def main():
"""
NAME
dipole_pinc.py
DESCRIPTION
gives GAD inclination at specified (paleo) latitude
SYNTAX
dipole_pinc.py [command line options]<filename
OPTIONS
-h prints help message and quits
-i allows interactive entry of latitude
-f file, specifies file name on command line
"""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
elif '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
f=open(file,'rU')
data=f.readlines()
elif '-i' not in sys.argv:
data=sys.stdin.readlines()
if '-i' not in sys.argv:
for line in data:
rec=line.split()
print '%7.1f'%(pmag.pinc(float(rec[0])))
else:
while 1:
try:
lat=raw_input("Paleolat for converting to inclination: <cntl-D> to quit ")
print '%7.1f'%(pmag.pinc(float(lat)))
except EOFError:
print '\n Good-bye \n'
sys.exit()
def main():
"""
NAME
strip_magic.py
DESCRIPTION
plots various parameters versus depth or age
SYNTAX
strip_magic.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file from magic,default='pmag_results.txt'
supported types=[pmag_specimens, pmag_samples, pmag_sites, pmag_results, magic_web]
-obj [sit,sam,all]: specify object to site,sample,all for pmag_result table, default is all
-fmt [svg,png,jpg], format for images - default is svg
-x [age,pos]: specify whether age or stratigraphic position
-y [dec,inc,int,chi,lat,lon,vdm,vadm]
(lat and lon are VGP lat and lon)
-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]
-mcd method_code, specify method code, default is first one encountered
NOTES
when x and/or y are not specified, a list of possibilities will be presented to the user for choosing
"""
xaxis,xplotind,yplotind="",0,0 # (0 for strat pos)
yaxis,Xinc="", ""
obj='all'
supported=['pmag_specimens', 'pmag_samples', 'pmag_sites', 'pmag_results','magic_web']
Depth_keys=['specimen_core_depth','specimen_height','specimen_elevation','specimen_composite_depth', 'sample_core_depth','sample_height','sample_elevation','sample_composite_depth', 'site_core_depth','site_height','site_elevation','site_composite_depth','average_height']
Age_keys=['specimen_inferred_age','sample_inferred_age','site_inferred_age','average_age']
Unit_keys={'specimen_inferred_age':'specimen_inferred_age_unit','sample_inferred_age':'sample_inferred_age_unit','site_inferred_age':'site_inferred_age_unit','average_age':'average_age_unit'}
Dec_keys=['measurement_dec','specimen_dec','sample_dec','site_dec','average_dec']
Inc_keys=['measurement_inc','specimen_inc','sample_inc','site_inc','average_inc']
Int_keys=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass','specimen_int','specimen_int_rel','sample_int','sample_int_rel','site_int','site_int_rel','average_int','average_int_rel']
Chi_keys=['measurement_chi_volume','measurement_chi_mass']
Lat_keys=['sample_lat','site_lat','average_lat']
VLat_keys=['vgp_lat']
VLon_keys=['vgp_lon']
Vdm_keys=['vdm']
Vadm_keys=['vadm']
X_keys=[Age_keys,Depth_keys]
Y_keys=[Dec_keys,Inc_keys,Int_keys,Chi_keys,VLat_keys,VLon_keys,Vdm_keys,Vadm_keys]
method,fmt="",'svg'
FIG={'strat':1}
plotexp,pTS=0,0
dir_path="./"
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
res_file=dir_path+'/pmag_results.txt'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
res_file=dir_path+'/'+sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
obj=sys.argv[ind+1]
if '-x' in sys.argv:
ind=sys.argv.index('-x')
xaxis=sys.argv[ind+1]
if '-y' in sys.argv:
ind=sys.argv.index('-y')
yaxis=sys.argv[ind+1]
if yaxis=='dec':ykeys=Dec_keys
if yaxis=='inc':ykeys=Inc_keys
if yaxis=='int':ykeys=Int_keys
if yaxis=='chi':ykeys=Chi_keys
if yaxis=='lat':ykeys=VLat_keys
if yaxis=='lon':ykeys=VLon_keys
if yaxis=='vdm':ykeys=Vdm_keys
if yaxis=='vadm':ykeys=Vadm_keys
if '-mcd' in sys.argv:
ind=sys.argv.index('-mcd')
method=sys.argv[ind+1]
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
if '-Iex' in sys.argv: plotexp=1
#
#
# get data read in
Results,file_type=pmag.magic_read(res_file)
if file_type not in supported:
print "Unsupported file type, try again"
sys.exit()
PltObjs=['all']
if file_type=='pmag_results': # find out what to plot
for rec in Results:
resname=rec['pmag_result_name'].split()
if 'Sample' in resname and 'sam' not in PltObjs:PltObjs.append('sam')
if 'Site' in resname and 'sit' not in PltObjs:PltObjs.append('sit')
methcodes=[]
if "magic_method_codes" in Results[0].keys(): # need to know all the measurement types from method_codes
for rec in Results:
meths=rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in methcodes and 'LP' in meth: methcodes.append(meth.strip()) # look for the lab treatments
#
# initialize some variables
X_unit="" # Unit for age or depth plotting (meters if depth)
Xplots,Yplots=[],[]
Xunits=[]
yplotind,xplotind=0,0
#
# step through possible plottable keys
#
if xaxis=="" or yaxis=="":
for key in Results[0].keys():
for keys in X_keys:
for xkeys in keys:
if key in xkeys:
for ResRec in Results:
if ResRec[key]!="":
Xplots.append(key) # only plot something if there is something to plot!
break
for keys in Y_keys:
for pkeys in keys:
if key in pkeys:
for ResRec in Results:
if ResRec[key]!="":
Yplots.append(key)
break
X,Y=[],[]
for plt in Xplots:
if plt in Age_keys and 'age' not in X: X.append('age')
if plt in Depth_keys and 'pos' not in X:X.append('pos')
for plt in Yplots:
if plt in Dec_keys and 'dec' not in Y:Y.append('dec')
if plt in Inc_keys and 'inc' not in Y:Y.append('inc')
if plt in Int_keys and 'int' not in Y:Y.append('int')
if plt in Chi_keys and 'chi' not in Y:Y.append('chi')
if plt in VLat_keys and 'lat' not in Y:Y.append('lat')
if plt in VLon_keys and 'lon' not in Y:Y.append('lon')
if plt in Vadm_keys and 'vadm' not in Y:Y.append('vadm')
if plt in Vdm_keys and 'vdm' not in Y:Y.append('vdm')
if file_type=='pmag_results':
print 'available objects for plotting: ',PltObjs
print 'available X plots: ',X
print 'available Y plots: ',Y
print 'available method codes: ',methcodes
f=open(dir_path+'/.striprc','w')
for x in X:
f.write('x:'+x+'\n')
for y in Y:
f.write('y:'+y+'\n')
for m in methcodes:
f.write('m:'+m+'\n')
for obj in PltObjs:
f.write('obj:'+obj+'\n')
sys.exit()
if plotexp==1:
for lkey in Lat_keys:
for key in Results[0].keys():
if key==lkey:
lat=float(Results[0][lkey])
Xinc=[pmag.pinc(lat),-pmag.pinc(lat)]
break
if Xinc=="":
print 'can not plot expected inc for site - lat unknown'
if method!="" and method not in methcodes:
print 'your method not available, but these are: '
print methcodes
print 'use ',methocodes[0],'? ^D to quit'
if xaxis=='age':
for akey in Age_keys:
for key in Results[0].keys():
if key==akey:
Xplots.append(key)
Xunits.append(Unit_keys[key])
if xaxis=='pos':
for dkey in Depth_keys:
for key in Results[0].keys():
if key==dkey:
Xplots.append(key)
if len(Xplots)==0:
print 'desired X axis information not found'
sys.exit()
if xaxis=='age':age_unit=Results[0][Xunits[0]]
if len(Xplots)>1:
print 'multiple X axis keys found, using: ',Xplots[xplotind]
for ykey in ykeys:
for key in Results[0].keys():
if key==ykey:Yplots.append(key)
if len(Yplots)==0:
print 'desired Y axis information not found'
sys.exit()
if len(Yplots)>1:
print 'multiple Y axis keys found, using: ',Yplots[yplotind]
# check if age or depth info
if len(Xplots)==0:
print "Must have either age or height info to plot "
sys.exit()
#
# check for variable to plot
#
#
# determine X axis (age or depth)
#
if xaxis=="age": plotind="1"
if method=="":method=methcodes[0]
if xaxis=='pos':
xlab="Stratigraphic Height (meters)"
else:
xlab="Age ("+age_unit+")"
Xkey=Xplots[xplotind]
Ykey=Yplots[yplotind]
ylab=Ykey
#
# collect the data for plotting
XY=[]
isign=1.
# if float(Results[0][Xkey])/float(Results[-1][Xkey])>0 and float(Results[0][Xkey])<0:
# isign=-1. # x axis all same sign and negative, take positive (e.g.,for depth in core)
# xlab="Stratigraphic Position (meters)"
# else:
# isign=1.
for rec in Results:
if "magic_method_codes" in rec.keys():
meths=rec["magic_method_codes"].split(":")
if method in meths: # make sure it is desired lab treatment step
if obj=='all' and rec[Xkey].strip()!="":
XY.append([isign*float(rec[Xkey]),float(rec[Ykey])])
elif rec[Xkey].strip()!="":
name=rec['pmag_result_name'].split()
if obj=='sit' and "Site" in name: XY.append([isign*float(rec[Xkey]),float(rec[Ykey])])
if obj=='sam' and "Sample" in name: XY.append([isign*float(rec[Xkey]),float(rec[Ykey])])
elif method =="":
if obj=='all' and rec[Xkey].strip()!="":
XY.append([isign*float(rec[Xkey]),float(rec[Ykey])])
elif rec[Xkey].strip()!="":
name=rec['pmag_result_name'].split()
if obj=='sit' and "Site" in name: XY.append([isign*float(rec[Xkey]),float(rec[Ykey])])
if obj=='sam' and "Sample" in name: XY.append([isign*float(rec[Xkey]),float(rec[Ykey])])
else:
print "Something wrong with your plotting choices"
break
XY.sort()
title=""
if "er_locations_names" in Results[0].keys(): title=Results[0]["er_location_names"]
if "er_locations_name" in Results[0].keys(): title=Results[0]["er_location_name"]
labels=[xlab,ylab,title]
pmagplotlib.plot_init(FIG['strat'],10,5)
pmagplotlib.plotSTRAT(FIG['strat'],XY,labels) # plot them
if plotexp==1: pmagplotlib.plotHs(FIG['strat'],Xinc,'b','--')
if yaxis=='inc' or yaxis=='lat':
pmagplotlib.plotHs(FIG['strat'],[0],'b','-')
pmagplotlib.plotHs(FIG['strat'],[-90,90],'g','-')
if pTS==1:
FIG['ts']=2
pmagplotlib.plot_init(FIG['ts'],10,5)
pmagplotlib.plotTS(FIG['ts'],[amin,amax],ts)
files={}
for key in FIG.keys():
files[key]=key+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
files={}
files['strat']=xaxis+'_'+yaxis+'_.'+fmt
files['ts']='ts.'+fmt
titles={}
titles['strat']='Depth/Time Series Plot'
titles['ts']='Time Series Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
else:
ans=raw_input(" S[a]ve to save plot, [q]uit without saving: ")
if ans=="a": pmagplotlib.saveP(FIG,files)
def main():
"""
NAME
magstrat_magic.py
DESCRIPTION
plots various parameters versus depth or age with optional time scale
SYNTAX
magstrat_magic.py [-h] [-i] [command line optins]
OPTIONS
-h prints help message and quits
-i allows interactive entry of options
-f FILE: specify input magic format file from magic,default='pmag_results.txt'
supported types=[pmag_specimens, pmag_samples, pmag_sites, pmag_results]
-X [age,pos]: specify whether age or stratigraphic position
-Y [dec,inc,int,lat,lon,vdm,vadm]
(lat and lon are VGP lat and lon)
-Iex: plot the expected inc at average_lat - only available for pmag_results
-ts TS: plot the GPTS for the time interval shown (only for age option)
TS: [ck95, gts04]
-mcd method_code, specify method code, default is first one encountered
NOTES
when X and/or Y are not specified, a list of possibilities will be presented to the user for choosing
"""
res_file='pmag_results.txt'
xaxis,xplotind,yplotind="",0,"" # (0 for strat pos)
yaxis=""
supported=['pmag_specimens', 'pmag_samples', 'pmag_sites', 'pmag_results','magic_web']
method,fignum="",1
plotexp,pTS=0,0
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
res_file=sys.argv[ind+1]
if '-X' in sys.argv:
ind=sys.argv.index('-X')
xaxis=sys.argv[ind+1]
