added missing string import in marc_addUserOutput (introduced with rev 3718) and removed unwanted imports and introduce use of damask.extendableParser in some other scripts

processing/pre/OIMang_hex2cub.py

@@ -2,37 +2,19 @@
 # -*- coding: UTF-8 no BOM -*-
 
 import string,os,sys
-from optparse import OptionParser, Option
+from optparse import OptionParser
+import damask
 
 scriptID   = string.replace('$Id$','\n','\\n')
 scriptName = scriptID.split()[1][:-3]
-
-#-------------------------------------------------------------------------------------------------
-class extendableOption(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
 #--------------------------------------------------------------------------------------------------
-parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
 Converts ang files (EBSD Data) from hexagonal grid to a pixel grid
-""" + string.replace(scriptID,'\n','\\n')
+
-)
+""", version = scriptID)
 
 parser.add_option('-x', dest='columnX', type='int', metavar='int', \
                         help='column containing x coordinates [%default]')

processing/pre/geom_fromMinimalSurface.py

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

processing/pre/geom_fromOsteonGeometry.py

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

processing/pre/geom_grainGrowth.py

@@ -1,11 +1,10 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,string,re,math,itertools
+import os,sys,string,math
 import numpy as np
 from optparse import OptionParser
 from scipy import ndimage
-from multiprocessing import Pool
 import damask
 
 scriptID   = string.replace('$Id$','\n','\\n')

processing/pre/geom_pack.py

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

processing/pre/geom_rescale.py

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

processing/pre/geom_toTable.py

@@ -1,33 +1,15 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,string,re,vtk
+import os,sys,string,vtk
 import numpy as np
-from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
+from optparse import OptionParser
 import damask
 
 scriptID   = string.replace('$Id$','\n','\\n')
 scriptName = scriptID.split()[1][:-3]
 
-#--------------------------------------------------------------------------------------------------
-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
 #--------------------------------------------------------------------------------------------------
@@ -48,11 +30,10 @@ mappings = {
         'microstructures': lambda x: int(x),
           }
 
-parser = OptionParser(option_class=extendedOption, usage='%prog [geomfile[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile[s]]', description = """
 Produce ASCIItable of structure data from geom description
 
-""" + string.replace(scriptID,'\n','\\n')
+""", version = scriptID)
-)
 
 (options, filenames) = parser.parse_args()
 

processing/pre/geom_translate.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,math
+import numpy as np
 import damask
-from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
+from optparse import OptionParser
 
 scriptID   = string.replace('$Id$','\n','\\n')
 scriptName = scriptID.split()[1][:-3]
 
-#--------------------------------------------------------------------------------------------------
-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
 #--------------------------------------------------------------------------------------------------
@@ -46,10 +29,10 @@ 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 = """
 translate microstructure indices (shift or substitute) and/or geometry origin.
-""" + string.replace(scriptID,'\n','\\n')
+
-)
+""", version=scriptID)
 
 parser.add_option('-o', '--origin', dest='origin', type='float', nargs = 3, \
                   help='offset from old to new origin of grid', metavar='float float float')
@@ -96,14 +79,14 @@ 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,
          }
   newInfo = {
-          'origin':  numpy.zeros(3,'d'),
+          'origin':  np.zeros(3,'d'),
           'microstructures': 0,
          }
   extra_header = []
@@ -129,15 +112,15 @@ 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
 
 #--- read data ------------------------------------------------------------------------------------
-  microstructure = numpy.zeros(info['grid'].prod(),'i')
+  microstructure = np.zeros(info['grid'].prod(),'i')
   i = 0
   theTable.data_rewind()
   while theTable.data_read():
@@ -153,7 +136,7 @@ for file in files:
     i += s
 
 #--- do work ------------------------------------------------------------------------------------
-  substituted = numpy.copy(microstructure)
+  substituted = np.copy(microstructure)
   for k, v in sub.iteritems(): substituted[microstructure==k] = v                                    # substitute microstructure indices
 
   substituted += options.microstructure                                                              # shift microstructure indices

processing/pre/geom_unpack.py

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

processing/pre/geom_vicinityOffset.py

@@ -1,9 +1,11 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,string,re,math,numpy, damask
+import os,sys,string,math
+import numpy as np
 from scipy import ndimage
-from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
+from optparse import OptionParser
+import damask
 
 scriptID   = string.replace('$Id$','\n','\\n')
 scriptName = scriptID.split()[1][:-3]
@@ -48,11 +50,11 @@ 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 = """
 Offset microstructure index for points which see a microstructure different from themselves within a given (cubic) vicinity,
 i.e. within the region close to a grain/phase boundary.
-""" + string.replace(scriptID,'\n','\\n')
+
-)
+""", version = scriptID)
 
 parser.add_option('-v', '--vicinity', dest='vicinity', type='int', metavar='int', \
                   help='voxel distance checked for presence of other microstructure [%default]')

processing/pre/gmsh_identifySurfaces.py

@@ -1,10 +1,9 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,string
+import os,sys,string,re
-import damask
-import re
 from optparse import OptionParser
+import damask
 
 scriptID   = string.replace('$Id$','\n','\\n')
 scriptName = scriptID.split()[1][:-3]

processing/pre/marc_addUserOutput.py

@@ -7,8 +7,9 @@ based on the files
 <modelname_jobname>.output<Homogenization/Crystallite/Constitutive>
 that are written during the first run of the model.
 '''
-import sys,os,re
+import sys,os,re,string
 from optparse import OptionParser
+import damask
 
 scriptID   = string.replace('$Id$','\n','\\n')
 scriptName = scriptID.split()[1][:-3]
@@ -54,8 +55,7 @@ def ParseOutputFormat(filename,what,me):
           format['outputs'].append([output,length])
   return format
 
-
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options] Marc.inputfile(s)', description="""
-parser = OptionParser(usage='%prog [options] Marc.inputfile(s)', description="""
 Transfer the output variables requested in the material.config to
 properly labelled user defined variables within the Marc input file (*.dat).
 
@@ -65,7 +65,10 @@ that are written during the first run of the model.
 
 Specify which user block format you want to apply by stating the homogenization, crystallite, and phase identifiers.
 Or have an existing set of user variables copied over from another *.dat file.
-""")
+
+""", version = scriptID)
+
+
 parser.add_option('-n','--number', dest='number', type='int', \
           help='maximum requested User Defined Variable [%default]')
 parser.add_option('--homogenization', dest='homog', \

processing/pre/mentat_pbcOnBoxMesh.py

@@ -1,8 +1,10 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import sys,os,pwd,math,re,string,numpy, damask
+import sys,os,pwd,math,string
+import numpy as np
 from optparse import OptionParser
+import damask
 
 scriptID   = string.replace('$Id$','\n','\\n')
 scriptName = scriptID.split()[1][:-3]
@@ -54,12 +56,12 @@ def servoLink():
 
   cmds = []
   base = ['x','y','z']
-  box = {'min': numpy.zeros(3,dtype='d'),
+  box = {'min': np.zeros(3,dtype='d'),
-         'max': numpy.zeros(3,dtype='d'),
+         'max': np.zeros(3,dtype='d'),
-       'delta': numpy.zeros(3,dtype='d'),
+       'delta': np.zeros(3,dtype='d'),
       }
   Nnodes = py_get_int("nnodes()")
-  NodeCoords = numpy.zeros((Nnodes,3),dtype='d')
+  NodeCoords = np.zeros((Nnodes,3),dtype='d')
   for node in xrange(Nnodes):
     NodeCoords[node,0] = py_get_float("node_x(%i)"%(node+1))
     NodeCoords[node,1] = py_get_float("node_y(%i)"%(node+1))
@@ -120,7 +122,7 @@ def servoLink():
     for dir in xrange(3):                         # check for each direction
       if node['faceMember'][dir]:                 # me on this front face
         linkCoord[0][dir] = box['min'][dir]       # project me onto rear face along dir
-        linkCoord.append(numpy.array(box['min'])) # append base corner
+        linkCoord.append(np.array(box['min'])) # append base corner
         
         linkCoord[-1][dir] = box['max'][dir]      # stretch it to corresponding control leg of "dir"
 
@@ -156,10 +158,10 @@ def servoLink():
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #-------------------------------------------------------------------------------------------------- 
-parser = OptionParser(usage='%prog [options]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage = '%prog [options]', description = """
 Set up servo linking to achieve periodic boundary conditions for a regular hexahedral mesh presently opened in MSC.Mentat
-""" + string.replace(scriptID,'\n','\\n')
+
-)
+""", version = scriptID)
 
 parser.add_option("-p", "--port", type="int",\
                                   dest="port",\

processing/pre/mentat_spectralBox.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import os, sys, math, re, threading, time, string
+import os, sys, string
 from optparse import OptionParser
 import damask
 

processing/pre/patchFromReconstructedBoundaries.py

@@ -1,8 +1,9 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import sys,os,math,re,string, damask
+import sys,os,math,re,string
-from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
+from optparse import OptionParser
+import damask
 
 scriptID   = string.replace('$Id$','\n','\\n')
 scriptName = scriptID.split()[1][:-3]
@@ -23,26 +24,6 @@ except:
   MentatCapability = False
 
 
-# -----------------------------
-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)
-
-
-
 def outMentat(cmd,locals):
   if cmd[0:3] == '(!)':
     exec(cmd[3:])
@@ -800,12 +781,11 @@ def fftbuild(rcData,height,xframe,yframe,resolution,extrusion):            # bui
 
 
 # ----------------------- MAIN -------------------------------
-  
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options] datafile[s]', description = """
-parser = OptionParser(option_class=extendedOption, usage='%prog [options] datafile[s]', description = """
 Produce image, spectral geometry description, and (auto) Mentat procedure from TSL/OIM
 reconstructed boundary file
-""" + string.replace(scriptID,'\n','\\n')
+
-)
+""", version = scriptID)
 
 parser.add_option("-o", "--output", action='extend', dest='output', \
         help="types of output [image, mentat, procedure, spectral]")

processing/pre/seeds_check.py

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

processing/pre/seeds_fromRandom.py

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