def main():
"""
NAME
trmaq_magic.py
DESCTIPTION
does non-linear trm acquisisiton correction
SYNTAX
trmaq_magic.py [-h][-i][command line options]
OPTIONS
-h prints help message and quits
-i allows interactive setting of file names
-f MFILE, sets magic_measurements input file
-ft TSPEC, sets thellier_specimens input file
-F OUT, sets output for non-linear TRM acquisition corrected data
DEFAULTS
MFILE: trmaq_measurements.txt
TSPEC: thellier_specimens.txt
OUT: NLT_specimens.txt
"""
meas_file = 'trmaq_measurements.txt'
tspec = "thellier_specimens.txt"
output = 'NLT_specimens.txt'
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-i' in sys.argv:
meas_file = input(
"Input magic_measurements file name? [trmaq_measurements.txt] ")
if meas_file == "": meas_file = "trmaq_measurements.txt"
tspec = input(
" thellier_specimens file name? [thellier_specimens.txt] ")
if tspec == "": tspec = "thellier_specimens.txt"
output = input(
"File for non-linear TRM adjusted specimen data: [NLTspecimens.txt] "
)
if output == "": output = "NLT_specimens.txt"
if '-f' in sys.argv:
ind = sys.argv.index('-f')
meas_file = sys.argv[ind + 1]
if '-ft' in sys.argv:
ind = sys.argv.index('-ft')
tspec = sys.argv[ind + 1]
if '-F' in sys.argv:
ind = sys.argv.index('-F')
output = sys.argv[ind + 1]
#
PLT = {'aq': 1}
pmagplotlib.plot_init(PLT['aq'], 5, 5)
#
# get name of file from command line
#
comment = ""
#
#
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print(file_type)
print(file_type, "This is not a valid magic_measurements file ")
sys.exit()
sids = pmag.get_specs(meas_data)
specimen = 0
#
# read in thellier_specimen data
#
nrm, file_type = pmag.magic_read(tspec)
PmagSpecRecs = []
while specimen < len(sids):
#
# find corresoponding paleointensity data for this specimen
#
s = sids[specimen]
blab, best = "", ""
for nrec in nrm: # pick out the Banc data for this spec
if nrec["er_specimen_name"] == s:
blab = float(nrec["specimen_lab_field_dc"])
best = float(nrec["specimen_int"])
TrmRec = nrec
break
if blab == "":
print("skipping ", s, " : no best ")
specimen += 1
else:
print(sids[specimen], specimen + 1, 'of ', len(sids), 'Best = ',
best * 1e6)
MeasRecs = []
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"] == s:
meths = rec["magic_method_codes"].split(":")
methcodes = []
for meth in meths:
methcodes.append(meth.strip())
if "LP-TRM" in methcodes: MeasRecs.append(rec)
if len(MeasRecs) < 2:
specimen += 1
print('skipping specimen - no trm acquisition data ', s)
#
# collect info for the PmagSpecRec dictionary
#
else:
TRMs, Bs = [], []
for rec in MeasRecs:
Bs.append(float(rec['treatment_dc_field']))
TRMs.append(float(rec['measurement_magn_moment']))
NLpars = nlt.NLtrm(
Bs, TRMs, best, blab, 0
) # calculate best fit parameters through TRM acquisition data, and get new banc
#
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
npred = nlt.TRM(
Bp[-1], NLpars['xopt'][0],
NLpars['xopt'][1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(PLT['aq'], Bs, TRMs, Bp, Mp, NLpars,
rec['magic_experiment_name'])
pmagplotlib.drawFIGS(PLT)
print('Banc= ', float(NLpars['banc']) * 1e6)
trmTC = {}
for key in list(TrmRec.keys()):
trmTC[key] = TrmRec[
key] # copy of info from thellier_specimens record
trmTC['specimen_int'] = '%8.3e' % (NLpars['banc'])
trmTC['magic_method_codes'] = TrmRec[
"magic_method_codes"] + ":DA-NL"
PmagSpecRecs.append(trmTC)
ans = input("Return for next specimen, s[a]ve plot ")
if ans == 'a':
Name = {'aq': rec['er_specimen_name'] + '_TRM.svg'}
pmagplotlib.saveP(PLT, Name)
specimen += 1
pmag.magic_write(output, PmagSpecRecs, 'pmag_specimens')
def main():
"""
NAME
microwave_magic.py
DESCRIPTION
plots microwave paleointensity data, allowing interactive setting of bounds.
Saves and reads interpretations
from a pmag_specimen formatted table, default: microwave_specimens.txt
SYNTAX
microwave_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEAS, set magic_measurements input file
-fsp PRIOR, set pmag_specimen prior interpretations file
-fcr CRIT, set criteria file for grading.
-fmt [svg,png,jpg], format for images - default is svg
-sav, saves plots with out review (default format)
-spc SPEC, plots single specimen SPEC, saves plot with specified format
with optional -b bounds adn quits
-b BEG END: sets bounds for calculation
BEG: starting step for slope calculation
END: ending step for slope calculation
DEFAULTS
MEAS: magic_measurements.txt
CRIT: NONE
PRIOR: microwave_specimens.txt
OUTPUT
figures:
ALL: numbers refer to temperature steps in command line window
1) Arai plot: closed circles are zero-field first/infield
open circles are infield first/zero-field
triangles are pTRM checks
squares are pTRM tail checks
VDS is vector difference sum
diamonds are bounds for interpretation
2) Zijderveld plot: closed (open) symbols are X-Y (X-Z) planes
X rotated to NRM direction
3) (De/Re)Magnetization diagram:
circles are NRM remaining
squares are pTRM gained
command line window:
list is: temperature step numbers, power (J), Dec, Inc, Int (units of magic_measuements)
list of possible commands: type letter followed by return to select option
saving of plots creates .svg format files with specimen_name, plot type as name
"""
#
# initializations
#
meas_file, critout, inspec = "magic_measurements.txt", "", "microwave_specimens.txt"
inlt = 0
version_num = pmag.get_version()
Tinit, DCZ, field, first_save = 0, 0, -1, 1
user, comment = "", ''
ans, specimen, recnum, start, end = 0, 0, 0, 0, 0
plots, pmag_out, samp_file, style = 0, "", "", "svg"
fmt = '.' + style
#
# default acceptance criteria
#
accept_keys = [
'specimen_int_ptrm_n', 'specimen_md', 'specimen_fvds',
'specimen_b_beta', 'specimen_dang', 'specimen_drats', 'specimen_Z'
