def main():
"""
NAME
lowrie.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie -h [command line options]
INPUT
takes SIO formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
"""
fmt='svg'
FIG={} # plot dictionary
FIG['lowrie']=1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'],6,6)
norm=1 # default is to normalize by maximum axis
if len(sys.argv)>1:
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv: norm=0 # don't normalize
if '-f' in sys.argv: # sets input filename
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
else:
print main.__doc__
print 'you must supply a file name'
sys.exit()
else:
print main.__doc__
print 'you must supply a file name'
sys.exit()
data=open(in_file).readlines() # open the SIO format file
PmagRecs=[] # set up a list for the results
keys=['specimen','treatment','csd','M','dec','inc']
for line in data:
PmagRec={}
rec=line.replace('\n','').split()
for k in range(len(keys)):
PmagRec[keys[k]]=rec[k]
PmagRecs.append(PmagRec)
specs=pmag.get_dictkey(PmagRecs,'specimen','')
sids=[]
for spec in specs:
if spec not in sids:sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print spc
specdata=pmag.get_dictitem(PmagRecs,'specimen',spc,'T') # get all this one's data
DIMs,Temps=[],[]
for dat in specdata: # step through the data
DIMs.append([float(dat['dec']),float(dat['inc']),float(dat['M'])*1e-3])
Temps.append(float(dat['treatment']))
carts=pmag.dir2cart(DIMs).transpose()
#if norm==1: # want to normalize
# nrm=max(max(abs(carts[0])),max(abs(carts[1])),max(abs(carts[2]))) # by maximum of x,y,z values
# ylab="M/M_max"
if norm==1: # want to normalize
nrm=(DIMs[0][2]) # normalize by NRM
ylab="M/M_o"
else:
nrm=1. # don't normalize
ylab="Magnetic moment (Am^2)"
xlab="Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[0])/nrm,sym='r-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[0])/nrm,sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[1])/nrm,sym='c-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[1])/nrm,sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[2])/nrm,sym='k-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[2])/nrm,sym='k^',title=spc,xlab=xlab,ylab=ylab) # Z direction
pmagplotlib.drawFIGS(FIG)
ans=raw_input('S[a]ve figure? [q]uit, <return> to continue ')
if ans=='a':
files={'lowrie':'lowrie:_'+spc+'_.'+fmt}
pmagplotlib.saveP(FIG,files)
elif ans=='q':
sys.exit()
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
lowrie_magic.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie -h [command line options]
INPUT
takes magic_measurements formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is magic_measurements.txt
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
"""
fmt='svg'
FIG={} # plot dictionary
FIG['lowrie']=1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'],6,6)
norm=1 # default is to normalize by maximum axis
in_file,dir_path='magic_measurements.txt','.'
if len(sys.argv)>1:
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv: norm=0 # don't normalize
if '-f' in sys.argv: # sets input filename
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
else:
print main.__doc__
print 'you must supply a file name'
sys.exit()
in_file=dir_path+'/'+in_file
print in_file
PmagRecs,file_type=pmag.magic_read(in_file)
if file_type!="magic_measurements":
print 'bad input file'
sys.exit()
PmagRecs=pmag.get_dictitem(PmagRecs,'magic_method_codes','LP-IRM-3D','has') # get all 3D IRM records
if len(PmagRecs)==0:
print 'no records found'
sys.exit()
specs=pmag.get_dictkey(PmagRecs,'er_specimen_name','')
sids=[]
for spec in specs:
if spec not in sids:sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print spc
specdata=pmag.get_dictitem(PmagRecs,'er_specimen_name',spc,'T') # get all this one's data
DIMs,Temps=[],[]
for dat in specdata: # step through the data
DIMs.append([float(dat['measurement_dec']),float(dat['measurement_inc']),float(dat['measurement_magn_moment'])])
Temps.append(float(dat['treatment_temp'])-273.)
carts=pmag.dir2cart(DIMs).transpose()
if norm==1: # want to normalize
nrm=(DIMs[0][2]) # normalize by NRM
ylab="M/M_o"
else:
nrm=1. # don't normalize
ylab="Magnetic moment (Am^2)"
xlab="Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[0])/nrm,sym='r-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[0])/nrm,sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[1])/nrm,sym='c-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[1])/nrm,sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[2])/nrm,sym='k-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[2])/nrm,sym='k^',title=spc,xlab=xlab,ylab=ylab) # Z direction
pmagplotlib.drawFIGS(FIG)
ans=raw_input('S[a]ve figure? [q]uit, <return> to continue ')
if ans=='a':
files={'lowrie':'lowrie:_'+spc+'_.'+fmt}
pmagplotlib.saveP(FIG,files)
elif ans=='q':
sys.exit()
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
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"
def main():
"""
NAME
sites_locations.py
DESCRIPTION
reads in er_sites.txt file and finds all locations and bounds of locations
outputs er_locations.txt file
SYNTAX
sites_locations.py [command line options]
OPTIONS
-h prints help message and quits
-f: specimen input er_sites format file, default is "er_sites.txt"
-F: locations table: default is "er_locations.txt"
"""
# set defaults
site_file = "er_sites.txt"
loc_file = "er_locations.txt"
Names, user = [], "unknown"
Done = []
version_num = pmag.get_version()
args = sys.argv
dir_path = "."
# get command line stuff
if "-WD" in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-f" in args:
ind = args.index("-f")
site_file = args[ind + 1]
if "-F" in args:
ind = args.index("-F")
loc_file = args[ind + 1]
#
site_file = dir_path + "/" + site_file
loc_file = dir_path + "/" + loc_file
Sites, file_type = pmag.magic_read(site_file)
if file_type != "er_sites":
print file_type
print file_type, "This is not a valid er_sites file "
sys.exit()
# read in site data
#
LocNames, Locations = [], []
for site in Sites:
if site["er_location_name"] not in LocNames: # new location name
LocNames.append(site["er_location_name"])
sites_locs = pmag.get_dictitem(
Sites, "er_location_name", site["er_location_name"], "T"
) # get all sites for this loc
lats = pmag.get_dictkey(sites_locs, "site_lat", "f") # get all the latitudes as floats
lons = pmag.get_dictkey(sites_locs, "site_lon", "f") # get all the longitudes as floats
LocRec = {
"er_citation_names": "This study",
"er_location_name": site["er_location_name"],
"location_type": "",
}
LocRec["location_begin_lat"] = str(min(lats))
LocRec["location_end_lat"] = str(max(lats))
LocRec["location_begin_lon"] = str(min(lons))
LocRec["location_end_lon"] = str(max(lons))
Locations.append(LocRec)
if len(Locations) > 0:
pmag.magic_write(loc_file, Locations, "er_locations")
print "Locations written to: ", loc_file
def main():
"""
NAME
plot_mapPTS.py
DESCRIPTION
plots points on map
SYNTAX
plot_mapPTS.py [command line options]
OPTIONS
-h prints help and quits
-sym [ro, bs, g^, r., b-, etc.] [1,5,10] symbol and size for points
colors are r=red,b=blue,g=green, etc.
symbols are '.' for points, ^, for triangle, s for square, etc.
-, for lines, -- for dotted lines, see matplotlib online documentation for plot()
-eye ELAT ELON [specify eyeball location]
-etp put on topography
-f FILE, specify input file
-o color ocean blue/land green (default is not)
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-fmt [pdf,eps, png] specify output format (default is pdf)
-R don't plot details of rivers
-B don't plot national/state boundaries, etc.
-pad [LAT LON] pad bounding box by LAT/LON (default is not)
-grd SPACE specify grid spacing
-sav save plot and quit
-prj PROJ, specify one of the supported projections: (see basemap.py online documentation)
aeqd = Azimuthal Equidistant
poly = Polyconic
gnom = Gnomonic
moll = Mollweide
tmerc = Transverse Mercator
nplaea = North-Polar Lambert Azimuthal
mill = Miller Cylindrical
merc = Mercator
stere = Stereographic
npstere = North-Polar Stereographic
geos = Geostationary
laea = Lambert Azimuthal Equal Area
sinu = Sinusoidal
spstere = South-Polar Stereographic
lcc = Lambert Conformal
npaeqd = North-Polar Azimuthal Equidistant
eqdc = Equidistant Conic
cyl = Cylindrical Equidistant
omerc = Oblique Mercator
aea = Albers Equal Area
spaeqd = South-Polar Azimuthal Equidistant
ortho = Orthographic
cass= Cassini-Soldner
splaea = South-Polar Lambert Azimuthal
robin = Robinson
Special codes for MagIC formatted input files:
-n
-l
INPUTS
space or tab delimited LON LAT data
OR:
standard MagIC formatted er_sites or pmag_results table
DEFAULTS
res: c
prj: mollweide; lcc for MagIC format files
ELAT,ELON = 0,0
pad LAT,LON=0,0
NB: high resolution or lines can be very slow
"""
dir_path='.'
