Merge branch 'config_from_dream3D' into 'development'
Config from DREAM.3D See merge request damask/DAMASK!358
This commit is contained in:
Francisco Jose Gallardo Basile
commit
ee8015cd55
2
PRIVATE
2
PRIVATE
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@ -1 +1 @@
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Subproject commit a4fed7a4b285496f547a7b940f6b6d54419f2384
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Subproject commit ba046ace284515cb82020b3930206eab84ff3121
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@ -65,7 +65,7 @@ if filenames == []: parser.error('no input file specified.')
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for name in filenames:
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damask.util.report(scriptName,name)
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geom = damask.Grid.load_DREAM3D(name,options.basegroup,options.pointwise)
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geom = damask.Grid.load_DREAM3D(name,'FeatureIds')
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damask.util.croak(geom)
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geom.save_ASCII(os.path.splitext(name)[0]+'.geom')
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@ -1,4 +1,7 @@
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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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from . import Config
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from . import Rotation
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@ -49,7 +52,7 @@ class ConfigMaterial(Config):
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@staticmethod
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def from_table(table,**kwargs):
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"""
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Load from an ASCII table.
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Generate from an ASCII table.
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Parameters
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----------
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@ -85,7 +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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@ -94,6 +97,79 @@ class ConfigMaterial(Config):
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return ConfigMaterial().material_add(**kwargs_)
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@staticmethod
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def load_DREAM3D(fname,
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grain_data=None,cell_data=None,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 DREAM.3D (HDF5) file.
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Data in DREAM.3D files can be stored per cell ('CellData')
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and/or per grain ('Grain Data'). Per default, cell-wise data
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is assumed.
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damask.Grid.load_DREAM3D allows to get the corresponding geometry
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for the grid solver.
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Parameters
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----------
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fname : str
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Filename of the DREAM.3D (HDF5) file.
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grain_data : str
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Name of the group (folder) containing grain-wise data. Defaults
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to None, in which case cell-wise data is used.
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cell_data : str
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Name of the group (folder) containing cell-wise data. Defaults to
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None in wich case it is automatically detected.
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cell_ensemble_data : str
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Name of the group (folder) containing data of cell ensembles. This
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group is used to inquire the name of the phases. Phases will get
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numeric IDs if this group is not found. Defaults to 'CellEnsembleData'.
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phases : str
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Name of the dataset containing the phase ID (cell-wise or grain-wise).
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Defaults to 'Phases'.
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Euler_angles : str
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Name of the dataset containing the crystallographic orientation as
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Euler angles in radians (cell-wise or grain-wise). Defaults to 'EulerAngles'.
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phase_names : str
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Name of the dataset containing the phase names. Phases will get
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numeric IDs if this dataset is not found. Defaults to 'PhaseName'.
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base_group : str
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Path to the group (folder) that contains geometry (_SIMPL_GEOMETRY),
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and grain- or cell-wise 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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c = util.DREAM3D_cell_data_group(fname) if cell_data is None else cell_data
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f = h5py.File(fname,'r')
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if grain_data is None:
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phase = f[os.path.join(b,c,phases)][()].flatten()
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O = Rotation.from_Euler_angles(f[os.path.join(b,c,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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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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if cell_ensemble_data is not None and phase_names is not None:
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try:
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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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except KeyError:
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pass
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base_config = ConfigMaterial({'phase':{k if isinstance(k,int) else str(k):'t.b.d.' for k in np.unique(phase)},
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'homogenization':{'direct':{'N_constituents':1}}})
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constituent = {k:np.atleast_1d(v[idx].squeeze()) for k,v in zip(['O','phase'],[O,phase])}
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return base_config.material_add(**constituent,homogenization='direct')
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@property
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def is_complete(self):
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"""Check for completeness."""
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@ -256,35 +256,62 @@ class Grid:
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@staticmethod
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def load_DREAM3D(fname,base_group,point_data=None,material='FeatureIds'):
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def load_DREAM3D(fname,
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feature_IDs=None,cell_data=None,
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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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Load DREAM.3D (HDF5) file.
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Data in DREAM.3D files can be stored per cell ('CellData')
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and/or per grain ('Grain Data'). Per default, cell-wise data
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is assumed.
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damask.ConfigMaterial.load_DREAM3D allows to get the
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corresponding material definition.
