improving import from DREAM.3D
- no duplicated entries even for non-segmented data - using phase labels from file - material.yaml: Dummy homogenization and phase - tests to ensure correct order and match between Grid and ConfigMaterial
This commit is contained in:
Martin Diehl
parent
cdcedd0d44
commit
394fda5f37
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@ -1,4 +1,4 @@
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from os import path
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import os.path
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import numpy as np
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import h5py
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@ -88,7 +88,7 @@ class ConfigMaterial(Config):
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phase: {}
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"""
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kwargs_ = {k:table.get(v) for k,v in kwargs.items()}
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kwargs_ = {k:table.get(v) for k,v in kwargs.items()}
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_,idx = np.unique(np.hstack(list(kwargs_.values())),return_index=True,axis=0)
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idx = np.sort(idx)
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@ -98,7 +98,10 @@ class ConfigMaterial(Config):
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@staticmethod
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def load_DREAM3D(fname,data_group,ori_data,phase_id,phase_name,base_group=None):
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def load_DREAM3D(fname,
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grain_data=None,cell_data='CellData',cell_ensemble_data='CellEnsembleData',
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phases='Phases',Euler_angles='EulerAngles',phase_names='PhaseName',
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base_group=None):
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"""
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Load material data from DREAM3D file.
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@ -107,70 +110,33 @@ class ConfigMaterial(Config):
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Parameters
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----------
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fname : str
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path to the DREAM3D file.
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Filename of the DREAM.3D (HDF5) file.
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base_group : str
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Name of the group (folder) below 'DataContainers',
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for example 'SyntheticVolumeDataContainer'.
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data_group : str
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Name of the group (folder) having relevant data for conversion,
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for example 'Grain Data' or 'CellData'.
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ori_data : str
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Name of the dataset having orientation data (working with Euler Angles in dream3D file),
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For example 'EulerAngles'.
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phase_id : str
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Name of the dataset containing phase IDs for each grain,
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for example 'Phases'.
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phase_name : list
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List with name of the phases.
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Examples
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--------
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for grain based data with single phase
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>>> import damask
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>>> import damask.ConfigMaterial as cm
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>>> cm.load_from_Dream3D('20grains16x16x16.dream3D','SyntheticVolumeDataContainer', 'Grain Data',
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... 'EulerAngles','Phases',['Ferrite'])
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for point based data with single phase
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>>> import damask
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>>> import damask.ConfigMaterial as cm
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>>> cm.load_from_Dream3D('20grains16x16x16.dream3D','SyntheticVolumeDataContainer', 'CellData',
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... 'EulerAngles','Phases',['Ferrite'])
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for grain based data with dual phase
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>>> import damask
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>>> import damask.ConfigMaterial as cm
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>>> cm.load_from_Dream3D('20grains16x16x16.dream3D','SyntheticVolumeDataContainer', 'Grain Data',
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... 'EulerAngles','Phases',['Ferrite','Martensite'])
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for point based data with dual phase
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>>> import damask
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>>> import damask.ConfigMaterial as cm
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>>> cm.load_from_Dream3D('20grains16x16x16.dream3D','SyntheticVolumeDataContainer', 'CellData',
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... 'EulerAngles','Phases',['Ferrite','Martensite'])
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Path to the group (folder) that contains the geometry (_SIMPL_GEOMETRY),
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and, optionally, the cell data. Defaults to None, in which case
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it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
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"""
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b = util.DREAM3D_base_group(fname) if base_group is None else base_group
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hdf = h5py.File(fname,'r')
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f = h5py.File(fname,'r')
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orientation_path = path.join(b,data_group,ori_data)
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if hdf[orientation_path].attrs['TupleDimensions'].shape == (3,):
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grain_orientations = np.array(hdf[orientation_path]).reshape(-1,3,order='F')
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if grain_data is None:
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phase = f[os.path.join(b,cell_data,phases)][()].flatten()
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O = Rotation.from_Euler_angles(f[os.path.join(b,cell_data,Euler_angles)]).as_quaternion().reshape(-1,4) # noqa
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_,idx = np.unique(np.hstack([O,phase.reshape(-1,1)]),return_index=True,axis=0)
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idx = np.sort(idx)
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else:
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grain_orientations = np.array(hdf[orientation_path])[1:]
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phase = f[os.path.join(b,grain_data,phases)][()]
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O = Rotation.from_Euler_angles(f[os.path.join(b,grain_data,Euler_angles)]).as_quaternion() # noqa
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idx = np.arange(phase.size)
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grain_quats = Rotation.from_Euler_angles(grain_orientations).as_quaternion()
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if cell_ensemble_data is not None:
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names = np.array([s.decode() for s in f[os.path.join(b,cell_ensemble_data,phase_names)]])
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phase = names[phase]
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phase_path = path.join(b,data_group,phase_id)
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if hdf[phase_path].attrs['TupleDimensions'].shape == (3,):
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grain_phase = np.array(hdf[phase_path]).reshape(-1,order='F')
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else:
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grain_phase = np.array(hdf[phase_path])[1:]
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grain_phase = grain_phase.reshape(len(grain_phase),)
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phase_name_list = [phase_name[i - 1] for i in grain_phase]
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return ConfigMaterial().material_add(phase=phase_name_list, O = grain_quats) # noqa
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material = {k:np.atleast_1d(v[idx].squeeze()) for k,v in zip(['O','phase'],[O,phase])}
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return ConfigMaterial({'phase':{k if isinstance(k,int) else str(k):'tbd' for k in np.unique(phase)},
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'homogenization':{'direct':{'N_constituents':1}}}).material_add(**material)
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@property
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@ -256,14 +256,17 @@ class Grid:
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@staticmethod
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def load_DREAM3D(fname,cell_data=None,material='FeatureIds',base_group=None):
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def load_DREAM3D(fname,
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feature_IDs=None,cell_data='CellData',
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phases='Phases',Euler_angles='EulerAngles',
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base_group=None):
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"""
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Load from DREAM.3D file.
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Parameters
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----------
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fname : str
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Filename of the DREAM.3D file
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Filename of the DREAM.3D (HDF5) file.
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cell_data : str, optional
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Name of the group (folder) containing the pointwise material data,
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for example 'CellData'. Defaults to None, in which case points are consecutively numbered.
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@ -274,16 +277,22 @@ class Grid:
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Path to the group (folder) that contains the geometry (_SIMPL_GEOMETRY),
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and, optionally, the cell data. Defaults to None, in which case
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it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
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"""
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b = util.DREAM3D_base_group(fname) if base_group is None else base_group
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f = h5py.File(fname, 'r')
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cells = f[os.path.join(b,'_SIMPL_GEOMETRY','DIMENSIONS')][()]
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size = f[os.path.join(b,'_SIMPL_GEOMETRY','SPACING')][()] * cells
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size = f[os.path.join(b,'_SIMPL_GEOMETRY','SPACING')] * cells
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origin = f[os.path.join(b,'_SIMPL_GEOMETRY','ORIGIN')][()]
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ma = np.arange(cells.prod(),dtype=int) if cell_data is None else \
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np.reshape(f[os.path.join(b,cell_data,material)],cells.prod())
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if feature_IDs is None:
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phase = f[os.path.join(b,cell_data,phases)][()].reshape(-1,1)
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O = Rotation.from_Euler_angles(f[os.path.join(b,cell_data,Euler_angles)]).as_quaternion().reshape(-1,4) # noqa
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unique,unique_inverse = np.unique(np.hstack([O,phase]),return_inverse=True,axis=0)
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ma = np.arange(cells.prod()) if len(unique) == cells.prod() else \
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np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
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else:
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ma = f[os.path.join(b,cell_data,feature_IDs)][()].flatten()
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return Grid(ma.reshape(cells,order='F'),size,origin,util.execution_stamp('Grid','load_DREAM3D'))
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@ -6,6 +6,7 @@ import numpy as np
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from damask import ConfigMaterial
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from damask import Table
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from damask import Rotation
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from damask import Grid
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@pytest.fixture
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def ref_path(ref_path_base):
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@ -108,3 +109,24 @@ class TestConfigMaterial:
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m = ConfigMaterial().material_add(**kw)
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assert len(m['material']) == N
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assert len(m['material'][0]['constituents']) == n
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@pytest.mark.parametrize('cell_ensemble_data',[None,'CellEnsembleData'])
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def test_load_DREAM3D(self,ref_path,cell_ensemble_data):
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grain_c = ConfigMaterial.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','Grain Data',
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cell_ensemble_data = cell_ensemble_data)
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point_c = ConfigMaterial.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d',
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cell_ensemble_data = cell_ensemble_data)
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assert point_c.is_valid and grain_c.is_valid
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assert len(point_c['material'])+1 == len(grain_c['material'])
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grain_m = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','FeatureIds').material.flatten()
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point_m = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d').material.flatten()
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for i in np.unique(point_m):
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j = int(grain_m[(point_m==i).nonzero()[0][0]])
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assert np.allclose(point_c['material'][i]['constituents'][0]['O'],
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grain_c['material'][j]['constituents'][0]['O'])
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assert point_c['material'][i]['constituents'][0]['phase'] == \
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grain_c['material'][j]['constituents'][0]['phase']
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@ -420,12 +420,22 @@ class TestGrid:
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t = Table(np.column_stack((coords.reshape(-1,3,order='F'),grid.material.flatten(order='F'))),{'c':3,'m':1})
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assert grid_equal(grid.sort().renumber(),Grid.from_table(t,'c',['m']))
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@pytest.mark.parametrize('periodic',[True,False])
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@pytest.mark.parametrize('direction',['x','y','z',['x','y'],'zy','xz',['x','y','z']])
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def test_get_grain_boundaries(self,update,ref_path,periodic,direction):
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grid=Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
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current=grid.get_grain_boundaries(periodic,direction)
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grid = Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
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current = grid.get_grain_boundaries(periodic,direction)
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if update:
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current.save(ref_path/f'get_grain_boundaries_8g12x15x20_{direction}_{periodic}.vtu',parallel=False)
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reference=VTK.load(ref_path/f'get_grain_boundaries_8g12x15x20_{"".join(direction)}_{periodic}.vtu')
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reference = VTK.load(ref_path/f'get_grain_boundaries_8g12x15x20_{"".join(direction)}_{periodic}.vtu')
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assert current.__repr__() == reference.__repr__()
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def test_load_DREAM3D(self,ref_path):
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grain = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','FeatureIds')
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point = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d')
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assert np.allclose(grain.origin,point.origin) and \
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np.allclose(grain.size,point.size) and \
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(grain.sort().material == point.material+1).all()
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