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Merge branch 'load-DREAM3d-improvements' into 'development' 

Load dream3d improvements

See merge request damask/DAMASK!821
This commit is contained in:
Philip Eisenlohr 2023-09-23 23:14:03 +00:00
parent 0604e510ec 4a943ff844
commit 57d8a6c438
4 changed files with 91 additions and 65 deletions
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60
python/damask/_configmaterial.py
View File

@ -106,15 +106,12 @@ class ConfigMaterial(Config):
Load DREAM.3D (HDF5) file.
Data in DREAM.3D files can be stored per cell ('CellData')
and/or per grain ('Grain Data'). Per default, cell-wise data
is assumed.
damask.Grid.load_DREAM3D allows to get the corresponding geometry
for the grid solver.
and/or per grain ('Grain Data'). Per default, i.e. if
'grain_data' is None, cell-wise data is assumed.
Parameters
----------
fname : str
fname : str or pathlib.Path
Filename of the DREAM.3D (HDF5) file.
grain_data : str
Name of the group (folder) containing grain-wise data. Defaults
@ -140,36 +137,43 @@ class ConfigMaterial(Config):
and grain- or cell-wise data. Defaults to None, in which case
it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
Notes
-----
Homogenization and phase entries are emtpy and need to be defined separately.
Returns
-------
loaded : damask.ConfigMaterial
Material configuration from file.
Notes
-----
damask.Grid.load_DREAM3D gives the corresponding geometry for
the grid solver.
For cell-wise data, only unique combinations of
orientation and phase are considered.
Homogenization and phase entries are emtpy and need to be
defined separately.
"""
b = util.DREAM3D_base_group(fname) if base_group is None else base_group
c = util.DREAM3D_cell_data_group(fname) if cell_data is None else cell_data
f = h5py.File(fname,'r')
with h5py.File(fname, 'r') as f:
b = util.DREAM3D_base_group(f) if base_group is None else base_group
c = util.DREAM3D_cell_data_group(f) if cell_data is None else cell_data
if grain_data is None:
phase = f['/'.join([b,c,phases])][()].flatten()
O = Rotation.from_Euler_angles(f['/'.join([b,c,Euler_angles])]).as_quaternion().reshape(-1,4) # noqa
_,idx = np.unique(np.hstack([O,phase.reshape(-1,1)]),return_index=True,axis=0)
idx = np.sort(idx)
else:
phase = f['/'.join([b,grain_data,phases])][()]
O = Rotation.from_Euler_angles(f['/'.join([b,grain_data,Euler_angles])]).as_quaternion() # noqa
idx = np.arange(phase.size)
if grain_data is None:
phase = f['/'.join([b,c,phases])][()].flatten()
O = Rotation.from_Euler_angles(f['/'.join([b,c,Euler_angles])]).as_quaternion().reshape(-1,4) # noqa
_,idx = np.unique(np.hstack([O,phase.reshape(-1,1)]),return_index=True,axis=0)
idx = np.sort(idx)
else:
phase = f['/'.join([b,grain_data,phases])][()]
O = Rotation.from_Euler_angles(f['/'.join([b,grain_data,Euler_angles])]).as_quaternion() # noqa
idx = np.arange(phase.size)
if cell_ensemble_data is not None and phase_names is not None:
try:
names = np.array([s.decode() for s in f['/'.join([b,cell_ensemble_data,phase_names])]])
phase = names[phase]
except KeyError:
pass
if cell_ensemble_data is not None and phase_names is not None:
try:
names = np.array([s.decode() for s in f['/'.join([b,cell_ensemble_data,phase_names])]])
phase = names[phase]
except KeyError:
pass
base_config = ConfigMaterial({'phase':{k if isinstance(k,int) else str(k): None for k in np.unique(phase)},