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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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feature_IDs : str
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Name of the dataset containing the mapping between cells and
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grain-wise data. Defaults to 'None', in which case cell-wise
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data is used.
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cell_data : str
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Name of the group (folder) containing cell-wise data. Defaults to
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None in wich case it is automatically detected.
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phases : str
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Name of the dataset containing the phase ID. It is not used for
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grain-wise data, i.e. when feature_IDs is not None.
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Defaults to 'Phases'.
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Euler_angles : str
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Name of the dataset containing the crystallographic orientation as
|
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Euler angles in radians It is not used for grain-wise data, i.e.
|
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when feature_IDs is not None. Defaults to 'EulerAngles'.
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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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point_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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material : str, optional
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Name of the dataset containing the material ID.
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Defaults to 'FeatureIds'.
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Path to the group (folder) that contains geometry (_SIMPL_GEOMETRY),
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and grain- or cell-wise data. Defaults to None, in which case
|
||||
it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
|
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"""
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root_dir ='DataContainers'
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b = util.DREAM3D_base_group(fname) if base_group is None else base_group
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c = util.DREAM3D_cell_data_group(fname) if cell_data is None else cell_data
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f = h5py.File(fname, 'r')
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g = os.path.join(root_dir,base_group,'_SIMPL_GEOMETRY')
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cells = f[os.path.join(g,'DIMENSIONS')][()]
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size = f[os.path.join(g,'SPACING')][()] * cells
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origin = f[os.path.join(g,'ORIGIN')][()]
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ma = np.arange(cells.prod(),dtype=int) \
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if point_data is None else \
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np.reshape(f[os.path.join(root_dir,base_group,point_data,material)],cells.prod())
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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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origin = f[os.path.join(b,'_SIMPL_GEOMETRY','ORIGIN')][()]
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if feature_IDs is None:
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phase = f[os.path.join(b,c,phases)][()].reshape(-1,1)
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O = Rotation.from_Euler_angles(f[os.path.join(b,c,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,c,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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@ -9,6 +9,7 @@ from functools import reduce
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from optparse import Option
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import numpy as np
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import h5py
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from . import version
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@ -27,7 +28,8 @@ __all__=[
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'extendableOption',
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'execution_stamp',
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'shapeshifter', 'shapeblender',
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'extend_docstring', 'extended_docstring'
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'extend_docstring', 'extended_docstring',
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'DREAM3D_base_group', 'DREAM3D_cell_data_group'
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]
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####################################################################################################
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@ -376,6 +378,53 @@ def extended_docstring(f,extra_docstring):
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return _decorator
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def DREAM3D_base_group(fname):
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"""
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Determine the base group of a DREAM.3D file.
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The base group is defined as the group (folder) that contains
|
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a 'SPACING' dataset in a '_SIMPL_GEOMETRY' group.
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Parameters
|
||||
----------
|
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fname : str
|
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Filename of the DREAM.3D (HDF5) file.
|
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|
||||
"""
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with h5py.File(fname,'r') as f:
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base_group = f.visit(lambda path: path.rsplit('/',2)[0] if '_SIMPL_GEOMETRY/SPACING' in path else None)
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|
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if base_group is None:
|
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raise ValueError(f'Could not determine base group in file {fname}.')
|
||||
|
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return base_group
|
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def DREAM3D_cell_data_group(fname):
|
||||
"""
|
||||
Determine the cell data group of a DREAM.3D file.
|
||||
|
||||
The cell data group is defined as the group (folder) that contains
|
||||
a dataset in the base group whose length matches the total number
|
||||
of points as specified in '_SIMPL_GEOMETRY/DIMENSIONS'.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
fname : str
|
||||
Filename of the DREAM.3D (HDF5) file.
|
||||
|
||||
"""
|
||||
base_group = DREAM3D_base_group(fname)
|
||||
with h5py.File(fname,'r') as f:
|
||||
cells = tuple(f[os.path.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
|
||||
|
||||
####################################################################################################
|
||||
# Classes
|
||||
####################################################################################################
|
||||
|
|
|
|||
|
|
@ -0,0 +1 @@
|
|||
../Grid/2phase_irregularGrid.dream3d
|
||||
|
|
@ -0,0 +1 @@
|
|||
../Grid/2phase_irregularGrid.json
|
||||
|
|
@ -0,0 +1 @@
|
|||
../Grid/2phase_irregularGrid.xdmf
|
||||
|
|
@ -0,0 +1 @@
|
|||
../Grid/measured.dream3d
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1 @@
|
|||
../Grid/measured.xdmf
|
||||
Binary file not shown.
