changed manual input/output close to class method

processing/post/addCalculation.py

@@ -115,7 +115,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/addCauchy.py

@@ -92,7 +92,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/addCompatibilityMismatch.py

@@ -129,6 +129,6 @@ for file in files:
 # ------------------------------------------ output result ---------------------------------------  
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table
+  table.input_close()                                                                               # close input ASCII table
-  file['output'].close()                                                                            # close output ASCII table
+  table.output_close()                                                                              # close output ASCII table
   os.rename(file['name']+'_tmp',file['name'])                                                       # overwrite old one with tmp new

processing/post/addCurl.py

@@ -149,6 +149,6 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------  
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table
+  table.input_close()                                                                               # close input ASCII table
-  file['output'].close()                                                                            # close output ASCII table
+  table.output_close()                                                                              # close output ASCII table
   os.rename(file['name']+'_tmp',file['name'])                                                       # overwrite old one with tmp new

processing/post/addDeformedConfiguration.py

@@ -124,6 +124,6 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table
+  table.input_close()                                                                               # close input ASCII table
-  file['output'].close()                                                                            # close output ASCII table
+  table.output_close()                                                                              # close output ASCII table
   os.rename(file['name']+'_tmp',file['name'])                                                       # overwrite old one with tmp new

processing/post/addDeterminant.py

@@ -88,7 +88,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/addDeviator.py

@@ -94,7 +94,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/addDivergence.py

@@ -172,6 +172,6 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table
+  table.input_close()                                                                               # close input ASCII table
-  file['output'].close()                                                                            # close output ASCII table
+  table.output_close()                                                                              # close output ASCII table
   os.rename(file['name']+'_tmp',file['name'])                                                       # overwrite old one with tmp new

processing/post/addEhkl.py

@@ -104,7 +104,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/addEuclideanDistance.py

@@ -199,6 +199,6 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table
+  table.input_close()                                                                               # close input ASCII table
-  file['output'].close()                                                                            # close output ASCII table
+  table.output_close()                                                                              # close output ASCII table
   os.rename(file['name']+'_tmp',file['name'])                                                       # overwrite old one with tmp new

processing/post/addIPFcolor.py

@@ -148,7 +148,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/addMapped.py

@@ -120,7 +120,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/addMises.py

@@ -100,7 +100,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/addNorm.py

@@ -111,7 +111,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/addOrientations.py

@@ -168,7 +168,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/addPK2.py

@@ -93,7 +93,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/addSchmidfactors.py

@@ -375,7 +375,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/addSpectralDecomposition.py

@@ -80,7 +80,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/addStrainTensors.py

@@ -138,7 +138,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/averageDown.py

@@ -133,7 +133,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------  
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table
+  table.input_close()                                                                               # close input ASCII table
-  file['output'].close()                                                                            # close output ASCII table
+  table.output_close()                                                                              # close output ASCII table
   os.rename(file['name']+'_tmp',\
             os.path.join(os.path.dirname(file['name']),prefix+os.path.basename(file['name'])))

processing/post/binXY.py

@@ -72,7 +72,7 @@ for file in files:
   skip = int(file['input'].readline().split()[0])
   for i in xrange(skip): headers = file['input'].readline().split()
   data = np.loadtxt(file['input'],usecols=np.array(options.data+((options.weight,) if options.weight != None else ()))-1)
-  file['input'].close()                                                                              # close input ASCII table
+  table.input_close()                                                                                # close input ASCII table
 
   for i in (0,1):                                                                                    # check data range for x and y
     if (range[i] == 0.0).all(): range[i] = [data[:,i].min(),data[:,i].max()]
@@ -113,7 +113,7 @@ for file in files:
   file['output'].write('1\thead\n')
   file['output'].write('bin_%s\tbin_%s\tz\n'%(headers[options.data[0]-1],headers[options.data[1]-1]))
   np.savetxt(file['output'],result)
-  file['output'].close()                                                                            # close output ASCII table
+  table.output_close()                                                                              # close output ASCII table
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',\
               os.path.join(os.path.dirname(file['name']),prefix+os.path.basename(file['name'])))

processing/post/blowUp.py

@@ -125,7 +125,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------  
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table
+  table.input_close()                                                                               # close input ASCII table
-  file['output'].close()                                                                            # close output ASCII table
+  table.output_close()                                                                              # close output ASCII table
   os.rename(file['name']+'_tmp',\
             os.path.join(os.path.dirname(file['name']),prefix+os.path.basename(file['name'])))

processing/post/deleteColumn.py

@@ -98,7 +98,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/deleteInfo.py

@@ -48,7 +48,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/filterTable.py

