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processing/pre/geom_fromAng.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,math,string
+import os,sys,math
 import numpy as np
 from optparse import OptionParser
 import damask
@@ -124,16 +124,22 @@ for name in filenames:
     continue
 
   eulerangles=np.around(eulerangles,int(options.precision))                                         # round to desired precision
+# ensure, that rounded euler angles are not out of bounds (modulo by limits)
   for i,angle in enumerate(['phi1','PHI','phi2']):
-    eulerangles[:,i]%=limits[i]                                                                     # ensure, that rounded euler angles are not out of bounds (modulo by limits)
+    eulerangles[:,i]%=limits[i]
 
+# scale angles by desired precision and convert to int. create unique integer key from three euler angles by
+# concatenating the string representation with leading zeros and store as integer and search unique euler angle keys.
+# Texture IDs are the indices of the first occurrence, the inverse is used to construct the microstructure
+# create a microstructure (texture/phase pair) for each point using unique texture IDs.
+# Use longInt (64bit, i8) because the keys might be long
   if options.compress:
     formatString='{0:0>'+str(int(options.precision)+3)+'}'
-    euleranglesRadInt = (eulerangles*10**int(options.precision)).astype('int')                      # scale by desired precision and convert to int
+    euleranglesRadInt = (eulerangles*10**int(options.precision)).astype('int')                      
     eulerKeys = np.array([int(''.join(map(formatString.format,euleranglesRadInt[i,:]))) \
-                                                             for i in xrange(info['grid'].prod())]) # create unique integer key from three euler angles by concatenating the string representation with leading zeros and store as integer
+                                                             for i in xrange(info['grid'].prod())]) 
-    devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)# search unique euler angle keys. Texture IDs are the indices of the first occurrence, the inverse is used to construct the microstructure
+    devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)
-    msFull = np.array([[eulerKeys_idx[i],phase[i]] for i in xrange(info['grid'].prod())],'i8')      # create a microstructure (texture/phase pair) for each point using unique texture IDs. Use longInt (64bit, i8) because the keys might be long
+    msFull = np.array([[eulerKeys_idx[i],phase[i]] for i in xrange(info['grid'].prod())],'i8')      
     devNull,msUnique,matPoints = np.unique(msFull.view('c16'),True,True)
     matPoints+=1
     microstructure = np.array([msFull[i] for i in msUnique])                                        # pick only unique microstructures

processing/pre/geom_fromVPSC.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,math,string
+import os,sys,math
 import numpy as np
 from optparse import OptionParser
 import damask
@@ -101,16 +101,22 @@ for name in filenames:
                                      %(angle,n,eulerangles[n,0],eulerangles[n,1],eulerangles[n,2]))
     continue
   eulerangles=np.around(eulerangles,int(options.precision))                                         # round to desired precision
+# ensure, that rounded euler angles are not out of bounds (modulo by limits)
   for i,angle in enumerate(['phi1','PHI','phi2']):
-    eulerangles[:,i]%=limits[i]                                                                     # ensure, that rounded euler angles are not out of bounds (modulo by limits)
+    eulerangles[:,i]%=limits[i]                                                                     
 
+# scale angles by desired precision and convert to int. create unique integer key from three euler angles by
+# concatenating the string representation with leading zeros and store as integer and search unique euler angle keys.
+# Texture IDs are the indices of the first occurrence, the inverse is used to construct the microstructure
+# create a microstructure (texture/phase pair) for each point using unique texture IDs.
+# Use longInt (64bit, i8) because the keys might be long
   if options.compress:
     formatString='{0:0>'+str(int(options.precision)+3)+'}'
-    euleranglesRadInt = (eulerangles*10**int(options.precision)).astype('int')                      # scale by desired precision and convert to int
+    euleranglesRadInt = (eulerangles*10**int(options.precision)).astype('int')
     eulerKeys = np.array([int(''.join(map(formatString.format,euleranglesRadInt[i,:]))) \
-                                                             for i in xrange(info['grid'].prod())]) # create unique integer key from three euler angles by concatenating the string representation with leading zeros and store as integer
+                                                             for i in xrange(info['grid'].prod())])
-    devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)# search unique euler angle keys. Texture IDs are the indices of the first occurence, the inverse is used to construct the microstructure
+    devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)
-    msFull = np.array([[eulerKeys_idx[i],phase[i]] for i in xrange(info['grid'].prod())],'i8')      # create a microstructure (texture/phase pair) for each point using unique texture IDs. Use longInt (64bit, i8) because the keys might be long
+    msFull = np.array([[eulerKeys_idx[i],phase[i]] for i in xrange(info['grid'].prod())],'i8')
     devNull,msUnique,matPoints = np.unique(msFull.view('c16'),True,True)
     matPoints+=1
     microstructure = np.array([msFull[i] for i in msUnique])                                        # pick only unique microstructures

processing/pre/geom_fromVoronoiTessellation.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,math,string
+import os,sys,math
 import numpy as np
 import multiprocessing
 from optparse import OptionParser
@@ -13,9 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 
 
 def meshgrid2(*arrs):
-  '''
+  """code inspired by http://stackoverflow.com/questions/1827489/numpy-meshgrid-in-3d"""
-  code inspired by http://stackoverflow.com/questions/1827489/numpy-meshgrid-in-3d
-  '''
   arrs = tuple(reversed(arrs))
   arrs = tuple(arrs)
   lens = np.array(map(len, arrs))
@@ -99,7 +97,8 @@ def laguerreTessellation(undeformed, coords, weights, grains, nonperiodic = Fals
         for i,arg in enumerate(arguments):
           closestSeeds[i] = findClosestSeed(arg)
 
