functionality for geom generation in python lib

processing/pre/geom_fromDREAM3D.py

@@ -1,12 +1,8 @@
 #!/usr/bin/env python3
 
 import os
-import sys
 from optparse import OptionParser
 
-import h5py
-import numpy as np
-
 import damask
 
 
@@ -64,88 +60,12 @@ parser.set_defaults(pointwise      = 'CellData',
 if options.basegroup is None:
   parser.error('No base group selected')
 
-rootDir ='DataContainers'
-
-
 if filenames == []: parser.error('no input file specified.')
 
 for name in filenames:
     damask.util.report(scriptName,name)
 
-  errors = []
+    geom = damask.Geom.load_DREAM3D(name,options.basegroup,options.pointwise)
-
-  inFile = h5py.File(name, 'r')
-  group_geom = os.path.join(rootDir,options.basegroup,'_SIMPL_GEOMETRY')
-  try:
-    size   = inFile[os.path.join(group_geom,'DIMENSIONS')][...] \
-           * inFile[os.path.join(group_geom,'SPACING')][...]
-    grid   = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
-    origin = inFile[os.path.join(group_geom,'ORIGIN')][...]
-  except KeyError:
-    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'
-
-    dataset = os.path.join(group_pointwise,options.quaternion)
-    try:
-      quats = np.reshape(inFile[dataset][...],(np.product(grid),4))
-      rot   = [damask.Rotation.from_quaternion(q,True,P=+1) for q in quats]
-    except KeyError:
-      errors.append('Pointwise orientation (quaternion) data ({}) not readable'.format(dataset))
-
-    dataset = os.path.join(group_pointwise,options.phase)
-    try:
-      phase = np.reshape(inFile[dataset][...],(np.product(grid)))
-    except KeyError:
-      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'
-
-    dataset = os.path.join(group_pointwise,options.microstructure)
-    try:
-      microstructure = np.transpose(inFile[dataset][...].reshape(grid[::-1]),(2,1,0))               # convert from C ordering
-    except KeyError:
-      errors.append('Link between pointwise and grain average data ({}) not readable'.format(dataset))
-
-    group_average = os.path.join(rootDir,options.basegroup,options.average)
-
-    dataset = os.path.join(group_average,options.quaternion)
-    try:
-      rot = [damask.Rotation.from_quaternion(q,True,P=+1) for q in inFile[dataset][...][1:]]        # skip first entry (unindexed)
-    except KeyError:
-      errors.append('Average orientation data ({}) not readable'.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 KeyError:
-      errors.append('Average phase data ({}) not readable'.format(dataset))
-
-  if errors != []:
-    damask.util.croak(errors)
-    continue
-
-  config_header = ['<texture>']
-  for i in range(np.nanmax(microstructure)):
-    config_header += ['[{}{}]'.format(label,i+1),
-                      '(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*rot[i].as_Eulers(degrees = True)),
-                     ]
-  config_header += ['<microstructure>']
-  for i in range(np.nanmax(microstructure)):
-    config_header += ['[{}{}]'.format(label,i+1),
-                      '(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(phase[i],i+1),
-                      ]
-
-  header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
-         + config_header
-  geom = damask.Geom(microstructure,size,origin,comments=header)
     damask.util.croak(geom)
 
     geom.save_ASCII(os.path.splitext(name)[0]+'.geom',compress=False)

processing/pre/geom_fromTable.py

@@ -2,11 +2,8 @@
 
 import os
 import sys
-from io import StringIO
 from optparse import OptionParser
 
-import numpy as np
-
 import damask
 
 
@@ -40,64 +37,20 @@ parser.add_option('-q', '--quaternion',
                   dest = 'quaternion',
                   type = 'string', metavar='string',
                   help = 'quaternion label')
-parser.add_option('--axes',
-                  dest = 'axes',
-                  type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
-                  help = 'orientation coordinate frame in terms of position coordinate frame [+x +y +z]')
 
-
+parser.set_defaults(pos= 'pos')
-parser.set_defaults(pos            = 'pos',
-                   )
 
 (options,filenames) = parser.parse_args()
 if filenames == []: filenames = [None]
 
