gaussian filter (wrapper no ndimage)

This commit is contained in:
Martin Diehl 2017-05-29 10:32:22 +02:00
parent 83f8795638
commit e5af0630fe
3 changed files with 140 additions and 2 deletions

@ -1 +1 @@
Subproject commit 19a53f6229603aeafb2466b58679a1cd04fc0142 Subproject commit 596ec41a5117c5f2a09356ffeee8cd8ce9a149d7

137
processing/post/addGaussian.py Executable file
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@ -0,0 +1,137 @@
#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os,sys
import numpy as np
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(s) [ASCIItable(s)]', description = """
Add column(s) containing gradient of requested column(s).
Operates on periodic ordered three-dimensional data sets.
Deals with both vector- and scalar fields.
""", 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 = 'scalar',
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')
parser.add_option('--sigma',
dest = 'sigma',
type = float,
metavar = 'float',
help = 'standard deviation')
parser.add_option('--periodic',
dest = 'periodic',
action = 'store_true',
help = 'assume periodic grain structure'
)
parser.set_defaults(pos = 'pos',
order = 0,
sigma = 1,
periodic = False
)
(options,filenames) = parser.parse_args()
if options.scalar is None:
parser.error('no data column specified.')
# --- loop over input files ------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try: table = damask.ASCIItable(name = name,buffered = False)
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
table.head_read()
# ------------------------------------------ sanity checks ----------------------------------------
items = {
'scalar': {'dim': 1, 'shape': [1], 'labels':options.scalar, 'active':[], 'column': []},
}
errors = []
remarks = []
column = {}
if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos))
else: colCoord = table.label_index(options.pos)
for type, data in items.iteritems():
for what in (data['labels'] if data['labels'] is not None else []):
dim = table.label_dimension(what)
if dim != data['dim']: remarks.append('column {} is not a {}.'.format(what,type))
else:
items[type]['active'].append(what)
items[type]['column'].append(table.label_index(what))
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ assemble header --------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
for type, data in items.iteritems():
for label in data['active']:
table.labels_append(['Gauss{}({})'.format(options.sigma,label)]) # extend ASCII header with new labels
table.head_write()
# --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray()
coords = [np.unique(table.data[:,colCoord+i]) for i in range(3)]
mincorner = np.array(map(min,coords))
maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 equal to smallest among other ones
# ------------------------------------------ process value field -----------------------------------
stack = [table.data]
for type, data in items.iteritems():
for i,label in enumerate(data['active']):
stack.append(ndimage.filters.gaussian_filter(table.data[:,data['column'][i]],
options.sigma,options.order,
mode = 'wrap' if options.periodic else 'nearest'
).reshape([table.data.shape[0],1])
)
# ------------------------------------------ output result -----------------------------------------
if len(stack) > 1: table.data = np.hstack(tuple(stack))
table.data_writeArray('%.12g')
# ------------------------------------------ output finalization -----------------------------------
table.close() # close input ASCII table (works for stdin)

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@ -23,7 +23,7 @@ Generate geometry description and material configuration from position, phase, a
parser.add_option('--coordinates', parser.add_option('--coordinates',
dest = 'pos', dest = 'pos',
type = 'string', metavar = 'string', type = 'string', metavar = 'string',
help = 'coordinates label') help = 'coordinates label (%default)')
parser.add_option('--phase', parser.add_option('--phase',
dest = 'phase', dest = 'phase',
type = 'string', metavar = 'string', type = 'string', metavar = 'string',
@ -90,6 +90,7 @@ parser.set_defaults(symmetry = [damask.Symmetry.lattices[-1]],
homogenization = 1, homogenization = 1,
crystallite = 1, crystallite = 1,
verbose = False, verbose = False,
pos = 'pos',
) )
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()