def main():
"""
NAME
probRo.py
DESCRIPTION
Calculates Ro as a test for randomness - if R exceeds Ro given N, then set is not random at 95% level of confindence
SYNTAX
probRo.py [command line options]
OPTIONS
-h prints this help message
-Nm number of Monte Carlo simulations (default is 10000)
-Nmax maximum number for dataset (default is 10)
"""
Ns,Nm=range(4,11),10000
files,fmt={},'svg'
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-Nm' in sys.argv:
ind=sys.argv.index('-Nm')
Nm=int(sys.argv[ind+1])
if '-Nmax' in sys.argv:
ind=sys.argv.index('-Nmax')
Nmax=int(sys.argv[ind+1])
Ns=range(3,Nmax+1)
PLT={'plt':1}
pmagplotlib.plot_init(PLT['plt'],5,5)
Ro=[]
for N in Ns:
Rs=[]
n=0
while n<Nm:
dirs=pmag.get_unf(N)
pars=pmag.fisher_mean(dirs)
Rs.append(pars['r'])
n+=1
Rs.sort()
crit=int(.95*Nm)
Ro.append(Rs[crit])
pmagplotlib.plotXY(PLT['plt'],Ns,Ro,'-','N','Ro','')
pmagplotlib.plotXY(PLT['plt'],Ns,Ro,'ro','N','Ro','')
pmagplotlib.drawFIGS(PLT)
for key in PLT.keys():
files[key]=key+'.'+fmt
ans=raw_input(" S[a]ve to save plot, [q]uit without saving: ")
if ans=="a": pmagplotlib.saveP(PLT,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
-x XMETH:key:step, specify method code for X axis (optional key and treatment values)
-y YMETH:key:step, specify method code for X axis
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is whole file
-n [V,M] plot volume or mass normalized data only
NOTES
if nothing is specified for x and y, the user will be presented with options
key = ['treatment_ac_field','treatment_dc_field',treatment_temp']
step in mT for fields, K for temperatures
"""
#
file='magic_measurements.txt'
methx,methy,fmt="","",'.svg'
plot_key=''
norm_by=""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
if '-n' in sys.argv:
ind=sys.argv.index('-n')
norm_by=sys.argv[ind+1]
xtreat_key,ytreat_key,xstep,ystep="","","",""
if '-x' in sys.argv:
ind=sys.argv.index('-x')
meths=sys.argv[ind+1].split(':')
methx=meths[0]
if len(meths)>1:
xtreat_key=meths[1]
xstep=float(meths[2])
if '-y' in sys.argv:
ind=sys.argv.index('-y')
meths=sys.argv[ind+1].split(':')
methy=meths[0]
if len(meths)>1:
ytreat_key=meths[1]
ystep=float(meths[2])
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
plot_by=sys.argv[ind+1]
if plot_by=='loc':plot_key='er_location_name'
if plot_by=='sit':plot_key='er_site_name'
if plot_by=='sam':plot_key='er_sample_name'
if plot_by=='spc':plot_key='er_specimen_name'
if '-i' in sys.argv:
#
# get name of file from command line
#
file=raw_input("Input magic_measurments file name? [magic_measurements.txt] ")
if file=="":file="magic_measurements.txt"
#
#
FIG={'fig':1}
pmagplotlib.plot_init(FIG['fig'],5,5)
data,file_type=pmag.magic_read(file)
if file_type!="magic_measurements":
print file_type,' not correct format for magic_measurments file'
sys.exit()
#
# collect method codes
methods,plotlist=[],[]
for rec in data:
if plot_key!="":
if rec[plot_key] not in plotlist:plotlist.append(rec[plot_key])
elif len(plotlist)==0:
plotlist.append('All')
meths=rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip() not in methods and meth.strip()!="LP-":
methods.append(meth.strip())
#
if '-i' in sys.argv:
print methods
elif methx =="" or methy=="":
print methods
sys.exit()
GoOn=1
while GoOn==1:
if '-i' in sys.argv:methx=raw_input('Select method for x axis: ')
if methx not in methods:
if '-i' in sys.argv:
print 'try again! method not available'
else:
print main.__doc__
print '\n must specify X axis method\n'
sys.exit()
else:
if pmagplotlib.verbose: print methx, ' selected for X axis'
GoOn=0
GoOn=1
while GoOn==1:
if '-i' in sys.argv:methy=raw_input('Select method for y axis: ')
if methy not in methods:
if '-i' in sys.argv:
print 'try again! method not available'
else:
print main.__doc__
print '\n must specify Y axis method\n'
sys.exit()
else:
if pmagplotlib.verbose: print methy, ' selected for Y axis'
GoOn=0
if norm_by=="":
measkeys=['measurement_magn_mass','measurement_magn_volume','measurement_magn_moment','measurement_magnitude','measurement_chi_volume','measurement_chi_mass','measurement_chi']
elif norm_by=="V":
measkeys=['measurement_magn_volume','measurement_chi_volume']
elif norm_by=="M":
measkeys=['measurement_magn_mass','measurement_chi_mass']
xmeaskey,ymeaskey="",""
plotlist.sort()
for plot in plotlist: # go through objects
if pmagplotlib.verbose: print plot
X,Y=[],[]
x,y='',''
for rec in data:
if plot_key!="" and rec[plot_key]!=plot:
pass
else:
meths=rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip()==methx:
if xmeaskey=="":
for key in measkeys:
if key in rec.keys() and rec[key]!="":
xmeaskey=key
if pmagplotlib.verbose: print xmeaskey,' being used for plotting X.'
break
if meth.strip()==methy:
if ymeaskey=="":
for key in measkeys:
if key in rec.keys() and rec[key]!="":
ymeaskey=key
if pmagplotlib.verbose: print ymeaskey,' being used for plotting Y'
break
if ymeaskey!="" and xmeaskey!="":
for rec in data:
x,y='',''
spec=rec['er_specimen_name'] # get the ydata for this specimen
if rec[ymeaskey]!="" and methy in rec['magic_method_codes'].split(':'):
if ytreat_key=="" or (ytreat_key in rec.keys() and float(rec[ytreat_key])==ystep):
y=float(rec[ymeaskey])
for rec in data: # now find the xdata
if rec['er_specimen_name']==spec and rec[xmeaskey]!="" and methx in rec['magic_method_codes'].split(':'):
if xtreat_key=="" or (xtreat_key in rec.keys() and float(rec[xtreat_key])==xstep):
x=float(rec[xmeaskey])
if x != '' and y!= '':
X.append(x)
Y.append(y)
if len(X)>0:
pmagplotlib.clearFIG(FIG['fig'])
pmagplotlib.plotXY(FIG['fig'],X,Y,'ro',methx,methy,plot+':Biplot')
if not pmagplotlib.isServer:
ans=raw_input('S[a]ve plots, [q]uit, Return for next plot ' )
if ans=='a':
files={}
for key in FIG.keys(): files[key]=plot+'_'+key+fmt
pmagplotlib.saveP(FIG,files)
if ans=='q':
print "Good-bye\n"
sys.exit()
else:
files={}
for key in FIG.keys(): files[key]=plot+'_'+key+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['fig']='X Y Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
else:
print 'nothing to plot for ',plot
def main():
"""
NAME
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
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
lowrie.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie -h [command line options]
INPUT
takes SIO formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
"""
fmt='svg'
FIG={} # plot dictionary
FIG['lowrie']=1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'],6,6)
norm=1 # default is to normalize by maximum axis
if len(sys.argv)>1:
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv: norm=0 # don't normalize
if '-f' in sys.argv: # sets input filename
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
else:
print main.__doc__
print 'you must supply a file name'
sys.exit()
else:
print main.__doc__
print 'you must supply a file name'
sys.exit()
data=open(in_file).readlines() # open the SIO format file
PmagRecs=[] # set up a list for the results
keys=['specimen','treatment','csd','M','dec','inc']
for line in data:
PmagRec={}
rec=line.replace('\n','').split()
for k in range(len(keys)):
PmagRec[keys[k]]=rec[k]
PmagRecs.append(PmagRec)
specs=pmag.get_dictkey(PmagRecs,'specimen','')
sids=[]
for spec in specs:
if spec not in sids:sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print spc
specdata=pmag.get_dictitem(PmagRecs,'specimen',spc,'T') # get all this one's data
DIMs,Temps=[],[]
for dat in specdata: # step through the data
DIMs.append([float(dat['dec']),float(dat['inc']),float(dat['M'])*1e-3])
Temps.append(float(dat['treatment']))
carts=pmag.dir2cart(DIMs).transpose()
#if norm==1: # want to normalize
# nrm=max(max(abs(carts[0])),max(abs(carts[1])),max(abs(carts[2]))) # by maximum of x,y,z values
# ylab="M/M_max"
if norm==1: # want to normalize
nrm=(DIMs[0][2]) # normalize by NRM
ylab="M/M_o"
else:
nrm=1. # don't normalize
ylab="Magnetic moment (Am^2)"
xlab="Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[0])/nrm,sym='r-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[0])/nrm,sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[1])/nrm,sym='c-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[1])/nrm,sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[2])/nrm,sym='k-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[2])/nrm,sym='k^',title=spc,xlab=xlab,ylab=ylab) # Z direction
pmagplotlib.drawFIGS(FIG)
ans=raw_input('S[a]ve figure? [q]uit, <return> to continue ')
if ans=='a':
files={'lowrie':'lowrie:_'+spc+'_.'+fmt}
pmagplotlib.saveP(FIG,files)
elif ans=='q':
sys.exit()
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
curie.py
DESCTIPTION
plots and interprets curie temperature data.