|
|
@ -0,0 +1,764 @@
|
|||
{
|
||||
"0": {
|
||||
"CellEnsembleAttributeMatrixName": "CellEnsembleData",
|
||||
"CrystalStructuresArrayName": "CrystalStructures",
|
||||
"Filter_Enabled": true,
|
||||
"Filter_Human_Label": "StatsGenerator",
|
||||
"Filter_Name": "StatsGeneratorFilter",
|
||||
"Filter_Uuid": "{f642e217-4722-5dd8-9df9-cee71e7b26ba}",
|
||||
"PhaseNamesArrayName": "PhaseName",
|
||||
"PhaseTypesArrayName": "PhaseTypes",
|
||||
"StatsDataArray": {
|
||||
"1": {
|
||||
"AxisODF-Weights": {
|
||||
},
|
||||
"Bin Count": 34,
|
||||
"BinNumber": [
|
||||
0.03019738383591175,
|
||||
1.031197428703308,
|
||||
2.0321974754333496,
|
||||
3.0331974029541016,
|
||||
4.0341973304748535,
|
||||
5.0351972579956055,
|
||||
6.036197185516357,
|
||||
7.037197113037109,
|
||||
8.03819751739502,
|
||||
9.03919792175293,
|
||||
10.04019832611084,
|
||||
11.04119873046875,
|
||||
12.04219913482666,
|
||||
13.04319953918457,
|
||||
14.04419994354248,
|
||||
15.04520034790039,
|
||||
16.046199798583984,
|
||||
17.047199249267578,
|
||||
18.048198699951172,
|
||||
19.049198150634766,
|
||||
20.05019760131836,
|
||||
21.051197052001953,
|
||||
22.052196502685547,
|
||||
23.05319595336914,
|
||||
24.054195404052734,
|
||||
25.055194854736328,
|
||||
26.056194305419922,
|
||||
27.057193756103516,
|
||||
28.05819320678711,
|
||||
29.059192657470703,
|
||||
30.060192108154297,
|
||||
31.06119155883789,
|
||||
32.062191009521484,
|
||||
33.06319046020508
|
||||
],
|
||||
"BoundaryArea": 0,
|
||||
"Crystal Symmetry": 1,
|
||||
"FeatureSize Distribution": {
|
||||
"Average": 0.5,
|
||||
"Standard Deviation": 1
|
||||
},
|
||||
"FeatureSize Vs B Over A Distributions": {
|
||||
"Alpha": [
|
||||
15.845513343811035,
|
||||
15.281289100646973,
|
||||
15.406131744384766,
|
||||
15.695631980895996
|
||||
],
|
||||
"Beta": [
|
||||
1.5363599061965942,
|
||||
1.3575199842453003,
|
||||
1.2908644676208496,
|
||||
1.6510697603225708
|
||||
],
|
||||
"Distribution Type": "Beta Distribution"
|
||||
},
|
||||
"FeatureSize Vs C Over A Distributions": {
|
||||
"Alpha": [
|
||||
15.83090591430664,
|
||||
15.119057655334473,
|
||||
15.210259437561035,
|
||||
15.403964042663574
|
||||
],
|
||||
"Beta": [
|
||||
1.4798208475112915,
|
||||
1.439164638519287,
|
||||
1.6361048221588135,
|
||||
1.3149876594543457
|
||||
],
|
||||
"Distribution Type": "Beta Distribution"
|
||||
},
|
||||
"FeatureSize Vs Neighbors Distributions": {
|
||||
"Average": [
|
||||
2.3025851249694824,
|
||||
2.4849066734313965,
|
||||
2.6390573978424072,
|
||||
2.7725887298583984
|
||||
],
|
||||
"Distribution Type": "Log Normal Distribution",
|
||||
"Standard Deviation": [
|
||||
0.4000000059604645,
|
||||
0.3499999940395355,
|
||||
0.30000001192092896,
|
||||
0.25
|
||||
]
|
||||
},
|
||||
"FeatureSize Vs Omega3 Distributions": {
|
||||
"Alpha": [
|
||||
10.906224250793457,
|
||||
10.030556678771973,
|
||||
10.367804527282715,
|
||||
10.777519226074219
|
||||
],
|
||||
"Beta": [
|
||||
1.7305665016174316,
|
||||
1.638364553451538,
|
||||
1.6687047481536865,
|
||||
1.6839183568954468
|
||||
],
|
||||
"Distribution Type": "Beta Distribution"
|
||||
},
|
||||
"Feature_Diameter_Info": [
|
||||
1.0010000467300415,
|
||||
33.11545181274414,
|
||||
0.03019738383591175
|
||||
],
|
||||
"MDF-Weights": {
|
||||
},
|
||||
"Name": "Primary",
|
||||
"ODF-Weights": {
|
||||
},
|
||||
"PhaseFraction": 0.8999999761581421,
|
||||
"PhaseType": "Primary"
|
||||
},
|
||||
"2": {
|
||||
"AxisODF-Weights": {
|
||||
},
|
||||
"Bin Count": 34,
|
||||
"BinNumber": [
|
||||
0.03019738383591175,
|
||||
1.031197428703308,
|
||||
2.0321974754333496,
|
||||
3.0331974029541016,
|
||||
4.0341973304748535,
|
||||
5.0351972579956055,
|
||||
6.036197185516357,
|
||||
7.037197113037109,
|
||||
8.03819751739502,
|
||||
9.03919792175293,
|
||||
10.04019832611084,
|
||||
11.04119873046875,
|
||||
12.04219913482666,
|
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"Attribute Matrix Name": "Synthetic Shape Parameters (Precipitate)",
|
||||
"Data Array Name": "",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"NumFeaturesArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "NumFeatures",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"PeriodicBoundaries": 0,
|
||||
"PrecipInputFile": "C:/Users/work",
|
||||
"SaveGeometricDescriptions": 0,
|
||||
"SelectedAttributeMatrixPath": {
|
||||
"Attribute Matrix Name": "",
|
||||
"Data Array Name": "",
|
||||
"Data Container Name": ""
|
||||
},
|
||||
"UseMask": 0
|
||||
},
|
||||
"6": {
|
||||
"BoundaryCellsArrayName": "BoundaryCells",
|
||||
"CellFeatureAttributeMatrixPath": {
|
||||
"Attribute Matrix Name": "Grain Data",
|
||||
"Data Array Name": "",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"FeatureIdsArrayPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "FeatureIds",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"FilterVersion": "6.5.138",
|
||||
"Filter_Enabled": true,
|
||||
"Filter_Human_Label": "Find Feature Neighbors",
|
||||
"Filter_Name": "FindNeighbors",
|
||||
"Filter_Uuid": "{97cf66f8-7a9b-5ec2-83eb-f8c4c8a17bac}",
|
||||
"NeighborListArrayName": "NeighborList",
|
||||
"NumNeighborsArrayName": "NumNeighbors",
|
||||
"SharedSurfaceAreaListArrayName": "SharedSurfaceAreaList",
|
||||
"StoreBoundaryCells": 0,
|
||||
"StoreSurfaceFeatures": 1,
|
||||
"SurfaceFeaturesArrayName": "SurfaceFeatures"
|
||||
},
|
||||
"7": {
|
||||
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|
||||
"CellEulerAnglesArrayName": "EulerAngles",
|
||||
"CrystalStructuresArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "CrystalStructures",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"FeatureEulerAnglesArrayName": "EulerAngles",
|
||||
"FeatureIdsArrayPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "FeatureIds",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"FeaturePhasesArrayPath": {
|
||||
"Attribute Matrix Name": "Grain Data",
|
||||
"Data Array Name": "Phases",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"FilterVersion": "6.5.138",
|
||||
"Filter_Enabled": true,
|
||||
"Filter_Human_Label": "Match Crystallography",
|
||||
"Filter_Name": "MatchCrystallography",
|
||||
"Filter_Uuid": "{7bfb6e4a-6075-56da-8006-b262d99dff30}",
|
||||
"InputStatsArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "Statistics",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"MaxIterations": 100,
|
||||
"NeighborListArrayPath": {
|
||||
"Attribute Matrix Name": "Grain Data",
|
||||
"Data Array Name": "NeighborList",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"NumFeaturesArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "NumFeatures",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"PhaseTypesArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "PhaseTypes",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"SharedSurfaceAreaListArrayPath": {
|
||||
"Attribute Matrix Name": "Grain Data",
|
||||
"Data Array Name": "SharedSurfaceAreaList",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"SurfaceFeaturesArrayPath": {
|
||||
"Attribute Matrix Name": "Grain Data",
|
||||
"Data Array Name": "SurfaceFeatures",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"VolumesArrayName": "Volumes"
|
||||
},
|
||||
"8": {
|
||||
"CellEulerAnglesArrayPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "EulerAngles",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"CellIPFColorsArrayName": "IPFColor",
|
||||
"CellPhasesArrayPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "Phases",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"CrystalStructuresArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "CrystalStructures",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"FilterVersion": "6.5.138",
|
||||
"Filter_Enabled": true,
|
||||
"Filter_Human_Label": "Generate IPF Colors",
|
||||
"Filter_Name": "GenerateIPFColors",
|
||||
"Filter_Uuid": "{a50e6532-8075-5de5-ab63-945feb0de7f7}",
|
||||
"GoodVoxelsArrayPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"ReferenceDir": {
|
||||
"x": 0,
|
||||
"y": 0,
|
||||
"z": 1
|
||||
},
|
||||
"UseGoodVoxels": 0
|
||||
},
|
||||
"9": {
|
||||
"FilterVersion": "1.2.812",
|
||||
"Filter_Enabled": true,
|
||||
"Filter_Human_Label": "Write DREAM.3D Data File",
|
||||
"Filter_Name": "DataContainerWriter",
|
||||
"Filter_Uuid": "{3fcd4c43-9d75-5b86-aad4-4441bc914f37}",
|
||||
"OutputFile": "C:\\Users\\work\\Desktop\\2phase_irregularGrid.dream3d",
|
||||
"WriteTimeSeries": 0,
|
||||
"WriteXdmfFile": 1
|
||||
},
|
||||
"PipelineBuilder": {
|
||||
"Name": "2phase_irregularGrid",
|
||||
"Number_Filters": 10,
|
||||
"Version": 6
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,42 @@
|
|||
<?xml version="1.0"?>
|
||||
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd"[]>
|
||||
<Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
|
||||
<Domain>
|
||||
<!-- *************** START OF SyntheticVolumeDataContainer *************** -->
|
||||
<Grid Name="SyntheticVolumeDataContainer" GridType="Uniform">
|
||||
<Topology TopologyType="3DCoRectMesh" Dimensions="11 9 14 "></Topology>
|
||||
<Geometry Type="ORIGIN_DXDYDZ">
|
||||
<!-- Origin Z, Y, X -->
|
||||
<DataItem Format="XML" Dimensions="3">0 0 0</DataItem>
|
||||
<!-- DxDyDz (Spacing/Resolution) Z, Y, X -->
|
||||
<DataItem Format="XML" Dimensions="3">0.8 0.8 0.8</DataItem>
|
||||
</Geometry>
|
||||
<Attribute Name="BoundaryCells" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="10 8 13 1" NumberType="Char" Precision="1" >
|
||||
2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/BoundaryCells
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="EulerAngles" AttributeType="Vector" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="10 8 13 3" NumberType="Float" Precision="4" >
|
||||
2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/EulerAngles
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="FeatureIds" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="10 8 13 1" NumberType="Int" Precision="4" >
|
||||
2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/FeatureIds
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="IPFColor" AttributeType="Vector" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="10 8 13 3" NumberType="UChar" Precision="1" >
|
||||
2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/IPFColor
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="Phases" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="10 8 13 1" NumberType="Int" Precision="4" >
|
||||
2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/Phases
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
</Grid>
|
||||
<!-- *************** END OF SyntheticVolumeDataContainer *************** -->
|
||||
</Domain>
|
||||
</Xdmf>
|
||||
Binary file not shown.
