def getvec_geocentric(gh, lat, lon):
"""
from pmagpy - itype = 2 and alt = 6371.004
Evaluates the vector at a given latitude and longitude for a specified
set of coefficients
Parameters
----------
gh : a list of gauss coefficients
lat : latitude of location
long : longitude of location
Returns
-------
vec : direction in [dec, inc, intensity]
"""
sv = []
pad = 120 - len(gh)
for x in range(pad):
gh.append(0.)
for x in range(len(gh)):
sv.append(0.)
#! convert to colatitude for MB routine
itype = 2
colat = 90. - lat
date, alt = 2000., 6371.004 # use a dummy date and altitude
x, y, z, f = pmag.magsyn(gh, sv, date, date, itype, alt, colat, lon)
vec = pmag.cart2dir([x, y, z])
vec[2] = f
return vec
def main():
"""
NAME
igrf.py
DESCRIPTION
This program calculates igrf field values
using the routine of Malin and Barraclough (1981)
based on d/igrfs from 1900 to 2010.
between 1900 and 1000BCE, it uses CALS3K.4, ARCH3K.1
Prior to 1000BCE, it uses PFM9k or CALS10k-4b
Calculates reference field vector at specified location and time.
SYNTAX
igrf.py [-h] [-i] -f FILE [< filename]
OPTIONS:
-h prints help message and quits
-i for interactive data entry
-f FILE specify file name with input data
-F FILE specify output file name
-ages MIN MAX INCR: specify age minimum in years (+/- AD), maximum and increment, default is line by line
-loc LAT LON; specify location, default is line by line
-alt ALT; specify altitude in km, default is sealevel (0)
-plt; make a plot of the time series
-sav, saves plot and quits
-fmt [pdf,jpg,eps,svg] specify format for output figure (default is svg)
-mod [arch3k,cals3k,pfm9k,hfm10k,cals10k_2,shadif14k,cals10k] specify model for 3ka to 1900 AD, default is cals10k
NB: program uses IGRF12 for dates 1900 to 2015.
INPUT FORMAT
interactive entry:
date: decimal year
alt: altitude in km
lat: positive north
lon: positive east
for file entry:
space delimited string: date alt lat long
OUTPUT FORMAT
Declination Inclination Intensity (nT) date alt lat long
MODELS: ARCH3K: (Korte et al., 2009);CALS3K (Korte & Contable, 2011); CALS10k (is .1b of Korte et al., 2011); PFM9K (Nilsson et al., 2014); HFM10k (is HFM.OL1.A1 of Constable et al., 2016); CALS10k_2 (is cals10k.2 of Constable et al., 2016), SHADIF14k (SHA.DIF.14K of Pavon-Carrasco et al., 2014).
"""
plot, fmt = 0, 'svg'
plt = 0
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if len(sys.argv) != 0 and '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-mod' in sys.argv:
ind = sys.argv.index('-mod')
mod = sys.argv[ind + 1]
else:
mod = 'cals10k'
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
input = numpy.loadtxt(file)
elif '-i' in sys.argv:
while 1:
try:
line = []
line.append(float(input("Decimal year: <cntrl-D to quit> ")))
alt = input("Elevation in km [0] ")
if alt == "": alt = "0"
line.append(float(alt))
line.append(float(input("Latitude (positive north) ")))
line.append(float(input("Longitude (positive east) ")))
if mod == '':
x, y, z, f = pmag.doigrf(line[3] % 360., line[2], line[1],
line[0])
else:
x, y, z, f = pmag.doigrf(line[3] % 360.,
line[2],
line[1],
line[0],
mod=mod)
Dir = pmag.cart2dir((x, y, z))
print('%8.2f %8.2f %8.0f' % (Dir[0], Dir[1], f))
except EOFError:
print("\n Good-bye\n")
sys.exit()
elif '-ages' in sys.argv:
ind = sys.argv.index('-ages')
agemin = float(sys.argv[ind + 1])
agemax = float(sys.argv[ind + 2])
ageincr = float(sys.argv[ind + 3])
if '-loc' in sys.argv:
ind = sys.argv.index('-loc')
lat = float(sys.argv[ind + 1])
lon = float(sys.argv[ind + 2])
else:
print("must specify lat/lon if using age range option")
sys.exit()
if '-alt' in sys.argv:
ind = sys.argv.index('-alt')
alt = float(sys.argv[ind + 1])
else:
alt = 0
ages = numpy.arange(agemin, agemax, ageincr)
lats = numpy.ones(len(ages)) * lat
lons = numpy.ones(len(ages)) * lon
alts = numpy.ones(len(ages)) * alt
input = numpy.array([ages, alts, lats, lons]).transpose()
else:
input = numpy.loadtxt(sys.stdin, dtype=numpy.float)
if '-F' in sys.argv:
ind = sys.argv.index('-F')
outfile = sys.argv[ind + 1]
out = open(outfile, 'w')
else:
outfile = ""
if '-sav' in sys.argv: plot = 1
if '-plt' in sys.argv:
plt = 1
import matplotlib
matplotlib.use("TkAgg")
import pylab
pylab.ion()
Ages, Decs, Incs, Ints, VADMs = [], [], [], [], []
for line in input:
#if mod=='':
# x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0])
#else:
# x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0],mod=mod)
x, y, z, f = pmag.doigrf(line[3] % 360.,
line[2],
line[1],
line[0],
mod=mod)
Dir = pmag.cart2dir((x, y, z))
if outfile != "":
out.write('%8.2f %8.2f %8.0f %7.1f %7.1f %7.1f %7.1f\n' %
(Dir[0], Dir[1], f, line[0], line[1], line[2], line[3]))
elif plt:
Ages.append(line[0])
if Dir[0] > 180: Dir[0] = Dir[0] - 360.0
Decs.append(Dir[0])
Incs.append(Dir[1])
Ints.append(f * 1e-3)
VADMs.append(pmag.b_vdm(f * 1e-9, line[2]) * 1e-21)
else:
print('%8.2f %8.2f %8.0f %7.1f %7.1f %7.1f %7.1f' %
(Dir[0], Dir[1], f, line[0], line[1], line[2], line[3]))
if plt:
fig = pylab.figure(num=1, figsize=(7, 9))
fig.add_subplot(411)
pylab.plot(Ages, Decs)
pylab.ylabel('Declination ($^{\circ}$)')
fig.add_subplot(412)
pylab.plot(Ages, Incs)
pylab.ylabel('Inclination ($^{\circ}$)')
fig.add_subplot(413)
pylab.plot(Ages, Ints)
pylab.ylabel('Intensity ($\mu$T)')
fig.add_subplot(414)
pylab.plot(Ages, VADMs)
pylab.ylabel('VADMs (ZAm$^2$)')
pylab.xlabel('Ages')
if plot == 0:
pylab.draw()
ans = input("S[a]ve to save figure, <Return> to quit ")
if ans == 'a':
pylab.savefig('igrf.' + fmt)
print('Figure saved as: ', 'igrf.' + fmt)
else:
pylab.savefig('igrf.' + fmt)
print('Figure saved as: ', 'igrf.' + fmt)
sys.exit()
def main(command_line=True, **kwargs):
"""
NAME
pmd_magic.py
DESCRIPTION
converts PMD (Enkin) format files to magic_measurements format files
SYNTAX
pmd_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify naming convention
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
PMD format files
"""
# initialize some stuff
noave=0
inst=""
samp_con,Z='1',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
specnum=-1
MagRecs=[]
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
DIspec=[]
MagFiles=[]
user=""
mag_file=""
dir_path='.'
ErSamps=[]
SampOuts=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind+1]
#try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind+1])
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args: noave=1
if "-mcd" in args:
ind=args.index("-mcd")
meth_code=args[ind+1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 0)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
print samp_con
# format variables
mag_file = input_dir_path+"/" + mag_file
meas_file = output_dir_path+"/" + meas_file
samp_file = output_dir_path+"/" + samp_file
if specnum!=0:specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print "naming convention option [4] must be in form 4-Z where Z is an integer"
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
# parse data
data=open(mag_file,'rU').readlines() # read in data from file
comment=data[0]
line=data[1].strip()
line=line.replace("=","= ") # make finding orientations easier
rec=line.split() # read in sample orientation, etc.
er_specimen_name=rec[0]
ErSampRec,ErSiteRec={},{} # make a sample record
if specnum!=0:
er_sample_name=rec[0][:specnum]
else:
er_sample_name=rec[0]
if len(ErSamps)>0: # need to copy existing
for samp in ErSamps:
if samp['er_sample_name']==er_sample_name:
ErSampRec=samp # we'll ammend this one
else:
SampOuts.append(samp) # keep all the others
if int(samp_con)<6:
er_site_name=pmag.parse_site(er_sample_name,samp_con,Z)
else:
if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampREc['er_site_name']
if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampREc['er_location_name']
az_ind=rec.index('a=')+1
ErSampRec['er_sample_name']=er_sample_name
ErSampRec['er_sample_description']=comment
ErSampRec['sample_azimuth']=rec[az_ind]
dip_ind=rec.index('b=')+1
dip=-float(rec[dip_ind])
ErSampRec['sample_dip']='%7.1f'%(dip)
strike_ind=rec.index('s=')+1
ErSampRec['sample_bed_dip_direction']='%7.1f'%(float(rec[strike_ind])+90.)
bd_ind=rec.index('d=')+1
ErSampRec['sample_bed_dip']=rec[bd_ind]
v_ind=rec.index('v=')+1
vol=rec[v_ind][:-3]
date=rec[-2]
time=rec[-1]
ErSampRec['magic_method_codes']=meth_code
if 'er_location_name' not in ErSampRec.keys():ErSampRec['er_location_name']=er_location_name
if 'er_site_name' not in ErSampRec.keys():ErSampRec['er_site_name']=er_site_name
if 'er_citation_names' not in ErSampRec.keys():ErSampRec['er_citation_names']='This study'
if 'magic_method_codes' not in ErSampRec.keys():ErSampRec['magic_method_codes']='SO-NO'
SampOuts.append(ErSampRec)
for k in range(3,len(data)): # read in data
line=data[k]
rec=line.split()
if len(rec)>1: # skip blank lines at bottom
MagRec={}
MagRec['measurement_description']='Date: '+date+' '+time
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['er_site_name']=er_site_name
MagRec['er_sample_name']=er_sample_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=er_specimen_name
if rec[0]=='NRM':
meas_type="LT-NO"
elif rec[0][0]=='M' or rec[0][0]=='H':
meas_type="LT-AF-Z"
elif rec[0][0]=='T':
meas_type="LT-T-Z"
else:
print "measurement type unknown"
return False, "measurement type unknown"
X=[float(rec[1]),float(rec[2]),float(rec[3])]
Vec=pmag.cart2dir(X)
MagRec["measurement_magn_moment"]='%10.3e'% (Vec[2]) # Am^2
MagRec["measurement_magn_volume"]=rec[4] # A/m
MagRec["measurement_dec"]='%7.1f'%(Vec[0])
MagRec["measurement_inc"]='%7.1f'%(Vec[1])
MagRec["treatment_ac_field"]='0'
if meas_type!='LT-NO':
treat=float(rec[0][1:])
else:
treat=0
if meas_type=="LT-AF-Z":
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif meas_type=="LT-T-Z":
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
pmag.magic_write(samp_file,SampOuts,'er_samples')
print "sample orientations put in ",samp_file
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
bgc_magic.py
DESCRIPTION
converts Berkeley Geochronology Center (BGC) format files to magic_measurements format files
SYNTAX
bgc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-loc LOCNAME : specify location/study name
-site SITENAME : specify site name
-A: don't average replicate measurements
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-v NUM : specify the volume in cc of the sample, default 2.5^3cc. Will use vol in data file if volume!=0 in file.
INPUT
BGC paleomag format file
"""
# initialize some stuff
noave = 0
volume = 0.025**3 #default volume is a 2.5cm cube
#inst=""
#samp_con,Z='1',""
#missing=1
#demag="N"
er_location_name = "unknown"
er_site_name = "unknown"
#citation='This study'
args = sys.argv
meth_code = "LP-NO"
#specnum=1
version_num = pmag.get_version()
mag_file = ""
dir_path = '.'
MagRecs = []
SampOuts = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
meth_code = ""
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind+1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind+1]
#try:
# open(samp_file,'r')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind+1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind+1]
if "-site" in args:
ind = args.index("-site")
er_site_name = args[ind+1]
if "-A" in args:
noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind+1]
#samp_con='5'
if "-v" in args:
ind = args.index("-v")
volume = float(args[ind+1]) * 1e-6 # enter volume in cc, convert to m^3
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
er_location_name = kwargs.get('er_location_name', '')
er_site_name = kwargs.get('er_site_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 0.025**3 #default volume is a 2.5 cm cube, translated to meters cubed
else:
#convert cm^3 to m^3
volume *= 1e-6
# format variables
if not mag_file:
return False, 'You must provide a BCG format file'
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
samp_file = os.path.join(output_dir_path, samp_file)
ErSampRec = {}
# parse data
# Open up the BGC file and read the header information
print('mag_file in bgc_magic', mag_file)
pre_data = open(mag_file, 'r')
line = pre_data.readline()
line_items = line.split(' ')
sample_name = line_items[2]
sample_name = sample_name.replace('\n', '')
line = pre_data.readline()
line = pre_data.readline()
line_items = line.split('\t')
sample_azimuth = float(line_items[1])
sample_dip = float(line_items[2])
sample_bed_dip = line_items[3]
sample_bed_azimuth = line_items[4]
sample_lon = line_items[5]
sample_lat = line_items[6]
tmp_volume = line_items[7]
if tmp_volume != 0.0:
volume = float(tmp_volume) * 1e-6
pre_data.close()
data = pd.read_csv(mag_file, sep='\t', header=3, index_col=False)
cart = np.array([data['X'], data['Y'], data['Z']]).transpose()
direction = pmag.cart2dir(cart).transpose()
data['measurement_dec'] = direction[0]
data['measurement_inc'] = direction[1]
data['measurement_magn_moment'] = old_div(direction[2], 1000) # the data are in EMU - this converts to Am^2
data['measurement_magn_volume'] = old_div((old_div(direction[2], 1000)), volume) # EMU - data converted to A/m
# Configure the er_sample table
ErSampRec['er_sample_name'] = sample_name
ErSampRec['sample_azimuth'] = sample_azimuth
ErSampRec['sample_dip'] = sample_dip
ErSampRec['sample_bed_dip_direction'] = sample_bed_azimuth
ErSampRec['sample_bed_dip'] = sample_bed_dip
ErSampRec['sample_lat'] = sample_lat
ErSampRec['sample_lon'] = sample_lon
ErSampRec['magic_method_codes'] = meth_code
ErSampRec['er_location_name'] = er_location_name
ErSampRec['er_site_name'] = er_site_name
ErSampRec['er_citation_names'] = 'This study'
SampOuts.append(ErSampRec.copy())
# Configure the magic_measurements table
for rowNum, row in data.iterrows():
MagRec = {}
MagRec['measurement_description'] = 'Date: ' + str(row['Date']) + ' Time: ' + str(row['Time'])
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = er_site_name
MagRec['er_sample_name'] = sample_name
MagRec['magic_software_packages'] = version_num
MagRec["treatment_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = rowNum
MagRec["er_specimen_name"] = sample_name
MagRec["treatment_ac_field"] = '0'
if row['DM Val'] == '0':
meas_type = "LT-NO"
elif int(row['DM Type']) > 0.0:
meas_type = "LT-AF-Z"
treat = float(row['DM Val'])
MagRec["treatment_ac_field"] = '%8.3e' %(treat*1e-3) # convert from mT to tesla
elif int(row['DM Type']) == -1:
meas_type = "LT-T-Z"
treat = float(row['DM Val'])
MagRec["treatment_temp"] = '%8.3e' % (treat+273.) # temp in kelvin
else:
print("measurement type unknown:", row['DM Type'], " in row ", rowNum)
MagRec["measurement_magn_moment"] = str(row['measurement_magn_moment'])
MagRec["measurement_magn_volume"] = str(row['measurement_magn_volume'])
MagRec["measurement_dec"] = str(row['measurement_dec'])
MagRec["measurement_inc"] = str(row['measurement_inc'])
MagRec['magic_method_codes'] = meas_type
MagRec['measurement_csd'] = '0.0' # added due to magic.write error
MagRec['measurement_positions'] = '1' # added due to magic.write error
MagRecs.append(MagRec.copy())
pmag.magic_write(samp_file, SampOuts, 'er_samples')
print("sample orientations put in ", samp_file)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print("results put in ", meas_file)
return True, meas_file
def average_duplicates(duplicates):
'''
avarage replicate measurements.
'''
carts_s,carts_g,carts_t=[],[],[]
for rec in duplicates:
moment=float(rec['moment'])
if 'dec_s' in list(rec.keys()) and 'inc_s' in list(rec.keys()):
if rec['dec_s']!="" and rec['inc_s']!="":
dec_s=float(rec['dec_s'])
inc_s=float(rec['inc_s'])
cart_s=pmag.dir2cart([dec_s,inc_s,moment])
carts_s.append(cart_s)
if 'dec_g' in list(rec.keys()) and 'inc_g' in list(rec.keys()):
if rec['dec_g']!="" and rec['inc_g']!="":
dec_g=float(rec['dec_g'])
inc_g=float(rec['inc_g'])
cart_g=pmag.dir2cart([dec_g,inc_g,moment])
carts_g.append(cart_g)
if 'dec_t' in list(rec.keys()) and 'inc_t' in list(rec.keys()):
if rec['dec_t']!="" and rec['inc_t']!="":
dec_t=float(rec['dec_t'])
inc_t=float(rec['inc_t'])
cart_t=pmag.dir2cart([dec_t,inc_t,moment])
carts_t.append(cart_t)
if len(carts_s)>0:
carts=scipy.array(carts_s)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_s="%.2f"%mean_dir[0]
mean_inc_s="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_s,mean_inc_s="",""
if len(carts_g)>0:
carts=scipy.array(carts_g)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_g="%.2f"%mean_dir[0]
mean_inc_g="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_g,mean_inc_g="",""
if len(carts_t)>0:
carts=scipy.array(carts_t)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_t="%.2f"%mean_dir[0]
mean_inc_t="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_t,mean_inc_t="",""
meanrec={}
for key in list(duplicates[0].keys()):
if key in ['dec_s','inc_s','dec_g','inc_g','dec_t','inc_t','moment']:
continue
else:
meanrec[key]=duplicates[0][key]
meanrec['dec_s']=mean_dec_s
meanrec['dec_g']=mean_dec_g
meanrec['dec_t']=mean_dec_t
meanrec['inc_s']=mean_inc_s
meanrec['inc_g']=mean_inc_g
meanrec['inc_t']=mean_inc_t
meanrec['moment']=mean_moment
return meanrec
def main(command_line=True, **kwargs):
"""
NAME
utrecht_magic.py
DESCRIPTION
converts Utrecht magnetometer data files to magic_measurements files
SYNTAX
utrecht_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-WD: output directory for MagIC files
-ncn: Site Naming Convention
Site to Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2: default] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
-spc: number of characters to remove to generate sample names from specimen names
-dmy: European date format
-loc LOCNAME : specify location/study name
-lat latitude of samples
-lon longitude of samples
-A: don't average replicate measurements
-mcd: [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-dc: B PHI THETA: dc lab field (in microTesla), phi,and theta must be input as a tuple "(DC,PHI,THETA)". If not input user will be asked for values, this is advantagious if there are differing dc fields between steps or specimens. Note: this currently only works with the decimal IZZI naming convetion (XXX.0,1,2,3 where XXX is the treatment temperature and 0 is a zero field step, 1 is in field, and 2 is a pTRM check, 3 is a tail check). All other steps are hardcoded dc_field = 0.
INPUT
Utrecht magnetometer data file
"""
# initialize some stuff
sample_lat = 0.0
sample_lon = 0.0
noave = 0
er_location_name = "unknown"
args = sys.argv
meth_code = "LP-NO"
version_num = pmag.get_version()
site_num = 1
mag_file = ""
dir_path = '.'
MagRecs = []
SpecOuts = []
SampOuts = []
SiteOuts = []
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
meth_code = ""
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=args[ind+1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind+1]
if '-Fsi' in args: # LORI addition
ind=args.index("-Fsi")
site_file=args[ind+1]
#try:
# open(samp_file,'r')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind+1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind+1]
if "-lat" in args:
ind = args.index("-lat")
site_lat = args[ind+1]
if "-lon" in args:
ind = args.index("-lon")
site_lon = args[ind+1]
if "-A" in args:
noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind+1]
#samp_con='5'
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
site_num=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
site_num=samp_con.split("-")[1]
samp_con="7"
else: samp_con="1"
if '-dc' in args:
ind=args.index('-dc')
DC_FIELD,DC_PHI,DC_THETA=list(map(float,args[ind+1].strip('( ) [ ]').split(',')))
DC_FIELD *= 1e-6
yn=''
GET_DC_PARAMS=False
else: DC_FIELD,DC_PHI,DC_THETA=0,0,-90
if '-spc' in args:
ind=args.index("-spc")
specnum=-int(args[ind+1])
else: specnum = 0
if '-dmy' in args:
ind=args.index("-dmy")
dmy_flag=True
else: dmy_flag=False
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file', 'er_specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt') # site outfile
er_location_name = kwargs.get('location_name', '')
site_lat = kwargs.get('site_lat', '')
site_lon = kwargs.get('site_lon', '')
#oave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
specnum = -int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '2')
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
site_num=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
site_num=samp_con.split("-")[1]
samp_con="7"
DC_FIELD,DC_PHI,DC_THETA = list(map(float, kwargs.get('dc_params', (0,0,-90))))
DC_FIELD *= 1e-6
noave = kwargs.get('avg', True)
dmy_flag = kwargs.get('dmy_flag', False)
# format variables
if not mag_file:
return False, 'You must provide a Utrecht formated file'
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
# parse data
# Open up the Utrecht file and read the header information
print('mag_file in utrecht_file', mag_file)
AF_or_T = mag_file.split('.')[-1]
data = open(mag_file, 'r')
line = data.readline()
line_items = line.split(',')
operator=line_items[0]
operator=operator.replace("\"","")
machine=line_items[1]
machine=machine.replace("\"","")
machine=machine.rstrip('\n')
print("operator=", operator)
print("machine=", machine)
#read in measurement data
line = data.readline()
while line != "END" and line != '"END"':
ErSpecRec,ErSampRec,ErSiteRec = {},{},{}
line_items = line.split(',')
spec_name=line_items[0]
spec_name=spec_name.replace("\"","")
print("spec_name=", spec_name)
free_string=line_items[1]
free_string=free_string.replace("\"","")
print("free_string=", free_string)
dec=line_items[2]
print("dec=", dec)
inc=line_items[3]
print("inc=", inc)
volume=float(line_items[4])
volume=volume * 1e-6 # enter volume in cm^3, convert to m^3
print("volume=", volume)
bed_plane=line_items[5]
print("bed_plane=", bed_plane)
bed_tilt=line_items[6]
print("bed_tilt=", bed_tilt)
# Configure et er_ tables
ErSpecRec['er_specimen_name'] = spec_name
if specnum==0: sample_name = spec_name
else: sample_name = spec_name[:specnum]
ErSampRec['er_sample_name'] = sample_name
ErSpecRec['er_sample_name'] = sample_name
er_site_name = pmag.parse_site(sample_name,samp_con,site_num)
ErSpecRec['er_site_name']=er_site_name
ErSpecRec['er_location_name']=er_location_name
ErSampRec['sample_azimuth'] = dec
ErSampRec['sample_dip'] = str(float(inc)-90)
ErSampRec['sample_bed_dip_direction'] = bed_plane
ErSampRec['sample_bed_tilt'] = bed_tilt
ErSiteRec['site_lat'] = site_lat
ErSiteRec['site_lon'] = site_lon
ErSpecRec['magic_method_codes'] = meth_code
ErSampRec['er_location_name'] = er_location_name
ErSiteRec['er_location_name'] = er_location_name
ErSiteRec['er_site_name'] = er_site_name
ErSampRec['er_site_name'] = er_site_name
ErSampRec['er_citation_names'] = 'This study'
SpecOuts.append(ErSpecRec)
SampOuts.append(ErSampRec)
SiteOuts.append(ErSiteRec)
#measurement data
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
while line != '9999':
print(line)
step=items[0]
step=step.split('.')
step_value=step[0]
step_type = ""
if len(step) == 2:
step_type=step[1]
if step_type=='5':
step_value = items[0]
A=float(items[1])
B=float(items[2])
C=float(items[3])
# convert to MagIC coordinates
Z=-A
X=-B
Y=C
cart = np.array([X, Y, Z]).transpose()
direction = pmag.cart2dir(cart).transpose()
measurement_dec = direction[0]
measurement_inc = direction[1]
measurement_magn_moment = direction[2] * 1.0e-12 # the data are in pico-Am^2 - this converts to Am^2
measurement_magn_volume = direction[2] * 1.0e-12 / volume # data volume normalized - converted to A/m
print("measurement_magn_moment=", measurement_magn_moment)
print("measurement_magn_volume=", measurement_magn_volume)
error = items[4]
date=items[5]
date=date.strip('"')
if date.count("-") > 0:
date=date.split("-")
elif date.count("/") > 0:
date=date.split("/")
else: print("date format seperator cannot be identified")
print(date)
time=items[6]
time=time.strip('"')
time=time.split(":")
print(time)
if dmy_flag:
date_time = date[1] + ":" + date[0] + ":" + date[2] + ":" + time[0] + ":" + time[1] + ":" + "0.0"
else:
date_time = date[0] + ":" + date[1] + ":" + date[2] + ":" + time[0] + ":" + time[1] + ":" + "0.0"
print(date_time)
MagRec = {}
MagRec["er_analyst_mail_names"] = operator
MagRec["magic_instrument_codes"] = "Utrecht_" + machine
MagRec["measurement_description"] = "free string = " + free_string
MagRec["measurement_date"] = date_time
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = er_site_name
MagRec['er_sample_name'] = sample_name
MagRec['magic_software_packages'] = version_num
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["magic_experiment_name"] = er_location_name + er_site_name + spec_name
MagRec["measurement_number"] = er_location_name + er_site_name + spec_name + items[0]
MagRec["er_specimen_name"] = spec_name
# MagRec["treatment_ac_field"] = '0'
if AF_or_T.lower() == "th":
MagRec["treatment_temp"] = '%8.3e' % (float(step_value)+273.) # temp in kelvin
MagRec['treatment_ac_field']='0'
meas_type = "LP-DIR-T:LT-T-Z"
else:
MagRec['treatment_temp']='273'
MagRec['treatment_ac_field']='%10.3e'%(float(step_value)*1e-3)
meas_type = "LP-DIR-AF:LT-AF-Z"
MagRec['treatment_dc_field']='0'
if step_value == '0':
meas_type = "LT-NO"
print("step_type=", step_type)
if step_type == '0' and AF_or_T.lower() == 'th':
if meas_type == "":
meas_type = "LT-T-Z"
else:
meas_type = meas_type + ":" + "LT-T-Z"
elif step_type == '1':
if meas_type == "":
meas_type = "LT-T-I"
else:
meas_type = meas_type + ":" + "LT-T-I"
MagRec['treatment_dc_field']='%1.2e'%DC_FIELD
elif step_type == '2':
if meas_type == "":
meas_type = "LT-PTRM-I"
else:
meas_type = meas_type + ":" + "LT-PTRM-I"
MagRec['treatment_dc_field']='%1.2e'%DC_FIELD
elif step_type == '3':
if meas_type == "" :
meas_type = "LT-PTRM-Z"
else:
meas_type = meas_type + ":" + "LT-PTRM-Z"
print("meas_type=", meas_type)
MagRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MagRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
MagRec['magic_method_codes'] = meas_type
MagRec["measurement_magn_moment"] = measurement_magn_moment
MagRec["measurement_magn_volume"] = measurement_magn_volume
MagRec["measurement_dec"] = measurement_dec
MagRec["measurement_inc"] = measurement_inc
MagRec['measurement_csd'] = error
# MagRec['measurement_positions'] = '1'
MagRecs.append(MagRec)
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
# write out the data to MagIC data files
pmag.magic_write(spec_file, SpecOuts, 'er_specimens')
pmag.magic_write(samp_file, SampOuts, 'er_samples')
pmag.magic_write(site_file, SiteOuts, 'er_sites')
# MagOuts = pmag.measurements_methods(MagRecs, noave)
# pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
pmag.magic_write(meas_file, MagRecs, 'magic_measurements')
print("results put in ", meas_file)
print("exit!")
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
old_iodp_jr6_magic.py
DESCRIPTION
converts shipboard .jr6 format files to magic_measurements format files
SYNTAX
old_iodp_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-fsa FILE: specify er_samples.txt file for sample name lookup ,
default is 'er_samples.txt'
-loc HOLE : specify hole name (U1456A)
-A: don't average replicate measurements
INPUT
JR6 .jr6 format file
"""
def fix_separation(filename, new_filename):
old_file = open(filename, 'rU')
data = old_file.readlines()
new_data = []
for line in data:
new_line = line.replace('-', ' -')
new_line = new_line.replace(' ', ' ')
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
old_file.close()
new_file.close()
return new_filename
def old_fix_separation(filename, new_filename):
old_file = open(filename, 'rU')
data = old_file.readlines()
new_data = []
for line in data:
new_line = []
for i in line.split():
if '-' in i[1:]:
lead_char = '-' if i[0] == '-' else ''
if lead_char:
v = i[1:].split('-')
else:
v = i.split('-')
new_line.append(lead_char + v[0])
new_line.append('-' + v[1])
else:
new_line.append(i)
new_line = (' '.join(new_line)) + '\n'
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
new_file.close()
old_file.close()
return new_filename
# initialize some stuff
noave=0
volume=2.5**3 #default volume is a 2.5cm cube
inst=""
samp_con,Z='5',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
version_num=pmag.get_version()
dir_path='.'
MagRecs=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
mag_file = ''
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-fsa' in args:
ind = args.index("-fsa")
samp_file = args[ind+1]
if samp_file[0]!='/':
samp_file = os.path.join(input_dir_path, samp_file)
try:
open(samp_file,'rU')
ErSamps,file_type=pmag.magic_read(samp_file)
except:
print samp_file,' not found: '
print ' download csv file and import to MagIC with iodp_samples_magic.py'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args:
noave=1
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file', '')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
if len(str(samp_con)) > 1:
samp_con, Z = samp_con.split('-')
else:
Z = ''
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
# format variables
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
if mag_file:
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = os.path.join(input_dir_path, samp_file)
meas_file = os.path.join(output_dir_path, meas_file)
# validate variables
if not mag_file:
print "You must provide an IODP_jr6 format file"
return False, "You must provide an IODP_jr6 format file"
if not os.path.exists(mag_file):
print 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(os.path.join(input_dir_path, mag_file))
return False, 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(magfile)
if not os.path.exists(samp_file):
print 'samp_file', samp_file
print "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(input_dir_path)
return False, "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(input_dir_path)
# parse data
temp = os.path.join(output_dir_path, 'temp.txt')
fix_separation(mag_file, temp)
#os.rename('temp.txt', mag_file)
#data = open(mag_file, 'rU').readlines()
data=pd.read_csv(temp, delim_whitespace=True,header=None)
os.remove(temp)
samples,filetype = pmag.magic_read(samp_file)
data.columns=['specname','step','negz','y','x','expon','sample_azimuth','sample_dip','sample_bed_dip_direction','sample_bed_dip','bed_dip_dir2','bed_dip2','param1','param2','param3','param4','measurement_csd']
cart=np.array([data['x'],data['y'],-data['negz']]).transpose()
dir= pmag.cart2dir(cart).transpose()
data['measurement_dec']=dir[0]
data['measurement_inc']=dir[1]
data['measurement_magn_volume']=dir[2]*(10.0**data['expon']) # A/m - data in A/m
data['measurement_flag']='g'
data['measurement_standard']='u'
data['measurement_number']='1'
data['measurement_temp']='273'
data['er_location_name']=er_location_name
for rowNum, row in data.iterrows():
MagRec={}
spec_text_id=row['specname'].split('_')[1]
SampRecs=pmag.get_dictitem(samples,'er_sample_alternatives',spec_text_id,'has') # retrieve sample record for this specimen
if len(SampRecs)>0: # found one
MagRec['er_specimen_name']=SampRecs[0]['er_sample_name']
MagRec['er_sample_name']=MagRec['er_specimen_name']
MagRec['er_site_name']=MagRec['er_specimen_name']
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["treatment_ac_field"]='0'
volume=float(SampRecs[0]['sample_volume'])
moment=row['measurement_magn_volume'] * volume
MagRec["measurement_magn_moment"]=str(moment)
MagRec["measurement_magn_volume"]=str(row['measurement_magn_volume'])
MagRec["measurement_dec"]='%7.1f'%(row['measurement_dec'])
MagRec["measurement_inc"]='%7.1f'%(row['measurement_inc'])
if row['step'] == 'NRM':
meas_type="LT-NO"
elif row['step'][0:2] == 'AD':
meas_type="LT-AF-Z"
treat=float(row['step'][2:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type="LT-T-Z"
treat=float(row['step'][2:])
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
elif row['step'][0:3]=='ARM': #
meas_type="LT-AF-I"
treat=float(row['step'][3:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
MagRec["treatment_dc_field"]='%8.3e' %(50e-6) # assume 50uT DC field
MagRec["measurement_description"]='Assumed DC field - actual unknown'
elif row['step'][0:3]=='IRM': #
meas_type="LT-IRM"
treat=float(row['step'][3:])
MagRec["treatment_dc_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
else:
print 'unknown treatment type for ',row
return False, 'unknown treatment type for ',row
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec.copy())
else:
print 'sample name not found: ',row['specname']
MagOuts=pmag.measurements_methods(MagRecs,noave)
file_created, error_message = pmag.magic_write(meas_file,MagOuts,'magic_measurements')
if file_created:
return True, meas_file
else:
return False, 'Results not written to file'
def main():
"""
NAME
cart_dir.py
DESCRIPTION
converts cartesian coordinates to geomagnetic elements
INPUT (COMMAND LINE ENTRY)
x1 x2 x3
if only two columns, assumes magnitude of unity
OUTPUT
declination inclination magnitude
SYNTAX
cart_dir.py [command line options] [< filename]
OPTIONS
-h prints help message and quits
-i for interactive data entry
-f FILE to specify input filename
-F OFILE to specify output filename (also prints to screen)
"""
ofile = ""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-F' in sys.argv:
ind = sys.argv.index('-F')
ofile = sys.argv[ind + 1]
outfile = open(ofile, 'w')
if '-i' in sys.argv:
cont = 1
while cont == 1:
cart = []
try:
ans = input('X: [ctrl-D to quit] ')
cart.append(float(ans))
ans = input('Y: ')
cart.append(float(ans))
ans = input('Z: ')
cart.append(float(ans))
except:
print("\n Good-bye \n")
sys.exit()
dir = pmag.cart2dir(
cart) # send dir to dir2cart and spit out result
print('%7.1f %7.1f %10.3e' % (dir[0], dir[1], dir[2]))
elif '-f' in sys.argv:
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
inp = numpy.loadtxt(file) # read from a file
else:
inp = numpy.loadtxt(sys.stdin,
dtype=numpy.float) # read from standard input
dir = pmag.cart2dir(inp)
if len(dir.shape) == 1:
line = dir
print('%7.1f %7.1f %10.3e' % (line[0], line[1], line[2]))
if ofile != "":
outstring = '%7.1f %7.1f %10.8e\n' % (line[0], line[1], line[2])
outfile.write(outstring)
else:
for line in dir:
print('%7.1f %7.1f %10.3e' % (line[0], line[1], line[2]))
if ofile != "":
outstring = '%7.1f %7.1f %10.8e\n' % (line[0], line[1],
line[2])
outfile.write(outstring)
def main(command_line=True, **kwargs):
"""
NAME
bgc_magic.py
DESCRIPTION
converts Berkeley Geochronology Center (BGC) format files to magic_measurements format files
SYNTAX
bgc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-loc LOCNAME : specify location/study name
-site SITENAME : specify site name
-A: don't average replicate measurements
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-v NUM : specify the volume in cc of the sample, default 2.5^3cc. Will use vol in data file if volume!=0 in file.
INPUT
BGC paleomag format file
"""
# initialize some stuff
noave = 0
volume = 0.025**3 #default volume is a 2.5cm cube
#inst=""
#samp_con,Z='1',""
#missing=1
#demag="N"
er_location_name = "unknown"
er_site_name = "unknown"
#citation='This study'
args = sys.argv
meth_code = "LP-NO"
#specnum=1
version_num = pmag.get_version()
mag_file = ""
dir_path = '.'
MagRecs = []
SampOuts = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
meth_code = ""
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
#try:
# open(samp_file,'r')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-site" in args:
ind = args.index("-site")
er_site_name = args[ind + 1]
if "-A" in args:
noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind + 1]
#samp_con='5'
if "-v" in args:
ind = args.index("-v")
volume = float(
args[ind + 1]) * 1e-6 # enter volume in cc, convert to m^3
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
er_location_name = kwargs.get('er_location_name', '')
er_site_name = kwargs.get('er_site_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 0.025**3 #default volume is a 2.5 cm cube, translated to meters cubed
else:
#convert cm^3 to m^3
volume *= 1e-6
# format variables
if not mag_file:
return False, 'You must provide a BCG format file'
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
samp_file = os.path.join(output_dir_path, samp_file)
ErSampRec = {}
# parse data
# Open up the BGC file and read the header information
print('mag_file in bgc_magic', mag_file)
pre_data = open(mag_file, 'r')
line = pre_data.readline()
line_items = line.split(' ')
sample_name = line_items[2]
sample_name = sample_name.replace('\n', '')
line = pre_data.readline()
line = pre_data.readline()
line_items = line.split('\t')
sample_azimuth = float(line_items[1])
sample_dip = float(line_items[2])
sample_bed_dip = line_items[3]
sample_bed_azimuth = line_items[4]
sample_lon = line_items[5]
sample_lat = line_items[6]
tmp_volume = line_items[7]
if tmp_volume != 0.0:
volume = float(tmp_volume) * 1e-6
pre_data.close()
data = pd.read_csv(mag_file, sep='\t', header=3, index_col=False)
cart = np.array([data['X'], data['Y'], data['Z']]).transpose()
direction = pmag.cart2dir(cart).transpose()
data['measurement_dec'] = direction[0]
data['measurement_inc'] = direction[1]
data['measurement_magn_moment'] = old_div(
direction[2], 1000) # the data are in EMU - this converts to Am^2
data['measurement_magn_volume'] = old_div(
(old_div(direction[2], 1000)), volume) # EMU - data converted to A/m
# Configure the er_sample table
ErSampRec['er_sample_name'] = sample_name
ErSampRec['sample_azimuth'] = sample_azimuth
ErSampRec['sample_dip'] = sample_dip
ErSampRec['sample_bed_dip_direction'] = sample_bed_azimuth
ErSampRec['sample_bed_dip'] = sample_bed_dip
ErSampRec['sample_lat'] = sample_lat
ErSampRec['sample_lon'] = sample_lon
ErSampRec['magic_method_codes'] = meth_code
ErSampRec['er_location_name'] = er_location_name
ErSampRec['er_site_name'] = er_site_name
ErSampRec['er_citation_names'] = 'This study'
SampOuts.append(ErSampRec.copy())
# Configure the magic_measurements table
for rowNum, row in data.iterrows():
MagRec = {}
MagRec['measurement_description'] = 'Date: ' + str(
row['Date']) + ' Time: ' + str(row['Time'])
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = er_site_name
MagRec['er_sample_name'] = sample_name
MagRec['magic_software_packages'] = version_num
MagRec["treatment_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = rowNum
MagRec["er_specimen_name"] = sample_name
MagRec["treatment_ac_field"] = '0'
if row['DM Val'] == '0':
meas_type = "LT-NO"
elif int(row['DM Type']) > 0.0:
meas_type = "LT-AF-Z"
treat = float(row['DM Val'])
MagRec["treatment_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif int(row['DM Type']) == -1:
meas_type = "LT-T-Z"
treat = float(row['DM Val'])
MagRec["treatment_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
else:
print("measurement type unknown:", row['DM Type'], " in row ",
rowNum)
MagRec["measurement_magn_moment"] = str(row['measurement_magn_moment'])
MagRec["measurement_magn_volume"] = str(row['measurement_magn_volume'])
MagRec["measurement_dec"] = str(row['measurement_dec'])
MagRec["measurement_inc"] = str(row['measurement_inc'])
MagRec['magic_method_codes'] = meas_type
MagRec['measurement_csd'] = '0.0' # added due to magic.write error
MagRec['measurement_positions'] = '1' # added due to magic.write error
MagRecs.append(MagRec.copy())
pmag.magic_write(samp_file, SampOuts, 'er_samples')
print("sample orientations put in ", samp_file)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print("results put in ", meas_file)
return True, meas_file
def convert(**kwargs):
# initialize some stuff
demag="N"
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
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')
mag_file = kwargs.get('mag_file', '')
site = kwargs.get('site', 'unknown')
expedition = kwargs.get('expedition', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', False) # default means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = kwargs.get('volume', 2.5**3)*1e-6#default volume is a 2.5cm cube
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
if not mag_file:
print("-W- You must provide an IODP_jr6 format file")
return False, "You must provide an IODP_jr6 format file"
mag_file = os.path.join(input_dir_path, mag_file)
# validate variables
if not os.path.isfile(mag_file):
print('The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(mag_file))
return False, 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(mag_file)
# parse data
temp = os.path.join(output_dir_path, 'temp.txt')
fix_separation(mag_file, temp)
infile = open(temp, 'r')
lines = infile.readlines()
infile.close()
try: os.remove(temp)
except OSError: print("problem with temp file")
citations="This Study"
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
for line in lines:
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
line = line.split()
spec_text_id = line[0]
specimen = spec_text_id
for dem in ['-','_']:
if dem in spec_text_id:
sample=dem.join(spec_text_id.split(dem)[:-1]); break
location = expedition + site
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
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']=line[6]
SampRec['dip']=line[7]
SampRec['bed_dip_direction']=line[8]
SampRec['bed_dip']=line[9]
SampRec['method_codes']=meth_code
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations']= 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
MeasRec["citations"]=citations
MeasRec['software_packages']=version_num
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["quality"]='g'
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
MeasRec["treat_ac_field"]='0'
x = float(line[4])
y = float(line[3])
negz = float(line[2])
cart=np.array([x,y,-negz]).transpose()
direction = pmag.cart2dir(cart).transpose()
expon = float(line[5])
magn_volume = direction[2] * (10.0**expon)
moment = magn_volume * volume
MeasRec["magn_moment"]=str(moment)
MeasRec["magn_volume"]=str(magn_volume)#str(direction[2] * (10.0 ** expon))
MeasRec["dir_dec"]='%7.1f'%(direction[0])
MeasRec["dir_inc"]='%7.1f'%(direction[1])
step = line[1]
if step == 'NRM':
meas_type="LT-NO"
elif step[0:2] == 'AD':
meas_type="LT-AF-Z"
treat=float(step[2:])
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif step[0:2] == 'TD':
meas_type="LT-T-Z"
treat=float(step[2:])
MeasRec["treat_temp"]='%8.3e'%(treat+273.) # temp in kelvin
elif step[0:3]=='ARM': #
meas_type="LT-AF-I"
treat=float(row['step'][3:])
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
MeasRec["treat_dc_field"]='%8.3e' %(50e-6) # assume 50uT DC field
MeasRec["measurement_description"]='Assumed DC field - actual unknown'
elif step[0] == 'A':
meas_type="LT-AF-Z"
treat=float(step[1:])
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif step[0] == 'T':
meas_type="LT-T-Z"
treat=float(step[1:])
MeasRec["treat_temp"]='%8.3e' % (treat+273.) # temp in kelvin
elif step[0:3]=='IRM': #
meas_type="LT-IRM"
treat=float(step[3:])
MeasRec["treat_dc_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
else:
print('unknown treatment type for ',row)
return False, 'unknown treatment type for ',row
MeasRec['method_codes']=meas_type
MeasRecs.append(MeasRec.copy())
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return (True, meas_file)
def convert(**kwargs):
"""
"""
#get kwargs
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
lat = kwargs.get('lat', 0)
lon = kwargs.get('lon', 0)
specnum = int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
version_num = pmag.get_version()
if specnum != 0: specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print(
"naming convention option [4] must be in form 4-Z where Z is an integer"
)
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
else:
Z = 1
# format variables
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
# parse data
data = open(mag_file, 'r').readlines() # read in data from file
comment = data[0]
line = data[1].strip()
line = line.replace("=", "= ") # make finding orientations easier
rec = line.split() # read in sample orientation, etc.
specimen = rec[0]
SpecRecs, SampRecs, SiteRecs, LocRecs, MeasRecs = [], [], [], [], []
SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {} # make a sample record
if specnum != 0:
sample = rec[0][:specnum]
else:
sample = rec[0]
if int(samp_con) < 6:
site = pmag.parse_site(sample, samp_con, Z)
else:
if 'site' in list(SampRec.keys()): site = ErSampREc['site']
if 'location' in list(SampRec.keys()): location = ErSampREc['location']
az_ind = rec.index('a=') + 1
SampRec['sample'] = sample
SampRec['description'] = comment
SampRec['azimuth'] = rec[az_ind]
dip_ind = rec.index('b=') + 1
dip = -float(rec[dip_ind])
SampRec['dip'] = '%7.1f' % (dip)
strike_ind = rec.index('s=') + 1
SampRec['bed_dip_direction'] = '%7.1f' % (float(rec[strike_ind]) + 90.)
bd_ind = rec.index('d=') + 1
SampRec['bed_dip'] = rec[bd_ind]
v_ind = rec.index('v=') + 1
vol = rec[v_ind][:-3]
date = rec[-2]
time = rec[-1]
SampRec['method_codes'] = meth_code
SampRec['site'] = site
SampRec['citations'] = 'This study'
SampRec['method_codes'] = 'SO-NO'
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['citations'] = 'This study'
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations'] = 'This study'
SiteRec['lat'] = lat
SiteRec['lon'] = lon
LocRec['location'] = location
LocRec['citations'] = 'This study'
LocRec['lat_n'] = lat
LocRec['lat_s'] = lat
LocRec['lon_e'] = lon
LocRec['lon_w'] = lon
SpecRecs.append(SpecRec)
SampRecs.append(SampRec)
SiteRecs.append(SiteRec)
LocRecs.append(LocRec)
for k in range(3, len(data)): # read in data
line = data[k]
rec = line.split()
if len(rec) > 1: # skip blank lines at bottom
MeasRec = {}
MeasRec['description'] = 'Date: ' + date + ' ' + time
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["specimen"] = specimen
if rec[0] == 'NRM':
meas_type = "LT-NO"
elif rec[0][0] == 'M' or rec[0][0] == 'H':
meas_type = "LT-AF-Z"
elif rec[0][0] == 'T':
meas_type = "LT-T-Z"
else:
print("measurement type unknown")
return False, "measurement type unknown"
X = [float(rec[1]), float(rec[2]), float(rec[3])]
Vec = pmag.cart2dir(X)
MeasRec["magn_moment"] = '%10.3e' % (Vec[2]) # Am^2
MeasRec["magn_volume"] = rec[4] # A/m
MeasRec["dir_dec"] = '%7.1f' % (Vec[0])
MeasRec["dir_inc"] = '%7.1f' % (Vec[1])
MeasRec["treat_ac_field"] = '0'
if meas_type != 'LT-NO':
treat = float(rec[0][1:])
else:
treat = 0
if meas_type == "LT-AF-Z":
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif meas_type == "LT-T-Z":
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
MeasRec['method_codes'] = meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
version_num = pmag.get_version()
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # Loc outfile
mag_file = kwargs.get('mag_file') #required
location = kwargs.get('location', 'unknown')
site = kwargs.get('site', '')
samp_con = kwargs.get('samp_con', '1')
specnum = int(kwargs.get('specnum', 0))
timezone = kwargs.get('timestamp', 'US/Pacific')
noave = kwargs.get('noave', False) # default False means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 0.025**3 #default volume is a 2.5 cm cube, translated to meters cubed
else:
volume *= 1e-6 #convert cm^3 to m^3
if specnum != 0:
specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z = int(samp_con.split("-")[1])
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z = int(samp_con.split("-")[1])
samp_con = "7"
else:
Z = 1
# format variables
if not os.path.isfile(mag_file):
print("%s is not a BGC file" % mag_file)
return False, 'You must provide a BCG format file'
mag_file = os.path.join(input_dir_path, mag_file)
# Open up the BGC file and read the header information
print('mag_file in bgc_magic', mag_file)
pre_data = open(mag_file, 'r')
line = pre_data.readline()
line_items = line.split(' ')
specimen = line_items[2]
specimen = specimen.replace('\n', '')
line = pre_data.readline()
line = pre_data.readline()
line_items = line.split('\t')
azimuth = float(line_items[1])
dip = float(line_items[2])
bed_dip = line_items[3]
sample_bed_azimuth = line_items[4]
lon = line_items[5]
lat = line_items[6]
tmp_volume = line_items[7]
if tmp_volume != 0.0:
volume = float(tmp_volume) * 1e-6
pre_data.close()
data = pd.read_csv(mag_file, sep='\t', header=3, index_col=False)
cart = np.array([data['X'], data['Y'], data['Z']]).transpose()
direction = pmag.cart2dir(cart).transpose()
data['dir_dec'] = direction[0]
data['dir_inc'] = direction[1]
data['magn_moment'] = old_div(
direction[2], 1000) # the data are in EMU - this converts to Am^2
data['magn_volume'] = old_div((old_div(direction[2], 1000)),
volume) # EMU - data converted to A/m
# Configure the magic_measurements table
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
for rowNum, row in data.iterrows():
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
if specnum != 0:
sample = specimen[:specnum]
else:
sample = specimen
if site == '':
site = pmag.parse_site(sample, samp_con, Z)
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['volume'] = volume
SpecRec['analysts'] = user
SpecRec['citations'] = 'This study'
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['azimuth'] = azimuth
SampRec['dip'] = dip
SampRec['bed_dip_direction'] = sample_bed_azimuth
SampRec['bed_dip'] = bed_dip
SampRec['method_codes'] = meth_code
SampRec['analysts'] = user
SampRec['citations'] = 'This study'
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRec['analysts'] = user
SiteRec['citations'] = 'This study'
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['analysts'] = user
LocRec['citations'] = 'This study'
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec['description'] = 'Date: ' + str(row['Date']) + ' Time: ' + str(
row['Time'])
if '.' in row['Date']: datelist = row['Date'].split('.')
elif '/' in row['Date']: datelist = row['Date'].split('/')
elif '-' in row['Date']: datelist = row['Date'].split('-')
else:
print(
"unrecogized date formating on one of the measurement entries for specimen %s"
% specimen)
datelist = ['', '', '']
if ':' in row['Time']: timelist = row['Time'].split(':')
else:
print(
"unrecogized time formating on one of the measurement entries for specimen %s"
% specimen)
timelist = ['', '', '']
datelist[2] = '19' + datelist[2] if len(
datelist[2]) <= 2 else datelist[2]
dt = ":".join([
datelist[1], datelist[0], datelist[2], timelist[0], timelist[1],
timelist[2]
])
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp = utc_dt.strftime("%Y-%m-%dT%H:%M:%S") + "Z"
MeasRec["timestamp"] = timestamp
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = rowNum
MeasRec["specimen"] = specimen
MeasRec["treat_ac_field"] = '0'
if row['DM Val'] == '0':
meas_type = "LT-NO"
elif int(row['DM Type']) > 0.0:
meas_type = "LT-AF-Z"
treat = float(row['DM Val'])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif int(row['DM Type']) == -1:
meas_type = "LT-T-Z"
treat = float(row['DM Val'])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
else:
print("measurement type unknown:", row['DM Type'], " in row ",
rowNum)
MeasRec["magn_moment"] = str(row['magn_moment'])
MeasRec["magn_volume"] = str(row['magn_volume'])
MeasRec["dir_dec"] = str(row['dir_dec'])
MeasRec["dir_inc"] = str(row['dir_inc'])
MeasRec['method_codes'] = meas_type
MeasRec['dir_csd'] = '0.0' # added due to magic.write error
MeasRec['meas_n_orient'] = '1' # added due to magic.write error
MeasRecs.append(MeasRec.copy())
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
utrecht_magic.py
DESCRIPTION
converts Utrecht magnetometer data files to magic_measurements files
SYNTAX
utrecht_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-WD: output directory for MagIC files
-ncn: Site Naming Convention
Site to Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2: default] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
-spc: number of characters to remove to generate sample names from specimen names
-dmy: European date format
-loc LOCNAME : specify location/study name
-lat latitude of samples
-lon longitude of samples
-A: don't average replicate measurements
-mcd: [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-dc: B PHI THETA: dc lab field (in microTesla), phi,and theta must be input as a tuple "(DC,PHI,THETA)". If not input user will be asked for values, this is advantagious if there are differing dc fields between steps or specimens. Note: this currently only works with the decimal IZZI naming convetion (XXX.0,1,2,3 where XXX is the treatment temperature and 0 is a zero field step, 1 is in field, and 2 is a pTRM check, 3 is a tail check). All other steps are hardcoded dc_field = 0.
INPUT
Utrecht magnetometer data file
"""
# initialize some stuff
sample_lat = 0.0
sample_lon = 0.0
noave = 0
er_location_name = "unknown"
args = sys.argv
meth_code = "LP-NO"
version_num = pmag.get_version()
site_num = 1
mag_file = ""
dir_path = '.'
MagRecs = []
SpecOuts = []
SampOuts = []
SiteOuts = []
meas_file = 'magic_measurements.txt'
spec_file = 'er_specimens.txt'
samp_file = 'er_samples.txt'
site_file = 'er_sites.txt'
meth_code = ""
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsp' in args:
ind = args.index("-Fsp")
spec_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
if '-Fsi' in args: # LORI addition
ind = args.index("-Fsi")
site_file = args[ind + 1]
#try:
# open(samp_file,'r')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-lat" in args:
ind = args.index("-lat")
site_lat = args[ind + 1]
if "-lon" in args:
ind = args.index("-lon")
site_lon = args[ind + 1]
if "-A" in args:
noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind + 1]
#samp_con='5'
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print(
"option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
site_num = samp_con.split("-")[1]
samp_con = "4"
elif "7" in samp_con:
if "-" not in samp_con:
print(
"option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
site_num = samp_con.split("-")[1]
samp_con = "7"
else:
samp_con = "1"
if '-dc' in args:
ind = args.index('-dc')
DC_FIELD, DC_PHI, DC_THETA = list(
map(float, args[ind + 1].strip('( ) [ ]').split(',')))
DC_FIELD *= 1e-6
yn = ''
GET_DC_PARAMS = False
else:
DC_FIELD, DC_PHI, DC_THETA = 0, 0, -90
if '-spc' in args:
ind = args.index("-spc")
specnum = -int(args[ind + 1])
else:
specnum = 0
if '-dmy' in args:
ind = args.index("-dmy")
dmy_flag = True
else:
dmy_flag = False
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file',
'er_specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt') # site outfile
er_location_name = kwargs.get('location_name', '')
site_lat = kwargs.get('site_lat', '')
site_lon = kwargs.get('site_lon', '')
#oave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
specnum = -int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '2')
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
site_num = samp_con.split("-")[1]
samp_con = "4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
site_num = samp_con.split("-")[1]
samp_con = "7"
DC_FIELD, DC_PHI, DC_THETA = list(
map(float, kwargs.get('dc_params', (0, 0, -90))))
DC_FIELD *= 1e-6
noave = kwargs.get('avg', True)
dmy_flag = kwargs.get('dmy_flag', False)
# format variables
if not mag_file:
return False, 'You must provide a Utrecht formated file'
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
# parse data
# Open up the Utrecht file and read the header information
print('mag_file in utrecht_file', mag_file)
AF_or_T = mag_file.split('.')[-1]
data = open(mag_file, 'r')
line = data.readline()
line_items = line.split(',')
operator = line_items[0]
operator = operator.replace("\"", "")
machine = line_items[1]
machine = machine.replace("\"", "")
machine = machine.rstrip('\n')
print("operator=", operator)
print("machine=", machine)
#read in measurement data
line = data.readline()
while line != "END" and line != '"END"':
ErSpecRec, ErSampRec, ErSiteRec = {}, {}, {}
line_items = line.split(',')
spec_name = line_items[0]
spec_name = spec_name.replace("\"", "")
print("spec_name=", spec_name)
free_string = line_items[1]
free_string = free_string.replace("\"", "")
print("free_string=", free_string)
dec = line_items[2]
print("dec=", dec)
inc = line_items[3]
print("inc=", inc)
volume = float(line_items[4])
volume = volume * 1e-6 # enter volume in cm^3, convert to m^3
print("volume=", volume)
bed_plane = line_items[5]
print("bed_plane=", bed_plane)
bed_tilt = line_items[6]
print("bed_tilt=", bed_tilt)
# Configure et er_ tables
ErSpecRec['er_specimen_name'] = spec_name
if specnum == 0: sample_name = spec_name
else: sample_name = spec_name[:specnum]
ErSampRec['er_sample_name'] = sample_name
ErSpecRec['er_sample_name'] = sample_name
er_site_name = pmag.parse_site(sample_name, samp_con, site_num)
ErSpecRec['er_site_name'] = er_site_name
ErSpecRec['er_location_name'] = er_location_name
ErSampRec['sample_azimuth'] = dec
ErSampRec['sample_dip'] = str(float(inc) - 90)
ErSampRec['sample_bed_dip_direction'] = bed_plane
ErSampRec['sample_bed_tilt'] = bed_tilt
ErSiteRec['site_lat'] = site_lat
ErSiteRec['site_lon'] = site_lon
ErSpecRec['magic_method_codes'] = meth_code
ErSampRec['er_location_name'] = er_location_name
ErSiteRec['er_location_name'] = er_location_name
ErSiteRec['er_site_name'] = er_site_name
ErSampRec['er_site_name'] = er_site_name
ErSampRec['er_citation_names'] = 'This study'
SpecOuts.append(ErSpecRec)
SampOuts.append(ErSampRec)
SiteOuts.append(ErSiteRec)
#measurement data
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
while line != '9999':
print(line)
step = items[0]
step = step.split('.')
step_value = step[0]
step_type = ""
if len(step) == 2:
step_type = step[1]
if step_type == '5':
step_value = items[0]
A = float(items[1])
B = float(items[2])
C = float(items[3])
# convert to MagIC coordinates
Z = -A
X = -B
Y = C
cart = np.array([X, Y, Z]).transpose()
direction = pmag.cart2dir(cart).transpose()
measurement_dec = direction[0]
measurement_inc = direction[1]
measurement_magn_moment = direction[
2] * 1.0e-12 # the data are in pico-Am^2 - this converts to Am^2
measurement_magn_volume = direction[
2] * 1.0e-12 / volume # data volume normalized - converted to A/m
print("measurement_magn_moment=", measurement_magn_moment)
print("measurement_magn_volume=", measurement_magn_volume)
error = items[4]
date = items[5]
date = date.strip('"')
if date.count("-") > 0:
date = date.split("-")
elif date.count("/") > 0:
date = date.split("/")
else:
print("date format seperator cannot be identified")
print(date)
time = items[6]
time = time.strip('"')
time = time.split(":")
print(time)
if dmy_flag:
date_time = date[1] + ":" + date[0] + ":" + date[
2] + ":" + time[0] + ":" + time[1] + ":" + "0.0"
else:
date_time = date[0] + ":" + date[1] + ":" + date[
2] + ":" + time[0] + ":" + time[1] + ":" + "0.0"
print(date_time)
MagRec = {}
MagRec["er_analyst_mail_names"] = operator
MagRec["magic_instrument_codes"] = "Utrecht_" + machine
MagRec["measurement_description"] = "free string = " + free_string
MagRec["measurement_date"] = date_time
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = er_site_name
MagRec['er_sample_name'] = sample_name
MagRec['magic_software_packages'] = version_num
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec[
"magic_experiment_name"] = er_location_name + er_site_name + spec_name
MagRec[
"measurement_number"] = er_location_name + er_site_name + spec_name + items[
0]
MagRec["er_specimen_name"] = spec_name
# MagRec["treatment_ac_field"] = '0'
if AF_or_T.lower() == "th":
MagRec["treatment_temp"] = '%8.3e' % (float(step_value) + 273.