the 1st derivative is calculated from smoothed M-T curve
(convolution with trianfular window with width= <-w> degrees)
the 2nd derivative is calculated from smoothed 1st derivative curve
( using the same sliding window width)
the estinated curie temp. is the maximum of the 2nd derivative
- the temperature steps should be in multiples of 1.0 degrees
INPUT
T,M
SYNTAX
curie.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, sets M,T input file (required)
-w size of sliding window in degrees (default - 3 degrees)
-t <min> <max> temperature range (optional)
example:
curie.py -f ex2.1 -w 30 -t 300 700
"""
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]
else:
print "missing -f\n"
sys.exit()
if '-w' in sys.argv:
ind=sys.argv.index('-w')
window_len=int(sys.argv[ind+1])
else:
window_len=3
if '-t' in sys.argv:
ind=sys.argv.index('-t')
t_begin=int(sys.argv[ind+1])
t_end=int(sys.argv[ind+2])
else:
t_begin=''
t_end=''
# read data from file
Data=numpy.loadtxt(meas_file,dtype=numpy.float)
T=Data.transpose()[0]
M=Data.transpose()[1]
# cut the data if -t is one of the flags
if t_begin:
while T[0]<t_begin:
M.pop(0);T.pop(0)
while T[-1]>t_end:
M.pop(-1);T.pop(-1)
# prepare the signal:
# from M(T) array with unequal deltaT
# to M(T) array with deltaT=(1 degree).
# if delataT is larger, then points are added using linear fit between
# consecutive data points.
# exit if deltaT is not integer
i=0
while i<(len(T)-1):
if (T[i+1]-T[i])%1>0.001:
print "delta T should be integer, this program will not work!"
print "temperature range:",T[i],T[i+1]
sys.exit()
if (T[i+1]-T[i])==0.:
M[i]=average([M[i],M[i+1]])
M.pop(i+1);T.pop(i+1)
elif (T[i+1]-T[i])<0.:
M.pop(i+1);T.pop(i+1)
print "check data in T=%.0f ,M[T] is ignored"%(T[i])
elif (T[i+1]-T[i])>1.:
slope,b=polyfit([T[i],T[i+1]],[M[i],M[i+1]],1)
for j in range(int(T[i+1])-int(T[i])-1):
M.insert(i+1,slope*(T[i]+1.)+b)
T.insert(i+1,(T[i]+1.))
