direct translation from DREAM.3D to DAMASK geom

needs test

processing/pre/geom_fromDREAM3D.py

@@ -0,0 +1,189 @@
+#!/usr/bin/env python3
+# -*- coding: UTF-8 no BOM -*-
+
+import os,sys,h5py
+import numpy as np
+from optparse import OptionParser
+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 [dream3dfile[s]]', description = """
+Convert DREAM3D file to geometry file. This can be done from cell data (direct pointwise takeover) or
+from grain data (individual grains are segmented). Requires orientation data as quaternion.
+
+""", version = scriptID)
+
+parser.add_option('-b','--basegroup',
+                  dest = 'basegroup', metavar = 'string',
+                  help = 'name of the group in "DataContainers" that contains all the data')
+parser.add_option('-p','--pointwise',
+                  dest = 'pointwise', metavar = 'string',
+                  help = 'name of the group in "DataContainers/<basegroup>" that contains pointwise data [%default]')
+parser.add_option('-a','--average',
+                  dest = 'average', metavar = 'string',
+                  help = 'name of the group in "DataContainers</basegroup>" that contains grain average data. '\
+                       + 'Leave empty for pointwise data')
+parser.add_option('--phase',
+                  dest = 'phase',
+                  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',
+                  help = 'name of the dataset connecting pointwise and average data [%default]')
+parser.add_option('-q', '--quaternion',
+                  dest = 'quaternion',
+                  type = 'string', metavar='string',
+                  help = 'name of the dataset containing pointwise/average orientation as quaternion [%default]')
+
+parser.set_defaults(pointwise      = 'CellData',
+                    quaternion     = 'Quats',
+                    phase          = 'Phases',
+                    microstructure = 'FeatureIds',
+                    crystallite    = 1,
+                   )
+
+(options, filenames) = parser.parse_args()
+
+if options.basegroup is None:
+  parser.error('No base group selected')
+
+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')][...] \
+                   * inFile[os.path.join(group_geom,'SPACING')][...]
+    info['grid']   = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
+    info['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'
+    N_microstructure = np.product(info['grid'])
+    
+    dataset = os.path.join(group_pointwise,options.quaternion)
+    try:
+      quats = np.reshape(inFile[dataset][...],(N_microstructure,3))
+    except:
+      errors.append('Pointwise orientation data ({}) not found'.format(dataset))
+      
+    texture = [damask.Rotation.fromQuaternion(q,P=+1) for q in quats]
+
+    dataset = os.path.join(group_pointwise,options.phase)
+    try:
+      phase = np.reshape(inFile[dataset][...],(N_microstructure))
+    except:
+      errors.append('Pointwise phase data ({}) not found'.format(dataset))
+
+    
+  else:
+    label = 'grain'
+    
+    dataset = os.path.join(group_pointwise,options.microstructure)
+    try:
+      microstructure = np.reshape(inFile[dataset][...],(np.product(info['grid'])))
+      N_microstructure = np.max(microstructure)
+    except:
+      errors.append('Link between pointwise and grain average data ({}) not found'.format(dataset))
+
+    group_average = os.path.join(rootDir,options.basegroup,options.average)
+    
+    dataset = os.path.join(group_average,options.quaternion)
+    try:
+      texture = [damask.Rotation.fromQuaternion(q,P=+1) for q in inFile[dataset][...][1:]]          # skip first entry (unindexed)
+    except:
+      errors.append('Average orientation data ({}) not found'.format(dataset))
+      
+    dataset = os.path.join(group_average,options.phase)
+    try:
+      phase = [i[0] for i in inFile[dataset][...]][1:]                                              # skip first entry (unindexed)
+    except:
+      errors.append('Average phase data ({}) not found'.format(dataset))
+
+  if errors != []:
+    damask.util.croak(errors)
+    table.close(dismiss = True)
+    continue
+    
+    
+  mat = damask.Material()
+  mat.verbose = False
+
+  # dummy <homogenization>
+  h = damask.config.material.Homogenization()
+  mat.add_section('Homogenization','none',h)
+  info['homogenization'] = 1
+  
+  # <crystallite> placeholder (same for all microstructures at the moment)
+  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()  

processing/pre/geom_fromTable.py

@@ -39,7 +39,7 @@ parser.add_option('-q', '--quaternion',
 parser.add_option('--axes',
                   dest = 'axes',
                   type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
-                  help = 'orientation coordinate frame in terms of position coordinate frame [same]')
+                  help = 'orientation coordinate frame in terms of position coordinate frame [+x +y +z]')
 
 parser.add_option('--homogenization',
                   dest = 'homogenization',
@@ -51,8 +51,7 @@ parser.add_option('--crystallite',
                   help = 'crystallite index to be used [%default]')
 
 
-parser.set_defaults(symmetry       = [damask.Symmetry.lattices[-1]],
+parser.set_defaults(homogenization = 1,
-                    homogenization = 1,
                     crystallite    = 1,
                     pos            = 'pos',
                    )
@@ -100,7 +99,7 @@ for name in filenames:
   if options.phase and table.label_dimension(options.phase) != 1:
     errors.append('phase column "{}" is not scalar.'.format(options.phase))
   
-  if errors  != []:
+  if errors != []:
     damask.util.croak(errors)
     table.close(dismiss = True)
     continue