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DAMASK_EICMD
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corrected the looping and target dir

This commit is contained in:
Vitesh Shah 2023-04-17 08:03:44 +02:00
parent 2ae1a20443
commit 029b830156
1 changed files with 79 additions and 72 deletions
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151
python/damask/_result.py
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@ -1945,7 +1945,8 @@ class Result:
v.save(vtk_dir/f'{self.fname.stem}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}', v.save(vtk_dir/f'{self.fname.stem}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}',
parallel=parallel) parallel=parallel)
def export_DREAM3D(self): def export_DREAM3D(self,
target_dir: Union[None, str, Path] = None):
""" """
Export the visible components to DREAM3D compatible files. Export the visible components to DREAM3D compatible files.
@ -1957,7 +1958,8 @@ class Result:
Parameters Parameters
---------- ----------
target_dir : str or pathlib.Path, optional
Directory to save DREAM3D files. Will be created if non-existent.
""" """
Crystal_structures = {'fcc': 1, Crystal_structures = {'fcc': 1,
'bcc': 1, 'bcc': 1,
@ -1970,93 +1972,98 @@ class Result:
at_cell_ph,in_data_ph,at_cell_ho,in_data_ho = self._mappings() at_cell_ph,in_data_ph,at_cell_ho,in_data_ho = self._mappings()
for inc in util.show_progress(self.visible['increments']): dream_dir = Path.cwd() if target_dir is None else Path(target_dir)
cell_orientation_array = np.zeros((np.prod(self.cells),3)) dream_dir.mkdir(parents=True,exist_ok=True)
phase_ID_array = np.zeros((np.prod(self.cells)),dtype=np.int32) #need to reshape it later
for c in range(self.N_constituents):
for count,label in enumerate(self.visible['phases']):
try:
data = ma.array(_read(f['/'.join([inc,'phase',label,'mechanical/O'])]))
cell_orientation_array[at_cell_ph[c][label],:] = Rotation(data[in_data_ph[c][label],:]).as_Euler_angles() # TODO: convert DAMASK quats to Dream3D quats?
except ValueError: #check if the exception is correct
print("Orientation data is not present")
exit() # need to check if such a statement would really work.
with h5py.File(self.fname,'r') as f:
for inc in util.show_progress(self.visible['increments']):
cell_orientation_array = np.zeros((np.prod(self.cells),3))
phase_ID_array = np.zeros((np.prod(self.cells)),dtype=np.int32) #need to reshape it later
for c in range(self.N_constituents):
for count,label in enumerate(self.visible['phases']):
try:
data = ma.array(_read(f['/'.join([inc,'phase',label,'mechanical/O'])]))
cell_orientation_array[at_cell_ph[c][label],:] = \
Rotation(data[in_data_ph[c][label],:]).as_Euler_angles()
# Dream3D handles euler angles better
except ValueError: #check if the exception is correct
print("Orientation data is not present")
exit() # need to check if such a statement would really work.
phase_ID_array[at_cell_ph[c][label]] = count + 1 #need to figure out these mappings a bit phase_ID_array[at_cell_ph[c][label]] = count + 1
job_file_no_ext = os.path.splitext(self.fname)[0] job_file_no_ext = os.path.splitext(self.fname)[0]
o = h5py.File(f'{job_file_no_ext}_increment{inc}.dream3D','w') o = h5py.File(f'{dream_dir}/{job_file_no_ext}_{inc}.dream3D','w')
o.attrs['DADF5toDREAM3D'] = '1.0' o.attrs['DADF5toDREAM3D'] = '1.0'
o.attrs['FileVersion'] = '7.0' o.attrs['FileVersion'] = '7.0'
for g in ['DataContainerBundles','Pipeline']: # empty groups (needed) for g in ['DataContainerBundles','Pipeline']: # empty groups (needed)
o.create_group(g) o.create_group(g)
data_container_label = 'DataContainers/SyntheticVolumeDataContainer' data_container_label = 'DataContainers/SyntheticVolumeDataContainer'
cell_data_label = data_container_label + '/CellData' cell_data_label = data_container_label + '/CellData'
# Data phases # Data phases
o[cell_data_label + '/Phases'] = np.reshape(phase_ID_array, \ o[cell_data_label + '/Phases'] = np.reshape(phase_ID_array, \
tuple(np.flip(self.cells))+(1,)) tuple(np.flip(self.cells))+(1,))
# Data eulers # Data eulers
orientation_data = cell_orientation_array.astype(np.float32) orientation_data = cell_orientation_array.astype(np.float32)
o[cell_data_label + '/Eulers'] = orientation_data.reshape(tuple(np.flip(self.cells))+(3,)) o[cell_data_label + '/Eulers'] = orientation_data.reshape(tuple(np.flip(self.cells))+(3,))
# Attributes to CellData group # Attributes to CellData group
o[cell_data_label].attrs['AttributeMatrixType'] = np.array([3],np.uint32) o[cell_data_label].attrs['AttributeMatrixType'] = np.array([3],np.uint32)
o[cell_data_label].attrs['TupleDimensions'] = np.array(self.cells,np.uint64) o[cell_data_label].attrs['TupleDimensions'] = np.array(self.cells,np.uint64)
# Common Attributes for groups in CellData # Common Attributes for groups in CellData
for group in ['/Phases','/Eulers']: for group in ['/Phases','/Eulers']:
o[cell_data_label + group].attrs['DataArrayVersion'] = np.array([2],np.int32) o[cell_data_label + group].attrs['DataArrayVersion'] = np.array([2],np.int32)
o[cell_data_label + group].attrs['Tuple Axis Dimensions'] = 'x={},y={},z={}'.format(*np.array(self.cells)) o[cell_data_label + group].attrs['Tuple Axis Dimensions'] = 'x={},y={},z={}'.format(*np.array(self.cells))
# phase attributes # phase attributes
o[cell_data_label + '/Phases'].attrs['ComponentDimensions'] = np.array([1],np.uint64) o[cell_data_label + '/Phases'].attrs['ComponentDimensions'] = np.array([1],np.uint64)
o[cell_data_label + '/Phases'].attrs['ObjectType'] = 'DataArray<int32_t>' o[cell_data_label + '/Phases'].attrs['ObjectType'] = 'DataArray<int32_t>'
o[cell_data_label + '/Phases'].attrs['TupleDimensions'] = np.array(self.cells,np.uint64) o[cell_data_label + '/Phases'].attrs['TupleDimensions'] = np.array(self.cells,np.uint64)
# Eulers attributes # Eulers attributes
o[cell_data_label + '/Eulers'].attrs['ComponentDimensions'] = np.array([3],np.uint64) o[cell_data_label + '/Eulers'].attrs['ComponentDimensions'] = np.array([3],np.uint64)
o[cell_data_label + '/Eulers'].attrs['ObjectType'] = 'DataArray<float>' o[cell_data_label + '/Eulers'].attrs['ObjectType'] = 'DataArray<float>'
o[cell_data_label + '/Eulers'].attrs['TupleDimensions'] = np.array(self.cells,np.uint64) o[cell_data_label + '/Eulers'].attrs['TupleDimensions'] = np.array(self.cells,np.uint64)
# Create EnsembleAttributeMatrix # Create EnsembleAttributeMatrix
ensemble_label = data_container_label + '/CellEnsembleData' ensemble_label = data_container_label + '/CellEnsembleData'
# Data CrystalStructures # Data CrystalStructures
o[ensemble_label + '/CrystalStructures'] = np.uint32(np.array([999] + [1]*len(self.phases))) o[ensemble_label + '/CrystalStructures'] = np.uint32(np.array([999] + [1]*len(self.phases)))
# assuming only cubic crystal structures # assuming only cubic crystal structures
# Damask can give the crystal structure info but need to look into dream3d which crystal structure corresponds to which number # Damask can give the crystal structure info but need to look into dream3d which crystal structure corresponds to which number
o[ensemble_label + '/PhaseTypes'] = np.uint32(np.array([999] + [Phase_types['Primary']]*len(self.phases))).reshape((len(self.phases)+1,1)) o[ensemble_label + '/PhaseTypes'] = np.uint32(np.array([999] + [Phase_types['Primary']]*len(self.phases))).reshape((len(self.phases)+1,1))
# also assuming Primary phases # also assuming Primary phases
# there can be precipitates etc as well # there can be precipitates etc as well
# Attributes Ensemble Matrix # Attributes Ensemble Matrix
o[ensemble_label].attrs['AttributeMatrixType'] = np.array([11],np.uint32) o[ensemble_label].attrs['AttributeMatrixType'] = np.array([11],np.uint32)
o[ensemble_label].attrs['TupleDimensions'] = np.array([len(self.phases) + 1], np.uint64) o[ensemble_label].attrs['TupleDimensions'] = np.array([len(self.phases) + 1], np.uint64)
# Attributes for data in Ensemble matrix # Attributes for data in Ensemble matrix
for group in ['CrystalStructures','PhaseTypes']: # 'PhaseName' not required MD: But would be nice to take the phase name mapping for group in ['CrystalStructures','PhaseTypes']: # 'PhaseName' not required MD: But would be nice to take the phase name mapping
o[ensemble_label+'/'+group].attrs['ComponentDimensions'] = np.array([1],np.uint64) o[ensemble_label+'/'+group].attrs['ComponentDimensions'] = np.array([1],np.uint64)
o[ensemble_label+'/'+group].attrs['Tuple Axis Dimensions'] = f'x={len(self.phases)+1}' o[ensemble_label+'/'+group].attrs['Tuple Axis Dimensions'] = f'x={len(self.phases)+1}'
o[ensemble_label+'/'+group].attrs['DataArrayVersion'] = np.array([2],np.int32) o[ensemble_label+'/'+group].attrs['DataArrayVersion'] = np.array([2],np.int32)
o[ensemble_label+'/'+group].attrs['ObjectType'] = 'DataArray<uint32_t>' o[ensemble_label+'/'+group].attrs['ObjectType'] = 'DataArray<uint32_t>'
o[ensemble_label+'/'+group].attrs['TupleDimensions'] = np.array([len(self.phases) + 1],np.uint64) o[ensemble_label+'/'+group].attrs['TupleDimensions'] = np.array([len(self.phases) + 1],np.uint64)
# Create geometry info # Create geometry info
geom_label = data_container_label + '/_SIMPL_GEOMETRY' geom_label = data_container_label + '/_SIMPL_GEOMETRY'
o[geom_label + '/DIMENSIONS'] = np.int64(np.array(self.cells)) o[geom_label + '/DIMENSIONS'] = np.int64(np.array(self.cells))
o[geom_label + '/ORIGIN'] = np.float32(np.zeros(3)) o[geom_label + '/ORIGIN'] = np.float32(np.zeros(3))
o[geom_label + '/SPACING'] = np.float32(dx) o[geom_label + '/SPACING'] = np.float32(dx)
o[geom_label].attrs['GeometryName'] = 'ImageGeometry' o[geom_label].attrs['GeometryName'] = 'ImageGeometry'
o[geom_label].attrs['GeometryTypeName'] = 'ImageGeometry' o[geom_label].attrs['GeometryTypeName'] = 'ImageGeometry'
o[geom_label].attrs['GeometryType'] = np.array([0],np.uint32) o[geom_label].attrs['GeometryType'] = np.array([0],np.uint32)
o[geom_label].attrs['SpatialDimensionality'] = np.array([3],np.uint32) o[geom_label].attrs['SpatialDimensionality'] = np.array([3],np.uint32)
o[geom_label].attrs['UnitDimensionality'] = np.array([3],np.uint32) o[geom_label].attrs['UnitDimensionality'] = np.array([3],np.uint32)