ensure closing of file
This commit is contained in:
Martin Diehl
parent
b5e34e7949
commit
5923aa2493
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@ -1989,63 +1989,63 @@ class Result:
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cell_orientation[at_cell_ph[c][label],:] = \
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Rotation(data[in_data_ph[c][label],:]).as_Euler_angles().astype(np.float32)
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except ValueError:
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except KeyError:
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crystal_structure.append(999)
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phase_ID_array[at_cell_ph[c][label]] = count + 1
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o = h5py.File(f'{out_dir}/{self.fname.stem}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}.dream3d','w')
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add_attribute(o,'FileVersion','7.0')
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with h5py.File(f'{out_dir}/{self.fname.stem}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}.dream3d','w') as f_out:
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add_attribute(f_out,'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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f_out.create_group(g)
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data_container = create_and_open(o,'DataContainers/SyntheticVolumeDataContainer')
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data_container = create_and_open(f_out,'DataContainers/SyntheticVolumeDataContainer')
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cell = create_and_open(data_container,'CellData')
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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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cell = create_and_open(data_container,'CellData')
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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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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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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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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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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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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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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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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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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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cell_ensemble = create_and_open(data_container,'CellEnsembleData')
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cell_ensemble = create_and_open(data_container,'CellEnsembleData')
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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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cell_ensemble.create_dataset(name='PhaseName',data = phase_name_list, dtype=h5py.Datatype(tid))
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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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cell_ensemble.create_dataset(name='PhaseName',data = phase_name_list, dtype=h5py.Datatype(tid))
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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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for group in ['CrystalStructures','PhaseTypes','PhaseName']:
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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], 'TupleDimensions', np.array([len(self.phases) + 1],np.uint64))
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for group in ['CrystalStructures','PhaseTypes']:
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add_attribute(cell_ensemble[group], 'ObjectType', 'DataArray<uint32_t>')
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add_attribute(cell_ensemble['PhaseName'], 'ObjectType', 'StringDataArray')
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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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for group in ['CrystalStructures','PhaseTypes','PhaseName']:
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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], 'TupleDimensions', np.array([len(self.phases) + 1],np.uint64))
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for group in ['CrystalStructures','PhaseTypes']:
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add_attribute(cell_ensemble[group], 'ObjectType', 'DataArray<uint32_t>')
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add_attribute(cell_ensemble['PhaseName'], 'ObjectType', 'StringDataArray')
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geom = create_and_open(data_container,'_SIMPL_GEOMETRY')
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geom['DIMENSIONS'] = np.array(self.cells,np.int64)
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geom['ORIGIN'] = np.array(self.origin,np.float32)
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geom['SPACING'] = np.float32(self.size/self.cells)
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names = ['GeometryName', 'GeometryTypeName','GeometryType','SpatialDimensionality','UnitDimensionality']
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values = ['ImageGeometry','ImageGeometry',np.array([0],np.uint32),np.array([3],np.uint32),np.array([3],np.uint32)]
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for name,value in zip(names,values):
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add_attribute(geom,name,value)
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geom = create_and_open(data_container,'_SIMPL_GEOMETRY')
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geom['DIMENSIONS'] = np.array(self.cells,np.int64)
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geom['ORIGIN'] = np.array(self.origin,np.float32)
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geom['SPACING'] = np.float32(self.size/self.cells)
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names = ['GeometryName', 'GeometryTypeName','GeometryType','SpatialDimensionality','UnitDimensionality']
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values = ['ImageGeometry','ImageGeometry', np.array([0],np.uint32)] + [np.array([3],np.uint32)]*2
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for name,value in zip(names,values):
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add_attribute(geom,name,value)
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def export_DADF5(self,
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