def save(ANIS, fmt, title):
files = {}
for key in list(ANIS.keys()):
if pmagplotlib.isServer:
files[key] = title + '_TY:_aniso-' + key + '_.' + fmt
else:
files[key] = title.replace('__', '_') + "_aniso-" + key + "." + fmt
pmagplotlib.saveP(ANIS, files)
def save(ANIS,fmt,title):
files = {}
for key in list(ANIS.keys()):
if pmagplotlib.isServer:
files[key] = title + '_TY:_aniso-' + key + '_.' + fmt
else:
files[key] = title.replace('__', '_') + "_aniso-" + key + "." + fmt
pmagplotlib.saveP(ANIS, files)
def main():
"""
NAME
plot_2cdfs.py
DESCRIPTION
makes plots of cdfs of data in input file
SYNTAX
plot_2cdfs.py [-h][command line options]
OPTIONS
-h prints help message and quits
-f FILE1 FILE2
-t TITLE
-fmt [svg,eps,png,pdf,jpg..] specify format of output figure, default is svg
"""
fmt = 'svg'
title = ""
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]
X = numpy.loadtxt(file)
file = sys.argv[ind + 2]
X2 = numpy.loadtxt(file)
# else:
# X=numpy.loadtxt(sys.stdin,dtype=numpy.float)
else:
print '-f option required'
print main.__doc__
sys.exit()
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if '-t' in sys.argv:
ind = sys.argv.index('-t')
title = sys.argv[ind + 1]
CDF = {'X': 1}
pmagplotlib.plot_init(CDF['X'], 5, 5)
pmagplotlib.plotCDF(CDF['X'], X, '', 'r', '')
pmagplotlib.plotCDF(CDF['X'], X2, title, 'b', '')
D, p = scipy.stats.ks_2samp(X, X2)
if p >= .05:
print D, p, ' not rejected at 95%'
else:
print D, p, ' rejected at 95%'
pmagplotlib.drawFIGS(CDF)
ans = raw_input('S[a]ve plot, <Return> to quit ')
if ans == 'a':
files = {'X': 'CDF_.' + fmt}
pmagplotlib.saveP(CDF, files)
def main():
"""
NAME
plot_2cdfs.py
DESCRIPTION
makes plots of cdfs of data in input file
SYNTAX
plot_2cdfs.py [-h][command line options]
OPTIONS
-h prints help message and quits
-f FILE1 FILE2
-t TITLE
-fmt [svg,eps,png,pdf,jpg..] specify format of output figure, default is svg
"""
fmt = "svg"
title = ""
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]
X = numpy.loadtxt(file)
file = sys.argv[ind + 2]
X2 = numpy.loadtxt(file)
# else:
# X=numpy.loadtxt(sys.stdin,dtype=numpy.float)
else:
print "-f option required"
print main.__doc__
sys.exit()
if "-fmt" in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if "-t" in sys.argv:
ind = sys.argv.index("-t")
title = sys.argv[ind + 1]
CDF = {"X": 1}
pmagplotlib.plot_init(CDF["X"], 5, 5)
pmagplotlib.plotCDF(CDF["X"], X, "", "r", "")
pmagplotlib.plotCDF(CDF["X"], X2, title, "b", "")
D, p = scipy.stats.ks_2samp(X, X2)
if p >= 0.05:
print D, p, " not rejected at 95%"
else:
print D, p, " rejected at 95%"
pmagplotlib.drawFIGS(CDF)
ans = raw_input("S[a]ve plot, <Return> to quit ")
if ans == "a":
files = {"X": "CDF_." + fmt}
pmagplotlib.saveP(CDF, files)
def main():
"""
NAME
plot_cdf.py
DESCRIPTION
makes plots of cdfs of data in input file
SYNTAX
plot_cdf.py [-h][command line options]
OPTIONS
-h prints help message and quits
-f FILE
-t TITLE
-fmt [svg,eps,png,pdf,jpg..] specify format of output figure, default is svg
-sav saves plot and quits
"""
fmt, plot = 'svg', 0
title = ""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-sav' in sys.argv: plot = 1
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
X = numpy.loadtxt(file)
# else:
# X=numpy.loadtxt(sys.stdin,dtype=numpy.float)
else:
print '-f option required'
print main.__doc__
sys.exit()
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if '-t' in sys.argv:
ind = sys.argv.index('-t')
title = sys.argv[ind + 1]
CDF = {'X': 1}
pmagplotlib.plot_init(CDF['X'], 5, 5)
pmagplotlib.plotCDF(CDF['X'], X, title, 'r', '')
files = {'X': 'CDF_.' + fmt}
if plot == 0:
pmagplotlib.drawFIGS(CDF)
ans = raw_input('S[a]ve plot, <Return> to quit ')
if ans == 'a':
pmagplotlib.saveP(CDF, files)
else:
pmagplotlib.saveP(CDF, files)
def main():
"""
NAME
plot_cdf.py
DESCRIPTION
makes plots of cdfs of data in input file
SYNTAX
plot_cdf.py [-h][command line options]
OPTIONS
-h prints help message and quits
-f FILE
-t TITLE
-fmt [svg,eps,png,pdf,jpg..] specify format of output figure, default is svg
-sav saves plot and quits
"""
fmt,plot='svg',0
title=""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-sav' in sys.argv:plot=1
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
X=numpy.loadtxt(file)
# else:
# X=numpy.loadtxt(sys.stdin,dtype=numpy.float)
else:
print '-f option required'
print main.__doc__
sys.exit()
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-t' in sys.argv:
ind=sys.argv.index('-t')
title=sys.argv[ind+1]
CDF={'X':1}
pmagplotlib.plot_init(CDF['X'],5,5)
pmagplotlib.plotCDF(CDF['X'],X,title,'r','')
files={'X':'CDF_.'+fmt}
if plot==0:
pmagplotlib.drawFIGS(CDF)
ans= raw_input('S[a]ve plot, <Return> to quit ')
if ans=='a':
pmagplotlib.saveP(CDF,files)
else:
pmagplotlib.saveP(CDF,files)
def main():
"""
NAME
qqunf.py
DESCRIPTION
makes qq plot from input data against uniform distribution
SYNTAX
qqunf.py [command line options]
OPTIONS
-h help message
-f FILE, specify file on command line
"""
fmt, plot = 'svg', 0
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
elif '-f' in sys.argv: # ask for filename
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
f = open(file, 'rU')
input = f.readlines()
Data = []
for line in input:
line.replace('\n', '')
if '\t' in line: # read in the data from standard input
rec = line.split('\t') # split each line on space to get records
else:
rec = line.split() # split each line on space to get records
Data.append(float(rec[0]))
#
if len(Data) >= 10:
QQ = {'unf1': 1}
pmagplotlib.plot_init(QQ['unf1'], 5, 5)
pmagplotlib.plotQQunf(QQ['unf1'], Data, 'QQ-Uniform') # make plot
else:
print 'you need N> 10'
sys.exit()
pmagplotlib.drawFIGS(QQ)
files = {}
for key in QQ.keys():
files[key] = key + '.' + fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['eq'] = 'Equal Area Plot'
EQ = pmagplotlib.addBorders(EQ, titles, black, purple)
pmagplotlib.saveP(QQ, files)
elif plot == 1:
files['qq'] = file + '.' + fmt
pmagplotlib.saveP(QQ, files)
else:
ans = raw_input(" S[a]ve to save plot, [q]uit without saving: ")
if ans == "a": pmagplotlib.saveP(QQ, files)
def main():
"""
NAME
qqunf.py
DESCRIPTION
makes qq plot from input data against uniform distribution
SYNTAX
qqunf.py [command line options]
OPTIONS
-h help message
-f FILE, specify file on command line
"""
fmt,plot='svg',0
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
elif '-f' in sys.argv: # ask for filename
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
f=open(file,'rU')
input=f.readlines()
Data=[]
for line in input:
line.replace('\n','')
if '\t' in line: # read in the data from standard input
rec=line.split('\t') # split each line on space to get records
else:
rec=line.split() # split each line on space to get records
Data.append(float(rec[0]))
#
if len(Data) >=10:
QQ={'unf1':1}
pmagplotlib.plot_init(QQ['unf1'],5,5)
pmagplotlib.plotQQunf(QQ['unf1'],Data,'QQ-Uniform') # make plot
else:
print 'you need N> 10'
sys.exit()
pmagplotlib.drawFIGS(QQ)
files={}
for key in QQ.keys():
files[key]=key+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='Equal Area Plot'
EQ = pmagplotlib.addBorders(EQ,titles,black,purple)
pmagplotlib.saveP(QQ,files)
elif plot==1:
files['qq']=file+'.'+fmt
pmagplotlib.saveP(QQ,files)
else:
ans=raw_input(" S[a]ve to save plot, [q]uit without saving: ")
if ans=="a": pmagplotlib.saveP(QQ,files)
def main():
"""
NAME
dayplot_magic.py
DESCRIPTION
makes 'day plots' (Day et al. 1977) and squareness/coercivity,
plots 'linear mixing' curve from Dunlop and Carter-Stiglitz (2006).
squareness coercivity of remanence (Neel, 1955) plots after
Tauxe et al. (2002)
SYNTAX
dayplot_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input hysteresis file, default is rmag_hysteresis.txt
-fr: specify input remanence file, default is rmag_remanence.txt
-fmt [svg,png,jpg] format for output plots
-sav saves plots and quits quietly
-n label specimen names
"""
args=sys.argv
hyst_file,rem_file="rmag_hysteresis.txt","rmag_remanence.txt"
dir_path='.'
verbose=pmagplotlib.verbose
fmt='svg' # default file format
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-f' in args:
ind=args.index("-f")
hyst_file=args[ind+1]
if '-fr' in args:
ind=args.index("-fr")
rem_file=args[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-sav' in sys.argv:
plots=1
verbose=0
else: plots=0
if '-n' in sys.argv:
label=1
else:
label=0
hyst_file = os.path.realpath(os.path.join(dir_path, hyst_file))
rem_file = os.path.realpath(os.path.join(dir_path, rem_file))
#
# initialize some variables
# define figure numbers for Day,S-Bc,S-Bcr
DSC={}
DSC['day'],DSC['S-Bc'],DSC['S-Bcr'],DSC['bcr1-bcr2']=1,2,3,4
pmagplotlib.plot_init(DSC['day'],5,5)
pmagplotlib.plot_init(DSC['S-Bc'],5,5)
pmagplotlib.plot_init(DSC['S-Bcr'],5,5)
pmagplotlib.plot_init(DSC['bcr1-bcr2'],5,5)
#
#
hyst_data,file_type=pmag.magic_read(hyst_file)
rem_data,file_type=pmag.magic_read(rem_file)
#
S,BcrBc,Bcr2,Bc,hsids,Bcr=[],[],[],[],[],[]
Ms,Bcr1,Bcr1Bc,S1=[],[],[],[]
names=[]
locations=''
for rec in hyst_data:
if 'er_location_name' in rec.keys() and rec['er_location_name'] not in locations: locations=locations+rec['er_location_name']+'_'
if rec['hysteresis_bcr'] !="" and rec['hysteresis_mr_moment']!="":
S.append(float(rec['hysteresis_mr_moment'])/float(rec['hysteresis_ms_moment']))
Bcr.append(float(rec['hysteresis_bcr']))
Bc.append(float(rec['hysteresis_bc']))
BcrBc.append(Bcr[-1]/Bc[-1])
if 'er_synthetic_name' in rec.keys() and rec['er_synthetic_name']!="":
rec['er_specimen_name']=rec['er_synthetic_name']
hsids.append(rec['er_specimen_name'])
names.append(rec['er_specimen_name'])
if len(rem_data)>0:
for rec in rem_data:
if rec['remanence_bcr'] !="" and float(rec['remanence_bcr'])>0:
try:
ind=hsids.index(rec['er_specimen_name'])
Bcr1.append(float(rec['remanence_bcr']))
Bcr1Bc.append(Bcr1[-1]/Bc[ind])
S1.append(S[ind])
Bcr2.append(Bcr[ind])
except ValueError:
if verbose:print('hysteresis data for ',rec['er_specimen_name'],' not found')
#
# now plot the day and S-Bc, S-Bcr plots
#
leglist=[]
if label==0:names=[]
if len(Bcr1)>0:
pmagplotlib.plotDay(DSC['day'],Bcr1Bc,S1,'ro',names=names)
pmagplotlib.plotSBcr(DSC['S-Bcr'],Bcr1,S1,'ro')
pmagplotlib.plot_init(DSC['bcr1-bcr2'],5,5)
pmagplotlib.plotBcr(DSC['bcr1-bcr2'],Bcr1,Bcr2)
else:
del DSC['bcr1-bcr2']
pmagplotlib.plotDay(DSC['day'],BcrBc,S,'bs',names=names)
pmagplotlib.plotSBcr(DSC['S-Bcr'],Bcr,S,'bs')
pmagplotlib.plotSBc(DSC['S-Bc'],Bc,S,'bs')
files={}
if len(locations)>0:locations=locations[:-1]
for key in DSC.keys():
if pmagplotlib.isServer: # use server plot naming convention
files[key] = 'LO:_'+locations+'_'+'SI:__SA:__SP:__TY:_'+key+'_.'+fmt
else: # use more readable plot naming convention
files[key] = '{}_{}.{}'.format(locations, key, fmt)
if verbose:
pmagplotlib.drawFIGS(DSC)
ans=raw_input(" S[a]ve to save plots, return to quit: ")
if ans=="a":
pmagplotlib.saveP(DSC,files)
else: sys.exit()
if plots: pmagplotlib.saveP(DSC,files)
def main():
"""
NAME
trmaq_magic.py
DESCTIPTION
does non-linear trm acquisisiton correction
SYNTAX
trmaq_magic.py [-h][-i][command line options]
OPTIONS
-h prints help message and quits
-i allows interactive setting of file names
-f MFILE, sets magic_measurements input file
-ft TSPEC, sets thellier_specimens input file
-F OUT, sets output for non-linear TRM acquisition corrected data
DEFAULTS
MFILE: trmaq_measurements.txt
TSPEC: thellier_specimens.txt
OUT: NLT_specimens.txt
"""
meas_file='trmaq_measurements.txt'
tspec="thellier_specimens.txt"
output='NLT_specimens.txt'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-i' in sys.argv:
meas_file=raw_input("Input magic_measurements file name? [trmaq_measurements.txt] ")
if meas_file=="":meas_file="trmaq_measurements.txt"
tspec=raw_input(" thellier_specimens file name? [thellier_specimens.txt] ")
if tspec=="":tspec="thellier_specimens.txt"
output=raw_input("File for non-linear TRM adjusted specimen data: [NLTspecimens.txt] ")
if output=="":output="NLT_specimens.txt"
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=sys.argv[ind+1]
if '-ft' in sys.argv:
ind=sys.argv.index('-ft')
tspec=sys.argv[ind+1]
if '-F' in sys.argv:
ind=sys.argv.index('-F')
output=sys.argv[ind+1]
#
PLT={'aq':1}
pmagplotlib.plot_init(PLT['aq'],5,5)
#
# get name of file from command line
#
comment=""
#
#
meas_data,file_type=pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
sids=pmag.get_specs(meas_data)
specimen=0
#
# read in thellier_specimen data
#
nrm,file_type=pmag.magic_read(tspec)
PmagSpecRecs=[]
while specimen < len(sids):
#
# find corresoponding paleointensity data for this specimen
#
s=sids[specimen]
blab,best="",""
for nrec in nrm: # pick out the Banc data for this spec
if nrec["er_specimen_name"]==s:
blab=float(nrec["specimen_lab_field_dc"])
best=float(nrec["specimen_int"])
TrmRec=nrec
break
if blab=="":
print "skipping ",s," : no best "
specimen+=1
else:
print sids[specimen],specimen+1, 'of ', len(sids),'Best = ',best*1e6
MeasRecs=[]
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"]==s:
meths=rec["magic_method_codes"].split(":")
methcodes=[]
for meth in meths:
methcodes.append(meth.strip())
if "LP-TRM" in methcodes: MeasRecs.append(rec)
if len(MeasRecs) <2:
specimen+=1
print 'skipping specimen - no trm acquisition data ', s
#
# collect info for the PmagSpecRec dictionary
#
else:
TRMs,Bs=[],[]
for rec in MeasRecs:
Bs.append(float(rec['treatment_dc_field']))
TRMs.append(float(rec['measurement_magn_moment']))
NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
#
Mp,Bp=[],[]
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(PLT['aq'],Bs,TRMs,Bp,Mp,NLpars,rec['magic_experiment_name'])
pmagplotlib.drawFIGS(PLT)
print 'Banc= ',float(NLpars['banc'])*1e6
trmTC={}
for key in TrmRec.keys():
trmTC[key]=TrmRec[key] # copy of info from thellier_specimens record
trmTC['specimen_int']='%8.3e'%(NLpars['banc'])
trmTC['magic_method_codes']=TrmRec["magic_method_codes"]+":DA-NL"
PmagSpecRecs.append(trmTC)
ans=raw_input("Return for next specimen, s[a]ve plot ")
if ans=='a':
Name={'aq':rec['er_specimen_name']+'_TRM.svg'}
pmagplotlib.saveP(PLT,Name)
specimen+=1
pmag.magic_write(output,PmagSpecRecs,'pmag_specimens')
def main():
"""
NAME
revtest_MM1990.py
DESCRIPTION
calculates Watson's V statistic from input files through Monte Carlo simulation in order to test whether normal and reversed populations could have been drawn from a common mean (equivalent to watsonV.py). Also provides the critical angle between the two sample mean directions and the corresponding McFadden and McElhinny (1990) classification.
INPUT FORMAT
takes dec/inc as first two columns in two space delimited files (one file for normal directions, one file for reversed directions).
SYNTAX
revtest_MM1990.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE
-f2 FILE
-P (don't plot the Watson V cdf)
OUTPUT
Watson's V between the two populations and the Monte Carlo Critical Value Vc.
M&M1990 angle, critical angle and classification
Plot of Watson's V CDF from Monte Carlo simulation (red line), V is solid and Vc is dashed.
"""
D1,D2=[],[]
plot=1
Flip=1
if '-h' in sys.argv: # check if help is needed
print(main.__doc__)
sys.exit() # graceful quit
if '-P' in sys.argv: plot=0
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file1=sys.argv[ind+1]
f1=open(file1,'r')
for line in f1.readlines():
rec=line.split()
Dec,Inc=float(rec[0]),float(rec[1])
D1.append([Dec,Inc,1.])
f1.close()
if '-f2' in sys.argv:
ind=sys.argv.index('-f2')
file2=sys.argv[ind+1]
f2=open(file2,'r')
print("be patient, your computer is doing 5000 simulations...")
for line in f2.readlines():
rec=line.split()
Dec,Inc=float(rec[0]),float(rec[1])
D2.append([Dec,Inc,1.])
f2.close()
#take the antipode for the directions in file 2
D2_flip=[]
for rec in D2:
d,i=(rec[0]-180.)%360.,-rec[1]
D2_flip.append([d,i,1.])
pars_1=pmag.fisher_mean(D1)
pars_2=pmag.fisher_mean(D2_flip)
cart_1=pmag.dir2cart([pars_1["dec"],pars_1["inc"],pars_1["r"]])
cart_2=pmag.dir2cart([pars_2['dec'],pars_2['inc'],pars_2["r"]])
Sw=pars_1['k']*pars_1['r']+pars_2['k']*pars_2['r'] # k1*r1+k2*r2
xhat_1=pars_1['k']*cart_1[0]+pars_2['k']*cart_2[0] # k1*x1+k2*x2
xhat_2=pars_1['k']*cart_1[1]+pars_2['k']*cart_2[1] # k1*y1+k2*y2
xhat_3=pars_1['k']*cart_1[2]+pars_2['k']*cart_2[2] # k1*z1+k2*z2
Rw=numpy.sqrt(xhat_1**2+xhat_2**2+xhat_3**2)
V=2*(Sw-Rw)
#
#keep weighted sum for later when determining the "critical angle" let's save it as Sr (notation of McFadden and McElhinny, 1990)
#
Sr=Sw
#
# do monte carlo simulation of datasets with same kappas, but common mean
#
counter,NumSims=0,5000
Vp=[] # set of Vs from simulations
for k in range(NumSims):
#
# get a set of N1 fisher distributed vectors with k1, calculate fisher stats
#
Dirp=[]
for i in range(pars_1["n"]):
Dirp.append(pmag.fshdev(pars_1["k"]))
pars_p1=pmag.fisher_mean(Dirp)
#
# get a set of N2 fisher distributed vectors with k2, calculate fisher stats
#
Dirp=[]
for i in range(pars_2["n"]):
Dirp.append(pmag.fshdev(pars_2["k"]))
pars_p2=pmag.fisher_mean(Dirp)
#
# get the V for these
#
Vk=pmag.vfunc(pars_p1,pars_p2)
Vp.append(Vk)
#
# sort the Vs, get Vcrit (95th percentile one)
#
Vp.sort()
k=int(.95*NumSims)
Vcrit=Vp[k]
#
# equation 18 of McFadden and McElhinny, 1990 calculates the critical value of R (Rwc)
#
Rwc=Sr-(old_div(Vcrit,2))
#
#following equation 19 of McFadden and McElhinny (1990) the critical angle is calculated.
#
k1=pars_1['k']
k2=pars_2['k']
R1=pars_1['r']
R2=pars_2['r']
critical_angle=numpy.degrees(numpy.arccos(old_div(((Rwc**2)-((k1*R1)**2)-((k2*R2)**2)),(2*k1*R1*k2*R2))))
D1_mean=(pars_1['dec'],pars_1['inc'])
D2_mean=(pars_2['dec'],pars_2['inc'])
angle=pmag.angle(D1_mean,D2_mean)
#
# print the results of the test
#
print("")
print("Results of Watson V test: ")
print("")
print("Watson's V: " '%.1f' %(V))
print("Critical value of V: " '%.1f' %(Vcrit))
if V<Vcrit:
print('"Pass": Since V is less than Vcrit, the null hypothesis that the two populations are drawn from distributions that share a common mean direction (antipodal to one another) cannot be rejected.')
elif V>Vcrit:
print('"Fail": Since V is greater than Vcrit, the two means can be distinguished at the 95% confidence level.')
print("")
print("M&M1990 classification:")
print("")
print("Angle between data set means: " '%.1f'%(angle))
print("Critical angle of M&M1990: " '%.1f'%(critical_angle))
if V>Vcrit:
print("")
elif V<Vcrit:
if critical_angle<5:
print("The McFadden and McElhinny (1990) classification for this test is: 'A'")
elif critical_angle<10:
print("The McFadden and McElhinny (1990) classification for this test is: 'B'")
elif critical_angle<20:
print("The McFadden and McElhinny (1990) classification for this test is: 'C'")
else:
print("The McFadden and McElhinny (1990) classification for this test is: 'INDETERMINATE;")
if plot==1:
CDF={'cdf':1}
pmagplotlib.plot_init(CDF['cdf'],5,5)
p1 = pmagplotlib.plotCDF(CDF['cdf'],Vp,"Watson's V",'r',"")
p2 = pmagplotlib.plotVs(CDF['cdf'],[V],'g','-')
p3 = pmagplotlib.plotVs(CDF['cdf'],[Vp[k]],'b','--')
pmagplotlib.drawFIGS(CDF)
files,fmt={},'svg'
if file2!="":
files['cdf']='WatsonsV_'+file1+'_'+file2+'.'+fmt
else:
files['cdf']='WatsonsV_'+file1+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['cdf']='Cumulative Distribution'
CDF = pmagplotlib.addBorders(CDF,titles,black,purple)
pmagplotlib.saveP(CDF,files)
else:
ans=input(" S[a]ve to save plot, [q]uit without saving: ")
if ans=="a": pmagplotlib.saveP(CDF,files)
def save(ANIS, fmt, title):
files = {}
for key in ANIS.keys():
files[key] = title + '_TY:_aniso-' + key + '_.' + fmt
pmagplotlib.saveP(ANIS, files)
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
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
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
dayplot_magic.py
DESCRIPTION
makes 'day plots' (Day et al. 1977) and squareness/coercivity,
plots 'linear mixing' curve from Dunlop and Carter-Stiglitz (2006).
squareness coercivity of remanence (Neel, 1955) plots after
Tauxe et al. (2002)
SYNTAX
dayplot_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input hysteresis file, default is specimens.txt
-fmt [svg,png,jpg] format for output plots
-sav saves plots and quits quietly
"""
args = sys.argv
if "-h" in args:
print(main.__doc__)
sys.exit()
verbose = pmagplotlib.verbose
dir_path = pmag.get_named_arg_from_sys('-WD', '.')
fmt = pmag.get_named_arg_from_sys('-fmt', 'svg')
if '-sav' in sys.argv:
plots = 1
verbose = False
else:
plots = 0
infile = pmag.get_named_arg_from_sys("-f", "specimens.txt")
fnames = {'specimens': infile}
con = nb.Contribution(dir_path, read_tables=['specimens'],
custom_filenames=fnames)
spec_container = con.tables['specimens']
spec_df = spec_container.df
#
# initialize some variables
# define figure numbers for Day,S-Bc,S-Bcr
DSC = {}
DSC['day'], DSC['S-Bc'], DSC['S-Bcr'], DSC['bcr1-bcr2'] = 1, 2, 3, 4
pmagplotlib.plot_init(DSC['day'], 5, 5)
pmagplotlib.plot_init(DSC['S-Bc'], 5, 5)
pmagplotlib.plot_init(DSC['S-Bcr'], 5, 5)
pmagplotlib.plot_init(DSC['bcr1-bcr2'], 5, 5)
S, BcrBc, Bcr2, Bc, hsids, Bcr = [], [], [], [], [], []
Bcr1, Bcr1Bc, S1 = [], [], []
locations = ''
if 'location' in spec_df.columns:
locations = spec_df['location'].unique()
do_rem = bool('rem_bcr' in spec_df.columns)
for ind, row in spec_df.iterrows():
if row['hyst_bcr'] and row['hyst_mr_moment']:
S.append(old_div(float(row['hyst_mr_moment']), float(row['hyst_ms_moment'])))
Bcr.append(float(row['hyst_bcr']))
Bc.append(float(row['hyst_bc']))
BcrBc.append(old_div(Bcr[-1], Bc[-1]))
hsids.append(row['specimen'])
if do_rem:
if row['rem_bcr'] and float(row['rem_bcr']) > 0:
try:
Bcr1.append(float(row['rem_bcr']))
Bcr1Bc.append(old_div(Bcr1[-1], Bc[-1]))
S1.append(S[-1])
Bcr2.append(Bcr[-1])
except ValueError:
if verbose:
print('hysteresis data for ', row['specimen'], end=' ')
print(' not found')
#
# now plot the day and S-Bc, S-Bcr plots
#
if len(Bcr1) > 0:
pmagplotlib.plotDay(DSC['day'], Bcr1Bc, S1, 'ro')
pmagplotlib.plotSBcr(DSC['S-Bcr'], Bcr1, S1, 'ro')
pmagplotlib.plot_init(DSC['bcr1-bcr2'], 5, 5)
pmagplotlib.plotBcr(DSC['bcr1-bcr2'], Bcr1, Bcr2)
else:
del DSC['bcr1-bcr2']
pmagplotlib.plotDay(DSC['day'], BcrBc, S, 'bs')
pmagplotlib.plotSBcr(DSC['S-Bcr'], Bcr, S, 'bs')
pmagplotlib.plotSBc(DSC['S-Bc'], Bc, S, 'bs')
files = {}
if len(locations) > 0:
locations = locations[:-1]
for key in list(DSC.keys()):
if pmagplotlib.isServer: # use server plot naming convention
files[key] = 'LO:_' + locations + '_' + 'SI:__SA:__SP:__TY:_' + key + '_.' + fmt
else: # use more readable plot naming convention
files[key] = '{}_{}.{}'.format(locations, key, fmt)
if verbose:
pmagplotlib.drawFIGS(DSC)
ans = input(" S[a]ve to save plots, return to quit: ")
if ans == "a":
pmagplotlib.saveP(DSC, files)
else:
sys.exit()
if plots:
pmagplotlib.saveP(DSC, files)
def main():
"""
NAME
eqarea.py
DESCRIPTION
makes equal area projections from declination/inclination data
INPUT FORMAT
takes dec/inc as first two columns in space delimited file
SYNTAX
eqarea.py [options]
OPTIONS
-f FILE, specify file on command line
-sav save figure and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
-s SIZE specify symbol size - default is 20
-Lsym SHAPE COLOR specify shape and color for lower hemisphere
-Usym SHAPE COLOR specify shape and color for upper hemisphere
shapes: 's': square,'o': circle,'^,>,v,<': [up,right,down,left] triangle, 'd': diamond,
'p': pentagram, 'h': hexagon, '8': octagon, '+': plus, 'x': cross
colors: [b]lue,[g]reen,[r]ed,[c]yan,[m]agenta,[y]ellow,blac[k],[w]hite
"""
title=""
files,fmt={},'svg'
sym={'lower':['o','r'],'upper':['o','w']}
plot=0
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-sav' in sys.argv: plot=1
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-s' in sys.argv:
ind=sys.argv.index('-s')
sym['size']=int(sys.argv[ind+1])
else:
sym['size']=20
if '-Lsym' in sys.argv:
ind=sys.argv.index('-Lsym')
sym['lower'][0]=sys.argv[ind+1]
sym['lower'][1]=sys.argv[ind+2]
if '-Usym' in sys.argv:
ind=sys.argv.index('-Usym')
sym['upper'][0]=sys.argv[ind+1]
sym['upper'][1]=sys.argv[ind+2]
if '-f' in sys.argv: # ask for filename
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
else:
print main.__doc__
print ' \n -f option required'
sys.exit() # graceful quit
DI=numpy.loadtxt(file)
EQ={'eq':1}
pmagplotlib.plot_init(EQ['eq'],5,5)
pmagplotlib.plotEQsym(EQ['eq'],DI,'Equal Area Plot',sym) # make plot
if plot==0:pmagplotlib.drawFIGS(EQ) # make it visible
for key in EQ.keys():
files[key]=key+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='Equal Area Plot'
EQ = pmagplotlib.addBorders(EQ,titles,black,purple)
pmagplotlib.saveP(EQ,files)
elif plot==1:
files['eq']=file+'.'+fmt
pmagplotlib.saveP(EQ,files)
else:
ans=raw_input(" S[a]ve to save plot, [q]uit without saving: ")
if ans=="a": pmagplotlib.saveP(EQ,files)
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
plotdi_e.py
DESCRIPTION
plots equal area projection from dec inc data and cones of confidence
(Fisher, kent or Bingham or bootstrap).