i=i+1
i=i+1
# calculate the smoothed signal
M=array(M,'f')
T=array(T,'f')
M_smooth=[]
M_smooth=smooth(M,window_len)
#plot the original data and the smooth data
PLT={'M_T':1,'der1':2,'der2':3,'Curie':4}
pmagplotlib.plot_init(PLT['M_T'],5,5)
string='M-T (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['M_T'],T,M_smooth,sym='-')
pmagplotlib.plotXY(PLT['M_T'],T,M,sym='--',xlab='Temperature C',ylab='Magnetization',title=string)
#calculate first derivative
d1,T_d1=[],[]
for i in range(len(M_smooth)-1):
Dy=M_smooth[i-1]-M_smooth[i+1]
Dx=T[i-1]-T[i+1]
d1.append(Dy/Dx)
T_d1=T[1:len(T-1)]
d1=array(d1,'f')
d1_smooth=smooth(d1,window_len)
#plot the first derivative
pmagplotlib.plot_init(PLT['der1'],5,5)
string='1st dervative (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['der1'],T_d1,d1_smooth,sym='-',xlab='Temperature C',title=string)
pmagplotlib.plotXY(PLT['der1'],T_d1,d1,sym='b--')
#calculate second derivative
d2,T_d2=[],[]
for i in range(len(d1_smooth)-1):
Dy=d1_smooth[i-1]-d1_smooth[i+1]
Dx=T[i-1]-T[i+1]
#print Dy/Dx
d2.append(Dy/Dx)
T_d2=T[2:len(T-2)]
d2=array(d2,'f')
d2_smooth=smooth(d2,window_len)
#plot the second derivative
pmagplotlib.plot_init(PLT['der2'],5,5)
string='2nd dervative (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['der2'],T_d2,d2,sym='-',xlab='Temperature C',title=string)
d2=list(d2)
print 'second deriative maximum is at T=%i'%int(T_d2[d2.index(max(d2))])
# calculate Curie temperature for different width of sliding windows
curie,curie_1=[],[]
wn=range(5,50,1)
for win in wn:
# calculate the smoothed signal
M_smooth=[]
M_smooth=smooth(M,win)
#calculate first derivative
d1,T_d1=[],[]
for i in range(len(M_smooth)-1):
Dy=M_smooth[i-1]-M_smooth[i+1]
Dx=T[i-1]-T[i+1]
d1.append(Dy/Dx)
T_d1=T[1:len(T-1)]
d1=array(d1,'f')
d1_smooth=smooth(d1,win)
#calculate second derivative
d2,T_d2=[],[]
for i in range(len(d1_smooth)-1):
Dy=d1_smooth[i-1]-d1_smooth[i+1]
Dx=T[i-1]-T[i+1]
d2.append(Dy/Dx)
T_d2=T[2:len(T-2)]
d2=array(d2,'f')
d2_smooth=smooth(d2,win)
d2=list(d2)
d2_smooth=list(d2_smooth)
curie.append(T_d2[d2.index(max(d2))])
curie_1.append(T_d2[d2_smooth.index(max(d2_smooth))])
#plot Curie temp for different sliding window length
pmagplotlib.plot_init(PLT['Curie'],5,5)
pmagplotlib.plotXY(PLT['Curie'],wn,curie,sym='.',xlab='Sliding Window Width (degrees)',ylab='Curie Temp',title='Curie Statistics')
pmagplotlib.drawFIGS(PLT)
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 PLT.keys():
files[key]=str(key) + ".svg"
pmagplotlib.saveP(PLT,files)
def main():
"""
NAME
plot_magic_keys.py
DESCRIPTION
picks out keys and makes and xy plot
SYNTAX
plot_magic_keys.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file
-xkey KEY: specify key for X
-ykey KEY: specify key for Y
-b xmin xmax ymin ymax, sets bounds
"""
dir_path="./"
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 '-f' in sys.argv:
ind=sys.argv.index('-f')
magic_file=dir_path+'/'+sys.argv[ind+1]
else:
print main.__doc__
sys.exit()
if '-xkey' in sys.argv:
ind=sys.argv.index('-xkey')
xkey=sys.argv[ind+1]
if '-ykey' in sys.argv:
ind=sys.argv.index('-ykey')
ykey=sys.argv[ind+1]
else:
print main.__doc__
sys.exit()
if '-b' in sys.argv:
ind=sys.argv.index('-b')
xmin=float(sys.argv[ind+1])
xmax=float(sys.argv[ind+2])
ymin=float(sys.argv[ind+3])
ymax=float(sys.argv[ind+4])
#
#
# get data read in
X,Y=[],[]
Data,file_type=pmag.magic_read(magic_file)
if len(Data)>0:
for rec in Data:
if xkey in rec.keys() and rec[xkey]!="" and ykey in rec.keys() and rec[ykey]!="":
try:
X.append(float(rec[xkey]))
Y.append(float(rec[ykey]))
except:
pass
FIG={'fig':1}
pmagplotlib.plot_init(FIG['fig'],5,5)
if '-b' in sys.argv:
pmagplotlib.plotXY(FIG['fig'],X,Y,sym='ro',xlab=xkey,ylab=ykey,xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax )
else:
pmagplotlib.plotXY(FIG['fig'],X,Y,sym='ro',xlab=xkey,ylab=ykey)
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]=str(key) + ".svg"
pmagplotlib.saveP(FIG,files)
sys.exit()
else:
print 'no data to plot'
def main():
"""
NAME
lowrie_magic.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie -h [command line options]
INPUT
takes magic_measurements formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is magic_measurements.txt
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
"""
fmt='svg'
FIG={} # plot dictionary
FIG['lowrie']=1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'],6,6)
norm=1 # default is to normalize by maximum axis
in_file,dir_path='magic_measurements.txt','.'