) # temp in kelvin
MagRec['treatment_ac_field'] = '0'
meas_type = "LP-DIR-T:LT-T-Z"
else:
MagRec['treatment_temp'] = '273'
MagRec['treatment_ac_field'] = '%10.3e' % (float(step_value) *
1e-3)
meas_type = "LP-DIR-AF:LT-AF-Z"
MagRec['treatment_dc_field'] = '0'
if step_value == '0':
meas_type = "LT-NO"
print("step_type=", step_type)
if step_type == '0' and AF_or_T.lower() == 'th':
if meas_type == "":
meas_type = "LT-T-Z"
else:
meas_type = meas_type + ":" + "LT-T-Z"
elif step_type == '1':
if meas_type == "":
meas_type = "LT-T-I"
else:
meas_type = meas_type + ":" + "LT-T-I"
MagRec['treatment_dc_field'] = '%1.2e' % DC_FIELD
elif step_type == '2':
if meas_type == "":
meas_type = "LT-PTRM-I"
else:
meas_type = meas_type + ":" + "LT-PTRM-I"
MagRec['treatment_dc_field'] = '%1.2e' % DC_FIELD
elif step_type == '3':
if meas_type == "":
meas_type = "LT-PTRM-Z"
else:
meas_type = meas_type + ":" + "LT-PTRM-Z"
print("meas_type=", meas_type)
MagRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MagRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
MagRec['magic_method_codes'] = meas_type
MagRec["measurement_magn_moment"] = measurement_magn_moment
MagRec["measurement_magn_volume"] = measurement_magn_volume
MagRec["measurement_dec"] = measurement_dec
MagRec["measurement_inc"] = measurement_inc
MagRec['measurement_csd'] = error
# MagRec['measurement_positions'] = '1'
MagRecs.append(MagRec)
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
# write out the data to MagIC data files
pmag.magic_write(spec_file, SpecOuts, 'er_specimens')
pmag.magic_write(samp_file, SampOuts, 'er_samples')
pmag.magic_write(site_file, SiteOuts, 'er_sites')
# MagOuts = pmag.measurements_methods(MagRecs, noave)
# pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
pmag.magic_write(meas_file, MagRecs, 'magic_measurements')
print("results put in ", meas_file)
print("exit!")
return True, meas_file
def plotMT(datablock, s, num, units, norm):
Ints = []
for plotrec in datablock:
Ints.append(plotrec[3])
Ints.sort()
T, M, Tv, recnum = [], [], [], 0
Mex, Tex, Vdif = [], [], []
recbak = []
for rec in datablock:
if rec[5] == 'g':
if units == "T":
T.append(rec[0] * 1e3)
Tv.append(rec[0] * 1e3)
if recnum > 0: Tv.append(rec[0] * 1e3)
elif units == "U":
T.append(rec[0])
Tv.append(rec[0])
if recnum > 0: Tv.append(rec[0])
elif units == "K":
T.append(rec[0] - 273)
Tv.append(rec[0] - 273)
if recnum > 0: Tv.append(rec[0] - 273)
elif "T" in units and "K" in units:
if rec[0] < 1.:
T.append(rec[0] * 1e3)
Tv.append(rec[0] * 1e3)
else:
T.append(rec[0] - 273)
Tv.append(rec[0] - 273)
if recnum > 0: Tv.append(rec[0] - 273)
else:
T.append(rec[0])
Tv.append(rec[0])
if recnum > 0: Tv.append(rec[0])
if norm == 1:
M.append(rec[3] / Ints[-1])
else:
M.append(rec[3])
if recnum > 0 and len(rec) > 0 and len(recbak) > 0:
v = []
if recbak[0] != rec[0]:
V0 = pmag.dir2cart([recbak[1], recbak[2], recbak[3]])
V1 = pmag.dir2cart([rec[1], rec[2], rec[3]])
for el in range(3):
v.append(abs(V1[el] - V0[el]))
vdir = pmag.cart2dir(v)
Vdif.append(vdir[2] / Ints[-1]) # append vector difference
Vdif.append(vdir[2] / Ints[-1]) #
recbak = []
for el in rec:
recbak.append(el)
delta = .02 * M[0]
if num == 1:
if recnum % 2 == 0:
plt.text(T[-1] + delta,
M[-1],
' ' * 3 + str(int(datablock[recnum][0] - 273)) +
'$\degree$C',
fontsize=9)
recnum += 1
else:
if rec[0] < 200: Tex.append(rec[0] * 1e3)
if rec[0] >= 200: Tex.append(rec[0] - 273)
Mex.append(rec[3] / Ints[-1])
recnum += 1
MTlist = T
MTlisty = M
if len(Mex) > 0 and len(Tex) > 0:
plt.scatter(Tex, Mex, marker='d', color='k')
if len(Vdif) > 0:
Vdif.append(vdir[2] / Ints[-1]) #
Vdif.append(0)
Tv.append(Tv[-1])
plt.plot(T, M)
plt.plot(T, M, 'ro')
if len(Tv) == len(Vdif) and norm == 1: plt.plot(Tv, Vdif, 'g-')
if units == "T":
plt.xlabel("Step (mT)")
elif units == "K":
plt.xlabel("Step (C)")
elif units == "J":
plt.xlabel("Step (J)")
else:
plt.xlabel("Step [mT,C]")
if norm == 1: plt.ylabel("Fractional Magnetization")
if norm == 0: plt.ylabel("Magnetization")
plt.axvline(0, color='k')
plt.axhline(0, color='k')
tstring = s
plt.title(tstring)
def main():
"""
NAME
cart_dir.py
DESCRIPTION
converts cartesian coordinates to geomagnetic elements
INPUT (COMMAND LINE ENTRY)
x1 x2 x3
if only two columns, assumes magnitude of unity
OUTPUT
declination inclination magnitude
SYNTAX
cart_dir.py [command line options] [< filename]
OPTIONS
-h prints help message and quits
-i for interactive data entry
-f FILE to specify input filename
-F OFILE to specify output filename (also prints to screen)
"""
ofile=""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-F' in sys.argv:
ind=sys.argv.index('-F')
ofile=sys.argv[ind+1]
outfile=open(ofile,'w')
if '-i' in sys.argv:
cont=1
while cont==1:
cart=[]
try:
ans=raw_input('X: [ctrl-D to quit] ')
cart.append(float(ans))
ans=raw_input('Y: ')
cart.append(float(ans))
ans=raw_input('Z: ')
cart.append(float(ans))
except:
print "\n Good-bye \n"
sys.exit()
dir= pmag.cart2dir(cart) # send dir to dir2cart and spit out result
print '%7.1f %7.1f %10.3e'%(dir[0],dir[1],dir[2])
elif '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
input=numpy.loadtxt(file) # read from a file
else:
input = numpy.loadtxt(sys.stdin,dtype=numpy.float) # read from standard input
dir=pmag.cart2dir(input)
if len(dir.shape)==1:
line=dir
print '%7.1f %7.1f %10.3e'%(line[0],line[1],line[2])
if ofile!="":
outstring='%7.1f %7.1f %10.8e\n' %(line[0],line[1],line[2])
outfile.write(outstring)
else:
for line in dir:
print '%7.1f %7.1f %10.3e'%(line[0],line[1],line[2])
if ofile!="":
outstring='%7.1f %7.1f %10.8e\n' %(line[0],line[1],line[2])
outfile.write(outstring)
def main():
"""
NAME
igrf.py
DESCRIPTION
This program calculates igrf field values
using the routine of Malin and Barraclough (1981)
based on d/igrfs from 1900 to 2010.
between 1900 and 1000BCE, it uses CALS3K.4, ARCH3K.1
Prior to 1000BCE, it uses PFM9k or CALS10k-4b
Calculates reference field vector at specified location and time.
SYNTAX
igrf.py [-h] [-i] -f FILE [< filename]
OPTIONS:
-h prints help message and quits
-i for interactive data entry
-f FILE specify file name with input data
-fgh FILE specify file with custom field coefficients in format: l m g h
-F FILE specify output file name
-ages MIN MAX INCR: specify age minimum in years (+/- AD), maximum and increment, default is line by line
-loc LAT LON; specify location, default is line by line
-alt ALT; specify altitude in km, default is sealevel (0)
-plt; make a plot of the time series
-sav, saves plot and quits
-fmt [pdf,jpg,eps,svg] specify format for output figure (default is svg)
-mod [arch3k,cals3k,pfm9k,hfm10k,cals10k_2,shadif14k,cals10k] specify model for 3ka to 1900 AD, default is cals10k
NB: program uses IGRF12 for dates 1900 to 2015.
INPUT FORMAT
interactive entry:
date: decimal year
alt: altitude in km
lat: positive north
lon: positive east
for file entry:
space delimited string: date alt lat long
OUTPUT FORMAT
Declination Inclination Intensity (nT) date alt lat long
MODELS: ARCH3K: (Korte et al., 2009);CALS3K (Korte & Contable, 2011); CALS10k (is .1b of Korte et al., 2011); PFM9K (Nilsson et al., 2014); HFM10k (is HFM.OL1.A1 of Constable et al., 2016); CALS10k_2 (is cals10k.2 of Constable et al., 2016), SHADIF14k (SHA.DIF.14K of Pavon-Carrasco et al., 2014).
"""
plot,fmt=0,'svg'
mod,alt,plt,lat,lon='cals10k',0,0,0,0
if '-loc' in sys.argv:
ind=sys.argv.index('-loc')
lat=float(sys.argv[ind+1])
lon=float(sys.argv[ind+2])
if '-alt' in sys.argv:
ind=sys.argv.index('-alt')
alt=float(sys.argv[ind+1])
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if len(sys.argv)!=0 and '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-mod' in sys.argv:
ind=sys.argv.index('-mod')
mod=sys.argv[ind+1]
if '-fgh' in sys.argv:
ind=sys.argv.index('-fgh')
ghfile=sys.argv[ind+1]
lmgh=numpy.loadtxt(ghfile)
gh=[]
lmgh=numpy.loadtxt(ghfile).transpose()
gh.append(lmgh[2][0])
for i in range(1,lmgh.shape[1]):
gh.append(lmgh[2][i])
gh.append(lmgh[3][i])
mod='custom'
inp=[[0,alt,lat,lon]]
elif '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
inp=numpy.loadtxt(file)
elif '-i' in sys.argv:
while 1:
try:
line=[]
if mod!='custom':
line.append(float(input("Decimal year: <cntrl-D to quit> ")))
else:
line.append(0)
alt=input("Elevation in km [0] ")
if alt=="":alt="0"
line.append(float(alt))
line.append(float(input("Latitude (positive north) ")))
line.append(float(input("Longitude (positive east) ")))
if mod=='':
x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0])
elif mod=='custom':
x,y,z,f = pmag.docustom(line[3]%360.,line[2], line[1], gh)
else:
x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0],mod=mod)
Dir=pmag.cart2dir((x,y,z))
print('%8.2f %8.2f %8.0f'%(Dir[0],Dir[1],f))
except EOFError:
print("\n Good-bye\n")
sys.exit()
elif '-ages' in sys.argv:
ind=sys.argv.index('-ages')
agemin=float(sys.argv[ind+1])
agemax=float(sys.argv[ind+2])
ageincr=float(sys.argv[ind+3])
ages=numpy.arange(agemin,agemax,ageincr)
lats=numpy.ones(len(ages))*lat
lons=numpy.ones(len(ages))*lon
alts=numpy.ones(len(ages))*alt
inp=numpy.array([ages,alts,lats,lons]).transpose()
else:
inp=numpy.loadtxt(sys.stdin,dtype=numpy.float)
if '-F' in sys.argv:
ind=sys.argv.index('-F')
outfile=sys.argv[ind+1]
out=open(outfile,'w')
else:outfile=""
if '-sav' in sys.argv:plot=1
if '-plt' in sys.argv:
plt=1
import matplotlib
matplotlib.use("TkAgg")
import pylab
pylab.ion()
Ages,Decs,Incs,Ints,VADMs=[],[],[],[],[]
for line in inp:
if mod!='custom':
x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0],mod=mod)
else:
x,y,z,f = pmag.docustom(line[3]%360.,line[2], line[1], gh)
Dir=pmag.cart2dir((x,y,z))
if outfile!="":
out.write('%8.2f %8.2f %8.0f %7.1f %7.1f %7.1f %7.1f\n'%(Dir[0],Dir[1],f,line[0],line[1],line[2],line[3]))
elif plt:
Ages.append(line[0])
if Dir[0]>180: Dir[0]=Dir[0]-360.0
Decs.append(Dir[0])
Incs.append(Dir[1])
Ints.append(f*1e-3)
VADMs.append(pmag.b_vdm(f*1e-9,line[2])*1e-21)
else:
print('%8.2f %8.2f %8.0f %7.1f %7.1f %7.1f %7.1f'%(Dir[0],Dir[1],f,line[0],line[1],line[2],line[3]))
if plt:
fig=pylab.figure(num=1,figsize=(7,9))
fig.add_subplot(411)
pylab.plot(Ages,Decs)
pylab.ylabel('Declination ($^{\circ}$)')
fig.add_subplot(412)
pylab.plot(Ages,Incs)
pylab.ylabel('Inclination ($^{\circ}$)')
fig.add_subplot(413)
pylab.plot(Ages,Ints)
pylab.ylabel('Intensity ($\mu$T)')
fig.add_subplot(414)
pylab.plot(Ages,VADMs)
pylab.ylabel('VADMs (ZAm$^2$)')
pylab.xlabel('Ages')
if plot==0:
pylab.draw()
ans=input("S[a]ve to save figure, <Return> to quit ")
if ans=='a':
pylab.savefig('igrf.'+fmt)
print('Figure saved as: ','igrf.'+fmt)
else:
pylab.savefig('igrf.'+fmt)
print('Figure saved as: ','igrf.'+fmt)
sys.exit()
def convert(**kwargs):
# initialize some stuff
version_num = pmag.get_version()
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs = [],[],[],[],[]
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # site outfile
location = kwargs.get('location', 'unknown')
dmy_flag = kwargs.get('dmy_flag', False)
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
#oave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
specnum = -int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '2')
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
site_num=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
site_num=samp_con.split("-")[1]
samp_con="7"
else: site_num=1
try:
DC_FIELD = float(kwargs.get('labfield',0))*1e-6
DC_PHI = float(kwargs.get('phi',0))
DC_THETA = float(kwargs.get('theta',0))
except ValueError: raise ValueError('problem with your dc parameters. please provide a labfield in microTesla and a phi and theta in degrees.')
noave = kwargs.get('noave', False)
dmy_flag = kwargs.get('dmy_flag', False)
meas_n_orient = kwargs.get('meas_n_orient', '8')
# format variables
if not mag_file:
return False, 'You must provide a Utrecht formated file'
mag_file = os.path.join(input_dir_path, mag_file)
# parse data
# Open up the Utrecht file and read the header information
AF_or_T = mag_file.split('.')[-1]
data = open(mag_file, 'r')
line = data.readline()
line_items = line.split(',')
operator=line_items[0]
operator=operator.replace("\"","")
machine=line_items[1]
machine=machine.replace("\"","")
machine=machine.rstrip('\n')
# print("operator=", operator)
# print("machine=", machine)
#read in measurement data
line = data.readline()
while line != "END" and line != '"END"':
SpecRec,SampRec,SiteRec,LocRec = {},{},{},{}
line_items = line.split(',')
spec_name=line_items[0]
spec_name=spec_name.replace("\"","")
# print("spec_name=", spec_name)
free_string=line_items[1]
free_string=free_string.replace("\"","")
# print("free_string=", free_string)
dec=line_items[2]
# print("dec=", dec)
inc=line_items[3]
# print("inc=", inc)
volume=float(line_items[4])
volume=volume * 1e-6 # enter volume in cm^3, convert to m^3
# print("volume=", volume)
bed_plane=line_items[5]
# print("bed_plane=", bed_plane)
bed_dip=line_items[6]
# print("bed_dip=", bed_dip)
# Configure et er_ tables
if specnum==0: sample_name = spec_name
else: sample_name = spec_name[:specnum]
site = pmag.parse_site(sample_name,samp_con,site_num)
SpecRec['specimen'] = spec_name
SpecRec['sample'] = sample_name
if volume!=0: SpecRec['volume']=volume
SpecRecs.append(SpecRec)
if sample_name!="" and sample_name not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample_name
SampRec['azimuth'] = dec
SampRec['dip'] = str(float(inc)-90)
SampRec['bed_dip_direction'] = bed_plane
SampRec['bed_dip'] = bed_dip
SampRec['method_codes'] = meth_code
SampRec['site'] = site
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
#measurement data
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
while line != '9999':
step=items[0]
step=step.split('.')
step_value=step[0]
step_type = ""
if len(step) == 2:
step_type=step[1]
if step_type=='5':
step_value = items[0]
A=float(items[1])
B=float(items[2])
C=float(items[3])
# convert to MagIC coordinates
Z=-A
X=-B
Y=C
cart = array([X, Y, Z]).transpose()
direction = pmag.cart2dir(cart).transpose()
measurement_dec = direction[0]
measurement_inc = direction[1]
magn_moment = direction[2] * 1.0e-12 # the data are in pico-Am^2 - this converts to Am^2
if volume!=0:
magn_volume = direction[2] * 1.0e-12 / volume # data volume normalized - converted to A/m
# print("magn_moment=", magn_moment)
# print("magn_volume=", magn_volume)
error = items[4]
date=items[5]
date=date.strip('"').replace(' ','')
if date.count("-") > 0:
date=date.split("-")
elif date.count("/") > 0:
date=date.split("/")
else: print("date format seperator cannot be identified")
# print(date)
time=items[6]
time=time.strip('"').replace(' ','')
time=time.split(":")
# print(time)
dt = date[0] + ":" + date[1] + ":" + date[2] + ":" + time[0] + ":" + time[1] + ":" + "0"
local = pytz.timezone("Europe/Amsterdam")
try:
if dmy_flag: naive = datetime.datetime.strptime(dt, "%d:%m:%Y:%H:%M:%S")
else: naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
except ValueError:
naive = datetime.datetime.strptime(dt, "%Y:%m:%d:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
# print(timestamp)
MeasRec = {}
MeasRec["timestamp"]=timestamp
MeasRec["analysts"] = operator
MeasRec["instrument_codes"] = "Utrecht_" + machine
MeasRec["description"] = "free string = " + free_string
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["experiments"] = location + site + spec_name
MeasRec["treat_step_num"] = location + site + spec_name + items[0]
MeasRec["specimen"] = spec_name
# MeasRec["treat_ac_field"] = '0'
if AF_or_T.lower() == "th":
MeasRec["treat_temp"] = '%8.3e' % (float(step_value)+273.) # temp in kelvin
MeasRec['treat_ac_field']='0'
lab_treat_type = "T"
else:
MeasRec['treat_temp']='273'
MeasRec['treat_ac_field']='%10.3e'%(float(step_value)*1e-3)
lab_treat_type = "AF"
MeasRec['treat_dc_field']='0'
if step_value == '0':
meas_type = "LT-NO"
# print("step_type=", step_type)
if step_type == '0' or step_type == '00':
meas_type = "LT-%s-Z"%lab_treat_type
elif step_type == '1' or step_type == '11':
meas_type = "LT-%s-I"%lab_treat_type
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
elif step_type == '2' or step_type == '12':
meas_type = "LT-PTRM-I"
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
elif step_type == '3' or step_type == '13':
meas_type = "LT-PTRM-Z"
# print("meas_type=", meas_type)
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['method_codes'] = meas_type
MeasRec["magn_moment"] = magn_moment
if volume!=0: MeasRec["magn_volume"] = magn_volume
MeasRec["dir_dec"] = measurement_dec
MeasRec["dir_inc"] = measurement_inc
MeasRec['dir_csd'] = error
MeasRec['meas_n_orient'] = meas_n_orient
# print(MeasRec)
MeasRecs.append(MeasRec)
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
data.close()
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave) #figures out method codes for measuremet data
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def average_duplicates(duplicates):
'''
avarage replicate measurements.