INPUT FORMAT
takes dec/inc as first two columns in space delimited file
SYNTAX
plotdi_e.py [command line options]
OPTIONS
-h prints help message and quits
-i for interactive parameter entry
-f FILE, sets input filename on command line
-Fish plots unit vector mean direction, alpha95
-Bing plots Principal direction, Bingham confidence ellipse
-Kent plots unit vector mean direction, confidence ellipse
-Boot E plots unit vector mean direction, bootstrapped confidence ellipse
-Boot V plots unit vector mean direction, distribution of bootstrapped means
"""
dist='F' # default distribution is Fisherian
mode=1
EQ={'eq':1}
if len(sys.argv) > 0:
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-i' in sys.argv: # ask for filename
file=raw_input("Enter file name with dec, inc data: ")
dist=raw_input("Enter desired distrubution: [Fish]er, [Bing]ham, [Kent] [Boot] [default is Fisher]: ")
if dist=="":dist="F"
if dist=="Boot":
type=raw_input(" Ellipses or distribution of vectors? [E]/V ")
if type=="" or type=="E":
dist="BE"
else:
dist="BE"
else:
#
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
else:
print 'you must specify a file name'
print main.__doc__
sys.exit()
if '-Bing' in sys.argv:dist='B'
if '-Kent' in sys.argv:dist='K'
if '-Boot' in sys.argv:
ind=sys.argv.index('-Boot')
type=sys.argv[ind+1]
if type=='E':
dist='BE'
elif type=='V':
dist='BV'
EQ['bdirs']=2
pmagplotlib.plot_init(EQ['bdirs'],5,5)
else:
print main.__doc__
sys.exit()
pmagplotlib.plot_init(EQ['eq'],5,5)
#
# get to work
f=open(file,'r')
data=f.readlines()
#
DIs= [] # set up list for dec inc data
DiRecs=[]
pars=[]
nDIs,rDIs,npars,rpars=[],[],[],[]
mode =1
for line in data: # read in the data from standard input
DiRec={}
rec=line.split() # split each line on space to get records
DIs.append((float(rec[0]),float(rec[1]),1.))
DiRec['dec']=rec[0]
DiRec['inc']=rec[1]
DiRec['direction_type']='l'
DiRecs.append(DiRec)
# split into two modes
ppars=pmag.doprinc(DIs) # get principal directions
for rec in DIs:
angle=pmag.angle([rec[0],rec[1]],[ppars['dec'],ppars['inc']])
if angle>90.:
rDIs.append(rec)
else:
nDIs.append(rec)
if dist=='B': # do on whole dataset
title="Bingham confidence ellipse"
bpars=pmag.dobingham(DIs)
for key in bpars.keys():
if key!='n':print " ",key, '%7.1f'%(bpars[key])
if key=='n':print " ",key, ' %i'%(bpars[key])
npars.append(bpars['dec'])
npars.append(bpars['inc'])
npars.append(bpars['Zeta'])
npars.append(bpars['Zdec'])
npars.append(bpars['Zinc'])
npars.append(bpars['Eta'])
npars.append(bpars['Edec'])
npars.append(bpars['Einc'])
if dist=='F':
title="Fisher confidence cone"
if len(nDIs)>3:
fpars=pmag.fisher_mean(nDIs)
print "mode ",mode
for key in fpars.keys():
if key!='n':print " ",key, '%7.1f'%(fpars[key])
if key=='n':print " ",key, ' %i'%(fpars[key])
mode+=1
npars.append(fpars['dec'])
npars.append(fpars['inc'])
npars.append(fpars['alpha95']) # Beta
npars.append(fpars['dec'])
isign=abs(fpars['inc'])/fpars['inc']
npars.append(fpars['inc']-isign*90.) #Beta inc
npars.append(fpars['alpha95']) # gamma
npars.append(fpars['dec']+90.) # Beta dec
npars.append(0.) #Beta inc
if len(rDIs)>3:
fpars=pmag.fisher_mean(rDIs)
print "mode ",mode
for key in fpars.keys():
if key!='n':print " ",key, '%7.1f'%(fpars[key])
if key=='n':print " ",key, ' %i'%(fpars[key])
mode+=1
rpars.append(fpars['dec'])
rpars.append(fpars['inc'])
rpars.append(fpars['alpha95']) # Beta
rpars.append(fpars['dec'])
isign=abs(fpars['inc'])/fpars['inc']
rpars.append(fpars['inc']-isign*90.) #Beta inc
rpars.append(fpars['alpha95']) # gamma
rpars.append(fpars['dec']+90.) # Beta dec
rpars.append(0.) #Beta inc
if dist=='K':
title="Kent confidence ellipse"
if len(nDIs)>3:
kpars=pmag.dokent(nDIs,len(nDIs))
print "mode ",mode
for key in kpars.keys():
if key!='n':print " ",key, '%7.1f'%(kpars[key])
if key=='n':print " ",key, ' %i'%(kpars[key])
mode+=1
npars.append(kpars['dec'])
npars.append(kpars['inc'])
npars.append(kpars['Zeta'])
npars.append(kpars['Zdec'])
npars.append(kpars['Zinc'])
npars.append(kpars['Eta'])
npars.append(kpars['Edec'])
npars.append(kpars['Einc'])
if len(rDIs)>3:
kpars=pmag.dokent(rDIs,len(rDIs))
print "mode ",mode
for key in kpars.keys():
if key!='n':print " ",key, '%7.1f'%(kpars[key])
if key=='n':print " ",key, ' %i'%(kpars[key])
mode+=1
rpars.append(kpars['dec'])
rpars.append(kpars['inc'])
rpars.append(kpars['Zeta'])
rpars.append(kpars['Zdec'])
rpars.append(kpars['Zinc'])
rpars.append(kpars['Eta'])
rpars.append(kpars['Edec'])
rpars.append(kpars['Einc'])
else: # assume bootstrap
if dist=='BE':
if len(nDIs)>5:
BnDIs=pmag.di_boot(nDIs)
Bkpars=pmag.dokent(BnDIs,1.)
print "mode ",mode
for key in Bkpars.keys():
if key!='n':print " ",key, '%7.1f'%(Bkpars[key])
if key=='n':print " ",key, ' %i'%(Bkpars[key])
mode+=1
npars.append(Bkpars['dec'])
npars.append(Bkpars['inc'])
npars.append(Bkpars['Zeta'])
npars.append(Bkpars['Zdec'])
npars.append(Bkpars['Zinc'])
npars.append(Bkpars['Eta'])
npars.append(Bkpars['Edec'])
npars.append(Bkpars['Einc'])
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
Bkpars=pmag.dokent(BrDIs,1.)
print "mode ",mode
for key in Bkpars.keys():
if key!='n':print " ",key, '%7.1f'%(Bkpars[key])
if key=='n':print " ",key, ' %i'%(Bkpars[key])
mode+=1
rpars.append(Bkpars['dec'])
rpars.append(Bkpars['inc'])
rpars.append(Bkpars['Zeta'])
rpars.append(Bkpars['Zdec'])
rpars.append(Bkpars['Zinc'])
rpars.append(Bkpars['Eta'])
rpars.append(Bkpars['Edec'])
rpars.append(Bkpars['Einc'])
title="Bootstrapped confidence ellipse"
elif dist=='BV':
if len(nDIs)>5:
pmagplotlib.plotEQ(EQ['eq'],nDIs,'Data')
BnDIs=pmag.di_boot(nDIs)
pmagplotlib.plotEQ(EQ['bdirs'],BnDIs,'Bootstrapped Eigenvectors')
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
if len(nDIs)>5: # plot on existing plots
pmagplotlib.plotDI(EQ['eq'],rDIs)
pmagplotlib.plotDI(EQ['bdirs'],BrDIs)
else:
pmagplotlib.plotEQ(EQ['eq'],rDIs,'Data')
pmagplotlib.plotEQ(EQ['bdirs'],BrDIs,'Bootstrapped Eigenvectors')
pmagplotlib.drawFIGS(EQ)
ans=raw_input('s[a]ve, [q]uit ')
if ans=='q':sys.exit()
if ans=='a':
files={}
for key in EQ.keys():
files[key]='BE_'+key+'.svg'
pmagplotlib.saveP(EQ,files)
sys.exit()
if len(nDIs)>5:
pmagplotlib.plotCONF(EQ['eq'],title,DiRecs,npars,1)
if len(rDIs)>5 and dist!='B':
pmagplotlib.plotCONF(EQ['eq'],title,[],rpars,0)
elif len(rDIs)>5 and dist!='B':
pmagplotlib.plotCONF(EQ['eq'],title,DiRecs,rpars,1)
pmagplotlib.drawFIGS(EQ)
ans=raw_input('s[a]ve, [q]uit ')
if ans=='q':sys.exit()
if ans=='a':
files={}
for key in EQ.keys():
files[key]=key+'.svg'
pmagplotlib.saveP(EQ,files)
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
print 'verbose?', 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
print 'verbose', verbose
#
#
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
cont_rot.py
DESCRIPTION
rotates continental fragments according to specified Euler pole
SYNTAX
cont_rot.py [command line options]
OPTIONS
-h prints help and quits
-con [af, congo, kala, aus, balt, eur, ind, sam, ant, grn, lau, nam, gond] , specify colon delimited list of continents to be displayed, e.g., af, af:aus], etc
-age use finite rotations of Torsvik et al. 2008 for specific age (5 Ma increments <325Ma)
rotates to paleomagnetic reference frame
available conts: [congo kala aus eur ind sam ant grn nam]
-sac include rotation of south african craton to pmag reference
-sym [ro, bs, g^, r., b-, etc.] [1,5,10] symbol and size for continent
colors are r=red,b=blue,g=green, etc.
symbols are '.' for points, ^, for triangle, s for square, etc.
-, for lines, -- for dotted lines, see matplotlib online documentation for plot()
-eye ELAT ELON [specify eyeball location]
-pfr PLAT PLON OMEGA [specify pole of finite rotation lat,lon and degrees]
-ffr FFILE, specifies series of finite rotations
vector in tab delimited file
-sr treat poles as sequential rotations
-fpp PFILE, specifies series of paleopoles from which
euler poles can be calculated: vector in tab delimited file
-pt LAT LON, specify a point to rotate along with continent
-fpt PTFILE, specifies file with a series of points to be plotted
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-fmt [png,jpg,svg,pdf] format for saved figure - pdf is default
-sav saves plots and quits
-prj PROJ, specify one of the supported projections: (see basemap.py online documentation)
aeqd = Azimuthal Equidistant
poly = Polyconic
gnom = Gnomonic
moll = Mollweide
tmerc = Transverse Mercator
nplaea = North-Polar Lambert Azimuthal
mill = Miller Cylindrical
merc = Mercator
stere = Stereographic
npstere = North-Polar Stereographic
geos = Geostationary
laea = Lambert Azimuthal Equal Area
sinu = Sinusoidal
spstere = South-Polar Stereographic
lcc = Lambert Conformal
npaeqd = North-Polar Azimuthal Equidistant
eqdc = Equidistant Conic
cyl = Cylindrical Equidistant
omerc = Oblique Mercator
aea = Albers Equal Area
spaeqd = South-Polar Azimuthal Equidistant
ortho = Orthographic
cass= Cassini-Soldner
splaea = South-Polar Lambert Azimuthal
robin = Robinson
DEFAULTS
con: nam
res: c
prj: mollweide
ELAT,ELON = 0,0
NB: high resolution or lines can be very slow
"""
dir_path='.'
ocean=0
res='c'
proj='moll'
euler_file=''
Conts=[]
Poles=[]
PTS=[]
lat_0,lon_0=0.,0.
fmt='pdf'
sym='r.'
symsize=5
plot=0
SEQ,age,SAC=0,0,0
rconts=['af','congo','kala','aus','eur','ind','sam','ant','grn','nam']
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 '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-con' in sys.argv:
ind = sys.argv.index('-con')
Conts=sys.argv[ind+1].split(':')
if '-age' in sys.argv:
ind = sys.argv.index('-age')
age=int(sys.argv[ind+1])
if age%5!=0 and age>320:
print main.__doc__
print 'age must be multiple of 5 less than 325'
sys.exit()
import pmagpy.frp as frp
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res=sys.argv[ind+1]
if res!= 'c' and res!='l':
print 'this resolution will take a while - be patient'
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj=sys.argv[ind+1]
if '-sav' in sys.argv: plot=1
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0=float(sys.argv[ind+1])
lon_0=float(sys.argv[ind+2])
if '-pt' in sys.argv:
ind = sys.argv.index('-pt')
pt_lat=float(sys.argv[ind+1])
pt_lon=float(sys.argv[ind+2])
PTS.append([pt_lat,pt_lon])
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym=sys.argv[ind+1]
symsize=int(sys.argv[ind+2])
# if '-rsym' in sys.argv:
# ind = sys.argv.index('-rsym')
# rsym=sys.argv[ind+1]
# rsymsize=int(sys.argv[ind+2])
if '-sr' in sys.argv: SEQ=1
if '-sac' in sys.argv: SAC=1
if '-pfr' in sys.argv:
ind = sys.argv.index('-pfr')
Poles.append([float(sys.argv[ind+1]),float(sys.argv[ind+2]),float(sys.argv[ind+3])])
elif '-ffr' in sys.argv:
ind = sys.argv.index('-ffr')
file=dir_path+'/'+sys.argv[ind+1]
f=open(file,'rU')
edata=f.readlines()
for line in edata:
rec=line.split()
Poles.append([float(rec[0]),float(rec[1]),float(rec[2])])
elif '-fpp' in sys.argv:
ind = sys.argv.index('-fpp')
file=dir_path+'/'+sys.argv[ind+1]
f=open(file,'rU')
pdata=f.readlines()
for line in pdata:
rec=line.split()
# transform paleopole to Euler pole taking shortest route
Poles.append([0.,float(rec[1])-90.,90.-float(rec[0])])
if '-fpt' in sys.argv:
ind = sys.argv.index('-fpt')
file=dir_path+'/'+sys.argv[ind+1]
f=open(file,'rU')
ptdata=f.readlines()
for line in ptdata:
rec=line.split()
PTS.append([float(rec[0]),float(rec[1])])
FIG={'map':1}
pmagplotlib.plot_init(FIG['map'],6,6)
# read in er_sites file
if res=='c':skip=8
if res=='l':skip=5
if res=='i':skip=2
if res=='h':skip=1
cnt=0
Opts={'latmin':-90,'latmax':90,'lonmin':0.,'lonmax':360.,'lat_0':lat_0,'lon_0':lon_0,'proj':proj,'sym':sym,'symsize':3,'pltgrid':0,'res':res,'boundinglat':0.}
if proj=='merc':
Opts['latmin']=-70
Opts['latmax']=70
Opts['lonmin']=-180
Opts['lonmax']=180
pmagplotlib.plotMAP(FIG['map'],[],[],Opts) # plot the basemap
Opts['pltgrid']=-1 # turn off replotting of gridlines
if '-pt' in sys.argv:
Opts['sym']=sym
Opts['symsize']=symsize
pmagplotlib.plotMAP(FIG['map'],[pt_lat],[pt_lon],Opts)
if plot==0:pmagplotlib.drawFIGS(FIG)
for cont in Conts:
Opts['sym']=sym
lats,lons=[],[]
if age!=0:
Poles=[]
rcont=cont
if rcont not in rconts:
print main.__doc__
print rcont
print 'continents must be one of following: '
print rconts
sys.exit()
if rcont=='congo':rcont='nwaf'
if rcont=='kala':rcont='neaf'
if rcont=='sam':rcont='sac'
if rcont=='ant':rcont='eant'
if rcont!='af':
Poles.append(frp.get_pole(rcont,age))
else:
Poles.append([0,0,0])
if SAC==1:Poles.append(frp.get_pole('saf',age))
SEQ=1
if Poles[-1]=='NONE':
print 'continent does not exist for rotation, try again '
sys.exit()
data=continents.get_continent(cont+'.asc')
for line in data:
if float(line[0])==0 and float(line[1])==0:line[0]='100.' # change stupid 0,0s to delimeters with lat=100
if float(line[0])>90:
lats.append(float(line[0]))
lons.append(float(line[1]))
elif cnt%skip==0:
lats.append(float(line[0]))
lons.append(float(line[1]))
cnt+=1
if len(lats)>0 and len(Poles)==0:
pmagplotlib.plotMAP(FIG['map'],lats,lons,Opts)
if plot==0:pmagplotlib.drawFIGS(FIG)
newlats,newlons=[],[]
for lat in lats:newlats.append(lat)
for lon in lons:newlons.append(lon)
Opts['pltgrid']=-1 # turns off replotting of meridians and parallels
for pole in Poles:
Rlats,Rlons=pmag.PTrot(pole,newlats,newlons)
Opts['sym']=sym
Opts['symsize']=3
if SEQ==0:
pmagplotlib.plotMAP(FIG['map'],Rlats,Rlons,Opts)
elif pole==Poles[-1]: # plot only last pole for sequential rotations
pmagplotlib.plotMAP(FIG['map'],Rlats,Rlons,Opts)
if plot==0:pmagplotlib.drawFIGS(FIG)
if SEQ==1: # treat poles as sequential rotations
newlats,newlons=[],[]
for lat in Rlats:newlats.append(lat)
for lon in Rlons:newlons.append(lon)
for pt in PTS:
pt_lat=pt[0]
pt_lon=pt[1]
Opts['sym']='r*'
Opts['symsize']=5
pmagplotlib.plotMAP(FIG['map'],[pt[0]],[pt[1]],Opts)
if plot==0:pmagplotlib.drawFIGS(FIG)
Opts['pltgrid']=-1 # turns off replotting of meridians and parallels
for pole in Poles:
Opts['sym']=sym
Opts['symsize']=symsize
Rlats,Rlons=pmag.PTrot(pole,[pt_lat],[pt_lon])
print Rlats,Rlons
pmagplotlib.plotMAP(FIG['map'],Rlats,Rlons,Opts)
if plot==0:pmagplotlib.drawFIGS(FIG)
Opts['sym']='g^'
Opts['symsize']=5
pmagplotlib.plotMAP(FIG['map'],[pole[0]],[pole[1]],Opts)
if plot==0:pmagplotlib.drawFIGS(FIG)
files={}
for key in FIG.keys():
files[key]='Cont_rot'+'.'+fmt
if plot==1:
pmagplotlib.saveP(FIG,files)
sys.exit()
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='Site Map'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
else:
pmagplotlib.drawFIGS(FIG)
ans=raw_input(" S[a]ve to save plot, Return to quit: ")
if ans=="a":
pmagplotlib.saveP(FIG,files)
def main():
"""
NAME
basemap_magic.py
NB: this program no longer maintained - use plot_mapPTS.py for greater functionality
DESCRIPTION
makes a map of locations in er_sites.txt
SYNTAX
basemap_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f SFILE, specify er_sites.txt or pmag_results.txt format file
-res [c,l,i,h] specify resolution (crude,low,intermediate,high)
-etp plot the etopo20 topographic mesh
-pad [LAT LON] pad bounding box by LAT/LON (default is [.5 .5] degrees)
-grd SPACE specify grid spacing
-prj [lcc] , specify projection (lcc=lambert conic conformable), default is mercator
-n print site names (default is not)
-l print location names (default is not)
-o color ocean blue/land green (default is not)
-R don't plot details of rivers
-B don't plot national/state boundaries, etc.
-sav save plot and quit quietly
-fmt [png,svg,eps,jpg,pdf] specify format for output, default is pdf
DEFAULTS
SFILE: 'er_sites.txt'
resolution: intermediate
saved images are in pdf
"""
dir_path='.'
sites_file='er_sites.txt'
ocean=0
res='i'
proj='merc'
prn_name=0
prn_loc=0
fancy=0
rivers,boundaries=0,0
padlon,padlat,gridspace,details=.5,.5,.5,1
fmt='pdf'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
sites_file=sys.argv[ind+1]
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res=sys.argv[ind+1]
if '-etp' in sys.argv:fancy=1
if '-n' in sys.argv:prn_name=1
if '-l' in sys.argv:prn_loc=1
if '-o' in sys.argv:ocean=1
if '-R' in sys.argv:rivers=0
if '-B' in sys.argv:boundaries=0
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj=sys.argv[ind+1]
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
verbose=pmagplotlib.verbose
if '-sav' in sys.argv:
verbose=0
if '-pad' in sys.argv:
ind = sys.argv.index('-pad')
padlat=float(sys.argv[ind+1])
padlon=float(sys.argv[ind+2])
if '-grd' in sys.argv:
ind = sys.argv.index('-grd')
gridspace=float(sys.argv[ind+1])
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
sites_file=dir_path+'/'+sites_file
location=""
FIG={'map':1}
pmagplotlib.plot_init(FIG['map'],6,6)
# read in er_sites file
Sites,file_type=pmag.magic_read(sites_file)
if 'results' in file_type:
latkey='average_lat'
lonkey='average_lon'
namekey='pmag_result_name'
lockey='er_location_names'
else:
latkey='site_lat'
lonkey='site_lon'
namekey='er_site_name'
lockey='er_location_name'
lats,lons=[],[]
slats,slons=[],[]
names,locs=[],[]
for site in Sites:
if prn_loc==1 and location=="":location=site['er_location_name']
lats.append(float(site[latkey]))
l=float(site[lonkey])
if l<0:l=l+360. # make positive
lons.append(l)
if prn_name==1:names.append(site[namekey])
if prn_loc==1:locs.append(site[lockey])
for lat in lats:slats.append(lat)
for lon in lons:slons.append(lon)
Opts={'res':res,'proj':proj,'loc_name':locs,'padlon':padlon,'padlat':padlat,'latmin':numpy.min(slats)-padlat,'latmax':numpy.max(slats)+padlat,'lonmin':numpy.min(slons)-padlon,'lonmax':numpy.max(slons)+padlon,'sym':'ro','boundinglat':0.,'pltgrid':1.}
Opts['lon_0']=0.5*(numpy.min(slons)+numpy.max(slons))
Opts['lat_0']=0.5*(numpy.min(slats)+numpy.max(slats))
Opts['names']=names
Opts['gridspace']=gridspace
Opts['details']={'coasts':1,'rivers':1,'states':1,'countries':1,'ocean':0}
if ocean==1:Opts['details']['ocean']=1
if rivers==1: Opts['details']['rivers']=0
if boundaries==1:
Opts['details']['states']=0
Opts['details']['countries']=0
Opts['details']['fancy']=fancy
pmagplotlib.plotMAP(FIG['map'],lats,lons,Opts)
if verbose:pmagplotlib.drawFIGS(FIG)
files={}
for key in FIG.keys():
files[key]='Site_map'+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['map']='Site Map'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
elif verbose:
ans=raw_input(" S[a]ve to save plot, Return to quit: ")
if ans=="a":
pmagplotlib.saveP(FIG,files)
else:
pmagplotlib.saveP(FIG,files)
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
eqarea.py
DESCRIPTION
makes equal area projections from declination/inclination data
INPUT FORMAT
takes dec/inc as first two columns in space delimited file
SYNTAX
eqarea.py [options]
OPTIONS
-f FILE, specify file on command line
-sav save figure and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
-s SIZE specify symbol size - default is 20
-Lsym SHAPE COLOR specify shape and color for lower hemisphere
-Usym SHAPE COLOR specify shape and color for upper hemisphere
shapes: 's': square,'o': circle,'^,>,v,<': [up,right,down,left] triangle, 'd': diamond,
'p': pentagram, 'h': hexagon, '8': octagon, '+': plus, 'x': cross
colors: [b]lue,[g]reen,[r]ed,[c]yan,[m]agenta,[y]ellow,blac[k],[w]hite
"""
title = ""
files, fmt = {}, 'svg'
sym = {'lower': ['o', 'r'], 'upper': ['o', 'w']}
plot = 0
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-sav' in sys.argv: plot = 1
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if '-s' in sys.argv:
ind = sys.argv.index('-s')
sym['size'] = int(sys.argv[ind + 1])
else:
sym['size'] = 20
if '-Lsym' in sys.argv:
ind = sys.argv.index('-Lsym')
sym['lower'][0] = sys.argv[ind + 1]
sym['lower'][1] = sys.argv[ind + 2]
if '-Usym' in sys.argv:
ind = sys.argv.index('-Usym')
sym['upper'][0] = sys.argv[ind + 1]
sym['upper'][1] = sys.argv[ind + 2]
if '-f' in sys.argv: # ask for filename
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
else:
print main.__doc__
print ' \n -f option required'
sys.exit() # graceful quit
DI = numpy.loadtxt(file)
EQ = {'eq': 1}
pmagplotlib.plot_init(EQ['eq'], 5, 5)
pmagplotlib.plotEQsym(EQ['eq'], DI, 'Equal Area Plot', sym) # make plot
if plot == 0: pmagplotlib.drawFIGS(EQ) # make it visible
for key in EQ.keys():
files[key] = key + '.' + fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['eq'] = 'Equal Area Plot'
EQ = pmagplotlib.addBorders(EQ, titles, black, purple)
pmagplotlib.saveP(EQ, files)
elif plot == 1:
files['eq'] = file + '.' + fmt
pmagplotlib.saveP(EQ, files)
else:
ans = raw_input(" S[a]ve to save plot, [q]uit without saving: ")
if ans == "a": pmagplotlib.saveP(EQ, files)
def main():
"""
NAME
plotdi_e.py
DESCRIPTION
plots equal area projection from dec inc data and cones of confidence
(Fisher, kent or Bingham or bootstrap).