if len(sys.argv)>1:
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv: norm=0 # don't normalize
if '-f' in sys.argv: # sets input filename
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
else:
print main.__doc__
print 'you must supply a file name'
sys.exit()
in_file=dir_path+'/'+in_file
print in_file
PmagRecs,file_type=pmag.magic_read(in_file)
if file_type!="magic_measurements":
print 'bad input file'
sys.exit()
PmagRecs=pmag.get_dictitem(PmagRecs,'magic_method_codes','LP-IRM-3D','has') # get all 3D IRM records
if len(PmagRecs)==0:
print 'no records found'
sys.exit()
specs=pmag.get_dictkey(PmagRecs,'er_specimen_name','')
sids=[]
for spec in specs:
if spec not in sids:sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print spc
specdata=pmag.get_dictitem(PmagRecs,'er_specimen_name',spc,'T') # get all this one's data
DIMs,Temps=[],[]
for dat in specdata: # step through the data
DIMs.append([float(dat['measurement_dec']),float(dat['measurement_inc']),float(dat['measurement_magn_moment'])])
Temps.append(float(dat['treatment_temp'])-273.)
carts=pmag.dir2cart(DIMs).transpose()
if norm==1: # want to normalize
nrm=(DIMs[0][2]) # normalize by NRM
ylab="M/M_o"
else:
nrm=1. # don't normalize
ylab="Magnetic moment (Am^2)"
xlab="Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[0])/nrm,sym='r-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[0])/nrm,sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[1])/nrm,sym='c-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[1])/nrm,sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[2])/nrm,sym='k-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[2])/nrm,sym='k^',title=spc,xlab=xlab,ylab=ylab) # Z direction
pmagplotlib.drawFIGS(FIG)
ans=raw_input('S[a]ve figure? [q]uit, <return> to continue ')
if ans=='a':
files={'lowrie':'lowrie:_'+spc+'_.'+fmt}
pmagplotlib.saveP(FIG,files)
elif ans=='q':
sys.exit()
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
site_edit_magic.py
DESCRIPTION
makes equal area projections site by site
from zeq_specimens_g.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 zeq_specimens_s.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 = "zeq_specimens_s.txt"
sampfile = "er_samples.txt"
out_file = ""
fmt, plot = "svg", 1
Crits = ""
M, N = 180.0, 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
#
in_file = dir_path + "/" + in_file
sampfile = dir_path + "/" + sampfile
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 = []
for spec in Specs:
if spec["er_site_name"] == site:
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"
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")
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"]) - 180.0,
-float(spec["sample_dip"]),
)
XY = pmag.dimap(d, i)
pmagplotlib.plotXY(EQ["eqarea"], [XY[0]], [XY[1]], "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"]) - 180.0,
float(spec["sample_dip"]),
)
XY = pmag.dimap(d, i)
pmagplotlib.plotXY(EQ["eqarea"], [XY[0]], [XY[1]], "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, "b.", "", "", "")
pmagplotlib.plotXY(EQ["eqarea"], X_up, Y_up, "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
curie_magic.py
DESCTIPTION
plots and interprets curie temperature data.
the 1st derivative is calculated from smoothed M-T curve
(convolution with trianfular window with width= <-w> degrees)
the 2nd derivative is calculated from smoothed 1st derivative curve
( using the same sliding window width)
the estinated curie temp. is the maximum of the 2nd derivative
- the temperature steps should be in multiples of 1.0 degrees
INPUT
magic_measurements formatted file
SYNTAX
curie_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, sets M,T magic_measurements formatted file, default is MsT_measurements.txt
-F RMAG, sets Rmag_results format file for appending results, default is not
-w size of sliding window in degrees (default - 3 degrees)
-t <min> <max> temperature range (optional)
"""
fmt,dir_path='svg','.'
