def main():
"""
NAME
core_depthplot.py
DESCRIPTION
plots various measurements versus core_depth or age. plots data flagged as 'FS-SS-C' as discrete samples.
SYNTAX
core_depthplot.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic_measurments format file from magi
-fsum FILE: specify input LIMS database (IODP) core summary csv file
-fwig FILE: specify input depth,wiggle to plot, in magic format with sample_core_depth key for depth
-fsa FILE: specify input er_samples format file from magic for depth
-fa FILE: specify input er_ages format file from magic for age
NB: must have either -fsa OR -fa (not both)
-fsp FILE sym size: specify input zeq_specimen format file from magic, sym and size
NB: PCAs will have specified color, while fisher means will be white with specified color as the edgecolor
-fres FILE specify input pmag_results file from magic, sym and size
-LP [AF,T,ARM,IRM, X] step [in mT,C,mT,mT, mass/vol] to plot
-S do not plot blanket treatment data (if this is set, you don't need the -LP)
-sym SYM SIZE, symbol, size for continuous points (e.g., ro 5, bs 10, g^ 10 for red dot, blue square, green triangle), default is blue dot at 5 pt
-D do not plot declination
-M do not plot magnetization
-log plot magnetization on a log scale
-L do not connect dots with a line
-I do not plot inclination
-d min max [in m] depth range to plot
-n normalize by weight in er_specimen table
-Iex: plot the expected inc at lat - only available for results with lat info in file
-ts TS amin amax: plot the GPTS for the time interval between amin and amax (numbers in Ma)
TS: [ck95, gts04, gts12]
-ds [mbsf,mcd] specify depth scale, mbsf default
-fmt [svg, eps, pdf, png] specify output format for plot (default: svg)
-sav save plot silently
DEFAULTS:
Measurements file: magic_measurements.txt
Samples file: er_samples.txt
NRM step
Summary file: none
"""
meas_file='magic_measurements.txt'
intlist=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
samp_file='er_samples.txt'
depth_scale='sample_core_depth'
wt_file=''
verbose=pmagplotlib.verbose
width=10
sym,size='bo',5
Ssym,Ssize='cs',5
method,fmt="LT-NO",'.svg'
step=0
pcol=3
pel=3
pltD,pltI,pltM,pltL,pltS=1,1,1,1,1
logit=0
maxInt=-1000
minInt=1e10
maxSuc=-1000
minSuc=10000
plotexp,pTS=0,0
dir_path="."
sum_file=""
suc_file=""
age_file=""
spc_file=""
res_file=""
ngr_file=""
wig_file=""
title,location="",""
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
norm=0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-L' in sys.argv:
pltL=0
if '-S' in sys.argv: pltS=0 # don't plot the bulk measurements at all
if '-D' in sys.argv:
pltD=0
pcol-=1
pel-=1
width-=2
if '-I' in sys.argv:
pltI=0
pcol-=1
pel-=1
width-=2
if '-M' in sys.argv:
pltM=0
pcol-=1
pel-=1
width-=2
if '-log' in sys.argv:logit=1
if '-ds' in sys.argv and 'mcd' in sys.argv:depth_scale='sample_composite_depth'
if '-sym' in sys.argv:
ind=sys.argv.index('-sym')
sym=sys.argv[ind+1]
size=float(sys.argv[ind+2])
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=sys.argv[ind+1]
if '-fsa' in sys.argv:
ind=sys.argv.index('-fsa')
samp_file=sys.argv[ind+1]
if '-fa' in sys.argv:
print(main.__doc__)
print('only -fsa OR -fa - not both')
sys.exit()
elif '-fa' in sys.argv:
ind=sys.argv.index('-fa')
age_file=sys.argv[ind+1]
if '-fsp' in sys.argv:
ind=sys.argv.index('-fsp')
spc_file=dir_path+'/'+sys.argv[ind+1]
spc_sym=sys.argv[ind+2]
spc_size=float(sys.argv[ind+3])
if '-fres' in sys.argv:
ind=sys.argv.index('-fres')
res_file=dir_path+'/'+sys.argv[ind+1]
res_sym=sys.argv[ind+2]
res_size=float(sys.argv[ind+3])
if '-fwig' in sys.argv:
ind=sys.argv.index('-fwig')
wig_file=dir_path+'/'+sys.argv[ind+1]
pcol+=1
width+=2
if '-fsum' in sys.argv:
ind=sys.argv.index('-fsum')
sum_file=dir_path+'/'+sys.argv[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
if '-LP' in sys.argv:
ind=sys.argv.index('-LP')
meth=sys.argv[ind+1]
if meth=="AF":
step=round(float(sys.argv[ind+2])*1e-3,6)
method='LT-AF-Z'
elif meth== 'T':
step=round(float(sys.argv[ind+2])+273,6)
method='LT-T-Z'
elif meth== 'ARM':
method='LT-AF-I'
step=round(float(sys.argv[ind+2])*1e-3,6)
elif meth== 'IRM':
method='LT-IRM'
step=round(float(sys.argv[ind+2])*1e-3,6)
elif meth== 'X':
method='LP-X'
pcol+=1
if sys.argv[ind+2]=='mass':
suc_key='measurement_chi_mass'
elif sys.argv[ind+2]=='vol':
suc_key='measurement_chi_volume'
else:
print('error in susceptibility units')
sys.exit()
else:
print('method not supported')
sys.exit()
if '-n' in sys.argv:
ind=sys.argv.index('-n')
wt_file=dir_path+'/'+sys.argv[ind+1]
norm=1
dmin,dmax=-1,-1
if '-d' in sys.argv:
ind=sys.argv.index('-d')
dmin=float(sys.argv[ind+1])
dmax=float(sys.argv[ind+2])
if '-ts' in sys.argv:
ind=sys.argv.index('-ts')
ts=sys.argv[ind+1]
amin=float(sys.argv[ind+2])
amax=float(sys.argv[ind+3])
pTS=1
pcol+=1
width+=2
#
#
# get data read in
meas_file=dir_path+'/'+meas_file
if age_file=="":
samp_file=dir_path+'/'+samp_file
Samps,file_type=pmag.magic_read(samp_file)
else:
depth_scale='age'
age_file=dir_path+'/'+age_file
Samps,file_type=pmag.magic_read(age_file)
age_unit=""
if spc_file!="":Specs,file_type=pmag.magic_read(spc_file)
if res_file!="":Results,file_type=pmag.magic_read(res_file)
if norm==1:
ErSpecs,file_type=pmag.magic_read(wt_file)
print(len(ErSpecs), ' specimens read in from ',wt_file)
Cores=[]
core_depth_key="Top depth cored CSF (m)"
if sum_file!="":
input=open(sum_file,'r').readlines()
if "Core Summary" in input[0]:
headline=1
else:
headline=0
keys=input[headline].replace('\n','').split(',')
if "Core Top (m)" in keys:core_depth_key="Core Top (m)"
if "Core Label" in keys:core_label_key="Core Label"
if "Core label" in keys:core_label_key="Core label"
for line in input[2:]:
if 'TOTALS' not in line:
CoreRec={}
for k in range(len(keys)):CoreRec[keys[k]]=line.split(',')[k]
Cores.append(CoreRec)
if len(Cores)==0:
print('no Core depth information available: import core summary file')
sum_file=""
Data=[]
if depth_scale=='sample_core_depth':
ylab="Depth (mbsf)"
elif depth_scale=='age':
ylab="Age"
else:
ylab="Depth (mcd)"
# collect the data for plotting declination
Depths,Decs,Incs,Ints=[],[],[],[]
SDepths,SDecs,SIncs,SInts=[],[],[],[]
SSucs=[]
samples=[]
methods,steps,m2=[],[],[]
if pltS: # plot the bulk measurement data
