def save_redo(SpecRecs,inspec):
SpecRecs,keys=pmag.fillkeys(SpecRecs)
pmag.magic_write(inspec,SpecRecs,'pmag_specimens')
def main(command_line=True, **kwargs):
"""
NAME
iodp_dscr_magic.py
DESCRIPTION
converts ODP LIMS discrete sample format files to magic_measurements format files
SYNTAX
iodp_descr_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input .csv file, default is all in directory
-F FILE: specify output measurements file, default is magic_measurements.txt
-A : don't average replicate measurements
INPUTS
IODP discrete sample .csv file format exported from LIMS database
"""
#
# initialize defaults
version_num = pmag.get_version()
meas_file = 'magic_measurements.txt'
csv_file = ''
MagRecs, Specs = [], []
citation = "This study"
dir_path, demag = '.', 'NRM'
args = sys.argv
noave = 0
# get command line args
if command_line:
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
if "-h" in args:
print(main.__doc__)
return False
if "-A" in args: noave = 1
if '-f' in args:
ind = args.index("-f")
csv_file = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
meas_file = 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 # rename dir_path after input_dir_path is set
noave = kwargs.get('noave', 0) # default (0) is DO average
csv_file = kwargs.get('csv_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
# format variables
meas_file = os.path.join(output_dir_path, meas_file)
if csv_file == "":
filelist = os.listdir(
input_dir_path) # read in list of files to import
else:
csv_file = os.path.join(input_dir_path, csv_file)
filelist = [csv_file]
# parsing the data
file_found = False
for fname in filelist: # parse each file
if fname[-3:].lower() == 'csv':
file_found = True
print('processing: ', fname)
with open(fname, 'r') as finput:
data = list(finput.readlines())
keys = data[0].replace('\n',
'').split(',') # splits on underscores
interval_key = "Offset (cm)"
demag_key = "Demag level (mT)"
offline_demag_key = "Treatment Value (mT or °C)"
offline_treatment_type = "Treatment type"
run_key = "Test No."
if "Inclination background + tray corrected (deg)" in keys:
inc_key = "Inclination background + tray corrected (deg)"
if "Inclination background & tray corrected (deg)" in keys:
inc_key = "Inclination background & tray corrected (deg)"
if "Declination background + tray corrected (deg)" in keys:
dec_key = "Declination background + tray corrected (deg)"
if "Declination background & tray corrected (deg)" in keys:
dec_key = "Declination background & tray corrected (deg)"
if "Intensity background + tray corrected (A/m)" in keys:
int_key = "Intensity background + tray corrected (A/m)"
if "Intensity background & tray corrected (A/m)" in keys:
int_key = "Intensity background & tray corrected (A/m)"
type = "Type"
sect_key = "Sect"
half_key = "A/W"
# need to add volume_key to LORE format!
if "Sample volume (cm^3)" in keys:
volume_key = "Sample volume (cm^3)"
if "Sample volume (cc)" in keys: volume_key = "Sample volume (cc)"
if "Sample volume (cm³)" in keys:
volume_key = "Sample volume (cm³)"
for line in data[1:]:
InRec = {}
for k in range(len(keys)):
InRec[keys[k]] = line.split(',')[k]
inst = "IODP-SRM"
MagRec = {}
expedition = InRec['Exp']
location = InRec['Site'] + InRec['Hole']
offsets = InRec[interval_key].split(
'.'
) # maintain consistency with er_samples convention of using top interval
if len(offsets) == 1:
offset = int(offsets[0])
else:
offset = int(offsets[0]) - 1
#interval=str(offset+1)# maintain consistency with er_samples convention of using top interval
interval = str(
offset
) # maintain consistency with er_samples convention of using top interval
specimen = expedition + '-' + location + '-' + InRec[
'Core'] + InRec[type] + "-" + InRec[
sect_key] + '_' + InRec[half_key] + '_' + interval
if specimen not in Specs: Specs.append(specimen)
MagRec['er_expedition_name'] = expedition
MagRec['er_location_name'] = location
MagRec['er_site_name'] = specimen
MagRec['er_citation_names'] = citation
MagRec['er_specimen_name'] = specimen
MagRec['er_sample_name'] = specimen
MagRec['er_site_name'] = specimen
# set up measurement record - default is NRM
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'
MagRec["measurement_flag"] = 'g' # assume all data are "good"
MagRec[
"measurement_standard"] = 'u' # assume all data are "good"
MagRec["measurement_csd"] = '0' # assume all data are "good"
volume = InRec[volume_key]
MagRec["magic_method_codes"] = 'LT-NO'
sort_by = 'treatment_ac_field' # set default to AF demag
if InRec[demag_key] != "0":
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst = inst + ':IODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value = float(
InRec[demag_key].strip('"')) * 1e-3 # convert mT => T
if sort_by == "treatment_ac_field":
MagRec[
"treatment_ac_field"] = treatment_value # AF demag in treat mT => T
else:
MagRec["treatment_ac_field"] = str(
treatment_value) # AF demag in treat mT => T
elif offline_treatment_type in list(
InRec.keys()) and InRec[offline_treatment_type] != "":
if "Lowrie" in InRec['Comments']:
MagRec['magic_method_codes'] = 'LP-IRM-3D'
treatment_value = float(InRec[offline_demag_key].strip(
'"')) + 273. # convert C => K
MagRec["treatment_temp"] = treatment_value
MagRec["treatment_ac_field"] = "0"
sort_by = 'treatment_temp'
elif 'Isothermal' in InRec[offline_treatment_type]:
MagRec['magic_method_codes'] = 'LT-IRM'
treatment_value = float(InRec[offline_demag_key].strip(
'"')) * 1e-3 # convert mT => T
MagRec["treatment_dc_field"] = treatment_value
MagRec["treatment_ac_field"] = "0"
sort_by = 'treatment_dc_field'
MagRec[
"measurement_standard"] = 'u' # assume all data are "good"
vol = float(volume) * 1e-6 # convert from cc to m^3
if run_key in list(InRec.keys()):
run_number = InRec[run_key]
MagRec['external_database_ids'] = run_number
MagRec['external_database_names'] = 'LIMS'
else:
MagRec['external_database_ids'] = ""
MagRec['external_database_names'] = ''
MagRec[
'measurement_description'] = 'sample orientation: ' + InRec[
'Sample orientation']
MagRec['measurement_inc'] = InRec[inc_key].strip('"')
MagRec['measurement_dec'] = InRec[dec_key].strip('"')
intens = InRec[int_key].strip('"')
MagRec['measurement_magn_moment'] = '%8.3e' % (
float(intens) * vol
) # convert intensity from A/m to Am^2 using vol
MagRec['magic_instrument_codes'] = inst
MagRec['measurement_number'] = '1'
MagRec['measurement_positions'] = ''
MagRecs.append(MagRec)
if not file_found:
print("No .csv files were found")
return False, "No .csv files were found"
MagOuts = []
for spec in Specs:
Speclist = pmag.get_dictitem(MagRecs, 'er_specimen_name', spec, 'T')
Meassorted = sorted(Speclist,
key=lambda x, y=None: int(
round(float(x[sort_by]) - float(y[sort_by])))
if y != None else 0)
for rec in Meassorted:
for key in list(rec.keys()):
rec[key] = str(rec[key])
MagOuts.append(rec)
Fixed = pmag.measurements_methods(MagOuts, noave)
Out, keys = pmag.fillkeys(Fixed)
if pmag.magic_write(meas_file, Out, 'magic_measurements'):
print('data stored in ', meas_file)
return True, meas_file
else:
print('no data found. bad magfile?')
return False, 'no data found. bad magfile?'
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():
"""
NAME
aniso_magic.py
DESCRIPTION
plots anisotropy data with either bootstrap or hext ellipses
SYNTAX
aniso_magic.py [-h] [command line options]
OPTIONS
-h plots help message and quits
-usr USER: set the user name
-f AFILE, specify rmag_anisotropy formatted file for input
-F RFILE, specify rmag_results formatted file for output
-x Hext [1963] and bootstrap
-B DON'T do bootstrap, do Hext
-par Tauxe [1998] parametric bootstrap
-v plot bootstrap eigenvectors instead of ellipses
-sit plot by site instead of entire file
-crd [s,g,t] coordinate system, default is specimen (g=geographic, t=tilt corrected)
-P don't make any plots - just make rmag_results table
-sav don't make the rmag_results table - just save all the plots
-fmt [svg, jpg, eps] format for output images, pdf default
-gtc DEC INC dec,inc of pole to great circle [down(up) in green (cyan)
-d Vi DEC INC; Vi (1,2,3) to compare to direction DEC INC
-n N; specifies the number of bootstraps - default is 1000
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
plot bootstrap ellipses of Constable & Tauxe [1987]
NOTES
minor axis: circles
major axis: triangles
principal axis: squares
directions are plotted on the lower hemisphere
for bootstrapped eigenvector components: Xs: blue, Ys: red, Zs: black
"""
#
dir_path = "."
version_num = pmag.get_version()
verbose = pmagplotlib.verbose
args = sys.argv
ipar, ihext, ivec, iboot, imeas, isite, iplot, vec = 0, 0, 0, 1, 1, 0, 1, 0
hpars, bpars, PDir = [], [], []
CS, crd = '-1', 's'
nb = 1000
fmt = 'pdf'
ResRecs = []
orlist = []
outfile, comp, Dir, gtcirc, PDir = 'rmag_results.txt', 0, [], 0, []
infile = 'rmag_anisotropy.txt'
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind+1]
if '-n' in args:
ind = args.index('-n')
nb = int(args[ind+1])
if '-usr' in args:
ind = args.index('-usr')
user = args[ind+1]
else:
user = ""
if '-B' in args:
iboot, ihext = 0, 1
if '-par' in args:
ipar = 1
if '-x' in args:
ihext = 1
if '-v' in args:
ivec = 1
if '-sit' in args:
isite = 1
if '-P' in args:
iplot = 0
if '-f' in args:
ind = args.index('-f')
infile = args[ind+1]
if '-F' in args:
ind = args.index('-F')
outfile = args[ind+1]
if '-crd' in sys.argv:
ind = sys.argv.index('-crd')
crd = sys.argv[ind+1]
if crd == 'g':
CS = '0'
if crd == 't':
CS = '100'
if '-fmt' in args:
ind = args.index('-fmt')
fmt = args[ind+1]
if '-sav' in args:
plots = 1
verbose = 0
else:
plots = 0
if '-gtc' in args:
ind = args.index('-gtc')
d, i = float(args[ind+1]), float(args[ind+2])
PDir.append(d)
PDir.append(i)
if '-d' in args:
comp = 1
ind = args.index('-d')
vec = int(args[ind+1])-1
Dir = [float(args[ind+2]), float(args[ind+3])]
#
# set up plots
#
if infile[0] != '/':
infile = dir_path+'/'+infile
if outfile[0] != '/':
outfile = dir_path+'/'+outfile
ANIS = {}
initcdf, inittcdf = 0, 0
ANIS['data'], ANIS['conf'] = 1, 2
if iboot == 1:
ANIS['tcdf'] = 3
if iplot == 1:
inittcdf = 1
pmagplotlib.plot_init(ANIS['tcdf'], 5, 5)
if comp == 1 and iplot == 1:
initcdf = 1
ANIS['vxcdf'], ANIS['vycdf'], ANIS['vzcdf'] = 4, 5, 6
pmagplotlib.plot_init(ANIS['vxcdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vycdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vzcdf'], 5, 5)
if iplot == 1:
pmagplotlib.plot_init(ANIS['conf'], 5, 5)
pmagplotlib.plot_init(ANIS['data'], 5, 5)
# read in the data
data, ifiletype = pmag.magic_read(infile)
for rec in data: # find all the orientation systems
if 'anisotropy_tilt_correction' not in rec.keys():
rec['anisotropy_tilt_correction'] = '-1'
if rec['anisotropy_tilt_correction'] not in orlist:
orlist.append(rec['anisotropy_tilt_correction'])
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = '-1'
if CS == '-1':
crd = 's'
if CS == '0':
crd = 'g'
if CS == '100':
crd = 't'
if verbose:
print("desired coordinate system not available, using available: ", crd)
if isite == 1:
sitelist = []
for rec in data:
if rec['er_site_name'] not in sitelist:
sitelist.append(rec['er_site_name'])
sitelist.sort()
plt = len(sitelist)
else:
plt = 1
k = 0
while k < plt:
site = ""
sdata, Ss = [], [] # list of S format data
Locs, Sites, Samples, Specimens, Cits = [], [], [], [], []
if isite == 0:
sdata = data
else:
site = sitelist[k]
for rec in data:
if rec['er_site_name'] == site:
sdata.append(rec)
anitypes = []
csrecs = pmag.get_dictitem(
sdata, 'anisotropy_tilt_correction', CS, 'T')
for rec in csrecs:
if rec['anisotropy_type'] not in anitypes:
anitypes.append(rec['anisotropy_type'])
if rec['er_location_name'] not in Locs:
Locs.append(rec['er_location_name'])
if rec['er_site_name'] not in Sites:
Sites.append(rec['er_site_name'])
if rec['er_sample_name'] not in Samples:
Samples.append(rec['er_sample_name'])
if rec['er_specimen_name'] not in Specimens:
Specimens.append(rec['er_specimen_name'])
if rec['er_citation_names'] not in Cits:
Cits.append(rec['er_citation_names'])
s = []
s.append(float(rec["anisotropy_s1"]))
s.append(float(rec["anisotropy_s2"]))
s.append(float(rec["anisotropy_s3"]))
s.append(float(rec["anisotropy_s4"]))
s.append(float(rec["anisotropy_s5"]))
s.append(float(rec["anisotropy_s6"]))
if s[0] <= 1.0:
Ss.append(s) # protect against crap
# tau,Vdirs=pmag.doseigs(s)
ResRec = {}
ResRec['er_location_names'] = rec['er_location_name']
ResRec['er_citation_names'] = rec['er_citation_names']
ResRec['er_site_names'] = rec['er_site_name']
ResRec['er_sample_names'] = rec['er_sample_name']
ResRec['er_specimen_names'] = rec['er_specimen_name']
ResRec['rmag_result_name'] = rec['er_specimen_name'] + \
":"+rec['anisotropy_type']
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
ResRec["anisotropy_type"] = rec['anisotropy_type']
if "anisotropy_n" not in rec.keys():
rec["anisotropy_n"] = "6"
if "anisotropy_sigma" not in rec.keys():
rec["anisotropy_sigma"] = "0"
fpars = pmag.dohext(
int(rec["anisotropy_n"])-6, float(rec["anisotropy_sigma"]), s)
ResRec["anisotropy_v1_dec"] = '%7.1f' % (fpars['v1_dec'])
ResRec["anisotropy_v2_dec"] = '%7.1f' % (fpars['v2_dec'])
ResRec["anisotropy_v3_dec"] = '%7.1f' % (fpars['v3_dec'])
ResRec["anisotropy_v1_inc"] = '%7.1f' % (fpars['v1_inc'])
ResRec["anisotropy_v2_inc"] = '%7.1f' % (fpars['v2_inc'])
ResRec["anisotropy_v3_inc"] = '%7.1f' % (fpars['v3_inc'])
ResRec["anisotropy_t1"] = '%10.8f' % (fpars['t1'])
ResRec["anisotropy_t2"] = '%10.8f' % (fpars['t2'])
ResRec["anisotropy_t3"] = '%10.8f' % (fpars['t3'])
ResRec["anisotropy_ftest"] = '%10.3f' % (fpars['F'])
ResRec["anisotropy_ftest12"] = '%10.3f' % (fpars['F12'])
ResRec["anisotropy_ftest23"] = '%10.3f' % (fpars['F23'])
ResRec["result_description"] = 'F_crit: ' + \
fpars['F_crit']+'; F12,F23_crit: '+fpars['F12_crit']
ResRec['anisotropy_type'] = pmag.makelist(anitypes)
ResRecs.append(ResRec)
if len(Ss) > 1:
if pmagplotlib.isServer:
title = "LO:_"+ResRec['er_location_names'] + \
'_SI:_'+site+'_SA:__SP:__CO:_'+crd
else:
title = ResRec['er_location_names']
if site:
title += "_{}".format(site)
title += '_{}'.format(crd)
ResRec['er_location_names'] = pmag.makelist(Locs)
bpars, hpars = pmagplotlib.plot_anis(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb)
if len(PDir) > 0:
pmagplotlib.plot_circ(ANIS['data'], PDir, 90., 'g')
pmagplotlib.plot_circ(ANIS['conf'], PDir, 90., 'g')
if verbose and plots == 0:
pmagplotlib.draw_figs(ANIS)
ResRec['er_location_names'] = pmag.makelist(Locs)
if plots == 1:
save(ANIS, fmt, title)
ResRec = {}
ResRec['er_citation_names'] = pmag.makelist(Cits)
ResRec['er_location_names'] = pmag.makelist(Locs)
ResRec['er_site_names'] = pmag.makelist(Sites)
ResRec['er_sample_names'] = pmag.makelist(Samples)
ResRec['er_specimen_names'] = pmag.makelist(Specimens)
ResRec['rmag_result_name'] = pmag.makelist(
Sites)+":"+pmag.makelist(anitypes)
ResRec['anisotropy_type'] = pmag.makelist(anitypes)
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
if isite == "0":
ResRec['result_description'] = "Study average using coordinate system: " + CS
if isite == "1":
ResRec['result_description'] = "Site average using coordinate system: " + CS
if hpars != [] and ihext == 1:
HextRec = {}
for key in ResRec.keys():
HextRec[key] = ResRec[key] # copy over stuff
HextRec["anisotropy_v1_dec"] = '%7.1f' % (hpars["v1_dec"])
HextRec["anisotropy_v2_dec"] = '%7.1f' % (hpars["v2_dec"])
HextRec["anisotropy_v3_dec"] = '%7.1f' % (hpars["v3_dec"])
HextRec["anisotropy_v1_inc"] = '%7.1f' % (hpars["v1_inc"])
HextRec["anisotropy_v2_inc"] = '%7.1f' % (hpars["v2_inc"])
HextRec["anisotropy_v3_inc"] = '%7.1f' % (hpars["v3_inc"])
HextRec["anisotropy_t1"] = '%10.8f' % (hpars["t1"])
HextRec["anisotropy_t2"] = '%10.8f' % (hpars["t2"])
HextRec["anisotropy_t3"] = '%10.8f' % (hpars["t3"])
HextRec["anisotropy_hext_F"] = '%7.1f ' % (hpars["F"])
HextRec["anisotropy_hext_F12"] = '%7.1f ' % (hpars["F12"])
HextRec["anisotropy_hext_F23"] = '%7.1f ' % (hpars["F23"])
HextRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v1_eta_dec"] = '%7.1f ' % (hpars["v2_dec"])
HextRec["anisotropy_v1_eta_inc"] = '%7.1f ' % (hpars["v2_inc"])
HextRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % (
hpars["e13"])
HextRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % (
hpars["v3_dec"])
HextRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % (
hpars["v3_inc"])
HextRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v2_eta_dec"] = '%7.1f ' % (hpars["v1_dec"])
HextRec["anisotropy_v2_eta_inc"] = '%7.1f ' % (hpars["v1_inc"])
HextRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % (
hpars["e23"])
HextRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % (
hpars["v3_dec"])
HextRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % (
hpars["v3_inc"])
HextRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v3_eta_dec"] = '%7.1f ' % (hpars["v1_dec"])
HextRec["anisotropy_v3_eta_inc"] = '%7.1f ' % (hpars["v1_inc"])
HextRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % (
hpars["e23"])
HextRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % (
hpars["v2_dec"])
HextRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % (
hpars["v2_inc"])
HextRec["magic_method_codes"] = 'LP-AN:AE-H'
if verbose:
print("Hext Statistics: ")
print(
" tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I")
print(HextRec["anisotropy_t1"], HextRec["anisotropy_v1_dec"], HextRec["anisotropy_v1_inc"], HextRec["anisotropy_v1_eta_semi_angle"], HextRec["anisotropy_v1_eta_dec"],
HextRec["anisotropy_v1_eta_inc"], HextRec["anisotropy_v1_zeta_semi_angle"], HextRec["anisotropy_v1_zeta_dec"], HextRec["anisotropy_v1_zeta_inc"])
print(HextRec["anisotropy_t2"], HextRec["anisotropy_v2_dec"], HextRec["anisotropy_v2_inc"], HextRec["anisotropy_v2_eta_semi_angle"], HextRec["anisotropy_v2_eta_dec"],
HextRec["anisotropy_v2_eta_inc"], HextRec["anisotropy_v2_zeta_semi_angle"], HextRec["anisotropy_v2_zeta_dec"], HextRec["anisotropy_v2_zeta_inc"])
print(HextRec["anisotropy_t3"], HextRec["anisotropy_v3_dec"], HextRec["anisotropy_v3_inc"], HextRec["anisotropy_v3_eta_semi_angle"], HextRec["anisotropy_v3_eta_dec"],
HextRec["anisotropy_v3_eta_inc"], HextRec["anisotropy_v3_zeta_semi_angle"], HextRec["anisotropy_v3_zeta_dec"], HextRec["anisotropy_v3_zeta_inc"])
HextRec['magic_software_packages'] = version_num
ResRecs.append(HextRec)
if bpars != []:
BootRec = {}
for key in ResRec.keys():
BootRec[key] = ResRec[key] # copy over stuff
BootRec["anisotropy_v1_dec"] = '%7.1f' % (bpars["v1_dec"])
BootRec["anisotropy_v2_dec"] = '%7.1f' % (bpars["v2_dec"])
BootRec["anisotropy_v3_dec"] = '%7.1f' % (bpars["v3_dec"])
