removed aliases 'resolution' and 'dimension' for 'grid' and 'size' because some scripts did not have it anyway and the rename happened quite a while ago

processing/pre/geom_addPrimitive.py

@@ -14,10 +14,6 @@ oversampling = 2.
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
-synonyms = {
-        'grid':   ['resolution'],
-        'size':   ['dimension'],
-          }
 identifiers = {
         'grid':   ['a','b','c'],
         'size':   ['x','y','z'],
@@ -37,8 +33,7 @@ Depending on the sign of the dimension parameters, these objects can be boxes, c
 
 """, version = scriptID)
 
-parser.add_option('-o', '--origin', 
+parser.add_option('-c', '--center',     dest='center', type='int', nargs = 3, metavar=' '.join(['int']*3),
-                  '-c', '--center',     dest='center', type='int', nargs = 3, metavar=' '.join(['int']*3),
                   help='a,b,c origin of primitive %default')
 parser.add_option('-d', '--dimension',  dest='dimension', type='int', nargs = 3, metavar=' '.join(['int']*3),
                   help='a,b,c extension of hexahedral box; negative values are diameters')
@@ -115,8 +110,6 @@ for file in files:
   for header in table.info:
     headitems = map(str.lower,header.split())
     if len(headitems) == 0: continue                                                              # skip blank lines
-    for synonym,alternatives in synonyms.iteritems():
-      if headitems[0] in alternatives: headitems[0] = synonym
     if headitems[0] in mappings.keys():
       if headitems[0] in identifiers.keys():
         for i in xrange(len(identifiers[headitems[0]])):

processing/pre/geom_canvas.py

@@ -12,12 +12,6 @@ scriptName = os.path.splitext(scriptID.split()[1])[0]
 # --------------------------------------------------------------------
 #                                MAIN
 # --------------------------------------------------------------------
-
-
-synonyms = {
-        'grid':   ['resolution'],
-        'size':   ['dimension'],
-          }
 identifiers = {
         'grid':   ['a','b','c'],
         'size':   ['x','y','z'],
@@ -44,7 +38,7 @@ parser.add_option('-f', '--fill',   dest='fill', type='int', metavar = 'int',
                                     help='(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
 
 parser.set_defaults(grid = ['0','0','0'])
-parser.set_defaults(offset = [0,0,0])
+parser.set_defaults(offset = (0,0,0))
 parser.set_defaults(fill = 0)
 
 (options, filenames) = parser.parse_args()
@@ -91,8 +85,6 @@ for file in files:
   for header in theTable.info:
     headitems = map(str.lower,header.split())
     if len(headitems) == 0: continue                                                              # skip blank lines
-    for synonym,alternatives in synonyms.iteritems():
-      if headitems[0] in alternatives: headitems[0] = synonym
     if headitems[0] in mappings.keys():
       if headitems[0] in identifiers.keys():
         for i in xrange(len(identifiers[headitems[0]])):

processing/pre/geom_check.py

@@ -12,10 +12,6 @@ scriptName = os.path.splitext(scriptID.split()[1])[0]
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
-synonyms = {
-        'grid':   ['resolution'],
-        'size':   ['dimension'],
-          }
 identifiers = {
         'grid':    ['a','b','c'],
         'size':    ['x','y','z'],
@@ -77,8 +73,6 @@ for file in files:
   for header in theTable.info:
     headitems = map(str.lower,header.split())
     if len(headitems) == 0: continue
-    for synonym,alternatives in synonyms.iteritems():
-      if headitems[0] in alternatives: headitems[0] = synonym
     if headitems[0] in mappings.keys():
       if headitems[0] in identifiers.keys():
         for i in xrange(len(identifiers[headitems[0]])):

processing/pre/geom_fromEuclideanDistance.py

@@ -34,10 +34,6 @@ def periodic_3Dpad(array, rimdim=(1,1,1)):
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
-synonyms = {
-        'grid':   ['resolution'],
-        'size':   ['dimension'],
-          }
 identifiers = {
         'grid':   ['a','b','c'],
         'size':   ['x','y','z'],
@@ -169,8 +165,6 @@ for file in files:
   for header in table.info:
     headitems = map(str.lower,header.split())
     if len(headitems) == 0: continue                                                              # skip blank lines
-    for synonym,alternatives in synonyms.iteritems():
-      if headitems[0] in alternatives: headitems[0] = synonym
     if headitems[0] in mappings.keys():
       if headitems[0] in identifiers.keys():
         for i in xrange(len(identifiers[headitems[0]])):

processing/pre/geom_grainGrowth.py

@@ -8,15 +8,11 @@ from scipy import ndimage
 import damask
 
 scriptID   = string.replace('$Id$','\n','\\n')
-scriptName = scriptID.split()[1][:-3]
+scriptName = os.path.splitext(scriptID.split()[1])[0]
 