INPUT FORMAT
takes dec/inc as first two columns in space delimited file
SYNTAX
plotdi_e.py [command line options]
OPTIONS
-h prints help message and quits
-i for interactive parameter entry
-f FILE, sets input filename on command line
-Fish plots unit vector mean direction, alpha95
-Bing plots Principal direction, Bingham confidence ellipse
-Kent plots unit vector mean direction, confidence ellipse
-Boot E plots unit vector mean direction, bootstrapped confidence ellipse
-Boot V plots unit vector mean direction, distribution of bootstrapped means
"""
dist = 'F' # default distribution is Fisherian
mode = 1
EQ = {'eq': 1}
if len(sys.argv) > 0:
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-i' in sys.argv: # ask for filename
file = raw_input("Enter file name with dec, inc data: ")
dist = raw_input(
"Enter desired distrubution: [Fish]er, [Bing]ham, [Kent] [Boot] [default is Fisher]: "
)
if dist == "": dist = "F"
if dist == "Boot":
type = raw_input(
" Ellipses or distribution of vectors? [E]/V ")
if type == "" or type == "E":
dist = "BE"
else:
dist = "BE"
else:
#
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
else:
print 'you must specify a file name'
print main.__doc__
sys.exit()
if '-Bing' in sys.argv: dist = 'B'
if '-Kent' in sys.argv: dist = 'K'
if '-Boot' in sys.argv:
ind = sys.argv.index('-Boot')
type = sys.argv[ind + 1]
if type == 'E':
dist = 'BE'
elif type == 'V':
dist = 'BV'
EQ['bdirs'] = 2
pmagplotlib.plot_init(EQ['bdirs'], 5, 5)
else:
print main.__doc__
sys.exit()
pmagplotlib.plot_init(EQ['eq'], 5, 5)
#
# get to work
f = open(file, 'r')
data = f.readlines()
#
DIs = [] # set up list for dec inc data
DiRecs = []
pars = []
nDIs, rDIs, npars, rpars = [], [], [], []
mode = 1
for line in data: # read in the data from standard input
DiRec = {}
rec = line.split() # split each line on space to get records
DIs.append((float(rec[0]), float(rec[1]), 1.))
DiRec['dec'] = rec[0]
DiRec['inc'] = rec[1]
DiRec['direction_type'] = 'l'
DiRecs.append(DiRec)
# split into two modes
ppars = pmag.doprinc(DIs) # get principal directions
for rec in DIs:
angle = pmag.angle([rec[0], rec[1]], [ppars['dec'], ppars['inc']])
if angle > 90.:
rDIs.append(rec)
else:
nDIs.append(rec)
if dist == 'B': # do on whole dataset
title = "Bingham confidence ellipse"
bpars = pmag.dobingham(DIs)
for key in bpars.keys():
if key != 'n': print " ", key, '%7.1f' % (bpars[key])
if key == 'n': print " ", key, ' %i' % (bpars[key])
npars.append(bpars['dec'])
npars.append(bpars['inc'])
npars.append(bpars['Zeta'])
npars.append(bpars['Zdec'])
npars.append(bpars['Zinc'])
npars.append(bpars['Eta'])
npars.append(bpars['Edec'])
npars.append(bpars['Einc'])
if dist == 'F':
title = "Fisher confidence cone"
if len(nDIs) > 3:
fpars = pmag.fisher_mean(nDIs)
print "mode ", mode
for key in fpars.keys():
if key != 'n': print " ", key, '%7.1f' % (fpars[key])
if key == 'n': print " ", key, ' %i' % (fpars[key])
mode += 1
npars.append(fpars['dec'])
npars.append(fpars['inc'])
npars.append(fpars['alpha95']) # Beta
npars.append(fpars['dec'])
isign = abs(fpars['inc']) / fpars['inc']
npars.append(fpars['inc'] - isign * 90.) #Beta inc
npars.append(fpars['alpha95']) # gamma
npars.append(fpars['dec'] + 90.) # Beta dec
npars.append(0.) #Beta inc
if len(rDIs) > 3:
fpars = pmag.fisher_mean(rDIs)
print "mode ", mode
for key in fpars.keys():
if key != 'n': print " ", key, '%7.1f' % (fpars[key])
if key == 'n': print " ", key, ' %i' % (fpars[key])
mode += 1
rpars.append(fpars['dec'])
rpars.append(fpars['inc'])
rpars.append(fpars['alpha95']) # Beta
rpars.append(fpars['dec'])
isign = abs(fpars['inc']) / fpars['inc']
rpars.append(fpars['inc'] - isign * 90.) #Beta inc
rpars.append(fpars['alpha95']) # gamma
rpars.append(fpars['dec'] + 90.) # Beta dec
rpars.append(0.) #Beta inc
if dist == 'K':
title = "Kent confidence ellipse"
if len(nDIs) > 3:
kpars = pmag.dokent(nDIs, len(nDIs))
print "mode ", mode
for key in kpars.keys():
if key != 'n': print " ", key, '%7.1f' % (kpars[key])
if key == 'n': print " ", key, ' %i' % (kpars[key])
mode += 1
npars.append(kpars['dec'])
npars.append(kpars['inc'])
npars.append(kpars['Zeta'])
npars.append(kpars['Zdec'])
npars.append(kpars['Zinc'])
npars.append(kpars['Eta'])
npars.append(kpars['Edec'])
npars.append(kpars['Einc'])
if len(rDIs) > 3:
kpars = pmag.dokent(rDIs, len(rDIs))
print "mode ", mode
for key in kpars.keys():
if key != 'n': print " ", key, '%7.1f' % (kpars[key])
if key == 'n': print " ", key, ' %i' % (kpars[key])
mode += 1
rpars.append(kpars['dec'])
rpars.append(kpars['inc'])
rpars.append(kpars['Zeta'])
rpars.append(kpars['Zdec'])
rpars.append(kpars['Zinc'])
rpars.append(kpars['Eta'])
rpars.append(kpars['Edec'])
rpars.append(kpars['Einc'])
else: # assume bootstrap
if dist == 'BE':
if len(nDIs) > 5:
BnDIs = pmag.di_boot(nDIs)
Bkpars = pmag.dokent(BnDIs, 1.)
print "mode ", mode
for key in Bkpars.keys():
if key != 'n': print " ", key, '%7.1f' % (Bkpars[key])
if key == 'n':
print " ", key, ' %i' % (Bkpars[key])
mode += 1
npars.append(Bkpars['dec'])
npars.append(Bkpars['inc'])
npars.append(Bkpars['Zeta'])
npars.append(Bkpars['Zdec'])
npars.append(Bkpars['Zinc'])
npars.append(Bkpars['Eta'])
npars.append(Bkpars['Edec'])
npars.append(Bkpars['Einc'])
if len(rDIs) > 5:
BrDIs = pmag.di_boot(rDIs)
Bkpars = pmag.dokent(BrDIs, 1.)
print "mode ", mode
for key in Bkpars.keys():
if key != 'n': print " ", key, '%7.1f' % (Bkpars[key])
if key == 'n':
print " ", key, ' %i' % (Bkpars[key])
mode += 1
rpars.append(Bkpars['dec'])
rpars.append(Bkpars['inc'])
rpars.append(Bkpars['Zeta'])
rpars.append(Bkpars['Zdec'])
rpars.append(Bkpars['Zinc'])
rpars.append(Bkpars['Eta'])
rpars.append(Bkpars['Edec'])
rpars.append(Bkpars['Einc'])
title = "Bootstrapped confidence ellipse"
elif dist == 'BV':
if len(nDIs) > 5:
pmagplotlib.plotEQ(EQ['eq'], nDIs, 'Data')
BnDIs = pmag.di_boot(nDIs)
pmagplotlib.plotEQ(EQ['bdirs'], BnDIs,
'Bootstrapped Eigenvectors')
if len(rDIs) > 5:
BrDIs = pmag.di_boot(rDIs)
if len(nDIs) > 5: # plot on existing plots
pmagplotlib.plotDI(EQ['eq'], rDIs)
pmagplotlib.plotDI(EQ['bdirs'], BrDIs)
else:
pmagplotlib.plotEQ(EQ['eq'], rDIs, 'Data')
pmagplotlib.plotEQ(EQ['bdirs'], BrDIs,
'Bootstrapped Eigenvectors')
pmagplotlib.drawFIGS(EQ)
ans = raw_input('s[a]ve, [q]uit ')
if ans == 'q': sys.exit()
if ans == 'a':
files = {}
for key in EQ.keys():
files[key] = 'BE_' + key + '.svg'
pmagplotlib.saveP(EQ, files)
sys.exit()
if len(nDIs) > 5:
pmagplotlib.plotCONF(EQ['eq'], title, DiRecs, npars, 1)
if len(rDIs) > 5 and dist != 'B':
pmagplotlib.plotCONF(EQ['eq'], title, [], rpars, 0)
elif len(rDIs) > 5 and dist != 'B':
pmagplotlib.plotCONF(EQ['eq'], title, DiRecs, rpars, 1)
pmagplotlib.drawFIGS(EQ)
ans = raw_input('s[a]ve, [q]uit ')
if ans == 'q': sys.exit()
if ans == 'a':
files = {}
for key in EQ.keys():
files[key] = key + '.svg'
pmagplotlib.saveP(EQ, files)
def main():
"""
NAME
eqarea_magic.py
DESCRIPTION
makes equal area projections from declination/inclination data
SYNTAX
eqarea_magic.py [command line options]
INPUT
takes magic formatted sites, samples, specimens, or measurements
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file from magic, default='sites.txt'
supported types=[measurements, specimens, samples, sites]
-fsp FILE: specify specimen file name, (required if you want to plot measurements by sample)
default='specimens.txt'
-fsa FILE: specify sample file name, (required if you want to plot specimens by site)
default='samples.txt'
-fsi FILE: specify site file name, default='sites.txt'
-obj OBJ: specify level of plot [all, sit, sam, spc], default is all
-crd [s,g,t]: specify coordinate system, [s]pecimen, [g]eographic, [t]ilt adjusted
default is geographic, unspecified assumed geographic
-fmt [svg,png,jpg] format for output plots
-ell [F,K,B,Be,Bv] plot Fisher, Kent, Bingham, Bootstrap ellipses or Boostrap eigenvectors
-c plot as colour contour
-sav save plot and quit quietly
NOTE
all: entire file; sit: site; sam: sample; spc: specimen
"""
# initialize some default variables
FIG = {} # plot dictionary
FIG['eqarea'] = 1 # eqarea is figure 1
plotE = 0
plt = 0 # default to not plotting
verbose = pmagplotlib.verbose
# extract arguments from sys.argv
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg_from_sys("-WD", default_val=".")
pmagplotlib.plot_init(FIG['eqarea'],5,5)
in_file = pmag.get_named_arg_from_sys("-f", default_val="sites.txt")
in_file = pmag.resolve_file_name(in_file, dir_path)
if "-WD" not in sys.argv:
dir_path = os.path.split(in_file)[0]
#full_in_file = os.path.join(dir_path, in_file)
plot_by = pmag.get_named_arg_from_sys("-obj", default_val="all").lower()
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")
if plot_by == 'all':
plot_key = 'all'
elif plot_by == 'sit':
plot_key = 'site'
elif plot_by == 'sam':
plot_key = 'sample'
elif plot_by == 'spc':
plot_key = 'specimen'
else:
plot_by = 'all'
plot_key = 'all'
if '-c' in sys.argv:
contour = 1
else:
contour = 0
if '-sav' in sys.argv:
plt = 1
verbose = 0
if '-ell' in sys.argv:
plotE = 1
ind = sys.argv.index('-ell')
ell_type = sys.argv[ind+1]
ell_type = pmag.get_named_arg_from_sys("-ell", "F")
dist = ell_type.upper()
# if dist type is unrecognized, use Fisher
if dist not in ['F', 'K', 'B', 'BE', 'BV']:
dist = 'F'
if dist == "BV":
FIG['bdirs'] = 2
pmagplotlib.plot_init(FIG['bdirs'],5,5)
crd = pmag.get_named_arg_from_sys("-crd", default_val="g")
if crd == "s":
coord = "-1"
elif crd == "t":
coord = "100"
else:
coord = "0"
fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
dec_key = 'dir_dec'
inc_key = 'dir_inc'
tilt_key = 'dir_tilt_correction'
#Dir_type_keys=['','site_direction_type','sample_direction_type','specimen_direction_type']
#
fnames = {"specimens": spec_file, "samples": samp_file, 'sites': site_file}
contribution = nb.Contribution(dir_path, custom_filenames=fnames,
single_file=in_file)
try:
contribution.propagate_location_to_samples()
contribution.propagate_location_to_specimens()
contribution.propagate_location_to_measurements()
except KeyError as ex:
pass
# the object that contains the DataFrame + useful helper methods:
table_name = list(contribution.tables.keys())[0]
data_container = contribution.tables[table_name]
# the actual DataFrame:
data = data_container.df
if plot_key != "all" and plot_key not in data.columns:
print("-E- You can't plot by {} with the data provided".format(plot_key))
return
# add tilt key into DataFrame columns if it isn't there already
if tilt_key not in data.columns:
data.loc[:, tilt_key] = None
if verbose:
print(len(data), ' records read from ', in_file)
# find desired dec,inc data:
dir_type_key = ''
#
# get plotlist if not plotting all records
#
plotlist=[]
if plot_key != "all":
# return all where plot_key is not blank
if plot_key not in data.columns:
print('Can\'t plot by "{}". That header is not in infile: {}'.format(plot_key, in_file))
return
plots = data[data[plot_key].notnull()]
plotlist = plots[plot_key].unique() # grab unique values
else:
plotlist.append('All')
for plot in plotlist:
if verbose:
print(plot)
if plot == 'All':
# plot everything at once
plot_data = data
else:
# pull out only partial data
plot_data = data[data[plot_key] == plot]
DIblock = []
GCblock = []
# SLblock, SPblock = [], []
title = plot
mode = 1
k = 0
if dec_key not in plot_data.columns:
print("-W- No dec/inc data")
continue
# get all records where dec & inc values exist
plot_data = plot_data[plot_data[dec_key].notnull() & plot_data[inc_key].notnull()]
if plot_data.empty:
continue
# this sorting out is done in get_di_bock
#if coord == '0': # geographic, use records with no tilt key (or tilt_key 0)
# cond1 = plot_data[tilt_key].fillna('') == coord
# cond2 = plot_data[tilt_key].isnull()
# plot_data = plot_data[cond1 | cond2]
#else: # not geographic coordinates, use only records with correct tilt_key
# plot_data = plot_data[plot_data[tilt_key] == coord]
# get metadata for naming the plot file
locations = data_container.get_name('location', df_slice=plot_data)
site = data_container.get_name('site', df_slice=plot_data)
sample = data_container.get_name('sample', df_slice=plot_data)
specimen = data_container.get_name('specimen', df_slice=plot_data)
# make sure method_codes is in plot_data
if 'method_codes' not in plot_data.columns:
plot_data['method_codes'] = ''
# get data blocks
DIblock = data_container.get_di_block(df_slice=plot_data,
tilt_corr=coord, excl=['DE-BFP'])
#SLblock = [[ind, row['method_codes']] for ind, row in plot_data.iterrows()]
# get great circles
great_circle_data = data_container.get_records_for_code('DE-BFP', incl=True,
use_slice=True, sli=plot_data)
if len(great_circle_data) > 0:
gc_cond = great_circle_data[tilt_key] == coord
GCblock = [[float(row[dec_key]), float(row[inc_key])] for ind, row in great_circle_data[gc_cond].iterrows()]
#SPblock = [[ind, row['method_codes']] for ind, row in great_circle_data[gc_cond].iterrows()]
if len(DIblock) > 0:
if contour == 0:
pmagplotlib.plotEQ(FIG['eqarea'], DIblock, title)
else:
pmagplotlib.plotEQcont(FIG['eqarea'], DIblock)
else:
pmagplotlib.plotNET(FIG['eqarea'])
if len(GCblock)>0:
for rec in GCblock:
pmagplotlib.plotC(FIG['eqarea'], rec, 90., 'g')
if len(DIblock) == 0 and len(GCblock) == 0:
if verbose:
print("no records for plotting")
continue
#sys.exit()
if plotE == 1:
ppars = pmag.doprinc(DIblock) # get principal directions
nDIs, rDIs, npars, rpars = [], [], [], []
for rec in DIblock:
angle=pmag.angle([rec[0],rec[1]],[ppars['dec'],ppars['inc']])
if angle>90.:
rDIs.append(rec)
else:
nDIs.append(rec)
if dist=='B': # do on whole dataset
etitle="Bingham confidence ellipse"
bpars=pmag.dobingham(DIblock)
for key in list(bpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(bpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(bpars[key]))
npars.append(bpars['dec'])
npars.append(bpars['inc'])
npars.append(bpars['Zeta'])
npars.append(bpars['Zdec'])
npars.append(bpars['Zinc'])
npars.append(bpars['Eta'])
npars.append(bpars['Edec'])
npars.append(bpars['Einc'])
if dist=='F':
etitle="Fisher confidence cone"
if len(nDIs)>2:
fpars=pmag.fisher_mean(nDIs)
for key in list(fpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(fpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(fpars[key]))
mode+=1
npars.append(fpars['dec'])
npars.append(fpars['inc'])
npars.append(fpars['alpha95']) # Beta
npars.append(fpars['dec'])
isign=old_div(abs(fpars['inc']),fpars['inc'])
npars.append(fpars['inc']-isign*90.) #Beta inc
npars.append(fpars['alpha95']) # gamma
npars.append(fpars['dec']+90.) # Beta dec
npars.append(0.) #Beta inc
if len(rDIs)>2:
fpars=pmag.fisher_mean(rDIs)
if verbose: print("mode ",mode)
for key in list(fpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(fpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(fpars[key]))
mode+=1
rpars.append(fpars['dec'])
rpars.append(fpars['inc'])
rpars.append(fpars['alpha95']) # Beta
rpars.append(fpars['dec'])
isign=old_div(abs(fpars['inc']),fpars['inc'])
rpars.append(fpars['inc']-isign*90.) #Beta inc
rpars.append(fpars['alpha95']) # gamma
rpars.append(fpars['dec']+90.) # Beta dec
rpars.append(0.) #Beta inc
if dist=='K':
etitle="Kent confidence ellipse"
if len(nDIs)>3:
kpars=pmag.dokent(nDIs,len(nDIs))
if verbose: print("mode ",mode)
for key in list(kpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(kpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(kpars[key]))
mode+=1
npars.append(kpars['dec'])
npars.append(kpars['inc'])
npars.append(kpars['Zeta'])
npars.append(kpars['Zdec'])
npars.append(kpars['Zinc'])
npars.append(kpars['Eta'])
npars.append(kpars['Edec'])
npars.append(kpars['Einc'])
if len(rDIs)>3:
kpars=pmag.dokent(rDIs,len(rDIs))
if verbose: print("mode ",mode)
for key in list(kpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(kpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(kpars[key]))
mode+=1
rpars.append(kpars['dec'])
rpars.append(kpars['inc'])
rpars.append(kpars['Zeta'])
rpars.append(kpars['Zdec'])
rpars.append(kpars['Zinc'])
rpars.append(kpars['Eta'])
rpars.append(kpars['Edec'])
rpars.append(kpars['Einc'])
else: # assume bootstrap
if dist=='BE':
if len(nDIs)>5:
BnDIs=pmag.di_boot(nDIs)
Bkpars=pmag.dokent(BnDIs,1.)
if verbose: print("mode ",mode)
for key in list(Bkpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(Bkpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(Bkpars[key]))
mode+=1
npars.append(Bkpars['dec'])
npars.append(Bkpars['inc'])
npars.append(Bkpars['Zeta'])
npars.append(Bkpars['Zdec'])
npars.append(Bkpars['Zinc'])
npars.append(Bkpars['Eta'])
npars.append(Bkpars['Edec'])
npars.append(Bkpars['Einc'])
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
Bkpars=pmag.dokent(BrDIs,1.)
if verbose: print("mode ",mode)
for key in list(Bkpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(Bkpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(Bkpars[key]))
mode+=1
rpars.append(Bkpars['dec'])
rpars.append(Bkpars['inc'])
rpars.append(Bkpars['Zeta'])
rpars.append(Bkpars['Zdec'])
rpars.append(Bkpars['Zinc'])
rpars.append(Bkpars['Eta'])
rpars.append(Bkpars['Edec'])
rpars.append(Bkpars['Einc'])
etitle="Bootstrapped confidence ellipse"
elif dist=='BV':
sym={'lower':['o','c'],'upper':['o','g'],'size':3,'edgecolor':'face'}
if len(nDIs)>5:
BnDIs=pmag.di_boot(nDIs)
pmagplotlib.plotEQsym(FIG['bdirs'],BnDIs,'Bootstrapped Eigenvectors', sym)
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
if len(nDIs)>5: # plot on existing plots
pmagplotlib.plotDIsym(FIG['bdirs'],BrDIs,sym)
else:
pmagplotlib.plotEQ(FIG['bdirs'],BrDIs,'Bootstrapped Eigenvectors')
if dist=='B':
if len(nDIs)> 3 or len(rDIs)>3: pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],npars,0)
elif len(nDIs)>3 and dist!='BV':
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],npars,0)
if len(rDIs)>3:
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],rpars,0)
elif len(rDIs)>3 and dist!='BV':
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],rpars,0)
for key in list(FIG.keys()):
files = {}
filename = pmag.get_named_arg_from_sys('-fname')
if filename: # use provided filename
filename+= '.' + fmt
elif pmagplotlib.isServer: # use server plot naming convention
filename='LO:_'+locations+'_SI:_'+site+'_SA:_'+sample+'_SP:_'+specimen+'_CO:_'+crd+'_TY:_'+key+'_.'+fmt
elif plot_key == 'all':
filename = 'all'
if 'location' in plot_data.columns:
locs = plot_data['location'].unique()
loc_string = "_".join([loc.replace(' ', '_') for loc in locs])
filename += "_" + loc_string
filename += "_" + crd + "_" + key
filename += ".{}".format(fmt)
else: # use more readable naming convention
filename = ''
# fix this if plot_by is location , for example
use_names = {'location': [locations], 'site': [locations, site],
'sample': [locations, site, sample],
'specimen': [locations, site, sample, specimen]}
use = use_names[plot_key]
use.extend([crd, key])
for item in use: #[locations, site, sample, specimen, crd, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key]=filename
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='Equal Area Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
if plt:
pmagplotlib.saveP(FIG,files)
continue
if verbose:
pmagplotlib.drawFIGS(FIG)
ans=input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans == "q":
sys.exit()
if ans == "a":
pmagplotlib.saveP(FIG,files)
continue
def main():
"""
NAME
plotdi_a.py
DESCRIPTION
plots equal area projection from dec inc data and fisher mean, cone of confidence
INPUT FORMAT
takes dec, inc, alpha95 as first three columns in space delimited file
SYNTAX
plotdi_a.py [-i][-f FILE]
OPTIONS
-f FILE to read file name from command line
-fmt [png,jpg,eps,pdf,svg] set plot file format ['svg' is default]
-sav save plot and quit
"""
fmt,plot='svg',0
if len(sys.argv) > 0:
if '-h' in sys.argv: # check if help is needed
print(main.__doc__)
sys.exit() # graceful quit
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-sav' in sys.argv:plot=1
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
f=open(file,'r')
data=f.readlines()
else:
data=sys.stdin.readlines() # read in data from standard input
DIs,Pars=[],[]
for line in data: # read in the data from standard input
pars=[]
rec=line.split() # split each line on space to get records
DIs.append([float(rec[0]),float(rec[1])])
pars.append(float(rec[0]))
pars.append(float(rec[1]))
pars.append(float(rec[2]))
pars.append(float(rec[0]))
isign=old_div(abs(float(rec[1])),float(rec[1]))
pars.append(float(rec[1])-isign*90.) #Beta inc
pars.append(float(rec[2])) # gamma
pars.append(float(rec[0])+90.) # Beta dec
pars.append(0.) #Beta inc
Pars.append(pars)
#
EQ={'eq':1} # make plot dictionary
pmagplotlib.plot_init(EQ['eq'],5,5)
title='Equal area projection'
pmagplotlib.plotEQ(EQ['eq'],DIs,title)# plot directions
for k in range(len(Pars)):
pmagplotlib.plotELL(EQ['eq'],Pars[k],'b',0,1) # plot ellipses
files={}
for key in list(EQ.keys()):
files[key]=key+'.'+fmt
titles={}
titles['eq']='Equal Area Plot'
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
EQ = pmagplotlib.addBorders(EQ,titles,black,purple)
pmagplotlib.saveP(EQ,files)
elif plot==0:
pmagplotlib.drawFIGS(EQ)
ans=input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans=="q": sys.exit()
if ans=="a":
pmagplotlib.saveP(EQ,files)
else:
pmagplotlib.saveP(EQ,files)
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
zeq.py
DESCRIPTION
plots demagnetization data. The equal area projection has the X direction (usually North in geographic coordinates)
to the top. The red line is the X axis of the Zijderveld diagram. Solid symbols are lower hemisphere.
The solid (open) symbols in the Zijderveld diagram are X,Y (X,Z) pairs. The demagnetization diagram plots the
fractional remanence remaining after each step. The green line is the fraction of the total remaence removed
between each step.
