using specialized class

processing/post/addEuclideanDistance.py

@@ -2,6 +2,7 @@
 
 import os
 import sys
+from io import StringIO
 from optparse import OptionParser
 import itertools
 

processing/post/addGaussian.py

@@ -2,9 +2,9 @@
 
 import os
 import sys
+from io import StringIO
 from optparse import OptionParser
 
-import numpy as np
 from scipy import ndimage
 
 import damask

processing/post/averageDown.py

@@ -65,7 +65,8 @@ for name in filenames:
                                     outname = os.path.join(os.path.dirname(name),
                                                            prefix+os.path.basename(name)) if name else name,
                                     buffered = False)
-  except: continue
+  except IOError:
+    continue
   damask.util.report(scriptName,name)
 
 # ------------------------------------------ read header ------------------------------------------
@@ -95,7 +96,7 @@ for name in filenames:
   table.data_readArray()
 
   if (options.grid is None or options.size is None):
-    grid,size = damask.util.coordGridAndSize(table.data[:,table.label_indexrange(options.pos)])
+    grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.data[:,table.label_indexrange(options.pos)])
   else:
     grid   = np.array(options.grid,'i')
     size   = np.array(options.size,'d')

processing/post/blowUp.py

@@ -55,7 +55,8 @@ for name in filenames:
                                     outname = os.path.join(os.path.dirname(name),
                                                            prefix+os.path.basename(name)) if name else name,
                                     buffered = False)
-  except: continue
+  except IOError:
+    continue
   damask.util.report(scriptName,name)
 
 # ------------------------------------------ read header ------------------------------------------
@@ -82,7 +83,7 @@ for name in filenames:
   table.data_readArray(options.pos)
   table.data_rewind()
 
-  grid,size = damask.util.coordGridAndSize(table.data)
+  grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.data)
   
   packing = np.array(options.packing,'i')
   outSize = grid*packing

python/damask/grid_filters.py

@@ -219,7 +219,7 @@ def cell_coord0_2_DNA(coord0,ordered=True):
 
 def coord0_check(coord0):
     """
-    Check whether coordinates lie on a regular grid
+    Check whether coordinates lie on a regular grid.
 
     Parameters
     ----------

python/damask/util.py

@@ -119,30 +119,6 @@ def execute(cmd,
   if process.returncode != 0: raise RuntimeError('{} failed with returncode {}'.format(cmd,process.returncode))
   return out,error
 
-def coordGridAndSize(coordinates):
-  """Determines grid count and overall physical size along each dimension of an ordered array of coordinates."""
-  dim    = coordinates.shape[1]
-  coords = [np.unique(coordinates[:,i]) for i in range(dim)]
-  mincorner = np.array(list(map(min,coords)))
-  maxcorner = np.array(list(map(max,coords)))
-  grid   = np.array(list(map(len,coords)),'i')
-  size   = grid/np.maximum(np.ones(dim,'d'), grid-1.0) * (maxcorner-mincorner)                      # size from edge to edge = dim * n/(n-1) 
-  size   = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1]))                             # spacing for grid==1 equal to smallest among other ones
-  delta  = size/grid
-  
-  N = grid.prod()
-  
-  if  N != len(coordinates):
-    raise ValueError('Data count {} does not match grid {}.'.format(len(coordinates),' x '.join(map(repr,grid))))
-    
-  if   np.any(np.abs(np.log10((coords[0][1:]-coords[0][:-1])/delta[0])) > 0.01) \
-    or np.any(np.abs(np.log10((coords[1][1:]-coords[1][:-1])/delta[1])) > 0.01):
-    raise ValueError('regular grid spacing {} violated.'.format(' x '.join(map(repr,delta))))
-  if dim==3 and np.any(np.abs(np.log10((coords[2][1:]-coords[2][:-1])/delta[2])) > 0.01):
-    raise ValueError('regular grid spacing {} violated.'.format(' x '.join(map(repr,delta))))  
-  
-  return grid,size
-  
 # -----------------------------
 class extendableOption(Option):
   """