]
accept = {}
accept['specimen_int_ptrm_n'] = 2
accept['specimen_md'] = 10
accept['specimen_fvds'] = 0.35
accept['specimen_b_beta'] = .1
accept['specimen_int_mad'] = 7
accept['specimen_dang'] = 10
accept['specimen_drats'] = 10
accept['specimen_Z'] = 10
#
# parse command line options
#
spc, BEG, END = "", "", ""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
meas_file = sys.argv[ind + 1]
if '-fsp' in sys.argv:
ind = sys.argv.index('-fsp')
inspec = sys.argv[ind + 1]
if '-fcr' in sys.argv:
ind = sys.argv.index('-fcr')
critout = sys.argv[ind + 1]
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = '.' + sys.argv[ind + 1]
if '-spc' in sys.argv:
ind = sys.argv.index('-spc')
spc = sys.argv[ind + 1]
if '-b' in sys.argv:
ind = sys.argv.index('-b')
BEG = int(sys.argv[ind + 1])
END = int(sys.argv[ind + 2])
if critout != "":
crit_data, file_type = pmag.magic_read(critout)
if pmagplotlib.verbose:
print "Acceptance criteria read in from ", critout
accept = {}
accept['specimen_int_ptrm_n'] = 2.0
for critrec in crit_data:
if critrec["pmag_criteria_code"] == "IE-SPEC":
for key in accept_keys:
if key not in critrec.keys():
accept[key] = -1
else:
accept[key] = float(critrec[key])
try:
open(inspec, 'rU')
PriorRecs, file_type = pmag.magic_read(inspec)
if file_type != 'pmag_specimens':
print file_type
print file_type, inspec, " is not a valid pmag_specimens file "
sys.exit()
for rec in PriorRecs:
if 'magic_software_packages' not in rec.keys():
rec['magic_software_packages'] = ""
except IOError:
PriorRecs = []
if pmagplotlib.verbose:
print "starting new specimen interpretation file: ", inspec
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print file_type
print file_type, "This is not a valid magic_measurements file "
sys.exit()
backup = 0
# define figure numbers for arai, zijderveld and
# de-,re-magization diagrams
AZD = {}
AZD['deremag'], AZD['zijd'], AZD['arai'], AZD['eqarea'] = 1, 2, 3, 4
pmagplotlib.plot_init(AZD['arai'], 4, 4)
pmagplotlib.plot_init(AZD['zijd'], 4, 4)
pmagplotlib.plot_init(AZD['deremag'], 4, 4)
pmagplotlib.plot_init(AZD['eqarea'], 4, 4)
#
#
#
# get list of unique specimen names
#
CurrRec = []
sids = pmag.get_specs(meas_data)
# get plots for specimen s - default is just to step through arai diagrams
#
if spc != "": specimen = sids.index(spc)
while specimen < len(sids):
methcodes = []
if pmagplotlib.verbose and spc != "":
print sids[specimen], specimen + 1, 'of ', len(sids)
MeasRecs = []
s = sids[specimen]
datablock, trmblock = [], []
PmagSpecRec = {}
PmagSpecRec["er_analyst_mail_names"] = user
PmagSpecRec["specimen_correction"] = 'u'
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"] == s:
MeasRecs.append(rec)
methods = rec["magic_method_codes"].split(":")
meths = []
for meth in methods:
meths.append(meth.strip()) # take off annoying spaces
methods = ""
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:
methcodes.append(meth.strip())
methods = methods + meth + ":"
methods = methods[:-1]
rec["magic_method_codes"] = methods
if "LP-PI-M" in meths: datablock.append(rec)
if "LP-MRM" in meths: trmblock.append(rec)
if len(trmblock) > 2 and inspec != "":
if Tinit == 0:
Tinit = 1
AZD['MRM'] = 4
pmagplotlib.plot_init(AZD['MRM'], 4, 4)
elif Tinit == 1:
pmagplotlib.clearFIG(AZD['MRM'])
if len(datablock) < 4:
if backup == 0:
specimen += 1
if pmagplotlib.verbose:
print 'skipping specimen - moving forward ', s
else:
specimen -= 1
if pmagplotlib.verbose:
print 'skipping specimen - moving backward ', s
#
# collect info for the PmagSpecRec dictionary
#
else:
rec = datablock[0]
PmagSpecRec["er_citation_names"] = "This study"
PmagSpecRec["er_specimen_name"] = s
PmagSpecRec["er_sample_name"] = rec["er_sample_name"]
PmagSpecRec["er_site_name"] = rec["er_site_name"]
PmagSpecRec["er_location_name"] = rec["er_location_name"]
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"] = ""
PmagSpecRec["magic_instrument_codes"] = rec[
"magic_instrument_codes"]
PmagSpecRec["measurement_step_unit"] = "J"
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"] = ""
else:
PmagSpecRec["magic_experiment_names"] = rec[
"magic_experiment_name"]
meths = rec["magic_method_codes"].split(':')
# sort data into types
if "LP-PI-M-D" in meths: # this is a double heating experiment
exp_type = "LP-PI-M-D"
elif "LP-PI-M-S" in meths:
exp_type = "LP-PI-M-S"
else:
print "experiment type not supported yet "
break
araiblock, field = pmag.sortmwarai(datablock, exp_type)
first_Z = araiblock[0]
first_I = araiblock[1]
GammaChecks = araiblock[-3]
ThetaChecks = araiblock[-2]
DeltaChecks = araiblock[-1]
if len(first_Z) < 3:
if backup == 0:
specimen += 1
if pmagplotlib.verbose:
print 'skipping specimen - moving forward ', s
else:
specimen -= 1
if pmagplotlib.verbose:
print 'skipping specimen - moving backward ', s
else:
backup = 0
zijdblock, units = pmag.find_dmag_rec(s, meas_data)
if exp_type == "LP-PI-M-D":
recnum = 0
print "ZStep Watts Dec Inc Int"
for plotrec in zijdblock:
if pmagplotlib.verbose:
print '%i %i %7.1f %7.1f %8.3e ' % (
recnum, plotrec[0], plotrec[1], plotrec[2],
plotrec[3])
recnum += 1
recnum = 1
if GammaChecks != "":
print "IStep Watts Gamma"
for gamma in GammaChecks:
if pmagplotlib.verbose:
print '%i %i %7.1f ' % (recnum, gamma[0],
gamma[1])
recnum += 1
if exp_type == "LP-PI-M-S":
if pmagplotlib.verbose:
print "IStep Watts Theta"
kk = 0
for theta in ThetaChecks:
kk += 1
print '%i %i %7.1f ' % (kk, theta[0], theta[1])
if pmagplotlib.verbose:
print "Watts Delta"
for delta in DeltaChecks:
print '%i %7.1f ' % (delta[0], delta[1])
pmagplotlib.plotAZ(AZD, araiblock, zijdblock, s, units[0])
if inspec != "":
if pmagplotlib.verbose:
print 'Looking up saved interpretation....'
