geom_check is now using vtk class, other scripts stop execution in case of invalid grid or size

processing/pre/geom_Osteon.py

@@ -81,7 +81,11 @@ file = {'name':'STDIN',
        }
 
 if numpy.any(options.grid < 2):
-  file['croak'].write('grid too low...\n')
+  file['croak'].write('grid too small...\n')
+  sys.exit()
+
+if numpy.any(options.size <= 0.0):
+  file['croak'].write('size too small...\n')
   sys.exit()
 
 options.omega  *= math.pi/180.0                                                                     # rescale ro radians
@@ -135,6 +139,13 @@ file['croak'].write('grid     a b c:  %s\n'%(' x '.join(map(str,info['grid'])))
                     'homogenization:  %i\n'%info['homogenization'])
 file['croak'].write("bounding box:    %s\n"%(numpy.sqrt(numpy.sum(box*box,0))))
 
+if numpy.any(info['grid'] < 1):
+  file['croak'].write('no valid grid info found.\n')
+  sys.exit()
+if numpy.any(info['size'] <= 0.0):
+  file['croak'].write('no valid size info found.\n')
+  sys.exit()
+
 # -------------------------------------- switch according to task ----------------------------------
 formatwidth = 1+int(math.floor(math.log10(info['microstructures']-1)))
 if options.config:

processing/pre/geom_check.py

@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,string,re,numpy
+import os,sys,string,re,numpy,vtk
 from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
 
-# -----------------------------
+#--------------------------------------------------------------------------------------------------
 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
     
@@ -22,75 +22,10 @@ class extendedOption(Option):
         else:
             Option.take_action(self, action, dest, opt, value, values, parser)
 
-
+     
-
+#--------------------------------------------------------------------------------------------------
-def outStdout(cmd,locals):
+#                                MAIN
-  if cmd[0:3] == '(!)':
+#--------------------------------------------------------------------------------------------------
-    exec(cmd[3:])
-  elif cmd[0:3] == '(?)':
-    cmd = eval(cmd[3:])
-    print cmd
-  else:
-    print cmd
-  return
-
-def outFile(cmd,locals):
-  if cmd[0:3] == '(!)':
-    exec(cmd[3:])
-  elif cmd[0:3] == '(?)':
-    cmd = eval(cmd[3:])
-    locals['filepointer'].write(cmd+'\n')
-  else:
-    locals['filepointer'].write(cmd+'\n')
-  return
-
-
-def output(cmds,locals,dest):
-  for cmd in cmds:
-    if isinstance(cmd,list):
-      output(cmd,locals,dest)
-    else:
-      {\
-      'File': outFile,\
-      'Stdout': outStdout,\
-      }[dest](str(cmd),locals)
-  return
-
-
-# +++++++++++++++++++++++++++++++++++++++++++++++++++
-def vtk_writeASCII_mesh(dim,res,origin,data):
-# +++++++++++++++++++++++++++++++++++++++++++++++++++
-  """ function writes data array defined on a rectilinear grid """
-  N  = res[0]*res[1]*res[2]
-  
-  cmds = [\
-          '# vtk DataFile Version 3.1',
-          string.replace('powered by $Id$','\n','\\n'),
-          'ASCII',
-          'DATASET RECTILINEAR_GRID',
-          'DIMENSIONS %i %i %i'%(res[0]+1,res[1]+1,res[2]+1),
-          'X_COORDINATES %i float'%(res[0]+1),
-          ' '.join(map(str,[i*dim[0]/res[0]+origin[0] for i in range(res[0]+1)])),
-          'Y_COORDINATES %i float'%(res[1]+1),
-          ' '.join(map(str,[i*dim[1]/res[1]+origin[1] for i in range(res[1]+1)])),
-          'Z_COORDINATES %i float'%(res[2]+1),
-          ' '.join(map(str,[i*dim[2]/res[2]+origin[2] for i in range(res[2]+1)])),
-          'CELL_DATA %i'%N,
-         ]
-  
-  for datatype in data:
-    for item in data[datatype]:
-      cmds += [\
-               '%s %s float'%(datatype.upper()+{True:'',False:'S'}[datatype.lower().endswith('s')],item),
-               'LOOKUP_TABLE default',
-               [[['\t'.join(map(str,data[datatype][item][:,j,k]))] for j in range(res[1])] for k in range(res[2])]
-              ]
-
-  return cmds
-
-
-# ----------------------- MAIN -------------------------------
-
 identifiers = {
         'grid':    ['a','b','c'],
         'size':    ['x','y','z'],
@@ -112,8 +47,7 @@ Produce VTK rectilinear mesh of structure data from geom description
 
 (options, filenames) = parser.parse_args()
 
-# ------------------------------------------ setup file handles ---------------------------------------  
+#--- setup file handles --------------------------------------------------------------------------  
-
 files = []
 if filenames == []:
   files.append({'name':'STDIN',
@@ -128,13 +62,10 @@ else:
                     'croak':sys.stdout,
                     })
 
-# ------------------------------------------ loop over input files ---------------------------------------  
+#--- loop over input files ------------------------------------------------------------------------
-
 for file in files:
   if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
 
-  #  get labels by either read the first row, or - if keyword header is present - the last line of the header
-
   firstline = file['input'].readline()
   m = re.search('(\d+)\s*head', firstline.lower())
   if m:
@@ -147,11 +78,13 @@ for file in files:
   content = file['input'].readlines()
   file['input'].close()
 
-  info = {'grid':           [0,0,0],
+#--- interprete header ----------------------------------------------------------------------------
-          'size':           [0.0,0.0,0.0],
+  info = {
-          'origin':         [0.0,0.0,0.0],
+          'grid':   numpy.zeros(3,'i'),
-          'homogenization':  0,
+          'size':   numpy.zeros(3,'d'),
+          'origin': numpy.zeros(3,'d'),
           'microstructures': 0,
+          'homogenization':  0
          }
 
   for header in headers:
@@ -166,36 +99,56 @@ for file in files:
       else:
         info[headitems[0]] = mappings[headitems[0]](headitems[1])
 
-  if numpy.all(info['grid'] == 0):
-    file['croak'].write('no grid info found.\n')
-    continue
-
-  if numpy.all(info['size'] == 0.0):
-    file['croak'].write('no size info found.\n')
-    continue
-
   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']))) + \
                       'homogenization:  %i\n'%info['homogenization'] + \
                       'microstructures: %i\n'%info['microstructures'])
-  
+
-  data = {'scalar':{'structure':numpy.zeros(info['grid'],'i')}}
+  if numpy.all(any['grid'] < 1):
-  i = 0
+    file['croak'].write('no valid grid info found.\n')
+    sys.exit()
+  if numpy.any(info['size'] <= 0.0):
+    file['croak'].write('no valid size info found.\n')
+    sys.exit()
+
+
+#--- generate grid --------------------------------------------------------------------------------
+  grid = vtk.vtkRectilinearGrid()
+  grid.SetDimensions([x+1 for x in info['grid']])
+  temp = vtk.vtkDoubleArray()
+  for i in xrange(3):
+    temp.SetNumberOfTuples(info['grid'][i]+1)
+    for j in range(info['grid'][i]+1):
+      temp.InsertTuple1(j,j*info['size'][i]/info['grid'][i]+info['origin'][i])
+      if i == 0: grid.SetXCoordinates(temp)
+      if i == 1: grid.SetYCoordinates(temp)
+      if i == 2: grid.SetZCoordinates(temp)
+
+#--- read microstructure information --------------------------------------------------------------
+  structure = vtk.vtkIntArray()
+  structure.SetName('Microstructures')
   for line in content:  
     for item in map(int,line.split()):
-      data['scalar']['structure'][i%info['grid'][0],(i/info['grid'][0])%info['grid'][1],i/info['grid'][0]/info['grid'][1]] = item
+      structure.InsertNextValue(item)
-      i += 1
 
+  grid.GetCellData().AddArray(structure)
 
-  out = {}
+#--- write data -----------------------------------------------------------------------------------
-  out['mesh'] = vtk_writeASCII_mesh(info['size'],info['grid'],info['origin'],data)
+  if file['name'] == 'STDIN':
-  
+    outWriter = vtk.vtkRectilinearGridWriter()
-  for what in out.keys():
+    outWriter.WriteToOutputStringOn()
-    if file['name'] == 'STDIN':
+    outWriter.SetFileTypeToASCII()
-      output(out[what],{},'Stdout')
+    outWriter.SetHeader('# powered by $Id$')
-    else:
+    outWriter.SetInput(grid)
-      (head,tail) = os.path.split(file['name'])
+    outWriter.Write()
-      vtk = open(os.path.join(head,what+'_'+os.path.splitext(tail)[0]+'.vtk'), 'w')
+    sys.stdout.write(outWriter.GetOutputString()[0:outWriter.GetOutputStringLength()])
-      output(out[what],{'filepointer':vtk},'File')
+  else:
-      vtk.close()
+    (head,tail) = os.path.split(file['name'])
+    outWriter = vtk.vtkXMLRectilinearGridWriter()
+    outWriter.SetDataModeToBinary()
+    outWriter.SetCompressorTypeToZLib()
+    outWriter.SetFileName(os.path.join(head,'mesh_'+os.path.splitext(tail)[0]
+                                                   +'.'+outWriter.GetDefaultFileExtension()))
+    outWriter.SetInput(grid)
+    outWriter.Write()

processing/pre/geom_euclideanDistance.py

@@ -202,18 +202,18 @@ for file in files:
     else:
       new_header.append(header)
 
-  if numpy.all(info['grid'] == 0):
-    file['croak'].write('no grid info found.\n')
-    continue
-  if numpy.all(info['size'] == 0.0):
-    file['croak'].write('no size info found.\n')
-    continue
-
   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']))) + \
                       'homogenization:  %i\n'%info['homogenization'] + \
                       'microstructures: %i\n'%info['microstructures'])
+  
+  if numpy.any(info['grid'] < 1):
+    file['croak'].write('no valid grid info found.\n')
+    sys.exit()
+  if numpy.any(info['size'] <= 0.0):
+    file['croak'].write('no valid size info found.\n')
+    sys.exit()
 
   new_header.append('$Id$\n')
   new_header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],))

processing/pre/geom_fromAng.py

@@ -79,7 +79,7 @@ for file in files:
 
   info = {
           'grid':   numpy.array([0,0,1]),
-          'size':   numpy.array([0.0,0.0,0.0]),
+          'size':   numpy.zeros(3,'d'),
           'origin': numpy.zeros(3,'d'),
           'microstructures': 0,
           'homogenization':  options.homogenization
@@ -126,6 +126,13 @@ for file in files:
                       'homogenization:  %i\n'%info['homogenization'] + \
                       'microstructures: %i\n\n'%info['microstructures'])
 
+  if numpy.any(info['grid'] < 1):
+    file['croak'].write('no valid grid info found.\n')
+    sys.exit()
+  if numpy.any(info['size'] <= 0.0):
+    file['croak'].write('no valid size info found.\n')
+    sys.exit()
+
 #--- write data -----------------------------------------------------------------------------------
   if options.config:
     file['output'].write('\n'.join(microstructure) + \

processing/pre/geom_fromMinimalSurface.py

@@ -74,21 +74,13 @@ file = {'name':'STDIN',
         'output':sys.stdout,
         'croak':sys.stderr,
        }
-
+info = {
-if numpy.any(options.grid < 1):
+        'grid':   numpy.array(options.grid),
-  file['croak'].write('invalid grid...\n')
+        'size':   numpy.array(options.size),
-  sys.exit()
+        'origin': numpy.zeros(3,'d'),
-
+        'microstructures': max(options.microstructure),
-if numpy.any(options.size < 0.0):
+        'homogenization':  options.homogenization
-  file['croak'].write('invalid size...\n')
+       }
-  sys.exit()
-  info = {
-          'grid':   numpy.array(options.grid),
-          'size':   numpy.array(options.size),
-          'origin': numpy.zeros(3,'d'),
-          'microstructures': max(options.microstructure),
-          'homogenization':  options.homogenization
-         }
 
 #--- report ---------------------------------------------------------------------------------------
 file['croak'].write('grid     a b c:  %s\n'%(' x '.join(map(str,info['grid']))) + \
@@ -97,6 +89,13 @@ file['croak'].write('grid     a b c:  %s\n'%(' x '.join(map(str,info['grid'])))
                     'homogenization:  %i\n'%info['homogenization'] + \
                     'microstructures: %i\n\n'%info['microstructures'])
 
+if numpy.any(info['grid'] < 1):
+  file['croak'].write('no valid grid info found.\n')
+  sys.exit()
+if numpy.any(info['size'] <= 0.0):
+  file['croak'].write('no valid size info found.\n')
+  sys.exit()
+
 #--- write header ---------------------------------------------------------------------------------
 header = ['$Id$\n']
 header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],))

processing/pre/geom_fromVPSC.py

@@ -77,8 +77,8 @@ for file in files:
   if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
 
   info = {
-          'grid':   numpy.array([0,0,0]),
+          'grid':   numpy.zeros(3,'i'),
-          'size':   numpy.array([0.0,0.0,0.0]),
+          'size':   numpy.zeros(3,'d'),
           'origin': numpy.zeros(3,'d'),
           'microstructures': 0,
           'homogenization':  options.homogenization
@@ -116,6 +116,13 @@ for file in files:
                       'homogenization:  %i\n'%info['homogenization'] + \
                       'microstructures: %i\n\n'%info['microstructures'])
 
+  if numpy.any(info['grid'] < 1):
+    file['croak'].write('no valid grid info found.\n')
+    sys.exit()
+  if numpy.any(info['size'] <= 0.0):
+    file['croak'].write('no valid size info found.\n')
+    sys.exit()
+
 #--- write data -----------------------------------------------------------------------------------
   if options.config:
     file['output'].write('\n'.join(microstructure) + \

processing/pre/geom_rescale.py

@@ -118,20 +118,20 @@ for file in files:
         info[headitems[0]] = mappings[headitems[0]](headitems[1])
     else:
       new_header.append(header)
-    
-  if numpy.all(info['grid'] == 0):
-    file['croak'].write('no grid info found.\n')
-    continue
-  if numpy.all(info['size'] == 0.0):
-    file['croak'].write('no size info found.\n')
-    continue
 
   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']))) + \
                       'homogenization:  %i\n'%info['homogenization'] + \
                       'microstructures: %i\n\n'%info['microstructures'])
-                      
+  
+  if numpy.any(info['grid'] < 1):
+    file['croak'].write('no valid grid info found.\n')
+    sys.exit()
+  if numpy.any(info['size'] <= 0.0):
+    file['croak'].write('no valid size info found.\n')
+    sys.exit()
+
   if numpy.all(info['grid'] == 0):
     newInfo['grid'] = info['grid']
   if numpy.all(info['size'] == 0.0)::
@@ -155,6 +155,13 @@ for file in files:
     file['croak'].write('--> size     x y z:  %s\n'%(' x '.join(map(str,newInfo['size']))))
   if (newInfo['microstructures'] != info['microstructures']):
     file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
+  
+  if numpy.any(newInfo['grid'] < 1):
+    file['croak'].write('no valid new grid info found.\n')
+    sys.exit()
+  if numpy.any(newInfo['size'] <= 0.0):
+    file['croak'].write('no valid new size info found.\n')
+    sys.exit()
 