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
meas_file=dir_path+'/MsT_measurements.txt'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=dir_path+'/'+sys.argv[ind+1]
Results,rmag_file=[],""
if '-F' in sys.argv:
ind=sys.argv.index('-F')
rmag_file=dir_path+'/'+sys.argv[ind+1]
try:
Results,file_type=pmag.magic_read(rmag_file)
if file_type!='rmag_results':
print 'bad results file, starting new one'
except:
pass
if '-w' in sys.argv:
ind=sys.argv.index('-w')
window_len=int(sys.argv[ind+1])
else:
window_len=3
if '-t' in sys.argv:
ind=sys.argv.index('-t')
t_begin=int(sys.argv[ind+1])
t_end=int(sys.argv[ind+2])
else:
t_begin=''
t_end=''
# read data from file
Data,file_type=pmag.magic_read(meas_file)
if file_type!='magic_measurements':
print 'bad measurements file'
sys.exit()
specs=[]
for rec in Data:
specname=""
if 'er_specimen_name' in rec.keys() and rec['er_specimen_name']!="":
specname=rec['er_specimen_name']
else:
rec['er_specimen_name']=""
if 'er_synthetic_name' in rec.keys() and rec['er_synthetic_name']!="":
specname=rec['er_synthetic_name']
else:
rec['er_synthetic_name']=""
if specname not in specs:specs.append(specname)
for spec in specs:
print 'processing: ',spec
M,T,curieT=[],[],0
for rec in Data:
if rec['er_specimen_name'] or rec['er_synthetic_name']==spec:
location,sample,site="","",""
if 'er_location_name' in rec.keys():location=rec['er_location_name']
if 'er_sample_name' in rec.keys():sample=rec['er_sample_name']
if 'er_site_name' in rec.keys():site=rec['er_site_name']
syn=""
if 'er_synthetic_name' in rec.keys():syn=rec['er_synthetic_name']
meths=rec['magic_method_codes'].strip().split(':')
expnames=rec['magic_experiment_name'].strip().split(':')
if 'LP-MW-I' in meths and 'Curie' in expnames:
method=rec['magic_method_codes']
expname=rec['magic_experiment_name']
T.append(float(rec['measurment_temp'])-273)
M.append(float(rec['measurement_magnitude']))
# cut the data if -t is one of the flags
if len(M)<10:
print 'not enough data for processing'
sys.exit()
if t_begin:
while T[0]<t_begin:
M.pop(0);T.pop(0)
while T[-1]>t_end:
M.pop(-1);T.pop(-1)
# prepare the signal:
# from M(T) array with unequal deltaT
# to M(T) array with deltaT=(1 degree).
# if delataT is larger, then points are added using linear fit between
# consecutive data points.
# exit if deltaT is not integer
i=0
while i<(len(T)-1):
if (T[i+1]-T[i])%1>0.001:
print "delta T should be integer, this program will not work!"
print "temperature range:",T[i],T[i+1]
sys.exit()
if (T[i+1]-T[i])==0.:
M[i]=average([M[i],M[i+1]])
M.pop(i+1);T.pop(i+1)
elif (T[i+1]-T[i])<0.:
M.pop(i+1);T.pop(i+1)
print "check data in T=%.0f ,M[T] is ignored"%(T[i])
elif (T[i+1]-T[i])>1.:
slope,b=polyfit([T[i],T[i+1]],[M[i],M[i+1]],1)
for j in range(int(T[i+1])-int(T[i])-1):
M.insert(i+1,slope*(T[i]+1.)+b)
T.insert(i+1,(T[i]+1.))
i=i+1
i=i+1
# calculate the smoothed signal
M=array(M,'f')
T=array(T,'f')
M_smooth=[]
M_smooth=smooth(M,window_len)
#plot the original data and the smooth data
PLT={'M_T':1,'der1':2,'der2':3,'Curie':4}
pmagplotlib.plot_init(PLT['M_T'],5,5)
string='M-T (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['M_T'],T,M,'--','Temperature C','Magnetization',string)
plot(T,M_smooth,'-')
