def test_core_depthplot_bad_params(self):
path = os.path.join(WD, 'data_files', 'core_depthplot')
program_ran, error_message = ipmag.core_depthplot(input_dir_path=path)
self.assertFalse(program_ran)
self.assertEqual(
'No data found to plot\nTry again with different parameters',
error_message)
def test_core_depthplot_with_sum_file(self):
path = os.path.join(WD, 'data_files', 'UTESTA', 'UTESTA_MagIC')
sum_file = 'CoreSummary_XXX_UTESTA.csv'
program_ran, plot_name = ipmag.core_depthplot(input_dir_path=path, spc_file='pmag_specimens.txt', samp_file='er_samples.txt', meth='AF', step=15, sum_file=sum_file)
self.assertTrue(program_ran)
outfile = 'UTESTA_m:_LT-AF-Z_core-depthplot.svg'
self.assertEqual(plot_name, outfile)
def test_core_depthplot_with_sum_file(self):
path = os.path.join(WD, 'data_files', 'UTESTA', 'UTESTA_MagIC')
sum_file = 'CoreSummary_XXX_UTESTA.csv'
program_ran, plot_name = ipmag.core_depthplot(input_dir_path=path, spc_file='pmag_specimens.txt', samp_file='er_samples.txt', meth='AF', step=15, sum_file=sum_file)
self.assertTrue(program_ran)
outfile = 'UTESTA_m:_LT-AF-Z_core-depthplot.svg'
self.assertEqual(plot_name, outfile)
def test_core_depthplot_bad_method(self):
path = os.path.join(WD, 'data_files', 'core_depthplot')
program_ran, error_message = ipmag.core_depthplot(input_dir_path=path,
step=5,
meth='NA')
self.assertFalse(program_ran)
self.assertEqual(error_message,
'method: "{}" not supported'.format('NA'))
def test_core_depthplot_data_model3_options(self):
path = os.path.join(WD, 'data_files', 'core_depthplot')
program_ran, plot_name = ipmag.core_depthplot(input_dir_path=path,
samp_file='samples.txt',
meth='AF',
step=15)
self.assertTrue(program_ran)
self.assertEqual(plot_name,
'DSDP Site 522_m:_LT-AF-Z_core-depthplot.svg')
def test_core_depthplot_data_model3(self):
path = os.path.join(WD, 'data_files', 'core_depthplot')
program_ran, plot_name = ipmag.core_depthplot(input_dir_path=path,
spc_file='specimens.txt',
age_file='ages.txt',
meth='AF', step=15,
fmt='png', pltInc=False,
logit=True, pltTime=True,
timescale='gts12',
amin=0, amax=3, data_model_num=3)
self.assertTrue(program_ran)
self.assertEqual(plot_name, 'DSDP Site 522_m:_LT-AF-Z_core-depthplot.png')
def test_core_depthplot_success_with_other_options(self):
path = os.path.join(WD, 'data_files', 'core_depthplot')
program_ran, plot_name = ipmag.core_depthplot(input_dir_path=path,
spc_file='pmag_specimens.txt',
age_file='er_ages.txt',
meth='AF', step=15,
fmt='png', pltInc=False,
logit=True, pltTime=True,
timescale='gts12',
amin=0, amax=3, data_model_num=2) # pltDec = False causes failure with these data
self.assertTrue(program_ran)
self.assertEqual(plot_name, 'DSDP Site 522_m:_LT-AF-Z_core-depthplot.png')
def test_core_depthplot_success(self):
path = os.path.join(WD, 'data_files', 'core_depthplot')
program_ran, plot_name = ipmag.core_depthplot(
input_dir_path=path,
spc_file='pmag_specimens.txt',
samp_file='er_samples.txt',
meth='AF',
step=15)
#program_ran, plot_name = True, 'DSDP Site 522_m:_LT-AF-Z_core-depthplot.svg'
self.assertTrue(program_ran)
self.assertEqual(plot_name,
'DSDP Site 522_m:_LT-AF-Z_core-depthplot.svg')
def test_core_depthplot_success_with_other_options(self):
path = os.path.join(WD, 'data_files', 'core_depthplot')
program_ran, plot_name = ipmag.core_depthplot(input_dir_path=path,
spc_file='pmag_specimens.txt',
age_file='er_ages.txt',
meth='AF', step=15,
fmt='png', pltInc=False,
logit=True, pltTime=True,
timescale='gts12',
amin=0, amax=3) # pltDec = False causes failure with these data
self.assertTrue(program_ran)
self.assertEqual(plot_name, 'DSDP Site 522_m:_LT-AF-Z_core-depthplot.png')
def test_core_depthplot_without_full_time_options(self):
path = os.path.join(WD, 'data_files', 'core_depthplot')
program_ran, error_message = ipmag.core_depthplot(
input_dir_path=path,
spc_file='pmag_specimens.txt',
samp_file='er_samples.txt',
meth='AF',
step=15,
fmt='png',
pltInc=False,
logit=True,
pltTime=True
) #, timescale='gts12', amin=0, amax=3) # pltDec = False causes failure with these data
self.assertFalse(program_ran)
self.assertEqual(
error_message,
"To plot time, you must provide amin, amax, and timescale")
def test_core_depthplot_data_model3(self):
path = os.path.join(WD, 'data_files', 'core_depthplot')
program_ran, plot_name = ipmag.core_depthplot(input_dir_path=path,
spc_file='specimens.txt',
age_file='ages.txt',
meth='AF',
step=15,
fmt='png',
pltInc=False,
logit=True,
pltTime=True,
timescale='gts12',
amin=0,
amax=3,
data_model_num=3)
self.assertTrue(program_ran)
self.assertEqual(plot_name,
'DSDP Site 522_m:_LT-AF-Z_core-depthplot.png')
def test_core_depthplot_bad_method(self):
path = os.path.join(WD, 'data_files', 'core_depthplot')
program_ran, error_message = ipmag.core_depthplot(input_dir_path=path, step=5, meth='NA')
self.assertFalse(program_ran)
self.assertEqual(error_message, 'method: "{}" not supported'.format('NA'))
def test_core_depthplot_data_model3_options(self):
path = os.path.join(WD, 'data_files', 'core_depthplot')
program_ran, plot_name = ipmag.core_depthplot(input_dir_path=path, samp_file='samples.txt',
meth='AF', step=15)
self.assertTrue(program_ran)
self.assertEqual(plot_name, 'DSDP Site 522_m:_LT-AF-Z_core-depthplot.svg')
def main():
"""
NAME
core_depthplot.py
DESCRIPTION
plots various measurements versus core_depth or age. plots data flagged as 'FS-SS-C' as discrete samples.
SYNTAX
core_depthplot.py [command line options]
# or, for Anaconda users:
core_depthplot_anaconda [command line options]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic_measurments format file from magi
-fsum FILE: specify input LIMS database (IODP) core summary csv file
-fwig FILE: specify input depth,wiggle to plot, in magic format with sample_core_depth key for depth
-fsa FILE: specify input er_samples format file from magic for depth
-fa FILE: specify input er_ages format file from magic for age
NB: must have either -fsa OR -fa (not both)
-fsp FILE sym size: specify input zeq_specimen format file from magic, sym and size
NB: PCAs will have specified color, while fisher means will be white with specified color as the edgecolor
-fres FILE specify input pmag_results file from magic, sym and size
-LP [AF,T,ARM,IRM, X] step [in mT,C,mT,mT, mass/vol] to plot
-S do not plot blanket treatment data (if this is set, you don't need the -LP)
-sym SYM SIZE, symbol, size for continuous points (e.g., ro 5, bs 10, g^ 10 for red dot, blue square, green triangle), default is blue dot at 5 pt
-D do not plot declination
-M do not plot magnetization
-log plot magnetization on a log scale
-L do not connect dots with a line
-I do not plot inclination
-d min max [in m] depth range to plot
-n normalize by weight in er_specimen table
-Iex: plot the expected inc at lat - only available for results with lat info in file
-ts TS amin amax: plot the GPTS for the time interval between amin and amax (numbers in Ma)
TS: [ck95, gts04, gts12]
-ds [mbsf,mcd] specify depth scale, mbsf default
-fmt [svg, eps, pdf, png] specify output format for plot (default: svg)
-sav save plot silently
DEFAULTS:
Measurements file: magic_measurements.txt
Samples file: er_samples.txt
NRM step
Summary file: none
"""
args = sys.argv
if '-h' in args:
print(main.__doc__)
sys.exit()
dataframe = extractor.command_line_dataframe([ ['f', False, 'magic_measurements.txt'], ['fsum', False, ''],
['fwig', False, ''], ['fsa', False, ''],
['fa', False, ''], ['fsp', False, ''],
['fres', False, '' ], ['fmt', False, 'svg'],
['LP', False, ''], ['n', False, False],
['d', False, '-1 -1'], ['ts', False, ''],
['WD', False, '.'], ['L', False, True],
['S', False, True], ['D', False, True],
