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
-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=""
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 '-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,'ro',methx,methy,plot+':Biplot')
if not pmagplotlib.isServer:
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
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
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_key='er_location_name'
if len(sys.argv)>1:
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv: norm=0
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=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
#
# get plotlist
#
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 plot in plotlist:
print plot,'plotting by: ',plot_key
PLTblock=pmag.get_dictitem(data,plot_key,plot,'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)
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 '-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)
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)
# 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)
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 -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
"""
fmt='svg'
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 '-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
pmagplotlib.drawFIGS(FIG)
ans=raw_input('S[a]ve figure? [q]uit, <return> to continue ')
if ans=='a':
files={'lowrie':'lowrie:_'+spc+'_.'+fmt}
pmagplotlib.saveP(FIG,files)
elif ans=='q':
sys.exit()
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
"""
fmt='svg'
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 '-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. # 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
pmagplotlib.drawFIGS(FIG)
ans=raw_input('S[a]ve figure? [q]uit, <return> to continue ')
if ans=='a':
files={'lowrie':'lowrie:_'+spc+'_.'+fmt}
pmagplotlib.saveP(FIG,files)
elif ans=='q':
sys.exit()
pmagplotlib.clearFIG(FIG['lowrie'])
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['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 and verbose:
pmag.magic_write(rmag_out,HystRecs,"rmag_hysteresis")
print "hysteresis parameters saved in ",rmag_out
if len(RemRecs)>0 and verbose:
pmag.magic_write(rmag_rem,RemRecs,"rmag_remanence")
print "remanence parameters saved in ",rmag_rem
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
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG={} # plot dictionary
FIG['exp']=1 # exp is figure 1
in_file,plot_key,LP='magic_measurements.txt','er_location_name',"LP-IRM"
units,dmag_key='T','treatment_dc_field'
XLP=[]
norm=1
if len(sys.argv)>1:
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv:norm=0
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=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 '-LP' in sys.argv:
# ind=sys.argv.index("-LT")
# LP='LP-'+sys.argv[ind+1] # get lab protocol for plotting
data,file_type=pmag.magic_read(in_file)
sids=pmag.get_specs(data)
pmagplotlib.plot_init(FIG['exp'],6,6)
print len(data),' records read from ',in_file
#
#
# find desired intensity data
#
# get plotlist
#
plotlist,intlist=[],['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
IntMeths=[]
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 LP in meths: plotlist.append(rec[plot_key])
plotlist.sort()
if len(IntMeths)==0:
print 'No intensity information found'
sys.exit()
int_key=IntMeths[0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
for plot in plotlist:
print plot
for spec in sids:
INTblock=[]
for rec in data:
if 'measurement_flag' not in rec.keys():rec['measurement_flag']='g'
if rec[plot_key]==plot and int_key in rec.keys() and rec[int_key]!="" and rec['er_specimen_name']==spec:
meths=[]
methcodes=rec['magic_method_codes'].split(':')
for meth in methcodes:
LPtest=meth.split('-')
if XLP not in LPtest: meths.append(meth.strip())
if len(meths)>0 and LP in meths or 'LT-NO' in meths:
title=rec[plot_key]
INTblock.append([float(rec[dmag_key]),0,0,float(rec[int_key]),1,rec['measurement_flag']])
Sdata=INTblock.sort()
if len(INTblock)>2: pmagplotlib.plotMT(FIG['exp'],INTblock,title,0,units,norm)
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+'_'+LP+'.svg'
pmagplotlib.saveP(FIG,files)
pmagplotlib.clearFIG(FIG['exp'])
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
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG={} # plot dictionary
FIG['exp']=1 # exp is figure 1
dir_path='./'
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 '-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 plot in plotlist:
print plot
INTblock=[]
data=pmag.get_dictitem(Ints[int_key],plot_key,plot,'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)
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+'_'+LP+'.svg'
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(): rec['measurement_temp']='300' # assume room T measurement unless otherwise specified
#
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
spec=pmag.get_dictitem(hyst_data,'er_specimen_name',s,'T') # get all measurements for this specimen
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:
meas_data=pmag.get_dictitem(spec,m,'','F') # get all non-blank data for this specimen
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.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
files={}
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
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"
