diff --git a/python/damask/_result.py b/python/damask/_result.py index 379ca24fa..d02811366 100644 --- a/python/damask/_result.py +++ b/python/damask/_result.py @@ -62,41 +62,6 @@ def _empty_like(dataset: np.ma.core.MaskedArray, fill_value = fill_float if dataset.dtype in np.sctypes['float'] else fill_int, mask = True) -class AttributeManagerNullterm(h5py.AttributeManager): - """ - Attribute management for DREAM.3D hdf5 files. - - String attribute values are stored as fixed-length string with NULLTERM - - References - ---------- - https://stackoverflow.com/questions/38267076 - https://stackoverflow.com/questions/52750232 - - """ - - def create(self, name, data, shape=None, dtype=None): - if isinstance(data,str): - tid = h5py.h5t.C_S1.copy() - tid.set_size(len(data + ' ')) - super().create(name=name,data=data+' ',dtype = h5py.Datatype(tid)) - else: - super().create(name=name,data=data,shape=shape,dtype=dtype) - -class ResetAttributeManager(h5py.AttributeManager): - """ - Reset the attribute management for DREAM.3D hdf5 files. - - References - ---------- - https://stackoverflow.com/questions/38267076 - https://stackoverflow.com/questions/52750232 - - """ - - def create(self, name, data, shape=None, dtype=None): - super().create(name=name,data=data,shape=shape,dtype=dtype) - class Result: """ @@ -1983,7 +1948,15 @@ class Result: Directory to save DREAM3D files. Will be created if non-existent. """ - h5py._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch' + def add_attribute(obj,name,data): + """DREAM.3D requires fixed length string.""" + if isinstance(data,str): + tid = h5py.h5t.C_S1.copy() + tid.set_size(len(data)+1) + obj.attrs.create(name,data,dtype=h5py.Datatype(tid)) + else: + obj.attrs.create(name,data) + if self.N_constituents != 1 or not self.structured: raise TypeError('DREAM3D output requires structured grid with single constituent.') @@ -2000,16 +1973,15 @@ class Result: 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)) + cell_orientation = 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'])])) - lattice_dict[label] = f['/'.join([inc,'phase',label,'mechanical/O'])].attrs['lattice'] - cell_orientation_array[at_cell_ph[c][label],:] = \ - Rotation(data[in_data_ph[c][label],:]).as_Euler_angles() - # Dream3D handles euler angles better + data = _read(f['/'.join([inc,'phase',label,'mechanical/O'])]) + lattice_dict[label] = data.dtype.metadata['lattice'] + cell_orientation[at_cell_ph[c][label],:] = \ + Rotation(data[in_data_ph[c][label],:]).as_Euler_angles().astype(np.float32) except ValueError: print("Orientation data is not present") exit() @@ -2017,41 +1989,34 @@ class Result: phase_ID_array[at_cell_ph[c][label]] = count + 1 o = h5py.File(f'{out_dir}/{self.fname.stem}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}.dream3d','w') - o.attrs['DADF5toDREAM3D'] = '1.0' - o.attrs['FileVersion'] = '7.0' + add_attribute(o,'FileVersion','7.0') - for g in ['DataContainerBundles','Pipeline']: # empty groups (needed) - o.create_group(g) + for g in ['DataContainerBundles','Pipeline']: # empty groups (needed) + o.create_group(g) data_container_label = 'DataContainers/SyntheticVolumeDataContainer' cell_data_label = data_container_label + '/CellData' - # Data phases - o[cell_data_label + '/Phases'] = np.reshape(phase_ID_array, \ - tuple(np.flip(self.cells))+(1,)) + o[cell_data_label + '/Phases'] = np.reshape(phase_ID_array,tuple(np.flip(self.cells))+(1,)) + o[cell_data_label + '/EulerAngles'] = cell_orientation.reshape(tuple(np.flip(self.cells))+(3,)) - # Data eulers - orientation_data = cell_orientation_array.astype(np.float32) - o[cell_data_label + '/EulerAngles'] = orientation_data.reshape(tuple(np.flip(self.cells))+(3,)) - - # Attributes to CellData group o[cell_data_label].attrs['AttributeMatrixType'] = np.array([3],np.uint32) o[cell_data_label].attrs['TupleDimensions'] = np.array(self.cells,np.uint64) # Common Attributes for groups in CellData for dataset in ['/Phases','/EulerAngles']: - o[cell_data_label + dataset].attrs['DataArrayVersion'] = np.array([2],np.int32) - o[cell_data_label + dataset].attrs['Tuple Axis Dimensions'] = 'x={},y={},z={}'.format(*np.array(self.cells)) + add_attribute(o[cell_data_label + dataset],'DataArrayVersion',np.array([2],np.int32)) + add_attribute(o[cell_data_label + dataset],'Tuple Axis Dimensions','x={},y={},z={}'.format(*np.array(self.cells))) # phase attributes - o[cell_data_label + '/Phases'].attrs['ComponentDimensions'] = np.array([1],np.uint64) - o[cell_data_label + '/Phases'].attrs['ObjectType'] = 'DataArray' - o[cell_data_label + '/Phases'].attrs['TupleDimensions'] = np.array(self.cells,np.uint64) + add_attribute(o[cell_data_label + '/Phases'], 'ComponentDimensions', np.array([1],np.uint64)) + add_attribute(o[cell_data_label + '/Phases'], 'ObjectType', 'DataArray') + add_attribute(o[cell_data_label + '/Phases'], 'TupleDimensions', np.array(self.cells,np.uint64)) # Eulers attributes - o[cell_data_label + '/EulerAngles'].attrs['ComponentDimensions'] = np.array([3],np.uint64) - o[cell_data_label + '/EulerAngles'].attrs['ObjectType'] = 'DataArray' - o[cell_data_label + '/EulerAngles'].attrs['TupleDimensions'] = np.array(self.cells,np.uint64) + add_attribute(o[cell_data_label + '/EulerAngles'], 'ComponentDimensions', np.array([3],np.uint64)) + add_attribute(o[cell_data_label + '/EulerAngles'], 'ObjectType', 'DataArray') + add_attribute(o[cell_data_label + '/EulerAngles'], 'TupleDimensions', np.array(self.cells,np.uint64)) # Create EnsembleAttributeMatrix ensemble_label = data_container_label + '/CellEnsembleData' @@ -2081,17 +2046,17 @@ class Result: # Attributes for data in Ensemble matrix for group in ['CrystalStructures','PhaseTypes']: - 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['DataArrayVersion'] = np.array([2],np.int32) - o[ensemble_label+'/'+group].attrs['ObjectType'] = 'DataArray' - o[ensemble_label+'/'+group].attrs['TupleDimensions'] = np.array([len(self.phases) + 1],np.uint64) + add_attribute(o[ensemble_label+'/'+group], 'ComponentDimensions', np.array([1],np.uint64)) + add_attribute(o[ensemble_label+'/'+group], 'Tuple Axis Dimensions', f'x={len(self.phases)+1}') + add_attribute(o[ensemble_label+'/'+group], 'DataArrayVersion', np.array([2],np.int32)) + add_attribute(o[ensemble_label+'/'+group], 'ObjectType', 'DataArray') + add_attribute(o[ensemble_label+'/'+group], 'TupleDimensions', np.array([len(self.phases) + 1],np.uint64)) - o[ensemble_label+'/PhaseName'].attrs['ComponentDimensions'] = np.array([1],np.uint64) - o[ensemble_label+'/PhaseName'].attrs['Tuple Axis Dimensions'] = f'x={len(self.phases)+1}' - o[ensemble_label+'/PhaseName'].attrs['DataArrayVersion'] = np.array([2],np.int32) - o[ensemble_label+'/PhaseName'].attrs['ObjectType'] = 'StringDataArray' - o[ensemble_label+'/PhaseName'].attrs['TupleDimensions'] = np.array([len(self.phases) + 1],np.uint64) + add_attribute(o[ensemble_label+'/PhaseName'], 'ComponentDimensions', np.array([1],np.uint64)) + add_attribute(o[ensemble_label+'/PhaseName'], 'Tuple Axis Dimensions', f'x={len(self.phases)+1}') + add_attribute(o[ensemble_label+'/PhaseName'], 'DataArrayVersion', np.array([2],np.int32)) + add_attribute(o[ensemble_label+'/PhaseName'], 'ObjectType', 'StringDataArray') + add_attribute(o[ensemble_label+'/PhaseName'], 'TupleDimensions', np.array([len(self.phases) + 1],np.uint64)) # Create geometry info geom_label = data_container_label + '/_SIMPL_GEOMETRY' @@ -2100,12 +2065,11 @@ class Result: o[geom_label + '/ORIGIN'] = np.float32(np.zeros(3)) o[geom_label + '/SPACING'] = np.float32(dx) - o[geom_label].attrs['GeometryName'] = 'ImageGeometry' - o[geom_label].attrs['GeometryTypeName'] = 'ImageGeometry' - o[geom_label].attrs['GeometryType'] = np.array([0],np.uint32) - o[geom_label].attrs['SpatialDimensionality'] = np.array([3],np.uint32) - o[geom_label].attrs['UnitDimensionality'] = np.array([3],np.uint32) - h5py._hl.attrs.AttributeManager = ResetAttributeManager # Reset the attribute manager to original: + add_attribute(o[geom_label], 'GeometryName', 'ImageGeometry') + add_attribute(o[geom_label], 'GeometryTypeName', 'ImageGeometry') + add_attribute(o[geom_label], 'GeometryType', np.array([0],np.uint32)) + add_attribute(o[geom_label], 'SpatialDimensionality', np.array([3],np.uint32)) + add_attribute(o[geom_label], 'UnitDimensionality', np.array([3],np.uint32)) def export_DADF5(self,