['I', False, True], ['M', False, True],
['log', False, 0],
['ds', False, 'sample_core_depth'],
['sym', False, 'bo 5'], ['ID', False, '.'],
['sav', False, False], ['DM', False, 3]])
checked_args = extractor.extract_and_check_args(args, dataframe)
meas_file, sum_file, wig_file, samp_file, age_file, spc_file, res_file, fmt, meth, norm, depth, timescale, dir_path, pltLine, pltSus, pltDec, pltInc, pltMag, logit, depth_scale, symbol, input_dir, save, data_model_num = extractor.get_vars(
['f', 'fsum', 'fwig', 'fsa', 'fa', 'fsp', 'fres', 'fmt', 'LP', 'n', 'd', 'ts', 'WD', 'L', 'S', 'D', 'I', 'M', 'log', 'ds', 'sym', 'ID', 'sav', 'DM'], checked_args)
# format some variables
# format symbol/size
try:
sym, size = symbol.split()
size = int(size)
except:
print('you should provide -sym in this format: ro 5')
print('using defaults instead')
sym, size = 'ro', 5
# format result file, symbol, size
if res_file:
try:
res_file, res_sym, res_size = res_file.split()
except:
print('you must provide -fres in this format: -fres filename symbol size')
print(
'could not parse {}, defaulting to using no result file'.format(res_file))
res_file, res_sym, res_size = '', '', 0
else:
res_file, res_sym, res_size = '', '', 0
# format specimen file, symbol, size
if spc_file:
try:
spc_file, spc_sym, spc_size = spc_file.split()
except:
print('you must provide -fsp in this format: -fsp filename symbol size')
print(
'could not parse {}, defaulting to using no specimen file'.format(spc_file))
spc_file, spc_sym, spc_size = '', '', 0
else:
spc_file, spc_sym, spc_size = '', '', 0
# format min/max depth
try:
dmin, dmax = depth.split()
except:
print('you must provide -d in this format: -d dmin dmax')
print('could not parse {}, defaulting to plotting all depths'.format(depth))
dmin, dmax = -1, -1
# format timescale, min/max time
if timescale:
try:
timescale, amin, amax = timescale.split()
pltTime = True
except:
print(
'you must provide -ts in this format: -ts timescale minimum_age maximum_age')
print(
'could not parse {}, defaulting to using no timescale'.format(timescale))
timescale, amin, amax = None, -1, -1
pltTime = False
else:
timescale, amin, amax = None, -1, -1
pltTime = False
# format norm and wt_file
if norm and not isinstance(norm, bool):
wt_file = norm
norm = True
else:
norm = False
wt_file = ''
# format list of protcols and step
try:
method, step = meth.split()
except:
print(
'To use the -LP flag you must provide both the protocol and the step in this format:\n-LP [AF,T,ARM,IRM, X] step [in mT,C,mT,mT, mass/vol] to plot')
print('Defaulting to using no protocol')
method, step = 'LT-NO', 0
# list of varnames
#['f', 'fsum', 'fwig', 'fsa', 'fa', 'fsp', 'fres', 'fmt', 'LP', 'n', 'd', 'ts', 'WD', 'L', 'S', 'D', 'I', 'M', 'log', 'ds', 'sym' ]
#meas_file, sum_file, wig_file, samp_file, age_file, spc_file, res_file, fmt, meth, norm, depth, timescale, dir_path, pltLine, pltSus, pltDec, pltInc, pltMag, logit, depth_scale, symbol
fig, figname = ipmag.core_depthplot(input_dir, meas_file, spc_file, samp_file, age_file, sum_file, wt_file, depth_scale, dmin, dmax, sym, size,
spc_sym, spc_size, method, step, fmt, pltDec, pltInc, pltMag, pltLine, pltSus, logit, pltTime, timescale, amin, amax, norm, data_model_num)
if not pmagplotlib.isServer:
figname = figname.replace(':', '_')
if fig and save:
print('-I- Created plot: {}'.format(figname))
plt.savefig(figname)
return
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_core_depthplot_with_no_files(self):
program_ran, error_message = ipmag.core_depthplot()
self.assertFalse(program_ran)
self.assertEqual(
"You must provide either a magic_measurements file or a pmag_specimens file",
error_message)
def main():
"""
NAME
core_depthplot.py
DESCRIPTION
plots various measurements versus core_depth or age. plots data flagged as 'FS-SS-C' as discrete samples.
SYNTAX
core_depthplot.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic_measurments format file from magi
-fsum FILE: specify input LIMS database (IODP) core summary csv file
-fwig FILE: specify input depth,wiggle to plot, in magic format with sample_core_depth key for depth
-fsa FILE: specify input er_samples format file from magic for depth
-fa FILE: specify input er_ages format file from magic for age
NB: must have either -fsa OR -fa (not both)
-fsp FILE sym size: specify input zeq_specimen format file from magic, sym and size
NB: PCAs will have specified color, while fisher means will be white with specified color as the edgecolor
-fres FILE specify input pmag_results file from magic, sym and size
-LP [AF,T,ARM,IRM, X] step [in mT,C,mT,mT, mass/vol] to plot
-S do not plot blanket treatment data (if this is set, you don't need the -LP)
-sym SYM SIZE, symbol, size for continuous points (e.g., ro 5, bs 10, g^ 10 for red dot, blue square, green triangle), default is blue dot at 5 pt
-D do not plot declination
-M do not plot magnetization
-log plot magnetization on a log scale
-L do not connect dots with a line
-I do not plot inclination
-d min max [in m] depth range to plot
-n normalize by weight in er_specimen table
-Iex: plot the expected inc at lat - only available for results with lat info in file
-ts TS amin amax: plot the GPTS for the time interval between amin and amax (numbers in Ma)
TS: [ck95, gts04, gts12]
-ds [mbsf,mcd] specify depth scale, mbsf default
-fmt [svg, eps, pdf, png] specify output format for plot (default: svg)
-sav save plot silently
DEFAULTS:
Measurements file: magic_measurements.txt
Samples file: er_samples.txt
NRM step
Summary file: none
"""
args = sys.argv
if '-h' in args:
print(main.__doc__)
sys.exit()
dataframe = extractor.command_line_dataframe([ ['f', False, 'magic_measurements.txt'], ['fsum', False, ''],
['fwig', False, ''], ['fsa', False, ''],
['fa', False, ''], ['fsp', False, ''],
['fres', False, '' ], ['fmt', False, 'svg'],
['LP', False, ''], ['n', False, False],
['d', False, '-1 -1'], ['ts', False, ''],
['WD', False, '.'], ['L', False, True],
['S', False, True], ['D', False, True],
['I', False, True], ['M', False, True],
['log', False, 0],
['ds', False, 'sample_core_depth'],
['sym', False, 'bo 5'], ['ID', False, '.'],
['sav', False, False]])
checked_args = extractor.extract_and_check_args(args, dataframe)
meas_file, sum_file, wig_file, samp_file, age_file, spc_file, res_file, fmt, meth, norm, depth, timescale, dir_path, pltLine, pltSus, pltDec, pltInc, pltMag, logit, depth_scale, symbol, input_dir, save = extractor.get_vars(['f', 'fsum', 'fwig', 'fsa', 'fa', 'fsp', 'fres', 'fmt', 'LP', 'n', 'd', 'ts', 'WD', 'L', 'S', 'D', 'I', 'M', 'log', 'ds', 'sym', 'ID', 'sav'], checked_args)
# format some variables
# format symbol/size
try:
sym, size = symbol.split()
size = int(size)
except:
print('you should provide -sym in this format: ro 5')
print('using defaults instead')
sym, size = 'ro', 5
# format result file, symbol, size
if res_file:
try:
res_file, res_sym, res_size = res_file.split()
except:
print('you must provide -fres in this format: -fres filename symbol size')
print('could not parse {}, defaulting to using no result file'.format(res_file))
res_file, res_sym, res_size = '', '', 0
else:
res_file, res_sym, res_size = '', '', 0
# format specimen file, symbol, size
if spc_file:
try:
spc_file, spc_sym, spc_size = spc_file.split()
except:
print('you must provide -fsp in this format: -fsp filename symbol size')
print('could not parse {}, defaulting to using no specimen file'.format(spc_file))
spc_file, spc_sym, spc_size = '', '', 0
else:
spc_file, spc_sym, spc_size = '', '', 0
# format min/max depth
try:
dmin, dmax = depth.split()
except:
print('you must provide -d in this format: -d dmin dmax')
print('could not parse {}, defaulting to plotting all depths'.format(depth))
dmin, dmax = -1, -1
# format timescale, min/max time
if timescale:
try:
timescale, amin, amax = timescale.split()
pltTime = True
except:
print('you must provide -ts in this format: -ts timescale minimum_age maximum_age')
print('could not parse {}, defaulting to using no timescale'.format(timescale))
timescale, amin, amax = None, -1, -1
pltTime = False
else:
timescale, amin, amax = None, -1, -1
pltTime = False
# format norm and wt_file
if norm and not isinstance(norm, bool):
wt_file = norm
norm = True
else:
norm = False
wt_file = ''
# format list of protcols and step
try:
method, step = meth.split()
except:
print('To use the -LP flag you must provide both the protocol and the step in this format:\n-LP [AF,T,ARM,IRM, X] step [in mT,C,mT,mT, mass/vol] to plot')
print('Defaulting to using no protocol')
method, step = 'LT-NO', 0
# list of varnames
#['f', 'fsum', 'fwig', 'fsa', 'fa', 'fsp', 'fres', 'fmt', 'LP', 'n', 'd', 'ts', 'WD', 'L', 'S', 'D', 'I', 'M', 'log', 'ds', 'sym' ]
#meas_file, sum_file, wig_file, samp_file, age_file, spc_file, res_file, fmt, meth, norm, depth, timescale, dir_path, pltLine, pltSus, pltDec, pltInc, pltMag, logit, depth_scale, symbol
fig, figname = ipmag.core_depthplot(input_dir, meas_file, spc_file, samp_file, age_file, sum_file, wt_file, depth_scale, dmin, dmax, sym, size, spc_sym, spc_size, method, step, fmt, pltDec, pltInc, pltMag, pltLine, pltSus, logit, pltTime, timescale, amin, amax, norm)
if not pmagplotlib.isServer:
figname = figname.replace(':', '_')
if fig and save:
plt.savefig(figname)
return
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_core_depthplot_without_full_time_options(self):
path = os.path.join(WD, 'data_files', 'core_depthplot')
program_ran, error_message = ipmag.core_depthplot(input_dir_path=path, spc_file='pmag_specimens.txt', samp_file='er_samples.txt', meth='AF', step=15, fmt='png', pltInc=False, logit=True, pltTime=True)#, timescale='gts12', amin=0, amax=3) # pltDec = False causes failure with these data
self.assertFalse(program_ran)
self.assertEqual(error_message, "To plot time, you must provide amin, amax, and timescale")
def test_core_depthplot_with_no_files(self):
program_ran, error_message = ipmag.core_depthplot()
self.assertFalse(program_ran)
self.assertEqual("You must provide either a magic_measurements file or a pmag_specimens file", error_message)
def test_core_depthplot_success(self):
path = os.path.join(WD, 'data_files', 'core_depthplot')
program_ran, plot_name = ipmag.core_depthplot(input_dir_path=path, spc_file='pmag_specimens.txt', samp_file='er_samples.txt', meth='AF', step=15)
#program_ran, plot_name = True, 'DSDP Site 522_m:_LT-AF-Z_core-depthplot.svg'
self.assertTrue(program_ran)
self.assertEqual(plot_name, 'DSDP Site 522_m:_LT-AF-Z_core-depthplot.svg')
def test_core_depthplot_bad_params(self):
path = os.path.join(WD, 'data_files', 'core_depthplot')
program_ran, error_message = ipmag.core_depthplot(input_dir_path=path)
self.assertFalse(program_ran)
self.assertEqual('No data found to plot\nTry again with different parameters', error_message)
