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
ODP_dcs_magic.py
DESCRIPTION
converts ODP discrete sample format files to magic_measurements format files
SYNTAX
ODP_dsc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file for appending, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-A : don't average replicate measurements
INPUT
Put data from separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in separate directory
"""
#
#
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-A" in args: noave=1
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=dir_path+'/'+args[ind+1]
ErSamps,file_type=pmag.magic_read(samp_file)
else:
samp_file=dir_path+'/'+samp_file
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in args: methcode="LT-AF-Z"
if'-dc' in args: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in args: methcode="LT-T-Z"
if '-dc' in args: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=raw_input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=raw_input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
spec_file=dir_path+'/'+spec_file
site_file=dir_path+'/'+site_file
meas_file=dir_path+'/'+meas_file
filelist=os.listdir(dir_path) # read in list of files to import
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs=[],[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
for file in filelist: # parse each file
if file[-3:].lower()=='dsc':
print 'processing: ',file
MagRec,SpecRec,SampRec={},{},{}
treatment_type,treatment_value,user="","",""
inst="ODP-SRM"
input=open(dir_path+'/'+file,'rU').readlines()
IDs=file.split('_') # splits on underscores
pieces=IDs[0].split('-')
expedition=pieces[0]
location=pieces[1]
if file[0]!='_':
while len(pieces[2])<4:pieces[2]='0'+pieces[2] # pad core to be 3 characters
specimen=""
else:
specimen="test"
for piece in pieces:
specimen=specimen+piece+'-'
specimen=specimen[:-1]
alt_spec=IDs[1] # alternate specimen is second field in field name
# set up specimen record for Er_specimens table
SpecRec['er_expedition_name']=expedition
SpecRec['er_location_name']=location
SpecRec['er_site_name']=specimen
SpecRec['er_sample_name']=specimen
SpecRec['er_citation_names']=citation
for key in SpecRec.keys():SampRec[key]=SpecRec[key]
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['magic_method_codes']='FS-C-DRILL-IODP:FS-SS-C:SO-V'
SpecRec['er_specimen_name']=specimen
for key in SpecRec.keys():MagRec[key]=SpecRec[key]
# set up measurement record - default is NRM
MagRec['er_analyst_mail_names']=user
MagRec['magic_method_codes']='LT-NO'
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]=0.
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
MagRec["measurement_csd"]='' # set csd to blank
SpecRec['er_specimen_alternatives']=alt_spec
vol=7e-6 # assume 7 cc samples
datestamp=input[1].split() # date time is second line of file
mmddyy=datestamp[0].split('/') # break into month day year
date=mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]
MagRec["measurement_date"]=date
for k in range(len(input)):
fields= input[k].split("=")
if 'treatment_type' in fields[0]:
if "Alternating Frequency Demagnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type="AF"
if "Anhysteretic Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-I'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type="ARM"
if "Isothermal Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-IRM'
inst=inst+':ODP-IMP' # measured on shipboard ASC IMPULSE magnetizer
treatment_type="IRM"
if "treatment_value" in fields[0]:
values=fields[1].split(',')
value=values[0]
if value!=" \n":
if treatment_type=="AF":
treatment_value=float(value)*1e-3
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
elif treatment_type=="IRM":
treatment_value=float(value)*1e-3
MagRec["treatment_dc_field"]='%8.3e'%(treatment_value) # IRM treat mT => T
if treatment_type=="ARM":
treatment_value=float(value)*1e-3
dc_value=float(values[1])*1e-3
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
MagRec["treatment_dc_field"]='%8.3e'%(dc_value) # DC mT => T
if 'user' in fields[0]:
user=fields[-1]
MagRec["er_analyst_mail_names"]=user
if 'sample_orientation' in fields[0]:
MagRec["measurement_description"]=fields[-1]
MagRec["measurement_standard"]='u' # assume all data are "good"
if 'sample_area' in fields[0]: vol=float(fields[1])*1e-6 # takes volume (cc) and converts to m^3
if 'run_number' in fields[0]:
MagRec['external_database_ids']=fields[1] # run number is the LIMS measurement number
MagRec['external_database_names']='LIMS'
if input[k][0:7]=='<MULTI>':
rec=input[k+1].split(',') # list of data
for item in rec:
items=item.split('=')
if items[0].strip()=='demag_level' and treatment_value=="" :
treat= float(items[1])
if treat!=0:
MagRec['magic_method_codes']='LT-AF-Z'
inst=inst+':ODP-SRM-AF'
MagRec["treatment_ac_field"]=treat*1e-3 # AF demag in treat mT => T
if items[0].strip()=='inclination_w_tray_w_bkgrd': MagRec['measurement_inc']=items[1]
if items[0].strip()=='declination_w_tray_w_bkgrd': MagRec['measurement_dec']=items[1]
if items[0].strip()=='intensity_w_tray_w_bkgrd': MagRec['measurement_magn_moment']='%8.3e'%(float(items[1])*vol) # convert intensity from A/m to Am^2 using vol
if items[0].strip()=='x_stdev':MagRec['measurement_x_sd']=items[1]
if items[0].strip()=='y_stdev':MagRec['measurement_y_sd']=items[1]
if items[0].strip()=='z_stdev':MagRec['measurement_z_sd']=items[1]
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
MagOuts=pmag.sort_diclist(MagRecs,'treatment_ac_field')
for MagRec in MagOuts:
MagRec["treatment_ac_field"]='%8.3e'%(MagRec["treatment_ac_field"]) # convert to string
pmag.magic_write(spec_file,SpecRecs,'er_specimens')
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
print 'samples stored in ',samp_file
pmag.magic_write(samp_file,SampRecs,'er_samples')
print 'specimens stored in ',spec_file
Fixed=pmag.measurements_methods(MagOuts,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print 'data stored in ',meas_file
def main(command_line=True, **kwargs):
"""
NAME
IODP_dscr_magic.py
DESCRIPTION
converts ODP LIMS discrete sample format files to magic_measurements format files
SYNTAX
IODP_descr_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input .csv file, default is all in directory
-F FILE: specify output measurements file, default is magic_measurements.txt
-A : don't average replicate measurements
INPUTS
IODP discrete sample .csv file format exported from LIMS database
"""
#
# initialize defaults
version_num = pmag.get_version()
meas_file = "magic_measurements.txt"
csv_file = ""
MagRecs, Specs = [], []
citation = "This study"
dir_path, demag = ".", "NRM"
args = sys.argv
noave = 0
# get command line args
if command_line:
if "-WD" in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-ID" in args:
ind = args.index("-ID")
input_dir_path = args[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if "-A" in args:
noave = 1
if "-f" in args:
ind = args.index("-f")
csv_file = args[ind + 1]
if "-F" in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if not command_line:
dir_path = kwargs.get("dir_path", ".")
input_dir_path = kwargs.get("input_dir_path", dir_path)
output_dir_path = dir_path # rename dir_path after input_dir_path is set
noave = kwargs.get("noave", 0) # default (0) is DO average
csv_file = kwargs.get("csv_file", "")
meas_file = kwargs.get("meas_file", "magic_measurements.txt")
# format variables
meas_file = os.path.join(output_dir_path, meas_file)
if csv_file == "":
filelist = os.listdir(input_dir_path) # read in list of files to import
else:
csv_file = os.path.join(input_dir_path, csv_file)
filelist = [csv_file]
# parsing the data
file_found = False
for file in filelist: # parse each file
if file[-3:].lower() == "csv":
file_found = True
print "processing: ", file
input = open(file, "rU").readlines()
keys = input[0].replace("\n", "").split(",") # splits on underscores
interval_key = "Offset (cm)"
demag_key = "Demag level (mT)"
offline_demag_key = "Treatment Value (mT or °C)"
offline_treatment_type = "Treatment type"
run_key = "Test No."