Meas,file_type=pmag.magic_read(meas_file)
meas_key='measurement_magn_moment'
print(len(Meas), ' measurements read in from ',meas_file)
for m in intlist: # find the intensity key with data
meas_data=pmag.get_dictitem(Meas,m,'','F') # get all non-blank data for this specimen
if len(meas_data)>0:
meas_key=m
break
m1=pmag.get_dictitem(Meas,'magic_method_codes',method,'has') # fish out the desired method code
if method=='LT-T-Z':
m2=pmag.get_dictitem(m1,'treatment_temp',str(step),'eval') # fish out the desired step
elif 'LT-AF' in method:
m2=pmag.get_dictitem(m1,'treatment_ac_field',str(step),'eval')
elif 'LT-IRM' in method:
m2=pmag.get_dictitem(m1,'treatment_dc_field',str(step),'eval')
elif 'LT-X' in method:
m2=pmag.get_dictitem(m1,suc_key,'','F')
if len(m2)>0:
for rec in m2: # fish out depths and weights
D=pmag.get_dictitem(Samps,'er_sample_name',rec['er_sample_name'],'T')
if not D: # if using an age_file, you may need to sort by site
D=pmag.get_dictitem(Samps,'er_site_name',rec['er_site_name'],'T')
depth=pmag.get_dictitem(D,depth_scale,'','F')
if len(depth)>0:
if ylab=='Age': ylab=ylab+' ('+depth[0]['age_unit']+')' # get units of ages - assume they are all the same!
rec['core_depth'] = float(depth[0][depth_scale])
rec['magic_method_codes'] = rec['magic_method_codes']+':'+depth[0]['magic_method_codes']
if norm==1:
specrecs=pmag.get_dictitem(ErSpecs,'er_specimen_name',rec['er_specimen_name'],'T')
specwts=pmag.get_dictitem(specrecs,'specimen_weight',"",'F')
if len(specwts)>0:
rec['specimen_weight'] = specwts[0]['specimen_weight']
Data.append(rec) # fish out data with core_depth and (if needed) weights
else:
Data.append(rec) # fish out data with core_depth and (if needed) weights
if title=="":
pieces=rec['er_sample_name'].split('-')
location=rec['er_location_name']
title=location
SData=pmag.sort_diclist(Data,'core_depth')
for rec in SData: # fish out bulk measurement data from desired depths
if dmax==-1 or float(rec['core_depth'])<dmax and float(rec['core_depth'])>dmin:
Depths.append((rec['core_depth']))
if method=="LP-X":
SSucs.append(float(rec[suc_key]))
else:
if pltD==1:Decs.append(float(rec['measurement_dec']))
if pltI==1:Incs.append(float(rec['measurement_inc']))
if norm==0 and pltM==1:Ints.append(float(rec[meas_key]))
if norm==1 and pltM==1:Ints.append(old_div(float(rec[meas_key]),float(rec['specimen_weight'])))
if len(SSucs)>0:
maxSuc=max(SSucs)
minSuc=min(SSucs)
if len(Ints)>1:
maxInt=max(Ints)
minInt=min(Ints)
if len(Depths)==0:
print('no bulk measurement data matched your request')
SpecDepths,SpecDecs,SpecIncs=[],[],[]
FDepths,FDecs,FIncs=[],[],[]
if spc_file!="": # add depths to spec data
print('spec file found')
BFLs=pmag.get_dictitem(Specs,'magic_method_codes','DE-BFL','has') # get all the discrete data with best fit lines
for spec in BFLs:
if location=="":
location=spec['er_location_name']
samp=pmag.get_dictitem(Samps,'er_sample_name',spec['er_sample_name'],'T')
if len(samp)>0 and depth_scale in list(samp[0].keys()) and samp[0][depth_scale]!="":
if ylab=='Age': ylab=ylab+' ('+samp[0]['age_unit']+')' # get units of ages - assume they are all the same!
