replace geom_canvas --blank with geom_fromScratch

PRIVATE

@@ -1 +1 @@
-Subproject commit d596982319b5e8bbded6c14a5724df6c9de2a0fd
+Subproject commit 36b3a1b44a71574e2b5dce93ed25963e9fe3e74a

processing/pre/geom_canvas.py

@@ -1,78 +1,98 @@
 #!/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 options [geomfile(s)]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
-Increases or decreases the (three-dimensional) canvas.
+Changes the (three-dimensional) canvas of a spectral geometry description.
 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','--grid',
+parser.add_option('-g',
+                  '--grid',
                   dest = 'grid',
                   type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
-                  help = 'a,b,c grid of hexahedral box')
+                  help = 'a,b,c grid of hexahedral box. [auto]')
-parser.add_option('-o','--offset',
+parser.add_option('-o',
+                  '--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','--fill',
+parser.add_option('-f',
+                  '--fill',
                   dest = 'fill',
-                  type = 'float', metavar = 'int',
+                  type = 'float', metavar = 'float',
-                  help = 'background microstructure index, defaults to max microstructure index + 1')
+                  help = '(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
 
-parser.set_defaults(offset = (0,0,0))
+parser.set_defaults(grid = ['0','0','0'],
+                    offset = (0,0,0),
+                   )
 
 (options, filenames) = parser.parse_args()
 
 
+# --- loop over input files -------------------------------------------------------------------------
+
 if filenames == []: filenames = [None]
 
 for name in filenames:
   damask.util.report(scriptName,name)
   
-  if name is None:
+  geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-    virt_file = StringIO(''.join(sys.stdin.read()))
+
-    geom = damask.Geom.from_file(virt_file)
-  else:
-    geom = damask.Geom.from_file(name)
   grid = geom.get_grid()
+  size = geom.get_size()
+  origin = geom.get_origin()
+  microstructure = geom.get_microstructure()
+  fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill
+  dtype = float if np.isnan(fill) or int(fill) != fill or microstructure.dtype==np.float else int
   
-  if options.grid is not None:
+# --- do work ------------------------------------------------------------------------------------
-    for i,g in enumerate(options.grid):
-      grid[i] = int(round(grid[i]*float(g.lower().replace('x','')))) if g.lower().endswith('x') \
-           else int(options.grid[i])
  
-  new  = np.full(grid,options.fill if options.fill is not None
+  new_grid = np.array([int(o*float(n.lower().replace('x',''))) if n.lower().endswith('x') \
-                 else np.nanmax(geom.microstructure)+1,geom.microstructure.dtype)
+                  else int(n) for o,n in zip(grid,options.grid)],dtype=int)
+  new_grid = np.where(new_grid > 0, new_grid,grid)
 
-  for x in range(geom.microstructure.shape[0]):
+  microstructure_cropped = np.zeros(new_grid,dtype=dtype)
-    X = x + options.offset[0]
+  microstructure_cropped.fill(fill)
-    if not 0 <= X < new.shape[0]: continue 
-    for y in range(geom.microstructure.shape[1]):
-      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]
   
-  damask.util.croak(geom.update(new,rescale=True))
+  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:

processing/pre/geom_fromScratch.py

@@ -0,0 +1,74 @@
+#!/usr/bin/env python3
+# -*- coding: UTF-8 no BOM -*-
+
+import os
+import sys
+import numpy as np
+import damask
+
+from optparse import OptionParser
+
+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 = """
+Generate homogeneous geometry.
+
+""", version = scriptID)
+
+parser.add_option('-g',
+                  '--grid',
+                  dest = 'grid',
+                  type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
+                  help = 'a,b,c grid of hexahedral box %default')
+parser.add_option('-s',
+                  '--size',
+                  dest = 'size',
+                  type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
+                  help = 'x,y,z of geometry size %default')
+parser.add_option('-o',
+                  '--origin',
+                  dest = 'origin',
+                  type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
+                  help = 'x,y,z of geometry origin %default')
+parser.add_option('--homogenization',
+                  dest = 'homogenization',
+                  type = 'int', metavar = 'int',
+                  help = 'homogenization index [%default]')
+parser.add_option('-f',
+                  '--fill',
+                  dest = 'fill',
+                  type = 'float', metavar = 'float',
+                  help = 'microstructure index [%default]')
+
+parser.set_defaults(grid = [16,16,16],
+                    size = [1.,1.,1.],
+                    origin = [0.,0.,0.],
+                    homogenization = 1,
+                    fill = 1,
+                   )
+
+(options, filenames) = parser.parse_args()
+
+dtype = float if np.isnan(options.fill) or int(options.fill) != options.fill else int
+grid   = list(map(  int,options.grid))
+size   = list(map(float,options.size))
+origin = list(map(float,options.origin))
+homogenization = int(options.homogenization)
+fill = float(options.fill)
+
+damask.util.report(scriptName,'')
+
+geom = damask.Geom(microstructure=(fill * np.ones(grid)).astype(dtype),
+                   size=size,
+                   origin=origin,
+                   homogenization=homogenization,
+                   comments=scriptID + ' ' + ' '.join(sys.argv[1:]))
+
+damask.util.croak(geom)
+  
+sys.stdout.write(str(geom.show()))