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