found = 0
for k in range(len(PriorRecs)):
try:
if PriorRecs[k]["er_specimen_name"] == s:
found = 1
CurrRec.append(PriorRecs[k])
for j in range(len(araiblock[0])):
if float(araiblock[0][j][0]) == float(
PriorRecs[k]
["measurement_step_min"]):
start = j
if float(araiblock[0][j][0]) == float(
PriorRecs[k]
["measurement_step_max"]):
end = j
pars, errcode = pmag.PintPars(
araiblock, zijdblock, start, end)
pars['measurement_step_unit'] = "J"
del PriorRecs[
k] # put in CurrRec, take out of PriorRecs
if errcode != 1:
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars[
"specimen_b"]
pars["er_specimen_name"] = s
if pmagplotlib.verbose:
print 'Saved interpretation: '
pars = pmag.scoreit(
pars, PmagSpecRec, accept, '', 0)
pmagplotlib.plotB(AZD, araiblock,
zijdblock, pars)
if len(trmblock) > 2:
blab = field
best = pars["specimen_int"]
Bs, TRMs = [], []
for trec in trmblock:
Bs.append(
float(
trec['treatment_dc_field'])
)
TRMs.append(
float(trec[
'measurement_magn_moment'])
)
NLpars = nlt.NLtrm(
Bs, TRMs, best, blab, 0
) # calculate best fit parameters through TRM acquisition data, and get new banc
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
npred = nlt.TRM(
Bp[-1], NLpars['xopt'][0],
NLpars['xopt'][1]
) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(
AZD['MRM'], Bs, TRMs, Bp, Mp,
NLpars,
trec['magic_experiment_name'])
print npred
print 'Banc= ', float(
NLpars['banc']) * 1e6
if pmagplotlib.verbose:
print 'Banc= ', float(
NLpars['banc']) * 1e6
pmagplotlib.drawFIGS(AZD)
else:
print 'error on specimen ', s
except:
pass
if pmagplotlib.verbose and found == 0:
print ' None found :( '
if spc != "":
if BEG != "":
pars, errcode = pmag.PintPars(araiblock, zijdblock,
BEG, END)
pars['measurement_step_unit'] = "J"
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars["specimen_b"]
pars["er_specimen_name"] = s
pars['specimen_grade'] = '' # ungraded
pmagplotlib.plotB(AZD, araiblock, zijdblock, pars)
if len(trmblock) > 2:
if inlt == 0:
donlt()
inlt = 1
blab = field
best = pars["specimen_int"]
Bs, TRMs = [], []
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(
float(trec['measurement_magn_moment']))
NLpars = nlt.NLtrm(
Bs, TRMs, best, blab, 0
) # calculate best fit parameters through TRM acquisition data, and get new banc
#
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
npred = nlt.TRM(
Bp[-1], NLpars['xopt'][0], NLpars['xopt']
[1]) # predicted NRM for this field
files = {}
for key in AZD.keys():
files[key] = s + '_' + key + fmt
pmagplotlib.saveP(AZD, files)
sys.exit()
if plots == 0:
ans = 'b'
while ans != "":
print """
s[a]ve plot, set [b]ounds for calculation, [d]elete current interpretation, [p]revious, [s]ample, [q]uit:
"""
ans = raw_input('Return for next specimen \n')
if ans == "":
specimen += 1
if ans == "d":
save_redo(PriorRecs, inspec)
CurrRec = []
pmagplotlib.plotAZ(AZD, araiblock, zijdblock, s,
units[0])
pmagplotlib.drawFIGS(AZD)
if ans == 'a':
files = {}
for key in AZD.keys():
files[key] = s + '_' + key + fmt
pmagplotlib.saveP(AZD, files)
ans = ""
if ans == 'q':
print "Good bye"
sys.exit()
if ans == 'p':
specimen = specimen - 1
backup = 1
ans = ""
if ans == 's':
keepon = 1
spec = raw_input(
'Enter desired specimen name (or first part there of): '
)
while keepon == 1:
try:
specimen = sids.index(spec)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if spec in sids[qq]:
tmplist.append(sids[qq])
print specimen, " not found, but this was: "
print tmplist
spec = raw_input(
'Select one or try again\n ')
ans = ""
if ans == 'b':
if end == 0 or end >= len(araiblock[0]):
end = len(araiblock[0]) - 1
GoOn = 0
while GoOn == 0:
print 'Enter index of first point for calculation: ', '[', start, ']'
answer = raw_input('return to keep default ')
if answer != "": start = int(answer)
print 'Enter index of last point for calculation: ', '[', end, ']'
answer = raw_input('return to keep default ')
if answer != "":
end = int(answer)
if start >= 0 and start < len(araiblock[
0]) - 2 and end > 0 and end < len(
araiblock[0]) and start < end:
GoOn = 1
else:
print "Bad endpoints - try again! "
start, end = 0, len(araiblock)
s = sids[specimen]
pars, errcode = pmag.PintPars(
araiblock, zijdblock, start, end)
pars['measurement_step_unit'] = "J"
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars[
"specimen_b"]
pars["er_specimen_name"] = s
pars = pmag.scoreit(pars, PmagSpecRec, accept, '',
0)
PmagSpecRec["measurement_step_min"] = '%8.3e' % (
pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"] = '%8.3e' % (
pars["measurement_step_max"])
PmagSpecRec["measurement_step_unit"] = "J"
PmagSpecRec["specimen_int_n"] = '%i' % (
pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"] = '%8.3e' % (
pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"] = '%8.3e ' % (
pars["specimen_int"])
PmagSpecRec["specimen_b"] = '%5.3f ' % (
pars["specimen_b"])
PmagSpecRec["specimen_q"] = '%5.1f ' % (
pars["specimen_q"])
PmagSpecRec["specimen_f"] = '%5.3f ' % (
pars["specimen_f"])
PmagSpecRec["specimen_fvds"] = '%5.3f' % (
pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"] = '%5.3f' % (
pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"] = '%7.1f' % (
pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"] = '%7.1f' % (
pars["specimen_Z"])
if pars["method_codes"] != "":
tmpcodes = pars["method_codes"].split(":")
for t in tmpcodes:
if t.strip() not in methcodes:
methcodes.append(t.strip())
PmagSpecRec["specimen_dec"] = '%7.1f' % (
pars["specimen_dec"])
PmagSpecRec["specimen_inc"] = '%7.1f' % (
pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"] = '-1'
PmagSpecRec["specimen_direction_type"] = 'l'
PmagSpecRec[
"direction_type"] = 'l' # this is redudant, but helpful - won't be imported
PmagSpecRec["specimen_dang"] = '%7.1f ' % (
pars["specimen_dang"])
PmagSpecRec["specimen_drats"] = '%7.1f ' % (
pars["specimen_drats"])
PmagSpecRec["specimen_int_ptrm_n"] = '%i ' % (
pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"] = '%6.4f ' % (
pars["specimen_rsc"])
PmagSpecRec["specimen_md"] = '%i ' % (int(
pars["specimen_md"]))
if PmagSpecRec["specimen_md"] == '-1':
PmagSpecRec["specimen_md"] = ""
PmagSpecRec["specimen_b_sigma"] = '%5.3f ' % (
pars["specimen_b_sigma"])
if "IE-TT" not in methcodes:
methcodes.append("IE-TT")
methods = ""
for meth in methcodes:
methods = methods + meth + ":"
PmagSpecRec["magic_method_codes"] = methods[:-1]
PmagSpecRec["specimen_description"] = comment
PmagSpecRec[
"magic_software_packages"] = version_num
pmagplotlib.plotAZ(AZD, araiblock, zijdblock, s,
units[0])
pmagplotlib.plotB(AZD, araiblock, zijdblock, pars)
if len(trmblock) > 2:
blab = field
best = pars["specimen_int"]
Bs, TRMs = [], []
for trec in trmblock:
Bs.append(float(
trec['treatment_dc_field']))
TRMs.append(
float(trec['measurement_magn_moment']))
NLpars = nlt.NLtrm(
Bs, TRMs, best, blab, 0
) # calculate best fit parameters through TRM acquisition data, and get new banc
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
npred = nlt.TRM(
Bp[-1], NLpars['xopt'][0],
NLpars['xopt']
[1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(
AZD['MRM'], Bs, TRMs, Bp, Mp, NLpars,
trec['magic_experiment_name'])
print 'Banc= ', float(NLpars['banc']) * 1e6
pmagplotlib.drawFIGS(AZD)
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars[
"specimen_b"]
saveit = raw_input(
"Save this interpretation? [y]/n \n")
if saveit != 'n':
specimen += 1
PriorRecs.append(
PmagSpecRec) # put back an interpretation
save_redo(PriorRecs, inspec)
ans = ""
else:
specimen += 1
if fmt != ".pmag":
basename = s + '_microwave' + fmt
files = {}
for key in AZD.keys():
files[key] = s + '_' + key + fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['deremag'] = 'DeReMag Plot'
titles['zijd'] = 'Zijderveld Plot'
titles['arai'] = 'Arai Plot'
AZD = pmagplotlib.addBorders(
AZD, titles, black, purple)
pmagplotlib.saveP(AZD, files)
# pmagplotlib.combineFigs(s,files,3)
if len(CurrRec) > 0:
for rec in CurrRec:
PriorRecs.append(rec)
CurrRec = []
if plots != 1:
ans = raw_input(" Save last plot? 1/[0] ")
if ans == "1":
if fmt != ".pmag":
files = {}
for key in AZD.keys():
files[key] = s + '_' + key + fmt
pmagplotlib.saveP(AZD, files)
if len(CurrRec) > 0:
PriorRecs.append(CurrRec) # put back an interpretation
if len(PriorRecs) > 0:
save_redo(PriorRecs, inspec)
print 'Updated interpretations saved in ', inspec
if pmagplotlib.verbose:
print "Good bye"
def main():
"""
NAME
thellier_magic.py
DESCRIPTION
plots Thellier-Thellier, allowing interactive setting of bounds
and customizing of selection criteria. Saves and reads interpretations
from a pmag_specimen formatted table, default: thellier_specimens.txt
SYNTAX
thellier_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEAS, set magic_measurements input file
-fsp PRIOR, set pmag_specimen prior interpretations file
-fan ANIS, set rmag_anisotropy file for doing the anisotropy corrections
-fcr CRIT, set criteria file for grading.
-fmt [svg,png,jpg], format for images - default is svg
-sav, saves plots with out review (default format)
-spc SPEC, plots single specimen SPEC, saves plot with specified format
with optional -b bounds adn quits
-b BEG END: sets bounds for calculation
BEG: starting step for slope calculation
END: ending step for slope calculation
-z use only z component difference for pTRM calculation
DEFAULTS
MEAS: magic_measurements.txt
REDO: thellier_redo
CRIT: NONE
PRIOR: NONE
OUTPUT
figures:
ALL: numbers refer to temperature steps in command line window
1) Arai plot: closed circles are zero-field first/infield
open circles are infield first/zero-field
triangles are pTRM checks
squares are pTRM tail checks
VDS is vector difference sum
diamonds are bounds for interpretation
2) Zijderveld plot: closed (open) symbols are X-Y (X-Z) planes
X rotated to NRM direction
3) (De/Re)Magnetization diagram:
circles are NRM remaining
squares are pTRM gained
4) equal area projections:
green triangles are pTRM gained direction
red (purple) circles are lower(upper) hemisphere of ZI step directions
blue (cyan) squares are lower(upper) hemisphere IZ step directions
5) Optional: TRM acquisition
6) Optional: TDS normalization
command line window:
list is: temperature step numbers, temperatures (C), Dec, Inc, Int (units of magic_measuements)
list of possible commands: type letter followed by return to select option
saving of plots creates .svg format files with specimen_name, plot type as name
"""
#
# initializations
#
meas_file, critout, inspec = "magic_measurements.txt", "", "thellier_specimens.txt"
first = 1
inlt = 0
version_num = pmag.get_version()
TDinit, Tinit, field, first_save = 0, 0, -1, 1
user, comment, AniSpec, locname = "", '', "", ""
ans, specimen, recnum, start, end = 0, 0, 0, 0, 0
plots, pmag_out, samp_file, style = 0, "", "", "svg"
verbose = pmagplotlib.verbose
fmt = '.' + style
#
# default acceptance criteria
#
accept = pmag.default_criteria(0)[0] # set the default criteria
#
# parse command line options
#
Zdiff, anis = 0, 0
spc, BEG, END = "", "", ""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
meas_file = sys.argv[ind + 1]
if '-fsp' in sys.argv:
ind = sys.argv.index('-fsp')
inspec = sys.argv[ind + 1]
if '-fan' in sys.argv:
ind = sys.argv.index('-fan')
anisfile = sys.argv[ind + 1]
anis = 1
anis_data, file_type = pmag.magic_read(anisfile)
if verbose:
print("Anisotropy data read in from ", anisfile)
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = '.' + sys.argv[ind + 1]
if '-dpi' in sys.argv:
ind = sys.argv.index('-dpi')
dpi = '.' + sys.argv[ind + 1]
else:
dpi = 100
if '-sav' in sys.argv:
plots = 1
verbose = 0
if '-z' in sys.argv:
Zdiff = 1
if '-spc' in sys.argv:
ind = sys.argv.index('-spc')
spc = sys.argv[ind + 1]
if '-b' in sys.argv:
ind = sys.argv.index('-b')
BEG = int(sys.argv[ind + 1])
END = int(sys.argv[ind + 2])
if '-fcr' in sys.argv:
ind = sys.argv.index('-fcr')
critout = sys.argv[ind + 1]
crit_data, file_type = pmag.magic_read(critout)
if file_type != 'pmag_criteria':
if verbose:
print('bad pmag_criteria file, using no acceptance criteria')
accept = pmag.default_criteria(1)[0]
else:
if verbose:
print("Acceptance criteria read in from ", critout)
accept = {
'pmag_criteria_code': 'ACCEPTANCE',
'er_citation_names': 'This study'
}
for critrec in crit_data:
if 'sample_int_sigma_uT' in critrec.keys(
): # accommodate Shaar's new criterion
critrec['sample_int_sigma'] = '%10.3e' % (
eval(critrec['sample_int_sigma_uT']) * 1e-6)
for key in critrec.keys():
if key not in accept.keys() and critrec[key] != '':
accept[key] = critrec[key]
try:
open(inspec, 'rU')
PriorRecs, file_type = pmag.magic_read(inspec)
if file_type != 'pmag_specimens':
print(file_type)
print(file_type, inspec, " is not a valid pmag_specimens file ")
sys.exit()
for rec in PriorRecs:
if 'magic_software_packages' not in rec.keys():
rec['magic_software_packages'] = ""
except IOError:
PriorRecs = []
if verbose:
print("starting new specimen interpretation file: ", inspec)
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print(file_type)
print(file_type, "This is not a valid magic_measurements file ")
sys.exit()
backup = 0
# define figure numbers for arai, zijderveld and
# de-,re-magization diagrams
AZD = {}
AZD['deremag'], AZD['zijd'], AZD['arai'], AZD['eqarea'] = 1, 2, 3, 4
pmagplotlib.plot_init(AZD['arai'], 5, 5)
pmagplotlib.plot_init(AZD['zijd'], 5, 5)
pmagplotlib.plot_init(AZD['deremag'], 5, 5)
pmagplotlib.plot_init(AZD['eqarea'], 5, 5)
#
#
#
# get list of unique specimen names
#
CurrRec = []
sids = pmag.get_specs(meas_data)
# get plots for specimen s - default is just to step through arai diagrams
#
if spc != "":
specimen = sids.index(spc)
while specimen < len(sids):
methcodes = []
if verbose:
print(sids[specimen], specimen + 1, 'of ', len(sids))
MeasRecs = []
s = sids[specimen]
datablock, trmblock, tdsrecs = [], [], []
PmagSpecRec = {}
if first == 0:
for key in keys:
# make sure all new records have same set of keys
PmagSpecRec[key] = ""
PmagSpecRec["er_analyst_mail_names"] = user
PmagSpecRec["specimen_correction"] = 'u'
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"] == s:
MeasRecs.append(rec)
if "magic_method_codes" not in rec.keys():
rec["magic_method_codes"] = ""
methods = rec["magic_method_codes"].split(":")
meths = []
for meth in methods:
meths.append(meth.strip()) # take off annoying spaces
methods = ""
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:
methcodes.append(meth.strip())
methods = methods + meth + ":"
methods = methods[:-1]
rec["magic_method_codes"] = methods
if "LP-PI-TRM" in meths:
datablock.append(rec)
if "LP-TRM" in meths:
trmblock.append(rec)
if "LP-TRM-TD" in meths:
tdsrecs.append(rec)
if len(trmblock) > 2 and inspec != "":
if Tinit == 0:
Tinit = 1
AZD['TRM'] = 5
pmagplotlib.plot_init(AZD['TRM'], 5, 5)
elif Tinit == 1: # clear the TRM figure if not needed
pmagplotlib.clearFIG(AZD['TRM'])
if len(tdsrecs) > 2:
if TDinit == 0:
TDinit = 1
AZD['TDS'] = 6
pmagplotlib.plot_init(AZD['TDS'], 5, 5)
elif TDinit == 1: # clear the TDS figure if not needed
pmagplotlib.clearFIG(AZD['TDS'])
if len(datablock) < 4:
if backup == 0:
specimen += 1
if verbose:
print('skipping specimen - moving forward ', s)
else:
specimen -= 1
if verbose:
print('skipping specimen - moving backward ', s)
#
# collect info for the PmagSpecRec dictionary
#
else:
rec = datablock[0]
PmagSpecRec["er_citation_names"] = "This study"
PmagSpecRec["er_specimen_name"] = s
PmagSpecRec["er_sample_name"] = rec["er_sample_name"]
PmagSpecRec["er_site_name"] = rec["er_site_name"]
PmagSpecRec["er_location_name"] = rec["er_location_name"]
locname = rec['er_location_name'].replace('/', '-')
if "er_expedition_name" in rec.keys():
PmagSpecRec["er_expedition_name"] = rec["er_expedition_name"]
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"] = ""
PmagSpecRec["magic_instrument_codes"] = rec[
"magic_instrument_codes"]
PmagSpecRec["measurement_step_unit"] = "K"
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"] = ""
else:
PmagSpecRec["magic_experiment_names"] = rec[
"magic_experiment_name"]
meths = rec["magic_method_codes"].split()
# sort data into types
araiblock, field = pmag.sortarai(datablock, s, Zdiff)
first_Z = araiblock[0]
GammaChecks = araiblock[5]
if len(first_Z) < 3:
if backup == 0:
specimen += 1
if verbose:
print('skipping specimen - moving forward ', s)
else:
specimen -= 1
if verbose:
print('skipping specimen - moving backward ', s)
else:
backup = 0
zijdblock, units = pmag.find_dmag_rec(s, meas_data)
recnum = 0
if verbose:
print("index step Dec Inc Int Gamma")
for plotrec in zijdblock:
if GammaChecks != "":
gamma = ""
for g in GammaChecks:
if g[0] == plotrec[0] - 273:
gamma = g[1]
break
if gamma != "":
print('%i %i %7.1f %7.1f %8.3e %7.1f' %
(recnum, plotrec[0] - 273, plotrec[1],
plotrec[2], plotrec[3], gamma))
else:
print('%i %i %7.1f %7.1f %8.3e ' %
(recnum, plotrec[0] - 273, plotrec[1],
plotrec[2], plotrec[3]))
recnum += 1
pmagplotlib.plot_arai_zij(AZD, araiblock, zijdblock, s,
units[0])
if verbose:
pmagplotlib.draw_figs(AZD)
if len(tdsrecs) > 2: # a TDS experiment
tdsblock = [] # make a list for the TDS data
Mkeys = [
'measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measuruement_magn_mass'
]
mkey, k = "", 0
# find which type of intensity
while mkey == "" and k < len(Mkeys) - 1:
key = Mkeys[k]
if key in tdsrecs[0].keys() and tdsrecs[0][key] != "":
mkey = key
k += 1
if mkey == "":
break # get outta here
Tnorm = ""
for tdrec in tdsrecs:
meths = tdrec['magic_method_codes'].split(":")
for meth in meths:
# strip off potential nasty spaces
meth.replace(" ", "")
if 'LT-T-I' in meths and Tnorm == "": # found first total TRM
# normalize by total TRM
Tnorm = float(tdrec[mkey])
# put in the zero step
tdsblock.append([273, zijdblock[0][3] / Tnorm, 1.])
# found a LP-TRM-TD demag step, now need complementary LT-T-Z from zijdblock
if 'LT-T-Z' in meths and Tnorm != "":
step = float(tdrec['treatment_temp'])
Tint = ""
if mkey != "":
Tint = float(tdrec[mkey])
if Tint != "":
for zrec in zijdblock:
if zrec[0] == step: # found matching
tdsblock.append([
step, zrec[3] / Tnorm, Tint / Tnorm
])
break
if len(tdsblock) > 2:
pmagplotlib.plot_tds(AZD['TDS'], tdsblock,
s + ':LP-PI-TDS:')
if verbose:
pmagplotlib(draw_figs(AZD))
else:
print("Something wrong here")
if anis == 1: # look up anisotropy data for this specimen
AniSpec = ""
for aspec in anis_data:
if aspec["er_specimen_name"] == PmagSpecRec[
"er_specimen_name"]:
AniSpec = aspec
if verbose:
print('Found anisotropy record...')
break
if inspec != "":
if verbose:
print('Looking up saved interpretation....')
found = 0
for k in range(len(PriorRecs)):
try:
if PriorRecs[k]["er_specimen_name"] == s:
found = 1
CurrRec.append(PriorRecs[k])
for j in range(len(zijdblock)):
if float(zijdblock[j][0]) == float(
PriorRecs[k]
["measurement_step_min"]):
start = j
if float(zijdblock[j][0]) == float(
PriorRecs[k]
["measurement_step_max"]):
end = j
pars, errcode = pmag.PintPars(
datablock, araiblock, zijdblock, start,
end, accept)
pars['measurement_step_unit'] = "K"
pars['experiment_type'] = 'LP-PI-TRM'
# put in CurrRec, take out of PriorRecs
del PriorRecs[k]
if errcode != 1:
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * \
field*pars["specimen_b"]
pars["er_specimen_name"] = s
if verbose:
print('Saved interpretation: ')
pars, kill = pmag.scoreit(
pars, PmagSpecRec, accept, '', verbose)
pmagplotlib.plot_b(AZD, araiblock,
zijdblock, pars)
if verbose:
pmagplotlib.draw_figs(AZD)
if len(trmblock) > 2:
blab = field
best = pars["specimen_int"]
Bs, TRMs = [], []
for trec in trmblock:
Bs.append(
float(
trec['treatment_dc_field'])
)
TRMs.append(
float(trec[
'measurement_magn_moment'])
)
# calculate best fit parameters through TRM acquisition data, and get new banc
NLpars = nlt.NLtrm(
Bs, TRMs, best, blab, 0)
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
# predicted NRM for this field
npred = nlt.TRM(
Bp[-1], NLpars['xopt'][0],
NLpars['xopt'][1])
Mp.append(npred)
pmagplotlib.plot_trm(
AZD['TRM'], Bs, TRMs, Bp, Mp,
NLpars,
trec['magic_experiment_name'])
PmagSpecRec['specimen_int'] = NLpars[
'banc']
if verbose:
print('Banc= ',
float(NLpars['banc']) * 1e6)
pmagplotlib.draw_figs(AZD)
mpars = pmag.domean(
araiblock[1], start, end, 'DE-BFL')
if verbose:
print(
'pTRM direction= ',
'%7.1f' % (mpars['specimen_dec']),
' %7.1f' % (mpars['specimen_inc']),
' MAD:',
'%7.1f' % (mpars['specimen_mad']))
if AniSpec != "":
CpTRM = pmag.Dir_anis_corr([
mpars['specimen_dec'],
mpars['specimen_inc']
], AniSpec)
AniSpecRec = pmag.doaniscorr(
PmagSpecRec, AniSpec)
if verbose:
print(
'Anisotropy corrected TRM direction= ',
'%7.1f' % (CpTRM[0]),
' %7.1f' % (CpTRM[1]))
print(
'Anisotropy corrected intensity= ',
float(
AniSpecRec['specimen_int'])
* 1e6)
else:
print('error on specimen ', s)
except:
pass
if verbose and found == 0:
print(' None found :( ')
if spc != "":
if BEG != "":
pars, errcode = pmag.PintPars(datablock, araiblock,
zijdblock, BEG, END,
accept)
pars['measurement_step_unit'] = "K"
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars["specimen_b"]
pars["er_specimen_name"] = s
pars['specimen_grade'] = '' # ungraded
pmagplotlib.plot_b(AZD, araiblock, zijdblock, pars)
if verbose:
pmagplotlib.draw_figs(AZD)
if len(trmblock) > 2:
if inlt == 0:
inlt = 1
blab = field
best = pars["specimen_int"]
Bs, TRMs = [], []
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(
float(trec['measurement_magn_moment']))
# calculate best fit parameters through TRM acquisition data, and get new banc
NLpars = nlt.NLtrm(Bs, TRMs, best, blab, 0)
#
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
# predicted NRM for this field
npred = nlt.TRM(Bp[-1], NLpars['xopt'][0],
NLpars['xopt'][1])
files = {}
for key in AZD.keys():
files[key] = s + '_' + key + fmt
pmagplotlib.save_plots(AZD, files, dpi=dpi)
sys.exit()
if verbose:
ans = 'b'
while ans != "":
print("""
s[a]ve plot, set [b]ounds for calculation, [d]elete current interpretation, [p]revious, [s]ample, [q]uit:
""")
ans = input('Return for next specimen \n')
if ans == "":
specimen += 1
if ans == "d":
save_redo(PriorRecs, inspec)
CurrRec = []
pmagplotlib.plot_arai_zij(AZD, araiblock,
zijdblock, s, units[0])
if verbose:
pmagplotlib.draw_figs(AZD)
if ans == 'a':
files = {}
for key in AZD.keys():
files[key] = "LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name'] + \
'_SA:_' + \
PmagSpecRec['er_sample_name'] + \
'_SP:_'+s+'_CO:_s_TY:_'+key+fmt
pmagplotlib.save_plots(AZD, files)
ans = ""
if ans == 'q':
print("Good bye")
sys.exit()
if ans == 'p':
specimen = specimen - 1
backup = 1
ans = ""
if ans == 's':
keepon = 1
spec = input(
'Enter desired specimen name (or first part there of): '
)
while keepon == 1:
try:
specimen = sids.index(spec)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if spec in sids[qq]:
tmplist.append(sids[qq])
print(specimen,
" not found, but this was: ")
print(tmplist)
spec = input('Select one or try again\n ')
ans = ""
if ans == 'b':
if end == 0 or end >= len(zijdblock):