if "Inclination background + tray corrected (deg)" in keys:
inc_key = "Inclination background + tray corrected (deg)"
if "Inclination background & tray corrected (deg)" in keys:
inc_key = "Inclination background & tray corrected (deg)"
if "Declination background + tray corrected (deg)" in keys:
dec_key = "Declination background + tray corrected (deg)"
if "Declination background & tray corrected (deg)" in keys:
dec_key = "Declination background & tray corrected (deg)"
if "Intensity background + tray corrected (A/m)" in keys:
int_key = "Intensity background + tray corrected (A/m)"
if "Intensity background & tray corrected (A/m)" in keys:
int_key = "Intensity background & tray corrected (A/m)"
type = "Type"
sect_key = "Sect"
half_key = "A/W"
# need to add volume_key to LORE format!
if "Sample volume (cm^3)" in keys:
volume_key = "Sample volume (cm^3)"
if "Sample volume (cc)" in keys:
volume_key = "Sample volume (cc)"
if "Sample volume (cm³)" in keys:
volume_key = "Sample volume (cm³)"
for line in input[1:]:
InRec = {}
for k in range(len(keys)):
InRec[keys[k]] = line.split(",")[k]
inst = "IODP-SRM"
MagRec = {}
expedition = InRec["Exp"]
location = InRec["Site"] + InRec["Hole"]
offsets = InRec[interval_key].split(
"."
) # maintain consistency with er_samples convention of using top interval
if len(offsets) == 1:
offset = int(offsets[0])
else:
offset = int(offsets[0]) - 1
# interval=str(offset+1)# maintain consistency with er_samples convention of using top interval
interval = str(offset) # maintain consistency with er_samples convention of using top interval
specimen = (
expedition
+ "-"
+ location
+ "-"
+ InRec["Core"]
+ InRec[type]
+ "-"
+ InRec[sect_key]
+ "_"
+ InRec[half_key]
+ "_"
+ interval
)
if specimen not in Specs:
Specs.append(specimen)
MagRec["er_expedition_name"] = expedition
MagRec["er_location_name"] = location
MagRec["er_site_name"] = specimen
MagRec["er_citation_names"] = citation
MagRec["er_specimen_name"] = specimen
MagRec["er_sample_name"] = specimen
MagRec["er_site_name"] = specimen
# set up measurement record - default is NRM
MagRec["magic_software_packages"] = version_num
MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["treatment_ac_field"] = "0"
MagRec["treatment_dc_field"] = "0"
MagRec["treatment_dc_field_phi"] = "0"
MagRec["treatment_dc_field_theta"] = "0"
MagRec["measurement_flag"] = "g" # assume all data are "good"
MagRec["measurement_standard"] = "u" # assume all data are "good"
MagRec["measurement_csd"] = "0" # assume all data are "good"
volume = InRec[volume_key]
MagRec["magic_method_codes"] = "LT-NO"
sort_by = "treatment_ac_field" # set default to AF demag
if InRec[demag_key] != "0":
MagRec["magic_method_codes"] = "LT-AF-Z"
inst = inst + ":IODP-SRM-AF" # measured on shipboard in-line 2G AF
treatment_value = float(InRec[demag_key].strip('"')) * 1e-3 # convert mT => T
if sort_by == "treatment_ac_field":
MagRec["treatment_ac_field"] = treatment_value # AF demag in treat mT => T
else:
MagRec["treatment_ac_field"] = str(treatment_value) # AF demag in treat mT => T
elif offline_treatment_type in InRec.keys() and InRec[offline_treatment_type] != "":
if "Lowrie" in InRec["Comments"]:
MagRec["magic_method_codes"] = "LP-IRM-3D"
treatment_value = float(InRec[offline_demag_key].strip('"')) + 273.0 # convert C => K
MagRec["treatment_temp"] = treatment_value
MagRec["treatment_ac_field"] = "0"
