change reading in to standard loop over files
getting bins now from header information format of linearODF now standard ASCII table style with header/keyword/label
This commit is contained in:
Martin Diehl
parent
f43afa13d8
commit
4581e22a0f
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@ -3,6 +3,7 @@
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import os,string,sys,re
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import os,string,sys,re
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from optparse import OptionParser
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from optparse import OptionParser
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import numpy as np
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import damask
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import damask
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scriptID = string.replace('$Id$','\n','\\n')
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scriptID = string.replace('$Id$','\n','\\n')
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@ -17,90 +18,88 @@ sampleSym = { 'Orthotropic' : (90,90,90),
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# --------------------------------------------------------------------
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Transform the OIM texture data into linear ODF data, the input file can be generated by software "TSL OIM Analysis",
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Transform the binned texture data from "TSL OIM Analysis" into linear ODF data,
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and the output file can be used by the script: "hybridIA_linODFsampling.py"
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""", version=string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-f', '--file', dest='file', type='string', metavar = 'string', \
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""", version = scriptID)
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help='file name')
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parser.add_option('-s', '--symmetry', dest='symmetry', choices=sampleSym.keys(),\
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parser.add_option('-s', '--symmetry', dest='symmetry', choices=sampleSym.keys(),
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help='Sample symmetry, the default is [%default]')
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help='Sample symmetry, the default is [%default]')
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parser.add_option('--step', dest='step', type='int', nargs=3,
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help='''Angle steps of: phi1, Phi, phi2. For example, if the
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range of phi1 is 360 degree, and the desired interval
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is 5 degree, then the angle step of phi1 is 72, but
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we will discard the 72th step, because 360 is
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identical with 0, the default depends on the sample
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symmetry. ''', \
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metavar='int int int')
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parser.set_defaults(symmetry = 'Triclinic')
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parser.set_defaults(symmetry = 'Triclinic')
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parser.set_defaults(step = None)
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options = parser.parse_args()[0]
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if options.step is None:
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(options,filenames) = parser.parse_args()
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options.step= [sampleSym[options.symmetry][i]/5 for i in xrange(3)]
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if not os.path.exists(options.file):
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#--- setup file handles ---------------------------------------------------------------------------
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parser.error('texture file does not exist'); sys.exit()
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files = []
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if filenames == []:
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files.append({'name':'STDIN',
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'input':sys.stdin,
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'output':sys.stdout,
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'croak':sys.stderr,
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})
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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,
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'input':open(name),
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'output':open(name+'_tmp','w'),
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'croak':sys.stdout,
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})
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inName = options.file
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#--- loop over input files ------------------------------------------------------------------------
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outName = os.path.splitext(inName)[0]+'.linearODF'
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for file in files:
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nPhi1,nPHI,nPhi2 = options.step
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file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n')
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dPhi1,dPHI,dPhi2 = [sampleSym[options.symmetry][i]/float(options.step[i]) for i in xrange(3)]
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N = (nPhi1-1)*(nPHI-1)*(nPhi2-1)
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while True: # read header (forward and get bin Size)
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line = file['input'].readline()
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words = line.split()
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if len(words)>=3:
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if words[1]=='Bin' and words[2]=='Size:': binSize=float(words[3][:-1])
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if not line.startswith('#'): break
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try:
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delta = [sampleSym[options.symmetry][i]/binSize for i in xrange(3)]
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inFile = open(inName,'r')