File diff suppressed because one or more lines are too long
|
|
@ -0,0 +1,77 @@
|
|||
<?xml version="1.0"?>
|
||||
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd"[]>
|
||||
<Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
|
||||
<Domain>
|
||||
<!-- *************** START OF Small IN100 *************** -->
|
||||
<Grid Name="Small IN100" GridType="Uniform">
|
||||
<Topology TopologyType="3DCoRectMesh" Dimensions="2 102 202 "></Topology>
|
||||
<Geometry Type="ORIGIN_DXDYDZ">
|
||||
<!-- Origin Z, Y, X -->
|
||||
<DataItem Format="XML" Dimensions="3">0 35 -294.7</DataItem>
|
||||
<!-- DxDyDz (Spacing/Resolution) Z, Y, X -->
|
||||
<DataItem Format="XML" Dimensions="3">0.35 0.35 0.35</DataItem>
|
||||
</Geometry>
|
||||
<Attribute Name="Confidence Index" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Confidence Index
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="EulerAngles" AttributeType="Vector" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 3" NumberType="Float" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/EulerAngles
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="FeatureIds" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Int" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/FeatureIds
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="Fit" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Fit
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="IPFColor" AttributeType="Vector" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 3" NumberType="UChar" Precision="1" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/IPFColor
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="Image Quality" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Image Quality
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="Mask" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="uchar" Precision="1" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Mask
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="ParentIds" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Int" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/ParentIds
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="Phases" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Int" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Phases
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="SEM Signal" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/SEM Signal
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="X Position" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/X Position
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="Y Position" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Y Position
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
</Grid>
|
||||
<!-- *************** END OF Small IN100 *************** -->
|
||||
</Domain>
|
||||
</Xdmf>
|
||||
|
|
@ -1,11 +1,12 @@
|
|||
import os
|
||||
|
||||
import filecmp
|
||||
import pytest
|
||||
import numpy as np
|
||||
|
||||
from damask import ConfigMaterial
|
||||
from damask import Table
|
||||
from damask import Rotation
|
||||
from damask import Grid
|
||||
|
||||
@pytest.fixture
|
||||
def ref_path(ref_path_base):
|
||||
|
|
@ -108,3 +109,32 @@ class TestConfigMaterial:
|
|||
m = ConfigMaterial().material_add(**kw)
|
||||
assert len(m['material']) == N
|
||||
assert len(m['material'][0]['constituents']) == n
|
||||
|
||||
|
||||
@pytest.mark.parametrize('cell_ensemble_data',[None,'CellEnsembleData'])
|
||||
def test_load_DREAM3D(self,ref_path,cell_ensemble_data):
|
||||
grain_c = ConfigMaterial.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','Grain Data',
|
||||
cell_ensemble_data = cell_ensemble_data)
|
||||
point_c = ConfigMaterial.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d',
|
||||
cell_ensemble_data = cell_ensemble_data)
|
||||
|
||||
assert point_c.is_valid and grain_c.is_valid and \
|
||||
len(point_c['material'])+1 == len(grain_c['material'])
|
||||
|
||||
grain_m = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','FeatureIds').material.flatten()
|
||||
point_m = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d').material.flatten()
|
||||
|
||||
for i in np.unique(point_m):
|
||||
j = int(grain_m[(point_m==i).nonzero()[0][0]])
|
||||
assert np.allclose(point_c['material'][i]['constituents'][0]['O'],
|
||||
grain_c['material'][j]['constituents'][0]['O'])
|
||||
assert point_c['material'][i]['constituents'][0]['phase'] == \
|
||||
grain_c['material'][j]['constituents'][0]['phase']
|
||||
|
||||
|
||||
def test_load_DREAM3D_reference(self,tmp_path,ref_path,update):
|
||||
config = ConfigMaterial.load_DREAM3D(ref_path/'measured.dream3d')
|
||||
config.save(tmp_path/'material.yaml')
|
||||
if update:
|
||||
config.save(ref_path/'measured.material_yaml')
|
||||
assert config.is_valid and filecmp.cmp(tmp_path/'material.yaml',ref_path/'measured.material_yaml')
|
||||
|
|
|
|||
|
|
@ -420,12 +420,31 @@ class TestGrid:
|
|||
t = Table(np.column_stack((coords.reshape(-1,3,order='F'),grid.material.flatten(order='F'))),{'c':3,'m':1})
|
||||
assert grid_equal(grid.sort().renumber(),Grid.from_table(t,'c',['m']))
|
||||
|
||||
|
||||
@pytest.mark.parametrize('periodic',[True,False])
|
||||
@pytest.mark.parametrize('direction',['x','y','z',['x','y'],'zy','xz',['x','y','z']])
|
||||
def test_get_grain_boundaries(self,update,ref_path,periodic,direction):
|
||||
grid=Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
|
||||
current=grid.get_grain_boundaries(periodic,direction)
|
||||
grid = Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
|
||||
current = grid.get_grain_boundaries(periodic,direction)
|
||||
if update:
|
||||
current.save(ref_path/f'get_grain_boundaries_8g12x15x20_{direction}_{periodic}.vtu',parallel=False)
|
||||
reference=VTK.load(ref_path/f'get_grain_boundaries_8g12x15x20_{"".join(direction)}_{periodic}.vtu')
|
||||
reference = VTK.load(ref_path/f'get_grain_boundaries_8g12x15x20_{"".join(direction)}_{periodic}.vtu')
|
||||
assert current.__repr__() == reference.__repr__()
|
||||
|
||||
|
||||
def test_load_DREAM3D(self,ref_path):
|
||||
grain = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','FeatureIds')
|
||||
point = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d')
|
||||
|
||||
assert np.allclose(grain.origin,point.origin) and \
|
||||
np.allclose(grain.size,point.size) and \
|
||||
(grain.sort().material == point.material+1).all()
|
||||
|
||||
|
||||
def test_load_DREAM3D_reference(self,ref_path,update):
|
||||
current = Grid.load_DREAM3D(ref_path/'measured.dream3d')
|
||||
reference = Grid.load(ref_path/'measured')
|
||||
if update:
|
||||
current.save(ref_path/'measured.vtr')
|
||||
|
||||
assert grid_equal(current,reference)
|
||||
|
|
|
|||
|
|
@ -1,6 +1,10 @@
|
|||
import random
|
||||
import os
|
||||
|
||||
import pytest
|
||||
import numpy as np
|
||||
from scipy import stats
|
||||
import h5py
|
||||
|
||||
from damask import util
|
||||
|
||||
|
|
@ -102,3 +106,36 @@ class TestUtil:
|
|||
@pytest.mark.parametrize('style',[util.emph,util.deemph,util.warn,util.strikeout])
|
||||
def test_decorate(self,style):
|
||||
assert 'DAMASK' in style('DAMASK')
|
||||
|
||||
@pytest.mark.parametrize('complete',[True,False])
|
||||
def test_D3D_base_group(self,tmp_path,complete):
|
||||
base_group = ''.join(random.choices('DAMASK', k=10))
|
||||
with h5py.File(tmp_path/'base_group.dream3d','w') as f:
|
||||
f.create_group(os.path.join(base_group,'_SIMPL_GEOMETRY'))
|
||||
if complete:
|
||||
f[os.path.join(base_group,'_SIMPL_GEOMETRY')].create_dataset('SPACING',data=np.ones(3))
|
||||
|
||||
if complete:
|
||||
assert base_group == util.DREAM3D_base_group(tmp_path/'base_group.dream3d')
|
||||
else:
|
||||
with pytest.raises(ValueError):
|
||||
util.DREAM3D_base_group(tmp_path/'base_group.dream3d')
|
||||
|
||||
@pytest.mark.parametrize('complete',[True,False])
|
||||
def test_D3D_cell_data_group(self,tmp_path,complete):
|
||||
base_group = ''.join(random.choices('DAMASK', k=10))
|
||||
cell_data_group = ''.join(random.choices('KULeuven', k=10))
|
||||
cells = np.random.randint(1,50,3)
|
||||
with h5py.File(tmp_path/'cell_data_group.dream3d','w') as f:
|
||||
f.create_group(os.path.join(base_group,'_SIMPL_GEOMETRY'))
|
||||
f[os.path.join(base_group,'_SIMPL_GEOMETRY')].create_dataset('SPACING',data=np.ones(3))
|
||||
f[os.path.join(base_group,'_SIMPL_GEOMETRY')].create_dataset('DIMENSIONS',data=cells[::-1])
|
||||
f[base_group].create_group(cell_data_group)
|
||||
if complete:
|
||||
f[os.path.join(base_group,cell_data_group)].create_dataset('data',shape=np.append(cells,1))
|
||||
|
||||
if complete:
|
||||
assert cell_data_group == util.DREAM3D_cell_data_group(tmp_path/'cell_data_group.dream3d')
|
||||
else:
|
||||
with pytest.raises(ValueError):
|
||||
util.DREAM3D_cell_data_group(tmp_path/'cell_data_group.dream3d')
|
||||
|
|
|
|||
Loading…
Reference in New Issue