@@ -95,7 +95,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/nodesFromCentroids.py

@@ -148,7 +148,7 @@ for file in files:
     undeformedCentroids[x,y,z] = numpy.array(map(float,table.data[columnUndeformed:columnUndeformed+3]),'d')
     defgrad[x,y,z] = numpy.array(map(float,table.data[columnDefgrad:columnDefgrad+9]),'d').reshape(3,3)
 
-  file['input'].close()                                                     # close input ASCII table
+  table.input_close()                                                       # close input ASCII table
 
 
 # ------------------------------------------ process value field ----------------------------

processing/post/perceptualUniformColorMap.py

@@ -166,4 +166,4 @@ myColormap = Colormap(leftColor,rightColor)
 for file in files:
   outColormap = myColormap.export(file['name'],file['outtype'],options.steps,list(options.trim))
   file['output'].write(outColormap)
-  file['output'].close()
+  table.output_close()  

processing/post/permuteData.py

@@ -90,6 +90,6 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------  
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table
+  table.input_close()                                                                               # close input ASCII table
-  file['output'].close()                                                                            # close output ASCII table
+  table.output_close()                                                                              # close output ASCII table
   os.rename(file['name']+'_tmp',file['name'])                                                       # overwrite old one with tmp new

processing/post/rotateData.py

@@ -110,7 +110,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush() 
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/scaleData.py

@@ -103,7 +103,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/shiftData.py

@@ -103,7 +103,7 @@ for file in files:
 # ------------------------------------------ output result -----------------------------------------
   outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
 
-  file['input'].close()                                                                             # close input ASCII table (works for stdin)
+  table.input_close()                                                                               # close input ASCII table (works for stdin)
-  file['output'].close()                                                                            # close output ASCII table (works for stdout)
+  table.output_close()                                                                              # close output ASCII table (works for stdout)
   if file['name'] != 'STDIN':
     os.rename(file['name']+'_tmp',file['name'])                                                     # overwrite old one with tmp new

processing/post/showTable.py

@@ -59,4 +59,4 @@ for file in files:
   outputAlive and table.output_flush()
 
   if file['name'] != 'STDIN':
-    file['input'].close()
+    table.input_close()  

processing/post/sortTable.py

@@ -98,7 +98,7 @@ for file in files:
 
   table.output_flush()                                      # just in case of buffered ASCII table
 
-  file['input'].close()                                                     # close input ASCII table
+  table.input_close()                                                       # close input ASCII table
   if file['name'] != 'STDIN':
-    file['output'].close()                                                  # close output ASCII table
+    table.output_close()                                                    # close output ASCII table
     os.rename(file['name']+'_tmp',file['name'])                             # overwrite old one with tmp new

processing/post/stddevDown.py

@@ -188,6 +188,6 @@ for file in files:
 # ------------------------------------------ close file handles ---------------------------------------  
 
 for file in files:
-  file['input'].close()                                                     # close input ASCII table
+  table.input_close()                                                       # close input ASCII table
   if file['name'] != 'STDIN':
-    file['output'].close()                                                  # close output ASCII table
+    table.output_close()                                                    # close output ASCII table

processing/post/tagLabel.py

@@ -119,7 +119,7 @@ for file in files:
 
   outputAlive and table.output_flush()                                      # just in case of buffered ASCII table
 
-  file['input'].close()                                                     # close input ASCII table
+  table.input_close()                                                       # close input ASCII table
   if file['name'] != 'STDIN':
     file['output'].close                                                    # close output ASCII table
     os.rename(file['name']+'_tmp',file['name'])                             # overwrite old one with tmp new

processing/post/vtk_addPointcloudData.py

@@ -127,7 +127,7 @@ for file in files:
         elif datatype == 'scalar':
           array[datatype][label].InsertNextValue(float(theData[0]))
 
-  file['input'].close()                                                   # close input ASCII table
+  table.input_close()                                                     # close input ASCII table
 
 # ------------------------------------------ add data ---------------------------------------  
 

processing/post/vtk_addVoxelcloudData.py

@@ -136,7 +136,7 @@ for file in files:
         elif datatype == 'scalar':
           array[datatype][label].InsertNextValue(float(theData[0]))
 
-  file['input'].close()                                                   # close input ASCII table
+  table.input_close()                                                     # close input ASCII table
 
 # ------------------------------------------ add data ---------------------------------------  
 

processing/post/vtk_pointcloud.py

@@ -112,4 +112,4 @@ for file in files:
       writer.SetInputData(Polydata)
   writer.Write()
 
-  file['input'].close()                                                   # close input ASCII table
+  table.input_close()                                                     # close input ASCII table

processing/post/vtk_voxelcloud.py

@@ -134,4 +134,4 @@ for file in files:
       writer.SetInputData(uGrid)
   writer.Write()
 
-  file['input'].close()                                                   # close input ASCII table
+  table.input_close()                                                     # close input ASCII table

processing/pre/geom_addPrimitive.py

@@ -223,6 +223,6 @@ for file in files:
     
 #--- output finalization --------------------------------------------------------------------------
   if file['name'] != 'STDIN':
-    file['input'].close()
+    table.input_close()  
-    file['output'].close()
+    table.output_close()  
     os.rename(file['name']+'_tmp',file['name'])

processing/pre/geom_canvas.py

@@ -217,6 +217,6 @@ for file in files:
     
 #--- output finalization --------------------------------------------------------------------------
   if file['name'] != 'STDIN':
-    file['input'].close()
+    table.input_close()  
-    file['output'].close()
+    table.output_close()  
     os.rename(file['name']+'_tmp',file['name'])

processing/pre/geom_fromAng.py

@@ -208,7 +208,7 @@ for file in files:
   
 #--- output finalization -------------------------------------------------------------------------- 
   if file['name'] != 'STDIN':
-    file['output'].close()
+    table.output_close()  
     os.rename(file['name']+'_tmp',os.path.splitext(file['name'])[0] + \
                                   {True: '_material.config',
                                    False:'.geom'}[options.config])

processing/pre/geom_fromEuclideanDistance.py

@@ -284,4 +284,4 @@ for file in files:
     
 #--- output finalization --------------------------------------------------------------------------
   if file['name'] != 'STDIN':
-    file['input'].close()
+    table.input_close()  

processing/pre/geom_fromOsteonGeometry.py

@@ -192,4 +192,4 @@ else:
   
 
 #--- output finalization --------------------------------------------------------------------------  
-file['output'].close()
+table.output_close()  

processing/pre/geom_fromVPSC.py

@@ -143,7 +143,7 @@ for file in files:
 
 #--- output finalization --------------------------------------------------------------------------  
   if file['name'] != 'STDIN':
-    file['output'].close()
+    table.output_close()  
     os.rename(file['name']+'_tmp',os.path.splitext(file['name'])[0] + \
                                   {True: '_material.config',
                                    False:'.geom'}[options.config])

processing/pre/geom_fromVoronoiTessellation.py

@@ -266,8 +266,8 @@ for file in files:
 #--- output finalization --------------------------------------------------------------------------
 
   if file['name'] != 'STDIN':
-    file['input'].close()
+    table.input_close()  
-    file['output'].close()
+    table.output_close()  
     os.rename(file['name']+'_tmp',os.path.splitext(file['name'])[0] + \
                                   {True: '_material.config',
                                    False:'.geom'}[options.config])

processing/pre/geom_pack.py

@@ -1,31 +1,14 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,string,re,math,numpy
+import os,sys,string,re,math
+import numpy as np
+from optparse import OptionParser
 import damask
-from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
 
 scriptID = '$Id$'
 scriptName = scriptID.split()[1]
 
-#--------------------------------------------------------------------------------------------------
-class extendedOption(Option):
-#--------------------------------------------------------------------------------------------------
-# used for definition of new option parser action 'extend', which enables to take multiple option arguments
-# taken from online tutorial http://docs.python.org/library/optparse.html
-    
-    ACTIONS = Option.ACTIONS + ("extend",)
-    STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
-    TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
-    ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
-
-    def take_action(self, action, dest, opt, value, values, parser):
-        if action == "extend":
-            lvalue = value.split(",")
-            values.ensure_value(dest, []).extend(lvalue)
-        else:
-            Option.take_action(self, action, dest, opt, value, values, parser)
-
 
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
@@ -47,29 +30,20 @@ mappings = {
         'microstructures': lambda x: int(x),
           }
 
-parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
 compress geometry files with ranges "a to b" and/or multiples "n of x".
-""" + string.replace(scriptID,'\n','\\n')
+""", version = scriptID)
-)
 
 (options, filenames) = parser.parse_args()
 
-#--- setup file handles --------------------------------------------------------------------------- 
+# ------------------------------------------ setup file handles ---------------------------------------  
 files = []
 if filenames == []:
-  files.append({'name':'STDIN',
+  files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
-                'input':sys.stdin,
-                'output':sys.stdout,
-                'croak':sys.stderr,
-               })
 else:
   for name in filenames:
     if os.path.exists(name):
-      files.append({'name':name,
+      files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
-                    'input':open(name),
-                    'output':open(name+'_tmp','w'),
-                    'croak':sys.stdout,
-                    })
 
 #--- loop over input files ------------------------------------------------------------------------
 for file in files:
@@ -82,9 +56,9 @@ for file in files:
 
 #--- interpret header ----------------------------------------------------------------------------
   info = {
-          'grid':    numpy.zeros(3,'i'),
+          'grid':    np.zeros(3,'i'),
-          'size':    numpy.zeros(3,'d'),
+          'size':    np.zeros(3,'d'),
-          'origin':  numpy.zeros(3,'d'),
+          'origin':  np.zeros(3,'d'),
           'homogenization':  0,
           'microstructures': 0,
          }
@@ -111,10 +85,10 @@ for file in files:
                       'homogenization:  %i\n'%info['homogenization'] + \
                       'microstructures: %i\n'%info['microstructures'])
 
-  if numpy.any(info['grid'] < 1):
+  if np.any(info['grid'] < 1):
     file['croak'].write('invalid grid a b c.\n')
     continue
-  if numpy.any(info['size'] <= 0.0):
+  if np.any(info['size'] <= 0.0):
     file['croak'].write('invalid size x y z.\n')
     continue
 
@@ -179,11 +153,10 @@ for file in files:
 
 
 # ------------------------------------------ output result ---------------------------------------  
-
   outputAlive and theTable.output_flush()                                   # just in case of buffered ASCII table
 
 #--- output finalization --------------------------------------------------------------------------
   if file['name'] != 'STDIN':
-    file['input'].close()                                                   # close input ASCII table
+    table.input_close()                                                     # close input ASCII table
-    file['output'].close()                                                   # close input ASCII table
+    table.output_close()                                                    # close input ASCII table
     os.rename(file['name']+'_tmp',file['name'])                             # overwrite old one with tmp new

processing/pre/geom_rescale.py

@@ -219,7 +219,7 @@ for file in files:
     
 #--- output finalization --------------------------------------------------------------------------
   if file['name'] != 'STDIN':
-    file['input'].close()
+    table.input_close()  
-    file['output'].close()
+    table.output_close()  
     os.rename(file['name']+'_tmp',file['name'])
   

processing/pre/geom_translate.py

@@ -188,6 +188,6 @@ for file in files:
     
 #--- output finalization --------------------------------------------------------------------------
   if file['name'] != 'STDIN':
-    file['input'].close()
+    table.input_close()  
-    file['output'].close()
+    table.output_close()  
     os.rename(file['name']+'_tmp',file['name'])

processing/pre/geom_unpack.py

@@ -162,6 +162,6 @@ for file in files:
     
 #--- output finalization --------------------------------------------------------------------------
   if file['name'] != 'STDIN':
-    file['input'].close()                                                   # close input ASCII table
+    table.input_close()                                                     # close input ASCII table
-    file['output'].close()                                                  # close input ASCII table
+    table.output_close()                                                    # close input ASCII table
     os.rename(file['name']+'_tmp',file['name'])                             # overwrite old one with tmp new

processing/pre/geom_vicinityOffset.py

@@ -181,7 +181,7 @@ for file in files:
     
 #--- output finalization --------------------------------------------------------------------------
   if file['name'] != 'STDIN':
-    file['input'].close()
+    table.input_close()  
-    file['output'].close()
+    table.output_close()  
     os.rename(file['name']+'_tmp',file['name'])
 

processing/pre/seeds_fromGeom.py

@@ -189,6 +189,6 @@ for file in files:
 
   outputDead or theTable.output_flush()                                        # just in case of buffered ASCII table
 
-  file['input'].close()                                                     # close input ASCII table
+  table.input_close()                                                       # close input ASCII table
   if file['name'] != 'STDIN':
-    file['output'].close()                                                  # close output ASCII table
+    table.output_close()                                                    # close output ASCII table

processing/pre/seeds_fromTable.py

@@ -177,6 +177,6 @@ for file in files:
   theTable.data_writeArray()
   theTable.output_flush()
   
-  file['input'].close()                                                     # close input ASCII table
+  table.input_close()                                                       # close input ASCII table
   if file['name'] != 'STDIN':
-    file['output'].close()                                                  # close output ASCII table
+    table.output_close()                                                    # close output ASCII table