44
python/damask/_grid.py
View File

@ -358,14 +358,14 @@ class Grid:
"""
Load DREAM.3D (HDF5) file.
Data in DREAM.3D files can be stored per cell ('CellData') and/or
per grain ('Grain Data'). Per default, cell-wise data is assumed.
Data in DREAM.3D files can be stored per cell ('CellData')
and/or per grain ('Grain Data'). Per default, i.e. if
'feature_IDs' is None, cell-wise data is assumed.
damask.ConfigMaterial.load_DREAM3D gives the corresponding material definition.
Parameters
----------
fname : str or or pathlib.Path
fname : str or pathlib.Path
Filename of the DREAM.3D (HDF5) file.
feature_IDs : str, optional
Name of the dataset containing the mapping between cells and
@ -392,23 +392,31 @@ class Grid:
loaded : damask.Grid
Grid-based geometry from file.
Notes
-----
damask.ConfigMaterial.load_DREAM3D gives the corresponding
material definition.
For cell-wise data, only unique combinations of
orientation and phase are considered.
"""
b = util.DREAM3D_base_group(fname) if base_group is None else base_group
c = util.DREAM3D_cell_data_group(fname) if cell_data is None else cell_data
f = h5py.File(fname, 'r')
with h5py.File(fname, 'r') as f:
b = util.DREAM3D_base_group(f) if base_group is None else base_group
c = util.DREAM3D_cell_data_group(f) if cell_data is None else cell_data
cells = f['/'.join([b,'_SIMPL_GEOMETRY','DIMENSIONS'])][()]
size = f['/'.join([b,'_SIMPL_GEOMETRY','SPACING'])] * cells
origin = f['/'.join([b,'_SIMPL_GEOMETRY','ORIGIN'])][()]
cells = f['/'.join([b,'_SIMPL_GEOMETRY','DIMENSIONS'])][()]
size = f['/'.join([b,'_SIMPL_GEOMETRY','SPACING'])] * cells
origin = f['/'.join([b,'_SIMPL_GEOMETRY','ORIGIN'])][()]
if feature_IDs is None:
phase = f['/'.join([b,c,phases])][()].reshape(-1,1)
O = Rotation.from_Euler_angles(f['/'.join([b,c,Euler_angles])]).as_quaternion().reshape(-1,4) # noqa
unique,unique_inverse = np.unique(np.hstack([O,phase]),return_inverse=True,axis=0)
ma = np.arange(cells.prod()) if len(unique) == cells.prod() else \
np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
else:
ma = f['/'.join([b,c,feature_IDs])][()].flatten()
if feature_IDs is None:
phase = f['/'.join([b,c,phases])][()].reshape(-1,1)
O = Rotation.from_Euler_angles(f['/'.join([b,c,Euler_angles])]).as_quaternion().reshape(-1,4) # noqa
unique,unique_inverse = np.unique(np.hstack([O,phase]),return_inverse=True,axis=0)
ma = np.arange(cells.prod()) if len(unique) == cells.prod() else \
np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
else:
ma = f['/'.join([b,c,feature_IDs])][()].flatten()
return Grid(material = ma.reshape(cells,order='F'),
size = size,

