explicit loop for simpler code

- no invalid combintations any more (allow to move the original
microstructure out of the new canvas)
- handling of origin needs discussion. When we want to recover the old
behavior, the origin might be located outside of the new geometry

processing/pre/geom_canvas.py

@@ -1,52 +1,46 @@
 #!/usr/bin/env python3
-# -*- coding: UTF-8 no BOM -*-
 
 import os
 import sys
-import numpy as np
-import damask
-
 from io import StringIO
 from optparse import OptionParser
 
+import numpy as np
+
+import damask
+
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
+
 # --------------------------------------------------------------------
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
-Changes the (three-dimensional) canvas of a spectral geometry description.
+Increases or decreases the (three-dimensional) canvas.
 Grid can be given as absolute or relative values, e.g. 16 16 16 or 2x 0.5x 32.
 
 """, version = scriptID)
 
-parser.add_option('-g',
+parser.add_option('-g','--grid',
-                  '--grid',
                   dest = 'grid',
                   type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
-                  help = 'a,b,c grid of hexahedral box. [auto]')
+                  help = 'a,b,c grid of hexahedral box')
-parser.add_option('-o',
+parser.add_option('-o','--offset',
-                  '--offset',
                   dest = 'offset',
                   type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
                   help = 'a,b,c offset from old to new origin of grid [%default]')
-parser.add_option('-f',
+parser.add_option('-f','--fill',
-                  '--fill',
                   dest = 'fill',
-                  type = 'float', metavar = 'float',
+                  type = 'float', metavar = 'int',
-                  help = '(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
+                  help = 'background microstructure index, defaults to max microstructure index + 1')
 
-parser.set_defaults(grid = ['0','0','0'],
+parser.set_defaults(offset = (0,0,0))
-                    offset = (0,0,0),
-                   )
 
 (options, filenames) = parser.parse_args()
 
 
-# --- loop over input files -------------------------------------------------------------------------
-
 if filenames == []: filenames = [None]
 
 for name in filenames:
@@ -55,44 +49,26 @@ for name in filenames:
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
   grid = geom.get_grid()
-  size = geom.get_size()
+  if options.grid is not None:
-  origin = geom.get_origin()
+    grid = np.array([int(o*float(n.lower().replace('x',''))) if n.lower().endswith('x') \
-  microstructure = geom.get_microstructure()
+                     else int(n) for o,n in zip(grid,options.grid)],dtype=int)
-  fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill
+  grid = np.maximum(grid,1)
-  dtype = float if np.isnan(fill) or int(fill) != fill or microstructure.dtype==np.float else int
+
+  new = np.full(grid,options.fill if options.fill is not None
+                else np.nanmax(geom.microstructure)+1,geom.microstructure.dtype)
   
-# --- do work ------------------------------------------------------------------------------------
+  for x in range(geom.microstructure.shape[0]):
- 
+    X = x + options.offset[0]
-  new_grid = np.array([int(o*float(n.lower().replace('x',''))) if n.lower().endswith('x') \
+    if not 0 <= X < new.shape[0]: continue 
-                  else int(n) for o,n in zip(grid,options.grid)],dtype=int)
+    for y in range(geom.microstructure.shape[1]):
-  new_grid = np.where(new_grid > 0, new_grid,grid)
+      Y = y + options.offset[1]
+      if not 0 <= Y < new.shape[1]: continue 
+      for z in range(geom.microstructure.shape[2]):
+        Z = z + options.offset[2]
+        if not 0 <= Z < new.shape[2]: continue
+        new[X,Y,Z] = geom.microstructure[x,y,z]
 
-  microstructure_cropped = np.zeros(new_grid,dtype=dtype)
+  damask.util.croak(geom.update(new,origin=(0,0,0),rescale=True))
-  microstructure_cropped.fill(fill)
-  
-  xindex = np.arange(max(options.offset[0],0),min(options.offset[0]+new_grid[0],grid[0]))
-  yindex = np.arange(max(options.offset[1],0),min(options.offset[1]+new_grid[1],grid[1]))
-  zindex = np.arange(max(options.offset[2],0),min(options.offset[2]+new_grid[2],grid[2]))
-  translate_x = [i - options.offset[0] for i in xindex]
-  translate_y = [i - options.offset[1] for i in yindex]
-  translate_z = [i - options.offset[2] for i in zindex]
-  if 0 in map(len,[xindex,yindex,zindex,translate_x,translate_y,translate_z]):
-    damask.util.croak('invaldid combination of grid and offset.')
-    continue
-  microstructure_cropped[min(translate_x):max(translate_x)+1,
-                         min(translate_y):max(translate_y)+1,
-                         min(translate_z):max(translate_z)+1] \
-        = microstructure[min(xindex):max(xindex)+1,
-                         min(yindex):max(yindex)+1,
-                         min(zindex):max(zindex)+1]
-
-  new_size   = size/grid*new_grid  if np.all(grid > 0) else new_grid
-  new_origin = origin + (size/grid if np.all(grid > 0) else new_size/new_grid) * options.offset
-
-  damask.util.croak(geom.update(microstructure=microstructure_cropped,
-                                size=new_size,
-                                origin=new_origin,
-                                ))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
   if name is None: