Merge branch 'PythonImprovements' into no-crystallite

processing/pre/geom_addPrimitive.py

@@ -132,7 +132,4 @@ for name in filenames:
   damask.util.croak(geom.update(np.where(mask,geom.microstructure,fill)))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_canvas.py

@@ -61,7 +61,7 @@ for name in filenames:
   canvas = np.full(new,options.fill if options.fill is not None
                   else np.nanmax(geom.microstructure)+1,geom.microstructure.dtype)
 
-  l = np.clip( offset,    0,np.minimum(old  +offset,new))
+  l = np.clip( offset,    0,np.minimum(old  +offset,new))                                           # noqa
   r = np.clip( offset+old,0,np.minimum(old*2+offset,new))
   L = np.clip(-offset,    0,np.minimum(new  -offset,old))
   R = np.clip(-offset+new,0,np.minimum(new*2-offset,old))
@@ -71,7 +71,4 @@ for name in filenames:
   damask.util.croak(geom.update(canvas,origin=origin+offset*size/old,rescale=True))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_clean.py

@@ -37,12 +37,6 @@ 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)
-
   damask.util.croak(geom.clean(options.stencil))
-
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-  if name is None:
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_fromDREAM3D.py

@@ -86,7 +86,7 @@ for name in filenames:
            * inFile[os.path.join(group_geom,'SPACING')][...]
     grid   = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
     origin = inFile[os.path.join(group_geom,'ORIGIN')][...]
-  except:
+  except KeyError:
     errors.append('Geometry data ({}) not found'.format(group_geom))
 
 
@@ -98,13 +98,13 @@ for name in filenames:
     try:
       quats = np.reshape(inFile[dataset][...],(np.product(grid),4))
       rot   = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats]
-    except:
+    except KeyError:
       errors.append('Pointwise orientation (quaternion) data ({}) not readable'.format(dataset))
 
     dataset = os.path.join(group_pointwise,options.phase)
     try:
       phase = np.reshape(inFile[dataset][...],(np.product(grid)))
-    except:
+    except KeyError:
       errors.append('Pointwise phase data ({}) not readable'.format(dataset))
 
     microstructure = np.arange(1,np.product(grid)+1,dtype=int).reshape(grid,order='F')
@@ -116,7 +116,7 @@ for name in filenames:
     dataset = os.path.join(group_pointwise,options.microstructure)
     try:
       microstructure = np.transpose(inFile[dataset][...].reshape(grid[::-1]),(2,1,0))               # convert from C ordering
-    except:
+    except KeyError:
       errors.append('Link between pointwise and grain average data ({}) not readable'.format(dataset))
 
     group_average = os.path.join(rootDir,options.basegroup,options.average)
@@ -124,13 +124,13 @@ for name in filenames:
     dataset = os.path.join(group_average,options.quaternion)
     try:
       rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in inFile[dataset][...][1:]]         # skip first entry (unindexed)
-    except:
+    except KeyError:
       errors.append('Average orientation data ({}) not readable'.format(dataset))
 
     dataset = os.path.join(group_average,options.phase)
     try:
       phase = [i[0] for i in inFile[dataset][...]][1:]                                              # skip first entry (unindexed)
-    except:
+    except KeyError:
       errors.append('Average phase data ({}) not readable'.format(dataset))
 
   if errors != []:
@@ -155,4 +155,4 @@ for name in filenames:
                      homogenization=options.homogenization,comments=header)
   damask.util.croak(geom)
 
-  geom.to_file(os.path.splitext(name)[0]+'.geom')
+  geom.to_file(os.path.splitext(name)[0]+'.geom',pack=False)

processing/pre/geom_fromMinimalSurface.py

@@ -89,7 +89,4 @@ geom=damask.Geom(microstructure,options.size,
                  comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
 damask.util.croak(geom)
 
-if name is None:
+geom.to_file(sys.stdout if name is None else name,pack=False)
-  sys.stdout.write(str(geom.show()))
-else:
-  geom.to_file(name)

processing/pre/geom_fromOsteonGeometry.py

@@ -145,7 +145,4 @@ geom = damask.Geom(microstructure.reshape(grid),
                    homogenization=options.homogenization,comments=header)
 damask.util.croak(geom)
 
-if name is None:
+geom.to_file(sys.stdout if name is None else name,pack=False)
-  sys.stdout.write(str(geom.show()))
-else:
-  geom.to_file(name)

processing/pre/geom_fromScratch.py

@@ -63,7 +63,4 @@ geom = damask.Geom(microstructure=np.full(options.grid,options.fill,dtype=dtype)
                    comments=scriptID + ' ' + ' '.join(sys.argv[1:]))
 damask.util.croak(geom)
 
-if name is None:
+geom.to_file(sys.stdout if name is None else name,pack=False)
-  sys.stdout.write(str(geom.show()))
-else:
-  geom.to_file(name)

processing/pre/geom_fromTable.py

@@ -152,7 +152,4 @@ for name in filenames:
                      homogenization=options.homogenization,comments=header)
   damask.util.croak(geom)
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(os.path.splitext(name)[0]+'.geom')

processing/pre/geom_fromVoronoiTessellation.py

@@ -302,7 +302,4 @@ for name in filenames:
                      homogenization=options.homogenization,comments=header)
   damask.util.croak(geom)
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(os.path.splitext(name)[0]+'.geom')

processing/pre/geom_grainGrowth.py

@@ -172,7 +172,4 @@ for name in filenames:
   damask.util.croak(geom.update(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]]))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_mirror.py

@@ -42,11 +42,6 @@ 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)
-
   damask.util.croak(geom.mirror(options.directions,options.reflect))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-  if name is None:
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_pack.py

@@ -34,41 +34,4 @@ for name in filenames:
   damask.util.croak(geom)
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
  
-  compressType = None
+  geom.to_file(sys.stdout if name is None else name,pack=True)
-  former = start = -1
-  reps = 0
-
-  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
-    elif current == former and start == former:
-      compressType = 'of'
-      reps += 1
-    else:
-      if   compressType is None:
-        f.write('\n'.join(geom.get_header())+'\n')
-      elif compressType == '.':
-        f.write('{}\n'.format(former))
-      elif compressType == 'to':
-        f.write('{} to {}\n'.format(start,former))
-      elif compressType == 'of':
-        f.write('{} of {}\n'.format(reps,former))
-
-      compressType = '.'
-      start = current
-      reps = 1
-
-    former = current
-
-  if compressType == '.':
-    f.write('{}\n'.format(former))
-  elif compressType == 'to':
-    f.write('{} to {}\n'.format(start,former))
-  elif compressType == 'of':
-    f.write('{} of {}\n'.format(reps,former))

processing/pre/geom_renumber.py

@@ -5,8 +5,6 @@ import sys
 from io import StringIO
 from optparse import OptionParser
 
-import numpy as np
-
 import damask
 
 
@@ -32,15 +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)
-
+  damask.util.croak(geom.renumber)
-  renumbered = np.empty(geom.get_grid(),dtype=geom.microstructure.dtype)
-  for i, oldID in enumerate(np.unique(geom.microstructure)):
-    renumbered = np.where(geom.microstructure == oldID, i+1, renumbered)
-
-  damask.util.croak(geom.update(renumbered))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-  if name is None:
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_rescale.py

@@ -2,11 +2,10 @@
 
 import os
 import sys
-import numpy as np
-
 from io import StringIO
 from optparse import OptionParser
-from scipy import ndimage
+
+import numpy as np
 
 import damask
 
@@ -55,20 +54,7 @@ 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)
 
-  damask.util.croak(geom.update(microstructure =
+  geom.scale(new_grid)
-                                ndimage.interpolation.zoom(
+  damask.util.croak(geom.update(microstructure = None,size = new_size))
-                                    geom.microstructure,
-                                    new_grid/grid,
-                                    output=geom.microstructure.dtype,
-                                    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:]))
-
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-  if name is None:
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_rotate.py

@@ -95,7 +95,4 @@ for name in filenames:
   damask.util.croak(geom.update(microstructure,origin=origin-(np.asarray(microstructure.shape)-grid)/2*size/grid,rescale=True))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_translate.py

@@ -58,7 +58,4 @@ for name in filenames:
   damask.util.croak(geom.update(substituted,origin=geom.get_origin()+options.origin))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_unpack.py

@@ -34,7 +34,4 @@ for name in filenames:
   damask.util.croak(geom)
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_vicinityOffset.py

@@ -82,7 +82,4 @@ for name in filenames:
                                            geom.microstructure + offset,geom.microstructure)))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name,pack=False)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

python/damask/geom.py

@@ -299,7 +299,7 @@ class Geom():
         return cls(microstructure.reshape(grid),size,origin,homogenization,comments)
 
 
-    def to_file(self,fname):
+    def to_file(self,fname,pack=None):
         """
         Writes a geom file.
 