34
python/damask/util.py
View File

@ -698,7 +698,7 @@ def pass_on(keyword: str,
return wrapper
return decorator
def DREAM3D_base_group(fname: _Union[str, _Path]) -> str:
def DREAM3D_base_group(fname: _Union[str, _Path, _h5py.File]) -> str:
"""
Determine the base group of a DREAM.3D file.
@ -707,7 +707,7 @@ def DREAM3D_base_group(fname: _Union[str, _Path]) -> str:
Parameters
----------
fname : str or pathlib.Path
fname : str, pathlib.Path, or _h5py.File
Filename of the DREAM.3D (HDF5) file.
Returns
@ -716,15 +716,19 @@ def DREAM3D_base_group(fname: _Union[str, _Path]) -> str:
Path to the base group.
"""
with _h5py.File(_Path(fname).expanduser(),'r') as f:
def get_base_group(f: _h5py.File) -> str:
base_group = f.visit(lambda path: path.rsplit('/',2)[0] if '_SIMPL_GEOMETRY/SPACING' in path else None)
if base_group is None:
raise ValueError(f'could not determine base group in file "{fname}"')
return base_group
if base_group is None:
raise ValueError(f'could not determine base group in file "{fname}"')
if isinstance(fname,_h5py.File):
return get_base_group(fname)
return base_group
with _h5py.File(_Path(fname).expanduser(),'r') as f:
return get_base_group(f)
def DREAM3D_cell_data_group(fname: _Union[str, _Path]) -> str:
def DREAM3D_cell_data_group(fname: _Union[str, _Path, _h5py.File]) -> str:
"""
Determine the cell data group of a DREAM.3D file.
@ -734,7 +738,7 @@ def DREAM3D_cell_data_group(fname: _Union[str, _Path]) -> str:
Parameters
----------
fname : str or pathlib.Path
fname : str, pathlib.Path, or h5py.File
Filename of the DREAM.3D (HDF5) file.
Returns
@ -743,17 +747,21 @@ def DREAM3D_cell_data_group(fname: _Union[str, _Path]) -> str:
Path to the cell data group.
"""
base_group = DREAM3D_base_group(fname)
with _h5py.File(_Path(fname).expanduser(),'r') as f:
def get_cell_data_group(f: _h5py.File) -> str:
base_group = DREAM3D_base_group(f)
cells = tuple(f['/'.join([base_group,'_SIMPL_GEOMETRY','DIMENSIONS'])][()][::-1])
cell_data_group = f[base_group].visititems(lambda path,obj: path.split('/')[0] \
if isinstance(obj,_h5py._hl.dataset.Dataset) and _np.shape(obj)[:-1] == cells \
else None)
if cell_data_group is None:
raise ValueError(f'could not determine cell-data group in file "{fname}/{base_group}"')
return cell_data_group
if cell_data_group is None:
raise ValueError(f'could not determine cell-data group in file "{fname}/{base_group}"')
if isinstance(fname,_h5py.File):
return get_cell_data_group(fname)
return cell_data_group
with _h5py.File(_Path(fname).expanduser(),'r') as f:
return get_cell_data_group(f)
def Bravais_to_Miller(*,

18
python/tests/test_util.py
View File

@ -146,21 +146,25 @@ class TestUtil:
assert 'DAMASK' in style('DAMASK')
@pytest.mark.parametrize('complete',[True,False])
def test_D3D_base_group(self,tmp_path,complete):
@pytest.mark.parametrize('fhandle',[True,False])
def test_D3D_base_group(self,tmp_path,complete,fhandle):
base_group = ''.join(random.choices('DAMASK', k=10))
with h5py.File(tmp_path/'base_group.dream3d','w') as f:
f.create_group('/'.join((base_group,'_SIMPL_GEOMETRY')))
if complete:
f['/'.join((base_group,'_SIMPL_GEOMETRY'))].create_dataset('SPACING',data=np.ones(3))
fname = tmp_path/'base_group.dream3d'
if fhandle: fname = h5py.File(fname)
if complete:
assert base_group == util.DREAM3D_base_group(tmp_path/'base_group.dream3d')
assert base_group == util.DREAM3D_base_group(fname)
else:
with pytest.raises(ValueError):
util.DREAM3D_base_group(tmp_path/'base_group.dream3d')
util.DREAM3D_base_group(fname)
@pytest.mark.parametrize('complete',[True,False])
def test_D3D_cell_data_group(self,tmp_path,complete):
@pytest.mark.parametrize('fhandle',[True,False])
def test_D3D_cell_data_group(self,tmp_path,complete,fhandle):
base_group = ''.join(random.choices('DAMASK', k=10))
cell_data_group = ''.join(random.choices('KULeuven', k=10))
cells = np.random.randint(1,50,3)
@ -172,11 +176,13 @@ class TestUtil:
if complete:
f['/'.join((base_group,cell_data_group))].create_dataset('data',shape=np.append(cells,1))
fname = tmp_path/'cell_data_group.dream3d'
if fhandle: fname = h5py.File(fname)
if complete:
assert cell_data_group == util.DREAM3D_cell_data_group(tmp_path/'cell_data_group.dream3d')
assert cell_data_group == util.DREAM3D_cell_data_group(fname)
else:
with pytest.raises(ValueError):
util.DREAM3D_cell_data_group(tmp_path/'cell_data_group.dream3d')
util.DREAM3D_cell_data_group(fname)
@pytest.mark.parametrize('full,reduced',[({}, {}),