sort_by = "treatment_temp"
elif "Isothermal" in InRec[offline_treatment_type]:
MagRec["magic_method_codes"] = "LT-IRM"
treatment_value = float(InRec[offline_demag_key].strip('"')) * 1e-3 # convert mT => T
MagRec["treatment_dc_field"] = treatment_value
MagRec["treatment_ac_field"] = "0"
sort_by = "treatment_dc_field"
MagRec["measurement_standard"] = "u" # assume all data are "good"
vol = float(volume) * 1e-6 # convert from cc to m^3
if run_key in InRec.keys():
run_number = InRec[run_key]
MagRec["external_database_ids"] = run_number
MagRec["external_database_names"] = "LIMS"
else:
MagRec["external_database_ids"] = ""
MagRec["external_database_names"] = ""
MagRec["measurement_description"] = "sample orientation: " + InRec["Sample orientation"]
MagRec["measurement_inc"] = InRec[inc_key].strip('"')
MagRec["measurement_dec"] = InRec[dec_key].strip('"')
intens = InRec[int_key].strip('"')
MagRec["measurement_magn_moment"] = "%8.3e" % (
float(intens) * vol
) # convert intensity from A/m to Am^2 using vol
MagRec["magic_instrument_codes"] = inst
MagRec["measurement_number"] = "1"
MagRec["measurement_positions"] = ""
MagRecs.append(MagRec)
if not file_found:
print "No .csv files were found"
return False, "No .csv files were found"
MagOuts = []
for spec in Specs:
Speclist = pmag.get_dictitem(MagRecs, "er_specimen_name", spec, "T")
sorted = pmag.sort_diclist(Speclist, sort_by)
for rec in sorted:
for key in rec.keys():
rec[key] = str(rec[key])
MagOuts.append(rec)
Fixed = pmag.measurements_methods(MagOuts, noave)
Out, keys = pmag.fillkeys(Fixed)
if pmag.magic_write(meas_file, Out, "magic_measurements"):
print "data stored in ", meas_file
return True, meas_file
else:
print "no data found. bad magfile?"
return False, "no data found. bad magfile?"
def main():
"""
NAME
ODP_depthplot.py
DESCRIPTION
plots various measurements versus core_depth
SYNTAX
ODP_depthplot.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic_measurments format file from magic
-fsum FILE: specify input ODP 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
-fsp FILE sym size: specify input zeq_specimen format file from magic, sym and size
-LP [AF,T,ARM,IRM, X] step [in mT,C,mT,mT, mass/vol] to plot
-sym SYM SIZE, symbol, size for data 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
-S do not plot subsample blanket treatment data
-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]
DEFAULTS:
Measurements file: magic_measurements.txt
Samples file: er_samples.txt
NRM step
Summary file: none
"""
meas_file='magic_measurements.txt'
samp_file='er_samples.txt'
wt_file=''
width=10
sym,size='bo',5
Ssym,Ssize='ws',5
method,fmt="LT-NO",'.pdf'
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=""
spc_file=""
ngr_file=""
wig_file=""
title=""
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
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 '-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 '-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 '-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=sys.argv[ind+1]
sum_file=dir_path+'/'+sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
if '-LP' in sys.argv:
ind=sys.argv.index('-LP')
meth=sys.argv[ind+1]
if meth=="AF":
step=float(sys.argv[ind+2])*1e-3
method='LT-AF-Z'
elif meth== 'T':
step=float(sys.argv[ind+2])+273
method='LT-T-Z'
elif meth== 'ARM':
method='LT-AF-I'
