0:0"
line = data.readline()
line = data.readline()
line = data.readline()
line = data.readline()
parsedLine = line.split()
specimenAngleDec = parsedLine[1]
specimenAngleInc = parsedLine[2]
while parsedLine[0] != 'MEAN':
line = data.readline()
parsedLine = line.split()
if len(parsedLine) == 0:
parsedLine = ["Hello"]
Mx = parsedLine[1]
My = parsedLine[2]
Mz = parsedLine[3]
line = data.readline()
line = data.readline()
parsedLine = line.split()
splitExp = parsedLine[2].split('A')
intensityVolStr = parsedLine[1] + splitExp[0]
intensityVol = float(intensityVolStr)
# check and see if Prec is too big and messes with the parcing.
precisionStr = ''
if len(parsedLine) == 6: #normal line
precisionStr = parsedLine[5][0:-1]
else:
precisionStr = parsedLine[4][0:-1]
precisionPer = float(precisionStr)
precision = intensityVol * precisionPer / 100
while parsedLine[0] != 'SPEC.':
line = data.readline()
parsedLine = line.split()
if len(parsedLine) == 0:
parsedLine = ["Hello"]
specimenDec = parsedLine[2]
specimenInc = parsedLine[3]
line = data.readline()
line = data.readline()
parsedLine = line.split()
geographicDec = parsedLine[1]
geographicInc = parsedLine[2]
# Add data to various MagIC data tables.
specimen = sampleName
if specnum != 0: sample = specimen[:specnum]
else: sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec["citations"] = "This study"
SpecRec["analysts"] = user
SpecRec['volume'] = volume
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec["citations"] = "This study"
SampRec["analysts"] = user
SampRec['azimuth'] = specimenAngleDec
sample_dip = str(float(specimenAngleInc) -
90.0) #convert to magic orientation
SampRec['dip'] = sample_dip
SampRec['method_codes'] = meth_code
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else ""
for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec["citations"] = "This study"
SiteRec["analysts"] = user
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec["citations"] = "This study"
LocRec["analysts"] = user
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(date, "%m-%d-%Y:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp = utc_dt.strftime("%Y-%m-%dT%H:%M:%S") + "Z"
MeasRec["specimen"] = specimen
MeasRec["timestamp"] = timestamp
MeasRec['description'] = ''
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["treat_ac_field"] = '0'
if demagLevel == 'NRM':
meas_type = "LT-NO"
elif demagLevel[0] == 'A':
meas_type = "LT-AF-Z"
treat = float(demagLevel[1:])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif demagLevel[0] == 'T':
meas_type = "LT-T-Z"
treat = float(demagLevel[1:])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
else:
print("measurement type unknown", demag_level)
return False, "measurement type unknown"
MeasRec["magn_moment"] = str(intensityVol * volume) # Am^2
MeasRec["magn_volume"] = intensityVolStr # A/m
MeasRec["dir_dec"] = specimenDec
MeasRec["dir_inc"] = specimenInc
MeasRec['method_codes'] = meas_type
MeasRecs.append(MeasRec)
#read lines till end of record
line = data.readline()
line = data.readline()
line = data.readline()
line = data.readline()
line = data.readline()
# read all the rest of the special characters. Some data files not consistantly formatted.
while (len(line) <= 3 and line != ''):
line = data.readline()
#end of data while loop
data.close()
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def main():
"""
NAME
s_magic.py
DESCRIPTION
converts .s format data to magic_measurements format.
SYNTAX
s_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f SFILE specifies the .s file name
-sig last column has sigma
-typ Anisotropy type: AMS,AARM,ATRM (default is AMS)
-F RFILE specifies the rmag_anisotropy file name
-usr USER specify username
-loc location specify location/study name
-spc NUM : specify number of characters to
designate a specimen, default = 0
-spn SPECNAME, this specimen has the name SPECNAME
-n first column has specimen name
-crd [s,g,t], specify coordinate system of data
s=specimen,g=geographic,t=tilt adjusted, default is 's'
-ncn NCON: naming conventionconvention NCON
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXXYYY: YYY is sample designation with Z characters from site XXX
[5] sample = site
[6] sample, site, location info in er_samples.txt -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
DEFAULT
RFILE: rmag_anisotropy.txt
INPUT
X11,X22,X33,X12,X23,X13 (.s format file)
X11,X22,X33,X12,X23,X13,sigma (.s format file with -sig option)
SID, X11,X22,X33,X12,X23,X13 (.s format file with -n option)
OUTPUT
rmag_anisotropy.txt format file
NOTE
because .s files do not have specimen names or location information, the output MagIC files
will have to be changed prior to importing to data base.
"""
sfile,anisfile="","rmag_anisotropy.txt"
location='unknown'
user=""
sitename,specnum='unknown',0
samp_con,Z="",1
user=""
dir_path='.'
name,sigma,spec=0,0,'unknown'
type='AMS'
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if "-spc" in sys.argv:
ind=sys.argv.index("-spc")
specnum=int(sys.argv[ind+1])
if specnum!=0:specnum=-specnum
if "-spn" in sys.argv:
ind=sys.argv.index("-spn")
spec=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index('-f')
sfile = sys.argv[ind+1]
if '-sig' in sys.argv: sigma=1
if '-typ' in sys.argv:
ind=sys.argv.index('-typ')
type = sys.argv[ind+1]
if '-F' in sys.argv:
ind=sys.argv.index('-F')
anisfile = sys.argv[ind+1]
if '-usr' in sys.argv:
ind=sys.argv.index('-usr')
user = sys.argv[ind+1]
if '-loc' in sys.argv:
ind=sys.argv.index('-loc')
location = sys.argv[ind+1]
if "-n" in sys.argv:
name=1
coord='-1'
if "-crd" in sys.argv:
ind=sys.argv.index("-crd")
coord=sys.argv[ind+1]
if coord=='s':coord='-1'
if coord=='g':coord='0'
if coord=='t':coord='100'
if "-ncn" in sys.argv:
ind=sys.argv.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if samp_con=='6':
Samps,filetype=pmag.magic_read(dirpath+'/er_samples.txt')
#
# get down to bidness
sfile=dir_path+'/'+sfile
anisfile=dir_path+'/'+anisfile
input=open(sfile,'r')
AnisRecs=[]
linecnt=0
citation="This study"
# read in data
for line in input.readlines():
AnisRec={}
rec=line.split()
if name==1:
k=1
spec=rec[0]
else:
k=0
trace=float(rec[k])+float(rec[k+1])+float(rec[k+2])
s1='%10.9e'%(old_div(float(rec[k]),trace))
s2='%10.9e'%(old_div(float(rec[k+1]),trace))
s3='%10.9e'%(old_div(float(rec[k+2]),trace))
s4='%10.9e'%(old_div(float(rec[k+3]),trace))
s5='%10.9e'%(old_div(float(rec[k+4]),trace))
s6='%10.9e'%(old_div(float(rec[k+5]),trace))
AnisRec["er_citation_names"]=citation
AnisRec["er_specimen_name"]=spec
if specnum!=0:
AnisRec["er_sample_name"]=spec[:specnum]
else:
AnisRec["er_sample_name"]=spec
if samp_con=="6":
for samp in Samps:
if samp['er_sample_name']==AnisRec["er_sample_name"]:
sitename=samp['er_site_name']
location=samp['er_location_name']
elif samp_con!="":
sitename=pmag.parse_site(AnisRec['er_sample_name'],samp_con,Z)
AnisRec["er_location_name"]=location
AnisRec["er_site_name"]=sitename
AnisRec["er_anylist_mail_names"]=user
if type=='AMS':
AnisRec["anisotropy_type"]="AMS"
AnisRec["magic_experiment_names"]=spec+":LP-X"
else:
AnisRec["anisotropy_type"]=type
AnisRec["magic_experiment_names"]=spec+":LP-"+type
AnisRec["anisotropy_s1"]=s1
AnisRec["anisotropy_s2"]=s2
AnisRec["anisotropy_s3"]=s3
AnisRec["anisotropy_s4"]=s4
AnisRec["anisotropy_s5"]=s5
AnisRec["anisotropy_s6"]=s6
if sigma==1: AnisRec["anisotropy_sigma"]='%10.8e'%(old_div(float(rec[k+6]),trace))
AnisRec["anisotropy_unit"]='SI'
AnisRec["anisotropy_tilt_correction"]=coord
AnisRec["magic_method_codes"]='LP-'+type
AnisRecs.append(AnisRec)
pmag.magic_write(anisfile,AnisRecs,'rmag_anisotropy')
print('data saved in ',anisfile)
def convert(**kwargs):
"""
"""
#get kwargs
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
lat = kwargs.get('lat', 0)
lon = kwargs.get('lon', 0)
specnum = int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
version_num=pmag.get_version()
if specnum!=0:specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print("naming convention option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
else: Z = 1
# format variables
mag_file = os.path.join(input_dir_path,mag_file)
meas_file = os.path.join(output_dir_path,meas_file)
spec_file = os.path.join(output_dir_path,spec_file)
samp_file = os.path.join(output_dir_path,samp_file)
site_file = os.path.join(output_dir_path,site_file)
# parse data
data=open(mag_file,'r').readlines() # read in data from file
comment=data[0]
line=data[1].strip()
line=line.replace("=","= ") # make finding orientations easier
rec=line.split() # read in sample orientation, etc.
specimen=rec[0]
SpecRecs,SampRecs,SiteRecs,LocRecs,MeasRecs = [],[],[],[],[]
SpecRec,SampRec,SiteRec,LocRec={},{},{},{} # make a sample record
if specnum!=0:
sample=rec[0][:specnum]
else:
sample=rec[0]
if int(samp_con)<6:
site=pmag.parse_site(sample,samp_con,Z)
else:
if 'site' in list(SampRec.keys()):site=ErSampREc['site']
if 'location' in list(SampRec.keys()):location=ErSampREc['location']
az_ind=rec.index('a=')+1
SampRec['sample']=sample
SampRec['description']=comment
SampRec['azimuth']=rec[az_ind]
dip_ind=rec.index('b=')+1
dip=-float(rec[dip_ind])
SampRec['dip']='%7.1f'%(dip)
strike_ind=rec.index('s=')+1
SampRec['bed_dip_direction']='%7.1f'%(float(rec[strike_ind])+90.)
bd_ind=rec.index('d=')+1
SampRec['bed_dip']=rec[bd_ind]
v_ind=rec.index('v=')+1
vol=rec[v_ind][:-3]
date=rec[-2]
time=rec[-1]
SampRec['method_codes']=meth_code
SampRec['site']=site
SampRec['citations']='This study'
SampRec['method_codes']='SO-NO'
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['citations']='This study'
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations']='This study'
SiteRec['lat'] = lat
SiteRec['lon']= lon
LocRec['location'] = location
LocRec['citations']='This study'
LocRec['lat_n'] = lat
LocRec['lat_s'] = lat
LocRec['lon_e'] = lon
LocRec['lon_w'] = lon
SpecRecs.append(SpecRec)
SampRecs.append(SampRec)
SiteRecs.append(SiteRec)
LocRecs.append(LocRec)
for k in range(3,len(data)): # read in data
line=data[k]
rec=line.split()
if len(rec)>1: # skip blank lines at bottom
MeasRec={}
MeasRec['description']='Date: '+date+' '+time
MeasRec["citations"]="This study"
MeasRec['software_packages']=version_num
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["quality"]='g'
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
MeasRec["specimen"]=specimen
if rec[0]=='NRM':
meas_type="LT-NO"
elif rec[0][0]=='M' or rec[0][0]=='H':
meas_type="LT-AF-Z"
elif rec[0][0]=='T':
meas_type="LT-T-Z"
else:
print("measurement type unknown")
return False, "measurement type unknown"
X=[float(rec[1]),float(rec[2]),float(rec[3])]
Vec=pmag.cart2dir(X)
MeasRec["magn_moment"]='%10.3e'% (Vec[2]) # Am^2
MeasRec["magn_volume"]=rec[4] # A/m
MeasRec["dir_dec"]='%7.1f'%(Vec[0])
MeasRec["dir_inc"]='%7.1f'%(Vec[1])
MeasRec["treat_ac_field"]='0'
if meas_type!='LT-NO':
treat=float(rec[0][1:])
else:
treat=0
if meas_type=="LT-AF-Z":
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif meas_type=="LT-T-Z":
MeasRec["treat_temp"]='%8.3e' % (treat+273.) # temp in kelvin
MeasRec['method_codes']=meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
version_num = pmag.get_version()
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # Loc outfile
mag_file = kwargs.get('mag_file', '') #required
location = kwargs.get('location', 'unknown')
site = kwargs.get('site', '')
samp_con = kwargs.get('samp_con', '1')
specnum = int(kwargs.get('specnum', 0))
timezone = kwargs.get('timestamp', 'US/Pacific')
append = kwargs.get('append', False)
noave = kwargs.get('noave', False) # default False means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume: volume = 0.025**3 #default volume is a 2.5 cm cube, translated to meters cubed
else: volume *= 1e-6 #convert cm^3 to m^3
if specnum!=0:
specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z=int(samp_con.split("-")[1])
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=int(samp_con.split("-")[1])
samp_con="7"
else: Z=1
# format variables
mag_file = os.path.join(input_dir_path, mag_file)
if not os.path.isfile(mag_file):
print("%s is not a BGC file"%mag_file)
return False, 'You must provide a BCG format file'
# Open up the BGC file and read the header information
print('mag_file in bgc_magic', mag_file)
pre_data = open(mag_file, 'r')
line = pre_data.readline()
line_items = line.split(' ')
specimen = line_items[2]
specimen = specimen.replace('\n', '')
line = pre_data.readline()
line = pre_data.readline()
line_items = line.split('\t')
azimuth = float(line_items[1])
dip = float(line_items[2])
bed_dip = line_items[3]
sample_bed_azimuth = line_items[4]
lon = line_items[5]
lat = line_items[6]
tmp_volume = line_items[7]
if tmp_volume != 0.0:
volume = float(tmp_volume) * 1e-6
pre_data.close()
data = pd.read_csv(mag_file, sep='\t', header=3, index_col=False)
cart = np.array([data['X'], data['Y'], data['Z']]).transpose()
direction = pmag.cart2dir(cart).transpose()
data['dir_dec'] = direction[0]
data['dir_inc'] = direction[1]
data['magn_moment'] = old_div(direction[2], 1000) # the data are in EMU - this converts to Am^2
data['magn_volume'] = old_div((old_div(direction[2], 1000)), volume) # EMU - data converted to A/m
# Configure the magic_measurements table
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
for rowNum, row in data.iterrows():
MeasRec,SpecRec,SampRec,SiteRec,LocRec = {},{},{},{},{}
if specnum!=0:
sample=specimen[:specnum]
else:
sample=specimen
if site=='':
site=pmag.parse_site(sample,samp_con,Z)
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['volume'] = volume
SpecRec['analysts']=user
SpecRec['citations'] = 'This study'
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['azimuth'] = azimuth
SampRec['dip'] = dip
SampRec['bed_dip_direction'] = sample_bed_azimuth
SampRec['bed_dip'] = bed_dip
SampRec['method_codes'] = meth_code
SampRec['analysts']=user
SampRec['citations'] = 'This study'
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRec['analysts']=user
SiteRec['citations'] = 'This study'
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['analysts']=user
LocRec['citations'] = 'This study'
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec['description'] = 'Date: ' + str(row['Date']) + ' Time: ' + str(row['Time'])
if '.' in row['Date']: datelist = row['Date'].split('.')