if '-Y' in sys.argv:
ind=sys.argv.index('-Y')
yaxis=sys.argv[ind+1]
if '-mcd' in sys.argv:
ind=sys.argv.index('-mcd')
method=sys.argv[ind+1]
if '-ts' in sys.argv:
ind=sys.argv.index('-ts')
ts=sys.argv[ind+1]
pTS=1
if xaxis=='pos':
print "Time scale option for age only, time scale will not be plotted"
pTS=0
if '-Iex' in sys.argv: plotexp=1
if '-i' in sys.argv:
yaxis,xaxis=="",""
#
# get name of file from command line
#
res_file=raw_input("Input pmag_results file name? [pmag_results.txt] ")
if res_file=="":res_file="pmag_results.txt"
#
#
# get data read in
Results,file_type=pmag.magic_read(res_file)
if file_type not in supported:
print "Unsupported file type, try again"
sys.exit()
methcodes=[]
if "magic_method_codes" in Results[0].keys(): # need to know all the measurement types from method_codes
for rec in Results:
meths=rec["magic_method_codes"]
if meths not in methcodes: methcodes.append(meths.strip()) # look for the lab treatments
#
# initialize some variables
age_unit="" # Unit for age or depth plotting (meters if depth)
Xplots,Yplots,Xplotind,Yplotind=[],[],0,""
#
# step through possible file formats
#
if file_type=="pmag_results":
if "average_age" in Results[0].keys():
Xplots.append("average_age")
age_unit=Results[0]["average_age_unit"]
if "average_height" in Results[0].keys(): Xplots.append("average_height")
if plotexp==1:
if "average_lat" in Results[0].keys():
lat=float(Results[0]['average_lat'])
Xinc=[pmag.pinc(lat),-pmag.pinc(lat)]
else:
print 'can not plot expected inc for site - lat unknown'
if xaxis=="pos":
xplotind=Xplots.index("average_height")
else:
xplotind=Xplots.index("average_age")
if "average_dec" in Results[0].keys():Yplots.append("average_dec")
if "average_inc" in Results[0].keys():Yplots.append("average_inc")
if "average_int" in Results[0].keys():Yplots.append("average_int")
if "average_int_rel" in Results[0].keys():Yplots.append("average_int_rel")
if "vgp_lat" in Results[0].keys():Yplots.append("vgp_lat")
if "vgp_lon" in Results[0].keys():Yplots.append("vgp_lon")
if "vdm" in Results[0].keys():Yplots.append("vdm")
if "vadm" in Results[0].keys():Yplots.append("vadm")
if yaxis=="dec" and "average_dec" in Yplots:yplotind=Yplots.index("average_dec")
if yaxis=="inc" and "average_inc" in Yplots:yplotind=Yplots.index("average_inc")
if yaxis=="int" and "average_int_rel" in Yplots:yplotind=Yplots.index("average_int_rel")
if yaxis=="int" and "average_int" in Yplots:yplotind=Yplots.index("average_int")
if yaxis=="lat" and "vgp_lat" in Yplots:yplotind=Yplots.index("vgp_lat")
if yaxis=="lon" and "vgp_lon" in Yplots:yplotind=Yplots.index("vgp_lon")
if yaxis=="vdm" and "vdm" in Yplots:yplotind=Yplots.index("vdm")
if yaxis=="vadm" and "vadm" in Yplots:yplotind=Yplots.index("vadm")
if yplotind=="":
print 'your choice not available, but these are: '
print Yplots
sys.exit()
else:
xplotind,plotexp=0,0
if xaxis=="pos":
print "Only age available for these types of files - try pmag_results "
sys.exit()
if file_type=="pmag_sites":
if "site_inferred_age" in Results[0].keys():
Xplots.append("site_inferred_age")
age_unit=Results[0]["site_inferred_age_unit"]
if "site_dec" in Results[0].keys():Yplots.append("site_dec")
if "site_inc" in Results[0].keys():Yplots.append("site_inc")
if "site_int" in Results[0].keys():Yplots.append("site_int")
if "site_int_rel" in Results[0].keys():Yplots.append("site_int_rel")
if yaxis=="dec" and "site_dec" in Yplots:yplotind=Yplots.index("site_dec")