if dmax==-1 or float(samp[0][depth_scale])<dmax and float(samp[0][depth_scale])>dmin: # filter for depth
SpecDepths.append(float(samp[0][depth_scale])) # fish out data with core_depth
SpecDecs.append(float(spec['specimen_dec'])) # fish out data with core_depth
SpecIncs.append(float(spec['specimen_inc'])) # fish out data with core_depth
else:
print('no core_depth found for: ',spec['er_specimen_name'])
FMs=pmag.get_dictitem(Specs,'magic_method_codes','DE-FM','has') # get all the discrete data with best fit lines
for spec in FMs:
if location=="":
location=spec['er_location_name']
samp=pmag.get_dictitem(Samps,'er_sample_name',spec['er_sample_name'],'T')
if len(samp)>0 and depth_scale in list(samp[0].keys()) and samp[0][depth_scale]!="":
if ylab=='Age': ylab=ylab+' ('+samp[0]['age_unit']+')' # get units of ages - assume they are all the same!
if dmax==-1 or float(samp[0][depth_scale])<dmax and float(samp[0][depth_scale])>dmin: # filter for depth
FDepths.append(float(samp[0][depth_scale]))# fish out data with core_depth
FDecs.append(float(spec['specimen_dec'])) # fish out data with core_depth
FIncs.append(float(spec['specimen_inc'])) # fish out data with core_depth
else:
print('no core_depth found for: ',spec['er_specimen_name'])
ResDepths,ResDecs,ResIncs=[],[],[]
if 'age' in depth_scale: # set y-key
res_scale='average_age'
else:
res_scale='average_height'
if res_file!="": #creates lists of Result Data
for res in Results:
meths=res['magic_method_codes'].split(":")
if 'DE-FM' in meths:
if dmax==-1 or float(res[res_scale])<dmax and float(res[res_scale])>dmin: # filter for depth
ResDepths.append(float(res[res_scale])) # fish out data with core_depth
ResDecs.append(float(res['average_dec'])) # fish out data with core_depth
ResIncs.append(float(res['average_inc'])) # fish out data with core_depth
Susc,Sus_depths=[],[]
if dmin==-1:
if len(Depths)>0: dmin,dmax=Depths[0],Depths[-1]
if len(FDepths)>0: dmin,dmax=Depths[0],Depths[-1]
if pltS==1 and len(SDepths)>0:
if SDepths[0]<dmin:dmin=SDepths[0]
if SDepths[-1]>dmax:dmax=SDepths[-1]
if len(SpecDepths)>0:
if min(SpecDepths)<dmin:dmin=min(SpecDepths)
if max(SpecDepths)>dmax:dmax=max(SpecDepths)
if len(ResDepths)>0:
if min(ResDepths)<dmin:dmin=min(ResDepths)
if max(ResDepths)>dmax:dmax=max(ResDepths)
if suc_file!="":
sucdat=open(suc_file,'r').readlines()
keys=sucdat[0].replace('\n','').split(',') # splits on underscores
for line in sucdat[1:]:
SucRec={}
for k in range(len(keys)):SucRec[keys[k]]=line.split(',')[k]
if float(SucRec['Top Depth (m)'])<dmax and float(SucRec['Top Depth (m)'])>dmin and SucRec['Magnetic Susceptibility (80 mm)']!="":
Susc.append(float(SucRec['Magnetic Susceptibility (80 mm)']))
if Susc[-1]>maxSuc:maxSuc=Susc[-1]
if Susc[-1]<minSuc:minSuc=Susc[-1]
Sus_depths.append(float(SucRec['Top Depth (m)']))
WIG,WIG_depths=[],[]
if wig_file!="":