elif '/' in row['Date']: datelist = row['Date'].split('/')
elif '-' in row['Date']: datelist = row['Date'].split('-')
else: print("unrecogized date formating on one of the measurement entries for specimen %s"%specimen); datelist=['','','']
if ':' in row['Time']: timelist = row['Time'].split(':')
else: print("unrecogized time formating on one of the measurement entries for specimen %s"%specimen); timelist=['','','']
datelist[2]='19'+datelist[2] if len(datelist[2])<=2 else datelist[2]
dt=":".join([datelist[1],datelist[0],datelist[2],timelist[0],timelist[1],timelist[2]])
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
MeasRec["timestamp"] = timestamp
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = rowNum
MeasRec["specimen"] = specimen
MeasRec["treat_ac_field"] = '0'
if row['DM Val'] == '0':
meas_type = "LT-NO"
elif int(row['DM Type']) > 0.0:
meas_type = "LT-AF-Z"
treat = float(row['DM Val'])
MeasRec["treat_ac_field"] = '%8.3e' %(treat*1e-3) # convert from mT to tesla
elif int(row['DM Type']) == -1:
meas_type = "LT-T-Z"
treat = float(row['DM Val'])
MeasRec["treat_temp"] = '%8.3e' % (treat+273.) # temp in kelvin
else:
print("measurement type unknown:", row['DM Type'], " in row ", rowNum)
MeasRec["magn_moment"] = str(row['magn_moment'])
MeasRec["magn_volume"] = str(row['magn_volume'])
MeasRec["dir_dec"] = str(row['dir_dec'])
MeasRec["dir_inc"] = str(row['dir_inc'])
MeasRec['method_codes'] = meas_type
MeasRec['dir_csd'] = '0.0' # added due to magic.write error
MeasRec['meas_n_orient'] = '1' # added due to magic.write error
MeasRecs.append(MeasRec.copy())
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.write_table_to_file('specimens', custom_name=spec_file, append=append)
con.write_table_to_file('samples', custom_name=samp_file, append=append)
con.write_table_to_file('sites', custom_name=site_file, append=append)
con.write_table_to_file('locations', custom_name=loc_file, append=append)
meas_file = con.write_table_to_file('measurements', custom_name=meas_file, append=append)
return True, meas_file
def main():
"""
NAME
s_magic.py
DESCRIPTION
converts .s format data to magic_measurements format.
SYNTAX
s_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f SFILE specifies the .s file name
-sig last column has sigma
-typ Anisotropy type: AMS,AARM,ATRM (default is AMS)
-F RFILE specifies the rmag_anisotropy file name
-usr USER specify username
-loc location specify location/study name
-spc NUM : specify number of characters to
designate a specimen, default = 0
-spn SPECNAME, this specimen has the name SPECNAME
-n first column has specimen name
-crd [s,g,t], specify coordinate system of data
s=specimen,g=geographic,t=tilt adjusted, default is 's'
-ncn NCON: naming conventionconvention NCON
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXXYYY: YYY is sample designation with Z characters from site XXX
[5] sample = site
[6] sample, site, location info in er_samples.txt -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
DEFAULT
RFILE: rmag_anisotropy.txt
INPUT
X11,X22,X33,X12,X23,X13 (.s format file)
X11,X22,X33,X12,X23,X13,sigma (.s format file with -sig option)
SID, X11,X22,X33,X12,X23,X13 (.s format file with -n option)
OUTPUT
rmag_anisotropy.txt format file
NOTE
because .s files do not have specimen names or location information, the output MagIC files
will have to be changed prior to importing to data base.
"""
sfile, anisfile = "", "rmag_anisotropy.txt"
location = 'unknown'
user = ""
sitename, specnum = 'unknown', 0
samp_con, Z = "", 1
user = ""
dir_path = '.'
name, sigma, spec = 0, 0, 'unknown'
type = 'AMS'
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if "-spc" in sys.argv:
ind = sys.argv.index("-spc")
specnum = int(sys.argv[ind + 1])
if specnum != 0: specnum = -specnum
if "-spn" in sys.argv:
ind = sys.argv.index("-spn")
spec = sys.argv[ind + 1]
if '-f' in sys.argv:
ind = sys.argv.index('-f')
sfile = sys.argv[ind + 1]
if '-sig' in sys.argv: sigma = 1
if '-typ' in sys.argv:
ind = sys.argv.index('-typ')
type = sys.argv[ind + 1]
if '-F' in sys.argv:
ind = sys.argv.index('-F')
anisfile = sys.argv[ind + 1]
if '-usr' in sys.argv:
ind = sys.argv.index('-usr')
user = sys.argv[ind + 1]
if '-loc' in sys.argv:
ind = sys.argv.index('-loc')
location = sys.argv[ind + 1]
if "-n" in sys.argv:
name = 1
coord = '-1'
if "-crd" in sys.argv:
ind = sys.argv.index("-crd")
coord = sys.argv[ind + 1]
if coord == 's': coord = '-1'
if coord == 'g': coord = '0'
if coord == 't': coord = '100'
if "-ncn" in sys.argv:
ind = sys.argv.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if samp_con == '6':
Samps, filetype = pmag.magic_read(dirpath + '/er_samples.txt')
#
# get down to bidness
sfile = dir_path + '/' + sfile
anisfile = dir_path + '/' + anisfile
input = open(sfile, 'r')
AnisRecs = []
linecnt = 0
citation = "This study"
# read in data
for line in input.readlines():
AnisRec = {}
rec = line.split()
if name == 1:
k = 1
spec = rec[0]
else:
k = 0
trace = float(rec[k]) + float(rec[k + 1]) + float(rec[k + 2])
s1 = '%10.9e' % (old_div(float(rec[k]), trace))
s2 = '%10.9e' % (old_div(float(rec[k + 1]), trace))
s3 = '%10.9e' % (old_div(float(rec[k + 2]), trace))
s4 = '%10.9e' % (old_div(float(rec[k + 3]), trace))
s5 = '%10.9e' % (old_div(float(rec[k + 4]), trace))
s6 = '%10.9e' % (old_div(float(rec[k + 5]), trace))
AnisRec["er_citation_names"] = citation
AnisRec["er_specimen_name"] = spec
if specnum != 0:
AnisRec["er_sample_name"] = spec[:specnum]
else:
AnisRec["er_sample_name"] = spec
if samp_con == "6":
for samp in Samps:
if samp['er_sample_name'] == AnisRec["er_sample_name"]:
sitename = samp['er_site_name']
location = samp['er_location_name']
elif samp_con != "":
sitename = pmag.parse_site(AnisRec['er_sample_name'], samp_con, Z)
AnisRec["er_location_name"] = location
AnisRec["er_site_name"] = sitename
AnisRec["er_anylist_mail_names"] = user
if type == 'AMS':
AnisRec["anisotropy_type"] = "AMS"
AnisRec["magic_experiment_names"] = spec + ":LP-X"
else:
AnisRec["anisotropy_type"] = type
AnisRec["magic_experiment_names"] = spec + ":LP-" + type
AnisRec["anisotropy_s1"] = s1
AnisRec["anisotropy_s2"] = s2
AnisRec["anisotropy_s3"] = s3
AnisRec["anisotropy_s4"] = s4
AnisRec["anisotropy_s5"] = s5
AnisRec["anisotropy_s6"] = s6
if sigma == 1:
AnisRec["anisotropy_sigma"] = '%10.8e' % (old_div(
float(rec[k + 6]), trace))
AnisRec["anisotropy_unit"] = 'SI'
AnisRec["anisotropy_tilt_correction"] = coord
AnisRec["magic_method_codes"] = 'LP-' + type
AnisRecs.append(AnisRec)
pmag.magic_write(anisfile, AnisRecs, 'rmag_anisotropy')
print('data saved in ', anisfile)
def main(command_line=True, **kwargs):
"""
NAME
ldeo_magic.py
DESCRIPTION
converts LDEO format files to magic_measurements format files
SYNTAX
ldeo_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .ldeo format input file, required
-F FILE: specify output file, default is magic_measurements.txt
-Fsy: specify er_synthetics file, default is er_sythetics.txt
-LP [colon delimited list of protocols, include all that apply]
AF: af demag
T: thermal including thellier but not trm acquisition
S: Shaw method
I: IRM (acquisition)
N: NRM only
TRM: trm acquisition
ANI: anisotropy experiment
D: double AF demag
G: triple AF demag (GRM protocol)
-V [1,2,3] units of IRM field in volts using ASC coil #1,2 or 3
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-syn INST TYPE: sets these specimens as synthetics created at institution INST and of type TYPE
-ins INST : specify which demag instrument was used (e.g, SIO-Suzy or SIO-Odette),default is ""
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-ARM_dc # default value is 50e-6
-ARM_temp # default is 600c
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] synthetic - has no site name
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in
seperate .mag files (eg. af.mag, thermal.mag, etc.)
Format of LDEO files:
isaf2.fix
LAT: .00 LON: .00
ID TREAT I CD J CDECL CINCL GDECL GINCL BDECL BINCL SUSC M/V
________________________________________________________________________________
is031c2 .0 SD 0 461.600 163.9 17.5 337.1 74.5 319.1 74.4 .0 .0
ID: specimen name
TREAT: treatment step
I: Instrument
CD: Circular standard devation
J: intensity. assumed to be total moment in 10^-4 (emu)
CDECL: Declination in specimen coordinate system
CINCL: Declination in specimen coordinate system
GDECL: Declination in geographic coordinate system
GINCL: Declination in geographic coordinate system
BDECL: Declination in bedding adjusted coordinate system
BINCL: Declination in bedding adjusted coordinate system
SUSC: magnetic susceptibility (in micro SI)a
M/V: mass or volume for nomalizing (0 won't normalize)
"""
# initialize some stuff
noave=0
codelist = ''
methcode,inst="LP-NO",""
phi,theta,peakfield,labfield=0,0,0,0
pTRM,MD,samp_con,Z=0,0,'1',1
dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0]
inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
tdec=[0,90,0,180,270,0,0,90,0]
tinc=[0,0,90,0,0,-90,0,0,90]
missing=1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
fmt='old'
syn=0
synfile='er_synthetics.txt'
magfile = ''
trm=0
irm=0
specnum=0
coil=""
arm_labfield = 50e-6
trm_peakT = 600+273
#
# get command line arguments
#
meas_file="magic_measurements.txt"
user=""
if command_line:
if "-h" in args:
print main.__doc__
return False
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsy' in args:
ind=args.index("-Fsy")
synfile=args[ind+1]
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
if "-dc" in args:
ind=args.index("-dc")
labfield=float(args[ind+1])*1e-6
phi=float(args[ind+2])
theta=float(args[ind+3])
if "-ac" in args:
ind=args.index("-ac")
peakfield=float(args[ind+1])*1e-3
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if '-syn' in args:
syn=1
ind=args.index("-syn")
institution=args[ind+1]
syntype=args[ind+2]
if '-fsy' in args:
ind=args.index("-fsy")
synfile=args[ind+1]
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-A" in args: noave=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
if "-V" in args:
ind=args.index("-V")
coil=args[ind+1]
if '-ARM_dc' in args:
ind = args.index("-ARM_dc")
arm_labfield = args[ind+1]
if '-ARM_temp' in args:
ind = args.index('-ARM_temp')
trm_peakT = args[ind+1]
if not command_line:
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
synfile = kwargs.get('synfile', 'er_synthetics.txt')
# rm samp_file = kwargs.get('samp_file', '')
magfile = kwargs.get('magfile', '')
labfield = int(kwargs.get('labfield', 0)) *1e-6
phi = int(kwargs.get('phi', 0))
theta = int(kwargs.get('theta', 0))
peakfield = int(kwargs.get('peakfield', 0))*1e-3
specnum = int(kwargs.get('specnum', 0))
er_location_name = kwargs.get('er_location_name', '')
# rm samp_infile = kwargs.get('samp_infile', '')
syn = kwargs.get('syn', 0)
institution = kwargs.get('institution', '')
syntype = kwargs.get('syntype', '')
inst = kwargs.get('inst', '')
noave = kwargs.get('noave', 0) # 0 means "do average", is default
samp_con = kwargs.get('samp_con', '1')
codelist = kwargs.get('codelist', '')
coil = kwargs.get('coil', '')
arm_labfield = kwargs.get('arm_labfield', 50e-6)
trm_peakT = kwargs.get('trm_peakT', 600+273)
# format/organize variables
if magfile:
try:
input=open(magfile,'rU')
except:
print "bad mag file name"
return False, "bad mag file name"
else:
print "mag_file field is required option"
print main.__doc__
return False, "mag_file field is required option"
if specnum!=0:specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print "naming convention option [4] must be in form 4-Z where Z is an integer"
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "naming convention option [7] must be in form 7-Z where Z is an integer"
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if not labfield: methcode="LT-AF-Z"
if labfield: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if not labfield: methcode="LT-T-Z"
if labfield: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
irmunits="mT"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
# should use arm_labfield and trm_peakT as well, but these values are currently never asked for
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if coil:
methcode="LP-IRM"
irmunits="V"
if coil not in ["1","2","3"]:
print main.__doc__
print 'not a valid coil specification'
return False, 'not a valid coil specification'
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
SynRecs,MagRecs=[],[]
version_num=pmag.get_version()
if 1: # ldeo file format
#
# find start of data:
#
DIspec=[]
Data,k=input.readlines(),0
for k in range(len(Data)):
rec=Data[k].split()
if rec[0][0]=="_" or rec[0][0:2]=="!_":
break
start=k+1
for k in range(start,len(Data)):
rec=Data[k].split()
if len(rec)>0:
MagRec={}
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=rec[0]
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
MagRec["er_location_name"]=er_location_name
MagRec["measurement_csd"]=rec[3]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[4])*1e-7) # moment in Am^2 (from 10^-4 emu)
#
#if samp_file!="" and MagRec["er_sample_name"] not in Samps: # create er_samples.txt file with these data
# cdec,cinc=float(rec[5]),float(rec[6])
# gdec,ginc=float(rec[7]),float(rec[8])
# az,pl=pmag.get_azpl(cdec,cinc,gdec,ginc)
# bdec,binc=float(rec[9]),float(rec[10])
# if rec[7]!=rec[9] and rec[6]!=rec[8]:
# dipdir,dip=pmag.get_tilt(gdec,ginc,bdec,binc)
# else:
# dipdir,dip=0,0
# ErSampRec={}
# ErSampRec['er_location_name']=MagRec['er_location_name']
# ErSampRec['er_sample_name']=MagRec['er_sample_name']
# ErSampRec['er_site_name']=MagRec['er_site_name']
# ErSampRec['sample_azimuth']='%7.1f'%(az)
# ErSampRec['sample_dip']='%7.1f'%(pl)
# ErSampRec['sample_bed_dip_direction']='%7.1f'%(dipdir)
# ErSampRec['sample_bed_dip']='%7.1f'%(dip)
# ErSampRec['sample_description']='az,pl,dip_dir and dip recalculated from [c,g,b][dec,inc] in ldeo file'
# ErSampRec['magic_method_codes']='SO-REC'
# ErSamps.append(ErSampRec)
# Samps.append(ErSampRec['er_sample_name'])
MagRec["measurement_dec"]=rec[5]
MagRec["measurement_inc"]=rec[6]
MagRec["measurement_chi"]='%10.3e'%(float(rec[11])*1e-5)#convert to SI (assume Bartington, 10-5 SI)
#MagRec["magic_instrument_codes"]=rec[2]
#MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"]="This study"
MagRec["magic_method_codes"]=meas_type
if demag=="AF":
if methcode != "LP-AN-ARM":
MagRec["treatment_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
else: # AARM experiment
if treat[1][0]=='0':
meas_type="LT-AF-Z"
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
else:
meas_type="LT-AF-I"
ipos=int(treat[0])-1
MagRec["treatment_dc_field_phi"]='%7.1f' %(dec[ipos])
MagRec["treatment_dc_field_theta"]='%7.1f'% (inc[ipos])
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
elif demag=="T":
if rec[1][0]==".":rec[1]="0"+rec[1]
treat=rec[1].split('.')
if len(treat)==1:treat.append('0')
MagRec["treatment_temp"]='%8.3e' % (float(rec[1])+273.) # temp in kelvin
meas_type="LT-T-Z"
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if trm==0: # demag=T and not trmaq
if treat[1][0]=='0':
meas_type="LT-T-Z"
else:
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step
if treat[1][0]=='2':
meas_type="LT-PTRM-I" # pTRM check
pTRM=1
if treat[1][0]=='3':
MagRec["treatment_dc_field"]='0' # this is a zero field step
meas_type="LT-PTRM-MD" # pTRM tail check
else:
meas_type="LT-T-I" # trm acquisition experiment
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
if len(SynRecs)>0:
pmag.magic_write(synfile,SynRecs,'er_synthetics')
print "synthetics put in ",synfile
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
pmd_magic.py
DESCRIPTION
converts PMD (Enkin) format files to magic_measurements format files
SYNTAX
pmd_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify naming convention
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
PMD format files
"""
# initialize some stuff
noave = 0
inst = ""
samp_con, Z = '1', ""
missing = 1
demag = "N"
er_location_name = "unknown"
citation = 'This study'
args = sys.argv
meth_code = "LP-NO"
specnum = -1
MagRecs = []
version_num = pmag.get_version()
Samps = [] # keeps track of sample orientations
DIspec = []
MagFiles = []
user = ""
mag_file = ""
dir_path = '.'
ErSamps = []
SampOuts = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
#try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-A" in args: noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind + 1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 0)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
print samp_con
# format variables
mag_file = input_dir_path + "/" + mag_file
meas_file = output_dir_path + "/" + meas_file
samp_file = output_dir_path + "/" + samp_file
if specnum != 0: specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print "naming convention option [4] must be in form 4-Z where Z is an integer"
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
# parse data
data = open(mag_file, 'rU').readlines() # read in data from file
comment = data[0]
line = data[1].strip()
line = line.replace("=", "= ") # make finding orientations easier
rec = line.split() # read in sample orientation, etc.
er_specimen_name = rec[0]
ErSampRec, ErSiteRec = {}, {} # make a sample record
if specnum != 0:
er_sample_name = rec[0][:specnum]
else:
er_sample_name = rec[0]
if len(ErSamps) > 0: # need to copy existing
for samp in ErSamps:
if samp['er_sample_name'] == er_sample_name:
ErSampRec = samp # we'll ammend this one
else:
SampOuts.append(samp) # keep all the others
if int(samp_con) < 6:
er_site_name = pmag.parse_site(er_sample_name, samp_con, Z)
else:
if 'er_site_name' in ErSampRec.keys():
er_site_name = ErSampREc['er_site_name']
if 'er_location_name' in ErSampRec.keys():
er_location_name = ErSampREc['er_location_name']
az_ind = rec.index('a=') + 1
ErSampRec['er_sample_name'] = er_sample_name
ErSampRec['er_sample_description'] = comment
ErSampRec['sample_azimuth'] = rec[az_ind]
dip_ind = rec.index('b=') + 1
dip = -float(rec[dip_ind])
ErSampRec['sample_dip'] = '%7.1f' % (dip)
strike_ind = rec.index('s=') + 1
ErSampRec['sample_bed_dip_direction'] = '%7.1f' % (float(rec[strike_ind]) +
90.)
bd_ind = rec.index('d=') + 1
ErSampRec['sample_bed_dip'] = rec[bd_ind]
v_ind = rec.index('v=') + 1
vol = rec[v_ind][:-3]
date = rec[-2]
time = rec[-1]
ErSampRec['magic_method_codes'] = meth_code
if 'er_location_name' not in ErSampRec.keys():
ErSampRec['er_location_name'] = er_location_name
if 'er_site_name' not in ErSampRec.keys():
ErSampRec['er_site_name'] = er_site_name
if 'er_citation_names' not in ErSampRec.keys():
ErSampRec['er_citation_names'] = 'This study'
if 'magic_method_codes' not in ErSampRec.keys():
ErSampRec['magic_method_codes'] = 'SO-NO'
SampOuts.append(ErSampRec)
for k in range(3, len(data)): # read in data
line = data[k]
rec = line.split()
if len(rec) > 1: # skip blank lines at bottom
MagRec = {}
MagRec['measurement_description'] = 'Date: ' + date + ' ' + time
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = er_site_name
MagRec['er_sample_name'] = er_sample_name
MagRec['magic_software_packages'] = version_num
MagRec["treatment_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = '1'
MagRec["er_specimen_name"] = er_specimen_name
if rec[0] == 'NRM':
meas_type = "LT-NO"
elif rec[0][0] == 'M' or rec[0][0] == 'H':
meas_type = "LT-AF-Z"
elif rec[0][0] == 'T':
meas_type = "LT-T-Z"
else:
print "measurement type unknown"
return False, "measurement type unknown"
X = [float(rec[1]), float(rec[2]), float(rec[3])]
Vec = pmag.cart2dir(X)
MagRec["measurement_magn_moment"] = '%10.3e' % (Vec[2]) # Am^2
MagRec["measurement_magn_volume"] = rec[4] # A/m
MagRec["measurement_dec"] = '%7.1f' % (Vec[0])
MagRec["measurement_inc"] = '%7.1f' % (Vec[1])
MagRec["treatment_ac_field"] = '0'
if meas_type != 'LT-NO':
treat = float(rec[0][1:])
else:
treat = 0
if meas_type == "LT-AF-Z":
MagRec["treatment_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif meas_type == "LT-T-Z":
MagRec["treatment_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
MagRec['magic_method_codes'] = meas_type
MagRecs.append(MagRec)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print "results put in ", meas_file
pmag.magic_write(samp_file, SampOuts, 'er_samples')
print "sample orientations put in ", samp_file
return True, meas_file
def main():
"""
NAME
susar4-asc_magic.py
DESCRIPTION
converts ascii files generated by SUSAR ver.4.0 to MagIC formated
files for use with PmagPy plotting software
SYNTAX
susar4-asc_magic.py -h [command line options]
OPTIONS
-h: prints the help message and quits
-f FILE: specify .asc input file name
-F MFILE: specify magic_measurements output file
-Fa AFILE: specify rmag_anisotropy output file
-Fr RFILE: specify rmag_results output file
-Fs SFILE: specify er_specimens output file with location, sample, site, etc. information
-usr USER: specify who made the measurements
-loc LOC: specify location name for study
-ins INST: specify instrument used
-spc SPEC: specify number of characters to specify specimen from sample
-ncn NCON: specify naming convention: default is #2 below
-k15 : specify static 15 position mode - default is spinning
-new : replace all existing magic files
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
SFILE: default is to create new er_specimen.txt file
USER: ""
LOC: "unknown"
INST: ""
SPEC: 0 sample name is same as site (if SPEC is 1, sample is all but last character)
appends to 'er_specimens.txt, er_samples.txt, er_sites.txt' files
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
"""
citation = 'This study'
cont = 0
samp_con, Z = "1", 1
AniRecSs,AniRecs,SpecRecs,SampRecs,SiteRecs,MeasRecs=[],[],[],[],[],[]
user, locname, specfile = "", "unknown", "er_specimens.txt"
isspec, inst, specnum = '0', "", 0
spin, new = 1, 0
dir_path = '.'
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
aoutput, routput, moutput = dir_path + '/rmag_anisotropy.txt', dir_path + '/rmag_results.txt', dir_path + '/magic_measurements.txt'
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-usr' in sys.argv:
ind = sys.argv.index('-usr')
user = sys.argv[ind + 1]
if "-ncn" in sys.argv:
ind = sys.argv.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if '-k15' in sys.argv: spin = 0
if '-f' in sys.argv:
ind = sys.argv.index('-f')
ascfile = dir_path + '/' + sys.argv[ind + 1]
if '-F' in sys.argv:
ind = sys.argv.index('-F')
moutput = dir_path + '/' + sys.argv[ind + 1]
if '-Fa' in sys.argv:
ind = sys.argv.index('-Fa')
aoutput = dir_path + '/' + sys.argv[ind + 1]
if '-Fr' in sys.argv:
ind = sys.argv.index('-Fr')
routput = dir_path + '/' + sys.argv[ind + 1]
if '-Fs' in sys.argv:
ind = sys.argv.index('-Fs')
specfile = dir_path + '/' + sys.argv[ind + 1]
isspec = '1'
elif '-loc' in sys.argv:
ind = sys.argv.index('-loc')
locname = sys.argv[ind + 1]
if '-spc' in sys.argv:
ind = sys.argv.index('-spc')
specnum = -(int(sys.argv[ind + 1]))
if specnum != 0: specnum = -specnum
if isspec == "1":
specs, file_type = pmag.magic_read(specfile)
specnames, sampnames, sitenames = [], [], []
if '-new' not in sys.argv: # see if there are already specimen,sample, site files lying around
try:
SpecRecs, file_type = pmag.magic_read(dir_path +
'/er_specimens.txt')
for spec in SpecRecs:
if spec['er_specimen_name'] not in specnames:
specnames.append(samp['er_specimen_name'])
except:
SpecRecs, specs = [], []
try:
SampRecs, file_type = pmag.magic_read(dir_path + '/er_samples.txt')
for samp in SampRecs:
if samp['er_sample_name'] not in sampnames:
sampnames.append(samp['er_sample_name'])
except:
sampnames, SampRecs = [], []
try:
SiteRecs, file_type = pmag.magic_read(dir_path + '/er_sites.txt')
for site in SiteRecs:
if site['er_site_names'] not in sitenames:
sitenames.append(site['er_site_name'])
except:
sitenames, SiteRecs = [], []
try:
input = open(ascfile, 'r')
except:
print('Error opening file: ', ascfile)
Data = input.readlines()
k = 0
while k < len(Data):
line = Data[k]
words = line.split()
if "ANISOTROPY" in words: # first line of data for the spec
MeasRec, AniRec, SpecRec, SampRec, SiteRec = {}, {}, {}, {}, {}
specname = words[0]
AniRec['er_specimen_name'] = specname
if isspec == "1":
for spec in specs:
if spec['er_specimen_name'] == specname:
AniRec['er_sample_name'] = spec['er_sample_name']
AniRec['er_site_name'] = spec['er_site_name']
AniRec['er_location_name'] = spec['er_location_name']
break
elif isspec == "0":
if specnum != 0:
sampname = specname[:specnum]
else:
sampname = specname
AniRec['er_sample_name'] = sampname
SpecRec['er_specimen_name'] = specname
SpecRec['er_sample_name'] = sampname
SampRec['er_sample_name'] = sampname
SiteRec['er_sample_name'] = sampname
SiteRec['site_description'] = 's'
AniRec['er_site_name'] = pmag.parse_site(
AniRec['er_sample_name'], samp_con, Z)
SpecRec['er_site_name'] = pmag.parse_site(
AniRec['er_sample_name'], samp_con, Z)
SampRec['er_site_name'] = pmag.parse_site(
AniRec['er_sample_name'], samp_con, Z)
SiteRec['er_site_name'] = pmag.parse_site(
AniRec['er_sample_name'], samp_con, Z)
AniRec['er_location_name'] = locname
SpecRec['er_location_name'] = locname
SampRec['er_location_name'] = locname
SiteRec['er_location_name'] = locname
AniRec['er_citation_names'] = "This study"
SpecRec['er_citation_names'] = "This study"
SampRec['er_citation_names'] = "This study"
SiteRec['er_citation_names'] = "This study"
AniRec['er_citation_names'] = "This study"
AniRec['magic_instrument_codes'] = inst
AniRec['magic_method_codes'] = "LP-X:AE-H:LP-AN-MS"
AniRec['magic_experiment_names'] = specname + ":" + "LP-AN-MS"
AniRec['er_analyst_mail_names'] = user
for key in list(AniRec.keys()):
MeasRec[key] = AniRec[key]
MeasRec['measurement_flag'] = 'g'
AniRec['anisotropy_flag'] = 'g'
MeasRec['measurement_standard'] = 'u'
MeasRec[
'measurement_description'] = 'Bulk sucsecptibility measurement'
AniRec['anisotropy_type'] = "AMS"
AniRec['anisotropy_unit'] = "Normalized by trace"
if spin == 1:
AniRec['anisotropy_n'] = "192"
else:
AniRec['anisotropy_n'] = "15"
if 'Azi' in words and isspec == '0':
SampRec['sample_azimuth'] = words[1]
labaz = float(words[1])
if 'Dip' in words:
SampRec['sample_dip'] = '%7.1f' % (-float(words[1]))
SpecRec['specimen_vol'] = '%8.3e' % (float(
words[10]) * 1e-6) # convert actual volume to m^3 from cm^3
labdip = float(words[1])
if 'T1' in words and 'F1' in words:
k += 2 # read in fourth line down
line = Data[k]
rec = line.split()
dd = rec[1].split('/')
dip_direction = int(dd[0]) + 90
SampRec['sample_bed_dip_direction'] = '%i' % (dip_direction)
SampRec['sample_bed_dip'] = dd[1]
bed_dip = float(dd[1])
if "Mean" in words:
k += 4 # read in fourth line down
line = Data[k]
rec = line.split()
MeasRec['measurement_chi_volume'] = rec[1]
sigma = .01 * float(rec[2]) / 3.
AniRec['anisotropy_sigma'] = '%7.4f' % (sigma)
AniRec['anisotropy_unit'] = 'SI'
if "factors" in words:
k += 4 # read in second line down
line = Data[k]
rec = line.split()
if "Specimen" in words: # first part of specimen data
AniRec['anisotropy_s1'] = '%7.4f' % (old_div(float(
words[5]), 3.)) # eigenvalues sum to unity - not 3
AniRec['anisotropy_s2'] = '%7.4f' % (old_div(float(words[6]), 3.))
AniRec['anisotropy_s3'] = '%7.4f' % (old_div(float(words[7]), 3.))
k += 1
line = Data[k]
rec = line.split()
AniRec['anisotropy_s4'] = '%7.4f' % (old_div(float(
rec[5]), 3.)) # eigenvalues sum to unity - not 3
AniRec['anisotropy_s5'] = '%7.4f' % (old_div(float(rec[6]), 3.))
AniRec['anisotropy_s6'] = '%7.4f' % (old_div(float(rec[7]), 3.))
AniRec['anisotropy_tilt_correction'] = '-1'
AniRecs.append(AniRec)
AniRecG, AniRecT = {}, {}
for key in list(AniRec.keys()):
AniRecG[key] = AniRec[key]
for key in list(AniRec.keys()):
AniRecT[key] = AniRec[key]
sbar = []
sbar.append(float(AniRec['anisotropy_s1']))
sbar.append(float(AniRec['anisotropy_s2']))
sbar.append(float(AniRec['anisotropy_s3']))
sbar.append(float(AniRec['anisotropy_s4']))
sbar.append(float(AniRec['anisotropy_s5']))
sbar.append(float(AniRec['anisotropy_s6']))
sbarg = pmag.dosgeo(sbar, labaz, labdip)
AniRecG["anisotropy_s1"] = '%12.10f' % (sbarg[0])
AniRecG["anisotropy_s2"] = '%12.10f' % (sbarg[1])
AniRecG["anisotropy_s3"] = '%12.10f' % (sbarg[2])
AniRecG["anisotropy_s4"] = '%12.10f' % (sbarg[3])
AniRecG["anisotropy_s5"] = '%12.10f' % (sbarg[4])
AniRecG["anisotropy_s6"] = '%12.10f' % (sbarg[5])
AniRecG["anisotropy_tilt_correction"] = '0'
AniRecs.append(AniRecG)
if bed_dip != "" and bed_dip != 0: # have tilt correction
sbart = pmag.dostilt(sbarg, dip_direction, bed_dip)
AniRecT["anisotropy_s1"] = '%12.10f' % (sbart[0])
AniRecT["anisotropy_s2"] = '%12.10f' % (sbart[1])
AniRecT["anisotropy_s3"] = '%12.10f' % (sbart[2])
AniRecT["anisotropy_s4"] = '%12.10f' % (sbart[3])
AniRecT["anisotropy_s5"] = '%12.10f' % (sbart[4])
AniRecT["anisotropy_s6"] = '%12.10f' % (sbart[5])
AniRecT["anisotropy_tilt_correction"] = '100'
AniRecs.append(AniRecT)
MeasRecs.append(MeasRec)
if SpecRec['er_specimen_name'] not in specnames:
SpecRecs.append(SpecRec)
specnames.append(SpecRec['er_specimen_name'])
if SampRec['er_sample_name'] not in sampnames:
SampRecs.append(SampRec)
sampnames.append(SampRec['er_sample_name'])
if SiteRec['er_site_name'] not in sitenames:
SiteRecs.append(SiteRec)
sitenames.append(SiteRec['er_site_name'])
k += 1 # skip to next specimen
pmag.magic_write(aoutput, AniRecs, 'rmag_anisotropy')
print("anisotropy tensors put in ", aoutput)
pmag.magic_write(moutput, MeasRecs, 'magic_measurements')
print("bulk measurements put in ", moutput)
if isspec == "0":
SpecOut, keys = pmag.fillkeys(SpecRecs)
output = dir_path + "/er_specimens.txt"
pmag.magic_write(output, SpecOut, 'er_specimens')
print("specimen info put in ", output)
output = dir_path + "/er_samples.txt"
SampOut, keys = pmag.fillkeys(SampRecs)
pmag.magic_write(output, SampOut, 'er_samples')
print("sample info put in ", output)
output = dir_path + "/er_sites.txt"
SiteOut, keys = pmag.fillkeys(SiteRecs)
pmag.magic_write(output, SiteOut, 'er_sites')
print("site info put in ", output)
print(""""
You can now import your data into the Magic Console and complete data entry,
for example the site locations, lithologies, etc. plotting can be done with aniso_magic.py
""")
def main():
"""
NAME
agm_magic.py
DESCRIPTION
converts Micromag agm files to magic format
SYNTAX
agm_magic.py [-h] [command line options]
OPTIONS
-usr USER: identify user, default is "" - put in quotation marks!
-bak: this is a IRM backfield curve
-f FILE, specify input file, required
-fsa SAMPFILE, specify er_samples.txt file relating samples, site and locations names,default is none
-F MFILE, specify magic measurements formatted output file, default is agm_measurements.txt
-spn SPEC, specimen name, default is base of input file name, e.g. SPECNAME.agm
-spc NUM, specify number of characters to designate a specimen, default = 0
-Fsp SPECFILE : name of er_specimens.txt file for appending data to
[default: er_specimens.txt]
-ncn NCON,: specify naming convention: default is #1 below
-syn SYN, synthetic specimen name
-loc LOCNAME : specify location/study name,
should have either LOCNAME or SAMPFILE (unless synthetic)
-ins INST : specify which instrument was used (e.g, SIO-Maud), default is ""
-u units: [cgs,SI], default is cgs
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
[8] specimen is a synthetic - it has no sample, site, location information
NB: all others you will have to customize your self
or e-mail [email protected] for help.