#calculate first derivative
d1,T_d1=[],[]
for i in range(len(M_smooth)-1):
Dy=M_smooth[i-1]-M_smooth[i+1]
Dx=T[i-1]-T[i+1]
d1.append(Dy/Dx)
T_d1=T[1:len(T-1)]
d1=array(d1,'f')
d1_smooth=smooth(d1,window_len)
#plot the first derivative
pmagplotlib.plot_init(PLT['der1'],5,5)
string='1st dervative (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['der1'],T_d1,d1_smooth,'-','temperatue C','',string)
plot(T_d1,d1,'--b')
#calculate second derivative
d2,T_d2=[],[]
for i in range(len(d1_smooth)-1):
Dy=d1_smooth[i-1]-d1_smooth[i+1]
Dx=T[i-1]-T[i+1]
#print Dy/Dx
d2.append(Dy/Dx)
T_d2=T[2:len(T-2)]
d2=array(d2,'f')
d2_smooth=smooth(d2,window_len)
#plot the second derivative
pmagplotlib.plot_init(PLT['der2'],5,5)
string='2nd dervative (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['der2'],T_d2,d2,'-','temperatue C','',string)
d2=list(d2)
print 'second deriative maximum is at T=%i'%int(T_d2[d2.index(max(d2))])
# calculate Curie temperature for different width of sliding windows
curie,curie_1=[],[]
wn=range(5,50,1)
for win in wn:
# calculate the smoothed signal
M_smooth=[]
M_smooth=smooth(M,win)
#calculate first derivative
d1,T_d1=[],[]
for i in range(len(M_smooth)-1):
Dy=M_smooth[i-1]-M_smooth[i+1]
Dx=T[i-1]-T[i+1]
d1.append(Dy/Dx)
T_d1=T[1:len(T-1)]
d1=array(d1,'f')
d1_smooth=smooth(d1,win)
#calculate second derivative
d2,T_d2=[],[]
for i in range(len(d1_smooth)-1):
Dy=d1_smooth[i-1]-d1_smooth[i+1]
Dx=T[i-1]-T[i+1]
d2.append(Dy/Dx)
T_d2=T[2:len(T-2)]
d2=array(d2,'f')
d2_smooth=smooth(d2,win)
d2=list(d2)
d2_smooth=list(d2_smooth)
curie.append(T_d2[d2.index(max(d2))])
if curie[-1]>curieT:curieT=curie[-1] # find maximum curie T
curie_1.append(T_d2[d2_smooth.index(max(d2_smooth))])
#plot Curie temp for different sliding window length
pmagplotlib.plot_init(PLT['Curie'],5,5)
pmagplotlib.plotXY(PLT['Curie'],wn,curie,'.','sliding window width (degrees)','curie temp','Inferred Curie Temperatures')
print 'Curie T is: ',curieT
pmagplotlib.drawFIGS(PLT)
files={}
for key in PLT.keys():
files[key]=spec+'_'+key+'.'+fmt
ans=raw_input(" S[a]ve to save plot, [q]uit, or return to continue: ")
if ans=='q':sys.exit()
if ans=='a':
pmagplotlib.saveP(PLT,files)
if rmag_file!="":
ResRec={}
ResRec['rmag_result_name']='Curie T: '+spec
ResRec['er_location_names']=location
ResRec['er_sample_names']=sample
ResRec['er_site_names']=site
ResRec['er_synthetic_names']=syn
if syn!="":
ResRec['er_specimen_names']=spec
else:
ResRec['er_specimen_names']=""
ResRec['magic_experiment_names']=expname
ResRec['magic_method_codes']=method+':SM-2DMAX'
ResRec['critical_temp']='%10.1f'%(curieT)
ResRec['critical_temp_type']="Curie"
ResRec['er_citation_names']="This study"
Results.append(ResRec)
if len(Results)>0 and rmag_file!="":
ResOuts,keys=pmag.fillkeys(Results)
pmag.magic_write(rmag_file,ResOuts,'rmag_results')
print 'Results stored in ',rmag_file
def main():
"""
NAME
quick_hyst.py
DESCRIPTION
makes plots of hysteresis data
SYNTAX
quick_hyst.py [command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f: specify input file, default is magic_measurements.txt
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args=sys.argv
PLT=1
plots=0
user,meas_file="","magic_measurements.txt"
pltspec=""
dir_path='.'
