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#!/usr/bin/env pythonw
import wx
import os
import sys
import matplotlib
if matplotlib.get_backend() != "WXAgg":
import matplotlib.pylab as plt
import pmagpy.command_line_extractor as extractor
import pmagpy.ipmag as ipmag
import dialogs.pmag_widgets as pw
import dialogs.pmag_menu_dialogs as pmag_menu_dialogs
def main():
plots tau, V3_inc, V1_dec, P and chi versus core_depth
SYNTAX [command line optins]
# or, for Anaconda users:
ani_depthplot_anaconda [command line options]
-h prints help message and quits
-f FILE: specify input rmag_anisotropy format file from magic (MagIC 2 only)
-fb FILE: specify input measurements format file from magic
-fsa FILE: specify input sample format file from magic
-fsp FILE: specify input specimen file (MagIC 3 only)
-fsum FILE : specify input LIMS database (IODP) core summary csv file
to print the core names, set lab to 1
-fa FILE: specify input ages format file from magic
-d min max [in m] depth range to plot
-ds [mcd,mbsf], specify depth scale, default is mbsf (core depth)
-sav save plot without review
-fmt specfiy format for figures - default is svg
Anisotropy file: specimens.txt
Bulk susceptibility file: measurements.txt
Samples file: samples.txt
args = sys.argv
if '-h' in args:
dataframe = extractor.command_line_dataframe([['f', False, 'rmag_anisotropy.txt'],
['fb', False, 'magic_measurements.txt'],
['fsa', False, 'er_samples.txt'],
['fa', False, None], ['fsum', False, None],
['fmt', False, 'svg'], ['ds', False, 'mbsf'],
['d', False, '-1 -1'], ['sav', False, False],
['WD', False, '.' ], ['DM', False, 3],
['fsp', False, 'specimens.txt']])
#args = sys.argv
checked_args = extractor.extract_and_check_args(args, dataframe)
ani_file, meas_file, samp_file, age_file, sum_file, fmt, depth_scale, depth, save_quietly, dir_path, data_model, spec_file = extractor.get_vars(['f', 'fb', 'fsa', 'fa', 'fsum', 'fmt', 'ds', 'd', 'sav', 'WD', 'DM', 'fsp'], checked_args)
# format min/max depth
dmin, dmax = depth.split()
dmin, dmax = float(dmin), float(dmax)
print('you must provide depth in this format: -d dmin dmax')
print('could not parse "{}", defaulting to plotting all depths'.format('-d ' + str(depth)))
dmin, dmax = -1, -1
if depth_scale:
if depth_scale not in ['age', 'mbsf', 'mcd']:
print('-W- Unrecognized option "{}" provided for depth scale.\n Options for depth scale are mbsf (meters below sea floor) or mcd (meters composite depth).\n Alternatively, if you provide an age file the depth scale will be automatically set to plot by age instead.\n Using default "mbsf"'.format(depth_scale))
depth_scale = 'sample_core_depth'
if age_file:
depth_scale = 'age'
elif 'mbsf' in depth_scale:
depth_scale = 'sample_core_depth'
elif 'mcd' in depth_scale:
depth_scale = 'sample_composite_depth'
data_model = int(float(data_model))
# MagIC 2
if data_model == 2:
fig, figname = ipmag.ani_depthplot2(ani_file, meas_file, samp_file, age_file, sum_file, fmt, dmin, dmax, depth_scale, dir_path)
# MagIC 3
if meas_file == "magic_measurements.txt":
meas_file = 'measurements.txt'
if samp_file in ['er_samples.txt', 'pmag_samples.txt']:
samp_file = "samples.txt"
site_file = 'sites.txt'
fig, figname = ipmag.ani_depthplot(spec_file, samp_file, meas_file, site_file, age_file, sum_file, fmt, dmin, dmax, depth_scale, dir_path)
if save_quietly:
if dir_path == '.':
dir_path = os.getcwd()
print('Saved file: {}'.format(figname))
return False
app = wx.App(redirect=False)
if not fig:
pw.simple_warning('No plot was able to be created with the data you provided.\nMake sure you have given all the required information and try again')
return False
dpi = fig.get_dpi()
pixel_width = dpi * fig.get_figwidth()
pixel_height = dpi * fig.get_figheight()
figname = os.path.join(dir_path, figname)
plot_frame = pmag_menu_dialogs.PlotFrame((int(pixel_width), int(pixel_height + 50)),
fig, figname, standalone=True)
if __name__ == "__main__":