plot=0
ocean=0
res='c'
proj='moll'
Lats,Lons=[],[]
fmt='pdf'
sym='ro'
symsize=5
fancy=0
rivers,boundaries,ocean=1,1,0
latmin,latmax,lonmin,lonmax,lat_0,lon_0=-90,90,0.,360.,0.,0.
padlat,padlon,gridspace=0,0,30
lat_0,lon_0="",""
prn_name,prn_loc,names,locs=0,0,[],[]
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res=sys.argv[ind+1]
if res!= 'c' and res!='l':
print 'this resolution will take a while - be patient'
if '-etp' in sys.argv: fancy=1
if '-sav' in sys.argv: plot=1
if '-R' in sys.argv:rivers=0
if '-B' in sys.argv:boundaries=0
if '-o' in sys.argv:ocean=1
if '-grd' in sys.argv:
ind = sys.argv.index('-grd')
gridspace=float(sys.argv[ind+1])
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0=float(sys.argv[ind+1])
lon_0=float(sys.argv[ind+2])
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym=sys.argv[ind+1]
symsize=int(sys.argv[ind+2])
if '-pad' in sys.argv:
ind = sys.argv.index('-pad')
padlat=float(sys.argv[ind+1])
padlon=float(sys.argv[ind+2])
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file=dir_path+'/'+sys.argv[ind+1]
header=open(file,'rU').readlines()[0].split('\t')
if 'tab' in header[0]:
if '-n' in sys.argv:prn_name=1
if '-l' in sys.argv:prn_loc=1
proj='lcc'
if 'results' in header[1]:
latkey='average_lat'
lonkey='average_lon'
namekey='pmag_result_name'
lockey='er_location_names'
elif 'sites' in header[1]:
latkey='site_lat'
lonkey='site_lon'
namekey='er_site_name'
lockey='er_location_name'
else:
print 'file type not supported'
print main.__doc__
sys.exit()
Sites,file_type=pmag.magic_read(file)
Lats=pmag.get_dictkey(Sites,latkey,'f')
Lons=pmag.get_dictkey(Sites,lonkey,'f')
if prn_name==1:names=pmag.get_dictkey(Sites,namekey,'')
if prn_loc==1:names=pmag.get_dictkey(Sites,lockey,'')
else:
f=open(file,'rU')
ptdata=numpy.loadtxt(file)
Lons=ptdata.transpose()[0]
Lats=ptdata.transpose()[1]
latmin=numpy.min(Lats)-padlat
lonmin=numpy.min(Lons)-padlon
latmax=numpy.max(Lats)+padlat
lonmax=numpy.max(Lons)+padlon
if lon_0=="":
lon_0=0.5*(lonmin+lonmax)
lat_0=0.5*(latmin+latmax)
else:
print "input file must be specified"
sys.exit()
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj=sys.argv[ind+1]
FIG={'map':1}
pmagplotlib.plot_init(FIG['map'],6,6)
if res=='c':skip=8
if res=='l':skip=5
if res=='i':skip=2
if res=='h':skip=1
cnt=0
Opts={'latmin':latmin,'latmax':latmax,'lonmin':lonmin,'lonmax':lonmax,'lat_0':lat_0,'lon_0':lon_0,'proj':proj,'sym':sym,'symsize':3,'pltgrid':1,'res':res,'boundinglat':0.,'padlon':padlon,'padlat':padlat,'gridspace':gridspace}
Opts['details']={}
Opts['details']['coasts']=1
Opts['details']['rivers']=rivers
Opts['details']['states']=boundaries
Opts['details']['countries']=boundaries
Opts['details']['ocean']=ocean
Opts['details']['fancy']=fancy
if len(names)>0:Opts['names']=names
if len(locs)>0:Opts['loc_name']=locs
if proj=='merc':
Opts['latmin']=-70
Opts['latmax']=70
Opts['lonmin']=-180
Opts['lonmax']=180
print 'please wait to draw points'
Opts['sym']=sym
Opts['symsize']=symsize
pmagplotlib.plotMAP(FIG['map'],Lats,Lons,Opts)
files={}
for key in FIG.keys():
files[key]='Map_PTS'+'.'+fmt
if pmagplotlib.isServer or plot:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='PT Map'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
else:
pmagplotlib.drawFIGS(FIG)
ans=raw_input(" S[a]ve to save plot, Return to quit: ")
if ans=="a": pmagplotlib.saveP(FIG,files)
