DAMASK_EICMD/processing/post/groupTable.py

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#!/usr/bin/env python3
import os
import sys
from optparse import OptionParser, OptionGroup
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import math # noqa
import numpy as np
import damask
def periodicAverage(coords, limits):
"""Centroid in periodic domain, see https://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions"""
theta = 2.0*np.pi * (coords - limits[0])/(limits[1] - limits[0])
theta_avg = np.pi + np.arctan2(-np.sin(theta).mean(axis=0), -np.cos(theta).mean(axis=0))
return limits[0] + theta_avg * (limits[1] - limits[0])/2.0/np.pi
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Apply a user-specified function to condense into a single row all those rows for which columns 'label' have identical values.
Output table will contain as many rows as there are different (unique) values in the grouping column(s).
Periodic domain averaging of coordinate values is supported.
Examples:
For grain averaged values, replace all rows of particular 'texture' with a single row containing their average.
{name} --label texture --function np.average data.txt
""".format(name = scriptName), version = scriptID)
parser.add_option('-l','--label',
dest = 'label',
action = 'extend', metavar = '<string LIST>',
help = 'column label(s) for grouping rows')
parser.add_option('-f','--function',
dest = 'function',
type = 'string', metavar = 'string',
help = 'mapping function [%default]')
parser.add_option('-a','--all',
dest = 'all',
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action = 'store_true',
help = 'apply mapping function also to grouping column(s)')
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group = OptionGroup(parser, "periodic averaging", "")
group.add_option ('-p','--periodic',
dest = 'periodic',
action = 'extend', metavar = '<string LIST>',
help = 'coordinate label(s) to average across periodic domain')
group.add_option ('--limits',
dest = 'boundary',
type = 'float', metavar = 'float float', nargs = 2,
help = 'min and max of periodic domain %default')
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parser.add_option_group(group)
parser.set_defaults(function = 'np.average',
all = False,
label = [],
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boundary = [0.0, 1.0])
(options,filenames) = parser.parse_args()
funcModule,funcName = options.function.split('.')
try:
mapFunction = getattr(locals().get(funcModule) or
globals().get(funcModule) or
__import__(funcModule),
funcName)
except:
mapFunction = None
if options.label is []:
parser.error('no grouping column specified.')
if not hasattr(mapFunction,'__call__'):
parser.error('function "{}" is not callable.'.format(options.function))
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
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try:
table = damask.ASCIItable(name = name)
except IOError:
continue
damask.util.report(scriptName,name)
# ------------------------------------------ sanity checks ---------------------------------------
remarks = []
errors = []
table.head_read()
grpColumns = table.label_index(options.label)[::-1]
grpColumns = grpColumns[np.where(grpColumns>=0)]
if len(grpColumns) == 0: errors.append('no valid grouping column present.')
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss=True)
continue
# ------------------------------------------ assemble info ---------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.head_write()
# ------------------------------------------ process data --------------------------------
table.data_readArray()
indexrange = table.label_indexrange(options.periodic) if options.periodic is not None else []
rows,cols = table.data.shape
table.data = table.data[np.lexsort(table.data[:,grpColumns].T)] # sort data by grpColumn(s)
values,index = np.unique(table.data[:,grpColumns], axis=0, return_index=True) # unique grpColumn values and their positions
index = sorted(np.append(index,rows)) # add termination position
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grpTable = np.empty((len(values), cols)) # initialize output
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for i in range(len(values)): # iterate over groups (unique values in grpColumn)
grpTable[i] = np.apply_along_axis(mapFunction,0,table.data[index[i]:index[i+1]]) # apply (general) mapping function
grpTable[i,indexrange] = \
periodicAverage(table.data[index[i]:index[i+1],indexrange],options.boundary) # apply periodicAverage mapping function
if not options.all: grpTable[i,grpColumns] = table.data[index[i],grpColumns] # restore grouping column value
table.data = grpTable
# ------------------------------------------ output result -------------------------------
table.data_writeArray()
table.close() # close ASCII table