-if np.sum([options.quaternion     is not None,
-           options.microstructure is not None]) != 1:
-  parser.error('need either microstructure or quaternion (and optionally phase) as input.')
-if options.microstructure is not None and options.phase is not None:
-  parser.error('need either microstructure or phase (and mandatory quaternion) as input.')
-if options.axes is not None and not set(options.axes).issubset(set(['x','+x','-x','y','+y','-y','z','+z','-z'])):
-  parser.error('invalid axes {} {} {}.'.format(*options.axes))
-
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    labels = []
-    table.sort_by(['{}_{}'.format(i,options.pos) for i in range(3,0,-1)])                           # x fast, y slow
+    for l in [options.quaternion,options.phase,options.microstructure]:
-    grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
+        if l is not None: labels.append(l)
 
-    config_header  = table.comments
+    geom = damask.Geom.load_table(name,options.pos,labels)
-
-    if   options.microstructure:
-        microstructure = table.get(options.microstructure).reshape(grid,order='F')
-
-    elif options.quaternion:
-        q     = table.get(options.quaternion)
-        phase = table.get(options.phase).astype(int) if options.phase else \
-                np.ones((table.data.shape[0],1),dtype=int)
-
-        unique,unique_inverse = np.unique(np.hstack((q,phase)),return_inverse=True,axis=0)
-        microstructure = unique_inverse.reshape(grid,order='F') + 1
-
-        config_header = ['<texture>']
-        for i,data in enumerate(unique):
-            ori = damask.Rotation(data[0:4])
-            config_header += ['[Grain{}]'.format(i+1),
-                              '(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*ori.as_Eulers(degrees = True)),
-                             ]
-            if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)]
-
-        config_header += ['<microstructure>']
-        for i,data in enumerate(unique):
-            config_header += ['[Grain{}]'.format(i+1),
-                              '(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(int(data[4]),i+1),
-                             ]
-
-    header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
-           + config_header
-    geom = damask.Geom(microstructure,size,origin,
-                       comments=header)
     damask.util.croak(geom)
 
     geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',compress=False)

python/damask/_geom.py

@@ -1,15 +1,18 @@
 import copy
 import multiprocessing as mp
 from functools import partial
+from os import path
 
 import numpy as np
+import h5py
 from scipy import ndimage,spatial
 
 from . import environment
-from . import Rotation
 from . import VTK
 from . import util
 from . import grid_filters
+from . import Table
+from . import Rotation
 
 
 class Geom:
@@ -397,6 +400,35 @@ class Geom:
                    )
 
 
+    @staticmethod
+    def load_DREAM3D(fname,base_group,point_data=None,material='FeatureIds'):
+        root_dir ='DataContainers'
+        f = h5py.File(fname, 'r')
+        g = path.join(root_dir,base_group,'_SIMPL_GEOMETRY')
+        size   = f[path.join(g,'DIMENSIONS')][()] * f[path.join(g,'SPACING')][()]
+        grid   = f[path.join(g,'DIMENSIONS')][()]
+        origin = f[path.join(g,'ORIGIN')][()]
+        group_pointwise = path.join(root_dir,base_group,point_data)
+
+        ma = np.arange(1,np.product(grid)+1,dtype=int) if point_data is None else \
+             np.reshape(f[path.join(group_pointwise,material)],grid.prod())
+
+        return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','from_DREAM3D'))
+
+
+    @staticmethod
+    def load_table(fname,coordinates,labels):
+        table = Table.load(fname).sort_by([f'{i}_{coordinates}' for i in range(3,0,-1)])
+
+        grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(table.get(coordinates))
+
+        labels_ = [labels] if isinstance(labels,str) else labels
+        _,unique_inverse = np.unique(np.hstack([table.get(l) for l in labels_]),return_inverse=True,axis=0)
+        ma = unique_inverse.reshape(grid,order='F') + 1
+
+        return Geom(ma,size,origin,util.execution_stamp('Geom','from_table'))
+
+
     def save(self,fname,compress=True):
         """
         Generates vtk rectilinear grid.
@@ -536,7 +568,7 @@ class Geom:
         coords_rot = R.broadcast_to(tuple(self.grid))@coords
 
         with np.errstate(all='ignore'):
-            mask = np.where(np.sum(np.power(coords_rot/r,2.0**exponent),axis=-1) > 1.0,True,False)
+            mask = np.sum(np.power(coords_rot/r,2.0**np.array(exponent)),axis=-1) > 1.0
 
         if periodic:                                                                                # translate back to center
             mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2))