end = len(zijdblock) - 1
GoOn = 0
while GoOn == 0:
answer = input(
'Enter index of first point for calculation: ['
+ str(start) + '] ')
try:
start = int(answer)
answer = input(
'Enter index of last point for calculation: ['
+ str(end) + '] ')
end = int(answer)
if start >= 0 and start < len(
zijdblock
) - 2 and end > 0 and end < len(
zijdblock) or start >= end:
GoOn = 1
else:
print("Bad endpoints - try again! ")
start, end = 0, len(zijdblock)
except ValueError:
print("Bad endpoints - try again! ")
start, end = 0, len(zijdblock)
s = sids[specimen]
pars, errcode = pmag.PintPars(
datablock, araiblock, zijdblock, start, end,
accept)
pars['measurement_step_unit'] = "K"
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars[
"specimen_b"]
pars["er_specimen_name"] = s
pars, kill = pmag.scoreit(pars, PmagSpecRec,
accept, '', 0)
PmagSpecRec['specimen_scat'] = pars[
'specimen_scat']
PmagSpecRec['specimen_frac'] = '%5.3f' % (
pars['specimen_frac'])
PmagSpecRec['specimen_gmax'] = '%5.3f' % (
pars['specimen_gmax'])
PmagSpecRec["measurement_step_min"] = '%8.3e' % (
pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"] = '%8.3e' % (
pars["measurement_step_max"])
PmagSpecRec["measurement_step_unit"] = "K"
PmagSpecRec["specimen_int_n"] = '%i' % (
pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"] = '%8.3e' % (
pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"] = '%9.4e ' % (
pars["specimen_int"])
PmagSpecRec["specimen_b"] = '%5.3f ' % (
pars["specimen_b"])
PmagSpecRec["specimen_q"] = '%5.1f ' % (
pars["specimen_q"])
PmagSpecRec["specimen_f"] = '%5.3f ' % (
pars["specimen_f"])
PmagSpecRec["specimen_fvds"] = '%5.3f' % (
pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"] = '%5.3f' % (
pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"] = '%7.1f' % (
pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"] = '%7.1f' % (
pars["specimen_Z"])
PmagSpecRec["specimen_gamma"] = '%7.1f' % (
pars["specimen_gamma"])
PmagSpecRec["specimen_grade"] = pars[
"specimen_grade"]
if pars["method_codes"] != "":
tmpcodes = pars["method_codes"].split(":")
for t in tmpcodes:
if t.strip() not in methcodes:
methcodes.append(t.strip())
PmagSpecRec["specimen_dec"] = '%7.1f' % (
pars["specimen_dec"])
PmagSpecRec["specimen_inc"] = '%7.1f' % (
pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"] = '-1'
PmagSpecRec["specimen_direction_type"] = 'l'
# this is redundant, but helpful - won't be imported
PmagSpecRec["direction_type"] = 'l'
PmagSpecRec["specimen_int_dang"] = '%7.1f ' % (
pars["specimen_int_dang"])
PmagSpecRec["specimen_drats"] = '%7.1f ' % (
pars["specimen_drats"])
PmagSpecRec["specimen_drat"] = '%7.1f ' % (
pars["specimen_drat"])
PmagSpecRec["specimen_int_ptrm_n"] = '%i ' % (
pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"] = '%6.4f ' % (
pars["specimen_rsc"])
PmagSpecRec["specimen_md"] = '%i ' % (int(
pars["specimen_md"]))
if PmagSpecRec["specimen_md"] == '-1':
PmagSpecRec["specimen_md"] = ""
PmagSpecRec["specimen_b_sigma"] = '%5.3f ' % (
pars["specimen_b_sigma"])
if "IE-TT" not in methcodes:
methcodes.append("IE-TT")
methods = ""
for meth in methcodes:
methods = methods + meth + ":"
PmagSpecRec["magic_method_codes"] = methods[:-1]
PmagSpecRec["specimen_description"] = comment
PmagSpecRec[
"magic_software_packages"] = version_num
pmagplotlib.plot_arai_zij(AZD, araiblock,
zijdblock, s, units[0])
pmagplotlib.plot_b(AZD, araiblock, zijdblock, pars)
if verbose:
pmagplotlib.draw_figs(AZD)
if len(trmblock) > 2:
blab = field
best = pars["specimen_int"]
Bs, TRMs = [], []
for trec in trmblock:
Bs.append(float(
trec['treatment_dc_field']))
TRMs.append(
float(trec['measurement_magn_moment']))
# calculate best fit parameters through TRM acquisition data, and get new banc
NLpars = nlt.NLtrm(Bs, TRMs, best, blab, 0)
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
# predicted NRM for this field
npred = nlt.TRM(Bp[-1], NLpars['xopt'][0],
NLpars['xopt'][1])
Mp.append(npred)
pmagplotlib.plot_trm(
AZD['TRM'], Bs, TRMs, Bp, Mp, NLpars,
trec['magic_experiment_name'])
if verbose:
print(
'Non-linear TRM corrected intensity= ',
float(NLpars['banc']) * 1e6)
if verbose:
pmagplotlib.draw_figs(AZD)
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars[
"specimen_b"]
pars, kill = pmag.scoreit(pars, PmagSpecRec,
accept, '', verbose)
saveit = input(
"Save this interpretation? [y]/n \n")
if saveit != 'n':
# put back an interpretation
PriorRecs.append(PmagSpecRec)
specimen += 1
save_redo(PriorRecs, inspec)
ans = ""
elif plots == 1:
specimen += 1
if fmt != ".pmag":
files = {}
for key in AZD.keys():
files[key] = "LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_' + \
PmagSpecRec['er_sample_name'] + \
'_SP:_'+s+'_CO:_s_TY:_'+key+'_'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['deremag'] = 'DeReMag Plot'
titles['zijd'] = 'Zijderveld Plot'
titles['arai'] = 'Arai Plot'
AZD = pmagplotlib.add_borders(
AZD, titles, black, purple)
pmagplotlib.save_plots(AZD, files, dpi=dpi)
# pmagplotlib.combineFigs(s,files,3)
else: # save in pmag format
script = "grep " + s + " output.mag | thellier -mfsi"
script = script + ' %8.4e' % (field)
min = '%i' % ((pars["measurement_step_min"] - 273))
Max = '%i' % ((pars["measurement_step_max"] - 273))
script = script + " " + min + " " + Max
script = script + " |plotxy;cat mypost >>thellier.ps\n"
pltf.write(script)
pmag.domagicmag(outf, MeasRecs)
if len(CurrRec) > 0:
for rec in CurrRec:
PriorRecs.append(rec)
CurrRec = []
if plots != 1 and verbose:
ans = input(" Save last plot? 1/[0] ")
if ans == "1":
if fmt != ".pmag":
files = {}
for key in AZD.keys():
files[key] = s + '_' + key + fmt
pmagplotlib.save_plots(AZD, files, dpi=dpi)
else:
print("\n Good bye\n")
sys.exit()
if len(CurrRec) > 0:
PriorRecs.append(CurrRec) # put back an interpretation
if len(PriorRecs) > 0:
save_redo(PriorRecs, inspec)
print('Updated interpretations saved in ', inspec)
if verbose:
print("Good bye")
def main():
"""
NAME
trmaq_magic.py
DESCTIPTION
does non-linear trm acquisisiton correction
SYNTAX
trmaq_magic.py [-h][-i][command line options]
OPTIONS
-h prints help message and quits
-i allows interactive setting of file names
-f MFILE, sets magic_measurements input file
-ft TSPEC, sets thellier_specimens input file
-F OUT, sets output for non-linear TRM acquisition corrected data
-sav save figures and quit
-fmt [png, svg, pdf]
-DM [2, 3] MagIC data model, default 3
DEFAULTS
MFILE: trmaq_measurements.txt
TSPEC: thellier_specimens.txt
OUT: NLT_specimens.txt
"""
meas_file = 'trmaq_measurements.txt'
tspec = "thellier_specimens.txt"
output = 'NLT_specimens.txt'
data_model_num = int(float(pmag.get_named_arg("-DM", 3)))
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-i' in sys.argv:
meas_file = input(
"Input magic_measurements file name? [trmaq_measurements.txt] ")
if meas_file == "":
meas_file = "trmaq_measurements.txt"
tspec = input(
" thellier_specimens file name? [thellier_specimens.txt] ")
if tspec == "":
tspec = "thellier_specimens.txt"
output = input(
"File for non-linear TRM adjusted specimen data: [NLTspecimens.txt] ")
if output == "":
output = "NLT_specimens.txt"
if '-f' in sys.argv:
ind = sys.argv.index('-f')
meas_file = sys.argv[ind+1]
if '-ft' in sys.argv:
ind = sys.argv.index('-ft')
tspec = sys.argv[ind+1]
if '-F' in sys.argv:
ind = sys.argv.index('-F')
output = sys.argv[ind+1]
if '-sav' in sys.argv:
save_plots = True
else:
save_plots = False
fmt = pmag.get_named_arg("-fmt", "svg")
#
PLT = {'aq': 1}
if not save_plots:
pmagplotlib.plot_init(PLT['aq'], 5, 5)
#
# get name of file from command line
#
comment = ""
#
#
meas_data, file_type = pmag.magic_read(meas_file)
if 'measurements' not in file_type:
print(file_type, "This is not a valid measurements file ")
sys.exit()
if data_model_num == 2:
spec_col = "er_specimen_name"
lab_field_dc_col = "specimen_lab_field_dc"
int_col = "specimen_int"
meth_col = "magic_method_codes"
treat_dc_col = "treatment_dc_field"
magn_moment_col = "measurement_magn_moment"
experiment_col = "magic_experiment_name"
outfile_type = "pmag_specimens"
else:
spec_col = "specimen"
lab_field_dc_col = "int_treat_dc_field"
int_col = "int_abs"
meth_col = "method_codes"
treat_dc_col = "treat_dc_field"
magn_moment_col = "magn_moment"
experiment_col = "experiment"
outfile_type = "specimens"
sids = pmag.get_specs(meas_data)
specimen = 0
#
# read in thellier_specimen data
#
nrm, file_type = pmag.magic_read(tspec)
PmagSpecRecs= []
while specimen < len(sids):
#
# find corresoponding paleointensity data for this specimen
#
s = sids[specimen]
blab, best = "", ""
for nrec in nrm: # pick out the Banc data for this spec
if nrec[spec_col] == s:
try:
blab = float(nrec[lab_field_dc_col])
except ValueError:
continue
best = float(nrec[int_col])
TrmRec = nrec
break
if blab == "":
print("skipping ", s, " : no best ")
specimen += 1
else:
print(sids[specimen], specimen+1, 'of ',
len(sids), 'Best = ', best*1e6)
MeasRecs = []
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec[spec_col] == s:
meths = rec[meth_col].split(":")
methcodes = []
for meth in meths:
methcodes.append(meth.strip())
if "LP-TRM" in methcodes:
MeasRecs.append(rec)
if len(MeasRecs) < 2:
specimen += 1
print('skipping specimen - no trm acquisition data ', s)
#
# collect info for the PmagSpecRec dictionary
#
else:
TRMs, Bs = [], []
for rec in MeasRecs:
Bs.append(float(rec[treat_dc_col]))
TRMs.append(float(rec[magn_moment_col]))
# calculate best fit parameters through TRM acquisition data, and get new banc
NLpars = nlt.NLtrm(Bs, TRMs, best, blab, 0)
#
Mp, Bp = [], []
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
# predicted NRM for this field
npred = nlt.TRM(Bp[-1], NLpars['xopt']
[0], NLpars['xopt'][1])
Mp.append(npred)
pmagplotlib.plot_trm(
PLT['aq'], Bs, TRMs, Bp, Mp, NLpars, rec[experiment_col])
if not save_plots:
pmagplotlib.draw_figs(PLT)
print('Banc= ', float(NLpars['banc'])*1e6)
trmTC = {}
for key in list(TrmRec.keys()):
# copy of info from thellier_specimens record
trmTC[key] = TrmRec[key]
trmTC[int_col] = '%8.3e' % (NLpars['banc'])
trmTC[meth_col] = TrmRec[meth_col]+":DA-NL"
PmagSpecRecs.append(trmTC)
if not save_plots:
ans = input("Return for next specimen, s[a]ve plot ")
if ans == 'a':
Name = {'aq': rec[spec_col]+'_TRM.{}'.format(fmt)}
pmagplotlib.save_plots(PLT, Name)
else:
Name = {'aq': rec[spec_col]+'_TRM.{}'.format(fmt)}
pmagplotlib.save_plots(PLT, Name)
specimen += 1
pmag.magic_write(output, PmagSpecRecs, outfile_type)