From f619cf4ff20bd4769aeba2300ecb23493ce9bf01 Mon Sep 17 00:00:00 2001 From: Vitesh Shah Date: Thu, 6 Apr 2023 20:56:42 +0200 Subject: [PATCH] making export DREAM3D compatible with results class --- python/damask/_result.py | 145 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 145 insertions(+) diff --git a/python/damask/_result.py b/python/damask/_result.py index 83c1e8298..1d782c905 100644 --- a/python/damask/_result.py +++ b/python/damask/_result.py @@ -63,6 +63,30 @@ 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) + + +h5py._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch' + class Result: """ Add data to and export data from a DADF5 file. @@ -1919,6 +1943,127 @@ class Result: v.save(vtk_dir/f'{self.fname.stem}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}', parallel=parallel) + + def export_DREAM3D(self): + """ + Export the visible components to DREAM3D compatible files. + + One DREAM3D file per visible increment is created. + The DREAM3D file is based on HDF5 file format. + Without any regridding. + Considers the original grid from DAMASK. + Needs orientation data, O, present in the file. + + Parameters + ---------- + + """ + Crystal_structures = {'fcc': 1, + 'bcc': 1, + 'hcp': 0, + 'bct': 7, + 'ort': 6} #TODO: is bct Tetragonal low/Tetragonal high? + Phase_types = {'Primary': 0} #further additions to these can be done by looking at 'Create Ensemble Info' filter, other options could be 'Precipitate' and so on. + + dx = self.size/self.cells + + for inc in util.show_progress(self.visible['increments']): + for label in self.visible['phases']: + try: + data = ma.array(_read(f['/'.join([inc,'phase',label,'mechanical/O'])])) + 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. + + 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 + + at_cell_ph,in_data_ph,at_cell_ho,in_data_ho = self._mappings() + for c in range(self.N_constituents): + for ph in self.phases: + cell_orientation_array[at_cell_ph[c][ph],:] = data[,:]# need to figure out these mappings a bit + cell_orientation_array[in_data_ph[ph],:] = # need to figure out these mappings a bit + phase_ID_array[phase_index] = count + 1 #need to figure out these mappings a bit + + job_file_no_ext = os.path.splitext(self.fname)[0] + o = h5py.File(f'{job_file_no_ext}_increment{inc}.dream3D','w') + o.attrs['DADF5toDREAM3D'] = '1.0' + o.attrs['FileVersion'] = '7.0' + + 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,)) + + # Data eulers + orientation_data = cell_orientation_array.astype(np.float32) + o[cell_data_label + '/Eulers'] = 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 group in ['/Phases','/Eulers']: + 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)) + + # 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) + + # Eulers attributes + o[cell_data_label + '/Eulers'].attrs['ComponentDimensions'] = np.array([3],np.uint64) + o[cell_data_label + '/Eulers'].attrs['ObjectType'] = 'DataArray' + o[cell_data_label + '/Eulers'].attrs['TupleDimensions'] = np.array(self.cells,np.uint64) + + # Create EnsembleAttributeMatrix + ensemble_label = data_container_label + '/CellEnsembleData' + + # Data CrystalStructures + o[ensemble_label + '/CrystalStructures'] = np.uint32(np.array([999] + [1]*len(self.phases))) + # 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 + 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 + # there can be precipitates etc as well + # Attributes Ensemble Matrix + o[ensemble_label].attrs['AttributeMatrixType'] = np.array([11],np.uint32) + o[ensemble_label].attrs['TupleDimensions'] = np.array([len(self.phases) + 1], np.uint64) + + # 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 + 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) + + # Create geometry info + geom_label = data_container_label + '/_SIMPL_GEOMETRY' + + o[geom_label + '/DIMENSIONS'] = np.int64(np.array(self.cells)) + 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) + + + + + + + def export_DADF5(self, fname,