compress functionality should be part of the geom class

automated decision is base on heuristic whether compression is memory
efficient

processing/pre/geom_clean.py

@@ -42,7 +42,4 @@ for name in filenames:
 
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_mirror.py

@@ -46,7 +46,4 @@ for name in filenames:
   damask.util.croak(geom.mirror(options.directions,options.reflect))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name)
-    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_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)

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()
-        format_string = '%g' if self.microstructure in np.sctypes['float'] else \
+        
-                        '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure)))))
+        if pack is None:
-        np.savetxt(fname,
+            plain = grid.prod()/np.unique(self.microstructure).size < 250
-                   self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
+        else:
-                   header='\n'.join(header), fmt=format_string, comments='')
+            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):
         """