input file handling now save for large file count.

streamlining of input column detection.
fixed bug iterating through “grainIDs” instead of “grain”.
proper closing and dismissal of output table file.

processing/pre/seeds_check.py

@@ -37,44 +37,38 @@ parser.set_defaults(size = [0.0,0.0,0.0])
 
 (options, filenames) = parser.parse_args()
 
-#--- setup file handles --------------------------------------------------------------------------  
-files = []
+# --- loop over input files -------------------------------------------------------------------------
 if filenames == []:
-  files.append({'name':'STDIN',
-                'input':sys.stdin,
-                'output':sys.stdout,
-                'croak':sys.stderr,
-               })
-else:
-  for name in filenames:
-    if os.path.exists(name):
-      files.append({'name':name,
-                    'input':open(name),
-                    'output':sys.stdout,
-                    'croak':sys.stdout,
-                    })
+  filenames = ['STDIN']
 
-#--- loop over input files ------------------------------------------------------------------------
-for file in files:
-  file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n')
+for name in filenames:
+  if name == 'STDIN':
+    file = {'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr}
+    file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
+  else:
+    if not os.path.exists(name): continue
+    file = {'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr}
+    file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
 
-  table = damask.ASCIItable(file['input'],file['output'])
+  table = damask.ASCIItable(file['input'],file['output'],buffered = False)
   table.head_read()
 
-  coordsCol = table.labels_index('1_coords')
-  if coordsCol < 0: 
-    coordsCol = table.labels_index('x')                                                            # try if file is in legacy format
-    if coordsCol < 0: 
-      file['croak'].write('column 1_coords/x not found...\n')
-      continue
 
-  grainCol = table.labels_index('microstructure')
-  hasGrains = grainCol != -1
+  if np.all(table.label_index(['1_coords','2_coords','3_coords']) != -1):
+    labels = ['1_coords','2_coords','3_coords']
+  elif np.all(table.label_index(['x','y','z']) != -1):
+    labels = ['x','y','z']
+  else:
+    file['croak'].write('no coordinate data (1/2/3_coords | x/y/z) found ...')
+    continue
 
-  table.data_readArray()
-  coords = table.data[:,coordsCol:coordsCol+3]
-  grain = table.data[:,grainCol] if hasGrains else 1+np.arange(len(coords))
-  grainIDs = np.unique(grain).astype('i')
+  hasGrains = table.label_index('microstructure') != -1
+  labels += ['microstructure'] if hasGrains else []
+
+  table.data_readArray(labels)                                                                      # read ASCIItable columns
+  coords = table.data[:,:3]                                                                         # assign coordinates
+  grain = table.data[:,3].astype('i') if hasGrains else 1+np.arange(len(coords),dtype='i')          # assign grains
+  grainIDs = np.unique(grain).astype('i')                                                           # find all grainIDs present
   
 #--- interpret header ----------------------------------------------------------------------------
   info = {
@@ -121,7 +115,7 @@ for file in files:
     pointIds = vtk.vtkIdList()
     pointIds.InsertId(0, pid)
     grid.InsertNextCell(1, pointIds)
-    IDs.InsertNextValue(grainIDs[i])
+    IDs.InsertNextValue(grain[i])
 
   grid.SetPoints(pts)
   grid.GetCellData().AddArray(IDs)
@@ -139,6 +133,7 @@ for file in files:
     writer.Write()
     sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
   else:
+    table.close(dismiss=True)
     (head,tail) = os.path.split(file['name'])
     writer = vtk.vtkXMLUnstructuredGridWriter()
     writer.SetDataModeToBinary()