195 lines
7.4 KiB
Python
195 lines
7.4 KiB
Python
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#!/usr/bin/env python
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import os,re,sys,math,string,damask,numpy
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from optparse import OptionParser, Option
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# -----------------------------
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class extendableOption(Option):
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# -----------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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def integerFactorization(i):
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j = int(math.floor(math.sqrt(float(i))))
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while (j>1 and int(i)%j != 0):
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j -= 1
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return j
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def positiveRadians(angle):
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angle = math.radians(float(angle))
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while angle < 0.0:
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angle += 2.0*math.pi
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return angle
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def getHeader(sizeX,sizeY,step):
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return [ \
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'# TEM_PIXperUM 1.000000', \
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'# x-star 0.509548', \
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'# y-star 0.795272', \
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'# z-star 0.611799', \
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'# WorkingDistance 18.000000', \
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'#', \
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'# Phase 1', \
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'# MaterialName Al', \
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'# Formula Fe', \
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'# Info', \
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'# Symmetry 43', \
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'# LatticeConstants 2.870 2.870 2.870 90.000 90.000 90.000', \
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'# NumberFamilies 4', \
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'# hklFamilies 1 1 0 1 0.000000 1', \
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'# hklFamilies 2 0 0 1 0.000000 1', \
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'# hklFamilies 2 1 1 1 0.000000 1', \
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'# hklFamilies 3 1 0 1 0.000000 1', \
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'# Categories 0 0 0 0 0 ', \
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'#', \
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'# GRID: SquareGrid', \
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'# XSTEP: ' + str(step), \
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'# YSTEP: ' + str(step), \
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'# NCOLS_ODD: ' + str(sizeX), \
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'# NCOLS_EVEN: ' + str(sizeX), \
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'# NROWS: ' + str(sizeY), \
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'#', \
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'# OPERATOR: ODFsammpling', \
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'#', \
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'# SAMPLEID: ', \
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'#', \
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'# SCANID: ', \
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'#', \
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]
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
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Builds an ang file out of ASCII table.
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""" + string.replace('$Id$','\n','\\n')
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)
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parser.add_option('--coords', dest='coords', type='string', \
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help='label of coords in ASCII table')
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parser.set_defaults(norm = 'ip')
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(options,filenames) = parser.parse_args()
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datainfo = {
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'vector': {'len':3,
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'label':[]}
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}
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datainfo['vector']['label'] += ['eulerangles']
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# ------------------------------------------ setup file handles ---------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout})
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else:
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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)})
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# ------------------------------------------ loop over input files ---------------------------------------
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for file in files:
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if file['name'] != 'STDIN': print file['name']
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table = damask.ASCIItable(file['input']) # open ASCII_table for reading
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table.head_read() # read ASCII header info
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# --------------- figure out dimension and resolution
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try:
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locationCol = table.labels.index('ip.x') # columns containing location data
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except ValueError:
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print 'no coordinate data found...'
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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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resolution = numpy.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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dimension = resolution/numpy.maximum(numpy.ones(3,'d'),resolution-1.0)* \
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numpy.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 resolution[2] == 1:
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dimension[2] = min(dimension[:2]/resolution[:2])
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N = resolution.prod()
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print '\t%s @ %s'%(dimension,resolution)
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# --------------- figure out columns to process
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active = {}
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column = {}
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values = {}
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divergence = {}
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head = []
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for datatype,info in datainfo.items():
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for label in info['label']:
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key = {True :'1_%s',
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False:'%s' }[info['len']>1]%label
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if key not in table.labels:
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sys.stderr.write('column %s not found...\n'%key)
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else:
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if datatype not in active: active[datatype] = []
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if datatype not in column: column[datatype] = {}
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if datatype not in values: values[datatype] = {}
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if datatype not in divergence: divergence[datatype] = {}
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if label not in divergence[datatype]: divergence[datatype][label] = {}
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active[datatype].append(label)
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column[datatype][label] = table.labels.index(key) # remember columns of requested data
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values[datatype][label] = numpy.array([0.0 for i in xrange(N*datainfo[datatype]['len'])])
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# ------------------------------------------ read value field ---------------------------------------
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table.data_rewind()
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print values['vector']['eulerangles']
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print numpy.shape(values['vector']['eulerangles'])
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idx = 0
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while table.data_read(): # read next data line of ASCII table
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for datatype,labels in active.items(): # loop over vector,tensor
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for label in labels: # loop over all requested curls
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values[datatype][label][idx:idx+3]= numpy.array(map(float,table.data[column[datatype][label]:
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column[datatype][label]+datainfo[datatype]['len']]),'d')
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idx+=3
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for z in xrange(resolution[2]):
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fileOut=open(os.path.join(os.path.dirname(name),os.path.splitext(os.path.basename(name))[0]+'_%s.ang'%z),'w')
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for line in getHeader(resolution[0],resolution[1],1.0):
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fileOut.write(line + '\n')
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# write data
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for counter in xrange(resolution[0]*resolution[1]):
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print z*resolution[0]*resolution[1]*3+counter*3,' - ',z*resolution[0]*resolution[1]*3+counter*3+3
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fileOut.write(''.join(['%10.5f'%positiveRadians(angle) for angle in values['vector']['eulerangles'][z*resolution[0]*resolution[1]*3+counter*3:z*resolution[0]*resolution[1]*3+counter*3+3]])+
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''.join(['%10.5f'%coord for coord in [counter%resolution[0],counter//resolution[1]]])+
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' 100.0 1.0 0 1 1.0\n')
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counter += 1
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fileOut.close()
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