@@ -307,15 +307,63 @@ class Geom():
         ----------
         fname : str or file handle
             geometry file to write.
+        pack : bool, optional
+            compress geometry with 'x of y' and 'a to b'.
 
         """
         header = self.get_header()
         grid   = self.get_grid()
+        
+        if pack is None:
+            plain = grid.prod()/np.unique(self.microstructure).size < 250
+        else:
+            plain = not pack
+
+        if plain:
             format_string = '%g' if self.microstructure in np.sctypes['float'] else \
                             '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure)))))
             np.savetxt(fname,
                        self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
                        header='\n'.join(header), fmt=format_string, comments='')
+        else:
+            if isinstance(fname,str):
+                f = open(fname,'w')
+            else:
+                f = fname
+
+            compressType = None
+            former = start = -1
+            reps = 0
+            for current in self.microstructure.flatten('F'):
+                if abs(current - former) == 1 and (start - current) == reps*(former - current):
+                    compressType = 'to'
+                    reps += 1
+                elif current == former and start == former:
+                    compressType = 'of'
+                    reps += 1
+                else:
+                    if   compressType is None:
+                        f.write('\n'.join(self.get_header())+'\n')
+                    elif compressType == '.':
+                        f.write('{}\n'.format(former))
+                    elif compressType == 'to':
+                        f.write('{} to {}\n'.format(start,former))
+                    elif compressType == 'of':
+                        f.write('{} of {}\n'.format(reps,former))
+
+                    compressType = '.'
+                    start = current
+                    reps = 1
+
+                former = current
+
+            if compressType == '.':
+                f.write('{}\n'.format(former))
+            elif compressType == 'to':
+                f.write('{} to {}\n'.format(start,former))
+            elif compressType == 'of':
+                f.write('{} of {}\n'.format(reps,former))
+
                  
     def to_vtk(self,fname=None):
         """
@@ -419,6 +467,29 @@ class Geom():
         #self.add_comments('tbd')
 
 
+    def scale(self,grid):
+        """
+        Scale microstructure to new grid.
+
+        Parameters
+        ----------
+        grid : iterable of int
+            new grid dimension
+
+        """
+        return self.update(
+                           ndimage.interpolation.zoom(
+                                                      self.microstructure,
+                                                      grid/self.get_grid(),
+                                                      output=self.microstructure.dtype,
+                                                      order=0,
+                                                      mode='nearest',
+                                                      prefilter=False
+                                                     )
+                          )
+        #self.add_comments('tbd')
+
+
     def clean(self,stencil=3):
         """
         Smooth microstructure by selecting most frequent index within given stencil at each location.
@@ -433,7 +504,20 @@ class Geom():
             unique, inverse = np.unique(arr, return_inverse=True)
             return unique[np.argmax(np.bincount(inverse))]
 
-        return self.update(ndimage.filters.generic_filter(self.microstructure,
+        return self.update(ndimage.filters.generic_filter(
+                                                          self.microstructure,
                                                           mostFrequent,
-                                                          size=(stencil,)*3).astype(self.microstructure.dtype))
+                                                          size=(stencil,)*3
+                                                         ).astype(self.microstructure.dtype)
+                          )
+        #self.add_comments('tbd')
+
+
+    def renumber(self):
+        """Renumber sorted microstructure indices to 1,...,N."""
+        renumbered = np.empty(self.get_grid(),dtype=self.microstructure.dtype)
+        for i, oldID in enumerate(np.unique(self.microstructure)):
+          renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
+
+        return self.update(renumbered)
         #self.add_comments('tbd')