diff --git a/PRIVATE b/PRIVATE index 19a53f622..596ec41a5 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 19a53f6229603aeafb2466b58679a1cd04fc0142 +Subproject commit 596ec41a5117c5f2a09356ffeee8cd8ce9a149d7 diff --git a/processing/post/addGaussian.py b/processing/post/addGaussian.py new file mode 100755 index 000000000..91d3e4667 --- /dev/null +++ b/processing/post/addGaussian.py @@ -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 = '', + 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) diff --git a/processing/pre/geom_fromTable.py b/processing/pre/geom_fromTable.py index 9af92888d..b10bc9f88 100755 --- a/processing/pre/geom_fromTable.py +++ b/processing/pre/geom_fromTable.py @@ -23,7 +23,7 @@ Generate geometry description and material configuration from position, phase, a parser.add_option('--coordinates', dest = 'pos', type = 'string', metavar = 'string', - help = 'coordinates label') + help = 'coordinates label (%default)') parser.add_option('--phase', dest = 'phase', type = 'string', metavar = 'string', @@ -90,6 +90,7 @@ parser.set_defaults(symmetry = [damask.Symmetry.lattices[-1]], homogenization = 1, crystallite = 1, verbose = False, + pos = 'pos', ) (options,filenames) = parser.parse_args()