some more scripts passed

processing/pre/OIMlinear2linearODF.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python
 # -*- coding: UTF-8 no BOM -*-
 
-import os,string,sys,re
+import os,sys
 from optparse import OptionParser
 import numpy as np
 import damask
@@ -73,7 +73,7 @@ for file in files:
   for iPhi1 in range(nPhi1):
     for iPHI in range(nPHI):
       for iPhi2 in range(nPhi2):
-        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)
+        ODF[iPhi1,iPHI,iPhi2] = float(line.split()[3])*0.125                                      # extract intensity (in column 4) and weight by 1/8
         line = file['input'].readline()
 
   for iPhi1 in range(nPhi1-1):

processing/pre/geom_fromBarycentric.py

@@ -10,10 +10,11 @@
 # maintain meaningful microstructure(reduce artifacts).
 
 
-import sys, os, string
+import os
 import numpy as np
 import argparse
 from scipy.spatial import Delaunay
+import damask
 
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
@@ -23,16 +24,14 @@ OFFSET = 0.1  #resize the seeded volume to give space for rim/pan
 PHANTOM_ID = -1  #grain ID for phantom seeds
 
 def d_print(info, data, separator=False):
-    '''quickly print debug information'''
+  """quickly print debug information"""
-    if(separator): print "*"*80
+  if(separator): print "*"*80
-    print info
+  print info
-    print data
+  print data
 
 
 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))
@@ -121,9 +120,9 @@ args = parser.parse_args()  # get all the arguments right after
 #quick help to user
 print "*"*80
 parser.print_help()
-print '''Sample usage:
+print """Sample usage:
 ./geoFromBarycentic.py 20grains.seeds -g 128 128 128 -S -r; geom_check seeds.geom; seeds_check new_seed.seeds.
-'''
+"""
 print "*"*80
 if (args.debug):
     d_print("args are:", parser.parse_args(),separator=True)

processing/pre/geom_rotate.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
 import damask
 from scipy import ndimage
@@ -49,7 +49,7 @@ parser.set_defaults(degrees = False,
 
 (options, filenames) = parser.parse_args()
 
-if sum(x != None for x in [options.rotation,options.eulers,options.matrix,options.quaternion]) !=1:
+if sum(x is not None for x in [options.rotation,options.eulers,options.matrix,options.quaternion]) !=1:
   parser.error('not exactly one rotation specified...')
 
 toRadian = math.pi/180. if options.degrees else 1.0

processing/pre/geom_translate.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
 import damask
 from optparse import OptionParser
@@ -95,8 +95,10 @@ for name in filenames:
 # --- report ---------------------------------------------------------------------------------------
 
   remarks = []
-  if (any(newInfo['origin']          != info['origin'])):         remarks.append('--> origin   x y z:  %s'%(' : '.join(map(str,newInfo['origin']))))
+  if (any(newInfo['origin']          != info['origin'])):
-  if (    newInfo['microstructures'] != info['microstructures']): remarks.append('--> microstructures: %i'%newInfo['microstructures'])
+    remarks.append('--> origin   x y z:  %s'%(' : '.join(map(str,newInfo['origin']))))
+  if (    newInfo['microstructures'] != info['microstructures']):
+    remarks.append('--> microstructures: %i'%newInfo['microstructures'])
   if remarks != []: damask.util.croak(remarks)
 
 # --- write header ---------------------------------------------------------------------------------

processing/pre/geom_unpack.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

processing/pre/geom_vicinityOffset.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 scipy import ndimage
 from optparse import OptionParser
@@ -87,9 +87,8 @@ for name in filenames:
 
 # --- report ---------------------------------------------------------------------------------------
 
-  remarks = []
+  if (newInfo['microstructures'] != info['microstructures']):
-  if (    newInfo['microstructures'] != info['microstructures']): remarks.append('--> microstructures: %i'%newInfo['microstructures'])
+    damask.util.croak('--> microstructures: %i'%newInfo['microstructures'])
-  if remarks != []: damask.util.croak(remarks)
 
 # --- write header ---------------------------------------------------------------------------------
 

processing/pre/seeds_check.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,string,vtk
+import os,sys,vtk
 import numpy as np
 import damask
 from optparse import OptionParser
@@ -66,8 +66,8 @@ for name in filenames:
       if info['size'][i] <= 0.0:                                                                    # any invalid size?
         info['size'][i] = float(info['grid'][i])/max(info['grid'])                                  # normalize to grid
         remarks.append('rescaling size {} to {}...'.format({0:'x',1:'y',2:'z'}[i],info['size'][i]))
-  if table.label_dimension(options.position) != 3: errors.append('columns "{}" have dimension {}'.format(options.position,
+  if table.label_dimension(options.position) != 3:
-                                                                                                         table.label_dimension(options.position)))
+    errors.append('columns "{}" have dimension {}'.format(options.position,table.label_dimension(options.position)))
   if remarks != []: damask.util.croak(remarks)
   if errors  != []:
     damask.util.croak(errors)
@@ -110,8 +110,7 @@ for name in filenames:
     (directory,filename) = os.path.split(name)
     writer.SetDataModeToBinary()
     writer.SetCompressorTypeToZLib()
-    writer.SetFileName(os.path.join(directory,os.path.splitext(filename)[0]
+    writer.SetFileName(os.path.join(directory,os.path.splitext(filename)[0]+'.'+writer.GetDefaultFileExtension()))
-                                              +'.'+writer.GetDefaultFileExtension()))
   else:
     writer = vtk.vtkDataSetWriter()
     writer.WriteToOutputStringOn()
@@ -120,7 +119,7 @@ for name in filenames:
   if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(grid)
   else:                          writer.SetInputData(grid)
   writer.Write()
-  if name == None:  sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
+  if name is None:  sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
 
   table.close()
 

processing/pre/seeds_fromGeom.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,string
+import os,sys
 import numpy as np
 from optparse import OptionParser
 import damask
@@ -88,8 +88,10 @@ for name in filenames:
   yy = np.tile(np.repeat(y,info['grid'][0]                ),info['grid'][2])
   zz =         np.repeat(z,info['grid'][0]*info['grid'][1])
 
-  mask = np.logical_and(np.in1d(microstructure,options.whitelist,invert=False) if options.whitelist != [] else np.full_like(microstructure,True,dtype=bool), 
+  mask = np.logical_and(np.in1d(microstructure,options.whitelist,invert=False) if options.whitelist != []
-                        np.in1d(microstructure,options.blacklist,invert=True ) if options.blacklist != [] else np.full_like(microstructure,True,dtype=bool))
+                                                                               else np.full_like(microstructure,True,dtype=bool), 
+                        np.in1d(microstructure,options.blacklist,invert=True ) if options.blacklist != []
+                                                                               else np.full_like(microstructure,True,dtype=bool))
 
 # ------------------------------------------ assemble header ---------------------------------------