Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development

VERSION

@@ -1 +1 @@
-v2.0.1-946-g5011e20
+v2.0.1-960-geddc2a6

processing/pre/3DRVEfrom2Dang.py

@@ -0,0 +1,119 @@
+#!/usr/bin/env python2.7
+# -*- coding: UTF-8 no BOM -*-
+
+import os,sys,math
+from optparse import OptionParser
+import damask
+import pipes
+
+scriptName = os.path.splitext(os.path.basename(__file__))[0]
+scriptID   = ' '.join([scriptName,damask.version])
+
+# --------------------------------------------------------------------
+#                                MAIN
+# --------------------------------------------------------------------
+
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', 
+                      description ='generate 3D RVE from .ang files of EBSD slices .',
+                      version = scriptID)
+
+parser.add_option('--offset',
+                  dest='offset',
+                  type='float',
+                  help='offset of EBSD slices [%default]',
+                  metavar='float')
+parser.add_option('--outname',
+                  dest='outName',
+                  type='string',
+                  help='output file name [%default]',  metavar='string')    
+parser.add_option('--vtr',
+                  action="store_true",
+                  dest='vtr')
+parser.add_option('--geom',
+                  action="store_true",
+                  dest='geom')
+parser.set_defaults(offset = 1.0,
+                    outName = 'RVE3D')
+
+(options,filenames) = parser.parse_args()
+
+numFiles = len(filenames)
+formatwidth = 1+int(math.log10(numFiles))
+
+# copy original files to tmp files to not alter originals
+for i in range(numFiles):
+  sliceID = 'slice' + str(i).zfill(formatwidth) + '.tmp'
+  strCommand = 'cp ' + pipes.quote(filenames[i]) + ' ' + sliceID
+  os.system(strCommand)
+
+# modify tmp files
+print('Add z-coordinates')
+for i in range(numFiles):
+  sliceID = 'slice' + str(i).zfill(formatwidth) + '.tmp'
+  strCommand = 'OIMgrainFile_toTable ' + sliceID
+  os.system(strCommand)
+  strCommand = 'addCalculation --label 3Dpos --formula "np.array(#pos#.tolist()+[' + str(i*options.offset) + '])" ' + sliceID
+  os.system(strCommand)
+
+# join temp files into one
+
+print('\n Colocate files')
+fileOut = open(options.outName + '.ang','w')
+
+# take header information from 1st file
+sliceID = 'slice' + str(0).zfill(formatwidth) + '.tmp'
+fileRead = open(sliceID)
+data = fileRead.readlines()
+fileRead.close()
+headerLines = int(data[0].split()[0])
+fileOut.write(str(headerLines+1) + '\t header\n')
+for line in data[1:headerLines]:
+  fileOut.write(line)
+fileOut.write(scriptID + '\t' + ' '.join(sys.argv[1:]) + '\n')
+for line in data[headerLines:]:
+  fileOut.write(line)
+
+# append other files content without header
+for i in range(numFiles-1):
+  sliceID = 'slice' + str(i+1).zfill(formatwidth) + '.tmp'
+  fileRead = open(sliceID)
+  data = fileRead.readlines()
+  fileRead.close()
+  headerLines = int(data[0].split()[0])
+  for line in data[headerLines+1:]:
+    fileOut.write(line)
+fileOut.close()
+
+# tidy up and add phase column 
+print('\n Remove temp data and add phase info')
+strCommand = 'filterTable --black pos ' + options.outName + '.ang'
+os.system(strCommand)
+strCommand = 'reLabel --label 3Dpos --substitute pos ' + options.outName + '.ang'
+os.system(strCommand)
+strCommand = 'addCalculation -l phase -f 1 ' + options.outName + '.ang'
+os.system(strCommand)
+
+
+# create geom file when asked for
+if options.geom:
+  print('\n Build geometry file')
+  strCommand = 'geom_fromTable --phase phase --eulers euler --coordinates pos ' + pipes.quote(options.outName) + '.ang'
+  os.system(strCommand)
+
+# create paraview file when asked for
+
+if options.vtr:
+  print('\n Build Paraview file')
+  strCommand = 'addIPFcolor --eulers euler --pole 0.0 0.0 1.0 ' + options.outName + '.ang'
+  os.system(strCommand)
+  strCommand = 'vtk_rectilinearGrid ' + pipes.quote(options.outName) + '.ang'
+  os.system(strCommand)
+  os.rename(pipes.quote(options.outName) + '_pos(cell)'+'.vtr', pipes.quote(options.outName) + '.vtr')
+  strCommand = 'vtk_addRectilinearGridData --vtk '+ pipes.quote(options.outName) + '.vtr --color IPF_001_cubic '\
+               + pipes.quote(options.outName) + '.ang'
+  os.system(strCommand)
+  
+# delete tmp files
+for i in range(numFiles):
+  sliceID = 'slice' + str(i).zfill(formatwidth) + '.tmp'
+  os.remove(sliceID)