 #--- assemble header ------------------------------------------------------------------------------
   new_header.append('$Id$\n')
@@ -167,12 +174,12 @@ for file in files:
   output += ''.join(new_header)
   
 #--- scale microstructure -------------------------------------------------------------------------
-  for c in xrange(options.grid[2]):
+  for c in xrange(newInfo['grid'][2]):
-    z = int(info['grid'][2]*(c+0.5)/options.grid[2])%info['grid'][2]
+    z = int(info['grid'][2]*(c+0.5)/newInfo['grid'][2])%info['grid'][2]
-    for b in xrange(options.grid[1]):
+    for b in xrange(newInfo['grid'][1]):
-      y = int(info['grid'][1]*(b+0.5)/options.grid[1])%info['grid'][1]
+      y = int(info['grid'][1]*(b+0.5)/newInfo['grid'][1])%info['grid'][1]
-      for a in xrange(options.grid[0]):
+      for a in xrange(newInfo['grid'][0]):
-        x = int(info['grid'][0]*(a+0.5)/options.grid[0])%info['grid'][0]
+        x = int(info['grid'][0]*(a+0.5)/newInfo['grid'][0])%info['grid'][0]
         output += str(microstructure[x,y,z]).rjust(formatwidth) + {True:' ',False:'\n'}[options.twoD]
       output += {True:'\n',False:''}[options.twoD]
   file['output'].write(output)

processing/pre/geom_translate.py

@@ -122,19 +122,20 @@ for file in files:
     else:
       new_header.append(header)
 
-  if numpy.all(info['grid'] == 0):
-    file['croak'].write('no grid info found.\n')
-    continue
-  if numpy.all(info['size'] == 0.0):
-    file['croak'].write('no size info found.\n')
-    continue
 
   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']))) + \
                       'homogenization:  %i\n'%info['homogenization'] + \
                       'microstructures: %i\n\n'%info['microstructures'])
-  
+
+  if numpy.any(info['grid'] < 1):
+    file['croak'].write('no valid grid info found.\n')
+    sys.exit()
+  if numpy.any(info['size'] <= 0.0):
+    file['croak'].write('no valid size info found.\n')
+    sys.exit()
+
 #--- process input --------------------------------------------------------------------------------  
   N = info['grid'][0]*info['grid'][1]*info['grid'][2]
   microstructure = numpy.zeros(N,'i')
@@ -161,7 +162,7 @@ for file in files:
     file['croak'].write('--> origin   x y z:  %s\n'%(' : '.join(map(str,newInfo['origin']))))
   if (newInfo['microstructures'] != info['microstructures']):
     file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
- 
+
   new_header.append('$Id$\n')
   new_header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],))
   new_header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][2],))

processing/pre/geom_vicinityOffset.py

@@ -119,19 +119,19 @@ for file in files:
     else:
       new_header.append(header)
 
-  if numpy.all(info['grid'] == 0):
-    file['croak'].write('no grid info found.\n')
-    continue
-  if numpy.all(info['size'] == 0.0):
-    file['croak'].write('no dimension info found.\n')
-    continue
-
   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']))) + \
                       'homogenization:  %i\n'%info['homogenization'] + \
                       'microstructures: %i\n'%info['microstructures'])
 
+  if numpy.any(info['grid'] < 1):
+    file['croak'].write('no valid grid info found.\n')
+    sys.exit()
+  if numpy.any(info['size'] <= 0.0):
+    file['croak'].write('no valid size info found.\n')
+    sys.exit()
+
 #--- read data ------------------------------------------------------------------------------------
   microstructure = numpy.zeros(info['grid'],'i')
   i = 0