save some memory (avoid copies if not needed)

processing/pre/geom_clean.py

@@ -45,12 +45,10 @@ for name in filenames:
   damask.util.report(scriptName,name)
   
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-  microstructure = geom.get_microstructure()
 
-  microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent,
+  damask.util.croak(geom.update(ndimage.filters.generic_filter(
-                                                  size=(options.stencil,)*3).astype(microstructure.dtype)
+                                  geom.microstructure,mostFrequent,
-
+                                  size=(options.stencil,)*3).astype(geom.microstructure.dtype)))
-  damask.util.croak(geom.update(microstructure))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
   if name is None:

processing/pre/geom_grainGrowth.py

@@ -60,11 +60,10 @@ for name in filenames:
   damask.util.report(scriptName,name)
   
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-  microstructure = geom.get_microstructure()
+  grid_original = geom.get_grid()
   damask.util.croak(geom)
   
-  grid_original = geom.get_grid()
+  microstructure = np.tile(geom.microstructure,np.where(grid_original == 1, 2,1))                # make one copy along dimensions with grid == 1
-  microstructure = np.tile(geom.get_microstructure(),np.where(grid_original == 1, 2,1))           # make one copy along dimensions with grid == 1
   grid = np.array(microstructure.shape)
 
 # --- initialize support data ---------------------------------------------------------------------

processing/pre/geom_pack.py

@@ -30,7 +30,6 @@ for name in filenames:
   damask.util.report(scriptName,name)
 
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-  microstructure = geom.get_microstructure().flatten('F')
   damask.util.croak(geom)
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
   
@@ -38,7 +37,12 @@ for name in filenames:
   former = start = -1
   reps = 0
 
-  for current in microstructure:
+  if name is None:
+    f = sys.stdout
+  else:
+    f= open(name,'w')
+
+  for current in geom.microstructure.flatten('F'):
     if abs(current - former) == 1 and (start - current) == reps*(former - current):
       compressType = 'to'
       reps += 1
@@ -47,13 +51,13 @@ for name in filenames:
       reps += 1
     else:
       if   compressType is None:
-        out = geom.get_header()
+        f.write('\n'.join(geom.get_header())+'\n')
       elif compressType == '.':
-        out.append('{}'.format(former))
+        f.write('{}\n'.format(former))
       elif compressType == 'to':
-        out.append('{} to {}'.format(start,former))
+        f.write('{} to {}\n'.format(start,former))
       elif compressType == 'of':
-        out.append('{} of {}'.format(reps,former))
+        f.write('{} of {}\n'.format(reps,former))
 
       compressType = '.'
       start = current
@@ -62,15 +66,8 @@ for name in filenames:
     former = current
    
   if compressType == '.':
-    out.append('{}'.format(former))
+    f.write('{}\n'.format(former))
   elif compressType == 'to':
-    out.append('{} to {}'.format(start,former))
+    f.write('{} to {}\n'.format(start,former))
   elif compressType == 'of':
-    out.append('{} of {}'.format(reps,former))
+    f.write('{} of {}\n'.format(reps,former))
- 
-  
-  if name is None:
-    sys.stdout.write('\n'.join(out)+'\n')
-  else:
-    with open(name,'w') as f:
-      f.write('\n'.join(out)+'\n')

processing/pre/geom_renumber.py

@@ -32,11 +32,10 @@ for name in filenames:
   damask.util.report(scriptName,name)
   
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-  microstructure = geom.get_microstructure()
   
-  renumbered = np.copy(microstructure)
+  renumbered = np.empty(geom.get_grid(),dtype=geom.microstructure.dtype)
-  for i, oldID in enumerate(np.unique(microstructure)):
+  for i, oldID in enumerate(np.unique(geom.microstructure)):
-    renumbered = np.where(microstructure == oldID, i+1, renumbered)
+    renumbered = np.where(geom.microstructure == oldID, i+1, renumbered)
 
   damask.util.croak(geom.update(renumbered))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))

processing/pre/geom_rescale.py

@@ -43,7 +43,6 @@ for name in filenames:
   damask.util.report(scriptName,name)
     
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-  microstructure = geom.get_microstructure()
   grid = geom.get_grid()
   size = geom.get_size()
 
@@ -55,11 +54,14 @@ for name in filenames:
              np.array([o*float(n.lower().replace('x','')) if n.lower().endswith('x') \
                   else float(n) for o,n in zip(size,options.size)],dtype=float)
 
-  if np.any(new_grid != grid):
+  damask.util.croak(geom.update(microstructure = 
-    microstructure = ndimage.interpolation.zoom(microstructure, new_grid/grid,output=microstructure.dtype,
+                                  ndimage.interpolation.zoom(
-                                                order=0,mode='nearest', prefilter=False)
+                                    geom.microstructure,
-
+                                    new_grid/grid,output=geom.microstructure.dtype,
-  damask.util.croak(geom.update(microstructure,new_size))
+                                    order=0,mode='nearest', prefilter=False\
+                                                            ) \
+                                 if np.any(new_grid != grid) else None,
+                                 size = new_size))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
   if name is None:

processing/pre/geom_rotate.py

@@ -88,7 +88,6 @@ for name in filenames:
   microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,
                                   prefilter=False,output=dtype,cval=fill)            # rotation around z
   
-
   damask.util.croak(geom.update(microstructure,rescale=True))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
   

processing/pre/geom_toTable.py

@@ -32,8 +32,7 @@ for name in filenames:
   damask.util.report(scriptName,name)
   
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-  damask.util.croak(geom)  
+  damask.util.croak(geom)
-  microstructure = geom.get_microstructure().flatten('F')
   grid           = geom.get_grid()
   size           = geom.get_size()
   origin         = geom.get_origin()
@@ -55,6 +54,6 @@ for name in filenames:
   table.labels_append(['{}_{}'.format(1+i,'pos') for i in range(3)]+['microstructure'])
   table.head_write()
   table.output_flush()
-  table.data = np.squeeze(np.dstack((xx,yy,zz,microstructure)),axis=0)
+  table.data = np.squeeze(np.dstack((xx,yy,zz,geom.microstructure.flatten('F'))),axis=0)
   table.data_writeArray()
   table.close()

processing/pre/geom_translate.py

@@ -51,10 +51,9 @@ for name in filenames:
   damask.util.report(scriptName,name)
   
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-  microstructure = geom.get_microstructure()
+  substituted = geom.get_microstructure()
-  substituted    = np.copy(microstructure)
   
-  for old,new in zip(sub[0::2],sub[1::2]): substituted[microstructure==old] = new                   # substitute microstructure indices
+  for old,new in zip(sub[0::2],sub[1::2]): substituted[substituted==old] = new                      # substitute microstructure indices
   substituted += options.microstructure                                                             # constant shift
   
   damask.util.croak(geom.update(substituted,origin=geom.get_origin()+options.origin))

processing/pre/geom_vicinityOffset.py

@@ -70,18 +70,16 @@ for name in filenames:
   damask.util.report(scriptName,name)
   
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-  microstructure = geom.get_microstructure()
 
-  offset = np.nanmax(microstructure) if options.offset is None else options.offset
+  offset = np.nanmax(geom.microstructure) if options.offset is None else options.offset
 
-  microstructure = np.where(ndimage.filters.generic_filter(microstructure,
+  damask.util.croak(geom.update(np.where(ndimage.filters.generic_filter(
-                                                           taintedNeighborhood,
+                                           geom.microstructure,
-                                                           size=1+2*options.vicinity,mode=options.mode,
+                                           taintedNeighborhood,
-                                                           extra_arguments=(),
+                                           size=1+2*options.vicinity,mode=options.mode,
-                                                           extra_keywords={"trigger":options.trigger,"size":1+2*options.vicinity}),
+                                           extra_arguments=(),
-                            microstructure + offset,microstructure)
+                                           extra_keywords={"trigger":options.trigger,"size":1+2*options.vicinity}),
-
+                                           geom.microstructure + offset,geom.microstructure)))
-  damask.util.croak(geom.update(microstructure))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
   
   if name is None: