def main():
"""
NAME
pmag_results_extract.py
DESCRIPTION
make a tab delimited output file from pmag_results table
SYNTAX
pmag_results_extract.py [command line options]
OPTIONS
-h prints help message and quits
-f RFILE, specify pmag_results table; default is pmag_results.txt
-fa AFILE, specify er_ages table; default is NONE
-fsp SFILE, specify pmag_specimens table, default is NONE
-fcr CFILE, specify pmag_criteria table, default is NONE
-g include specimen_grade in table - only works for PmagPy generated pmag_specimen formatted files.
-tex, output in LaTeX format
"""
do_help = pmag.get_flag_arg_from_sys('-h')
if do_help:
print(main.__doc__)
return False
res_file = pmag.get_named_arg_from_sys('-f', 'pmag_results.txt')
crit_file = pmag.get_named_arg_from_sys('-fcr', '')
spec_file = pmag.get_named_arg_from_sys('-fsp', '')
age_file = pmag.get_named_arg_from_sys('-fa', '')
grade = pmag.get_flag_arg_from_sys('-g')
latex = pmag.get_flag_arg_from_sys('-tex')
WD = pmag.get_named_arg_from_sys('-WD', os.getcwd())
ipmag.pmag_results_extract(res_file, crit_file, spec_file, age_file, latex, grade, WD)
def main():
"""
NAME
pmag_results_extract.py
DESCRIPTION
make a tab delimited output file from pmag_results table
SYNTAX
pmag_results_extract.py [command line options]
OPTIONS
-h prints help message and quits
-f RFILE, specify pmag_results table; default is pmag_results.txt
-fa AFILE, specify er_ages table; default is NONE
-fsp SFILE, specify pmag_specimens table, default is NONE
-fcr CFILE, specify pmag_criteria table, default is NONE
-g include specimen_grade in table - only works for PmagPy generated pmag_specimen formatted files.
-tex, output in LaTeX format
"""
do_help = pmag.get_flag_arg_from_sys('-h')
if do_help:
print(main.__doc__)
return False
res_file = pmag.get_named_arg('-f', 'pmag_results.txt')
crit_file = pmag.get_named_arg('-fcr', '')
spec_file = pmag.get_named_arg('-fsp', '')
age_file = pmag.get_named_arg('-fa', '')
grade = pmag.get_flag_arg_from_sys('-g')
latex = pmag.get_flag_arg_from_sys('-tex')
WD = pmag.get_named_arg('-WD', os.getcwd())
ipmag.pmag_results_extract(res_file, crit_file, spec_file, age_file, latex, grade, WD)
def main():
"""
NAME
dmag_magic.py
DESCRIPTION
plots intensity decay curves for demagnetization experiments
SYNTAX
dmag_magic -h [command line options]
INPUT
takes magic formatted measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot,
default is by location
-LT [AF,T,M]: specify lab treatment type, default AF
-XLP [PI]: exclude specific lab protocols,
(for example, method codes like LP-PI)
-N do not normalize by NRM magnetization
-sav save plots silently and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
# initialize variables from command line + defaults
dir_path = pmag.get_named_arg("-WD", default_val=".")
input_dir_path = pmag.get_named_arg('-ID', '')
if not input_dir_path:
input_dir_path = dir_path
in_file = pmag.get_named_arg("-f", default_val="measurements.txt")
in_file = pmag.resolve_file_name(in_file, input_dir_path)
if "-ID" not in sys.argv:
input_dir_path = os.path.split(in_file)[0]
plot_by = pmag.get_named_arg("-obj", default_val="loc")
LT = pmag.get_named_arg("-LT", "AF")
no_norm = pmag.get_flag_arg_from_sys("-N")
norm = False if no_norm else True
interactive = True
save_plots = pmag.get_flag_arg_from_sys("-sav")
if save_plots:
interactive = False
fmt = pmag.get_named_arg("-fmt", "svg")
XLP = pmag.get_named_arg("-XLP", "")
spec_file = pmag.get_named_arg("-fsp", default_val="specimens.txt")
samp_file = pmag.get_named_arg("-fsa", default_val="samples.txt")
site_file = pmag.get_named_arg("-fsi", default_val="sites.txt")
loc_file = pmag.get_named_arg("-flo", default_val="locations.txt")
ipmag.dmag_magic(in_file, dir_path, input_dir_path, spec_file, samp_file,
site_file, loc_file, plot_by, LT, norm, XLP,
save_plots, fmt, interactive)
def main():
"""
NAME
dmag_magic.py
DESCRIPTION
plots intensity decay curves for demagnetization experiments
SYNTAX
dmag_magic -h [command line options]
INPUT
takes magic formatted measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot,
default is by location
-LT [AF,T,M]: specify lab treatment type, default AF
-XLP [PI]: exclude specific lab protocols,
(for example, method codes like LP-PI)
-N do not normalize by NRM magnetization
-sav save plots silently and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
# initialize variables from command line + defaults
dir_path = pmag.get_named_arg("-WD", default_val=".")
input_dir_path = pmag.get_named_arg('-ID', '')
if not input_dir_path:
input_dir_path = dir_path
in_file = pmag.get_named_arg("-f", default_val="measurements.txt")
in_file = pmag.resolve_file_name(in_file, input_dir_path)
if "-ID" not in sys.argv:
input_dir_path = os.path.split(in_file)[0]
plot_by = pmag.get_named_arg("-obj", default_val="loc")
LT = pmag.get_named_arg("-LT", "AF")
no_norm = pmag.get_flag_arg_from_sys("-N")
norm = False if no_norm else True
interactive = True
save_plots = pmag.get_flag_arg_from_sys("-sav")
if save_plots:
interactive = False
fmt = pmag.get_named_arg("-fmt", "svg")
XLP = pmag.get_named_arg("-XLP", "")
spec_file = pmag.get_named_arg("-fsp", default_val="specimens.txt")
samp_file = pmag.get_named_arg("-fsa", default_val="samples.txt")
site_file = pmag.get_named_arg("-fsi", default_val="sites.txt")
loc_file = pmag.get_named_arg("-flo", default_val="locations.txt")
ipmag.dmag_magic(in_file, dir_path, input_dir_path, spec_file, samp_file,
site_file, loc_file, plot_by, LT, norm, XLP,
save_plots, fmt, interactive, n_plots="all")
def main():
"""
NAME
download_magic.py
DESCRIPTION
unpacks a magic formatted smartbook .txt file from the MagIC database into the
tab delimited MagIC format txt files for use with the MagIC-Py programs.
SYNTAX
download_magic.py command line options]
INPUT
takes either the upload.txt file created by upload_magic.py or a file
downloaded from the MagIC database (http://earthref.org/MagIC)
OPTIONS
-h prints help message and quits
-i allows interactive entry of filename
-f FILE specifies input file name
-sep write location data to separate subdirectories (Location_*), (default False)
-O do not overwrite duplicate Location_* directories while downloading
-DM data model (2 or 3, default 3)
"""
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]
# interactive entry
if '-i' in sys.argv:
infile = input("Magic txt file for unpacking? ")
dir_path = '.'
input_dir_path = '.'
# non-interactive
else:
infile = pmag.get_named_arg("-f", reqd=True)
# if -O flag is present, overwrite is False
overwrite = pmag.get_flag_arg_from_sys("-O", true=False, false=True)
# if -sep flag is present, sep is True
sep = pmag.get_flag_arg_from_sys("-sep", true=True, false=False)
data_model = pmag.get_named_arg("-DM", default_val=3, reqd=False)
dir_path = pmag.get_named_arg("-WD", default_val=".", reqd=False)
input_dir_path = pmag.get_named_arg("-ID", default_val=".", reqd=False)
#if '-ID' not in sys.argv and '-WD' in sys.argv:
# input_dir_path = dir_path
if "-WD" not in sys.argv and "-ID" not in sys.argv:
input_dir_path = os.path.split(infile)[0]
if not input_dir_path:
input_dir_path = "."
ipmag.download_magic(infile, dir_path, input_dir_path, overwrite, True,
data_model, sep)
def main():
"""
NAME
download_magic.py
DESCRIPTION
unpacks a magic formatted smartbook .txt file from the MagIC database into the
tab delimited MagIC format txt files for use with the MagIC-Py programs.
SYNTAX
download_magic.py command line options]
INPUT
takes either the upload.txt file created by upload_magic.py or a file
downloaded from the MagIC database (http://earthref.org/MagIC)
OPTIONS
-h prints help message and quits
-i allows interactive entry of filename
-f FILE specifies input file name
-sep write location data to separate subdirectories (Location_*), (default False)
-O do not overwrite duplicate Location_* directories while downloading
-DM data model (2 or 3, default 3)
"""
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]
# interactive entry
if '-i' in sys.argv:
infile=input("Magic txt file for unpacking? ")
dir_path = '.'
input_dir_path = '.'
# non-interactive
else:
infile = pmag.get_named_arg("-f", reqd=True)
# if -O flag is present, overwrite is False
overwrite = pmag.get_flag_arg_from_sys("-O", true=False, false=True)
# if -sep flag is present, sep is True
sep = pmag.get_flag_arg_from_sys("-sep", true=True, false=False)
data_model = pmag.get_named_arg("-DM", default_val=3, reqd=False)
dir_path = pmag.get_named_arg("-WD", default_val=".", reqd=False)
input_dir_path = pmag.get_named_arg("-ID", default_val=".", reqd=False)
#if '-ID' not in sys.argv and '-WD' in sys.argv:
# input_dir_path = dir_path
if "-WD" not in sys.argv and "-ID" not in sys.argv:
input_dir_path = os.path.split(infile)[0]
if not input_dir_path:
input_dir_path = "."
ipmag.download_magic(infile, dir_path, input_dir_path, overwrite, True, data_model, sep)
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
-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, png 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
-n 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__)
return
dir_path = pmag.get_named_arg("-WD", ".")
if '-ID' in args and dir_path == '.':
dir_path = pmag.get_named_arg("-ID", ".")
iboot, vec = 1, 0
num_bootstraps = pmag.get_named_arg("-n", 1000)
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)
if ivec:
vec = 3
#iplot = pmag.get_flag_arg_from_sys("-P", true=0, false=1)
isite = pmag.get_flag_arg_from_sys("-sit", true=1, false=0)
infile = pmag.get_named_arg('-f', 'specimens.txt')
samp_file = pmag.get_named_arg('-fsa', 'samples.txt')
site_file = pmag.get_named_arg('-fsi', 'sites.txt')
#outfile = pmag.get_named_arg("-F", "rmag_results.txt")
fmt = pmag.get_named_arg("-fmt", "png")
crd = pmag.get_named_arg("-crd", "s")
comp, Dir, PDir = 0, [], []
user = pmag.get_named_arg("-usr", "")
if '-B' in args:
iboot, ihext = 0, 1
save_plots, verbose, interactive = False, True, True
if '-sav' in args:
save_plots = True
verbose = False
interactive = False
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])]
ipmag.aniso_magic_nb(infile, samp_file, site_file, verbose,
ipar, ihext, ivec, isite, False, iboot,
vec, Dir, PDir, crd, num_bootstraps,
dir_path, save_plots=save_plots, interactive=interactive,
fmt=fmt)
def main():
"""
NAME
dmag_magic.py
DESCRIPTION
plots intensity decay curves for demagnetization experiments
SYNTAX
dmag_magic -h [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: magic_measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot,
default is by location
-LT [AF,T,M]: specify lab treatment type, default AF
-XLP [PI]: exclude specific lab protocols,
(for example, method codes like LP-PI)
-N do not normalize by NRM magnetization
-sav save plots silently and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
# initialize variables from command line + defaults
FIG = {} # plot dictionary
FIG['demag'] = 1 # demag is figure 1
in_file = pmag.get_named_arg_from_sys("-f", default_val="measurements.txt")
plot_by = pmag.get_named_arg_from_sys("-obj", default_val="loc")
name_dict = {
'loc': 'location',
'sit': 'site',
'sam': 'sample',
'spc': 'specimen'
}
plot_key = name_dict[plot_by]
LT = "LT-" + pmag.get_named_arg_from_sys("-LT", "AF") + "-Z"
if LT == "LT-T-Z":
units, dmag_key = 'K', 'treat_temp'
elif LT == "LT-AF-Z":
units, dmag_key = 'T', 'treat_ac_field'
elif LT == 'LT-M-Z':
units, dmag_key = 'J', 'treat_mw_energy'
else:
units = 'U'
no_norm = pmag.get_flag_arg_from_sys("-N")
norm = 0 if no_norm else 1
no_plot = pmag.get_flag_arg_from_sys("-sav")
plot = 0 if no_plot else 1
fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
XLP = pmag.get_named_arg_from_sys("-XLP", "")
dir_path = pmag.get_named_arg_from_sys("-WD", os.getcwd())
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")
# create contribution and add required headers
fnames = {"specimens": spec_file, "samples": samp_file, 'sites': site_file}
contribution = nb.Contribution(dir_path,
single_file=in_file,
custom_filenames=fnames)
file_type = list(contribution.tables.keys())[0]
print(len(contribution.tables['measurements'].df), ' records read from ',
in_file)
# add plot_key into measurements table
if plot_key not in contribution.tables['measurements'].df.columns:
#contribution.propagate_name_down(plot_key, 'measurements')
contribution.propagate_location_to_measurements()
data_container = contribution.tables[file_type]
# pare down to only records with useful data
# grab records that have the requested code
data_slice = data_container.get_records_for_code(LT)
# and don't have the offending code
data = data_container.get_records_for_code(XLP,
incl=False,
use_slice=True,
sli=data_slice,
strict_match=False)
# make sure quality is in the dataframe
if 'quality' not in data.columns:
data['quality'] = 'g'
# get intensity key and make sure intensity data is not blank
intlist = ['magn_moment', 'magn_volume', 'magn_mass']
IntMeths = [col_name for col_name in data.columns if col_name in intlist]
# get rid of any entirely blank intensity columns
for col_name in IntMeths:
if not data[col_name].any():
data.drop(col_name, axis=1, inplace=True)
IntMeths = [col_name for col_name in data.columns if col_name in intlist]
if len(IntMeths) == 0:
print('No intensity headers found')
sys.exit()
int_key = IntMeths[
0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
data = data[data[int_key].notnull()]
# make list of individual plots
# by default, will be by location_name
plotlist = data[plot_key].unique()
plotlist.sort()
pmagplotlib.plot_init(FIG['demag'], 5, 5)
# iterate through and plot the data
for plt in plotlist:
plot_data = data[data[plot_key] == plt].copy()
if plot:
print(plt, 'plotting by: ', plot_key)
if len(plot_data) > 2:
title = plt
spcs = []
spcs = plot_data['specimen'].unique()
for spc in spcs:
INTblock = []
spec_data = plot_data[plot_data['specimen'] == spc]
for ind, rec in spec_data.iterrows():
INTblock.append([
float(rec[dmag_key]), 0, 0,
float(rec[int_key]), 1, rec['quality']
])
if len(INTblock) > 2:
pmagplotlib.plotMT(FIG['demag'], INTblock, title, 0, units,
norm)
if not plot:
files = {}
for key in list(FIG.keys()):
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
#sys.exit()
else:
pmagplotlib.drawFIGS(FIG)
prompt = " S[a]ve to save plot, [q]uit, Return to continue: "
ans = input(prompt)
if ans == 'q':
sys.exit()
if ans == "a":
files = {}
for key in list(FIG.keys()):
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['demag'])
def main():
"""
NAME
biplot_magic.py
DESCRIPTION
makes a biplot of specified variables from magic_measurements.txt format file
SYNTAX
biplot_magic.py [-h] [-i] [command line options]
INPUT
takes magic formated magic_measurments file
OPTIONS
-h prints help message and quits
-i interactively set filename and axes for plotting
-f FILE: specifies file name, default: magic_measurements.txt
-fmt [svg,png,jpg], format for images - default is svg
-sav figure and quit
-x XMETH:key:step, specify method code for X axis (optional key and treatment values)
-y YMETH:key:step, specify method code for X axis
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is whole file
-n [V,M] plot volume or mass normalized data only
NOTES
if nothing is specified for x and y, the user will be presented with options
key = ['treatment_ac_field','treatment_dc_field',treatment_temp']
step in mT for fields, K for temperatures
"""
#
file='magic_measurements.txt'
methx,methy,fmt="","",'.svg'
plot_key=''
norm_by=""
#plot=0
no_plot = pmag.get_flag_arg_from_sys('-sav')
if not no_plot:
do_plot = True
else:
do_plot = False
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
if '-n' in sys.argv:
ind=sys.argv.index('-n')
norm_by=sys.argv[ind+1]
xtreat_key,ytreat_key,xstep,ystep="","","",""
if '-x' in sys.argv:
ind=sys.argv.index('-x')
meths=sys.argv[ind+1].split(':')
methx=meths[0]
if len(meths)>1:
xtreat_key=meths[1]
xstep=float(meths[2])
if '-y' in sys.argv:
ind=sys.argv.index('-y')
meths=sys.argv[ind+1].split(':')
methy=meths[0]
if len(meths)>1:
ytreat_key=meths[1]
ystep=float(meths[2])
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
plot_by=sys.argv[ind+1]
if plot_by=='loc':plot_key='er_location_name'
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 '-h' in sys.argv:
do_plot = False
if '-i' in sys.argv:
#
# get name of file from command line
#
file=raw_input("Input magic_measurments file name? [magic_measurements.txt] ")
if file=="":file="magic_measurements.txt"
#
#
FIG={'fig':1}
pmagplotlib.plot_init(FIG['fig'],5,5)
data,file_type=pmag.magic_read(file)
if file_type!="magic_measurements":
print file_type,' not correct format for magic_measurments file'
sys.exit()
#
# collect method codes
methods,plotlist=[],[]
for rec in data:
if plot_key!="":
if rec[plot_key] not in plotlist:plotlist.append(rec[plot_key])
elif len(plotlist)==0:
plotlist.append('All')
meths=rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip() not in methods and meth.strip()!="LP-":
methods.append(meth.strip())
#
if '-i' in sys.argv:
print methods
elif methx =="" or methy=="":
print methods
sys.exit()
GoOn=1
while GoOn==1:
if '-i' in sys.argv:methx=raw_input('Select method for x axis: ')
if methx not in methods:
if '-i' in sys.argv:
print 'try again! method not available'
else:
print main.__doc__
print '\n must specify X axis method\n'
sys.exit()
else:
if pmagplotlib.verbose: print methx, ' selected for X axis'
GoOn=0
GoOn=1
while GoOn==1:
if '-i' in sys.argv:methy=raw_input('Select method for y axis: ')
if methy not in methods:
if '-i' in sys.argv:
print 'try again! method not available'
else:
print main.__doc__
print '\n must specify Y axis method\n'
sys.exit()
else:
if pmagplotlib.verbose: print methy, ' selected for Y axis'
GoOn=0
if norm_by=="":
measkeys=['measurement_magn_mass','measurement_magn_volume','measurement_magn_moment','measurement_magnitude','measurement_chi_volume','measurement_chi_mass','measurement_chi']
elif norm_by=="V":
measkeys=['measurement_magn_volume','measurement_chi_volume']
elif norm_by=="M":
measkeys=['measurement_magn_mass','measurement_chi_mass']
xmeaskey,ymeaskey="",""
plotlist.sort()
for plot in plotlist: # go through objects
if pmagplotlib.verbose:
print plot
X,Y=[],[]
x,y='',''
for rec in data:
if plot_key!="" and rec[plot_key]!=plot:
pass
else:
meths=rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip()==methx:
if xmeaskey=="":
for key in measkeys:
if key in rec.keys() and rec[key]!="":
xmeaskey=key
if pmagplotlib.verbose:
print xmeaskey,' being used for plotting X.'
break
if meth.strip()==methy:
if ymeaskey=="":
for key in measkeys:
if key in rec.keys() and rec[key]!="":
ymeaskey=key
if pmagplotlib.verbose:
print ymeaskey,' being used for plotting Y'
break
if ymeaskey!="" and xmeaskey!="":
for rec in data:
x,y='',''
spec=rec['er_specimen_name'] # get the ydata for this specimen
if rec[ymeaskey]!="" and methy in rec['magic_method_codes'].split(':'):
if ytreat_key=="" or (ytreat_key in rec.keys() and float(rec[ytreat_key])==ystep):
y=float(rec[ymeaskey])
for rec in data: # now find the xdata
if rec['er_specimen_name']==spec and rec[xmeaskey]!="" and methx in rec['magic_method_codes'].split(':'):
if xtreat_key=="" or (xtreat_key in rec.keys() and float(rec[xtreat_key])==xstep):
x=float(rec[xmeaskey])
if x != '' and y!= '':
X.append(x)
Y.append(y)
if len(X)>0:
pmagplotlib.clearFIG(FIG['fig'])
pmagplotlib.plotXY(FIG['fig'],X,Y,sym='ro',xlab=methx,ylab=methy,title=plot+':Biplot')
if not pmagplotlib.isServer and do_plot:
pmagplotlib.drawFIGS(FIG)
ans=raw_input('S[a]ve plots, [q]uit, Return for next plot ' )
if ans=='a':
files={}
for key in FIG.keys(): files[key]=plot+'_'+key+fmt
pmagplotlib.saveP(FIG,files)
if ans=='q':
print "Good-bye\n"
sys.exit()
else:
files={}
for key in FIG.keys(): files[key]=plot+'_'+key+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['fig']='X Y Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
else:
print 'nothing to plot for ',plot
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
-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, png 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
-n 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(new.__doc__)
return
dir_path = pmag.get_named_arg("-WD", ".")
if '-ID' in args and dir_path == '.':
dir_path = pmag.get_named_arg("-ID", ".")
iboot, vec = 1, 0
num_bootstraps = pmag.get_named_arg("-n", 1000)
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)
if ivec:
vec = 3
#iplot = pmag.get_flag_arg_from_sys("-P", true=0, false=1)
isite = pmag.get_flag_arg_from_sys("-sit", true=1, false=0)
infile = pmag.get_named_arg('-f', 'specimens.txt')
samp_file = pmag.get_named_arg('-fsa', 'samples.txt')
site_file = pmag.get_named_arg('-fsi', 'sites.txt')
#outfile = pmag.get_named_arg("-F", "rmag_results.txt")
fmt = pmag.get_named_arg("-fmt", "png")
crd = pmag.get_named_arg("-crd", "s")
comp, Dir, PDir = 0, [], []
user = pmag.get_named_arg("-usr", "")
if '-B' in args:
iboot, ihext = 0, 1
save_plots, verbose, interactive = False, True, True
if '-sav' in args:
save_plots = True
verbose = False
interactive = False
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])]
ipmag.aniso_magic_nb(infile, samp_file, site_file, verbose,
ipar, ihext, ivec, isite, False, iboot,
vec, Dir, PDir, crd, num_bootstraps,
dir_path, save_plots=save_plots, interactive=interactive,
fmt=fmt)
def main():
"""
NAME
s_magic.py
DESCRIPTION
converts .s format data to measurements format.
SYNTAX
s_magic.py [command line options]
OPTIONS
-h prints help message and quits
-DM DATA_MODEL_NUM data model number (default is 3)
-f SFILE specifies the .s file name
-sig last column has sigma
-typ Anisotropy type: AMS,AARM,ATRM (default is AMS)
-F FILE specifies the specimens formatted file name
-usr USER specify username
-loc location specify location/study name
-spc NUM : specify number of characters to
designate a specimen, default = 0
-spn SPECNAME, this specimen has the name SPECNAME
-n first column has specimen name
-crd [s,g,t], specify coordinate system of data
s=specimen,g=geographic,t=tilt adjusted, default is 's'
-ncn NCON: naming convention
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXXYYY: YYY is sample designation with Z characters from site XXX
[5] sample = site
[6] sample, site, location info in er_samples.txt -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
DEFAULT
FILE: specimens.txt
INPUT
X11,X22,X33,X12,X23,X13 (.s format file)
X11,X22,X33,X12,X23,X13,sigma (.s format file with -sig option)
SID, X11,X22,X33,X12,X23,X13 (.s format file with -n option)
OUTPUT
specimens.txt format file
NOTE
because .s files do not have specimen names or location information, the output MagIC files
will have to be changed prior to importing to data base.
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
data_model_num = pmag.get_named_arg("-DM", 3)
data_model_num = int(float(data_model_num))
sfile = pmag.get_named_arg("-f", reqd=True)
if data_model_num == 2:
anisfile = pmag.get_named_arg("-F", "rmag_anisotropy.txt")
else:
anisfile = pmag.get_named_arg("-F", "specimens.txt")
location = pmag.get_named_arg("-loc", "unknown")
user = pmag.get_named_arg("-usr", "")
sitename = pmag.get_named_arg("unknown", "")
specnum = pmag.get_named_arg("-spc", 0)
specnum = -int(specnum)
dir_path = pmag.get_named_arg("-WD", ".")
name = pmag.get_flag_arg_from_sys("-n")
sigma = pmag.get_flag_arg_from_sys("-sig")
spec = pmag.get_named_arg("-spn", "unknown")
atype = pmag.get_named_arg("-typ", 'AMS')
samp_con = pmag.get_named_arg("-ncn", "1")
#if '-sig' in sys.argv:
# sigma = 1
#if "-n" in sys.argv:
# name = 1
coord_type = pmag.get_named_arg("-crd", 's')
convert.s_magic(sfile, anisfile, dir_path, atype,
coord_type, sigma, samp_con, specnum,
location, spec, sitename, user, data_model_num, name)
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
vgpmap_magic.py
DESCRIPTION
makes a map of vgps and a95/dp,dm for site means in a sites table
SYNTAX
vgpmap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE sites format file, [default is sites.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-etp plot the etopo20 topographpy data (requires high resolution data set)
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 5 : small red circles
bs 10 : intermediate blue squares
g^ 20 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to plot all site VGPs
-fmt [pdf, png, eps...] specify output format, default is pdf
-sav save and quit
DEFAULTS
FILE: pmag_results.txt
res: c
prj: ortho
ELAT,ELON = 0,0
SYM SIZE: ro 8
RSYM RSIZE: g^ 8
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg_from_sys("-WD", ".")
# plot: default is 0, if -sav in sys.argv should be 1
plot = pmag.get_flag_arg_from_sys("-sav", true=1, false=0)
fmt = pmag.get_named_arg_from_sys("-fmt", "pdf")
res = pmag.get_named_arg_from_sys("-res", "c")
proj = pmag.get_named_arg_from_sys("-prj", "ortho")
anti = pmag.get_flag_arg_from_sys("-S", true=1, false=0)
fancy = pmag.get_flag_arg_from_sys("-etp", true=1, false=0)
ell = pmag.get_flag_arg_from_sys("-ell", true=1, false=0)
ages = pmag.get_flag_arg_from_sys("-age", true=1, false=0)
if '-rev' in sys.argv:
flip = 1
ind = sys.argv.index('-rev')
rsym = (sys.argv[ind + 1])
rsize = int(sys.argv[ind + 2])
else:
flip, rsym, rsize = 0, "g^", 8
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym = (sys.argv[ind + 1])
size = int(sys.argv[ind + 2])
else:
sym, size = 'ro', 8
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0 = float(sys.argv[ind + 1])
lon_0 = float(sys.argv[ind + 2])
else:
lat_0, lon_0 = 90., 0.
crd = pmag.get_named_arg_from_sys("-crd", "")
coord_dict = {'g': 0, 't': 100}
coord = coord_dict[crd] if crd else ""
results_file = pmag.get_named_arg_from_sys("-f", "sites.txt")
con = nb.Contribution(dir_path, single_file=results_file)
if not list(con.tables.keys()):
print("-W - Couldn't read in data")
return
FIG = {'map': 1}
pmagplotlib.plot_init(FIG['map'], 6, 6)
# read in er_sites file
lats, lons = [], []
Pars = []
dates, rlats, rlons = [], [], []
site_container = con.tables['sites']
site_df = site_container.df
# use individual results
site_df = site_df[site_df['result_type'] == 'i']
# use records with vgp_lat and vgp_lon
cond1, cond2 = site_df['vgp_lat'].notnull(), site_df['vgp_lon'].notnull()
Results = site_df[cond1 & cond2]
# use tilt correction
if coord and 'dir_tilt_correction' in Results.columns:
Results = Results[Results['dir_tilt_correction'] == coord]
# get location name and average ages
location = ":".join(Results['location'].unique())
if 'average_age' in Results.columns and ages == 1:
dates = Results['average_age'].unique()
# go through rows and extract data
for ind, row in Results.iterrows():
lat, lon = float(row['vgp_lat']), float(row['vgp_lon'])
if anti == 1:
lats.append(-lat)
lon = lon + 180.
if lon > 360:
lon = lon - 360.
lons.append(lon)
elif flip == 0:
lats.append(lat)
lons.append(lon)
elif flip == 1:
if lat < 0:
rlats.append(-lat)
lon = lon + 180.
if lon > 360:
lon = lon - 360
rlons.append(lon)
else:
lats.append(lat)
lons.append(lon)
ppars = []
ppars.append(lon)
ppars.append(lat)
ell1, ell2 = "", ""
if 'vgp_dm' in list(row.keys()) and row['vgp_dm']:
ell1 = float(row['vgp_dm'])
if 'vgp_dp' in list(row.keys()) and row['vgp_dp']:
ell2 = float(row['vgp_dp'])
if 'vgp_alpha95' in list(row.keys()) and row['vgp_alpha95'].notnull():
ell1, ell2 = float(row['vgp_alpha95']), float(row['vgp_alpha95'])
if ell1 and ell2:
ppars = []
ppars.append(lons[-1])
ppars.append(lats[-1])
ppars.append(ell1)
ppars.append(lons[-1])
isign = old_div(abs(lats[-1]), lats[-1])
ppars.append(lats[-1] - isign * 90.)
ppars.append(ell2)
ppars.append(lons[-1] + 90.)
ppars.append(0.)
Pars.append(ppars)
location = location.strip(':')
Opts = {
'latmin': -90,
'latmax': 90,
'lonmin': 0.,
'lonmax': 360.,
'lat_0': lat_0,
'lon_0': lon_0,
'proj': proj,
'sym': 'bs',
'symsize': 3,
'pltgrid': 0,
'res': res,
'boundinglat': 0.
}
Opts['details'] = {
'coasts': 1,
'rivers': 0,
'states': 0,
'countries': 0,
'ocean': 1,
'fancy': fancy
}
# make the base map with a blue triangle at the pole
pmagplotlib.plotMAP(FIG['map'], [90.], [0.], Opts)
Opts['pltgrid'] = -1
Opts['sym'] = sym
Opts['symsize'] = size
if len(dates) > 0:
Opts['names'] = dates
if len(lats) > 0:
# add the lats and lons of the poles
pmagplotlib.plotMAP(FIG['map'], lats, lons, Opts)
Opts['names'] = []
if len(rlats) > 0:
Opts['sym'] = rsym
Opts['symsize'] = rsize
# add the lats and lons of the poles
pmagplotlib.plotMAP(FIG['map'], rlats, rlons, Opts)
if plot == 0:
pmagplotlib.drawFIGS(FIG)
if ell == 1: # add ellipses if desired.
Opts['details'] = {
'coasts': 0,
'rivers': 0,
'states': 0,
'countries': 0,
'ocean': 0,
'fancy': fancy
}
Opts['pltgrid'] = -1 # turn off meridian replotting
Opts['symsize'] = 2
Opts['sym'] = 'g-'
for ppars in Pars:
if ppars[2] != 0:
PTS = pmagplotlib.plotELL(FIG['map'], ppars, 'g.', 0, 0)
elats, elons = [], []
for pt in PTS:
elons.append(pt[0])
elats.append(pt[1])
# make the base map with a blue triangle at the pole
pmagplotlib.plotMAP(FIG['map'], elats, elons, Opts)
if plot == 0:
pmagplotlib.drawFIGS(FIG)
files = {}
for key in list(FIG.keys()):
if pmagplotlib.isServer: # use server plot naming convention
files[key] = 'LO:_' + location + '_VGP_map.' + fmt
else: # use more readable naming convention
files[key] = '{}_VGP_map.{}'.format(location, fmt)
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['eq'] = 'LO:_' + location + '_VGP_map'
FIG = pmagplotlib.addBorders(FIG, titles, black, purple)
pmagplotlib.saveP(FIG, files)
elif plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = input(" S[a]ve to save plot, Return to quit: ")
if ans == "a":
pmagplotlib.saveP(FIG, files)
else:
print("Good bye")
sys.exit()
else:
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
vgpmap_magic.py
DESCRIPTION
makes a map of vgps and a95/dp,dm for site means in a sites table
SYNTAX
vgpmap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE sites format file, [default is sites.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-etp plot the etopo20 topographpy data (requires high resolution data set)
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 5 : small red circles
bs 10 : intermediate blue squares
g^ 20 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to plot all site VGPs
-fmt [pdf, png, eps...] specify output format, default is pdf
-sav save and quit
DEFAULTS
FILE: pmag_results.txt
res: c
prj: ortho
ELAT,ELON = 0,0
SYM SIZE: ro 8
RSYM RSIZE: g^ 8
"""
if "-h" in sys.argv:
print main.__doc__
sys.exit()
dir_path = pmag.get_named_arg_from_sys("-WD", ".")
# plot: default is 0, if -sav in sys.argv should be 1
plot = pmag.get_flag_arg_from_sys("-sav", true=1, false=0)
fmt = pmag.get_named_arg_from_sys("-fmt", "pdf")
res = pmag.get_named_arg_from_sys("-res", "c")
proj = pmag.get_named_arg_from_sys("-prj", "ortho")
anti = pmag.get_flag_arg_from_sys("-S", true=1, false=0)
fancy = pmag.get_flag_arg_from_sys("-etp", true=1, false=0)
ell = pmag.get_flag_arg_from_sys("-ell", true=1, false=0)
ages = pmag.get_flag_arg_from_sys("-age", true=1, false=0)
if "-rev" in sys.argv:
flip = 1
ind = sys.argv.index("-rev")
rsym = sys.argv[ind + 1]
rsize = int(sys.argv[ind + 2])
else:
flip, rsym, rsize = 0, "g^", 8
if "-sym" in sys.argv:
ind = sys.argv.index("-sym")
sym = sys.argv[ind + 1]
size = int(sys.argv[ind + 2])
else:
sym, size = "ro", 8
if "-eye" in sys.argv:
ind = sys.argv.index("-eye")
lat_0 = float(sys.argv[ind + 1])
lon_0 = float(sys.argv[ind + 2])
else:
lat_0, lon_0 = 90.0, 0.0
crd = pmag.get_named_arg_from_sys("-crd", "")
coord_dict = {"g": 0, "t": 100}
coord = coord_dict[crd] if crd else ""
results_file = pmag.get_named_arg_from_sys("-f", "sites.txt")
con = nb.Contribution(dir_path, single_file=results_file)
if not con.tables.keys():
print "-W - Couldn't read in data"
return
FIG = {"map": 1}
pmagplotlib.plot_init(FIG["map"], 6, 6)
# read in er_sites file
lats, lons = [], []
Pars = []
dates, rlats, rlons = [], [], []
site_container = con.tables["sites"]
site_df = site_container.df
# use individual results
site_df = site_df[site_df["result_type"] == "i"]
# use records with vgp_lat and vgp_lon
cond1, cond2 = site_df["vgp_lat"].notnull(), site_df["vgp_lon"].notnull()
Results = site_df[cond1 & cond2]
# use tilt correction
if coord and "dir_tilt_correction" in Results.columns:
Results = Results[Results["dir_tilt_correction"] == coord]
# get location name and average ages
location = ":".join(Results["location"].unique())
if "average_age" in Results.columns and ages == 1:
dates = Results["average_age"].unique()
# go through rows and extract data
for ind, row in Results.iterrows():
lat, lon = float(row["vgp_lat"]), float(row["vgp_lon"])
if anti == 1:
lats.append(-lat)
lon = lon + 180.0
if lon > 360:
lon = lon - 360.0
lons.append(lon)
elif flip == 0:
lats.append(lat)
lons.append(lon)
elif flip == 1:
if lat < 0:
rlats.append(-lat)
lon = lon + 180.0
if lon > 360:
lon = lon - 360
rlons.append(lon)
else:
lats.append(lat)
lons.append(lon)
ppars = []
ppars.append(lon)
ppars.append(lat)
ell1, ell2 = "", ""
if "vgp_dm" in row.keys() and row["vgp_dm"]:
ell1 = float(row["vgp_dm"])
if "vgp_dp" in row.keys() and row["vgp_dp"]:
ell2 = float(row["vgp_dp"])
if "vgp_alpha95" in row.keys() and row["vgp_alpha95"].notnull():
ell1, ell2 = float(row["vgp_alpha95"]), float(row["vgp_alpha95"])
if ell1 and ell2:
ppars = []
ppars.append(lons[-1])
ppars.append(lats[-1])
ppars.append(ell1)
ppars.append(lons[-1])
isign = abs(lats[-1]) / lats[-1]
ppars.append(lats[-1] - isign * 90.0)
ppars.append(ell2)
ppars.append(lons[-1] + 90.0)
ppars.append(0.0)
Pars.append(ppars)
location = location.strip(":")
Opts = {
"latmin": -90,
"latmax": 90,
"lonmin": 0.0,
"lonmax": 360.0,
"lat_0": lat_0,
"lon_0": lon_0,
"proj": proj,
"sym": "bs",
"symsize": 3,
"pltgrid": 0,
"res": res,
"boundinglat": 0.0,
}
Opts["details"] = {"coasts": 1, "rivers": 0, "states": 0, "countries": 0, "ocean": 1, "fancy": fancy}
# make the base map with a blue triangle at the pole
pmagplotlib.plotMAP(FIG["map"], [90.0], [0.0], Opts)
Opts["pltgrid"] = -1
Opts["sym"] = sym
Opts["symsize"] = size
if len(dates) > 0:
Opts["names"] = dates
if len(lats) > 0:
# add the lats and lons of the poles
pmagplotlib.plotMAP(FIG["map"], lats, lons, Opts)
Opts["names"] = []
if len(rlats) > 0:
Opts["sym"] = rsym
Opts["symsize"] = rsize
# add the lats and lons of the poles
pmagplotlib.plotMAP(FIG["map"], rlats, rlons, Opts)
if plot == 0:
pmagplotlib.drawFIGS(FIG)
if ell == 1: # add ellipses if desired.
Opts["details"] = {"coasts": 0, "rivers": 0, "states": 0, "countries": 0, "ocean": 0, "fancy": fancy}
Opts["pltgrid"] = -1 # turn off meridian replotting
Opts["symsize"] = 2
Opts["sym"] = "g-"
for ppars in Pars:
if ppars[2] != 0:
PTS = pmagplotlib.plotELL(FIG["map"], ppars, "g.", 0, 0)
elats, elons = [], []
for pt in PTS:
elons.append(pt[0])
elats.append(pt[1])
# make the base map with a blue triangle at the pole
pmagplotlib.plotMAP(FIG["map"], elats, elons, Opts)
if plot == 0:
pmagplotlib.drawFIGS(FIG)
files = {}
for key in FIG.keys():
files[key] = "LO:_" + location + "_VGP_map." + fmt
if pmagplotlib.isServer:
black = "#000000"
purple = "#800080"
titles = {}
titles["eq"] = "LO:_" + location + "_VGP_map"
FIG = pmagplotlib.addBorders(FIG, titles, black, purple)
pmagplotlib.saveP(FIG, files)
elif plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = raw_input(" S[a]ve to save plot, Return to quit: ")
if ans == "a":
pmagplotlib.saveP(FIG, files)
else:
print "Good bye"
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
def main():
"""
NAME
polemap_magic.py
DESCRIPTION
makes a map of paleomagnetic poles and a95/dp,dm for pole in a locations table
SYNTAX
polemap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE location format file, [default is locations.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-etp plot the etopo20 topographpy data (requires high resolution data set)
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 5 : small red circles
bs 10 : intermediate blue squares
g^ 20 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to plot all location poles
-fmt [pdf, png, eps...] specify output format, default is pdf
-sav save and quit
DEFAULTS
FILE: locations.txt
res: c
prj: ortho
ELAT,ELON = 0,0
SYM SIZE: ro 8
RSYM RSIZE: g^ 8
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg("-WD", ".")
# plot: default is 0, if -sav in sys.argv should be 1
plot = pmag.get_flag_arg_from_sys("-sav", true=1, false=0)
fmt = pmag.get_named_arg("-fmt", "pdf")
res = pmag.get_named_arg("-res", "c")
proj = pmag.get_named_arg("-prj", "ortho")
anti = pmag.get_flag_arg_from_sys("-S", true=1, false=0)
fancy = pmag.get_flag_arg_from_sys("-etp", true=1, false=0)
ell = pmag.get_flag_arg_from_sys("-ell", true=1, false=0)
ages = pmag.get_flag_arg_from_sys("-age", true=1, false=0)
if '-rev' in sys.argv:
flip = 1
ind = sys.argv.index('-rev')
rsym = (sys.argv[ind + 1])
rsize = int(sys.argv[ind + 2])
else:
flip, rsym, rsize = 0, "g^", 8
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym = (sys.argv[ind + 1])
size = int(sys.argv[ind + 2])
else:
sym, size = 'ro', 8
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0 = float(sys.argv[ind + 1])
lon_0 = float(sys.argv[ind + 2])
else:
lat_0, lon_0 = 90., 0.
crd = pmag.get_named_arg("-crd", "")
coord_dict = {'g': 0, 't': 100}
coord = coord_dict[crd] if crd else ""
results_file = pmag.get_named_arg("-f", "locations.txt")
con = cb.Contribution(dir_path, single_file=results_file)
if not list(con.tables.keys()):
print("-W - Couldn't read in data")
return False, "Couldn't read in data"
FIG = {'map': 1}
pmagplotlib.plot_init(FIG['map'], 6, 6)
# read in location file
lats, lons = [], []
Pars = []
dates, rlats, rlons = [], [], []
polarities = []
pole_container = con.tables['locations']
pole_df = pole_container.df
# use individual results
if not pmagplotlib.isServer:
if 'result_type' in pole_df.columns:
pole_df = pole_df[pole_df['result_type'] == 'a']
if 'pole_lat' not in pole_df.columns or 'pole_lon' not in pole_df.columns:
print(
"-W- pole_lat and pole_lon are required columns to run polemap_magic.py"
)
return False, "pole_lat and pole_lon are required columns to run polemap_magic.py"
# use records with pole_lat and pole_lon
cond1, cond2 = pole_df['pole_lat'].notnull(), pole_df['pole_lon'].notnull()
Results = pole_df[cond1 & cond2]
# use tilt correction
if coord and 'dir_tilt_correction' in Results.columns:
Results = Results[Results['dir_tilt_correction'] == coord]
# get location name and average ages
loc_list = Results['location'].values
locations = ":".join(Results['location'].unique())
if 'age' not in Results.columns and 'age_low' in Results.columns and 'age_high' in Results.columns:
Results['age'] = Results['age_low']+0.5 * \
(Results['age_high']-Results['age_low'])
if 'age' in Results.columns and ages == 1:
dates = Results['age'].unique()
if not any(Results.index):
print("-W- No poles could be plotted")
return False, "No poles could be plotted"
# go through rows and extract data
for ind, row in Results.iterrows():
lat, lon = float(row['pole_lat']), float(row['pole_lon'])
if 'dir_polarity' in row:
polarities.append(row['dir_polarity'])
if anti == 1:
lats.append(-lat)
lon = lon + 180.
if lon > 360:
lon = lon - 360.
lons.append(lon)
elif flip == 0:
lats.append(lat)
lons.append(lon)
elif flip == 1:
if lat < 0:
rlats.append(-lat)
lon = lon + 180.
if lon > 360:
lon = lon - 360
rlons.append(lon)
else:
lats.append(lat)
lons.append(lon)
ppars = []
ppars.append(lon)
ppars.append(lat)
ell1, ell2 = "", ""
if 'pole_dm' in list(row.keys()) and row['pole_dm']:
ell1 = float(row['pole_dm'])
if 'pole_dp' in list(row.keys()) and row['pole_dp']:
ell2 = float(row['pole_dp'])
if 'pole_alpha95' in list(row.keys()) and row['pole_alpha95']:
ell1, ell2 = float(row['pole_alpha95']), float(row['pole_alpha95'])
if ell1 and ell2:
ppars = []
ppars.append(lons[-1])
ppars.append(lats[-1])
ppars.append(ell1)
ppars.append(lons[-1])
isign = abs(lats[-1]) / lats[-1]
ppars.append(lats[-1] - isign * 90.)
ppars.append(ell2)
ppars.append(lons[-1] + 90.)
ppars.append(0.)
Pars.append(ppars)
locations = locations.strip(':')
Opts = {
'latmin': -90,
'latmax': 90,
'lonmin': 0.,
'lonmax': 360.,
'lat_0': lat_0,
'lon_0': lon_0,
'proj': proj,
'sym': 'bs',
'symsize': 3,
'pltgrid': 0,
'res': res,
'boundinglat': 0.
}
Opts['details'] = {
'coasts': 1,
'rivers': 0,
'states': 0,
'countries': 0,
'ocean': 1,
'fancy': fancy
}
base_Opts = Opts.copy()
# make the base map with a blue triangle at the pole
pmagplotlib.plot_map(FIG['map'], [90.], [0.], Opts)
Opts['pltgrid'] = -1
Opts['sym'] = sym
Opts['symsize'] = size
if len(dates) > 0:
Opts['names'] = dates
if len(lats) > 0:
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], lats, lons, Opts)
Opts['names'] = []
titles = {}
files = {}
if pmagplotlib.isServer:
# plot each indvidual pole for the server
for ind in range(len(lats)):
lat = lats[ind]
lon = lons[ind]
polarity = ""
if 'polarites' in locals():
polarity = polarities[ind]
polarity = "_" + polarity if polarity else ""
location = loc_list[ind]
FIG["map_{}".format(ind)] = ind + 2
pmagplotlib.plot_init(FIG['map'], 6, 6)
# if with baseOpts, lat/lon don't show
# if with Opts, grid lines don't show
pmagplotlib.plot_map(ind + 2, [90], [0.], base_Opts)
pmagplotlib.plot_map(ind + 2, [lat], [lon], Opts)
titles["map_{}".format(ind)] = location
files["map_{}".format(ind)] = "LO:_{}{}_TY:_POLE_map_.{}".format(
location, polarity, fmt)
# truncate location names so that ultra long filenames are not created
if len(locations) > 50:
locations = locations[:50]
if pmagplotlib.isServer:
# use server plot naming convention
if 'contribution' in con.tables:
# try to get contribution id
con_id = con.tables['contribution'].df.iloc[0].id
files['map'] = 'MC:_{}_TY:_POLE_map.{}'.format(con_id, fmt)
else:
# no contribution id available
files['map'] = 'LO:_' + locations + '_TY:_POLE_map.' + fmt
else:
# use readable naming convention for non-database use
files['map'] = '{}_POLE_map.{}'.format(locations, fmt)
#
if len(rlats) > 0:
Opts['sym'] = rsym
Opts['symsize'] = rsize
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], rlats, rlons, Opts)
if plot == 0 and not set_env.IS_WIN:
pmagplotlib.draw_figs(FIG)
if ell == 1: # add ellipses if desired.
Opts['details'] = {
'coasts': 0,
'rivers': 0,
'states': 0,
'countries': 0,
'ocean': 0,
'fancy': fancy
}
Opts['pltgrid'] = -1 # turn off meridian replotting
Opts['symsize'] = 2
Opts['sym'] = 'g-'
for ppars in Pars:
if ppars[2] != 0:
PTS = pmagplotlib.plot_ell(FIG['map'], ppars, 'g.', 0, 0)
elats, elons = [], []
for pt in PTS:
elons.append(pt[0])
elats.append(pt[1])
# make the base map with a blue triangle at the pole
pmagplotlib.plot_map(FIG['map'], elats, elons, Opts)
if plot == 0 and not set_env.IS_WIN:
pmagplotlib.draw_figs(FIG)
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles['map'] = 'LO:_' + locations + '_POLE_map'
if 'contribution' in con.tables:
con_id = con.tables['contribution'].df.iloc[0].id
titles['map'] = "MagIC contribution {} all locations".format(
con_id)
FIG = pmagplotlib.add_borders(FIG, titles, black, purple)
pmagplotlib.save_plots(FIG, files)
elif plot == 0:
pmagplotlib.draw_figs(FIG)
ans = input(" S[a]ve to save plot, Return to quit: ")
if ans == "a":
pmagplotlib.save_plots(FIG, files)
else:
print("Good bye")
else:
pmagplotlib.save_plots(FIG, files)
return True, files
def main():
"""
NAME
dmag_magic.py
DESCRIPTION
plots intensity decay curves for demagnetization experiments
SYNTAX
dmag_magic -h [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: magic_measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot,
default is by location
-LT [AF,T,M]: specify lab treatment type, default AF
-XLP [PI]: exclude specific lab protocols,
(for example, method codes like LP-PI)
-N do not normalize by NRM magnetization
-sav save plots silently and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
# initialize variables from command line + defaults
FIG = {} # plot dictionary
FIG['demag'] = 1 # demag is figure 1
in_file = pmag.get_named_arg_from_sys("-f", default_val="measurements.txt")
plot_by = pmag.get_named_arg_from_sys("-obj", default_val="loc")
name_dict = {'loc': 'location', 'sit': 'site',
'sam': 'sample', 'spc': 'specimen'}
plot_key = name_dict[plot_by]
LT = "LT-" + pmag.get_named_arg_from_sys("-LT", "AF") + "-Z"
if LT == "LT-T-Z":
units, dmag_key = 'K', 'treat_temp'
elif LT == "LT-AF-Z":
units, dmag_key = 'T', 'treat_ac_field'
elif LT == 'LT-M-Z':
units, dmag_key = 'J', 'treat_mw_energy'
else:
units = 'U'
no_norm = pmag.get_flag_arg_from_sys("-N")
norm = 0 if no_norm else 1
no_plot = pmag.get_flag_arg_from_sys("-sav")
plot = 0 if no_plot else 1
fmt = pmag.get_named_arg_from_sys("-fmt", "svg")
XLP = pmag.get_named_arg_from_sys("-XLP", "")
dir_path = pmag.get_named_arg_from_sys("-WD", os.getcwd())
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")
# create contribution and add required headers
fnames = {"specimens": spec_file, "samples": samp_file, 'sites': site_file}
contribution = nb.Contribution(dir_path, single_file=in_file,
custom_filenames=fnames)
file_type = contribution.tables.keys()[0]
print len(contribution.tables['measurements'].df), ' records read from ', in_file
# add plot_key into measurements table
if plot_key not in contribution.tables['measurements'].df.columns:
contribution.propagate_name_down(plot_key, 'measurements')
data_container = contribution.tables[file_type]
# pare down to only records with useful data
# grab records that have the requested code
data_slice = data_container.get_records_for_code(LT)
# and don't have the offending code
data = data_container.get_records_for_code(XLP, incl=False, use_slice=True,
sli=data_slice, strict_match=False)
# make sure quality is in the dataframe
if 'quality' not in data.columns:
data['quality'] = 'g'
# get intensity key and make sure intensity data is not blank
intlist = ['magn_moment', 'magn_volume', 'magn_mass']
IntMeths = [col_name for col_name in data.columns if col_name in intlist]
# get rid of any entirely blank intensity columns
for col_name in IntMeths:
if not data[col_name].any():
data.drop(col_name, axis=1, inplace=True)
IntMeths = [col_name for col_name in data.columns if col_name in intlist]
if len(IntMeths) == 0:
print 'No intensity headers found'
sys.exit()
int_key = IntMeths[0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
data = data[data[int_key].notnull()]
# make list of individual plots
# by default, will be by location_name
plotlist = data[plot_key].unique()
plotlist.sort()
pmagplotlib.plot_init(FIG['demag'], 5, 5)
# iterate through and plot the data
for plt in plotlist:
plot_data = data[data[plot_key] == plt].copy()
if plot:
print plt, 'plotting by: ', plot_key
if len(plot_data) > 2:
title = plt
spcs = []
spcs = plot_data['specimen'].unique()
for spc in spcs:
INTblock = []
spec_data = plot_data[plot_data['specimen'] == spc]
for ind, rec in spec_data.iterrows():
INTblock.append([float(rec[dmag_key]), 0, 0, float(rec[int_key]), 1, rec['quality']])
if len(INTblock) > 2:
pmagplotlib.plotMT(FIG['demag'], INTblock,
title, 0, units, norm)
if not plot:
files = {}
for key in FIG.keys():
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
#sys.exit()
else:
pmagplotlib.drawFIGS(FIG)
prompt = " S[a]ve to save plot, [q]uit, Return to continue: "
ans = raw_input(prompt)
if ans == 'q':
sys.exit()
if ans == "a":
files = {}
for key in FIG.keys():
files[key] = title + '_' + LT + '.' + fmt
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['demag'])
def main():
"""
NAME
polemap_magic.py
DESCRIPTION
makes a map of paleomagnetic poles and a95/dp,dm for pole in a locations table
SYNTAX
polemap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE location format file, [default is locations.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-etp plot the etopo20 topographpy data (requires high resolution data set)
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 20 : small red circles
bs 30 : intermediate blue squares
g^ 40 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to prioritize tilt-corrected
-fmt [pdf, png, eps...] specify output format, default is pdf
-sav save and quit
DEFAULTS
FILE: locations.txt
res: c
prj: ortho
ELAT,ELON = 0,0
SYM SIZE: ro 40
RSYM RSIZE: g^ 40
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg("-WD", ".")
# do_plot: default is 0, if -sav in sys.argv should be 1
save_plots = pmag.get_flag_arg_from_sys("-sav", true=1, false=0)
interactive = True
if save_plots:
interactive = False
fmt = pmag.get_named_arg("-fmt", "pdf")
res = pmag.get_named_arg("-res", "c")
proj = pmag.get_named_arg("-prj", "ortho")
anti = pmag.get_flag_arg_from_sys("-S", true=1, false=0)
fancy = pmag.get_flag_arg_from_sys("-etp", true=1, false=0)
ell = pmag.get_flag_arg_from_sys("-ell", true=1, false=0)
ages = pmag.get_flag_arg_from_sys("-age", true=1, false=0)
if '-rev' in sys.argv:
flip = True
ind = sys.argv.index('-rev')
try:
rsym = (sys.argv[ind + 1])
rsize = int(sys.argv[ind + 2])
except (IndexError, ValueError, KeyError):
flip, rsym, rsize = True, "g^", 40
else:
flip, rsym, rsize = False, "g^", 40
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym = (sys.argv[ind + 1])
size = int(sys.argv[ind + 2])
else:
sym, size = 'ro', 40
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0 = float(sys.argv[ind + 1])
lon_0 = float(sys.argv[ind + 2])
else:
lat_0, lon_0 = 90., 0.
crd = pmag.get_named_arg("-crd", "")
loc_file = pmag.get_named_arg("-f", "locations.txt")
ipmag.polemap_magic(loc_file, dir_path, interactive, crd,
sym, size, rsym, rsize, fmt, res,
proj, flip, anti, fancy, ell, ages, lat_0, lon_0,
save_plots)
def main():
"""
NAME
vgpmap_magic.py
DESCRIPTION
makes a map of vgps and a95/dp,dm for site means in a sites table
SYNTAX
vgpmap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE sites format file, [default is sites.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-etp plot the etopo20 topographpy data (requires high resolution data set)
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 5 : small red circles
bs 10 : intermediate blue squares
g^ 20 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to plot all site VGPs
-fmt [pdf, png, eps...] specify output format, default is pdf
-sav save and quit
DEFAULTS
FILE: sites.txt
res: c
prj: ortho
ELAT,ELON = 0,0
SYM SIZE: ro 8
RSYM RSIZE: g^ 8
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg("-WD", ".")
# plot: default is 0, if -sav in sys.argv should be 1
plot = pmag.get_flag_arg_from_sys("-sav", true=1, false=0)
fmt = pmag.get_named_arg("-fmt", "pdf")
res = pmag.get_named_arg("-res", "c")
proj = pmag.get_named_arg("-prj", "ortho")
anti = pmag.get_flag_arg_from_sys("-S", true=1, false=0)
fancy = pmag.get_flag_arg_from_sys("-etp", true=1, false=0)
ell = pmag.get_flag_arg_from_sys("-ell", true=1, false=0)
ages = pmag.get_flag_arg_from_sys("-age", true=1, false=0)
if '-rev' in sys.argv:
flip = 1
ind = sys.argv.index('-rev')
rsym = (sys.argv[ind + 1])
rsize = int(sys.argv[ind + 2])
else:
flip, rsym, rsize = 0, "g^", 8
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym = (sys.argv[ind + 1])
size = int(sys.argv[ind + 2])
else:
sym, size = 'ro', 8
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0 = float(sys.argv[ind + 1])
lon_0 = float(sys.argv[ind + 2])
else:
lat_0, lon_0 = 90., 0.
crd = pmag.get_named_arg("-crd", "")
coord_dict = {'g': 0, 't': 100}
coord = coord_dict[crd] if crd else ""
results_file = pmag.get_named_arg("-f", "sites.txt")
con = cb.Contribution(dir_path, single_file=results_file)
if not list(con.tables.keys()):
print("-W - Couldn't read in data")
return
FIG = {'map': 1}
pmagplotlib.plot_init(FIG['map'], 6, 6)
# read in er_sites file
lats, lons = [], []
Pars = []
dates, rlats, rlons = [], [], []
site_container = con.tables['sites']
site_df = site_container.df
# use records with vgp_lat and vgp_lon
if 'vgp_lat' in site_df.columns and 'vgp_lon' in site_df.columns:
cond1, cond2 = site_df['vgp_lat'].notnull(), site_df['vgp_lon'].notnull()
else:
print ('nothing to plot')
sys.exit()
Results = site_df[cond1 & cond2]
# use tilt correction
if coord and 'dir_tilt_correction' in Results.columns:
Results = Results[Results['dir_tilt_correction'] == coord]
# get location name and average ages
locs = Results['location'].unique()
if len(locs):
location = ":".join(Results['location'].unique())
else:
location = ""
if 'age' in Results.columns and ages == 1:
dates = Results['age'].unique()
# go through rows and extract data
for ind, row in Results.iterrows():
lat, lon = float(row['vgp_lat']), float(row['vgp_lon'])
if anti == 1:
lats.append(-lat)
lon = lon + 180.
if lon > 360:
lon = lon - 360.
lons.append(lon)
elif flip == 0:
lats.append(lat)
lons.append(lon)
elif flip == 1:
if lat < 0:
rlats.append(-lat)
lon = lon + 180.
if lon > 360:
lon = lon - 360
rlons.append(lon)
else:
lats.append(lat)
lons.append(lon)
ppars = []
ppars.append(lon)
ppars.append(lat)
ell1, ell2 = "", ""
if 'vgp_dm' in list(row.keys()) and row['vgp_dm']:
ell1 = float(row['vgp_dm'])
if 'vgp_dp' in list(row.keys()) and row['vgp_dp']:
ell2 = float(row['vgp_dp'])
if 'vgp_alpha95' in list(row.keys()) and (row['vgp_alpha95'] or row['vgp_alpha95'] == 0):
ell1, ell2 = float(row['vgp_alpha95']), float(row['vgp_alpha95'])
if ell1 and ell2:
ppars = []
ppars.append(lons[-1])
ppars.append(lats[-1])
ppars.append(ell1)
ppars.append(lons[-1])
try:
isign = abs(lats[-1]) / lats[-1]
except ZeroDivisionError:
isign = 1
ppars.append(lats[-1] - isign * 90.)
ppars.append(ell2)
ppars.append(lons[-1] + 90.)
ppars.append(0.)
Pars.append(ppars)
location = location.strip(':')
Opts = {'latmin': -90, 'latmax': 90, 'lonmin': 0., 'lonmax': 360.,
'lat_0': lat_0, 'lon_0': lon_0, 'proj': proj, 'sym': 'bs',
'symsize': 3, 'pltgrid': 0, 'res': res, 'boundinglat': 0.}
Opts['details'] = {'coasts': 1, 'rivers': 0, 'states': 0,
'countries': 0, 'ocean': 1, 'fancy': fancy}
# make the base map with a blue triangle at the pole
pmagplotlib.plot_map(FIG['map'], [90.], [0.], Opts)
Opts['pltgrid'] = -1
Opts['sym'] = sym
Opts['symsize'] = size
if len(dates) > 0:
Opts['names'] = dates
if len(lats) > 0:
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], lats, lons, Opts)
Opts['names'] = []
if len(rlats) > 0:
Opts['sym'] = rsym
Opts['symsize'] = rsize
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], rlats, rlons, Opts)
if plot == 0 and not set_env.IS_WIN:
pmagplotlib.draw_figs(FIG)
if ell == 1: # add ellipses if desired.
Opts['details'] = {'coasts': 0, 'rivers': 0, 'states': 0,
'countries': 0, 'ocean': 0, 'fancy': fancy}
Opts['pltgrid'] = -1 # turn off meridian replotting
Opts['symsize'] = 2
Opts['sym'] = 'g-'
for ppars in Pars:
if ppars[2] != 0:
PTS = pmagplotlib.plot_ell(FIG['map'], ppars, 'g.', 0, 0)
elats, elons = [], []
for pt in PTS:
elons.append(pt[0])
elats.append(pt[1])
# make the base map with a blue triangle at the pole
pmagplotlib.plot_map(FIG['map'], elats, elons, Opts)
if plot == 0 and not set_env.IS_WIN:
pmagplotlib.draw_figs(FIG)
files = {}
for key in list(FIG.keys()):
if pmagplotlib.isServer: # use server plot naming convention
files[key] = 'LO:_' + location + '_TY:_VGP_map.' + fmt
else: # use more readable naming convention
files[key] = '{}_VGP_map.{}'.format(location, fmt)
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['map'] = location + ' VGP map'
FIG = pmagplotlib.add_borders(FIG, titles, black, purple)
pmagplotlib.save_plots(FIG, files)
elif plot == 0:
pmagplotlib.draw_figs(FIG)
ans = input(" S[a]ve to save plot, Return to quit: ")
if ans == "a":
pmagplotlib.save_plots(FIG, files)
else:
print("Good bye")
sys.exit()
else:
pmagplotlib.save_plots(FIG, files)
def main():
"""
NAME
vgpmap_magic.py
DESCRIPTION
makes a map of vgps and a95/dp,dm for site means in a sites table
SYNTAX
vgpmap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE sites format file, [default is sites.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-etp plot the etopo20 topographpy data (requires high resolution data set)
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 5 : small red circles
bs 10 : intermediate blue squares
g^ 20 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to plot all site VGPs
-fmt [pdf, png, eps...] specify output format, default is pdf
-sav save and quit
DEFAULTS
FILE: sites.txt
res: c
prj: ortho
ELAT,ELON = 0,0
SYM SIZE: ro 8
RSYM RSIZE: g^ 8
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg("-WD", ".")
# plot: default is 0, if -sav in sys.argv should be 1
interactive = True
save_plots = pmag.get_flag_arg_from_sys("-sav", true=1, false=0)
if save_plots:
interactive = False
fmt = pmag.get_named_arg("-fmt", "pdf")
res = pmag.get_named_arg("-res", "c")
proj = pmag.get_named_arg("-prj", "ortho")
anti = pmag.get_flag_arg_from_sys("-S", true=1, false=0)
fancy = pmag.get_flag_arg_from_sys("-etp", true=1, false=0)
ell = pmag.get_flag_arg_from_sys("-ell", true=1, false=0)
ages = pmag.get_flag_arg_from_sys("-age", true=1, false=0)
if '-rev' in sys.argv:
flip = 1
ind = sys.argv.index('-rev')
rsym = (sys.argv[ind + 1])
rsize = int(sys.argv[ind + 2])
else:
flip, rsym, rsize = 0, "g^", 8
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym = (sys.argv[ind + 1])
size = int(sys.argv[ind + 2])
else:
sym, size = 'ro', 8
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0 = float(sys.argv[ind + 1])
lon_0 = float(sys.argv[ind + 2])
else:
lat_0, lon_0 = 90., 0.
crd = pmag.get_named_arg("-crd", "")
results_file = pmag.get_named_arg("-f", "sites.txt")
ipmag.vgpmap_magic(dir_path, results_file, crd, sym, size, rsym, rsize,
fmt, res, proj, flip, anti, fancy, ell, ages, lat_0,
lon_0, save_plots, interactive)
def main():
"""
NAME
plot_magmap.py
DESCRIPTION
makes a color contour map of desired field model
SYNTAX
plot_magmap.py [command line options]
OPTIONS
-h prints help and quits
-f FILE specify field model file with format: l m g h
-fmt [pdf,eps,svg,png] specify format for output figure (default is png)
-mod [arch3k,cals3k,pfm9k,hfm10k,cals10k.2,shadif14k,cals10k.1b] specify model for 3ka to 1900 CE, default is cals10k
-alt ALT; specify altitude in km, default is sealevel (0)
-age specify date in decimal year, default is 2016
-lon0: 0 longitude for map, default is 0
-el: [D,I,B,Br] specify element for plotting
-cm: [see https://matplotlib.org/users/colormaps.html] specify color map for plotting (default is RdYlBu)
"""
cmap = 'RdYlBu'
date = 2016.
if not Basemap:
print("-W- You must intstall the Basemap module to run plot_magmap.py")
sys.exit()
dir_path = '.'
lincr = 1 # level increment for contours
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if fmt == 'jpg':
print('jpg not a supported option')
print(main.__doc__)
sys.exit()
else:
fmt = 'png'
if '-cm' in sys.argv:
ind = sys.argv.index('-cm')
cmap = sys.argv[ind + 1]
if '-el' in sys.argv:
ind = sys.argv.index('-el')
el = sys.argv[ind + 1]
else:
el = 'B'
if '-alt' in sys.argv:
ind = sys.argv.index('-alt')
alt = sys.argv[ind + 1]
else:
alt = 0
if '-lon0' in sys.argv:
ind = sys.argv.index('-lon0')
lon_0 = float(sys.argv[ind + 1])
else:
lon_0 = 0
if '-mod' in sys.argv:
ind = sys.argv.index('-mod')
mod = sys.argv[ind + 1]
ghfile = ''
elif '-f' in sys.argv:
ind = sys.argv.index('-f')
ghfile = sys.argv[ind + 1]
mod = 'custom'
date = ''
else:
mod, ghfile = 'cals10k', ''
if '-age' in sys.argv:
ind = sys.argv.index('-age')
date = float(sys.argv[ind + 1])
if '-alt' in sys.argv:
ind = sys.argv.index('-alt')
alt = float(sys.argv[ind + 1])
else:
alt = 0
save = pmag.get_flag_arg_from_sys("-sav")
if mod == 'custom':
d = 'Custom'
else:
d = str(date)
Ds, Is, Bs, Brs, lons, lats = pmag.do_mag_map(date,
mod=mod,
lon_0=lon_0,
alt=alt,
file=ghfile)
if el == 'D':
element = Ds
elif el == 'I':
element = Is
elif el == 'B':
element = Bs
elif el == 'Br':
element = Brs
elif el == 'I':
element = Is
else:
print(main.__doc__)
sys.exit()
pmagplotlib.plot_mag_map(1, element, lons, lats, el, lon_0=0, date=date)
if not save:
pmagplotlib.draw_figs({'map': 1})
res = pmagplotlib.save_or_quit()
if res == 'a':
figname = 'igrf' + d + '.' + fmt
print("1 saved in ", figname)
plt.savefig('igrf' + d + '.' + fmt)
sys.exit()
plt.savefig('igrf' + d + '.' + fmt)
print('Figure saved as: ', 'igrf' + d + '.' + fmt)
def main():
"""
NAME
biplot_magic.py
DESCRIPTION
makes a biplot of specified variables from magic_measurements.txt format file
SYNTAX
biplot_magic.py [-h] [-i] [command line options]
INPUT
takes magic formated magic_measurments file
OPTIONS
-h prints help message and quits
-i interactively set filename and axes for plotting
-f FILE: specifies file name, default: magic_measurements.txt
-fmt [svg,png,jpg], format for images - default is svg
-sav figure and quit
-x XMETH:key:step, specify method code for X axis (optional key and treatment values)
-y YMETH:key:step, specify method code for X axis
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is whole file
-n [V,M] plot volume or mass normalized data only
NOTES
if nothing is specified for x and y, the user will be presented with options
key = ['treatment_ac_field','treatment_dc_field',treatment_temp']
step in mT for fields, K for temperatures
"""
#
file = 'magic_measurements.txt'
methx, methy, fmt = "", "", '.svg'
plot_key = ''
norm_by = ""
#plot=0
no_plot = pmag.get_flag_arg_from_sys('-sav')
if not no_plot:
do_plot = True
else:
do_plot = False
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = '.' + sys.argv[ind + 1]
if '-n' in sys.argv:
ind = sys.argv.index('-n')
norm_by = sys.argv[ind + 1]
xtreat_key, ytreat_key, xstep, ystep = "", "", "", ""
if '-x' in sys.argv:
ind = sys.argv.index('-x')
meths = sys.argv[ind + 1].split(':')
methx = meths[0]
if len(meths) > 1:
xtreat_key = meths[1]
xstep = float(meths[2])
if '-y' in sys.argv:
ind = sys.argv.index('-y')
meths = sys.argv[ind + 1].split(':')
methy = meths[0]
if len(meths) > 1:
ytreat_key = meths[1]
ystep = float(meths[2])
if '-obj' in sys.argv:
ind = sys.argv.index('-obj')
plot_by = sys.argv[ind + 1]
if plot_by == 'loc': plot_key = 'er_location_name'
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 '-h' in sys.argv:
do_plot = False
if '-i' in sys.argv:
#
# get name of file from command line
#
file = input(
"Input magic_measurments file name? [magic_measurements.txt] ")
if file == "": file = "magic_measurements.txt"
#
#
FIG = {'fig': 1}
pmagplotlib.plot_init(FIG['fig'], 5, 5)
data, file_type = pmag.magic_read(file)
if file_type != "magic_measurements":
print(file_type, ' not correct format for magic_measurments file')
sys.exit()
#
# collect method codes
methods, plotlist = [], []
for rec in data:
if plot_key != "":
if rec[plot_key] not in plotlist: plotlist.append(rec[plot_key])
elif len(plotlist) == 0:
plotlist.append('All')
meths = rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip() not in methods and meth.strip() != "LP-":
methods.append(meth.strip())
#
if '-i' in sys.argv:
print(methods)
elif methx == "" or methy == "":
print(methods)
sys.exit()
GoOn = 1
while GoOn == 1:
if '-i' in sys.argv: methx = input('Select method for x axis: ')
if methx not in methods:
if '-i' in sys.argv:
print('try again! method not available')
else:
print(main.__doc__)
print('\n must specify X axis method\n')
sys.exit()
else:
if pmagplotlib.verbose: print(methx, ' selected for X axis')
GoOn = 0
GoOn = 1
while GoOn == 1:
if '-i' in sys.argv: methy = input('Select method for y axis: ')
if methy not in methods:
if '-i' in sys.argv:
print('try again! method not available')
else:
print(main.__doc__)
print('\n must specify Y axis method\n')
sys.exit()
else:
if pmagplotlib.verbose: print(methy, ' selected for Y axis')
GoOn = 0
if norm_by == "":
measkeys = [
'measurement_magn_mass', 'measurement_magn_volume',
'measurement_magn_moment', 'measurement_magnitude',
'measurement_chi_volume', 'measurement_chi_mass', 'measurement_chi'
]
elif norm_by == "V":
measkeys = ['measurement_magn_volume', 'measurement_chi_volume']
elif norm_by == "M":
measkeys = ['measurement_magn_mass', 'measurement_chi_mass']
xmeaskey, ymeaskey = "", ""
plotlist.sort()
for plot in plotlist: # go through objects
if pmagplotlib.verbose:
print(plot)
X, Y = [], []
x, y = '', ''
for rec in data:
if plot_key != "" and rec[plot_key] != plot:
pass
else:
meths = rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip() == methx:
if xmeaskey == "":
for key in measkeys:
if key in list(rec.keys()) and rec[key] != "":
xmeaskey = key
if pmagplotlib.verbose:
print(xmeaskey,
' being used for plotting X.')
break
if meth.strip() == methy:
if ymeaskey == "":
for key in measkeys:
if key in list(rec.keys()) and rec[key] != "":
ymeaskey = key
if pmagplotlib.verbose:
print(ymeaskey,
' being used for plotting Y')
break
if ymeaskey != "" and xmeaskey != "":
for rec in data:
x, y = '', ''
spec = rec[
'er_specimen_name'] # get the ydata for this specimen
if rec[ymeaskey] != "" and methy in rec[
'magic_method_codes'].split(':'):
if ytreat_key == "" or (ytreat_key in list(rec.keys()) and
float(rec[ytreat_key]) == ystep):
y = float(rec[ymeaskey])
for rec in data: # now find the xdata
if rec['er_specimen_name'] == spec and rec[
xmeaskey] != "" and methx in rec[
'magic_method_codes'].split(':'):
if xtreat_key == "" or (
xtreat_key in list(rec.keys())
and float(rec[xtreat_key]) == xstep):
x = float(rec[xmeaskey])
if x != '' and y != '':
X.append(x)
Y.append(y)
if len(X) > 0:
pmagplotlib.clearFIG(FIG['fig'])
pmagplotlib.plotXY(FIG['fig'],
X,
Y,
sym='ro',
xlab=methx,
ylab=methy,
title=plot + ':Biplot')
if not pmagplotlib.isServer and do_plot:
pmagplotlib.drawFIGS(FIG)
ans = input('S[a]ve plots, [q]uit, Return for next plot ')
if ans == 'a':
files = {}
for key in list(FIG.keys()):
files[key] = plot + '_' + key + fmt
pmagplotlib.saveP(FIG, files)
if ans == 'q':
print("Good-bye\n")
sys.exit()
else:
files = {}
for key in list(FIG.keys()):
files[key] = plot + '_' + key + fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['fig'] = 'X Y Plot'
FIG = pmagplotlib.addBorders(FIG, titles, black, purple)
pmagplotlib.saveP(FIG, files)
else:
print('nothing to plot for ', plot)