129 lines
6.7 KiB
Python
Executable File
129 lines
6.7 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,re,sys,math,string
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import numpy as np
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from collections import defaultdict
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from optparse import OptionParser
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import damask
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scriptID = string.replace('$Id$','\n','\\n')
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scriptName = scriptID.split()[1]
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options file[s]', description = """
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Add column(s) containing deformed configuration of requested column(s).
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Operates on periodic ordered three-dimensional data sets.
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""", version = scriptID)
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parser.add_option('-c','--coordinates', dest='coords', action='store', type='string', metavar='string',
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help='column heading for coordinates [%default]')
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parser.add_option('-f','--defgrad', dest='defgrad', action='store', type='string', metavar='string',
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help='heading of columns containing tensor field values')
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parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',
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help='use linear reconstruction of geometry [%default]')
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parser.set_defaults(coords = 'ip')
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parser.set_defaults(defgrad = 'f' )
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parser.set_defaults(linearreconstruction = False)
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(options,filenames) = parser.parse_args()
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datainfo = { # list of requested labels per datatype
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'defgrad': {'len':9,
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'label':[]},
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}
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datainfo['defgrad']['label'].append(options.defgrad)
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# ------------------------------------------ setup file handles -------------------------------------
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files = []
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
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#--- loop over input files ------------------------------------------------------------------------
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for file in files:
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file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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# --------------- figure out dimension and resolution ----------------------------------------------
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try:
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locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data
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except ValueError:
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file['croak'].write('no coordinate data (%s.x) found...\n'%options.coords)
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continue
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grid = [{},{},{}]
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while table.data_read(): # read next data line of ASCII table
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for j in xrange(3):
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grid[j][str(table.data[locationCol+j])] = True # remember coordinate along x,y,z
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res = np.array([len(grid[0]),\
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len(grid[1]),\
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len(grid[2]),],'i') # resolution is number of distinct coordinates found
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geomdim = res/np.maximum(np.ones(3,'d'),res-1.0)* \
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np.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\
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max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\
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max(map(float,grid[2].keys()))-min(map(float,grid[2].keys())),\
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],'d') # dimension from bounding box, corrected for cell-centeredness
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if res[2] == 1:
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geomdim[2] = min(geomdim[:2]/res[:2])
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N = res.prod()
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# --------------- figure out columns to process ---------------------------------------------------
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missingColumns = False
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for label in datainfo['defgrad']['label']:
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key = '1_%s'%label
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if key not in table.labels:
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file['croak'].write('column %s not found...\n'%key)
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missingColumns = True
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else:
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column = table.labels.index(key) # remember columns of requested data
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if missingColumns:
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continue
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# ------------------------------------------ assemble header ---------------------------------------
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table.labels_append(['%s_coords'%(coord+1) for coord in xrange(3)]) # extend ASCII header with new labels
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table.head_write()
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# ------------------------------------------ read deformation gradient field -----------------------
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table.data_rewind()
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F = np.array([0.0 for i in xrange(N*9)]).reshape([3,3]+list(res))
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idx = 0
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while table.data_read():
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(x,y,z) = damask.util.gridLocation(idx,res) # figure out (x,y,z) position from line count
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idx += 1
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F[0:3,0:3,x,y,z] = np.array(map(float,table.data[column:column+9]),'d').reshape(3,3)
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# ------------------------------------------ calculate coordinates ---------------------------------
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Favg = damask.core.math.tensorAvg(F)
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if options.linearreconstruction:
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centroids = damask.core.mesh.deformedCoordsLin(geomdim,F,Favg)
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else:
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centroids = damask.core.mesh.deformedCoordsFFT(geomdim,F,Favg)
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# ------------------------------------------ process data ------------------------------------------
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table.data_rewind()
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idx = 0
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outputAlive = True
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while outputAlive and table.data_read(): # read next data line of ASCII table
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(x,y,z) = damask.util.gridLocation(idx,res) # figure out (x,y,z) position from line count
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idx += 1
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table.data_append(list(centroids[:,x,y,z]))
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outputAlive = table.data_write() # output processed line
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# ------------------------------------------ output result ---------------------------------------
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outputAlive and table.output_flush() # just in case of buffered ASCII table
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file['input'].close() # close input ASCII table (works for stdin)
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file['output'].close() # close output ASCII table (works for stdout)
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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