wigdat,file_type=pmag.magic_read(wig_file)
swigdat=pmag.sort_diclist(wigdat,depth_scale)
keys=list(wigdat[0].keys())
for key in keys:
if key!=depth_scale:
plt_key=key
break
for wig in swigdat:
if float(wig[depth_scale])<dmax and float(wig[depth_scale])>dmin:
WIG.append(float(wig[plt_key]))
WIG_depths.append(float(wig[depth_scale]))
tint=4.5
plt=1
if len(Decs)>0 and len(Depths)>0 or (len(SpecDecs)>0 and len(SpecDepths)>0) or (len(ResDecs)>0 and len(ResDepths)>0) or (len(SDecs)>0 and len(SDepths)>0) or (len(SInts)>0 and len(SDepths)>0) or (len(SIncs)>0 and len(SDepths)>0):
pylab.figure(1,figsize=(width,8))
version_num=pmag.get_version()
pylab.figtext(.02,.01,version_num)
if pltD==1:
ax=pylab.subplot(1,pcol,plt)
if pltL==1:
pylab.plot(Decs,Depths,'k')
if len(Decs)>0:
pylab.plot(Decs,Depths,sym,markersize=size)
if len(Decs)==0 and pltL==1 and len(SDecs)>0:
pylab.plot(SDecs,SDepths,'k')
if len(SDecs)>0:
pylab.plot(SDecs,SDepths,Ssym,markersize=Ssize)
if spc_file!="":
pylab.plot(SpecDecs,SpecDepths,spc_sym,markersize=spc_size)
if spc_file!="" and len(FDepths)>0:
pylab.scatter(FDecs,FDepths,marker=spc_sym[-1],edgecolor=spc_sym[0],facecolor='white',s=spc_size**2)
if res_file!="":
pylab.plot(ResDecs,ResDepths,res_sym,markersize=res_size)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
if depth>dmin and depth<dmax:
pylab.plot([0,360.],[depth,depth],'b--')
if pel==plt:pylab.text(360,depth+tint,core[core_label_key])
if pel==plt:
pylab.axis([0,400,dmax,dmin])
else:
pylab.axis([0,360.,dmax,dmin])
pylab.xlabel('Declination')
pylab.ylabel(ylab)
plt+=1
pmagplotlib.delticks(ax) # dec xticks are too crowded otherwise
if pltI==1:
pylab.subplot(1,pcol,plt)
if pltL==1:pylab.plot(Incs,Depths,'k')
if len(Incs)>0:pylab.plot(Incs,Depths,sym,markersize=size)
if len(Incs)==0 and pltL==1 and len(SIncs)>0:pylab.plot(SIncs,SDepths,'k')
if len(SIncs)>0:pylab.plot(SIncs,SDepths,Ssym,markersize=Ssize)
if spc_file!="" and len(SpecDepths)>0:pylab.plot(SpecIncs,SpecDepths,spc_sym,markersize=spc_size)
if spc_file!="" and len(FDepths)>0:
pylab.scatter(FIncs,FDepths,marker=spc_sym[-1],edgecolor=spc_sym[0],facecolor='white',s=spc_size**2)
if res_file!="":pylab.plot(ResIncs,ResDepths,res_sym,markersize=res_size)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
if depth>dmin and depth<dmax:
if pel==plt:pylab.text(90,depth+tint,core[core_label_key])
pylab.plot([-90,90],[depth,depth],'b--')
pylab.plot([0,0],[dmax,dmin],'k-')
if pel==plt:
pylab.axis([-90,110,dmax,dmin])
else:
pylab.axis([-90,90,dmax,dmin])
pylab.xlabel('Inclination')
pylab.ylabel('')
plt+=1
if pltM==1 and len(Ints)>0 or len(SInts)>0:
pylab.subplot(1,pcol,plt)
for pow in range(-10,10):
if maxInt*10**pow>1:break
if logit==0:
for k in range(len(Ints)):
Ints[k]=Ints[k]*10**pow
for k in range(len(SInts)):
SInts[k]=SInts[k]*10**pow
if pltL==1 and len(Ints)>0: pylab.plot(Ints,Depths,'k')
