def main():
"""
NAME
eqarea_magic.py
DESCRIPTION
makes equal area projections from declination/inclination data
SYNTAX
eqarea_magic.py [command line options]
INPUT
takes magic formatted sites, samples, specimens, or measurements
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file from magic, default='sites.txt'
supported types=[measurements, specimens, samples, sites]
-fsp FILE: specify specimen file name, (required if you want to plot measurements by sample)
default='specimens.txt'
-fsa FILE: specify sample file name, (required if you want to plot specimens by site)
default='samples.txt'
-fsi FILE: specify site file name, default='sites.txt'
-obj OBJ: specify level of plot [all, sit, sam, spc], default is all
-crd [s,g,t]: specify coordinate system, [s]pecimen, [g]eographic, [t]ilt adjusted
default is geographic, unspecified assumed geographic
-fmt [svg,png,jpg] format for output plots
-ell [F,K,B,Be,Bv] plot Fisher, Kent, Bingham, Bootstrap ellipses or Boostrap eigenvectors
-c plot as colour contour
-sav save plot and quit quietly
NOTE
all: entire file; sit: site; sam: sample; spc: specimen
"""
# initialize some default variables
FIG = {} # plot dictionary
FIG['eqarea'] = 1 # eqarea is figure 1
plotE = 0
plt = 0 # default to not plotting
verbose = pmagplotlib.verbose
# extract arguments from sys.argv
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg_from_sys("-WD", default_val=".")
pmagplotlib.plot_init(FIG['eqarea'],5,5)
in_file = pmag.get_named_arg_from_sys("-f", default_val="sites.txt")
in_file = pmag.resolve_file_name(in_file, dir_path)
if "-WD" not in sys.argv:
dir_path = os.path.split(in_file)[0]
#full_in_file = os.path.join(dir_path, in_file)
plot_by = pmag.get_named_arg_from_sys("-obj", default_val="all").lower()
spec_file = pmag.get_named_arg_from_sys("-fsp", default_val="specimens.txt")
samp_file = pmag.get_named_arg_from_sys("-fsa", default_val="samples.txt")
site_file = pmag.get_named_arg_from_sys("-fsi", default_val="sites.txt")
if plot_by == 'all':
plot_key = 'all'
elif plot_by == 'sit':
plot_key = 'site'
elif plot_by == 'sam':
plot_key = 'sample'
elif plot_by == 'spc':
plot_key = 'specimen'
else:
plot_by = 'all'
plot_key = 'all'
if '-c' in sys.argv:
contour = 1
else:
contour = 0
if '-sav' in sys.argv:
plt = 1
verbose = 0
if '-ell' in sys.argv:
plotE = 1
ind = sys.argv.index('-ell')
ell_type = sys.argv[ind+1]
ell_type = pmag.get_named_arg_from_sys("-ell", "F")
dist = ell_type.upper()
# if dist type is unrecognized, use Fisher
if dist not in ['F', 'K', 'B', 'BE', 'BV']:
dist = 'F'
if dist == "BV":
FIG['bdirs'] = 2
pmagplotlib.plot_init(FIG['bdirs'],5,5)
crd = pmag.get_named_arg_from_sys("-crd", default_val="g")
if crd == "s":
coord = "-1"
elif crd == "t":
coord = "100"
else:
coord = "0"
fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
dec_key = 'dir_dec'
inc_key = 'dir_inc'
tilt_key = 'dir_tilt_correction'
#Dir_type_keys=['','site_direction_type','sample_direction_type','specimen_direction_type']
#
fnames = {"specimens": spec_file, "samples": samp_file, 'sites': site_file}
contribution = nb.Contribution(dir_path, custom_filenames=fnames,
single_file=in_file)
try:
contribution.propagate_location_to_samples()
contribution.propagate_location_to_specimens()
contribution.propagate_location_to_measurements()
except KeyError as ex:
pass
# the object that contains the DataFrame + useful helper methods:
table_name = list(contribution.tables.keys())[0]
data_container = contribution.tables[table_name]
# the actual DataFrame:
data = data_container.df
if plot_key != "all" and plot_key not in data.columns:
print("-E- You can't plot by {} with the data provided".format(plot_key))
return
# add tilt key into DataFrame columns if it isn't there already
if tilt_key not in data.columns:
data.loc[:, tilt_key] = None
if verbose:
print(len(data), ' records read from ', in_file)
# find desired dec,inc data:
dir_type_key = ''
#
# get plotlist if not plotting all records
#
plotlist=[]
if plot_key != "all":
# return all where plot_key is not blank
if plot_key not in data.columns:
print('Can\'t plot by "{}". That header is not in infile: {}'.format(plot_key, in_file))
return
plots = data[data[plot_key].notnull()]
plotlist = plots[plot_key].unique() # grab unique values
else:
plotlist.append('All')
for plot in plotlist:
if verbose:
print(plot)
if plot == 'All':
# plot everything at once
plot_data = data
else:
# pull out only partial data
plot_data = data[data[plot_key] == plot]
DIblock = []
GCblock = []
# SLblock, SPblock = [], []
title = plot
mode = 1
k = 0
if dec_key not in plot_data.columns:
print("-W- No dec/inc data")
continue
# get all records where dec & inc values exist
plot_data = plot_data[plot_data[dec_key].notnull() & plot_data[inc_key].notnull()]
if plot_data.empty:
continue
# this sorting out is done in get_di_bock
#if coord == '0': # geographic, use records with no tilt key (or tilt_key 0)
# cond1 = plot_data[tilt_key].fillna('') == coord
# cond2 = plot_data[tilt_key].isnull()
# plot_data = plot_data[cond1 | cond2]
#else: # not geographic coordinates, use only records with correct tilt_key
# plot_data = plot_data[plot_data[tilt_key] == coord]
# get metadata for naming the plot file
locations = data_container.get_name('location', df_slice=plot_data)
site = data_container.get_name('site', df_slice=plot_data)
sample = data_container.get_name('sample', df_slice=plot_data)
specimen = data_container.get_name('specimen', df_slice=plot_data)
# make sure method_codes is in plot_data
if 'method_codes' not in plot_data.columns:
plot_data['method_codes'] = ''
# get data blocks
DIblock = data_container.get_di_block(df_slice=plot_data,
tilt_corr=coord, excl=['DE-BFP'])
#SLblock = [[ind, row['method_codes']] for ind, row in plot_data.iterrows()]
# get great circles
great_circle_data = data_container.get_records_for_code('DE-BFP', incl=True,
use_slice=True, sli=plot_data)
if len(great_circle_data) > 0:
gc_cond = great_circle_data[tilt_key] == coord
GCblock = [[float(row[dec_key]), float(row[inc_key])] for ind, row in great_circle_data[gc_cond].iterrows()]
#SPblock = [[ind, row['method_codes']] for ind, row in great_circle_data[gc_cond].iterrows()]
if len(DIblock) > 0:
if contour == 0:
pmagplotlib.plotEQ(FIG['eqarea'], DIblock, title)
else:
pmagplotlib.plotEQcont(FIG['eqarea'], DIblock)
else:
pmagplotlib.plotNET(FIG['eqarea'])
if len(GCblock)>0:
for rec in GCblock:
pmagplotlib.plotC(FIG['eqarea'], rec, 90., 'g')
if len(DIblock) == 0 and len(GCblock) == 0:
if verbose:
print("no records for plotting")
continue
#sys.exit()
if plotE == 1:
ppars = pmag.doprinc(DIblock) # get principal directions
nDIs, rDIs, npars, rpars = [], [], [], []
for rec in DIblock:
angle=pmag.angle([rec[0],rec[1]],[ppars['dec'],ppars['inc']])
if angle>90.:
rDIs.append(rec)
else:
nDIs.append(rec)
if dist=='B': # do on whole dataset
etitle="Bingham confidence ellipse"
bpars=pmag.dobingham(DIblock)
for key in list(bpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(bpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(bpars[key]))
npars.append(bpars['dec'])
npars.append(bpars['inc'])
npars.append(bpars['Zeta'])
npars.append(bpars['Zdec'])
npars.append(bpars['Zinc'])
npars.append(bpars['Eta'])
npars.append(bpars['Edec'])
npars.append(bpars['Einc'])
if dist=='F':
etitle="Fisher confidence cone"
if len(nDIs)>2:
fpars=pmag.fisher_mean(nDIs)
for key in list(fpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(fpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(fpars[key]))
mode+=1
npars.append(fpars['dec'])
npars.append(fpars['inc'])
npars.append(fpars['alpha95']) # Beta
npars.append(fpars['dec'])
isign=old_div(abs(fpars['inc']),fpars['inc'])
npars.append(fpars['inc']-isign*90.) #Beta inc
npars.append(fpars['alpha95']) # gamma
npars.append(fpars['dec']+90.) # Beta dec
npars.append(0.) #Beta inc
if len(rDIs)>2:
fpars=pmag.fisher_mean(rDIs)
if verbose: print("mode ",mode)
for key in list(fpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(fpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(fpars[key]))
mode+=1
rpars.append(fpars['dec'])
rpars.append(fpars['inc'])
rpars.append(fpars['alpha95']) # Beta
rpars.append(fpars['dec'])
isign=old_div(abs(fpars['inc']),fpars['inc'])
rpars.append(fpars['inc']-isign*90.) #Beta inc
rpars.append(fpars['alpha95']) # gamma
rpars.append(fpars['dec']+90.) # Beta dec
rpars.append(0.) #Beta inc
if dist=='K':
etitle="Kent confidence ellipse"
if len(nDIs)>3:
kpars=pmag.dokent(nDIs,len(nDIs))
if verbose: print("mode ",mode)
for key in list(kpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(kpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(kpars[key]))
mode+=1
npars.append(kpars['dec'])
npars.append(kpars['inc'])
npars.append(kpars['Zeta'])
npars.append(kpars['Zdec'])
npars.append(kpars['Zinc'])
npars.append(kpars['Eta'])
npars.append(kpars['Edec'])
npars.append(kpars['Einc'])
if len(rDIs)>3:
kpars=pmag.dokent(rDIs,len(rDIs))
if verbose: print("mode ",mode)
for key in list(kpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(kpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(kpars[key]))
mode+=1
rpars.append(kpars['dec'])
rpars.append(kpars['inc'])
rpars.append(kpars['Zeta'])
rpars.append(kpars['Zdec'])
rpars.append(kpars['Zinc'])
rpars.append(kpars['Eta'])
rpars.append(kpars['Edec'])
rpars.append(kpars['Einc'])
else: # assume bootstrap
if dist=='BE':
if len(nDIs)>5:
BnDIs=pmag.di_boot(nDIs)
Bkpars=pmag.dokent(BnDIs,1.)
if verbose: print("mode ",mode)
for key in list(Bkpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(Bkpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(Bkpars[key]))
mode+=1
npars.append(Bkpars['dec'])
npars.append(Bkpars['inc'])
npars.append(Bkpars['Zeta'])
npars.append(Bkpars['Zdec'])
npars.append(Bkpars['Zinc'])
npars.append(Bkpars['Eta'])
npars.append(Bkpars['Edec'])
npars.append(Bkpars['Einc'])
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
Bkpars=pmag.dokent(BrDIs,1.)
if verbose: print("mode ",mode)
for key in list(Bkpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(Bkpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(Bkpars[key]))
mode+=1
rpars.append(Bkpars['dec'])
rpars.append(Bkpars['inc'])
rpars.append(Bkpars['Zeta'])
rpars.append(Bkpars['Zdec'])
rpars.append(Bkpars['Zinc'])
rpars.append(Bkpars['Eta'])
rpars.append(Bkpars['Edec'])
rpars.append(Bkpars['Einc'])
etitle="Bootstrapped confidence ellipse"
elif dist=='BV':
sym={'lower':['o','c'],'upper':['o','g'],'size':3,'edgecolor':'face'}
if len(nDIs)>5:
BnDIs=pmag.di_boot(nDIs)
pmagplotlib.plotEQsym(FIG['bdirs'],BnDIs,'Bootstrapped Eigenvectors', sym)
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
if len(nDIs)>5: # plot on existing plots
pmagplotlib.plotDIsym(FIG['bdirs'],BrDIs,sym)
else:
pmagplotlib.plotEQ(FIG['bdirs'],BrDIs,'Bootstrapped Eigenvectors')
if dist=='B':
if len(nDIs)> 3 or len(rDIs)>3: pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],npars,0)
elif len(nDIs)>3 and dist!='BV':
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],npars,0)
if len(rDIs)>3:
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],rpars,0)
elif len(rDIs)>3 and dist!='BV':
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],rpars,0)
for key in list(FIG.keys()):
files = {}
filename = pmag.get_named_arg_from_sys('-fname')
if filename: # use provided filename
filename+= '.' + fmt
elif pmagplotlib.isServer: # use server plot naming convention
filename='LO:_'+locations+'_SI:_'+site+'_SA:_'+sample+'_SP:_'+specimen+'_CO:_'+crd+'_TY:_'+key+'_.'+fmt
elif plot_key == 'all':
filename = 'all'
if 'location' in plot_data.columns:
locs = plot_data['location'].unique()
loc_string = "_".join([loc.replace(' ', '_') for loc in locs])
filename += "_" + loc_string
filename += "_" + crd + "_" + key
filename += ".{}".format(fmt)
else: # use more readable naming convention
filename = ''
# fix this if plot_by is location , for example
use_names = {'location': [locations], 'site': [locations, site],
'sample': [locations, site, sample],
'specimen': [locations, site, sample, specimen]}
use = use_names[plot_key]
use.extend([crd, key])
for item in use: #[locations, site, sample, specimen, crd, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key]=filename
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='Equal Area Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
if plt:
pmagplotlib.saveP(FIG,files)
continue
if verbose:
pmagplotlib.drawFIGS(FIG)
ans=input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans == "q":
sys.exit()
if ans == "a":
pmagplotlib.saveP(FIG,files)
continue
def main():
"""
NAME
eqarea_magic.py
DESCRIPTION
makes equal area projections from declination/inclination data
SYNTAX
eqarea_magic.py [command line options]
INPUT
takes magic formatted sites, samples, specimens, or measurements
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file from magic, default='sites.txt'
supported types=[measurements, specimens, samples, sites]
-fsp FILE: specify specimen file name, (required if you want to plot measurements by sample)
default='specimens.txt'
-fsa FILE: specify sample file name, (required if you want to plot specimens by site)
default='samples.txt'
-fsi FILE: specify site file name, default='sites.txt'
-obj OBJ: specify level of plot [all, sit, sam, spc], default is all
-crd [s,g,t]: specify coordinate system, [s]pecimen, [g]eographic, [t]ilt adjusted
default is geographic, unspecified assumed geographic
-fmt [svg,png,jpg] format for output plots
-ell [F,K,B,Be,Bv] plot Fisher, Kent, Bingham, Bootstrap ellipses or Boostrap eigenvectors
-c plot as colour contour
-sav save plot and quit quietly
NOTE
all: entire file; sit: site; sam: sample; spc: specimen
"""
# initialize some default variables
FIG = {} # plot dictionary
FIG['eqarea'] = 1 # eqarea is figure 1
plotE = 0
plt = 0 # default to not plotting
verbose = pmagplotlib.verbose
# extract arguments from sys.argv
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg_from_sys("-WD", default_val=os.getcwd())
pmagplotlib.plot_init(FIG['eqarea'],5,5)
in_file = pmag.get_named_arg_from_sys("-f", default_val="sites.txt")
full_in_file = os.path.join(dir_path, in_file)
plot_by = pmag.get_named_arg_from_sys("-obj", default_val="all").lower()
spec_file = pmag.get_named_arg_from_sys("-fsp", default_val="specimens.txt")
samp_file = pmag.get_named_arg_from_sys("-fsa", default_val="samples.txt")
site_file = pmag.get_named_arg_from_sys("-fsi", default_val="sites.txt")
if plot_by == 'all':
plot_key = 'all'
elif plot_by == 'sit':
plot_key = 'site'
elif plot_by == 'sam':
plot_key = 'sample'
elif plot_by == 'spc':
plot_key = 'specimen'
else:
plot_key = 'all'
if '-c' in sys.argv:
contour = 1
else:
contour = 0
if '-sav' in sys.argv:
plt = 1
verbose = 0
if '-ell' in sys.argv:
plotE = 1
ind = sys.argv.index('-ell')
ell_type = sys.argv[ind+1]
ell_type = pmag.get_named_arg_from_sys("-ell", "F")
dist = ell_type.upper()
# if dist type is unrecognized, use Fisher
if dist not in ['F', 'K', 'B', 'BE', 'BV']:
dist = 'F'
if dist == "BV":
FIG['bdirs'] = 2
pmagplotlib.plot_init(FIG['bdirs'],5,5)
crd = pmag.get_named_arg_from_sys("-crd", default_val="g")
if crd == "s":
coord = "-1"
elif crd == "t":
coord = "100"
else:
coord = "0"
fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
dec_key = 'dir_dec'
inc_key = 'dir_inc'
tilt_key = 'dir_tilt_correction'
#Dir_type_keys=['','site_direction_type','sample_direction_type','specimen_direction_type']
#
fnames = {"specimens": spec_file, "samples": samp_file, 'sites': site_file}
contribution = nb.Contribution(dir_path, custom_filenames=fnames,
single_file=in_file)
# the object that contains the DataFrame + useful helper methods:
table_name = list(contribution.tables.keys())[0]
data_container = contribution.tables[table_name]
# the actual DataFrame:
data = data_container.df
# uses sample infile to add temporary site_name
# column to the specimen table
data_container = contribution.tables[table_name]
data = data_container.df
if (plot_key != "all") and (plot_key not in data.columns):
contribution.propagate_location_to_measurements()
contribution.propagate_location_to_specimens()
# add tilt key into DataFrame columns if it isn't there already
if tilt_key not in data.columns:
data.loc[:, tilt_key] = None
if verbose:
print(len(data), ' records read from ', in_file)
# find desired dec,inc data:
dir_type_key = ''
#
# get plotlist if not plotting all records
#
plotlist=[]
if plot_key != "all":
# return all where plot_key is not blank
if plot_key not in data.columns:
print('Can\'t plot by "{}". That header is not in infile: {}'.format(plot_key, in_file))
return
plots = data[data[plot_key].notnull()]
plotlist = plots[plot_key].unique() # grab unique values
else:
plotlist.append('All')
for plot in plotlist:
if verbose:
print(plot)
if plot == 'All':
# plot everything at once
plot_data = data
else:
# pull out only partial data
plot_data = data[data[plot_key] == plot]
DIblock = []
GCblock = []
# SLblock, SPblock = [], []
title = plot
mode = 1
k = 0
if dec_key not in plot_data.columns:
print("-W- No dec/inc data")
continue
# get all records where dec & inc values exist
plot_data = plot_data[plot_data[dec_key].notnull() & plot_data[inc_key].notnull()]
if plot_data.empty:
continue
# this sorting out is done in get_di_bock
#if coord == '0': # geographic, use records with no tilt key (or tilt_key 0)
# cond1 = plot_data[tilt_key].fillna('') == coord
# cond2 = plot_data[tilt_key].isnull()
# plot_data = plot_data[cond1 | cond2]
#else: # not geographic coordinates, use only records with correct tilt_key
# plot_data = plot_data[plot_data[tilt_key] == coord]
# get metadata for naming the plot file
locations = data_container.get_name('location', df_slice=plot_data)
site = data_container.get_name('site', df_slice=plot_data)
sample = data_container.get_name('sample', df_slice=plot_data)
specimen = data_container.get_name('specimen', df_slice=plot_data)
# make sure method_codes is in plot_data
if 'method_codes' not in plot_data.columns:
plot_data['method_codes'] = ''
# get data blocks
DIblock = data_container.get_di_block(df_slice=plot_data,
tilt_corr=coord, excl=['DE-BFP'])
#SLblock = [[ind, row['method_codes']] for ind, row in plot_data.iterrows()]
# get great circles
great_circle_data = data_container.get_records_for_code('DE-BFP', incl=True,
use_slice=True, sli=plot_data)
if len(great_circle_data) > 0:
gc_cond = great_circle_data[tilt_key] == coord
GCblock = [[float(row[dec_key]), float(row[inc_key])] for ind, row in great_circle_data[gc_cond].iterrows()]
#SPblock = [[ind, row['method_codes']] for ind, row in great_circle_data[gc_cond].iterrows()]
if len(DIblock) > 0:
if contour == 0:
pmagplotlib.plotEQ(FIG['eqarea'], DIblock, title)
else:
pmagplotlib.plotEQcont(FIG['eqarea'], DIblock)
else:
pmagplotlib.plotNET(FIG['eqarea'])
if len(GCblock)>0:
for rec in GCblock:
pmagplotlib.plotC(FIG['eqarea'], rec, 90., 'g')
if len(DIblock) == 0 and len(GCblock) == 0:
if verbose:
print("no records for plotting")
continue
#sys.exit()
if plotE == 1:
ppars = pmag.doprinc(DIblock) # get principal directions
nDIs, rDIs, npars, rpars = [], [], [], []
for rec in DIblock:
angle=pmag.angle([rec[0],rec[1]],[ppars['dec'],ppars['inc']])
if angle>90.:
rDIs.append(rec)
else:
nDIs.append(rec)
if dist=='B': # do on whole dataset
etitle="Bingham confidence ellipse"
bpars=pmag.dobingham(DIblock)
for key in list(bpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(bpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(bpars[key]))
npars.append(bpars['dec'])
npars.append(bpars['inc'])
npars.append(bpars['Zeta'])
npars.append(bpars['Zdec'])
npars.append(bpars['Zinc'])
npars.append(bpars['Eta'])
npars.append(bpars['Edec'])
npars.append(bpars['Einc'])
if dist=='F':
etitle="Fisher confidence cone"
if len(nDIs)>2:
fpars=pmag.fisher_mean(nDIs)
for key in list(fpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(fpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(fpars[key]))
mode+=1
npars.append(fpars['dec'])
npars.append(fpars['inc'])
npars.append(fpars['alpha95']) # Beta
npars.append(fpars['dec'])
isign=old_div(abs(fpars['inc']),fpars['inc'])
npars.append(fpars['inc']-isign*90.) #Beta inc
npars.append(fpars['alpha95']) # gamma
npars.append(fpars['dec']+90.) # Beta dec
npars.append(0.) #Beta inc
if len(rDIs)>2:
fpars=pmag.fisher_mean(rDIs)
if verbose: print("mode ",mode)
for key in list(fpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(fpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(fpars[key]))
mode+=1
rpars.append(fpars['dec'])
rpars.append(fpars['inc'])
rpars.append(fpars['alpha95']) # Beta
rpars.append(fpars['dec'])
isign=old_div(abs(fpars['inc']),fpars['inc'])
rpars.append(fpars['inc']-isign*90.) #Beta inc
rpars.append(fpars['alpha95']) # gamma
rpars.append(fpars['dec']+90.) # Beta dec
rpars.append(0.) #Beta inc
if dist=='K':
etitle="Kent confidence ellipse"
if len(nDIs)>3:
kpars=pmag.dokent(nDIs,len(nDIs))
if verbose: print("mode ",mode)
for key in list(kpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(kpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(kpars[key]))
mode+=1
npars.append(kpars['dec'])
npars.append(kpars['inc'])
npars.append(kpars['Zeta'])
npars.append(kpars['Zdec'])
npars.append(kpars['Zinc'])
npars.append(kpars['Eta'])
npars.append(kpars['Edec'])
npars.append(kpars['Einc'])
if len(rDIs)>3:
kpars=pmag.dokent(rDIs,len(rDIs))
if verbose: print("mode ",mode)
for key in list(kpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(kpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(kpars[key]))
mode+=1
rpars.append(kpars['dec'])
rpars.append(kpars['inc'])
rpars.append(kpars['Zeta'])
rpars.append(kpars['Zdec'])
rpars.append(kpars['Zinc'])
rpars.append(kpars['Eta'])
rpars.append(kpars['Edec'])
rpars.append(kpars['Einc'])
else: # assume bootstrap
if dist=='BE':
if len(nDIs)>5:
BnDIs=pmag.di_boot(nDIs)
Bkpars=pmag.dokent(BnDIs,1.)
if verbose: print("mode ",mode)
for key in list(Bkpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(Bkpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(Bkpars[key]))
mode+=1
npars.append(Bkpars['dec'])
npars.append(Bkpars['inc'])
npars.append(Bkpars['Zeta'])
npars.append(Bkpars['Zdec'])
npars.append(Bkpars['Zinc'])
npars.append(Bkpars['Eta'])
npars.append(Bkpars['Edec'])
npars.append(Bkpars['Einc'])
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
Bkpars=pmag.dokent(BrDIs,1.)
if verbose: print("mode ",mode)
for key in list(Bkpars.keys()):
if key!='n' and verbose: print(" ",key, '%7.1f'%(Bkpars[key]))
if key=='n' and verbose: print(" ",key, ' %i'%(Bkpars[key]))
mode+=1
rpars.append(Bkpars['dec'])
rpars.append(Bkpars['inc'])
rpars.append(Bkpars['Zeta'])
rpars.append(Bkpars['Zdec'])
rpars.append(Bkpars['Zinc'])
rpars.append(Bkpars['Eta'])
rpars.append(Bkpars['Edec'])
rpars.append(Bkpars['Einc'])
etitle="Bootstrapped confidence ellipse"
elif dist=='BV':
sym={'lower':['o','c'],'upper':['o','g'],'size':3,'edgecolor':'face'}
if len(nDIs)>5:
BnDIs=pmag.di_boot(nDIs)
pmagplotlib.plotEQsym(FIG['bdirs'],BnDIs,'Bootstrapped Eigenvectors', sym)
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
if len(nDIs)>5: # plot on existing plots
pmagplotlib.plotDIsym(FIG['bdirs'],BrDIs,sym)
else:
pmagplotlib.plotEQ(FIG['bdirs'],BrDIs,'Bootstrapped Eigenvectors')
if dist=='B':
if len(nDIs)> 3 or len(rDIs)>3: pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],npars,0)
elif len(nDIs)>3 and dist!='BV':
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],npars,0)
if len(rDIs)>3:
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],rpars,0)
elif len(rDIs)>3 and dist!='BV':
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],rpars,0)
for key in list(FIG.keys()):
files = {}
filename = pmag.get_named_arg_from_sys('-fname')
if filename: # use provided filename
filename+= '.' + fmt
elif pmagplotlib.isServer: # use server plot naming convention
filename='LO:_'+locations+'_SI:_'+site+'_SA:_'+sample+'_SP:_'+specimen+'_CO:_'+crd+'_TY:_'+key+'_.'+fmt
else: # use more readable naming convention
filename = ''
for item in [locations, site, sample, specimen, crd, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key]=filename
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='Equal Area Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
if plt:
pmagplotlib.saveP(FIG,files)
continue
if verbose:
pmagplotlib.drawFIGS(FIG)
ans=input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans == "q":
sys.exit()
if ans == "a":
pmagplotlib.saveP(FIG,files)
continue
def main():
"""
NAME
aniso_magic.py
DESCRIPTION
plots anisotropy data with either bootstrap or hext ellipses
SYNTAX
aniso_magic.py [-h] [command line options]
OPTIONS
-h plots help message and quits
-usr USER: set the user name
-f AFILE, specify rmag_anisotropy formatted file for input
-F RFILE, specify rmag_results formatted file for output
-x Hext [1963] and bootstrap
-B DON'T do bootstrap, do Hext
-par Tauxe [1998] parametric bootstrap
-v plot bootstrap eigenvectors instead of ellipses
-sit plot by site instead of entire file
-crd [s,g,t] coordinate system, default is specimen (g=geographic, t=tilt corrected)
-P don't make any plots - just make rmag_results table
-sav don't make the rmag_results table - just save all the plots
-fmt [svg, jpg, eps] format for output images, pdf default
-gtc DEC INC dec,inc of pole to great circle [down(up) in green (cyan)
-d Vi DEC INC; Vi (1,2,3) to compare to direction DEC INC
-nb N; specifies the number of bootstraps - default is 1000
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
plot bootstrap ellipses of Constable & Tauxe [1987]
NOTES
minor axis: circles
major axis: triangles
principal axis: squares
directions are plotted on the lower hemisphere
for bootstrapped eigenvector components: Xs: blue, Ys: red, Zs: black
"""
#
dir_path = "."
version_num = pmag.get_version()
verbose = pmagplotlib.verbose
args = sys.argv
ipar, ihext, ivec, iboot, imeas, isite, iplot, vec = 0, 0, 0, 1, 1, 0, 1, 0
hpars, bpars, PDir = [], [], []
CS, crd = '-1', 's'
nb = 1000
fmt = 'pdf'
ResRecs = []
orlist = []
outfile, comp, Dir, gtcirc, PDir = 'rmag_results.txt', 0, [], 0, []
infile = 'rmag_anisotropy.txt'
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind + 1]
if '-nb' in args:
ind = args.index('-nb')
nb = int(args[ind + 1])
if '-usr' in args:
ind = args.index('-usr')
user = args[ind + 1]
else:
user = ""
if '-B' in args: iboot, ihext = 0, 1
if '-par' in args: ipar = 1
if '-x' in args: ihext = 1
if '-v' in args: ivec = 1
if '-sit' in args: isite = 1
if '-P' in args: iplot = 0
if '-f' in args:
ind = args.index('-f')
infile = args[ind + 1]
if '-F' in args:
ind = args.index('-F')
outfile = args[ind + 1]
if '-crd' in sys.argv:
ind = sys.argv.index('-crd')
crd = sys.argv[ind + 1]
if crd == 'g': CS = '0'
if crd == 't': CS = '100'
if '-fmt' in args:
ind = args.index('-fmt')
fmt = args[ind + 1]
if '-sav' in args:
plots = 1
verbose = 0
else:
plots = 0
if '-gtc' in args:
ind = args.index('-gtc')
d, i = float(args[ind + 1]), float(args[ind + 2])
PDir.append(d)
PDir.append(i)
if '-d' in args:
comp = 1
ind = args.index('-d')
vec = int(args[ind + 1]) - 1
Dir = [float(args[ind + 2]), float(args[ind + 3])]
#
# set up plots
#
if infile[0] != '/': infile = dir_path + '/' + infile
if outfile[0] != '/': outfile = dir_path + '/' + outfile
ANIS = {}
initcdf, inittcdf = 0, 0
ANIS['data'], ANIS['conf'] = 1, 2
if iboot == 1:
ANIS['tcdf'] = 3
if iplot == 1:
inittcdf = 1
pmagplotlib.plot_init(ANIS['tcdf'], 5, 5)
if comp == 1 and iplot == 1:
initcdf = 1
ANIS['vxcdf'], ANIS['vycdf'], ANIS['vzcdf'] = 4, 5, 6
pmagplotlib.plot_init(ANIS['vxcdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vycdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vzcdf'], 5, 5)
if iplot == 1:
pmagplotlib.plot_init(ANIS['conf'], 5, 5)
pmagplotlib.plot_init(ANIS['data'], 5, 5)
# read in the data
data, ifiletype = pmag.magic_read(infile)
for rec in data: # find all the orientation systems
if 'anisotropy_tilt_correction' not in rec.keys():
rec['anisotropy_tilt_correction'] = '-1'
if rec['anisotropy_tilt_correction'] not in orlist:
orlist.append(rec['anisotropy_tilt_correction'])
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = '-1'
if CS == '-1': crd = 's'
if CS == '0': crd = 'g'
if CS == '100': crd = 't'
if verbose:
print("desired coordinate system not available, using available: ",
crd)
if isite == 1:
sitelist = []
for rec in data:
if rec['er_site_name'] not in sitelist:
sitelist.append(rec['er_site_name'])
sitelist.sort()
plt = len(sitelist)
else:
plt = 1
k = 0
while k < plt:
site = ""
sdata, Ss = [], [] # list of S format data
Locs, Sites, Samples, Specimens, Cits = [], [], [], [], []
if isite == 0:
sdata = data
else:
site = sitelist[k]
for rec in data:
if rec['er_site_name'] == site: sdata.append(rec)
anitypes = []
csrecs = pmag.get_dictitem(sdata, 'anisotropy_tilt_correction', CS,
'T')
for rec in csrecs:
if rec['anisotropy_type'] not in anitypes:
anitypes.append(rec['anisotropy_type'])
if rec['er_location_name'] not in Locs:
Locs.append(rec['er_location_name'])
if rec['er_site_name'] not in Sites:
Sites.append(rec['er_site_name'])
if rec['er_sample_name'] not in Samples:
Samples.append(rec['er_sample_name'])
if rec['er_specimen_name'] not in Specimens:
Specimens.append(rec['er_specimen_name'])
if rec['er_citation_names'] not in Cits:
Cits.append(rec['er_citation_names'])
s = []
s.append(float(rec["anisotropy_s1"]))
s.append(float(rec["anisotropy_s2"]))
s.append(float(rec["anisotropy_s3"]))
s.append(float(rec["anisotropy_s4"]))
s.append(float(rec["anisotropy_s5"]))
s.append(float(rec["anisotropy_s6"]))