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
-synonyms = {
-        'grid':   ['resolution'],
-        'size':   ['dimension'],
-          }
 identifiers = {
         'grid':   ['a','b','c'],
         'size':   ['x','y','z'],
@@ -35,8 +31,8 @@ Smoothens out interface roughness by simulated curvature flow.
 This is achieved by the diffusion of each initially sharply bounded grain volume within the periodic domain
 up to a given distance 'd' voxels.
 The final geometry is assembled by selecting at each voxel that grain index for which the concentration remains largest.
-""" + string.replace(scriptID,'\n','\\n')
+
-)
+""", version = scriptID)
 
 parser.add_option('-d', '--distance', dest='d', type='int', metavar='int',
                   help='diffusion distance in voxels [%default]')
@@ -97,8 +93,6 @@ for file in files:
   for header in theTable.info:
     headitems = map(str.lower,header.split())
     if len(headitems) == 0: continue
-    for synonym,alternatives in synonyms.iteritems():
-      if headitems[0] in alternatives: headitems[0] = synonym
     if headitems[0] in mappings.keys():
       if headitems[0] in identifiers.keys():
         for i in xrange(len(identifiers[headitems[0]])):
@@ -243,6 +237,6 @@ for file in files:
     
 #--- output finalization --------------------------------------------------------------------------
   if file['name'] != 'STDIN':
-    theTable.__IO__['in'].close()
+    theTable.input_close() 
-    theTable.__IO__['out'].close()
+    theTable.output_close() 
     os.rename(file['name']+'_tmp',file['name'])

processing/pre/geom_pack.py

@@ -12,10 +12,6 @@ scriptName = os.path.splitext(scriptID.split()[1])[0]
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
-synonyms = {
-        'grid':   ['resolution'],
-        'size':   ['dimension'],
-          }
 identifiers = {
         'grid':    ['a','b','c'],
         'size':    ['x','y','z'],
@@ -74,8 +70,6 @@ for file in files:
   for header in table.info:
     headitems = map(str.lower,header.split())
     if len(headitems) == 0: continue
-    for synonym,alternatives in synonyms.iteritems():
-      if headitems[0] in alternatives: headitems[0] = synonym
     if headitems[0] in mappings.keys():
       if headitems[0] in identifiers.keys():
         for i in xrange(len(identifiers[headitems[0]])):

processing/pre/geom_rescale.py

@@ -12,10 +12,6 @@ scriptName = os.path.splitext(scriptID.split()[1])[0]
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
-synonyms = {
-        'grid':   ['resolution'],
-        'size':   ['dimension'],
-          }
 identifiers = {
         'grid':   ['a','b','c'],
         'size':   ['x','y','z'],
@@ -91,8 +87,6 @@ for file in files:
   for header in table.info:
     headitems = map(str.lower,header.split())
     if len(headitems) == 0: continue
-    for synonym,alternatives in synonyms.iteritems():
-      if headitems[0] in alternatives: headitems[0] = synonym
     if headitems[0] in mappings.keys():
       if headitems[0] in identifiers.keys():
         for i in xrange(len(identifiers[headitems[0]])):

processing/pre/geom_toTable.py

@@ -7,16 +7,12 @@ from optparse import OptionParser
 import damask
 
 scriptID   = string.replace('$Id$','\n','\\n')
-scriptName = scriptID.split()[1][:-3]
+scriptName = os.path.splitext(scriptID.split()[1])[0]
 
 
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
-synonyms = {
-        'grid':   ['resolution'],
-        'size':   ['dimension'],
-          }
 identifiers = {
         'grid':    ['a','b','c'],
         'size':    ['x','y','z'],
@@ -76,8 +72,6 @@ for file in files:
   for header in theTable.info:
     headitems = map(str.lower,header.split())
     if len(headitems) == 0: continue
-    for synonym,alternatives in synonyms.iteritems():
-      if headitems[0] in alternatives: headitems[0] = synonym
     if headitems[0] in mappings.keys():
       if headitems[0] in identifiers.keys():
         for i in xrange(len(identifiers[headitems[0]])):

processing/pre/geom_translate.py

@@ -12,10 +12,6 @@ scriptName = os.path.splitext(scriptID.split()[1])[0]
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
-synonyms = {
-        'grid':   ['resolution'],
-        'size':   ['dimension'],
-          }
 identifiers = {
         'grid':    ['a','b','c'],
         'size':    ['x','y','z'],
@@ -34,14 +30,14 @@ translate microstructure indices (shift or substitute) and/or geometry origin.
 
 """, version=scriptID)
 
-parser.add_option('-o', '--origin', dest='origin', type='float', nargs = 3, \
+parser.add_option('-o', '--origin', dest='origin', type='float', nargs = 3,
-                  help='offset from old to new origin of grid', metavar='float float float')
+                  help='offset from old to new origin of grid', metavar=' '.join(['float']*3))
-parser.add_option('-m', '--microstructure', dest='microstructure', type='int', \
+parser.add_option('-m', '--microstructure', dest='microstructure', type='int',
                   help='offset from old to new microstructure indices', metavar='int')
-parser.add_option('-s', '--substitute', action='extend', dest='substitute', \
+parser.add_option('-s', '--substitute', action='extend', dest='substitute',
                   help='substitutions of microstructure indices from,to,from,to,...', metavar='<string LIST>')
 
-parser.set_defaults(origin = [0.0,0.0,0.0])
+parser.set_defaults(origin = (0.0,0.0,0.0))
 parser.set_defaults(microstructure = 0)
 parser.set_defaults(substitute = [])
 parser.set_defaults(twoD = False)
@@ -93,8 +89,6 @@ for file in files:
   for header in theTable.info:
     headitems = map(str.lower,header.split())
     if len(headitems) == 0: continue
-    for synonym,alternatives in synonyms.iteritems():
-      if headitems[0] in alternatives: headitems[0] = synonym
     if headitems[0] in mappings.keys():
       if headitems[0] in identifiers.keys():
         for i in xrange(len(identifiers[headitems[0]])):

processing/pre/geom_unpack.py

@@ -12,10 +12,6 @@ scriptName = os.path.splitext(scriptID.split()[1])[0]
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
-synonyms = {
-        'grid':   ['resolution'],
-        'size':   ['dimension'],
-          }
 identifiers = {
         'grid':      ['a','b','c'],
         'size':      ['x','y','z'],
@@ -70,8 +66,6 @@ for file in files:
   for header in table.info:
     headitems = map(str.lower,header.split())
     if len(headitems) == 0: continue
-    for synonym,alternatives in synonyms.iteritems():
-      if headitems[0] in alternatives: headitems[0] = synonym
     if headitems[0] in mappings.keys():
       if headitems[0] in identifiers.keys():
         for i in xrange(len(identifiers[headitems[0]])):

processing/pre/geom_vicinityOffset.py

@@ -10,33 +10,9 @@ import damask
 scriptID   = string.replace('$Id$','\n','\\n')
 scriptName = os.path.splitext(scriptID.split()[1])[0]
 
-#--------------------------------------------------------------------------------------------------
-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
 #--------------------------------------------------------------------------------------------------
-
-synonyms = {
-        'grid':   ['resolution'],
-        'size':   ['dimension'],
-          }
 identifiers = {
         'grid':   ['a','b','c'],
         'size':   ['x','y','z'],
@@ -107,8 +83,6 @@ for file in files:
   for header in theTable.info:
     headitems = map(str.lower,header.split())
     if len(headitems) == 0: continue
-    for synonym,alternatives in synonyms.iteritems():
-      if headitems[0] in alternatives: headitems[0] = synonym
     if headitems[0] in mappings.keys():
       if headitems[0] in identifiers.keys():
         for i in xrange(len(identifiers[headitems[0]])):

processing/pre/gmsh_identifySurfaces.py

@@ -6,7 +6,7 @@ from optparse import OptionParser
 import damask
 
 scriptID   = string.replace('$Id$','\n','\\n')
-scriptName = scriptID.split()[1][:-3]
+scriptName = os.path.splitext(scriptID.split()[1])[0]
 
 def all_same(items,a):
   return all(x == a for x in items)

processing/pre/seeds_check.py

@@ -12,10 +12,6 @@ scriptName = os.path.splitext(scriptID.split()[1])[0]
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
-synonyms = {
-        'grid':   ['resolution'],
-        'size':   ['dimension'],
-          }
 identifiers = {
         'grid':    ['a','b','c'],
         'size':    ['x','y','z'],
@@ -78,8 +74,6 @@ for file in files:
   for header in theTable.info:
     headitems = map(str.lower,header.split())
     if len(headitems) == 0: continue
-    for synonym,alternatives in synonyms.iteritems():
-      if headitems[0] in alternatives: headitems[0] = synonym
     if headitems[0] in mappings.keys():
       if headitems[0] in identifiers.keys():
         for i in xrange(len(identifiers[headitems[0]])):

processing/pre/seeds_fromGeom.py

@@ -12,10 +12,6 @@ scriptName = os.path.splitext(scriptID.split()[1])[0]
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
-synonyms = {
-        'grid':   ['resolution'],
-        'size':   ['dimension'],
-          }
 identifiers = {
         'grid':   ['a','b','c'],
         'size':   ['x','y','z'],
@@ -90,8 +86,6 @@ for file in files:
   for header in table.info:
     headitems = map(str.lower,header.split())
     if len(headitems) == 0: continue                                                              # skip blank lines
-    for synonym,alternatives in synonyms.iteritems():
-      if headitems[0] in alternatives: headitems[0] = synonym
     if headitems[0] in mappings.keys():
       if headitems[0] in identifiers.keys():
         for i in xrange(len(identifiers[headitems[0]])):

processing/pre/seeds_fromTable.py

@@ -10,14 +10,9 @@ import damask
 scriptID   = string.replace('$Id$','\n','\\n')
 scriptName = os.path.splitext(scriptID.split()[1])[0]
 
-
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
-synonyms = {
-        'grid':   ['resolution'],
-        'size':   ['dimension'],
-          }
 identifiers = {
         'grid':   ['a','b','c'],
         'size':   ['x','y','z'],
@@ -31,7 +26,6 @@ mappings = {
         'microstructures': lambda x: int(x),
           }
 
-
 parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
 Create seed file by taking microstructure indices from given ASCIItable column.
 White and black-listing of microstructure indices is possible.