if len(Ints)>0:pylab.plot(Ints,Depths,sym,markersize=size)
if len(Ints)==0 and pltL==1 and len(SInts)>0:pylab.plot(SInts,SDepths,'k-')
if len(SInts)>0:pylab.plot(SInts,SDepths,Ssym,markersize=Ssize)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
pylab.plot([0,maxInt*10**pow+.1],[depth,depth],'b--')
if depth>dmin and depth<dmax:pylab.text(maxInt*10**pow-.2*maxInt*10**pow,depth+tint,core[core_label_key])
pylab.axis([0,maxInt*10**pow+.1,dmax,dmin])
if norm==0:
pylab.xlabel('%s %i %s'%('Intensity (10^-',pow,' Am^2)'))
else:
pylab.xlabel('%s %i %s'%('Intensity (10^-',pow,' Am^2/kg)'))
else:
if pltL==1: pylab.semilogx(Ints,Depths,'k')
if len(Ints)>0:pylab.semilogx(Ints,Depths,sym,markersize=size)
if len(Ints)==0 and pltL==1 and len(SInts)>0:pylab.semilogx(SInts,SDepths,'k')
if len(Ints)==0 and pltL==1 and len(SInts)>0:pylab.semilogx(SInts,SDepths,'k')
if len(SInts)>0:pylab.semilogx(SInts,SDepths,Ssym,markersize=Ssize)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
pylab.semilogx([minInt,maxInt],[depth,depth],'b--')
if depth>dmin and depth<dmax:pylab.text(maxInt-.2*maxInt,depth+tint,core[core_label_key])
pylab.axis([0,maxInt,dmax,dmin])
if norm==0:
pylab.xlabel('Intensity (Am^2)')
else:
pylab.xlabel('Intensity (Am^2/kg)')
plt+=1
if suc_file!="" or len(SSucs)>0:
pylab.subplot(1,pcol,plt)
if len(Susc)>0:
if pltL==1:pylab.plot(Susc,Sus_depths,'k')
if logit==0:pylab.plot(Susc,Sus_depths,sym,markersize=size)
if logit==1:pylab.semilogx(Susc,Sus_depths,sym,markersize=size)
if len(SSucs)>0:
if logit==0:pylab.plot(SSucs,SDepths,sym,markersize=size)
if logit==1:pylab.semilogx(SSucs,SDepths,sym,markersize=size)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
if logit==0:pylab.plot([minSuc,maxSuc],[depth,depth],'b--')
if logit==1:pylab.semilogx([minSuc,maxSuc],[depth,depth],'b--')
pylab.axis([minSuc,maxSuc,dmax,dmin])
pylab.xlabel('Susceptibility')
plt+=1
if wig_file!="":
pylab.subplot(1,pcol,plt)
pylab.plot(WIG,WIG_depths,'k')
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
pylab.plot([WIG[0],WIG[-1]],[depth,depth],'b--')
pylab.axis([min(WIG),max(WIG),dmax,dmin])
pylab.xlabel(plt_key)
plt+=1
if pTS==1:
ax1=pylab.subplot(1,pcol,plt)
ax1.axis([-.25,1.5,amax,amin])
plt+=1
TS,Chrons=pmag.get_ts(ts)
X,Y,Y2=[0,1],[],[]
cnt=0
if amin<TS[1]: # in the Brunhes
Y=[amin,amin] # minimum age
Y1=[TS[1],TS[1]] # age of the B/M boundary
ax1.fill_between(X,Y,Y1,facecolor='black') # color in Brunhes, black
for d in TS[1:]:
pol=cnt%2
cnt+=1
if d<=amax and d>=amin:
ind=TS.index(d)
Y=[TS[ind],TS[ind]]
Y1=[TS[ind+1],TS[ind+1]]
if pol: ax1.fill_between(X,Y,Y1,facecolor='black') # fill in every other time
ax1.plot([0,1,1,0,0],[amin,amin,amax,amax,amin],'k-')
ax2=ax1.twinx()
pylab.ylabel("Age (Ma): "+ts)
for k in range(len(Chrons)-1):
c=Chrons[k]
cnext=Chrons[k+1]
d=cnext[1]-old_div((cnext[1]-c[1]),3.)