'''
carts_s,carts_g,carts_t=[],[],[]
for rec in duplicates:
moment=float(rec['moment'])
if 'dec_s' in list(rec.keys()) and 'inc_s' in list(rec.keys()):
if rec['dec_s']!="" and rec['inc_s']!="":
dec_s=float(rec['dec_s'])
inc_s=float(rec['inc_s'])
cart_s=pmag.dir2cart([dec_s,inc_s,moment])
carts_s.append(cart_s)
if 'dec_g' in list(rec.keys()) and 'inc_g' in list(rec.keys()):
if rec['dec_g']!="" and rec['inc_g']!="":
dec_g=float(rec['dec_g'])
inc_g=float(rec['inc_g'])
cart_g=pmag.dir2cart([dec_g,inc_g,moment])
carts_g.append(cart_g)
if 'dec_t' in list(rec.keys()) and 'inc_t' in list(rec.keys()):
if rec['dec_t']!="" and rec['inc_t']!="":
dec_t=float(rec['dec_t'])
inc_t=float(rec['inc_t'])
cart_t=pmag.dir2cart([dec_t,inc_t,moment])
carts_t.append(cart_t)
if len(carts_s)>0:
carts=scipy.array(carts_s)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_s="%.2f"%mean_dir[0]
mean_inc_s="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_s,mean_inc_s="",""
if len(carts_g)>0:
carts=scipy.array(carts_g)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_g="%.2f"%mean_dir[0]
mean_inc_g="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_g,mean_inc_g="",""
if len(carts_t)>0:
carts=scipy.array(carts_t)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_t="%.2f"%mean_dir[0]
mean_inc_t="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_t,mean_inc_t="",""
meanrec={}
for key in list(duplicates[0].keys()):
if key in ['dec_s','inc_s','dec_g','inc_g','dec_t','inc_t','moment']:
continue
else:
meanrec[key]=duplicates[0][key]
meanrec['dec_s']=mean_dec_s
meanrec['dec_g']=mean_dec_g
meanrec['dec_t']=mean_dec_t
meanrec['inc_s']=mean_inc_s
meanrec['inc_g']=mean_inc_g
meanrec['inc_t']=mean_inc_t
meanrec['moment']=mean_moment
return meanrec
def calculate_aniso_parameters(B,K):
aniso_parameters={}
S_bs=dot(B,K)
# normalize by trace
trace=S_bs[0]+S_bs[1]+S_bs[2]
S_bs=S_bs/trace
s1,s2,s3,s4,s5,s6=S_bs[0],S_bs[1],S_bs[2],S_bs[3],S_bs[4],S_bs[5]
s_matrix=[[s1,s4,s6],[s4,s2,s5],[s6,s5,s3]]
# calculate eigen vector,
t,evectors=eig(s_matrix)
# sort vectors
t=list(t)
t1=max(t)
ix_1=t.index(t1)
t3=min(t)
ix_3=t.index(t3)
for tt in range(3):
if t[tt]!=t1 and t[tt]!=t3:
t2=t[tt]
ix_2=t.index(t2)
v1=[evectors[0][ix_1],evectors[1][ix_1],evectors[2][ix_1]]
v2=[evectors[0][ix_2],evectors[1][ix_2],evectors[2][ix_2]]
v3=[evectors[0][ix_3],evectors[1][ix_3],evectors[2][ix_3]]
DIR_v1=pmag.cart2dir(v1)
DIR_v2=pmag.cart2dir(v2)
DIR_v3=pmag.cart2dir(v3)
aniso_parameters['anisotropy_s1']="%f"%s1
aniso_parameters['anisotropy_s2']="%f"%s2
aniso_parameters['anisotropy_s3']="%f"%s3
aniso_parameters['anisotropy_s4']="%f"%s4
aniso_parameters['anisotropy_s5']="%f"%s5
aniso_parameters['anisotropy_s6']="%f"%s6
aniso_parameters['anisotropy_degree']="%f"%(t1/t3)
aniso_parameters['anisotropy_t1']="%f"%t1
aniso_parameters['anisotropy_t2']="%f"%t2
aniso_parameters['anisotropy_t3']="%f"%t3
aniso_parameters['anisotropy_v1_dec']="%.1f"%DIR_v1[0]
aniso_parameters['anisotropy_v1_inc']="%.1f"%DIR_v1[1]
aniso_parameters['anisotropy_v2_dec']="%.1f"%DIR_v2[0]
aniso_parameters['anisotropy_v2_inc']="%.1f"%DIR_v2[1]
aniso_parameters['anisotropy_v3_dec']="%.1f"%DIR_v3[0]
aniso_parameters['anisotropy_v3_inc']="%.1f"%DIR_v3[1]
# modified from pmagpy:
if len(K)/3==9 or len(K)/3==6 or len(K)/3==15:
n_pos=len(K)/3
tmpH = Matrices[n_pos]['tmpH']
a=s_matrix
S=0.
comp=zeros((n_pos*3),'f')
for i in range(n_pos):
for j in range(3):
index=i*3+j
compare=a[j][0]*tmpH[i][0]+a[j][1]*tmpH[i][1]+a[j][2]*tmpH[i][2]
comp[index]=compare
for i in range(n_pos*3):
d=K[i]/trace - comp[i] # del values
S+=d*d
nf=float(n_pos*3-6) # number of degrees of freedom
if S >0:
sigma=math.sqrt(S/nf)
hpars=pmag.dohext(nf,sigma,[s1,s2,s3,s4,s5,s6])
aniso_parameters['anisotropy_sigma']="%f"%sigma
aniso_parameters['anisotropy_ftest']="%f"%hpars["F"]
aniso_parameters['anisotropy_ftest12']="%f"%hpars["F12"]
aniso_parameters['anisotropy_ftest23']="%f"%hpars["F23"]
aniso_parameters['result_description']="Critical F: %s"%(hpars['F_crit'])
aniso_parameters['anisotropy_F_crit']="%f"%float(hpars['F_crit'])
aniso_parameters['anisotropy_n']=n_pos
return(aniso_parameters)
def convert(**kwargs):
"""
"""
#get kwargs
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
lat = kwargs.get('lat', 0)
lon = kwargs.get('lon', 0)
specnum = int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
version_num=pmag.get_version()
if specnum!=0:specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print("naming convention option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
else: Z = 1
# format variables
mag_file = os.path.join(input_dir_path,mag_file)
meas_file = os.path.join(output_dir_path,meas_file)
spec_file = os.path.join(output_dir_path,spec_file)
samp_file = os.path.join(output_dir_path,samp_file)
site_file = os.path.join(output_dir_path,site_file)
# parse data
data=open(mag_file,'r').readlines() # read in data from file
comment=data[0]
line=data[1].strip()
line=line.replace("=","= ") # make finding orientations easier
rec=line.split() # read in sample orientation, etc.
specimen=rec[0]
SpecRecs,SampRecs,SiteRecs,LocRecs,MeasRecs = [],[],[],[],[]
SpecRec,SampRec,SiteRec,LocRec={},{},{},{} # make a sample record
if specnum!=0:
sample=rec[0][:specnum]
else:
sample=rec[0]
if int(samp_con)<6:
site=pmag.parse_site(sample,samp_con,Z)
else:
if 'site' in list(SampRec.keys()):site=ErSampREc['site']
if 'location' in list(SampRec.keys()):location=ErSampREc['location']
az_ind=rec.index('a=')+1
SampRec['sample']=sample
SampRec['description']=comment
SampRec['azimuth']=rec[az_ind]
dip_ind=rec.index('b=')+1
dip=-float(rec[dip_ind])
SampRec['dip']='%7.1f'%(dip)
strike_ind=rec.index('s=')+1
SampRec['bed_dip_direction']='%7.1f'%(float(rec[strike_ind])+90.)
bd_ind=rec.index('d=')+1
SampRec['bed_dip']=rec[bd_ind]
v_ind=rec.index('v=')+1
vol=rec[v_ind][:-3]
date=rec[-2]
time=rec[-1]
SampRec['method_codes']=meth_code
SampRec['site']=site
SampRec['citations']='This study'
SampRec['method_codes']='SO-NO'
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['citations']='This study'
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations']='This study'
SiteRec['lat'] = lat
SiteRec['lon']= lon
LocRec['location'] = location
LocRec['citations']='This study'
LocRec['lat_n'] = lat
LocRec['lat_s'] = lat
LocRec['lon_e'] = lon
LocRec['lon_w'] = lon
SpecRecs.append(SpecRec)
SampRecs.append(SampRec)
SiteRecs.append(SiteRec)
LocRecs.append(LocRec)
for k in range(3,len(data)): # read in data
line=data[k]
rec=line.split()
if len(rec)>1: # skip blank lines at bottom
MeasRec={}
MeasRec['description']='Date: '+date+' '+time
MeasRec["citations"]="This study"
MeasRec['software_packages']=version_num
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["quality"]='g'
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
MeasRec["specimen"]=specimen
if rec[0]=='NRM':
meas_type="LT-NO"
elif rec[0][0]=='M' or rec[0][0]=='H':
meas_type="LT-AF-Z"
elif rec[0][0]=='T':
meas_type="LT-T-Z"
else:
print("measurement type unknown")
return False, "measurement type unknown"
X=[float(rec[1]),float(rec[2]),float(rec[3])]
Vec=pmag.cart2dir(X)
MeasRec["magn_moment"]='%10.3e'% (Vec[2]) # Am^2
MeasRec["magn_volume"]=rec[4] # A/m
MeasRec["dir_dec"]='%7.1f'%(Vec[0])
MeasRec["dir_inc"]='%7.1f'%(Vec[1])
MeasRec["treat_ac_field"]='0'
if meas_type!='LT-NO':
treat=float(rec[0][1:])
else:
treat=0
if meas_type=="LT-AF-Z":
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif meas_type=="LT-T-Z":
MeasRec["treat_temp"]='%8.3e' % (treat+273.) # temp in kelvin
MeasRec['method_codes']=meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
utrecht_magic.py
DESCRIPTION
converts Utrecht magnetometer data files to magic_measurements files
SYNTAX
utrecht_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-loc LOCNAME : specify location/study name
-site SITENAME : specify site name
-lat latitude of samples
-lon longitude of samples
-A: don't average replicate measurements
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
INPUT
Utrecht magnetometer data file
"""
# initialize some stuff
sample_lat = 0.0
sample_lon = 0.0
noave = 0
er_location_name = "unknown"
er_site_name = "unknown"
args = sys.argv
meth_code = "LP-NO"
version_num = pmag.get_version()
mag_file = ""
dir_path = '.'
MagRecs = []
SampOuts = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
meth_code = ""
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind+1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind+1]
#try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind+1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind+1]
if "-lat" in args:
ind = args.index("-lat")
sample_lat = args[ind+1]
if "-lon" in args:
ind = args.index("-lon")
sample_lon = args[ind+1]
if "-site" in args:
ind = args.index("-site")
er_site_name = args[ind+1]
if "-A" in args:
noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind+1]
#samp_con='5'
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
er_location_name = kwargs.get('er_location_name', '')
er_site_name = kwargs.get('er_site_name', '')
sample_lat = kwargs.get('sample_lat', '')
sample_lon = kwargs.get('sample_lon', '')
#oave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
# format variables
if not mag_file:
return False, 'You must provide a Utrecht formated file'
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
samp_file = os.path.join(output_dir_path, samp_file)
ErSampRec = {}
# parse data
# Open up the Utrecht file and read the header information
print 'mag_file in utrecht_file', mag_file
data = open(mag_file, 'rU')
line = data.readline()
line_items = line.split(',')
operator=line_items[0]
operator=operator.replace("\"","")
machine=line_items[1]
machine=machine.replace("\"","")
machine=machine.rstrip('\n')
print "operator=", operator
print "machine=", machine
line = data.readline()
while line != '"END"' :
line_items = line.split(',')
sample_name=line_items[0]
sample_name=sample_name.replace("\"","")
print "sample_name=", sample_name
free_string=line_items[1]
free_string=free_string.replace("\"","")
print "free_string=", free_string
dec=line_items[2]
print "dec=", dec
inc=line_items[3]
print "inc=", inc
volume=float(line_items[4])
volume=volume * 1e-6 # enter volume in cm^3, convert to m^3
print "volume=", volume
bed_plane=line_items[5]
print "bed_plane=", bed_plane
bed_tilt=line_items[6]
print "bed_tilt=", bed_tilt
# Configure et er_samples table
ErSampRec['er_sample_name'] = sample_name
ErSampRec['sample_azimuth'] = dec
ErSampRec['sample_dip'] = inc
ErSampRec['sample_bed_dip_direction'] = bed_plane
ErSampRec['sample_bed_tilt'] = bed_tilt
ErSampRec['sample_lat'] = sample_lat
ErSampRec['sample_lon'] = sample_lon
ErSampRec['magic_method_codes'] = meth_code
ErSampRec['er_location_name'] = er_location_name
ErSampRec['er_site_name'] = er_site_name
ErSampRec['er_citation_names'] = 'This study'
SampOuts.append(ErSampRec.copy())
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
# exit()
while line != '9999' :
print line
step=items[0]
step=step.split('.')
step_value=step[0]
step_type = ""
if len(step) == 2:
step_type=step[1]
A=float(items[1])
B=float(items[2])
C=float(items[3])
# convert to MagIC coordinates
Z=-A
X=-B
Y=C
cart = np.array([X, Y, Z]).transpose()
direction = pmag.cart2dir(cart).transpose()
measurement_dec = direction[0]
measurement_inc = direction[1]
measurement_magn_moment = direction[2] * 1.0e-12 # the data are in pico-Am^2 - this converts to Am^2
measurement_magn_volume = direction[2] * 1.0e-12 / volume # data volume normalized - converted to A/m
print "measurement_magn_moment=", measurement_magn_moment
print "measurement_magn_volume=", measurement_magn_volume
error = items[4]
date=items[5]
date=date.strip('"')
date=date.split("-")
print date
time=items[6]
time=time.strip('"')
time=time.split(":")
print time
date_time = date[0] + ":" + date[1] + ":" + date[2] + ":" + time[0] + ":" + time[1] + ":" + "0.0"
print date_time
MagRec = {}
MagRec["er_analyst_mail_names"] = operator
MagRec["magic_instrument_codes"] = "Utrecht_" + machine
MagRec["measurement_description"] = "free string = " + free_string
MagRec["measurement_date"] = date_time
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = er_site_name
MagRec['er_sample_name'] = sample_name
MagRec['magic_software_packages'] = version_num
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["magic_experiment_name"] = er_location_name + er_site_name + sample_name
MagRec["measurement_number"] = er_location_name + er_site_name + sample_name + items[0]
MagRec["er_specimen_name"] = sample_name
# MagRec["treatment_ac_field"] = '0'
MagRec["treatment_temp"] = '%8.3e' % (float(step_value)+273.) # temp in kelvin
meas_type = "LP-DIR-T"
if step_value == '0':
meas_type = "LT-NO"
print "step_type=", step_type
if step_type == '0':
if meas_type == "" :
meas_type = "LT-T-Z"
else:
meas_type = meas_type + ":" + "LT-T-Z"
elif step_type == '1':
if meas_type == "" :
meas_type = "LT-T-I"
else:
meas_type = meas_type + ":" + "LT-T-I"
elif step_type == '2':
if meas_type == "" :
meas_type = "LT-PTRM-I"
else:
meas_type = meas_type + ":" + "LT-PTRM-I"
elif step_type == '3':
if meas_type == "" :
meas_type = "LT-PTRM-Z"
else:
meas_type = meas_type + ":" + "LT-PTRM-Z"
print "meas_type=", meas_type
MagRec['magic_method_codes'] = meas_type
MagRec["measurement_magn_moment"] = measurement_magn_moment
MagRec["measurement_magn_volume"] = measurement_magn_volume
MagRec["measurement_dec"] = measurement_dec
MagRec["measurement_inc"] = measurement_inc
MagRec['measurement_csd'] = error
# MagRec['measurement_positions'] = '1'
MagRecs.append(MagRec.copy())
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
# write out the data to MagIC data files
pmag.magic_write(samp_file, SampOuts, 'er_samples')
print "sample orientations put in ", samp_file
# MagOuts = pmag.measurements_methods(MagRecs, noave)
# pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
pmag.magic_write(meas_file, MagRecs, 'magic_measurements')
print "results put in ", meas_file
print "exit!"
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
pmd_magic.py
DESCRIPTION
converts PMD (Enkin) format files to magic_measurements format files
SYNTAX
pmd_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify naming convention
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
PMD format files
"""
# initialize some stuff
noave = 0
inst = ""
samp_con, Z = '1', ""
missing = 1
demag = "N"
er_location_name = "unknown"
citation = 'This study'
args = sys.argv
meth_code = "LP-NO"
specnum = -1
MagRecs = []
version_num = pmag.get_version()
Samps = [] # keeps track of sample orientations
DIspec = []
MagFiles = []
user = ""
mag_file = ""
dir_path = '.'
ErSamps = []
SampOuts = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
#try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-A" in args: noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind + 1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 0)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
print samp_con
# format variables
mag_file = input_dir_path + "/" + mag_file
meas_file = output_dir_path + "/" + meas_file
samp_file = output_dir_path + "/" + samp_file
if specnum != 0: specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print "naming convention option [4] must be in form 4-Z where Z is an integer"
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
# parse data
data = open(mag_file, 'rU').readlines() # read in data from file
comment = data[0]
line = data[1].strip()
line = line.replace("=", "= ") # make finding orientations easier
rec = line.split() # read in sample orientation, etc.
er_specimen_name = rec[0]
ErSampRec, ErSiteRec = {}, {} # make a sample record
if specnum != 0:
er_sample_name = rec[0][:specnum]
else:
er_sample_name = rec[0]
if len(ErSamps) > 0: # need to copy existing
for samp in ErSamps:
if samp['er_sample_name'] == er_sample_name:
ErSampRec = samp # we'll ammend this one
else:
SampOuts.append(samp) # keep all the others
if int(samp_con) < 6:
er_site_name = pmag.parse_site(er_sample_name, samp_con, Z)
else:
if 'er_site_name' in ErSampRec.keys():
er_site_name = ErSampREc['er_site_name']
if 'er_location_name' in ErSampRec.keys():
er_location_name = ErSampREc['er_location_name']
az_ind = rec.index('a=') + 1
ErSampRec['er_sample_name'] = er_sample_name
ErSampRec['er_sample_description'] = comment
ErSampRec['sample_azimuth'] = rec[az_ind]
dip_ind = rec.index('b=') + 1
dip = -float(rec[dip_ind])
ErSampRec['sample_dip'] = '%7.1f' % (dip)
strike_ind = rec.index('s=') + 1
ErSampRec['sample_bed_dip_direction'] = '%7.1f' % (float(rec[strike_ind]) +
90.)
bd_ind = rec.index('d=') + 1
ErSampRec['sample_bed_dip'] = rec[bd_ind]
v_ind = rec.index('v=') + 1
vol = rec[v_ind][:-3]
date = rec[-2]
time = rec[-1]
ErSampRec['magic_method_codes'] = meth_code
if 'er_location_name' not in ErSampRec.keys():
ErSampRec['er_location_name'] = er_location_name
if 'er_site_name' not in ErSampRec.keys():
ErSampRec['er_site_name'] = er_site_name
if 'er_citation_names' not in ErSampRec.keys():
ErSampRec['er_citation_names'] = 'This study'
if 'magic_method_codes' not in ErSampRec.keys():
ErSampRec['magic_method_codes'] = 'SO-NO'
SampOuts.append(ErSampRec)
for k in range(3, len(data)): # read in data
line = data[k]
rec = line.split()
if len(rec) > 1: # skip blank lines at bottom
MagRec = {}
MagRec['measurement_description'] = 'Date: ' + date + ' ' + time
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = er_site_name
MagRec['er_sample_name'] = er_sample_name
MagRec['magic_software_packages'] = version_num
MagRec["treatment_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = '1'
MagRec["er_specimen_name"] = er_specimen_name
if rec[0] == 'NRM':
meas_type = "LT-NO"
elif rec[0][0] == 'M' or rec[0][0] == 'H':
meas_type = "LT-AF-Z"
elif rec[0][0] == 'T':
meas_type = "LT-T-Z"
else:
print "measurement type unknown"
return False, "measurement type unknown"
X = [float(rec[1]), float(rec[2]), float(rec[3])]
Vec = pmag.cart2dir(X)
MagRec["measurement_magn_moment"] = '%10.3e' % (Vec[2]) # Am^2
MagRec["measurement_magn_volume"] = rec[4] # A/m
MagRec["measurement_dec"] = '%7.1f' % (Vec[0])
MagRec["measurement_inc"] = '%7.1f' % (Vec[1])
MagRec["treatment_ac_field"] = '0'
if meas_type != 'LT-NO':
treat = float(rec[0][1:])
else:
treat = 0
if meas_type == "LT-AF-Z":
MagRec["treatment_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif meas_type == "LT-T-Z":
MagRec["treatment_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
MagRec['magic_method_codes'] = meas_type
MagRecs.append(MagRec)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print "results put in ", meas_file
pmag.magic_write(samp_file, SampOuts, 'er_samples')
print "sample orientations put in ", samp_file
return True, meas_file
def convert(**kwargs):
version_num = pmag.get_version()
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # Loc outfile
mag_file = kwargs.get('mag_file', '') #required
location = kwargs.get('location', 'unknown')
site = kwargs.get('site', '')
samp_con = kwargs.get('samp_con', '1')
specnum = int(kwargs.get('specnum', 0))
timezone = kwargs.get('timestamp', 'US/Pacific')
append = kwargs.get('append', False)
noave = kwargs.get('noave', False) # default False means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume: volume = 0.025**3 #default volume is a 2.5 cm cube, translated to meters cubed
else: volume *= 1e-6 #convert cm^3 to m^3
if specnum!=0:
specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z=int(samp_con.split("-")[1])
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=int(samp_con.split("-")[1])
samp_con="7"
else: Z=1
# format variables
mag_file = os.path.join(input_dir_path, mag_file)
if not os.path.isfile(mag_file):
print("%s is not a BGC file"%mag_file)
return False, 'You must provide a BCG format file'
# Open up the BGC file and read the header information
print('mag_file in bgc_magic', mag_file)
pre_data = open(mag_file, 'r')
line = pre_data.readline()
line_items = line.split(' ')
specimen = line_items[2]
specimen = specimen.replace('\n', '')
line = pre_data.readline()
line = pre_data.readline()
line_items = line.split('\t')
azimuth = float(line_items[1])
dip = float(line_items[2])
bed_dip = line_items[3]
sample_bed_azimuth = line_items[4]
lon = line_items[5]
lat = line_items[6]
tmp_volume = line_items[7]
if tmp_volume != 0.0:
volume = float(tmp_volume) * 1e-6
pre_data.close()
data = pd.read_csv(mag_file, sep='\t', header=3, index_col=False)
cart = np.array([data['X'], data['Y'], data['Z']]).transpose()
direction = pmag.cart2dir(cart).transpose()
data['dir_dec'] = direction[0]
data['dir_inc'] = direction[1]
data['magn_moment'] = old_div(direction[2], 1000) # the data are in EMU - this converts to Am^2
data['magn_volume'] = old_div((old_div(direction[2], 1000)), volume) # EMU - data converted to A/m
# Configure the magic_measurements table
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
for rowNum, row in data.iterrows():
MeasRec,SpecRec,SampRec,SiteRec,LocRec = {},{},{},{},{}
if specnum!=0:
sample=specimen[:specnum]
else:
sample=specimen
if site=='':
site=pmag.parse_site(sample,samp_con,Z)
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['volume'] = volume
SpecRec['analysts']=user
SpecRec['citations'] = 'This study'
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['azimuth'] = azimuth
SampRec['dip'] = dip
SampRec['bed_dip_direction'] = sample_bed_azimuth
SampRec['bed_dip'] = bed_dip
SampRec['method_codes'] = meth_code
SampRec['analysts']=user
SampRec['citations'] = 'This study'
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRec['analysts']=user
SiteRec['citations'] = 'This study'
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['analysts']=user
LocRec['citations'] = 'This study'
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec['description'] = 'Date: ' + str(row['Date']) + ' Time: ' + str(row['Time'])
if '.' in row['Date']: datelist = row['Date'].split('.')
elif '/' in row['Date']: datelist = row['Date'].split('/')
elif '-' in row['Date']: datelist = row['Date'].split('-')
else: print("unrecogized date formating on one of the measurement entries for specimen %s"%specimen); datelist=['','','']
if ':' in row['Time']: timelist = row['Time'].split(':')
else: print("unrecogized time formating on one of the measurement entries for specimen %s"%specimen); timelist=['','','']
datelist[2]='19'+datelist[2] if len(datelist[2])<=2 else datelist[2]
dt=":".join([datelist[1],datelist[0],datelist[2],timelist[0],timelist[1],timelist[2]])
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
MeasRec["timestamp"] = timestamp
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = rowNum
MeasRec["specimen"] = specimen
MeasRec["treat_ac_field"] = '0'
if row['DM Val'] == '0':
meas_type = "LT-NO"
elif int(row['DM Type']) > 0.0:
meas_type = "LT-AF-Z"
treat = float(row['DM Val'])
MeasRec["treat_ac_field"] = '%8.3e' %(treat*1e-3) # convert from mT to tesla
elif int(row['DM Type']) == -1:
meas_type = "LT-T-Z"
treat = float(row['DM Val'])
MeasRec["treat_temp"] = '%8.3e' % (treat+273.) # temp in kelvin
else:
print("measurement type unknown:", row['DM Type'], " in row ", rowNum)
MeasRec["magn_moment"] = str(row['magn_moment'])
MeasRec["magn_volume"] = str(row['magn_volume'])
MeasRec["dir_dec"] = str(row['dir_dec'])
MeasRec["dir_inc"] = str(row['dir_inc'])
MeasRec['method_codes'] = meas_type
MeasRec['dir_csd'] = '0.0' # added due to magic.write error
MeasRec['meas_n_orient'] = '1' # added due to magic.write error
MeasRecs.append(MeasRec.copy())
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.write_table_to_file('specimens', custom_name=spec_file, append=append)
con.write_table_to_file('samples', custom_name=samp_file, append=append)
con.write_table_to_file('sites', custom_name=site_file, append=append)
con.write_table_to_file('locations', custom_name=loc_file, append=append)
meas_file = con.write_table_to_file('measurements', custom_name=meas_file, append=append)
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
jr6_jr6_magic.py
DESCRIPTION
converts JR6 .jr6 format files to magic_measurements format files
SYNTAX
jr6_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify sample naming convention (6 and 7 not yet implemented)
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-JR IODP samples measured on the JOIDES RESOLUTION
-v NUM : specify the volume in cc of the sample, default 2.5^3cc
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
JR6 .jr6 format file
"""
# initialize some stuff
noave=0
#volume=2.5**3 #default volume is a 2.5cm cube
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
inst=""
samp_con,Z='1',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
specnum=1
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
user=""
mag_file=""
dir_path='.'
MagRecs=[]
ErSamps=[]
SampOuts=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
tmp_file= "fixed.jr6"
meth_code,JR="",0
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind+1]
#try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind+1])
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args: noave=1
if "-mcd" in args:
ind=args.index("-mcd")
meth_code=args[ind+1]
if "-JR" in args:
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
JR=1
samp_con='5'
if "-v" in args:
ind=args.index("-v")
volume=float(args[ind+1])*1e-6 # enter volume in cc, convert to m^3
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
else:
#convert cm^3 to m^3
volume *= 1e-6
JR = kwargs.get('JR', 0)
if JR:
if meth_code == "LP-NO":
meth_code = ""
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
samp_con='5'
# format variables
mag_file = input_dir_path+"/" + mag_file
meas_file = output_dir_path+"/" + meas_file
samp_file = output_dir_path+"/" + samp_file
tmp_file = output_dir_path+"/" + tmp_file
if specnum!=0:
specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
ErSampRec,ErSiteRec={},{}
# parse data
# fix .jr6 file so that there are spaces between all the columns.
pre_data=open(mag_file, 'rU')
tmp_data=open(tmp_file, 'w')
line=pre_data.readline()
while line !='':
line=line.replace('-',' -')
#print "line=", line
tmp_data.write(line)
line=pre_data.readline()
tmp_data.close()
pre_data.close()
data=pd.read_csv(tmp_file, delim_whitespace=True,header=None)
if JR==0: #
data.columns=['er_specimen_name','step','x','y','z','expon','sample_azimuth','sample_dip', 'sample_bed_dip_direction','sample_bed_dip','bed_dip_dir2','bed_dip2','param1','param2','param3','param4','measurement_csd']
cart=np.array([data['x'],data['y'],data['z']]).transpose()
else: # measured on the Joides Resolution JR6
data.columns=['er_specimen_name','step','negz','y','x','expon','sample_azimuth','sample_dip', 'sample_bed_dip_direction','sample_bed_dip','bed_dip_dir2','bed_dip2','param1','param2','param3','param4','measurement_csd']
cart=np.array([data['x'],data['y'],-data['negz']]).transpose()
dir= pmag.cart2dir(cart).transpose()
data['measurement_dec']=dir[0]
data['measurement_inc']=dir[1]
data['measurement_magn_moment']=dir[2]*(10.0**data['expon'])*volume # the data are in A/m - this converts to Am^2
data['measurement_magn_volume']=dir[2]*(10.0**data['expon']) # A/m - data in A/m
data['sample_dip']=-data['sample_dip']
DGEOs,IGEOs=[],[]
for ind in range(len(data)):
dgeo,igeo=pmag.dogeo(data.ix[ind]['measurement_dec'],data.ix[ind]['measurement_inc'],data.ix[ind]['sample_azimuth'],data.ix[ind]['sample_dip'])
DGEOs.append(dgeo)
IGEOs.append(igeo)
data['specimen_dec']=DGEOs
data['specimen_inc']=IGEOs
data['specimen_tilt']='1'
if specnum!=0:
data['er_sample_name']=data['er_specimen_name'][:specnum]
else:
data['er_sample_name']=data['er_specimen_name']
if int(samp_con) in [1, 2, 3, 4, 5, 7]:
data['er_site_name']=pmag.parse_site(data['er_sample_name'],samp_con,Z)
# else:
# if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampRec['er_site_name']
# if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampRec['er_location_name']
# Configure the er_sample table
for rowNum, row in data.iterrows():
sampleFlag=0
for sampRec in SampOuts:
if sampRec['er_sample_name'] == row['er_sample_name']:
sampleFlag=1
break
if sampleFlag == 0:
ErSampRec['er_sample_name']=row['er_sample_name']
ErSampRec['sample_azimuth']=str(row['sample_azimuth'])
ErSampRec['sample_dip']=str(row['sample_dip'])
ErSampRec['magic_method_codes']=meth_code
ErSampRec['er_location_name']=er_location_name
ErSampRec['er_site_name']=row['er_site_name']
ErSampRec['er_citation_names']='This study'
SampOuts.append(ErSampRec.copy())
# Configure the magic_measurements table
for rowNum, row in data.iterrows():
MagRec={}
# MagRec['measurement_description']='Date: '+date
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['er_site_name']=row['er_site_name']
MagRec['er_sample_name']=row['er_sample_name']
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=row['er_specimen_name']
MagRec["treatment_ac_field"]='0'
if row['step'] == 'NRM':
meas_type="LT-NO"
elif row['step'][0:2] == 'AD':
meas_type="LT-AF-Z"
treat=float(row['step'][2:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type="LT-T-Z"
treat=float(row['step'][2:])
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
else: # need to add IRM, and ARM options
print "measurement type unknown", row['step']
return False, "measurement type unknown"
MagRec["measurement_magn_moment"]=str(row['measurement_magn_moment'])
MagRec["measurement_magn_volume"]=str(row['measurement_magn_volume'])
MagRec["measurement_dec"]=str(row['measurement_dec'])
MagRec["measurement_inc"]=str(row['measurement_inc'])
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec.copy())
pmag.magic_write(samp_file,SampOuts,'er_samples')
print "sample orientations put in ",samp_file
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
print "exit!"
return True, meas_file
def convert(**kwargs):
# initialize some stuff
version_num = pmag.get_version()
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # site outfile
location = kwargs.get('location', 'unknown')
dmy_flag = kwargs.get('dmy_flag', False)
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
#oave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
specnum = -int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '2')
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
site_num = samp_con.split("-")[1]
samp_con = "4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
site_num = samp_con.split("-")[1]
samp_con = "7"
else:
site_num = 1
try:
DC_FIELD = float(kwargs.get('labfield', 0)) * 1e-6
DC_PHI = float(kwargs.get('phi', 0))
DC_THETA = float(kwargs.get('theta', 0))
except ValueError:
raise ValueError(
'problem with your dc parameters. please provide a labfield in microTesla and a phi and theta in degrees.'
)
noave = kwargs.get('noave', False)
dmy_flag = kwargs.get('dmy_flag', False)
meas_n_orient = kwargs.get('meas_n_orient', '8')
# format variables
if not mag_file:
return False, 'You must provide a Utrecht formated file'
mag_file = os.path.join(input_dir_path, mag_file)
# parse data
# Open up the Utrecht file and read the header information
AF_or_T = mag_file.split('.')[-1]
data = open(mag_file, 'r')
line = data.readline()
line_items = line.split(',')
operator = line_items[0]
operator = operator.replace("\"", "")
machine = line_items[1]
machine = machine.replace("\"", "")
machine = machine.rstrip('\n')
# print("operator=", operator)
# print("machine=", machine)
#read in measurement data
line = data.readline()
while line != "END" and line != '"END"':
SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}
line_items = line.split(',')
spec_name = line_items[0]
spec_name = spec_name.replace("\"", "")
# print("spec_name=", spec_name)
free_string = line_items[1]
free_string = free_string.replace("\"", "")
# print("free_string=", free_string)
dec = line_items[2]
# print("dec=", dec)
inc = line_items[3]
# print("inc=", inc)
volume = float(line_items[4])
volume = volume * 1e-6 # enter volume in cm^3, convert to m^3
# print("volume=", volume)
bed_plane = line_items[5]
# print("bed_plane=", bed_plane)
bed_dip = line_items[6]
# print("bed_dip=", bed_dip)
# Configure et er_ tables
if specnum == 0: sample_name = spec_name
else: sample_name = spec_name[:specnum]
site = pmag.parse_site(sample_name, samp_con, site_num)
SpecRec['specimen'] = spec_name
SpecRec['sample'] = sample_name
if volume != 0: SpecRec['volume'] = volume
SpecRecs.append(SpecRec)
if sample_name != "" and sample_name not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample_name
SampRec['azimuth'] = dec
SampRec['dip'] = str(float(inc) - 90)
SampRec['bed_dip_direction'] = bed_plane
SampRec['bed_dip'] = bed_dip
SampRec['method_codes'] = meth_code
SampRec['site'] = site
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
#measurement data
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
while line != '9999':
step = items[0]
step = step.split('.')
step_value = step[0]
step_type = ""
if len(step) == 2:
step_type = step[1]
if step_type == '5':
step_value = items[0]
A = float(items[1])
B = float(items[2])
C = float(items[3])
# convert to MagIC coordinates
Z = -A
X = -B
Y = C
cart = array([X, Y, Z]).transpose()
direction = pmag.cart2dir(cart).transpose()
measurement_dec = direction[0]
measurement_inc = direction[1]
magn_moment = direction[
2] * 1.0e-12 # the data are in pico-Am^2 - this converts to Am^2
if volume != 0:
magn_volume = direction[
2] * 1.0e-12 / volume # data volume normalized - converted to A/m
# print("magn_moment=", magn_moment)
# print("magn_volume=", magn_volume)
error = items[4]
date = items[5]
date = date.strip('"').replace(' ', '')
if date.count("-") > 0:
date = date.split("-")
elif date.count("/") > 0:
date = date.split("/")
else:
print("date format seperator cannot be identified")
# print(date)
time = items[6]
time = time.strip('"').replace(' ', '')
time = time.split(":")
# print(time)
dt = date[0] + ":" + date[1] + ":" + date[2] + ":" + time[
0] + ":" + time[1] + ":" + "0"
local = pytz.timezone("Europe/Amsterdam")
try:
if dmy_flag:
naive = datetime.datetime.strptime(dt, "%d:%m:%Y:%H:%M:%S")
else:
naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
except ValueError:
naive = datetime.datetime.strptime(dt, "%Y:%m:%d:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp = utc_dt.strftime("%Y-%m-%dT%H:%M:%S") + "Z"
# print(timestamp)
MeasRec = {}
MeasRec["timestamp"] = timestamp
MeasRec["analysts"] = operator
MeasRec["instrument_codes"] = "Utrecht_" + machine
MeasRec["description"] = "free string = " + free_string
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["experiments"] = location + site + spec_name
MeasRec["treat_step_num"] = location + site + spec_name + items[0]
MeasRec["specimen"] = spec_name
# MeasRec["treat_ac_field"] = '0'
if AF_or_T.lower() == "th":
MeasRec["treat_temp"] = '%8.3e' % (float(step_value) + 273.
) # temp in kelvin
MeasRec['treat_ac_field'] = '0'
lab_treat_type = "T"
else:
MeasRec['treat_temp'] = '273'
MeasRec['treat_ac_field'] = '%10.3e' % (float(step_value) *
1e-3)
lab_treat_type = "AF"
MeasRec['treat_dc_field'] = '0'
if step_value == '0':
meas_type = "LT-NO"
# print("step_type=", step_type)
if step_type == '0' or step_type == '00':
meas_type = "LT-%s-Z" % lab_treat_type
elif step_type == '1' or step_type == '11':
meas_type = "LT-%s-I" % lab_treat_type
MeasRec['treat_dc_field'] = '%1.2e' % DC_FIELD
elif step_type == '2' or step_type == '12':
meas_type = "LT-PTRM-I"
MeasRec['treat_dc_field'] = '%1.2e' % DC_FIELD
elif step_type == '3' or step_type == '13':
meas_type = "LT-PTRM-Z"
# print("meas_type=", meas_type)
MeasRec['treat_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['method_codes'] = meas_type
MeasRec["magn_moment"] = magn_moment
if volume != 0: MeasRec["magn_volume"] = magn_volume
MeasRec["dir_dec"] = measurement_dec
MeasRec["dir_inc"] = measurement_inc
MeasRec['dir_csd'] = error
MeasRec['meas_n_orient'] = meas_n_orient
# print(MeasRec)
MeasRecs.append(MeasRec)
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
data.close()
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(
MeasRecs, noave) #figures out method codes for measuremet data
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
# initialize some stuff
demag = "N"
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
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')
mag_file = kwargs.get('mag_file', '')
site = kwargs.get('site', 'unknown')
expedition = kwargs.get('expedition', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', False) # default means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = kwargs.get('volume', 2.5**
3) * 1e-6 #default volume is a 2.5cm cube
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
if not mag_file:
print("-W- You must provide an IODP_jr6 format file")
return False, "You must provide an IODP_jr6 format file"
mag_file = os.path.join(input_dir_path, mag_file)
# validate variables
if not os.path.isfile(mag_file):
print(
'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'
.format(mag_file))
return False, 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(
mag_file)
# parse data
temp = os.path.join(output_dir_path, 'temp.txt')
fix_separation(mag_file, temp)
infile = open(temp, 'r')
lines = infile.readlines()
infile.close()
try:
os.remove(temp)
except OSError:
print("problem with temp file")
citations = "This Study"
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
for line in lines:
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
line = line.split()
spec_text_id = line[0]
specimen = spec_text_id
for dem in ['-', '_']:
if dem in spec_text_id:
sample = dem.join(spec_text_id.split(dem)[:-1])
break
location = expedition + site
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
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'] = line[6]
SampRec['dip'] = line[7]
SampRec['bed_dip_direction'] = line[8]
SampRec['bed_dip'] = line[9]
SampRec['method_codes'] = meth_code
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations'] = 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
MeasRec["citations"] = citations
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["treat_ac_field"] = '0'
x = float(line[4])
y = float(line[3])
negz = float(line[2])
cart = np.array([x, y, -negz]).transpose()
direction = pmag.cart2dir(cart).transpose()
expon = float(line[5])
magn_volume = direction[2] * (10.0**expon)
moment = magn_volume * volume
MeasRec["magn_moment"] = str(moment)
MeasRec["magn_volume"] = str(
magn_volume) #str(direction[2] * (10.0 ** expon))
MeasRec["dir_dec"] = '%7.1f' % (direction[0])
MeasRec["dir_inc"] = '%7.1f' % (direction[1])
step = line[1]
if step == 'NRM':
meas_type = "LT-NO"
elif step[0:2] == 'AD':
meas_type = "LT-AF-Z"
treat = float(step[2:])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif step[0:2] == 'TD':
meas_type = "LT-T-Z"
treat = float(step[2:])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
elif step[0:3] == 'ARM': #
meas_type = "LT-AF-I"
treat = float(row['step'][3:])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
MeasRec["treat_dc_field"] = '%8.3e' % (50e-6
) # assume 50uT DC field
MeasRec[
"measurement_description"] = 'Assumed DC field - actual unknown'
elif step[0] == 'A':
meas_type = "LT-AF-Z"
treat = float(step[1:])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif step[0] == 'T':
meas_type = "LT-T-Z"
treat = float(step[1:])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
elif step[0:3] == 'IRM': #
meas_type = "LT-IRM"
treat = float(step[3:])
MeasRec["treat_dc_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
else:
print('unknown treatment type for ', row)
return False, 'unknown treatment type for ', row
MeasRec['method_codes'] = meas_type
MeasRecs.append(MeasRec.copy())
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return (True, meas_file)
def calculate_aniso_parameters(B, K):
aniso_parameters = {}
S_bs = dot(B, K)
# normalize by trace
trace = S_bs[0] + S_bs[1] + S_bs[2]
S_bs = S_bs / trace
s1, s2, s3, s4, s5, s6 = S_bs[0], S_bs[1], S_bs[2], S_bs[3], S_bs[
4], S_bs[5]
s_matrix = [[s1, s4, s6], [s4, s2, s5], [s6, s5, s3]]
# calculate eigen vector,
t, evectors = eig(s_matrix)
# sort vectors
t = list(t)
t1 = max(t)
ix_1 = t.index(t1)
t3 = min(t)
ix_3 = t.index(t3)
for tt in range(3):
if t[tt] != t1 and t[tt] != t3:
t2 = t[tt]
ix_2 = t.index(t2)
v1 = [evectors[0][ix_1], evectors[1][ix_1], evectors[2][ix_1]]
v2 = [evectors[0][ix_2], evectors[1][ix_2], evectors[2][ix_2]]
v3 = [evectors[0][ix_3], evectors[1][ix_3], evectors[2][ix_3]]
DIR_v1 = pmag.cart2dir(v1)
DIR_v2 = pmag.cart2dir(v2)
DIR_v3 = pmag.cart2dir(v3)
aniso_parameters['anisotropy_s1'] = "%f" % s1
aniso_parameters['anisotropy_s2'] = "%f" % s2
aniso_parameters['anisotropy_s3'] = "%f" % s3
aniso_parameters['anisotropy_s4'] = "%f" % s4
aniso_parameters['anisotropy_s5'] = "%f" % s5
aniso_parameters['anisotropy_s6'] = "%f" % s6
aniso_parameters['anisotropy_degree'] = "%f" % (t1 / t3)
aniso_parameters['anisotropy_t1'] = "%f" % t1
aniso_parameters['anisotropy_t2'] = "%f" % t2
aniso_parameters['anisotropy_t3'] = "%f" % t3
aniso_parameters['anisotropy_v1_dec'] = "%.1f" % DIR_v1[0]
aniso_parameters['anisotropy_v1_inc'] = "%.1f" % DIR_v1[1]
aniso_parameters['anisotropy_v2_dec'] = "%.1f" % DIR_v2[0]
aniso_parameters['anisotropy_v2_inc'] = "%.1f" % DIR_v2[1]
aniso_parameters['anisotropy_v3_dec'] = "%.1f" % DIR_v3[0]
aniso_parameters['anisotropy_v3_inc'] = "%.1f" % DIR_v3[1]
# modified from pmagpy:
if len(K) / 3 == 9 or len(K) / 3 == 6 or len(K) / 3 == 15:
n_pos = len(K) / 3
tmpH = Matrices[n_pos]['tmpH']
a = s_matrix
S = 0.
comp = zeros((n_pos * 3), 'f')
for i in range(n_pos):
for j in range(3):
index = i * 3 + j
compare = a[j][0] * tmpH[i][0] + a[j][1] * tmpH[i][1] + a[
j][2] * tmpH[i][2]
comp[index] = compare
for i in range(n_pos * 3):
d = K[i] / trace - comp[i] # del values
S += d * d
nf = float(n_pos * 3 - 6) # number of degrees of freedom
if S > 0:
sigma = math.sqrt(S / nf)
hpars = pmag.dohext(nf, sigma, [s1, s2, s3, s4, s5, s6])
aniso_parameters['anisotropy_sigma'] = "%f" % sigma
aniso_parameters['anisotropy_ftest'] = "%f" % hpars["F"]
aniso_parameters['anisotropy_ftest12'] = "%f" % hpars["F12"]
aniso_parameters['anisotropy_ftest23'] = "%f" % hpars["F23"]
aniso_parameters['result_description'] = "Critical F: %s" % (
hpars['F_crit'])
aniso_parameters['anisotropy_F_crit'] = "%f" % float(
hpars['F_crit'])
aniso_parameters['anisotropy_n'] = n_pos
return (aniso_parameters)
def main(command_line=True, **kwargs):
"""
NAME
iodp_jr6_magic.py
DESCRIPTION
converts shipboard .jr6 format files to magic_measurements format files
SYNTAX
iodp_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-fsa FILE: specify er_samples.txt file for sample name lookup ,
default is 'er_samples.txt'
-loc HOLE : specify hole name (U1456A)
-A: don't average replicate measurements
INPUT
JR6 .jr6 format file
"""
def fix_separation(filename, new_filename):
old_file = open(filename, 'r')
data = old_file.readlines()
new_data = []
for line in data:
new_line = line.replace('-', ' -')
new_line = new_line.replace(' ', ' ')
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
old_file.close()
new_file.close()
return new_filename
def old_fix_separation(filename, new_filename):
old_file = open(filename, 'r')
data = old_file.readlines()
new_data = []
for line in data:
new_line = []
for i in line.split():
if '-' in i[1:]:
lead_char = '-' if i[0] == '-' else ''
if lead_char:
v = i[1:].split('-')
else:
v = i.split('-')
new_line.append(lead_char + v[0])
new_line.append('-' + v[1])
else:
new_line.append(i)
new_line = (' '.join(new_line)) + '\n'
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
new_file.close()
old_file.close()
return new_filename
# initialize some stuff
noave = 0
volume = 2.5**3 #default volume is a 2.5cm cube
inst = ""
samp_con, Z = '5', ""
missing = 1
demag = "N"
er_location_name = "unknown"
citation = 'This study'
args = sys.argv
meth_code = "LP-NO"
version_num = pmag.get_version()
dir_path = '.'
MagRecs = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
mag_file = ''
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-fsa' in args:
ind = args.index("-fsa")
samp_file = args[ind + 1]
if samp_file[0] != '/':
samp_file = os.path.join(input_dir_path, samp_file)
try:
open(samp_file, 'r')
ErSamps, file_type = pmag.magic_read(samp_file)
except:
print(samp_file, ' not found: ')
print(
' download csv file and import to MagIC with iodp_samples_magic.py'
)
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-A" in args:
noave = 1
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file', '')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
if len(str(samp_con)) > 1:
samp_con, Z = samp_con.split('-')
else:
Z = ''
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
# format variables
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
if mag_file:
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = os.path.join(input_dir_path, samp_file)
meas_file = os.path.join(output_dir_path, meas_file)
# validate variables
if not mag_file:
print("You must provide an IODP_jr6 format file")
return False, "You must provide an IODP_jr6 format file"
if not os.path.exists(mag_file):
print(
'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'
.format(mag_file))
return False, 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(
mag_file)
if not os.path.exists(samp_file):
print(
"Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one"
.format(input_dir_path))
return False, "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(
input_dir_path)
# parse data
temp = os.path.join(output_dir_path, 'temp.txt')
fix_separation(mag_file, temp)
samples, filetype = pmag.magic_read(samp_file)
with open(temp, 'r') as finput:
lines = finput.readlines()
os.remove(temp)
for line in lines:
MagRec = {}
line = line.split()
spec_text_id = line[0].split('_')[1]
SampRecs = pmag.get_dictitem(samples, 'er_sample_alternatives',
spec_text_id, 'has')
if len(SampRecs) > 0: # found one
MagRec['er_specimen_name'] = SampRecs[0]['er_sample_name']
MagRec['er_sample_name'] = MagRec['er_specimen_name']
MagRec['er_site_name'] = MagRec['er_specimen_name']
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['magic_software_packages'] = version_num
MagRec["treatment_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = '1'
MagRec["treatment_ac_field"] = '0'
volume = float(SampRecs[0]['sample_volume'])
x = float(line[4])
y = float(line[3])
negz = float(line[2])
cart = np.array([x, y, -negz]).transpose()
direction = pmag.cart2dir(cart).transpose()
expon = float(line[5])
magn_volume = direction[2] * (10.0**expon)
moment = magn_volume * volume
MagRec["measurement_magn_moment"] = str(moment)
MagRec["measurement_magn_volume"] = str(
magn_volume) #str(direction[2] * (10.0 ** expon))
MagRec["measurement_dec"] = '%7.1f' % (direction[0])
MagRec["measurement_inc"] = '%7.1f' % (direction[1])
step = line[1]
if step == 'NRM':
meas_type = "LT-NO"
elif step[0:2] == 'AD':
meas_type = "LT-AF-Z"
treat = float(step[2:])
MagRec["treatment_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif step[0:2] == 'TD':
meas_type = "LT-T-Z"
treat = float(step[2:])
MagRec["treatment_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
elif step[0:3] == 'ARM': #
meas_type = "LT-AF-I"
treat = float(row['step'][3:])
MagRec["treatment_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
MagRec["treatment_dc_field"] = '%8.3e' % (
50e-6) # assume 50uT DC field
MagRec[
"measurement_description"] = 'Assumed DC field - actual unknown'
elif step[0:3] == 'IRM': #
meas_type = "LT-IRM"
treat = float(step[3:])
MagRec["treatment_dc_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
else:
print('unknown treatment type for ', row)
return False, 'unknown treatment type for ', row
MagRec['magic_method_codes'] = meas_type
MagRecs.append(MagRec.copy())
else:
print('sample name not found: ', row['specname'])
MagOuts = pmag.measurements_methods(MagRecs, noave)
file_created, error_message = pmag.magic_write(meas_file, MagOuts,
'magic_measurements')
if file_created:
return True, meas_file
else:
return False, 'Results not written to file'
def main(**kwargs):
version_num = pmag.get_version()
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
mag_file = kwargs.get('mag_file')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 2.5)) * 1e-6
JR = kwargs.get('JR', False)
if JR:
if meth_code == "LP-NO":
meth_code = ""
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
samp_con = '5'
# format variables
tmp_file = mag_file.split(os.extsep)[0] + os.extsep + 'tmp'
mag_file = os.path.join(input_dir_path, mag_file)
if specnum != 0: specnum = -int(specnum)
if samp_con.startswith("4"):
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
elif samp_con.startswith("7"):
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
else:
Z = 1
# parse data
# fix .jr6 file so that there are spaces between all the columns.
pre_data = open(mag_file, 'r')
tmp_data = open(tmp_file, 'w')
if samp_con != '2': fixed_data = pre_data.read().replace('-', ' -')
else:
fixed_data = ""
for line in pre_data.readlines():
entries = line.split()
if len(entries) < 2: continue
fixed_line = entries[0] + ' ' + reduce(
lambda x, y: x + ' ' + y,
[x.replace('-', ' -') for x in entries[1:]])
fixed_data += fixed_line + os.linesep
tmp_data.write(fixed_data)
tmp_data.close()
pre_data.close()
if not JR:
column_names = [
'specimen', 'step', 'x', 'y', 'z', 'expon', 'azimuth', 'dip',
'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2',
'param1', 'param2', 'param3', 'param4', 'dir_csd'
]
else: # measured on the Joides Resolution JR6
column_names = [
'specimen', 'step', 'negz', 'y', 'x', 'expon', 'azimuth', 'dip',
'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2',
'param1', 'param2', 'param3', 'param4', 'dir_csd'
]
data = pd.read_csv(tmp_file,
delim_whitespace=True,
names=column_names,
index_col=False)
if isinstance(data['x'][0], str):
column_names = [
'specimen', 'step', 'step_unit', 'x', 'y', 'z', 'expon', 'azimuth',
'dip', 'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2',
'param1', 'param2', 'param3', 'param4', 'dir_csd'
]
data = pd.read_csv(tmp_file,
delim_whitespace=True,
names=column_names,
index_col=False)
if JR: data['z'] = -data['negz']
cart = np.array([data['x'], data['y'], data['z']]).transpose()
dir_dat = pmag.cart2dir(cart).transpose()
data['dir_dec'] = dir_dat[0]
data['dir_inc'] = dir_dat[1]
data['magn_moment'] = dir_dat[2] * (
10.0**
data['expon']) * volume # the data are in A/m - this converts to Am^2
data['magn_volume'] = dir_dat[2] * (10.0**data['expon']
) # A/m - data in A/m
data['dip'] = -data['dip']
data['specimen']
# put data into magic tables
MagRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
for rowNum, row in data.iterrows():
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
specimen = row['specimen']
if specnum != 0: sample = specimen[:specnum]
else: sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec["citations"] = "This study"
SpecRec["analysts"] = user
SpecRec['volume'] = volume
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec["citations"] = "This study"
SampRec["analysts"] = user
SampRec['azimuth'] = row['azimuth']
SampRec['dip'] = row['dip']
SampRec['bed_dip_direction'] = row['bed_dip_direction']
SampRec['bed_dip'] = row['bed_dip']
SampRec['method_codes'] = meth_code
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec["citations"] = "This study"
SiteRec["analysts"] = user
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec["citations"] = "This study"
LocRec["analysts"] = user
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec["citations"] = "This study"
MeasRec["analysts"] = user
MeasRec["specimen"] = specimen
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["treat_ac_field"] = '0'
if row['step'] == 'NRM':
meas_type = "LT-NO"
elif 'step_unit' in row and row['step_unit'] == 'C':
meas_type = "LT-T-Z"
treat = float(row['step'])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
elif row['step'][0:2] == 'AD':
meas_type = "LT-AF-Z"
treat = float(row['step'][2:])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif row['step'][0] == 'A':
meas_type = "LT-AF-Z"
treat = float(row['step'][1:])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type = "LT-T-Z"
treat = float(row['step'][2:])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
elif row['step'][0] == 'T':
meas_type = "LT-T-Z"
treat = float(row['step'][1:])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
else: # need to add IRM, and ARM options
print("measurement type unknown", row['step'])
return False, "measurement type unknown"
MeasRec["magn_moment"] = str(row['magn_moment'])
MeasRec["magn_volume"] = str(row['magn_volume'])
MeasRec["dir_dec"] = str(row['dir_dec'])
MeasRec["dir_inc"] = str(row['dir_inc'])
MeasRec['method_codes'] = meas_type
MagRecs.append(MeasRec)
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
try:
os.remove(tmp_file)
except (OSError, IOError) as e:
print("couldn't remove temperary fixed JR6 file %s" % tmp_file)
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
utrecht_magic.py
DESCRIPTION
converts Utrecht magnetometer data files to magic_measurements files
SYNTAX
utrecht_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-loc LOCNAME : specify location/study name
-site SITENAME : specify site name
-lat latitude of samples
-lon longitude of samples
-A: don't average replicate measurements
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
INPUT
Utrecht magnetometer data file
"""
# initialize some stuff
sample_lat = 0.0
sample_lon = 0.0
noave = 0
er_location_name = "unknown"
er_site_name = "unknown"
args = sys.argv
meth_code = "LP-NO"
version_num = pmag.get_version()
mag_file = ""
dir_path = '.'
MagRecs = []
SampOuts = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
meth_code = ""
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
#try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-lat" in args:
ind = args.index("-lat")
sample_lat = args[ind + 1]
if "-lon" in args:
ind = args.index("-lon")
sample_lon = args[ind + 1]
if "-site" in args:
ind = args.index("-site")
er_site_name = args[ind + 1]
if "-A" in args:
noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind + 1]
#samp_con='5'
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
er_location_name = kwargs.get('er_location_name', '')
er_site_name = kwargs.get('er_site_name', '')
sample_lat = kwargs.get('sample_lat', '')
sample_lon = kwargs.get('sample_lon', '')
#oave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
# format variables
if not mag_file:
return False, 'You must provide a Utrecht formated file'
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
samp_file = os.path.join(output_dir_path, samp_file)
ErSampRec = {}
# parse data
# Open up the Utrecht file and read the header information
print 'mag_file in utrecht_file', mag_file
data = open(mag_file, 'rU')
line = data.readline()
line_items = line.split(',')
operator = line_items[0]
operator = operator.replace("\"", "")
machine = line_items[1]
machine = machine.replace("\"", "")
machine = machine.rstrip('\n')
print "operator=", operator
print "machine=", machine
line = data.readline()
while line != '"END"':
line_items = line.split(',')
sample_name = line_items[0]
sample_name = sample_name.replace("\"", "")
print "sample_name=", sample_name
free_string = line_items[1]
free_string = free_string.replace("\"", "")
print "free_string=", free_string
dec = line_items[2]
print "dec=", dec
inc = line_items[3]
print "inc=", inc
volume = float(line_items[4])
volume = volume * 1e-6 # enter volume in cm^3, convert to m^3
print "volume=", volume
bed_plane = line_items[5]
print "bed_plane=", bed_plane
bed_tilt = line_items[6]
print "bed_tilt=", bed_tilt
# Configure et er_samples table
ErSampRec['er_sample_name'] = sample_name
ErSampRec['sample_azimuth'] = dec
ErSampRec['sample_dip'] = inc
ErSampRec['sample_bed_dip_direction'] = bed_plane
ErSampRec['sample_bed_tilt'] = bed_tilt
ErSampRec['sample_lat'] = sample_lat
ErSampRec['sample_lon'] = sample_lon
ErSampRec['magic_method_codes'] = meth_code
ErSampRec['er_location_name'] = er_location_name
ErSampRec['er_site_name'] = er_site_name
ErSampRec['er_citation_names'] = 'This study'
SampOuts.append(ErSampRec.copy())
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
# exit()
while line != '9999':
print line
step = items[0]
step = step.split('.')
step_value = step[0]
step_type = ""
if len(step) == 2:
step_type = step[1]
A = float(items[1])
B = float(items[2])
C = float(items[3])
# convert to MagIC coordinates
Z = -A
X = -B
Y = C
cart = np.array([X, Y, Z]).transpose()
direction = pmag.cart2dir(cart).transpose()
measurement_dec = direction[0]
measurement_inc = direction[1]
measurement_magn_moment = direction[
2] * 1.0e-12 # the data are in pico-Am^2 - this converts to Am^2
measurement_magn_volume = direction[
2] * 1.0e-12 / volume # data volume normalized - converted to A/m
print "measurement_magn_moment=", measurement_magn_moment
print "measurement_magn_volume=", measurement_magn_volume
error = items[4]
date = items[5]
date = date.strip('"')
date = date.split("-")
print date
time = items[6]
time = time.strip('"')
time = time.split(":")
print time
date_time = date[0] + ":" + date[1] + ":" + date[2] + ":" + time[
0] + ":" + time[1] + ":" + "0.0"
print date_time
MagRec = {}
MagRec["er_analyst_mail_names"] = operator
MagRec["magic_instrument_codes"] = "Utrecht_" + machine
MagRec["measurement_description"] = "free string = " + free_string
MagRec["measurement_date"] = date_time
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = er_site_name
MagRec['er_sample_name'] = sample_name
MagRec['magic_software_packages'] = version_num
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec[
"magic_experiment_name"] = er_location_name + er_site_name + sample_name
MagRec[
"measurement_number"] = er_location_name + er_site_name + sample_name + items[
0]
MagRec["er_specimen_name"] = sample_name
# MagRec["treatment_ac_field"] = '0'
MagRec["treatment_temp"] = '%8.3e' % (float(step_value) + 273.
