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
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:PmagSpecRec[key]="" # make sure all new records have same set of keys
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.plotAZ(AZD,araiblock,zijdblock,s,units[0])
if verbose:pmagplotlib.drawFIGS(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
while mkey=="" and k<len(Mkeys)-1: # find which type of intensity
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: meth.replace(" ","") # strip off potential nasty spaces
if 'LT-T-I' in meths and Tnorm=="": # found first total TRM
Tnorm=float(tdrec[mkey]) # normalize by total TRM
tdsblock.append([273,zijdblock[0][3]/Tnorm,1.]) # put in the zero step
if 'LT-T-Z' in meths and Tnorm!="": # found a LP-TRM-TD demag step, now need complementary LT-T-Z from zijdblock
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.plotTDS(AZD['TDS'],tdsblock,s+':LP-PI-TDS:')
if verbose:pmagplotlib(drawFIGS(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'
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 verbose:
print 'Saved interpretation: '
pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',verbose)
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
if verbose:pmagplotlib.drawFIGS(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']))
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['TRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name'])
PmagSpecRec['specimen_int']=NLpars['banc']
if verbose:
print 'Banc= ',float(NLpars['banc'])*1e6
pmagplotlib.drawFIGS(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.plotB(AZD,araiblock,zijdblock,pars)
if verbose:pmagplotlib.drawFIGS(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']))
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,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=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])
if verbose:pmagplotlib.drawFIGS(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.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(zijdblock):end=len(zijdblock)-1
GoOn=0
while GoOn==0:
answer=raw_input('Enter index of first point for calculation: ['+str(start)+'] ')
try:
start=int(answer)
answer=raw_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'
PmagSpecRec["direction_type"]='l' # this is redundant, but helpful - won't be imported
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.plotAZ(AZD,araiblock,zijdblock,s,units[0])
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
if verbose:pmagplotlib.drawFIGS(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']))
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['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.drawFIGS(AZD)
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',verbose)
saveit=raw_input("Save this interpretation? [y]/n \n")
if saveit!='n':
PriorRecs.append(PmagSpecRec) # put back an interpretation
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.addBorders(AZD,titles,black,purple)
pmagplotlib.saveP(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=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,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
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
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 list(critrec.keys()):
accept[key]=-1
else:
accept[key]=float(critrec[key])
try:
open(inspec,'r')
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 list(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 list(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 list(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 list(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=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 list(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=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(araiblock[0]):end=len(araiblock[0])-1
GoOn=0
while GoOn==0:
print('Enter index of first point for calculation: ','[',start,']')
answer=input('return to keep default ')
if answer != "":start=int(answer)
print('Enter index of last point for calculation: ','[',end,']')
answer=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=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 list(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=input(" Save last plot? 1/[0] ")
if ans=="1":
if fmt != ".pmag":
files={}
for key in list(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")