DAMASK_EICMD/processing/post/addGaussian.py

#!/usr/bin/env python3

import os
import sys
from io import StringIO
from optparse import OptionParser

from scipy import ndimage

import damask


scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID   = ' '.join([scriptName,damask.version])


# --------------------------------------------------------------------
#                                MAIN
# --------------------------------------------------------------------

parser = OptionParser(option_class=damask.extendableOption, usage='%prog option [ASCIItable(s)]', description = """
Add column(s) containing Gaussian filtered values of requested column(s).
Operates on periodic and non-periodic ordered three-dimensional data sets.
For details see scipy.ndimage documentation.

""", version = scriptID)

parser.add_option('-p','--pos','--periodiccellcenter',
                  dest = 'pos',
                  type = 'string', metavar = 'string',
                  help = 'label of coordinates [%default]')
parser.add_option('-s','--scalar',
                  dest = 'labels',
                  action = 'extend', metavar = '<string LIST>',
                  help = 'label(s) of scalar field values')
parser.add_option('-o','--order',
                  dest = 'order',
                  type = int,
                  metavar = 'int',
                  help = 'order of the filter [%default]')
parser.add_option('--sigma',
                  dest = 'sigma',
                  type = float,
                  metavar = 'float',
                  help = 'standard deviation [%default]')
parser.add_option('--periodic',
                  dest = 'periodic',
                  action = 'store_true',
                  help = 'assume periodic grain structure')



parser.set_defaults(pos = 'pos',
                    order = 0,
                    sigma = 1,
                   )

(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]

if options.labels is None: parser.error('no data column specified.')

for name in filenames:
    damask.util.report(scriptName,name)

    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
    damask.grid_filters.coord0_check(table.get(options.pos))

    for label in options.labels:
        table = table.add('Gauss{}({})'.format(options.sigma,label),
                          ndimage.filters.gaussian_filter(table.get(label).reshape(-1),
                                                          options.sigma,options.order,
                                                          mode = 'wrap' if options.periodic else 'nearest'),
                          scriptID+' '+' '.join(sys.argv[1:]))

    table.save((sys.stdout if name is None else name), legacy=True)