def test_aniso_depthplot_with_sum_file(self):
dir_path = os.path.join(WD, 'data_files', 'UTESTA', 'UTESTA_MagIC')
sum_file = 'CoreSummary_XXX_UTESTA.csv'
main_plot, plot_name = ipmag.aniso_depthplot(dir_path=dir_path,
sum_file=sum_file)
assert (isinstance(main_plot, matplotlib.figure.Figure))
self.assertEqual(plot_name, 'UTESTA_ani_depthplot.svg')
def test_aniso_depthplot_with_no_files(self):
program_ran, error_message = ipmag.aniso_depthplot()
expected_file = os.path.join('.', 'rmag_anisotropy.txt')
self.assertFalse(program_ran)
self.assertEqual(
error_message,
"Could not find rmag_anisotropy type file: {}.\nPlease provide a valid file path and try again"
.format(expected_file))
def test_aniso_depthplot_with_options(self):
main_plot, plot_name = ipmag.aniso_depthplot(
dmin=20,
dmax=40,
depth_scale='sample_core_depth',
fmt='png',
dir_path=self.aniso_WD)
assert (isinstance(main_plot, matplotlib.figure.Figure))
self.assertEqual(plot_name, 'U1361A_ani_depthplot.png')
def test_aniso_depthplot_with_age_option(self):
main_plot, plot_name = ipmag.aniso_depthplot(age_file='er_ages.txt',
dir_path=self.aniso_WD)
assert (isinstance(main_plot, matplotlib.figure.Figure))
self.assertEqual(plot_name, 'U1361A_ani_depthplot.svg')
def test_aniso_depthplot_with_files(self):
#dir_path = os.path.join(WD, 'data_files', 'UTESTA')
main_plot, plot_name = ipmag.aniso_depthplot(
dir_path=self.aniso_WD, sum_file='CoreSummary_XXX_UTESTA.csv')
assert (isinstance(main_plot, matplotlib.figure.Figure))
self.assertEqual(plot_name, 'U1361A_ani_depthplot.svg')
def test_aniso_depthplot_with_options(self):
main_plot, plot_name = ipmag.aniso_depthplot(dmin=20, dmax=40, depth_scale='sample_core_depth', fmt='png', dir_path=self.aniso_WD)
assert(isinstance(main_plot, matplotlib.figure.Figure))
self.assertEqual(plot_name, 'U1361A_ani_depthplot.png')
def main():
"""
NAME
ani_depthplot.py
DESCRIPTION
plots tau, V3_inc, V1_dec, P and chi versus core_depth
SYNTAX
ani_depthplot.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input rmag_anisotropy format file from magic
-fb FILE: specify input magic_measurements format file from magic
-fsa FILE: specify input er_samples format file from magic
-fsum FILE : specify input LIMS database (IODP) core summary csv file
to print the core names, set lab to 1
-fa FILE: specify input er_ages format file from magic
-d min max [in m] depth range to plot
-ds [mcd,mbsf], specify depth scale, default is mbsf
-sav save plot without review
-fmt specfiy format for figures - default is svg
DEFAULTS:
Anisotropy file: rmag_anisotropy.txt
Bulk susceptibility file: magic_measurements.txt
Samples file: er_samples.txt
"""
args = sys.argv
if '-h' in args:
print main.__doc__
sys.exit()
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, '.' ]])
#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 = extractor.get_vars(['f', 'fb', 'fsa', 'fa', 'fsum', 'fmt', 'ds', 'd', 'sav', 'WD'], checked_args)
# format min/max depth
try:
dmin, dmax = depth.split()
dmin, dmax = float(dmin), float(dmax)
except:
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 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'
else:
print 'Warning: Unrecognized option "{}" provided for depth scale.\nOptions for depth scale are mbsf -- meters below sea floor -- or mcd -- meters composite depth.\nAlternatively, if you provide an age file the depth scale will be automatically set to plot by age instead.\nUsing default "mbsf"'.format(depth_scale)
depth_scale = 'sample_composite_depth'
fig, figname = ipmag.aniso_depthplot(ani_file, meas_file, samp_file, age_file, sum_file, fmt, dmin, dmax, depth_scale, dir_path)
if save_quietly:
if dir_path == '.':
dir_path = os.getcwd()
plt.savefig(figname)
plt.clf()
print 'Saved file: {} in folder: {}'.format(figname, dir_path)
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)
app.MainLoop()
def test_aniso_depthplot_with_age_option(self):
main_plot, plot_name = ipmag.aniso_depthplot(age_file='er_ages.txt', dir_path=self.aniso_WD)
assert(isinstance(main_plot, matplotlib.figure.Figure))
self.assertEqual(plot_name, 'U1361A_ani_depthplot.svg')
def test_aniso_depthplot_with_sum_file(self):
dir_path = os.path.join(WD, 'data_files', 'UTESTA', 'UTESTA_MagIC')
sum_file = 'CoreSummary_XXX_UTESTA.csv'
main_plot, plot_name = ipmag.aniso_depthplot(dir_path=dir_path, sum_file=sum_file)
assert(isinstance(main_plot, matplotlib.figure.Figure))
self.assertEqual(plot_name, 'UTESTA_ani_depthplot.svg')
def test_aniso_depthplot_with_files(self):
#dir_path = os.path.join(WD, 'data_files', 'UTESTA')
main_plot, plot_name = ipmag.aniso_depthplot(dir_path=self.aniso_WD, sum_file='CoreSummary_XXX_UTESTA.csv')
assert(isinstance(main_plot, matplotlib.figure.Figure))
self.assertEqual(plot_name, 'U1361A_ani_depthplot.svg')
def test_aniso_depthplot_with_no_files(self):
program_ran, error_message = ipmag.aniso_depthplot()
expected_file = os.path.join('.', 'rmag_anisotropy.txt')
self.assertFalse(program_ran)
self.assertEqual(error_message, "Could not find rmag_anisotropy type file: {}.\nPlease provide a valid file path and try again".format(expected_file))
def main():
"""
NAME
ani_depthplot.py
DESCRIPTION
plots tau, V3_inc, V1_dec, P and chi versus core_depth
SYNTAX
ani_depthplot.py [command line optins]
# or, for Anaconda users:
ani_depthplot_anaconda [command line options]
OPTIONS
-h prints help message and quits
-f FILE: specify input rmag_anisotropy format file from magic
-fb FILE: specify input magic_measurements format file from magic
-fsa FILE: specify input er_samples format file from magic
-fsum FILE : specify input LIMS database (IODP) core summary csv file
to print the core names, set lab to 1
-fa FILE: specify input er_ages format file from magic
-d min max [in m] depth range to plot
-ds [mcd,mbsf], specify depth scale, default is mbsf
-sav save plot without review
-fmt specfiy format for figures - default is svg
DEFAULTS:
Anisotropy file: rmag_anisotropy.txt
Bulk susceptibility file: magic_measurements.txt
Samples file: er_samples.txt
"""
args = sys.argv
if '-h' in args:
print(main.__doc__)
sys.exit()
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, '.']])
#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 = extractor.get_vars(
['f', 'fb', 'fsa', 'fa', 'fsum', 'fmt', 'ds', 'd', 'sav', 'WD'],
checked_args)
# format min/max depth
try:
dmin, dmax = depth.split()
dmin, dmax = float(dmin), float(dmax)
except:
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 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'
else:
print(
'Warning: Unrecognized option "{}" provided for depth scale.\nOptions for depth scale are mbsf -- meters below sea floor -- or mcd -- meters composite depth.\nAlternatively, if you provide an age file the depth scale will be automatically set to plot by age instead.\nUsing default "mbsf"'
.format(depth_scale))
depth_scale = 'sample_composite_depth'
fig, figname = ipmag.aniso_depthplot(ani_file, meas_file, samp_file,
age_file, sum_file, fmt, dmin, dmax,
depth_scale, dir_path)
if save_quietly:
if dir_path == '.':
dir_path = os.getcwd()
plt.savefig(figname)
plt.clf()
print('Saved file: {} in folder: {}'.format(figname, dir_path))
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)
app.MainLoop()