BootRec["anisotropy_v1_inc"] = '%7.1f' % (bpars["v1_inc"])
BootRec["anisotropy_v2_inc"] = '%7.1f' % (bpars["v2_inc"])
BootRec["anisotropy_v3_inc"] = '%7.1f' % (bpars["v3_inc"])
BootRec["anisotropy_t1"] = '%10.8f' % (bpars["t1"])
BootRec["anisotropy_t2"] = '%10.8f' % (bpars["t2"])
BootRec["anisotropy_t3"] = '%10.8f' % (bpars["t3"])
BootRec["anisotropy_v1_eta_inc"] = '%7.1f ' % (
bpars["v1_eta_inc"])
BootRec["anisotropy_v1_eta_dec"] = '%7.1f ' % (
bpars["v1_eta_dec"])
BootRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % (
bpars["v1_eta"])
BootRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % (
bpars["v1_zeta_inc"])
BootRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % (
bpars["v1_zeta_dec"])
BootRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % (
bpars["v1_zeta"])
BootRec["anisotropy_v2_eta_inc"] = '%7.1f ' % (
bpars["v2_eta_inc"])
BootRec["anisotropy_v2_eta_dec"] = '%7.1f ' % (
bpars["v2_eta_dec"])
BootRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % (
bpars["v2_eta"])
BootRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % (
bpars["v2_zeta_inc"])
BootRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % (
bpars["v2_zeta_dec"])
BootRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % (
bpars["v2_zeta"])
BootRec["anisotropy_v3_eta_inc"] = '%7.1f ' % (
bpars["v3_eta_inc"])
BootRec["anisotropy_v3_eta_dec"] = '%7.1f ' % (
bpars["v3_eta_dec"])
BootRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % (
bpars["v3_eta"])
BootRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % (
bpars["v3_zeta_inc"])
BootRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % (
bpars["v3_zeta_dec"])
BootRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % (
bpars["v3_zeta"])
BootRec["anisotropy_hext_F"] = ''
BootRec["anisotropy_hext_F12"] = ''
BootRec["anisotropy_hext_F23"] = ''
# regular bootstrap
BootRec["magic_method_codes"] = 'LP-AN:AE-H:AE-BS'
if ipar == 1:
# parametric bootstrap
BootRec["magic_method_codes"] = 'LP-AN:AE-H:AE-BS-P'
if verbose:
print("Boostrap Statistics: ")
print(
" tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I")
print(BootRec["anisotropy_t1"], BootRec["anisotropy_v1_dec"], BootRec["anisotropy_v1_inc"], BootRec["anisotropy_v1_eta_semi_angle"], BootRec["anisotropy_v1_eta_dec"],
BootRec["anisotropy_v1_eta_inc"], BootRec["anisotropy_v1_zeta_semi_angle"], BootRec["anisotropy_v1_zeta_dec"], BootRec["anisotropy_v1_zeta_inc"])
print(BootRec["anisotropy_t2"], BootRec["anisotropy_v2_dec"], BootRec["anisotropy_v2_inc"], BootRec["anisotropy_v2_eta_semi_angle"], BootRec["anisotropy_v2_eta_dec"],
BootRec["anisotropy_v2_eta_inc"], BootRec["anisotropy_v2_zeta_semi_angle"], BootRec["anisotropy_v2_zeta_dec"], BootRec["anisotropy_v2_zeta_inc"])
print(BootRec["anisotropy_t3"], BootRec["anisotropy_v3_dec"], BootRec["anisotropy_v3_inc"], BootRec["anisotropy_v3_eta_semi_angle"], BootRec["anisotropy_v3_eta_dec"],
BootRec["anisotropy_v3_eta_inc"], BootRec["anisotropy_v3_zeta_semi_angle"], BootRec["anisotropy_v3_zeta_dec"], BootRec["anisotropy_v3_zeta_inc"])
BootRec['magic_software_packages'] = version_num
ResRecs.append(BootRec)
k += 1
goon = 1
while goon == 1 and iplot == 1 and verbose:
if iboot == 1:
print("compare with [d]irection ")
print(
" plot [g]reat circle, change [c]oord. system, change [e]llipse calculation, s[a]ve plots, [q]uit ")
if isite == 1:
print(" [p]revious, [s]ite, [q]uit, <return> for next ")
ans = input("")
if ans == "q":
sys.exit()
if ans == "e":
iboot, ipar, ihext, ivec = 1, 0, 0, 0
e = input("Do Hext Statistics 1/[0]: ")
if e == "1":
ihext = 1
e = input("Suppress bootstrap 1/[0]: ")
if e == "1":
iboot = 0
if iboot == 1:
e = input("Parametric bootstrap 1/[0]: ")
if e == "1":
ipar = 1
e = input("Plot bootstrap eigenvectors: 1/[0]: ")
if e == "1":
ivec = 1
if iplot == 1:
if inittcdf == 0:
ANIS['tcdf'] = 3
pmagplotlib.plot_init(ANIS['tcdf'], 5, 5)
inittcdf = 1
bpars, hpars = pmagplotlib.plot_anis(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb)
if verbose and plots == 0:
pmagplotlib.draw_figs(ANIS)
if ans == "c":
print("Current Coordinate system is: ")
if CS == '-1':
print(" Specimen")
if CS == '0':
print(" Geographic")
if CS == '100':
print(" Tilt corrected")
key = input(
" Enter desired coordinate system: [s]pecimen, [g]eographic, [t]ilt corrected ")
if key == 's':
CS = '-1'
if key == 'g':
CS = '0'
if key == 't':
CS = '100'
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = '-1'
if CS == '-1':
crd = 's'
if CS == '0':
crd = 'g'
if CS == '100':
crd = 't'
print(
"desired coordinate system not available, using available: ", crd)
k -= 1
goon = 0
if ans == "":
if isite == 1:
goon = 0
else:
print("Good bye ")
sys.exit()
if ans == 'd':
if initcdf == 0:
initcdf = 1
ANIS['vxcdf'], ANIS['vycdf'], ANIS['vzcdf'] = 4, 5, 6
pmagplotlib.plot_init(ANIS['vxcdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vycdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vzcdf'], 5, 5)
Dir, comp = [], 1
print("""
Input: Vi D I to compare eigenvector Vi with direction D/I
where Vi=1: principal
Vi=2: major
Vi=3: minor
D= declination of comparison direction
I= inclination of comparison direction""")
con = 1
while con == 1:
try:
vdi = input("Vi D I: ").split()
vec = int(vdi[0])-1
Dir = [float(vdi[1]), float(vdi[2])]
con = 0
except IndexError:
print(" Incorrect entry, try again ")
bpars, hpars = pmagplotlib.plot_anis(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb)
Dir, comp = [], 0
if ans == 'g':
con, cnt = 1, 0
while con == 1:
try:
print(
" Input: input pole to great circle ( D I) to plot a great circle: ")
di = input(" D I: ").split()
PDir.append(float(di[0]))
PDir.append(float(di[1]))
con = 0
except:
cnt += 1
if cnt < 10:
print(
" enter the dec and inc of the pole on one line ")
else:
print(
"ummm - you are doing something wrong - i give up")
sys.exit()
pmagplotlib.plot_circ(ANIS['data'], PDir, 90., 'g')
pmagplotlib.plot_circ(ANIS['conf'], PDir, 90., 'g')
if verbose and plots == 0:
pmagplotlib.draw_figs(ANIS)
if ans == "p":
k -= 2
goon = 0
if ans == "q":
k = plt
goon = 0
if ans == "s":
keepon = 1
site = input(" print site or part of site desired: ")
while keepon == 1:
try:
k = sitelist.index(site)
keepon = 0
except:
tmplist = []
for qq in range(len(sitelist)):
if site in sitelist[qq]:
tmplist.append(sitelist[qq])
print(site, " not found, but this was: ")
print(tmplist)
site = input('Select one or try again\n ')
k = sitelist.index(site)
goon, ans = 0, ""
if ans == "a":
locs = pmag.makelist(Locs)
if pmagplotlib.isServer: # use server plot naming convention
title = "LO:_"+locs+'_SI:__'+'_SA:__SP:__CO:_'+crd
else: # use more readable plot naming convention
title = "{}_{}".format(locs, crd)
save(ANIS, fmt, title)
goon = 0
else:
if verbose:
print('skipping plot - not enough data points')
k += 1
# put rmag_results stuff here
if len(ResRecs) > 0:
ResOut, keylist = pmag.fillkeys(ResRecs)
pmag.magic_write(outfile, ResOut, 'rmag_results')
if verbose:
print(" Good bye ")
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 main(command_line=True, **kwargs):
"""
NAME
iodp_srm_magic.py
DESCRIPTION
converts IODP LIMS and LORE SRM archive half sample format files to magic_measurements format files
SYNTAX
iodp_srm_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input .csv file, default is all in directory
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-A : don't average replicate measurements
INPUTS
IODP .csv file format exported from LIMS database
"""
#
# initialize defaults
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
csv_file=''
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
depth_method='a'
# get command line args
if command_line:
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
if "-h" in args:
print main.__doc__
return False
if "-A" in args: noave=1
if '-f' in args:
ind=args.index("-f")
csv_file=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 '-Fsi' in args:
ind=args.index("-Fsi")
site_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file = 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 # rename dir_path after input_dir_path is set
noave = kwargs.get('noave', 0) # default (0) is DO average
csv_file = kwargs.get('csv_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
spec_file = kwargs.get('spec_file', 'er_specimens.txt')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt')
# format variables
meas_file = os.path.join(output_dir_path, meas_file)
spec_file = os.path.join(output_dir_path, spec_file)
Specs,file_type = pmag.magic_read(spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
ErSamps,file_type = pmag.magic_read(samp_file)
site_file = os.path.join(output_dir_path, site_file)
if csv_file=="":
filelist=os.listdir(input_dir_path) # read in list of files to import
else:
csv_file = os.path.join(input_dir_path, csv_file)
filelist=[csv_file]
# parsing the data
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs,SiteRecs=[],[],[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
file_found = False
for f in filelist: # parse each file
if f[-3:].lower()=='csv':
file_found = True
print 'processing: ',f
full_file = os.path.join(input_dir_path, f)
file_input=open(full_file,'rU').readlines()
keys=file_input[0].replace('\n','').split(',') # splits on underscores
if "Interval Top (cm) on SHLF" in keys:interval_key="Interval Top (cm) on SHLF"
if " Interval Bot (cm) on SECT" in keys:interval_key=" Interval Bot (cm) on SECT"
if "Offset (cm)" in keys: interval_key="Offset (cm)"
if "Top Depth (m)" in keys:depth_key="Top Depth (m)"
if "CSF-A Top (m)" in keys:depth_key="CSF-A Top (m)"
if "Depth CSF-A (m)" in keys:depth_key="Depth CSF-A (m)"
if "CSF-B Top (m)" in keys:
comp_depth_key="CSF-B Top (m)" # use this model if available
elif "Depth CSF-B (m)" in keys:
comp_depth_key="Depth CSF-B (m)"
else:
comp_depth_key=""
if "Demag level (mT)" in keys:demag_key="Demag level (mT)"
if "Demag Level (mT)" in keys: demag_key="Demag Level (mT)"
if "Inclination (Tray- and Bkgrd-Corrected) (deg)" in keys:inc_key="Inclination (Tray- and Bkgrd-Corrected) (deg)"
if "Inclination background + tray corrected (deg)" in keys:inc_key="Inclination background + tray corrected (deg)"
if "Inclination background + tray corrected (\xc2\xb0)" in keys:inc_key="Inclination background + tray corrected (\xc2\xb0)"
if "Inclination background & tray corrected (deg)" in keys:inc_key="Inclination background & tray corrected (deg)"
if "Declination (Tray- and Bkgrd-Corrected) (deg)" in keys:dec_key="Declination (Tray- and Bkgrd-Corrected) (deg)"
if "Declination background + tray corrected (deg)" in keys:dec_key="Declination background + tray corrected (deg)"
if "Declination background + tray corrected (\xc2\xb0)" in keys:dec_key="Declination background + tray corrected (\xc2\xb0)"
if "Declination background & tray corrected (deg)" in keys:dec_key="Declination background & tray corrected (deg)"
if "Intensity (Tray- and Bkgrd-Corrected) (A/m)" in keys:int_key="Intensity (Tray- and Bkgrd-Corrected) (A/m)"
if "Intensity background + tray corrected (A/m)" in keys:int_key="Intensity background + tray corrected (A/m)"
if "Intensity background & tray corrected (A/m)" in keys:int_key="Intensity background & tray corrected (A/m)"
if "Core Type" in keys:
core_type="Core Type"
else: core_type="Type"
if 'Run Number' in keys: run_number_key='Run Number'
if 'Test No.' in keys: run_number_key='Test No.'
if 'Test Changed On' in keys: date_key='Test Changed On'
if "Timestamp (UTC)" in keys: date_key="Timestamp (UTC)"
if "Section" in keys: sect_key="Section"
if "Sect" in keys: sect_key="Sect"
if 'Section Half' in keys: half_key='Section Half'
if "A/W" in keys: half_key="A/W"
if "Text ID" in keys: text_id="Text ID"
if "Text Id" in keys: text_id="Text Id"
for line in file_input[1:]:
InRec={}
test=0
recs=line.split(',')
for k in range(len(keys)):
if len(recs)==len(keys):
InRec[keys[k]]=line.split(',')[k]
if InRec['Exp']!="": test=1 # get rid of pesky blank lines
if test==1:
run_number=""
inst="IODP-SRM"
volume='15.59' # set default volume to this
MagRec,SpecRec,SampRec,SiteRec={},{},{},{}
expedition=InRec['Exp']
location=InRec['Site']+InRec['Hole']
# Maintain backward compatibility for the ever-changing LIMS format (Argh!)
while len(InRec['Core'])<3:
InRec['Core']='0'+InRec['Core']
if "Last Tray Measurment" in InRec.keys() and "SHLF" not in InRec[text_id] or 'dscr' in csv_file : # assume discrete sample
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[core_type]+"-"+InRec[sect_key]+'-'+InRec[half_key]+'-'+str(InRec[interval_key])
else: # mark as continuous measurements
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[core_type]+"_"+InRec[sect_key]+InRec[half_key]+'-'+str(InRec[interval_key])
SpecRec['er_expedition_name']=expedition
SpecRec['er_location_name']=location
SpecRec['er_site_name']=specimen
SpecRec['er_citation_names']=citation
for key in SpecRec.keys():SampRec[key]=SpecRec[key]
for key in SpecRec.keys():SiteRec[key]=SpecRec[key]
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['sample_core_depth']=InRec[depth_key]
if comp_depth_key!='':
SampRec['sample_composite_depth']=InRec[comp_depth_key]
if "SHLF" not in InRec[text_id]:
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SP-SS-C:SO-V'
else:
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SO-V'
SpecRec['er_specimen_name']=specimen
SpecRec['er_sample_name']=specimen
SampRec['er_sample_name']=specimen
SampRec['er_specimen_names']=specimen
SiteRec['er_specimen_names']=specimen
for key in SpecRec.keys():MagRec[key]=SpecRec[key]
# set up measurement record - default is NRM
#MagRec['er_analyst_mail_names']=InRec['Test Entered By']
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'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
SpecRec['er_specimen_alternatives']=InRec[text_id]
if 'Sample Area (cm?)' in InRec.keys() and InRec['Sample Area (cm?)']!= "": volume=InRec['Sample Area (cm?)']
if InRec[run_number_key]!= "": run_number=InRec[run_number_key]
datestamp=InRec[date_key].split() # date time is second line of file
if '/' in datestamp[0]:
mmddyy=datestamp[0].split('/') # break into month day year
if len(mmddyy[0])==1: mmddyy[0]='0'+mmddyy[0] # make 2 characters
if len(mmddyy[1])==1: mmddyy[1]='0'+mmddyy[1] # make 2 characters
if len(datestamp[1])==1: datestamp[1]='0'+datestamp[1] # make 2 characters
date='20'+mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]+":00.00"
if '-' in datestamp[0]:
mmddyy=datestamp[0].split('-') # break into month day year
date=mmddyy[0]+':'+mmddyy[1]+":"+mmddyy[2] +':' +datestamp[1]+":00.00"
MagRec["measurement_date"]=date
MagRec["magic_method_codes"]='LT-NO'
if InRec[demag_key]!="0":
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':IODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
if 'Treatment Type' in InRec.keys() and InRec['Treatment Type']!="":
if 'Alternating Frequency' in InRec['Treatment Type']:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':I`ODP-DTECH' # measured on shipboard Dtech D2000
treatment_value=float(InRec['Treatment Value'])*1e-3 # convert mT => T
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
elif 'Thermal' in InRec['Treatment Type']:
MagRec['magic_method_codes'] = 'LT-T-Z'
inst=inst+':IODP-TDS' # measured on shipboard Schonstedt thermal demagnetizer
treatment_value=float(InRec['Treatment Value'])+273 # convert C => K
MagRec["treatment_temp"]='%8.3e'%(treatment_value) #
MagRec["measurement_standard"]='u' # assume all data are "good"
vol=float(volume)*1e-6 # convert from cc to m^3
if run_number!="":
MagRec['external_database_ids']=run_number
MagRec['external_database_names']='LIMS'
else:
MagRec['external_database_ids']=""
MagRec['external_database_names']=''
MagRec['measurement_inc']=InRec[inc_key].strip('"')
MagRec['measurement_dec']=InRec[dec_key].strip('"')
intens= InRec[int_key].strip('"')
MagRec['measurement_magn_moment']='%8.3e'%(float(intens)*vol) # convert intensity from A/m to Am^2 using vol
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
MagRec['measurement_csd']=''
MagRec['measurement_positions']=''
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
if MagRec['er_site_name'] not in sites:
sites.append(MagRec['er_site_name'])
SiteRecs.append(SiteRec)
#except:
# print 'Boo-boo somewhere - no idea where'
if not file_found:
print "No .csv files were found"
return False, "No .csv files were found"
if len(SpecRecs)>0:
print 'spec_file', spec_file
pmag.magic_write(spec_file,SpecRecs,'er_specimens')
#print 'specimens stored in ',spec_file
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
#print 'samples stored in ',samp_file
if len(SiteRecs)>0:
pmag.magic_write(site_file,SiteRecs,'er_sites')
#print 'sites stored in ',site_file
MagSort=pmag.sortbykeys(MagRecs,["er_specimen_name","treatment_ac_field"])
MagOuts=[]
for MagRec in MagSort:
MagRec["treatment_ac_field"]='%8.3e'%(MagRec['treatment_ac_field']) # convert to string
MagOuts.append(MagRec)
Fixed=pmag.measurements_methods(MagOuts,noave)
if pmag.magic_write(meas_file,Fixed,'magic_measurements'):
print 'data stored in ',meas_file
return True, meas_file
else:
print 'no data found. bad magfile?'
return False, 'no data found. bad magfile?'
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
aniso_magic.py
DESCRIPTION
plots anisotropy data with either bootstrap or hext ellipses
SYNTAX
aniso_magic.py [-h] [command line options]
OPTIONS
-h plots help message and quits
-usr USER: set the user name
-f AFILE, specify rmag_anisotropy formatted file for input
-F RFILE, specify rmag_results formatted file for output
-x Hext [1963] and bootstrap
-B DON'T do bootstrap, do Hext
-par Tauxe [1998] parametric bootstrap
-v plot bootstrap eigenvectors instead of ellipses
-sit plot by site instead of entire file
-crd [s,g,t] coordinate system, default is specimen (g=geographic, t=tilt corrected)
-P don't make any plots - just make rmag_results table
-sav don't make the rmag_results table - just save all the plots
-fmt [svg, jpg, eps] format for output images, pdf default
-gtc DEC INC dec,inc of pole to great circle [down(up) in green (cyan)
-d Vi DEC INC; Vi (1,2,3) to compare to direction DEC INC
-nb N; specifies the number of bootstraps - default is 1000
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
plot bootstrap ellipses of Constable & Tauxe [1987]
NOTES
minor axis: circles
major axis: triangles
principal axis: squares
directions are plotted on the lower hemisphere
for bootstrapped eigenvector components: Xs: blue, Ys: red, Zs: black
"""
#
dir_path = "."
