using class

still a very complex script

processing/pre/geom_fromVoronoiTessellation.py

@@ -1,11 +1,14 @@
 #!/usr/bin/env python3
-# -*- coding: UTF-8 no BOM -*-
 
-import os,sys,math
-import numpy as np
+import os
+import sys 
 import multiprocessing
+from io import StringIO
 from optparse import OptionParser,OptionGroup
+
+import numpy as np
 from scipy import spatial
+
 import damask
 
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
@@ -29,15 +32,15 @@ def meshgrid2(*arrs):
     ans.insert(0,arr2)
   return tuple(ans)
 
-def findClosestSeed(fargs):
+
+def laguerreTessellation(undeformed, coords, weights, grains, periodic = True, cpus = 2):
+
+  def findClosestSeed(fargs):
     point, seeds, myWeights = fargs
     tmp = np.repeat(point.reshape(3,1), len(seeds), axis=1).T
     dist = np.sum((tmp - seeds)**2,axis=1) -myWeights
     return np.argmin(dist)                                                                          # seed point closest to point
     
-
-def laguerreTessellation(undeformed, coords, weights, grains, periodic = True, cpus = 2):
-
   copies = \
     np.array([
               [ -1,-1,-1 ],
@@ -220,10 +223,7 @@ parser.set_defaults(pos            = 'pos',
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  try:    table = damask.ASCIItable(name = name,
-                                    outname = os.path.splitext(name)[0]+'.geom' if name else name,
-                                    buffered = False)
-  except: continue
+  table = damask.ASCIItable(name = name, readonly = True)
   damask.util.report(scriptName,name)
 
 # --- read header ----------------------------------------------------------------------------
@@ -281,7 +281,7 @@ for name in filenames:
         else  table.data[:,table.label_indexrange(options.pos)] - info['origin']
   eulers    = table.data[:,table.label_indexrange(options.eulers)] if hasEulers \
               else np.zeros(3*len(coords))
-  grains    = table.data[:,table.label_indexrange(options.microstructure)].astype('i') if hasGrains \
+  grains    = table.data[:,table.label_indexrange(options.microstructure)].astype(int) if hasGrains \
               else 1+np.arange(len(coords))
   weights   = table.data[:,table.label_indexrange(options.weight)] if hasWeights \
               else np.zeros(len(coords))
@@ -299,20 +299,8 @@ for name in filenames:
   grid = np.vstack(meshgrid2(x, y, z)).reshape(3,-1).T
   indices = laguerreTessellation(grid, coords, weights, grains, options.periodic, options.cpus)
     
-# --- write header ------------------------------------------------------------------------
-
-  usedGrainIDs = np.intersect1d(grainIDs,indices)
-  info['microstructures'] = len(usedGrainIDs)
-
-  if info['homogenization'] == 0: info['homogenization'] = options.homogenization
-  
-  damask.util.report_geom(info,['grid','size','origin','homogenization',])
-  damask.util.croak(['microstructures: {}{}'.format(info['microstructures'],
-                    (' out of {}'.format(NgrainIDs) if NgrainIDs != info['microstructures'] else '')),
-                    ])
-
   config_header = []
-  formatwidth = 1+int(math.log10(NgrainIDs))
+  formatwidth = 1+int(np.log10(NgrainIDs))
 
   if options.config:
     config_header += ['<microstructure>']
@@ -331,24 +319,10 @@ for name in filenames:
                          ] + theAxes
     config_header += ['<!skip>']
   
-  table.labels_clear()
-  table.info_clear()
-  table.info_append([
-    scriptID + ' ' + ' '.join(sys.argv[1:]),
-    "grid\ta {}\tb {}\tc {}".format(*info['grid']),
-    "size\tx {}\ty {}\tz {}".format(*info['size']),
-    "origin\tx {}\ty {}\tz {}".format(*info['origin']),
-    "homogenization\t{}".format(info['homogenization']),
-    "microstructures\t{}".format(info['microstructures']),
-    config_header,
-    ])
-  table.head_write()
+  geom = damask.Geom(indices.reshape(info['grid'],order='F'),info['size'],options.homogenization,comments=config_header)
+  damask.util.croak(geom)
   
-# --- write microstructure information ------------------------------------------------------------
-
-  table.data = indices.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
-  table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
-    
-#--- output finalization --------------------------------------------------------------------------
-
-  table.close()  
+  if name is None:
+    sys.stdout.write(str(geom.show()))
+  else:
+    geom.to_file(os.path.splitext(name)[0]+'.geom')

python/damask/geom.py

@@ -12,7 +12,7 @@ class Geom():
 
     if len(microstructure.shape) != 3:
       raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape))
-    elif microstructure.dtype not in ['int','float']:
+    elif microstructure.dtype not in [int,float]:
       raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype))
     else:
       self.microstructure = microstructure