avoid monkey patching
This commit is contained in:
Martin Diehl
parent
7a5e08c14d
commit
213e8aa4be
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@ -62,41 +62,6 @@ def _empty_like(dataset: np.ma.core.MaskedArray,
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fill_value = fill_float if dataset.dtype in np.sctypes['float'] else fill_int,
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mask = True)
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class AttributeManagerNullterm(h5py.AttributeManager):
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"""
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Attribute management for DREAM.3D hdf5 files.
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String attribute values are stored as fixed-length string with NULLTERM
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References
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----------
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https://stackoverflow.com/questions/38267076
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https://stackoverflow.com/questions/52750232
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"""
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def create(self, name, data, shape=None, dtype=None):
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if isinstance(data,str):
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tid = h5py.h5t.C_S1.copy()
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tid.set_size(len(data + ' '))
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super().create(name=name,data=data+' ',dtype = h5py.Datatype(tid))
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else:
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super().create(name=name,data=data,shape=shape,dtype=dtype)
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class ResetAttributeManager(h5py.AttributeManager):
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"""
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Reset the attribute management for DREAM.3D hdf5 files.
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References
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----------
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https://stackoverflow.com/questions/38267076
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https://stackoverflow.com/questions/52750232
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"""
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def create(self, name, data, shape=None, dtype=None):
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super().create(name=name,data=data,shape=shape,dtype=dtype)
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class Result:
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"""
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@ -1983,7 +1948,15 @@ class Result:
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Directory to save DREAM3D files. Will be created if non-existent.
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"""
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h5py._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch'
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def add_attribute(obj,name,data):
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"""DREAM.3D requires fixed length string."""
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if isinstance(data,str):
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tid = h5py.h5t.C_S1.copy()
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tid.set_size(len(data)+1)
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obj.attrs.create(name,data,dtype=h5py.Datatype(tid))
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else:
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obj.attrs.create(name,data)
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if self.N_constituents != 1 or not self.structured:
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raise TypeError('DREAM3D output requires structured grid with single constituent.')
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@ -2000,16 +1973,15 @@ class Result:
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with h5py.File(self.fname,'r') as f:
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for inc in util.show_progress(self.visible['increments']):
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cell_orientation_array = np.zeros((np.prod(self.cells),3))
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cell_orientation = np.zeros((np.prod(self.cells),3))
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phase_ID_array = np.zeros((np.prod(self.cells)),dtype=np.int32) #need to reshape it later
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for c in range(self.N_constituents):
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for count,label in enumerate(self.visible['phases']):
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try:
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data = ma.array(_read(f['/'.join([inc,'phase',label,'mechanical/O'])]))
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lattice_dict[label] = f['/'.join([inc,'phase',label,'mechanical/O'])].attrs['lattice']
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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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# Dream3D handles euler angles better
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data = _read(f['/'.join([inc,'phase',label,'mechanical/O'])])
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lattice_dict[label] = data.dtype.metadata['lattice']
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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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print("Orientation data is not present")
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exit()
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@ -2017,41 +1989,34 @@ class Result:
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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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o.attrs['DADF5toDREAM3D'] = '1.0'
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o.attrs['FileVersion'] = '7.0'
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add_attribute(o,'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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o.create_group(g)
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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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o[cell_data_label + '/Phases'] = np.reshape(phase_ID_array,tuple(np.flip(self.cells))+(1,))
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o[cell_data_label + '/EulerAngles'] = cell_orientation.reshape(tuple(np.flip(self.cells))+(3,))
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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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# Attributes to CellData group
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o[cell_data_label].attrs['AttributeMatrixType'] = np.array([3],np.uint32)
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o[cell_data_label].attrs['TupleDimensions'] = np.array(self.cells,np.uint64)
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# Common Attributes for groups in CellData
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for dataset in ['/Phases','/EulerAngles']:
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o[cell_data_label + dataset].attrs['DataArrayVersion'] = np.array([2],np.int32)
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o[cell_data_label + dataset].attrs['Tuple Axis Dimensions'] = 'x={},y={},z={}'.format(*np.array(self.cells))
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add_attribute(o[cell_data_label + dataset],'DataArrayVersion',np.array([2],np.int32))
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add_attribute(o[cell_data_label + dataset],'Tuple Axis Dimensions','x={},y={},z={}'.format(*np.array(self.cells)))
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# phase attributes
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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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add_attribute(o[cell_data_label + '/Phases'], 'ComponentDimensions', np.array([1],np.uint64))
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add_attribute(o[cell_data_label + '/Phases'], 'ObjectType', 'DataArray<int32_t>')
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add_attribute(o[cell_data_label + '/Phases'], '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['TupleDimensions'] = np.array(self.cells,np.uint64)
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add_attribute(o[cell_data_label + '/EulerAngles'], 'ComponentDimensions', np.array([3],np.uint64))
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add_attribute(o[cell_data_label + '/EulerAngles'], 'ObjectType', 'DataArray<float>')
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add_attribute(o[cell_data_label + '/EulerAngles'], '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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@ -2081,17 +2046,17 @@ class Result:
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# Attributes for data in Ensemble matrix
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for group in ['CrystalStructures','PhaseTypes']:
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o[ensemble_label+'/'+group].attrs['ComponentDimensions'] = np.array([1],np.uint64)
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o[ensemble_label+'/'+group].attrs['Tuple Axis Dimensions'] = f'x={len(self.phases)+1}'
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o[ensemble_label+'/'+group].attrs['DataArrayVersion'] = np.array([2],np.int32)
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o[ensemble_label+'/'+group].attrs['ObjectType'] = 'DataArray<uint32_t>'
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o[ensemble_label+'/'+group].attrs['TupleDimensions'] = np.array([len(self.phases) + 1],np.uint64)
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add_attribute(o[ensemble_label+'/'+group], 'ComponentDimensions', np.array([1],np.uint64))
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add_attribute(o[ensemble_label+'/'+group], 'Tuple Axis Dimensions', f'x={len(self.phases)+1}')
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add_attribute(o[ensemble_label+'/'+group], 'DataArrayVersion', np.array([2],np.int32))
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add_attribute(o[ensemble_label+'/'+group], 'ObjectType', 'DataArray<uint32_t>')
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add_attribute(o[ensemble_label+'/'+group], 'TupleDimensions', np.array([len(self.phases) + 1],np.uint64))
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o[ensemble_label+'/PhaseName'].attrs['ComponentDimensions'] = np.array([1],np.uint64)
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o[ensemble_label+'/PhaseName'].attrs['Tuple Axis Dimensions'] = f'x={len(self.phases)+1}'
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o[ensemble_label+'/PhaseName'].attrs['DataArrayVersion'] = np.array([2],np.int32)
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o[ensemble_label+'/PhaseName'].attrs['ObjectType'] = 'StringDataArray'
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o[ensemble_label+'/PhaseName'].attrs['TupleDimensions'] = np.array([len(self.phases) + 1],np.uint64)
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add_attribute(o[ensemble_label+'/PhaseName'], 'ComponentDimensions', np.array([1],np.uint64))
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add_attribute(o[ensemble_label+'/PhaseName'], 'Tuple Axis Dimensions', f'x={len(self.phases)+1}')
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add_attribute(o[ensemble_label+'/PhaseName'], 'DataArrayVersion', np.array([2],np.int32))
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add_attribute(o[ensemble_label+'/PhaseName'], 'ObjectType', 'StringDataArray')
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add_attribute(o[ensemble_label+'/PhaseName'], 'TupleDimensions', np.array([len(self.phases) + 1],np.uint64))
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# Create geometry info
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geom_label = data_container_label + '/_SIMPL_GEOMETRY'
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@ -2100,12 +2065,11 @@ class Result:
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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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h5py._hl.attrs.AttributeManager = ResetAttributeManager # Reset the attribute manager to original:
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add_attribute(o[geom_label], 'GeometryName', 'ImageGeometry')
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add_attribute(o[geom_label], 'GeometryTypeName', 'ImageGeometry')
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add_attribute(o[geom_label], 'GeometryType', np.array([0],np.uint32))
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add_attribute(o[geom_label], 'SpatialDimensionality', np.array([3],np.uint32))
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add_attribute(o[geom_label], 'UnitDimensionality', np.array([3],np.uint32))
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def export_DADF5(self,
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