fmt='png'
verbose=pmagplotlib.verbose
version_num=pmag.get_version()
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-f' in args:
ind=args.index("-f")
meas_file=args[ind+1]
if '-sav' in args:
verbose=0
plots=1
if '-spc' in args:
ind=args.index("-spc")
pltspec= args[ind+1]
verbose=0
plots=1
if '-fmt' in args:
ind=args.index("-fmt")
fmt=args[ind+1]
meas_file=dir_path+'/'+meas_file
#
#
meas_data,file_type=pmag.magic_read(meas_file)
if file_type!='magic_measurements':
print main.__doc__
print 'bad file'
sys.exit()
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs,RemRecs=[],[]
HDD={}
HDD['hyst']=1
pmagplotlib.plot_init(HDD['hyst'],5,5)
#
# get list of unique experiment names and specimen names
#
experiment_names,sids=[],[]
hyst_data=pmag.get_dictitem(meas_data,'magic_method_codes','LP-HYS','has') # get all hysteresis data
for rec in hyst_data:
if 'er_synthetic_name' in rec.keys() and rec['er_synthetic_name']!="":
rec['er_specimen_name']=rec['er_synthetic_name']
if rec['magic_experiment_name'] not in experiment_names:experiment_names.append(rec['magic_experiment_name'])
if rec['er_specimen_name'] not in sids:sids.append(rec['er_specimen_name'])
if 'measurement_temp' not in rec.keys(): rec['measurement_temp']='300' # assume room T measurement unless otherwise specified
#
k=0
if pltspec!="":
k=sids.index(pltspec)
intlist=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
while k < len(sids):
locname,site,sample,synth='','','',''
s=sids[k]
hmeths=[]
if verbose:print s, k+1 , 'out of ',len(sids)
#
#
B,M=[],[] #B,M for hysteresis, Bdcd,Mdcd for irm-dcd data
spec=pmag.get_dictitem(hyst_data,'er_specimen_name',s,'T') # get all measurements for this specimen
if 'er_location_name' in spec[0].keys():
locname=spec[0]['er_location_name']
if 'er_site_name' in spec[0].keys():
site=spec[0]['er_site_name']
if 'er_sample_name' in spec[0].keys():
sample=spec[0]['er_sample_name']
if 'er_synthetic_name' in spec[0].keys():
synth=spec[0]['er_synthetic_name']
for m in intlist:
meas_data=pmag.get_dictitem(spec,m,'','F') # get all non-blank data for this specimen
if len(meas_data)>0: break
c=['k-','b-','c-','g-','m-','r-','y-']
cnum=0
if len(meas_data)>0:
Temps=[]
xlab,ylab,title='','',''
for rec in meas_data:
if rec['measurement_temp'] not in Temps:Temps.append(rec['measurement_temp'])
for t in Temps:
print 'working on t: ',t
t_data=pmag.get_dictitem(meas_data,'measurement_temp',t,'T')
B,M=[],[]
for rec in t_data:
B.append(float(rec['measurement_lab_field_dc']))
M.append(float(rec[m]))
# now plot the hysteresis curve(s)
#
if len(B)>0:
B=numpy.array(B)
M=numpy.array(M)
if t==Temps[-1]:
xlab='Field (T)'
ylab=m
title='Hysteresis: '+s
if t==Temps[0]:
pmagplotlib.clearFIG(HDD['hyst'])
pmagplotlib.plotXY(HDD['hyst'],B,M,sym=c[cnum],xlab=xlab,ylab=ylab,title=title)
pmagplotlib.plotXY(HDD['hyst'],[1.1*B.min(),1.1*B.max()],[0,0],sym='k-',xlab=xlab,ylab=ylab,title=title)
pmagplotlib.plotXY(HDD['hyst'],[0,0],[1.1*M.min(),1.1*M.max()],sym='k-',xlab=xlab,ylab=ylab,title=title)
if verbose:pmagplotlib.drawFIGS(HDD)
cnum+=1
if cnum==len(c):cnum=0
#
files={}
if plots:
if pltspec!="":s=pltspec
files={}
for key in HDD.keys():
if synth=='':
files[key]="LO:_"+locname+'_SI:_'+site+'_SA:_'+sample+'_SP:_'+s+'_TY:_'+key+'_.'+fmt
else:
files[key]='SY:_'+synth+'_TY:_'+key+'_.'+fmt
pmagplotlib.saveP(HDD,files)
if pltspec!="":sys.exit()
if verbose:
pmagplotlib.drawFIGS(HDD)
ans=raw_input("S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n ")
if ans=="a":
files={}
for key in HDD.keys():
files[key]="LO:_"+locname+'_SI:_'+site+'_SA:_'+sample+'_SP:_'+s+'_TY:_'+key+'_.'+fmt
pmagplotlib.saveP(HDD,files)
if ans=='':k+=1
if ans=="p":
del HystRecs[-1]
k-=1
if ans=='q':
print "Good bye"
sys.exit()
if ans=='s':
keepon=1
specimen=raw_input('Enter desired specimen name (or first part there of): ')
while keepon==1:
try:
k =sids.index(specimen)
keepon=0
except:
tmplist=[]
for qq in range(len(sids)):
if specimen in sids[qq]:tmplist.append(sids[qq])
print specimen," not found, but this was: "
print tmplist
specimen=raw_input('Select one or try again\n ')
k =sids.index(specimen)
else:
k+=1
if len(B)==0:
if verbose:print 'skipping this one - no hysteresis data'
k+=1