if s[0] <= 1.0: Ss.append(s) # protect against crap
#tau,Vdirs=pmag.doseigs(s)
ResRec = {}
ResRec['er_location_names'] = rec['er_location_name']
ResRec['er_citation_names'] = rec['er_citation_names']
ResRec['er_site_names'] = rec['er_site_name']
ResRec['er_sample_names'] = rec['er_sample_name']
ResRec['er_specimen_names'] = rec['er_specimen_name']
ResRec['rmag_result_name'] = rec['er_specimen_name'] + ":" + rec[
'anisotropy_type']
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
ResRec["anisotropy_type"] = rec['anisotropy_type']
if "anisotropy_n" not in rec.keys(): rec["anisotropy_n"] = "6"
if "anisotropy_sigma" not in rec.keys():
rec["anisotropy_sigma"] = "0"
fpars = pmag.dohext(
int(rec["anisotropy_n"]) - 6, float(rec["anisotropy_sigma"]),
s)
ResRec["anisotropy_v1_dec"] = '%7.1f' % (fpars['v1_dec'])
ResRec["anisotropy_v2_dec"] = '%7.1f' % (fpars['v2_dec'])
ResRec["anisotropy_v3_dec"] = '%7.1f' % (fpars['v3_dec'])
ResRec["anisotropy_v1_inc"] = '%7.1f' % (fpars['v1_inc'])
ResRec["anisotropy_v2_inc"] = '%7.1f' % (fpars['v2_inc'])
ResRec["anisotropy_v3_inc"] = '%7.1f' % (fpars['v3_inc'])
ResRec["anisotropy_t1"] = '%10.8f' % (fpars['t1'])
ResRec["anisotropy_t2"] = '%10.8f' % (fpars['t2'])
ResRec["anisotropy_t3"] = '%10.8f' % (fpars['t3'])
ResRec["anisotropy_ftest"] = '%10.3f' % (fpars['F'])
ResRec["anisotropy_ftest12"] = '%10.3f' % (fpars['F12'])
ResRec["anisotropy_ftest23"] = '%10.3f' % (fpars['F23'])
ResRec["result_description"] = 'F_crit: ' + fpars[
'F_crit'] + '; F12,F23_crit: ' + fpars['F12_crit']
ResRec['anisotropy_type'] = pmag.makelist(anitypes)
ResRecs.append(ResRec)
if len(Ss) > 1:
if pmagplotlib.isServer:
title = "LO:_" + ResRec[
'er_location_names'] + '_SI:_' + site + '_SA:__SP:__CO:_' + crd
else:
title = ResRec['er_location_names']
if site:
title += "_{}".format(site)
title += '_{}'.format(crd)
ResRec['er_location_names'] = pmag.makelist(Locs)
bpars, hpars = pmagplotlib.plotANIS(ANIS, Ss, iboot, ihext, ivec,
ipar, title, iplot, comp, vec,
Dir, nb)
if len(PDir) > 0:
pmagplotlib.plotC(ANIS['data'], PDir, 90., 'g')
pmagplotlib.plotC(ANIS['conf'], PDir, 90., 'g')
if verbose and plots == 0: pmagplotlib.drawFIGS(ANIS)
ResRec['er_location_names'] = pmag.makelist(Locs)
if plots == 1:
save(ANIS, fmt, title)
ResRec = {}
ResRec['er_citation_names'] = pmag.makelist(Cits)
ResRec['er_location_names'] = pmag.makelist(Locs)
ResRec['er_site_names'] = pmag.makelist(Sites)
ResRec['er_sample_names'] = pmag.makelist(Samples)
ResRec['er_specimen_names'] = pmag.makelist(Specimens)
ResRec['rmag_result_name'] = pmag.makelist(
Sites) + ":" + pmag.makelist(anitypes)
ResRec['anisotropy_type'] = pmag.makelist(anitypes)
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
if isite == "0":
ResRec[
'result_description'] = "Study average using coordinate system: " + CS
if isite == "1":
ResRec[
'result_description'] = "Site average using coordinate system: " + CS
if hpars != [] and ihext == 1:
HextRec = {}
for key in ResRec.keys():
HextRec[key] = ResRec[key] # copy over stuff
HextRec["anisotropy_v1_dec"] = '%7.1f' % (hpars["v1_dec"])
HextRec["anisotropy_v2_dec"] = '%7.1f' % (hpars["v2_dec"])
HextRec["anisotropy_v3_dec"] = '%7.1f' % (hpars["v3_dec"])
HextRec["anisotropy_v1_inc"] = '%7.1f' % (hpars["v1_inc"])
HextRec["anisotropy_v2_inc"] = '%7.1f' % (hpars["v2_inc"])
HextRec["anisotropy_v3_inc"] = '%7.1f' % (hpars["v3_inc"])
HextRec["anisotropy_t1"] = '%10.8f' % (hpars["t1"])
HextRec["anisotropy_t2"] = '%10.8f' % (hpars["t2"])
HextRec["anisotropy_t3"] = '%10.8f' % (hpars["t3"])
HextRec["anisotropy_hext_F"] = '%7.1f ' % (hpars["F"])
HextRec["anisotropy_hext_F12"] = '%7.1f ' % (hpars["F12"])
HextRec["anisotropy_hext_F23"] = '%7.1f ' % (hpars["F23"])
HextRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v1_eta_dec"] = '%7.1f ' % (hpars["v2_dec"])
HextRec["anisotropy_v1_eta_inc"] = '%7.1f ' % (hpars["v2_inc"])
HextRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % (
hpars["e13"])
HextRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % (
hpars["v3_dec"])
HextRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % (
hpars["v3_inc"])
HextRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v2_eta_dec"] = '%7.1f ' % (hpars["v1_dec"])
HextRec["anisotropy_v2_eta_inc"] = '%7.1f ' % (hpars["v1_inc"])
HextRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % (
hpars["e23"])
HextRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % (
hpars["v3_dec"])
HextRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % (
hpars["v3_inc"])
HextRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v3_eta_dec"] = '%7.1f ' % (hpars["v1_dec"])
HextRec["anisotropy_v3_eta_inc"] = '%7.1f ' % (hpars["v1_inc"])
HextRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % (
hpars["e23"])
HextRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % (
hpars["v2_dec"])
HextRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % (
hpars["v2_inc"])
HextRec["magic_method_codes"] = 'LP-AN:AE-H'
if verbose:
print("Hext Statistics: ")
print(
" tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
)
print(HextRec["anisotropy_t1"],
HextRec["anisotropy_v1_dec"],
HextRec["anisotropy_v1_inc"],
HextRec["anisotropy_v1_eta_semi_angle"],
HextRec["anisotropy_v1_eta_dec"],
HextRec["anisotropy_v1_eta_inc"],
HextRec["anisotropy_v1_zeta_semi_angle"],
HextRec["anisotropy_v1_zeta_dec"],
HextRec["anisotropy_v1_zeta_inc"])
print(HextRec["anisotropy_t2"],
HextRec["anisotropy_v2_dec"],
HextRec["anisotropy_v2_inc"],
HextRec["anisotropy_v2_eta_semi_angle"],
HextRec["anisotropy_v2_eta_dec"],
HextRec["anisotropy_v2_eta_inc"],
HextRec["anisotropy_v2_zeta_semi_angle"],
HextRec["anisotropy_v2_zeta_dec"],
HextRec["anisotropy_v2_zeta_inc"])
print(HextRec["anisotropy_t3"],
HextRec["anisotropy_v3_dec"],
HextRec["anisotropy_v3_inc"],
HextRec["anisotropy_v3_eta_semi_angle"],
HextRec["anisotropy_v3_eta_dec"],
HextRec["anisotropy_v3_eta_inc"],
HextRec["anisotropy_v3_zeta_semi_angle"],
HextRec["anisotropy_v3_zeta_dec"],
HextRec["anisotropy_v3_zeta_inc"])
HextRec['magic_software_packages'] = version_num
ResRecs.append(HextRec)
if bpars != []:
BootRec = {}
for key in ResRec.keys():
BootRec[key] = ResRec[key] # copy over stuff
BootRec["anisotropy_v1_dec"] = '%7.1f' % (bpars["v1_dec"])
BootRec["anisotropy_v2_dec"] = '%7.1f' % (bpars["v2_dec"])
BootRec["anisotropy_v3_dec"] = '%7.1f' % (bpars["v3_dec"])
BootRec["anisotropy_v1_inc"] = '%7.1f' % (bpars["v1_inc"])
BootRec["anisotropy_v2_inc"] = '%7.1f' % (bpars["v2_inc"])
BootRec["anisotropy_v3_inc"] = '%7.1f' % (bpars["v3_inc"])
BootRec["anisotropy_t1"] = '%10.8f' % (bpars["t1"])
BootRec["anisotropy_t2"] = '%10.8f' % (bpars["t2"])
BootRec["anisotropy_t3"] = '%10.8f' % (bpars["t3"])
BootRec["anisotropy_v1_eta_inc"] = '%7.1f ' % (
bpars["v1_eta_inc"])
BootRec["anisotropy_v1_eta_dec"] = '%7.1f ' % (
bpars["v1_eta_dec"])
BootRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % (
bpars["v1_eta"])
BootRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % (
bpars["v1_zeta_inc"])
BootRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % (
bpars["v1_zeta_dec"])
BootRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % (
bpars["v1_zeta"])
BootRec["anisotropy_v2_eta_inc"] = '%7.1f ' % (
bpars["v2_eta_inc"])
BootRec["anisotropy_v2_eta_dec"] = '%7.1f ' % (
bpars["v2_eta_dec"])
BootRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % (
bpars["v2_eta"])
BootRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % (
bpars["v2_zeta_inc"])
BootRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % (
bpars["v2_zeta_dec"])
BootRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % (
bpars["v2_zeta"])
BootRec["anisotropy_v3_eta_inc"] = '%7.1f ' % (
bpars["v3_eta_inc"])
BootRec["anisotropy_v3_eta_dec"] = '%7.1f ' % (
bpars["v3_eta_dec"])
BootRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % (
bpars["v3_eta"])
BootRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % (
bpars["v3_zeta_inc"])
BootRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % (
bpars["v3_zeta_dec"])
BootRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % (
bpars["v3_zeta"])
BootRec["anisotropy_hext_F"] = ''
BootRec["anisotropy_hext_F12"] = ''
BootRec["anisotropy_hext_F23"] = ''
BootRec[
"magic_method_codes"] = 'LP-AN:AE-H:AE-BS' # regular bootstrap
if ipar == 1:
BootRec[
"magic_method_codes"] = 'LP-AN:AE-H:AE-BS-P' # parametric bootstrap
if verbose:
print("Boostrap Statistics: ")
print(
" tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
)
print(BootRec["anisotropy_t1"],
BootRec["anisotropy_v1_dec"],
BootRec["anisotropy_v1_inc"],
BootRec["anisotropy_v1_eta_semi_angle"],
BootRec["anisotropy_v1_eta_dec"],
BootRec["anisotropy_v1_eta_inc"],
BootRec["anisotropy_v1_zeta_semi_angle"],
BootRec["anisotropy_v1_zeta_dec"],
BootRec["anisotropy_v1_zeta_inc"])
print(BootRec["anisotropy_t2"],
BootRec["anisotropy_v2_dec"],
BootRec["anisotropy_v2_inc"],
BootRec["anisotropy_v2_eta_semi_angle"],
BootRec["anisotropy_v2_eta_dec"],
BootRec["anisotropy_v2_eta_inc"],
BootRec["anisotropy_v2_zeta_semi_angle"],
BootRec["anisotropy_v2_zeta_dec"],
BootRec["anisotropy_v2_zeta_inc"])
print(BootRec["anisotropy_t3"],
BootRec["anisotropy_v3_dec"],
BootRec["anisotropy_v3_inc"],
BootRec["anisotropy_v3_eta_semi_angle"],
BootRec["anisotropy_v3_eta_dec"],
BootRec["anisotropy_v3_eta_inc"],
BootRec["anisotropy_v3_zeta_semi_angle"],
BootRec["anisotropy_v3_zeta_dec"],
BootRec["anisotropy_v3_zeta_inc"])
BootRec['magic_software_packages'] = version_num
ResRecs.append(BootRec)
k += 1
goon = 1
while goon == 1 and iplot == 1 and verbose:
if iboot == 1: print("compare with [d]irection ")
print(
" plot [g]reat circle, change [c]oord. system, change [e]llipse calculation, s[a]ve plots, [q]uit "
)
if isite == 1:
print(" [p]revious, [s]ite, [q]uit, <return> for next ")
ans = input("")
if ans == "q":
sys.exit()
if ans == "e":
iboot, ipar, ihext, ivec = 1, 0, 0, 0
e = input("Do Hext Statistics 1/[0]: ")
if e == "1": ihext = 1
e = input("Suppress bootstrap 1/[0]: ")
if e == "1": iboot = 0
if iboot == 1:
e = input("Parametric bootstrap 1/[0]: ")
if e == "1": ipar = 1
e = input("Plot bootstrap eigenvectors: 1/[0]: ")
if e == "1": ivec = 1
if iplot == 1:
if inittcdf == 0:
ANIS['tcdf'] = 3
pmagplotlib.plot_init(ANIS['tcdf'], 5, 5)
inittcdf = 1
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp,
vec, Dir, nb)
if verbose and plots == 0: pmagplotlib.drawFIGS(ANIS)
if ans == "c":
print("Current Coordinate system is: ")
if CS == '-1': print(" Specimen")
if CS == '0': print(" Geographic")
if CS == '100': print(" Tilt corrected")
key = input(
" Enter desired coordinate system: [s]pecimen, [g]eographic, [t]ilt corrected "
)
if key == 's': CS = '-1'
if key == 'g': CS = '0'
if key == 't': CS = '100'
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = '-1'
if CS == '-1': crd = 's'
if CS == '0': crd = 'g'
if CS == '100': crd = 't'
print(
"desired coordinate system not available, using available: ",
crd)
k -= 1
goon = 0
if ans == "":
if isite == 1:
goon = 0
else:
print("Good bye ")
sys.exit()
if ans == 'd':
if initcdf == 0:
initcdf = 1
ANIS['vxcdf'], ANIS['vycdf'], ANIS['vzcdf'] = 4, 5, 6
pmagplotlib.plot_init(ANIS['vxcdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vycdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vzcdf'], 5, 5)
Dir, comp = [], 1
print("""
Input: Vi D I to compare eigenvector Vi with direction D/I
where Vi=1: principal
Vi=2: major
Vi=3: minor
D= declination of comparison direction
I= inclination of comparison direction""")
con = 1
while con == 1:
try:
vdi = input("Vi D I: ").split()
vec = int(vdi[0]) - 1
Dir = [float(vdi[1]), float(vdi[2])]
con = 0
except IndexError:
print(" Incorrect entry, try again ")
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp,
vec, Dir, nb)
Dir, comp = [], 0
if ans == 'g':
con, cnt = 1, 0
while con == 1:
try:
print(
" Input: input pole to great circle ( D I) to plot a great circle: "
)
di = input(" D I: ").split()
PDir.append(float(di[0]))
PDir.append(float(di[1]))
con = 0
except:
cnt += 1
if cnt < 10:
print(
" enter the dec and inc of the pole on one line "
)
else:
print(
"ummm - you are doing something wrong - i give up"
)
sys.exit()
pmagplotlib.plotC(ANIS['data'], PDir, 90., 'g')
pmagplotlib.plotC(ANIS['conf'], PDir, 90., 'g')
if verbose and plots == 0: pmagplotlib.drawFIGS(ANIS)
if ans == "p":
k -= 2
goon = 0
if ans == "q":
k = plt
goon = 0
if ans == "s":
keepon = 1
site = input(" print site or part of site desired: ")
while keepon == 1:
try:
k = sitelist.index(site)
keepon = 0
except:
tmplist = []
for qq in range(len(sitelist)):
if site in sitelist[qq]:
tmplist.append(sitelist[qq])
print(site, " not found, but this was: ")
print(tmplist)
site = input('Select one or try again\n ')
k = sitelist.index(site)
goon, ans = 0, ""
if ans == "a":
locs = pmag.makelist(Locs)
if pmagplotlib.isServer: # use server plot naming convention
title = "LO:_" + locs + '_SI:__' + '_SA:__SP:__CO:_' + crd
else: # use more readable plot naming convention
title = "{}_{}".format(locs, crd)
save(ANIS, fmt, title)
goon = 0
else:
if verbose: print('skipping plot - not enough data points')
k += 1
# put rmag_results stuff here
if len(ResRecs) > 0:
ResOut, keylist = pmag.fillkeys(ResRecs)
pmag.magic_write(outfile, ResOut, 'rmag_results')
if verbose:
print(" Good bye ")
def main():
"""
NAME
aniso_magic.py
DESCRIPTION
plots anisotropy data with either bootstrap or hext ellipses
SYNTAX
aniso_magic.py [-h] [command line options]
OPTIONS
-h plots help message and quits
-usr USER: set the user name
-f AFILE, specify specimens.txt formatted file for input
-fsa SAMPFILE, specify samples.txt file (required to plot by site)
-fsi SITEFILE, specify site file (required to include location information)
-x Hext [1963] and bootstrap
-B DON'T do bootstrap, do Hext
-par Tauxe [1998] parametric bootstrap
-v plot bootstrap eigenvectors instead of ellipses
-sit plot by site instead of entire file
-crd [s,g,t] coordinate system, default is specimen (g=geographic, t=tilt corrected)
-P don't make any plots - just fill in the specimens, samples, sites tables
-sav don't make the tables - just save all the plots
-fmt [svg, jpg, eps] format for output images, pdf default
-gtc DEC INC dec,inc of pole to great circle [down(up) in green (cyan)
-d Vi DEC INC; Vi (1,2,3) to compare to direction DEC INC
-nb N; specifies the number of bootstraps - default is 1000
DEFAULTS
AFILE: specimens.txt
plot bootstrap ellipses of Constable & Tauxe [1987]
NOTES
minor axis: circles
major axis: triangles
principal axis: squares
directions are plotted on the lower hemisphere
for bootstrapped eigenvector components: Xs: blue, Ys: red, Zs: black
"""
args = sys.argv
if "-h" in args:
print(main.__doc__)
sys.exit()
#version_num = pmag.get_version()
verbose = pmagplotlib.verbose
dir_path = pmag.get_named_arg_from_sys("-WD", ".")
num_bootstraps = pmag.get_named_arg_from_sys("-nb", 1000)
#user = pmag.get_named_arg_from_sys("-usr", "")
ipar = pmag.get_flag_arg_from_sys("-par", true=1, false=0)
ihext = pmag.get_flag_arg_from_sys("-x", true=1, false=0)
ivec = pmag.get_flag_arg_from_sys("-v", true=1, false=0)
iplot = pmag.get_flag_arg_from_sys("-P", true=0, false=1)
isite = pmag.get_flag_arg_from_sys("-sit", true=1, false=0)
iboot, vec = 1, 0
infile = pmag.get_named_arg_from_sys('-f', 'specimens.txt')
samp_file = pmag.get_named_arg_from_sys('-fsa', 'samples.txt')
site_file = pmag.get_named_arg_from_sys('-fsi', 'sites.txt')
#outfile = pmag.get_named_arg_from_sys("-F", "rmag_results.txt")
fmt = pmag.get_named_arg_from_sys("-fmt", "pdf")
hpars, bpars = [], []
CS, crd = -1, 's'
ResRecs = []
comp, Dir, PDir = 0, [], []
if '-B' in args:
iboot, ihext = 0, 1
if '-crd' in sys.argv:
ind = sys.argv.index('-crd')
crd = sys.argv[ind + 1]
if crd == 'g':
CS = 0
if crd == 't':
CS = 100
if '-sav' in args:
plots = 1
verbose = 0
else:
plots = 0
if '-gtc' in args:
ind = args.index('-gtc')
d, i = float(args[ind + 1]), float(args[ind + 2])
PDir.append(d)
PDir.append(i)
if '-d' in args:
comp = 1
ind = args.index('-d')
vec = int(args[ind + 1]) - 1
Dir = [float(args[ind + 2]), float(args[ind + 3])]
#
# set up plots
#
ANIS = {}
initcdf, inittcdf = 0, 0
ANIS['data'], ANIS['conf'] = 1, 2
if iboot == 1:
ANIS['tcdf'] = 3
if iplot == 1:
inittcdf = 1
pmagplotlib.plot_init(ANIS['tcdf'], 5, 5)
if comp == 1 and iplot == 1:
initcdf = 1
ANIS['vxcdf'], ANIS['vycdf'], ANIS['vzcdf'] = 4, 5, 6
pmagplotlib.plot_init(ANIS['vxcdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vycdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vzcdf'], 5, 5)
if iplot == 1:
pmagplotlib.plot_init(ANIS['conf'], 5, 5)
pmagplotlib.plot_init(ANIS['data'], 5, 5)
# read in the data
fnames = {'specimens': infile, 'samples': samp_file, 'sites': site_file}
con = nb.Contribution(dir_path,
read_tables=['specimens', 'samples', 'sites'],
custom_filenames=fnames)
con.propagate_location_to_specimens()
spec_container = con.tables['specimens']
# get only anisotropy records
spec_df = spec_container.get_records_for_code('AE-', strict_match=False)
if 'aniso_tilt_correction' not in spec_df.columns:
spec_df['aniso_tilt_correction'] = None
orlist = spec_df['aniso_tilt_correction'].dropna().unique()
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = -1
if CS == -1:
crd = 's'
if CS == 0:
crd = 'g'
if CS == 100:
crd = 't'
if verbose:
print("desired coordinate system not available, using available: ",
crd)
if isite == 1:
sitelist = spec_df['site'].unique()
sitelist.sort()
plt = len(sitelist)
else:
plt = 1
k = 0
while k < plt:
site = ""
loc_name = ""
sdata, Ss = [], [] # list of S format data
if isite == 0:
sdata = spec_df
if 'location' in sdata.columns:
loc_name = ':'.join(sdata['location'].unique())
else:
site = sitelist[k]
sdata = spec_df[spec_df['site'] == site]
if 'location' in sdata.columns:
loc_name = sdata['location'][0]
csrecs = sdata[sdata['aniso_tilt_correction'] == CS]
#anitypes = csrecs['aniso_type'].unique()
for name in ['citations', 'location', 'site', 'sample']:
if name not in csrecs:
csrecs[name] = ""
Locs = csrecs['location'].unique()
#Sites = csrecs['site'].unique()
#Samples = csrecs['sample'].unique()
#Specimens = csrecs['specimen'].unique()
#Cits = csrecs['citations'].unique()
for ind, rec in csrecs.iterrows():
s = [float(i.strip()) for i in rec['aniso_s'].split(':')]
if s[0] <= 1.0:
Ss.append(s) # protect against crap
# tau,Vdirs=pmag.doseigs(s)
# do we need fpars somewhere???
# fpars = pmag.dohext(int(rec["aniso_s_n_measurements"]) -6, float(rec["aniso_s_sigma"]), s)
# fill in ResRecs (ignoring this for now, grab it from aniso_magic if needed)
if len(Ss) > 1:
if pmagplotlib.isServer: # use server plot naming convention
title = "LO:_" + loc_name + '_SI:_' + site + '_SA:__SP:__CO:_' + crd
else: # use more readable plot naming convention
title = "{}_{}_{}".format(loc_name, site, crd)
bpars, hpars = pmagplotlib.plotANIS(ANIS, Ss, iboot, ihext, ivec,
ipar, title, iplot, comp, vec,
Dir, num_bootstraps)
if len(PDir) > 0:
pmagplotlib.plotC(ANIS['data'], PDir, 90., 'g')
pmagplotlib.plotC(ANIS['conf'], PDir, 90., 'g')
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
if plots == 1:
save(ANIS, fmt, title)
if hpars != [] and ihext == 1:
HextRec = {}
#for key in ResRec.keys():HextRec[key]=ResRec[key] # copy over stuff
HextRec["anisotropy_v1_dec"] = '%7.1f' % (hpars["v1_dec"])
HextRec["anisotropy_v2_dec"] = '%7.1f' % (hpars["v2_dec"])
HextRec["anisotropy_v3_dec"] = '%7.1f' % (hpars["v3_dec"])
HextRec["anisotropy_v1_inc"] = '%7.1f' % (hpars["v1_inc"])
HextRec["anisotropy_v2_inc"] = '%7.1f' % (hpars["v2_inc"])
HextRec["anisotropy_v3_inc"] = '%7.1f' % (hpars["v3_inc"])
HextRec["anisotropy_t1"] = '%10.8f' % (hpars["t1"])
HextRec["anisotropy_t2"] = '%10.8f' % (hpars["t2"])
HextRec["anisotropy_t3"] = '%10.8f' % (hpars["t3"])
HextRec["anisotropy_hext_F"] = '%7.1f ' % (hpars["F"])
HextRec["anisotropy_hext_F12"] = '%7.1f ' % (hpars["F12"])
HextRec["anisotropy_hext_F23"] = '%7.1f ' % (hpars["F23"])
HextRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v1_eta_dec"] = '%7.1f ' % (hpars["v2_dec"])
HextRec["anisotropy_v1_eta_inc"] = '%7.1f ' % (hpars["v2_inc"])
HextRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % (
hpars["e13"])
HextRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % (
hpars["v3_dec"])
HextRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % (
hpars["v3_inc"])
HextRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v2_eta_dec"] = '%7.1f ' % (hpars["v1_dec"])
HextRec["anisotropy_v2_eta_inc"] = '%7.1f ' % (hpars["v1_inc"])
HextRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % (
hpars["e23"])
HextRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % (
hpars["v3_dec"])
HextRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % (
hpars["v3_inc"])
HextRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v3_eta_dec"] = '%7.1f ' % (hpars["v1_dec"])
HextRec["anisotropy_v3_eta_inc"] = '%7.1f ' % (hpars["v1_inc"])
HextRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % (
hpars["e23"])
HextRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % (
hpars["v2_dec"])
HextRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % (
hpars["v2_inc"])
HextRec["magic_method_codes"] = 'LP-AN:AE-H'
if verbose:
print("Hext Statistics: ")
print(
" tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
)
print(HextRec["anisotropy_t1"],
HextRec["anisotropy_v1_dec"],
end=' ')
print(HextRec["anisotropy_v1_inc"],
HextRec["anisotropy_v1_eta_semi_angle"],
end=' ')
print(HextRec["anisotropy_v1_eta_dec"],
HextRec["anisotropy_v1_eta_inc"],
end=' ')
print(HextRec["anisotropy_v1_zeta_semi_angle"],
HextRec["anisotropy_v1_zeta_dec"],
end=' ')
print(HextRec["anisotropy_v1_zeta_inc"])
#
print(HextRec["anisotropy_t2"],
HextRec["anisotropy_v2_dec"],
end=' ')
print(HextRec["anisotropy_v2_inc"],
HextRec["anisotropy_v2_eta_semi_angle"],
end=' ')
print(HextRec["anisotropy_v2_eta_dec"],
HextRec["anisotropy_v2_eta_inc"],
end=' ')
print(HextRec["anisotropy_v2_zeta_semi_angle"],
HextRec["anisotropy_v2_zeta_dec"],
end=' ')
print(HextRec["anisotropy_v2_zeta_inc"])
#
print(HextRec["anisotropy_t3"],
HextRec["anisotropy_v3_dec"],
end=' ')
print(HextRec["anisotropy_v3_inc"],
HextRec["anisotropy_v3_eta_semi_angle"],
end=' ')
print(HextRec["anisotropy_v3_eta_dec"],
HextRec["anisotropy_v3_eta_inc"],
end=' ')
print(HextRec["anisotropy_v3_zeta_semi_angle"],
HextRec["anisotropy_v3_zeta_dec"],
end=' ')
print(HextRec["anisotropy_v3_zeta_inc"])
#HextRec['magic_software_packages']=version_num
#ResRecs.append(HextRec)
if bpars != []:
BootRec = {}
#for key in ResRec.keys():BootRec[key]=ResRec[key] # copy over stuff
BootRec["anisotropy_v1_dec"] = '%7.1f' % (bpars["v1_dec"])
BootRec["anisotropy_v2_dec"] = '%7.1f' % (bpars["v2_dec"])
BootRec["anisotropy_v3_dec"] = '%7.1f' % (bpars["v3_dec"])
BootRec["anisotropy_v1_inc"] = '%7.1f' % (bpars["v1_inc"])
BootRec["anisotropy_v2_inc"] = '%7.1f' % (bpars["v2_inc"])
BootRec["anisotropy_v3_inc"] = '%7.1f' % (bpars["v3_inc"])
BootRec["anisotropy_t1"] = '%10.8f' % (bpars["t1"])
BootRec["anisotropy_t2"] = '%10.8f' % (bpars["t2"])
BootRec["anisotropy_t3"] = '%10.8f' % (bpars["t3"])
BootRec["anisotropy_v1_eta_inc"] = '%7.1f ' % (
bpars["v1_eta_inc"])
BootRec["anisotropy_v1_eta_dec"] = '%7.1f ' % (
bpars["v1_eta_dec"])
BootRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % (
bpars["v1_eta"])
BootRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % (
bpars["v1_zeta_inc"])
BootRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % (
bpars["v1_zeta_dec"])
BootRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % (
bpars["v1_zeta"])
BootRec["anisotropy_v2_eta_inc"] = '%7.1f ' % (
bpars["v2_eta_inc"])
BootRec["anisotropy_v2_eta_dec"] = '%7.1f ' % (
bpars["v2_eta_dec"])
BootRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % (
bpars["v2_eta"])
BootRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % (
bpars["v2_zeta_inc"])
BootRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % (
bpars["v2_zeta_dec"])
BootRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % (
bpars["v2_zeta"])
BootRec["anisotropy_v3_eta_inc"] = '%7.1f ' % (
bpars["v3_eta_inc"])
BootRec["anisotropy_v3_eta_dec"] = '%7.1f ' % (
bpars["v3_eta_dec"])
BootRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % (
bpars["v3_eta"])
BootRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % (
bpars["v3_zeta_inc"])
BootRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % (
bpars["v3_zeta_dec"])
BootRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % (
bpars["v3_zeta"])
BootRec["anisotropy_hext_F"] = ''
BootRec["anisotropy_hext_F12"] = ''
BootRec["anisotropy_hext_F23"] = ''
BootRec[
"magic_method_codes"] = 'LP-AN:AE-H:AE-BS' # regular bootstrap
if ipar == 1:
BootRec[
"magic_method_codes"] = 'LP-AN:AE-H:AE-BS-P' # parametric bootstrap
if verbose:
print("Boostrap Statistics: ")
print(
" tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
)
print(BootRec["anisotropy_t1"],
BootRec["anisotropy_v1_dec"],
end=' ')
print(BootRec["anisotropy_v1_inc"],
BootRec["anisotropy_v1_eta_semi_angle"],
end=' ')
print(BootRec["anisotropy_v1_eta_dec"],
BootRec["anisotropy_v1_eta_inc"],
end=' ')
print(BootRec["anisotropy_v1_zeta_semi_angle"],
BootRec["anisotropy_v1_zeta_dec"],
end=' ')
print(BootRec["anisotropy_v1_zeta_inc"])
#
print(BootRec["anisotropy_t2"],
BootRec["anisotropy_v2_dec"],
BootRec["anisotropy_v2_inc"],
end=' ')
print(BootRec["anisotropy_v2_eta_semi_angle"],
BootRec["anisotropy_v2_eta_dec"],
end=' ')
print(BootRec["anisotropy_v2_eta_inc"],
BootRec["anisotropy_v2_zeta_semi_angle"],
end=' ')
print(BootRec["anisotropy_v2_zeta_dec"],
BootRec["anisotropy_v2_zeta_inc"])
#
print(BootRec["anisotropy_t3"],
BootRec["anisotropy_v3_dec"],
BootRec["anisotropy_v3_inc"],
end=' ')
print(BootRec["anisotropy_v3_eta_semi_angle"],
BootRec["anisotropy_v3_eta_dec"],
end=' ')
print(BootRec["anisotropy_v3_eta_inc"],
BootRec["anisotropy_v3_zeta_semi_angle"],
end=' ')
print(BootRec["anisotropy_v3_zeta_dec"],
BootRec["anisotropy_v3_zeta_inc"])
#BootRec['magic_software_packages'] = version_num
ResRecs.append(BootRec)
k += 1
goon = 1
while goon == 1 and iplot == 1 and verbose:
if iboot == 1:
print("compare with [d]irection ")
print(
" plot [g]reat circle, change [c]oord. system, change [e]llipse calculation, s[a]ve plots, [q]uit "
)
if isite == 1:
print(" [p]revious, [s]ite, [q]uit, <return> for next ")
ans = input("")
if ans == "q":
sys.exit()
if ans == "e":
iboot, ipar, ihext, ivec = 1, 0, 0, 0
e = input("Do Hext Statistics 1/[0]: ")
if e == "1":
ihext = 1
e = input("Suppress bootstrap 1/[0]: ")
if e == "1":
iboot = 0
if iboot == 1:
e = input("Parametric bootstrap 1/[0]: ")
if e == "1":
ipar = 1
e = input("Plot bootstrap eigenvectors: 1/[0]: ")
if e == "1":
ivec = 1
if iplot == 1:
if inittcdf == 0:
ANIS['tcdf'] = 3
pmagplotlib.plot_init(ANIS['tcdf'], 5, 5)
inittcdf = 1
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp,
vec, Dir, num_bootstraps)
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
if ans == "c":
print("Current Coordinate system is: ")
if CS == -1:
print(" Specimen")
if CS == 0:
print(" Geographic")
if CS == 100:
print(" Tilt corrected")
key = input(
" Enter desired coordinate system: [s]pecimen, [g]eographic, [t]ilt corrected "
)
if key == 's':
CS = -1
if key == 'g':
CS = 0
if key == 't':
CS = 100
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = -1
if CS == -1:
crd = 's'
if CS == 0:
crd = 'g'
if CS == 100:
crd = 't'
print(
"desired coordinate system not available, using available: ",
crd)
k -= 1
goon = 0
if ans == "":
if isite == 1:
goon = 0
else:
print("Good bye ")
sys.exit()
if ans == 'd':
if initcdf == 0:
initcdf = 1
ANIS['vxcdf'], ANIS['vycdf'], ANIS['vzcdf'] = 4, 5, 6
pmagplotlib.plot_init(ANIS['vxcdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vycdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vzcdf'], 5, 5)
Dir, comp = [], 1
print("""
Input: Vi D I to compare eigenvector Vi with direction D/I
where Vi=1: principal
Vi=2: major
Vi=3: minor
D= declination of comparison direction
I= inclination of comparison direction""")
con = 1
while con == 1:
try:
vdi = input("Vi D I: ").split()
vec = int(vdi[0]) - 1
Dir = [float(vdi[1]), float(vdi[2])]
con = 0
except IndexError:
print(" Incorrect entry, try again ")
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp,
vec, Dir, num_bootstraps)
Dir, comp = [], 0
if ans == 'g':
con, cnt = 1, 0
while con == 1:
try:
print(
" Input: input pole to great circle ( D I) to plot a great circle: "
)
di = input(" D I: ").split()
PDir.append(float(di[0]))
PDir.append(float(di[1]))
con = 0
except:
cnt += 1
if cnt < 10:
print(
" enter the dec and inc of the pole on one line "
)
else:
print(
"ummm - you are doing something wrong - i give up"
)
sys.exit()
pmagplotlib.plotC(ANIS['data'], PDir, 90., 'g')
pmagplotlib.plotC(ANIS['conf'], PDir, 90., 'g')
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
if ans == "p":
k -= 2
goon = 0
if ans == "q":
k = plt
goon = 0
if ans == "s":
keepon = 1
site = input(" print site or part of site desired: ")
while keepon == 1:
try:
k = sitelist.index(site)
keepon = 0
except:
tmplist = []
for qq in range(len(sitelist)):
if site in sitelist[qq]:
tmplist.append(sitelist[qq])
print(site, " not found, but this was: ")
print(tmplist)
site = input('Select one or try again\n ')
k = sitelist.index(site)
goon, ans = 0, ""
if ans == "a":
locs = pmag.makelist(Locs)
site_name = "_"
if isite:
site_name = site
if pmagplotlib.isServer: # use server plot naming convention
title = "LO:_" + locs + '_SI:_' + site_name + '_SA:__SP:__CO:_' + crd
else: # use more readable plot naming convention
title = "{}_{}_{}".format(locs, site_name, crd)
save(ANIS, fmt, title)
goon = 0
else:
if verbose:
print('skipping plot - not enough data points')
k += 1
# put rmag_results stuff here
#if len(ResRecs)>0:
# ResOut,keylist=pmag.fillkeys(ResRecs)
# pmag.magic_write(outfile,ResOut,'rmag_results')
if verbose:
print(" Good bye ")
def main():
"""
NAME
eqarea_magic.py
DESCRIPTION
makes equal area projections from declination/inclination data
SYNTAX
eqarea_magic.py [command line options]
INPUT
takes magic formatted pmag_results, pmag_sites, pmag_samples or pmag_specimens
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file from magic,default='pmag_results.txt'
supported types=[magic_measurements,pmag_specimens, pmag_samples, pmag_sites, pmag_results, magic_web]
-obj OBJ: specify level of plot [all, sit, sam, spc], default is all
-crd [s,g,t]: specify coordinate system, [s]pecimen, [g]eographic, [t]ilt adjusted
default is geographic, unspecified assumed geographic
-fmt [svg,png,jpg] format for output plots
-ell [F,K,B,Be,Bv] plot Fisher, Kent, Bingham, Bootstrap ellipses or Boostrap eigenvectors
-c plot as colour contour
-sav save plot and quit quietly
NOTE
all: entire file; sit: site; sam: sample; spc: specimen
"""
FIG={} # plot dictionary
FIG['eqarea']=1 # eqarea is figure 1
in_file,plot_key,coord,crd='pmag_results.txt','all',"0",'g'
plotE,contour=0,0
dir_path='.'
fmt='svg'
verbose=pmagplotlib.verbose
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
pmagplotlib.plot_init(FIG['eqarea'],5,5)
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=dir_path+"/"+sys.argv[ind+1]
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
plot_by=sys.argv[ind+1]
if plot_by=='all':plot_key='all'
if plot_by=='sit':plot_key='er_site_name'
if plot_by=='sam':plot_key='er_sample_name'
if plot_by=='spc':plot_key='er_specimen_name'
if '-c' in sys.argv: contour=1
plt=0
if '-sav' in sys.argv:
plt=1
verbose=0
if '-ell' in sys.argv:
plotE=1
ind=sys.argv.index('-ell')
ell_type=sys.argv[ind+1]
if ell_type=='F':dist='F'
if ell_type=='K':dist='K'
if ell_type=='B':dist='B'
if ell_type=='Be':dist='BE'
if ell_type=='Bv':
dist='BV'
FIG['bdirs']=2
pmagplotlib.plot_init(FIG['bdirs'],5,5)
if '-crd' in sys.argv:
ind=sys.argv.index("-crd")
crd=sys.argv[ind+1]
if crd=='s':coord="-1"
if crd=='g':coord="0"
if crd=='t':coord="100"
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
Dec_keys=['site_dec','sample_dec','specimen_dec','measurement_dec','average_dec','none']
Inc_keys=['site_inc','sample_inc','specimen_inc','measurement_inc','average_inc','none']
Tilt_keys=['tilt_correction','site_tilt_correction','sample_tilt_correction','specimen_tilt_correction','none']
Dir_type_keys=['','site_direction_type','sample_direction_type','specimen_direction_type']
Name_keys=['er_specimen_name','er_sample_name','er_site_name','pmag_result_name']
data,file_type=pmag.magic_read(in_file)
if file_type=='pmag_results' and plot_key!="all":plot_key=plot_key+'s' # need plural for results table
if verbose:
print len(data),' records read from ',in_file
#
#
# find desired dec,inc data:
#
dir_type_key=''
#
# get plotlist if not plotting all records
#
plotlist=[]
if plot_key!="all":
plots=pmag.get_dictitem(data,plot_key,'','F')
for rec in plots:
if rec[plot_key] not in plotlist:
plotlist.append(rec[plot_key])
plotlist.sort()
else:
plotlist.append('All')
for plot in plotlist:
#if verbose: print plot
DIblock=[]
GCblock=[]
SLblock,SPblock=[],[]
title=plot
mode=1
dec_key,inc_key,tilt_key,name_key,k="","","","",0
if plot!="All":
odata=pmag.get_dictitem(data,plot_key,plot,'T')
else: odata=data # data for this obj
for dec_key in Dec_keys:
Decs=pmag.get_dictitem(odata,dec_key,'','F') # get all records with this dec_key not blank
if len(Decs)>0: break
for inc_key in Inc_keys:
Incs=pmag.get_dictitem(Decs,inc_key,'','F') # get all records with this inc_key not blank
if len(Incs)>0: break
for tilt_key in Tilt_keys:
if tilt_key in Incs[0].keys(): break # find the tilt_key for these records
if tilt_key=='none': # no tilt key in data, need to fix this with fake data which will be unknown tilt
tilt_key='tilt_correction'
for rec in Incs:rec[tilt_key]=''
cdata=pmag.get_dictitem(Incs,tilt_key,coord,'T') # get all records matching specified coordinate system
if coord=='0': # geographic
udata=pmag.get_dictitem(Incs,tilt_key,'','T') # get all the blank records - assume geographic
if len(cdata)==0: crd=''
if len(udata)>0:
for d in udata:cdata.append(d)
crd=crd+'u'
for name_key in Name_keys:
Names=pmag.get_dictitem(cdata,name_key,'','F') # get all records with this name_key not blank
if len(Names)>0: break
for dir_type_key in Dir_type_keys:
Dirs=pmag.get_dictitem(cdata,dir_type_key,'','F') # get all records with this direction type
if len(Dirs)>0: break
if dir_type_key=="":dir_type_key='direction_type'
locations,site,sample,specimen="","","",""
for rec in cdata: # pick out the data
if 'er_location_name' in rec.keys() and rec['er_location_name']!="" and rec['er_location_name'] not in locations:locations=locations+rec['er_location_name'].replace("/","")+"_"
if 'er_location_names' in rec.keys() and rec['er_location_names']!="":
locs=rec['er_location_names'].split(':')
for loc in locs:
if loc not in locations:locations=locations+loc.replace("/","")+'_'
if plot_key=='er_site_name' or plot_key=='er_sample_name' or plot_key=='er_specimen_name':
site=rec['er_site_name']
if plot_key=='er_sample_name' or plot_key=='er_specimen_name':
sample=rec['er_sample_name']
if plot_key=='er_specimen_name':
specimen=rec['er_specimen_name']
if plot_key=='er_site_names' or plot_key=='er_sample_names' or plot_key=='er_specimen_names':
site=rec['er_site_names']
if plot_key=='er_sample_names' or plot_key=='er_specimen_names':
sample=rec['er_sample_names']
if plot_key=='er_specimen_names':
specimen=rec['er_specimen_names']
if dir_type_key not in rec.keys() or rec[dir_type_key]=="":rec[dir_type_key]='l'
if 'magic_method_codes' not in rec.keys():rec['magic_method_codes']=""
DIblock.append([float(rec[dec_key]),float(rec[inc_key])])
SLblock.append([rec[name_key],rec['magic_method_codes']])
if rec[tilt_key]==coord and rec[dir_type_key]!='l' and rec[dec_key]!="" and rec[inc_key]!="":
GCblock.append([float(rec[dec_key]),float(rec[inc_key])])
SPblock.append([rec[name_key],rec['magic_method_codes']])
if len(DIblock)==0 and len(GCblock)==0:
if verbose: print "no records for plotting"
sys.exit()
if verbose:
for k in range(len(SLblock)):
print '%s %s %7.1f %7.1f'%(SLblock[k][0],SLblock[k][1],DIblock[k][0],DIblock[k][1])
for k in range(len(SPblock)):
print '%s %s %7.1f %7.1f'%(SPblock[k][0],SPblock[k][1],GCblock[k][0],GCblock[k][1])
if len(DIblock)>0:
if contour==0:
pmagplotlib.plotEQ(FIG['eqarea'],DIblock,title)
else:
pmagplotlib.plotEQcont(FIG['eqarea'],DIblock)
else: pmagplotlib.plotNET(FIG['eqarea'])
if len(GCblock)>0:
for rec in GCblock: pmagplotlib.plotC(FIG['eqarea'],rec,90.,'g')
if plotE==1:
ppars=pmag.doprinc(DIblock) # get principal directions
nDIs,rDIs,npars,rpars=[],[],[],[]
for rec in DIblock:
angle=pmag.angle([rec[0],rec[1]],[ppars['dec'],ppars['inc']])
if angle>90.:
rDIs.append(rec)
else:
nDIs.append(rec)
if dist=='B': # do on whole dataset
etitle="Bingham confidence ellipse"
bpars=pmag.dobingham(DIblock)
for key in bpars.keys():
if key!='n' and verbose:print " ",key, '%7.1f'%(bpars[key])
if key=='n' and verbose:print " ",key, ' %i'%(bpars[key])
npars.append(bpars['dec'])
npars.append(bpars['inc'])
npars.append(bpars['Zeta'])
npars.append(bpars['Zdec'])
npars.append(bpars['Zinc'])
npars.append(bpars['Eta'])
npars.append(bpars['Edec'])
npars.append(bpars['Einc'])
if dist=='F':
etitle="Fisher confidence cone"
if len(nDIs)>2:
fpars=pmag.fisher_mean(nDIs)
for key in fpars.keys():
if key!='n' and verbose:print " ",key, '%7.1f'%(fpars[key])
if key=='n' and verbose:print " ",key, ' %i'%(fpars[key])
mode+=1
npars.append(fpars['dec'])
npars.append(fpars['inc'])
npars.append(fpars['alpha95']) # Beta
npars.append(fpars['dec'])
isign=abs(fpars['inc'])/fpars['inc']
npars.append(fpars['inc']-isign*90.) #Beta inc
npars.append(fpars['alpha95']) # gamma
npars.append(fpars['dec']+90.) # Beta dec
npars.append(0.) #Beta inc
if len(rDIs)>2:
fpars=pmag.fisher_mean(rDIs)
if verbose:print "mode ",mode
for key in fpars.keys():
if key!='n' and verbose:print " ",key, '%7.1f'%(fpars[key])
if key=='n' and verbose:print " ",key, ' %i'%(fpars[key])
mode+=1
rpars.append(fpars['dec'])
rpars.append(fpars['inc'])
rpars.append(fpars['alpha95']) # Beta
rpars.append(fpars['dec'])
isign=abs(fpars['inc'])/fpars['inc']
rpars.append(fpars['inc']-isign*90.) #Beta inc
rpars.append(fpars['alpha95']) # gamma
rpars.append(fpars['dec']+90.) # Beta dec
rpars.append(0.) #Beta inc
if dist=='K':
etitle="Kent confidence ellipse"
if len(nDIs)>3:
kpars=pmag.dokent(nDIs,len(nDIs))
if verbose:print "mode ",mode
for key in kpars.keys():
if key!='n' and verbose:print " ",key, '%7.1f'%(kpars[key])
if key=='n' and verbose:print " ",key, ' %i'%(kpars[key])
mode+=1
npars.append(kpars['dec'])
npars.append(kpars['inc'])
npars.append(kpars['Zeta'])
npars.append(kpars['Zdec'])
npars.append(kpars['Zinc'])
npars.append(kpars['Eta'])
npars.append(kpars['Edec'])
npars.append(kpars['Einc'])
if len(rDIs)>3:
kpars=pmag.dokent(rDIs,len(rDIs))
if verbose:print "mode ",mode
for key in kpars.keys():
if key!='n' and verbose:print " ",key, '%7.1f'%(kpars[key])
if key=='n' and verbose:print " ",key, ' %i'%(kpars[key])
mode+=1
rpars.append(kpars['dec'])
rpars.append(kpars['inc'])
rpars.append(kpars['Zeta'])
rpars.append(kpars['Zdec'])
rpars.append(kpars['Zinc'])
rpars.append(kpars['Eta'])
rpars.append(kpars['Edec'])
rpars.append(kpars['Einc'])
else: # assume bootstrap
if dist=='BE':
if len(nDIs)>5:
BnDIs=pmag.di_boot(nDIs)
Bkpars=pmag.dokent(BnDIs,1.)
if verbose:print "mode ",mode
for key in Bkpars.keys():
if key!='n' and verbose:print " ",key, '%7.1f'%(Bkpars[key])
if key=='n' and verbose:print " ",key, ' %i'%(Bkpars[key])
mode+=1
npars.append(Bkpars['dec'])
npars.append(Bkpars['inc'])
npars.append(Bkpars['Zeta'])
npars.append(Bkpars['Zdec'])
npars.append(Bkpars['Zinc'])
npars.append(Bkpars['Eta'])
npars.append(Bkpars['Edec'])
npars.append(Bkpars['Einc'])
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
Bkpars=pmag.dokent(BrDIs,1.)
if verbose:print "mode ",mode
for key in Bkpars.keys():
if key!='n' and verbose:print " ",key, '%7.1f'%(Bkpars[key])
if key=='n' and verbose:print " ",key, ' %i'%(Bkpars[key])
mode+=1
rpars.append(Bkpars['dec'])
rpars.append(Bkpars['inc'])
rpars.append(Bkpars['Zeta'])
rpars.append(Bkpars['Zdec'])
rpars.append(Bkpars['Zinc'])
rpars.append(Bkpars['Eta'])
rpars.append(Bkpars['Edec'])
rpars.append(Bkpars['Einc'])
etitle="Bootstrapped confidence ellipse"
elif dist=='BV':
sym={'lower':['o','c'],'upper':['o','g'],'size':3,'edgecolor':'face'}
if len(nDIs)>5:
BnDIs=pmag.di_boot(nDIs)
pmagplotlib.plotEQsym(FIG['bdirs'],BnDIs,'Bootstrapped Eigenvectors', sym)
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
if len(nDIs)>5: # plot on existing plots
pmagplotlib.plotDIsym(FIG['bdirs'],BrDIs,sym)
else:
pmagplotlib.plotEQ(FIG['bdirs'],BrDIs,'Bootstrapped Eigenvectors')
if dist=='B':
if len(nDIs)> 3 or len(rDIs)>3: pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],npars,0)
elif len(nDIs)>3 and dist!='BV':
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],npars,0)
if len(rDIs)>3:
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],rpars,0)
elif len(rDIs)>3 and dist!='BV':
pmagplotlib.plotCONF(FIG['eqarea'],etitle,[],rpars,0)
if verbose:pmagplotlib.drawFIGS(FIG)
#
files={}
locations=locations[:-1]
for key in FIG.keys():
filename='LO:_'+locations+'_SI:_'+site+'_SA:_'+sample+'_SP:_'+specimen+'_CO:_'+crd+'_TY:_'+key+'_.'+fmt
files[key]=filename
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='Equal Area Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
elif verbose:
ans=raw_input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans=="q": sys.exit()
if ans=="a": pmagplotlib.saveP(FIG,files)
if plt:
pmagplotlib.saveP(FIG,files)
def main():
"""
NAME
aniso_magic.py
DESCRIPTION
plots anisotropy data with either bootstrap or hext ellipses
SYNTAX
aniso_magic.py [-h] [command line options]
OPTIONS
-h plots help message and quits
-usr USER: set the user name
-f AFILE, specify specimens.txt formatted file for input
-fsa SAMPFILE, specify samples.txt file (required to plot by site)
-fsi SITEFILE, specify site file (required to include location information)
-x Hext [1963] and bootstrap
-B DON'T do bootstrap, do Hext
-par Tauxe [1998] parametric bootstrap
-v plot bootstrap eigenvectors instead of ellipses
-sit plot by site instead of entire file
-crd [s,g,t] coordinate system, default is specimen (g=geographic, t=tilt corrected)
-P don't make any plots - just fill in the specimens, samples, sites tables
-sav don't make the tables - just save all the plots
-fmt [svg, jpg, eps] format for output images, pdf default
-gtc DEC INC dec,inc of pole to great circle [down(up) in green (cyan)
-d Vi DEC INC; Vi (1,2,3) to compare to direction DEC INC
-nb N; specifies the number of bootstraps - default is 1000
DEFAULTS
AFILE: specimens.txt
plot bootstrap ellipses of Constable & Tauxe [1987]
NOTES
minor axis: circles
major axis: triangles
principal axis: squares
directions are plotted on the lower hemisphere
for bootstrapped eigenvector components: Xs: blue, Ys: red, Zs: black
"""
args = sys.argv
if "-h" in args:
print main.__doc__
sys.exit()
#version_num = pmag.get_version()
verbose = pmagplotlib.verbose
dir_path = pmag.get_named_arg_from_sys("-WD", ".")
num_bootstraps = pmag.get_named_arg_from_sys("-nb", 1000)
#user = pmag.get_named_arg_from_sys("-usr", "")
ipar = pmag.get_flag_arg_from_sys("-par", true=1, false=0)
ihext = pmag.get_flag_arg_from_sys("-x", true=1, false=0)
ivec = pmag.get_flag_arg_from_sys("-v", true=1, false=0)
iplot = pmag.get_flag_arg_from_sys("-P", true=0, false=1)
isite = pmag.get_flag_arg_from_sys("-sit", true=1, false=0)
iboot, vec = 1, 0
infile = pmag.get_named_arg_from_sys('-f', 'specimens.txt')
samp_file = pmag.get_named_arg_from_sys('-fsa', 'samples.txt')
site_file = pmag.get_named_arg_from_sys('-fsi', 'sites.txt')
#outfile = pmag.get_named_arg_from_sys("-F", "rmag_results.txt")
fmt = pmag.get_named_arg_from_sys("-fmt", "pdf")
hpars, bpars = [], []
CS, crd = -1, 's'
ResRecs = []
comp, Dir, PDir = 0, [], []
if '-B' in args:
iboot, ihext = 0, 1
if '-crd' in sys.argv:
ind = sys.argv.index('-crd')
crd = sys.argv[ind+1]
if crd == 'g':
CS = 0
if crd == 't':
CS = 100
if '-sav' in args:
plots = 1
verbose = 0
else:
plots = 0
if '-gtc' in args:
ind = args.index('-gtc')
d, i = float(args[ind+1]), float(args[ind+2])
PDir.append(d)
PDir.append(i)
if '-d' in args:
comp = 1
ind = args.index('-d')
vec = int(args[ind+1])-1
Dir = [float(args[ind+2]), float(args[ind+3])]
#
# set up plots
#
ANIS = {}
initcdf, inittcdf = 0, 0
ANIS['data'], ANIS['conf'] = 1, 2
if iboot == 1:
ANIS['tcdf'] = 3
if iplot == 1:
inittcdf = 1
pmagplotlib.plot_init(ANIS['tcdf'], 5, 5)
if comp == 1 and iplot == 1:
initcdf = 1
ANIS['vxcdf'], ANIS['vycdf'], ANIS['vzcdf'] = 4, 5, 6
pmagplotlib.plot_init(ANIS['vxcdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vycdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vzcdf'], 5, 5)
if iplot == 1:
pmagplotlib.plot_init(ANIS['conf'], 5, 5)
pmagplotlib.plot_init(ANIS['data'], 5, 5)
# read in the data
fnames = {'specimens': infile, 'samples': samp_file, 'sites': site_file}
con = nb.Contribution(dir_path, read_tables=['specimens', 'samples', 'sites'],
custom_filenames=fnames)
spec_container = con.tables['specimens']
spec_df = con.propagate_name_down('location', 'specimens')
# get only anisotropy records
spec_df = spec_container.get_records_for_code('AE-', strict_match=False)
if 'aniso_tilt_correction' not in spec_df.columns:
spec_df['aniso_tilt_correction'] = None
orlist = spec_df['aniso_tilt_correction'].dropna().unique()
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = -1
if CS == -1:
crd = 's'
if CS == 0:
crd = 'g'
if CS == 100:
crd = 't'
if verbose:
print "desired coordinate system not available, using available: ", crd
if isite == 1:
sitelist = spec_df['site'].unique()
sitelist.sort()
plt = len(sitelist)
else:
plt = 1
k = 0
while k < plt:
site = ""
loc_name = ""
sdata, Ss = [], [] # list of S format data
if isite == 0:
sdata = spec_df
if 'location' in sdata.columns:
loc_name = ':'.join(sdata['location'].unique())
else:
site = sitelist[k]
sdata = spec_df[spec_df['site'] == site]
if 'location' in sdata.columns:
loc_name = sdata['location'][0]
csrecs = sdata[sdata['aniso_tilt_correction'] == CS]
#anitypes = csrecs['aniso_type'].unique()
for name in ['citations', 'location', 'site', 'sample']:
if name not in csrecs:
csrecs[name] = ""
Locs = csrecs['location'].unique()
#Sites = csrecs['site'].unique()
#Samples = csrecs['sample'].unique()
#Specimens = csrecs['specimen'].unique()
#Cits = csrecs['citations'].unique()
for ind, rec in csrecs.iterrows():
s = [float(i.strip()) for i in rec['aniso_s'].split(':')]
if s[0] <= 1.0:
Ss.append(s) # protect against crap
# tau,Vdirs=pmag.doseigs(s)
# do we need fpars somewhere???
# fpars = pmag.dohext(int(rec["aniso_s_n_measurements"]) -6, float(rec["aniso_s_sigma"]), s)
# fill in ResRecs (ignoring this for now, grab it from aniso_magic if needed)
if len(Ss) > 1:
title = "LO:_" + loc_name + '_SI:_' + site + '_SA:__SP:__CO:_' + crd
bpars, hpars = pmagplotlib.plotANIS(ANIS, Ss, iboot, ihext, ivec, ipar,
title, iplot, comp, vec, Dir, num_bootstraps)
if len(PDir) > 0:
pmagplotlib.plotC(ANIS['data'], PDir, 90., 'g')
pmagplotlib.plotC(ANIS['conf'], PDir, 90., 'g')
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
if plots == 1:
save(ANIS,fmt,title)
if hpars != [] and ihext == 1:
HextRec = {}
#for key in ResRec.keys():HextRec[key]=ResRec[key] # copy over stuff
HextRec["anisotropy_v1_dec"] = '%7.1f'%(hpars["v1_dec"])
HextRec["anisotropy_v2_dec"] = '%7.1f'%(hpars["v2_dec"])
HextRec["anisotropy_v3_dec"] = '%7.1f'%(hpars["v3_dec"])
HextRec["anisotropy_v1_inc"] = '%7.1f'%(hpars["v1_inc"])
HextRec["anisotropy_v2_inc"] = '%7.1f'%(hpars["v2_inc"])
HextRec["anisotropy_v3_inc"] = '%7.1f'%(hpars["v3_inc"])
HextRec["anisotropy_t1"] = '%10.8f'%(hpars["t1"])
HextRec["anisotropy_t2"] = '%10.8f'%(hpars["t2"])
HextRec["anisotropy_t3"] = '%10.8f'%(hpars["t3"])
HextRec["anisotropy_hext_F"] = '%7.1f '%(hpars["F"])
HextRec["anisotropy_hext_F12"] = '%7.1f '%(hpars["F12"])
HextRec["anisotropy_hext_F23"] = '%7.1f '%(hpars["F23"])
HextRec["anisotropy_v1_eta_semi_angle"] = '%7.1f '%(hpars["e12"])
HextRec["anisotropy_v1_eta_dec"] = '%7.1f '%(hpars["v2_dec"])
HextRec["anisotropy_v1_eta_inc"] = '%7.1f '%(hpars["v2_inc"])
HextRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f '%(hpars["e13"])
HextRec["anisotropy_v1_zeta_dec"] = '%7.1f '%(hpars["v3_dec"])
HextRec["anisotropy_v1_zeta_inc"] = '%7.1f '%(hpars["v3_inc"])
HextRec["anisotropy_v2_eta_semi_angle"] = '%7.1f '%(hpars["e12"])
HextRec["anisotropy_v2_eta_dec"] = '%7.1f '%(hpars["v1_dec"])
HextRec["anisotropy_v2_eta_inc"] = '%7.1f '%(hpars["v1_inc"])
HextRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f '%(hpars["e23"])
HextRec["anisotropy_v2_zeta_dec"] = '%7.1f '%(hpars["v3_dec"])
HextRec["anisotropy_v2_zeta_inc"] = '%7.1f '%(hpars["v3_inc"])
HextRec["anisotropy_v3_eta_semi_angle"] = '%7.1f '%(hpars["e12"])
HextRec["anisotropy_v3_eta_dec"] = '%7.1f '%(hpars["v1_dec"])
HextRec["anisotropy_v3_eta_inc"] = '%7.1f '%(hpars["v1_inc"])
HextRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f '%(hpars["e23"])
HextRec["anisotropy_v3_zeta_dec"] = '%7.1f '%(hpars["v2_dec"])
HextRec["anisotropy_v3_zeta_inc"] = '%7.1f '%(hpars["v2_inc"])
HextRec["magic_method_codes"] = 'LP-AN:AE-H'
if verbose:
print "Hext Statistics: "
print " tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
print HextRec["anisotropy_t1"], HextRec["anisotropy_v1_dec"],
print HextRec["anisotropy_v1_inc"], HextRec["anisotropy_v1_eta_semi_angle"],
print HextRec["anisotropy_v1_eta_dec"], HextRec["anisotropy_v1_eta_inc"],
print HextRec["anisotropy_v1_zeta_semi_angle"], HextRec["anisotropy_v1_zeta_dec"],
print HextRec["anisotropy_v1_zeta_inc"]
#
print HextRec["anisotropy_t2"],HextRec["anisotropy_v2_dec"],
print HextRec["anisotropy_v2_inc"], HextRec["anisotropy_v2_eta_semi_angle"],
print HextRec["anisotropy_v2_eta_dec"], HextRec["anisotropy_v2_eta_inc"],
print HextRec["anisotropy_v2_zeta_semi_angle"], HextRec["anisotropy_v2_zeta_dec"],
print HextRec["anisotropy_v2_zeta_inc"]
#
print HextRec["anisotropy_t3"], HextRec["anisotropy_v3_dec"],
print HextRec["anisotropy_v3_inc"], HextRec["anisotropy_v3_eta_semi_angle"],
print HextRec["anisotropy_v3_eta_dec"], HextRec["anisotropy_v3_eta_inc"],
print HextRec["anisotropy_v3_zeta_semi_angle"], HextRec["anisotropy_v3_zeta_dec"],
print HextRec["anisotropy_v3_zeta_inc"]
#HextRec['magic_software_packages']=version_num
#ResRecs.append(HextRec)
if bpars != []:
BootRec = {}
#for key in ResRec.keys():BootRec[key]=ResRec[key] # copy over stuff
BootRec["anisotropy_v1_dec"] = '%7.1f'%(bpars["v1_dec"])
BootRec["anisotropy_v2_dec"] = '%7.1f'%(bpars["v2_dec"])
BootRec["anisotropy_v3_dec"] = '%7.1f'%(bpars["v3_dec"])
BootRec["anisotropy_v1_inc"] = '%7.1f'%(bpars["v1_inc"])
BootRec["anisotropy_v2_inc"] = '%7.1f'%(bpars["v2_inc"])
BootRec["anisotropy_v3_inc"] = '%7.1f'%(bpars["v3_inc"])
BootRec["anisotropy_t1"] = '%10.8f'%(bpars["t1"])
BootRec["anisotropy_t2"] = '%10.8f'%(bpars["t2"])
BootRec["anisotropy_t3"] = '%10.8f'%(bpars["t3"])
BootRec["anisotropy_v1_eta_inc"] = '%7.1f '%(bpars["v1_eta_inc"])
BootRec["anisotropy_v1_eta_dec"] = '%7.1f '%(bpars["v1_eta_dec"])
BootRec["anisotropy_v1_eta_semi_angle"] = '%7.1f '%(bpars["v1_eta"])
BootRec["anisotropy_v1_zeta_inc"] = '%7.1f '%(bpars["v1_zeta_inc"])
BootRec["anisotropy_v1_zeta_dec"] = '%7.1f '%(bpars["v1_zeta_dec"])
BootRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f '%(bpars["v1_zeta"])
BootRec["anisotropy_v2_eta_inc"] = '%7.1f '%(bpars["v2_eta_inc"])
BootRec["anisotropy_v2_eta_dec"] = '%7.1f '%(bpars["v2_eta_dec"])
BootRec["anisotropy_v2_eta_semi_angle"] = '%7.1f '%(bpars["v2_eta"])
BootRec["anisotropy_v2_zeta_inc"] = '%7.1f '%(bpars["v2_zeta_inc"])
BootRec["anisotropy_v2_zeta_dec"] = '%7.1f '%(bpars["v2_zeta_dec"])
BootRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f '%(bpars["v2_zeta"])
BootRec["anisotropy_v3_eta_inc"] = '%7.1f '%(bpars["v3_eta_inc"])
BootRec["anisotropy_v3_eta_dec"] = '%7.1f '%(bpars["v3_eta_dec"])
BootRec["anisotropy_v3_eta_semi_angle"] = '%7.1f '%(bpars["v3_eta"])
BootRec["anisotropy_v3_zeta_inc"] = '%7.1f '%(bpars["v3_zeta_inc"])
BootRec["anisotropy_v3_zeta_dec"] = '%7.1f '%(bpars["v3_zeta_dec"])
BootRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f '%(bpars["v3_zeta"])
BootRec["anisotropy_hext_F"] = ''
BootRec["anisotropy_hext_F12"] = ''
BootRec["anisotropy_hext_F23"] = ''
BootRec["magic_method_codes"] = 'LP-AN:AE-H:AE-BS' # regular bootstrap
if ipar == 1:
BootRec["magic_method_codes"] = 'LP-AN:AE-H:AE-BS-P' # parametric bootstrap
if verbose:
print "Boostrap Statistics: "
print " tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
print BootRec["anisotropy_t1"], BootRec["anisotropy_v1_dec"],
print BootRec["anisotropy_v1_inc"], BootRec["anisotropy_v1_eta_semi_angle"],
print BootRec["anisotropy_v1_eta_dec"], BootRec["anisotropy_v1_eta_inc"],
print BootRec["anisotropy_v1_zeta_semi_angle"], BootRec["anisotropy_v1_zeta_dec"],
print BootRec["anisotropy_v1_zeta_inc"]
#
print BootRec["anisotropy_t2"], BootRec["anisotropy_v2_dec"], BootRec["anisotropy_v2_inc"],
print BootRec["anisotropy_v2_eta_semi_angle"], BootRec["anisotropy_v2_eta_dec"],
print BootRec["anisotropy_v2_eta_inc"], BootRec["anisotropy_v2_zeta_semi_angle"],
print BootRec["anisotropy_v2_zeta_dec"], BootRec["anisotropy_v2_zeta_inc"]
#
print BootRec["anisotropy_t3"], BootRec["anisotropy_v3_dec"], BootRec["anisotropy_v3_inc"],
print BootRec["anisotropy_v3_eta_semi_angle"], BootRec["anisotropy_v3_eta_dec"],
print BootRec["anisotropy_v3_eta_inc"], BootRec["anisotropy_v3_zeta_semi_angle"],
print BootRec["anisotropy_v3_zeta_dec"], BootRec["anisotropy_v3_zeta_inc"]
#BootRec['magic_software_packages'] = version_num
ResRecs.append(BootRec)
k += 1
goon = 1
while goon == 1 and iplot == 1 and verbose:
if iboot == 1:
print "compare with [d]irection "
print " plot [g]reat circle, change [c]oord. system, change [e]llipse calculation, s[a]ve plots, [q]uit "
if isite == 1:
print " [p]revious, [s]ite, [q]uit, <return> for next "
ans = raw_input("")
if ans == "q":
sys.exit()
if ans == "e":
iboot, ipar, ihext, ivec = 1, 0, 0, 0
e = raw_input("Do Hext Statistics 1/[0]: ")
if e == "1":
ihext = 1
e = raw_input("Suppress bootstrap 1/[0]: ")
if e == "1":
iboot = 0
if iboot == 1:
e = raw_input("Parametric bootstrap 1/[0]: ")
if e == "1":
ipar = 1
e = raw_input("Plot bootstrap eigenvectors: 1/[0]: ")
if e == "1":
ivec=1
if iplot == 1:
if inittcdf == 0:
ANIS['tcdf'] = 3
pmagplotlib.plot_init(ANIS['tcdf'], 5, 5)
inittcdf = 1
bpars, hpars = pmagplotlib.plotANIS(ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot,
comp, vec, Dir, num_bootstraps)
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
if ans == "c":
print "Current Coordinate system is: "
if CS == -1:
print " Specimen"
if CS == 0:
print " Geographic"
if CS == 100:
print " Tilt corrected"
key = raw_input(" Enter desired coordinate system: [s]pecimen, [g]eographic, [t]ilt corrected ")
if key == 's':
CS = -1
if key == 'g':
CS = 0
if key == 't':
CS = 100
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = -1
if CS == -1:
crd = 's'
if CS == 0:
crd = 'g'
if CS == 100:
crd = 't'
print "desired coordinate system not available, using available: ", crd
k -= 1
goon = 0
if ans == "":
if isite == 1:
goon = 0
else:
print "Good bye "
sys.exit()
if ans == 'd':
if initcdf == 0:
initcdf = 1
ANIS['vxcdf'], ANIS['vycdf'], ANIS['vzcdf'] = 4, 5, 6
pmagplotlib.plot_init(ANIS['vxcdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vycdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vzcdf'], 5, 5)
Dir, comp = [], 1
print """
Input: Vi D I to compare eigenvector Vi with direction D/I
where Vi=1: principal
Vi=2: major
Vi=3: minor
D= declination of comparison direction
I= inclination of comparison direction"""
con = 1
while con == 1:
try:
vdi = raw_input("Vi D I: ").split()
vec = int(vdi[0])-1
Dir = [float(vdi[1]), float(vdi[2])]
con = 0
except IndexError:
print " Incorrect entry, try again "
bpars, hpars = pmagplotlib.plotANIS(ANIS, Ss, iboot, ihext, ivec, ipar, title,
iplot, comp, vec, Dir, num_bootstraps)
Dir, comp = [], 0
if ans == 'g':
con, cnt = 1, 0
while con == 1:
try:
print " Input: input pole to great circle ( D I) to plot a great circle: "
di = raw_input(" D I: ").split()
PDir.append(float(di[0]))
PDir.append(float(di[1]))
con=0
except:
cnt += 1
if cnt < 10:
print " enter the dec and inc of the pole on one line "
else:
print "ummm - you are doing something wrong - i give up"
sys.exit()
pmagplotlib.plotC(ANIS['data'], PDir, 90., 'g')
pmagplotlib.plotC(ANIS['conf'], PDir, 90., 'g')
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
if ans == "p":
k -= 2
goon = 0
if ans == "q":
k = plt
goon = 0
if ans == "s":
keepon = 1
site = raw_input(" print site or part of site desired: ")
while keepon == 1:
try:
k = sitelist.index(site)
keepon = 0
except:
tmplist = []
for qq in range(len(sitelist)):
if site in sitelist[qq]:
tmplist.append(sitelist[qq])
print site, " not found, but this was: "
print tmplist
site = raw_input('Select one or try again\n ')
k = sitelist.index(site)
goon, ans = 0, ""
if ans == "a":
locs = pmag.makelist(Locs)
site_name = "_"
if isite:
site_name = site
title = "LO:_" + locs + '_SI:_' + site_name + '_SA:__SP:__CO:_' + crd
save(ANIS, fmt, title)
goon = 0
else:
if verbose:
print 'skipping plot - not enough data points'
k += 1
# put rmag_results stuff here
#if len(ResRecs)>0:
# ResOut,keylist=pmag.fillkeys(ResRecs)
# pmag.magic_write(outfile,ResOut,'rmag_results')
if verbose:
print " Good bye "
def main():
"""
NAME
eqarea_magic.py
DESCRIPTION
makes equal area projections from declination/inclination data
SYNTAX
eqarea_magic.py [command line options]
INPUT
takes magic formatted sites, samples, specimens, or measurements
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file from magic, default='sites.txt'
supported types=[measurements, specimens, samples, sites]
-fsp FILE: specify specimen file name, (required if you want to plot measurements by sample)
default='specimens.txt'
-fsa FILE: specify sample file name, (required if you want to plot specimens by site)
default='samples.txt'
-fsi FILE: specify site file name, default='sites.txt'
-obj OBJ: specify level of plot [all, sit, sam, spc], default is all
-crd [s,g,t]: specify coordinate system, [s]pecimen, [g]eographic, [t]ilt adjusted
default is geographic, unspecified assumed geographic
-fmt [svg,png,jpg] format for output plots
-ell [F,K,B,Be,Bv] plot Fisher, Kent, Bingham, Bootstrap ellipses or Boostrap eigenvectors
-c plot as colour contour
-sav save plot and quit quietly
NOTE
all: entire file; sit: site; sam: sample; spc: specimen
"""
# initialize some default variables
FIG = {} # plot dictionary
