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

processing/misc/DREAM3D_toTable.py

@@ -0,0 +1,74 @@
+#!/usr/bin/env python2.7
+# -*- coding: UTF-8 no BOM -*-
+
+import os,h5py
+import numpy as np
+from optparse import OptionParser
+import damask
+
+scriptName = os.path.splitext(os.path.basename(__file__))[0]
+scriptID   = ' '.join([scriptName,damask.version])
+
+
+#--------------------------------------------------------------------------------------------------
+#                                MAIN
+#--------------------------------------------------------------------------------------------------
+
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile[s]]', description = """
+Convert DREAM3D file to ASCIItable
+
+""", version = scriptID)
+
+(options, filenames) = parser.parse_args()
+
+rootDir ='DataContainers/ImageDataContainer'
+
+# --- loop over input files -------------------------------------------------------------------------
+
+if filenames == []: parser.error('no input file specified.')
+
+for name in filenames:
+  try:
+    table = damask.ASCIItable(outname = os.path.splitext(name)[0]+'.txt',
+                              buffered = False
+                              )
+  except: continue
+  damask.util.report(scriptName,name)
+
+  inFile = h5py.File(name, 'r')
+      
+  grid = inFile[rootDir+'/_SIMPL_GEOMETRY/DIMENSIONS'][...]
+
+  
+# --- read comments --------------------------------------------------------------------------------
+                    
+  coords = (np.mgrid[0:grid[2], 0:grid[1], 0: grid[0]]).reshape(3, -1).T
+  coords = (np.fliplr(coords)*inFile[rootDir+'/_SIMPL_GEOMETRY/SPACING'][...] \
+            + inFile[rootDir+'/_SIMPL_GEOMETRY/ORIGIN'][...] \
+            + inFile[rootDir+'/_SIMPL_GEOMETRY/SPACING'][...]*0.5)
+
+  table.data = np.hstack( (coords,
+                           inFile[rootDir+'/CellData/EulerAngles'][...].reshape(grid.prod(),3),
+                           inFile[rootDir+'/CellData/Phases'][...].reshape(grid.prod(),1),
+                           inFile[rootDir+'/CellData/Confidence Index'][...].reshape(grid.prod(),1),
+                           inFile[rootDir+'/CellData/Fit'][...].reshape(grid.prod(),1),
+                           inFile[rootDir+'/CellData/Image Quality'][...].reshape(grid.prod(),1)))
+                    
+  
+  labels = ['1_pos','2_pos','3_pos',
+            '1_Euler','2_Euler','3_Euler',
+            'PhaseID','CI','Fit','IQ']
+  try:
+    table.data = np.hstack((table.data, inFile[rootDir+'/CellData/FeatureIds'][...].reshape(grid.prod(),1)))
+    labels.append(['FeatureID'])
+  except Exception:
+    pass
+    
+# ------------------------------------------ assemble header ---------------------------------------
+  table.labels_clear()
+  table.labels_append(labels,reset = True)
+  table.head_write()
+  
+# ------------------------------------------ finalize output ---------------------------------------
+  table.data_writeArray() #(fmt='%e2.2')
+  table.close()