def main():
"""
NAME
dmag_magic.py
DESCRIPTION
plots intensity decay curves for demagnetization experiments
SYNTAX
dmag_magic -h [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: magic_measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is by location
-LT [AF,T,M]: specify lab treatment type, default AF
-XLP [PI]: exclude specific lab protocols (for example, method codes like LP-PI)
-N do not normalize by NRM magnetization
-sav save plots silently and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG={} # plot dictionary
FIG['demag']=1 # demag is figure 1
in_file,plot_key,LT='magic_measurements.txt','er_location_name',"LT-AF-Z"
XLP=""
norm=1
LT='LT-AF-Z'
units,dmag_key='T','treatment_ac_field'
plot=0
fmt='svg'
if len(sys.argv)>1:
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv: norm=0
if '-sav' in sys.argv:
plot=1
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
plot_by=sys.argv[ind+1]
if plot_by=='sit':plot_key='er_site_name'
if plot_by=='sam':plot_key='er_sample_name'
if plot_by=='spc':plot_key='er_specimen_name'
if '-XLP' in sys.argv:
ind=sys.argv.index("-XLP")
XLP=sys.argv[ind+1] # get lab protocol for excluding
if '-LT' in sys.argv:
ind=sys.argv.index("-LT")
LT='LT-'+sys.argv[ind+1]+'-Z' # get lab treatment for plotting
if LT=='LT-T-Z':
units,dmag_key='K','treatment_temp'
elif LT=='LT-AF-Z':
units,dmag_key='T','treatment_ac_field'
elif LT=='LT-M-Z':
units,dmag_key='J','treatment_mw_energy'
else:
units='U'
data,file_type=pmag.magic_read(in_file)
sids=pmag.get_specs(data)
pmagplotlib.plot_init(FIG['demag'],5,5)
print len(data),' records read from ',in_file
#
#
# find desired intensity data
#
#
plotlist,intlist=[],['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
IntMeths=[]
FixData=[]
for rec in data:
meths=[]
methcodes=rec['magic_method_codes'].split(':')
for meth in methcodes:meths.append(meth.strip())
for key in rec.keys():
if key in intlist and rec[key]!="":
if key not in IntMeths:IntMeths.append(key)
if rec[plot_key] not in plotlist and LT in meths: plotlist.append(rec[plot_key])
if 'measurement_flag' not in rec.keys():rec['measurement_flag']='g'
FixData.append(rec)
plotlist.sort()
if len(IntMeths)==0:
print 'No intensity information found'
sys.exit()
data=FixData
int_key=IntMeths[0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
for plt in plotlist:
if plot==0: print plt,'plotting by: ',plot_key
PLTblock=pmag.get_dictitem(data,plot_key,plt,'T') # fish out all the data for this type of plot
PLTblock=pmag.get_dictitem(PLTblock,'magic_method_codes',LT,'has') # fish out all the dmag for this experiment type
PLTblock=pmag.get_dictitem(PLTblock,int_key,'','F') # get all with this intensity key non-blank
if XLP!="":PLTblock=pmag.get_dictitem(PLTblock,'magic_method_codes',XLP,'not') # reject data with XLP in method_code
if len(PLTblock)>2:
title=PLTblock[0][plot_key]
spcs=[]
for rec in PLTblock:
if rec['er_specimen_name'] not in spcs:spcs.append(rec['er_specimen_name'])
for spc in spcs:
SPCblock=pmag.get_dictitem(PLTblock,'er_specimen_name',spc,'T') # plot specimen by specimen
INTblock=[]
for rec in SPCblock:
INTblock.append([float(rec[dmag_key]),0,0,float(rec[int_key]),1,rec['measurement_flag']])
if len(INTblock)>2:
pmagplotlib.plotMT(FIG['demag'],INTblock,title,0,units,norm)
if plot==1:
files={}
for key in FIG.keys():
files[key]=title+'_'+LT+'.'+fmt
pmagplotlib.saveP(FIG,files)
sys.exit()
else:
pmagplotlib.drawFIGS(FIG)
ans=raw_input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans=='q':sys.exit()
if ans=="a":
files={}
for key in FIG.keys():
files[key]=title+'_'+LT+'.svg'
pmagplotlib.saveP(FIG,files)
pmagplotlib.clearFIG(FIG['demag'])
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
lowrie_magic.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie_magic.py -h [command line options]
INPUT
takes magic_measurements formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is magic_measurements.txt
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav saves plots and quits
"""
fmt, plot = 'svg', 0
FIG = {} # plot dictionary
FIG['lowrie'] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'], 6, 6)
norm = 1 # default is to normalize by maximum axis
in_file, dir_path = 'magic_measurements.txt', '.'
if len(sys.argv) > 1:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-N' in sys.argv: norm = 0 # don't normalize
if '-sav' in sys.argv: plot = 1 # don't normalize
if '-fmt' in sys.argv: # sets input filename
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-f' in sys.argv: # sets input filename
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
in_file = dir_path + '/' + in_file
print(in_file)
PmagRecs, file_type = pmag.magic_read(in_file)
if file_type != "magic_measurements":
print('bad input file')
sys.exit()
PmagRecs = pmag.get_dictitem(PmagRecs, 'magic_method_codes', 'LP-IRM-3D',
'has') # get all 3D IRM records
if len(PmagRecs) == 0:
print('no records found')
sys.exit()
specs = pmag.get_dictkey(PmagRecs, 'er_specimen_name', '')
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print(spc)
specdata = pmag.get_dictitem(PmagRecs, 'er_specimen_name', spc,
'T') # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append([
float(dat['measurement_dec']),
float(dat['measurement_inc']),
float(dat['measurement_magn_moment'])
])
Temps.append(float(dat['treatment_temp']) - 273.)
carts = pmag.dir2cart(DIMs).transpose()
if norm == 1: # want to normalize
nrm = (DIMs[0][2]) # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1. # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[0]), nrm),
sym='r-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[0]), nrm),
sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[1]), nrm),
sym='c-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[1]), nrm),
sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[2]), nrm),
sym='k-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[2]), nrm),
sym='k^',
title=spc,
xlab=xlab,
ylab=ylab) # Z direction
files = {'lowrie': 'lowrie:_' + spc + '_.' + fmt}
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = input('S[a]ve figure? [q]uit, <return> to continue ')
if ans == 'a':
pmagplotlib.saveP(FIG, files)
elif ans == 'q':
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
hysteresis_magic.py
DESCRIPTION
calculates hystereis parameters and saves them in 3.0 specimen format file
makes plots if option selected
SYNTAX
hysteresis_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input file, default is agm_measurements.txt
-F: specify specimens.txt output file
-P: do not make the plots
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args=sys.argv
PLT=1
plots=0
fmt=pmag.get_named_arg_from_sys('-fmt','svg')
dir_path=pmag.get_named_arg_from_sys('-WD','.')
dir_path=os.path.realpath(dir_path)
verbose=pmagplotlib.verbose
version_num=pmag.get_version()
user=pmag.get_named_arg_from_sys('-usr','')
if "-h" in args:
print(main.__doc__)
sys.exit()
meas_file=pmag.get_named_arg_from_sys('-f','agm_measurements.txt')
spec_file=pmag.get_named_arg_from_sys('-F','specimens.txt')
if '-P' in args:
PLT=0
irm_init,imag_init=-1,-1
if '-sav' in args:
verbose=0
plots=1
pltspec=pmag.get_named_arg_from_sys('-spc',0)
if pltspec:
#pltspec= args[ind+1]
verbose=0
plots=1
spec_file=dir_path+'/'+spec_file
meas_file=dir_path+'/'+meas_file
SpecRecs=[]
#
#
meas_data,file_type=pmag.magic_read(meas_file)
if file_type!='measurements':
print(main.__doc__)
print('bad file')
sys.exit()
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs,RemRecs=[],[]
HDD={}
if verbose:
if verbose and PLT:print("Plots may be on top of each other - use mouse to place ")
if PLT:
HDD['hyst'],HDD['deltaM'],HDD['DdeltaM']=1,2,3
pmagplotlib.plot_init(HDD['DdeltaM'],5,5)
pmagplotlib.plot_init(HDD['deltaM'],5,5)
pmagplotlib.plot_init(HDD['hyst'],5,5)
imag_init=0
irm_init=0
else:
HDD['hyst'],HDD['deltaM'],HDD['DdeltaM'],HDD['irm'],HDD['imag']=0,0,0,0,0
#
if spec_file: prior_data,file_type=pmag.magic_read(spec_file)
#
# get list of unique experiment names and specimen names
#
experiment_names,sids=[],[]
hys_data=pmag.get_dictitem(meas_data,'method_codes','LP-HYS','has')
dcd_data=pmag.get_dictitem(meas_data,'method_codes','LP-IRM-DCD','has')
imag_data=pmag.get_dictitem(meas_data,'method_codes','LP-IMAG','has')
for rec in hys_data:
if rec['experiment'] not in experiment_names:experiment_names.append(rec['experiment'])
if rec['specimen'] not in sids:sids.append(rec['specimen'])
#
k=0
if pltspec:
k=sids.index(pltspec)
print(sids[k])
while k < len(sids):
specimen=sids[k]
HystRec={'specimen':specimen,'experiment':""} # initialize a new specimen hysteresis record
if verbose and PLT:print(specimen, k+1 , 'out of ',len(sids))
#
#
B,M,Bdcd,Mdcd=[],[],[],[] #B,M for hysteresis, Bdcd,Mdcd for irm-dcd data
Bimag,Mimag=[],[] #Bimag,Mimag for initial magnetization curves
spec_data=pmag.get_dictitem(hys_data,'specimen',specimen,'T') # fish out all the LP-HYS data for this specimen
if len(spec_data)>0:
meths=spec_data[0]['method_codes'].split(':')
e=spec_data[0]['experiment']
HystRec['experiment']=spec_data[0]['experiment']
for rec in spec_data:
B.append(float(rec['meas_field_dc']))
M.append(float(rec['magn_moment']))
spec_data=pmag.get_dictitem(dcd_data,'specimen',specimen,'T') # fish out all the data for this specimen
if len(spec_data)>0:
HystRec['experiment']=HystRec['experiment']+':'+spec_data[0]['experiment']
irm_exp=spec_data[0]['experiment']
for rec in spec_data:
Bdcd.append(float(rec['treat_dc_field']))
Mdcd.append(float(rec['magn_moment']))
spec_data=pmag.get_dictitem(imag_data,'specimen',specimen,'T') # fish out all the data for this specimen
if len(spec_data)>0:
imag_exp=spec_data[0]['experiment']
for rec in spec_data:
Bimag.append(float(rec['meas_field_dc']))
Mimag.append(float(rec['magn_moment']))
#
# now plot the hysteresis curve
#
if len(B)>0:
hmeths=[]
for meth in meths: hmeths.append(meth)
hpars=pmagplotlib.plotHDD(HDD,B,M,e)
if verbose and PLT:pmagplotlib.drawFIGS(HDD)
#
if verbose:pmagplotlib.plotHPARS(HDD,hpars,'bs')
HystRec['hyst_mr_moment']=hpars['hysteresis_mr_moment']
HystRec['hyst_ms_moment']=hpars['hysteresis_ms_moment']
HystRec['hyst_bc']=hpars['hysteresis_bc']
HystRec['hyst_bcr']=hpars['hysteresis_bcr']
HystRec['susc_h']=hpars['hysteresis_xhf']
HystRec['experiments']=e
HystRec['software_packages']=version_num
if hpars["magic_method_codes"] not in hmeths:hmeths.append(hpars["magic_method_codes"])
methods=""
for meth in hmeths:
methods=methods+meth.strip()+":"
HystRec["method_codes"]=methods[:-1]
HystRec["citations"]="This study"
#
if len(Bdcd)>0:
rmeths=[]
for meth in meths: rmeths.append(meth)
if verbose and PLT:print('plotting IRM')
if irm_init==0:
HDD['irm']=5
pmagplotlib.plot_init(HDD['irm'],5,5)
irm_init=1
rpars=pmagplotlib.plotIRM(HDD['irm'],Bdcd,Mdcd,irm_exp)
HystRec['rem_mr_moment']=rpars['remanence_mr_moment']
HystRec['rem_bcr']=rpars['remanence_bcr']
HystRec['experiments']=specimen+':'+irm_exp
if rpars["magic_method_codes"] not in meths:meths.append(rpars["magic_method_codes"])
methods=""
for meth in rmeths:
methods=methods+meth.strip()+":"
HystRec["method_codes"]=HystRec['method_codes']+':'+methods[:-1]
HystRec["citations"]="This study"
else:
if irm_init:pmagplotlib.clearFIG(HDD['irm'])
if len(Bimag)>0:
if verbose and PLT:print('plotting initial magnetization curve')
# first normalize by Ms
Mnorm=[]
for m in Mimag: Mnorm.append(old_div(m,float(hpars['hysteresis_ms_moment'])))
if imag_init==0:
HDD['imag']=4
pmagplotlib.plot_init(HDD['imag'],5,5)
imag_init=1
pmagplotlib.plotIMAG(HDD['imag'],Bimag,Mnorm,imag_exp)
else:
if imag_init:pmagplotlib.clearFIG(HDD['imag'])
if len(list(HystRec.keys()))>0:HystRecs.append(HystRec)
#
files={}
if plots:
if pltspec:s=pltspec
files={}
for key in list(HDD.keys()):
files[key]=s+'_'+key+'.'+fmt
pmagplotlib.saveP(HDD,files)
if pltspec:sys.exit()
if verbose and PLT:
pmagplotlib.drawFIGS(HDD)
ans=input("S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n ")
if ans=="a":
files={}
for key in list(HDD.keys()):
files[key]=specimen+'_'+key+'.'+fmt
pmagplotlib.saveP(HDD,files)
if ans=='':k+=1
if ans=="p":
del HystRecs[-1]
k-=1
if ans=='q':
print("Good bye")
sys.exit()
if ans=='s':
keepon=1
specimen=input('Enter desired specimen name (or first part there of): ')
while keepon==1:
try:
k =sids.index(specimen)
keepon=0
except:
tmplist=[]
for qq in range(len(sids)):
if specimen in sids[qq]:tmplist.append(sids[qq])
print(specimen," not found, but this was: ")
print(tmplist)
specimen=input('Select one or try again\n ')
k =sids.index(specimen)
else:
k+=1
if len(B)==0 and len(Bdcd)==0:
if verbose:print('skipping this one - no hysteresis data')
k+=1
if len(HystRecs)>0:
# go through prior_data, clean out prior results and save combined file as spec_file
SpecRecs,keys=[],list(HystRecs[0].keys())
if len(prior_data)>0:
prior_keys=list(prior_data[0].keys())
else: prior_keys=[]
for rec in prior_data:
for key in keys:
if key not in list(rec.keys()):rec[key]=""
if 'LP-HYS' not in rec['method_codes']:
SpecRecs.append(rec)
for rec in HystRecs:
for key in prior_keys:
if key not in list(rec.keys()):rec[key]=""
prior=pmag.get_dictitem(prior_data,'specimen',rec['specimen'],'T')
if len(prior)>0 and 'sample' in list(prior[0].keys()):
rec['sample']=prior[0]['sample'] # pull sample name from prior specimens table
SpecRecs.append(rec)
pmag.magic_write(spec_file,SpecRecs,"specimens")
if verbose:print("hysteresis parameters saved in ",spec_file)
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
dmag_magic.py
DESCRIPTION
plots intensity decay curves for demagnetization experiments
SYNTAX
dmag_magic -h [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: magic_measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is by location
-LT [AF,T,M]: specify lab treatment type, default AF
-XLP [PI]: exclude specific lab protocols (for example, method codes like LP-PI)
-N do not normalize by NRM magnetization
-sav save plots silently and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG = {} # plot dictionary
FIG['demag'] = 1 # demag is figure 1
in_file, plot_key, LT = 'magic_measurements.txt', 'er_location_name', "LT-AF-Z"
XLP = ""
norm = 1
LT = 'LT-AF-Z'
units, dmag_key = 'T', 'treatment_ac_field'
plot = 0
fmt = 'svg'
if len(sys.argv) > 1:
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-N' in sys.argv: norm = 0
if '-sav' in sys.argv:
plot = 1
if '-f' in sys.argv:
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-obj' in sys.argv:
ind = sys.argv.index('-obj')
plot_by = sys.argv[ind + 1]
if plot_by == 'sit': plot_key = 'er_site_name'
if plot_by == 'sam': plot_key = 'er_sample_name'
if plot_by == 'spc': plot_key = 'er_specimen_name'
if '-XLP' in sys.argv:
ind = sys.argv.index("-XLP")
XLP = sys.argv[ind + 1] # get lab protocol for excluding
if '-LT' in sys.argv:
ind = sys.argv.index("-LT")
LT = 'LT-' + sys.argv[ind +
1] + '-Z' # get lab treatment for plotting
if LT == 'LT-T-Z':
units, dmag_key = 'K', 'treatment_temp'
elif LT == 'LT-AF-Z':
units, dmag_key = 'T', 'treatment_ac_field'
elif LT == 'LT-M-Z':
units, dmag_key = 'J', 'treatment_mw_energy'
else:
units = 'U'
data, file_type = pmag.magic_read(in_file)
sids = pmag.get_specs(data)
pmagplotlib.plot_init(FIG['demag'], 5, 5)
print(len(data), ' records read from ', in_file)
#
#
# find desired intensity data
#
#
plotlist, intlist = [], [
'measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measurement_magn_mass'
]
IntMeths = []
FixData = []
for rec in data:
meths = []
methcodes = rec['magic_method_codes'].split(':')
for meth in methcodes:
meths.append(meth.strip())
for key in rec.keys():
if key in intlist and rec[key] != "":
if key not in IntMeths: IntMeths.append(key)
if rec[plot_key] not in plotlist and LT in meths:
plotlist.append(rec[plot_key])
if 'measurement_flag' not in rec.keys():
rec['measurement_flag'] = 'g'
FixData.append(rec)
plotlist.sort()
if len(IntMeths) == 0:
print('No intensity information found')
sys.exit()
data = FixData
int_key = IntMeths[
0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
for plt in plotlist:
if plot == 0: print(plt, 'plotting by: ', plot_key)
PLTblock = pmag.get_dictitem(
data, plot_key, plt,
'T') # fish out all the data for this type of plot
PLTblock = pmag.get_dictitem(
PLTblock, 'magic_method_codes', LT,
'has') # fish out all the dmag for this experiment type
PLTblock = pmag.get_dictitem(
PLTblock, int_key, '',
'F') # get all with this intensity key non-blank
if XLP != "":
PLTblock = pmag.get_dictitem(
PLTblock, 'magic_method_codes', XLP,
'not') # reject data with XLP in method_code
if len(PLTblock) > 2:
title = PLTblock[0][plot_key]
spcs = []
for rec in PLTblock:
if rec['er_specimen_name'] not in spcs:
spcs.append(rec['er_specimen_name'])
for spc in spcs:
SPCblock = pmag.get_dictitem(PLTblock, 'er_specimen_name', spc,
'T') # plot specimen by specimen
INTblock = []
for rec in SPCblock:
INTblock.append([
float(rec[dmag_key]), 0, 0,
float(rec[int_key]), 1, rec['measurement_flag']
])
if len(INTblock) > 2:
pmagplotlib.plotMT(FIG['demag'], INTblock, title, 0, units,
norm)
if plot == 1:
files = {}
for key in FIG.keys():
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
sys.exit()
else:
pmagplotlib.drawFIGS(FIG)
ans = raw_input(
" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans == 'q': sys.exit()
if ans == "a":
files = {}
for key in FIG.keys():
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['demag'])
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
hysteresis_magic.py
DESCRIPTION
calculates hystereis parameters and saves them in 3.0 specimen format file
makes plots if option selected
SYNTAX
hysteresis_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input file, default is agm_measurements.txt
-F: specify specimens.txt output file
-P: do not make the plots
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
PLT = 1
plots = 0
fmt = pmag.get_named_arg_from_sys('-fmt', 'svg')
dir_path = pmag.get_named_arg_from_sys('-WD', '.')
dir_path = os.path.realpath(dir_path)
verbose = pmagplotlib.verbose
version_num = pmag.get_version()
user = pmag.get_named_arg_from_sys('-usr', '')
if "-h" in args:
print(main.__doc__)
sys.exit()
meas_file = pmag.get_named_arg_from_sys('-f', 'agm_measurements.txt')
spec_file = pmag.get_named_arg_from_sys('-F', 'specimens.txt')
if '-P' in args:
PLT = 0
irm_init, imag_init = -1, -1
if '-sav' in args:
verbose = 0
plots = 1
pltspec = pmag.get_named_arg_from_sys('-spc', 0)
if pltspec:
#pltspec= args[ind+1]
verbose = 0
plots = 1
spec_file = dir_path + '/' + spec_file
meas_file = dir_path + '/' + meas_file
SpecRecs = []
#
#
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != 'measurements':
print(main.__doc__)
print('bad file')
sys.exit()
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs, RemRecs = [], []
HDD = {}
if verbose:
if verbose and PLT:
print("Plots may be on top of each other - use mouse to place ")
if PLT:
HDD['hyst'], HDD['deltaM'], HDD['DdeltaM'] = 1, 2, 3
pmagplotlib.plot_init(HDD['DdeltaM'], 5, 5)
pmagplotlib.plot_init(HDD['deltaM'], 5, 5)
pmagplotlib.plot_init(HDD['hyst'], 5, 5)
imag_init = 0
irm_init = 0
else:
HDD['hyst'], HDD['deltaM'], HDD['DdeltaM'], HDD['irm'], HDD[
'imag'] = 0, 0, 0, 0, 0
#
if spec_file: prior_data, file_type = pmag.magic_read(spec_file)
#
# get list of unique experiment names and specimen names
#
experiment_names, sids = [], []
hys_data = pmag.get_dictitem(meas_data, 'method_codes', 'LP-HYS', 'has')
dcd_data = pmag.get_dictitem(meas_data, 'method_codes', 'LP-IRM-DCD',
'has')
imag_data = pmag.get_dictitem(meas_data, 'method_codes', 'LP-IMAG', 'has')
for rec in hys_data:
if rec['experiment'] not in experiment_names:
experiment_names.append(rec['experiment'])
if rec['specimen'] not in sids: sids.append(rec['specimen'])
#
k = 0
if pltspec:
k = sids.index(pltspec)
print(sids[k])
while k < len(sids):
specimen = sids[k]
HystRec = {
'specimen': specimen,
'experiment': ""
} # initialize a new specimen hysteresis record
if verbose and PLT: print(specimen, k + 1, 'out of ', len(sids))
#
#
B, M, Bdcd, Mdcd = [], [], [], [
] #B,M for hysteresis, Bdcd,Mdcd for irm-dcd data
Bimag, Mimag = [], [] #Bimag,Mimag for initial magnetization curves
spec_data = pmag.get_dictitem(
hys_data, 'specimen', specimen,
'T') # fish out all the LP-HYS data for this specimen
if len(spec_data) > 0:
meths = spec_data[0]['method_codes'].split(':')
e = spec_data[0]['experiment']
HystRec['experiment'] = spec_data[0]['experiment']
for rec in spec_data:
B.append(float(rec['meas_field_dc']))
M.append(float(rec['magn_moment']))
spec_data = pmag.get_dictitem(
dcd_data, 'specimen', specimen,
'T') # fish out all the data for this specimen
if len(spec_data) > 0:
HystRec['experiment'] = HystRec['experiment'] + ':' + spec_data[0][
'experiment']
irm_exp = spec_data[0]['experiment']
for rec in spec_data:
Bdcd.append(float(rec['treat_dc_field']))
Mdcd.append(float(rec['magn_moment']))
spec_data = pmag.get_dictitem(
imag_data, 'specimen', specimen,
'T') # fish out all the data for this specimen
if len(spec_data) > 0:
imag_exp = spec_data[0]['experiment']
for rec in spec_data:
Bimag.append(float(rec['meas_field_dc']))
Mimag.append(float(rec['magn_moment']))
#
# now plot the hysteresis curve
#
if len(B) > 0:
hmeths = []
for meth in meths:
hmeths.append(meth)
hpars = pmagplotlib.plotHDD(HDD, B, M, e)
if verbose and PLT: pmagplotlib.drawFIGS(HDD)
#
if verbose: pmagplotlib.plotHPARS(HDD, hpars, 'bs')
HystRec['hyst_mr_moment'] = hpars['hysteresis_mr_moment']
HystRec['hyst_ms_moment'] = hpars['hysteresis_ms_moment']
HystRec['hyst_bc'] = hpars['hysteresis_bc']
HystRec['hyst_bcr'] = hpars['hysteresis_bcr']
HystRec['hyst_xhf'] = hpars['hysteresis_xhf']
HystRec['experiments'] = e
HystRec['software_packages'] = version_num
if hpars["magic_method_codes"] not in hmeths:
hmeths.append(hpars["magic_method_codes"])
methods = ""
for meth in hmeths:
methods = methods + meth.strip() + ":"
HystRec["method_codes"] = methods[:-1]
HystRec["citations"] = "This study"
#
if len(Bdcd) > 0:
rmeths = []
for meth in meths:
rmeths.append(meth)
if verbose and PLT: print('plotting IRM')
if irm_init == 0:
HDD['irm'] = 5
pmagplotlib.plot_init(HDD['irm'], 5, 5)
irm_init = 1
rpars = pmagplotlib.plotIRM(HDD['irm'], Bdcd, Mdcd, irm_exp)
HystRec['rem_mr_moment'] = rpars['remanence_mr_moment']
HystRec['rem_bcr'] = rpars['remanence_bcr']
HystRec['experiments'] = specimen + ':' + irm_exp
if rpars["magic_method_codes"] not in meths:
meths.append(rpars["magic_method_codes"])
methods = ""
for meth in rmeths:
methods = methods + meth.strip() + ":"
HystRec[
"method_codes"] = HystRec['method_codes'] + ':' + methods[:-1]
HystRec["citations"] = "This study"
else:
if irm_init: pmagplotlib.clearFIG(HDD['irm'])
if len(Bimag) > 0:
if verbose and PLT: print('plotting initial magnetization curve')
# first normalize by Ms
Mnorm = []
for m in Mimag:
Mnorm.append(old_div(m, float(hpars['hysteresis_ms_moment'])))
if imag_init == 0:
HDD['imag'] = 4
pmagplotlib.plot_init(HDD['imag'], 5, 5)
imag_init = 1
pmagplotlib.plotIMAG(HDD['imag'], Bimag, Mnorm, imag_exp)
else:
if imag_init: pmagplotlib.clearFIG(HDD['imag'])
if len(list(HystRec.keys())) > 0: HystRecs.append(HystRec)
#
files = {}
if plots:
if pltspec:
s = pltspec
else:
s = specimen
files = {}
for key in list(HDD.keys()):
files[key] = s + '_' + key + '.' + fmt
pmagplotlib.saveP(HDD, files)
if pltspec: sys.exit()
if verbose and PLT:
pmagplotlib.drawFIGS(HDD)
ans = input(
"S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n "
)
if ans == "a":
files = {}
for key in list(HDD.keys()):
files[key] = specimen + '_' + key + '.' + fmt
pmagplotlib.saveP(HDD, files)
if ans == '': k += 1
if ans == "p":
del HystRecs[-1]
k -= 1
if ans == 'q':
print("Good bye")
sys.exit()
if ans == 's':
keepon = 1
specimen = input(
'Enter desired specimen name (or first part there of): ')
while keepon == 1:
try:
k = sids.index(specimen)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if specimen in sids[qq]: tmplist.append(sids[qq])
print(specimen, " not found, but this was: ")
print(tmplist)
specimen = input('Select one or try again\n ')
k = sids.index(specimen)
else:
k += 1
if len(B) == 0 and len(Bdcd) == 0:
if verbose: print('skipping this one - no hysteresis data')
k += 1
if len(HystRecs) > 0:
# go through prior_data, clean out prior results and save combined file as spec_file
SpecRecs, keys = [], list(HystRecs[0].keys())
if len(prior_data) > 0:
prior_keys = list(prior_data[0].keys())
else:
prior_keys = []
for rec in prior_data:
for key in keys:
if key not in list(rec.keys()): rec[key] = ""
if 'LP-HYS' not in rec['method_codes']:
SpecRecs.append(rec)
for rec in HystRecs:
for key in prior_keys:
if key not in list(rec.keys()): rec[key] = ""
prior = pmag.get_dictitem(prior_data, 'specimen', rec['specimen'],
'T')
if len(prior) > 0 and 'sample' in list(prior[0].keys()):
rec['sample'] = prior[0][
'sample'] # pull sample name from prior specimens table
SpecRecs.append(rec)
# drop unnecessary/duplicate rows
dir_path = os.path.split(spec_file)[0]
con = nb.Contribution(dir_path, read_tables=[])
con.add_magic_table_from_data('specimens', SpecRecs)
con.tables['specimens'].drop_duplicate_rows(ignore_cols=[
'specimen', 'sample', 'citations', 'software_packages'
])
con.tables['specimens'].df = con.tables[
'specimens'].df.drop_duplicates()
con.write_table_to_file('specimens', custom_name=spec_file)
# old way:
##pmag.magic_write(spec_file,SpecRecs,"specimens")
if verbose: print("hysteresis parameters saved in ", spec_file)
def main():
"""
NAME
irmaq_magic.py
DESCRIPTION
plots IRM acquisition curves from magic_measurements file
SYNTAX
irmaq_magic [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: magic_measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is by location
-N ; do not normalize by last point - use original units
-fmt [png,jpg,eps,pdf] set plot file format [default is svg]
-sav save plot[s] and quit
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG={} # plot dictionary
FIG['exp']=1 # exp is figure 1
dir_path='./'
plot,fmt=0,'svg'
units,dmag_key='T','treatment_dc_field'
XLP=[]
norm=1
in_file,plot_key,LP='magic_measurements.txt','er_location_name',"LP-IRM"
if len(sys.argv)>1:
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv:norm=0
if '-sav' in sys.argv:plot=1
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
in_file=dir_path+'/'+in_file
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
plot_by=sys.argv[ind+1]
if plot_by=='sit':plot_key='er_site_name'
if plot_by=='sam':plot_key='er_sample_name'
if plot_by=='spc':plot_key='er_specimen_name'
data,file_type=pmag.magic_read(in_file)
sids=pmag.get_specs(data)
pmagplotlib.plot_init(FIG['exp'],6,6)
#
#
# find desired intensity data
#
# get plotlist
#
plotlist,intlist=[],['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
IntMeths=[]
data=pmag.get_dictitem(data,'magic_method_codes',LP,'has') # get all the records with this lab protocol
Ints={}
NoInts,int_key=1,""
for key in intlist:
Ints[key]=pmag.get_dictitem(data,key,'','F') # get all non-blank data for intensity type
if len(Ints[key])>0:
NoInts=0
if int_key=="":int_key=key
if NoInts==1:
print 'No intensity information found'
sys.exit()
for rec in Ints[int_key]:
if rec[plot_key] not in plotlist: plotlist.append(rec[plot_key])
plotlist.sort()
for plt in plotlist:
print plt
INTblock=[]
data=pmag.get_dictitem(Ints[int_key],plot_key,plt,'T') # get data with right intensity info whose plot_key matches plot
sids=pmag.get_specs(data) # get a list of specimens with appropriate data
if len(sids)>0:
title=data[0][plot_key]
for s in sids:
INTblock=[]
sdata=pmag.get_dictitem(data,'er_specimen_name',s,'T') # get data for each specimen
for rec in sdata:
INTblock.append([float(rec[dmag_key]),0,0,float(rec[int_key]),1,'g'])
pmagplotlib.plotMT(FIG['exp'],INTblock,title,0,units,norm)
files={}
for key in FIG.keys():
files[key]=title+'_'+LP+'.'+fmt
if plot==0:
pmagplotlib.drawFIGS(FIG)
ans=raw_input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans=='q':sys.exit()
if ans=="a":
pmagplotlib.saveP(FIG,files)
else:
pmagplotlib.saveP(FIG,files)
pmagplotlib.clearFIG(FIG['exp'])
def main():
"""
NAME
lowrie.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie -h [command line options]
INPUT
takes SIO formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav save plots and quit
"""
fmt, plot = 'svg', 0
FIG = {} # plot dictionary
FIG['lowrie'] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'], 6, 6)
norm = 1 # default is to normalize by maximum axis
if len(sys.argv) > 1:
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-N' in sys.argv:
norm = 0 # don't normalize
if '-sav' in sys.argv:
plot = 1 # don't normalize
if '-fmt' in sys.argv: # sets input filename
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-f' in sys.argv: # sets input filename
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
data = pmag.open_file(in_file)
PmagRecs = [] # set up a list for the results
keys = ['specimen', 'treatment', 'csd', 'M', 'dec', 'inc']
for line in data:
PmagRec = {}
rec = line.replace('\n', '').split()
for k in range(len(keys)):
PmagRec[keys[k]] = rec[k]
PmagRecs.append(PmagRec)
specs = pmag.get_dictkey(PmagRecs, 'specimen', '')
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print(spc)
specdata = pmag.get_dictitem(
PmagRecs, 'specimen', spc, 'T') # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append([float(dat['dec']), float(
dat['inc']), float(dat['M']) * 1e-3])
Temps.append(float(dat['treatment']))
carts = pmag.dir2cart(DIMs).transpose()
# if norm==1: # want to normalize
# nrm=max(max(abs(carts[0])),max(abs(carts[1])),max(abs(carts[2]))) # by maximum of x,y,z values
# ylab="M/M_max"
if norm == 1: # want to normalize
nrm = (DIMs[0][2]) # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1. # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[0]), nrm), sym='r-')
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[0]), nrm), sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[1]), nrm), sym='c-')
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[1]), nrm), sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[2]), nrm), sym='k-')
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[2]), nrm), sym='k^', title=spc, xlab=xlab, ylab=ylab) # Z direction
files = {'lowrie': 'lowrie:_' + spc + '_.' + fmt}
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = input('S[a]ve figure? [q]uit, <return> to continue ')
if ans == 'a':
pmagplotlib.saveP(FIG, files)
elif ans == 'q':
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
dmag_magic.py
DESCRIPTION
plots intensity decay curves for demagnetization experiments
SYNTAX
dmag_magic -h [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: magic_measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot,
default is by location
-LT [AF,T,M]: specify lab treatment type, default AF
-XLP [PI]: exclude specific lab protocols,
(for example, method codes like LP-PI)
-N do not normalize by NRM magnetization
-sav save plots silently and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
# initialize variables from command line + defaults
FIG = {} # plot dictionary
FIG['demag'] = 1 # demag is figure 1
in_file = pmag.get_named_arg_from_sys("-f", default_val="measurements.txt")
plot_by = pmag.get_named_arg_from_sys("-obj", default_val="loc")
name_dict = {'loc': 'location', 'sit': 'site',
'sam': 'sample', 'spc': 'specimen'}
plot_key = name_dict[plot_by]
LT = "LT-" + pmag.get_named_arg_from_sys("-LT", "AF") + "-Z"
if LT == "LT-T-Z":
units, dmag_key = 'K', 'treat_temp'
elif LT == "LT-AF-Z":
units, dmag_key = 'T', 'treat_ac_field'
elif LT == 'LT-M-Z':
units, dmag_key = 'J', 'treat_mw_energy'
else:
units = 'U'
no_norm = pmag.get_flag_arg_from_sys("-N")
norm = 0 if no_norm else 1
no_plot = pmag.get_flag_arg_from_sys("-sav")
plot = 0 if no_plot else 1
fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
XLP = pmag.get_named_arg_from_sys("-XLP", "")
dir_path = pmag.get_named_arg_from_sys("-WD", os.getcwd())
spec_file = pmag.get_named_arg_from_sys("-fsp", default_val="specimens.txt")
samp_file = pmag.get_named_arg_from_sys("-fsa", default_val="samples.txt")
site_file = pmag.get_named_arg_from_sys("-fsi", default_val="sites.txt")
# create contribution and add required headers
fnames = {"specimens": spec_file, "samples": samp_file, 'sites': site_file}
contribution = nb.Contribution(dir_path, single_file=in_file,
custom_filenames=fnames)
file_type = contribution.tables.keys()[0]
print len(contribution.tables['measurements'].df), ' records read from ', in_file
# add plot_key into measurements table
if plot_key not in contribution.tables['measurements'].df.columns:
contribution.propagate_name_down(plot_key, 'measurements')
data_container = contribution.tables[file_type]
# pare down to only records with useful data
# grab records that have the requested code
data_slice = data_container.get_records_for_code(LT)
# and don't have the offending code
data = data_container.get_records_for_code(XLP, incl=False, use_slice=True,
sli=data_slice, strict_match=False)
# make sure quality is in the dataframe
if 'quality' not in data.columns:
data['quality'] = 'g'
# get intensity key and make sure intensity data is not blank
intlist = ['magn_moment', 'magn_volume', 'magn_mass']
IntMeths = [col_name for col_name in data.columns if col_name in intlist]
# get rid of any entirely blank intensity columns
for col_name in IntMeths:
if not data[col_name].any():
data.drop(col_name, axis=1, inplace=True)
IntMeths = [col_name for col_name in data.columns if col_name in intlist]
if len(IntMeths) == 0:
print 'No intensity headers found'
sys.exit()
int_key = IntMeths[0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
data = data[data[int_key].notnull()]
# make list of individual plots
# by default, will be by location_name
plotlist = data[plot_key].unique()
plotlist.sort()
pmagplotlib.plot_init(FIG['demag'], 5, 5)
# iterate through and plot the data
for plt in plotlist:
plot_data = data[data[plot_key] == plt].copy()
if plot:
print plt, 'plotting by: ', plot_key
if len(plot_data) > 2:
title = plt
spcs = []
spcs = plot_data['specimen'].unique()
for spc in spcs:
INTblock = []
spec_data = plot_data[plot_data['specimen'] == spc]
for ind, rec in spec_data.iterrows():
INTblock.append([float(rec[dmag_key]), 0, 0, float(rec[int_key]), 1, rec['quality']])
if len(INTblock) > 2:
pmagplotlib.plotMT(FIG['demag'], INTblock,
title, 0, units, norm)
if not plot:
files = {}
for key in FIG.keys():
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
#sys.exit()
else:
pmagplotlib.drawFIGS(FIG)
prompt = " S[a]ve to save plot, [q]uit, Return to continue: "
ans = raw_input(prompt)
if ans == 'q':
sys.exit()
if ans == "a":
files = {}
for key in FIG.keys():
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['demag'])
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")
def main():
"""
NAME
lowrie_magic.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie_magic.py -h [command line options]
INPUT
takes measurements formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is magic_measurements.txt
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav saves plots and quits
-DM [2, 3] MagIC data model number
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if len(sys.argv) <= 1:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
FIG = {} # plot dictionary
FIG['lowrie'] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'], 6, 6)
norm = 1 # default is to normalize by maximum axis
in_file = pmag.get_named_arg("-f", "measurements.txt")
dir_path = pmag.get_named_arg("-WD", ".")
in_file = pmag.resolve_file_name(in_file, dir_path)
data_model = pmag.get_named_arg("-DM", 3)
data_model = int(float(data_model))
fmt = pmag.get_named_arg("-fmt", "svg")
if '-N' in sys.argv:
norm = 0 # don't normalize
if '-sav' in sys.argv:
plot = 1 # silently save and quit
else:
plot = 0 # generate plots
print(in_file)
# read in data
PmagRecs, file_type = pmag.magic_read(in_file)
if data_model == 2 and file_type != "magic_measurements":
print('bad input file', file_type)
sys.exit()
if data_model == 3 and file_type != "measurements":
print('bad input file', file_type)
sys.exit()
if data_model == 2:
meth_code_col = 'magic_method_codes'
spec_col = 'er_specimen_name'
dec_col = "measurement_dec"
inc_col = 'measurement_inc'
moment_col = 'measurement_magn_moment'
temp_col = 'treatment_temp'
else:
meth_code_col = 'method_codes'
spec_col = 'specimen'
dec_col = 'dir_dec'
inc_col = 'dir_inc'
moment_col = 'magn_moment'
temp_col = "treat_temp"
PmagRecs = pmag.get_dictitem(
PmagRecs, meth_code_col, 'LP-IRM-3D', 'has') # get all 3D IRM records
if len(PmagRecs) == 0:
print('no records found with the method code LP-IRM-3D')
sys.exit()
specs = pmag.get_dictkey(PmagRecs, spec_col, '')
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print(spc)
specdata = pmag.get_dictitem(
PmagRecs, spec_col, spc, 'T') # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append([float(dat[dec_col]), float(
dat[inc_col]), float(dat[moment_col])])
Temps.append(float(dat[temp_col])-273.)
carts = pmag.dir2cart(DIMs).transpose()
if norm == 1: # want to normalize
nrm = (DIMs[0][2]) # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1. # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[0]) / nrm, sym='r-')
pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[0]) / nrm, sym='ro') # X direction
pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[1]) / nrm, sym='c-')
pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[1]) / nrm, sym='cs') # Y direction
pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[2]) / nrm, sym='k-')
pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[2]) / nrm, sym='k^', title=spc, xlab=xlab, ylab=ylab) # Z direction
files = {'lowrie': 'lowrie:_'+spc+'_.'+fmt}
if plot == 0:
pmagplotlib.draw_figs(FIG)
ans = input('S[a]ve figure? [q]uit, <return> to continue ')
if ans == 'a':
pmagplotlib.save_plots(FIG, files)
elif ans == 'q':
sys.exit()
else:
pmagplotlib.save_plots(FIG, files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
lowrie_magic.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie_magic.py -h [command line options]
INPUT
takes measurements formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is magic_measurements.txt
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav saves plots and quits
-DM [2, 3] MagIC data model number
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if len(sys.argv) <= 1:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
FIG = {} # plot dictionary
FIG['lowrie'] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'], 6, 6)
norm = 1 # default is to normalize by maximum axis
in_file = pmag.get_named_arg("-f", "measurements.txt")
dir_path = pmag.get_named_arg("-WD", ".")
in_file = pmag.resolve_file_name(in_file, dir_path)
data_model = pmag.get_named_arg("-DM", 3)
data_model = int(float(data_model))
fmt = pmag.get_named_arg("-fmt", "svg")
if '-N' in sys.argv:
norm = 0 # don't normalize
if '-sav' in sys.argv:
plot = 1 # silently save and quit
else:
plot = 0 # generate plots
print(in_file)
# read in data
PmagRecs, file_type = pmag.magic_read(in_file)
if data_model == 2 and file_type != "magic_measurements":
print('bad input file', file_type)
sys.exit()
if data_model == 3 and file_type != "measurements":
print('bad input file', file_type)
sys.exit()
if data_model == 2:
meth_code_col = 'magic_method_codes'
spec_col = 'er_specimen_name'
dec_col = "measurement_dec"
inc_col = 'measurement_inc'
moment_col = 'measurement_magn_moment'
temp_col = 'treatment_temp'
else:
meth_code_col = 'method_codes'
spec_col = 'specimen'
dec_col = 'dir_dec'
inc_col = 'dir_inc'
moment_col = 'magn_moment'
temp_col = "treat_temp"
PmagRecs = pmag.get_dictitem(PmagRecs, meth_code_col, 'LP-IRM-3D',
'has') # get all 3D IRM records
if len(PmagRecs) == 0:
print('no records found with the method code LP-IRM-3D')
sys.exit()
specs = pmag.get_dictkey(PmagRecs, spec_col, '')
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print(spc)
specdata = pmag.get_dictitem(PmagRecs, spec_col, spc,
'T') # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append([
float(dat[dec_col]),
float(dat[inc_col]),
float(dat[moment_col])
])
Temps.append(float(dat[temp_col]) - 273.)
carts = pmag.dir2cart(DIMs).transpose()
if norm == 1: # want to normalize
nrm = (DIMs[0][2]) # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1. # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plot_xy(FIG['lowrie'],
Temps,
abs(carts[0]) / nrm,
sym='r-')
pmagplotlib.plot_xy(FIG['lowrie'],
Temps,
abs(carts[0]) / nrm,
sym='ro') # X direction
pmagplotlib.plot_xy(FIG['lowrie'],
Temps,
abs(carts[1]) / nrm,
sym='c-')
pmagplotlib.plot_xy(FIG['lowrie'],
Temps,
abs(carts[1]) / nrm,
sym='cs') # Y direction
pmagplotlib.plot_xy(FIG['lowrie'],
Temps,
abs(carts[2]) / nrm,
sym='k-')
pmagplotlib.plot_xy(FIG['lowrie'],
Temps,
abs(carts[2]) / nrm,
sym='k^',
title=spc,
xlab=xlab,
ylab=ylab) # Z direction
files = {'lowrie': 'lowrie:_' + spc + '_.' + fmt}
if plot == 0:
pmagplotlib.draw_figs(FIG)
ans = input('S[a]ve figure? [q]uit, <return> to continue ')
if ans == 'a':
pmagplotlib.save_plots(FIG, files)
elif ans == 'q':
sys.exit()
else:
pmagplotlib.save_plots(FIG, files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
quick_hyst.py
DESCRIPTION
makes plots of hysteresis data
SYNTAX
quick_hyst.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input file, default is measurements.txt
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
if "-h" in args:
print main.__doc__
sys.exit()
plots = 0
pltspec = ""
verbose = pmagplotlib.verbose
# version_num = pmag.get_version()
dir_path = pmag.get_named_arg_from_sys("-WD", ".")
dir_path = os.path.realpath(dir_path)
meas_file = pmag.get_named_arg_from_sys("-f", "measurements.txt")
fmt = pmag.get_named_arg_from_sys("-fmt", "png")
if "-sav" in args:
verbose = 0
plots = 1
if "-spc" in args:
ind = args.index("-spc")
pltspec = args[ind + 1]
verbose = 0
plots = 1
#
con = nb.Contribution(dir_path, read_tables=["measurements"], custom_filenames={"measurements": meas_file})
# get as much name data as possible (used for naming plots)
if not "measurements" in con.tables:
print "-W- No measurement file found"
return
con.propagate_name_down("location", "measurements")
if "measurements" not in con.tables:
print main.__doc__
print "bad file"
sys.exit()
meas_container = con.tables["measurements"]
# meas_df = meas_container.df
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs = []
HDD = {}
HDD["hyst"] = 1
pmagplotlib.plot_init(HDD["hyst"], 5, 5)
#
# get list of unique experiment names and specimen names
#
sids = []
hyst_data = meas_container.get_records_for_code("LP-HYS")
# experiment_names = hyst_data['experiment_name'].unique()
if not len(hyst_data):
print "-W- No hysteresis data found"
return
sids = hyst_data["specimen"].unique()
# if 'treat_temp' is provided, use that value, otherwise assume 300
hyst_data["treat_temp"].where(hyst_data["treat_temp"], "300", inplace=True)
# start at first specimen, or at provided specimen ('-spc')
k = 0
if pltspec != "":
try:
print sids
k = list(sids).index(pltspec)
except ValueError:
print "-W- No specimen named: {}.".format(pltspec)
print "-W- Please provide a valid specimen name"
return
intlist = ["magn_moment", "magn_volume", "magn_mass"]
while k < len(sids):
locname, site, sample, synth = "", "", "", ""
s = sids[k]
if verbose:
print s, k + 1, "out of ", len(sids)
# B, M for hysteresis, Bdcd,Mdcd for irm-dcd data
B, M = [], []
# get all measurements for this specimen
spec = hyst_data[hyst_data["specimen"] == s]
# get names
if "location" in spec:
locname = spec["location"][0]
if "site" in spec:
site = spec["sample"][0]
if "sample" in spec:
sample = spec["sample"][0]
# get all records with non-blank values in any intlist column
# find intensity data
for int_column in intlist:
if int_column in spec.columns:
int_col = int_column
break
meas_data = spec[spec[int_column].notnull()]
if len(meas_data) == 0:
break
#
c = ["k-", "b-", "c-", "g-", "m-", "r-", "y-"]
cnum = 0
Temps = []
xlab, ylab, title = "", "", ""
Temps = meas_data["treat_temp"].unique()
for t in Temps:
print "working on t: ", t
t_data = meas_data[meas_data["treat_temp"] == t]
m = int_col
B = t_data["meas_field_dc"].astype(float).values
M = t_data[m].astype(float).values
# now plot the hysteresis curve(s)
#
if len(B) > 0:
B = numpy.array(B)
M = numpy.array(M)
if t == Temps[-1]:
xlab = "Field (T)"
ylab = m
title = "Hysteresis: " + s
if t == Temps[0]:
pmagplotlib.clearFIG(HDD["hyst"])
pmagplotlib.plotXY(HDD["hyst"], B, M, sym=c[cnum], xlab=xlab, ylab=ylab, title=title)
pmagplotlib.plotXY(
HDD["hyst"], [1.1 * B.min(), 1.1 * B.max()], [0, 0], sym="k-", xlab=xlab, ylab=ylab, title=title
)
pmagplotlib.plotXY(
HDD["hyst"], [0, 0], [1.1 * M.min(), 1.1 * M.max()], sym="k-", xlab=xlab, ylab=ylab, title=title
)
if verbose:
pmagplotlib.drawFIGS(HDD)
cnum += 1
if cnum == len(c):
cnum = 0
#
files = {}
if plots:
if pltspec != "":
s = pltspec
for key in HDD.keys():
if synth == "":
files[key] = (
"LO:_" + locname + "_SI:_" + site + "_SA:_" + sample + "_SP:_" + s + "_TY:_" + key + "_." + fmt
)
else:
files[key] = "SY:_" + synth + "_TY:_" + key + "_." + fmt
pmagplotlib.saveP(HDD, files)
if pltspec != "":
sys.exit()
if verbose:
pmagplotlib.drawFIGS(HDD)
ans = raw_input("S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n ")
if ans == "a":
files = {}
for key in HDD.keys():
files[key] = (
"LO:_" + locname + "_SI:_" + site + "_SA:_" + sample + "_SP:_" + s + "_TY:_" + key + "_." + fmt
)
pmagplotlib.saveP(HDD, files)
if ans == "":
k += 1
if ans == "p":
del HystRecs[-1]
k -= 1
if ans == "q":
print "Good bye"
sys.exit()
if ans == "s":
keepon = 1
specimen = raw_input("Enter desired specimen name (or first part there of): ")
while keepon == 1:
try:
k = sids.index(specimen)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if specimen in sids[qq]:
tmplist.append(sids[qq])
print specimen, " not found, but this was: "
print tmplist
specimen = raw_input("Select one or try again\n ")
k = sids.index(specimen)
else:
k += 1
if len(B) == 0:
if verbose:
print "skipping this one - no hysteresis data"
k += 1
def main():
"""
NAME
thellier_magic.py
DESCRIPTION
plots Thellier-Thellier data in version 3.0 format
Reads saved interpretations from a specimen formatted table, default: specimens.txt
SYNTAX
thellier_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEAS, set measurements input file, default is 'measurements.txt'
-fsp PRIOR, set specimens.txt prior interpretations file, default is 'specimens.txt'
-fcr CRIT, set criteria file for grading. # not yet implemented
-fmt [svg,png,jpg], format for images - default is svg
-sav, saves plots with out review (in format specified by -fmt key or default)
-spc SPEC, plots single specimen SPEC, saves plot with specified format
with optional -b bounds and quits
-b BEG END: sets bounds for calculation
BEG: starting step number for slope calculation
END: ending step number for slope calculation
-z use only z component difference for pTRM calculation
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 measuements)
list of possible commands: type letter followed by return to select option
saving of plots creates image files with specimen, plot type as name
"""
#
# initializations
#
version_num=pmag.get_version()
verbose=pmagplotlib.verbose
#
# default acceptance criteria
#
accept=pmag.default_criteria(0)[0] # set the default criteria
#
# parse command line options
#
plots,fmt,Zdiff=0,'svg',0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg_from_sys("-WD", default_val=os.getcwd())
meas_file = pmag.get_named_arg_from_sys("-f", default_val="measurements.txt")
spec_file=pmag.get_named_arg_from_sys("-fsp", default_val="specimens.txt")
crit_file=pmag.get_named_arg_from_sys("-fcr", default_val="criteria.txt")
spec_file=os.path.join(dir_path,spec_file)
meas_file=os.path.join(dir_path,meas_file)
crit_file=os.path.join(dir_path,crit_file)
fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
if '-sav' in sys.argv: plots,verbose=1,0
if '-z' in sys.argv: Zdiff=1
specimen=pmag.get_named_arg_from_sys("-spc",default_val="")
if '-b' in sys.argv:
ind=sys.argv.index('-b')
start=int(sys.argv[ind+1])
end=int(sys.argv[ind+2])
else:
start,end="",""
fnames = {'measurements': meas_file, 'specimens': spec_file, 'criteria': crit_file}
contribution = nb.Contribution(dir_path, custom_filenames=fnames, read_tables=['measurements', 'specimens', 'criteria'])
#
# import prior interpretations from specimen file
#
specimen_cols = ['analysts', 'aniso_ftest', 'aniso_ftest12', 'aniso_ftest23', 'aniso_s', 'aniso_s_mean', 'aniso_s_n_measurements', 'aniso_s_sigma', 'aniso_s_unit', 'aniso_tilt_correction', 'aniso_type', 'aniso_v1', 'aniso_v2', 'aniso_v3', 'citations', 'description', 'dir_alpha95', 'dir_comp', 'dir_dec', 'dir_inc', 'dir_mad_free', 'dir_n_measurements', 'dir_tilt_correction', 'experiments', 'geologic_classes', 'geologic_types', 'hyst_bc', 'hyst_bcr', 'hyst_mr_moment', 'hyst_ms_moment', 'int_abs', 'int_b', 'int_b_beta', 'int_b_sigma', 'int_corr', 'int_dang', 'int_drats', 'int_f', 'int_fvds', 'int_gamma', 'int_mad_free', 'int_md', 'int_n_measurements', 'int_n_ptrm', 'int_q', 'int_rsc', 'int_treat_dc_field', 'lithologies', 'meas_step_max', 'meas_step_min', 'meas_step_unit', 'method_codes', 'sample', 'software_packages', 'specimen']
if 'specimens' in contribution.tables:
spec_container = contribution.tables['specimens']
prior_spec_data=spec_container.get_records_for_code('LP-PI-TRM',strict_match=False) # look up all prior intensity interpretations
else:
spec_container, prior_spec_data = None, []
backup=0
#
Mkeys = ['magn_moment', 'magn_volume', 'magn_mass']
#
# create measurement dataframe
#
meas_container = contribution.tables['measurements']
meas_data = meas_container.df
#
meas_data['method_codes']=meas_data['method_codes'].str.replace(" ","") # get rid of nasty spaces
meas_data= meas_data[meas_data['method_codes'].str.contains('LP-PI-TRM|LP-TRM|LP-TRM-TD')==True] # fish out zero field steps for plotting
intensity_types = [col_name for col_name in meas_data.columns if col_name in Mkeys]
int_key = intensity_types[0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
meas_data = meas_data[meas_data[int_key].notnull()] # get all the non-null intensity records of the same type
if 'flag' not in meas_data.columns: meas_data['flag'] = 'g' # set the default flag to good
meas_data = meas_data[meas_data['flag'].str.contains('g')==True] # only the 'good' measurements
thel_data = meas_data[meas_data['method_codes'].str.contains('LP-PI-TRM')==True] # get all the Thellier data
trm_data = meas_data[meas_data['method_codes'].str.contains('LP-TRM')==True] # get all the TRM acquisition data
td_data = meas_data[meas_data['method_codes'].str.contains('LP-TRM-TD')==True] # get all the TD data
anis_data = meas_data[meas_data['method_codes'].str.contains('LP-AN')==True] # get all the anisotropy data
#
# get list of unique specimen names from measurement data
#
specimen_names= meas_data.specimen.unique() # this is a Series of all the specimen names
specimen_names= specimen_names.tolist() # turns it into a list
specimen_names.sort() # sorts by specimen name
#
# set up new DataFrame for this sessions specimen interpretations
#
spec_container = nb.MagicDataFrame(dtype='specimens', columns=specimen_cols)
current_spec_data = spec_container.df # this is for interpretations from this session
if specimen=="": # do all specimens
k = 0
else:
k=specimen_names.index(specimen) # just do this one
# define figure numbers for arai, zijderveld and
# de-,re-magnetization 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)
if len(trm_data)>0:
AZD['TRM']=5
pmagplotlib.plot_init(AZD['TRM'],5,5)
if len(td_data)>0:
AZD['TDS']=6
pmagplotlib.plot_init(AZD['TDS'],5,5)
#
while k < len(specimen_names):
this_specimen=specimen_names[k] # set the current specimen for plotting
if verbose and this_specimen!="":print(this_specimen, k+1 , 'out of ',len(specimen_names))
#
# set up datablocks
#
thelblock= thel_data[thel_data['specimen'].str.contains(this_specimen)==True] # fish out this specimen
trmblock= trm_data[trm_data['specimen'].str.contains(this_specimen)==True] # fish out this specimen
tdsrecs= td_data[td_data['specimen'].str.contains(this_specimen)==True] # fish out this specimen
anisblock= anis_data[anis_data['specimen'].str.contains(this_specimen)==True] # fish out the anisotropy data
prior_specimen_interpretations= prior_spec_data[prior_spec_data['specimen'].str.contains(this_specimen)==True] # fish out prior interpretation
#
# sort data into types
#
araiblock,field=pmag.sortarai(thelblock,this_specimen,Zdiff,version=3)
first_Z=araiblock[0]
GammaChecks=araiblock[5]
if len(first_Z)<3:
if backup==0:
k+=1
if verbose:
print('skipping specimen - moving forward ', this_specimen)
else:
k-=1
if verbose:
print('skipping specimen - moving backward ', this_specimen)
else:
backup=0
zijdblock,units=pmag.find_dmag_rec(this_specimen,thelblock,version=3)
if start=="" and len(prior_specimen_interpretations)>0:
if verbose: print('Looking up saved interpretation....')
#
# get prior interpretation steps
#
beg_int=pd.to_numeric(prior_specimen_interpretations.meas_step_min.values).tolist()[0]
end_int=pd.to_numeric(prior_specimen_interpretations.meas_step_max.values).tolist()[0]
else: beg_int,end_int="",""
recnum=0
if verbose: print("index step Dec Inc Int Gamma")
for plotrec in zijdblock:
if plotrec[0]==beg_int:start=recnum # while we are at it, collect these bounds
if plotrec[0]==end_int:end=recnum
if verbose:
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
for fig in list(AZD.keys()):pmagplotlib.clearFIG(AZD[fig]) # clear all figures
pmagplotlib.plotAZ(AZD,araiblock,zijdblock,this_specimen,units[0])
if verbose:pmagplotlib.drawFIGS(AZD)
pars,errcode=pmag.PintPars(thelblock,araiblock,zijdblock,start,end,accept,version=3)
pars['measurement_step_unit']="K"
pars['experiment_type']='LP-PI-TRM'
#
# work on saving interpretations stuff later
#
if errcode!=1: # no problem in PintPars
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars["er_specimen_name"]=this_specimen
#pars,kill=pmag.scoreit(pars,this_specimen_interpretation,accept,'',verbose) # deal with this later
pars["specimen_grade"]='None'
pars['measurement_step_min']=pars['meas_step_min']
pars['measurement_step_max']=pars['meas_step_max']
if pars['measurement_step_unit']=='K':
outstr= "specimen Tmin Tmax N lab_field B_anc b q f(coe) Fvds beta MAD Dang Drats Nptrm Grade R MD% sigma Gamma_max \n"
pars_out= (this_specimen,(pars["meas_step_min"]-273),(pars["meas_step_max"]-273),(pars["specimen_int_n"]),1e6*(pars["specimen_lab_field_dc"]),1e6*(pars["specimen_int"]),pars["specimen_b"],pars["specimen_q"],pars["specimen_f"],pars["specimen_fvds"],pars["specimen_b_beta"],pars["int_mad_free"],pars["int_dang"],pars["int_drats"],pars["int_n_ptrm"],pars["specimen_grade"],np.sqrt(pars["specimen_rsc"]),int(pars["int_md"]), pars["specimen_b_sigma"],pars['specimen_gamma'])
outstring= '%s %4.0f %4.0f %i %4.1f %4.1f %5.3f %5.1f %5.3f %5.3f %5.3f %7.1f %7.1f %7.1f %s %s %6.3f %i %5.3f %7.1f' % pars_out +'\n'
elif pars['measurement_step_unit']=='J':
outstr= "specimen Wmin Wmax N lab_field B_anc b q f(coe) Fvds beta MAD Dang Drats Nptrm Grade R MD% sigma ThetaMax DeltaMax GammaMax\n"
pars_out= (this_specimen,(pars["meas_step_min"]),(pars["meas_step_max"]),(pars["specimen_int_n"]),1e6*(pars["specimen_lab_field_dc"]),1e6*(pars["specimen_int"]),pars["specimen_b"],pars["specimen_q"],pars["specimen_f"],pars["specimen_fvds"],pars["specimen_b_beta"],pars["specimen_int_mad"],pars["specimen_int_dang"],pars["specimen_drats"],pars["specimen_int_ptrm_n"],pars["specimen_grade"],np.sqrt(pars["specimen_rsc"]),int(pars["specimen_md"]), pars["specimen_b_sigma"],pars["specimen_theta"],pars["specimen_delta"],pars["specimen_gamma"])
outstring= '%s %4.0f %4.0f %i %4.1f %4.1f %5.3f %5.1f %5.3f %5.3f %5.3f %7.1f %7.1f %7.1f %s %s %6.3f %i %5.3f %7.1f %7.1f %7.1f' % pars_out +'\n'
print(outstr)
print(outstring)
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
mpars=pmag.domean(araiblock[1],start,end,'DE-BFL')
if verbose:
pmagplotlib.drawFIGS(AZD)
print('pTRM direction= ','%7.1f'%(mpars['specimen_dec']),' %7.1f'%(mpars['specimen_inc']),' MAD:','%7.1f'%(mpars['specimen_mad']))
if len(anisblock)>0: # this specimen has anisotropy data
if verbose: print('Found anisotropy record... but ignoring for now ')
if plots==1:
if fmt != "pmag":
files={}
for key in list(AZD.keys()):
files[key]='SP:_'+this_specimen+'_TY:_'+key+'_'+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['deremag']='DeReMag Plot'
titles['zijd']='Zijderveld Plot'
titles['arai']='Arai Plot'
titles['TRM']='TRM Acquisition data'
AZD = pmagplotlib.addBorders(AZD,titles,black,purple)
pmagplotlib.saveP(AZD,files)
else: # save in pmag format
print('pmag format no longer supported')
#script="grep "+this_specimen+" 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 specimen!="": sys.exit() # syonara
if verbose:
ans=input('Return for next specimen, q to quit: ')
if ans=='q':sys.exit()
k+=1 # moving on
def main():
"""
NAME
dmag_magic.py
DESCRIPTION
plots intensity decay curves for demagnetization experiments
SYNTAX
dmag_magic -h [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: magic_measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot,
default is by location
-LT [AF,T,M]: specify lab treatment type, default AF
-XLP [PI]: exclude specific lab protocols,
(for example, method codes like LP-PI)
-N do not normalize by NRM magnetization
-sav save plots silently and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
# initialize variables from command line + defaults
FIG = {} # plot dictionary
FIG['demag'] = 1 # demag is figure 1
in_file = pmag.get_named_arg_from_sys("-f", default_val="measurements.txt")
plot_by = pmag.get_named_arg_from_sys("-obj", default_val="loc")
name_dict = {
'loc': 'location',
'sit': 'site',
'sam': 'sample',
'spc': 'specimen'
}
plot_key = name_dict[plot_by]
LT = "LT-" + pmag.get_named_arg_from_sys("-LT", "AF") + "-Z"
if LT == "LT-T-Z":
units, dmag_key = 'K', 'treat_temp'
elif LT == "LT-AF-Z":
units, dmag_key = 'T', 'treat_ac_field'
elif LT == 'LT-M-Z':
units, dmag_key = 'J', 'treat_mw_energy'
else:
units = 'U'
no_norm = pmag.get_flag_arg_from_sys("-N")
norm = 0 if no_norm else 1
no_plot = pmag.get_flag_arg_from_sys("-sav")
plot = 0 if no_plot else 1
fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
XLP = pmag.get_named_arg_from_sys("-XLP", "")
dir_path = pmag.get_named_arg_from_sys("-WD", os.getcwd())
spec_file = pmag.get_named_arg_from_sys("-fsp",
default_val="specimens.txt")
samp_file = pmag.get_named_arg_from_sys("-fsa", default_val="samples.txt")
site_file = pmag.get_named_arg_from_sys("-fsi", default_val="sites.txt")
# create contribution and add required headers
fnames = {"specimens": spec_file, "samples": samp_file, 'sites': site_file}
contribution = nb.Contribution(dir_path,
single_file=in_file,
custom_filenames=fnames)
file_type = list(contribution.tables.keys())[0]
print(len(contribution.tables['measurements'].df), ' records read from ',
in_file)
# add plot_key into measurements table
if plot_key not in contribution.tables['measurements'].df.columns:
#contribution.propagate_name_down(plot_key, 'measurements')
contribution.propagate_location_to_measurements()
data_container = contribution.tables[file_type]
# pare down to only records with useful data
# grab records that have the requested code
data_slice = data_container.get_records_for_code(LT)
# and don't have the offending code
data = data_container.get_records_for_code(XLP,
incl=False,
use_slice=True,
sli=data_slice,
strict_match=False)
# make sure quality is in the dataframe
if 'quality' not in data.columns:
data['quality'] = 'g'
# get intensity key and make sure intensity data is not blank
intlist = ['magn_moment', 'magn_volume', 'magn_mass']
IntMeths = [col_name for col_name in data.columns if col_name in intlist]
# get rid of any entirely blank intensity columns
for col_name in IntMeths:
if not data[col_name].any():
data.drop(col_name, axis=1, inplace=True)
IntMeths = [col_name for col_name in data.columns if col_name in intlist]
if len(IntMeths) == 0:
print('No intensity headers found')
sys.exit()
int_key = IntMeths[
0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
data = data[data[int_key].notnull()]
# make list of individual plots
# by default, will be by location_name
plotlist = data[plot_key].unique()
plotlist.sort()
pmagplotlib.plot_init(FIG['demag'], 5, 5)
# iterate through and plot the data
for plt in plotlist:
plot_data = data[data[plot_key] == plt].copy()
if plot:
print(plt, 'plotting by: ', plot_key)
if len(plot_data) > 2:
title = plt
spcs = []
spcs = plot_data['specimen'].unique()
for spc in spcs:
INTblock = []
spec_data = plot_data[plot_data['specimen'] == spc]
for ind, rec in spec_data.iterrows():
INTblock.append([
float(rec[dmag_key]), 0, 0,
float(rec[int_key]), 1, rec['quality']
])
if len(INTblock) > 2:
pmagplotlib.plotMT(FIG['demag'], INTblock, title, 0, units,
norm)
if not plot:
files = {}
for key in list(FIG.keys()):
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
#sys.exit()
else:
pmagplotlib.drawFIGS(FIG)
prompt = " S[a]ve to save plot, [q]uit, Return to continue: "
ans = input(prompt)
if ans == 'q':
sys.exit()
if ans == "a":
files = {}
for key in list(FIG.keys()):
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['demag'])
def main():
"""
NAME
irmaq_magic.py
DESCRIPTION
plots IRM acquisition curves from measurements file
SYNTAX
irmaq_magic [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: magic_measurements.txt/measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is by location
-N ; do not normalize by last point - use original units
-fmt [png,jpg,eps,pdf] set plot file format [default is svg]
-sav save plot[s] and quit
-DM MagIC data model number, default is 3
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG = {} # plot dictionary
FIG['exp'] = 1 # exp is figure 1
dir_path = './'
plot, fmt = 0, 'svg'
units = 'T',
XLP = []
norm = 1
LP = "LP-IRM"
if len(sys.argv) > 1:
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
data_model = int(pmag.get_named_arg("-DM", 3))
if '-N' in sys.argv:
norm = 0
if '-sav' in sys.argv:
plot = 1
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if data_model == 3:
in_file = pmag.get_named_arg("-f", 'measurements.txt')
else:
in_file = pmag.get_named_arg("-f", 'magic_measurements.txt')
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
dir_path = os.path.realpath(dir_path)
in_file = pmag.resolve_file_name(in_file, dir_path)
if '-WD' not in sys.argv:
dir_path = os.path.split(in_file)[0]
plot_by = pmag.get_named_arg("-obj", "loc")
if data_model == 3:
plot_key = 'location'
if plot_by == 'sit':
plot_key = 'site'
if plot_by == 'sam':
plot_key = 'sample'
if plot_by == 'spc':
plot_key = 'specimen'
else:
plot_key = 'er_location_name'
if plot_by == 'sit':
plot_key = 'er_site_name'
if plot_by == 'sam':
plot_key = 'er_sample_name'
if plot_by == 'spc':
plot_key = 'er_specimen_name'
# set defaults and get more information if needed
if data_model == 3:
dmag_key = 'treat_dc_field'
else:
dmag_key = 'treatment_dc_field'
#
if data_model == 3 and plot_key != 'specimen':
# gonna need to read in more files
print('-W- You are trying to plot measurements by {}'.format(plot_key))
print(
' By default, this information is not available in your measurement file.'
)
print(
' Trying to acquire this information from {}'.format(dir_path))
con = cb.Contribution(dir_path)
meas_df = con.propagate_location_to_measurements()
if meas_df is None:
print('-W- No data found in {}'.format(dir_path))
return
if plot_key not in meas_df.columns:
print('-W- Could not find required data.')
print(' Try a different plot key.')
return
else:
print('-I- Found {} information, continuing with plotting'.format(
plot_key))
# need to take the data directly from the contribution here, to keep
# location/site/sample columns in the measurements table
data = con.tables['measurements'].convert_to_pmag_data_list()
file_type = "measurements"
else:
data, file_type = pmag.magic_read(in_file)
# read in data
sids = pmag.get_specs(data)
pmagplotlib.plot_init(FIG['exp'], 6, 6)
#
#
# find desired intensity data
#
# get plotlist
#
plotlist = []
if data_model == 3:
intlist = ['magn_moment', 'magn_volume', 'magn_mass', 'magnitude']
else:
intlist = [
'measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measurement_magn_mass'
]
IntMeths = []
# get all the records with this lab protocol
#print('data', len(data))
#print('data[0]', data[0])
if data_model == 3:
data = pmag.get_dictitem(data, 'method_codes', LP, 'has')
else:
data = pmag.get_dictitem(data, 'magic_method_codes', LP, 'has')
Ints = {}
NoInts, int_key = 1, ""
for key in intlist:
# get all non-blank data for intensity type
Ints[key] = pmag.get_dictitem(data, key, '', 'F')
if len(Ints[key]) > 0:
NoInts = 0
if int_key == "":
int_key = key
if NoInts == 1:
print('No intensity information found')
sys.exit()
for rec in Ints[int_key]:
if rec[plot_key] not in plotlist:
plotlist.append(rec[plot_key])
plotlist.sort()
for plt in plotlist:
print(plt)
INTblock = []
# get data with right intensity info whose plot_key matches plot
data = pmag.get_dictitem(Ints[int_key], plot_key, plt, 'T')
# get a list of specimens with appropriate data
sids = pmag.get_specs(data)
if len(sids) > 0:
title = data[0][plot_key]
for s in sids:
INTblock = []
# get data for each specimen
if data_model == 3:
sdata = pmag.get_dictitem(data, 'specimen', s, 'T')
else:
sdata = pmag.get_dictitem(data, 'er_specimen_name', s, 'T')
for rec in sdata:
INTblock.append(
[float(rec[dmag_key]), 0, 0,
float(rec[int_key]), 1, 'g'])
pmagplotlib.plot_mag(FIG['exp'], INTblock, title, 0, units, norm)
files = {}
for key in list(FIG.keys()):
files[key] = title + '_' + LP + '.' + fmt
if plot == 0:
pmagplotlib.draw_figs(FIG)
ans = input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans == 'q':
sys.exit()
if ans == "a":
pmagplotlib.save_plots(FIG, files)
if plt != plotlist[
-1]: # if it isn't the last plot, init the next one
pmagplotlib.plot_init(FIG['exp'], 6, 6)
else:
pmagplotlib.save_plots(FIG, files)
pmagplotlib.clearFIG(FIG['exp'])
def main():
"""
NAME
hysteresis_magic.py
DESCRIPTION
calculates hystereis parameters and saves them in rmag_hystereis format file
makes plots if option selected
SYNTAX
hysteresis_magic.py [command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f: specify input file, default is agm_measurements.txt
-fh: specify rmag_hysteresis.txt input file
-F: specify output file, default is rmag_hysteresis.txt
-P: do not make the plots
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args=sys.argv
PLT=1
plots=0
user,meas_file,rmag_out,rmag_file="","agm_measurements.txt","rmag_hysteresis.txt",""
pltspec=""
dir_path='.'
fmt='svg'
verbose=pmagplotlib.verbose
version_num=pmag.get_version()
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-f' in args:
ind=args.index("-f")
meas_file=args[ind+1]
if '-F' in args:
ind=args.index("-F")
rmag_out=args[ind+1]
if '-fh' in args:
ind=args.index("-fh")
rmag_file=args[ind+1]
rmag_file=dir_path+'/'+rmag_file
if '-P' in args:
PLT=0
irm_init,imag_init=-1,-1
if '-sav' in args:
verbose=0
plots=1
if '-spc' in args:
ind=args.index("-spc")
pltspec= args[ind+1]
verbose=0
plots=1
if '-fmt' in args:
ind=args.index("-fmt")
fmt=args[ind+1]
rmag_out=dir_path+'/'+rmag_out
meas_file=dir_path+'/'+meas_file
rmag_rem=dir_path+"/rmag_remanence.txt"
#
#
meas_data,file_type=pmag.magic_read(meas_file)
if file_type!='magic_measurements':
print(main.__doc__)
print('bad file')
sys.exit()
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs,RemRecs=[],[]
HDD={}
if verbose:
if verbose and PLT:print("Plots may be on top of each other - use mouse to place ")
if PLT:
HDD['hyst'],HDD['deltaM'],HDD['DdeltaM']=1,2,3
pmagplotlib.plot_init(HDD['DdeltaM'],5,5)
pmagplotlib.plot_init(HDD['deltaM'],5,5)
pmagplotlib.plot_init(HDD['hyst'],5,5)
imag_init=0
irm_init=0
else:
HDD['hyst'],HDD['deltaM'],HDD['DdeltaM'],HDD['irm'],HDD['imag']=0,0,0,0,0
#
if rmag_file!="":hyst_data,file_type=pmag.magic_read(rmag_file)
#
# get list of unique experiment names and specimen names
#
experiment_names,sids=[],[]
for rec in meas_data:
meths=rec['magic_method_codes'].split(':')
methods=[]
for meth in meths:
methods.append(meth.strip())
if 'LP-HYS' in methods:
if 'er_synthetic_name' in list(rec.keys()) and rec['er_synthetic_name']!="":
rec['er_specimen_name']=rec['er_synthetic_name']
if rec['magic_experiment_name'] not in experiment_names:experiment_names.append(rec['magic_experiment_name'])
if rec['er_specimen_name'] not in sids:sids.append(rec['er_specimen_name'])
#
k=0
locname=''
if pltspec!="":
k=sids.index(pltspec)
print(sids[k])
while k < len(sids):
s=sids[k]
if verbose and PLT:print(s, k+1 , 'out of ',len(sids))
#
#
B,M,Bdcd,Mdcd=[],[],[],[] #B,M for hysteresis, Bdcd,Mdcd for irm-dcd data
Bimag,Mimag=[],[] #Bimag,Mimag for initial magnetization curves
first_dcd_rec,first_rec,first_imag_rec=1,1,1
for rec in meas_data:
methcodes=rec['magic_method_codes'].split(':')
meths=[]
for meth in methcodes:
meths.append(meth.strip())
if rec['er_specimen_name']==s and "LP-HYS" in meths:
B.append(float(rec['measurement_lab_field_dc']))
M.append(float(rec['measurement_magn_moment']))
if first_rec==1:
e=rec['magic_experiment_name']
HystRec={}
first_rec=0
if "er_location_name" in list(rec.keys()):
HystRec["er_location_name"]=rec["er_location_name"]
locname=rec['er_location_name'].replace('/','-')
if "er_sample_name" in list(rec.keys()):HystRec["er_sample_name"]=rec["er_sample_name"]
if "er_site_name" in list(rec.keys()):HystRec["er_site_name"]=rec["er_site_name"]
if "er_synthetic_name" in list(rec.keys()) and rec['er_synthetic_name']!="":
HystRec["er_synthetic_name"]=rec["er_synthetic_name"]
else:
HystRec["er_specimen_name"]=rec["er_specimen_name"]
if rec['er_specimen_name']==s and "LP-IRM-DCD" in meths:
Bdcd.append(float(rec['treatment_dc_field']))
Mdcd.append(float(rec['measurement_magn_moment']))
if first_dcd_rec==1:
RemRec={}
irm_exp=rec['magic_experiment_name']
first_dcd_rec=0
if "er_location_name" in list(rec.keys()):RemRec["er_location_name"]=rec["er_location_name"]
if "er_sample_name" in list(rec.keys()):RemRec["er_sample_name"]=rec["er_sample_name"]
if "er_site_name" in list(rec.keys()):RemRec["er_site_name"]=rec["er_site_name"]
if "er_synthetic_name" in list(rec.keys()) and rec['er_synthetic_name']!="":
RemRec["er_synthetic_name"]=rec["er_synthetic_name"]
else:
RemRec["er_specimen_name"]=rec["er_specimen_name"]
if rec['er_specimen_name']==s and "LP-IMAG" in meths:
if first_imag_rec==1:
imag_exp=rec['magic_experiment_name']
first_imag_rec=0
Bimag.append(float(rec['measurement_lab_field_dc']))
Mimag.append(float(rec['measurement_magn_moment']))
#
# now plot the hysteresis curve
#
if len(B)>0:
hmeths=[]
for meth in meths: hmeths.append(meth)
hpars=pmagplotlib.plotHDD(HDD,B,M,e)
if verbose and PLT:pmagplotlib.drawFIGS(HDD)
#
# get prior interpretations from hyst_data
if rmag_file!="":
hpars_prior={}
for rec in hyst_data:
if rec['magic_experiment_names']==e:
if rec['hysteresis_bcr'] !="" and rec['hysteresis_mr_moment']!="":
hpars_prior['hysteresis_mr_moment']=rec['hysteresis_mr_moment']
hpars_prior['hysteresis_ms_moment']=rec['hysteresis_ms_moment']
hpars_prior['hysteresis_bc']=rec['hysteresis_bc']
hpars_prior['hysteresis_bcr']=rec['hysteresis_bcr']
break
if verbose:pmagplotlib.plotHPARS(HDD,hpars_prior,'ro')
else:
if verbose:pmagplotlib.plotHPARS(HDD,hpars,'bs')
HystRec['hysteresis_mr_moment']=hpars['hysteresis_mr_moment']
HystRec['hysteresis_ms_moment']=hpars['hysteresis_ms_moment']
HystRec['hysteresis_bc']=hpars['hysteresis_bc']
HystRec['hysteresis_bcr']=hpars['hysteresis_bcr']
HystRec['hysteresis_xhf']=hpars['hysteresis_xhf']
HystRec['magic_experiment_names']=e
HystRec['magic_software_packages']=version_num
if hpars["magic_method_codes"] not in hmeths:hmeths.append(hpars["magic_method_codes"])
methods=""
for meth in hmeths:
methods=methods+meth.strip()+":"
HystRec["magic_method_codes"]=methods[:-1]
HystRec["er_citation_names"]="This study"
HystRecs.append(HystRec)
#
if len(Bdcd)>0:
rmeths=[]
for meth in meths: rmeths.append(meth)
if verbose and PLT:print('plotting IRM')
if irm_init==0:
HDD['irm']=5
pmagplotlib.plot_init(HDD['irm'],5,5)
irm_init=1
rpars=pmagplotlib.plotIRM(HDD['irm'],Bdcd,Mdcd,irm_exp)
RemRec['remanence_mr_moment']=rpars['remanence_mr_moment']
RemRec['remanence_bcr']=rpars['remanence_bcr']
RemRec['magic_experiment_names']=irm_exp
if rpars["magic_method_codes"] not in meths:meths.append(rpars["magic_method_codes"])
methods=""
for meth in rmeths:
methods=methods+meth.strip()+":"
RemRec["magic_method_codes"]=methods[:-1]
RemRec["er_citation_names"]="This study"
RemRecs.append(RemRec)
else:
if irm_init:pmagplotlib.clearFIG(HDD['irm'])
if len(Bimag)>0:
if verbose:print('plotting initial magnetization curve')
# first normalize by Ms
Mnorm=[]
for m in Mimag: Mnorm.append(old_div(m,float(hpars['hysteresis_ms_moment'])))
if imag_init==0:
HDD['imag']=4
pmagplotlib.plot_init(HDD['imag'],5,5)
imag_init=1
pmagplotlib.plotIMAG(HDD['imag'],Bimag,Mnorm,imag_exp)
else:
if imag_init:pmagplotlib.clearFIG(HDD['imag'])
#
files={}
if plots:
if pltspec!="":s=pltspec
files={}
for key in list(HDD.keys()):
files[key]=locname+'_'+s+'_'+key+'.'+fmt
pmagplotlib.saveP(HDD,files)
if pltspec!="":sys.exit()
if verbose and PLT:
pmagplotlib.drawFIGS(HDD)
ans=input("S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n ")
if ans=="a":
files={}
for key in list(HDD.keys()):
files[key]=locname+'_'+s+'_'+key+'.'+fmt
pmagplotlib.saveP(HDD,files)
if ans=='':k+=1
if ans=="p":
del HystRecs[-1]
k-=1
if ans=='q':
print("Good bye")
sys.exit()
if ans=='s':
keepon=1
specimen=input('Enter desired specimen name (or first part there of): ')
while keepon==1:
try:
k =sids.index(specimen)
keepon=0
except:
tmplist=[]
for qq in range(len(sids)):
if specimen in sids[qq]:tmplist.append(sids[qq])
print(specimen," not found, but this was: ")
print(tmplist)
specimen=input('Select one or try again\n ')
k =sids.index(specimen)
else:
k+=1
if len(B)==0 and len(Bdcd)==0:
if verbose:print('skipping this one - no hysteresis data')
k+=1
if rmag_out=="" and ans=='s' and verbose:
really=input(" Do you want to overwrite the existing rmag_hystersis.txt file? 1/[0] ")
if really=="":
print('i thought not - goodbye')
sys.exit()
rmag_out="rmag_hysteresis.txt"
if len(HystRecs)>0:
pmag.magic_write(rmag_out,HystRecs,"rmag_hysteresis")
if verbose:print("hysteresis parameters saved in ",rmag_out)
if len(RemRecs)>0:
pmag.magic_write(rmag_rem,RemRecs,"rmag_remanence")
if verbose:print("remanence parameters saved in ",rmag_rem)
def main():
"""
NAME
irmaq_magic.py
DESCRIPTION
plots IRM acquisition curves from measurements file
SYNTAX
irmaq_magic [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: magic_measurements.txt/measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is by location
-N ; do not normalize by last point - use original units
-fmt [png,jpg,eps,pdf] set plot file format [default is svg]
-sav save plot[s] and quit
-DM MagIC data model number, default is 3
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG = {} # plot dictionary
FIG['exp'] = 1 # exp is figure 1
dir_path = './'
plot, fmt = 0, 'svg'
units = 'T',
XLP = []
norm = 1
LP = "LP-IRM"
if len(sys.argv) > 1:
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
data_model = int(pmag.get_named_arg("-DM", 3))
if '-N' in sys.argv:
norm = 0
if '-sav' in sys.argv:
plot = 1
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if data_model == 3:
in_file = pmag.get_named_arg("-f", 'measurements.txt')
else:
in_file = pmag.get_named_arg("-f", 'magic_measurements.txt')
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
dir_path = os.path.realpath(dir_path)
in_file = pmag.resolve_file_name(in_file, dir_path)
if '-WD' not in sys.argv:
dir_path = os.path.split(in_file)[0]
plot_by = pmag.get_named_arg("-obj", "loc")
if data_model == 3:
plot_key = 'location'
if plot_by == 'sit':
plot_key = 'site'
if plot_by == 'sam':
plot_key = 'sample'
if plot_by == 'spc':
plot_key = 'specimen'
else:
plot_key = 'er_location_name'
if plot_by == 'sit':
plot_key = 'er_site_name'
if plot_by == 'sam':
plot_key = 'er_sample_name'
if plot_by == 'spc':
plot_key = 'er_specimen_name'
# set defaults and get more information if needed
if data_model == 3:
dmag_key = 'treat_dc_field'
else:
dmag_key = 'treatment_dc_field'
#
if data_model == 3 and plot_key != 'specimen':
# gonna need to read in more files
print('-W- You are trying to plot measurements by {}'.format(plot_key))
print(' By default, this information is not available in your measurement file.')
print(' Trying to acquire this information from {}'.format(dir_path))
con = cb.Contribution(dir_path)
meas_df = con.propagate_location_to_measurements()
if meas_df is None:
print('-W- No data found in {}'.format(dir_path))
return
if plot_key not in meas_df.columns:
print('-W- Could not find required data.')
print(' Try a different plot key.')
return
else:
print('-I- Found {} information, continuing with plotting'.format(plot_key))
# need to take the data directly from the contribution here, to keep
# location/site/sample columns in the measurements table
data = con.tables['measurements'].convert_to_pmag_data_list()
file_type = "measurements"
else:
data, file_type = pmag.magic_read(in_file)
# read in data
sids = pmag.get_specs(data)
pmagplotlib.plot_init(FIG['exp'], 6, 6)
#
#
# find desired intensity data
#
# get plotlist
#
plotlist = []
if data_model == 3:
intlist = ['magn_moment', 'magn_volume', 'magn_mass', 'magnitude']
else:
intlist = ['measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measurement_magn_mass']
IntMeths = []
# get all the records with this lab protocol
#print('data', len(data))
#print('data[0]', data[0])
if data_model == 3:
data = pmag.get_dictitem(data, 'method_codes', LP, 'has')
else:
data = pmag.get_dictitem(data, 'magic_method_codes', LP, 'has')
Ints = {}
NoInts, int_key = 1, ""
for key in intlist:
# get all non-blank data for intensity type
Ints[key] = pmag.get_dictitem(data, key, '', 'F')
if len(Ints[key]) > 0:
NoInts = 0
if int_key == "":
int_key = key
if NoInts == 1:
print('No intensity information found')
sys.exit()
for rec in Ints[int_key]:
if rec[plot_key] not in plotlist:
plotlist.append(rec[plot_key])
plotlist.sort()
for plt in plotlist:
print(plt)
INTblock = []
# get data with right intensity info whose plot_key matches plot
data = pmag.get_dictitem(Ints[int_key], plot_key, plt, 'T')
# get a list of specimens with appropriate data
sids = pmag.get_specs(data)
if len(sids) > 0:
title = data[0][plot_key]
for s in sids:
INTblock = []
# get data for each specimen
if data_model == 3:
sdata = pmag.get_dictitem(data, 'specimen', s, 'T')
else:
sdata = pmag.get_dictitem(data, 'er_specimen_name', s, 'T')
for rec in sdata:
INTblock.append([float(rec[dmag_key]), 0, 0,
float(rec[int_key]), 1, 'g'])
pmagplotlib.plot_mag(FIG['exp'], INTblock, title, 0, units, norm)
files = {}
for key in list(FIG.keys()):
files[key] = title + '_' + LP + '.' + fmt
if plot == 0:
pmagplotlib.draw_figs(FIG)
ans = input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans == 'q':
sys.exit()
if ans == "a":
pmagplotlib.save_plots(FIG, files)
if plt != plotlist[-1]: # if it isn't the last plot, init the next one
pmagplotlib.plot_init(FIG['exp'], 6, 6)
else:
pmagplotlib.save_plots(FIG, files)
pmagplotlib.clearFIG(FIG['exp'])
def plot(in_file="measurements.txt", dir_path=".", input_dir_path="",
spec_file="specimens.txt", samp_file="samples.txt",
site_file="sites.txt", loc_file="locations.txt",
plot_by="loc", LT="AF", norm=True, XLP="",
save_plots=True, fmt="svg"):
"""
plots intensity decay curves for demagnetization experiments
Parameters
----------
in_file : str, default "measurements.txt"
dir_path : str
output directory, default "."
input_dir_path : str
input file directory (if different from dir_path), default ""
spec_file : str
input specimen file name, default "specimens.txt"
samp_file: str
input sample file name, default "samples.txt"
site_file : str
input site file name, default "sites.txt"
loc_file : str
input location file name, default "locations.txt"
plot_by : str
[spc, sam, sit, loc] (specimen, sample, site, location), default "loc"
LT : str
lab treatment [T, AF, M], default AF
norm : bool
normalize by NRM magnetization, default True
XLP : str
exclude specific lab protocols, (for example, method codes like LP-PI)
default ""
save_plots : bool
plot and save non-interactively, default True
fmt : str
["png", "svg", "pdf", "jpg"], default "svg"
Returns
---------
type - Tuple : (True or False indicating if conversion was sucessful, file name(s) written)
"""
dir_path = os.path.realpath(dir_path)
if not input_dir_path:
input_dir_path = dir_path
input_dir_path = os.path.realpath(input_dir_path)
# format plot_key
name_dict = {'loc': 'location', 'sit': 'site',
'sam': 'sample', 'spc': 'specimen'}
if plot_by not in name_dict.values():
try:
plot_key = name_dict[plot_by]
except KeyError:
print('Unrecognized plot_by {}, falling back to plot by location'.format(plot_by))
plot_key = "loc"
else:
plot_key = plot_by
# figure out what kind of experiment
LT = "LT-" + LT + "-Z"
print('LT', LT)
if LT == "LT-T-Z":
units, dmag_key = 'K', 'treat_temp'
elif LT == "LT-AF-Z":
units, dmag_key = 'T', 'treat_ac_field'
elif LT == 'LT-M-Z':
units, dmag_key = 'J', 'treat_mw_energy'
else:
units = 'U'
# init
FIG = {} # plot dictionary
FIG['demag'] = 1 # demag is figure 1
# create contribution and add required headers
fnames = {"specimens": spec_file, "samples": samp_file,
'sites': site_file, 'locations': loc_file}
if not os.path.exists(pmag.resolve_file_name(in_file, input_dir_path)):
print('-E- Could not find {}'.format(in_file))
return False, []
contribution = cb.Contribution(input_dir_path, single_file=in_file,
custom_filenames=fnames)
file_type = list(contribution.tables.keys())[0]
print(len(contribution.tables['measurements'].df), ' records read from ', in_file)
# add plot_key into measurements table
if plot_key not in contribution.tables['measurements'].df.columns:
#contribution.propagate_name_down(plot_key, 'measurements')
contribution.propagate_location_to_measurements()
data_container = contribution.tables[file_type]
# pare down to only records with useful data
# grab records that have the requested code
data_slice = data_container.get_records_for_code(LT)
# and don't have the offending code
data = data_container.get_records_for_code(XLP, incl=False, use_slice=True,
sli=data_slice, strict_match=False)
# make sure quality is in the dataframe
if 'quality' not in data.columns:
data['quality'] = 'g'
# get intensity key and make sure intensity data is not blank
intlist = ['magn_moment', 'magn_volume', 'magn_mass']
IntMeths = [col_name for col_name in data.columns if col_name in intlist]
# get rid of any entirely blank intensity columns
for col_name in IntMeths:
if not data[col_name].any():
data.drop(col_name, axis=1, inplace=True)
IntMeths = [col_name for col_name in data.columns if col_name in intlist]
if len(IntMeths) == 0:
print('-E- No intensity headers found')
return False, []
int_key = IntMeths[0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
data = data[data[int_key].notnull()]
# make list of individual plots
# by default, will be by location_name
plotlist = data[plot_key].unique()
plotlist.sort()
pmagplotlib.plot_init(FIG['demag'], 5, 5)
last_plot = False
# iterate through and plot the data
for plt in plotlist:
if plt == plotlist[-1]:
last_plot = True
plot_data = data[data[plot_key] == plt].copy()
if not save_plots:
print(plt, 'plotting by: ', plot_key)
if len(plot_data) > 2:
title = plt
spcs = []
spcs = plot_data['specimen'].unique()
for spc in spcs:
INTblock = []
spec_data = plot_data[plot_data['specimen'] == spc]
for ind, rec in spec_data.iterrows():
INTblock.append([float(rec[dmag_key]), 0, 0, float(rec[int_key]), 1, rec['quality']])
if len(INTblock) > 2:
pmagplotlib.plot_mag(FIG['demag'], INTblock,
title, 0, units, norm)
if save_plots:
files = {}
for key in list(FIG.keys()):
if pmagplotlib.isServer:
files[key] = title + '_' + LT + '.' + fmt
incl_dir = False
else: # if not server, include directory in output path
files[key] = os.path.join(dir_path, title + '_' + LT + '.' + fmt)
incl_dir = True
pmagplotlib.save_plots(FIG, files, incl_directory=incl_dir)
else:
pmagplotlib.draw_figs(FIG)
prompt = " S[a]ve to save plot, [q]uit, Return to continue: "
ans = input(prompt)
if ans == 'q':
return True, []
if ans == "a":
files = {}
for key in list(FIG.keys()):
if pmagplotlib.isServer:
files[key] = title + '_' + LT + '.' + fmt
incl_dir = False
else: # if not server, include directory in output path
files[key] = os.path.join(dir_path, title + '_' + LT + '.' + fmt)
incl_dir = True
pmagplotlib.save_plots(FIG, files, incl_directory=incl_dir)
pmagplotlib.clearFIG(FIG['demag'])
if last_plot:
return True, []
def main():
"""
NAME
biplot_magic.py
DESCRIPTION
makes a biplot of specified variables from magic_measurements.txt format file
SYNTAX
biplot_magic.py [-h] [-i] [command line options]
INPUT
takes magic formated magic_measurments file
OPTIONS
-h prints help message and quits
-i interactively set filename and axes for plotting
-f FILE: specifies file name, default: magic_measurements.txt
-fmt [svg,png,jpg], format for images - default is svg
-sav figure and quit
-x XMETH:key:step, specify method code for X axis (optional key and treatment values)
-y YMETH:key:step, specify method code for X axis
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is whole file
-n [V,M] plot volume or mass normalized data only
NOTES
if nothing is specified for x and y, the user will be presented with options
key = ['treatment_ac_field','treatment_dc_field',treatment_temp']
step in mT for fields, K for temperatures
"""
#
file = 'magic_measurements.txt'
methx, methy, fmt = "", "", '.svg'
plot_key = ''
norm_by = ""
#plot=0
no_plot = pmag.get_flag_arg_from_sys('-sav')
if not no_plot:
do_plot = True
else:
do_plot = False
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = '.' + sys.argv[ind + 1]
if '-n' in sys.argv:
ind = sys.argv.index('-n')
norm_by = sys.argv[ind + 1]
xtreat_key, ytreat_key, xstep, ystep = "", "", "", ""
if '-x' in sys.argv:
ind = sys.argv.index('-x')
meths = sys.argv[ind + 1].split(':')
methx = meths[0]
if len(meths) > 1:
xtreat_key = meths[1]
xstep = float(meths[2])
if '-y' in sys.argv:
ind = sys.argv.index('-y')
meths = sys.argv[ind + 1].split(':')
methy = meths[0]
if len(meths) > 1:
ytreat_key = meths[1]
ystep = float(meths[2])
if '-obj' in sys.argv:
ind = sys.argv.index('-obj')
plot_by = sys.argv[ind + 1]
if plot_by == 'loc': plot_key = 'er_location_name'
if plot_by == 'sit': plot_key = 'er_site_name'
if plot_by == 'sam': plot_key = 'er_sample_name'
if plot_by == 'spc': plot_key = 'er_specimen_name'
if '-h' in sys.argv:
do_plot = False
if '-i' in sys.argv:
#
# get name of file from command line
#
file = input(
"Input magic_measurments file name? [magic_measurements.txt] ")
if file == "": file = "magic_measurements.txt"
#
#
FIG = {'fig': 1}
pmagplotlib.plot_init(FIG['fig'], 5, 5)
data, file_type = pmag.magic_read(file)
if file_type != "magic_measurements":
print(file_type, ' not correct format for magic_measurments file')
sys.exit()
#
# collect method codes
methods, plotlist = [], []
for rec in data:
if plot_key != "":
if rec[plot_key] not in plotlist: plotlist.append(rec[plot_key])
elif len(plotlist) == 0:
plotlist.append('All')
meths = rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip() not in methods and meth.strip() != "LP-":
methods.append(meth.strip())
#
if '-i' in sys.argv:
print(methods)
elif methx == "" or methy == "":
print(methods)
sys.exit()
GoOn = 1
while GoOn == 1:
if '-i' in sys.argv: methx = input('Select method for x axis: ')
if methx not in methods:
if '-i' in sys.argv:
print('try again! method not available')
else:
print(main.__doc__)
print('\n must specify X axis method\n')
sys.exit()
else:
if pmagplotlib.verbose: print(methx, ' selected for X axis')
GoOn = 0
GoOn = 1
while GoOn == 1:
if '-i' in sys.argv: methy = input('Select method for y axis: ')
if methy not in methods:
if '-i' in sys.argv:
print('try again! method not available')
else:
print(main.__doc__)
print('\n must specify Y axis method\n')
sys.exit()
else:
if pmagplotlib.verbose: print(methy, ' selected for Y axis')
GoOn = 0
if norm_by == "":
measkeys = [
'measurement_magn_mass', 'measurement_magn_volume',
'measurement_magn_moment', 'measurement_magnitude',
'measurement_chi_volume', 'measurement_chi_mass', 'measurement_chi'
]
elif norm_by == "V":
measkeys = ['measurement_magn_volume', 'measurement_chi_volume']
elif norm_by == "M":
measkeys = ['measurement_magn_mass', 'measurement_chi_mass']
xmeaskey, ymeaskey = "", ""
plotlist.sort()
for plot in plotlist: # go through objects
if pmagplotlib.verbose:
print(plot)
X, Y = [], []
x, y = '', ''
for rec in data:
if plot_key != "" and rec[plot_key] != plot:
pass
else:
meths = rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip() == methx:
if xmeaskey == "":
for key in measkeys:
if key in list(rec.keys()) and rec[key] != "":
xmeaskey = key
if pmagplotlib.verbose:
print(xmeaskey,
' being used for plotting X.')
break
if meth.strip() == methy:
if ymeaskey == "":
for key in measkeys:
if key in list(rec.keys()) and rec[key] != "":
ymeaskey = key
if pmagplotlib.verbose:
print(ymeaskey,
' being used for plotting Y')
break
if ymeaskey != "" and xmeaskey != "":
for rec in data:
x, y = '', ''
spec = rec[
'er_specimen_name'] # get the ydata for this specimen
if rec[ymeaskey] != "" and methy in rec[
'magic_method_codes'].split(':'):
if ytreat_key == "" or (ytreat_key in list(rec.keys()) and
float(rec[ytreat_key]) == ystep):
y = float(rec[ymeaskey])
for rec in data: # now find the xdata
if rec['er_specimen_name'] == spec and rec[
xmeaskey] != "" and methx in rec[
'magic_method_codes'].split(':'):
if xtreat_key == "" or (
xtreat_key in list(rec.keys())
and float(rec[xtreat_key]) == xstep):
x = float(rec[xmeaskey])
if x != '' and y != '':
X.append(x)
Y.append(y)
if len(X) > 0:
pmagplotlib.clearFIG(FIG['fig'])
pmagplotlib.plotXY(FIG['fig'],
X,
Y,
sym='ro',
xlab=methx,
ylab=methy,
title=plot + ':Biplot')
if not pmagplotlib.isServer and do_plot:
pmagplotlib.drawFIGS(FIG)
ans = input('S[a]ve plots, [q]uit, Return for next plot ')
if ans == 'a':
files = {}
for key in list(FIG.keys()):
files[key] = plot + '_' + key + fmt
pmagplotlib.saveP(FIG, files)
if ans == 'q':
print("Good-bye\n")
sys.exit()
else:
files = {}
for key in list(FIG.keys()):
files[key] = plot + '_' + key + fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['fig'] = 'X Y Plot'
FIG = pmagplotlib.addBorders(FIG, titles, black, purple)
pmagplotlib.saveP(FIG, files)
else:
print('nothing to plot for ', plot)
def main():
"""
NAME
lowrie.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie -h [command line options]
INPUT
takes SIO formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav save plots and quit
"""
fmt, plot = 'svg', 0
FIG = {} # plot dictionary
FIG['lowrie'] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'], 6, 6)
norm = 1 # default is to normalize by maximum axis
if len(sys.argv) > 1:
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-N' in sys.argv:
norm = 0 # don't normalize
if '-sav' in sys.argv:
plot = 1 # don't normalize
if '-fmt' in sys.argv: # sets input filename
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-f' in sys.argv: # sets input filename
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
data = pmag.open_file(in_file)
PmagRecs = [] # set up a list for the results
keys = ['specimen', 'treatment', 'csd', 'M', 'dec', 'inc']
for line in data:
PmagRec = {}
rec = line.replace('\n', '').split()
for k in range(len(keys)):
PmagRec[keys[k]] = rec[k]
PmagRecs.append(PmagRec)
specs = pmag.get_dictkey(PmagRecs, 'specimen', '')
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print(spc)
specdata = pmag.get_dictitem(PmagRecs, 'specimen', spc,
'T') # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append(
[float(dat['dec']),
float(dat['inc']),
float(dat['M']) * 1e-3])
Temps.append(float(dat['treatment']))
carts = pmag.dir2cart(DIMs).transpose()
# if norm==1: # want to normalize
# nrm=max(max(abs(carts[0])),max(abs(carts[1])),max(abs(carts[2]))) # by maximum of x,y,z values
# ylab="M/M_max"
if norm == 1: # want to normalize
nrm = (DIMs[0][2]) # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1. # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[0]), nrm),
sym='r-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[0]), nrm),
sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[1]), nrm),
sym='c-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[1]), nrm),
sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[2]), nrm),
sym='k-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[2]), nrm),
sym='k^',
title=spc,
xlab=xlab,
ylab=ylab) # Z direction
files = {'lowrie': 'lowrie:_' + spc + '_.' + fmt}
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = input('S[a]ve figure? [q]uit, <return> to continue ')
if ans == 'a':
pmagplotlib.saveP(FIG, files)
elif ans == 'q':
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
lowrie_magic.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie_magic.py -h [command line options]
INPUT
takes magic_measurements formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is magic_measurements.txt
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav saves plots and quits
"""
fmt,plot='svg',0
FIG={} # plot dictionary
FIG['lowrie']=1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'],6,6)
norm=1 # default is to normalize by maximum axis
in_file,dir_path='magic_measurements.txt','.'
if len(sys.argv)>1:
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv: norm=0 # don't normalize
if '-sav' in sys.argv: plot=1 # don't normalize
if '-fmt' in sys.argv: # sets input filename
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-f' in sys.argv: # sets input filename
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
else:
print main.__doc__
print 'you must supply a file name'
sys.exit()
in_file=dir_path+'/'+in_file
print in_file
PmagRecs,file_type=pmag.magic_read(in_file)
if file_type!="magic_measurements":
print 'bad input file'
sys.exit()
PmagRecs=pmag.get_dictitem(PmagRecs,'magic_method_codes','LP-IRM-3D','has') # get all 3D IRM records
if len(PmagRecs)==0:
print 'no records found'
sys.exit()
specs=pmag.get_dictkey(PmagRecs,'er_specimen_name','')
sids=[]
for spec in specs:
if spec not in sids:sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print spc
specdata=pmag.get_dictitem(PmagRecs,'er_specimen_name',spc,'T') # get all this one's data
DIMs,Temps=[],[]
for dat in specdata: # step through the data
DIMs.append([float(dat['measurement_dec']),float(dat['measurement_inc']),float(dat['measurement_magn_moment'])])
Temps.append(float(dat['treatment_temp'])-273.)
carts=pmag.dir2cart(DIMs).transpose()
if norm==1: # want to normalize
nrm=(DIMs[0][2]) # normalize by NRM
ylab="M/M_o"
else:
nrm=1. # don't normalize
ylab="Magnetic moment (Am^2)"
xlab="Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[0])/nrm,sym='r-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[0])/nrm,sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[1])/nrm,sym='c-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[1])/nrm,sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[2])/nrm,sym='k-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[2])/nrm,sym='k^',title=spc,xlab=xlab,ylab=ylab) # Z direction
files={'lowrie':'lowrie:_'+spc+'_.'+fmt}
if plot==0:
pmagplotlib.drawFIGS(FIG)
ans=raw_input('S[a]ve figure? [q]uit, <return> to continue ')
if ans=='a':
pmagplotlib.saveP(FIG,files)
elif ans=='q':
sys.exit()
else:
pmagplotlib.saveP(FIG,files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
lowrie.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie -h [command line options]
INPUT
takes SIO formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav save plots and quit
"""
fmt, plot = "svg", 0
FIG = {} # plot dictionary
FIG["lowrie"] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG["lowrie"], 6, 6)
norm = 1 # default is to normalize by maximum axis
if len(sys.argv) > 1:
if "-h" in sys.argv:
print main.__doc__
sys.exit()
if "-N" in sys.argv:
norm = 0 # don't normalize
if "-sav" in sys.argv:
plot = 1 # don't normalize
if "-fmt" in sys.argv: # sets input filename
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if "-f" in sys.argv: # sets input filename
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
else:
print main.__doc__
print "you must supply a file name"
sys.exit()
else:
print main.__doc__
print "you must supply a file name"
sys.exit()
data = open(in_file).readlines() # open the SIO format file
PmagRecs = [] # set up a list for the results
keys = ["specimen", "treatment", "csd", "M", "dec", "inc"]
for line in data:
PmagRec = {}
rec = line.replace("\n", "").split()
for k in range(len(keys)):
PmagRec[keys[k]] = rec[k]
PmagRecs.append(PmagRec)
specs = pmag.get_dictkey(PmagRecs, "specimen", "")
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print spc
specdata = pmag.get_dictitem(PmagRecs, "specimen", spc, "T") # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append([float(dat["dec"]), float(dat["inc"]), float(dat["M"]) * 1e-3])
Temps.append(float(dat["treatment"]))
carts = pmag.dir2cart(DIMs).transpose()
# if norm==1: # want to normalize
# nrm=max(max(abs(carts[0])),max(abs(carts[1])),max(abs(carts[2]))) # by maximum of x,y,z values
# ylab="M/M_max"
if norm == 1: # want to normalize
nrm = DIMs[0][2] # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1.0 # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[0]) / nrm, sym="r-")
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[0]) / nrm, sym="ro") # X direction
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[1]) / nrm, sym="c-")
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[1]) / nrm, sym="cs") # Y direction
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[2]) / nrm, sym="k-")
pmagplotlib.plotXY(
FIG["lowrie"], Temps, abs(carts[2]) / nrm, sym="k^", title=spc, xlab=xlab, ylab=ylab
) # Z direction
files = {"lowrie": "lowrie:_" + spc + "_." + fmt}
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = raw_input("S[a]ve figure? [q]uit, <return> to continue ")
if ans == "a":
pmagplotlib.saveP(FIG, files)
elif ans == "q":
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG["lowrie"])
def main():
"""
NAME
irmaq_magic.py
DESCRIPTION
plots IRM acquisition curves from magic_measurements file
SYNTAX
irmaq_magic [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: magic_measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is by location
-N ; do not normalize by last point - use original units
-fmt [png,jpg,eps,pdf] set plot file format [default is svg]
-sav save plot[s] and quit
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG = {} # plot dictionary
FIG['exp'] = 1 # exp is figure 1
dir_path = './'
plot, fmt = 0, 'svg'
units, dmag_key = 'T', 'treatment_dc_field'
XLP = []
norm = 1
in_file, plot_key, LP = 'magic_measurements.txt', 'er_location_name', "LP-IRM"
if len(sys.argv) > 1:
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv: norm = 0
if '-sav' in sys.argv: plot = 1
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-f' in sys.argv:
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
in_file = dir_path + '/' + in_file
if '-obj' in sys.argv:
ind = sys.argv.index('-obj')
plot_by = sys.argv[ind + 1]
if plot_by == 'sit': plot_key = 'er_site_name'
if plot_by == 'sam': plot_key = 'er_sample_name'
if plot_by == 'spc': plot_key = 'er_specimen_name'
data, file_type = pmag.magic_read(in_file)
sids = pmag.get_specs(data)
pmagplotlib.plot_init(FIG['exp'], 6, 6)
#
#
# find desired intensity data
#
# get plotlist
#
plotlist, intlist = [], [
'measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measurement_magn_mass'
]
IntMeths = []
data = pmag.get_dictitem(
data, 'magic_method_codes', LP,
'has') # get all the records with this lab protocol
Ints = {}
NoInts, int_key = 1, ""
for key in intlist:
Ints[key] = pmag.get_dictitem(
data, key, '', 'F') # get all non-blank data for intensity type
if len(Ints[key]) > 0:
NoInts = 0
if int_key == "": int_key = key
if NoInts == 1:
print 'No intensity information found'
sys.exit()
for rec in Ints[int_key]:
if rec[plot_key] not in plotlist: plotlist.append(rec[plot_key])
plotlist.sort()
for plt in plotlist:
print plt
INTblock = []
data = pmag.get_dictitem(
Ints[int_key], plot_key, plt, 'T'
) # get data with right intensity info whose plot_key matches plot
sids = pmag.get_specs(
data) # get a list of specimens with appropriate data
if len(sids) > 0:
title = data[0][plot_key]
for s in sids:
INTblock = []
sdata = pmag.get_dictitem(data, 'er_specimen_name', s,
'T') # get data for each specimen
for rec in sdata:
INTblock.append(
[float(rec[dmag_key]), 0, 0,
float(rec[int_key]), 1, 'g'])
pmagplotlib.plotMT(FIG['exp'], INTblock, title, 0, units, norm)
files = {}
for key in FIG.keys():
files[key] = title + '_' + LP + '.' + fmt
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = raw_input(
" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans == 'q': sys.exit()
if ans == "a":
pmagplotlib.saveP(FIG, files)
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['exp'])
def main():
"""
NAME
quick_hyst.py
DESCRIPTION
makes plots of hysteresis data
SYNTAX
quick_hyst.py [command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f: specify input file, default is magic_measurements.txt
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
PLT = 1
plots = 0
user, meas_file = "", "magic_measurements.txt"
pltspec = ""
dir_path = '.'
fmt = 'png'
verbose = pmagplotlib.verbose
version_num = pmag.get_version()
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind+1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind+1]
if '-f' in args:
ind = args.index("-f")
meas_file = args[ind+1]
if '-sav' in args:
verbose = 0
plots = 1
if '-spc' in args:
ind = args.index("-spc")
pltspec = args[ind+1]
verbose = 0
plots = 1
if '-fmt' in args:
ind = args.index("-fmt")
fmt = args[ind+1]
meas_file = dir_path+'/'+meas_file
#
#
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print(main.__doc__)
print('bad file')
sys.exit()
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs, RemRecs = [], []
HDD = {}
HDD['hyst'] = 1
pmagplotlib.plot_init(HDD['hyst'], 5, 5)
#
# get list of unique experiment names and specimen names
#
experiment_names, sids = [], []
hyst_data = pmag.get_dictitem(
meas_data, 'magic_method_codes', 'LP-HYS', 'has') # get all hysteresis data
for rec in hyst_data:
if 'er_synthetic_name' in rec.keys() and rec['er_synthetic_name'] != "":
rec['er_specimen_name'] = rec['er_synthetic_name']
if rec['magic_experiment_name'] not in experiment_names:
experiment_names.append(rec['magic_experiment_name'])
if rec['er_specimen_name'] not in sids:
sids.append(rec['er_specimen_name'])
if 'measurement_temp' not in rec.keys():
# assume room T measurement unless otherwise specified
rec['measurement_temp'] = '300'
#
k = 0
if pltspec != "":
k = sids.index(pltspec)
intlist = ['measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measurement_magn_mass']
while k < len(sids):
locname, site, sample, synth = '', '', '', ''
s = sids[k]
hmeths = []
if verbose:
print(s, k+1, 'out of ', len(sids))
#
#
B, M = [], [] # B,M for hysteresis, Bdcd,Mdcd for irm-dcd data
# get all measurements for this specimen
spec = pmag.get_dictitem(hyst_data, 'er_specimen_name', s, 'T')
if 'er_location_name' in spec[0].keys():
locname = spec[0]['er_location_name']
if 'er_site_name' in spec[0].keys():
site = spec[0]['er_site_name']
if 'er_sample_name' in spec[0].keys():
sample = spec[0]['er_sample_name']
if 'er_synthetic_name' in spec[0].keys():
synth = spec[0]['er_synthetic_name']
for m in intlist:
# get all non-blank data for this specimen
meas_data = pmag.get_dictitem(spec, m, '', 'F')
if len(meas_data) > 0:
break
c = ['k-', 'b-', 'c-', 'g-', 'm-', 'r-', 'y-']
cnum = 0
if len(meas_data) > 0:
Temps = []
xlab, ylab, title = '', '', ''
for rec in meas_data:
if rec['measurement_temp'] not in Temps:
Temps.append(rec['measurement_temp'])
for t in Temps:
print('working on t: ', t)
t_data = pmag.get_dictitem(
meas_data, 'measurement_temp', t, 'T')
B, M = [], []
for rec in t_data:
B.append(float(rec['measurement_lab_field_dc']))
M.append(float(rec[m]))
# now plot the hysteresis curve(s)
#
if len(B) > 0:
B = numpy.array(B)
M = numpy.array(M)
if t == Temps[-1]:
xlab = 'Field (T)'
ylab = m
title = 'Hysteresis: '+s
if t == Temps[0]:
pmagplotlib.clearFIG(HDD['hyst'])
pmagplotlib.plot_xy(
HDD['hyst'], B, M, sym=c[cnum], xlab=xlab, ylab=ylab, title=title)
pmagplotlib.plot_xy(HDD['hyst'], [
1.1*B.min(), 1.1*B.max()], [0, 0], sym='k-', xlab=xlab, ylab=ylab, title=title)
pmagplotlib.plot_xy(HDD['hyst'], [0, 0], [
1.1*M.min(), 1.1*M.max()], sym='k-', xlab=xlab, ylab=ylab, title=title)
if verbose:
pmagplotlib.draw_figs(HDD)
cnum += 1
if cnum == len(c):
cnum = 0
#
files = {}
if plots:
if pltspec != "":
s = pltspec
files = {}
for key in HDD.keys():
if pmagplotlib.isServer: # use server plot naming convention
if synth == '':
filename = "LO:_"+locname+'_SI:_'+site + \
'_SA:_'+sample+'_SP:_'+s+'_TY:_'+key+'_.'+fmt
else:
filename = 'SY:_'+synth+'_TY:_'+key+'_.'+fmt
files[key] = filename
else: # use more readable plot naming convention
if synth == '':
filename = ''
for item in [locname, site, sample, s, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
else:
filename = synth+'_'+key+'.fmt'
files[key] = filename
pmagplotlib.save_plots(HDD, files)
if pltspec != "":
sys.exit()
if verbose:
pmagplotlib.draw_figs(HDD)
ans = raw_input(
"S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n ")
if ans == "a":
files = {}
for key in HDD.keys():
if pmagplotlib.isServer:
print('server')
files[key] = "LO:_"+locname+'_SI:_'+site + \
'_SA:_'+sample+'_SP:_'+s+'_TY:_'+key+'_.'+fmt
else:
print('not server')
filename = ''
for item in [locname, site, sample, s, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key] = filename
print('files', files)
pmagplotlib.save_plots(HDD, files)
if ans == '':
k += 1
if ans == "p":
del HystRecs[-1]
k -= 1
if ans == 'q':
print("Good bye")
sys.exit()
if ans == 's':
keepon = 1
specimen = raw_input(
'Enter desired specimen name (or first part there of): ')
while keepon == 1:
try:
k = sids.index(specimen)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if specimen in sids[qq]:
tmplist.append(sids[qq])
print(specimen, " not found, but this was: ")
print(tmplist)
specimen = raw_input('Select one or try again\n ')
k = sids.index(specimen)
else:
k += 1
if len(B) == 0:
if verbose:
print('skipping this one - no hysteresis data')
k += 1
def main():
"""
NAME
thellier_magic.py
DESCRIPTION
plots Thellier-Thellier data in version 3.0 format
Reads saved interpretations from a specimen formatted table, default: specimens.txt
SYNTAX
thellier_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEAS, set measurements input file, default is 'measurements.txt'
-fsp PRIOR, set specimens.txt prior interpretations file, default is 'specimens.txt'
-fcr CRIT, set criteria file for grading. # not yet implemented
-fmt [svg,png,jpg], format for images - default is svg
-sav, saves plots with out review (in format specified by -fmt key or default)
-spc SPEC, plots single specimen SPEC, saves plot with specified format
with optional -b bounds and quits
-b BEG END: sets bounds for calculation
BEG: starting step number for slope calculation
END: ending step number for slope calculation
-z use only z component difference for pTRM calculation
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 measuements)
list of possible commands: type letter followed by return to select option
saving of plots creates image files with specimen, plot type as name
"""
#
# initializations
#
version_num = pmag.get_version()
verbose = pmagplotlib.verbose
#
# default acceptance criteria
#
accept = pmag.default_criteria(0)[0] # set the default criteria
#
# parse command line options
#
plots, fmt, Zdiff = 0, 'svg', 0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg_from_sys("-WD", default_val=os.getcwd())
meas_file = pmag.get_named_arg_from_sys("-f",
default_val="measurements.txt")
spec_file = pmag.get_named_arg_from_sys("-fsp",
default_val="specimens.txt")
crit_file = pmag.get_named_arg_from_sys("-fcr", default_val="criteria.txt")
spec_file = os.path.join(dir_path, spec_file)
meas_file = os.path.join(dir_path, meas_file)
crit_file = os.path.join(dir_path, crit_file)
fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
if '-sav' in sys.argv: plots, verbose = 1, 0
if '-z' in sys.argv: Zdiff = 1
specimen = pmag.get_named_arg_from_sys("-spc", default_val="")
if '-b' in sys.argv:
ind = sys.argv.index('-b')
start = int(sys.argv[ind + 1])
end = int(sys.argv[ind + 2])
else:
start, end = "", ""
fnames = {
'measurements': meas_file,
'specimens': spec_file,
'criteria': crit_file
}
contribution = nb.Contribution(
dir_path,
custom_filenames=fnames,
read_tables=['measurements', 'specimens', 'criteria'])
#
# import prior interpretations from specimen file
#
specimen_cols = [
'analysts', 'aniso_ftest', 'aniso_ftest12', 'aniso_ftest23', 'aniso_s',
'aniso_s_mean', 'aniso_s_n_measurements', 'aniso_s_sigma',
'aniso_s_unit', 'aniso_tilt_correction', 'aniso_type', 'aniso_v1',
'aniso_v2', 'aniso_v3', 'citations', 'description', 'dir_alpha95',
'dir_comp', 'dir_dec', 'dir_inc', 'dir_mad_free', 'dir_n_measurements',
'dir_tilt_correction', 'experiments', 'geologic_classes',
'geologic_types', 'hyst_bc', 'hyst_bcr', 'hyst_mr_moment',
'hyst_ms_moment', 'int_abs', 'int_b', 'int_b_beta', 'int_b_sigma',
'int_corr', 'int_dang', 'int_drats', 'int_f', 'int_fvds', 'int_gamma',
'int_mad_free', 'int_md', 'int_n_measurements', 'int_n_ptrm', 'int_q',
'int_rsc', 'int_treat_dc_field', 'lithologies', 'meas_step_max',
'meas_step_min', 'meas_step_unit', 'method_codes', 'sample',
'software_packages', 'specimen'
]
if 'specimens' in contribution.tables:
spec_container = contribution.tables['specimens']
prior_spec_data = spec_container.get_records_for_code(
'LP-PI-TRM',
strict_match=False) # look up all prior intensity interpretations
else:
spec_container, prior_spec_data = None, []
backup = 0
#
Mkeys = ['magn_moment', 'magn_volume', 'magn_mass']
#
# create measurement dataframe
#
meas_container = contribution.tables['measurements']
meas_data = meas_container.df
#
meas_data['method_codes'] = meas_data['method_codes'].str.replace(
" ", "") # get rid of nasty spaces
meas_data = meas_data[meas_data['method_codes'].str.contains(
'LP-PI-TRM|LP-TRM|LP-TRM-TD') ==
True] # fish out zero field steps for plotting
intensity_types = [
col_name for col_name in meas_data.columns if col_name in Mkeys
]
int_key = intensity_types[
0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
meas_data = meas_data[meas_data[int_key].notnull(
)] # get all the non-null intensity records of the same type
if 'flag' not in meas_data.columns:
meas_data['flag'] = 'g' # set the default flag to good
meas_data = meas_data[meas_data['flag'].str.contains('g') ==
True] # only the 'good' measurements
thel_data = meas_data[meas_data['method_codes'].str.contains('LP-PI-TRM')
== True] # get all the Thellier data
trm_data = meas_data[meas_data['method_codes'].str.contains('LP-TRM') ==
True] # get all the TRM acquisition data
td_data = meas_data[meas_data['method_codes'].str.contains('LP-TRM-TD') ==
True] # get all the TD data
anis_data = meas_data[meas_data['method_codes'].str.contains('LP-AN') ==
True] # get all the anisotropy data
#
# get list of unique specimen names from measurement data
#
specimen_names = meas_data.specimen.unique(
) # this is a Series of all the specimen names
specimen_names = specimen_names.tolist() # turns it into a list
specimen_names.sort() # sorts by specimen name
#
# set up new DataFrame for this sessions specimen interpretations
#
spec_container = nb.MagicDataFrame(dtype='specimens',
columns=specimen_cols)
current_spec_data = spec_container.df # this is for interpretations from this session
if specimen == "": # do all specimens
k = 0
else:
k = specimen_names.index(specimen) # just do this one
# define figure numbers for arai, zijderveld and
# de-,re-magnetization 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)
if len(trm_data) > 0:
AZD['TRM'] = 5
pmagplotlib.plot_init(AZD['TRM'], 5, 5)
if len(td_data) > 0:
AZD['TDS'] = 6
pmagplotlib.plot_init(AZD['TDS'], 5, 5)
#
while k < len(specimen_names):
this_specimen = specimen_names[
k] # set the current specimen for plotting
if verbose and this_specimen != "":
print(this_specimen, k + 1, 'out of ', len(specimen_names))
#
# set up datablocks
#
thelblock = thel_data[thel_data['specimen'].str.contains(this_specimen)
== True] # fish out this specimen
trmblock = trm_data[trm_data['specimen'].str.contains(this_specimen) ==
True] # fish out this specimen
tdsrecs = td_data[td_data['specimen'].str.contains(this_specimen) ==
True] # fish out this specimen
anisblock = anis_data[anis_data['specimen'].str.contains(this_specimen)
== True] # fish out the anisotropy data
prior_specimen_interpretations = prior_spec_data[
prior_spec_data['specimen'].str.contains(
this_specimen) == True] # fish out prior interpretation
#
# sort data into types
#
araiblock, field = pmag.sortarai(thelblock,
this_specimen,
Zdiff,
version=3)
first_Z = araiblock[0]
GammaChecks = araiblock[5]
if len(first_Z) < 3:
if backup == 0:
k += 1
if verbose:
print('skipping specimen - moving forward ', this_specimen)
else:
k -= 1
if verbose:
print('skipping specimen - moving backward ',
this_specimen)
else:
backup = 0
zijdblock, units = pmag.find_dmag_rec(this_specimen,
thelblock,
version=3)
if start == "" and len(prior_specimen_interpretations) > 0:
if verbose: print('Looking up saved interpretation....')
#
# get prior interpretation steps
#
beg_int = pd.to_numeric(prior_specimen_interpretations.
meas_step_min.values).tolist()[0]
end_int = pd.to_numeric(prior_specimen_interpretations.
meas_step_max.values).tolist()[0]
else:
beg_int, end_int = "", ""
recnum = 0
if verbose: print("index step Dec Inc Int Gamma")
for plotrec in zijdblock:
if plotrec[0] == beg_int:
start = recnum # while we are at it, collect these bounds
if plotrec[0] == end_int: end = recnum
if verbose:
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
for fig in list(AZD.keys()):
pmagplotlib.clearFIG(AZD[fig]) # clear all figures
pmagplotlib.plotAZ(AZD, araiblock, zijdblock, this_specimen,
units[0])
if verbose: pmagplotlib.drawFIGS(AZD)
pars, errcode = pmag.PintPars(thelblock,
araiblock,
zijdblock,
start,
end,
accept,
version=3)
pars['measurement_step_unit'] = "K"
pars['experiment_type'] = 'LP-PI-TRM'
#
# work on saving interpretations stuff later
#
if errcode != 1: # no problem in PintPars
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars["specimen_b"]
pars["er_specimen_name"] = this_specimen
#pars,kill=pmag.scoreit(pars,this_specimen_interpretation,accept,'',verbose) # deal with this later
pars["specimen_grade"] = 'None'
pars['measurement_step_min'] = pars['meas_step_min']
pars['measurement_step_max'] = pars['meas_step_max']
if pars['measurement_step_unit'] == 'K':
outstr = "specimen Tmin Tmax N lab_field B_anc b q f(coe) Fvds beta MAD Dang Drats Nptrm Grade R MD% sigma Gamma_max \n"
pars_out = (this_specimen, (pars["meas_step_min"] - 273),
(pars["meas_step_max"] -
273), (pars["specimen_int_n"]),
1e6 * (pars["specimen_lab_field_dc"]),
1e6 * (pars["specimen_int"]),
pars["specimen_b"], pars["specimen_q"],
pars["specimen_f"], pars["specimen_fvds"],
pars["specimen_b_beta"], pars["int_mad_free"],
pars["int_dang"], pars["int_drats"],
pars["int_n_ptrm"], pars["specimen_grade"],
np.sqrt(pars["specimen_rsc"]),
int(pars["int_md"]), pars["specimen_b_sigma"],
pars['specimen_gamma'])
outstring = '%s %4.0f %4.0f %i %4.1f %4.1f %5.3f %5.1f %5.3f %5.3f %5.3f %7.1f %7.1f %7.1f %s %s %6.3f %i %5.3f %7.1f' % pars_out + '\n'
elif pars['measurement_step_unit'] == 'J':
outstr = "specimen Wmin Wmax N lab_field B_anc b q f(coe) Fvds beta MAD Dang Drats Nptrm Grade R MD% sigma ThetaMax DeltaMax GammaMax\n"
pars_out = (
this_specimen, (pars["meas_step_min"]),
(pars["meas_step_max"]), (pars["specimen_int_n"]),
1e6 * (pars["specimen_lab_field_dc"]),
1e6 * (pars["specimen_int"]), pars["specimen_b"],
pars["specimen_q"], pars["specimen_f"],
pars["specimen_fvds"], pars["specimen_b_beta"],
pars["specimen_int_mad"], pars["specimen_int_dang"],
pars["specimen_drats"], pars["specimen_int_ptrm_n"],
pars["specimen_grade"], np.sqrt(pars["specimen_rsc"]),
int(pars["specimen_md"]), pars["specimen_b_sigma"],
pars["specimen_theta"], pars["specimen_delta"],
pars["specimen_gamma"])
outstring = '%s %4.0f %4.0f %i %4.1f %4.1f %5.3f %5.1f %5.3f %5.3f %5.3f %7.1f %7.1f %7.1f %s %s %6.3f %i %5.3f %7.1f %7.1f %7.1f' % pars_out + '\n'
print(outstr)
print(outstring)
pmagplotlib.plotB(AZD, araiblock, zijdblock, pars)
mpars = pmag.domean(araiblock[1], start, end, 'DE-BFL')
if verbose:
pmagplotlib.drawFIGS(AZD)
print('pTRM direction= ',
'%7.1f' % (mpars['specimen_dec']),
' %7.1f' % (mpars['specimen_inc']), ' MAD:',
'%7.1f' % (mpars['specimen_mad']))
if len(anisblock) > 0: # this specimen has anisotropy data
if verbose:
print('Found anisotropy record... but ignoring for now ')
if plots == 1:
if fmt != "pmag":
files = {}
for key in list(AZD.keys()):
files[
key] = 'SP:_' + this_specimen + '_TY:_' + key + '_' + '.' + fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['deremag'] = 'DeReMag Plot'
titles['zijd'] = 'Zijderveld Plot'
titles['arai'] = 'Arai Plot'
titles['TRM'] = 'TRM Acquisition data'
AZD = pmagplotlib.addBorders(AZD, titles, black,
purple)
pmagplotlib.saveP(AZD, files)
else: # save in pmag format
print('pmag format no longer supported')
#script="grep "+this_specimen+" 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 specimen != "": sys.exit() # syonara
if verbose:
ans = input('Return for next specimen, q to quit: ')
if ans == 'q': sys.exit()
k += 1 # moving on
def main():
"""
NAME
hysteresis_magic.py
DESCRIPTION
calculates hystereis parameters and saves them in rmag_hystereis format file
makes plots if option selected
SYNTAX
hysteresis_magic.py [command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f: specify input file, default is agm_measurements.txt
-fh: specify rmag_hysteresis.txt input file
-F: specify output file, default is rmag_hysteresis.txt
-P: do not make the plots
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
PLT = 1
plots = 0
user, meas_file, rmag_out, rmag_file = "", "agm_measurements.txt", "rmag_hysteresis.txt", ""
pltspec = ""
dir_path = '.'
fmt = 'svg'
verbose = pmagplotlib.verbose
version_num = pmag.get_version()
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind + 1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if '-f' in args:
ind = args.index("-f")
meas_file = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
rmag_out = args[ind + 1]
if '-fh' in args:
ind = args.index("-fh")
rmag_file = args[ind + 1]
rmag_file = dir_path + '/' + rmag_file
if '-P' in args:
PLT = 0
irm_init, imag_init = -1, -1
if '-sav' in args:
verbose = 0
plots = 1
if '-spc' in args:
ind = args.index("-spc")
pltspec = args[ind + 1]
verbose = 0
plots = 1
if '-fmt' in args:
ind = args.index("-fmt")
fmt = args[ind + 1]
rmag_out = dir_path + '/' + rmag_out
meas_file = dir_path + '/' + meas_file
rmag_rem = dir_path + "/rmag_remanence.txt"
#
#
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print main.__doc__
print 'bad file'
sys.exit()
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs, RemRecs = [], []
HDD = {}
if verbose:
if verbose and PLT:
print "Plots may be on top of each other - use mouse to place "
if PLT:
HDD['hyst'], HDD['deltaM'], HDD['DdeltaM'] = 1, 2, 3
pmagplotlib.plot_init(HDD['DdeltaM'], 5, 5)
pmagplotlib.plot_init(HDD['deltaM'], 5, 5)
pmagplotlib.plot_init(HDD['hyst'], 5, 5)
imag_init = 0
irm_init = 0
else:
HDD['hyst'], HDD['deltaM'], HDD['DdeltaM'], HDD['irm'], HDD[
'imag'] = 0, 0, 0, 0, 0
#
if rmag_file != "": hyst_data, file_type = pmag.magic_read(rmag_file)
#
# get list of unique experiment names and specimen names
#
experiment_names, sids = [], []
for rec in meas_data:
meths = rec['magic_method_codes'].split(':')
methods = []
for meth in meths:
methods.append(meth.strip())
if 'LP-HYS' in methods:
if 'er_synthetic_name' in rec.keys(
) and rec['er_synthetic_name'] != "":
rec['er_specimen_name'] = rec['er_synthetic_name']
if rec['magic_experiment_name'] not in experiment_names:
experiment_names.append(rec['magic_experiment_name'])
if rec['er_specimen_name'] not in sids:
sids.append(rec['er_specimen_name'])
#
k = 0
locname = ''
if pltspec != "":
k = sids.index(pltspec)
print sids[k]
while k < len(sids):
s = sids[k]
if verbose and PLT: print s, k + 1, 'out of ', len(sids)
#
#
B, M, Bdcd, Mdcd = [], [], [], [
] #B,M for hysteresis, Bdcd,Mdcd for irm-dcd data
Bimag, Mimag = [], [] #Bimag,Mimag for initial magnetization curves
first_dcd_rec, first_rec, first_imag_rec = 1, 1, 1
for rec in meas_data:
methcodes = rec['magic_method_codes'].split(':')
meths = []
for meth in methcodes:
meths.append(meth.strip())
if rec['er_specimen_name'] == s and "LP-HYS" in meths:
B.append(float(rec['measurement_lab_field_dc']))
M.append(float(rec['measurement_magn_moment']))
if first_rec == 1:
e = rec['magic_experiment_name']
HystRec = {}
first_rec = 0
if "er_location_name" in rec.keys():
HystRec["er_location_name"] = rec["er_location_name"]
locname = rec['er_location_name'].replace('/', '-')
if "er_sample_name" in rec.keys():
HystRec["er_sample_name"] = rec["er_sample_name"]
if "er_site_name" in rec.keys():
HystRec["er_site_name"] = rec["er_site_name"]
if "er_synthetic_name" in rec.keys(
) and rec['er_synthetic_name'] != "":
HystRec["er_synthetic_name"] = rec["er_synthetic_name"]
else:
HystRec["er_specimen_name"] = rec["er_specimen_name"]
if rec['er_specimen_name'] == s and "LP-IRM-DCD" in meths:
Bdcd.append(float(rec['treatment_dc_field']))
Mdcd.append(float(rec['measurement_magn_moment']))
if first_dcd_rec == 1:
RemRec = {}
irm_exp = rec['magic_experiment_name']
first_dcd_rec = 0
if "er_location_name" in rec.keys():
RemRec["er_location_name"] = rec["er_location_name"]
if "er_sample_name" in rec.keys():
RemRec["er_sample_name"] = rec["er_sample_name"]
if "er_site_name" in rec.keys():
RemRec["er_site_name"] = rec["er_site_name"]
if "er_synthetic_name" in rec.keys(
) and rec['er_synthetic_name'] != "":
RemRec["er_synthetic_name"] = rec["er_synthetic_name"]
else:
RemRec["er_specimen_name"] = rec["er_specimen_name"]
if rec['er_specimen_name'] == s and "LP-IMAG" in meths:
if first_imag_rec == 1:
imag_exp = rec['magic_experiment_name']
first_imag_rec = 0
Bimag.append(float(rec['measurement_lab_field_dc']))
Mimag.append(float(rec['measurement_magn_moment']))
#
# now plot the hysteresis curve
#
if len(B) > 0:
hmeths = []
for meth in meths:
hmeths.append(meth)
hpars = pmagplotlib.plotHDD(HDD, B, M, e)
if verbose and PLT: pmagplotlib.drawFIGS(HDD)
#
# get prior interpretations from hyst_data
if rmag_file != "":
hpars_prior = {}
for rec in hyst_data:
if rec['magic_experiment_names'] == e:
if rec['hysteresis_bcr'] != "" and rec[
'hysteresis_mr_moment'] != "":
hpars_prior['hysteresis_mr_moment'] = rec[
'hysteresis_mr_moment']
hpars_prior['hysteresis_ms_moment'] = rec[
'hysteresis_ms_moment']
hpars_prior['hysteresis_bc'] = rec['hysteresis_bc']
hpars_prior['hysteresis_bcr'] = rec[
'hysteresis_bcr']
break
if verbose: pmagplotlib.plotHPARS(HDD, hpars_prior, 'ro')
else:
if verbose: pmagplotlib.plotHPARS(HDD, hpars, 'bs')
HystRec['hysteresis_mr_moment'] = hpars['hysteresis_mr_moment']
HystRec['hysteresis_ms_moment'] = hpars['hysteresis_ms_moment']
HystRec['hysteresis_bc'] = hpars['hysteresis_bc']
HystRec['hysteresis_bcr'] = hpars['hysteresis_bcr']
HystRec['hysteresis_xhf'] = hpars['hysteresis_xhf']
HystRec['magic_experiment_names'] = e
HystRec['magic_software_packages'] = version_num
if hpars["magic_method_codes"] not in hmeths:
hmeths.append(hpars["magic_method_codes"])
methods = ""
for meth in hmeths:
methods = methods + meth.strip() + ":"
HystRec["magic_method_codes"] = methods[:-1]
HystRec["er_citation_names"] = "This study"
HystRecs.append(HystRec)
#
if len(Bdcd) > 0:
rmeths = []
for meth in meths:
rmeths.append(meth)
if verbose and PLT: print 'plotting IRM'
if irm_init == 0:
HDD['irm'] = 5
pmagplotlib.plot_init(HDD['irm'], 5, 5)
irm_init = 1
rpars = pmagplotlib.plotIRM(HDD['irm'], Bdcd, Mdcd, irm_exp)
RemRec['remanence_mr_moment'] = rpars['remanence_mr_moment']
RemRec['remanence_bcr'] = rpars['remanence_bcr']
RemRec['magic_experiment_names'] = irm_exp
if rpars["magic_method_codes"] not in meths:
meths.append(rpars["magic_method_codes"])
methods = ""
for meth in rmeths:
methods = methods + meth.strip() + ":"
RemRec["magic_method_codes"] = methods[:-1]
RemRec["er_citation_names"] = "This study"
RemRecs.append(RemRec)
else:
if irm_init: pmagplotlib.clearFIG(HDD['irm'])
if len(Bimag) > 0:
if verbose: print 'plotting initial magnetization curve'
# first normalize by Ms
Mnorm = []
for m in Mimag:
Mnorm.append(m / float(hpars['hysteresis_ms_moment']))
if imag_init == 0:
HDD['imag'] = 4
pmagplotlib.plot_init(HDD['imag'], 5, 5)
imag_init = 1
pmagplotlib.plotIMAG(HDD['imag'], Bimag, Mnorm, imag_exp)
else:
if imag_init: pmagplotlib.clearFIG(HDD['imag'])
#
files = {}
if plots:
if pltspec != "": s = pltspec
files = {}
for key in HDD.keys():
files[key] = locname + '_' + s + '_' + key + '.' + fmt
pmagplotlib.saveP(HDD, files)
if pltspec != "": sys.exit()
if verbose and PLT:
pmagplotlib.drawFIGS(HDD)
ans = raw_input(
"S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n "
)
if ans == "a":
files = {}
for key in HDD.keys():
files[key] = locname + '_' + s + '_' + key + '.' + fmt
pmagplotlib.saveP(HDD, files)
if ans == '': k += 1
if ans == "p":
del HystRecs[-1]
k -= 1
if ans == 'q':
print "Good bye"
sys.exit()
if ans == 's':
keepon = 1
specimen = raw_input(
'Enter desired specimen name (or first part there of): ')
while keepon == 1:
try:
k = sids.index(specimen)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if specimen in sids[qq]: tmplist.append(sids[qq])
print specimen, " not found, but this was: "
print tmplist
specimen = raw_input('Select one or try again\n ')
k = sids.index(specimen)
else:
k += 1
if len(B) == 0 and len(Bdcd) == 0:
if verbose: print 'skipping this one - no hysteresis data'
k += 1
if rmag_out == "" and ans == 's' and verbose:
really = raw_input(
" Do you want to overwrite the existing rmag_hystersis.txt file? 1/[0] "
)
if really == "":
print 'i thought not - goodbye'
sys.exit()
rmag_out = "rmag_hysteresis.txt"
if len(HystRecs) > 0:
pmag.magic_write(rmag_out, HystRecs, "rmag_hysteresis")
if verbose: print "hysteresis parameters saved in ", rmag_out
if len(RemRecs) > 0:
pmag.magic_write(rmag_rem, RemRecs, "rmag_remanence")
if verbose: print "remanence parameters saved in ", rmag_rem
def main():
"""
NAME
biplot_magic.py
DESCRIPTION
makes a biplot of specified variables from magic_measurements.txt format file
SYNTAX
biplot_magic.py [-h] [-i] [command line options]
INPUT
takes magic formated magic_measurments file
OPTIONS
-h prints help message and quits
-i interactively set filename and axes for plotting
-f FILE: specifies file name, default: magic_measurements.txt
-fmt [svg,png,jpg], format for images - default is svg
-sav figure and quit
-x XMETH:key:step, specify method code for X axis (optional key and treatment values)
-y YMETH:key:step, specify method code for X axis
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is whole file
-n [V,M] plot volume or mass normalized data only
NOTES
if nothing is specified for x and y, the user will be presented with options
key = ['treatment_ac_field','treatment_dc_field',treatment_temp']
step in mT for fields, K for temperatures
"""
#
file='magic_measurements.txt'
methx,methy,fmt="","",'.svg'
plot_key=''
norm_by=""
#plot=0
no_plot = pmag.get_flag_arg_from_sys('-sav')
if not no_plot:
do_plot = True
else:
do_plot = False
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
if '-n' in sys.argv:
ind=sys.argv.index('-n')
norm_by=sys.argv[ind+1]
xtreat_key,ytreat_key,xstep,ystep="","","",""
if '-x' in sys.argv:
ind=sys.argv.index('-x')
meths=sys.argv[ind+1].split(':')
methx=meths[0]
if len(meths)>1:
xtreat_key=meths[1]
xstep=float(meths[2])
if '-y' in sys.argv:
ind=sys.argv.index('-y')
meths=sys.argv[ind+1].split(':')
methy=meths[0]
if len(meths)>1:
ytreat_key=meths[1]
ystep=float(meths[2])
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
plot_by=sys.argv[ind+1]
if plot_by=='loc':plot_key='er_location_name'
if plot_by=='sit':plot_key='er_site_name'
if plot_by=='sam':plot_key='er_sample_name'
if plot_by=='spc':plot_key='er_specimen_name'
if '-h' in sys.argv:
do_plot = False
if '-i' in sys.argv:
#
# get name of file from command line
#
file=raw_input("Input magic_measurments file name? [magic_measurements.txt] ")
if file=="":file="magic_measurements.txt"
#
#
FIG={'fig':1}
pmagplotlib.plot_init(FIG['fig'],5,5)
data,file_type=pmag.magic_read(file)
if file_type!="magic_measurements":
print file_type,' not correct format for magic_measurments file'
sys.exit()
#
# collect method codes
methods,plotlist=[],[]
for rec in data:
if plot_key!="":
if rec[plot_key] not in plotlist:plotlist.append(rec[plot_key])
elif len(plotlist)==0:
plotlist.append('All')
meths=rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip() not in methods and meth.strip()!="LP-":
methods.append(meth.strip())
#
if '-i' in sys.argv:
print methods
elif methx =="" or methy=="":
print methods
sys.exit()
GoOn=1
while GoOn==1:
if '-i' in sys.argv:methx=raw_input('Select method for x axis: ')
if methx not in methods:
if '-i' in sys.argv:
print 'try again! method not available'
else:
print main.__doc__
print '\n must specify X axis method\n'
sys.exit()
else:
if pmagplotlib.verbose: print methx, ' selected for X axis'
GoOn=0
GoOn=1
while GoOn==1:
if '-i' in sys.argv:methy=raw_input('Select method for y axis: ')
if methy not in methods:
if '-i' in sys.argv:
print 'try again! method not available'
else:
print main.__doc__
print '\n must specify Y axis method\n'
sys.exit()
else:
if pmagplotlib.verbose: print methy, ' selected for Y axis'
GoOn=0
if norm_by=="":
measkeys=['measurement_magn_mass','measurement_magn_volume','measurement_magn_moment','measurement_magnitude','measurement_chi_volume','measurement_chi_mass','measurement_chi']
elif norm_by=="V":
measkeys=['measurement_magn_volume','measurement_chi_volume']
elif norm_by=="M":
measkeys=['measurement_magn_mass','measurement_chi_mass']
xmeaskey,ymeaskey="",""
plotlist.sort()
for plot in plotlist: # go through objects
if pmagplotlib.verbose:
print plot
X,Y=[],[]
x,y='',''
for rec in data:
if plot_key!="" and rec[plot_key]!=plot:
pass
else:
meths=rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip()==methx:
if xmeaskey=="":
for key in measkeys:
if key in rec.keys() and rec[key]!="":
xmeaskey=key
if pmagplotlib.verbose:
print xmeaskey,' being used for plotting X.'
break
if meth.strip()==methy:
if ymeaskey=="":
for key in measkeys:
if key in rec.keys() and rec[key]!="":
ymeaskey=key
if pmagplotlib.verbose:
print ymeaskey,' being used for plotting Y'
break
if ymeaskey!="" and xmeaskey!="":
for rec in data:
x,y='',''
spec=rec['er_specimen_name'] # get the ydata for this specimen
if rec[ymeaskey]!="" and methy in rec['magic_method_codes'].split(':'):
if ytreat_key=="" or (ytreat_key in rec.keys() and float(rec[ytreat_key])==ystep):
y=float(rec[ymeaskey])
for rec in data: # now find the xdata
if rec['er_specimen_name']==spec and rec[xmeaskey]!="" and methx in rec['magic_method_codes'].split(':'):
if xtreat_key=="" or (xtreat_key in rec.keys() and float(rec[xtreat_key])==xstep):
x=float(rec[xmeaskey])
if x != '' and y!= '':
X.append(x)
Y.append(y)
if len(X)>0:
pmagplotlib.clearFIG(FIG['fig'])
pmagplotlib.plotXY(FIG['fig'],X,Y,sym='ro',xlab=methx,ylab=methy,title=plot+':Biplot')
if not pmagplotlib.isServer and do_plot:
pmagplotlib.drawFIGS(FIG)
ans=raw_input('S[a]ve plots, [q]uit, Return for next plot ' )
if ans=='a':
files={}
for key in FIG.keys(): files[key]=plot+'_'+key+fmt
pmagplotlib.saveP(FIG,files)
if ans=='q':
print "Good-bye\n"
sys.exit()
else:
files={}
for key in FIG.keys(): files[key]=plot+'_'+key+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['fig']='X Y Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
else:
print 'nothing to plot for ',plot
def main():
"""
NAME
quick_hyst.py
DESCRIPTION
makes plots of hysteresis data
SYNTAX
quick_hyst.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input file, default is measurements.txt
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
if "-h" in args:
print(main.__doc__)
sys.exit()
plots = 0
pltspec = ""
verbose = pmagplotlib.verbose
#version_num = pmag.get_version()
dir_path = pmag.get_named_arg_from_sys('-WD', '.')
dir_path = os.path.realpath(dir_path)
meas_file = pmag.get_named_arg_from_sys('-f', 'measurements.txt')
fmt = pmag.get_named_arg_from_sys('-fmt', 'png')
if '-sav' in args:
verbose = 0
plots = 1
if '-spc' in args:
ind = args.index("-spc")
pltspec = args[ind + 1]
verbose = 0
plots = 1
#
con = nb.Contribution(dir_path,
read_tables=['measurements'],
custom_filenames={'measurements': meas_file})
# get as much name data as possible (used for naming plots)
if not 'measurements' in con.tables:
print("-W- No measurement file found")
return
con.propagate_location_to_measurements()
if 'measurements' not in con.tables:
print(main.__doc__)
print('bad file')
sys.exit()
meas_container = con.tables['measurements']
#meas_df = meas_container.df
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs = []
HDD = {}
HDD['hyst'] = 1
pmagplotlib.plot_init(HDD['hyst'], 5, 5)
#
# get list of unique experiment names and specimen names
#
sids = []
hyst_data = meas_container.get_records_for_code('LP-HYS')
#experiment_names = hyst_data['experiment_name'].unique()
if not len(hyst_data):
print("-W- No hysteresis data found")
return
sids = hyst_data['specimen'].unique()
# if 'treat_temp' is provided, use that value, otherwise assume 300
hyst_data['treat_temp'].where(hyst_data['treat_temp'].notnull(),
'300',
inplace=True)
# start at first specimen, or at provided specimen ('-spc')
k = 0
if pltspec != "":
try:
print(sids)
k = list(sids).index(pltspec)
except ValueError:
print('-W- No specimen named: {}.'.format(pltspec))
print('-W- Please provide a valid specimen name')
return
intlist = ['magn_moment', 'magn_volume', 'magn_mass']
while k < len(sids):
locname, site, sample, synth = '', '', '', ''
s = sids[k]
if verbose:
print(s, k + 1, 'out of ', len(sids))
# B, M for hysteresis, Bdcd,Mdcd for irm-dcd data
B, M = [], []
# get all measurements for this specimen
spec = hyst_data[hyst_data['specimen'] == s]
# get names
if 'location' in spec:
locname = spec['location'][0]
if 'site' in spec:
site = spec['sample'][0]
if 'sample' in spec:
sample = spec['sample'][0]
# get all records with non-blank values in any intlist column
# find intensity data
for int_column in intlist:
if int_column in spec.columns:
int_col = int_column
break
meas_data = spec[spec[int_column].notnull()]
if len(meas_data) == 0:
break
#
c = ['k-', 'b-', 'c-', 'g-', 'm-', 'r-', 'y-']
cnum = 0
Temps = []
xlab, ylab, title = '', '', ''
Temps = meas_data['treat_temp'].unique()
for t in Temps:
print('working on t: ', t)
t_data = meas_data[meas_data['treat_temp'] == t]
m = int_col
B = t_data['meas_field_dc'].astype(float).values
M = t_data[m].astype(float).values
# now plot the hysteresis curve(s)
#
if len(B) > 0:
B = numpy.array(B)
M = numpy.array(M)
if t == Temps[-1]:
xlab = 'Field (T)'
ylab = m
title = 'Hysteresis: ' + s
if t == Temps[0]:
pmagplotlib.clearFIG(HDD['hyst'])
pmagplotlib.plotXY(HDD['hyst'],
B,
M,
sym=c[cnum],
xlab=xlab,
ylab=ylab,
title=title)
pmagplotlib.plotXY(HDD['hyst'], [1.1 * B.min(), 1.1 * B.max()],
[0, 0],
sym='k-',
xlab=xlab,
ylab=ylab,
title=title)
pmagplotlib.plotXY(HDD['hyst'], [0, 0],
[1.1 * M.min(), 1.1 * M.max()],
sym='k-',
xlab=xlab,
ylab=ylab,
title=title)
if verbose:
pmagplotlib.drawFIGS(HDD)
cnum += 1
if cnum == len(c):
cnum = 0
#
files = {}
if plots:
if pltspec != "":
s = pltspec
for key in list(HDD.keys()):
if pmagplotlib.isServer:
if synth == '':
files[
key] = "LO:_" + locname + '_SI:_' + site + '_SA:_' + sample + '_SP:_' + s + '_TY:_' + key + '_.' + fmt
else:
files[
key] = 'SY:_' + synth + '_TY:_' + key + '_.' + fmt
else:
if synth == '':
filename = ''
for item in [locname, site, sample, s, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key] = filename
else:
files[key] = "{}_{}.{}".format(synth, key, fmt)
pmagplotlib.saveP(HDD, files)
if pltspec != "":
sys.exit()
if verbose:
pmagplotlib.drawFIGS(HDD)
ans = input(
"S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n "
)
if ans == "a":
files = {}
for key in list(HDD.keys()):
if pmagplotlib.isServer: # use server plot naming convention
files[
key] = "LO:_" + locname + '_SI:_' + site + '_SA:_' + sample + '_SP:_' + s + '_TY:_' + key + '_.' + fmt
else: # use more readable plot naming convention
filename = ''
for item in [locname, site, sample, s, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key] = filename
pmagplotlib.saveP(HDD, files)
if ans == '':
k += 1
if ans == "p":
del HystRecs[-1]
k -= 1
if ans == 'q':
print("Good bye")
sys.exit()
if ans == 's':
keepon = 1
specimen = input(
'Enter desired specimen name (or first part there of): ')
while keepon == 1:
try:
k = sids.index(specimen)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if specimen in sids[qq]:
tmplist.append(sids[qq])
print(specimen, " not found, but this was: ")
print(tmplist)
specimen = input('Select one or try again\n ')
k = sids.index(specimen)
else:
k += 1
if len(B) == 0:
if verbose:
print('skipping this one - no hysteresis data')
k += 1
def main():
"""
NAME
quick_hyst.py
DESCRIPTION
makes plots of hysteresis data
SYNTAX
quick_hyst.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input file, default is measurements.txt
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
if "-h" in args:
print(main.__doc__)
sys.exit()
plots = 0
pltspec = ""
verbose = pmagplotlib.verbose
#version_num = pmag.get_version()
dir_path = pmag.get_named_arg('-WD', '.')
dir_path = os.path.realpath(dir_path)
meas_file = pmag.get_named_arg('-f', 'measurements.txt')
fmt = pmag.get_named_arg('-fmt', 'png')
if '-sav' in args:
verbose = 0
plots = 1
if '-spc' in args:
ind = args.index("-spc")
pltspec = args[ind+1]
verbose = 0
plots = 1
#
con = cb.Contribution(dir_path, read_tables=['measurements'],
custom_filenames={'measurements': meas_file})
# get as much name data as possible (used for naming plots)
if not 'measurements' in con.tables:
print("-W- No measurement file found")
return
con.propagate_location_to_measurements()
if 'measurements' not in con.tables:
print(main.__doc__)
print('bad file')
sys.exit()
meas_container = con.tables['measurements']
#meas_df = meas_container.df
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs = []
HDD = {}
HDD['hyst'] = 1
pmagplotlib.plot_init(HDD['hyst'], 5, 5)
#
# get list of unique experiment names and specimen names
#
sids = []
hyst_data = meas_container.get_records_for_code('LP-HYS')
#experiment_names = hyst_data['experiment_name'].unique()
if not len(hyst_data):
print("-W- No hysteresis data found")
return
sids = hyst_data['specimen'].unique()
# if 'treat_temp' is provided, use that value, otherwise assume 300
hyst_data['treat_temp'].where(hyst_data['treat_temp'].notnull(), '300', inplace=True)
# start at first specimen, or at provided specimen ('-spc')
k = 0
if pltspec != "":
try:
print(sids)
k = list(sids).index(pltspec)
except ValueError:
print('-W- No specimen named: {}.'.format(pltspec))
print('-W- Please provide a valid specimen name')
return
intlist = ['magn_moment', 'magn_volume', 'magn_mass']
while k < len(sids):
locname, site, sample, synth = '', '', '', ''
s = sids[k]
if verbose:
print(s, k + 1, 'out of ', len(sids))
# B, M for hysteresis, Bdcd,Mdcd for irm-dcd data
B, M = [], []
# get all measurements for this specimen
spec = hyst_data[hyst_data['specimen'] == s]
# get names
if 'location' in spec:
locname = spec['location'].iloc[0]
if 'site' in spec:
site = spec['sample'].iloc[0]
if 'sample' in spec:
sample = spec['sample'].iloc[0]
# get all records with non-blank values in any intlist column
# find intensity data
for int_column in intlist:
if int_column in spec.columns:
int_col = int_column
break
meas_data = spec[spec[int_column].notnull()]
if len(meas_data) == 0:
break
#
c = ['k-', 'b-', 'c-', 'g-', 'm-', 'r-', 'y-']
cnum = 0
Temps = []
xlab, ylab, title = '', '', ''
Temps = meas_data['treat_temp'].unique()
for t in Temps:
print('working on t: ', t)
t_data = meas_data[meas_data['treat_temp'] == t]
m = int_col
B = t_data['meas_field_dc'].astype(float).values
M = t_data[m].astype(float).values
# now plot the hysteresis curve(s)
#
if len(B) > 0:
B = numpy.array(B)
M = numpy.array(M)
if t == Temps[-1]:
xlab = 'Field (T)'
ylab = m
title = 'Hysteresis: ' + s
if t == Temps[0]:
pmagplotlib.clearFIG(HDD['hyst'])
pmagplotlib.plot_xy(HDD['hyst'],B,M,sym=c[cnum],xlab=xlab,ylab=ylab,title=title)
pmagplotlib.plot_xy(HDD['hyst'],[1.1*B.min(),1.1*B.max()],[0,0],sym='k-',xlab=xlab,ylab=ylab,title=title)
pmagplotlib.plot_xy(HDD['hyst'],[0,0],[1.1*M.min(),1.1*M.max()],sym='k-',xlab=xlab,ylab=ylab,title=title)
if verbose and not set_env.IS_WIN:
pmagplotlib.draw_figs(HDD)
cnum += 1
if cnum == len(c):
cnum = 0
#
files = {}
if plots:
if pltspec != "":
s = pltspec
for key in list(HDD.keys()):
if pmagplotlib.isServer:
if synth == '':
files[key] = "LO:_"+locname+'_SI:_'+site+'_SA:_'+sample+'_SP:_'+s+'_TY:_'+key+'_.'+fmt
else:
files[key] = 'SY:_'+synth+'_TY:_'+key+'_.'+fmt
else:
if synth == '':
filename = ''
for item in [locname, site, sample, s, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key] = filename
else:
files[key] = "{}_{}.{}".format(synth, key, fmt)
pmagplotlib.save_plots(HDD, files)
if pltspec != "":
sys.exit()
if verbose:
pmagplotlib.draw_figs(HDD)
ans = input("S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n ")
if ans == "a":
files = {}
for key in list(HDD.keys()):
if pmagplotlib.isServer: # use server plot naming convention
locname = locname if locname else ""
site = site if site else ""
sample = sample if sample else ""
files[key] = "LO:_"+locname+'_SI:_'+site+'_SA:_'+sample+'_SP:_'+s+'_TY:_'+key+'_.'+fmt
else: # use more readable plot naming convention
filename = ''
for item in [locname, site, sample, s, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key] = filename
pmagplotlib.save_plots(HDD, files)
if ans == '':
k += 1
if ans == "p":
del HystRecs[-1]
k -= 1
if ans == 'q':
print("Good bye")
sys.exit()
if ans == 's':
keepon = 1
specimen = input('Enter desired specimen name (or first part there of): ')
while keepon == 1:
try:
k = sids.index(specimen)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if specimen in sids[qq]:
tmplist.append(sids[qq])
print(specimen, " not found, but this was: ")
print(tmplist)
specimen = input('Select one or try again\n ')
k = sids.index(specimen)
else:
k += 1
if len(B) == 0:
if verbose:
print('skipping this one - no hysteresis data')
k += 1
