switched importing from "msc_tools" to "damask"

patchFrom... now skips blank lines, has more commenting, treats (artificial) bi-crystal (somewhat) gracefully.

processing/post/mentat_colorMap.py

@@ -1,10 +1,10 @@
 #!/usr/bin/env python 
 
-import sys, os, msc_tools, string
+import sys, os, string, damask
 from colorsys import *
 from optparse import OptionParser
 
-sys.path.append(msc_tools.MSC_TOOLS().libraryPath(sys.argv[0],'../../'))
+sys.path.append(damask.solver.Marc().libraryPath('../../'))
 
 try:
   from py_mentat import *

processing/post/postResults.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python 
 
 import pdb, os, sys, gc, math, re, threading, time, struct, string
-import msc_tools
+import damask
 from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
 
 
@@ -755,7 +755,7 @@ if options.filetype not in ['marc','spectral']:
   parser.error('file type "%s" not supported...'%options.filetype)
 
 if options.filetype == 'marc':
-  sys.path.append(msc_tools.MSC_TOOLS().libraryPath(sys.argv[0],'../../'))
+  sys.path.append(damask.solver.Marc().libraryPath('../../'))
   
   try:
     from py_post import *
@@ -838,7 +838,7 @@ for opt in ['nodalScalar','elemScalar','elemTensor','homogenizationResult','crys
 
 if options.info:
   if options.filetype == 'marc':
-    print '\n\nMentat release %s'%msc_tools.MSC_TOOLS().version(sys.argv[0],'../../')
+    print '\n\nMentat release %s'%damask.solver.Marc().version('../../')
   if options.filetype == 'spectral':
     print '\n\n',p
 

processing/pre/mentat_pbcOnBoxMesh.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python
 
-import sys,os,pwd,math,re,string,msc_tools
+import sys,os,pwd,math,re,string, damask
 from optparse import OptionParser
 
-sys.path.append(msc_tools.MSC_TOOLS().libraryPath(sys.argv[0],'../../'))
+sys.path.append(damask.solver.Marc().libraryPath('../../'))
 
 try:
   from py_mentat import *

processing/pre/mentat_spectralBox.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-import os, sys, math, re, threading, time, string, msc_tools
+import os, sys, math, re, threading, time, string, damask
 from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
 
 
@@ -251,7 +251,7 @@ parser.set_defaults(homogenization = 1)
 (options, args) = parser.parse_args()
 
 
-sys.path.append(msc_tools.MSC_TOOLS().libraryPath(sys.argv[0],'../../'))
+sys.path.append(damask.solver.Marc().libraryPath('../../'))
 
 try:
   from py_mentat import *

processing/pre/patchFromReconstructedBoundaries.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-import sys,os,math,re,string, msc_tools
+import sys,os,math,re,string, damask
 from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
 
 
@@ -10,7 +10,7 @@ try:                                        # check for Python Image Lib
 except:
   ImageCapability = False
 
-sys.path.append(msc_tools.MSC_TOOLS().libraryPath(sys.argv[0],'../../'))
+sys.path.append(damask.solver.Marc().libraryPath('../../'))
 
 try:                                        # check for MSC.Mentat Python interface
   from py_mentat import *
@@ -79,7 +79,8 @@ def rcbOrientationParser(content):
   grains = []
   myOrientation = [0.0,0.0,0.0]
   for line in content:
-    if line[0] != '#':                      # skip comments
+    m = re.match(r'\s*(#|$)',line)
+    if m: continue                                            # skip comments and blank lines
     for grain in range(2):
       myID = int(line.split()[12+grain])                      # get grain id
       myOrientation = map(float,line.split())[3*grain:3+3*grain]  # get orientation
@@ -99,7 +100,8 @@ def rcbParser(content,M,size,tolerance):                      # parser for TSL-O
   x = [0.,0.]
   y = [0.,0.]
   for line in content:
-    if line[0] != '#':                                          # skip comments
+    m = re.match(r'\s*(#|$)',line)
+    if m: continue                                            # skip comments and blank lines
     (x[0],y[0],x[1],y[1]) = map(float,line.split())[8:12]     # get start and end coordinates of each segment.
     (x[0],y[0]) = (M[0]*x[0]+M[1]*y[0],M[2]*x[0]+M[3]*y[0])   # apply transformation to coordinates
     (x[1],y[1]) = (M[0]*x[1]+M[1]*y[1],M[2]*x[1]+M[3]*y[1])   # to get rcb --> Euler system
@@ -122,7 +124,8 @@ def rcbParser(content,M,size,tolerance):                      # parser for TSL-O
   grainNeighbors = []
   
   for line in content:
-    if line[0] != '#':                                          # skip comments
+    m = re.match(r'\s*(#|$)',line)
+    if m: continue                                # skip comments and blank lines
     (x[0],y[0],x[1],y[1]) = map(float,line.split())[8:12]     # get start and end coordinates of each segment
     (x[0],y[0]) = (M[0]*x[0]+M[1]*y[0],M[2]*x[0]+M[3]*y[0])   # apply transformation to coordinates
     (x[1],y[1]) = (M[0]*x[1]+M[1]*y[1],M[2]*x[1]+M[3]*y[1])   # to get rcb --> Euler system
@@ -295,18 +298,23 @@ def rcbParser(content,M,size,tolerance):                      # parser for TSL-O
     rcData['segment'].append(segment)
   print "  built %i segments"%(len(rcData['segment']))
 
-  for grain in grains['legs']:  
+  for legs in grains['legs']:                                                             # loop over grains
-    rcData['grain'].append(grain)
+    rcData['grain'].append(legs)                                                          # store list of boundary segments
     myNeighbors = {}
-    for leg in grain:
+    for leg in legs:                                                                      # test each boundary segment
-      if leg < len(grainNeighbors):
+      if leg < len(grainNeighbors):                                                       # a valid segment index?
-        for side in range(2):
+        for side in range(2):                                                             # look at both sides of the segment
-          if grainNeighbors[leg][side] in myNeighbors:
+          if grainNeighbors[leg][side] in myNeighbors:                                    # count occurrence of grain IDs
             myNeighbors[grainNeighbors[leg][side]] += 1
           else:
             myNeighbors[grainNeighbors[leg][side]] = 1
-    if myNeighbors:   # do I have any neighbors
+    if myNeighbors:                                                                       # do I have any neighbors (i.e., non-bounding box segment)
-      rcData['grainMapping'].append(sorted(myNeighbors.iteritems(), key=lambda (k,v): (v,k), reverse=True)[0][0])   # most frequent grain is me
+      candidateGrains = sorted(myNeighbors.iteritems(), key=lambda (k,v): (v,k), reverse=True)  # sort grain counting
+      if candidateGrains[0][0] not in rcData['grainMapping']:                                   # most frequent one not yet seen?
+        rcData['grainMapping'].append(candidateGrains[0][0])                                    # must be me then
+      else:
+        rcData['grainMapping'].append(candidateGrains[1][0])                                    # special case of bi-crystal situation...
+      
   print "  found %i grains\n"%(len(rcData['grain']))
 
   rcData['box'] = grains['box']