OUTPUT
MagIC format files: magic_measurements, er_specimens, er_sample, er_site
"""
citation='This study'
MeasRecs=[]
units='cgs'
meth="LP-HYS"
version_num=pmag.get_version()
args=sys.argv
fmt='old'
er_sample_name,er_site_name,er_location_name="","",""
inst=""
er_location_name="unknown"
er_synthetic_name=""
user=""
er_site_name=""
dir_path='.'
dm=3
if "-WD" in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-ID" in args:
ind = args.index("-ID")
input_dir_path = args[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
specfile = output_dir_path+'/er_specimens.txt'
output = output_dir_path+"/agm_measurements.txt"
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-bak" in args:
meth="LP-IRM-DCD"
output = output_dir_path+"/irm_measurements.txt"
if "-new" in args: fmt='new'
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
output = output_dir_path+'/'+args[ind+1]
if '-f' in args:
ind=args.index("-f")
agm_file= input_dir_path+'/'+args[ind+1]
er_specimen_name=args[ind+1].split('.')[0]
else:
print("agm_file field is required option")
print(main.__doc__)
sys.exit()
if '-Fsp' in args:
ind=args.index("-Fsp")
specfile= output_dir_path+'/'+args[ind+1]
specnum,samp_con,Z=0,'1',1
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-spn" in args:
ind=args.index("-spn")
er_specimen_name=args[ind+1]
#elif "-syn" not in args:
# print "you must specify a specimen name"
# sys.exit()
if "-syn" in args:
ind=args.index("-syn")
er_synthetic_name=args[ind+1]
er_specimen_name=""
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
sampfile = input_dir_path+'/'+args[ind+1]
Samps,file_type=pmag.magic_read(sampfile)
print('sample_file successfully read in')
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-u" in args:
ind=args.index("-u")
units=args[ind+1]
dm = pmag.get_named_arg_from_sys("-DM", 2)
ErSpecRecs,filetype=pmag.magic_read(specfile)
ErSpecRec,MeasRec={},{}
ErSpecRec['er_citation_names']="This study"
ErSpecRec['er_specimen_name']=er_specimen_name
ErSpecRec['er_synthetic_name']=er_synthetic_name
if specnum!=0:
ErSpecRec["er_sample_name"]=er_specimen_name[:specnum]
else:
ErSpecRec["er_sample_name"]=er_specimen_name
if "-fsa" in args and er_synthetic_name=="":
for samp in Samps:
if samp["er_sample_name"] == ErSpecRec["er_sample_name"]:
ErSpecRec["er_location_name"]=samp["er_location_name"]
ErSpecRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6 and int(samp_con)!=8:
site=pmag.parse_site(ErSpecRec['er_sample_name'],samp_con,Z)
ErSpecRec["er_site_name"]=site
ErSpecRec["er_location_name"]=er_location_name
ErSpecRec['er_scientist_mail_names']=user.strip()
insert=1
for rec in ErSpecRecs:
if rec['er_specimen_name']==er_specimen_name:
insert=0
break
if insert==1:
ErSpecRecs.append(ErSpecRec)
ErSpecRecs,keylist=pmag.fillkeys(ErSpecRecs)
pmag.magic_write(specfile,ErSpecRecs,'er_specimens')
print("specimen name put in ",specfile)
f=open(agm_file,'r')
Data=f.readlines()
if "ASCII" not in Data[0]:fmt='new'
measnum,start=1,""
if fmt=='new': # new Micromag formatted file
end=2
for skip in range(len(Data)):
line=Data[skip]
rec=line.split()
if 'Units' in line:units=rec[-1]
if "Raw" in rec:
start=skip+2
if "Field" in rec and "Moment" in rec and start=="":
start=skip+2
break
else:
start = 2
end=1
for i in range(start,len(Data)-end): # skip header stuff
MeasRec={}
for key in list(ErSpecRec.keys()):
MeasRec[key]=ErSpecRec[key]
MeasRec['magic_instrument_codes']=inst
MeasRec['magic_method_codes']=meth
if 'er_synthetic_name' in list(MeasRec.keys()) and MeasRec['er_synthetic_name']!="":
MeasRec['magic_experiment_name']=er_synthetic_name+':'+meth
else:
MeasRec['magic_experiment_name']=er_specimen_name+':'+meth
line=Data[i]
rec=line.split(',') # data comma delimited
if rec[0]!='\n':
if units=='cgs':
field =float(rec[0])*1e-4 # convert from oe to tesla
else:
field =float(rec[0]) # field in tesla
if meth=="LP-HYS":
MeasRec['measurement_lab_field_dc']='%10.3e'%(field)
MeasRec['treatment_dc_field']=''
else:
MeasRec['measurement_lab_field_dc']=''
MeasRec['treatment_dc_field']='%10.3e'%(field)
if units=='cgs':
MeasRec['measurement_magn_moment']='%10.3e'%(float(rec[1])*1e-3) # convert from emu to Am^2
else:
MeasRec['measurement_magn_moment']='%10.3e'%(float(rec[1])) # Am^2
MeasRec['treatment_temp']='273' # temp in kelvin
MeasRec['measurement_temp']='273' # temp in kelvin
MeasRec['measurement_flag']='g'
MeasRec['measurement_standard']='u'
MeasRec['measurement_number']='%i'%(measnum)
measnum+=1
MeasRec['magic_software_packages']=version_num
MeasRecs.append(MeasRec)
# now we have to relabel LP-HYS method codes. initial loop is LP-IMT, minor loops are LP-M - do this in measurements_methods function
if meth=='LP-HYS':
recnum=0
while float(MeasRecs[recnum]['measurement_lab_field_dc'])<float(MeasRecs[recnum+1]['measurement_lab_field_dc']) and recnum+1<len(MeasRecs): # this is LP-IMAG
MeasRecs[recnum]['magic_method_codes']='LP-IMAG'
MeasRecs[recnum]['magic_experiment_name']=MeasRecs[recnum]['er_specimen_name']+":"+'LP-IMAG'
recnum+=1
#
if int(dm)==2:
pmag.magic_write(output,MeasRecs,'magic_measurements')
else:
print ('MagIC 3 is not supported yet')
sys.exit()
pmag.magic_write(output,MeasRecs,'measurements')
print("results put in ", output)
def convert(**kwargs):
# initialize some stuff
version_num = pmag.get_version()
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # site outfile
location = kwargs.get('location', 'unknown')
dmy_flag = kwargs.get('dmy_flag', False)
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
#oave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
specnum = -int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '2')
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
site_num = samp_con.split("-")[1]
samp_con = "4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
site_num = samp_con.split("-")[1]
samp_con = "7"
else:
site_num = 1
try:
DC_FIELD = float(kwargs.get('labfield', 0)) * 1e-6
DC_PHI = float(kwargs.get('phi', 0))
DC_THETA = float(kwargs.get('theta', 0))
except ValueError:
raise ValueError(
'problem with your dc parameters. please provide a labfield in microTesla and a phi and theta in degrees.'
)
noave = kwargs.get('noave', False)
dmy_flag = kwargs.get('dmy_flag', False)
meas_n_orient = kwargs.get('meas_n_orient', '8')
# format variables
if not mag_file:
return False, 'You must provide a Utrecht formated file'
mag_file = os.path.join(input_dir_path, mag_file)
# parse data
# Open up the Utrecht file and read the header information
AF_or_T = mag_file.split('.')[-1]
data = open(mag_file, 'r')
line = data.readline()
line_items = line.split(',')
operator = line_items[0]
operator = operator.replace("\"", "")
machine = line_items[1]
machine = machine.replace("\"", "")
machine = machine.rstrip('\n')
# print("operator=", operator)
# print("machine=", machine)
#read in measurement data
line = data.readline()
while line != "END" and line != '"END"':
SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}
line_items = line.split(',')
spec_name = line_items[0]
spec_name = spec_name.replace("\"", "")
# print("spec_name=", spec_name)
free_string = line_items[1]
free_string = free_string.replace("\"", "")
# print("free_string=", free_string)
dec = line_items[2]
# print("dec=", dec)
inc = line_items[3]
# print("inc=", inc)
volume = float(line_items[4])
volume = volume * 1e-6 # enter volume in cm^3, convert to m^3
# print("volume=", volume)
bed_plane = line_items[5]
# print("bed_plane=", bed_plane)
bed_dip = line_items[6]
# print("bed_dip=", bed_dip)
# Configure et er_ tables
if specnum == 0: sample_name = spec_name
else: sample_name = spec_name[:specnum]
site = pmag.parse_site(sample_name, samp_con, site_num)
SpecRec['specimen'] = spec_name
SpecRec['sample'] = sample_name
if volume != 0: SpecRec['volume'] = volume
SpecRecs.append(SpecRec)
if sample_name != "" and sample_name not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample_name
SampRec['azimuth'] = dec
SampRec['dip'] = str(float(inc) - 90)
SampRec['bed_dip_direction'] = bed_plane
SampRec['bed_dip'] = bed_dip
SampRec['method_codes'] = meth_code
SampRec['site'] = site
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
#measurement data
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
while line != '9999':
step = items[0]
step = step.split('.')
step_value = step[0]
step_type = ""
if len(step) == 2:
step_type = step[1]
if step_type == '5':
step_value = items[0]
A = float(items[1])
B = float(items[2])
C = float(items[3])
# convert to MagIC coordinates
Z = -A
X = -B
Y = C
cart = array([X, Y, Z]).transpose()
direction = pmag.cart2dir(cart).transpose()
measurement_dec = direction[0]
measurement_inc = direction[1]
magn_moment = direction[
2] * 1.0e-12 # the data are in pico-Am^2 - this converts to Am^2
if volume != 0:
magn_volume = direction[
2] * 1.0e-12 / volume # data volume normalized - converted to A/m
# print("magn_moment=", magn_moment)
# print("magn_volume=", magn_volume)
error = items[4]
date = items[5]
date = date.strip('"').replace(' ', '')
if date.count("-") > 0:
date = date.split("-")
elif date.count("/") > 0:
date = date.split("/")
else:
print("date format seperator cannot be identified")
# print(date)
time = items[6]
time = time.strip('"').replace(' ', '')
time = time.split(":")
# print(time)
dt = date[0] + ":" + date[1] + ":" + date[2] + ":" + time[
0] + ":" + time[1] + ":" + "0"
local = pytz.timezone("Europe/Amsterdam")
try:
if dmy_flag:
naive = datetime.datetime.strptime(dt, "%d:%m:%Y:%H:%M:%S")
else:
naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
except ValueError:
naive = datetime.datetime.strptime(dt, "%Y:%m:%d:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp = utc_dt.strftime("%Y-%m-%dT%H:%M:%S") + "Z"
# print(timestamp)
MeasRec = {}
MeasRec["timestamp"] = timestamp
MeasRec["analysts"] = operator
MeasRec["instrument_codes"] = "Utrecht_" + machine
MeasRec["description"] = "free string = " + free_string
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["experiments"] = location + site + spec_name
MeasRec["treat_step_num"] = location + site + spec_name + items[0]
MeasRec["specimen"] = spec_name
# MeasRec["treat_ac_field"] = '0'
if AF_or_T.lower() == "th":
MeasRec["treat_temp"] = '%8.3e' % (float(step_value) + 273.
) # temp in kelvin
MeasRec['treat_ac_field'] = '0'
lab_treat_type = "T"
else:
MeasRec['treat_temp'] = '273'
MeasRec['treat_ac_field'] = '%10.3e' % (float(step_value) *
1e-3)
lab_treat_type = "AF"
MeasRec['treat_dc_field'] = '0'
if step_value == '0':
meas_type = "LT-NO"
# print("step_type=", step_type)
if step_type == '0' or step_type == '00':
meas_type = "LT-%s-Z" % lab_treat_type
elif step_type == '1' or step_type == '11':
meas_type = "LT-%s-I" % lab_treat_type
MeasRec['treat_dc_field'] = '%1.2e' % DC_FIELD
elif step_type == '2' or step_type == '12':
meas_type = "LT-PTRM-I"
MeasRec['treat_dc_field'] = '%1.2e' % DC_FIELD
elif step_type == '3' or step_type == '13':
meas_type = "LT-PTRM-Z"
# print("meas_type=", meas_type)
MeasRec['treat_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['method_codes'] = meas_type
MeasRec["magn_moment"] = magn_moment
if volume != 0: MeasRec["magn_volume"] = magn_volume
MeasRec["dir_dec"] = measurement_dec
MeasRec["dir_inc"] = measurement_inc
MeasRec['dir_csd'] = error
MeasRec['meas_n_orient'] = meas_n_orient
# print(MeasRec)
MeasRecs.append(MeasRec)
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
data.close()
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(
MeasRecs, noave) #figures out method codes for measuremet data
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
jr6_magic.py
DESCRIPTION
converts JR6 format files to magic_measurements format files
SYNTAX
jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
# -Fsa: specify er_samples format file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify sample naming convention (6 and 7 not yet implemented)
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
JR6 .txt format file
"""
# initialize some stuff
noave=0
samp_con,Z='1',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
specnum=1
MagRecs=[]
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
user=""
mag_file=""
dir_path='.'
ErSamps=[]
SampOuts=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind+1]
#try:
# open(samp_file,'r')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind+1])
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args:
noave=1
if "-mcd" in args:
ind=args.index("-mcd")
meth_code=args[ind+1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
# format variables
mag_file = input_dir_path+"/" + mag_file
meas_file = output_dir_path+"/" + meas_file
samp_file = output_dir_path+"/" + samp_file
if specnum!=0:
specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False
else:
Z=samp_con.split("-")[1]
samp_con="7"
ErSampRec,ErSiteRec={},{}
# parse data
data=open(mag_file,'r')
line=data.readline()
line=data.readline()
line=data.readline()
while line !='':
parsedLine=line.split()
sampleName=parsedLine[0]
demagLevel=parsedLine[2]
date=parsedLine[3]
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
parsedLine=line.split()
specimenAngleDec=parsedLine[1]
specimenAngleInc=parsedLine[2]
while parsedLine[0] != 'MEAN' :
line=data.readline()
parsedLine=line.split()
if len(parsedLine) == 0:
parsedLine=["Hello"]
Mx=parsedLine[1]
My=parsedLine[2]
Mz=parsedLine[3]
line=data.readline()
line=data.readline()
parsedLine=line.split()
splitExp = parsedLine[2].split('A')
intensityStr=parsedLine[1] + splitExp[0]
intensity = float(intensityStr)
# check and see if Prec is too big and messes with the parcing.
precisionStr=''
if len(parsedLine) == 6: #normal line
precisionStr=parsedLine[5][0:-1]
else:
precisionStr=parsedLine[4][0:-1]
precisionPer = float(precisionStr)
precision=intensity*precisionPer/100
while parsedLine[0] != 'SPEC.' :
line=data.readline()
parsedLine=line.split()
if len(parsedLine) == 0:
parsedLine=["Hello"]
specimenDec=parsedLine[2]
specimenInc=parsedLine[3]
line=data.readline()
line=data.readline()
parsedLine=line.split()
geographicDec=parsedLine[1]
geographicInc=parsedLine[2]
# Add data to various MagIC data tables.
er_specimen_name = sampleName
if specnum!=0:
er_sample_name=er_specimen_name[:specnum]
else:
er_sample_name=er_specimen_name
if int(samp_con) in [1, 2, 3, 4, 5, 7]:
er_site_name=pmag.parse_site(er_sample_name,samp_con,Z)
# else:
# if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampRec['er_site_name']
# if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampRec['er_location_name']
# check sample list(SampOuts) to see if sample already exists in list before adding new sample info
sampleFlag=0
for sampRec in SampOuts:
if sampRec['er_sample_name'] == er_sample_name:
sampleFlag=1
break
if sampleFlag == 0:
ErSampRec['er_sample_name']=er_sample_name
ErSampRec['sample_azimuth']=specimenAngleDec
ErSampRec['sample_dip']=specimenAngleInc
ErSampRec['magic_method_codes']=meth_code
ErSampRec['er_location_name']=er_location_name
ErSampRec['er_site_name']=er_site_name
ErSampRec['er_citation_names']='This study'
SampOuts.append(ErSampRec.copy())
MagRec={}
MagRec['measurement_description']='Date: '+date
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['er_site_name']=er_site_name
MagRec['er_sample_name']=er_sample_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=er_specimen_name
MagRec["treatment_ac_field"]='0'
if demagLevel == 'NRM':
meas_type="LT-NO"
elif demagLevel[0] == 'A':
meas_type="LT-AF-Z"
treat=float(demagLevel[1:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif demagLevel[0] == 'T':
meas_type="LT-T-Z"
treat=float(demagLevel[1:])
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
else:
print("measurement type unknown")
return False
# X=[float(Mx),float(My),float(Mz)]
# Vec=pmag.cart2dir(X)
# MagRec["measurement_magn_moment"]='%10.3e'% (Vec[2]) # Am^2
MagRec["measurement_magn_moment"]=str(intensity*0.025*0.025*0.025) # Am^2 assume 2.5cm cube sample
MagRec["measurement_magn_volume"]=intensityStr
MagRec["measurement_dec"]=specimenDec
MagRec["measurement_inc"]=specimenInc
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec.copy())
#read lines till end of record
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
# read all the rest of the special characters. Some data files not consistantly formatted.
while (len(line) <=3 and line!=''):
line=data.readline()
#end of data while loop
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(samp_file,SampOuts,'er_samples')
print("sample orientations put in ",samp_file)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print("results put in ",meas_file)
return True
def main(**kwargs):
version_num = pmag.get_version()
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
mag_file = kwargs.get('mag_file')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 2.5)) * 1e-6
JR = kwargs.get('JR', False)
if JR:
if meth_code == "LP-NO":
meth_code = ""
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
samp_con = '5'
# format variables
tmp_file = mag_file.split(os.extsep)[0] + os.extsep + 'tmp'
mag_file = os.path.join(input_dir_path, mag_file)
if specnum != 0: specnum = -int(specnum)
if samp_con.startswith("4"):
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
elif samp_con.startswith("7"):
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
else:
Z = 1
# parse data
# fix .jr6 file so that there are spaces between all the columns.
pre_data = open(mag_file, 'r')
tmp_data = open(tmp_file, 'w')
if samp_con != '2': fixed_data = pre_data.read().replace('-', ' -')
else:
fixed_data = ""
for line in pre_data.readlines():
entries = line.split()
if len(entries) < 2: continue
fixed_line = entries[0] + ' ' + reduce(
lambda x, y: x + ' ' + y,
[x.replace('-', ' -') for x in entries[1:]])
fixed_data += fixed_line + os.linesep
tmp_data.write(fixed_data)
tmp_data.close()
pre_data.close()
if not JR:
column_names = [
'specimen', 'step', 'x', 'y', 'z', 'expon', 'azimuth', 'dip',
'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2',
'param1', 'param2', 'param3', 'param4', 'dir_csd'
]
else: # measured on the Joides Resolution JR6
column_names = [
'specimen', 'step', 'negz', 'y', 'x', 'expon', 'azimuth', 'dip',
'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2',
'param1', 'param2', 'param3', 'param4', 'dir_csd'
]
data = pd.read_csv(tmp_file,
delim_whitespace=True,
names=column_names,
index_col=False)
if isinstance(data['x'][0], str):
column_names = [
'specimen', 'step', 'step_unit', 'x', 'y', 'z', 'expon', 'azimuth',
'dip', 'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2',
'param1', 'param2', 'param3', 'param4', 'dir_csd'
]
data = pd.read_csv(tmp_file,
delim_whitespace=True,
names=column_names,
index_col=False)
if JR: data['z'] = -data['negz']
cart = np.array([data['x'], data['y'], data['z']]).transpose()
dir_dat = pmag.cart2dir(cart).transpose()
data['dir_dec'] = dir_dat[0]
data['dir_inc'] = dir_dat[1]
data['magn_moment'] = dir_dat[2] * (
10.0**
data['expon']) * volume # the data are in A/m - this converts to Am^2
data['magn_volume'] = dir_dat[2] * (10.0**data['expon']
) # A/m - data in A/m
data['dip'] = -data['dip']
data['specimen']
# put data into magic tables
MagRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
for rowNum, row in data.iterrows():
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
specimen = row['specimen']
if specnum != 0: sample = specimen[:specnum]
else: sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec["citations"] = "This study"
SpecRec["analysts"] = user
SpecRec['volume'] = volume
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec["citations"] = "This study"
SampRec["analysts"] = user
SampRec['azimuth'] = row['azimuth']
SampRec['dip'] = row['dip']
SampRec['bed_dip_direction'] = row['bed_dip_direction']
SampRec['bed_dip'] = row['bed_dip']
SampRec['method_codes'] = meth_code
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec["citations"] = "This study"
SiteRec["analysts"] = user
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec["citations"] = "This study"
LocRec["analysts"] = user
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec["citations"] = "This study"
MeasRec["analysts"] = user
MeasRec["specimen"] = specimen
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["treat_ac_field"] = '0'
if row['step'] == 'NRM':
meas_type = "LT-NO"
elif 'step_unit' in row and row['step_unit'] == 'C':
meas_type = "LT-T-Z"
treat = float(row['step'])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
elif row['step'][0:2] == 'AD':
meas_type = "LT-AF-Z"
treat = float(row['step'][2:])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif row['step'][0] == 'A':
meas_type = "LT-AF-Z"
treat = float(row['step'][1:])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type = "LT-T-Z"
treat = float(row['step'][2:])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
elif row['step'][0] == 'T':
meas_type = "LT-T-Z"
treat = float(row['step'][1:])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
else: # need to add IRM, and ARM options
print("measurement type unknown", row['step'])
return False, "measurement type unknown"
MeasRec["magn_moment"] = str(row['magn_moment'])
MeasRec["magn_volume"] = str(row['magn_volume'])
MeasRec["dir_dec"] = str(row['dir_dec'])
MeasRec["dir_inc"] = str(row['dir_inc'])
MeasRec['method_codes'] = meas_type
MagRecs.append(MeasRec)
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
try:
os.remove(tmp_file)
except (OSError, IOError) as e:
print("couldn't remove temperary fixed JR6 file %s" % tmp_file)
return True, meas_file
def main():
"""
NAME
huji_sample_magic.py
DESCRIPTION
takes tab delimited Hebrew University sample file and converts to MagIC formatted tables
SYNTAX
huji_sample_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-Fsa FILE: specify sample output file, default is: er_samples.txt
-Fsi FILE: specify site output file, default is: er_sites.txt
-Iso: import sample orientation info - default is to set sample_az/dip to 0,0
-ncn NCON: specify naming convention: default is #1 below
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-ASC an ASC orientation device was used
SO-MAG orientation with magnetic compass
-loc: location name, default="unknown"
INPUT FORMAT
Input files must be tab delimited:
Samp Az Dip Dip_dir Dip
Orientation convention:
Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
e.g. field_dip is degrees from horizontal of drill direction
Magnetic declination convention:
Az is already corrected in file
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
OUTPUT
output saved in er_samples.txt will overwrite any existing files
"""
#
# initialize variables
#
version_num = pmag.get_version()
samp_file, or_con, corr = "er_samples.txt", "1", "1"
site_file = 'er_sites.txt'
args = sys.argv
date, lat, lon = "", "", "" # date of sampling, latitude (pos North), longitude (pos East)
bed_dip, bed_dip_dir = "", ""
participantlist = ""
sites = [] # list of site names
Lats, Lons = [], [] # list of latitudes and longitudes
SampRecs, SiteRecs, ImageRecs, imagelist = [], [], [], [
] # lists of Sample records and Site records
samp_con, Z, average_bedding = "1", 1, "0"
newbaseline, newbeddir, newbeddip = "", "", ""
meths = 'FS-FD:SO-POM:SO-SUN'
delta_u = "0"
sclass, lithology, type = "", "", ""
newclass, newlith, newtype = '', '', ''
user = ""
or_con = '3'
corr == "3"
DecCorr = 0.
location_name = "unknown"
ignore = 1
#
#
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-f" in args:
ind = args.index("-f")
orient_file = sys.argv[ind + 1]
else:
"Must have orientation file name"
sys.exit()
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = sys.argv[ind + 1]
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 3-Z where Z is an integer")
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
print(samp_con, Z)
if "-mcd" in args:
ind = args.index("-mcd")
meths = (sys.argv[ind + 1])
if "-loc" in args:
ind = args.index("-loc")
location_name = (sys.argv[ind + 1])
if "-Iso" in args: ignore = 0
#
# read in file to convert
#
azfile = open(orient_file, 'r')
AzDipDat = azfile.readlines()
azfile.close()
SampOut = []
SiteOut = []
for line in AzDipDat[1:]:
orec = line.split()
if len(orec) > 1:
labaz, labdip = pmag.orient(float(orec[1]), float(orec[2]), or_con)
bed_dip_dir = (orec[3])
bed_dip = (orec[4])
SampRec = {}
SiteRec = {}
SampRec["er_location_name"] = location_name
SampRec["er_citation_names"] = "This study"
SiteRec["er_location_name"] = location_name
SiteRec["er_citation_names"] = "This study"
SiteRec["site_class"] = ""
SiteRec["site_lithology"] = ""
SiteRec["site_type"] = ""
SiteRec["site_definition"] = "s"
SiteRec["er_citation_names"] = "This study"
#
# parse information common to all orientation methods
#
SampRec["er_sample_name"] = orec[0]
SampRec["sample_bed_dip_direction"] = orec[3]
SampRec["sample_bed_dip"] = orec[4]
SiteRec["site_bed_dip_direction"] = orec[3]
SiteRec["site_bed_dip"] = orec[4]
if ignore == 0:
SampRec["sample_dip"] = '%7.1f' % (labdip)
SampRec["sample_azimuth"] = '%7.1f' % (labaz)
else:
SampRec["sample_dip"] = '0'
SampRec["sample_azimuth"] = '0'
SampRec["sample_lat"] = orec[5]
SampRec["sample_lon"] = orec[6]
SiteRec["site_lat"] = orec[5]
SiteRec["site_lon"] = orec[6]
methods = meths.split(":")
SampRec["magic_method_codes"] = meths
site = pmag.parse_site(orec[0], samp_con,
Z) # parse out the site name
SampRec["er_site_name"] = site
SampRec['magic_software_packages'] = version_num
SiteRec["er_site_name"] = site
SiteRec['magic_software_packages'] = version_num
SampOut.append(SampRec)
SiteOut.append(SiteRec)
pmag.magic_write(samp_file, SampOut, "er_samples")
print("Sample info saved in ", samp_file)
pmag.magic_write(site_file, SiteOut, "er_sites")
print("Site info saved in ", site_file)
def main():
"""
NAME
susar4-asc_magic.py
DESCRIPTION
converts ascii files generated by SUSAR ver.4.0 to MagIC formated
files for use with PmagPy plotting software
SYNTAX
susar4-asc_magic.py -h [command line options]
OPTIONS
-h: prints the help message and quits
-f FILE: specify .asc input file name
-F MFILE: specify magic_measurements output file
-Fa AFILE: specify rmag_anisotropy output file
-Fr RFILE: specify rmag_results output file
-Fs SFILE: specify er_specimens output file with location, sample, site, etc. information
-usr USER: specify who made the measurements
-loc LOC: specify location name for study
-ins INST: specify instrument used
-spc SPEC: specify number of characters to specify specimen from sample
-ncn NCON: specify naming convention: default is #2 below
-k15 : specify static 15 position mode - default is spinning
-new : replace all existing magic files
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
SFILE: default is to create new er_specimen.txt file
USER: ""
LOC: "unknown"
INST: ""
SPEC: 0 sample name is same as site (if SPEC is 1, sample is all but last character)
appends to 'er_specimens.txt, er_samples.txt, er_sites.txt' files
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
"""
citation='This study'
cont=0
samp_con,Z="1",1
AniRecSs,AniRecs,SpecRecs,SampRecs,SiteRecs,MeasRecs=[],[],[],[],[],[]
user,locname,specfile="","unknown","er_specimens.txt"
isspec,inst,specnum='0',"",0
spin,new=1,0
dir_path='.'
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
aoutput,routput,moutput=dir_path+'/rmag_anisotropy.txt',dir_path+'/rmag_results.txt',dir_path+'/magic_measurements.txt'
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-usr' in sys.argv:
ind=sys.argv.index('-usr')
user=sys.argv[ind+1]
if "-ncn" in sys.argv:
ind=sys.argv.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
if '-k15' in sys.argv:spin=0
if '-f' in sys.argv:
ind=sys.argv.index('-f')
ascfile=dir_path+'/'+sys.argv[ind+1]
if '-F' in sys.argv:
ind=sys.argv.index('-F')
moutput=dir_path+'/'+sys.argv[ind+1]
if '-Fa' in sys.argv:
ind=sys.argv.index('-Fa')
aoutput=dir_path+'/'+sys.argv[ind+1]
if '-Fr' in sys.argv:
ind=sys.argv.index('-Fr')
routput=dir_path+'/'+sys.argv[ind+1]
if '-Fs' in sys.argv:
ind=sys.argv.index('-Fs')
specfile=dir_path+'/'+sys.argv[ind+1]
isspec='1'
elif '-loc' in sys.argv:
ind=sys.argv.index('-loc')
locname=sys.argv[ind+1]
if '-spc' in sys.argv:
ind=sys.argv.index('-spc')
specnum=-(int(sys.argv[ind+1]))
if specnum!=0:specnum=-specnum
if isspec=="1":
specs,file_type=pmag.magic_read(specfile)
specnames,sampnames,sitenames=[],[],[]
if '-new' not in sys.argv: # see if there are already specimen,sample, site files lying around
try:
SpecRecs,file_type=pmag.magic_read(dir_path+'/er_specimens.txt')
for spec in SpecRecs:
if spec['er_specimen_name'] not in specnames:specnames.append(samp['er_specimen_name'])
except:
SpecRecs,specs=[],[]
try:
SampRecs,file_type=pmag.magic_read(dir_path+'/er_samples.txt')
for samp in SampRecs:
if samp['er_sample_name'] not in sampnames:sampnames.append(samp['er_sample_name'])
except:
sampnames,SampRecs=[],[]
try:
SiteRecs,file_type=pmag.magic_read(dir_path+'/er_sites.txt')
for site in SiteRecs:
if site['er_site_names'] not in sitenames:sitenames.append(site['er_site_name'])
except:
sitenames,SiteRecs=[],[]
try:
input=open(ascfile,'r')
except:
print('Error opening file: ', ascfile)
Data=input.readlines()
k=0
while k<len(Data):
line = Data[k]
words=line.split()
if "ANISOTROPY" in words: # first line of data for the spec
MeasRec,AniRec,SpecRec,SampRec,SiteRec={},{},{},{},{}
specname=words[0]
AniRec['er_specimen_name']=specname
if isspec=="1":
for spec in specs:
if spec['er_specimen_name']==specname:
AniRec['er_sample_name']=spec['er_sample_name']
AniRec['er_site_name']=spec['er_site_name']
AniRec['er_location_name']=spec['er_location_name']
break
elif isspec=="0":
if specnum!=0:
sampname=specname[:specnum]
else:
sampname=specname
AniRec['er_sample_name']=sampname
SpecRec['er_specimen_name']=specname
SpecRec['er_sample_name']=sampname
SampRec['er_sample_name']=sampname
SiteRec['er_sample_name']=sampname
SiteRec['site_description']='s'
AniRec['er_site_name']=pmag.parse_site(AniRec['er_sample_name'],samp_con,Z)
SpecRec['er_site_name']=pmag.parse_site(AniRec['er_sample_name'],samp_con,Z)
SampRec['er_site_name']=pmag.parse_site(AniRec['er_sample_name'],samp_con,Z)
SiteRec['er_site_name']=pmag.parse_site(AniRec['er_sample_name'],samp_con,Z)
AniRec['er_location_name']=locname
SpecRec['er_location_name']=locname
SampRec['er_location_name']=locname
SiteRec['er_location_name']=locname
AniRec['er_citation_names']="This study"
SpecRec['er_citation_names']="This study"
SampRec['er_citation_names']="This study"
SiteRec['er_citation_names']="This study"
AniRec['er_citation_names']="This study"
AniRec['magic_instrument_codes']=inst
AniRec['magic_method_codes']="LP-X:AE-H:LP-AN-MS"
AniRec['magic_experiment_names']=specname+":"+"LP-AN-MS"
AniRec['er_analyst_mail_names']=user
for key in list(AniRec.keys()):MeasRec[key]=AniRec[key]
MeasRec['measurement_flag']='g'
AniRec['anisotropy_flag']='g'
MeasRec['measurement_standard']='u'
MeasRec['measurement_description']='Bulk sucsecptibility measurement'
AniRec['anisotropy_type']="AMS"
AniRec['anisotropy_unit']="Normalized by trace"
if spin==1:
AniRec['anisotropy_n']="192"
else:
AniRec['anisotropy_n']="15"
if 'Azi' in words and isspec=='0':
SampRec['sample_azimuth']=words[1]
labaz=float(words[1])
if 'Dip' in words:
SampRec['sample_dip']='%7.1f'%(-float(words[1]))
SpecRec['specimen_vol']='%8.3e'%(float(words[10])*1e-6) # convert actual volume to m^3 from cm^3
labdip=float(words[1])
if 'T1' in words and 'F1' in words:
k+=2 # read in fourth line down
line=Data[k]
rec=line.split()
dd=rec[1].split('/')
dip_direction=int(dd[0])+90
SampRec['sample_bed_dip_direction']='%i'%(dip_direction)
SampRec['sample_bed_dip']=dd[1]
bed_dip=float(dd[1])
if "Mean" in words:
k+=4 # read in fourth line down
line=Data[k]
rec=line.split()
MeasRec['measurement_chi_volume']=rec[1]
sigma=.01*float(rec[2])/3.
AniRec['anisotropy_sigma']='%7.4f'%(sigma)
AniRec['anisotropy_unit']='SI'
if "factors" in words:
k+=4 # read in second line down
line=Data[k]
rec=line.split()
if "Specimen" in words: # first part of specimen data
AniRec['anisotropy_s1']='%7.4f'%(old_div(float(words[5]),3.)) # eigenvalues sum to unity - not 3
AniRec['anisotropy_s2']='%7.4f'%(old_div(float(words[6]),3.))
AniRec['anisotropy_s3']='%7.4f'%(old_div(float(words[7]),3.))
k+=1
line=Data[k]
rec=line.split()
AniRec['anisotropy_s4']='%7.4f'%(old_div(float(rec[5]),3.)) # eigenvalues sum to unity - not 3
AniRec['anisotropy_s5']='%7.4f'%(old_div(float(rec[6]),3.))
AniRec['anisotropy_s6']='%7.4f'%(old_div(float(rec[7]),3.))
AniRec['anisotropy_tilt_correction']='-1'
AniRecs.append(AniRec)
AniRecG,AniRecT={},{}
for key in list(AniRec.keys()):AniRecG[key]=AniRec[key]
for key in list(AniRec.keys()):AniRecT[key]=AniRec[key]
sbar=[]
sbar.append(float(AniRec['anisotropy_s1']))
sbar.append(float(AniRec['anisotropy_s2']))
sbar.append(float(AniRec['anisotropy_s3']))
sbar.append(float(AniRec['anisotropy_s4']))
sbar.append(float(AniRec['anisotropy_s5']))
sbar.append(float(AniRec['anisotropy_s6']))
sbarg=pmag.dosgeo(sbar,labaz,labdip)
AniRecG["anisotropy_s1"]='%12.10f'%(sbarg[0])
AniRecG["anisotropy_s2"]='%12.10f'%(sbarg[1])
AniRecG["anisotropy_s3"]='%12.10f'%(sbarg[2])
AniRecG["anisotropy_s4"]='%12.10f'%(sbarg[3])
AniRecG["anisotropy_s5"]='%12.10f'%(sbarg[4])
AniRecG["anisotropy_s6"]='%12.10f'%(sbarg[5])
AniRecG["anisotropy_tilt_correction"]='0'
AniRecs.append(AniRecG)
if bed_dip!="" and bed_dip!=0: # have tilt correction
sbart=pmag.dostilt(sbarg,dip_direction,bed_dip)
AniRecT["anisotropy_s1"]='%12.10f'%(sbart[0])
AniRecT["anisotropy_s2"]='%12.10f'%(sbart[1])
AniRecT["anisotropy_s3"]='%12.10f'%(sbart[2])
AniRecT["anisotropy_s4"]='%12.10f'%(sbart[3])
AniRecT["anisotropy_s5"]='%12.10f'%(sbart[4])
AniRecT["anisotropy_s6"]='%12.10f'%(sbart[5])
AniRecT["anisotropy_tilt_correction"]='100'
AniRecs.append(AniRecT)
MeasRecs.append(MeasRec)
if SpecRec['er_specimen_name'] not in specnames:
SpecRecs.append(SpecRec)
specnames.append(SpecRec['er_specimen_name'])
if SampRec['er_sample_name'] not in sampnames:
SampRecs.append(SampRec)
sampnames.append(SampRec['er_sample_name'])
if SiteRec['er_site_name'] not in sitenames:
SiteRecs.append(SiteRec)
sitenames.append(SiteRec['er_site_name'])
k+=1 # skip to next specimen
pmag.magic_write(aoutput,AniRecs,'rmag_anisotropy')
print("anisotropy tensors put in ",aoutput)
pmag.magic_write(moutput,MeasRecs,'magic_measurements')
print("bulk measurements put in ",moutput)
if isspec=="0":
SpecOut,keys=pmag.fillkeys(SpecRecs)
output=dir_path+"/er_specimens.txt"
pmag.magic_write(output,SpecOut,'er_specimens')
print("specimen info put in ",output)
output=dir_path+"/er_samples.txt"
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(output,SampOut,'er_samples')
print("sample info put in ",output)
output=dir_path+"/er_sites.txt"
SiteOut,keys=pmag.fillkeys(SiteRecs)
pmag.magic_write(output,SiteOut,'er_sites')
print("site info put in ",output)
print(""""
You can now import your data into the Magic Console and complete data entry,
for example the site locations, lithologies, etc. plotting can be done with aniso_magic.py
""")
def main(command_line=True, **kwargs):
"""
NAME
cit_magic.py
DESCRIPTION
converts CIT and .sam format files to magic_measurements format files
SYNTAX
cit_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .sam format input file, required
-fsi SITEFILE : specify file with site names and locations [tab delimited magic file]
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt # LORI
-n [gm,kg,cc,m3]: specify normalization
-A: don't average replicate measurements
-spc NUM : specify number of characters to designate a specimen, default = 0
-ncn NCON: specify naming convention
-loc LOCNAME : specify location/study name, must have either LOCNAME or SITEFILE or be a synthetic
-mcd [FS-FD:SO-MAG,.....] colon delimited list for method codes applied to all specimens in .sam file
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-dm: specify which magic data model you want your output in 3.0 or 2.5 default is 2.5
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.)
NOTES:
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
"""
#
#initialize variables
norm='cc'
samp_con,Z='3',1
meas_file='measurements.txt'
spec_file='specimens.txt'
samp_file='samples.txt'
site_file='sites.txt'
Specs,Samps,Sites,Locs=[],[],[],[]
MeasRecs=[]
specnum,units,locname=0,"1","unknown"
citation="This study"
dir_path='.'
args=sys.argv
if command_line:
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print(main.__doc__)
return False
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
if '-Fsi' in args: # LORI addition
ind=args.index("-Fsi")
site_file=args[ind+1]
if '-loc' in args:
ind=args.index("-loc")
locname=args[ind+1]
if '-mcd' in args:
ind=args.index("-mcd")
methods=args[ind+1]
else:
methods='SO-MAG'
if '-spc' in args:
ind=args.index("-spc")
specnum=-int(args[ind+1])
if '-n' in args:
ind=args.index("-n")
norm=args[ind+1]
if "-A" in args:
avg=1
else:
avg=0
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if '-dm' in args:
dmi = args.index('-dm')
data_model = args[dmi+1]
# if you are running as a module:
elif not command_line:
dir_path = kwargs.get('dir_path', '.')
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
data_model = kwargs.get('data_model', 2.5) # data_model to output as
locname = kwargs.get('locname', '')
methods = kwargs.get('methods', ['SO-MAG'])
specnum = -int(kwargs.get('specnum', 0))
norm = kwargs.get('norm', 'cc')
avg = kwargs.get('avg', 0) # 0 means do average, 1 means don't
samp_con = kwargs.get('samp_con', '3')
magfile = kwargs.get('magfile', '')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
# done with module-specific stuff
# formatting and checking variables
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
magfile = os.path.join(input_dir_path, magfile)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
meas_file= os.path.join(output_dir_path, meas_file)
try:
file_input=open(magfile,'r')
except Exception as ex:
print("bad sam file name: ", magfile)
return False, "bad sam file name"
File = file_input.readlines()
if len(File) == 1: File = File[0].split('\r'); File = [x+"\r\n" for x in File]
sids,ln,format=[],0,'CIT'
formats=['CIT','2G','APP','JRA']
if File[ln].strip()=='CIT': ln+=1
LocRec={}
LocRec["er_location_name"]=locname
LocRec["er_citation_names"]=citation
comment=File[ln]
if comment=='CIT':
format=comment
ln+=1
comment=File[ln]
print(comment)
ln+=1
specimens,samples,sites=[],[],[]
if format=='CIT':
line=File[ln].split()
site_lat=line[0]
site_lon=line[1]
LocRec["location_begin_lat"]=site_lat
LocRec["location_begin_lon"]=site_lon
LocRec["location_end_lat"]=site_lat
LocRec["location_end_lon"]=site_lon
Locs.append(LocRec)
try: Cdec=float(line[2])
except ValueError: pdb.set_trace()
for k in range(ln+1,len(File)):
line=File[k]
rec=line.split()
if rec == []: continue
specimen=rec[0]
specimens.append(specimen)
for specimen in specimens:
SpecRec,SampRec,SiteRec={},{},{}
if specnum!=0:
sample=specimen[:specnum]
else: sample=specimen
site=pmag.parse_site(sample,samp_con,Z)
SpecRec['er_specimen_name']=specimen
SpecRec['er_sample_name']=sample
SpecRec['er_site_name']=site
SpecRec['er_location_name']=locname
SpecRec['er_citation_names']=citation
SampRec['er_sample_name']=sample
SampRec['er_site_name']=site
SampRec['er_location_name']=locname
SampRec['er_citation_names']=citation
SampRec['magic_method_codes']=methods
SampRec['sample_declination_correction']='%7.1f'%(Cdec)
SiteRec['er_site_name']=site
SiteRec['er_location_name']=locname
SiteRec['er_citation_names']=citation
SiteRec['site_lat']=site_lat
SiteRec['site_lon']=site_lon
f=open(input_dir_path+'/'+specimen,'rU')
Lines=f.readlines()
comment=""
line=Lines[0].split()
if len(line)>2:
comment=line[2]
info=Lines[1].split()
vol=float(info[-1])
if vol!=1.0:
if norm=='cc':units="1"
if norm=='m3':units="2"
SpecRec['specimen_weight']=""
if units=="1" or "":
SpecRec['specimen_volume']='%10.3e'%(vol*1e-6)
else:
SpecRec['specimen_volume']='%10.3e'%(vol)
else:
if norm=='cc':units="1"
if norm=='m3':units="2"
SpecRec['specimen_volume']=""
if units=="1" or "":
SpecRec['specimen_weight']='%10.3e'%(vol*1e-3)
else:
SpecRec['specimen_weight']='%10.3e'%(vol)
dip=float(info[-2])
dip_direction=float(info[-3])+Cdec+90.
sample_dip=-float(info[-4])
sample_azimuth=float(info[-5])+Cdec-90.
if len(info)>5:
SampRec['sample_height']=info[-6]
else:
SampRec['sample_height']='0'
SampRec['sample_azimuth']='%7.1f'%(sample_azimuth)
SampRec['sample_dip']='%7.1f'%(sample_dip)
SampRec['sample_bed_dip']='%7.1f'%(dip)
SampRec['sample_bed_dip_direction']='%7.1f'%(dip_direction)
SampRec['sample_class']=''
SampRec['sample_type']=''
SampRec['sample_lithology']=''
if Cdec!=0 or Cdec!="":
SampRec['magic_method_codes']='SO-CMD-NORTH'
else:
SampRec['magic_method_codes']='SO-MAG'
for line in Lines[2:len(Lines)]:
#print 'line:', line
MeasRec=SpecRec.copy()
# Remove specimen_volume and specimen_weight as they do not exits in the magic_measurement table
del MeasRec["specimen_volume"]
del MeasRec["specimen_weight"]
treat_type=line[0:3]
treat=line[2:6]
try: float(treat)
except ValueError: treat = line[3:6]
if treat_type.startswith('NRM'):
MeasRec['magic_method_codes']='LT-NO'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_ac_field']='0'
elif treat_type.startswith('AF'):
MeasRec['magic_method_codes']='LT-AF-Z'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
if treat.strip() == '':
MeasRec['treatment_ac_field']='0'
else:
MeasRec['treatment_ac_field']='%10.3e'%(float(treat)*1e-3)
elif treat_type.startswith('ARM'):
MeasRec['magic_method_codes']="LP-ARM"
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
if treat.strip() == '':
MeasRec['treatment_ac_field']='0'
else:
MeasRec['magic_method_codes']="LP-ARM-AFD"
MeasRec['treatment_ac_field']='%10.3e'%(float(treat)*1e-3)
elif treat_type.startswith('TT'):
MeasRec['magic_method_codes']='LT-T-Z'
MeasRec['measurement_temp']='273'
if treat.strip() == '':
MeasRec['treatment_temp']='273'
else:
MeasRec['treatment_temp']='%7.1f'%(float(treat)+273)
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_ac_field']='0'
elif treat_type.startswith('LT') or treat_type.startswith('LN2'):
MeasRec['magic_method_codes']='LT-LT-Z'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='77'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_ac_field']='0'
else:
print("trouble with your treatment steps")
MeasRec['measurement_dec']=line[46:51]
MeasRec['measurement_inc']=line[52:58]
M='%8.2e'%(float(line[31:39])*vol*1e-3) # convert to Am2
MeasRec['measurement_magn_moment']=M
MeasRec['measurement_csd']='%7.1f'%(eval(line[41:46]))
MeasRec["measurement_positions"]='1'
MeasRec['measurement_standard']='u'
if len(line)>60:
MeasRec['magic_instrument_codes']=line[85:].strip('\n \r \t "')
MeasRec['measurement_sd_x']='%8.2e'%(float(line[58:67])*1e-8) #(convert e-5emu to Am2)
MeasRec['measurement_sd_y']='%8.2e'%(float(line[67:76])*1e-8)
MeasRec['measurement_sd_z']='%8.2e'%(float(line[76:85])*1e-8)
MeasRecs.append(MeasRec)
Specs.append(SpecRec)
if sample not in samples:
samples.append(sample)
Samps.append(SampRec)
site=pmag.parse_site(sample,samp_con,Z)
if site not in sites:
sites.append(site)
Sites.append(SiteRec)
if float(data_model)==3.0:
con = nb.Contribution('.',read_tables=[])
con.add_empty_magic_table('specimens')
con.add_empty_magic_table('samples')
con.add_empty_magic_table('sites')
con.add_empty_magic_table('locations')
con.add_empty_magic_table('measurements')
con.tables['specimens'].df = DataFrame(Specs).rename(columns=mapm.spec_magic2_2_magic3_map)
con.tables['samples'].df = DataFrame(Samps).rename(columns=mapm.samp_magic2_2_magic3_map)
con.tables['sites'].df = DataFrame(Sites).rename(columns=mapm.site_magic2_2_magic3_map)
con.tables['locations'].df = DataFrame(Locs).rename(columns=mapm.loc_magic2_2_magic3_map)
Fixed=pmag.measurements_methods(MeasRecs,avg)
con.tables['measurements'].df = DataFrame(Fixed).rename(columns=mapm.meas_magic2_2_magic3_map)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
print('specimens stored in ',spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
print('samples stored in ',samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
print('sites stored in ', site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
print('locations stored in ', loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
print('data stored in ',meas_file)
else:
pmag.magic_write(spec_file,Specs,'er_specimens')
print('specimens stored in ',spec_file)
pmag.magic_write(samp_file,Samps,'er_samples')
print('samples stored in ',samp_file)
pmag.magic_write(site_file,Sites,'er_sites')
print('sites stored in ', site_file)
Fixed=pmag.measurements_methods(MeasRecs,avg)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print('data stored in ',meas_file)
return True, meas_file
return True, meas_file
def main(**kwargs):
version_num=pmag.get_version()
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
mag_file = kwargs.get('mag_file')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 2.5))* 1e-6
JR = kwargs.get('JR', False)
if JR:
if meth_code == "LP-NO":
meth_code = ""
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
samp_con='5'
# format variables
tmp_file = mag_file.split(os.extsep)[0]+os.extsep+'tmp'
mag_file = os.path.join(input_dir_path, mag_file)
if specnum!=0: specnum=-int(specnum)
if samp_con.startswith("4"):
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
elif samp_con.startswith("7"):
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
else: Z=1
# parse data
# fix .jr6 file so that there are spaces between all the columns.
pre_data=open(mag_file, 'r')
tmp_data=open(tmp_file, 'w')
if samp_con!='2': fixed_data=pre_data.read().replace('-',' -')
else:
fixed_data=""
for line in pre_data.readlines():
entries=line.split()
if len(entries)<2: continue
fixed_line = entries[0] + ' ' + reduce(lambda x,y: x+' '+y, [x.replace('-',' -') for x in entries[1:]])
fixed_data += fixed_line+os.linesep
tmp_data.write(fixed_data)
tmp_data.close()
pre_data.close()
if not JR:
column_names=['specimen', 'step', 'x', 'y', 'z', 'expon', 'azimuth', 'dip', 'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2', 'param3', 'param4', 'dir_csd']
else: # measured on the Joides Resolution JR6
column_names=['specimen', 'step', 'negz', 'y', 'x', 'expon', 'azimuth', 'dip', 'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2', 'param3', 'param4', 'dir_csd']
data=pd.read_csv(tmp_file, delim_whitespace=True, names=column_names, index_col=False)
if isinstance(data['x'][0],str):
column_names=['specimen', 'step', 'step_unit', 'x', 'y', 'z', 'expon', 'azimuth', 'dip', 'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2', 'param3', 'param4', 'dir_csd']
data=pd.read_csv(tmp_file, delim_whitespace=True, names=column_names, index_col=False)
if JR: data['z']=-data['negz']
cart=np.array([data['x'],data['y'],data['z']]).transpose()
dir_dat= pmag.cart2dir(cart).transpose()
data['dir_dec']=dir_dat[0]
data['dir_inc']=dir_dat[1]
data['magn_moment']=dir_dat[2]*(10.0**data['expon'])*volume # the data are in A/m - this converts to Am^2
data['magn_volume']=dir_dat[2]*(10.0**data['expon']) # A/m - data in A/m
data['dip']=-data['dip']
data['specimen']
# put data into magic tables
MagRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
for rowNum, row in data.iterrows():
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
specimen=row['specimen']
if specnum!=0: sample=specimen[:specnum]
else: sample=specimen
site=pmag.parse_site(sample,samp_con,Z)
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec["citations"]="This study"
SpecRec["analysts"]=user
SpecRec['volume'] = volume
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec["citations"]="This study"
SampRec["analysts"]=user
SampRec['azimuth'] = row['azimuth']
SampRec['dip'] = row['dip']
SampRec['bed_dip_direction'] = row['bed_dip_direction']
SampRec['bed_dip'] = row['bed_dip']
SampRec['method_codes']=meth_code
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec["citations"]="This study"
SiteRec["analysts"]=user
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec["citations"]="This study"
LocRec["analysts"]=user
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec["citations"]="This study"
MeasRec["analysts"]=user
MeasRec["specimen"]=specimen
MeasRec['software_packages']=version_num
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["quality"]='g'
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
MeasRec["treat_ac_field"]='0'
if row['step'] == 'NRM':
meas_type="LT-NO"
elif 'step_unit' in row and row['step_unit']=='C':
meas_type="LT-T-Z"
treat=float(row['step'])
MeasRec["treat_temp"]='%8.3e' % (treat+273.) # temp in kelvin
elif row['step'][0:2] == 'AD':
meas_type="LT-AF-Z"
treat=float(row['step'][2:])
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif row['step'][0] == 'A':
meas_type="LT-AF-Z"
treat=float(row['step'][1:])
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type="LT-T-Z"
treat=float(row['step'][2:])
MeasRec["treat_temp"]='%8.3e' % (treat+273.) # temp in kelvin
elif row['step'][0] == 'T':
meas_type="LT-T-Z"
treat=float(row['step'][1:])
MeasRec["treat_temp"]='%8.3e' % (treat+273.) # temp in kelvin
else: # need to add IRM, and ARM options
print("measurement type unknown", row['step'])
return False, "measurement type unknown"
MeasRec["magn_moment"]=str(row['magn_moment'])
MeasRec["magn_volume"]=str(row['magn_volume'])
MeasRec["dir_dec"]=str(row['dir_dec'])
MeasRec["dir_inc"]=str(row['dir_inc'])
MeasRec['method_codes']=meas_type
MagRecs.append(MeasRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
try: os.remove(tmp_file)
except (OSError,IOError) as e: print("couldn't remove temperary fixed JR6 file %s"%tmp_file)
return True, meas_file