version_num = pmag.get_version()
verbose = pmagplotlib.verbose
args = sys.argv
ipar, ihext, ivec, iboot, imeas, isite, iplot, vec = 0, 0, 0, 1, 1, 0, 1, 0
hpars, bpars, PDir = [], [], []
CS, crd = '-1', 's'
nb = 1000
fmt = 'pdf'
ResRecs = []
orlist = []
outfile, comp, Dir, gtcirc, PDir = 'rmag_results.txt', 0, [], 0, []
infile = 'rmag_anisotropy.txt'
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind + 1]
if '-nb' in args:
ind = args.index('-nb')
nb = int(args[ind + 1])
if '-usr' in args:
ind = args.index('-usr')
user = args[ind + 1]
else:
user = ""
if '-B' in args: iboot, ihext = 0, 1
if '-par' in args: ipar = 1
if '-x' in args: ihext = 1
if '-v' in args: ivec = 1
if '-sit' in args: isite = 1
if '-P' in args: iplot = 0
if '-f' in args:
ind = args.index('-f')
infile = args[ind + 1]
if '-F' in args:
ind = args.index('-F')
outfile = args[ind + 1]
if '-crd' in sys.argv:
ind = sys.argv.index('-crd')
crd = sys.argv[ind + 1]
if crd == 'g': CS = '0'
if crd == 't': CS = '100'
if '-fmt' in args:
ind = args.index('-fmt')
fmt = args[ind + 1]
if '-sav' in args:
plots = 1
verbose = 0
else:
plots = 0
if '-gtc' in args:
ind = args.index('-gtc')
d, i = float(args[ind + 1]), float(args[ind + 2])
PDir.append(d)
PDir.append(i)
if '-d' in args:
comp = 1
ind = args.index('-d')
vec = int(args[ind + 1]) - 1
Dir = [float(args[ind + 2]), float(args[ind + 3])]
#
# set up plots
#
if infile[0] != '/': infile = dir_path + '/' + infile
if outfile[0] != '/': outfile = dir_path + '/' + outfile
ANIS = {}
initcdf, inittcdf = 0, 0
ANIS['data'], ANIS['conf'] = 1, 2
if iboot == 1:
ANIS['tcdf'] = 3
if iplot == 1:
inittcdf = 1
pmagplotlib.plot_init(ANIS['tcdf'], 5, 5)
if comp == 1 and iplot == 1:
initcdf = 1
ANIS['vxcdf'], ANIS['vycdf'], ANIS['vzcdf'] = 4, 5, 6
pmagplotlib.plot_init(ANIS['vxcdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vycdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vzcdf'], 5, 5)
if iplot == 1:
pmagplotlib.plot_init(ANIS['conf'], 5, 5)
pmagplotlib.plot_init(ANIS['data'], 5, 5)
# read in the data
data, ifiletype = pmag.magic_read(infile)
for rec in data: # find all the orientation systems
if 'anisotropy_tilt_correction' not in rec.keys():
rec['anisotropy_tilt_correction'] = '-1'
if rec['anisotropy_tilt_correction'] not in orlist:
orlist.append(rec['anisotropy_tilt_correction'])
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = '-1'
if CS == '-1': crd = 's'
if CS == '0': crd = 'g'
if CS == '100': crd = 't'
if verbose:
print("desired coordinate system not available, using available: ",
crd)
if isite == 1:
sitelist = []
for rec in data:
if rec['er_site_name'] not in sitelist:
sitelist.append(rec['er_site_name'])
sitelist.sort()
plt = len(sitelist)
else:
plt = 1
k = 0
while k < plt:
site = ""
sdata, Ss = [], [] # list of S format data
Locs, Sites, Samples, Specimens, Cits = [], [], [], [], []
if isite == 0:
sdata = data
else:
site = sitelist[k]
for rec in data:
if rec['er_site_name'] == site: sdata.append(rec)
anitypes = []
csrecs = pmag.get_dictitem(sdata, 'anisotropy_tilt_correction', CS,
'T')
for rec in csrecs:
if rec['anisotropy_type'] not in anitypes:
anitypes.append(rec['anisotropy_type'])
if rec['er_location_name'] not in Locs:
Locs.append(rec['er_location_name'])
if rec['er_site_name'] not in Sites:
Sites.append(rec['er_site_name'])
if rec['er_sample_name'] not in Samples:
Samples.append(rec['er_sample_name'])
if rec['er_specimen_name'] not in Specimens:
Specimens.append(rec['er_specimen_name'])
if rec['er_citation_names'] not in Cits:
Cits.append(rec['er_citation_names'])
s = []
s.append(float(rec["anisotropy_s1"]))
s.append(float(rec["anisotropy_s2"]))
s.append(float(rec["anisotropy_s3"]))
s.append(float(rec["anisotropy_s4"]))
s.append(float(rec["anisotropy_s5"]))
s.append(float(rec["anisotropy_s6"]))
if s[0] <= 1.0: Ss.append(s) # protect against crap
#tau,Vdirs=pmag.doseigs(s)
ResRec = {}
ResRec['er_location_names'] = rec['er_location_name']
ResRec['er_citation_names'] = rec['er_citation_names']
ResRec['er_site_names'] = rec['er_site_name']
ResRec['er_sample_names'] = rec['er_sample_name']
ResRec['er_specimen_names'] = rec['er_specimen_name']
ResRec['rmag_result_name'] = rec['er_specimen_name'] + ":" + rec[
'anisotropy_type']
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
ResRec["anisotropy_type"] = rec['anisotropy_type']
if "anisotropy_n" not in rec.keys(): rec["anisotropy_n"] = "6"
if "anisotropy_sigma" not in rec.keys():
rec["anisotropy_sigma"] = "0"
fpars = pmag.dohext(
int(rec["anisotropy_n"]) - 6, float(rec["anisotropy_sigma"]),
s)
ResRec["anisotropy_v1_dec"] = '%7.1f' % (fpars['v1_dec'])
ResRec["anisotropy_v2_dec"] = '%7.1f' % (fpars['v2_dec'])
ResRec["anisotropy_v3_dec"] = '%7.1f' % (fpars['v3_dec'])
ResRec["anisotropy_v1_inc"] = '%7.1f' % (fpars['v1_inc'])
ResRec["anisotropy_v2_inc"] = '%7.1f' % (fpars['v2_inc'])
ResRec["anisotropy_v3_inc"] = '%7.1f' % (fpars['v3_inc'])
ResRec["anisotropy_t1"] = '%10.8f' % (fpars['t1'])
ResRec["anisotropy_t2"] = '%10.8f' % (fpars['t2'])
ResRec["anisotropy_t3"] = '%10.8f' % (fpars['t3'])
ResRec["anisotropy_ftest"] = '%10.3f' % (fpars['F'])
ResRec["anisotropy_ftest12"] = '%10.3f' % (fpars['F12'])
ResRec["anisotropy_ftest23"] = '%10.3f' % (fpars['F23'])
ResRec["result_description"] = 'F_crit: ' + fpars[
'F_crit'] + '; F12,F23_crit: ' + fpars['F12_crit']
ResRec['anisotropy_type'] = pmag.makelist(anitypes)
ResRecs.append(ResRec)
if len(Ss) > 1:
if pmagplotlib.isServer:
title = "LO:_" + ResRec[
'er_location_names'] + '_SI:_' + site + '_SA:__SP:__CO:_' + crd
else:
title = ResRec['er_location_names']
if site:
title += "_{}".format(site)
title += '_{}'.format(crd)
ResRec['er_location_names'] = pmag.makelist(Locs)
bpars, hpars = pmagplotlib.plotANIS(ANIS, Ss, iboot, ihext, ivec,
ipar, title, iplot, comp, vec,
Dir, nb)
if len(PDir) > 0:
pmagplotlib.plotC(ANIS['data'], PDir, 90., 'g')
pmagplotlib.plotC(ANIS['conf'], PDir, 90., 'g')
if verbose and plots == 0: pmagplotlib.drawFIGS(ANIS)
ResRec['er_location_names'] = pmag.makelist(Locs)
if plots == 1:
save(ANIS, fmt, title)
ResRec = {}
ResRec['er_citation_names'] = pmag.makelist(Cits)
ResRec['er_location_names'] = pmag.makelist(Locs)
ResRec['er_site_names'] = pmag.makelist(Sites)
ResRec['er_sample_names'] = pmag.makelist(Samples)
ResRec['er_specimen_names'] = pmag.makelist(Specimens)
ResRec['rmag_result_name'] = pmag.makelist(
Sites) + ":" + pmag.makelist(anitypes)
ResRec['anisotropy_type'] = pmag.makelist(anitypes)
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
if isite == "0":
ResRec[
'result_description'] = "Study average using coordinate system: " + CS
if isite == "1":
ResRec[
'result_description'] = "Site average using coordinate system: " + CS
if hpars != [] and ihext == 1:
HextRec = {}
for key in ResRec.keys():
HextRec[key] = ResRec[key] # copy over stuff
HextRec["anisotropy_v1_dec"] = '%7.1f' % (hpars["v1_dec"])
HextRec["anisotropy_v2_dec"] = '%7.1f' % (hpars["v2_dec"])
HextRec["anisotropy_v3_dec"] = '%7.1f' % (hpars["v3_dec"])
HextRec["anisotropy_v1_inc"] = '%7.1f' % (hpars["v1_inc"])
HextRec["anisotropy_v2_inc"] = '%7.1f' % (hpars["v2_inc"])
HextRec["anisotropy_v3_inc"] = '%7.1f' % (hpars["v3_inc"])
HextRec["anisotropy_t1"] = '%10.8f' % (hpars["t1"])
HextRec["anisotropy_t2"] = '%10.8f' % (hpars["t2"])
HextRec["anisotropy_t3"] = '%10.8f' % (hpars["t3"])
HextRec["anisotropy_hext_F"] = '%7.1f ' % (hpars["F"])
HextRec["anisotropy_hext_F12"] = '%7.1f ' % (hpars["F12"])
HextRec["anisotropy_hext_F23"] = '%7.1f ' % (hpars["F23"])
HextRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v1_eta_dec"] = '%7.1f ' % (hpars["v2_dec"])
HextRec["anisotropy_v1_eta_inc"] = '%7.1f ' % (hpars["v2_inc"])
HextRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % (
hpars["e13"])
HextRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % (
hpars["v3_dec"])
HextRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % (
hpars["v3_inc"])
HextRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v2_eta_dec"] = '%7.1f ' % (hpars["v1_dec"])
HextRec["anisotropy_v2_eta_inc"] = '%7.1f ' % (hpars["v1_inc"])
HextRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % (
hpars["e23"])
HextRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % (
hpars["v3_dec"])
HextRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % (
hpars["v3_inc"])
HextRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v3_eta_dec"] = '%7.1f ' % (hpars["v1_dec"])
HextRec["anisotropy_v3_eta_inc"] = '%7.1f ' % (hpars["v1_inc"])
HextRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % (
hpars["e23"])
HextRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % (
hpars["v2_dec"])
HextRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % (
hpars["v2_inc"])
HextRec["magic_method_codes"] = 'LP-AN:AE-H'
if verbose:
print("Hext Statistics: ")
print(
" tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
)
print(HextRec["anisotropy_t1"],
HextRec["anisotropy_v1_dec"],
HextRec["anisotropy_v1_inc"],
HextRec["anisotropy_v1_eta_semi_angle"],
HextRec["anisotropy_v1_eta_dec"],
HextRec["anisotropy_v1_eta_inc"],
HextRec["anisotropy_v1_zeta_semi_angle"],
HextRec["anisotropy_v1_zeta_dec"],
HextRec["anisotropy_v1_zeta_inc"])
print(HextRec["anisotropy_t2"],
HextRec["anisotropy_v2_dec"],
HextRec["anisotropy_v2_inc"],
HextRec["anisotropy_v2_eta_semi_angle"],
HextRec["anisotropy_v2_eta_dec"],
HextRec["anisotropy_v2_eta_inc"],
HextRec["anisotropy_v2_zeta_semi_angle"],
HextRec["anisotropy_v2_zeta_dec"],
HextRec["anisotropy_v2_zeta_inc"])
print(HextRec["anisotropy_t3"],
HextRec["anisotropy_v3_dec"],
HextRec["anisotropy_v3_inc"],
HextRec["anisotropy_v3_eta_semi_angle"],
HextRec["anisotropy_v3_eta_dec"],
HextRec["anisotropy_v3_eta_inc"],
HextRec["anisotropy_v3_zeta_semi_angle"],
HextRec["anisotropy_v3_zeta_dec"],
HextRec["anisotropy_v3_zeta_inc"])
HextRec['magic_software_packages'] = version_num
ResRecs.append(HextRec)
if bpars != []:
BootRec = {}
for key in ResRec.keys():
BootRec[key] = ResRec[key] # copy over stuff
BootRec["anisotropy_v1_dec"] = '%7.1f' % (bpars["v1_dec"])
BootRec["anisotropy_v2_dec"] = '%7.1f' % (bpars["v2_dec"])
BootRec["anisotropy_v3_dec"] = '%7.1f' % (bpars["v3_dec"])
BootRec["anisotropy_v1_inc"] = '%7.1f' % (bpars["v1_inc"])
BootRec["anisotropy_v2_inc"] = '%7.1f' % (bpars["v2_inc"])
BootRec["anisotropy_v3_inc"] = '%7.1f' % (bpars["v3_inc"])
BootRec["anisotropy_t1"] = '%10.8f' % (bpars["t1"])
BootRec["anisotropy_t2"] = '%10.8f' % (bpars["t2"])
BootRec["anisotropy_t3"] = '%10.8f' % (bpars["t3"])
BootRec["anisotropy_v1_eta_inc"] = '%7.1f ' % (
bpars["v1_eta_inc"])
BootRec["anisotropy_v1_eta_dec"] = '%7.1f ' % (
bpars["v1_eta_dec"])
BootRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % (
bpars["v1_eta"])
BootRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % (
bpars["v1_zeta_inc"])
BootRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % (
bpars["v1_zeta_dec"])
BootRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % (
bpars["v1_zeta"])
BootRec["anisotropy_v2_eta_inc"] = '%7.1f ' % (
bpars["v2_eta_inc"])
BootRec["anisotropy_v2_eta_dec"] = '%7.1f ' % (
bpars["v2_eta_dec"])
BootRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % (
bpars["v2_eta"])
BootRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % (
bpars["v2_zeta_inc"])
BootRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % (
bpars["v2_zeta_dec"])
BootRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % (
bpars["v2_zeta"])
BootRec["anisotropy_v3_eta_inc"] = '%7.1f ' % (
bpars["v3_eta_inc"])
BootRec["anisotropy_v3_eta_dec"] = '%7.1f ' % (
bpars["v3_eta_dec"])
BootRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % (
bpars["v3_eta"])
BootRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % (
bpars["v3_zeta_inc"])
BootRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % (
bpars["v3_zeta_dec"])
BootRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % (
bpars["v3_zeta"])
BootRec["anisotropy_hext_F"] = ''
BootRec["anisotropy_hext_F12"] = ''
BootRec["anisotropy_hext_F23"] = ''
BootRec[
"magic_method_codes"] = 'LP-AN:AE-H:AE-BS' # regular bootstrap
if ipar == 1:
BootRec[
"magic_method_codes"] = 'LP-AN:AE-H:AE-BS-P' # parametric bootstrap
if verbose:
print("Boostrap Statistics: ")
print(
" tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
)
print(BootRec["anisotropy_t1"],
BootRec["anisotropy_v1_dec"],
BootRec["anisotropy_v1_inc"],
BootRec["anisotropy_v1_eta_semi_angle"],
BootRec["anisotropy_v1_eta_dec"],
BootRec["anisotropy_v1_eta_inc"],
BootRec["anisotropy_v1_zeta_semi_angle"],
BootRec["anisotropy_v1_zeta_dec"],
BootRec["anisotropy_v1_zeta_inc"])
print(BootRec["anisotropy_t2"],
BootRec["anisotropy_v2_dec"],
BootRec["anisotropy_v2_inc"],
BootRec["anisotropy_v2_eta_semi_angle"],
BootRec["anisotropy_v2_eta_dec"],
BootRec["anisotropy_v2_eta_inc"],
BootRec["anisotropy_v2_zeta_semi_angle"],
BootRec["anisotropy_v2_zeta_dec"],
BootRec["anisotropy_v2_zeta_inc"])
print(BootRec["anisotropy_t3"],
BootRec["anisotropy_v3_dec"],
BootRec["anisotropy_v3_inc"],
BootRec["anisotropy_v3_eta_semi_angle"],
BootRec["anisotropy_v3_eta_dec"],
BootRec["anisotropy_v3_eta_inc"],
BootRec["anisotropy_v3_zeta_semi_angle"],
BootRec["anisotropy_v3_zeta_dec"],
BootRec["anisotropy_v3_zeta_inc"])
BootRec['magic_software_packages'] = version_num
ResRecs.append(BootRec)
k += 1
goon = 1
while goon == 1 and iplot == 1 and verbose:
if iboot == 1: print("compare with [d]irection ")
print(
" plot [g]reat circle, change [c]oord. system, change [e]llipse calculation, s[a]ve plots, [q]uit "
)
if isite == 1:
print(" [p]revious, [s]ite, [q]uit, <return> for next ")
ans = input("")
if ans == "q":
sys.exit()
if ans == "e":
iboot, ipar, ihext, ivec = 1, 0, 0, 0
e = input("Do Hext Statistics 1/[0]: ")
if e == "1": ihext = 1
e = input("Suppress bootstrap 1/[0]: ")
if e == "1": iboot = 0
if iboot == 1:
e = input("Parametric bootstrap 1/[0]: ")
if e == "1": ipar = 1
e = input("Plot bootstrap eigenvectors: 1/[0]: ")
if e == "1": ivec = 1
if iplot == 1:
if inittcdf == 0:
ANIS['tcdf'] = 3
pmagplotlib.plot_init(ANIS['tcdf'], 5, 5)
inittcdf = 1
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp,
vec, Dir, nb)
if verbose and plots == 0: pmagplotlib.drawFIGS(ANIS)
if ans == "c":
print("Current Coordinate system is: ")
if CS == '-1': print(" Specimen")
if CS == '0': print(" Geographic")
if CS == '100': print(" Tilt corrected")
key = input(
" Enter desired coordinate system: [s]pecimen, [g]eographic, [t]ilt corrected "
)
if key == 's': CS = '-1'
if key == 'g': CS = '0'
if key == 't': CS = '100'
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = '-1'
if CS == '-1': crd = 's'
if CS == '0': crd = 'g'
if CS == '100': crd = 't'
print(
"desired coordinate system not available, using available: ",
crd)
k -= 1
goon = 0
if ans == "":
if isite == 1:
goon = 0
else:
print("Good bye ")
sys.exit()
if ans == 'd':
if initcdf == 0:
initcdf = 1
ANIS['vxcdf'], ANIS['vycdf'], ANIS['vzcdf'] = 4, 5, 6
pmagplotlib.plot_init(ANIS['vxcdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vycdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vzcdf'], 5, 5)
Dir, comp = [], 1
print("""
Input: Vi D I to compare eigenvector Vi with direction D/I
where Vi=1: principal
Vi=2: major
Vi=3: minor
D= declination of comparison direction
I= inclination of comparison direction""")
con = 1
while con == 1:
try:
vdi = input("Vi D I: ").split()
vec = int(vdi[0]) - 1
Dir = [float(vdi[1]), float(vdi[2])]
con = 0
except IndexError:
print(" Incorrect entry, try again ")
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp,
vec, Dir, nb)
Dir, comp = [], 0
if ans == 'g':
con, cnt = 1, 0
while con == 1:
try:
print(
" Input: input pole to great circle ( D I) to plot a great circle: "
)
di = input(" D I: ").split()
PDir.append(float(di[0]))
PDir.append(float(di[1]))
con = 0
except:
cnt += 1
if cnt < 10:
print(
" enter the dec and inc of the pole on one line "
)
else:
print(
"ummm - you are doing something wrong - i give up"
)
sys.exit()
pmagplotlib.plotC(ANIS['data'], PDir, 90., 'g')
pmagplotlib.plotC(ANIS['conf'], PDir, 90., 'g')
if verbose and plots == 0: pmagplotlib.drawFIGS(ANIS)
if ans == "p":
k -= 2
goon = 0
if ans == "q":
k = plt
goon = 0
if ans == "s":
keepon = 1
site = input(" print site or part of site desired: ")
while keepon == 1:
try:
k = sitelist.index(site)
keepon = 0
except:
tmplist = []
for qq in range(len(sitelist)):
if site in sitelist[qq]:
tmplist.append(sitelist[qq])
print(site, " not found, but this was: ")
print(tmplist)
site = input('Select one or try again\n ')
k = sitelist.index(site)
goon, ans = 0, ""
if ans == "a":
locs = pmag.makelist(Locs)
if pmagplotlib.isServer: # use server plot naming convention
title = "LO:_" + locs + '_SI:__' + '_SA:__SP:__CO:_' + crd
else: # use more readable plot naming convention
title = "{}_{}".format(locs, crd)
save(ANIS, fmt, title)
goon = 0
else:
if verbose: print('skipping plot - not enough data points')
k += 1
# put rmag_results stuff here
if len(ResRecs) > 0:
ResOut, keylist = pmag.fillkeys(ResRecs)
pmag.magic_write(outfile, ResOut, 'rmag_results')
if verbose:
print(" Good bye ")
def main():
"""
NAME
replace_AC_specimens.py
DESCRIPTION
finds anisotropy corrected data and
replaces that specimen with it.
puts in pmag_specimen format file
SYNTAX
replace_AC_specimens.py [command line options]
OPTIONS
-h prints help message and quits
-i allows interactive setting of file names
-fu TFILE uncorrected pmag_specimen format file with thellier interpretations
created by thellier_magic_redo.py
-fc AFILE anisotropy corrected pmag_specimen format file
created by thellier_magic_redo.py
-F FILE pmag_specimens format output file
DEFAULTS
TFILE: thellier_specimens.txt
AFILE: AC_specimens.txt
FILE: TorAC_specimens.txt
"""
dir_path='.'
tspec="thellier_specimens.txt"
aspec="AC_specimens.txt"
ofile="TorAC_specimens.txt"
critfile="pmag_criteria.txt"
ACSamplist,Samplist,sigmin=[],[],10000
GoodSamps,SpecOuts=[],[]
# get arguments from command line
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-fu' in sys.argv:
ind=sys.argv.index('-fu')
tspec=sys.argv[ind+1]
if '-fc' in sys.argv:
ind=sys.argv.index('-fc')
aspec=sys.argv[ind+1]
if '-F' in sys.argv:
ind=sys.argv.index('-F')
ofile=sys.argv[ind+1]
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
# read in pmag_specimens file
tspec=dir_path+'/'+tspec
aspec=dir_path+'/'+aspec
ofile=dir_path+'/'+ofile
Specs,file_type=pmag.magic_read(tspec)
Specs,file_type=pmag.magic_read(tspec)
Speclist=pmag.get_specs(Specs)
ACSpecs,file_type=pmag.magic_read(aspec)
ACspeclist=pmag.get_specs(ACSpecs)
for spec in Specs:
if spec["er_sample_name"] not in Samplist:Samplist.append(spec["er_sample_name"])
for spec in ACSpecs:
if spec["er_sample_name"] not in ACSamplist:ACSamplist.append(spec["er_sample_name"])
#
for samp in Samplist:
useAC,Ints,ACInts,GoodSpecs,AC,UC=0,[],[],[],[],[]
for spec in Specs:
if spec["er_sample_name"].lower()==samp.lower():
UC.append(spec)
if samp in ACSamplist:
for spec in ACSpecs:
if spec["er_sample_name"].lower()==samp.lower():
AC.append(spec)
if len(AC)>0:
AClist=[]
for spec in AC:
SpecOuts.append(spec)
AClist.append(spec['er_specimen_name'])
print('using AC: ',spec['er_specimen_name'],'%7.1f'%(1e6*float(spec['specimen_int'])))
for spec in UC:
if spec['er_specimen_name'] not in AClist:
SpecOuts.append(spec)
# print 'using UC: ',spec['er_specimen_name'],'%7.1f'%(1e6*float(spec['specimen_int']))
else:
for spec in UC:
SpecOuts.append(spec)
# print 'using UC: ',spec['er_specimen_name'],'%7.1f'%(1e6*float(spec['specimen_int']))
SpecOuts,keys=pmag.fillkeys(SpecOuts)
pmag.magic_write(ofile,SpecOuts,'pmag_specimens')
print('thellier data assessed for AC correction put in ', ofile)
def main():
"""
NAME
specimens_results_magic.py
DESCRIPTION
combines pmag_specimens.txt file with age, location, acceptance criteria and
outputs pmag_results table along with other MagIC tables necessary for uploading to the database
SYNTAX
specimens_results_magic.py [command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f: specimen input magic_measurements format file, default is "magic_measurements.txt"
-fsp: specimen input pmag_specimens format file, default is "pmag_specimens.txt"
-fsm: sample input er_samples format file, default is "er_samples.txt"
-fsi: specimen input er_sites format file, default is "er_sites.txt"
-fla: specify a file with paleolatitudes for calculating VADMs, default is not to calculate VADMS
format is: site_name paleolatitude (space delimited file)
-fa AGES: specify er_ages format file with age information
-crd [s,g,t,b]: specify coordinate system
(s, specimen, g geographic, t, tilt corrected, b, geographic and tilt corrected)
Default is to assume geographic
NB: only the tilt corrected data will appear on the results table, if both g and t are selected.
-cor [AC:CR:NL]: colon delimited list of required data adjustments for all specimens
included in intensity calculations (anisotropy, cooling rate, non-linear TRM)
unless specified, corrections will not be applied
-pri [TRM:ARM] colon delimited list of priorities for anisotropy correction (-cor must also be set to include AC). default is TRM, then ARM
-age MIN MAX UNITS: specify age boundaries and units
-exc: use exiting selection criteria (in pmag_criteria.txt file), default is default criteria
-C: no acceptance criteria
-aD: average directions per sample, default is NOT
-aI: average multiple specimen intensities per sample, default is by site
-aC: average all components together, default is NOT
-pol: calculate polarity averages
-sam: save sample level vgps and v[a]dms, default is by site
-xSi: skip the site level intensity calculation
-p: plot directions and look at intensities by site, default is NOT
-fmt: specify output for saved images, default is svg (only if -p set)
-lat: use present latitude for calculating VADMs, default is not to calculate VADMs
-xD: skip directions
-xI: skip intensities
OUPUT
writes pmag_samples, pmag_sites, pmag_results tables
"""
# set defaults
Comps = [] # list of components
version_num = pmag.get_version()
args = sys.argv
DefaultAge = ["none"]
skipdirs, coord, excrit, custom, vgps, average, Iaverage, plotsites, opt = 1, 0, 0, 0, 0, 0, 0, 0, 0
get_model_lat = 0 # this skips VADM calculation altogether, when get_model_lat=1, uses present day
fmt = 'svg'
dir_path = "."
model_lat_file = ""
Caverage = 0
infile = 'pmag_specimens.txt'
measfile = "magic_measurements.txt"
sampfile = "er_samples.txt"
sitefile = "er_sites.txt"
agefile = "er_ages.txt"
specout = "er_specimens.txt"
sampout = "pmag_samples.txt"
siteout = "pmag_sites.txt"
resout = "pmag_results.txt"
critout = "pmag_criteria.txt"
instout = "magic_instruments.txt"
sigcutoff, OBJ = "", ""
noDir, noInt = 0, 0
polarity = 0
coords = ['0']
Dcrit, Icrit, nocrit = 0, 0, 0
corrections = []
nocorrection = ['DA-NL', 'DA-AC', 'DA-CR']
priorities = ['DA-AC-ARM',
'DA-AC-TRM'] # priorities for anisotropy correction
# get command line stuff
if "-h" in args:
print main.__doc__
sys.exit()
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if '-cor' in args:
ind = args.index('-cor')
cors = args[ind + 1].split(':') # list of required data adjustments
for cor in cors:
nocorrection.remove('DA-' + cor)
corrections.append('DA-' + cor)
if '-pri' in args:
ind = args.index('-pri')
priorities = args[ind + 1].split(
':') # list of required data adjustments
for p in priorities:
p = 'DA-AC-' + p
if '-f' in args:
ind = args.index("-f")
measfile = args[ind + 1]
if '-fsp' in args:
ind = args.index("-fsp")
infile = args[ind + 1]
if '-fsi' in args:
ind = args.index("-fsi")
sitefile = args[ind + 1]
if "-crd" in args:
ind = args.index("-crd")
coord = args[ind + 1]
if coord == 's': coords = ['-1']
if coord == 'g': coords = ['0']
if coord == 't': coords = ['100']
if coord == 'b': coords = ['0', '100']
if "-usr" in args:
ind = args.index("-usr")
user = sys.argv[ind + 1]
else:
user = ""
if "-C" in args: Dcrit, Icrit, nocrit = 1, 1, 1 # no selection criteria
if "-sam" in args: vgps = 1 # save sample level VGPS/VADMs
if "-xSi" in args:
nositeints = 1 # skip site level intensity
else:
nositeints = 0
if "-age" in args:
ind = args.index("-age")
DefaultAge[0] = args[ind + 1]
DefaultAge.append(args[ind + 2])
DefaultAge.append(args[ind + 3])
Daverage, Iaverage, Caverage = 0, 0, 0
if "-aD" in args: Daverage = 1 # average by sample directions
if "-aI" in args: Iaverage = 1 # average by sample intensities
if "-aC" in args:
Caverage = 1 # average all components together ??? why???
if "-pol" in args: polarity = 1 # calculate averages by polarity
if '-xD' in args: noDir = 1
if '-xI' in args:
noInt = 1
elif "-fla" in args:
if '-lat' in args:
print "you should set a paleolatitude file OR use present day lat - not both"
sys.exit()
ind = args.index("-fla")
model_lat_file = dir_path + '/' + args[ind + 1]
get_model_lat = 2
mlat = open(model_lat_file, 'rU')
ModelLats = []
for line in mlat.readlines():
ModelLat = {}
tmp = line.split()
ModelLat["er_site_name"] = tmp[0]
ModelLat["site_model_lat"] = tmp[1]
ModelLat["er_sample_name"] = tmp[0]
ModelLat["sample_lat"] = tmp[1]
ModelLats.append(ModelLat)
get_model_lat = 2
elif '-lat' in args:
get_model_lat = 1
if "-p" in args:
plotsites = 1
if "-fmt" in args:
ind = args.index("-fmt")
fmt = args[ind + 1]
if noDir == 0: # plot by site - set up plot window
import pmagplotlib
EQ = {}
EQ['eqarea'] = 1
pmagplotlib.plot_init(
EQ['eqarea'], 5, 5) # define figure 1 as equal area projection
pmagplotlib.plotNET(
EQ['eqarea']
) # I don't know why this has to be here, but otherwise the first plot never plots...
pmagplotlib.drawFIGS(EQ)
if '-WD' in args:
infile = dir_path + '/' + infile
measfile = dir_path + '/' + measfile
instout = dir_path + '/' + instout
sampfile = dir_path + '/' + sampfile
sitefile = dir_path + '/' + sitefile
agefile = dir_path + '/' + agefile
specout = dir_path + '/' + specout
sampout = dir_path + '/' + sampout
siteout = dir_path + '/' + siteout
resout = dir_path + '/' + resout
critout = dir_path + '/' + critout
if "-exc" in args: # use existing pmag_criteria file
if "-C" in args:
print 'you can not use both existing and no criteria - choose either -exc OR -C OR neither (for default)'
sys.exit()
crit_data, file_type = pmag.magic_read(critout)
print "Acceptance criteria read in from ", critout
else: # use default criteria (if nocrit set, then get really loose criteria as default)
crit_data = pmag.default_criteria(nocrit)
if nocrit == 0:
print "Acceptance criteria are defaults"
else:
print "No acceptance criteria used "
accept = {}
for critrec in crit_data:
for key in critrec.keys():
# need to migrate specimen_dang to specimen_int_dang for intensity data using old format
if 'IE-SPEC' in critrec.keys() and 'specimen_dang' in critrec.keys(
) and 'specimen_int_dang' not in critrec.keys():
critrec['specimen_int_dang'] = critrec['specimen_dang']
del critrec['specimen_dang']
# need to get rid of ron shaars sample_int_sigma_uT
if 'sample_int_sigma_uT' in critrec.keys():
critrec['sample_int_sigma'] = '%10.3e' % (
eval(critrec['sample_int_sigma_uT']) * 1e-6)
if key not in accept.keys() and critrec[key] != '':
accept[key] = critrec[key]
#
#
if "-exc" not in args and "-C" not in args:
print "args", args
pmag.magic_write(critout, [accept], 'pmag_criteria')
print "\n Pmag Criteria stored in ", critout, '\n'
#
# now we're done slow dancing
#
SiteNFO, file_type = pmag.magic_read(
sitefile) # read in site data - has the lats and lons
SampNFO, file_type = pmag.magic_read(
sampfile) # read in site data - has the lats and lons
height_nfo = pmag.get_dictitem(SiteNFO, 'site_height', '',
'F') # find all the sites with height info.
if agefile != "":
AgeNFO, file_type = pmag.magic_read(
agefile) # read in the age information
Data, file_type = pmag.magic_read(
infile) # read in specimen interpretations
IntData = pmag.get_dictitem(Data, 'specimen_int', '',
'F') # retrieve specimens with intensity data
comment, orient = "", []
samples, sites = [], []
for rec in Data: # run through the data filling in missing keys and finding all components, coordinates available
# fill in missing fields, collect unique sample and site names
if 'er_sample_name' not in rec.keys():
rec['er_sample_name'] = ""
elif rec['er_sample_name'] not in samples:
samples.append(rec['er_sample_name'])
if 'er_site_name' not in rec.keys():
rec['er_site_name'] = ""
elif rec['er_site_name'] not in sites:
sites.append(rec['er_site_name'])
if 'specimen_int' not in rec.keys(): rec['specimen_int'] = ''
if 'specimen_comp_name' not in rec.keys(
) or rec['specimen_comp_name'] == "":
rec['specimen_comp_name'] = 'A'
if rec['specimen_comp_name'] not in Comps:
Comps.append(rec['specimen_comp_name'])
rec['specimen_tilt_correction'] = rec[
'specimen_tilt_correction'].strip('\n')
if "specimen_tilt_correction" not in rec.keys():
rec["specimen_tilt_correction"] = "-1" # assume sample coordinates
if rec["specimen_tilt_correction"] not in orient:
orient.append(rec["specimen_tilt_correction"]
) # collect available coordinate systems
if "specimen_direction_type" not in rec.keys():
rec["specimen_direction_type"] = 'l' # assume direction is line - not plane
if "specimen_dec" not in rec.keys():
rec["specimen_direction_type"] = '' # if no declination, set direction type to blank
if "specimen_n" not in rec.keys(): rec["specimen_n"] = '' # put in n
if "specimen_alpha95" not in rec.keys():
rec["specimen_alpha95"] = '' # put in alpha95
if "magic_method_codes" not in rec.keys():
rec["magic_method_codes"] = ''
#
# start parsing data into SpecDirs, SpecPlanes, SpecInts
SpecInts, SpecDirs, SpecPlanes = [], [], []
samples.sort() # get sorted list of samples and sites
sites.sort()
if noInt == 0: # don't skip intensities
IntData = pmag.get_dictitem(
Data, 'specimen_int', '',
'F') # retrieve specimens with intensity data
if nocrit == 0: # use selection criteria
for rec in IntData: # do selection criteria
kill = pmag.grade(rec, accept, 'specimen_int')
if len(kill) == 0:
SpecInts.append(
rec
) # intensity record to be included in sample, site calculations
else:
SpecInts = IntData[:] # take everything - no selection criteria
# check for required data adjustments
if len(corrections) > 0 and len(SpecInts) > 0:
for cor in corrections:
SpecInts = pmag.get_dictitem(
SpecInts, 'magic_method_codes', cor,
'has') # only take specimens with the required corrections
if len(nocorrection) > 0 and len(SpecInts) > 0:
for cor in nocorrection:
SpecInts = pmag.get_dictitem(
SpecInts, 'magic_method_codes', cor, 'not'
) # exclude the corrections not specified for inclusion
# take top priority specimen of its name in remaining specimens (only one per customer)
PrioritySpecInts = []
specimens = pmag.get_specs(SpecInts) # get list of uniq specimen names
for spec in specimens:
ThisSpecRecs = pmag.get_dictitem(
SpecInts, 'er_specimen_name', spec,
'T') # all the records for this specimen
if len(ThisSpecRecs) == 1:
PrioritySpecInts.append(ThisSpecRecs[0])
elif len(ThisSpecRecs) > 1: # more than one
prec = []
for p in priorities:
ThisSpecRecs = pmag.get_dictitem(
SpecInts, 'magic_method_codes', p,
'has') # all the records for this specimen
if len(ThisSpecRecs) > 0: prec.append(ThisSpecRecs[0])
PrioritySpecInts.append(prec[0]) # take the best one
SpecInts = PrioritySpecInts # this has the first specimen record
if noDir == 0: # don't skip directions
AllDirs = pmag.get_dictitem(
Data, 'specimen_direction_type', '',
'F') # retrieve specimens with directed lines and planes
Ns = pmag.get_dictitem(
AllDirs, 'specimen_n', '',
'F') # get all specimens with specimen_n information
if nocrit != 1: # use selection criteria
for rec in Ns: # look through everything with specimen_n for "good" data
kill = pmag.grade(rec, accept, 'specimen_dir')
if len(kill) == 0: # nothing killed it
SpecDirs.append(rec)
else: # no criteria
SpecDirs = AllDirs[:] # take them all
# SpecDirs is now the list of all specimen directions (lines and planes) that pass muster
#
PmagSamps, SampDirs = [], [
] # list of all sample data and list of those that pass the DE-SAMP criteria
PmagSites, PmagResults = [], [
] # list of all site data and selected results
SampInts = []
for samp in samples: # run through the sample names
if Daverage == 1: # average by sample if desired
SampDir = pmag.get_dictitem(
SpecDirs, 'er_sample_name', samp,
'T') # get all the directional data for this sample
if len(SampDir) > 0: # there are some directions
for coord in coords: # step through desired coordinate systems
CoordDir = pmag.get_dictitem(
SampDir, 'specimen_tilt_correction', coord,
'T') # get all the directions for this sample
if len(CoordDir
) > 0: # there are some with this coordinate system
if Caverage == 0: # look component by component
for comp in Comps:
CompDir = pmag.get_dictitem(
CoordDir, 'specimen_comp_name', comp, 'T'
) # get all directions from this component
if len(CompDir) > 0: # there are some
PmagSampRec = pmag.lnpbykey(
CompDir, 'sample', 'specimen'
) # get a sample average from all specimens
PmagSampRec["er_location_name"] = CompDir[0][
'er_location_name'] # decorate the sample record
PmagSampRec["er_site_name"] = CompDir[0][
'er_site_name']
PmagSampRec["er_sample_name"] = samp
PmagSampRec[
"er_citation_names"] = "This study"
PmagSampRec["er_analyst_mail_names"] = user
PmagSampRec[
'magic_software_packages'] = version_num
if nocrit != 1:
PmagSampRec[
'pmag_criteria_codes'] = "ACCEPT"
if agefile != "":
PmagSampRec = pmag.get_age(
PmagSampRec, "er_site_name",
"sample_inferred_", AgeNFO,
DefaultAge)
site_height = pmag.get_dictitem(
height_nfo, 'er_site_name',
PmagSampRec['er_site_name'], 'T')
if len(site_height) > 0:
PmagSampRec[
"sample_height"] = site_height[0][
'site_height'] # add in height if available
PmagSampRec['sample_comp_name'] = comp
PmagSampRec[
'sample_tilt_correction'] = coord
PmagSampRec[
'er_specimen_names'] = pmag.get_list(
CompDir, 'er_specimen_name'
) # get a list of the specimen names used
PmagSampRec[
'magic_method_codes'] = pmag.get_list(
CompDir, 'magic_method_codes'
) # get a list of the methods used
if nocrit != 1: # apply selection criteria
kill = pmag.grade(
PmagSampRec, accept, 'sample_dir')
else:
kill = []
if len(kill) == 0:
SampDirs.append(PmagSampRec)
if vgps == 1: # if sample level VGP info desired, do that now
PmagResRec = pmag.getsampVGP(
PmagSampRec, SiteNFO)
if PmagResRec != "":
PmagResults.append(PmagResRec)
PmagSamps.append(PmagSampRec)
if Caverage == 1: # average all components together basically same as above
PmagSampRec = pmag.lnpbykey(
CoordDir, 'sample', 'specimen')
PmagSampRec["er_location_name"] = CoordDir[0][
'er_location_name']
PmagSampRec["er_site_name"] = CoordDir[0][
'er_site_name']
PmagSampRec["er_sample_name"] = samp
PmagSampRec["er_citation_names"] = "This study"
PmagSampRec["er_analyst_mail_names"] = user
PmagSampRec[
'magic_software_packages'] = version_num
if nocrit != 1:
PmagSampRec['pmag_criteria_codes'] = ""
if agefile != "":
PmagSampRec = pmag.get_age(
PmagSampRec, "er_site_name",
"sample_inferred_", AgeNFO, DefaultAge)
site_height = pmag.get_dictitem(
height_nfo, 'er_site_name', site, 'T')
if len(site_height) > 0:
PmagSampRec["sample_height"] = site_height[0][
'site_height'] # add in height if available
PmagSampRec['sample_tilt_correction'] = coord
PmagSampRec['sample_comp_name'] = pmag.get_list(
CoordDir,
'specimen_comp_name') # get components used
PmagSampRec['er_specimen_names'] = pmag.get_list(
CoordDir, 'er_specimen_name'
) # get specimne names averaged
PmagSampRec['magic_method_codes'] = pmag.get_list(
CoordDir,
'magic_method_codes') # assemble method codes
if nocrit != 1: # apply selection criteria
kill = pmag.grade(PmagSampRec, accept,
'sample_dir')
if len(kill) == 0: # passes the mustard
SampDirs.append(PmagSampRec)
if vgps == 1:
PmagResRec = pmag.getsampVGP(
PmagSampRec, SiteNFO)
if PmagResRec != "":
PmagResults.append(PmagResRec)
else: # take everything
SampDirs.append(PmagSampRec)
if vgps == 1:
PmagResRec = pmag.getsampVGP(
PmagSampRec, SiteNFO)
if PmagResRec != "":
PmagResults.append(PmagResRec)
PmagSamps.append(PmagSampRec)
if Iaverage == 1: # average by sample if desired
SampI = pmag.get_dictitem(
SpecInts, 'er_sample_name', samp,
'T') # get all the intensity data for this sample
if len(SampI) > 0: # there are some
PmagSampRec = pmag.average_int(
SampI, 'specimen', 'sample') # get average intensity stuff
PmagSampRec[
"sample_description"] = "sample intensity" # decorate sample record
PmagSampRec["sample_direction_type"] = ""
PmagSampRec['er_site_name'] = SampI[0]["er_site_name"]
PmagSampRec['er_sample_name'] = samp
PmagSampRec['er_location_name'] = SampI[0]["er_location_name"]
PmagSampRec["er_citation_names"] = "This study"
PmagSampRec["er_analyst_mail_names"] = user
if agefile != "":
PmagSampRec = pmag.get_age(PmagSampRec, "er_site_name",
"sample_inferred_", AgeNFO,
DefaultAge)
site_height = pmag.get_dictitem(height_nfo, 'er_site_name',
PmagSampRec['er_site_name'],
'T')
if len(site_height) > 0:
PmagSampRec["sample_height"] = site_height[0][
'site_height'] # add in height if available
PmagSampRec['er_specimen_names'] = pmag.get_list(
SampI, 'er_specimen_name')
PmagSampRec['magic_method_codes'] = pmag.get_list(
SampI, 'magic_method_codes')
if nocrit != 1: # apply criteria!
kill = pmag.grade(PmagSampRec, accept, 'sample_int')
if len(kill) == 0:
PmagSampRec['pmag_criteria_codes'] = "ACCEPT"
SampInts.append(PmagSampRec)
PmagSamps.append(PmagSampRec)
else:
PmagSampRec = {} # sample rejected
else: # no criteria
SampInts.append(PmagSampRec)
PmagSamps.append(PmagSampRec)
PmagSampRec['pmag_criteria_codes'] = ""
if vgps == 1 and get_model_lat != 0 and PmagSampRec != {}: #
if get_model_lat == 1: # use sample latitude
PmagResRec = pmag.getsampVDM(PmagSampRec, SampNFO)
del (PmagResRec['model_lat']
) # get rid of the model lat key
elif get_model_lat == 2: # use model latitude
PmagResRec = pmag.getsampVDM(PmagSampRec, ModelLats)
if PmagResRec != {}:
PmagResRec['magic_method_codes'] = PmagResRec[
'magic_method_codes'] + ":IE-MLAT"
if PmagResRec != {}:
PmagResRec['er_specimen_names'] = PmagSampRec[
'er_specimen_names']
PmagResRec['er_sample_names'] = PmagSampRec[
'er_sample_name']
PmagResRec['pmag_criteria_codes'] = 'ACCEPT'
PmagResRec['average_int_sigma_perc'] = PmagSampRec[
'sample_int_sigma_perc']
PmagResRec['average_int_sigma'] = PmagSampRec[
'sample_int_sigma']
PmagResRec['average_int_n'] = PmagSampRec[
'sample_int_n']
PmagResRec['vadm_n'] = PmagSampRec['sample_int_n']
PmagResRec['data_type'] = 'i'
PmagResults.append(PmagResRec)
if len(PmagSamps) > 0:
TmpSamps, keylist = pmag.fillkeys(
PmagSamps) # fill in missing keys from different types of records
pmag.magic_write(sampout, TmpSamps,
'pmag_samples') # save in sample output file
print ' sample averages written to ', sampout
#
#create site averages from specimens or samples as specified
#
for site in sites:
if Daverage == 0:
key, dirlist = 'specimen', SpecDirs # if specimen averages at site level desired
if Daverage == 1:
key, dirlist = 'sample', SampDirs # if sample averages at site level desired
tmp = pmag.get_dictitem(dirlist, 'er_site_name', site,
'T') # get all the sites with directions
tmp1 = pmag.get_dictitem(
tmp, key + '_tilt_correction', coords[-1],
'T') # use only the last coordinate if Caverage==0
sd = pmag.get_dictitem(
SiteNFO, 'er_site_name', site,
'T') # fish out site information (lat/lon, etc.)
if len(sd) > 0:
sitedat = sd[0]
if Caverage == 0: # do component wise averaging
for comp in Comps:
siteD = pmag.get_dictitem(tmp1, key + '_comp_name', comp,
'T') # get all components comp
if len(
siteD
) > 0: # there are some for this site and component name
PmagSiteRec = pmag.lnpbykey(
siteD, 'site', key) # get an average for this site
PmagSiteRec[
'site_comp_name'] = comp # decorate the site record
PmagSiteRec["er_location_name"] = siteD[0][
'er_location_name']
PmagSiteRec["er_site_name"] = siteD[0]['er_site_name']
PmagSiteRec['site_tilt_correction'] = coords[-1]
PmagSiteRec['site_comp_name'] = pmag.get_list(
siteD, key + '_comp_name')
if Daverage == 1:
PmagSiteRec['er_sample_names'] = pmag.get_list(
siteD, 'er_sample_name')
else:
PmagSiteRec['er_specimen_names'] = pmag.get_list(
siteD, 'er_specimen_name')
# determine the demagnetization code (DC3,4 or 5) for this site
AFnum = len(
pmag.get_dictitem(siteD, 'magic_method_codes',
'LP-DIR-AF', 'has'))
Tnum = len(
pmag.get_dictitem(siteD, 'magic_method_codes',
'LP-DIR-T', 'has'))
DC = 3
if AFnum > 0: DC += 1
if Tnum > 0: DC += 1
PmagSiteRec['magic_method_codes'] = pmag.get_list(
siteD,
'magic_method_codes') + ':' + 'LP-DC' + str(DC)
PmagSiteRec['magic_method_codes'].strip(":")
if plotsites == 1:
print PmagSiteRec['er_site_name']
pmagplotlib.plotSITE(EQ['eqarea'], PmagSiteRec,
siteD,
key) # plot and list the data
pmagplotlib.drawFIGS(EQ)
PmagSites.append(PmagSiteRec)
else: # last component only
siteD = tmp1[:] # get the last orientation system specified
if len(siteD) > 0: # there are some
PmagSiteRec = pmag.lnpbykey(
siteD, 'site', key) # get the average for this site
PmagSiteRec["er_location_name"] = siteD[0][
'er_location_name'] # decorate the record
PmagSiteRec["er_site_name"] = siteD[0]['er_site_name']
PmagSiteRec['site_comp_name'] = comp
PmagSiteRec['site_tilt_correction'] = coords[-1]
PmagSiteRec['site_comp_name'] = pmag.get_list(
siteD, key + '_comp_name')
PmagSiteRec['er_specimen_names'] = pmag.get_list(
siteD, 'er_specimen_name')
PmagSiteRec['er_sample_names'] = pmag.get_list(
siteD, 'er_sample_name')
AFnum = len(
pmag.get_dictitem(siteD, 'magic_method_codes',
'LP-DIR-AF', 'has'))
Tnum = len(
pmag.get_dictitem(siteD, 'magic_method_codes',
'LP-DIR-T', 'has'))
DC = 3
if AFnum > 0: DC += 1
if Tnum > 0: DC += 1
PmagSiteRec['magic_method_codes'] = pmag.get_list(
siteD, 'magic_method_codes') + ':' + 'LP-DC' + str(DC)
PmagSiteRec['magic_method_codes'].strip(":")
if Daverage == 0:
PmagSiteRec['site_comp_name'] = pmag.get_list(
siteD, key + '_comp_name')
if plotsites == 1:
pmagplotlib.plotSITE(EQ['eqarea'], PmagSiteRec, siteD,
key)
pmagplotlib.drawFIGS(EQ)
PmagSites.append(PmagSiteRec)
else:
print 'site information not found in er_sites for site, ', site, ' site will be skipped'
for PmagSiteRec in PmagSites: # now decorate each dictionary some more, and calculate VGPs etc. for results table
PmagSiteRec["er_citation_names"] = "This study"
PmagSiteRec["er_analyst_mail_names"] = user
PmagSiteRec['magic_software_packages'] = version_num
if agefile != "":
PmagSiteRec = pmag.get_age(PmagSiteRec, "er_site_name",
"site_inferred_", AgeNFO, DefaultAge)
PmagSiteRec['pmag_criteria_codes'] = 'ACCEPT'
if 'site_n_lines' in PmagSiteRec.keys(
) and 'site_n_planes' in PmagSiteRec.keys() and PmagSiteRec[
'site_n_lines'] != "" and PmagSiteRec['site_n_planes'] != "":
if int(PmagSiteRec["site_n_planes"]) > 0:
PmagSiteRec["magic_method_codes"] = PmagSiteRec[
'magic_method_codes'] + ":DE-FM-LP"
elif int(PmagSiteRec["site_n_lines"]) > 2:
PmagSiteRec["magic_method_codes"] = PmagSiteRec[
'magic_method_codes'] + ":DE-FM"
kill = pmag.grade(PmagSiteRec, accept, 'site_dir')
if len(kill) == 0:
PmagResRec = {
} # set up dictionary for the pmag_results table entry
PmagResRec['data_type'] = 'i' # decorate it a bit
PmagResRec['magic_software_packages'] = version_num
PmagSiteRec[
'site_description'] = 'Site direction included in results table'
PmagResRec['pmag_criteria_codes'] = 'ACCEPT'
dec = float(PmagSiteRec["site_dec"])
inc = float(PmagSiteRec["site_inc"])
if 'site_alpha95' in PmagSiteRec.keys(
) and PmagSiteRec['site_alpha95'] != "":
a95 = float(PmagSiteRec["site_alpha95"])
else:
a95 = 180.
sitedat = pmag.get_dictitem(
SiteNFO, 'er_site_name', PmagSiteRec['er_site_name'],
'T')[0] # fish out site information (lat/lon, etc.)
