Merge branch 'geom_from_xx' into development

.gitattributes

@@ -8,6 +8,7 @@
 *.jpg binary
 *.hdf5 binary
 *.pdf binary
+*.dream3d binary
 
 # ignore files from MSC.Marc in language statistics
 installation/mods_MarcMentat/20*/*  linguist-vendored

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 +37,21 @@ 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
+    t = damask.Table.load(name)
-
+    geom = damask.Geom.from_table(t,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/__init__.py

@@ -10,21 +10,21 @@ with open(_Path(__file__).parent/_Path('VERSION')) as _f:
 # make classes directly accessible as damask.Class
 from ._environment import Environment as _ # noqa
 environment = _()
-from ._table           import Table            # noqa
-from ._vtk             import VTK              # noqa
-from ._colormap        import Colormap         # noqa
-from ._rotation        import Rotation         # noqa
-from ._lattice         import Symmetry, Lattice# noqa
-from ._orientation     import Orientation      # noqa
-from ._result          import Result           # noqa
-from ._geom            import Geom             # noqa
-from ._config          import Config           # noqa
-from ._configmaterial  import ConfigMaterial   # noqa
-from .                 import solver           # noqa
 from .                 import util             # noqa
 from .                 import seeds            # noqa
-from .                 import grid_filters     # noqa
 from .                 import mechanics        # noqa
+from .                 import solver           # noqa
+from .                 import grid_filters     # noqa
+from ._lattice         import Symmetry, Lattice# noqa
+from ._table           import Table            # noqa
+from ._rotation        import Rotation         # noqa
+from ._vtk             import VTK              # noqa
+from ._colormap        import Colormap         # noqa
+from ._orientation     import Orientation      # noqa
+from ._config          import Config           # noqa
+from ._configmaterial  import ConfigMaterial   # noqa
+from ._geom            import Geom             # noqa
+from ._result          import Result           # noqa
 
 
 

python/damask/_configmaterial.py

@@ -2,6 +2,7 @@ import copy
 
 import numpy as np
 
+from . import grid_filters
 from . import Config
 from . import Lattice
 from . import Rotation
@@ -17,12 +18,73 @@ class ConfigMaterial(Config):
         ----------
         fname : file, str, or pathlib.Path, optional
             Filename or file for writing. Defaults to 'material.yaml'.
-        **kwargs : dict
+        **kwargs
             Keyword arguments parsed to yaml.dump.
 
         """
         super().save(fname,**kwargs)
 
+
+    @staticmethod
+    def from_table(table,coordinates=None,constituents={},**kwargs):
+        """
+        Load from an ASCII table.
+
+        Parameters
+        ----------
+        table : damask.Table
+            Table that contains material information.
+        coordinates : str, optional
+            Label of spatial coordiates. Used for sorting and performing a
+            sanity check. Default to None, in which case no sorting or checking is
+            peformed.
+        constituents : dict, optional
+            Entries for 'constituents'. The key is the name and the value specifies
+            the label of the data column in the table
+        **kwargs
+            Keyword arguments where the key is the name and  the value specifies
+            the label of the data column in the table
+
+        Examples
+        --------
+        >>> import damask
+        >>> import damask.ConfigMaterial as cm
+        >>> t = damask.Table.load('small.txt')
+        >>> t
+            pos  pos  pos   qu   qu    qu    qu   phase    homog
+        0    0    0    0  0.19  0.8   0.24 -0.51  Aluminum SX
+        1    1    0    0  0.8   0.19  0.24 -0.51  Steel    SX
+        >>> cm.from_table(t,'pos',{'O':'qu','phase':'phase'},homogenization='homog')
+        material:
+          - constituents:
+              - O: [0.19, 0.8, 0.24, -0.51]
+                fraction: 1.0
+                phase: Aluminum
+            homogenization: SX
+          - constituents:
+              - O: [0.8, 0.19, 0.24, -0.51]
+                fraction: 1.0
+                phase: Steel
+            homogenization: SX
+
+        """
+        if coordinates is not None:
+            t = table.sort_by([f'{i}_{coordinates}' for i in range(3,0,-1)])
+            grid_filters.coord0_check(t.get(coordinates))
+        else:
+            t = table
+
+        constituents_ = {k:t.get(v) for k,v in constituents.items()}
+        kwargs_       = {k:t.get(v) for k,v in kwargs.items()}
+
+        _,idx = np.unique(np.hstack(list({**constituents_,**kwargs_}.values())),return_index=True,axis=0)
+
+        constituents_ = {k:v[idx].squeeze() for k,v in constituents_.items()}
+        kwargs_       = {k:v[idx].squeeze() for k,v in kwargs_.items()}
+
+        return ConfigMaterial().material_add(constituents_,**kwargs_)
+
+
     @property
     def is_complete(self):
         """Check for completeness."""
@@ -62,10 +124,10 @@ class ConfigMaterial(Config):
                     print(f'No lattice specified in phase {k}')
                     ok = False
 
-            #for k,v in self['homogenization'].items():
+            for k,v in self['homogenization'].items():
-            #    if 'N_constituents' not in v:
+                if 'N_constituents' not in v:
-            #        print(f'No. of constituents not specified in homogenization {k}'}
+                    print(f'No. of constituents not specified in homogenization {k}')
-            #        ok = False
+                    ok = False
 
             if phase - set(self['phase']):
                 print(f'Phase(s) {phase-set(self["phase"])} missing')
@@ -158,3 +220,80 @@ class ConfigMaterial(Config):
             except KeyError:
                 continue
         return dup
+
+
+    def material_add(self,constituents,**kwargs):
+        """
+        Add material entries.
+
+        Parameters
+        ----------
+        constituents : dict
+            Entries for 'constituents'. The key is the name and the value specifies
+            the label of the data column in the table
+        **kwargs
+            Keyword arguments where the key is the name and  the value specifies
+            the label of the data column in the table
+
+        Examples
+        --------
+        >>> import damask
+        >>> m = damask.ConfigMaterial()
+        >>> O = damask.Rotation.from_random(3).as_quaternion()
+        >>> phase = ['Aluminum','Steel','Aluminum']
+        >>> m.material_add(constituents={'phase':phase,'O':O},homogenization='SX')
+        material:
+          - constituents:
+              - O: [0.577764, -0.146299, -0.617669, 0.513010]
+                fraction: 1.0
+                phase: Aluminum
+            homogenization: SX
+          - constituents:
+              - O: [0.184176, 0.340305, 0.737247, 0.553840]
+                fraction: 1.0
+                phase: Steel
+            homogenization: SX
+          - constituents:
+              - O: [0.0886257, -0.144848, 0.615674, -0.769487]
+                fraction: 1.0
+                phase: Aluminum
+            homogenization: SX
+
+        """
+        c = [{'constituents':u} for u in ConfigMaterial._constituents(**constituents)]
+        for k,v in kwargs.items():
+            if hasattr(v,'__len__') and not isinstance(v,str):
+                if len(v) != len(c):
+                    raise ValueError('len mismatch 1')
+                for i,vv in enumerate(v):
+                    c[i][k] = [w.item() for w in vv] if isinstance(vv,np.ndarray) else vv.item()
+            else:
+                for i in range(len(c)):
+                    c[i][k] = v
+        dup = copy.deepcopy(self)
+        if 'material' not in dup: dup['material'] = []
+        dup['material'] +=c
+
+        return dup
+
+
+    @staticmethod
+    def _constituents(N=1,**kwargs):
+        """Construct list of constituents."""
+        for v in kwargs.values():
+            if hasattr(v,'__len__') and not isinstance(v,str): N_material = len(v)
+
+        if N == 1:
+            m = [[{'fraction':1.0}] for _ in range(N_material)]
+            for k,v in kwargs.items():
+                if hasattr(v,'__len__') and not isinstance(v,str):
+                    if len(v) != N_material:
+                        raise ValueError('len mismatch 2')
+                    for i,vv in enumerate(np.array(v)):
+                        m[i][0][k] = [w.item() for w in vv] if isinstance(vv,np.ndarray) else vv.item()
+                else:
+                    for i in range(N_material):
+                        m[i][0][k] = v
+            return m
+        else:
+            raise NotImplementedError

python/damask/_geom.py

@@ -1,15 +1,17 @@
 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 Rotation
 
 
 class Geom:
@@ -207,6 +209,68 @@ class Geom:
         return Geom(material.reshape(grid,order='F'),size,origin,comments)
 
 
+
+    @staticmethod
+    def load_DREAM3D(fname,base_group,point_data=None,material='FeatureIds'):
+        """
+        Load a DREAM.3D file.
+
+        Parameters
+        ----------
+        fname : str
+            Filename of the DREAM.3D file
+        base_group : str
+            Name of the group (folder) below 'DataContainers'. For example
+            'SyntheticVolumeDataContainer'.
+        point_data : str, optional
+            Name of the group (folder) containing the point wise material data,
+            for example 'CellData'. Defaults to None, in which case points consecutively numbered.
+        material : str, optional
+            Name of the dataset containing the material ID. Defaults to
+            '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','load_DREAM3D'))
+
+
+    @staticmethod
+    def from_table(table,coordinates,labels):
+        """
+        Load an ASCII table.
+
+        Parameters
+        ----------
+        table : damask.Table
+            Table that contains material information.
+        coordinates : str
+            Label of the column containing the spatial coordinates.
+        labels : str or list of str
+            Label(s) of the columns containing the material definition.
+            Each unique combintation of values results in a material.
+
+        """
+        t = table.sort_by([f'{i}_{coordinates}' for i in range(3,0,-1)])
+
+        grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(t.get(coordinates))
+
+        labels_ = [labels] if isinstance(labels,str) else labels
+        _,unique_inverse = np.unique(np.hstack([t.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'))
+
+
     @staticmethod
     def _find_closest_seed(seeds, weights, point):
         return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)
@@ -399,7 +463,7 @@ class Geom:
 
     def save(self,fname,compress=True):
         """
-        Generates vtk rectilinear grid.
+        Store as vtk rectilinear grid.
 
         Parameters
         ----------
@@ -536,7 +600,7 @@ 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))

python/damask/_table.py

@@ -33,6 +33,10 @@ class Table:
         """Brief overview."""
         return util.srepr(self.comments)+'\n'+self.data.__repr__()
 
+    def __len__(self):
+        """Number of rows."""
+        return len(self.data)
+
     def __copy__(self):
         """Copy Table."""
         return copy.deepcopy(self)

python/tests/reference/ConfigMaterial/material.yaml

@@ -1,8 +1,10 @@
 homogenization:
   SX:
+    N_constituents: 2
     mech: {type: none}
   Taylor:
-    mech: {N_constituents: 2, type: isostrain}
+    N_constituents: 2
+    mech: {type: isostrain}
 
 material:
   - constituents: