From 4aa63e1ab950c90829ead4988f6f0f57794f7d50 Mon Sep 17 00:00:00 2001
From: Martin	Diehl <m.diehl@mpie.de>
Date: Fri, 10 Apr 2015 16:59:08 +0000
Subject: [PATCH] handling of seeds files without microstructure (but
 eulerangles)

---
 processing/pre/seeds_check.py | 56 +++++++++++++++++++----------------
 1 file changed, 30 insertions(+), 26 deletions(-)

diff --git a/processing/pre/seeds_check.py b/processing/pre/seeds_check.py
index 48f738a19..8f6bef459 100755
--- a/processing/pre/seeds_check.py
+++ b/processing/pre/seeds_check.py
@@ -13,9 +13,9 @@ scriptName = os.path.splitext(scriptID.split()[1])[0]
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
 identifiers = {
-        'grid':    ['a','b','c'],
-        'size':    ['x','y','z'],
-        'origin':  ['x','y','z'],
+        'grid':   ['a','b','c'],
+        'size':   ['x','y','z'],
+        'origin': ['x','y','z'],
           }
 mappings = {
         'grid':            lambda x: int(x),
@@ -30,12 +30,9 @@ Produce VTK point mesh from seeds file
 
 """, version = scriptID)
 
-parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, metavar='int int int', \
-                  help='a,b,c grid of hexahedral box [from seeds file]')
 parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, metavar='float float float',\
                   help='x,y,z size of hexahedral box [1.0 along largest grid point number]')
 
-parser.set_defaults(grid = [0,0,0])
 parser.set_defaults(size = [0.0,0.0,0.0])
 
 (options, filenames) = parser.parse_args()
@@ -61,17 +58,32 @@ else:
 for file in files:
   file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n')
 
-  theTable = damask.ASCIItable(file['input'],file['output'])
-  theTable.head_read()
+  table = damask.ASCIItable(file['input'],file['output'])
+  table.head_read()
+
+  labels = ['x','y','z']
+  grainCol = table.labels_index('microstructure')
+  hasGrains = grainCol != -1
+
+  if hasGrains:
+    labels += ['microstructure']
+
+
+  table.data_readArray(labels)
+  coords = table.data[:,0:3]
+
+  grain = table.data[:,grainCol] if hasGrains else 1+np.arange(len(coords))
+  grainIDs = np.unique(grain).astype('i')
   
 #--- interpret header ----------------------------------------------------------------------------
   info = {
-          'grid':   np.zeros(3,'i'),
-          'size':   np.zeros(3,'d'),
-          'origin': np.zeros(3,'d'),
+          'grid':    np.zeros(3,'i'),
+          'size':    np.array(options.size),
+          'origin':  np.zeros(3,'d'),
+          'microstructures':  0,
          }
 
-  for header in theTable.info:
+  for header in table.info:
     headitems = map(str.lower,header.split())
     if len(headitems) == 0: continue
     if headitems[0] in mappings.keys():
@@ -82,26 +94,18 @@ for file in files:
       else:
         info[headitems[0]] = mappings[headitems[0]](headitems[1])
 
-  file['croak'].write('grid     a b c:  %s\n'%(' x '.join(map(str,info['grid']))) + \
-                      'size     x y z:  %s\n'%(' x '.join(map(str,info['size']))) + \
-                      'origin   x y z:  %s\n'%(' : '.join(map(str,info['origin']))))
-  if 0 not in options.grid:                                                                         # user-specified grid
-    info['grid'] = np.array(options.grid)
+  if info['microstructures'] != len(grainIDs):
+    file['croak'].write('grain data not matching grain count (%i)...\n'%(len(grainIDs)))
+    info['microstructures'] = len(grainIDs)
   if np.any(info['grid'] < 1):
     file['croak'].write('invalid grid a b c.\n')
-#    continue
+    continue
 
   for i in xrange(3):
     if info['size'][i] <= 0.0:                                                                      # any invalid size?
       info['size'][i] = float(info['grid'][i])/max(info['grid'])
       file['croak'].write('rescaling size %s...\n'%{0:'x',1:'y',2:'z'}[i])
 
-
-#--- read data --------------------------------------------------------------------------------
-  theTable.data_readArray(['x','y','z','microstructure'])
-  theTable.data[:,0:3] *= info['size']
-  theTable.data[:,0:3] += info['origin']
-
 #--- generate grid --------------------------------------------------------------------------------
   grid = vtk.vtkUnstructuredGrid()
   pts = vtk.vtkPoints()
@@ -111,12 +115,12 @@ for file in files:
   IDs.SetNumberOfComponents(1)
   IDs.SetName("GrainID")
 
-  for item in theTable.data:
+  for i,item in enumerate(coords):
     pid = pts.InsertNextPoint(item[0:3])
     pointIds = vtk.vtkIdList()
     pointIds.InsertId(0, pid)
     grid.InsertNextCell(1, pointIds)
-    IDs.InsertNextValue(int(item[3]))
+    IDs.InsertNextValue(grainIDs[i])
 
   grid.SetPoints(pts)
   grid.GetCellData().AddArray(IDs)