INPUT FORMAT
takes specimen_name treatment intensity declination inclination in space
delimited file
SYNTAX
zeq.py [command line options
OPTIONS
-f FILE for reading from command line
-u [mT,C] specify units of mT OR C, default is unscaled
-sav save figure and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
-beg [step number] treatment step for beginning of PCA calculation, 0 is default
-end [step number] treatment step for end of PCA calculation, last step is default
-ct [l,p,f] Calculation Type: best-fit line, plane or fisher mean; line is default
"""
files, fmt, plot = {}, 'svg', 0
end_pca, beg_pca = "", ""
calculation_type = 'DE-BFL'
if '-h' in sys.argv: # check if help is needed
print(main.__doc__)
sys.exit() # graceful quit
else:
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
else:
print(main.__doc__)
sys.exit()
if '-u' in sys.argv:
ind = sys.argv.index('-u')
units = sys.argv[ind + 1]
if units == "C": SIunits = "K"
if units == "mT": SIunits = "T"
else:
units = "U"
SIunits = "U"
if '-sav' in sys.argv: plot = 1
if '-ct' in sys.argv:
ind = sys.argv.index('-ct')
ct = sys.argv[ind + 1]
if ct == 'f': calculation_type = 'DE-FM'
if ct == 'p': calculation_type = 'DE-BFP'
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if '-beg' in sys.argv:
ind = sys.argv.index('-beg')
beg_pca = int(sys.argv[ind + 1])
if '-end' in sys.argv:
ind = sys.argv.index('-end')
end_pca = int(sys.argv[ind + 1])
f = open(file, 'r')
data = f.readlines()
#
datablock = [] # set up list for data
s = "" # initialize specimen name
angle = 0.
for line in data: # read in the data from standard input
rec = line.split() # split each line on space to get records
if angle == "": angle = float(rec[3])
if s == "": s = rec[0]
if units == 'mT':
datablock.append([
float(rec[1]) * 1e-3,
float(rec[3]),
float(rec[4]), 1e-3 * float(rec[2]), '', 'g'
]) # treatment, dec, inc, int # convert to T and Am^2 (assume emu)
if units == 'C':
datablock.append([
float(rec[1]) + 273.,
float(rec[3]),
float(rec[4]), 1e-3 * float(rec[2]), '', 'g'
]) # treatment, dec, inc, int, convert to K and Am^2, assume emu
if units == 'U':
datablock.append([
float(rec[1]),
float(rec[3]),
float(rec[4]),
float(rec[2]), '', 'g'
]) # treatment, dec, inc, int, using unscaled units
# define figure numbers in a dictionary for equal area, zijderveld,
# and intensity vs. demagnetiztion step respectively
ZED = {}
ZED['eqarea'], ZED['zijd'], ZED['demag'] = 1, 2, 3
pmagplotlib.plot_init(ZED['eqarea'], 5, 5) # initialize plots
pmagplotlib.plot_init(ZED['zijd'], 5, 5)
pmagplotlib.plot_init(ZED['demag'], 5, 5)
#
#
pmagplotlib.plotZED(ZED, datablock, angle, s, SIunits) # plot the data
if plot == 0: pmagplotlib.drawFIGS(ZED)
#
# print out data for this sample to screen
#
recnum = 0
for plotrec in datablock:
if units == 'mT':
print(
'%i %7.1f %8.3e %7.1f %7.1f ' %
(recnum, plotrec[0] * 1e3, plotrec[3], plotrec[1], plotrec[2]))
if units == 'C':
print('%i %7.1f %8.3e %7.1f %7.1f ' %
(recnum, plotrec[0] - 273., plotrec[3], plotrec[1],
plotrec[2]))
if units == 'U':
print('%i %7.1f %8.3e %7.1f %7.1f ' %
(recnum, plotrec[0], plotrec[3], plotrec[1], plotrec[2]))
recnum += 1
if plot == 0:
while 1:
if beg_pca != "" and end_pca != "" and calculation_type != "":
pmagplotlib.plotZED(ZED, datablock, angle, s,
SIunits) # plot the data
mpars = pmag.domean(
datablock, beg_pca, end_pca,
calculation_type) # get best-fit direction/great circle
pmagplotlib.plotDir(
ZED, mpars, datablock,
angle) # plot the best-fit direction/great circle
print('Specimen, calc_type, N, min, max, MAD, dec, inc')
if units == 'mT':
print('%s %s %i %6.2f %6.2f %6.1f %7.1f %7.1f' %
(s, calculation_type, mpars["specimen_n"],
mpars["measurement_step_min"] * 1e3,
mpars["measurement_step_max"] * 1e3,
mpars["specimen_mad"], mpars["specimen_dec"],
mpars["specimen_inc"]))
if units == 'C':
print('%s %s %i %6.2f %6.2f %6.1f %7.1f %7.1f' %
(s, calculation_type, mpars["specimen_n"],
mpars["measurement_step_min"] - 273,
mpars["measurement_step_max"] - 273,
mpars["specimen_mad"], mpars["specimen_dec"],
mpars["specimen_inc"]))
if units == 'U':
print(
'%s %s %i %6.2f %6.2f %6.1f %7.1f %7.1f' %
(s, calculation_type, mpars["specimen_n"],
mpars["measurement_step_min"],
mpars["measurement_step_max"], mpars["specimen_mad"],
mpars["specimen_dec"], mpars["specimen_inc"]))
if end_pca == "":
end_pca = len(
datablock
) - 1 # initialize end_pca, beg_pca to first and last measurement
if beg_pca == "": beg_pca = 0
ans = input(
" s[a]ve plot, [b]ounds for pca and calculate, change [h]orizontal projection angle, [q]uit: "
)
if ans == 'q':
sys.exit()
if ans == 'a':
files = {}
for key in list(ZED.keys()):
files[key] = s + '_' + key + '.' + fmt
pmagplotlib.saveP(ZED, files)
if ans == 'h':
angle = float(
input(" Declination to project onto horizontal axis? "))
pmagplotlib.plotZED(ZED, datablock, angle, s,
SIunits) # plot the data
if ans == 'b':
GoOn = 0
while GoOn == 0: # keep going until reasonable bounds are set
print('Enter index of first point for pca: ', '[', beg_pca,
']')
answer = input('return to keep default ')
if answer != "": beg_pca = int(answer)
print('Enter index of last point for pca: ', '[', end_pca,
']')
answer = input('return to keep default ')
if answer != "":
end_pca = int(answer)
if beg_pca >= 0 and beg_pca <= len(
datablock) - 2 and end_pca > 0 and end_pca < len(
datablock):
GoOn = 1
else:
print("Bad entry of indices - try again")
end_pca = len(datablock) - 1
beg_pca = 0
GoOn = 0
while GoOn == 0:
ct = input(
'Enter Calculation Type: best-fit line, plane or fisher mean [l]/p/f : '
)
if ct == "" or ct == "l":
calculation_type = "DE-BFL"
GoOn = 1 # all good
elif ct == 'p':
calculation_type = "DE-BFP"
GoOn = 1 # all good
elif ct == 'f':
calculation_type = "DE-FM"
GoOn = 1 # all good
else:
print("bad entry of calculation type: try again. "
) # keep going
pmagplotlib.plotZED(ZED, datablock, angle, s,
SIunits) # plot the data
mpars = pmag.domean(
datablock, beg_pca, end_pca, calculation_type
) # get best-fit direction/great circle
pmagplotlib.plotDir(
ZED, mpars, datablock,
angle) # plot the best-fit direction/great circle
print('Specimen, calc_type, N, min, max, MAD, dec, inc')
if units == 'mT':
print('%s %s %i %6.2f %6.2f %6.1f %7.1f %7.1f' %
(s, calculation_type, mpars["specimen_n"],
mpars["measurement_step_min"] * 1e3,
mpars["measurement_step_max"] * 1e3,
mpars["specimen_mad"], mpars["specimen_dec"],
mpars["specimen_inc"]))
if units == 'C':
print('%s %s %i %6.2f %6.2f %6.1f %7.1f %7.1f' %
(s, calculation_type, mpars["specimen_n"],
mpars["measurement_step_min"] - 273,
mpars["measurement_step_max"] - 273,
mpars["specimen_mad"], mpars["specimen_dec"],
mpars["specimen_inc"]))
if units == 'U':
print('%s %s %i %6.2f %6.2f %6.1f %7.1f %7.1f' %
(s, calculation_type, mpars["specimen_n"],
mpars["measurement_step_min"],
mpars["measurement_step_max"],
mpars["specimen_mad"], mpars["specimen_dec"],
mpars["specimen_inc"]))
pmagplotlib.drawFIGS(ZED)
else:
print(beg_pca, end_pca)
if beg_pca != "" and end_pca != "":
pmagplotlib.plotZED(ZED, datablock, angle, s,
SIunits) # plot the data
mpars = pmag.domean(
datablock, beg_pca, end_pca,
calculation_type) # get best-fit direction/great circle
pmagplotlib.plotDir(
ZED, mpars, datablock,
angle) # plot the best-fit direction/great circle
print('Specimen, calc_type, N, min, max, MAD, dec, inc')
if units == 'mT':
print('%s %s %i %6.2f %6.2f %6.1f %7.1f %7.1f' %
(s, calculation_type, mpars["specimen_n"],
mpars["measurement_step_min"] * 1e3,
mpars["measurement_step_max"] * 1e3,
mpars["specimen_mad"], mpars["specimen_dec"],
mpars["specimen_inc"]))
if units == 'C':
print('%s %s %i %6.2f %6.2f %6.1f %7.1f %7.1f' %
(s, calculation_type, mpars["specimen_n"],
mpars["measurement_step_min"] - 273,
mpars["measurement_step_max"] - 273,
mpars["specimen_mad"], mpars["specimen_dec"],
mpars["specimen_inc"]))
if units == 'U':
print('%s %s %i %6.2f %6.2f %6.1f %7.1f %7.1f' %
(s, calculation_type, mpars["specimen_n"],
mpars["measurement_step_min"],
mpars["measurement_step_max"], mpars["specimen_mad"],
mpars["specimen_dec"], mpars["specimen_inc"]))
files = {}
for key in list(ZED.keys()):
files[key] = s + '_' + key + '.' + fmt
pmagplotlib.saveP(ZED, files)
def main():
"""
NAME
revtest.py
DESCRIPTION
calculates bootstrap statistics to test for antipodality
INPUT FORMAT
takes dec/inc as first two columns in space delimited file
SYNTAX
revtest.py [-h] [command line options]
OPTION
-h prints help message and quits
-f FILE, sets input filename on command line
-fmt [svg,png,jpg], sets format for image output
-sav saves the figures silently and quits
"""
fmt,plot='svg',0
if '-h' in sys.argv: # check if help is needed
print(main.__doc__)
sys.exit() # graceful quit
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
data=numpy.loadtxt(file).transpose()
D=numpy.array([data[0],data[1]]).transpose()
else:
print('-f is a required switch')
print(main.__doc__)
print(sys.exit())
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-sav' in sys.argv:plot=1
# set up plots
d=""
CDF={'X':1,'Y':2,'Z':3}
pmagplotlib.plot_init(CDF['X'],5,5)
pmagplotlib.plot_init(CDF['Y'],5,5)
pmagplotlib.plot_init(CDF['Z'],5,5)
#
# flip reverse mode
#
D1,D2=pmag.flip(D)
counter,NumSims=0,500
#
# get bootstrapped means for each data set
#
print('doing first mode, be patient')
BDI1=pmag.di_boot(D1)
print('doing second mode, be patient')
BDI2=pmag.di_boot(D2)
pmagplotlib.plotCOM(CDF,BDI1,BDI2,[""])
files={}
for key in list(CDF.keys()):
files[key]='REV'+'_'+key+'.'+fmt
if plot==0:
pmagplotlib.drawFIGS(CDF)
ans= input("s[a]ve plots, [q]uit: ")
if ans=='a':
pmagplotlib.saveP(CDF,files)
print('good bye')
sys.exit()
else:
pmagplotlib.saveP(CDF,files)
def main():
"""
NAME
eqarea_ell.py
DESCRIPTION
makes equal area projections from declination/inclination data
and plot ellipses
SYNTAX
eqarea_ell.py -h [command line options]
INPUT
takes space delimited Dec/Inc data
OPTIONS
-h prints help message and quits
-f FILE
-fmt [svg,png,jpg] format for output plots
-sav saves figures and quits
-ell [F,K,B,Be,Bv] plot Fisher, Kent, Bingham, Bootstrap ellipses or Boostrap eigenvectors
"""
FIG={} # plot dictionary
FIG['eq']=1 # eqarea is figure 1
fmt,dist,mode,plot='svg','F',1,0
sym={'lower':['o','r'],'upper':['o','w'],'size':10}
plotE=0
if '-h' in sys.argv:
print main.__doc__
sys.exit()
pmagplotlib.plot_init(FIG['eq'],5,5)
if '-sav' in sys.argv:plot=1
if '-f' in sys.argv:
ind=sys.argv.index("-f")
title=sys.argv[ind+1]
data=numpy.loadtxt(title).transpose()
if '-ell' in sys.argv:
plotE=1
ind=sys.argv.index('-ell')
ell_type=sys.argv[ind+1]
if ell_type=='F':dist='F'
if ell_type=='K':dist='K'
if ell_type=='B':dist='B'
if ell_type=='Be':dist='BE'
if ell_type=='Bv':
dist='BV'
FIG['bdirs']=2
pmagplotlib.plot_init(FIG['bdirs'],5,5)
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
DIblock=numpy.array([data[0],data[1]]).transpose()
if len(DIblock)>0:
pmagplotlib.plotEQsym(FIG['eq'],DIblock,title,sym)
if plot==0:pmagplotlib.drawFIGS(FIG)
else:
print "no data to plot"
sys.exit()
if plotE==1:
ppars=pmag.doprinc(DIblock) # get principal directions
nDIs,rDIs,npars,rpars=[],[],[],[]
for rec in DIblock:
angle=pmag.angle([rec[0],rec[1]],[ppars['dec'],ppars['inc']])
if angle>90.:
rDIs.append(rec)
else:
nDIs.append(rec)
if dist=='B': # do on whole dataset
etitle="Bingham confidence ellipse"
bpars=pmag.dobingham(DIblock)
for key in bpars.keys():
if key!='n' and pmagplotlib.verbose:print " ",key, '%7.1f'%(bpars[key])
if key=='n' and pmagplotlib.verbose:print " ",key, ' %i'%(bpars[key])
npars.append(bpars['dec'])
npars.append(bpars['inc'])
npars.append(bpars['Zeta'])
npars.append(bpars['Zdec'])
npars.append(bpars['Zinc'])
npars.append(bpars['Eta'])
npars.append(bpars['Edec'])
npars.append(bpars['Einc'])
if dist=='F':
etitle="Fisher confidence cone"
if len(nDIs)>3:
fpars=pmag.fisher_mean(nDIs)
for key in fpars.keys():
if key!='n' and pmagplotlib.verbose:print " ",key, '%7.1f'%(fpars[key])
if key=='n' and pmagplotlib.verbose:print " ",key, ' %i'%(fpars[key])
mode+=1
npars.append(fpars['dec'])
npars.append(fpars['inc'])
npars.append(fpars['alpha95']) # Beta
npars.append(fpars['dec'])
isign=abs(fpars['inc'])/fpars['inc']
npars.append(fpars['inc']-isign*90.) #Beta inc
npars.append(fpars['alpha95']) # gamma
npars.append(fpars['dec']+90.) # Beta dec
npars.append(0.) #Beta inc
if len(rDIs)>3:
fpars=pmag.fisher_mean(rDIs)
if pmagplotlib.verbose:print "mode ",mode
for key in fpars.keys():
if key!='n' and pmagplotlib.verbose:print " ",key, '%7.1f'%(fpars[key])
if key=='n' and pmagplotlib.verbose:print " ",key, ' %i'%(fpars[key])
mode+=1
rpars.append(fpars['dec'])
rpars.append(fpars['inc'])
rpars.append(fpars['alpha95']) # Beta
rpars.append(fpars['dec'])
isign=abs(fpars['inc'])/fpars['inc']
rpars.append(fpars['inc']-isign*90.) #Beta inc
rpars.append(fpars['alpha95']) # gamma
rpars.append(fpars['dec']+90.) # Beta dec
rpars.append(0.) #Beta inc
if dist=='K':
etitle="Kent confidence ellipse"
if len(nDIs)>3:
kpars=pmag.dokent(nDIs,len(nDIs))
if pmagplotlib.verbose:print "mode ",mode
for key in kpars.keys():
if key!='n' and pmagplotlib.verbose:print " ",key, '%7.1f'%(kpars[key])
if key=='n' and pmagplotlib.verbose:print " ",key, ' %i'%(kpars[key])
mode+=1
npars.append(kpars['dec'])
npars.append(kpars['inc'])
npars.append(kpars['Zeta'])
npars.append(kpars['Zdec'])
npars.append(kpars['Zinc'])
npars.append(kpars['Eta'])
npars.append(kpars['Edec'])
npars.append(kpars['Einc'])
if len(rDIs)>3:
kpars=pmag.dokent(rDIs,len(rDIs))
if pmagplotlib.verbose:print "mode ",mode
for key in kpars.keys():
if key!='n' and pmagplotlib.verbose:print " ",key, '%7.1f'%(kpars[key])
if key=='n' and pmagplotlib.verbose:print " ",key, ' %i'%(kpars[key])
mode+=1
rpars.append(kpars['dec'])
rpars.append(kpars['inc'])
rpars.append(kpars['Zeta'])
rpars.append(kpars['Zdec'])
rpars.append(kpars['Zinc'])
rpars.append(kpars['Eta'])
rpars.append(kpars['Edec'])
rpars.append(kpars['Einc'])
else: # assume bootstrap
if len(nDIs)<10 and len(rDIs)<10:
print 'too few data points for bootstrap'
sys.exit()
if dist=='BE':
print 'Be patient for bootstrap...'
if len(nDIs)>=10:
BnDIs=pmag.di_boot(nDIs)
Bkpars=pmag.dokent(BnDIs,1.)
if pmagplotlib.verbose:print "mode ",mode
for key in Bkpars.keys():
if key!='n' and pmagplotlib.verbose:print " ",key, '%7.1f'%(Bkpars[key])
if key=='n' and pmagplotlib.verbose:print " ",key, ' %i'%(Bkpars[key])
mode+=1
npars.append(Bkpars['dec'])
npars.append(Bkpars['inc'])
npars.append(Bkpars['Zeta'])
npars.append(Bkpars['Zdec'])
npars.append(Bkpars['Zinc'])
npars.append(Bkpars['Eta'])
npars.append(Bkpars['Edec'])
npars.append(Bkpars['Einc'])
if len(rDIs)>=10:
BrDIs=pmag.di_boot(rDIs)
Bkpars=pmag.dokent(BrDIs,1.)
if pmagplotlib.verbose:print "mode ",mode
for key in Bkpars.keys():
if key!='n' and pmagplotlib.verbose:print " ",key, '%7.1f'%(Bkpars[key])
if key=='n' and pmagplotlib.verbose:print " ",key, ' %i'%(Bkpars[key])
mode+=1
rpars.append(Bkpars['dec'])
rpars.append(Bkpars['inc'])
rpars.append(Bkpars['Zeta'])
rpars.append(Bkpars['Zdec'])
rpars.append(Bkpars['Zinc'])
rpars.append(Bkpars['Eta'])
rpars.append(Bkpars['Edec'])
rpars.append(Bkpars['Einc'])
etitle="Bootstrapped confidence ellipse"
elif dist=='BV':
print 'Be patient for bootstrap...'
vsym={'lower':['+','k'],'upper':['x','k'],'size':5}
if len(nDIs)>5:
BnDIs=pmag.di_boot(nDIs)
pmagplotlib.plotEQsym(FIG['bdirs'],BnDIs,'Bootstrapped Eigenvectors',vsym)
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
if len(nDIs)>5: # plot on existing plots
pmagplotlib.plotDIsym(FIG['bdirs'],BrDIs,vsym)
else:
pmagplotlib.plotEQ(FIG['bdirs'],BrDIs,'Bootstrapped Eigenvectors',vsym)
if dist=='B':
if len(nDIs)> 3 or len(rDIs)>3: pmagplotlib.plotCONF(FIG['eq'],etitle,[],npars,0)
elif len(nDIs)>3 and dist!='BV':
pmagplotlib.plotCONF(FIG['eq'],etitle,[],npars,0)
if len(rDIs)>3:
pmagplotlib.plotCONF(FIG['eq'],etitle,[],rpars,0)
elif len(rDIs)>3 and dist!='BV':
pmagplotlib.plotCONF(FIG['eq'],etitle,[],rpars,0)
if plot==0:pmagplotlib.drawFIGS(FIG)
if plot==0:pmagplotlib.drawFIGS(FIG)
#
files={}
for key in FIG.keys():
files[key]=title+'_'+key+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='Equal Area Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
elif plot==0:
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)
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
chi_magic.py
DESCRIPTION
plots magnetic susceptibility as a function of frequency and temperature and AC field
SYNTAX
chi_magic.py [command line options]
OPTIONS
-h prints help message and quits
-i allows interactive setting of FILE and temperature step
-f FILE, specify magic_measurements format file
-T IND, specify temperature step to plot
-e EXP, specify experiment name to plot
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
-sav save figure and quit
DEFAULTS
FILE: magic_measurements.txt
IND: first
SPEC: step through one by one
"""
cont, FTinit, BTinit, k = "", 0, 0, 0
meas_file = "magic_measurements.txt"
spec = ""
Tind, cont = 0, ""
EXP = ""
fmt = 'svg' # default image type for saving
plot = 0
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-i' in sys.argv:
file = raw_input(
"Input magic_measurements file name? [magic_measurements.txt] ")
if file != "": meas_file = file
if '-e' in sys.argv:
ind = sys.argv.index('-e')
EXP = sys.argv[ind + 1]
if '-f' in sys.argv:
ind = sys.argv.index('-f')
meas_file = sys.argv[ind + 1]
if '-T' in sys.argv:
ind = sys.argv.index('-T')
Tind = int(sys.argv[ind + 1])
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if '-sav' in sys.argv: plot = 1
#
meas_data, file_type = pmag.magic_read(meas_file)
#
# get list of unique experiment names
#
# initialize some variables (a continuation flag, plot initialization flags and the experiment counter
experiment_names = []
for rec in meas_data:
if rec['magic_experiment_name'] not in experiment_names:
experiment_names.append(rec['magic_experiment_name'])
#
# hunt through by experiment name
if EXP != "":
try:
k = experiment_names.index(EXP)
except:
print "Bad experiment name"
sys.exit()
while k < len(experiment_names):
e = experiment_names[k]
if EXP == "": print e, k + 1, 'out of ', len(experiment_names)
#
# initialize lists of data, susceptibility, temperature, frequency and field
X, T, F, B = [], [], [], []
for rec in meas_data:
methcodes = rec['magic_method_codes']
meths = methcodes.strip().split(':')
if rec['magic_experiment_name'] == e and "LP-X" in meths: # looking for chi measurement
if 'measurement_temp' not in rec.keys():
rec['measurement_temp'] = '300' # set defaults
if 'measurement_freq' not in rec.keys():
rec['measurement_freq'] = '0' # set defaults
if 'measurement_lab_field_ac' not in rec.keys():
rec['measurement_lab_field_ac'] = '0' # set default
X.append(float(rec['measurement_x']))
T.append(float(rec['measurement_temp']))
F.append(float(rec['measurement_freq']))
B.append(float(rec['measurement_lab_field_ac']))
#
# get unique list of Ts,Fs, and Bs
#
Ts, Fs, Bs = [], [], []
for k in range(len(X)): # hunt through all the measurements
if T[k] not in Ts: Ts.append(T[k]) # append if not in list
if F[k] not in Fs: Fs.append(F[k])
if B[k] not in Bs: Bs.append(B[k])
Ts.sort() # sort list of temperatures, frequencies and fields
Fs.sort()
Bs.sort()
if '-x' in sys.argv:
k = len(experiment_names) + 1 # just plot the one
else:
k += 1 # increment experiment number
#
# plot chi versus T and F holding B constant
#
plotnum = 1 # initialize plot number to 1
if len(X) > 2: # if there are any data to plot, continue
b = Bs[-1] # keeping field constant and at maximum
XTF = [] # initialize list of chi versus Temp and freq
for f in Fs: # step through frequencies sequentially
XT = [] # initialize list of chi versus temp
for kk in range(len(X)): # hunt through all the data
if F[kk] == f and B[
kk] == b: # select data with given freq and field
XT.append([X[kk], T[kk]]) # append to list
XTF.append(XT) # append list to list of frequencies
if len(XT) > 1: # if there are any temperature dependent data
pmagplotlib.plot_init(plotnum, 5, 5) # initialize plot
pmagplotlib.plotXTF(plotnum, XTF, Fs, e,
b) # call the plotting function
if plot == 0:
pmagplotlib.drawFIGS({'fig': plotnum}) #make it visible
plotnum += 1 # increment plot number
f = Fs[0] # set frequency to minimum
XTB = [] # initialize list if chi versus Temp and field
for b in Bs: # step through field values
XT = [] # initial chi versus temp list for this field
for kk in range(len(X)): # hunt through all the data
if F[kk] == f and B[
kk] == b: # select data with given freq and field
XT.append([X[kk], T[kk]]) # append to list
XTB.append(XT)
if len(XT) > 1: # if there are any temperature dependent data
pmagplotlib.plot_init(plotnum, 5, 5) # set up plot
pmagplotlib.plotXTB(plotnum, XTB, Bs, e,
f) # call the plotting function
if plot == 0: pmagplotlib.drawFIGS({'fig': plotnum})
plotnum += 1 # increment plot number
if '-i' in sys.argv:
for ind in range(
len(Ts)): # print list of temperatures available
print ind, int(Ts[ind])
cont = raw_input(
"Enter index of desired temperature step, s[a]ve plots, [return] to quit "
)
if cont == 'a':
files = {}
PLTS = {}
for p in range(1, plotnum):
key = str(p)
files[key] = e + '_' + key + '.' + fmt
PLTS[key] = key
pmagplotlib.saveP(PLTS, files)
cont = raw_input(
"Enter index of desired temperature step, s[a]ve plots, [return] to quit "
)
if cont == "": cont = 'q'
while cont != "q":
if '-i' in sys.argv: Tind = int(cont) # set temperature index
b = Bs[-1] # set field to max available
XF = [] # initial chi versus frequency list
for kk in range(len(X)): # hunt through the data
if T[kk] == Ts[Tind] and B[
kk] == b: # if temperature and field match,
XF.append([X[kk], F[kk]]) # append the data
if len(XF) > 1: # if there are any data to plot
if FTinit == 0: # if not already initialized, initialize plot
#print 'initializing ',plotnum
pmagplotlib.plot_init(plotnum, 5, 5)
FTinit = 1
XFplot = plotnum
plotnum += 1 # increment plotnum
pmagplotlib.plotXFT(XFplot, XF, Ts[Tind], e, b)
if plot == 0: pmagplotlib.drawFIGS({'fig': plotnum})
else:
print '\n *** Skipping susceptibitily-frequency plot as a function of temperature *** \n'
f = Fs[0] # set frequency to minimum available
XB = [] # initialize chi versus field list
for kk in range(len(X)): # hunt through the data
if T[kk] == Ts[Tind] and F[
kk] == f: # if temperature and field match those desired
XB.append([X[kk], B[kk]]) # append the data to list
if len(XB) > 4: # if there are any data
if BTinit == 0: # if plot not already initialized
pmagplotlib.plot_init(plotnum, 5, 5) # do it
BTinit = 1
pmagplotlib.plotXBT(plotnum, XB, Ts[Tind], e,
f) # and call plotting function
if plot == 0: pmagplotlib.drawFIGS({'fig': plotnum})
else:
print 'Skipping susceptibitily - AC field plot as a function of temperature'
files = {}
PLTS = {}
for p in range(1, plotnum):
key = str(p)
files[key] = e + '_' + key + '.' + fmt
PLTS[key] = p
if '-i' in sys.argv:
for ind in range(
len(Ts)
): # just in case you forgot, print out a new list of temperatures
print ind, int(Ts[ind])
cont = raw_input(
"Enter index of next temperature step, s[a]ve plots, [return] to quit "
) # ask for new temp
if cont == "": sys.exit()
if cont == 'a':
pmagplotlib.saveP(PLTS, files)
cont = raw_input(
"Enter index of desired temperature step, s[a]ve plots, [return] to quit "
)
if cont == "": sys.exit()
elif plot == 0:
ans = raw_input(
"enter s[a]ve to save files, [return] to quit ")
if ans == 'a':
pmagplotlib.saveP(PLTS, files)
sys.exit()
else:
sys.exit()
else:
pmagplotlib.saveP(PLTS, files)
sys.exit()
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
eqarea_magic.py
DESCRIPTION
makes equal area projections from declination/inclination data
SYNTAX
eqarea_magic.py [command line options]
INPUT
takes magic formatted sites, samples, specimens, or measurements
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file from magic, default='sites.txt'
supported types=[measurements, specimens, samples, sites]
-fsp FILE: specify specimen file name, (required if you want to plot measurements by sample)
default='specimens.txt'
-fsa FILE: specify sample file name, (required if you want to plot specimens by site)
default='samples.txt'
-fsi FILE: specify site file name, default='sites.txt'
-obj OBJ: specify level of plot [all, sit, sam, spc], default is all
-crd [s,g,t]: specify coordinate system, [s]pecimen, [g]eographic, [t]ilt adjusted
default is geographic, unspecified assumed geographic
-fmt [svg,png,jpg] format for output plots
-ell [F,K,B,Be,Bv] plot Fisher, Kent, Bingham, Bootstrap ellipses or Boostrap eigenvectors
-c plot as colour contour
-sav save plot and quit quietly
NOTE
all: entire file; sit: site; sam: sample; spc: specimen
"""
# initialize some default variables
FIG = {} # plot dictionary
FIG['eqarea'] = 1 # eqarea is figure 1
plotE = 0
plt = 0 # default to not plotting
verbose = pmagplotlib.verbose
# extract arguments from sys.argv
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg_from_sys("-WD", default_val=os.getcwd())
pmagplotlib.plot_init(FIG['eqarea'],5,5)
in_file = pmag.get_named_arg_from_sys("-f", default_val="sites.txt")
full_in_file = os.path.join(dir_path, in_file)
plot_by = pmag.get_named_arg_from_sys("-obj", default_val="all").lower()
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")
if plot_by == 'all':
plot_key = 'all'
elif plot_by == 'sit':
plot_key = 'site'
elif plot_by == 'sam':
plot_key = 'sample'
elif plot_by == 'spc':
plot_key = 'specimen'
else:
plot_key = 'all'
if '-c' in sys.argv:
contour = 1
else:
contour = 0
if '-sav' in sys.argv:
plt = 1
verbose = 0
if '-ell' in sys.argv:
plotE = 1
ind = sys.argv.index('-ell')
ell_type = sys.argv[ind+1]
ell_type = pmag.get_named_arg_from_sys("-ell", "F")
dist = ell_type.upper()
# if dist type is unrecognized, use Fisher
if dist not in ['F', 'K', 'B', 'BE', 'BV']:
dist = 'F'
if dist == "BV":
FIG['bdirs'] = 2
pmagplotlib.plot_init(FIG['bdirs'],5,5)
crd = pmag.get_named_arg_from_sys("-crd", default_val="g")
if crd == "s":
coord = "-1"
elif crd == "t":
coord = "100"
else:
coord = "0"
fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
dec_key = 'dir_dec'
inc_key = 'dir_inc'
tilt_key = 'dir_tilt_correction'
#Dir_type_keys=['','site_direction_type','sample_direction_type','specimen_direction_type']
#
fnames = {"specimens": spec_file, "samples": samp_file, 'sites': site_file}
contribution = nb.Contribution(dir_path, custom_filenames=fnames,
single_file=in_file)
# the object that contains the DataFrame + useful helper methods:
table_name = list(contribution.tables.keys())[0]
data_container = contribution.tables[table_name]
# the actual DataFrame:
data = data_container.df
# uses sample infile to add temporary site_name
# column to the specimen table
data_container = contribution.tables[table_name]
data = data_container.df
if (plot_key != "all") and (plot_key not in data.columns):
contribution.propagate_location_to_measurements()
contribution.propagate_location_to_specimens()
# add tilt key into DataFrame columns if it isn't there already
if tilt_key not in data.columns:
data.loc[:, tilt_key] = None
if verbose:
print(len(data), ' records read from ', in_file)
# find desired dec,inc data:
dir_type_key = ''
#
# get plotlist if not plotting all records
#
plotlist=[]
if plot_key != "all":
# return all where plot_key is not blank
if plot_key not in data.columns:
print('Can\'t plot by "{}". That header is not in infile: {}'.format(plot_key, in_file))
return
plots = data[data[plot_key].notnull()]
plotlist = plots[plot_key].unique() # grab unique values
else:
plotlist.append('All')
for plot in plotlist:
if verbose:
print(plot)
if plot == 'All':
# plot everything at once
plot_data = data
else:
# pull out only partial data
plot_data = data[data[plot_key] == plot]
DIblock = []
GCblock = []
# SLblock, SPblock = [], []
title = plot
mode = 1
k = 0
if dec_key not in plot_data.columns:
print("-W- No dec/inc data")
continue
# get all records where dec & inc values exist
plot_data = plot_data[plot_data[dec_key].notnull() & plot_data[inc_key].notnull()]
if plot_data.empty:
continue
# this sorting out is done in get_di_bock
#if coord == '0': # geographic, use records with no tilt key (or tilt_key 0)
# cond1 = plot_data[tilt_key].fillna('') == coord
# cond2 = plot_data[tilt_key].isnull()
# plot_data = plot_data[cond1 | cond2]
#else: # not geographic coordinates, use only records with correct tilt_key
# plot_data = plot_data[plot_data[tilt_key] == coord]
# get metadata for naming the plot file
locations = data_container.get_name('location', df_slice=plot_data)
site = data_container.get_name('site', df_slice=plot_data)
sample = data_container.get_name('sample', df_slice=plot_data)
specimen = data_container.get_name('specimen', df_slice=plot_data)
# make sure method_codes is in plot_data
if 'method_codes' not in plot_data.columns:
plot_data['method_codes'] = ''
# get data blocks
DIblock = data_container.get_di_block(df_slice=plot_data,
tilt_corr=coord, excl=['DE-BFP'])
#SLblock = [[ind, row['method_codes']] for ind, row in plot_data.iterrows()]
# get great circles
great_circle_data = data_container.get_records_for_code('DE-BFP', incl=True,
use_slice=True, sli=plot_data)
if len(great_circle_data) > 0:
gc_cond = great_circle_data[tilt_key] == coord
GCblock = [[float(row[dec_key]), float(row[inc_key])] for ind, row in great_circle_data[gc_cond].iterrows()]
#SPblock = [[ind, row['method_codes']] for ind, row in great_circle_data[gc_cond].iterrows()]
if len(DIblock) > 0:
if contour == 0:
pmagplotlib.plotEQ(FIG['eqarea'], DIblock, title)
else:
pmagplotlib.plotEQcont(FIG['eqarea'], DIblock)
else:
pmagplotlib.plotNET(FIG['eqarea'])
if len(GCblock)>0:
for rec in GCblock:
pmagplotlib.plotC(FIG['eqarea'], rec, 90., 'g')
if len(DIblock) == 0 and len(GCblock) == 0:
if verbose:
print("no records for plotting")
continue
#sys.exit()
if plotE == 1:
ppars = pmag.doprinc(DIblock) # get principal directions
nDIs, rDIs, npars, rpars = [], [], [], []
for rec in DIblock:
angle=pmag.angle([rec[0],rec[1]],[ppars['dec'],ppars['inc']])
if angle>90.:
rDIs.append(rec)
else:
nDIs.append(rec)
if dist=='B': # do on whole dataset
etitle="Bingham confidence ellipse"
bpars=pmag.dobingham(DIblock)
for key in list(bpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(bpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(bpars[key]))
npars.append(bpars['dec'])
npars.append(bpars['inc'])
npars.append(bpars['Zeta'])
npars.append(bpars['Zdec'])
npars.append(bpars['Zinc'])
npars.append(bpars['Eta'])
npars.append(bpars['Edec'])
npars.append(bpars['Einc'])
if dist=='F':
etitle="Fisher confidence cone"
if len(nDIs)>2:
fpars=pmag.fisher_mean(nDIs)
for key in list(fpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(fpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(fpars[key]))
mode+=1
npars.append(fpars['dec'])
npars.append(fpars['inc'])
npars.append(fpars['alpha95']) # Beta
npars.append(fpars['dec'])
isign=old_div(abs(fpars['inc']),fpars['inc'])
npars.append(fpars['inc']-isign*90.) #Beta inc
npars.append(fpars['alpha95']) # gamma
npars.append(fpars['dec']+90.) # Beta dec
npars.append(0.) #Beta inc
if len(rDIs)>2:
fpars=pmag.fisher_mean(rDIs)
if verbose: print("mode ",mode)
for key in list(fpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(fpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(fpars[key]))
mode+=1
rpars.append(fpars['dec'])
rpars.append(fpars['inc'])
rpars.append(fpars['alpha95']) # Beta
rpars.append(fpars['dec'])
isign=old_div(abs(fpars['inc']),fpars['inc'])
rpars.append(fpars['inc']-isign*90.) #Beta inc
rpars.append(fpars['alpha95']) # gamma
rpars.append(fpars['dec']+90.) # Beta dec
rpars.append(0.) #Beta inc
if dist=='K':
etitle="Kent confidence ellipse"
if len(nDIs)>3:
kpars=pmag.dokent(nDIs,len(nDIs))
if verbose: print("mode ",mode)
for key in list(kpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(kpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(kpars[key]))
mode+=1
npars.append(kpars['dec'])
npars.append(kpars['inc'])
npars.append(kpars['Zeta'])
npars.append(kpars['Zdec'])
npars.append(kpars['Zinc'])
npars.append(kpars['Eta'])
npars.append(kpars['Edec'])
npars.append(kpars['Einc'])
if len(rDIs)>3:
kpars=pmag.dokent(rDIs,len(rDIs))
if verbose: print("mode ",mode)
for key in list(kpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(kpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(kpars[key]))
mode+=1
rpars.append(kpars['dec'])
rpars.append(kpars['inc'])
rpars.append(kpars['Zeta'])
rpars.append(kpars['Zdec'])
rpars.append(kpars['Zinc'])
rpars.append(kpars['Eta'])
rpars.append(kpars['Edec'])
rpars.append(kpars['Einc'])
else: # assume bootstrap
if dist=='BE':
if len(nDIs)>5:
BnDIs=pmag.di_boot(nDIs)
Bkpars=pmag.dokent(BnDIs,1.)
if verbose: print("mode ",mode)
for key in list(Bkpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(Bkpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(Bkpars[key]))
mode+=1
npars.append(Bkpars['dec'])
npars.append(Bkpars['inc'])
npars.append(Bkpars['Zeta'])
npars.append(Bkpars['Zdec'])
npars.append(Bkpars['Zinc'])
npars.append(Bkpars['Eta'])
npars.append(Bkpars['Edec'])
npars.append(Bkpars['Einc'])
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
Bkpars=pmag.dokent(BrDIs,1.)
if verbose: print("mode ",mode)
for key in list(Bkpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(Bkpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(Bkpars[key]))
mode+=1
rpars.append(Bkpars['dec'])
rpars.append(Bkpars['inc'])
rpars.append(Bkpars['Zeta'])
rpars.append(Bkpars['Zdec'])
rpars.append(Bkpars['Zinc'])
rpars.append(Bkpars['Eta'])
rpars.append(Bkpars['Edec'])
rpars.append(Bkpars['Einc'])
etitle="Bootstrapped confidence ellipse"
elif dist=='BV':
sym={'lower':['o','c'],'upper':['o','g'],'size':3,'edgecolor':'face'}
if len(nDIs)>5:
BnDIs=pmag.di_boot(nDIs)
pmagplotlib.plotEQsym(FIG['bdirs'],BnDIs,'Bootstrapped Eigenvectors', sym)
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
if len(nDIs)>5: # plot on existing plots
pmagplotlib.plotDIsym(FIG['bdirs'],BrDIs,sym)
else:
pmagplotlib.plotEQ(FIG['bdirs'],BrDIs,'Bootstrapped Eigenvectors')
if dist=='B':
if len(nDIs)> 3 or len(rDIs)>3: pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],npars,0)
elif len(nDIs)>3 and dist!='BV':
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],npars,0)
if len(rDIs)>3:
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],rpars,0)
elif len(rDIs)>3 and dist!='BV':
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],rpars,0)
for key in list(FIG.keys()):
files = {}
filename = pmag.get_named_arg_from_sys('-fname')
if filename: # use provided filename
filename+= '.' + fmt
elif pmagplotlib.isServer: # use server plot naming convention
filename='LO:_'+locations+'_SI:_'+site+'_SA:_'+sample+'_SP:_'+specimen+'_CO:_'+crd+'_TY:_'+key+'_.'+fmt
else: # use more readable naming convention
filename = ''
for item in [locations, site, sample, specimen, crd, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key]=filename
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='Equal Area Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
if plt:
pmagplotlib.saveP(FIG,files)
continue
if verbose:
pmagplotlib.drawFIGS(FIG)
ans=input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans == "q":
sys.exit()
if ans == "a":
pmagplotlib.saveP(FIG,files)
continue
def main():
"""
NAME
plot_geomagia.py
DESCRIPTION
makes a map and VADM plot of geomagia download file
SYNTAX
plot_geomagia.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, specify geomagia download file
-res [c,l,i,h] specify resolution (crude,low,intermediate,high)
-etp plot the etopo20 topographic mesh
-pad [LAT LON] pad bounding box by LAT/LON (default is [.5 .5] degrees)
-grd SPACE specify grid spacing
-prj [lcc] , specify projection (lcc=lambert conic conformable), default is mercator
-o color ocean blue/land green (default is not)
-d plot details of rivers, boundaries, etc.
-sav save plot and quit quietly
-fmt [png,svg,eps,jpg,pdf] specify format for output, default is pdf
DEFAULTS
resolution: intermediate
saved images are in pdf
"""
dir_path='.'
names,res,proj,locs,padlon,padlat,fancy,gridspace,details=[],'l','lcc','',0,0,0,15,1
Age_bounds=[-5000,2000]
Lat_bounds=[20,45]
Lon_bounds=[15,55]
fmt='pdf'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
sites_file=sys.argv[ind+1]
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res=sys.argv[ind+1]
if '-etp' in sys.argv:fancy=1
if '-o' in sys.argv:ocean=1
if '-d' in sys.argv:details=1
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj=sys.argv[ind+1]
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
verbose=pmagplotlib.verbose
if '-sav' in sys.argv:
verbose=0
if '-pad' in sys.argv:
ind = sys.argv.index('-pad')
padlat=float(sys.argv[ind+1])
padlon=float(sys.argv[ind+2])
if '-grd' in sys.argv:
ind = sys.argv.index('-grd')
gridspace=float(sys.argv[ind+1])
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
sites_file=dir_path+'/'+sites_file
geo_in=open(sites_file,'rU').readlines()
Age,AgeErr,Vadm,VadmErr,slats,slons=[],[],[],[],[],[]
for line in geo_in[2:]: # skip top two rows`
rec=line.split()
if float(rec[0])>Age_bounds[0] and float(rec[0])<Age_bounds[1] \
and float(rec[12])>Lat_bounds[0] and float(rec[12]) < Lat_bounds[1]\
and float(rec[13])>Lon_bounds[0] and float(rec[13])<Lon_bounds[1]:
Age.append(float(rec[0]))
AgeErr.append(float(rec[1]))
Vadm.append(10.*float(rec[6]))
VadmErr.append(10.*float(rec[7]))
slats.append(float(rec[12]))
slons.append(float(rec[13]))
FIGS={'map':1,'vadms':2}
pmagplotlib.plot_init(FIGS['map'],6,6)
pmagplotlib.plot_init(FIGS['vadms'],6,6)
Opts={'res':res,'proj':proj,'loc_name':locs,'padlon':padlon,'padlat':padlat,'latmin':numpy.min(slats)-padlat,'latmax':numpy.max(slats)+padlat,'lonmin':numpy.min(slons)-padlon,'lonmax':numpy.max(slons)+padlon,'sym':'ro','boundinglat':0.,'pltgrid':1}
Opts['lon_0']=int(0.5*(numpy.min(slons)+numpy.max(slons)))
Opts['lat_0']=int(0.5*(numpy.min(slats)+numpy.max(slats)))
Opts['gridspace']=gridspace
if details==1:
Opts['details']={'coasts':1,'rivers':0,'states':1,'countries':1,'ocean':1}
else:
Opts['details']={'coasts':1,'rivers':0,'states':0,'countries':0,'ocean':1}
Opts['details']['fancy']=fancy
pmagplotlib.plotMAP(FIGS['map'],slats,slons,Opts)
pmagplotlib.plotXY(FIGS['vadms'],Age,Vadm,sym='bo',xlab='Age (Years CE)',ylab=r'VADM (ZAm$^2$)')
if verbose:pmagplotlib.drawFIGS(FIGS)
files={}
for key in FIGS.keys():
files[key]=key+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['map']='Map'
titles['vadms']='VADMs'
FIG = pmagplotlib.addBorders(FIGS,titles,black,purple)
pmagplotlib.saveP(FIGS,files)
elif verbose:
ans=raw_input(" S[a]ve to save plot, Return to quit: ")
if ans=="a":
pmagplotlib.saveP(FIGS,files)
else:
pmagplotlib.saveP(FIGS,files)
def main():
"""
NAME
vgpmap_magic.py
DESCRIPTION
makes a map of vgps and a95/dp,dm for site means in a pmag_results table
SYNTAX
vgpmap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE pmag_results format file, [default is pmag_results.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-etp plot the etopo20 topographpy data (requires high resolution data set)
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 5 : small red circles
bs 10 : intermediate blue squares
g^ 20 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to plot all site VGPs
-fmt [pdf, png, eps...] specify output format, default is pdf
-sav save and quit
DEFAULTS
FILE: pmag_results.txt
res: c
prj: ortho
ELAT,ELON = 0,0
SYM SIZE: ro 8
RSYM RSIZE: g^ 8
"""
dir_path='.'
res,ages='c',0
plot=0
proj='ortho'
results_file='pmag_results.txt'
ell,flip=0,0
lat_0,lon_0=90.,0.
fmt='pdf'
sym,size='ro',8
rsym,rsize='g^',8
anti=0
fancy=0
coord=""
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 '-S' in sys.argv:anti=1
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-sav' in sys.argv:plot=1
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res=sys.argv[ind+1]
if '-etp' in sys.argv:fancy=1
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj=sys.argv[ind+1]
if '-rev' in sys.argv:
flip=1
ind = sys.argv.index('-rev')
rsym=(sys.argv[ind+1])
rsize=int(sys.argv[ind+2])
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym=(sys.argv[ind+1])
size=int(sys.argv[ind+2])
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0=float(sys.argv[ind+1])
lon_0=float(sys.argv[ind+2])
if '-ell' in sys.argv: ell=1
if '-age' in sys.argv: ages=1
if '-f' in sys.argv:
ind = sys.argv.index('-f')
results_file=sys.argv[ind+1]
if '-crd' in sys.argv:
ind = sys.argv.index('-crd')
crd=sys.argv[ind+1]
if crd=='g':coord='0'
if crd=='t':coord='100'
results_file=dir_path+'/'+results_file
data,file_type=pmag.magic_read(results_file)
if file_type!='pmag_results':
print "bad results file"
sys.exit()
FIG={'map':1}
pmagplotlib.plot_init(FIG['map'],6,6)
# read in er_sites file
lats,lons,dp,dm,a95=[],[],[],[],[]
Pars=[]
dates,rlats,rlons=[],[],[]
if 'data_type' in data[0].keys():
Results=pmag.get_dictitem(data,'data_type','i','T') # get all site level data
else:
Results=data
Results=pmag.get_dictitem(Results,'vgp_lat','','F') # get all non-blank latitudes
Results=pmag.get_dictitem(Results,'vgp_lon','','F') # get all non-blank longitudes
if coord!="":Results=pmag.get_dictitem(Results,'tilt_correction',coord,'T') # get specified coordinate system
location=""
for rec in Results:
if rec['er_location_names'] not in location:location = location+':'+rec['er_location_names']
if 'average_age' in rec.keys() and rec['average_age']!="" and ages==1:
dates.append(rec['average_age'])
lat=float(rec['vgp_lat'])
lon=float(rec['vgp_lon'])
if flip==0:
lats.append(lat)
lons.append(lon)
elif flip==1:
if lat<0:
rlats.append(-lat)
lon=lon+180.
if lon>360:lon=lon-360.
rlons.append(lon)
else:
lats.append(lat)
lons.append(lon)
elif anti==1:
lats.append(-lat)
lon=lon+180.
if lon>360:lon=lon-360.
lons.append(lon)
ppars=[]
ppars.append(lon)
ppars.append(lat)
ell1,ell2="",""
if 'vgp_dm' in rec.keys() and rec['vgp_dm']!="":ell1=float(rec['vgp_dm'])
if 'vgp_dp' in rec.keys() and rec['vgp_dp']!="":ell2=float(rec['vgp_dp'])
if 'vgp_alpha95' in rec.keys() and rec['vgp_alpha95']!="":ell1,ell2=float(rec['vgp_alpha95']),float(rec['vgp_alpha95'])
if ell1!="" and ell2!="":
ppars=[]
ppars.append(lons[-1])
ppars.append(lats[-1])
ppars.append(ell1)
ppars.append(lons[-1])
isign=abs(lats[-1])/lats[-1]
ppars.append(lats[-1]-isign*90.)
ppars.append(ell2)
ppars.append(lons[-1]+90.)
ppars.append(0.)
Pars.append(ppars)
location=location.strip(':')
Opts={'latmin':-90,'latmax':90,'lonmin':0.,'lonmax':360.,'lat_0':lat_0,'lon_0':lon_0,'proj':proj,'sym':'bs','symsize':3,'pltgrid':0,'res':res,'boundinglat':0.}
Opts['details']={'coasts':1,'rivers':0, 'states':0, 'countries':0,'ocean':1,'fancy':fancy}
pmagplotlib.plotMAP(FIG['map'],[90.],[0.],Opts) # make the base map with a blue triangle at the pole`
Opts['pltgrid']=-1
Opts['sym']=sym
Opts['symsize']=size
if len(dates)>0:Opts['names']=dates
if len(lats)>0:pmagplotlib.plotMAP(FIG['map'],lats,lons,Opts) # add the lats and lons of the poles
Opts['names']=[]
if len(rlats)>0:
Opts['sym']=rsym
Opts['symsize']=rsize
pmagplotlib.plotMAP(FIG['map'],rlats,rlons,Opts) # add the lats and lons of the poles
if plot==0:
pmagplotlib.drawFIGS(FIG)
if ell==1: # add ellipses if desired.
Opts['details']={'coasts':0,'rivers':0, 'states':0, 'countries':0,'ocean':0}
Opts['pltgrid']=-1 # turn off meridian replotting
Opts['symsize']=2
Opts['sym']='g-'
for ppars in Pars:
if ppars[2]!=0:
PTS=pmagplotlib.plotELL(FIG['map'],ppars,'g.',0,0)
elats,elons=[],[]
for pt in PTS:
elons.append(pt[0])
elats.append(pt[1])
pmagplotlib.plotMAP(FIG['map'],elats,elons,Opts) # make the base map with a blue triangle at the pole`
if plot==0:pmagplotlib.drawFIGS(FIG)
files={}
for key in FIG.keys():
files[key]='LO:_'+location+'_VGP_map.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='LO:_'+location+'_VGP_map'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
elif plot==0:
pmagplotlib.drawFIGS(FIG)
ans=raw_input(" S[a]ve to save plot, Return to quit: ")
if ans=="a":
pmagplotlib.saveP(FIG,files)
else:
print "Good bye"
sys.exit()
else:
pmagplotlib.saveP(FIG,files)
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
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
qqplot.py
DESCRIPTION
makes qq plot of input data against a Normal distribution.
INPUT FORMAT
takes real numbers in single column
SYNTAX
qqplot.py [-h][-i][-f FILE]
OPTIONS
-f FILE, specify file on command line
-fmt [png,svg,jpg,eps] set plot output format [default is svg]
-sav saves and quits
OUTPUT
calculates the K-S D and the D expected for a normal distribution
when D<Dc, distribution is normal (at 95% level of confidence).
"""
fmt,plot='svg',0
if '-h' in sys.argv: # check if help is needed
print(main.__doc__)
sys.exit() # graceful quit
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: # ask for filename
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
f=open(file,'r')
data=f.readlines()
X= [] # set up list for data
for line in data: # read in the data from standard input
rec=line.split() # split each line on space to get records
X.append(float(rec[0])) # append data to X
#
QQ={'qq':1}
pmagplotlib.plot_init(QQ['qq'],5,5)
pmagplotlib.plotQQnorm(QQ['qq'],X,'Q-Q Plot') # make plot
if plot==0:
pmagplotlib.drawFIGS(QQ)
files={}
for key in list(QQ.keys()):
files[key]=key+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='Q-Q Plot'
QQ = pmagplotlib.addBorders(EQ,titles,black,purple)
pmagplotlib.saveP(QQ,files)
elif plot==0:
ans=input(" S[a]ve to save plot, [q]uit without saving: ")
if ans=="a":
pmagplotlib.saveP(QQ,files)
else:
pmagplotlib.saveP(QQ,files)
def main():
"""
NAME
foldtest.py
DESCRIPTION
does a fold test (Tauxe, 2010) on data
INPUT FORMAT
dec inc dip_direction dip
SYNTAX
foldtest.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE file with input data
-F FILE for confidence bounds on fold test
-u ANGLE (circular standard deviation) for uncertainty on bedding poles
-b MIN MAX bounds for quick search of percent untilting [default is -10 to 150%]
-n NB number of bootstrap samples [default is 1000]
-fmt FMT, specify format - default is svg
-sav save figures and quit
INPUT FILE
Dec Inc Dip_Direction Dip in space delimited file
OUTPUT PLOTS
Geographic: is an equal area projection of the input data in
original coordinates
Stratigraphic: is an equal area projection of the input data in
tilt adjusted coordinates
% Untilting: The dashed (red) curves are representative plots of
maximum eigenvalue (tau_1) as a function of untilting
The solid line is the cumulative distribution of the
% Untilting required to maximize tau for all the
bootstrapped data sets. The dashed vertical lines
are 95% confidence bounds on the % untilting that yields
the most clustered result (maximum tau_1).
Command line: prints out the bootstrapped iterations and
finally the confidence bounds on optimum untilting.
If the 95% conf bounds include 0, then a post-tilt magnetization is indicated
If the 95% conf bounds include 100, then a pre-tilt magnetization is indicated
If the 95% conf bounds exclude both 0 and 100, syn-tilt magnetization is
possible as is vertical axis rotation or other pathologies
Geographic: is an equal area projection of the input data in
OPTIONAL OUTPUT FILE:
The output file has the % untilting within the 95% confidence bounds
nd the number of bootstrap samples
"""
kappa = 0
fmt, plot = 'svg', 0
nb = 1000 # number of bootstraps
min, max = -10, 150
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-F' in sys.argv:
ind = sys.argv.index('-F')
outfile = open(sys.argv[ind + 1], 'w')
else:
outfile = ""
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
DIDDs = numpy.loadtxt(file)
else:
print main.__doc__
sys.exit()
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if '-sav' in sys.argv: plot = 1
if '-b' in sys.argv:
ind = sys.argv.index('-b')
min = int(sys.argv[ind + 1])
max = int(sys.argv[ind + 2])
if '-n' in sys.argv:
ind = sys.argv.index('-n')
nb = int(sys.argv[ind + 1])
if '-u' in sys.argv:
ind = sys.argv.index('-u')
csd = float(sys.argv[ind + 1])
kappa = (81. / csd)**2
#
# get to work
#
PLTS = {'geo': 1, 'strat': 2, 'taus': 3} # make plot dictionary
pmagplotlib.plot_init(PLTS['geo'], 5, 5)
pmagplotlib.plot_init(PLTS['strat'], 5, 5)
pmagplotlib.plot_init(PLTS['taus'], 5, 5)
pmagplotlib.plotEQ(PLTS['geo'], DIDDs, 'Geographic')
D, I = pmag.dotilt_V(DIDDs)
TCs = numpy.array([D, I]).transpose()
pmagplotlib.plotEQ(PLTS['strat'], TCs, 'Stratigraphic')
if plot == 0: pmagplotlib.drawFIGS(PLTS)
Percs = range(min, max)
Cdf, Untilt = [], []
pylab.figure(num=PLTS['taus'])
print 'doing ', nb, ' iterations...please be patient.....'
for n in range(
nb): # do bootstrap data sets - plot first 25 as dashed red line
if n % 50 == 0: print n
Taus = [] # set up lists for taus
PDs = pmag.pseudo(DIDDs)
if kappa != 0:
for k in range(len(PDs)):
d, i = pmag.fshdev(kappa)
dipdir, dip = pmag.dodirot(d, i, PDs[k][2], PDs[k][3])
PDs[k][2] = dipdir
PDs[k][3] = dip
for perc in Percs:
tilt = numpy.array([1., 1., 1., 0.01 * perc])
D, I = pmag.dotilt_V(PDs * tilt)
TCs = numpy.array([D, I]).transpose()
ppars = pmag.doprinc(TCs) # get principal directions
Taus.append(ppars['tau1'])
if n < 25: pylab.plot(Percs, Taus, 'r--')
Untilt.append(Percs[Taus.index(
numpy.max(Taus))]) # tilt that gives maximum tau
Cdf.append(float(n) / float(nb))
pylab.plot(Percs, Taus, 'k')
pylab.xlabel('% Untilting')
pylab.ylabel('tau_1 (red), CDF (green)')
Untilt.sort() # now for CDF of tilt of maximum tau
pylab.plot(Untilt, Cdf, 'g')
lower = int(.025 * nb)
upper = int(.975 * nb)
pylab.axvline(x=Untilt[lower], ymin=0, ymax=1, linewidth=1, linestyle='--')
pylab.axvline(x=Untilt[upper], ymin=0, ymax=1, linewidth=1, linestyle='--')
tit = '%i - %i %s' % (Untilt[lower], Untilt[upper], 'Percent Unfolding')
print tit
print 'range of all bootstrap samples: ', Untilt[0], ' - ', Untilt[-1]
pylab.title(tit)
outstring = '%i - %i; %i\n' % (Untilt[lower], Untilt[upper], nb)
if outfile != "": outfile.write(outstring)
files = {}
for key in PLTS.keys():
files[key] = ('foldtest_' + '%s' % (key.strip()[:2]) + '.' + fmt)
if plot == 0:
pmagplotlib.drawFIGS(PLTS)
ans = raw_input('S[a]ve all figures, <Return> to quit ')
if ans != 'a':
print "Good bye"
sys.exit()
pmagplotlib.saveP(PLTS, files)
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
print('verbose', verbose)
#
#
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 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.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():
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.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
find_EI.py
DESCRIPTION
Applies series of assumed flattening factor and "unsquishes" inclinations assuming tangent function.
Finds flattening factor that gives elongation/inclination pair consistent with TK03.
Finds bootstrap confidence bounds
SYNTAX
find_EI.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE specify input file name
-nb N specify number of bootstraps - the more the better, but slower!, default is 1000
-sc uses a "site-level" correction to a Fisherian distribution instead
of a "study-level" correction to a TK03-consistent distribution.
Note that many directions (~ 100) are needed for this correction to be reliable.
-fmt [svg,png,eps,pdf..] change plot format, default is svg
-sav saves the figures and quits
INPUT
dec/inc pairs, delimited with space or tabs
OUTPUT
four plots: 1) equal area plot of original directions
2) Elongation/inclination pairs as a function of f, data plus 25 bootstrap samples
3) Cumulative distribution of bootstrapped optimal inclinations plus uncertainties.
Estimate from original data set plotted as solid line
4) Orientation of principle direction through unflattening
NOTE: If distribution does not have a solution, plot labeled: Pathological. Some bootstrap samples may have
valid solutions and those are plotted in the CDFs and E/I plot.
"""
fmt, nb = 'svg', 1000
plot = 0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit() # graceful quit
elif '-f' in sys.argv:
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
else:
print(main.__doc__)
sys.exit()
if '-nb' in sys.argv:
ind = sys.argv.index('-nb')
nb = int(sys.argv[ind + 1])
if '-sc' in sys.argv:
site_correction = True
else:
site_correction = False
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if '-sav' in sys.argv: plot = 1
data = numpy.loadtxt(file)
upper, lower = int(round(.975 * nb)), int(round(.025 * nb))
E, I = [], []
PLTS = {'eq': 1, 'ei': 2, 'cdf': 3, 'v2': 4}
pmagplotlib.plot_init(PLTS['eq'], 6, 6)
pmagplotlib.plot_init(PLTS['ei'], 5, 5)
pmagplotlib.plot_init(PLTS['cdf'], 5, 5)
pmagplotlib.plot_init(PLTS['v2'], 5, 5)
pmagplotlib.plotEQ(PLTS['eq'], data, 'Data')
if plot == 0: pmagplotlib.drawFIGS(PLTS)
ppars = pmag.doprinc(data)
Io = ppars['inc']
n = ppars["N"]
Es, Is, Fs, V2s = pmag.find_f(data)
if site_correction:
Inc, Elong = Is[Es.index(min(Es))], Es[Es.index(min(Es))]
flat_f = Fs[Es.index(min(Es))]
else:
Inc, Elong = Is[-1], Es[-1]
flat_f = Fs[-1]
pmagplotlib.plotEI(PLTS['ei'], Es, Is, flat_f)
pmagplotlib.plotV2s(PLTS['v2'], V2s, Is, flat_f)
b = 0
print("Bootstrapping.... be patient")
while b < nb:
bdata = pmag.pseudo(data)
Esb, Isb, Fsb, V2sb = pmag.find_f(bdata)
if b < 25:
pmagplotlib.plotEI(PLTS['ei'], Esb, Isb, Fsb[-1])
if Esb[-1] != 0:
ppars = pmag.doprinc(bdata)
if site_correction:
I.append(abs(Isb[Esb.index(min(Esb))]))
E.append(Esb[Esb.index(min(Esb))])
else:
I.append(abs(Isb[-1]))
E.append(Esb[-1])
b += 1
if b % 25 == 0: print(b, ' out of ', nb)
I.sort()
E.sort()
Eexp = []
for i in I:
Eexp.append(pmag.EI(i))
if Inc == 0:
title = 'Pathological Distribution: ' + '[%7.1f, %7.1f]' % (I[lower],
I[upper])
else:
title = '%7.1f [%7.1f, %7.1f]' % (Inc, I[lower], I[upper])
pmagplotlib.plotEI(PLTS['ei'], Eexp, I, 1)
pmagplotlib.plotCDF(PLTS['cdf'], I, 'Inclinations', 'r', title)
pmagplotlib.plotVs(PLTS['cdf'], [I[lower], I[upper]], 'b', '--')
pmagplotlib.plotVs(PLTS['cdf'], [Inc], 'g', '-')
pmagplotlib.plotVs(PLTS['cdf'], [Io], 'k', '-')
if plot == 0:
pmagplotlib.drawFIGS(PLTS)
print("Io Inc I_lower, I_upper, Elon, E_lower, E_upper")
print('%7.1f %s %7.1f _ %7.1f ^ %7.1f: %6.4f _ %6.4f ^ %6.4f' %
(Io, " => ", Inc, I[lower], I[upper], Elong, E[lower], E[upper]))
ans = input("S[a]ve plots - <return> to quit: ")
if ans != 'a':
print("\n Good bye\n")
sys.exit()
files = {}
files['eq'] = 'findEI_eq.' + fmt
files['ei'] = 'findEI_ei.' + fmt
files['cdf'] = 'findEI_cdf.' + fmt
files['v2'] = 'findEI_v2.' + fmt
pmagplotlib.saveP(PLTS, files)
def main():
"""
NAME
watsons_v.py
DESCRIPTION
calculates Watson's V statistic from input files
INPUT FORMAT
takes dec/inc as first two columns in two space delimited files
SYNTAX
watsons_v.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE (with optional second)
-f2 FILE (second file)
-ant, flip antipodal directions to opposite direction
in first file if only one file or flip all in second, if two files
-P (don't save or show plot)
-sav save figure and quit silently
-fmt [png,svg,eps,pdf,jpg] format for saved figure
OUTPUT
Watson's V and the Monte Carlo Critical Value Vc.
in plot, V is solid and Vc is dashed.
"""
Flip = 0
show, plot = 1, 0
fmt = 'svg'
file2 = ""
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-ant' in sys.argv: Flip = 1
if '-sav' in sys.argv: show, plot = 0, 1 # don't display, but do save plot
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if '-P' in sys.argv: show = 0 # don't display or save plot
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file1 = sys.argv[ind + 1]
data = numpy.loadtxt(file1).transpose()
D1 = numpy.array([data[0], data[1]]).transpose()
else:
print "-f is required"
print main.__doc__
sys.exit()
if '-f2' in sys.argv:
ind = sys.argv.index('-f2')
file2 = sys.argv[ind + 1]
data2 = numpy.loadtxt(file2).transpose()
D2 = numpy.array([data2[0], data2[1]]).transpose()
if Flip == 1:
D2, D = pmag.flip(D2) # D2 are now flipped
if len(D2) != 0:
if len(D) != 0:
D2 = numpy.concatenate(D, D2) # put all in D2
elif len(D) != 0:
D2 = D
else:
print 'length of second file is zero'
sys.exit()
elif Flip == 1:
D2, D1 = pmag.flip(D1) # peel out antipodal directions, put in D2
#
counter, NumSims = 0, 5000
#
# first calculate the fisher means and cartesian coordinates of each set of Directions
#
pars_1 = pmag.fisher_mean(D1)
pars_2 = pmag.fisher_mean(D2)
#
# get V statistic for these
#
V = pmag.vfunc(pars_1, pars_2)
#
# do monte carlo simulation of datasets with same kappas, but common mean
#
Vp = [] # set of Vs from simulations
if show == 1: print "Doing ", NumSims, " simulations"
for k in range(NumSims):
counter += 1
if counter == 50:
if show == 1: print k + 1
counter = 0
Dirp = []
# get a set of N1 fisher distributed vectors with k1, calculate fisher stats
for i in range(pars_1["n"]):
Dirp.append(pmag.fshdev(pars_1["k"]))
pars_p1 = pmag.fisher_mean(Dirp)
# get a set of N2 fisher distributed vectors with k2, calculate fisher stats
Dirp = []
for i in range(pars_2["n"]):
Dirp.append(pmag.fshdev(pars_2["k"]))
pars_p2 = pmag.fisher_mean(Dirp)
# get the V for these
Vk = pmag.vfunc(pars_p1, pars_p2)
Vp.append(Vk)
#
# sort the Vs, get Vcrit (95th one)
#
Vp.sort()
k = int(.95 * NumSims)
if show == 1:
print "Watson's V, Vcrit: "
print ' %10.1f %10.1f' % (V, Vp[k])
if show == 1 or plot == 1:
print "Watson's V, Vcrit: "
print ' %10.1f %10.1f' % (V, Vp[k])
CDF = {'cdf': 1}
pmagplotlib.plot_init(CDF['cdf'], 5, 5)
pmagplotlib.plotCDF(CDF['cdf'], Vp, "Watson's V", 'r', "")
pmagplotlib.plotVs(CDF['cdf'], [V], 'g', '-')
pmagplotlib.plotVs(CDF['cdf'], [Vp[k]], 'b', '--')
if plot == 0: pmagplotlib.drawFIGS(CDF)
files = {}
if file2 != "":
files['cdf'] = 'watsons_v_' + file1 + '_' + file2 + '.' + fmt
else:
files['cdf'] = 'watsons_v_' + file1 + '.' + fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['cdf'] = 'Cumulative Distribution'
CDF = pmagplotlib.addBorders(CDF, titles, black, purple)
pmagplotlib.saveP(CDF, files)
elif plot == 0:
ans = raw_input(" S[a]ve to save plot, [q]uit without saving: ")
if ans == "a": pmagplotlib.saveP(CDF, files)
if plot == 1: # save and quit silently
pmagplotlib.saveP(CDF, files)
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
trmaq_magic.py
DESCTIPTION
does non-linear trm acquisisiton correction
SYNTAX
trmaq_magic.py [-h][-i][command line options]
OPTIONS
-h prints help message and quits
-i allows interactive setting of file names
-f MFILE, sets magic_measurements input file
-ft TSPEC, sets thellier_specimens input file
-F OUT, sets output for non-linear TRM acquisition corrected data
DEFAULTS
MFILE: trmaq_measurements.txt
TSPEC: thellier_specimens.txt
OUT: NLT_specimens.txt
"""
meas_file = 'trmaq_measurements.txt'
tspec = "thellier_specimens.txt"
output = 'NLT_specimens.txt'
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-i' in sys.argv:
meas_file = input(
"Input magic_measurements file name? [trmaq_measurements.txt] ")
if meas_file == "": meas_file = "trmaq_measurements.txt"
tspec = input(
" thellier_specimens file name? [thellier_specimens.txt] ")
if tspec == "": tspec = "thellier_specimens.txt"
output = input(
"File for non-linear TRM adjusted specimen data: [NLTspecimens.txt] "
)
if output == "": output = "NLT_specimens.txt"
if '-f' in sys.argv:
ind = sys.argv.index('-f')
meas_file = sys.argv[ind + 1]
if '-ft' in sys.argv:
ind = sys.argv.index('-ft')
tspec = sys.argv[ind + 1]
if '-F' in sys.argv:
ind = sys.argv.index('-F')
output = sys.argv[ind + 1]
#
PLT = {'aq': 1}
pmagplotlib.plot_init(PLT['aq'], 5, 5)
#
# get name of file from command line
#
comment = ""
#
#
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print(file_type)
print(file_type, "This is not a valid magic_measurements file ")
sys.exit()
sids = pmag.get_specs(meas_data)
specimen = 0
#
# read in thellier_specimen data
#
nrm, file_type = pmag.magic_read(tspec)
PmagSpecRecs = []
while specimen < len(sids):
#
# find corresoponding paleointensity data for this specimen
#
s = sids[specimen]
blab, best = "", ""
for nrec in nrm: # pick out the Banc data for this spec
if nrec["er_specimen_name"] == s:
blab = float(nrec["specimen_lab_field_dc"])
best = float(nrec["specimen_int"])
TrmRec = nrec
break
if blab == "":
print("skipping ", s, " : no best ")
specimen += 1
else:
print(sids[specimen], specimen + 1, 'of ', len(sids), 'Best = ',
best * 1e6)
MeasRecs = []
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"] == s:
meths = rec["magic_method_codes"].split(":")
methcodes = []
for meth in meths:
methcodes.append(meth.strip())
if "LP-TRM" in methcodes: MeasRecs.append(rec)
if len(MeasRecs) < 2:
specimen += 1
print('skipping specimen - no trm acquisition data ', s)
#
# collect info for the PmagSpecRec dictionary
#
else:
TRMs, Bs = [], []
for rec in MeasRecs:
Bs.append(float(rec['treatment_dc_field']))
TRMs.append(float(rec['measurement_magn_moment']))
NLpars = nlt.NLtrm(
Bs, TRMs, best, blab, 0
) # calculate best fit parameters through TRM acquisition data, and get new banc
#
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
npred = nlt.TRM(
Bp[-1], NLpars['xopt'][0],
NLpars['xopt'][1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(PLT['aq'], Bs, TRMs, Bp, Mp, NLpars,
rec['magic_experiment_name'])
pmagplotlib.drawFIGS(PLT)
print('Banc= ', float(NLpars['banc']) * 1e6)
trmTC = {}
for key in list(TrmRec.keys()):
trmTC[key] = TrmRec[
key] # copy of info from thellier_specimens record
trmTC['specimen_int'] = '%8.3e' % (NLpars['banc'])
trmTC['magic_method_codes'] = TrmRec[
"magic_method_codes"] + ":DA-NL"
PmagSpecRecs.append(trmTC)
ans = input("Return for next specimen, s[a]ve plot ")
if ans == 'a':
Name = {'aq': rec['er_specimen_name'] + '_TRM.svg'}
pmagplotlib.saveP(PLT, Name)
specimen += 1
pmag.magic_write(output, PmagSpecRecs, 'pmag_specimens')
def main():
"""
NAME
plot_map_pts.py
DESCRIPTION
plots points on map
SYNTAX
plot_map_pts.py [command line options]
OPTIONS
-h prints help and quits
-sym [ro, bs, g^, r., b-, etc.] [1,5,10] symbol and size for points
colors are r=red,b=blue,g=green, etc.
symbols are '.' for points, ^, for triangle, s for square, etc.
-, for lines, -- for dotted lines, see matplotlib online documentation for plot()
-eye ELAT ELON [specify eyeball location]
-etp put on topography
-f FILE, specify input file
-o color ocean blue/land green (default is not)
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-fmt [pdf,eps, png] specify output format (default is pdf)
-R don't plot details of rivers
-B don't plot national/state boundaries, etc.
-pad [LAT LON] pad bounding box by LAT/LON (default is not)
-grd SPACE specify grid spacing
-sav save plot and quit
-prj PROJ, specify one of the supported projections: (see basemap.py online documentation)
aeqd = Azimuthal Equidistant
poly = Polyconic
gnom = Gnomonic
moll = Mollweide
tmerc = Transverse Mercator
nplaea = North-Polar Lambert Azimuthal
mill = Miller Cylindrical
merc = Mercator
stere = Stereographic
npstere = North-Polar Stereographic
geos = Geostationary
laea = Lambert Azimuthal Equal Area
sinu = Sinusoidal
spstere = South-Polar Stereographic
lcc = Lambert Conformal
npaeqd = North-Polar Azimuthal Equidistant
eqdc = Equidistant Conic
cyl = Cylindrical Equidistant
omerc = Oblique Mercator
aea = Albers Equal Area
spaeqd = South-Polar Azimuthal Equidistant
ortho = Orthographic
cass= Cassini-Soldner
splaea = South-Polar Lambert Azimuthal
robin = Robinson
Special codes for MagIC formatted input files:
-n
-l
INPUTS
space or tab delimited LON LAT data
OR:
standard MagIC formatted er_sites or pmag_results table
DEFAULTS
res: c
prj: mollweide; lcc for MagIC format files
ELAT,ELON = 0,0
pad LAT,LON=0,0
NB: high resolution or lines can be very slow
"""
dir_path='.'
plot=0
ocean=0
res='c'
proj='moll'
Lats,Lons=[],[]
fmt='pdf'
sym='ro'
symsize=5
fancy=0
rivers,boundaries,ocean=1,1,0
latmin,latmax,lonmin,lonmax,lat_0,lon_0=-90,90,0.,360.,0.,0.
padlat,padlon,gridspace=0,0,30
lat_0,lon_0="",""
prn_name,prn_loc,names,locs=0,0,[],[]
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 '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res=sys.argv[ind+1]
if res!= 'c' and res!='l':
print('this resolution will take a while - be patient')
if '-etp' in sys.argv: fancy=1
if '-sav' in sys.argv: plot=1
if '-R' in sys.argv:rivers=0
if '-B' in sys.argv:boundaries=0
if '-o' in sys.argv:ocean=1
if '-grd' in sys.argv:
ind = sys.argv.index('-grd')
gridspace=float(sys.argv[ind+1])
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0=float(sys.argv[ind+1])
lon_0=float(sys.argv[ind+2])
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym=sys.argv[ind+1]
symsize=int(sys.argv[ind+2])
if '-pad' in sys.argv:
ind = sys.argv.index('-pad')
padlat=float(sys.argv[ind+1])
padlon=float(sys.argv[ind+2])
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file=dir_path+'/'+sys.argv[ind+1]
header=open(file,'r').readlines()[0].split('\t')
if 'tab' in header[0]:
if '-n' in sys.argv:prn_name=1
if '-l' in sys.argv:prn_loc=1
proj='lcc'
if 'results' in header[1]:
latkey='average_lat'
lonkey='average_lon'
namekey='pmag_result_name'
lockey='er_location_names'
elif 'sites' in header[1]:
latkey='site_lat'
lonkey='site_lon'
namekey='er_site_name'
lockey='er_location_name'
else:
print('file type not supported')
print(main.__doc__)
sys.exit()
Sites,file_type=pmag.magic_read(file)
Lats=pmag.get_dictkey(Sites,latkey,'f')
Lons=pmag.get_dictkey(Sites,lonkey,'f')
if prn_name==1:names=pmag.get_dictkey(Sites,namekey,'')
if prn_loc==1:names=pmag.get_dictkey(Sites,lockey,'')
else:
ptdata=numpy.loadtxt(file)
Lons=ptdata.transpose()[0]
Lats=ptdata.transpose()[1]
latmin=numpy.min(Lats)-padlat
lonmin=numpy.min(Lons)-padlon
latmax=numpy.max(Lats)+padlat
lonmax=numpy.max(Lons)+padlon
if lon_0=="":
lon_0=0.5*(lonmin+lonmax)
lat_0=0.5*(latmin+latmax)
else:
print("input file must be specified")
sys.exit()
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj=sys.argv[ind+1]
FIG={'map':1}
pmagplotlib.plot_init(FIG['map'],6,6)
if res=='c':skip=8
if res=='l':skip=5
if res=='i':skip=2
if res=='h':skip=1
cnt=0
Opts={'latmin':latmin,'latmax':latmax,'lonmin':lonmin,'lonmax':lonmax,'lat_0':lat_0,'lon_0':lon_0,'proj':proj,'sym':sym,'symsize':3,'pltgrid':1,'res':res,'boundinglat':0.,'padlon':padlon,'padlat':padlat,'gridspace':gridspace}
Opts['details']={}
Opts['details']['coasts']=1
Opts['details']['rivers']=rivers
Opts['details']['states']=boundaries
Opts['details']['countries']=boundaries
Opts['details']['ocean']=ocean
Opts['details']['fancy']=fancy
if len(names)>0:Opts['names']=names
if len(locs)>0:Opts['loc_name']=locs
if proj=='merc':
Opts['latmin']=-70
Opts['latmax']=70
Opts['lonmin']=-180
Opts['lonmax']=180
print('please wait to draw points')
Opts['sym']=sym
Opts['symsize']=symsize
pmagplotlib.plotMAP(FIG['map'],Lats,Lons,Opts)
files={}
titles={}
titles['map']='PT Map'
for key in list(FIG.keys()):
files[key]='Map_PTS'+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
if plot==1:
pmagplotlib.saveP(FIG,files)
else:
pmagplotlib.drawFIGS(FIG)
ans=input(" S[a]ve to save plot, Return to quit: ")
if ans=="a": pmagplotlib.saveP(FIG,files)
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
chi_magic.py
DESCRIPTION
plots magnetic susceptibility as a function of frequency and temperature and AC field
SYNTAX
chi_magic.py [command line options]
OPTIONS
-h prints help message and quits
-i allows interactive setting of FILE and temperature step
-f FILE, specify magic_measurements format file
-T IND, specify temperature step to plot
-e EXP, specify experiment name to plot
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
-sav save figure and quit
DEFAULTS
FILE: magic_measurements.txt
IND: first
SPEC: step through one by one
"""
cont,FTinit,BTinit,k="",0,0,0
meas_file="magic_measurements.txt"
spec=""
Tind,cont=0,""
EXP=""
fmt='svg' # default image type for saving
plot=0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-i' in sys.argv:
file=input("Input magic_measurements file name? [magic_measurements.txt] ")
if file!="":meas_file=file
if '-e' in sys.argv:
ind=sys.argv.index('-e')
EXP=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=sys.argv[ind+1]
if '-T' in sys.argv:
ind=sys.argv.index('-T')
Tind=int(sys.argv[ind+1])
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-sav' in sys.argv:plot=1
#
meas_data,file_type=pmag.magic_read(meas_file)
#
# get list of unique experiment names
#
# initialize some variables (a continuation flag, plot initialization flags and the experiment counter
experiment_names=[]
for rec in meas_data:
if rec['magic_experiment_name'] not in experiment_names:experiment_names.append(rec['magic_experiment_name'])
#
# hunt through by experiment name
if EXP!="":
try:
k=experiment_names.index(EXP)
except:
print("Bad experiment name")
sys.exit()
while k < len(experiment_names):
e=experiment_names[k]
if EXP=="":print(e, k+1 , 'out of ',len(experiment_names))
#
# initialize lists of data, susceptibility, temperature, frequency and field
X,T,F,B=[],[],[],[]
for rec in meas_data:
methcodes=rec['magic_method_codes']
meths=methcodes.strip().split(':')
if rec['magic_experiment_name']==e and "LP-X" in meths: # looking for chi measurement
if 'measurement_temp' not in list(rec.keys()):rec['measurement_temp']='300' # set defaults
if 'measurement_freq' not in list(rec.keys()):rec['measurement_freq']='0' # set defaults
if 'measurement_lab_field_ac' not in list(rec.keys()):rec['measurement_lab_field_ac']='0' # set default
X.append(float(rec['measurement_x']))
T.append(float(rec['measurement_temp']))
F.append(float(rec['measurement_freq']))
B.append(float(rec['measurement_lab_field_ac']))
#
# get unique list of Ts,Fs, and Bs
#
Ts,Fs,Bs=[],[],[]
for k in range(len(X)): # hunt through all the measurements
if T[k] not in Ts:Ts.append(T[k]) # append if not in list
if F[k] not in Fs:Fs.append(F[k])
if B[k] not in Bs:Bs.append(B[k])
Ts.sort() # sort list of temperatures, frequencies and fields
Fs.sort()
Bs.sort()
if '-x' in sys.argv:
k=len(experiment_names)+1 # just plot the one
else:
k+=1 # increment experiment number
#
# plot chi versus T and F holding B constant
#
plotnum=1 # initialize plot number to 1
if len(X)>2: # if there are any data to plot, continue
b=Bs[-1] # keeping field constant and at maximum
XTF=[] # initialize list of chi versus Temp and freq
for f in Fs: # step through frequencies sequentially
XT=[] # initialize list of chi versus temp
for kk in range(len(X)): # hunt through all the data
if F[kk]==f and B[kk]==b: # select data with given freq and field
XT.append([X[kk],T[kk]]) # append to list
XTF.append(XT) # append list to list of frequencies
if len(XT)>1: # if there are any temperature dependent data
pmagplotlib.plot_init(plotnum,5,5) # initialize plot
pmagplotlib.plotXTF(plotnum,XTF,Fs,e,b) # call the plotting function
if plot==0:pmagplotlib.drawFIGS({'fig':plotnum}) #make it visible
plotnum+=1 # increment plot number
f=Fs[0] # set frequency to minimum
XTB=[] # initialize list if chi versus Temp and field
for b in Bs: # step through field values
XT=[] # initial chi versus temp list for this field
for kk in range(len(X)): # hunt through all the data
if F[kk]==f and B[kk]==b: # select data with given freq and field
XT.append([X[kk],T[kk]]) # append to list
XTB.append(XT)
if len(XT)>1: # if there are any temperature dependent data
pmagplotlib.plot_init(plotnum,5,5) # set up plot
pmagplotlib.plotXTB(plotnum,XTB,Bs,e,f) # call the plotting function
if plot==0:pmagplotlib.drawFIGS({'fig':plotnum})
plotnum+=1 # increment plot number
if '-i' in sys.argv:
for ind in range(len(Ts)): # print list of temperatures available
print(ind,int(Ts[ind]))
cont=input("Enter index of desired temperature step, s[a]ve plots, [return] to quit ")
if cont=='a':
files={}
PLTS={}
for p in range(1,plotnum):
key=str(p)
files[key]=e+'_'+key+'.'+fmt
PLTS[key]=key
pmagplotlib.saveP(PLTS,files)
cont=input("Enter index of desired temperature step, s[a]ve plots, [return] to quit ")
if cont=="":cont='q'
while cont!="q":
if '-i' in sys.argv:Tind=int(cont) # set temperature index
b=Bs[-1] # set field to max available
XF=[] # initial chi versus frequency list
for kk in range(len(X)): # hunt through the data
if T[kk]==Ts[Tind] and B[kk]==b: # if temperature and field match,
XF.append([X[kk],F[kk]]) # append the data
if len(XF)>1: # if there are any data to plot
if FTinit==0: # if not already initialized, initialize plot
#print 'initializing ',plotnum
pmagplotlib.plot_init(plotnum,5,5)
FTinit=1
XFplot=plotnum
plotnum+=1 # increment plotnum
pmagplotlib.plotXFT(XFplot,XF,Ts[Tind],e,b)
if plot==0:pmagplotlib.drawFIGS({'fig':plotnum})
else:
print('\n *** Skipping susceptibitily-frequency plot as a function of temperature *** \n')
f=Fs[0] # set frequency to minimum available
XB=[] # initialize chi versus field list
for kk in range(len(X)): # hunt through the data
if T[kk]==Ts[Tind] and F[kk]==f: # if temperature and field match those desired
XB.append([X[kk],B[kk]]) # append the data to list
if len(XB)>4: # if there are any data
if BTinit==0: # if plot not already initialized
pmagplotlib.plot_init(plotnum,5,5) # do it
BTinit=1
pmagplotlib.plotXBT(plotnum,XB,Ts[Tind],e,f) # and call plotting function
if plot==0:pmagplotlib.drawFIGS({'fig':plotnum})
else:
print('Skipping susceptibitily - AC field plot as a function of temperature')
files={}
PLTS={}
for p in range(1,plotnum):
key=str(p)
files[key]=e+'_'+key+'.'+fmt
PLTS[key]=p
if '-i' in sys.argv:
for ind in range(len(Ts)): # just in case you forgot, print out a new list of temperatures
print(ind,int(Ts[ind]))
cont=input("Enter index of next temperature step, s[a]ve plots, [return] to quit ") # ask for new temp
if cont=="":sys.exit()
if cont=='a':
pmagplotlib.saveP(PLTS,files)
cont=input("Enter index of desired temperature step, s[a]ve plots, [return] to quit ")
if cont=="":sys.exit()
elif plot==0:
ans=input("enter s[a]ve to save files, [return] to quit ")
if ans=='a':
pmagplotlib.saveP(PLTS,files)
sys.exit()
else:
sys.exit()
else:
pmagplotlib.saveP(PLTS,files)
sys.exit()
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
vgpmap_magic.py
DESCRIPTION
makes a map of vgps and a95/dp,dm for site means in a pmag_results table
SYNTAX
vgpmap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE pmag_results format file, [default is pmag_results.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-etp plot the etopo20 topographpy data (requires high resolution data set)
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 5 : small red circles
bs 10 : intermediate blue squares
g^ 20 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to plot all site VGPs
-fmt [pdf, png, eps...] specify output format, default is pdf
-sav save and quit
DEFAULTS
FILE: pmag_results.txt
res: c
prj: ortho
ELAT,ELON = 0,0
SYM SIZE: ro 8
RSYM RSIZE: g^ 8
"""
dir_path = '.'
