From b5b6c2d69557860c392de96547c251537c97f7ab Mon Sep 17 00:00:00 2001 From: Vitesh Shah Date: Thu, 4 May 2023 11:07:26 +0200 Subject: [PATCH] fixed typos and other python warnings --- python/damask/_result.py | 74 +++++++++++++++++-------------------- python/tests/test_Result.py | 4 +- 2 files changed, 36 insertions(+), 42 deletions(-) diff --git a/python/damask/_result.py b/python/damask/_result.py index be09cbf35..5e132d6a8 100644 --- a/python/damask/_result.py +++ b/python/damask/_result.py @@ -1944,32 +1944,31 @@ 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, target_dir: Union[None, str, Path] = None): """ - Export the visible components to DREAM3D compatible files. - + 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. - + 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 ---------- target_dir : str or pathlib.Path, optional Directory to save DREAM3D files. Will be created if non-existent. + """ - 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. + 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. + # also crystal structures be added in a similar way dx = self.size/self.cells - + at_cell_ph,in_data_ph,at_cell_ho,in_data_ho = self._mappings() dream_dir = Path.cwd() if target_dir is None else Path(target_dir) @@ -1984,29 +1983,29 @@ class Result: try: data = ma.array(_read(f['/'.join([inc,'phase',label,'mechanical/O'])])) cell_orientation_array[at_cell_ph[c][label],:] = \ - Rotation(data[in_data_ph[c][label],:]).as_Euler_angles() + Rotation(data[in_data_ph[c][label],:]).as_Euler_angles() # Dream3D handles euler angles better - except ValueError: #check if the exception is correct + except ValueError: print("Orientation data is not present") - exit() # need to check if such a statement would really work. + exit() # need to check if such a statement would really work. - phase_ID_array[at_cell_ph[c][label]] = count + 1 + phase_ID_array[at_cell_ph[c][label]] = count + 1 - job_file_no_ext = self.fname.stem + job_file_no_ext = self.fname.stem o = h5py.File(f'{dream_dir}/{job_file_no_ext}_{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' + + 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 + '/EulerAngles'] = orientation_data.reshape(tuple(np.flip(self.cells))+(3,)) @@ -2024,20 +2023,22 @@ class Result: 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 + '/EulerAngles'].attrs['ComponentDimensions'] = np.array([3],np.uint64) - o[cell_data_label + '/EulerAngles'].attrs['ObjectType'] = 'DataArray' + o[cell_data_label + '/EulerAngles'].attrs['ObjectType'] = 'DataArray' o[cell_data_label + '/EulerAngles'].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)) + # 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 @@ -2054,23 +2055,16 @@ class Result: # 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) - - - - - - - + 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, diff --git a/python/tests/test_Result.py b/python/tests/test_Result.py index b81b0ad0d..35adfb16f 100644 --- a/python/tests/test_Result.py +++ b/python/tests/test_Result.py @@ -499,13 +499,13 @@ class TestResult: for dataset in ['DIMENSIONS','ORIGIN','SPACING']: results_val = np.array(results_file[geom_label + '/' + dataset]) ref_val = np.array(ref_file[geom_label + '/' + dataset]) - if not np.array_equal(ref_val,actual_val): + if not np.array_equal(ref_val,results_val): error_messages.append(f'The {dataset} values are incorrect') for attrs in ['GeometryName','GeometryTypeName','GeometryType','SpatialDimensionality','UnitDimensionality']: ref_value = ref_file[geom_label].attrs[attrs] actual_val = results_file[geom_label].attrs[attrs] - if not np.array_equal(ref_val,actual_val): + if not np.array_equal(ref_value,actual_val): error_messages.append("Geometry attributes do not match") assert not error_messages