step=float(sys.argv[ind+2])*1e-3
elif meth== 'IRM':
method='LT-IRM'
step=float(sys.argv[ind+2])*1e-3
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
samp_file=dir_path+'/'+samp_file
Meas,file_type=pmag.magic_read(meas_file)
print len(Meas), ' measurements read in from ',meas_file
Samps,file_type=pmag.magic_read(samp_file)
if spc_file!="":Specs,file_type=pmag.magic_read(spc_file)
if norm==1:
ErSpecs,file_type=pmag.magic_read(wt_file)
print len(ErSpecs), ' specimens read in from ',wt_file
Cores=[]
if sum_file!="":
input=open(sum_file,'rU').readlines()
keys=input[1].replace('\n','').split(',') # splits on underscores
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=[]
for rec in Meas:
for samp in Samps:
if samp['er_sample_name']== rec['er_sample_name'] and 'sample_core_depth' in samp.keys() and samp['sample_core_depth']!="":
rec['core_depth'] = float(samp['sample_core_depth'])
rec['magic_method_codes'] = rec['magic_method_codes']+':'+samp['magic_method_codes']
if norm==1:
for spec in ErSpecs:
if spec['er_sample_name']== rec['er_sample_name'] and 'specimen_weight' in spec.keys() and spec['specimen_weight']!="":
rec['specimen_weight'] = spec['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=samp['er_sample_name'].split('-')
title=pieces[0]+'-'+pieces[1]
SData=pmag.sort_diclist(Data,'core_depth')
xlab="Depth (mbsf)"
# collect the data for plotting declination
Depths,Decs,Incs,Ints=[],[],[],[]
SDepths,SDecs,SIncs,SInts=[],[],[],[]
SSucs=[]
samples=[]
methods,steps=[],[]
for rec in SData:
if "magic_method_codes" in rec.keys():
meths=rec["magic_method_codes"].split(":")
if method in meths:
if step==0 or ('LT-AF-Z' in method and float(rec['treatment_ac_field'])==step) or ('LT-T-Z' in method and float(rec['treatment_temp'])==step) or ('LT-AF-I' in method and float(rec['treatment_ac_field'])==step) or ('LT-IRM' in method and float(rec['treatment_dc_field'])==step) or ('LP-X' in method and rec[suc_key] in rec.keys() and rec[suc_key]!=""):
if dmax==-1 or float(rec['core_depth'])<dmax and float(rec['core_depth'])>dmin:
if 'FS-SS-C' not in meths: # make sure it is desired lab treatment step
Depths.append((rec['core_depth']))
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['measurement_magn_moment']))
if norm==1 and pltM==1:Ints.append(float(rec['measurement_magn_moment'])/float(rec['specimen_weight']))
if len(Ints)>1 and Ints[-1]>maxInt:maxInt=Ints[-1]
if len(Ints)>1 and Ints[-1]<minInt:minInt=Ints[-1]
elif pltS==1: # make sure it is desired lab treatment step
SDepths.append((rec['core_depth']))
if pltD==1:SDecs.append(float(rec['measurement_dec']))
if pltI==1:SIncs.append(float(rec['measurement_inc']))
if norm==0 and pltM==1:SInts.append(float(rec['measurement_magn_moment']))
if norm==1 and pltM==1:SInts.append(float(rec['measurement_magn_moment'])/float(rec['specimen_weight']))
if len(SInts)>1 and SInts[-1]>maxInt:maxInt=SInts[-1]
if len(SInts)>1 and SInts[-1]<minInt:minInt=SInts[-1]
if method=="LP-X":
SSucs.append(float(rec[suc_key]))
if SSucs[-1]>maxSuc:maxSuc=SSucs[-1]
if SSucs[-1]<minSuc:minSuc=SSucs[-1]
elif len(Depths) and len(SDepths)==0:
for meth in meths:
if 'LT-AF-Z' in meth:
thisstep='%7.1f'%(float(rec['treatment_ac_field'])*1e3)
if thisstep not in steps:steps.append(thisstep)
if 'AF' not in methods:methods.append('AF')
if 'LT-T-Z' in meth:
thisstep='%7.1f'%(float(rec['treatment_ac_field'])-273.)