lat = float(sitedat['site_lat'])
lon = float(sitedat['site_lon'])
plong, plat, dp, dm = pmag.dia_vgp(
dec, inc, a95, lat, lon) # get the VGP for this site
if PmagSiteRec['site_tilt_correction'] == '-1':
C = ' (spec coord) '
if PmagSiteRec['site_tilt_correction'] == '0':
C = ' (geog. coord) '
if PmagSiteRec['site_tilt_correction'] == '100':
C = ' (strat. coord) '
PmagResRec["pmag_result_name"] = "VGP Site: " + PmagSiteRec[
"er_site_name"] # decorate some more
PmagResRec[
"result_description"] = "Site VGP, coord system = " + str(
coord) + ' component: ' + comp
PmagResRec['er_site_names'] = PmagSiteRec['er_site_name']
PmagResRec['pmag_criteria_codes'] = 'ACCEPT'
PmagResRec['er_citation_names'] = 'This study'
PmagResRec['er_analyst_mail_names'] = user
PmagResRec["er_location_names"] = PmagSiteRec[
"er_location_name"]
if Daverage == 1:
PmagResRec["er_sample_names"] = PmagSiteRec[
"er_sample_names"]
else:
PmagResRec["er_specimen_names"] = PmagSiteRec[
"er_specimen_names"]
PmagResRec["tilt_correction"] = PmagSiteRec[
'site_tilt_correction']
PmagResRec["pole_comp_name"] = PmagSiteRec['site_comp_name']
PmagResRec["average_dec"] = PmagSiteRec["site_dec"]
PmagResRec["average_inc"] = PmagSiteRec["site_inc"]
PmagResRec["average_alpha95"] = PmagSiteRec["site_alpha95"]
PmagResRec["average_n"] = PmagSiteRec["site_n"]
PmagResRec["average_n_lines"] = PmagSiteRec["site_n_lines"]
PmagResRec["average_n_planes"] = PmagSiteRec["site_n_planes"]
PmagResRec["vgp_n"] = PmagSiteRec["site_n"]
PmagResRec["average_k"] = PmagSiteRec["site_k"]
PmagResRec["average_r"] = PmagSiteRec["site_r"]
PmagResRec["average_lat"] = '%10.4f ' % (lat)
PmagResRec["average_lon"] = '%10.4f ' % (lon)
if agefile != "":
PmagResRec = pmag.get_age(PmagResRec, "er_site_names",
"average_", AgeNFO, DefaultAge)
site_height = pmag.get_dictitem(height_nfo, 'er_site_name',
site, 'T')
if len(site_height) > 0:
PmagResRec["average_height"] = site_height[0][
'site_height']
PmagResRec["vgp_lat"] = '%7.1f ' % (plat)
PmagResRec["vgp_lon"] = '%7.1f ' % (plong)
PmagResRec["vgp_dp"] = '%7.1f ' % (dp)
PmagResRec["vgp_dm"] = '%7.1f ' % (dm)
PmagResRec["magic_method_codes"] = PmagSiteRec[
"magic_method_codes"]
if PmagSiteRec['site_tilt_correction'] == '0':
PmagSiteRec['magic_method_codes'] = PmagSiteRec[
'magic_method_codes'] + ":DA-DIR-GEO"
if PmagSiteRec['site_tilt_correction'] == '100':
PmagSiteRec['magic_method_codes'] = PmagSiteRec[
'magic_method_codes'] + ":DA-DIR-TILT"
PmagSiteRec['site_polarity'] = ""
if polarity == 1: # assign polarity based on angle of pole lat to spin axis - may want to re-think this sometime
angle = pmag.angle([0, 0], [0, (90 - plat)])
if angle <= 55.: PmagSiteRec["site_polarity"] = 'n'
if angle > 55. and angle < 125.:
PmagSiteRec["site_polarity"] = 't'
if angle >= 125.: PmagSiteRec["site_polarity"] = 'r'
PmagResults.append(PmagResRec)
if polarity == 1:
crecs = pmag.get_dictitem(PmagSites, 'site_tilt_correction', '100',
'T') # find the tilt corrected data
if len(crecs) < 2:
crecs = pmag.get_dictitem(
PmagSites, 'site_tilt_correction', '0',
'T') # if there aren't any, find the geographic corrected data
if len(crecs) > 2: # if there are some,
comp = pmag.get_list(
crecs,
'site_comp_name').split(':')[0] # find the first component
crecs = pmag.get_dictitem(
crecs, 'site_comp_name', comp,
'T') # fish out all of the first component
precs = []
for rec in crecs:
precs.append({
'dec': rec['site_dec'],
'inc': rec['site_inc'],
'name': rec['er_site_name'],
'loc': rec['er_location_name']
})
polpars = pmag.fisher_by_pol(
precs) # calculate average by polarity
for mode in polpars.keys(
): # hunt through all the modes (normal=A, reverse=B, all=ALL)
PolRes = {}
PolRes['er_citation_names'] = 'This study'
PolRes[
"pmag_result_name"] = "Polarity Average: Polarity " + mode #
PolRes["data_type"] = "a"
PolRes["average_dec"] = '%7.1f' % (polpars[mode]['dec'])
PolRes["average_inc"] = '%7.1f' % (polpars[mode]['inc'])
PolRes["average_n"] = '%i' % (polpars[mode]['n'])
PolRes["average_r"] = '%5.4f' % (polpars[mode]['r'])
PolRes["average_k"] = '%6.0f' % (polpars[mode]['k'])
PolRes["average_alpha95"] = '%7.1f' % (
polpars[mode]['alpha95'])
PolRes['er_site_names'] = polpars[mode]['sites']
PolRes['er_location_names'] = polpars[mode]['locs']
PolRes['magic_software_packages'] = version_num
PmagResults.append(PolRes)
if noInt != 1 and nositeints != 1:
for site in sites: # now do intensities for each site
if plotsites == 1: print site
if Iaverage == 0:
key, intlist = 'specimen', SpecInts # if using specimen level data
if Iaverage == 1:
key, intlist = 'sample', PmagSamps # if using sample level data
Ints = pmag.get_dictitem(
intlist, 'er_site_name', site,
'T') # get all the intensities for this site
if len(Ints) > 0: # there are some
PmagSiteRec = pmag.average_int(
Ints, key,
'site') # get average intensity stuff for site table
PmagResRec = pmag.average_int(
Ints, key,
'average') # get average intensity stuff for results table
if plotsites == 1: # if site by site examination requested - print this site out to the screen
for rec in Ints:
print rec['er_' + key + '_name'], ' %7.1f' % (
1e6 * float(rec[key + '_int']))
if len(Ints) > 1:
print 'Average: ', '%7.1f' % (1e6 * float(
PmagResRec['average_int'])), 'N: ', len(Ints)
print 'Sigma: ', '%7.1f' % (
1e6 * float(PmagResRec['average_int_sigma'])
), 'Sigma %: ', PmagResRec['average_int_sigma_perc']
raw_input('Press any key to continue\n')
er_location_name = Ints[0]["er_location_name"]
PmagSiteRec[
"er_location_name"] = er_location_name # decorate the records
PmagSiteRec["er_citation_names"] = "This study"
PmagResRec["er_location_names"] = er_location_name
PmagResRec["er_citation_names"] = "This study"
PmagSiteRec["er_analyst_mail_names"] = user
PmagResRec["er_analyst_mail_names"] = user
PmagResRec["data_type"] = 'i'
if Iaverage == 0:
PmagSiteRec['er_specimen_names'] = pmag.get_list(
Ints, 'er_specimen_name') # list of all specimens used
PmagResRec['er_specimen_names'] = pmag.get_list(
Ints, 'er_specimen_name')
PmagSiteRec['er_sample_names'] = pmag.get_list(
Ints, 'er_sample_name') # list of all samples used
PmagResRec['er_sample_names'] = pmag.get_list(
Ints, 'er_sample_name')
PmagSiteRec['er_site_name'] = site
PmagResRec['er_site_names'] = site
PmagSiteRec['magic_method_codes'] = pmag.get_list(
Ints, 'magic_method_codes')
PmagResRec['magic_method_codes'] = pmag.get_list(
Ints, 'magic_method_codes')
kill = pmag.grade(PmagSiteRec, accept, 'site_int')
if nocrit == 1 or len(kill) == 0:
b, sig = float(PmagResRec['average_int']), ""
if (PmagResRec['average_int_sigma']) != "":
sig = float(PmagResRec['average_int_sigma'])
sdir = pmag.get_dictitem(PmagResults, 'er_site_names',
site,
'T') # fish out site direction
if len(sdir) > 0 and sdir[-1][
'average_inc'] != "": # get the VDM for this record using last average inclination (hope it is the right one!)
inc = float(sdir[0]['average_inc']) #
mlat = pmag.magnetic_lat(
inc) # get magnetic latitude using dipole formula
PmagResRec["vdm"] = '%8.3e ' % (pmag.b_vdm(
b, mlat)) # get VDM with magnetic latitude
PmagResRec["vdm_n"] = PmagResRec['average_int_n']
if 'average_int_sigma' in PmagResRec.keys(
) and PmagResRec['average_int_sigma'] != "":
vdm_sig = pmag.b_vdm(
float(PmagResRec['average_int_sigma']), mlat)
PmagResRec["vdm_sigma"] = '%8.3e ' % (vdm_sig)
else:
PmagResRec["vdm_sigma"] = ""
mlat = "" # define a model latitude
if get_model_lat == 1: # use present site latitude
mlats = pmag.get_dictitem(SiteNFO, 'er_site_name',
site, 'T')
if len(mlats) > 0: mlat = mlats[0]['site_lat']
elif get_model_lat == 2: # use a model latitude from some plate reconstruction model (or something)
mlats = pmag.get_dictitem(ModelLats, 'er_site_name',
site, 'T')
if len(mlats) > 0:
PmagResRec['model_lat'] = mlats[0][
'site_model_lat']
mlat = PmagResRec['model_lat']
if mlat != "":
PmagResRec["vadm"] = '%8.3e ' % (
pmag.b_vdm(b, float(mlat))
) # get the VADM using the desired latitude
if sig != "":
vdm_sig = pmag.b_vdm(
float(PmagResRec['average_int_sigma']),
float(mlat))
PmagResRec["vadm_sigma"] = '%8.3e ' % (vdm_sig)
PmagResRec["vadm_n"] = PmagResRec['average_int_n']
else:
PmagResRec["vadm_sigma"] = ""
sitedat = pmag.get_dictitem(
SiteNFO, 'er_site_name', PmagSiteRec['er_site_name'],
'T') # fish out site information (lat/lon, etc.)
if len(sitedat) > 0:
sitedat = sitedat[0]
PmagResRec['average_lat'] = sitedat['site_lat']
PmagResRec['average_lon'] = sitedat['site_lon']
else:
PmagResRec['average_lon'] = 'UNKNOWN'
PmagResRec['average_lon'] = 'UNKNOWN'
PmagResRec['magic_software_packages'] = version_num
PmagResRec["pmag_result_name"] = "V[A]DM: Site " + site
PmagResRec["result_description"] = "V[A]DM of site"
PmagResRec["pmag_criteria_codes"] = "ACCEPT"
if agefile != "":
PmagResRec = pmag.get_age(PmagResRec, "er_site_names",
"average_", AgeNFO,
DefaultAge)
site_height = pmag.get_dictitem(height_nfo, 'er_site_name',
site, 'T')
if len(site_height) > 0:
PmagResRec["average_height"] = site_height[0][
'site_height']
PmagSites.append(PmagSiteRec)
PmagResults.append(PmagResRec)
if len(PmagSites) > 0:
Tmp, keylist = pmag.fillkeys(PmagSites)
pmag.magic_write(siteout, Tmp, 'pmag_sites')
print ' sites written to ', siteout
else:
print "No Site level table"
if len(PmagResults) > 0:
TmpRes, keylist = pmag.fillkeys(PmagResults)
pmag.magic_write(resout, TmpRes, 'pmag_results')
print ' results written to ', resout
else:
print "No Results level table"
def main(command_line=True, **kwargs):
"""
NAME
iodp_dscr_magic.py
DESCRIPTION
converts ODP LIMS discrete sample format files to magic_measurements format files
SYNTAX
iodp_descr_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input .csv file, default is all in directory
-F FILE: specify output measurements file, default is magic_measurements.txt
-A : don't average replicate measurements
INPUTS
IODP discrete sample .csv file format exported from LIMS database
"""
#
# initialize defaults
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
csv_file=''
MagRecs,Specs=[],[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
# get command line args
if command_line:
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
if "-h" in args:
print(main.__doc__)
return False
if "-A" in args: noave=1
if '-f' in args:
ind=args.index("-f")
csv_file=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=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 # rename dir_path after input_dir_path is set
noave = kwargs.get('noave', 0) # default (0) is DO average
csv_file = kwargs.get('csv_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
# format variables
meas_file= os.path.join(output_dir_path, meas_file)
if csv_file=="":
filelist=os.listdir(input_dir_path) # read in list of files to import
else:
csv_file = os.path.join(input_dir_path, csv_file)
filelist=[csv_file]
# parsing the data
file_found = False
for fname in filelist: # parse each file
if fname[-3:].lower()=='csv':
file_found = True
print('processing: ',fname)
with open(fname, 'r') as finput:
data = list(finput.readlines())
keys = data[0].replace('\n','').split(',') # splits on underscores
interval_key="Offset (cm)"
demag_key="Demag level (mT)"
offline_demag_key="Treatment Value (mT or °C)"
offline_treatment_type="Treatment type"
run_key="Test No."
if "Inclination background + tray corrected (deg)" in keys: inc_key="Inclination background + tray corrected (deg)"
if "Inclination background & tray corrected (deg)" in keys: inc_key="Inclination background & tray corrected (deg)"
if "Declination background + tray corrected (deg)" in keys: dec_key="Declination background + tray corrected (deg)"
if "Declination background & tray corrected (deg)" in keys: dec_key="Declination background & tray corrected (deg)"
if "Intensity background + tray corrected (A/m)" in keys: int_key="Intensity background + tray corrected (A/m)"
if "Intensity background & tray corrected (A/m)" in keys: int_key="Intensity background & tray corrected (A/m)"
type="Type"
sect_key="Sect"
half_key="A/W"
# need to add volume_key to LORE format!
if "Sample volume (cm^3)" in keys:volume_key="Sample volume (cm^3)"
if "Sample volume (cc)" in keys:volume_key="Sample volume (cc)"
if "Sample volume (cm³)" in keys:volume_key="Sample volume (cm³)"
for line in data[1:]:
InRec={}
for k in range(len(keys)):InRec[keys[k]]=line.split(',')[k]
inst="IODP-SRM"
MagRec={}
expedition=InRec['Exp']
location=InRec['Site']+InRec['Hole']
offsets=InRec[interval_key].split('.') # maintain consistency with er_samples convention of using top interval
if len(offsets)==1:
offset=int(offsets[0])
else:
offset=int(offsets[0])-1
#interval=str(offset+1)# maintain consistency with er_samples convention of using top interval
interval=str(offset)# maintain consistency with er_samples convention of using top interval
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[type]+"-"+InRec[sect_key]+'_'+InRec[half_key]+'_'+interval
if specimen not in Specs:Specs.append(specimen)
MagRec['er_expedition_name']=expedition
MagRec['er_location_name']=location
MagRec['er_site_name']=specimen
MagRec['er_citation_names']=citation
MagRec['er_specimen_name']=specimen
MagRec['er_sample_name']=specimen
MagRec['er_site_name']=specimen
# set up measurement record - default is NRM
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'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
MagRec["measurement_csd"]='0' # assume all data are "good"
volume=InRec[volume_key]
MagRec["magic_method_codes"]='LT-NO'
sort_by='treatment_ac_field' # set default to AF demag
if InRec[demag_key]!="0":
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':IODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T
if sort_by =="treatment_ac_field":
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
else:
MagRec["treatment_ac_field"]=str(treatment_value)# AF demag in treat mT => T
elif offline_treatment_type in list(InRec.keys()) and InRec[offline_treatment_type]!="":
if "Lowrie" in InRec['Comments']:
MagRec['magic_method_codes'] = 'LP-IRM-3D'
treatment_value=float(InRec[offline_demag_key].strip('"'))+273. # convert C => K
MagRec["treatment_temp"]=treatment_value
MagRec["treatment_ac_field"]="0"
sort_by='treatment_temp'
elif 'Isothermal' in InRec[offline_treatment_type]:
MagRec['magic_method_codes'] = 'LT-IRM'
treatment_value=float(InRec[offline_demag_key].strip('"'))*1e-3 # convert mT => T
MagRec["treatment_dc_field"]=treatment_value
MagRec["treatment_ac_field"]="0"
sort_by='treatment_dc_field'
MagRec["measurement_standard"]='u' # assume all data are "good"
vol=float(volume)*1e-6 # convert from cc to m^3
if run_key in list(InRec.keys()):
run_number=InRec[run_key]
MagRec['external_database_ids']=run_number
MagRec['external_database_names']='LIMS'
else:
MagRec['external_database_ids']=""
MagRec['external_database_names']=''
MagRec['measurement_description']='sample orientation: '+InRec['Sample orientation']
MagRec['measurement_inc']=InRec[inc_key].strip('"')
MagRec['measurement_dec']=InRec[dec_key].strip('"')
intens= InRec[int_key].strip('"')
MagRec['measurement_magn_moment']='%8.3e'%(float(intens)*vol) # convert intensity from A/m to Am^2 using vol
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
MagRec['measurement_positions']=''
MagRecs.append(MagRec)
if not file_found:
print("No .csv files were found")
return False, "No .csv files were found"
MagOuts=[]
for spec in Specs:
Speclist=pmag.get_dictitem(MagRecs,'er_specimen_name',spec,'T')
Meassorted=sorted(Speclist, key=lambda x,y=None: int(round(float(x[sort_by])-float(y[sort_by]))) if y!=None else 0)
for rec in Meassorted:
for key in list(rec.keys()): rec[key]=str(rec[key])
MagOuts.append(rec)
Fixed=pmag.measurements_methods(MagOuts,noave)
Out,keys=pmag.fillkeys(Fixed)
if pmag.magic_write(meas_file,Out,'magic_measurements'):
print('data stored in ',meas_file)
return True, meas_file
else:
print('no data found. bad magfile?')
return False, 'no data found. bad magfile?'
def main(command_line=True, **kwargs):
"""
NAME
iodp_srm_magic.py
DESCRIPTION
converts IODP LIMS and LORE SRM archive half sample format files to magic_measurements format files
SYNTAX
iodp_srm_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input .csv file, default is all in directory
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-A : don't average replicate measurements
INPUTS
IODP .csv file format exported from LIMS database
"""
#
# initialize defaults
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
csv_file=''
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
depth_method='a'
# get command line args
if command_line:
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
if "-h" in args:
print(main.__doc__)
return False
if "-A" in args: noave=1
if '-f' in args:
ind=args.index("-f")
csv_file=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 '-Fsi' in args:
ind=args.index("-Fsi")
site_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file = 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 # rename dir_path after input_dir_path is set
noave = kwargs.get('noave', 0) # default (0) is DO average
csv_file = kwargs.get('csv_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
spec_file = kwargs.get('spec_file', 'er_specimens.txt')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt')
# format variables
meas_file = os.path.join(output_dir_path, meas_file)
spec_file = os.path.join(output_dir_path, spec_file)
Specs,file_type = pmag.magic_read(spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
ErSamps,file_type = pmag.magic_read(samp_file)
site_file = os.path.join(output_dir_path, site_file)
if csv_file=="":
filelist=os.listdir(input_dir_path) # read in list of files to import
else:
csv_file = os.path.join(input_dir_path, csv_file)
filelist=[csv_file]
# parsing the data
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs,SiteRecs=[],[],[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
file_found = False
for f in filelist: # parse each file
if f[-3:].lower()=='csv':
file_found = True
print('processing: ',f)
full_file = os.path.join(input_dir_path, f)
with open(full_file, 'r') as fin:
file_input = fin.readlines()
keys=file_input[0].replace('\n','').split(',') # splits on underscores
if "Interval Top (cm) on SHLF" in keys:interval_key="Interval Top (cm) on SHLF"
if " Interval Bot (cm) on SECT" in keys:interval_key=" Interval Bot (cm) on SECT"
if "Offset (cm)" in keys: interval_key="Offset (cm)"
if "Top Depth (m)" in keys:depth_key="Top Depth (m)"
if "CSF-A Top (m)" in keys:depth_key="CSF-A Top (m)"
if "Depth CSF-A (m)" in keys:depth_key="Depth CSF-A (m)"
if "CSF-B Top (m)" in keys:
comp_depth_key="CSF-B Top (m)" # use this model if available
elif "Depth CSF-B (m)" in keys:
comp_depth_key="Depth CSF-B (m)"
else:
comp_depth_key=""
if "Demag level (mT)" in keys:demag_key="Demag level (mT)"
if "Demag Level (mT)" in keys: demag_key="Demag Level (mT)"
if "Inclination (Tray- and Bkgrd-Corrected) (deg)" in keys:inc_key="Inclination (Tray- and Bkgrd-Corrected) (deg)"
if "Inclination background + tray corrected (deg)" in keys:inc_key="Inclination background + tray corrected (deg)"
if "Inclination background + tray corrected (\xc2\xb0)" in keys:inc_key="Inclination background + tray corrected (\xc2\xb0)"
if "Inclination background & tray corrected (deg)" in keys:inc_key="Inclination background & tray corrected (deg)"
if "Declination (Tray- and Bkgrd-Corrected) (deg)" in keys:dec_key="Declination (Tray- and Bkgrd-Corrected) (deg)"
if "Declination background + tray corrected (deg)" in keys:dec_key="Declination background + tray corrected (deg)"
if "Declination background + tray corrected (\xc2\xb0)" in keys:dec_key="Declination background + tray corrected (\xc2\xb0)"
if "Declination background & tray corrected (deg)" in keys:dec_key="Declination background & tray corrected (deg)"
if "Intensity (Tray- and Bkgrd-Corrected) (A/m)" in keys:int_key="Intensity (Tray- and Bkgrd-Corrected) (A/m)"
if "Intensity background + tray corrected (A/m)" in keys:int_key="Intensity background + tray corrected (A/m)"
if "Intensity background & tray corrected (A/m)" in keys:int_key="Intensity background & tray corrected (A/m)"
if "Core Type" in keys:
core_type="Core Type"
else: core_type="Type"
if 'Run Number' in keys: run_number_key='Run Number'
if 'Test No.' in keys: run_number_key='Test No.'
if 'Test Changed On' in keys: date_key='Test Changed On'
if "Timestamp (UTC)" in keys: date_key="Timestamp (UTC)"
if "Section" in keys: sect_key="Section"
if "Sect" in keys: sect_key="Sect"
if 'Section Half' in keys: half_key='Section Half'
if "A/W" in keys: half_key="A/W"
if "Text ID" in keys: text_id="Text ID"
if "Text Id" in keys: text_id="Text Id"
for line in file_input[1:]:
InRec={}
test=0
recs=line.split(',')
for k in range(len(keys)):
if len(recs)==len(keys):
InRec[keys[k]]=line.split(',')[k]
if InRec['Exp']!="": test=1 # get rid of pesky blank lines
if test==1:
run_number=""
inst="IODP-SRM"
volume='15.59' # set default volume to this
MagRec,SpecRec,SampRec,SiteRec={},{},{},{}
expedition=InRec['Exp']
location=InRec['Site']+InRec['Hole']
# Maintain backward compatibility for the ever-changing LIMS format (Argh!)
while len(InRec['Core'])<3:
InRec['Core']='0'+InRec['Core']
if "Last Tray Measurment" in list(InRec.keys()) and "SHLF" not in InRec[text_id] or 'dscr' in csv_file : # assume discrete sample
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[core_type]+"-"+InRec[sect_key]+'-'+InRec[half_key]+'-'+str(InRec[interval_key])
else: # mark as continuous measurements
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[core_type]+"_"+InRec[sect_key]+InRec[half_key]+'-'+str(InRec[interval_key])
SpecRec['er_expedition_name']=expedition
SpecRec['er_location_name']=location
SpecRec['er_site_name']=specimen
SpecRec['er_citation_names']=citation
for key in list(SpecRec.keys()):SampRec[key]=SpecRec[key]
for key in list(SpecRec.keys()):SiteRec[key]=SpecRec[key]
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['sample_core_depth']=InRec[depth_key]
if comp_depth_key!='':
SampRec['sample_composite_depth']=InRec[comp_depth_key]
if "SHLF" not in InRec[text_id]:
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SP-SS-C:SO-V'
else:
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SO-V'
SpecRec['er_specimen_name']=specimen
SpecRec['er_sample_name']=specimen
SampRec['er_sample_name']=specimen
SampRec['er_specimen_names']=specimen
SiteRec['er_specimen_names']=specimen
for key in list(SpecRec.keys()):MagRec[key]=SpecRec[key]
# set up measurement record - default is NRM
#MagRec['er_analyst_mail_names']=InRec['Test Entered By']
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'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
SpecRec['er_specimen_alternatives']=InRec[text_id]
if 'Sample Area (cm?)' in list(InRec.keys()) and InRec['Sample Area (cm?)']!= "": volume=InRec['Sample Area (cm?)']
if InRec[run_number_key]!= "": run_number=InRec[run_number_key]
datestamp=InRec[date_key].split() # date time is second line of file
if '/' in datestamp[0]:
mmddyy=datestamp[0].split('/') # break into month day year
if len(mmddyy[0])==1: mmddyy[0]='0'+mmddyy[0] # make 2 characters
if len(mmddyy[1])==1: mmddyy[1]='0'+mmddyy[1] # make 2 characters
if len(datestamp[1])==1: datestamp[1]='0'+datestamp[1] # make 2 characters
date='20'+mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]+":00.00"
if '-' in datestamp[0]:
mmddyy=datestamp[0].split('-') # break into month day year
date=mmddyy[0]+':'+mmddyy[1]+":"+mmddyy[2] +':' +datestamp[1]+":00.00"
MagRec["measurement_date"]=date
MagRec["magic_method_codes"]='LT-NO'
if InRec[demag_key]!="0":
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':IODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
if 'Treatment Type' in list(InRec.keys()) and InRec['Treatment Type']!="":
if 'Alternating Frequency' in InRec['Treatment Type']:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':I`ODP-DTECH' # measured on shipboard Dtech D2000
treatment_value=float(InRec['Treatment Value'])*1e-3 # convert mT => T
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
elif 'Thermal' in InRec['Treatment Type']:
MagRec['magic_method_codes'] = 'LT-T-Z'
inst=inst+':IODP-TDS' # measured on shipboard Schonstedt thermal demagnetizer
treatment_value=float(InRec['Treatment Value'])+273 # convert C => K
MagRec["treatment_temp"]='%8.3e'%(treatment_value) #
MagRec["measurement_standard"]='u' # assume all data are "good"
vol=float(volume)*1e-6 # convert from cc to m^3
if run_number!="":
MagRec['external_database_ids']=run_number
MagRec['external_database_names']='LIMS'
else:
MagRec['external_database_ids']=""
MagRec['external_database_names']=''
MagRec['measurement_inc']=InRec[inc_key].strip('"')
MagRec['measurement_dec']=InRec[dec_key].strip('"')
intens= InRec[int_key].strip('"')
MagRec['measurement_magn_moment']='%8.3e'%(float(intens)*vol) # convert intensity from A/m to Am^2 using vol
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
MagRec['measurement_csd']=''
MagRec['measurement_positions']=''
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
if MagRec['er_site_name'] not in sites:
sites.append(MagRec['er_site_name'])
SiteRecs.append(SiteRec)
#except:
# print 'Boo-boo somewhere - no idea where'
if not file_found:
print("No .csv files were found")
return False, "No .csv files were found"
if len(SpecRecs)>0:
print('spec_file', spec_file)
pmag.magic_write(spec_file,SpecRecs,'er_specimens')
#print 'specimens stored in ',spec_file
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
#print 'samples stored in ',samp_file
if len(SiteRecs)>0:
pmag.magic_write(site_file,SiteRecs,'er_sites')
#print 'sites stored in ',site_file
MagSort=pmag.sortbykeys(MagRecs,["er_specimen_name","treatment_ac_field"])
MagOuts=[]
for MagRec in MagSort:
MagRec["treatment_ac_field"]='%8.3e'%(MagRec['treatment_ac_field']) # convert to string
MagOuts.append(MagRec)
Fixed=pmag.measurements_methods(MagOuts,noave)
if pmag.magic_write(meas_file,Fixed,'magic_measurements'):
print('data stored in ',meas_file)
return True, meas_file
else:
print('no data found. bad magfile?')
return False, 'no data found. bad magfile?'
def main():
"""
NAME
specimens_results_magic.py
DESCRIPTION
combines pmag_specimens.txt file with age, location, acceptance criteria and
outputs pmag_results table along with other MagIC tables necessary for uploading to the database
SYNTAX
specimens_results_magic.py [command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f: specimen input magic_measurements format file, default is "magic_measurements.txt"
-fsp: specimen input pmag_specimens format file, default is "pmag_specimens.txt"
-fsm: sample input er_samples format file, default is "er_samples.txt"
-fsi: specimen input er_sites format file, default is "er_sites.txt"
-fla: specify a file with paleolatitudes for calculating VADMs, default is not to calculate VADMS
format is: site_name paleolatitude (space delimited file)
-fa AGES: specify er_ages format file with age information
-crd [s,g,t,b]: specify coordinate system
(s, specimen, g geographic, t, tilt corrected, b, geographic and tilt corrected)
Default is to assume geographic
NB: only the tilt corrected data will appear on the results table, if both g and t are selected.
-cor [AC:CR:NL]: colon delimited list of required data adjustments for all specimens
included in intensity calculations (anisotropy, cooling rate, non-linear TRM)
unless specified, corrections will not be applied
-pri [TRM:ARM] colon delimited list of priorities for anisotropy correction (-cor must also be set to include AC). default is TRM, then ARM
-age MIN MAX UNITS: specify age boundaries and units
-exc: use exiting selection criteria (in pmag_criteria.txt file), default is default criteria
-C: no acceptance criteria
-aD: average directions per sample, default is NOT
-aI: average multiple specimen intensities per sample, default is by site
-aC: average all components together, default is NOT
-pol: calculate polarity averages
-sam: save sample level vgps and v[a]dms, default is by site
-xSi: skip the site level intensity calculation
-p: plot directions and look at intensities by site, default is NOT
-fmt: specify output for saved images, default is svg (only if -p set)
-lat: use present latitude for calculating VADMs, default is not to calculate VADMs
-xD: skip directions
-xI: skip intensities
OUPUT
writes pmag_samples, pmag_sites, pmag_results tables
"""
# set defaults
Comps=[] # list of components
version_num=pmag.get_version()
args=sys.argv
DefaultAge=["none"]
skipdirs,coord,excrit,custom,vgps,average,Iaverage,plotsites,opt=1,0,0,0,0,0,0,0,0
get_model_lat=0 # this skips VADM calculation altogether, when get_model_lat=1, uses present day
fmt='svg'
dir_path="."
model_lat_file=""
Caverage=0
infile='pmag_specimens.txt'
measfile="magic_measurements.txt"
sampfile="er_samples.txt"
sitefile="er_sites.txt"
agefile="er_ages.txt"
specout="er_specimens.txt"
sampout="pmag_samples.txt"
siteout="pmag_sites.txt"
resout="pmag_results.txt"
critout="pmag_criteria.txt"
instout="magic_instruments.txt"
sigcutoff,OBJ="",""
noDir,noInt=0,0
polarity=0
coords=['0']
Dcrit,Icrit,nocrit=0,0,0
corrections=[]
nocorrection=['DA-NL','DA-AC','DA-CR']
priorities=['DA-AC-ARM','DA-AC-TRM'] # priorities for anisotropy correction
# get command line stuff
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if '-cor' in args:
ind=args.index('-cor')
cors=args[ind+1].split(':') # list of required data adjustments
for cor in cors:
nocorrection.remove('DA-'+cor)
corrections.append('DA-'+cor)
if '-pri' in args:
ind=args.index('-pri')
priorities=args[ind+1].split(':') # list of required data adjustments
for p in priorities:
p='DA-AC-'+p
if '-f' in args:
ind=args.index("-f")
measfile=args[ind+1]
if '-fsp' in args:
ind=args.index("-fsp")
infile=args[ind+1]
if '-fsi' in args:
ind=args.index("-fsi")
sitefile=args[ind+1]
if "-crd" in args:
ind=args.index("-crd")
coord=args[ind+1]
if coord=='s':coords=['-1']
if coord=='g':coords=['0']
if coord=='t':coords=['100']
if coord=='b':coords=['0','100']
if "-usr" in args:
ind=args.index("-usr")
user=sys.argv[ind+1]
else: user=""
if "-C" in args: Dcrit,Icrit,nocrit=1,1,1 # no selection criteria
if "-sam" in args: vgps=1 # save sample level VGPS/VADMs
if "-xSi" in args:
nositeints=1 # skip site level intensity
else:
nositeints=0
if "-age" in args:
ind=args.index("-age")
DefaultAge[0]=args[ind+1]
DefaultAge.append(args[ind+2])
DefaultAge.append(args[ind+3])
Daverage,Iaverage,Caverage=0,0,0
if "-aD" in args: Daverage=1 # average by sample directions
if "-aI" in args: Iaverage=1 # average by sample intensities
if "-aC" in args: Caverage=1 # average all components together ??? why???
if "-pol" in args: polarity=1 # calculate averages by polarity
if '-xD' in args:noDir=1
if '-xI' in args:
noInt=1
elif "-fla" in args:
if '-lat' in args:
print("you should set a paleolatitude file OR use present day lat - not both")
sys.exit()
ind=args.index("-fla")
model_lat_file=dir_path+'/'+args[ind+1]
get_model_lat=2
mlat=open(model_lat_file,'r')
ModelLats=[]
for line in mlat.readlines():
ModelLat={}
tmp=line.split()
ModelLat["er_site_name"]=tmp[0]
ModelLat["site_model_lat"]=tmp[1]
ModelLat["er_sample_name"]=tmp[0]
ModelLat["sample_lat"]=tmp[1]
ModelLats.append(ModelLat)
get_model_lat=2
elif '-lat' in args:
get_model_lat=1
if "-p" in args:
plotsites=1
if "-fmt" in args:
ind=args.index("-fmt")
fmt=args[ind+1]
if noDir==0: # plot by site - set up plot window
import pmagplotlib
EQ={}
EQ['eqarea']=1
pmagplotlib.plot_init(EQ['eqarea'],5,5) # define figure 1 as equal area projection
pmagplotlib.plotNET(EQ['eqarea']) # I don't know why this has to be here, but otherwise the first plot never plots...
pmagplotlib.drawFIGS(EQ)
if '-WD' in args:
infile=dir_path+'/'+infile
measfile=dir_path+'/'+measfile
instout=dir_path+'/'+instout
sampfile=dir_path+'/'+sampfile
sitefile=dir_path+'/'+sitefile
agefile=dir_path+'/'+agefile
specout=dir_path+'/'+specout
sampout=dir_path+'/'+sampout
siteout=dir_path+'/'+siteout
resout=dir_path+'/'+resout
critout=dir_path+'/'+critout
if "-exc" in args: # use existing pmag_criteria file
if "-C" in args:
print('you can not use both existing and no criteria - choose either -exc OR -C OR neither (for default)')
sys.exit()
crit_data,file_type=pmag.magic_read(critout)
print("Acceptance criteria read in from ", critout)
else : # use default criteria (if nocrit set, then get really loose criteria as default)
crit_data=pmag.default_criteria(nocrit)
if nocrit==0:
print("Acceptance criteria are defaults")
else:
print("No acceptance criteria used ")
accept={}
for critrec in crit_data:
for key in list(critrec.keys()):
# need to migrate specimen_dang to specimen_int_dang for intensity data using old format
if 'IE-SPEC' in list(critrec.keys()) and 'specimen_dang' in list(critrec.keys()) and 'specimen_int_dang' not in list(critrec.keys()):
critrec['specimen_int_dang']=critrec['specimen_dang']
del critrec['specimen_dang']
# need to get rid of ron shaars sample_int_sigma_uT
if 'sample_int_sigma_uT' in list(critrec.keys()):
critrec['sample_int_sigma']='%10.3e'%(eval(critrec['sample_int_sigma_uT'])*1e-6)
if key not in list(accept.keys()) and critrec[key]!='':
accept[key]=critrec[key]
#
#
if "-exc" not in args and "-C" not in args:
print("args",args)
pmag.magic_write(critout,[accept],'pmag_criteria')
print("\n Pmag Criteria stored in ",critout,'\n')
#
# now we're done slow dancing
#
SiteNFO,file_type=pmag.magic_read(sitefile) # read in site data - has the lats and lons
SampNFO,file_type=pmag.magic_read(sampfile) # read in site data - has the lats and lons
height_nfo=pmag.get_dictitem(SiteNFO,'site_height','','F') # find all the sites with height info.
if agefile !="":AgeNFO,file_type=pmag.magic_read(agefile) # read in the age information
Data,file_type=pmag.magic_read(infile) # read in specimen interpretations
IntData=pmag.get_dictitem(Data,'specimen_int','','F') # retrieve specimens with intensity data
comment,orient="",[]
samples,sites=[],[]
for rec in Data: # run through the data filling in missing keys and finding all components, coordinates available
# fill in missing fields, collect unique sample and site names
if 'er_sample_name' not in list(rec.keys()):
rec['er_sample_name']=""
elif rec['er_sample_name'] not in samples:
samples.append(rec['er_sample_name'])
if 'er_site_name' not in list(rec.keys()):
rec['er_site_name']=""
elif rec['er_site_name'] not in sites:
sites.append(rec['er_site_name'])
if 'specimen_int' not in list(rec.keys()):rec['specimen_int']=''
if 'specimen_comp_name' not in list(rec.keys()) or rec['specimen_comp_name']=="":rec['specimen_comp_name']='A'
if rec['specimen_comp_name'] not in Comps:Comps.append(rec['specimen_comp_name'])
rec['specimen_tilt_correction']=rec['specimen_tilt_correction'].strip('\n')
if "specimen_tilt_correction" not in list(rec.keys()): rec["specimen_tilt_correction"]="-1" # assume sample coordinates
if rec["specimen_tilt_correction"] not in orient: orient.append(rec["specimen_tilt_correction"]) # collect available coordinate systems
if "specimen_direction_type" not in list(rec.keys()): rec["specimen_direction_type"]='l' # assume direction is line - not plane
if "specimen_dec" not in list(rec.keys()): rec["specimen_direction_type"]='' # if no declination, set direction type to blank
if "specimen_n" not in list(rec.keys()): rec["specimen_n"]='' # put in n
if "specimen_alpha95" not in list(rec.keys()): rec["specimen_alpha95"]='' # put in alpha95
if "magic_method_codes" not in list(rec.keys()): rec["magic_method_codes"]=''
#
# start parsing data into SpecDirs, SpecPlanes, SpecInts
SpecInts,SpecDirs,SpecPlanes=[],[],[]
samples.sort() # get sorted list of samples and sites
sites.sort()
if noInt==0: # don't skip intensities
IntData=pmag.get_dictitem(Data,'specimen_int','','F') # retrieve specimens with intensity data
if nocrit==0: # use selection criteria
for rec in IntData: # do selection criteria
kill=pmag.grade(rec,accept,'specimen_int')
if len(kill)==0: SpecInts.append(rec) # intensity record to be included in sample, site calculations
else:
SpecInts=IntData[:] # take everything - no selection criteria
# check for required data adjustments
if len(corrections)>0 and len(SpecInts)>0:
for cor in corrections:
SpecInts=pmag.get_dictitem(SpecInts,'magic_method_codes',cor,'has') # only take specimens with the required corrections
if len(nocorrection)>0 and len(SpecInts)>0:
for cor in nocorrection:
SpecInts=pmag.get_dictitem(SpecInts,'magic_method_codes',cor,'not') # exclude the corrections not specified for inclusion
# take top priority specimen of its name in remaining specimens (only one per customer)
PrioritySpecInts=[]
specimens=pmag.get_specs(SpecInts) # get list of uniq specimen names
for spec in specimens:
ThisSpecRecs=pmag.get_dictitem(SpecInts,'er_specimen_name',spec,'T') # all the records for this specimen
if len(ThisSpecRecs)==1:
PrioritySpecInts.append(ThisSpecRecs[0])
elif len(ThisSpecRecs)>1: # more than one
prec=[]
for p in priorities:
ThisSpecRecs=pmag.get_dictitem(SpecInts,'magic_method_codes',p,'has') # all the records for this specimen
if len(ThisSpecRecs)>0:prec.append(ThisSpecRecs[0])
PrioritySpecInts.append(prec[0]) # take the best one
SpecInts=PrioritySpecInts # this has the first specimen record
if noDir==0: # don't skip directions
AllDirs=pmag.get_dictitem(Data,'specimen_direction_type','','F') # retrieve specimens with directed lines and planes
Ns=pmag.get_dictitem(AllDirs,'specimen_n','','F') # get all specimens with specimen_n information
if nocrit!=1: # use selection criteria
for rec in Ns: # look through everything with specimen_n for "good" data
kill=pmag.grade(rec,accept,'specimen_dir')
if len(kill)==0: # nothing killed it
SpecDirs.append(rec)
else: # no criteria
SpecDirs=AllDirs[:] # take them all
# SpecDirs is now the list of all specimen directions (lines and planes) that pass muster
#
PmagSamps,SampDirs=[],[] # list of all sample data and list of those that pass the DE-SAMP criteria
PmagSites,PmagResults=[],[] # list of all site data and selected results
SampInts=[]
for samp in samples: # run through the sample names
if Daverage==1: # average by sample if desired
SampDir=pmag.get_dictitem(SpecDirs,'er_sample_name',samp,'T') # get all the directional data for this sample
if len(SampDir)>0: # there are some directions
for coord in coords: # step through desired coordinate systems
CoordDir=pmag.get_dictitem(SampDir,'specimen_tilt_correction',coord,'T') # get all the directions for this sample
if len(CoordDir)>0: # there are some with this coordinate system
if Caverage==0: # look component by component
for comp in Comps:
CompDir=pmag.get_dictitem(CoordDir,'specimen_comp_name',comp,'T') # get all directions from this component
if len(CompDir)>0: # there are some
PmagSampRec=pmag.lnpbykey(CompDir,'sample','specimen') # get a sample average from all specimens
PmagSampRec["er_location_name"]=CompDir[0]['er_location_name'] # decorate the sample record
PmagSampRec["er_site_name"]=CompDir[0]['er_site_name']
PmagSampRec["er_sample_name"]=samp
PmagSampRec["er_citation_names"]="This study"
PmagSampRec["er_analyst_mail_names"]=user
PmagSampRec['magic_software_packages']=version_num
if nocrit!=1:PmagSampRec['pmag_criteria_codes']="ACCEPT"
if agefile != "": PmagSampRec= pmag.get_age(PmagSampRec,"er_site_name","sample_inferred_",AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',PmagSampRec['er_site_name'],'T')
if len(site_height)>0:PmagSampRec["sample_height"]=site_height[0]['site_height'] # add in height if available
PmagSampRec['sample_comp_name']=comp
PmagSampRec['sample_tilt_correction']=coord
PmagSampRec['er_specimen_names']= pmag.get_list(CompDir,'er_specimen_name') # get a list of the specimen names used
PmagSampRec['magic_method_codes']= pmag.get_list(CompDir,'magic_method_codes') # get a list of the methods used
if nocrit!=1: # apply selection criteria
kill=pmag.grade(PmagSampRec,accept,'sample_dir')
else:
kill=[]
if len(kill)==0:
SampDirs.append(PmagSampRec)
if vgps==1: # if sample level VGP info desired, do that now
PmagResRec=pmag.getsampVGP(PmagSampRec,SiteNFO)
if PmagResRec!="":PmagResults.append(PmagResRec)
PmagSamps.append(PmagSampRec)
if Caverage==1: # average all components together basically same as above
PmagSampRec=pmag.lnpbykey(CoordDir,'sample','specimen')
PmagSampRec["er_location_name"]=CoordDir[0]['er_location_name']
PmagSampRec["er_site_name"]=CoordDir[0]['er_site_name']
PmagSampRec["er_sample_name"]=samp
PmagSampRec["er_citation_names"]="This study"
PmagSampRec["er_analyst_mail_names"]=user
PmagSampRec['magic_software_packages']=version_num
if nocrit!=1:PmagSampRec['pmag_criteria_codes']=""
if agefile != "": PmagSampRec= pmag.get_age(PmagSampRec,"er_site_name","sample_inferred_",AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',site,'T')
if len(site_height)>0:PmagSampRec["sample_height"]=site_height[0]['site_height'] # add in height if available
PmagSampRec['sample_tilt_correction']=coord
PmagSampRec['sample_comp_name']= pmag.get_list(CoordDir,'specimen_comp_name') # get components used
PmagSampRec['er_specimen_names']= pmag.get_list(CoordDir,'er_specimen_name') # get specimne names averaged
PmagSampRec['magic_method_codes']= pmag.get_list(CoordDir,'magic_method_codes') # assemble method codes
if nocrit!=1: # apply selection criteria
kill=pmag.grade(PmagSampRec,accept,'sample_dir')
if len(kill)==0: # passes the mustard
SampDirs.append(PmagSampRec)
if vgps==1:
PmagResRec=pmag.getsampVGP(PmagSampRec,SiteNFO)
if PmagResRec!="":PmagResults.append(PmagResRec)
else: # take everything
SampDirs.append(PmagSampRec)
if vgps==1:
PmagResRec=pmag.getsampVGP(PmagSampRec,SiteNFO)
if PmagResRec!="":PmagResults.append(PmagResRec)
PmagSamps.append(PmagSampRec)
if Iaverage==1: # average by sample if desired
SampI=pmag.get_dictitem(SpecInts,'er_sample_name',samp,'T') # get all the intensity data for this sample
if len(SampI)>0: # there are some
PmagSampRec=pmag.average_int(SampI,'specimen','sample') # get average intensity stuff
PmagSampRec["sample_description"]="sample intensity" # decorate sample record
PmagSampRec["sample_direction_type"]=""
PmagSampRec['er_site_name']=SampI[0]["er_site_name"]
PmagSampRec['er_sample_name']=samp
PmagSampRec['er_location_name']=SampI[0]["er_location_name"]
PmagSampRec["er_citation_names"]="This study"
PmagSampRec["er_analyst_mail_names"]=user
if agefile != "": PmagSampRec=pmag.get_age(PmagSampRec,"er_site_name","sample_inferred_", AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',PmagSampRec['er_site_name'],'T')
if len(site_height)>0:PmagSampRec["sample_height"]=site_height[0]['site_height'] # add in height if available
PmagSampRec['er_specimen_names']= pmag.get_list(SampI,'er_specimen_name')
PmagSampRec['magic_method_codes']= pmag.get_list(SampI,'magic_method_codes')
if nocrit!=1: # apply criteria!
kill=pmag.grade(PmagSampRec,accept,'sample_int')
if len(kill)==0:
PmagSampRec['pmag_criteria_codes']="ACCEPT"
SampInts.append(PmagSampRec)
PmagSamps.append(PmagSampRec)
else:PmagSampRec={} # sample rejected
else: # no criteria
SampInts.append(PmagSampRec)
PmagSamps.append(PmagSampRec)
PmagSampRec['pmag_criteria_codes']=""
if vgps==1 and get_model_lat!=0 and PmagSampRec!={}: #
if get_model_lat==1: # use sample latitude
PmagResRec=pmag.getsampVDM(PmagSampRec,SampNFO)
del(PmagResRec['model_lat']) # get rid of the model lat key
elif get_model_lat==2: # use model latitude
PmagResRec=pmag.getsampVDM(PmagSampRec,ModelLats)
if PmagResRec!={}:PmagResRec['magic_method_codes']=PmagResRec['magic_method_codes']+":IE-MLAT"
if PmagResRec!={}:
PmagResRec['er_specimen_names']=PmagSampRec['er_specimen_names']
PmagResRec['er_sample_names']=PmagSampRec['er_sample_name']
PmagResRec['pmag_criteria_codes']='ACCEPT'
PmagResRec['average_int_sigma_perc']=PmagSampRec['sample_int_sigma_perc']
PmagResRec['average_int_sigma']=PmagSampRec['sample_int_sigma']
PmagResRec['average_int_n']=PmagSampRec['sample_int_n']
PmagResRec['vadm_n']=PmagSampRec['sample_int_n']
PmagResRec['data_type']='i'
PmagResults.append(PmagResRec)
if len(PmagSamps)>0:
TmpSamps,keylist=pmag.fillkeys(PmagSamps) # fill in missing keys from different types of records
pmag.magic_write(sampout,TmpSamps,'pmag_samples') # save in sample output file
print(' sample averages written to ',sampout)
#
#create site averages from specimens or samples as specified
#
for site in sites:
if Daverage==0: key,dirlist='specimen',SpecDirs # if specimen averages at site level desired
if Daverage==1: key,dirlist='sample',SampDirs # if sample averages at site level desired
tmp=pmag.get_dictitem(dirlist,'er_site_name',site,'T') # get all the sites with directions
tmp1=pmag.get_dictitem(tmp,key+'_tilt_correction',coords[-1],'T') # use only the last coordinate if Caverage==0
sd=pmag.get_dictitem(SiteNFO,'er_site_name',site,'T') # fish out site information (lat/lon, etc.)
if len(sd)>0:
sitedat=sd[0]
if Caverage==0: # do component wise averaging
for comp in Comps:
siteD=pmag.get_dictitem(tmp1,key+'_comp_name',comp,'T') # get all components comp
if len(siteD)>0: # there are some for this site and component name
PmagSiteRec=pmag.lnpbykey(siteD,'site',key) # get an average for this site
PmagSiteRec['site_comp_name']=comp # decorate the site record
PmagSiteRec["er_location_name"]=siteD[0]['er_location_name']
PmagSiteRec["er_site_name"]=siteD[0]['er_site_name']
PmagSiteRec['site_tilt_correction']=coords[-1]
PmagSiteRec['site_comp_name']= pmag.get_list(siteD,key+'_comp_name')
if Daverage==1:
PmagSiteRec['er_sample_names']= pmag.get_list(siteD,'er_sample_name')
else:
PmagSiteRec['er_specimen_names']= pmag.get_list(siteD,'er_specimen_name')
# determine the demagnetization code (DC3,4 or 5) for this site
AFnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-AF','has'))
Tnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-T','has'))
DC=3
if AFnum>0:DC+=1
if Tnum>0:DC+=1
PmagSiteRec['magic_method_codes']= pmag.get_list(siteD,'magic_method_codes')+':'+ 'LP-DC'+str(DC)
PmagSiteRec['magic_method_codes'].strip(":")
if plotsites==1:
print(PmagSiteRec['er_site_name'])
pmagplotlib.plotSITE(EQ['eqarea'],PmagSiteRec,siteD,key) # plot and list the data
pmagplotlib.drawFIGS(EQ)
PmagSites.append(PmagSiteRec)
else: # last component only
siteD=tmp1[:] # get the last orientation system specified
if len(siteD)>0: # there are some
PmagSiteRec=pmag.lnpbykey(siteD,'site',key) # get the average for this site
PmagSiteRec["er_location_name"]=siteD[0]['er_location_name'] # decorate the record
PmagSiteRec["er_site_name"]=siteD[0]['er_site_name']
PmagSiteRec['site_comp_name']=comp
PmagSiteRec['site_tilt_correction']=coords[-1]
PmagSiteRec['site_comp_name']= pmag.get_list(siteD,key+'_comp_name')
PmagSiteRec['er_specimen_names']= pmag.get_list(siteD,'er_specimen_name')
PmagSiteRec['er_sample_names']= pmag.get_list(siteD,'er_sample_name')
AFnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-AF','has'))
Tnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-T','has'))
DC=3
if AFnum>0:DC+=1
if Tnum>0:DC+=1
PmagSiteRec['magic_method_codes']= pmag.get_list(siteD,'magic_method_codes')+':'+ 'LP-DC'+str(DC)
PmagSiteRec['magic_method_codes'].strip(":")
if Daverage==0:PmagSiteRec['site_comp_name']= pmag.get_list(siteD,key+'_comp_name')
if plotsites==1:
pmagplotlib.plotSITE(EQ['eqarea'],PmagSiteRec,siteD,key)
pmagplotlib.drawFIGS(EQ)
PmagSites.append(PmagSiteRec)
else:
print('site information not found in er_sites for site, ',site,' site will be skipped')
for PmagSiteRec in PmagSites: # now decorate each dictionary some more, and calculate VGPs etc. for results table
PmagSiteRec["er_citation_names"]="This study"
PmagSiteRec["er_analyst_mail_names"]=user
PmagSiteRec['magic_software_packages']=version_num
if agefile != "": PmagSiteRec= pmag.get_age(PmagSiteRec,"er_site_name","site_inferred_",AgeNFO,DefaultAge)
PmagSiteRec['pmag_criteria_codes']='ACCEPT'
if 'site_n_lines' in list(PmagSiteRec.keys()) and 'site_n_planes' in list(PmagSiteRec.keys()) and PmagSiteRec['site_n_lines']!="" and PmagSiteRec['site_n_planes']!="":
if int(PmagSiteRec["site_n_planes"])>0:
PmagSiteRec["magic_method_codes"]=PmagSiteRec['magic_method_codes']+":DE-FM-LP"
elif int(PmagSiteRec["site_n_lines"])>2:
PmagSiteRec["magic_method_codes"]=PmagSiteRec['magic_method_codes']+":DE-FM"
kill=pmag.grade(PmagSiteRec,accept,'site_dir')
if len(kill)==0:
PmagResRec={} # set up dictionary for the pmag_results table entry
PmagResRec['data_type']='i' # decorate it a bit
PmagResRec['magic_software_packages']=version_num
PmagSiteRec['site_description']='Site direction included in results table'
PmagResRec['pmag_criteria_codes']='ACCEPT'
dec=float(PmagSiteRec["site_dec"])
inc=float(PmagSiteRec["site_inc"])
if 'site_alpha95' in list(PmagSiteRec.keys()) and PmagSiteRec['site_alpha95']!="":
a95=float(PmagSiteRec["site_alpha95"])
else:a95=180.
sitedat=pmag.get_dictitem(SiteNFO,'er_site_name',PmagSiteRec['er_site_name'],'T')[0] # fish out site information (lat/lon, etc.)
lat=float(sitedat['site_lat'])
lon=float(sitedat['site_lon'])
plong,plat,dp,dm=pmag.dia_vgp(dec,inc,a95,lat,lon) # get the VGP for this site
if PmagSiteRec['site_tilt_correction']=='-1':C=' (spec coord) '
if PmagSiteRec['site_tilt_correction']=='0':C=' (geog. coord) '
if PmagSiteRec['site_tilt_correction']=='100':C=' (strat. coord) '
PmagResRec["pmag_result_name"]="VGP Site: "+PmagSiteRec["er_site_name"] # decorate some more
PmagResRec["result_description"]="Site VGP, coord system = "+str(coord)+' component: '+comp
PmagResRec['er_site_names']=PmagSiteRec['er_site_name']
PmagResRec['pmag_criteria_codes']='ACCEPT'
PmagResRec['er_citation_names']='This study'
PmagResRec['er_analyst_mail_names']=user
PmagResRec["er_location_names"]=PmagSiteRec["er_location_name"]
if Daverage==1:
PmagResRec["er_sample_names"]=PmagSiteRec["er_sample_names"]
else:
PmagResRec["er_specimen_names"]=PmagSiteRec["er_specimen_names"]
PmagResRec["tilt_correction"]=PmagSiteRec['site_tilt_correction']
PmagResRec["pole_comp_name"]=PmagSiteRec['site_comp_name']
PmagResRec["average_dec"]=PmagSiteRec["site_dec"]
PmagResRec["average_inc"]=PmagSiteRec["site_inc"]
PmagResRec["average_alpha95"]=PmagSiteRec["site_alpha95"]
PmagResRec["average_n"]=PmagSiteRec["site_n"]
PmagResRec["average_n_lines"]=PmagSiteRec["site_n_lines"]
PmagResRec["average_n_planes"]=PmagSiteRec["site_n_planes"]
PmagResRec["vgp_n"]=PmagSiteRec["site_n"]
PmagResRec["average_k"]=PmagSiteRec["site_k"]
PmagResRec["average_r"]=PmagSiteRec["site_r"]
PmagResRec["average_lat"]='%10.4f ' %(lat)
PmagResRec["average_lon"]='%10.4f ' %(lon)
if agefile != "": PmagResRec= pmag.get_age(PmagResRec,"er_site_names","average_",AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',site,'T')
if len(site_height)>0:PmagResRec["average_height"]=site_height[0]['site_height']
PmagResRec["vgp_lat"]='%7.1f ' % (plat)
PmagResRec["vgp_lon"]='%7.1f ' % (plong)
PmagResRec["vgp_dp"]='%7.1f ' % (dp)
PmagResRec["vgp_dm"]='%7.1f ' % (dm)
PmagResRec["magic_method_codes"]= PmagSiteRec["magic_method_codes"]
if PmagSiteRec['site_tilt_correction']=='0':PmagSiteRec['magic_method_codes']=PmagSiteRec['magic_method_codes']+":DA-DIR-GEO"
if PmagSiteRec['site_tilt_correction']=='100':PmagSiteRec['magic_method_codes']=PmagSiteRec['magic_method_codes']+":DA-DIR-TILT"
PmagSiteRec['site_polarity']=""
if polarity==1: # assign polarity based on angle of pole lat to spin axis - may want to re-think this sometime
angle=pmag.angle([0,0],[0,(90-plat)])
if angle <= 55.: PmagSiteRec["site_polarity"]='n'
if angle > 55. and angle < 125.: PmagSiteRec["site_polarity"]='t'
if angle >= 125.: PmagSiteRec["site_polarity"]='r'
PmagResults.append(PmagResRec)
if polarity==1:
crecs=pmag.get_dictitem(PmagSites,'site_tilt_correction','100','T') # find the tilt corrected data
if len(crecs)<2:crecs=pmag.get_dictitem(PmagSites,'site_tilt_correction','0','T') # if there aren't any, find the geographic corrected data
if len(crecs)>2: # if there are some,
comp=pmag.get_list(crecs,'site_comp_name').split(':')[0] # find the first component
crecs=pmag.get_dictitem(crecs,'site_comp_name',comp,'T') # fish out all of the first component
precs=[]
for rec in crecs:
precs.append({'dec':rec['site_dec'],'inc':rec['site_inc'],'name':rec['er_site_name'],'loc':rec['er_location_name']})
polpars=pmag.fisher_by_pol(precs) # calculate average by polarity
for mode in list(polpars.keys()): # hunt through all the modes (normal=A, reverse=B, all=ALL)
PolRes={}
PolRes['er_citation_names']='This study'
PolRes["pmag_result_name"]="Polarity Average: Polarity "+mode #
PolRes["data_type"]="a"
PolRes["average_dec"]='%7.1f'%(polpars[mode]['dec'])
PolRes["average_inc"]='%7.1f'%(polpars[mode]['inc'])
PolRes["average_n"]='%i'%(polpars[mode]['n'])
PolRes["average_r"]='%5.4f'%(polpars[mode]['r'])
PolRes["average_k"]='%6.0f'%(polpars[mode]['k'])
PolRes["average_alpha95"]='%7.1f'%(polpars[mode]['alpha95'])
PolRes['er_site_names']= polpars[mode]['sites']
PolRes['er_location_names']= polpars[mode]['locs']
PolRes['magic_software_packages']=version_num
PmagResults.append(PolRes)
if noInt!=1 and nositeints!=1:
for site in sites: # now do intensities for each site
if plotsites==1:print(site)
if Iaverage==0: key,intlist='specimen',SpecInts # if using specimen level data
if Iaverage==1: key,intlist='sample',PmagSamps # if using sample level data
Ints=pmag.get_dictitem(intlist,'er_site_name',site,'T') # get all the intensities for this site
if len(Ints)>0: # there are some
PmagSiteRec=pmag.average_int(Ints,key,'site') # get average intensity stuff for site table
PmagResRec=pmag.average_int(Ints,key,'average') # get average intensity stuff for results table
if plotsites==1: # if site by site examination requested - print this site out to the screen
for rec in Ints:print(rec['er_'+key+'_name'],' %7.1f'%(1e6*float(rec[key+'_int'])))
if len(Ints)>1:
print('Average: ','%7.1f'%(1e6*float(PmagResRec['average_int'])),'N: ',len(Ints))
print('Sigma: ','%7.1f'%(1e6*float(PmagResRec['average_int_sigma'])),'Sigma %: ',PmagResRec['average_int_sigma_perc'])
input('Press any key to continue\n')
er_location_name=Ints[0]["er_location_name"]
PmagSiteRec["er_location_name"]=er_location_name # decorate the records
PmagSiteRec["er_citation_names"]="This study"
PmagResRec["er_location_names"]=er_location_name
PmagResRec["er_citation_names"]="This study"
PmagSiteRec["er_analyst_mail_names"]=user
PmagResRec["er_analyst_mail_names"]=user
PmagResRec["data_type"]='i'
if Iaverage==0:
PmagSiteRec['er_specimen_names']= pmag.get_list(Ints,'er_specimen_name') # list of all specimens used
PmagResRec['er_specimen_names']= pmag.get_list(Ints,'er_specimen_name')
PmagSiteRec['er_sample_names']= pmag.get_list(Ints,'er_sample_name') # list of all samples used
PmagResRec['er_sample_names']= pmag.get_list(Ints,'er_sample_name')
PmagSiteRec['er_site_name']= site
PmagResRec['er_site_names']= site
PmagSiteRec['magic_method_codes']= pmag.get_list(Ints,'magic_method_codes')
PmagResRec['magic_method_codes']= pmag.get_list(Ints,'magic_method_codes')
kill=pmag.grade(PmagSiteRec,accept,'site_int')
if nocrit==1 or len(kill)==0:
b,sig=float(PmagResRec['average_int']),""
if(PmagResRec['average_int_sigma'])!="":sig=float(PmagResRec['average_int_sigma'])
sdir=pmag.get_dictitem(PmagResults,'er_site_names',site,'T') # fish out site direction
if len(sdir)>0 and sdir[-1]['average_inc']!="": # get the VDM for this record using last average inclination (hope it is the right one!)
inc=float(sdir[0]['average_inc']) #
mlat=pmag.magnetic_lat(inc) # get magnetic latitude using dipole formula
PmagResRec["vdm"]='%8.3e '% (pmag.b_vdm(b,mlat)) # get VDM with magnetic latitude
PmagResRec["vdm_n"]=PmagResRec['average_int_n']
if 'average_int_sigma' in list(PmagResRec.keys()) and PmagResRec['average_int_sigma']!="":
vdm_sig=pmag.b_vdm(float(PmagResRec['average_int_sigma']),mlat)
PmagResRec["vdm_sigma"]='%8.3e '% (vdm_sig)
else:
PmagResRec["vdm_sigma"]=""
mlat="" # define a model latitude
if get_model_lat==1: # use present site latitude
mlats=pmag.get_dictitem(SiteNFO,'er_site_name',site,'T')
if len(mlats)>0: mlat=mlats[0]['site_lat']
elif get_model_lat==2: # use a model latitude from some plate reconstruction model (or something)
mlats=pmag.get_dictitem(ModelLats,'er_site_name',site,'T')
if len(mlats)>0: PmagResRec['model_lat']=mlats[0]['site_model_lat']
mlat=PmagResRec['model_lat']
if mlat!="":
PmagResRec["vadm"]='%8.3e '% (pmag.b_vdm(b,float(mlat))) # get the VADM using the desired latitude
if sig!="":
vdm_sig=pmag.b_vdm(float(PmagResRec['average_int_sigma']),float(mlat))
PmagResRec["vadm_sigma"]='%8.3e '% (vdm_sig)
PmagResRec["vadm_n"]=PmagResRec['average_int_n']
else:
PmagResRec["vadm_sigma"]=""
sitedat=pmag.get_dictitem(SiteNFO,'er_site_name',PmagSiteRec['er_site_name'],'T') # fish out site information (lat/lon, etc.)
if len(sitedat)>0:
sitedat=sitedat[0]
PmagResRec['average_lat']=sitedat['site_lat']
PmagResRec['average_lon']=sitedat['site_lon']
else:
PmagResRec['average_lon']='UNKNOWN'
PmagResRec['average_lon']='UNKNOWN'
PmagResRec['magic_software_packages']=version_num
PmagResRec["pmag_result_name"]="V[A]DM: Site "+site
PmagResRec["result_description"]="V[A]DM of site"
PmagResRec["pmag_criteria_codes"]="ACCEPT"
if agefile != "": PmagResRec= pmag.get_age(PmagResRec,"er_site_names","average_",AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',site,'T')
if len(site_height)>0:PmagResRec["average_height"]=site_height[0]['site_height']
PmagSites.append(PmagSiteRec)
PmagResults.append(PmagResRec)
if len(PmagSites)>0:
Tmp,keylist=pmag.fillkeys(PmagSites)
pmag.magic_write(siteout,Tmp,'pmag_sites')
print(' sites written to ',siteout)
else: print("No Site level table")
if len(PmagResults)>0:
TmpRes,keylist=pmag.fillkeys(PmagResults)
pmag.magic_write(resout,TmpRes,'pmag_results')
print(' results written to ',resout)
else: print("No Results level table")
def convert(**kwargs):
# initialize defaults
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 # rename dir_path after input_dir_path is set
noave = kwargs.get('noave', False) # default is DO average
csv_file = kwargs.get('csv_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')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
volume = kwargs.get('volume', 2.5**
3) * 1e-6 #default volume is a 2.5cm cube
# format variables
if csv_file == "":
filelist = os.listdir(
input_dir_path) # read in list of files to import
else:
csv_file = os.path.join(input_dir_path, csv_file)
filelist = [csv_file]
# parsing the data
file_found, citations = False, "This Study"
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
for fin in filelist: # parse each file
if fin[-3:].lower() == 'csv':
file_found = True
print('processing: ', fin)
indata = open(fin, 'r').readlines()
keys = indata[0].replace('\n',
'').split(',') # splits on underscores
keys = [k.strip('"') for k in keys]
interval_key = "Offset (cm)"
if "Treatment Value (mT or \xc2\xb0C)" in keys:
demag_key = "Treatment Value (mT or \xc2\xb0C)"
elif "Treatment Value" in keys:
demag_key = "Treatment Value"
elif "Treatment Value (mT or °C)" in keys:
demag_key = "Treatment Value (mT or °C)"
elif "Demag level (mT)" in keys:
demag_key = "Demag level (mT)"
else:
print("couldn't find demag level")
if "Treatment type" in keys: treatment_type = "Treatment type"
elif "Treatment Type" in keys: treatment_type = "Treatment Type"
else: treatment_type = ""
run_key = "Test No."
if "Inclination background + tray corrected (deg)" in keys:
inc_key = "Inclination background + tray corrected (deg)"
elif "Inclination background & tray corrected (deg)" in keys:
inc_key = "Inclination background & tray corrected (deg)"
elif "Inclination background & tray corrected (deg)" in keys:
inc_key = "Inclination background & tray corrected (deg)"
elif "Inclination background & drift corrected (deg)" in keys:
inc_key = "Inclination background & drift corrected (deg)"
else:
print("couldn't find inclination")
if "Declination background + tray corrected (deg)" in keys:
dec_key = "Declination background + tray corrected (deg)"
elif "Declination background & tray corrected (deg)" in keys:
dec_key = "Declination background & tray corrected (deg)"
elif "Declination background & tray corrected (deg)" in keys:
dec_key = "Declination background & tray corrected (deg)"
elif "Declination background & drift corrected (deg)" in keys:
dec_key = "Declination background & drift corrected (deg)"
else:
print("couldn't find declination")
if "Intensity background + tray corrected (A/m)" in keys:
int_key = "Intensity background + tray corrected (A/m)"
elif "Intensity background & tray corrected (A/m)" in keys:
int_key = "Intensity background & tray corrected (A/m)"
elif "Intensity background & tray corrected (A/m)" in keys:
int_key = "Intensity background & tray corrected (A/m)"
elif "Intensity background & drift corrected (A/m)" in keys:
int_key = "Intensity background & drift corrected (A/m)"
else:
print("couldn't find magnetic moment")
type_val = "Type"
sect_key = "Sect"
half_key = "A/W"
# need to add volume_key to LORE format!
if "Sample volume (cm^3)" in keys:
volume_key = "Sample volume (cm^3)"
elif "Sample volume (cc)" in keys:
volume_key = "Sample volume (cc)"
elif "Sample volume (cm³)" in keys:
volume_key = "Sample volume (cm³)"
elif "Sample volume (cm\xc2\xb3)" in keys:
volume_key = "Sample volume (cm\xc2\xb3)"
else:
volume_key = ""
for line in indata[1:]:
InRec = {}
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
for k in range(len(keys)):
InRec[keys[k]] = line.split(',')[k].strip('"')
inst = "IODP-SRM"
expedition = InRec['Exp']
location = InRec['Site'] + InRec['Hole']
offsets = InRec[interval_key].split(
'.'
) # maintain consistency with er_samples convention of using top interval
if len(offsets) == 1:
offset = int(offsets[0])
else:
offset = int(offsets[0]) - 1
#interval=str(offset+1)# maintain consistency with er_samples convention of using top interval
interval = str(
offset
) # maintain consistency with er_samples convention of using top interval
specimen = expedition + '-' + location + '-' + InRec[
'Core'] + InRec[type_val] + "-" + InRec[
sect_key] + '-' + InRec[half_key] + '-' + str(
InRec[interval_key])
sample = expedition + '-' + location + '-' + InRec[
'Core'] + InRec[type_val]
site = expedition + '-' + location
if volume_key in list(InRec.keys()): volume = InRec[volume_key]
if not InRec[dec_key].strip(
""" " ' """) or not InRec[inc_key].strip(""" " ' """):
print("No dec or inc found for specimen %s, skipping" %
specimen)
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['citations'] = citations
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'] = citations
SampRec['azimuth'] = '0'
SampRec['dip'] = '0'
SampRec['method_codes'] = 'FS-C-DRILL-IODP:SO-V'
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'] = citations
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'] = citations
LocRec['expedition_name'] = expedition
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec['specimen'] = specimen
# set up measurement record - default is NRM
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["treat_ac_field"] = '0'
MeasRec["treat_dc_field"] = '0'
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
MeasRec["quality"] = 'g' # assume all data are "good"
MeasRec["standard"] = 'u' # assume all data are "good"
MeasRec["dir_csd"] = '0' # assume all data are "good"
MeasRec["method_codes"] = 'LT-NO'
sort_by = 'treat_ac_field' # set default to AF demag
if treatment_type in list(
InRec.keys()) and InRec[treatment_type] != "":
if "AF" in InRec[treatment_type].upper():
MeasRec['method_codes'] = 'LT-AF-Z'
inst = inst + ':IODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value = float(InRec[demag_key].strip(
'"')) * 1e-3 # convert mT => T
MeasRec["treat_ac_field"] = str(
treatment_value) # AF demag in treat mT => T
elif "T" in InRec[treatment_type].upper():
MeasRec['method_codes'] = 'LT-T-Z'
inst = inst + ':IODP-TDS' # measured on shipboard Schonstedt thermal demagnetizer
treatment_value = float(InRec[demag_key].strip(
'"')) + 273 # convert C => K
MeasRec["treat_temp"] = str(treatment_value)
elif "Lowrie" in InRec['Comments']:
MeasRec['method_codes'] = 'LP-IRM-3D'
treatment_value = float(InRec[demag_key].strip(
'"')) + 273. # convert C => K
MeasRec["treat_temp"] = str(treatment_value)
MeasRec["treat_ac_field"] = "0"
sort_by = 'treat_temp'
elif 'Isothermal' in InRec[treatment_type]:
MeasRec['method_codes'] = 'LT-IRM'
treatment_value = float(InRec[demag_key].strip(
'"')) * 1e-3 # convert mT => T
MeasRec["treat_dc_field"] = str(treatment_value)
MeasRec["treat_ac_field"] = "0"
sort_by = 'treat_dc_field'
elif InRec[demag_key] != "0" and InRec[
demag_key] != "": #Assume AF if there is no Treatment typ info
MeasRec['method_codes'] = 'LT-AF-Z'
inst = inst + ':IODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value = float(
InRec[demag_key].strip('"')) * 1e-3 # convert mT => T
MeasRec[
"treat_ac_field"] = treatment_value # AF demag in treat mT => T
MeasRec["standard"] = 'u' # assume all data are "good"
vol = float(volume)
if run_key in list(InRec.keys()):
run_number = InRec[run_key]
MeasRec['external_database_ids'] = {'LIMS': run_number}
else:
MeasRec['external_database_ids'] = ""
MeasRec['description'] = 'sample orientation: ' + InRec[
'Sample orientation']
MeasRec['dir_inc'] = InRec[inc_key].strip('"')
MeasRec['dir_dec'] = InRec[dec_key].strip('"')
intens = InRec[int_key].strip('"')
MeasRec['magn_moment'] = '%8.3e' % (
float(intens) * vol
) # convert intensity from A/m to Am^2 using vol
MeasRec['instrument_codes'] = inst
MeasRec['treat_step_num'] = '1'
MeasRec['meas_n_orient'] = ''
MeasRecs.append(MeasRec)
if not file_found:
print("No .csv files were found")
return False, "No .csv files were found"
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)
MeasSort = sorted(
MeasRecs,
lambda x, y=None: int(round(float(x[sort_by]) - float(y[sort_by])))
if y != None else 0)
MeasFixed = pmag.measurements_methods3(MeasSort, noave)
MeasOuts, keys = pmag.fillkeys(MeasFixed)
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
replace_AC_specimens.py
DESCRIPTION
finds anisotropy corrected data and
replaces that specimen with it.
puts in pmag_specimen format file
SYNTAX
replace_AC_specimens.py [command line options]
OPTIONS
-h prints help message and quits
-i allows interactive setting of file names
-fu TFILE uncorrected pmag_specimen format file with thellier interpretations
created by thellier_magic_redo.py
-fc AFILE anisotropy corrected pmag_specimen format file
created by thellier_magic_redo.py
-F FILE pmag_specimens format output file
DEFAULTS
TFILE: thellier_specimens.txt
AFILE: AC_specimens.txt
FILE: TorAC_specimens.txt
"""
dir_path = '.'
tspec = "thellier_specimens.txt"
aspec = "AC_specimens.txt"
ofile = "TorAC_specimens.txt"
critfile = "pmag_criteria.txt"
ACSamplist, Samplist, sigmin = [], [], 10000
GoodSamps, SpecOuts = [], []
# get arguments from command line
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-fu' in sys.argv:
ind = sys.argv.index('-fu')
tspec = sys.argv[ind + 1]
if '-fc' in sys.argv:
ind = sys.argv.index('-fc')
aspec = sys.argv[ind + 1]
if '-F' in sys.argv:
ind = sys.argv.index('-F')
ofile = sys.argv[ind + 1]
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
# read in pmag_specimens file
tspec = dir_path + '/' + tspec
aspec = dir_path + '/' + aspec
ofile = dir_path + '/' + ofile
Specs, file_type = pmag.magic_read(tspec)
Specs, file_type = pmag.magic_read(tspec)
Speclist = pmag.get_specs(Specs)
ACSpecs, file_type = pmag.magic_read(aspec)
ACspeclist = pmag.get_specs(ACSpecs)
for spec in Specs:
if spec["er_sample_name"] not in Samplist:
Samplist.append(spec["er_sample_name"])
for spec in ACSpecs:
if spec["er_sample_name"] not in ACSamplist:
ACSamplist.append(spec["er_sample_name"])
#
for samp in Samplist:
useAC, Ints, ACInts, GoodSpecs, AC, UC = 0, [], [], [], [], []
for spec in Specs:
if spec["er_sample_name"].lower() == samp.lower():
UC.append(spec)
if samp in ACSamplist:
for spec in ACSpecs:
if spec["er_sample_name"].lower() == samp.lower():
AC.append(spec)
if len(AC) > 0:
AClist = []
for spec in AC:
SpecOuts.append(spec)
AClist.append(spec['er_specimen_name'])
print('using AC: ', spec['er_specimen_name'],
'%7.1f' % (1e6 * float(spec['specimen_int'])))
for spec in UC:
if spec['er_specimen_name'] not in AClist:
SpecOuts.append(spec)
# print 'using UC: ',spec['er_specimen_name'],'%7.1f'%(1e6*float(spec['specimen_int']))
else:
for spec in UC:
SpecOuts.append(spec)
# print 'using UC: ',spec['er_specimen_name'],'%7.1f'%(1e6*float(spec['specimen_int']))
SpecOuts, keys = pmag.fillkeys(SpecOuts)
pmag.magic_write(ofile, SpecOuts, 'pmag_specimens')
print('thellier data assessed for AC correction put in ', ofile)
def main():
"""
NAME
odp_dcs_magic.py
DESCRIPTION
converts ODP discrete sample format files to magic_measurements format files
SYNTAX
odp_dsc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file for appending, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-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
-A : don't average replicate measurements
INPUT
Put data from separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in separate directory
"""
#
#
version_num = pmag.get_version()
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 = [], [], [], [], []
MagRecs = []
citation = "This study"
dir_path, demag = '.', 'NRM'
args = sys.argv
noave = 0
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-A" in args: noave = 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 = dir_path + '/' + args[ind + 1]
ErSamps, file_type = pmag.magic_read(samp_file)
else:
samp_file = dir_path + '/' + samp_file
if '-LP' in args:
ind = args.index("-LP")
codelist = args[ind + 1]
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"
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 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
spec_file = dir_path + '/' + spec_file
site_file = dir_path + '/' + site_file
meas_file = dir_path + '/' + meas_file
filelist = os.listdir(dir_path) # read in list of files to import
specimens, samples, sites = [], [], []
MagRecs, SpecRecs, SampRecs = [], [], []
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
for file in filelist: # parse each file
if file[-3:].lower() == 'dsc':
print('processing: ', file)
MagRec, SpecRec, SampRec = {}, {}, {}
treatment_type, treatment_value, user = "", "", ""
inst = "ODP-SRM"
input = open(dir_path + '/' + file, 'r').readlines()
IDs = file.split('_') # splits on underscores
pieces = IDs[0].split('-')
expedition = pieces[0]
location = pieces[1]
if file[0] != '_':
while len(pieces[2]) < 4:
pieces[2] = '0' + pieces[2] # pad core to be 3 characters
specimen = ""
else:
specimen = "test"
for piece in pieces:
specimen = specimen + piece + '-'
specimen = specimen[:-1]
alt_spec = IDs[
1] # alternate specimen is second field in field name
# set up specimen record for Er_specimens table
SpecRec['er_expedition_name'] = expedition
SpecRec['er_location_name'] = location
SpecRec['er_site_name'] = specimen
SpecRec['er_sample_name'] = specimen
SpecRec['er_citation_names'] = citation
for key in list(SpecRec.keys()):
SampRec[key] = SpecRec[key]
SampRec['sample_azimuth'] = '0'
SampRec['sample_dip'] = '0'
SampRec['magic_method_codes'] = 'FS-C-DRILL-IODP:SP-SS-C:SO-V'
SpecRec['er_specimen_name'] = specimen
SampRec['er_specimen_names'] = specimen
for key in list(SpecRec.keys()):
MagRec[key] = SpecRec[key]
# set up measurement record - default is NRM
MagRec['er_analyst_mail_names'] = user
MagRec['magic_method_codes'] = 'LT-NO'
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'
MagRec["measurement_flag"] = 'g' # assume all data are "good"
MagRec["measurement_standard"] = 'u' # assume all data are "good"
MagRec["measurement_csd"] = '' # set csd to blank
SpecRec['er_specimen_alternatives'] = alt_spec
vol = 7e-6 # assume 7 cc samples
datestamp = input[1].split() # date time is second line of file
mmddyy = datestamp[0].split('/') # break into month day year
date = mmddyy[2] + ':' + mmddyy[0] + ":" + mmddyy[
1] + ':' + datestamp[1]
MagRec["measurement_date"] = date
for k in range(len(input)):
fields = input[k].split("=")
if 'treatment_type' in fields[0]:
if "Alternating Frequency Demagnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst = inst + ':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type = "AF"
if "Anhysteretic Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-I'
inst = inst + ':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type = "ARM"
if "Isothermal Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-IRM'
inst = inst + ':ODP-IMP' # measured on shipboard ASC IMPULSE magnetizer
treatment_type = "IRM"
if "treatment_value" in fields[0]:
values = fields[1].split(',')
value = values[0]
if value != " \n":
if treatment_type == "AF":
treatment_value = float(value) * 1e-3
MagRec[
"treatment_ac_field"] = treatment_value # AF demag in treat mT => T
elif treatment_type == "IRM":
treatment_value = float(value) * 1e-3
MagRec["treatment_dc_field"] = '%8.3e' % (
treatment_value) # IRM treat mT => T
if treatment_type == "ARM":
treatment_value = float(value) * 1e-3
dc_value = float(values[1]) * 1e-3
MagRec[
"treatment_ac_field"] = treatment_value # AF demag in treat mT => T
MagRec["treatment_dc_field"] = '%8.3e' % (
dc_value) # DC mT => T
if 'user' in fields[0]:
user = fields[-1]
MagRec["er_analyst_mail_names"] = user
if 'sample_orientation' in fields[0]:
MagRec["measurement_description"] = fields[-1]
MagRec[
"measurement_standard"] = 'u' # assume all data are "good"
if 'sample_area' in fields[0]:
vol = float(
fields[1]
) * 1e-6 # takes volume (cc) and converts to m^3
if 'run_number' in fields[0]:
MagRec['external_database_ids'] = fields[
1] # run number is the LIMS measurement number
MagRec['external_database_names'] = 'LIMS'
if input[k][0:7] == '<MULTI>':
rec = input[k + 1].split(',') # list of data
for item in rec:
items = item.split('=')
if items[0].strip(
) == 'demag_level' and treatment_value == "":
treat = float(items[1])
if treat != 0:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst = inst + ':ODP-SRM-AF'
MagRec[
"treatment_ac_field"] = treat * 1e-3 # AF demag in treat mT => T
if items[0].strip() == 'inclination_w_tray_w_bkgrd':
MagRec['measurement_inc'] = items[1]
if items[0].strip() == 'declination_w_tray_w_bkgrd':
MagRec['measurement_dec'] = items[1]
if items[0].strip() == 'intensity_w_tray_w_bkgrd':
MagRec['measurement_magn_moment'] = '%8.3e' % (
float(items[1]) * vol
) # convert intensity from A/m to Am^2 using vol
if items[0].strip() == 'x_stdev':
MagRec['measurement_x_sd'] = items[1]
if items[0].strip() == 'y_stdev':
MagRec['measurement_y_sd'] = items[1]
if items[0].strip() == 'z_stdev':
MagRec['measurement_sd_z'] = items[1]
MagRec['magic_instrument_codes'] = inst
MagRec['measurement_number'] = '1'
MagRec['measurement_positions'] = ''
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
MagOuts = pmag.sort_diclist(MagRecs, 'treatment_ac_field')
for MagRec in MagOuts:
MagRec["treatment_ac_field"] = '%8.3e' % (MagRec["treatment_ac_field"]
) # convert to string
pmag.magic_write(spec_file, SpecRecs, 'er_specimens')
if len(SampRecs) > 0:
SampOut, keys = pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file, SampOut, 'er_samples')
print('samples stored in ', samp_file)
pmag.magic_write(samp_file, SampRecs, 'er_samples')
print('specimens stored in ', spec_file)
Fixed = pmag.measurements_methods(MagOuts, noave)
pmag.magic_write(meas_file, Fixed, 'magic_measurements')
print('data stored in ', 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 save_redo(SpecRecs, inspec):
SpecRecs, keys = pmag.fillkeys(SpecRecs)
pmag.magic_write(inspec, SpecRecs, 'pmag_specimens')
def main():
"""
NAME
odp_dcs_magic.py
DESCRIPTION
converts ODP discrete sample format files to magic_measurements format files
SYNTAX
odp_dsc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file for appending, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-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
-A : don't average replicate measurements
INPUT
Put data from separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in separate directory
"""
#
#
version_num=pmag.get_version()
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=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-A" in args: noave=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=dir_path+'/'+args[ind+1]
ErSamps,file_type=pmag.magic_read(samp_file)
else:
samp_file=dir_path+'/'+samp_file
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
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"
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 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
spec_file=dir_path+'/'+spec_file
site_file=dir_path+'/'+site_file
meas_file=dir_path+'/'+meas_file
filelist=os.listdir(dir_path) # read in list of files to import
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs=[],[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
for file in filelist: # parse each file
if file[-3:].lower()=='dsc':
print('processing: ',file)
MagRec,SpecRec,SampRec={},{},{}
treatment_type,treatment_value,user="","",""
inst="ODP-SRM"
input=open(dir_path+'/'+file,'r').readlines()
IDs=file.split('_') # splits on underscores
pieces=IDs[0].split('-')
expedition=pieces[0]
location=pieces[1]
if file[0]!='_':
while len(pieces[2])<4:pieces[2]='0'+pieces[2] # pad core to be 3 characters
specimen=""
else:
specimen="test"
for piece in pieces:
specimen=specimen+piece+'-'
specimen=specimen[:-1]
alt_spec=IDs[1] # alternate specimen is second field in field name
# set up specimen record for Er_specimens table
SpecRec['er_expedition_name']=expedition
SpecRec['er_location_name']=location
SpecRec['er_site_name']=specimen
SpecRec['er_sample_name']=specimen
SpecRec['er_citation_names']=citation
for key in list(SpecRec.keys()):SampRec[key]=SpecRec[key]
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SP-SS-C:SO-V'
SpecRec['er_specimen_name']=specimen
SampRec['er_specimen_names']=specimen
for key in list(SpecRec.keys()):MagRec[key]=SpecRec[key]
# set up measurement record - default is NRM
MagRec['er_analyst_mail_names']=user
MagRec['magic_method_codes']='LT-NO'
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'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
MagRec["measurement_csd"]='' # set csd to blank
SpecRec['er_specimen_alternatives']=alt_spec
vol=7e-6 # assume 7 cc samples
datestamp=input[1].split() # date time is second line of file
mmddyy=datestamp[0].split('/') # break into month day year
date=mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]
MagRec["measurement_date"]=date
for k in range(len(input)):
fields= input[k].split("=")
if 'treatment_type' in fields[0]:
if "Alternating Frequency Demagnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type="AF"
if "Anhysteretic Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-I'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type="ARM"
if "Isothermal Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-IRM'
inst=inst+':ODP-IMP' # measured on shipboard ASC IMPULSE magnetizer
treatment_type="IRM"
if "treatment_value" in fields[0]:
values=fields[1].split(',')
value=values[0]
if value!=" \n":
if treatment_type=="AF":
treatment_value=float(value)*1e-3
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
elif treatment_type=="IRM":
treatment_value=float(value)*1e-3
MagRec["treatment_dc_field"]='%8.3e'%(treatment_value) # IRM treat mT => T
if treatment_type=="ARM":
treatment_value=float(value)*1e-3
dc_value=float(values[1])*1e-3
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
MagRec["treatment_dc_field"]='%8.3e'%(dc_value) # DC mT => T
if 'user' in fields[0]:
user=fields[-1]
MagRec["er_analyst_mail_names"]=user
if 'sample_orientation' in fields[0]:
MagRec["measurement_description"]=fields[-1]
MagRec["measurement_standard"]='u' # assume all data are "good"
if 'sample_area' in fields[0]: vol=float(fields[1])*1e-6 # takes volume (cc) and converts to m^3
if 'run_number' in fields[0]:
MagRec['external_database_ids']=fields[1] # run number is the LIMS measurement number
MagRec['external_database_names']='LIMS'
if input[k][0:7]=='<MULTI>':
rec=input[k+1].split(',') # list of data
for item in rec:
items=item.split('=')
if items[0].strip()=='demag_level' and treatment_value=="" :
treat= float(items[1])
if treat!=0:
MagRec['magic_method_codes']='LT-AF-Z'
inst=inst+':ODP-SRM-AF'
MagRec["treatment_ac_field"]=treat*1e-3 # AF demag in treat mT => T
if items[0].strip()=='inclination_w_tray_w_bkgrd': MagRec['measurement_inc']=items[1]
if items[0].strip()=='declination_w_tray_w_bkgrd': MagRec['measurement_dec']=items[1]
if items[0].strip()=='intensity_w_tray_w_bkgrd': MagRec['measurement_magn_moment']='%8.3e'%(float(items[1])*vol) # convert intensity from A/m to Am^2 using vol
if items[0].strip()=='x_stdev':MagRec['measurement_x_sd']=items[1]
if items[0].strip()=='y_stdev':MagRec['measurement_y_sd']=items[1]
if items[0].strip()=='z_stdev':MagRec['measurement_sd_z']=items[1]
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
MagRec['measurement_positions']=''
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
MagOuts=pmag.sort_diclist(MagRecs,'treatment_ac_field')
for MagRec in MagOuts:
MagRec["treatment_ac_field"]='%8.3e'%(MagRec["treatment_ac_field"]) # convert to string
pmag.magic_write(spec_file,SpecRecs,'er_specimens')
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
print('samples stored in ',samp_file)
pmag.magic_write(samp_file,SampRecs,'er_samples')
print('specimens stored in ',spec_file)
Fixed=pmag.measurements_methods(MagOuts,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print('data stored in ',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 convert(**kwargs):
# initialize defaults
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 # rename dir_path after input_dir_path is set
noave = kwargs.get('noave', False) # default is DO average
csv_file = kwargs.get('csv_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')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
volume = kwargs.get('volume', 2.5**3)*1e-6#default volume is a 2.5cm cube
# format variables
if csv_file=="":
filelist=os.listdir(input_dir_path) # read in list of files to import
else:
csv_file = os.path.join(input_dir_path, csv_file)
filelist=[csv_file]
# parsing the data
file_found,citations = False,"This Study"
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
for fin in filelist: # parse each file
if fin[-3:].lower()=='csv':
file_found = True
print('processing: ',fin)
indata=open(fin,'r').readlines()
keys=indata[0].replace('\n','').split(',') # splits on underscores
keys=[k.strip('"') for k in keys]
interval_key="Offset (cm)"
if "Treatment Value (mT or \xc2\xb0C)" in keys:demag_key="Treatment Value (mT or \xc2\xb0C)"
elif "Treatment Value" in keys:demag_key="Treatment Value"
elif "Treatment Value (mT or °C)" in keys:demag_key="Treatment Value (mT or °C)"
elif "Demag level (mT)" in keys:demag_key="Demag level (mT)"
else: print("couldn't find demag level")
if "Treatment type" in keys:treatment_type="Treatment type"
elif "Treatment Type" in keys:treatment_type="Treatment Type"
else: treatment_type=""
run_key="Test No."
if "Inclination background + tray corrected (deg)" in keys: inc_key="Inclination background + tray corrected (deg)"
elif "Inclination background & tray corrected (deg)" in keys: inc_key="Inclination background & tray corrected (deg)"
elif "Inclination background & tray corrected (deg)" in keys:inc_key="Inclination background & tray corrected (deg)"
elif "Inclination background & drift corrected (deg)" in keys:inc_key="Inclination background & drift corrected (deg)"
else: print("couldn't find inclination")
if "Declination background + tray corrected (deg)" in keys: dec_key="Declination background + tray corrected (deg)"
elif "Declination background & tray corrected (deg)" in keys: dec_key="Declination background & tray corrected (deg)"
elif "Declination background & tray corrected (deg)" in keys:dec_key="Declination background & tray corrected (deg)"
elif "Declination background & drift corrected (deg)" in keys:dec_key="Declination background & drift corrected (deg)"
else: print("couldn't find declination")
if "Intensity background + tray corrected (A/m)" in keys: int_key="Intensity background + tray corrected (A/m)"
elif "Intensity background & tray corrected (A/m)" in keys: int_key="Intensity background & tray corrected (A/m)"
elif "Intensity background & tray corrected (A/m)" in keys:int_key="Intensity background & tray corrected (A/m)"
elif "Intensity background & drift corrected (A/m)" in keys:int_key="Intensity background & drift corrected (A/m)"
else: print("couldn't find magnetic moment")
type_val="Type"
sect_key="Sect"
half_key="A/W"
# need to add volume_key to LORE format!
if "Sample volume (cm^3)" in keys:volume_key="Sample volume (cm^3)"
elif "Sample volume (cc)" in keys:volume_key="Sample volume (cc)"
elif "Sample volume (cm³)" in keys:volume_key="Sample volume (cm³)"
elif "Sample volume (cm\xc2\xb3)" in keys:volume_key="Sample volume (cm\xc2\xb3)"
else: volume_key=""
for line in indata[1:]:
InRec={}
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
for k in range(len(keys)):InRec[keys[k]]=line.split(',')[k].strip('"')
inst="IODP-SRM"
expedition=InRec['Exp']
location=InRec['Site']+InRec['Hole']
offsets=InRec[interval_key].split('.') # maintain consistency with er_samples convention of using top interval
if len(offsets)==1:
offset=int(offsets[0])
else:
offset=int(offsets[0])-1
#interval=str(offset+1)# maintain consistency with er_samples convention of using top interval
interval=str(offset)# maintain consistency with er_samples convention of using top interval
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[type_val]+"-"+InRec[sect_key]+'-'+InRec[half_key]+'-'+str(InRec[interval_key])
sample = expedition+'-'+location+'-'+InRec['Core']+InRec[type_val]
site = expedition+'-'+location
if volume_key in list(InRec.keys()): volume=InRec[volume_key]
if not InRec[dec_key].strip(""" " ' """) or not InRec[inc_key].strip(""" " ' """):
print("No dec or inc found for specimen %s, skipping"%specimen)
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['citations']=citations
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']=citations
SampRec['azimuth']='0'
SampRec['dip']='0'
SampRec['method_codes']='FS-C-DRILL-IODP:SO-V'
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']=citations
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']=citations
LocRec['expedition_name']=expedition
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec['specimen']=specimen
# set up measurement record - default is NRM
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["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
MeasRec["quality"]='g' # assume all data are "good"
MeasRec["standard"]='u' # assume all data are "good"
MeasRec["dir_csd"]='0' # assume all data are "good"
MeasRec["method_codes"]='LT-NO'
sort_by='treat_ac_field' # set default to AF demag
if treatment_type in list(InRec.keys()) and InRec[treatment_type]!="":
if "AF" in InRec[treatment_type].upper():
MeasRec['method_codes'] = 'LT-AF-Z'
inst=inst+':IODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T
MeasRec["treat_ac_field"]=str(treatment_value) # AF demag in treat mT => T
elif "T" in InRec[treatment_type].upper():
MeasRec['method_codes'] = 'LT-T-Z'
inst=inst+':IODP-TDS' # measured on shipboard Schonstedt thermal demagnetizer
treatment_value=float(InRec[demag_key].strip('"'))+273 # convert C => K
MeasRec["treat_temp"]=str(treatment_value)
elif "Lowrie" in InRec['Comments']:
MeasRec['method_codes'] = 'LP-IRM-3D'
treatment_value=float(InRec[demag_key].strip('"'))+273. # convert C => K
MeasRec["treat_temp"]=str(treatment_value)
MeasRec["treat_ac_field"]="0"
sort_by='treat_temp'
elif 'Isothermal' in InRec[treatment_type]:
MeasRec['method_codes'] = 'LT-IRM'
treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T
MeasRec["treat_dc_field"]=str(treatment_value)
MeasRec["treat_ac_field"]="0"
sort_by='treat_dc_field'
elif InRec[demag_key]!="0" and InRec[demag_key]!="": #Assume AF if there is no Treatment typ info
MeasRec['method_codes'] = 'LT-AF-Z'
inst=inst+':IODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T
MeasRec["treat_ac_field"]=treatment_value # AF demag in treat mT => T
MeasRec["standard"]='u' # assume all data are "good"
vol=float(volume)
if run_key in list(InRec.keys()):
run_number=InRec[run_key]
MeasRec['external_database_ids']={'LIMS':run_number}
else:
MeasRec['external_database_ids']=""
MeasRec['description']='sample orientation: '+InRec['Sample orientation']
MeasRec['dir_inc']=InRec[inc_key].strip('"')
MeasRec['dir_dec']=InRec[dec_key].strip('"')
intens= InRec[int_key].strip('"')
MeasRec['magn_moment']='%8.3e'%(float(intens)*vol) # convert intensity from A/m to Am^2 using vol
MeasRec['instrument_codes']=inst
MeasRec['treat_step_num']='1'
MeasRec['meas_n_orient']=''
MeasRecs.append(MeasRec)
if not file_found:
print("No .csv files were found")
return False, "No .csv files were found"
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)
MeasSort=sorted(MeasRecs, lambda x,y=None: int(round(float(x[sort_by])-float(y[sort_by]))) if y!=None else 0)
MeasFixed=pmag.measurements_methods3(MeasSort,noave)
MeasOuts,keys=pmag.fillkeys(MeasFixed)
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