-    return grains[closestSeeds%coords.shape[0]]                                                   # closestSeed is modulo number of original seed points (i.e. excluding periodic copies)
+# closestSeed is modulo number of original seed points (i.e. excluding periodic copies)
+    return grains[closestSeeds%coords.shape[0]]                                                   
 
 # --------------------------------------------------------------------
 #                                MAIN
@@ -210,9 +209,9 @@ for name in filenames:
   table.head_read()
   info,extra_header = table.head_getGeom()
   
-  if options.grid   != None: info['grid']   = options.grid
+  if options.grid   is not None: info['grid']   = options.grid
-  if options.size   != None: info['size']   = options.size
+  if options.size   is not None: info['size']   = options.size
-  if options.origin != None: info['origin'] = options.origin
+  if options.origin is not None: info['origin'] = options.origin
   
 # ------------------------------------------ sanity checks ---------------------------------------  
 
@@ -298,7 +297,7 @@ for name in filenames:
   phase = options.phase * np.ones(info['microstructures'],'i')
   if int(options.secondphase*info['microstructures']) > 0:
     phase[0:int(options.secondphase*info['microstructures'])] += 1
-    randomSeed = int(os.urandom(4).encode('hex'), 16)  if options.randomSeed == None \
+    randomSeed = int(os.urandom(4).encode('hex'), 16)  if options.randomSeed is None \
                                                        else options.randomSeed                      # random seed for second phase
     np.random.seed(randomSeed)
     np.random.shuffle(phase)
@@ -317,7 +316,7 @@ for name in filenames:
       config_header += ['[Grain%s]'%(str(ID).zfill(formatwidth)),
                         '(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0'%tuple(eulers[eulerID])
                        ]
-      if options.axes != None: config_header.append('axes\t%s %s %s'%tuple(options.axes))
+      if options.axes is not None: config_header.append('axes\t%s %s %s'%tuple(options.axes))
   
   table.labels_clear()
   table.info_clear()

processing/pre/geom_rescale.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,string,math
+import os,sys,math
 import numpy as np
 from optparse import OptionParser
 import damask
@@ -82,8 +82,12 @@ for name in filenames:
              'microstructures': 0,
             }
 
-  newInfo['grid'] = np.array([{True:round(o*float(n.translate(None,'xX'))), False: round(float(n.translate(None,'xX')))}[n[-1].lower() == 'x'] for o,n in zip(info['grid'],options.grid)],'i')
+  newInfo['grid'] = np.array([{True:round(o*float(n.translate(None,'xX'))), 
-  newInfo['size'] = np.array([{True:      o*float(n.translate(None,'xX')) , False:       float(n.translate(None,'xX')) }[n[-1].lower() == 'x'] for o,n in zip(info['size'],options.size)],'d')
+                               False: round(float(n.translate(None,'xX')))}[n[-1].lower() == 'x']
+                                                  for o,n in zip(info['grid'],options.grid)],'i')
+  newInfo['size'] = np.array([{True:      o*float(n.translate(None,'xX')) ,
+                               False:       float(n.translate(None,'xX')) }[n[-1].lower() == 'x']
+                                                  for o,n in zip(info['size'],options.size)],'d')
   newInfo['grid'] = np.where(newInfo['grid'] <= 0  , info['grid'],newInfo['grid'])
   newInfo['size'] = np.where(newInfo['size'] <= 0.0, info['size'],newInfo['size'])
 
@@ -97,11 +101,8 @@ for name in filenames:
       last = this
 
   microstructure = microstructure.reshape(info['grid'],order='F')
-  microstructure = np.repeat(
+  microstructure = np.repeat(np.repeat(np.repeat(microstructure,
-                   np.repeat(
+                   multiplicity[0], axis=0),multiplicity[1], axis=1),multiplicity[2], axis=2)
-                   np.repeat(microstructure,multiplicity[0], axis=0),
-                                            multiplicity[1], axis=1),
-                                            multiplicity[2], axis=2)
 # --- renumber to sequence 1...Ngrains if requested ------------------------------------------------
 #  http://stackoverflow.com/questions/10741346/np-frequency-counts-for-unique-values-in-an-array  
 
@@ -119,9 +120,12 @@ for name in filenames:
   remarks = []
   errors  = []
 
-  if (any(newInfo['grid']            != info['grid'])):           remarks.append('--> grid     a b c:  %s'%(' x '.join(map(str,newInfo['grid']))))
+  if (any(newInfo['grid']            != info['grid'])):
-  if (any(newInfo['size']            != info['size'])):           remarks.append('--> size     x y z:  %s'%(' x '.join(map(str,newInfo['size']))))
+    remarks.append('--> grid     a b c:  %s'%(' x '.join(map(str,newInfo['grid']))))
-  if (    newInfo['microstructures'] != info['microstructures']): remarks.append('--> microstructures: %i'%newInfo['microstructures'])
+  if (any(newInfo['size']            != info['size'])):
+    remarks.append('--> size     x y z:  %s'%(' x '.join(map(str,newInfo['size']))))
+  if (    newInfo['microstructures'] != info['microstructures']):
+    remarks.append('--> microstructures: %i'%newInfo['microstructures'])
 
   if np.any(newInfo['grid'] < 1):    errors.append('invalid new grid a b c.')
   if np.any(newInfo['size'] <= 0.0): errors.append('invalid new size x y z.')

processing/pre/geom_toTable.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,string,vtk
+import os,sys
 import numpy as np
 from optparse import OptionParser
 import damask