if thisstep not in steps:steps.append(thisstep)
if 'T' not in methods:methods.append('T')
if 'LT-T-I' in meth:
thisstep='%7.1f'%(float(rec['treatment_ac_field'])*1e3)
if thisstep not in steps:steps.append(thisstep)
if 'ARM' not in methods:methods.append('ARM')
if 'LT-IRM' in meth:
thisstep='%7.1f'%(float(rec['treatment_dc_field'])*1e3)
if thisstep not in steps:steps.append(thisstep)
if 'IRM' not in methods:methods.append('IRM')
if len(Depths)==0 and len(SDepths)==0:
print 'no data matched your request, try a different lab treatment '
print 'available treatment types: ',methods
print 'available treatment steps: ',steps
# sys.exit()
if dmin==-1:
if len(Depths)>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]
SpecDepths,SpecDecs,SpecIncs=[],[],[]
if spc_file!="" and pltS==1: # add depths to spec data
for spec in Specs:
for samp in Samps:
if samp['er_sample_name']== spec['er_sample_name'] and 'sample_core_depth' in samp.keys() and samp['sample_core_depth']!="":
meths=samp['magic_method_codes'].split(":")
if 'DE-BFP' not in meths:
SpecDepths.append(float(samp['sample_core_depth'])) # 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
Susc,Sus_depths=[],[]
if suc_file!="":
sucdat=open(suc_file,'rU').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,'sample_core_depth')
keys=wigdat[0].keys()
for key in keys:
if key!="sample_core_depth":
plt_key=key
break
for wig in swigdat:
if float(wig['sample_core_depth'])<dmax and float(wig['sample_core_depth'])>dmin:
WIG.append(float(wig[plt_key]))
WIG_depths.append(float(wig['sample_core_depth']))
tint=4.5
plt=1
if len(Decs)>0 and len(Depths)>0 or (len(SpecDecs)>0 and len(SpecDepths)>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):
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
pylab.figure(1,figsize=(width,8))
version_num=pmag.get_version()
pylab.figtext(.02,.01,version_num)
if pltD==1:
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 sum_file!="":
for core in Cores:
depth=float(core['Core Top (m)'])
if depth>dmin and depth<dmax:
pylab.plot([0,360.],[depth,depth],'b--')
if pel==plt:pylab.text(360,depth+tint,core['Core #']+core['Core Type'])
if pel==plt:
pylab.axis([0,400,dmax,dmin])
else:
pylab.axis([0,360.,dmax,dmin])
pylab.xlabel('Declination')
pylab.ylabel('Depth (mbsf)')
if title!="":pylab.title(title)
title=""
plt+=1
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!="":pylab.plot(SpecIncs,SpecDepths,spc_sym,markersize=spc_size)
if sum_file!="":
for core in Cores:
depth=float(core['Core Top (m)'])
if depth>dmin and depth<dmax:
if pel==plt:pylab.text(90,depth+tint,core['Core #']+core['Core Type'])
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('')
if title!="":pylab.title(title)
title=""
plt+=1
if pltM==1 and len(Ints)>0 or len(SInts)>0:
pylab.subplot(1,pcol,plt)
if logit==0:
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 Top (m)'])
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 #']+core['Core Type'])
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 Top (m)'])
pylab.semilogx([minInt,maxInt],[depth,depth],'b--')
if depth>dmin and depth<dmax:pylab.text(maxInt-.2*maxInt,depth+tint,core['Core #']+core['Core Type'])
pylab.axis([0,maxInt,dmax,dmin])
if norm==0:
pylab.xlabel('Intensity (Am^2)')
else:
pylab.xlabel('Intensity (Am^2/kg)')
if title!="":pylab.title(title)
title=""
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 Top (m)'])
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')
if title!="":pylab.title(title)
title=""
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 Top (m)'])
pylab.plot([WIG[0],WIG[-1]],[depth,depth],'b--')
pylab.axis([min(WIG),max(WIG),dmax,dmin])
pylab.xlabel(plt_key)
if title!="":pylab.title(title)
title=""
plt+=1
if pTS==1:
ax1=pylab.subplot(1,pcol,plt)
plt+=1
TS,Chrons=pmag.get_TS(ts)
p=1
X,Y=[],[]
for d in TS:
if d<=amax and d>=amin:
if len(X)==0:
ind=TS.index(d)
X.append(TS[ind-1])
Y.append(p%2)
X.append(d)
Y.append(p%2)
p+=1
X.append(d)
Y.append(p%2)
else:
X.append(amax)
Y.append(p%2)
# isign=-1
ax1.plot(Y,X,'k')
ax1.plot([0,1,1,0,0],[amin,amin,amax,amax,amin],'k-')
ax1.axis([-.25,1.5,amax,amin])
ax2=ax1.twinx()
pylab.ylabel("Age (Ma): "+ts)
for c in Chrons:
# isign=-1*isign
# if isign>0: off=1.05
if c[1]>=amin and c[1]<amax:
ax2.text(1.05,c[1],c[0])
ax2.axis([-.25,1.5,amax,amin])
pylab.draw()
ans=raw_input("Press return to quit ")
sys.exit()