if yaxis=="inc" and "site_inc" in Yplots:yplotind=Yplots.index("site_inc")
if yaxis=="int" and "site_int_rel" in Yplots:yplotind=Yplots.index("site_int_rel")
if yaxis=="int" and "site_int" in Yplots:yplotind=Yplots.index("site_int")
if file_type=="pmag_samples":
if "sample_inferred_age" in Results[0].keys():
Xplots.append("sample_inferred_age")
age_unit=Results[0]["sample_inferred_age_unit"]
if "sample_dec" in Results[0].keys():Yplots.append("sample_dec")
if "sample_inc" in Results[0].keys():Yplots.append("sample_inc")
if "sample_int" in Results[0].keys():Yplots.append("sample_int")
if "sample_int_rel" in Results[0].keys():Yplots.append("sample_int_rel")
if yaxis=="dec" and "sample_dec" in Yplots:yplotind=Yplots.index("sample_dec")
if yaxis=="inc" and "sample_inc" in Yplots:yplotind=Yplots.index("sample_inc")
if yaxis=="int" and "sample_int_rel" in Yplots:yplotind=Yplots.index("sample_int_rel")
if yaxis=="int" and "sample_int" in Yplots:yplotind=Yplots.index("sample_int")
if file_type=="pmag_specimens":
if "specimen_inferred_age" in Results[0].keys():
Xplots.append("specimen_inferred_age")
age_unit=Results[0]["specimen_inferred_age_unit"]
if "specimen_dec" in Results[0].keys():Yplots.append("specimen_dec")
if "specimen_inc" in Results[0].keys():Yplots.append("specimen_inc")
if "specimen_int" in Results[0].keys():Yplots.append("specimen_int")
if "specimen_int_rel" in Results[0].keys():Yplots.append("specimen_int_rel")
if yaxis=="dec" and "specimen_dec" in Yplots:yplotind=Yplots.index("specimen_dec")
if yaxis=="inc" and "specimen_inc" in Yplots:yplotind=Yplots.index("specimen_inc")
if yaxis=="int" and "specimen_int_rel" in Yplots:yplotind=Yplots.index("specimen_int_rel")
if yaxis=="int" and "specimen_int" in Yplots:yplotind=Yplots.index("specimen_int")
if yplotind=="":
print 'your choice not available, but these are: '
print Yplots
sys.exit()
#
# check if age or depth info
if len(Xplots)==0:
print "Must have either age or height info to plot "
sys.exit()
#
# check for variable to plot
#
if len(Yplots)==0:
print "Must have something to plot! "
sys.exit()
#
# determine X axis (age or depth)
#
if '-i' in sys.argv:
if len(Xplots)==2:
print "0: ",Xplots[0],"1: ",Xplots[1]
plotind=raw_input("Which type of plot [0]/1 " )
xplotind=int(plotind)
if xplotind==1:xaxis='age'
# inquire about which lab treatment step desired
method=methcodes[0]
if len(methcodes)>1:
print " There are several different experiments. "
print " Select type you want to plot. "
for k in range(len(methcodes)):
print methcodes[k], " [",k,"] "
ans=int(raw_input())
method=methcodes[ans]
# now get Y axis (whatever)
if len(Yplots)>1:
for yplotind in range(len(Yplots)):
print yplotind, Yplots[yplotind]
# if len(methcodes)>1: print "Be careful to select the one that goes with your lab treatment! "
yplotind=raw_input("Which type of plot [0] " )
if yplotind=="":yplotind=0
yplotind=int(yplotind)
else:
if xaxis=="age": plotind="1"
if method=="":method=methcodes[0]
if xaxis=='pos':
xlab="Stratigraphic Height (meters)"
else:
xlab="Age ("+age_unit+")"
Xkey=Xplots[xplotind]
Ykey=Yplots[yplotind]
ylab=Ykey
#
# collect the data for plotting
X,Y=[],[]
if float(Results[0][Xkey])/float(Results[-1][Xkey])>0 and float(Results[0][Xkey])<0:
isign=-1. # x axis all same signa and negative, take positive (e.g.,for depth in core)
xlab="Stratigraphic Depth (meters)"
else:
isign=1.
for rec in Results:
if "magic_method_codes" in rec.keys():
meths=rec["magic_method_codes"]
if method == meths: # make sure it is desired lab treatment step
X.append(isign*float(rec[Xkey]))
Y.append(float(rec[Ykey]))
elif method =="":
X.append(isign*float(rec[Xkey]))
Y.append(float(rec[Ykey]))
else:
print "Something wrong with your plotting choices"
break
data=[X,Y] # pack them up for shipping
title=""
if "er_locations_names" in Results[0].keys(): title=Results[0]["er_location_names"]
if "er_locations_name" in Results[0].keys(): title=Results[0]["er_location_name"]
labels=[xlab,ylab,title]
pmagplotlib.plotSTRAT(fignum,data,labels) # plot them
if plotexp==1: pmagplotlib.plotHs(fignum,Xinc,'b','--')
if yaxis=='inc' or yaxis=='lat':
pmagplotlib.plotHs(fignum,[0],'b','-')
pmagplotlib.plotHs(fignum,[-90,90],'g','-')
if pTS==1: pmagplotlib.plotTS(fignum+1,[X[0],X[-1]],ts)
raw_input()
def main():
"""
NAME
ODP_incplot.py
DESCRIPTION
plots various measurements versus core_depth
SYNTAX
ODP_incplot.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic_measurments format file from magic
-fsa FILE: specify input er_samples format file from magic
-AF step [in mT] to plot
-T step [in C] to plot
-d min max [in m] depth range to plot
-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
"""
method,fmt="LT-NO",'.svg'
step=0
pcol=3
plotexp,pTS=0,0
dir_path="./"
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
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')
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 '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
if '-AF' in sys.argv:
ind=sys.argv.index('-AF')
step=float(sys.argv[ind+1])*1e-3
method='LT-AF-Z'
if '-T' in sys.argv:
ind=sys.argv.index('-T')
step=float(sys.argv[ind+1])+273
method='LT-T-Z'
dmin,dmax=-1,1e6
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,pcol=1,4
if '-Iex' in sys.argv: plotexp=1
#
#
# get data read in
Meas,file_type=pmag.magic_read(meas_file)
Samps,file_type=pmag.magic_read(samp_file)
Data=[]
for rec in Meas:
for samp in Samps:
if samp['er_sample_name']== rec['er_sample_name'] and 'core_depth' in samp.keys() and samp['core_depth']!="":
rec['core_depth'] = samp['core_depth']
Data.append(rec) # fish out data with core_depth
if plotexp==1:
for lkey in Lat_keys:
for key in Results[0].keys():
if key==lkey:
lat=float(Results[0][lkey])
Xinc=[pmag.pinc(lat),-pmag.pinc(lat)]
break
if Xinc=="":
print 'can not plot expected inc for site - lat unknown'
xlab="Core Depth (m)"
# collect the data for plotting declination
XY=[]
maxInt=-1000
samples=[]
for rec in Data:
if "magic_method_codes" in rec.keys():
meths=rec["magic_method_codes"].split(":")
if method in meths: # make sure it is desired lab treatment step
if float(rec['core_depth'])<dmax and float(rec['core_depth'])>dmin and ('LT-AF-Z' in method and float(rec['treatment_ac_field'])==step) or ('LT-NO' in method and step == 0) or ('LT-T-Z' in method and float(rec['treatment_temp'])==step):
XY.append([float(rec['core_depth']),float(rec['measurement_inc'])])
if len(XY)>0 :
FIG={'strat':1,'ts':2}
pmagplotlib.plot_init(FIG['strat'],10,5)
labels=['Depth below sea floor (m)','Inclination','']
pmagplotlib.plotSTRAT(FIG['strat'],XY,labels)
if pTS==1:
pmagplotlib.plot_init(FIG['ts'],10,5)
pmagplotlib.plotTS(FIG['ts'],[amin,amax],ts)
else:
print "No data points met your criteria - try again"
sys.exit()
files,fmt={},'svg'
for key in FIG.keys():
files[key]=key+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
files={}
files['strat']=xaxis+'_'+yaxis+'_'+fmt
files['ts']='ts'+fmt
titles={}
titles['strat']='Depth/Time Series Plot'
titles['ts']='Time Series Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
else:
ans=raw_input(" S[a]ve to save plot, [q]uit without saving: ")
if ans=="a": pmagplotlib.saveP(FIG,files)
def main():
"""
NAME
Core_depthplot.py
DESCRIPTION
plots various measurements versus core_depth
SYNTAX
Core_depthplot.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic_measurments format file from magic
-fsa FILE: specify input er_samples format file from magic
-AF step [in mT] to plot
-T step [in C] to plot
-d min max [in m] depth range to plot
-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
"""
method,fmt="LT-NO",'.svg'
step=0
pcol=3
plotexp,pTS=0,0
dir_path="./"
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
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')
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 '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
if '-AF' in sys.argv:
ind=sys.argv.index('-AF')
step=float(sys.argv[ind+1])*1e-3
method='LT-AF-Z'
if '-T' in sys.argv:
ind=sys.argv.index('-T')
step=float(sys.argv[ind+1])+273
method='LT-T-Z'
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,pcol=1,4
if '-Iex' in sys.argv: plotexp=1
#
#
# get data read in
Meas,file_type=pmag.magic_read(meas_file)
Samps,file_type=pmag.magic_read(samp_file)
Data=[]
for rec in Meas:
for samp in Samps:
if samp['er_sample_name']== rec['er_sample_name'] and 'core_depth' in samp.keys() and samp['core_depth']!="":
rec['core_depth'] = samp['core_depth']
Data.append(rec) # fish out data with core_depth
if plotexp==1:
for lkey in Lat_keys:
for key in Results[0].keys():
if key==lkey:
lat=float(Results[0][lkey])
Xinc=[pmag.pinc(lat),-pmag.pinc(lat)]
break
if Xinc=="":
print 'can not plot expected inc for site - lat unknown'
xlab="Core Depth (m)"
# collect the data for plotting declination
Depths,Decs,Incs,Ints=[],[],[],[]
maxInt=-1000
samples=[]
for rec in Data:
if "magic_method_codes" in rec.keys():
meths=rec["magic_method_codes"].split(":")
if method in meths: # make sure it is desired lab treatment step
if ('LT-AF-Z' in method and float(rec['treatment_ac_field'])==step) or ('LT-NO' in method and step == 0) or ('LT-T-Z' in method and float(rec['treatment_temp'])==step):
Depths.append(float(rec['core_depth']))
Decs.append(float(rec['measurement_dec']))
Incs.append(float(rec['measurement_inc']))
Ints.append(float(rec['measurement_magn_moment']))
if len(Ints)>1 and Ints[-1]>maxInt:maxInt=Ints[-1]
if dmin==-1:
dmin,dmax=Depths[0],Depths[-1]
if len(Decs)>0 and len(Depths)>0:
for pow in range(-10,10):
if maxInt*10**pow>1:break
for k in range(len(Ints)):
Ints[k]=Ints[k]*10**pow
pylab.figure(1,figsize=(10,8))
pylab.subplot(1,pcol,1)
pylab.plot(Decs,Depths,'ro',Decs,Depths,'k')
pylab.axis([0,360,dmax,dmin])
pylab.xlabel('Declination')
pylab.ylabel('Depth in core (m)')
pylab.subplot(1,pcol,2)
pylab.plot(Incs,Depths,'bo',Incs,Depths,'k')
pylab.axis([-90,90,dmax,dmin])
pylab.xlabel('Inclination')
pylab.ylabel('')
pylab.subplot(1,pcol,3)
pylab.plot(Ints,Depths,'ko',Ints,Depths,'k')
pylab.axis([0,maxInt*10**pow+.1,dmax,dmin])
pylab.xlabel('%s %i %s'%('Intensity (x 10^',pow,' Am^2)'))
if pTS==1:
pylab.subplot(1,pcol,4)
TS,Chrons=pmag.get_TS(ts)
p=1
X,Y=[],[]
for d in TS:
if d<=amax:
if 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)
pylab.plot(Y,X,'k')
pylab.axvline(x=0,ymin=amin,ymax=amax,linewidth=1,color='w',linestyle='-')
# pylab.axhline(y=1.1,xmin=0,xmax=1,linewidth=1,color='w',linestyle='-')
# pylab.axvline(y=-.1,xmin=0,xmax=1,linewidth=1,color='w',linestyle='-')
# pylab.xlabel("Age (Ma): "+ts)
isign=-1
for c in Chrons:
off=-.1
isign=-1*isign
if isign>0: off=1.05
if c[1]>=X[0] and c[1]<X[-1]:
pylab.text(c[1]-.2,off,c[0])
pylab.axis([-.25,1.25,amax,amin])
pylab.draw()
ans=raw_input("Press return to quit ")
sys.exit()
else:
print "No data points met your criteria - try again"