FIG["eqarea"] = 1 # eqarea is figure 1
plotE = 0
plt = 0 # default to not plotting
verbose = pmagplotlib.verbose
# extract arguments from sys.argv
if "-h" in sys.argv:
print main.__doc__
sys.exit()
dir_path = pmag.get_named_arg_from_sys("-WD", default_val=os.getcwd())
pmagplotlib.plot_init(FIG["eqarea"], 5, 5)
in_file = pmag.get_named_arg_from_sys("-f", default_val="sites.txt")
full_in_file = os.path.join(dir_path, in_file)
plot_by = pmag.get_named_arg_from_sys("-obj", default_val="all").lower()
spec_file = pmag.get_named_arg_from_sys("-fsp", default_val="specimens.txt")
samp_file = pmag.get_named_arg_from_sys("-fsa", default_val="samples.txt")
site_file = pmag.get_named_arg_from_sys("-fsi", default_val="sites.txt")
if plot_by == "all":
plot_key = "all"
elif plot_by == "sit":
plot_key = "site"
elif plot_by == "sam":
plot_key = "sample"
elif plot_by == "spc":
plot_key = "specimen"
else:
plot_key = "all"
if "-c" in sys.argv:
contour = 1
else:
contour = 0
if "-sav" in sys.argv:
plt = 1
verbose = 0
if "-ell" in sys.argv:
plotE = 1
ind = sys.argv.index("-ell")
ell_type = sys.argv[ind + 1]
ell_type = pmag.get_named_arg_from_sys("-ell", "F")
dist = ell_type.upper()
# if dist type is unrecognized, use Fisher
if dist not in ["F", "K", "B", "BE", "BV"]:
dist = "F"
if dist == "BV":
FIG["bdirs"] = 2
pmagplotlib.plot_init(FIG["bdirs"], 5, 5)
crd = pmag.get_named_arg_from_sys("-crd", default_val="g")
if crd == "s":
coord = "-1"
elif crd == "t":
coord = "100"
else:
coord = "0"
fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
dec_key = "dir_dec"
inc_key = "dir_inc"
tilt_key = "dir_tilt_correction"
# Dir_type_keys=['','site_direction_type','sample_direction_type','specimen_direction_type']
#
fnames = {"specimens": spec_file, "samples": samp_file, "sites": site_file}
contribution = nb.Contribution(dir_path, custom_filenames=fnames, single_file=in_file)
# the object that contains the DataFrame + useful helper methods:
table_name = contribution.tables.keys()[0]
data_container = contribution.tables[table_name]
# the actual DataFrame:
data = data_container.df
# uses sample infile to add temporary site_name
# column to the specimen table
data_container = contribution.tables[table_name]
data = data_container.df
if (plot_key != "all") and (plot_key not in data.columns):
data = contribution.propagate_name_down(plot_key, table_name)
# add tilt key into DataFrame columns if it isn't there already
if tilt_key not in data.columns:
data.loc[:, tilt_key] = None
if verbose:
print len(data), " records read from ", in_file
# find desired dec,inc data:
dir_type_key = ""
#
# get plotlist if not plotting all records
#
plotlist = []
if plot_key != "all":
# return all where plot_key is not blank
if plot_key not in data.columns:
print 'Can\'t plot by "{}". That header is not in infile: {}'.format(plot_key, in_file)
return
plots = data[data[plot_key].notnull()]
plotlist = plots[plot_key].unique() # grab unique values
else:
plotlist.append("All")
for plot in plotlist:
if verbose:
print plot
if plot == "All":
# plot everything at once
plot_data = data
else:
# pull out only partial data
plot_data = data[data[plot_key] == plot]
DIblock = []
GCblock = []
# SLblock, SPblock = [], []
title = plot
mode = 1
k = 0
if dec_key not in plot_data.columns:
print "-W- No dec/inc data"
continue
# get all records where dec & inc values exist
plot_data = plot_data[plot_data[dec_key].notnull() & plot_data[inc_key].notnull()]
if plot_data.empty:
continue
# this sorting out is done in get_di_bock
# if coord == '0': # geographic, use records with no tilt key (or tilt_key 0)
# cond1 = plot_data[tilt_key].fillna('') == coord
# cond2 = plot_data[tilt_key].isnull()
# plot_data = plot_data[cond1 | cond2]
# else: # not geographic coordinates, use only records with correct tilt_key
# plot_data = plot_data[plot_data[tilt_key] == coord]
# get metadata for naming the plot file
locations = data_container.get_name("location", df_slice=plot_data)
site = data_container.get_name("site", df_slice=plot_data)
sample = data_container.get_name("sample", df_slice=plot_data)
specimen = data_container.get_name("specimen", df_slice=plot_data)
# make sure method_codes is in plot_data
if "method_codes" not in plot_data.columns:
plot_data["method_codes"] = ""
# get data blocks
DIblock = data_container.get_di_block(df_slice=plot_data, tilt_corr=coord, excl=["DE-BFP"])
# SLblock = [[ind, row['method_codes']] for ind, row in plot_data.iterrows()]
# get great circles
great_circle_data = data_container.get_records_for_code("DE-BFP", incl=True, use_slice=True, sli=plot_data)
if len(great_circle_data) > 0:
gc_cond = great_circle_data[tilt_key] == coord
GCblock = [[float(row[dec_key]), float(row[inc_key])] for ind, row in great_circle_data[gc_cond].iterrows()]
# SPblock = [[ind, row['method_codes']] for ind, row in great_circle_data[gc_cond].iterrows()]
if len(DIblock) > 0:
if contour == 0:
pmagplotlib.plotEQ(FIG["eqarea"], DIblock, title)
else:
pmagplotlib.plotEQcont(FIG["eqarea"], DIblock)
else:
pmagplotlib.plotNET(FIG["eqarea"])
if len(GCblock) > 0:
for rec in GCblock:
pmagplotlib.plotC(FIG["eqarea"], rec, 90.0, "g")
if len(DIblock) == 0 and len(GCblock) == 0:
if verbose:
print "no records for plotting"
continue
# sys.exit()
if plotE == 1:
ppars = pmag.doprinc(DIblock) # get principal directions
nDIs, rDIs, npars, rpars = [], [], [], []
for rec in DIblock:
angle = pmag.angle([rec[0], rec[1]], [ppars["dec"], ppars["inc"]])
if angle > 90.0:
rDIs.append(rec)
else:
nDIs.append(rec)
if dist == "B": # do on whole dataset
etitle = "Bingham confidence ellipse"
bpars = pmag.dobingham(DIblock)
for key in bpars.keys():
if key != "n" and verbose:
print " ", key, "%7.1f" % (bpars[key])
if key == "n" and verbose:
print " ", key, " %i" % (bpars[key])
npars.append(bpars["dec"])
npars.append(bpars["inc"])
npars.append(bpars["Zeta"])
npars.append(bpars["Zdec"])
npars.append(bpars["Zinc"])
npars.append(bpars["Eta"])
npars.append(bpars["Edec"])
npars.append(bpars["Einc"])
if dist == "F":
etitle = "Fisher confidence cone"
if len(nDIs) > 2:
fpars = pmag.fisher_mean(nDIs)
for key in fpars.keys():
if key != "n" and verbose:
print " ", key, "%7.1f" % (fpars[key])
if key == "n" and verbose:
print " ", key, " %i" % (fpars[key])
mode += 1
npars.append(fpars["dec"])
npars.append(fpars["inc"])
npars.append(fpars["alpha95"]) # Beta
npars.append(fpars["dec"])
isign = abs(fpars["inc"]) / fpars["inc"]
npars.append(fpars["inc"] - isign * 90.0) # Beta inc
npars.append(fpars["alpha95"]) # gamma
npars.append(fpars["dec"] + 90.0) # Beta dec
npars.append(0.0) # Beta inc
if len(rDIs) > 2:
fpars = pmag.fisher_mean(rDIs)
if verbose:
print "mode ", mode
for key in fpars.keys():
if key != "n" and verbose:
print " ", key, "%7.1f" % (fpars[key])
if key == "n" and verbose:
print " ", key, " %i" % (fpars[key])
mode += 1
rpars.append(fpars["dec"])
rpars.append(fpars["inc"])
rpars.append(fpars["alpha95"]) # Beta
rpars.append(fpars["dec"])
isign = abs(fpars["inc"]) / fpars["inc"]
rpars.append(fpars["inc"] - isign * 90.0) # Beta inc
rpars.append(fpars["alpha95"]) # gamma
rpars.append(fpars["dec"] + 90.0) # Beta dec
rpars.append(0.0) # Beta inc
if dist == "K":
etitle = "Kent confidence ellipse"
if len(nDIs) > 3:
kpars = pmag.dokent(nDIs, len(nDIs))
if verbose:
print "mode ", mode
for key in kpars.keys():
if key != "n" and verbose:
print " ", key, "%7.1f" % (kpars[key])
if key == "n" and verbose:
print " ", key, " %i" % (kpars[key])
mode += 1
npars.append(kpars["dec"])
npars.append(kpars["inc"])
npars.append(kpars["Zeta"])
npars.append(kpars["Zdec"])
npars.append(kpars["Zinc"])
npars.append(kpars["Eta"])
npars.append(kpars["Edec"])
npars.append(kpars["Einc"])
if len(rDIs) > 3:
kpars = pmag.dokent(rDIs, len(rDIs))
if verbose:
print "mode ", mode
for key in kpars.keys():
if key != "n" and verbose:
print " ", key, "%7.1f" % (kpars[key])
if key == "n" and verbose:
print " ", key, " %i" % (kpars[key])
mode += 1
rpars.append(kpars["dec"])
rpars.append(kpars["inc"])
rpars.append(kpars["Zeta"])
rpars.append(kpars["Zdec"])
rpars.append(kpars["Zinc"])
rpars.append(kpars["Eta"])
rpars.append(kpars["Edec"])
rpars.append(kpars["Einc"])
else: # assume bootstrap
if dist == "BE":
if len(nDIs) > 5:
BnDIs = pmag.di_boot(nDIs)
Bkpars = pmag.dokent(BnDIs, 1.0)
if verbose:
print "mode ", mode
for key in Bkpars.keys():
if key != "n" and verbose:
print " ", key, "%7.1f" % (Bkpars[key])
if key == "n" and verbose:
print " ", key, " %i" % (Bkpars[key])
mode += 1
npars.append(Bkpars["dec"])
npars.append(Bkpars["inc"])
npars.append(Bkpars["Zeta"])
npars.append(Bkpars["Zdec"])
npars.append(Bkpars["Zinc"])
npars.append(Bkpars["Eta"])
npars.append(Bkpars["Edec"])
npars.append(Bkpars["Einc"])
if len(rDIs) > 5:
BrDIs = pmag.di_boot(rDIs)
Bkpars = pmag.dokent(BrDIs, 1.0)
if verbose:
print "mode ", mode
for key in Bkpars.keys():
if key != "n" and verbose:
print " ", key, "%7.1f" % (Bkpars[key])
if key == "n" and verbose:
print " ", key, " %i" % (Bkpars[key])
mode += 1
rpars.append(Bkpars["dec"])
rpars.append(Bkpars["inc"])
rpars.append(Bkpars["Zeta"])
rpars.append(Bkpars["Zdec"])
rpars.append(Bkpars["Zinc"])
rpars.append(Bkpars["Eta"])
rpars.append(Bkpars["Edec"])
rpars.append(Bkpars["Einc"])
etitle = "Bootstrapped confidence ellipse"
elif dist == "BV":
sym = {"lower": ["o", "c"], "upper": ["o", "g"], "size": 3, "edgecolor": "face"}
if len(nDIs) > 5:
BnDIs = pmag.di_boot(nDIs)
pmagplotlib.plotEQsym(FIG["bdirs"], BnDIs, "Bootstrapped Eigenvectors", sym)
if len(rDIs) > 5:
BrDIs = pmag.di_boot(rDIs)
if len(nDIs) > 5: # plot on existing plots
pmagplotlib.plotDIsym(FIG["bdirs"], BrDIs, sym)
else:
pmagplotlib.plotEQ(FIG["bdirs"], BrDIs, "Bootstrapped Eigenvectors")
if dist == "B":
if len(nDIs) > 3 or len(rDIs) > 3:
pmagplotlib.plotCONF(FIG["eqarea"], etitle, [], npars, 0)
elif len(nDIs) > 3 and dist != "BV":
pmagplotlib.plotCONF(FIG["eqarea"], etitle, [], npars, 0)
if len(rDIs) > 3:
pmagplotlib.plotCONF(FIG["eqarea"], etitle, [], rpars, 0)
elif len(rDIs) > 3 and dist != "BV":
pmagplotlib.plotCONF(FIG["eqarea"], etitle, [], rpars, 0)
for key in FIG.keys():
files = {}
filename = pmag.get_named_arg_from_sys("-fname")
if filename:
filename += "." + fmt
else:
filename = (
"LO:_"
+ locations
+ "_SI:_"
+ site
+ "_SA:_"
+ sample
+ "_SP:_"
+ specimen
+ "_CO:_"
+ crd
+ "_TY:_"
+ key
+ "_."
+ fmt
)
files[key] = filename
if pmagplotlib.isServer:
black = "#000000"
purple = "#800080"
titles = {}
titles["eq"] = "Equal Area Plot"
FIG = pmagplotlib.addBorders(FIG, titles, black, purple)
pmagplotlib.saveP(FIG, files)
if plt:
pmagplotlib.saveP(FIG, files)
continue
if verbose:
pmagplotlib.drawFIGS(FIG)
ans = raw_input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans == "q":
sys.exit()
if ans == "a":
pmagplotlib.saveP(FIG, files)
continue
def main():
"""
NAME
aniso_magic.py
DESCRIPTION
plots anisotropy data with either bootstrap or hext ellipses
SYNTAX
aniso_magic.py [-h] [command line options]
OPTIONS
-h plots help message and quits
-usr USER: set the user name
-f AFILE, specify rmag_anisotropy formatted file for input
-F RFILE, specify rmag_results formatted file for output
-x Hext [1963] and bootstrap
-B DON'T do bootstrap, do Hext
-par Tauxe [1998] parametric bootstrap
-v plot bootstrap eigenvectors instead of ellipses
-sit plot by site instead of entire file
-crd [s,g,t] coordinate system, default is specimen (g=geographic, t=tilt corrected)
-P don't make any plots - just make rmag_results table
-sav don't make the rmag_results table - just save all the plots
-fmt [svg, jpg, eps] format for output images, pdf default
-gtc DEC INC dec,inc of pole to great circle [down(up) in green (cyan)
-d Vi DEC INC; Vi (1,2,3) to compare to direction DEC INC
-nb N; specifies the number of bootstraps - default is 1000
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
plot bootstrap ellipses of Constable & Tauxe [1987]
NOTES
minor axis: circles
major axis: triangles
principal axis: squares
directions are plotted on the lower hemisphere
for bootstrapped eigenvector components: Xs: blue, Ys: red, Zs: black
"""
#
dir_path="."
version_num=pmag.get_version()
verbose=pmagplotlib.verbose
args=sys.argv
ipar,ihext,ivec,iboot,imeas,isite,iplot,vec=0,0,0,1,1,0,1,0
hpars,bpars,PDir=[],[],[]
CS,crd='-1','s'
nb=1000
fmt='pdf'
ResRecs=[]
orlist=[]
outfile,comp,Dir,gtcirc,PDir='rmag_results.txt',0,[],0,[]
infile='rmag_anisotropy.txt'
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
if '-nb' in args:
ind=args.index('-nb')
nb=int(args[ind+1])
if '-usr' in args:
ind=args.index('-usr')
user=args[ind+1]
else:
user=""
if '-B' in args:iboot,ihext=0,1
if '-par' in args:ipar=1
if '-x' in args:ihext=1
if '-v' in args:ivec=1
if '-sit' in args:isite=1
if '-P' in args:iplot=0
if '-f' in args:
ind=args.index('-f')
infile=args[ind+1]
if '-F' in args:
ind=args.index('-F')
outfile=args[ind+1]
if '-crd' in sys.argv:
ind=sys.argv.index('-crd')
crd=sys.argv[ind+1]
if crd=='g':CS='0'
if crd=='t': CS='100'
if '-fmt' in args:
ind=args.index('-fmt')
fmt=args[ind+1]
if '-sav' in args:
plots=1
verbose=0
else:
plots=0
if '-gtc' in args:
ind=args.index('-gtc')
d,i=float(args[ind+1]),float(args[ind+2])
PDir.append(d)
PDir.append(i)
if '-d' in args:
comp=1
ind=args.index('-d')
vec=int(args[ind+1])-1
Dir=[float(args[ind+2]),float(args[ind+3])]
#
# set up plots
#
if infile[0]!='/':infile=dir_path+'/'+infile
if outfile[0]!='/':outfile=dir_path+'/'+outfile
ANIS={}
initcdf,inittcdf=0,0
ANIS['data'],ANIS['conf']=1,2
if iboot==1:
ANIS['tcdf']=3
if iplot==1:
inittcdf=1
pmagplotlib.plot_init(ANIS['tcdf'],5,5)
if comp==1 and iplot==1:
initcdf=1
ANIS['vxcdf'],ANIS['vycdf'],ANIS['vzcdf']=4,5,6
pmagplotlib.plot_init(ANIS['vxcdf'],5,5)
pmagplotlib.plot_init(ANIS['vycdf'],5,5)
pmagplotlib.plot_init(ANIS['vzcdf'],5,5)
if iplot==1:
pmagplotlib.plot_init(ANIS['conf'],5,5)
pmagplotlib.plot_init(ANIS['data'],5,5)
# read in the data
data,ifiletype=pmag.magic_read(infile)
for rec in data: # find all the orientation systems
if 'anisotropy_tilt_correction' not in rec.keys():rec['anisotropy_tilt_correction']='-1'
if rec['anisotropy_tilt_correction'] not in orlist:
orlist.append(rec['anisotropy_tilt_correction'])
if CS not in orlist:
if len(orlist)>0:
CS=orlist[0]
else:
CS='-1'
if CS=='-1':crd='s'
if CS=='0':crd='g'
if CS=='100':crd='t'
if verbose:print("desired coordinate system not available, using available: ",crd)
if isite==1:
sitelist=[]
for rec in data:
if rec['er_site_name'] not in sitelist:sitelist.append(rec['er_site_name'])
sitelist.sort()
plt=len(sitelist)
else:plt=1
k=0
while k<plt:
site=""
sdata,Ss=[],[] # list of S format data
Locs,Sites,Samples,Specimens,Cits=[],[],[],[],[]
if isite==0:
sdata=data
else:
site=sitelist[k]
for rec in data:
if rec['er_site_name']==site:sdata.append(rec)
anitypes=[]
csrecs=pmag.get_dictitem(sdata,'anisotropy_tilt_correction',CS,'T')
for rec in csrecs:
if rec['anisotropy_type'] not in anitypes:anitypes.append(rec['anisotropy_type'])
if rec['er_location_name'] not in Locs:Locs.append(rec['er_location_name'])
if rec['er_site_name'] not in Sites:Sites.append(rec['er_site_name'])
if rec['er_sample_name'] not in Samples:Samples.append(rec['er_sample_name'])
if rec['er_specimen_name'] not in Specimens:Specimens.append(rec['er_specimen_name'])
if rec['er_citation_names'] not in Cits:Cits.append(rec['er_citation_names'])
s=[]
s.append(float(rec["anisotropy_s1"]))
s.append(float(rec["anisotropy_s2"]))
s.append(float(rec["anisotropy_s3"]))
s.append(float(rec["anisotropy_s4"]))
s.append(float(rec["anisotropy_s5"]))
s.append(float(rec["anisotropy_s6"]))
if s[0]<=1.0:Ss.append(s) # protect against crap
#tau,Vdirs=pmag.doseigs(s)
ResRec={}
ResRec['er_location_names']=rec['er_location_name']
ResRec['er_citation_names']=rec['er_citation_names']
ResRec['er_site_names']=rec['er_site_name']
ResRec['er_sample_names']=rec['er_sample_name']
ResRec['er_specimen_names']=rec['er_specimen_name']
ResRec['rmag_result_name']=rec['er_specimen_name']+":"+rec['anisotropy_type']
ResRec["er_analyst_mail_names"]=user
ResRec["tilt_correction"]=CS
ResRec["anisotropy_type"]=rec['anisotropy_type']
if "anisotropy_n" not in rec.keys(): rec["anisotropy_n"]="6"
if "anisotropy_sigma" not in rec.keys(): rec["anisotropy_sigma"]="0"
fpars=pmag.dohext(int(rec["anisotropy_n"])-6,float(rec["anisotropy_sigma"]),s)
ResRec["anisotropy_v1_dec"]='%7.1f'%(fpars['v1_dec'])
ResRec["anisotropy_v2_dec"]='%7.1f'%(fpars['v2_dec'])
ResRec["anisotropy_v3_dec"]='%7.1f'%(fpars['v3_dec'])
ResRec["anisotropy_v1_inc"]='%7.1f'%(fpars['v1_inc'])
ResRec["anisotropy_v2_inc"]='%7.1f'%(fpars['v2_inc'])
ResRec["anisotropy_v3_inc"]='%7.1f'%(fpars['v3_inc'])
ResRec["anisotropy_t1"]='%10.8f'%(fpars['t1'])
ResRec["anisotropy_t2"]='%10.8f'%(fpars['t2'])
ResRec["anisotropy_t3"]='%10.8f'%(fpars['t3'])
ResRec["anisotropy_ftest"]='%10.3f'%(fpars['F'])
ResRec["anisotropy_ftest12"]='%10.3f'%(fpars['F12'])
ResRec["anisotropy_ftest23"]='%10.3f'%(fpars['F23'])
ResRec["result_description"]='F_crit: '+fpars['F_crit']+'; F12,F23_crit: '+fpars['F12_crit']
ResRec['anisotropy_type']=pmag.makelist(anitypes)
ResRecs.append(ResRec)
if len(Ss)>1:
if pmagplotlib.isServer:
title="LO:_"+ResRec['er_location_names']+'_SI:_'+site+'_SA:__SP:__CO:_'+crd
else:
title=ResRec['er_location_names']
if site:
title += "_{}".format(site)
title += '_{}'.format(crd)
ResRec['er_location_names']=pmag.makelist(Locs)
bpars,hpars=pmagplotlib.plotANIS(ANIS,Ss,iboot,ihext,ivec,ipar,title,iplot,comp,vec,Dir,nb)
if len(PDir)>0:
pmagplotlib.plotC(ANIS['data'],PDir,90.,'g')
pmagplotlib.plotC(ANIS['conf'],PDir,90.,'g')
if verbose and plots==0:pmagplotlib.drawFIGS(ANIS)
ResRec['er_location_names']=pmag.makelist(Locs)
if plots==1:
save(ANIS,fmt,title)
ResRec={}
ResRec['er_citation_names']=pmag.makelist(Cits)
ResRec['er_location_names']=pmag.makelist(Locs)
ResRec['er_site_names']=pmag.makelist(Sites)
ResRec['er_sample_names']=pmag.makelist(Samples)
ResRec['er_specimen_names']=pmag.makelist(Specimens)
ResRec['rmag_result_name']=pmag.makelist(Sites)+":"+pmag.makelist(anitypes)
ResRec['anisotropy_type']=pmag.makelist(anitypes)
ResRec["er_analyst_mail_names"]=user
ResRec["tilt_correction"]=CS
if isite=="0":ResRec['result_description']="Study average using coordinate system: "+ CS
if isite=="1":ResRec['result_description']="Site average using coordinate system: " +CS
if hpars!=[] and ihext==1:
HextRec={}
for key in ResRec.keys():HextRec[key]=ResRec[key] # copy over stuff
HextRec["anisotropy_v1_dec"]='%7.1f'%(hpars["v1_dec"])
HextRec["anisotropy_v2_dec"]='%7.1f'%(hpars["v2_dec"])
HextRec["anisotropy_v3_dec"]='%7.1f'%(hpars["v3_dec"])
HextRec["anisotropy_v1_inc"]='%7.1f'%(hpars["v1_inc"])
HextRec["anisotropy_v2_inc"]='%7.1f'%(hpars["v2_inc"])
HextRec["anisotropy_v3_inc"]='%7.1f'%(hpars["v3_inc"])
HextRec["anisotropy_t1"]='%10.8f'%(hpars["t1"])
HextRec["anisotropy_t2"]='%10.8f'%(hpars["t2"])
HextRec["anisotropy_t3"]='%10.8f'%(hpars["t3"])
HextRec["anisotropy_hext_F"]='%7.1f '%(hpars["F"])
HextRec["anisotropy_hext_F12"]='%7.1f '%(hpars["F12"])
HextRec["anisotropy_hext_F23"]='%7.1f '%(hpars["F23"])
HextRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars["e12"])
HextRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars["v2_dec"])
HextRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars["v2_inc"])
HextRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars["e13"])
HextRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars["v3_dec"])
HextRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars["v3_inc"])
HextRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars["e12"])
HextRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars["v1_dec"])
HextRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars["v1_inc"])
HextRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars["e23"])
HextRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars["v3_dec"])
HextRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars["v3_inc"])
HextRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars["e12"])
HextRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars["v1_dec"])
HextRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars["v1_inc"])
HextRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars["e23"])
HextRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars["v2_dec"])
HextRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars["v2_inc"])
HextRec["magic_method_codes"]='LP-AN:AE-H'
if verbose:
print("Hext Statistics: ")
print(" tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I")
print(HextRec["anisotropy_t1"], HextRec["anisotropy_v1_dec"], HextRec["anisotropy_v1_inc"], HextRec["anisotropy_v1_eta_semi_angle"], HextRec["anisotropy_v1_eta_dec"], HextRec["anisotropy_v1_eta_inc"], HextRec["anisotropy_v1_zeta_semi_angle"], HextRec["anisotropy_v1_zeta_dec"], HextRec["anisotropy_v1_zeta_inc"])
print(HextRec["anisotropy_t2"],HextRec["anisotropy_v2_dec"], HextRec["anisotropy_v2_inc"], HextRec["anisotropy_v2_eta_semi_angle"], HextRec["anisotropy_v2_eta_dec"], HextRec["anisotropy_v2_eta_inc"], HextRec["anisotropy_v2_zeta_semi_angle"], HextRec["anisotropy_v2_zeta_dec"], HextRec["anisotropy_v2_zeta_inc"])
print(HextRec["anisotropy_t3"], HextRec["anisotropy_v3_dec"], HextRec["anisotropy_v3_inc"], HextRec["anisotropy_v3_eta_semi_angle"], HextRec["anisotropy_v3_eta_dec"], HextRec["anisotropy_v3_eta_inc"], HextRec["anisotropy_v3_zeta_semi_angle"], HextRec["anisotropy_v3_zeta_dec"], HextRec["anisotropy_v3_zeta_inc"])
HextRec['magic_software_packages']=version_num
ResRecs.append(HextRec)
if bpars!=[]:
BootRec={}
for key in ResRec.keys():BootRec[key]=ResRec[key] # copy over stuff
BootRec["anisotropy_v1_dec"]='%7.1f'%(bpars["v1_dec"])
BootRec["anisotropy_v2_dec"]='%7.1f'%(bpars["v2_dec"])
BootRec["anisotropy_v3_dec"]='%7.1f'%(bpars["v3_dec"])
BootRec["anisotropy_v1_inc"]='%7.1f'%(bpars["v1_inc"])
BootRec["anisotropy_v2_inc"]='%7.1f'%(bpars["v2_inc"])
BootRec["anisotropy_v3_inc"]='%7.1f'%(bpars["v3_inc"])
BootRec["anisotropy_t1"]='%10.8f'%(bpars["t1"])
BootRec["anisotropy_t2"]='%10.8f'%(bpars["t2"])
BootRec["anisotropy_t3"]='%10.8f'%(bpars["t3"])
BootRec["anisotropy_v1_eta_inc"]='%7.1f '%(bpars["v1_eta_inc"])
BootRec["anisotropy_v1_eta_dec"]='%7.1f '%(bpars["v1_eta_dec"])
BootRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(bpars["v1_eta"])
BootRec["anisotropy_v1_zeta_inc"]='%7.1f '%(bpars["v1_zeta_inc"])
BootRec["anisotropy_v1_zeta_dec"]='%7.1f '%(bpars["v1_zeta_dec"])
BootRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(bpars["v1_zeta"])
BootRec["anisotropy_v2_eta_inc"]='%7.1f '%(bpars["v2_eta_inc"])
BootRec["anisotropy_v2_eta_dec"]='%7.1f '%(bpars["v2_eta_dec"])
BootRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(bpars["v2_eta"])
BootRec["anisotropy_v2_zeta_inc"]='%7.1f '%(bpars["v2_zeta_inc"])
BootRec["anisotropy_v2_zeta_dec"]='%7.1f '%(bpars["v2_zeta_dec"])
BootRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(bpars["v2_zeta"])
BootRec["anisotropy_v3_eta_inc"]='%7.1f '%(bpars["v3_eta_inc"])
BootRec["anisotropy_v3_eta_dec"]='%7.1f '%(bpars["v3_eta_dec"])
BootRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(bpars["v3_eta"])
BootRec["anisotropy_v3_zeta_inc"]='%7.1f '%(bpars["v3_zeta_inc"])
BootRec["anisotropy_v3_zeta_dec"]='%7.1f '%(bpars["v3_zeta_dec"])
BootRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(bpars["v3_zeta"])
BootRec["anisotropy_hext_F"]=''
BootRec["anisotropy_hext_F12"]=''
BootRec["anisotropy_hext_F23"]=''
BootRec["magic_method_codes"]='LP-AN:AE-H:AE-BS' # regular bootstrap
if ipar==1:BootRec["magic_method_codes"]='LP-AN:AE-H:AE-BS-P' # parametric bootstrap
if verbose:
print("Boostrap Statistics: ")
print(" tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I")
print(BootRec["anisotropy_t1"], BootRec["anisotropy_v1_dec"], BootRec["anisotropy_v1_inc"], BootRec["anisotropy_v1_eta_semi_angle"], BootRec["anisotropy_v1_eta_dec"], BootRec["anisotropy_v1_eta_inc"], BootRec["anisotropy_v1_zeta_semi_angle"], BootRec["anisotropy_v1_zeta_dec"], BootRec["anisotropy_v1_zeta_inc"])
print(BootRec["anisotropy_t2"],BootRec["anisotropy_v2_dec"], BootRec["anisotropy_v2_inc"], BootRec["anisotropy_v2_eta_semi_angle"], BootRec["anisotropy_v2_eta_dec"], BootRec["anisotropy_v2_eta_inc"], BootRec["anisotropy_v2_zeta_semi_angle"], BootRec["anisotropy_v2_zeta_dec"], BootRec["anisotropy_v2_zeta_inc"])
print(BootRec["anisotropy_t3"], BootRec["anisotropy_v3_dec"], BootRec["anisotropy_v3_inc"], BootRec["anisotropy_v3_eta_semi_angle"], BootRec["anisotropy_v3_eta_dec"], BootRec["anisotropy_v3_eta_inc"], BootRec["anisotropy_v3_zeta_semi_angle"], BootRec["anisotropy_v3_zeta_dec"], BootRec["anisotropy_v3_zeta_inc"])
BootRec['magic_software_packages']=version_num
ResRecs.append(BootRec)
k+=1
goon=1
while goon==1 and iplot==1 and verbose:
if iboot==1: print("compare with [d]irection ")
print(" plot [g]reat circle, change [c]oord. system, change [e]llipse calculation, s[a]ve plots, [q]uit ")
if isite==1: print(" [p]revious, [s]ite, [q]uit, <return> for next ")
ans=raw_input("")
if ans=="q":
sys.exit()
if ans=="e":
iboot,ipar,ihext,ivec=1,0,0,0
e=raw_input("Do Hext Statistics 1/[0]: ")
if e=="1":ihext=1
e=raw_input("Suppress bootstrap 1/[0]: ")
if e=="1":iboot=0
if iboot==1:
e=raw_input("Parametric bootstrap 1/[0]: ")
if e=="1":ipar=1
e=raw_input("Plot bootstrap eigenvectors: 1/[0]: ")
if e=="1":ivec=1
if iplot==1:
if inittcdf==0:
ANIS['tcdf']=3
pmagplotlib.plot_init(ANIS['tcdf'],5,5)
inittcdf=1
bpars,hpars=pmagplotlib.plotANIS(ANIS,Ss,iboot,ihext,ivec,ipar,title,iplot,comp,vec,Dir,nb)
if verbose and plots==0:pmagplotlib.drawFIGS(ANIS)
if ans=="c":
print("Current Coordinate system is: ")
if CS=='-1':print(" Specimen")
if CS=='0':print(" Geographic")
if CS=='100':print(" Tilt corrected")
key=raw_input(" Enter desired coordinate system: [s]pecimen, [g]eographic, [t]ilt corrected ")
if key=='s':CS='-1'
if key=='g':CS='0'
if key=='t': CS='100'
if CS not in orlist:
if len(orlist)>0:
CS=orlist[0]
else:
CS='-1'
if CS=='-1':crd='s'
if CS=='0':crd='g'
if CS=='100':crd='t'
print("desired coordinate system not available, using available: ",crd)
k-=1
goon=0
if ans=="":
if isite==1:
goon=0
else:
print("Good bye ")
sys.exit()
if ans=='d':
if initcdf==0:
initcdf=1
ANIS['vxcdf'],ANIS['vycdf'],ANIS['vzcdf']=4,5,6
pmagplotlib.plot_init(ANIS['vxcdf'],5,5)
pmagplotlib.plot_init(ANIS['vycdf'],5,5)
pmagplotlib.plot_init(ANIS['vzcdf'],5,5)
Dir,comp=[],1
print("""
Input: Vi D I to compare eigenvector Vi with direction D/I
where Vi=1: principal
Vi=2: major
Vi=3: minor
D= declination of comparison direction
I= inclination of comparison direction""")
con=1
while con==1:
try:
vdi=raw_input("Vi D I: ").split()
vec=int(vdi[0])-1
Dir=[float(vdi[1]),float(vdi[2])]
con=0
except IndexError:
print(" Incorrect entry, try again ")
bpars,hpars=pmagplotlib.plotANIS(ANIS,Ss,iboot,ihext,ivec,ipar,title,iplot,comp,vec,Dir,nb)
Dir,comp=[],0
if ans=='g':
con,cnt=1,0
while con==1:
try:
print(" Input: input pole to great circle ( D I) to plot a great circle: ")
di=raw_input(" D I: ").split()
PDir.append(float(di[0]))
PDir.append(float(di[1]))
con=0
except:
cnt+=1
if cnt<10:
print(" enter the dec and inc of the pole on one line ")
else:
print("ummm - you are doing something wrong - i give up")
sys.exit()
pmagplotlib.plotC(ANIS['data'],PDir,90.,'g')
pmagplotlib.plotC(ANIS['conf'],PDir,90.,'g')
if verbose and plots==0:pmagplotlib.drawFIGS(ANIS)
if ans=="p":
k-=2
goon=0
if ans=="q":
k=plt
goon=0
if ans=="s":
keepon=1
site=raw_input(" print site or part of site desired: ")
while keepon==1:
try:
k=sitelist.index(site)
keepon=0
except:
tmplist=[]
for qq in range(len(sitelist)):
if site in sitelist[qq]:tmplist.append(sitelist[qq])
print(site," not found, but this was: ")
print(tmplist)
site=raw_input('Select one or try again\n ')
k=sitelist.index(site)
goon,ans=0,""
if ans=="a":
locs=pmag.makelist(Locs)
if pmagplotlib.isServer: # use server plot naming convention
title="LO:_"+locs+'_SI:__'+'_SA:__SP:__CO:_'+crd
else: # use more readable plot naming convention
title="{}_{}".format(locs, crd)
save(ANIS,fmt,title)
goon=0
else:
if verbose:print('skipping plot - not enough data points')
k+=1
# put rmag_results stuff here
if len(ResRecs)>0:
ResOut,keylist=pmag.fillkeys(ResRecs)
pmag.magic_write(outfile,ResOut,'rmag_results')
if verbose:
print(" Good bye ")