res, ages = 'c', 0
plot = 0
proj = 'ortho'
results_file = 'pmag_results.txt'
ell, flip = 0, 0
lat_0, lon_0 = 90., 0.
fmt = 'pdf'
sym, size = 'ro', 8
rsym, rsize = 'g^', 8
anti = 0
fancy = 0
coord = ""
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 '-S' in sys.argv: anti = 1
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if '-sav' in sys.argv: plot = 1
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res = sys.argv[ind + 1]
if '-etp' in sys.argv: fancy = 1
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj = sys.argv[ind + 1]
if '-rev' in sys.argv:
flip = 1
ind = sys.argv.index('-rev')
rsym = (sys.argv[ind + 1])
rsize = int(sys.argv[ind + 2])
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym = (sys.argv[ind + 1])
size = int(sys.argv[ind + 2])
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0 = float(sys.argv[ind + 1])
lon_0 = float(sys.argv[ind + 2])
if '-ell' in sys.argv: ell = 1
if '-age' in sys.argv: ages = 1
if '-f' in sys.argv:
ind = sys.argv.index('-f')
results_file = sys.argv[ind + 1]
if '-crd' in sys.argv:
ind = sys.argv.index('-crd')
crd = sys.argv[ind + 1]
if crd == 'g': coord = '0'
if crd == 't': coord = '100'
results_file = dir_path + '/' + results_file
data, file_type = pmag.magic_read(results_file)
if file_type != 'pmag_results':
print "bad results file"
sys.exit()
FIG = {'map': 1}
pmagplotlib.plot_init(FIG['map'], 6, 6)
# read in er_sites file
lats, lons, dp, dm, a95 = [], [], [], [], []
Pars = []
dates, rlats, rlons = [], [], []
if 'data_type' in data[0].keys():
Results = pmag.get_dictitem(data, 'data_type', 'i',
'T') # get all site level data
else:
Results = data
Results = pmag.get_dictitem(Results, 'vgp_lat', '',
'F') # get all non-blank latitudes
Results = pmag.get_dictitem(Results, 'vgp_lon', '',
'F') # get all non-blank longitudes
if coord != "":
Results = pmag.get_dictitem(Results, 'tilt_correction', coord,
'T') # get specified coordinate system
location = ""
for rec in Results:
if rec['er_location_names'] not in location:
location = location + ':' + rec['er_location_names']
if 'average_age' in rec.keys(
) and rec['average_age'] != "" and ages == 1:
dates.append(rec['average_age'])
lat = float(rec['vgp_lat'])
lon = float(rec['vgp_lon'])
if flip == 0:
lats.append(lat)
lons.append(lon)
elif flip == 1:
if lat < 0:
rlats.append(-lat)
lon = lon + 180.
if lon > 360: lon = lon - 360.
rlons.append(lon)
else:
lats.append(lat)
lons.append(lon)
elif anti == 1:
lats.append(-lat)
lon = lon + 180.
if lon > 360: lon = lon - 360.
lons.append(lon)
ppars = []
ppars.append(lon)
ppars.append(lat)
ell1, ell2 = "", ""
if 'vgp_dm' in rec.keys() and rec['vgp_dm'] != "":
ell1 = float(rec['vgp_dm'])
if 'vgp_dp' in rec.keys() and rec['vgp_dp'] != "":
ell2 = float(rec['vgp_dp'])
if 'vgp_alpha95' in rec.keys() and rec['vgp_alpha95'] != "":
ell1, ell2 = float(rec['vgp_alpha95']), float(rec['vgp_alpha95'])
if ell1 != "" and ell2 != "":
ppars = []
ppars.append(lons[-1])
ppars.append(lats[-1])
ppars.append(ell1)
ppars.append(lons[-1])
isign = abs(lats[-1]) / lats[-1]
ppars.append(lats[-1] - isign * 90.)
ppars.append(ell2)
ppars.append(lons[-1] + 90.)
ppars.append(0.)
Pars.append(ppars)
location = location.strip(':')
Opts = {
'latmin': -90,
'latmax': 90,
'lonmin': 0.,
'lonmax': 360.,
'lat_0': lat_0,
'lon_0': lon_0,
'proj': proj,
'sym': 'bs',
'symsize': 3,
'pltgrid': 0,
'res': res,
'boundinglat': 0.
}
Opts['details'] = {
'coasts': 1,
'rivers': 0,
'states': 0,
'countries': 0,
'ocean': 1,
'fancy': fancy
}
pmagplotlib.plotMAP(
FIG['map'], [90.], [0.],
Opts) # make the base map with a blue triangle at the pole`
Opts['pltgrid'] = -1
Opts['sym'] = sym
Opts['symsize'] = size
if len(dates) > 0: Opts['names'] = dates
if len(lats) > 0:
pmagplotlib.plotMAP(FIG['map'], lats, lons,
Opts) # add the lats and lons of the poles
Opts['names'] = []
if len(rlats) > 0:
Opts['sym'] = rsym
Opts['symsize'] = rsize
pmagplotlib.plotMAP(FIG['map'], rlats, rlons,
Opts) # add the lats and lons of the poles
if plot == 0:
pmagplotlib.drawFIGS(FIG)
if ell == 1: # add ellipses if desired.
Opts['details'] = {
'coasts': 0,
'rivers': 0,
'states': 0,
'countries': 0,
'ocean': 0
}
Opts['pltgrid'] = -1 # turn off meridian replotting
Opts['symsize'] = 2
Opts['sym'] = 'g-'
for ppars in Pars:
if ppars[2] != 0:
PTS = pmagplotlib.plotELL(FIG['map'], ppars, 'g.', 0, 0)
elats, elons = [], []
for pt in PTS:
elons.append(pt[0])
elats.append(pt[1])
pmagplotlib.plotMAP(
FIG['map'], elats, elons, Opts
) # make the base map with a blue triangle at the pole`
if plot == 0: pmagplotlib.drawFIGS(FIG)
files = {}
for key in FIG.keys():
files[key] = 'LO:_' + location + '_VGP_map.' + fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['eq'] = 'LO:_' + location + '_VGP_map'
FIG = pmagplotlib.addBorders(FIG, titles, black, purple)
pmagplotlib.saveP(FIG, files)
elif plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = raw_input(" S[a]ve to save plot, Return to quit: ")
if ans == "a":
pmagplotlib.saveP(FIG, files)
else:
print "Good bye"
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
def main():
"""
NAME
foldtest.py
DESCRIPTION
does a fold test (Tauxe, 2010) on data
INPUT FORMAT
dec inc dip_direction dip
SYNTAX
foldtest.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE file with input data
-F FILE for confidence bounds on fold test
-u ANGLE (circular standard deviation) for uncertainty on bedding poles
-b MIN MAX bounds for quick search of percent untilting [default is -10 to 150%]
-n NB number of bootstrap samples [default is 1000]
-fmt FMT, specify format - default is svg
-sav save figures and quit
INPUT FILE
Dec Inc Dip_Direction Dip in space delimited file
OUTPUT PLOTS
Geographic: is an equal area projection of the input data in
original coordinates
Stratigraphic: is an equal area projection of the input data in
tilt adjusted coordinates
% Untilting: The dashed (red) curves are representative plots of
maximum eigenvalue (tau_1) as a function of untilting
The solid line is the cumulative distribution of the
% Untilting required to maximize tau for all the
bootstrapped data sets. The dashed vertical lines
are 95% confidence bounds on the % untilting that yields
the most clustered result (maximum tau_1).
Command line: prints out the bootstrapped iterations and
finally the confidence bounds on optimum untilting.
If the 95% conf bounds include 0, then a post-tilt magnetization is indicated
If the 95% conf bounds include 100, then a pre-tilt magnetization is indicated
If the 95% conf bounds exclude both 0 and 100, syn-tilt magnetization is
possible as is vertical axis rotation or other pathologies
Geographic: is an equal area projection of the input data in
OPTIONAL OUTPUT FILE:
The output file has the % untilting within the 95% confidence bounds
nd the number of bootstrap samples
"""
kappa=0
fmt,plot='svg',0
nb=1000 # number of bootstraps
min,max=-10,150
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-F' in sys.argv:
ind=sys.argv.index('-F')
outfile=open(sys.argv[ind+1],'w')
else:
outfile=""
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
DIDDs=numpy.loadtxt(file)
else:
print main.__doc__
sys.exit()
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-sav' in sys.argv:plot=1
if '-b' in sys.argv:
ind=sys.argv.index('-b')
min=int(sys.argv[ind+1])
max=int(sys.argv[ind+2])
if '-n' in sys.argv:
ind=sys.argv.index('-n')
nb=int(sys.argv[ind+1])
if '-u' in sys.argv:
ind=sys.argv.index('-u')
csd=float(sys.argv[ind+1])
kappa=(81./csd)**2
#
# get to work
#
PLTS={'geo':1,'strat':2,'taus':3} # make plot dictionary
pmagplotlib.plot_init(PLTS['geo'],5,5)
pmagplotlib.plot_init(PLTS['strat'],5,5)
pmagplotlib.plot_init(PLTS['taus'],5,5)
pmagplotlib.plotEQ(PLTS['geo'],DIDDs,'Geographic')
D,I=pmag.dotilt_V(DIDDs)
TCs=numpy.array([D,I]).transpose()
pmagplotlib.plotEQ(PLTS['strat'],TCs,'Stratigraphic')
if plot==0:pmagplotlib.drawFIGS(PLTS)
Percs=range(min,max)
Cdf,Untilt=[],[]
pylab.figure(num=PLTS['taus'])
print 'doing ',nb,' iterations...please be patient.....'
for n in range(nb): # do bootstrap data sets - plot first 25 as dashed red line
if n%50==0:print n
Taus=[] # set up lists for taus
PDs=pmag.pseudo(DIDDs)
if kappa!=0:
for k in range(len(PDs)):
d,i=pmag.fshdev(kappa)
dipdir,dip=pmag.dodirot(d,i,PDs[k][2],PDs[k][3])
PDs[k][2]=dipdir
PDs[k][3]=dip
for perc in Percs:
tilt=numpy.array([1.,1.,1.,0.01*perc])
D,I=pmag.dotilt_V(PDs*tilt)
TCs=numpy.array([D,I]).transpose()
ppars=pmag.doprinc(TCs) # get principal directions
Taus.append(ppars['tau1'])
if n<25:pylab.plot(Percs,Taus,'r--')
Untilt.append(Percs[Taus.index(numpy.max(Taus))]) # tilt that gives maximum tau
Cdf.append(float(n)/float(nb))
pylab.plot(Percs,Taus,'k')
pylab.xlabel('% Untilting')
pylab.ylabel('tau_1 (red), CDF (green)')
Untilt.sort() # now for CDF of tilt of maximum tau
pylab.plot(Untilt,Cdf,'g')
lower=int(.025*nb)
upper=int(.975*nb)
pylab.axvline(x=Untilt[lower],ymin=0,ymax=1,linewidth=1,linestyle='--')
pylab.axvline(x=Untilt[upper],ymin=0,ymax=1,linewidth=1,linestyle='--')
tit= '%i - %i %s'%(Untilt[lower],Untilt[upper],'Percent Unfolding')
print tit
print 'range of all bootstrap samples: ', Untilt[0], ' - ', Untilt[-1]
pylab.title(tit)
outstring= '%i - %i; %i\n'%(Untilt[lower],Untilt[upper],nb)
if outfile!="":outfile.write(outstring)
files={}
for key in PLTS.keys():
files[key]=('foldtest_'+'%s'%(key.strip()[:2])+'.'+fmt)
if plot==0:
pmagplotlib.drawFIGS(PLTS)
ans= raw_input('S[a]ve all figures, <Return> to quit ')
if ans!='a':
print "Good bye"
sys.exit()
pmagplotlib.saveP(PLTS,files)
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
zeq_magic.py
DESCRIPTION
reads in magic_measurements formatted file, makes plots of remanence decay
during demagnetization experiments. Reads in prior interpretations saved in
a pmag_specimens formatted file [and allows re-interpretations of best-fit lines
and planes and saves (revised or new) interpretations in a pmag_specimens file.
interpretations are saved in the coordinate system used. Also allows judicious editting of
measurements to eliminate "bad" measurements. These are marked as such in the magic_measurements
input file. they are NOT deleted, just ignored. ] Bracketed part not yet implemented
SYNTAX
zeq_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEASFILE: sets measurements format input file, default: measurements.txt
-fsp SPECFILE: sets specimens format file with prior interpreations, default: specimens.txt
-fsa SAMPFILE: sets samples format file sample=>site information, default: samples.txt
-fsi SITEFILE: sets sites format file with site=>location informationprior interpreations, default: samples.txt
-Fp PLTFILE: sets filename for saved plot, default is name_type.fmt (where type is zijd, eqarea or decay curve)
-crd [s,g,t]: sets coordinate system, g=geographic, t=tilt adjusted, default: specimen coordinate system
-spc SPEC plots single specimen SPEC, saves plot with specified format
with optional -dir settings and quits
-dir [L,P,F][beg][end]: sets calculation type for principal component analysis, default is none
beg: starting step for PCA calculation
end: ending step for PCA calculation
[L,P,F]: calculation type for line, plane or fisher mean
must be used with -spc option
-fmt FMT: set format of saved plot [png,svg,jpg]
-A: suppresses averaging of replicate measurements, default is to average
-sav: saves all plots without review
SCREEN OUTPUT:
Specimen, N, a95, StepMin, StepMax, Dec, Inc, calculation type
"""
# initialize some variables
doave, e, b = 1, 0, 0 # average replicates, initial end and beginning step
intlist = ['magn_moment', 'magn_volume', 'magn_mass', 'magnitude']
plots, coord = 0, 's'
noorient = 0
version_num = pmag.get_version()
verbose = pmagplotlib.verbose
calculation_type, fmt = "", "svg"
user, spec_keys, locname = "", [], ''
geo, tilt, ask = 0, 0, 0
PriorRecs = [] # empty list for prior interpretations
backup = 0
specimen = "" # can skip everything and just plot one specimen with bounds e,b
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")
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")
#meas_file = os.path.join(dir_path, meas_file)
#spec_file = os.path.join(dir_path, spec_file)
#samp_file = os.path.join(dir_path, samp_file)
#site_file = os.path.join(dir_path, site_file)
plot_file = pmag.get_named_arg_from_sys("-Fp", default_val="")
crd = pmag.get_named_arg_from_sys("-crd", default_val="s")
if crd == "s":
coord = "-1"
elif crd == "t":
coord = "100"
else:
coord = "0"
fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
specimen = pmag.get_named_arg_from_sys("-spc", default_val="")
beg_pca, end_pca = "", ""
if '-dir' in sys.argv:
ind = sys.argv.index('-dir')
direction_type = sys.argv[ind + 1]
beg_pca = int(sys.argv[ind + 2])
end_pca = int(sys.argv[ind + 3])
if direction_type == 'L':
calculation_type = 'DE-BFL'
if direction_type == 'P':
calculation_type = 'DE-BFP'
if direction_type == 'F':
calculation_type = 'DE-FM'
if '-A' in sys.argv:
doave = 0
if '-sav' in sys.argv:
plots, verbose = 1, 0
#
first_save = 1
fnames = {
'measurements': meas_file,
'specimens': spec_file,
'samples': samp_file,
'sites': site_file
}
contribution = nb.Contribution(
dir_path,
custom_filenames=fnames,
read_tables=['measurements', 'specimens', 'samples', 'sites'])
#
# import specimens
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:
# contribution.propagate_name_down('sample','measurements')
spec_container = contribution.tables['specimens']
prior_spec_data = spec_container.get_records_for_code(
'LP-DIR', strict_match=False
) # look up all prior directional interpretations
#
# tie sample names to measurement data
#
else:
spec_container, prior_spec_data = None, []
#
# import samples for orientation info
#
if 'samples' in contribution.tables:
# contribution.propagate_name_down('site','measurements')
contribution.propagate_cols(
col_names=['azimuth', 'dip', 'orientation_flag'],
target_df_name='measurements',
source_df_name='samples')
#
# define figure numbers for equal area, zijderveld,
# and intensity vs. demagnetiztion step respectively
#
ZED = {}
ZED['eqarea'], ZED['zijd'], ZED['demag'] = 1, 2, 3
pmagplotlib.plot_init(ZED['eqarea'], 6, 6)
pmagplotlib.plot_init(ZED['zijd'], 6, 6)
pmagplotlib.plot_init(ZED['demag'], 6, 6)
# save_pca=0
angle, direction_type, setangle = "", "", 0
# create measurement dataframe
#
meas_container = contribution.tables['measurements']
meas_data = meas_container.df
#
meas_data = meas_data[meas_data['method_codes'].str.contains(
'LT-NO|LT-AF-Z|LT-T-Z|LT-M-Z') == True] # fish out steps for plotting
meas_data = meas_data[meas_data['method_codes'].str.contains(
'AN|ARM|LP-TRM|LP-PI-ARM') == False] # strip out unwanted experiments
intensity_types = [
col_name for col_name in meas_data.columns if col_name in intlist
]
# plot first intensity method found - normalized to initial value anyway -
# doesn't matter which used
int_key = intensity_types[0]
# get all the non-null intensity records of the same type
meas_data = meas_data[meas_data[int_key].notnull()]
if 'flag' not in meas_data.columns:
meas_data['flag'] = 'g' # set the default flag to good
# need to treat LP-NO specially for af data, treatment should be zero,
# otherwise 273.
meas_data['treatment'] = meas_data['treat_ac_field'].where(
cond=meas_data['treat_ac_field'] != '0', other=meas_data['treat_temp'])
meas_data['ZI'] = 1 # initialize these to one
meas_data['instrument_codes'] = "" # initialize these to blank
# for unusual case of microwave power....
if 'treat_mw_power' in meas_data.columns:
meas_data.loc[
meas_data.treat_mw_power != 0,
'treatment'] = meas_data.treat_mw_power * meas_data.treat_mw_time
#
# get list of unique specimen names from measurement data
#
# this is a list of all the specimen names
specimen_names = meas_data.specimen.unique()
specimen_names = specimen_names.tolist()
specimen_names.sort()
#
# set up new DataFrame for this sessions specimen interpretations
#
data_container = nb.MagicDataFrame(dtype='specimens',
columns=specimen_cols)
# this is for interpretations from this session
current_spec_data = data_container.df
locname = 'LookItUp'
if specimen == "":
k = 0
else:
k = specimen_names.index(specimen)
# let's look at the data now
while k < len(specimen_names):
# set the current specimen for plotting
this_specimen = specimen_names[k]
if verbose and this_specimen != "":
print(this_specimen, k + 1, 'out of ', len(specimen_names))
if setangle == 0:
angle = ""
this_specimen_measurements = meas_data[
meas_data['specimen'].str.contains(
this_specimen) == True] # fish out this specimen
this_specimen_measurements = this_specimen_measurements[
this_specimen_measurements['flag'].str.contains(
'g') == True] # fish out this specimen
if len(this_specimen_measurements) != 0: # if there are measurements
#
# set up datablock [[treatment,dec, inc, int, direction_type],[....]]
#
#
# figure out the method codes
#
units, methods, title = "", "", this_specimen
# this is a list of all the specimen method codes`
meas_meths = this_specimen_measurements.method_codes.unique()
tr = pd.to_numeric(this_specimen_measurements.treatment).tolist()
if set(tr) == set([0]):
k += 1
continue
for m in meas_meths:
if 'LT-AF-Z' in m:
units = 'T' # units include tesla
tr[0] = 0
if 'LT-T-Z' in m:
units = units + ":K" # units include kelvin
if 'LT-M-Z' in m:
units = units + ':J' # units include joules
tr[0] = 0
units = units.strip(':') # strip off extra colons
if 'LP-' in m:
methods = methods + ":" + m
decs = pd.to_numeric(this_specimen_measurements.dir_dec).tolist()
incs = pd.to_numeric(this_specimen_measurements.dir_inc).tolist()
#
# fix the coordinate system
#
if coord != '-1': # need to transform coordinates to geographic
azimuths = pd.to_numeric(this_specimen_measurements.azimuth
).tolist() # get the azimuths
# get the azimuths
dips = pd.to_numeric(this_specimen_measurements.dip).tolist()
dirs = [decs, incs, azimuths, dips]
# this transposes the columns and rows of the list of lists
dirs_geo = np.array(list(map(list, list(zip(*dirs)))))
decs, incs = pmag.dogeo_V(dirs_geo)
if coord == '100': # need to do tilt correction too
bed_dip_dirs = pd.to_numeric(
this_specimen_measurements.bed_dip_dir).tolist(
) # get the azimuths
bed_dips = pd.to_numeric(this_specimen_measurements.bed_dip
).tolist() # get the azimuths
dirs = [decs, incs, bed_dip_dirs, bed_dips]
# this transposes the columns and rows of the list of lists
dirs_tilt = np.array(list(map(list, list(zip(*dirs)))))
decs, incs = pmag.dotilt_V(dirs_tilt)
title = title + '_t'
else:
title = title + '_g'
if angle == "":
angle = decs[0]
ints = pd.to_numeric(this_specimen_measurements[int_key]).tolist()
ZI = this_specimen_measurements.ZI.tolist()
flags = this_specimen_measurements.flag.tolist()
codes = this_specimen_measurements.instrument_codes.tolist()
datalist = [tr, decs, incs, ints, ZI, flags, codes]
# this transposes the columns and rows of the list of lists
datablock = list(map(list, list(zip(*datalist))))
pmagplotlib.plotZED(ZED, datablock, angle, title, units)
if verbose:
pmagplotlib.drawFIGS(ZED)
#
# collect info for current_specimen_interpretation dictionary
#
if beg_pca == "" and len(prior_spec_data) != 0:
#
# find prior interpretation
#
prior_specimen_interpretations = prior_spec_data[
prior_spec_data['specimen'].str.contains(
this_specimen) == True]
beg_pcas = pd.to_numeric(prior_specimen_interpretations.
meas_step_min.values).tolist()
end_pcas = pd.to_numeric(prior_specimen_interpretations.
meas_step_max.values).tolist()
spec_methods = prior_specimen_interpretations.method_codes.tolist(
)
# step through all prior interpretations and plot them
for ind in range(len(beg_pcas)):
spec_meths = spec_methods[ind].split(':')
for m in spec_meths:
if 'DE-BFL' in m:
calculation_type = 'DE-BFL' # best fit line
if 'DE-BFP' in m:
calculation_type = 'DE-BFP' # best fit plane
if 'DE-FM' in m:
calculation_type = 'DE-FM' # fisher mean
if 'DE-BFL-A' in m:
calculation_type = 'DE-BFL-A' # anchored best fit line
start, end = tr.index(beg_pcas[ind]), tr.index(
end_pcas[ind]
) # getting the starting and ending points
# calculate direction/plane
mpars = pmag.domean(datablock, start, end,
calculation_type)
if mpars["specimen_direction_type"] != "Error":
# put it on the plot
pmagplotlib.plotDir(ZED, mpars, datablock, angle)
if verbose:
pmagplotlib.drawFIGS(ZED)
else:
start, end = int(beg_pca), int(end_pca)
# calculate direction/plane
mpars = pmag.domean(datablock, start, end, calculation_type)
if mpars["specimen_direction_type"] != "Error":
# put it on the plot
pmagplotlib.plotDir(ZED, mpars, datablock, angle)
if verbose:
pmagplotlib.drawFIGS(ZED)
if plots == 1 or specimen != "":
if plot_file == "":
basename = title
else:
basename = plot_file
files = {}
for key in list(ZED.keys()):
files[key] = basename + '_' + key + '.' + fmt
pmagplotlib.saveP(ZED, files)
if specimen != "":
sys.exit()
if verbose:
recnum = 0
for plotrec in datablock:
if units == 'T':
print('%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' %
(plotrec[5], recnum, plotrec[0] * 1e3, " mT",
plotrec[3], plotrec[1], plotrec[2], plotrec[6]))
if units == "K":
print('%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' %
(plotrec[5], recnum, plotrec[0] - 273, ' C',
plotrec[3], plotrec[1], plotrec[2], plotrec[6]))
if units == "J":
print('%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' %
(plotrec[5], recnum, plotrec[0], ' J',
plotrec[3], plotrec[1], plotrec[2], plotrec[6]))
if 'K' in units and 'T' in units:
if plotrec[0] >= 1.:
print('%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' %
(plotrec[5], recnum, plotrec[0] - 273, ' C',
plotrec[3], plotrec[1], plotrec[2],
plotrec[6]))
if plotrec[0] < 1.:
print('%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' %
(plotrec[5], recnum, plotrec[0] * 1e3, " mT",
plotrec[3], plotrec[1], plotrec[2],
plotrec[6]))
recnum += 1
# we have a current interpretation
elif mpars["specimen_direction_type"] != "Error":
#
# create a new specimen record for the interpreation for this
# specimen
this_specimen_interpretation = {
col: ""
for col in specimen_cols
}
# this_specimen_interpretation["analysts"]=user
this_specimen_interpretation['software_packages'] = version_num
this_specimen_interpretation['specimen'] = this_specimen
this_specimen_interpretation["method_codes"] = calculation_type
this_specimen_interpretation["meas_step_unit"] = units
this_specimen_interpretation["meas_step_min"] = tr[start]
this_specimen_interpretation["meas_step_max"] = tr[end]
this_specimen_interpretation["dir_dec"] = '%7.1f' % (
mpars['specimen_dec'])
this_specimen_interpretation["dir_inc"] = '%7.1f' % (
mpars['specimen_inc'])
this_specimen_interpretation["dir_dang"] = '%7.1f' % (
mpars['specimen_dang'])
this_specimen_interpretation["dir_n_measurements"] = '%i' % (
mpars['specimen_n'])
this_specimen_interpretation["dir_tilt_correction"] = coord
methods = methods.replace(" ", "")
if "T" in units:
methods = methods + ":LP-DIR-AF"
if "K" in units:
methods = methods + ":LP-DIR-T"
if "J" in units:
methods = methods + ":LP-DIR-M"
this_specimen_interpretation["method_codes"] = methods.strip(
':')
this_specimen_interpretation[
"experiments"] = this_specimen_measurements.experiment.unique(
)[0]
#
# print some stuff
#
if calculation_type != 'DE-FM':
this_specimen_interpretation["dir_mad_free"] = '%7.1f' % (
mpars['specimen_mad'])
this_specimen_interpretation["dir_alpha95"] = ''
if verbose:
if units == 'K':
print(
'%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n'
%
(this_specimen_interpretation["specimen"],
int(this_specimen_interpretation[
"dir_n_measurements"]),
float(this_specimen_interpretation[
"dir_mad_free"]),
float(
this_specimen_interpretation["dir_dang"]),
float(this_specimen_interpretation[
"meas_step_min"]) - 273,
float(this_specimen_interpretation[
"meas_step_max"]) - 273,
float(
this_specimen_interpretation["dir_dec"]),
float(
this_specimen_interpretation["dir_inc"]),
calculation_type))
elif units == 'T':
print(
'%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n'
%
(this_specimen_interpretation["specimen"],
int(this_specimen_interpretation[
"dir_n_measurements"]),
float(this_specimen_interpretation[
"dir_mad_free"]),
float(
this_specimen_interpretation["dir_dang"]),
float(this_specimen_interpretation[
"meas_step_min"]) * 1e3,
float(this_specimen_interpretation[
"meas_step_max"]) * 1e3,
float(
this_specimen_interpretation["dir_dec"]),
float(
this_specimen_interpretation["dir_inc"]),
calculation_type))
elif 'T' in units and 'K' in units:
if float(this_specimen_interpretation[
'meas_step_min']) < 1.0:
min = float(this_specimen_interpretation[
'meas_step_min']) * 1e3
else:
min = float(this_specimen_interpretation[
'meas_step_min']) - 273
if float(this_specimen_interpretation[
'meas_step_max']) < 1.0:
max = float(this_specimen_interpretation[
'meas_step_max']) * 1e3
else:
max = float(this_specimen_interpretation[
'meas_step_max']) - 273
print(
'%s %i %7.1f %i %i %7.1f %7.1f %7.1f %s \n' %
(this_specimen_interpretation["specimen"],
int(this_specimen_interpretation[
"dir_n_measurements"]),
float(this_specimen_interpretation[
"dir_mad_free"]),
float(
this_specimen_interpretation["dir_dang"]),
min, max,
float(
this_specimen_interpretation["dir_dec"]),
float(
this_specimen_interpretation["dir_inc"]),
calculation_type))
else:
print(
'%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n'
%
(this_specimen_interpretation["specimen"],
int(this_specimen_interpretation[
"dir_n_measurements"]),
float(this_specimen_interpretation[
"dir_mad_free"]),
float(
this_specimen_interpretation["dir_dang"]),
float(this_specimen_interpretation[
"meas_step_min"]),
float(this_specimen_interpretation[
"meas_step_max"]),
float(
this_specimen_interpretation["dir_dec"]),
float(
this_specimen_interpretation["dir_inc"]),
calculation_type))
else:
this_specimen_interpretation["dir_alpha95"] = '%7.1f' % (
mpars['specimen_alpha95'])
this_specimen_interpretation["dir_mad_free"] = ''
if verbose:
if 'K' in units:
print(
'%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n'
%
(this_specimen_interpretation["specimen"],
int(this_specimen_interpretation[
"dir_n_measurments"]),
float(this_specimen_interpretation[
"dir_mad_free"]),
float(
this_specimen_interpretation["dir_dang"]),
float(this_specimen_interpretation[
"meas_step_min"]) - 273,
float(this_specimen_interpretation[
"meas_step_max"]) - 273,
float(
this_specimen_interpretation["dir_dec"]),
float(
this_specimen_interpretation["dir_inc"]),
calculation_type))
elif 'T' in units:
print(
'%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s \n'
%
(this_specimen_interpretation["specimen"],
int(this_specimen_interpretation[
"dir_n_measurements"]),
float(this_specimen_interpretation[
"dir_alpha95"]),
float(
this_specimen_interpretation["dir_dang"]),
float(this_specimen_interpretation[
"meas_step_min"]) * 1e3,
float(this_specimen_interpretation[
"meas_step_max"]) * 1e3,
float(
this_specimen_interpretation["dir_dec"]),
float(
this_specimen_interpretation["dir_inc"]),
calculation_type))
elif 'T' in units and 'K' in units:
if float(this_specimen_interpretation[
'meas_step_min']) < 1.0:
min = float(this_specimen_interpretation[
'meas_step_min']) * 1e3
else:
min = float(this_specimen_interpretation[
'meas_step_min']) - 273
if float(this_specimen_interpretation[
'meas_step_max']) < 1.0:
max = float(this_specimen_interpretation[
'meas_step_max']) * 1e3
else:
max = float(this_specimen_interpretation[
'meas_step_max']) - 273
print('%s %i %7.1f %i %i %7.1f %7.1f %s \n' % (
this_specimen_interpretation["specimen"],
int(this_specimen_interpretation[
"dir_n_measurements"]),
float(
this_specimen_interpretation["dir_alpha95"]
), min, max,
float(this_specimen_interpretation["dir_dec"]),
float(this_specimen_interpretation["dir_inc"]),
calculation_type))
else:
print(
'%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %s \n' %
(this_specimen_interpretation["specimen"],
int(this_specimen_interpretation[
"dir_n_measurements"]),
float(this_specimen_interpretation[
"dir_alpha95"]),
float(this_specimen_interpretation[
"meas_step_min"]),
float(this_specimen_interpretation[
"meas_step_max"]),
float(
this_specimen_interpretation["dir_dec"]),
float(
this_specimen_interpretation["dir_inc"]),
calculation_type))
if verbose:
saveit = input("Save this interpretation? [y]/n \n")
# START HERE
#
# if len(current_spec_data)==0: # no interpretations yet for this session
# print "no current interpretation"
# beg_pca,end_pca="",""
# calculation_type=""
# get the ones that meet the current coordinate system
else:
print("no data")
if verbose:
input('Ready for next specimen ')
k += 1
def main():
"""
NAME
lnp_magic.py
DESCRIPTION
makes equal area projections site by site
from pmag_specimen formatted file with
Fisher confidence ellipse using McFadden and McElhinny (1988)
technique for combining lines and planes
SYNTAX
lnp_magic [command line options]
INPUT
takes magic formatted pmag_specimens file
OUPUT
prints site_name n_lines n_planes K alpha95 dec inc R
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is 'pmag_specimens.txt'
-crd [s,g,t]: specify coordinate system, [s]pecimen, [g]eographic, [t]ilt adjusted
default is specimen
-fmt [svg,png,jpg] format for plots, default is svg
-sav save plots and quit
-P: do not plot
-F FILE, specify output file of dec, inc, alpha95 data for plotting with plotdi_a and plotdi_e
-exc use criteria in pmag_criteria.txt
"""
dir_path='.'
FIG={} # plot dictionary
FIG['eqarea']=1 # eqarea is figure 1
in_file,plot_key,coord='pmag_specimens.txt','er_site_name',"-1"
out_file=""
fmt,plt,plot='svg',1,0
Crits=""
M,N,acutoff,kcutoff=180.,1,180.,0.
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-exc' in sys.argv:
Crits,file_type=pmag.magic_read(dir_path+'/pmag_criteria.txt')
for crit in Crits:
if 'specimen_mad' in crit: M=float(crit['specimen_mad'])
if 'specimen_n' in crit: N=float(crit['specimen_n'])
if 'site_alpha95' in crit: acutoff=float(crit['site_alpha95'])
if 'site_k' in crit: kcutoff=float(crit['site_k'])
if '-F' in sys.argv:
ind=sys.argv.index("-F")
out_file=sys.argv[ind+1]
out=open(dir_path+'/'+out_file,'w')
if '-crd' in sys.argv:
ind=sys.argv.index("-crd")
crd=sys.argv[ind+1]
if crd=='s':coord="-1"
if crd=='g':coord="0"
if crd=='t':coord="100"
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-P' in sys.argv:plt=0
if '-sav' in sys.argv:plot=1
#
in_file=dir_path+'/'+in_file
Specs,file_type=pmag.magic_read(in_file)
if file_type!='pmag_specimens':
print('Error opening file')
sys.exit()
sitelist=[]
for rec in Specs:
if rec['er_site_name'] not in sitelist: sitelist.append(rec['er_site_name'])
sitelist.sort()
if plt==1:
EQ={}
EQ['eqarea']=1
pmagplotlib.plot_init(EQ['eqarea'],4,4)
for site in sitelist:
print(site)
data=[]
for spec in Specs:
if 'specimen_tilt_correction' not in list(spec.keys()):spec['specimen_tilt_correction']='-1' # assume unoriented
if spec['er_site_name']==site:
if 'specimen_mad' not in list(spec.keys()) or spec['specimen_mad']=="":
if 'specimen_alpha95' in list(spec.keys()) and spec['specimen_alpha95']!="":
spec['specimen_mad']=spec['specimen_alpha95']
else:
spec['specimen_mad']='180'
if spec['specimen_tilt_correction']==coord and float(spec['specimen_mad'])<=M and float(spec['specimen_n'])>=N:
rec={}
for key in list(spec.keys()):rec[key]=spec[key]
rec["dec"]=float(spec['specimen_dec'])
rec["inc"]=float(spec['specimen_inc'])
rec["tilt_correction"]=spec['specimen_tilt_correction']
data.append(rec)
if len(data)>2:
fpars=pmag.dolnp(data,'specimen_direction_type')
print("Site lines planes kappa a95 dec inc")
print(site, fpars["n_lines"], fpars["n_planes"], fpars["K"], fpars["alpha95"], fpars["dec"], fpars["inc"], fpars["R"])
if out_file!="":
if float(fpars["alpha95"])<=acutoff and float(fpars["K"])>=kcutoff:
out.write('%s %s %s\n'%(fpars["dec"],fpars['inc'],fpars['alpha95']))
print('% tilt correction: ',coord)
if plt==1:
files={}
files['eqarea']=site+'_'+crd+'_'+'eqarea'+'.'+fmt
pmagplotlib.plotLNP(EQ['eqarea'],site,data,fpars,'specimen_direction_type')
if plot==0:
pmagplotlib.drawFIGS(EQ)
ans=input("s[a]ve plot, [q]uit, <return> to continue:\n ")
if ans=="a":
pmagplotlib.saveP(EQ,files)
if ans=="q": sys.exit()
else:
pmagplotlib.saveP(EQ,files)
else:
print('skipping site - not enough data with specified coordinate system')
def main():
"""
NAME
site_edit_magic.py
DESCRIPTION
makes equal area projections site by site
from pmag_specimens.txt file with
Fisher confidence ellipse using McFadden and McElhinny (1988)
technique for combining lines and planes
allows testing and reject specimens for bad orientations
SYNTAX
site_edit_magic.py [command line options]
OPTIONS
-h: prints help and quits
-f: specify pmag_specimen format file, default is pmag_specimens.txt
-fsa: specify er_samples.txt file
-exc: use existing pmag_criteria.txt file
-N: reset all sample flags to good
OUPUT
edited er_samples.txt file
"""
dir_path='.'
FIG={} # plot dictionary
FIG['eqarea']=1 # eqarea is figure 1
in_file='pmag_specimens.txt'
sampfile='er_samples.txt'
out_file=""
fmt,plot='svg',1
Crits=""
M,N=180.,1
repeat=''
renew=0
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-fsa' in sys.argv:
ind=sys.argv.index("-fsa")
sampfile=sys.argv[ind+1]
if '-exc' in sys.argv:
Crits,file_type=pmag.magic_read(dir_path+'/pmag_criteria.txt')
for crit in Crits:
if crit['pmag_criteria_code']=='DE-SPEC':
M=float(crit['specimen_mad'])
N=float(crit['specimen_n'])
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-N' in sys.argv: renew=1
#
if in_file[0]!="/":in_file=dir_path+'/'+in_file
if sampfile[0]!="/":sampfile=dir_path+'/'+sampfile
crd='s'
Specs,file_type=pmag.magic_read(in_file)
if file_type!='pmag_specimens':
print ' bad pmag_specimen input file'
sys.exit()
Samps,file_type=pmag.magic_read(sampfile)
if file_type!='er_samples':
print ' bad er_samples input file'
sys.exit()
SO_methods=[]
for rec in Samps:
if 'sample_orientation_flag' not in rec.keys(): rec['sample_orientation_flag']='g'
if 'sample_description' not in rec.keys(): rec['sample_description']=''
if renew==1:
rec['sample_orientation_flag']='g'
description=rec['sample_description']
if '#' in description:
newdesc=""
c=0
while description[c]!='#' and c<len(description)-1: # look for first pound sign
newdesc=newdesc+description[c]
c+=1
while description[c]=='#':
c+=1# skip first set of pound signs
while description[c]!='#':c+=1 # find second set of pound signs
while description[c]=='#' and c<len(description)-1:c+=1 # skip second set of pound signs
while c<len(description)-1: # look for first pound sign
newdesc=newdesc+description[c]
c+=1
rec['sample_description']=newdesc # edit out old comment about orientations
if "magic_method_codes" in rec:
methlist=rec["magic_method_codes"]
for meth in methlist.split(":"):
if "SO" in meth.strip() and "SO-POM" not in meth.strip():
if meth.strip() not in SO_methods: SO_methods.append(meth.strip())
pmag.magic_write(sampfile,Samps,'er_samples')
SO_priorities=pmag.set_priorities(SO_methods,0)
sitelist=[]
for rec in Specs:
if rec['er_site_name'] not in sitelist: sitelist.append(rec['er_site_name'])
sitelist.sort()
EQ={}
EQ['eqarea']=1
pmagplotlib.plot_init(EQ['eqarea'],5,5)
k=0
while k<len(sitelist):
site=sitelist[k]
print site
data=[]
ThisSiteSpecs=pmag.get_dictitem(Specs,'er_site_name',site,'T')
ThisSiteSpecs=pmag.get_dictitem(ThisSiteSpecs,'specimen_tilt_correction','-1','T') # get all the unoriented data
for spec in ThisSiteSpecs:
if spec['specimen_mad']!="" and spec['specimen_n']!="" and float(spec['specimen_mad'])<=M and float(spec['specimen_n'])>=N:
# good spec, now get orientation....
redo,p=1,0
if len(SO_methods)<=1:
az_type=SO_methods[0]
orient=pmag.find_samp_rec(spec["er_sample_name"],Samps,az_type)
redo=0
while redo==1:
if p>=len(SO_priorities):
print "no orientation data for ",spec['er_sample_name']
orient["sample_azimuth"]=""
orient["sample_dip"]=""
redo=0
else:
az_type=SO_methods[SO_methods.index(SO_priorities[p])]
orient=pmag.find_samp_rec(spec["er_sample_name"],Samps,az_type)
if orient["sample_azimuth"] !="":
redo=0
p+=1
if orient['sample_azimuth']!="":
rec={}
for key in spec.keys():rec[key]=spec[key]
rec['dec'],rec['inc']=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(orient['sample_azimuth']),float(orient['sample_dip']))
rec["tilt_correction"]='1'
crd='g'
rec['sample_azimuth']=orient['sample_azimuth']
rec['sample_dip']=orient['sample_dip']
data.append(rec)
if len(data)>2:
print 'specimen, dec, inc, n_meas/MAD,| method codes '
for i in range(len(data)):
print '%s: %7.1f %7.1f %s / %s | %s' % (data[i]['er_specimen_name'], data[i]['dec'], data[i]['inc'], data[i]['specimen_n'], data[i]['specimen_mad'], data[i]['magic_method_codes'])
fpars=pmag.dolnp(data,'specimen_direction_type')
print "\n Site lines planes kappa a95 dec inc"
print site, fpars["n_lines"], fpars["n_planes"], fpars["K"], fpars["alpha95"], fpars["dec"], fpars["inc"], fpars["R"]
if out_file!="":
if float(fpars["alpha95"])<=acutoff and float(fpars["K"])>=kcutoff:
out.write('%s %s %s\n'%(fpars["dec"],fpars['inc'],fpars['alpha95']))
pmagplotlib.plotLNP(EQ['eqarea'],site,data,fpars,'specimen_direction_type')
pmagplotlib.drawFIGS(EQ)
if k!=0 and repeat!='y':
ans=raw_input("s[a]ve plot, [q]uit, [e]dit specimens, [p]revious site, <return> to continue:\n ")
elif k==0 and repeat!='y':
ans=raw_input("s[a]ve plot, [q]uit, [e]dit specimens, <return> to continue:\n ")
if ans=="p": k-=2
if ans=="a":
files={}
files['eqarea']=site+'_'+crd+'_eqarea'+'.'+fmt
pmagplotlib.saveP(EQ,files)
if ans=="q": sys.exit()
if ans=="e" and Samps==[]:
print "can't edit samples without orientation file, sorry"
elif ans=="e":
# k-=1
testspec=raw_input("Enter name of specimen to check: ")
for spec in data:
if spec['er_specimen_name']==testspec:
# first test wrong direction of drill arrows (flip drill direction in opposite direction and re-calculate d,i
d,i=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(spec['sample_azimuth'])-180.,-float(spec['sample_dip']))
XY=pmag.dimap(d,i)
pmagplotlib.plotXY(EQ['eqarea'],[XY[0]],[XY[1]],sym='g^')
# first test wrong end of compass (take az-180.)
d,i=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(spec['sample_azimuth'])-180.,float(spec['sample_dip']))
XY=pmag.dimap(d,i)
pmagplotlib.plotXY(EQ['eqarea'],[XY[0]],[XY[1]],sym='kv')
# did the sample spin in the hole?
# now spin around specimen's z
X_up,Y_up,X_d,Y_d=[],[],[],[]
for incr in range(0,360,5):
d,i=pmag.dogeo(float(spec['specimen_dec'])+incr,float(spec['specimen_inc']),float(spec['sample_azimuth']),float(spec['sample_dip']))
XY=pmag.dimap(d,i)
if i>=0:
X_d.append(XY[0])
Y_d.append(XY[1])
else:
X_up.append(XY[0])
Y_up.append(XY[1])
pmagplotlib.plotXY(EQ['eqarea'],X_d,Y_d,sym='b.')
pmagplotlib.plotXY(EQ['eqarea'],X_up,Y_up,sym='c.')
pmagplotlib.drawFIGS(EQ)
break
print "Triangle: wrong arrow for drill direction."
print "Delta: wrong end of compass."
print "Small circle: wrong mark on sample. [cyan upper hemisphere]"
deleteme=raw_input("Mark this sample as bad? y/[n] ")
if deleteme=='y':
reason=raw_input("Reason: [1] broke, [2] wrong drill direction, [3] wrong compass direction, [4] bad mark, [5] displaced block [6] other ")
if reason=='1':
description=' sample broke while drilling'
if reason=='2':
description=' wrong drill direction '
if reason=='3':
description=' wrong compass direction '
if reason=='4':
description=' bad mark in field'
if reason=='5':
description=' displaced block'
if reason=='6':
description=raw_input('Enter brief reason for deletion: ')
for samp in Samps:
if samp['er_sample_name']==spec['er_sample_name']:
samp['sample_orientation_flag']='b'
samp['sample_description']=samp['sample_description']+' ## direction deleted because: '+description+'##' # mark description
pmag.magic_write(sampfile,Samps,'er_samples')
repeat=raw_input("Mark another sample, this site? y/[n] ")
if repeat=='y': k-=1
else:
print 'skipping site - not enough data with specified coordinate system'
k+=1
print "sample flags stored in ",sampfile
def main():
"""
NAME
dayplot_magic.py
DESCRIPTION
makes 'day plots' (Day et al. 1977) and squareness/coercivity,
plots 'linear mixing' curve from Dunlop and Carter-Stiglitz (2006).
squareness coercivity of remanence (Neel, 1955) plots after
Tauxe et al. (2002)
SYNTAX
dayplot_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input hysteresis file, default is rmag_hysteresis.txt
-fr: specify input remanence file, default is rmag_remanence.txt
-fmt [svg,png,jpg] format for output plots
-sav saves plots and quits quietly
-n label specimen names
"""
args = sys.argv
hyst_file, rem_file = "rmag_hysteresis.txt", "rmag_remanence.txt"
dir_path = '.'
verbose = pmagplotlib.verbose
fmt = 'svg' # default file format
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind + 1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-f' in args:
ind = args.index("-f")
hyst_file = args[ind + 1]
if '-fr' in args:
ind = args.index("-fr")
rem_file = args[ind + 1]
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-sav' in sys.argv:
plots = 1
verbose = 0
else:
plots = 0
if '-n' in sys.argv:
label = 1
else:
label = 0
hyst_file = os.path.realpath(os.path.join(dir_path, hyst_file))
rem_file = os.path.realpath(os.path.join(dir_path, rem_file))
#
# initialize some variables
# define figure numbers for Day,S-Bc,S-Bcr
DSC = {}
DSC['day'], DSC['S-Bc'], DSC['S-Bcr'], DSC['bcr1-bcr2'] = 1, 2, 3, 4
pmagplotlib.plot_init(DSC['day'], 5, 5)
pmagplotlib.plot_init(DSC['S-Bc'], 5, 5)
pmagplotlib.plot_init(DSC['S-Bcr'], 5, 5)
pmagplotlib.plot_init(DSC['bcr1-bcr2'], 5, 5)
#
#
hyst_data, file_type = pmag.magic_read(hyst_file)
rem_data, file_type = pmag.magic_read(rem_file)
#
S, BcrBc, Bcr2, Bc, hsids, Bcr = [], [], [], [], [], []
Ms, Bcr1, Bcr1Bc, S1 = [], [], [], []
names = []
locations = ''
for rec in hyst_data:
if 'er_location_name' in rec.keys(
) and rec['er_location_name'] not in locations:
locations = locations + rec['er_location_name'] + '_'
if rec['hysteresis_bcr'] != "" and rec['hysteresis_mr_moment'] != "":
S.append(
float(rec['hysteresis_mr_moment']) /
float(rec['hysteresis_ms_moment']))
Bcr.append(float(rec['hysteresis_bcr']))
Bc.append(float(rec['hysteresis_bc']))
BcrBc.append(Bcr[-1] / Bc[-1])
if 'er_synthetic_name' in rec.keys(
) and rec['er_synthetic_name'] != "":
rec['er_specimen_name'] = rec['er_synthetic_name']
hsids.append(rec['er_specimen_name'])
names.append(rec['er_specimen_name'])
if len(rem_data) > 0:
for rec in rem_data:
if rec['remanence_bcr'] != "" and float(rec['remanence_bcr']) > 0:
try:
ind = hsids.index(rec['er_specimen_name'])
Bcr1.append(float(rec['remanence_bcr']))
Bcr1Bc.append(Bcr1[-1] / Bc[ind])
S1.append(S[ind])
Bcr2.append(Bcr[ind])
except ValueError:
if verbose:
print('hysteresis data for ', rec['er_specimen_name'],
' not found')
#
# now plot the day and S-Bc, S-Bcr plots
#
leglist = []
if label == 0: names = []
if len(Bcr1) > 0:
pmagplotlib.plotDay(DSC['day'], Bcr1Bc, S1, 'ro', names=names)
pmagplotlib.plotSBcr(DSC['S-Bcr'], Bcr1, S1, 'ro')
pmagplotlib.plot_init(DSC['bcr1-bcr2'], 5, 5)
pmagplotlib.plotBcr(DSC['bcr1-bcr2'], Bcr1, Bcr2)
else:
del DSC['bcr1-bcr2']
pmagplotlib.plotDay(DSC['day'], BcrBc, S, 'bs', names=names)
pmagplotlib.plotSBcr(DSC['S-Bcr'], Bcr, S, 'bs')
pmagplotlib.plotSBc(DSC['S-Bc'], Bc, S, 'bs')
files = {}
if len(locations) > 0: locations = locations[:-1]
for key in DSC.keys():
if pmagplotlib.isServer: # use server plot naming convention
files[
key] = 'LO:_' + locations + '_' + 'SI:__SA:__SP:__TY:_' + key + '_.' + fmt
else: # use more readable plot naming convention
files[key] = '{}_{}.{}'.format(locations, key, fmt)
if verbose:
pmagplotlib.drawFIGS(DSC)
ans = raw_input(" S[a]ve to save plots, return to quit: ")
if ans == "a":
pmagplotlib.saveP(DSC, files)
else:
sys.exit()
if plots: pmagplotlib.saveP(DSC, files)