fixed typos and other python warnings
This commit is contained in:
Vitesh Shah
parent
8de19f0c3b
commit
b5b6c2d695
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@ -1944,32 +1944,31 @@ class Result:
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v.save(vtk_dir/f'{self.fname.stem}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}',
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parallel=parallel)
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def export_DREAM3D(self,
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target_dir: Union[None, str, Path] = None):
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"""
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Export the visible components to DREAM3D compatible files.
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Export the visible components to DREAM3D compatible files.
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One DREAM3D file per visible increment is created.
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The DREAM3D file is based on HDF5 file format.
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Without any regridding.
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Considers the original grid from DAMASK.
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Needs orientation data, O, present in the file.
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The DREAM3D file is based on HDF5 file format.
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Without any regridding.
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Considers the original grid from DAMASK.
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Needs orientation data, O, present in the file.
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Parameters
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----------
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target_dir : str or pathlib.Path, optional
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Directory to save DREAM3D files. Will be created if non-existent.
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"""
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Crystal_structures = {'fcc': 1,
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'bcc': 1,
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'hcp': 0,
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'bct': 7,
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'ort': 6} #TODO: is bct Tetragonal low/Tetragonal high?
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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.
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Phase_types = {'Primary': 0}
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#further additions to these can be done by looking at 'Create Ensemble Info' filter
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# other options could be 'Precipitate' and so on.
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# also crystal structures be added in a similar way
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dx = self.size/self.cells
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at_cell_ph,in_data_ph,at_cell_ho,in_data_ho = self._mappings()
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dream_dir = Path.cwd() if target_dir is None else Path(target_dir)
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@ -1984,29 +1983,29 @@ class Result:
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try:
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data = ma.array(_read(f['/'.join([inc,'phase',label,'mechanical/O'])]))
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cell_orientation_array[at_cell_ph[c][label],:] = \
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Rotation(data[in_data_ph[c][label],:]).as_Euler_angles()
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Rotation(data[in_data_ph[c][label],:]).as_Euler_angles()
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# Dream3D handles euler angles better
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except ValueError: #check if the exception is correct
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except ValueError:
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print("Orientation data is not present")
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exit() # need to check if such a statement would really work.
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exit() # need to check if such a statement would really work.
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phase_ID_array[at_cell_ph[c][label]] = count + 1
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phase_ID_array[at_cell_ph[c][label]] = count + 1
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job_file_no_ext = self.fname.stem
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job_file_no_ext = self.fname.stem
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o = h5py.File(f'{dream_dir}/{job_file_no_ext}_{inc}.dream3d','w')
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o.attrs['DADF5toDREAM3D'] = '1.0'
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o.attrs['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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data_container_label = 'DataContainers/SyntheticVolumeDataContainer'
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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 phases
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o[cell_data_label + '/Phases'] = np.reshape(phase_ID_array, \
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tuple(np.flip(self.cells))+(1,))
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# Data eulers
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orientation_data = cell_orientation_array.astype(np.float32)
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o[cell_data_label + '/EulerAngles'] = orientation_data.reshape(tuple(np.flip(self.cells))+(3,))
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@ -2024,20 +2023,22 @@ class Result:
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o[cell_data_label + '/Phases'].attrs['ComponentDimensions'] = np.array([1],np.uint64)
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o[cell_data_label + '/Phases'].attrs['ObjectType'] = 'DataArray<int32_t>'
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o[cell_data_label + '/Phases'].attrs['TupleDimensions'] = np.array(self.cells,np.uint64)
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# Eulers attributes
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o[cell_data_label + '/EulerAngles'].attrs['ComponentDimensions'] = np.array([3],np.uint64)
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o[cell_data_label + '/EulerAngles'].attrs['ObjectType'] = 'DataArray<float>'
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o[cell_data_label + '/EulerAngles'].attrs['ObjectType'] = 'DataArray<float>'
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o[cell_data_label + '/EulerAngles'].attrs['TupleDimensions'] = np.array(self.cells,np.uint64)
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# Create EnsembleAttributeMatrix
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ensemble_label = data_container_label + '/CellEnsembleData'
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# Data CrystalStructures
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o[ensemble_label + '/CrystalStructures'] = np.uint32(np.array([999] + [1]*len(self.phases)))
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# assuming only cubic crystal structures
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# Damask can give the crystal structure info but need to look into dream3d which crystal structure corresponds to which number
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o[ensemble_label + '/PhaseTypes'] = np.uint32(np.array([999] + [Phase_types['Primary']]*len(self.phases))).reshape((len(self.phases)+1,1))
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# Damask can give the crystal structure info
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# but need to look into dream3d which crystal structure corresponds to which number
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o[ensemble_label + '/PhaseTypes'] = np.uint32(np.array([999] + [Phase_types['Primary']]*len(self.phases)))\
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.reshape((len(self.phases)+1,1))
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# also assuming Primary phases
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# there can be precipitates etc as well
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# Attributes Ensemble Matrix
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@ -2054,23 +2055,16 @@ class Result:
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# Create geometry info
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geom_label = data_container_label + '/_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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o[geom_label].attrs['GeometryName'] = 'ImageGeometry'
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o[geom_label].attrs['GeometryTypeName'] = 'ImageGeometry'
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o[geom_label].attrs['GeometryType'] = np.array([0],np.uint32)
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o[geom_label].attrs['SpatialDimensionality'] = np.array([3],np.uint32)
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o[geom_label].attrs['UnitDimensionality'] = np.array([3],np.uint32)
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o[geom_label].attrs['GeometryType'] = np.array([0],np.uint32)
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o[geom_label].attrs['SpatialDimensionality'] = np.array([3],np.uint32)
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o[geom_label].attrs['UnitDimensionality'] = np.array([3],np.uint32)
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def export_DADF5(self,
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fname,
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@ -499,13 +499,13 @@ class TestResult:
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for dataset in ['DIMENSIONS','ORIGIN','SPACING']:
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results_val = np.array(results_file[geom_label + '/' + dataset])
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ref_val = np.array(ref_file[geom_label + '/' + dataset])
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if not np.array_equal(ref_val,actual_val):
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if not np.array_equal(ref_val,results_val):
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error_messages.append(f'The {dataset} values are incorrect')
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for attrs in ['GeometryName','GeometryTypeName','GeometryType','SpatialDimensionality','UnitDimensionality']:
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ref_value = ref_file[geom_label].attrs[attrs]
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actual_val = results_file[geom_label].attrs[attrs]
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if not np.array_equal(ref_val,actual_val):
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if not np.array_equal(ref_value,actual_val):
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error_messages.append("Geometry attributes do not match")
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assert not error_messages
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