) # temp in kelvin
meas_type = "LP-DIR-T"
if step_value == '0':
meas_type = "LT-NO"
print "step_type=", step_type
if step_type == '0':
if meas_type == "":
meas_type = "LT-T-Z"
else:
meas_type = meas_type + ":" + "LT-T-Z"
elif step_type == '1':
if meas_type == "":
meas_type = "LT-T-I"
else:
meas_type = meas_type + ":" + "LT-T-I"
elif step_type == '2':
if meas_type == "":
meas_type = "LT-PTRM-I"
else:
meas_type = meas_type + ":" + "LT-PTRM-I"
elif step_type == '3':
if meas_type == "":
meas_type = "LT-PTRM-Z"
else:
meas_type = meas_type + ":" + "LT-PTRM-Z"
print "meas_type=", meas_type
MagRec['magic_method_codes'] = meas_type
MagRec["measurement_magn_moment"] = measurement_magn_moment
MagRec["measurement_magn_volume"] = measurement_magn_volume
MagRec["measurement_dec"] = measurement_dec
MagRec["measurement_inc"] = measurement_inc
MagRec['measurement_csd'] = error
# MagRec['measurement_positions'] = '1'
MagRecs.append(MagRec.copy())
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
# write out the data to MagIC data files
pmag.magic_write(samp_file, SampOuts, 'er_samples')
print "sample orientations put in ", samp_file
# MagOuts = pmag.measurements_methods(MagRecs, noave)
# pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
pmag.magic_write(meas_file, MagRecs, 'magic_measurements')
print "results put in ", meas_file
print "exit!"
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
jr6_jr6_magic.py
DESCRIPTION
converts JR6 .jr6 format files to magic_measurements format files
SYNTAX
jr6_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify sample naming convention (6 and 7 not yet implemented)
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-JR IODP samples measured on the JOIDES RESOLUTION
-v NUM : specify the volume in cc of the sample, default 2.5^3cc
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
JR6 .jr6 format file
"""
# initialize some stuff
noave = 0
#volume=2.5**3 #default volume is a 2.5cm cube
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
inst = ""
samp_con, Z = '1', ""
missing = 1
demag = "N"
er_location_name = "unknown"
citation = 'This study'
args = sys.argv
meth_code = "LP-NO"
specnum = 1
version_num = pmag.get_version()
Samps = [] # keeps track of sample orientations
user = ""
mag_file = ""
dir_path = '.'
MagRecs = []
ErSamps = []
SampOuts = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
tmp_file = "fixed.jr6"
meth_code, JR = "", 0
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
#try:
# open(samp_file,'r')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-A" in args: noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind + 1]
if "-JR" in args:
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
JR = 1
samp_con = '5'
if "-v" in args:
ind = args.index("-v")
volume = float(
args[ind + 1]) * 1e-6 # enter volume in cc, convert to m^3
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
else:
#convert cm^3 to m^3
volume *= 1e-6
JR = kwargs.get('JR', 0)
if JR:
if meth_code == "LP-NO":
meth_code = ""
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
samp_con = '5'
# format variables
mag_file = input_dir_path + "/" + mag_file
meas_file = output_dir_path + "/" + meas_file
samp_file = output_dir_path + "/" + samp_file
tmp_file = output_dir_path + "/" + tmp_file
if specnum != 0:
specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
ErSampRec, ErSiteRec = {}, {}
# parse data
# fix .jr6 file so that there are spaces between all the columns.
pre_data = open(mag_file, 'r')
tmp_data = open(tmp_file, 'w')
line = pre_data.readline()
while line != '':
line = line.replace('-', ' -')
#print "line=", line
tmp_data.write(line)
line = pre_data.readline()
tmp_data.close()
pre_data.close()
data = pd.read_csv(tmp_file, delim_whitespace=True, header=None)
if JR == 0: #
data.columns = [
'er_specimen_name', 'step', 'x', 'y', 'z', 'expon',
'sample_azimuth', 'sample_dip', 'sample_bed_dip_direction',
'sample_bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2',
'param3', 'param4', 'measurement_csd'
]
cart = np.array([data['x'], data['y'], data['z']]).transpose()
else: # measured on the Joides Resolution JR6
data.columns = [
'er_specimen_name', 'step', 'negz', 'y', 'x', 'expon',
'sample_azimuth', 'sample_dip', 'sample_bed_dip_direction',
'sample_bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2',
'param3', 'param4', 'measurement_csd'
]
cart = np.array([data['x'], data['y'], -data['negz']]).transpose()
dir = pmag.cart2dir(cart).transpose()
data['measurement_dec'] = dir[0]
data['measurement_inc'] = dir[1]
data['measurement_magn_moment'] = dir[2] * (
10.0**
data['expon']) * volume # the data are in A/m - this converts to Am^2
data['measurement_magn_volume'] = dir[2] * (10.0**data['expon']
) # A/m - data in A/m
data['sample_dip'] = -data['sample_dip']
DGEOs, IGEOs = [], []
for ind in range(len(data)):
dgeo, igeo = pmag.dogeo(data.iloc[ind]['measurement_dec'],
data.iloc[ind]['measurement_inc'],
data.iloc[ind]['sample_azimuth'],
data.iloc[ind]['sample_dip'])
DGEOs.append(dgeo)
IGEOs.append(igeo)
data['specimen_dec'] = DGEOs
data['specimen_inc'] = IGEOs
data['specimen_tilt'] = '1'
if specnum != 0:
data['er_sample_name'] = data['er_specimen_name'][:specnum]
else:
data['er_sample_name'] = data['er_specimen_name']
if int(samp_con) in [1, 2, 3, 4, 5, 7]:
data['er_site_name'] = pmag.parse_site(data['er_sample_name'],
samp_con, Z)
# else:
# if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampRec['er_site_name']
# if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampRec['er_location_name']
# Configure the er_sample table
for rowNum, row in data.iterrows():
sampleFlag = 0
for sampRec in SampOuts:
if sampRec['er_sample_name'] == row['er_sample_name']:
sampleFlag = 1
break
if sampleFlag == 0:
ErSampRec['er_sample_name'] = row['er_sample_name']
ErSampRec['sample_azimuth'] = str(row['sample_azimuth'])
ErSampRec['sample_dip'] = str(row['sample_dip'])
ErSampRec['magic_method_codes'] = meth_code
ErSampRec['er_location_name'] = er_location_name
ErSampRec['er_site_name'] = row['er_site_name']
ErSampRec['er_citation_names'] = 'This study'
SampOuts.append(ErSampRec.copy())
# Configure the magic_measurements table
for rowNum, row in data.iterrows():
MagRec = {}
# MagRec['measurement_description']='Date: '+date
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = row['er_site_name']
MagRec['er_sample_name'] = row['er_sample_name']
MagRec['magic_software_packages'] = version_num
MagRec["treatment_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = '1'
MagRec["er_specimen_name"] = row['er_specimen_name']
MagRec["treatment_ac_field"] = '0'
if row['step'] == 'NRM':
meas_type = "LT-NO"
elif row['step'][0:2] == 'AD':
meas_type = "LT-AF-Z"
treat = float(row['step'][2:])
MagRec["treatment_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type = "LT-T-Z"
treat = float(row['step'][2:])
MagRec["treatment_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
else: # need to add IRM, and ARM options
print("measurement type unknown", row['step'])
return False, "measurement type unknown"
MagRec["measurement_magn_moment"] = str(row['measurement_magn_moment'])
MagRec["measurement_magn_volume"] = str(row['measurement_magn_volume'])
MagRec["measurement_dec"] = str(row['measurement_dec'])
MagRec["measurement_inc"] = str(row['measurement_inc'])
MagRec['magic_method_codes'] = meas_type
MagRecs.append(MagRec.copy())
pmag.magic_write(samp_file, SampOuts, 'er_samples')
print("sample orientations put in ", samp_file)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print("results put in ", meas_file)
print("exit!")
return True, meas_file
def main():
"""
NAME
igrf.py
DESCRIPTION
This program calculates igrf field values
using the routine of Malin and Barraclough (1981)
based on d/igrfs from 1900 to 2010.
between 1900 and 1000BCE, it uses CALS3K.4, ARCH3K.1 , or PFM9K
Prior to 1000BCE, it uses CALS10k-4b
Calculates reference field vector at specified location and time.
SYNTAX
igrf.py [-h] [-i] -f FILE [< filename]
OPTIONS:
-h prints help message and quits
-i for interactive data entry
-f FILE specify file name with input data
-F FILE specify output file name
-ages MIN MAX INCR: specify age minimum in years (+/- AD), maximum and increment, default is line by line
-loc LAT LON; specify location, default is line by line
-alt ALT; specify altitude in km, default is sealevel (0)
-plt; make a plot of the time series
-sav, saves plot and quits
-fmt [pdf,jpg,eps,svg] specify format for output figure (default is svg)
-mod [arch3k,cals3k,pfm9k] specify model for 3ka to 1900 AD, default is cals3k.4b
NB: program uses IGRF12 for dates 1900 to 2015.
INPUT FORMAT
interactive entry:
date: decimal year
alt: altitude in km
lat: positive north
lon: positive east
for file entry:
space delimited string: date alt lat long
OUTPUT FORMAT
Declination Inclination Intensity (nT) date alt lat long
"""
plot,fmt=0,'svg'
plt=0
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if len(sys.argv)!=0 and '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-mod' in sys.argv:
ind=sys.argv.index('-mod')
mod=sys.argv[ind+1]
else: mod='cals3k'
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
input=numpy.loadtxt(file)
elif '-i' in sys.argv:
while 1:
try:
line=[]
line.append(float(raw_input("Decimal year: <cntrl-D to quit> ")))
alt=raw_input("Elevation in km [0] ")
if alt=="":alt="0"
line.append(float(alt))
line.append(float(raw_input("Latitude (positive north) ")))
line.append(float(raw_input("Longitude (positive east) ")))
if mod=='':
x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0])
else:
x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0],mod=mod)
Dir=pmag.cart2dir((x,y,z))
print '%8.2f %8.2f %8.0f'%(Dir[0],Dir[1],f)
except EOFError:
print "\n Good-bye\n"
sys.exit()
elif '-ages' in sys.argv:
ind=sys.argv.index('-ages')
agemin=float(sys.argv[ind+1])
agemax=float(sys.argv[ind+2])
ageincr=float(sys.argv[ind+3])
if '-loc' in sys.argv:
ind=sys.argv.index('-loc')
lat=float(sys.argv[ind+1])
lon=float(sys.argv[ind+2])
else:
print "must specify lat/lon if using age range option"
sys.exit()
if '-alt' in sys.argv:
ind=sys.argv.index('-alt')
alt=float(sys.argv[ind+1])
else: alt=0
ages=numpy.arange(agemin,agemax,ageincr)
lats=numpy.ones(len(ages))*lat
lons=numpy.ones(len(ages))*lon
alts=numpy.ones(len(ages))*alt
input=numpy.array([ages,alts,lats,lons]).transpose()
else:
input=numpy.loadtxt(sys.stdin,dtype=numpy.float)
if '-F' in sys.argv:
ind=sys.argv.index('-F')
outfile=sys.argv[ind+1]
out=open(outfile,'w')
else:outfile=""
if '-sav' in sys.argv:plot=1
if '-plt' in sys.argv:
plt=1
import matplotlib
matplotlib.use("TkAgg")
import pylab
pylab.ion()
Ages,Decs,Incs,Ints,VADMs=[],[],[],[],[]
for line in input:
if mod=='':
x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0])
else:
x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0],mod=mod)
Dir=pmag.cart2dir((x,y,z))
if outfile!="":
out.write('%8.2f %8.2f %8.0f %7.1f %7.1f %7.1f %7.1f\n'%(Dir[0],Dir[1],f,line[0],line[1],line[2],line[3]))
elif plt:
Ages.append(line[0])
if Dir[0]>180: Dir[0]=Dir[0]-360.0
Decs.append(Dir[0])
Incs.append(Dir[1])
Ints.append(f*1e-3)
VADMs.append(pmag.b_vdm(f*1e-9,line[2])*1e-21)
else:
print '%8.2f %8.2f %8.0f %7.1f %7.1f %7.1f %7.1f'%(Dir[0],Dir[1],f,line[0],line[1],line[2],line[3])
if plt:
fig=pylab.figure(num=1,figsize=(7,9))
fig.add_subplot(411)
pylab.plot(Ages,Decs)
pylab.ylabel('Declination ($^{\circ}$)')
fig.add_subplot(412)
pylab.plot(Ages,Incs)
pylab.ylabel('Inclination ($^{\circ}$)')
fig.add_subplot(413)
pylab.plot(Ages,Ints)
pylab.ylabel('Intensity ($\mu$T)')
fig.add_subplot(414)
pylab.plot(Ages,VADMs)
pylab.ylabel('VADMs (ZAm$^2$)')
pylab.xlabel('Ages')
if plot==0:
pylab.draw()
ans=raw_input("S[a]ve to save figure, <Return> to quit ")
if ans=='a':
pylab.savefig('igrf.'+fmt)
print 'Figure saved as: ','igrf.'+fmt
else:
pylab.savefig('igrf.'+fmt)
print 'Figure saved as: ','igrf.'+fmt
sys.exit()
def main(**kwargs):
version_num=pmag.get_version()
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
mag_file = kwargs.get('mag_file')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 2.5))* 1e-6
JR = kwargs.get('JR', False)
if JR:
if meth_code == "LP-NO":
meth_code = ""
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
samp_con='5'
# format variables
tmp_file = mag_file.split(os.extsep)[0]+os.extsep+'tmp'
mag_file = os.path.join(input_dir_path, mag_file)
if specnum!=0: specnum=-int(specnum)
if samp_con.startswith("4"):
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
elif samp_con.startswith("7"):
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
else: Z=1
# parse data
# fix .jr6 file so that there are spaces between all the columns.
pre_data=open(mag_file, 'r')
tmp_data=open(tmp_file, 'w')
if samp_con!='2': fixed_data=pre_data.read().replace('-',' -')
else:
fixed_data=""
for line in pre_data.readlines():
entries=line.split()
if len(entries)<2: continue
fixed_line = entries[0] + ' ' + reduce(lambda x,y: x+' '+y, [x.replace('-',' -') for x in entries[1:]])
fixed_data += fixed_line+os.linesep
tmp_data.write(fixed_data)
tmp_data.close()
pre_data.close()
if not JR:
column_names=['specimen', 'step', 'x', 'y', 'z', 'expon', 'azimuth', 'dip', 'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2', 'param3', 'param4', 'dir_csd']
else: # measured on the Joides Resolution JR6
column_names=['specimen', 'step', 'negz', 'y', 'x', 'expon', 'azimuth', 'dip', 'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2', 'param3', 'param4', 'dir_csd']
data=pd.read_csv(tmp_file, delim_whitespace=True, names=column_names, index_col=False)
if isinstance(data['x'][0],str):
column_names=['specimen', 'step', 'step_unit', 'x', 'y', 'z', 'expon', 'azimuth', 'dip', 'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2', 'param3', 'param4', 'dir_csd']
data=pd.read_csv(tmp_file, delim_whitespace=True, names=column_names, index_col=False)
if JR: data['z']=-data['negz']
cart=np.array([data['x'],data['y'],data['z']]).transpose()
dir_dat= pmag.cart2dir(cart).transpose()
data['dir_dec']=dir_dat[0]
data['dir_inc']=dir_dat[1]
data['magn_moment']=dir_dat[2]*(10.0**data['expon'])*volume # the data are in A/m - this converts to Am^2
data['magn_volume']=dir_dat[2]*(10.0**data['expon']) # A/m - data in A/m
data['dip']=-data['dip']
data['specimen']
# put data into magic tables
MagRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
for rowNum, row in data.iterrows():
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
specimen=row['specimen']
if specnum!=0: sample=specimen[:specnum]
else: sample=specimen
site=pmag.parse_site(sample,samp_con,Z)
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec["citations"]="This study"
SpecRec["analysts"]=user
SpecRec['volume'] = volume
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec["citations"]="This study"
SampRec["analysts"]=user
SampRec['azimuth'] = row['azimuth']
SampRec['dip'] = row['dip']
SampRec['bed_dip_direction'] = row['bed_dip_direction']
SampRec['bed_dip'] = row['bed_dip']
SampRec['method_codes']=meth_code
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec["citations"]="This study"
SiteRec["analysts"]=user
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec["citations"]="This study"
LocRec["analysts"]=user
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec["citations"]="This study"
MeasRec["analysts"]=user
MeasRec["specimen"]=specimen
MeasRec['software_packages']=version_num
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["quality"]='g'
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
MeasRec["treat_ac_field"]='0'
if row['step'] == 'NRM':
meas_type="LT-NO"
elif 'step_unit' in row and row['step_unit']=='C':
meas_type="LT-T-Z"
treat=float(row['step'])
MeasRec["treat_temp"]='%8.3e' % (treat+273.) # temp in kelvin
elif row['step'][0:2] == 'AD':
meas_type="LT-AF-Z"
treat=float(row['step'][2:])
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif row['step'][0] == 'A':
meas_type="LT-AF-Z"
treat=float(row['step'][1:])
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type="LT-T-Z"
treat=float(row['step'][2:])
MeasRec["treat_temp"]='%8.3e' % (treat+273.) # temp in kelvin
elif row['step'][0] == 'T':
meas_type="LT-T-Z"
treat=float(row['step'][1:])
MeasRec["treat_temp"]='%8.3e' % (treat+273.) # temp in kelvin
else: # need to add IRM, and ARM options
print("measurement type unknown", row['step'])
return False, "measurement type unknown"
MeasRec["magn_moment"]=str(row['magn_moment'])
MeasRec["magn_volume"]=str(row['magn_volume'])
MeasRec["dir_dec"]=str(row['dir_dec'])
MeasRec["dir_inc"]=str(row['dir_inc'])
MeasRec['method_codes']=meas_type
MagRecs.append(MeasRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
try: os.remove(tmp_file)
except (OSError,IOError) as e: print("couldn't remove temperary fixed JR6 file %s"%tmp_file)
return True, meas_file