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content = inFile.readlines()
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except:
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print 'unable to read:',inName
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sys.exit(1)
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try:
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outFile = open(outName,'w')
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except:
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print 'unable to write:',outName
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sys.exit(1)
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ODF = [[[[None] for k in range(nPhi2)] for j in range(nPHI)] for i in range(nPhi1)]
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nPhi1,nPHI,nPhi2 = map(int,delta)
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linear = [None]*N
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dPhi1,dPHI,dPhi2 = [sampleSym[options.symmetry][i]/delta[i] for i in xrange(3)]
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line = 0
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while (content[line].startswith('#')): # skip comments at start of file
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N = (nPhi1-1)*(nPHI-1)*(nPhi2-1)
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line += 1
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for iPhi1 in range(nPhi1):
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for iPHI in range(nPHI):
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for iPhi2 in range(nPhi2):
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words = content[line].split()
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ODF[iPhi1][iPHI][iPhi2] = float(words[3]) # extract intensity (in column 4)
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line += 1
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for iPhi1 in range(nPhi1-1):
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for iPHI in range(nPHI-1):
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for iPhi2 in range(nPhi2-1):
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linear[iPhi1*(nPHI-1)*(nPhi2-1)+iPHI*(nPhi2-1)+iPhi2] = (\
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ODF[iPhi1 ][iPHI ][iPhi2 ] + \
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ODF[iPhi1 ][iPHI ][iPhi2+1] + \
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ODF[iPhi1 ][iPHI+1][iPhi2 ] + \
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ODF[iPhi1 ][iPHI+1][iPhi2+1] + \
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ODF[iPhi1+1][iPHI ][iPhi2 ] + \
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ODF[iPhi1+1][iPHI ][iPhi2+1] + \
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ODF[iPhi1+1][iPHI+1][iPhi2 ] + \
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ODF[iPhi1+1][iPHI+1][iPhi2+1] \
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) / 8.0
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inFile.close()
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ODF = [[[[None] for k in range(nPhi2)] for j in range(nPHI)] for i in range(nPhi1)]
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outFile.write('%-6i%-6i%-6i #Ranges of phi1, Phi, phi2\n'%sampleSym[options.symmetry])
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linear = [None]*N
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outFile.write('%-6.2f%-6.2f%-6.2f #Deltas of phi1, Phi, phi2\n'%(dPhi1,dPHI,dPhi2))
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#outFile.write('%-6i%-6i%-6i #Angular steps needed to be converted\n'%(nPhi1-1,nPHI-1,nPhi2-1))
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outFile.write('cell-centered data\n')
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outFile.write('\n')
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for i in range(N):
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ODF = np.empty([nPhi1,nPHI,nPhi2],'d')
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outFile.write('%g\n'%(linear[i]))
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for iPhi1 in range(nPhi1):
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for iPHI in range(nPHI):
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for iPhi2 in range(nPhi2):
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ODF[iPhi1,iPHI,iPhi2] = float(line.split()[3])*0.125 # extract intensity (in column 4) and weight by 1/8 (since we convert from the 8 corners to the center later on)
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line = file['input'].readline()
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for iPhi1 in range(nPhi1-1):
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for iPHI in range(nPHI-1):
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for iPhi2 in range(nPhi2-1):
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linear[iPhi1*(nPHI-1)*(nPhi2-1)+iPHI*(nPhi2-1)+iPhi2] =\
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ODF[iPhi1 ,iPHI ,iPhi2 ] +\
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ODF[iPhi1 ,iPHI ,iPhi2+1] +\
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ODF[iPhi1 ,iPHI+1,iPhi2 ] +\
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ODF[iPhi1 ,iPHI+1,iPhi2+1] +\
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ODF[iPhi1+1,iPHI ,iPhi2 ] +\
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ODF[iPhi1+1,iPHI ,iPhi2+1] +\
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ODF[iPhi1+1,iPHI+1,iPhi2 ] +\
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ODF[iPhi1+1,iPHI+1,iPhi2+1]
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file['output'].write('4 header\n')
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file['output'].write('limit phi1 %-6.2f Phi %-6.2f phi2 %-6.2f\n'%sampleSym[options.symmetry])
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file['output'].write('delta phi1 %-6.2f Phi %-6.2f phi2 %-6.2f\n'%(dPhi1,dPHI,dPhi2))
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file['output'].write('centration cell-centered\n')
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file['output'].write('density\n')
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for i in range(N):
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file['output'].write('%g\n'%(linear[i]))
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outFile.close()
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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file['output'].close()
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os.rename(file['name']+'_tmp',os.path.splitext(file['name'])[0] +'.linearODF')
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