if d>=amin and d<amax:
ax2.plot([1,1.5],[c[1],c[1]],'k-') # make the Chron boundary tick
ax2.text(1.05,d,c[0]) #
ax2.axis([-.25,1.5,amax,amin])
figname=location+'_m:_'+method+'_core-depthplot'+fmt
pylab.title(location)
if verbose:
pylab.draw()
ans=input("S[a]ve plot? ")
if ans=='a':
pylab.savefig(figname)
print('Plot saved as ',figname)
elif plots:
pylab.savefig(figname)
print('Plot saved as ',figname)
sys.exit()
def main():
"""
NAME
ani_depthplot.py
DESCRIPTION
plots tau, V3_inc, P and chi versus core_depth
SYNTAX
ani_depthplot.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input rmag_anisotropy format file from magic
-fb FILE: specify input magic_measurements format file from magic
-fsa FILE: specify input er_samples format file from magic
-fa FILE: specify input er_ages format file from magic
-d min max [in m] depth range to plot
-ds [mcd,mbsf], specify depth scale, default is mbsf
-sav save plot without review
-fmt specfiy format for figures - default is svg
DEFAULTS:
Anisotropy file: rmag_anisotropy.txt
Bulk susceptibility file: magic_measurements.txt
Samples file: er_samples.txt
"""
fmt='.svg'
dir_path="./"
pcol=3
verbose=pmagplotlib.verbose
plots=0
age_file=""
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
ani_file=dir_path+'/rmag_anisotropy.txt'
meas_file=dir_path+'/magic_measurements.txt'
samp_file=dir_path+'/er_samples.txt'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
ani_file=dir_path+'/'+sys.argv[ind+1]
if '-fb' in sys.argv:
ind=sys.argv.index('-fb')
meas_file=dir_path+'/'+sys.argv[ind+1]
if '-fsa' in sys.argv:
ind=sys.argv.index('-fsa')
samp_file=dir_path+'/'+sys.argv[ind+1]
if '-fa' in sys.argv:
print main.__doc__
print 'only -fsa OR -fa - not both'
sys.exit()
elif '-fa' in sys.argv:
ind=sys.argv.index('-fa')
age_file=dir_path+"/"+sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
dmin,dmax=-1,-1
if '-d' in sys.argv:
ind=sys.argv.index('-d')
dmin=float(sys.argv[ind+1])
dmax=float(sys.argv[ind+2])
if '-ds' in sys.argv and 'mcd' in sys.argv: # sets depth scale to meters composite depth (as opposed to meters below sea floor)
depth_scale='sample_composite_depth'
elif age_file=="":
depth_scale='sample_core_depth'
else:
depth_scale='age'
if '-sav' in sys.argv:
plots=1
verbose=0
#
# get data read in
isbulk=0 # tests if there are bulk susceptibility measurements
AniData,file_type=pmag.magic_read(ani_file) # read in tensor elements
if age_file=="":
Samps,file_type=pmag.magic_read(samp_file) # read in sample depth info from er_sample.txt format file
else:
Samps,file_type=pmag.magic_read(age_file) # read in sample age info from er_ages.txt format file
age_unit=Samps[0]['age_unit']
for s in Samps:s['er_sample_name']=s['er_sample_name'].upper() # change to upper case for every sample name
Meas,file_type=pmag.magic_read(meas_file)
if file_type=='magic_measurements':isbulk=1
Data=[]
Bulks=[]
BulkDepths=[]
for rec in AniData:
samprecs=pmag.get_dictitem(Samps,'er_sample_name',rec['er_sample_name'].upper(),'T') # look for depth record for this sample
sampdepths=pmag.get_dictitem(samprecs,depth_scale,'','F') # see if there are non-blank depth data
if dmax!=-1:
sampdepths=pmag.get_dictitem(sampdepths,depth_scale,dmax,'max') # fishes out records within depth bounds
sampdepths=pmag.get_dictitem(sampdepths,depth_scale,dmin,'min')
if len(sampdepths)>0: # if there are any....
rec['core_depth'] = sampdepths[0][depth_scale] # set the core depth of this record
Data.append(rec) # fish out data with core_depth
if isbulk: # if there are bulk data
chis=pmag.get_dictitem(Meas,'er_specimen_name',rec['er_specimen_name'],'T')
chis=pmag.get_dictitem(chis,'measurement_chi_volume','','F') # get the non-zero values for this specimen
if len(chis)>0: # if there are any....
Bulks.append(1e6*float(chis[0]['measurement_chi_volume'])) # put in microSI
BulkDepths.append(float(sampdepths[0][depth_scale]))
if len(Bulks)>0: # set min and max bulk values
bmin=min(Bulks)
bmax=max(Bulks)
xlab="Depth (m)"
if len(Data)>0:
location=Data[0]['er_location_name']
else:
print 'no data to plot'
sys.exit()
# collect the data for plotting tau and V3_inc
Depths,Tau1,Tau2,Tau3,V3Incs,P=[],[],[],[],[],[]
Axs=[] # collect the plot ids
if len(Bulks)>0: pcol+=1
s1=pmag.get_dictkey(Data,'anisotropy_s1','f') # get all the s1 values from Data as floats
s2=pmag.get_dictkey(Data,'anisotropy_s2','f')
s3=pmag.get_dictkey(Data,'anisotropy_s3','f')
s4=pmag.get_dictkey(Data,'anisotropy_s4','f')
s5=pmag.get_dictkey(Data,'anisotropy_s5','f')
s6=pmag.get_dictkey(Data,'anisotropy_s6','f')
Depths=pmag.get_dictkey(Data,'core_depth','f')
Ss=numpy.array([s1,s4,s5,s4,s2,s6,s5,s6,s3]).transpose() # make an array
Ts=numpy.reshape(Ss,(len(Ss),3,-1)) # and re-shape to be n-length array of 3x3 sub-arrays
for k in range(len(Depths)):
tau,Evecs= pmag.tauV(Ts[k]) # get the sorted eigenvalues and eigenvectors
v3=pmag.cart2dir(Evecs[2])[1] # convert to inclination of the minimum eigenvector
V3Incs.append(v3)
Tau1.append(tau[0])
Tau2.append(tau[1])
Tau3.append(tau[2])
P.append(tau[0]/tau[2])
if len(Depths)>0:
if dmax==-1:
dmax=max(Depths)
dmin=min(Depths)
tau_max=max(Tau1)
tau_min=min(Tau3)
P_max=max(P)
P_min=min(P)
#dmax=dmax+.05*dmax
#dmin=dmin-.05*dmax
pylab.figure(1,figsize=(10,8)) # make the figure
version_num=pmag.get_version()
pylab.figtext(.02,.01,version_num) # attach the pmagpy version number
ax=pylab.subplot(1,pcol,1) # make the first column
Axs.append(ax)
ax.plot(Tau1,Depths,'rs')
ax.plot(Tau2,Depths,'b^')
ax.plot(Tau3,Depths,'ko')
ax.axis([tau_min,tau_max,dmax,dmin])
ax.set_xlabel('Eigenvalues')
if depth_scale=='sample_core_depth':
ax.set_ylabel('Depth (mbsf)')
elif depth_scale=='age':
ax.set_ylabel('Age ('+age_unit+')')
else:
ax.set_ylabel('Depth (mcd)')
ax2=pylab.subplot(1,pcol,2) # make the second column
ax2.plot(P,Depths,'rs')
ax2.axis([P_min,P_max,dmax,dmin])
ax2.set_xlabel('P')
ax2.set_title(location)
Axs.append(ax2)
ax3=pylab.subplot(1,pcol,3)
Axs.append(ax3)
ax3.plot(V3Incs,Depths,'ko')
ax3.axis([0,90,dmax,dmin])
ax3.set_xlabel('V3 Inclination')
if pcol==4:
ax4=pylab.subplot(1,pcol,4)
Axs.append(ax4)
ax4.plot(Bulks,BulkDepths,'bo')
ax4.axis([bmin-1,bmax+1,dmax,dmin])
ax4.set_xlabel('Bulk Susc. (uSI)')
for x in Axs:pmagplotlib.delticks(x) # this makes the x-tick labels more reasonable - they were overcrowded using the defaults
figname=location+'_ani-depthplot'+fmt
if verbose:
pylab.draw()
ans=raw_input("S[a]ve plot? Return to quit ")
if ans=='a':
pylab.savefig(figname)
print 'Plot saved as ',figname
elif plots:
pylab.savefig(figname)
print 'Plot saved as ',figname
sys.exit()
else:
print "No data points met your criteria - try again"
