using geom class

- dropped the use of the material class as it does not allow to have
empty phase and crystallite. The material.config class needs a severe
refurbishing (no crystallite, use orderedDict instead of hand written
solution, drop of texture components). Probably best solution is to
postpone this until we have a yaml/json reader for Fortran.

processing/pre/geom_fromDREAM3D.py

@@ -1,11 +1,15 @@
 #!/usr/bin/env python3
-# -*- coding: UTF-8 no BOM -*-
 
-import os,sys,h5py
+import os
-import numpy as np
+import sys
 from optparse import OptionParser
+
+import h5py
+import numpy as np
+
 import damask
 
+
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
@@ -14,40 +18,50 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog [dream3dfile[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [DREAM.3Dfile(s)]', description = """
-Convert DREAM3D file to geometry file. This can be done from cell data (direct pointwise takeover) or
+Converts DREAM.3D file. Input can be cell data (direct pointwise takeover) or grain data (individual
-from grain data (individual grains are segmented). Requires orientation data as quaternion.
+grains are segmented). Requires orientation data as quaternion.
 
 """, version = scriptID)
 
 parser.add_option('-b','--basegroup',
-                  dest = 'basegroup', metavar = 'string',
+                  dest = 'basegroup',
+                  metavar = 'string',
                   help = 'name of the group in "DataContainers" containing the pointwise (and, if applicable grain average) data')
 parser.add_option('-p','--pointwise',
-                  dest = 'pointwise', metavar = 'string',
+                  dest = 'pointwise',
+                  metavar = 'string',
                   help = 'name of the group in "DataContainers/<basegroup>" containing pointwise data [%default]')
 parser.add_option('-a','--average',
-                  dest = 'average', metavar = 'string',
+                  dest = 'average',
+                  metavar = 'string',
                   help = 'name of the group in "DataContainers</basegroup>" containing grain average data. '\
                        + 'Leave empty for pointwise data')
 parser.add_option('--phase',
                   dest = 'phase',
-                  type = 'string', metavar = 'string',
+                  type = 'string',
+                  metavar = 'string',
                   help = 'name of the dataset containing pointwise/average phase IDs [%default]')
 parser.add_option('--microstructure',
                   dest = 'microstructure',
-                  type = 'string', metavar = 'string',
+                  type = 'string',
+                  metavar = 'string',
                   help = 'name of the dataset connecting pointwise and average data [%default]')
 parser.add_option('-q', '--quaternion',
                   dest = 'quaternion',
-                  type = 'string', metavar='string',
+                  type = 'string',
+                  metavar='string',
                   help = 'name of the dataset containing pointwise/average orientation as quaternion [%default]')
+parser.add_option('--homogenization',
+                  dest = 'homogenization',
+                  type = 'int', metavar = 'int',
+                  help = 'homogenization index to be used [%default]')
 
 parser.set_defaults(pointwise      = 'CellData',
                     quaternion     = 'Quats',
                     phase          = 'Phases',
                     microstructure = 'FeatureIds',
-                    crystallite    = 1,
+                    homogenization = 1,
                    )
 
 (options, filenames) = parser.parse_args()
@@ -57,59 +71,51 @@ if options.basegroup is None:
 
 rootDir ='DataContainers'
 
-# --- loop over input files -------------------------------------------------------------------------
 
 if filenames == []: parser.error('no input file specified.')
 
 for name in filenames:
-  try:
-    table = damask.ASCIItable(outname = os.path.splitext(name)[0]+'.geom',
-                              buffered = False, labeled=False,
-                              )
-  except: continue
   damask.util.report(scriptName,name)
 
   errors = []
   
-  info = {}
-  ori  = []
   inFile = h5py.File(name, 'r')
   group_geom = os.path.join(rootDir,options.basegroup,'_SIMPL_GEOMETRY')
   try:
-    info['size']   = inFile[os.path.join(group_geom,'DIMENSIONS')][...] \
+    size   = inFile[os.path.join(group_geom,'DIMENSIONS')][...] \
-                   * inFile[os.path.join(group_geom,'SPACING')][...]
+           * inFile[os.path.join(group_geom,'SPACING')][...]
-    info['grid']   = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
+    grid   = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
-    info['origin'] = inFile[os.path.join(group_geom,'ORIGIN')][...]
+    origin = inFile[os.path.join(group_geom,'ORIGIN')][...]
   except:
     errors.append('Geometry data ({}) not found'.format(group_geom))
     
     
   group_pointwise = os.path.join(rootDir,options.basegroup,options.pointwise)
   if options.average is None:
-    label = 'point'
+    label = 'Point'
-    N_microstructure = np.product(info['grid'])
 
     dataset = os.path.join(group_pointwise,options.quaternion)
     try:
-      quats   = np.reshape(inFile[dataset][...],(N_microstructure,4))
+      quats = np.reshape(inFile[dataset][...],(np.product(grid),4))
-      texture = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats]
+      rot   = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats]
     except:
       errors.append('Pointwise orientation (quaternion) data ({}) not readable'.format(dataset))
       
     dataset = os.path.join(group_pointwise,options.phase)
     try:
-      phase = np.reshape(inFile[dataset][...],(N_microstructure))
+      phase = np.reshape(inFile[dataset][...],(np.product(grid)))
     except:
       errors.append('Pointwise phase data ({}) not readable'.format(dataset))
     
+    microstructure = np.arange(1,np.product(grid)+1,dtype=int).reshape(grid,order='F')
+
     
   else:
-    label = 'grain'
+    label = 'Grain'
     
     dataset = os.path.join(group_pointwise,options.microstructure)
     try:
-      microstructure = np.reshape(inFile[dataset][...],(np.product(info['grid'])))
+      microstructure = np.transpose(inFile[dataset][...].reshape(grid[::-1]),(2,1,0))               # convert from C ordering
-      N_microstructure = np.max(microstructure)
     except:
       errors.append('Link between pointwise and grain average data ({}) not readable'.format(dataset))
     
@@ -117,7 +123,7 @@ for name in filenames:
     
     dataset = os.path.join(group_average,options.quaternion)
     try:
-      texture = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in inFile[dataset][...][1:]]     # skip first entry (unindexed)
+      rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in inFile[dataset][...][1:]]         # skip first entry (unindexed)
     except:
       errors.append('Average orientation data ({}) not readable'.format(dataset))
       
@@ -129,60 +135,25 @@ for name in filenames:
 
   if errors != []:
     damask.util.croak(errors)
-    table.close(dismiss = True)
     continue
     
+  config_header = ['<microstructure>']
+  for i in range(np.nanmax(microstructure)):
+    config_header += ['[{}{}]'.format(label,i+1),
+                      'crystallite 1',
+                      '(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(phase[i],i+1),
+                      ]
   
-  mat = damask.Material()
+  config_header += ['<texture>']
-  mat.verbose = False
+  for i in range(np.nanmax(microstructure)):
+    config_header += ['[{}{}]'.format(label,i+1),
+                      '(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*rot[i].asEulers(degrees = True)),
+                     ]
     
-  # dummy <homogenization>
+  header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
-  h = damask.config.material.Homogenization()
+         + config_header
-  mat.add_section('Homogenization','none',h)
+  geom = damask.Geom(microstructure,size,origin,
-  info['homogenization'] = 1
+                     homogenization=options.homogenization,comments=header)
+  damask.util.croak(geom)
 
-  # <crystallite> placeholder (same for all microstructures at the moment)
+  geom.to_file(os.path.splitext(name)[0]+'.geom')
-  c = damask.config.material.Crystallite()
-  mat.add_section('Crystallite','tbd',c)
-  
-  # <phase> placeholders
-  for i in range(np.max(phase)):
-    p = damask.config.material.Phase()
-    mat.add_section('phase','phase{}-tbd'.format(i+1),p)
-
-  # <texture>
-  for i,o in enumerate(texture):
-    t = damask.config.material.Texture()
-    t.add_component('gauss',{'eulers':o.asEulers(degrees=True)})
-    mat.add_section(part='texture', section='{}{}'.format(label,i+1),initialData=t)
-  
-  # <microstructure>
-  for i in range(N_microstructure):
-    m = damask.config.material.Microstructure()
-    mat.add_section('microstructure','{}{}'.format(label,i+1),m)
-    mat.add_microstructure('{}{}'.format(label,i+1),
-                           {'phase':  'phase{}-tbd'.format(phase[i]),
-                            'texture':'{}{}'.format(label,i+1),
-                            'crystallite':'tbd',
-                            'fraction':1
-                            })
-    
-  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']),
-    str(mat).split('\n')
-    ])
-  table.head_write()
-  
-  if options.average is None:
-    table.data = [1, 'to', format(N_microstructure)]
-    table.data_write()
-  else:
-    table.data = microstructure.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
-    table.data_writeArray()
-    
-    
-  table.close()