simplified
This commit is contained in:
Martin Diehl
parent
213e8aa4be
commit
ffd3cfe951
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@ -1957,6 +1957,10 @@ class Result:
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else:
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obj.attrs.create(name,data)
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def create_and_open(obj,name):
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obj.create_group(name)
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return obj[name]
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if self.N_constituents != 1 or not self.structured:
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raise TypeError('DREAM3D output requires structured grid with single constituent.')
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@ -1994,32 +1998,30 @@ class Result:
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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 = create_and_open(o,'DataContainers/SyntheticVolumeDataContainer')
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cell = create_and_open(data_container,'CellData')
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o[cell_data_label + '/Phases'] = np.reshape(phase_ID_array,tuple(np.flip(self.cells))+(1,))
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o[cell_data_label + '/EulerAngles'] = cell_orientation.reshape(tuple(np.flip(self.cells))+(3,))
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cell['Phases'] = np.reshape(phase_ID_array,tuple(np.flip(self.cells))+(1,))
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cell['EulerAngles'] = cell_orientation.reshape(tuple(np.flip(self.cells))+(3,))
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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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add_attribute(cell,'AttributeMatrixType',np.array([3],np.uint32))
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add_attribute(cell,'TupleDimensions', np.array(self.cells,np.uint64))
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# Common Attributes for groups in CellData
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for dataset in ['/Phases','/EulerAngles']:
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add_attribute(o[cell_data_label + dataset],'DataArrayVersion',np.array([2],np.int32))
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add_attribute(o[cell_data_label + dataset],'Tuple Axis Dimensions','x={},y={},z={}'.format(*np.array(self.cells)))
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for dataset in ['Phases','EulerAngles']:
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add_attribute(cell[dataset],'DataArrayVersion',np.array([2],np.int32))
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add_attribute(cell[dataset],'Tuple Axis Dimensions','x={},y={},z={}'.format(*np.array(self.cells)))
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add_attribute(cell[dataset],'TupleDimensions', np.array(self.cells,np.uint64))
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# phase attributes
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add_attribute(o[cell_data_label + '/Phases'], 'ComponentDimensions', np.array([1],np.uint64))
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add_attribute(o[cell_data_label + '/Phases'], 'ObjectType', 'DataArray<int32_t>')
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add_attribute(o[cell_data_label + '/Phases'], 'TupleDimensions', np.array(self.cells,np.uint64))
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add_attribute(cell['Phases'], 'ComponentDimensions', np.array([1],np.uint64))
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add_attribute(cell['Phases'], 'ObjectType', 'DataArray<int32_t>')
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# Eulers attributes
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add_attribute(o[cell_data_label + '/EulerAngles'], 'ComponentDimensions', np.array([3],np.uint64))
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add_attribute(o[cell_data_label + '/EulerAngles'], 'ObjectType', 'DataArray<float>')
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add_attribute(o[cell_data_label + '/EulerAngles'], 'TupleDimensions', np.array(self.cells,np.uint64))
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add_attribute(cell['EulerAngles'], 'ComponentDimensions', np.array([3],np.uint64))
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add_attribute(cell['EulerAngles'], 'ObjectType', 'DataArray<float>')
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# Create EnsembleAttributeMatrix
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ensemble_label = data_container_label + '/CellEnsembleData'
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cell_ensemble = create_and_open(data_container,'CellEnsembleData')
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# Map to DREAM.3D IDs
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crystal_structure = [999]
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@ -2031,45 +2033,44 @@ class Result:
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elif lattice_dict[label] in ['tI']:
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crystal_structure.append(8)
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o[ensemble_label + '/CrystalStructures'] = np.array(crystal_structure,np.uint32).reshape(-1,1)
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o[ensemble_label + '/PhaseTypes'] = np.array([999] + [0]*len(self.phases),np.uint32).reshape(-1,1)
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phase_name_list = ['Unknown Phase Type']
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phase_name_list.extend(i for i in self.visible['phases'])
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cell_ensemble['CrystalStructures'] = np.array(crystal_structure,np.uint32).reshape(-1,1)
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cell_ensemble['PhaseTypes'] = np.array([999] + [0]*len(self.phases),np.uint32).reshape(-1,1)
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phase_name_list = ['Unknown Phase Type'] + [p for p in self.visible['phases']]
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tid = h5py.h5t.C_S1.copy()
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tid.set_size(h5py.h5t.VARIABLE)
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tid.set_cset(h5py.h5t.CSET_ASCII)
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o[ensemble_label].create_dataset(name='PhaseName',data = phase_name_list, dtype=h5py.Datatype(tid))
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cell_ensemble.create_dataset(name='PhaseName',data = phase_name_list, dtype=h5py.Datatype(tid))
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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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cell_ensemble.attrs['AttributeMatrixType'] = np.array([11],np.uint32)
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cell_ensemble.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']:
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add_attribute(o[ensemble_label+'/'+group], 'ComponentDimensions', np.array([1],np.uint64))
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add_attribute(o[ensemble_label+'/'+group], 'Tuple Axis Dimensions', f'x={len(self.phases)+1}')
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add_attribute(o[ensemble_label+'/'+group], 'DataArrayVersion', np.array([2],np.int32))
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add_attribute(o[ensemble_label+'/'+group], 'ObjectType', 'DataArray<uint32_t>')
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add_attribute(o[ensemble_label+'/'+group], 'TupleDimensions', np.array([len(self.phases) + 1],np.uint64))
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add_attribute(cell_ensemble[group], 'ComponentDimensions', np.array([1],np.uint64))
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add_attribute(cell_ensemble[group], 'Tuple Axis Dimensions', f'x={len(self.phases)+1}')
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add_attribute(cell_ensemble[group], 'DataArrayVersion', np.array([2],np.int32))
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add_attribute(cell_ensemble[group], 'ObjectType', 'DataArray<uint32_t>')
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add_attribute(cell_ensemble[group], 'TupleDimensions', np.array([len(self.phases) + 1],np.uint64))
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add_attribute(o[ensemble_label+'/PhaseName'], 'ComponentDimensions', np.array([1],np.uint64))
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add_attribute(o[ensemble_label+'/PhaseName'], 'Tuple Axis Dimensions', f'x={len(self.phases)+1}')
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add_attribute(o[ensemble_label+'/PhaseName'], 'DataArrayVersion', np.array([2],np.int32))
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add_attribute(o[ensemble_label+'/PhaseName'], 'ObjectType', 'StringDataArray')
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add_attribute(o[ensemble_label+'/PhaseName'], 'TupleDimensions', np.array([len(self.phases) + 1],np.uint64))
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add_attribute(cell_ensemble['PhaseName'], 'ComponentDimensions', np.array([1],np.uint64))
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add_attribute(cell_ensemble['PhaseName'], 'Tuple Axis Dimensions', f'x={len(self.phases)+1}')
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add_attribute(cell_ensemble['PhaseName'], 'DataArrayVersion', np.array([2],np.int32))
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add_attribute(cell_ensemble['PhaseName'], 'ObjectType', 'StringDataArray')
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add_attribute(cell_ensemble['PhaseName'], '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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geom = create_and_open(data_container,'_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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geom['DIMENSIONS'] = np.int64(np.array(self.cells))
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geom['ORIGIN'] = np.float32(np.zeros(3))
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geom['SPACING'] = np.float32(dx)
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add_attribute(o[geom_label], 'GeometryName', 'ImageGeometry')
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add_attribute(o[geom_label], 'GeometryTypeName', 'ImageGeometry')
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add_attribute(o[geom_label], 'GeometryType', np.array([0],np.uint32))
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add_attribute(o[geom_label], 'SpatialDimensionality', np.array([3],np.uint32))
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add_attribute(o[geom_label], 'UnitDimensionality', np.array([3],np.uint32))
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add_attribute(geom, 'GeometryName', 'ImageGeometry')
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add_attribute(geom, 'GeometryTypeName', 'ImageGeometry')
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add_attribute(geom, 'GeometryType', np.array([0],np.uint32))
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add_attribute(geom, 'SpatialDimensionality', np.array([3],np.uint32))
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add_attribute(geom, 'UnitDimensionality', np.array([3],np.uint32))
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def export_DADF5(self,
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