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 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 (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
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, '.'],
['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
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 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
else:
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()
plt.savefig(figname)
plt.clf()
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)
app.MainLoop()