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docstring adjustments

This commit is contained in:
Martin Diehl 2022-01-12 23:13:38 +01:00
parent 2c1231a806
commit 3acabcdc7f
8 changed files with 41 additions and 41 deletions
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2
python/damask/_colormap.py
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@ -205,7 +205,7 @@ class Colormap(mpl.colors.ListedColormap):
Returns Returns
------- -------
color : np.ndarray, shape(...,4) color : numpy.ndarray, shape(...,4)
RGBA values of interpolated color(s). RGBA values of interpolated color(s).
Examples Examples

22
python/damask/_grid.py
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@ -39,7 +39,7 @@ class Grid:
Parameters Parameters
---------- ----------
material : numpy.ndarray of shape (:,:,:) material : numpy.ndarray, shape (:,:,:)
Material indices. The shape of the material array defines Material indices. The shape of the material array defines
the number of cells. the number of cells.
size : sequence of float, len (3) size : sequence of float, len (3)
@ -406,14 +406,14 @@ class Grid:
Number of cells in x,y,z direction. Number of cells in x,y,z direction.
size : sequence of float, len (3) size : sequence of float, len (3)
Physical size of the grid in meter. Physical size of the grid in meter.
seeds : numpy.ndarray of shape (:,3) seeds : numpy.ndarray, shape (:,3)
Position of the seed points in meter. All points need to lay within the box. Position of the seed points in meter. All points need to lay within the box.
weights : sequence of float, len (seeds.shape[0]) weights : sequence of float, len (seeds.shape[0])
Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation. Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
material : sequence of int, len (seeds.shape[0]), optional material : sequence of int, len (seeds.shape[0]), optional
Material ID of the seeds. Material ID of the seeds.
Defaults to None, in which case materials are consecutively numbered. Defaults to None, in which case materials are consecutively numbered.
periodic : Boolean, optional periodic : bool, optional
Assume grid to be periodic. Defaults to True. Assume grid to be periodic. Defaults to True.
Returns Returns
@ -462,12 +462,12 @@ class Grid:
Number of cells in x,y,z direction. Number of cells in x,y,z direction.
size : sequence of float, len (3) size : sequence of float, len (3)
Physical size of the grid in meter. Physical size of the grid in meter.
seeds : numpy.ndarray of shape (:,3) seeds : numpy.ndarray, shape (:,3)
Position of the seed points in meter. All points need to lay within the box. Position of the seed points in meter. All points need to lay within the box.
material : sequence of int, len (seeds.shape[0]), optional material : sequence of int, len (seeds.shape[0]), optional
Material ID of the seeds. Material ID of the seeds.
Defaults to None, in which case materials are consecutively numbered. Defaults to None, in which case materials are consecutively numbered.
periodic : Boolean, optional periodic : bool, optional
Assume grid to be periodic. Defaults to True. Assume grid to be periodic. Defaults to True.
Returns Returns
@ -706,10 +706,10 @@ class Grid:
Fill value for primitive. Defaults to material.max()+1. Fill value for primitive. Defaults to material.max()+1.
R : damask.Rotation, optional R : damask.Rotation, optional
Rotation of primitive. Defaults to no rotation. Rotation of primitive. Defaults to no rotation.
inverse : Boolean, optional inverse : bool, optional
Retain original materials within primitive and fill outside. Retain original materials within primitive and fill outside.
Defaults to False. Defaults to False.
periodic : Boolean, optional periodic : bool, optional
Assume grid to be periodic. Defaults to True. Assume grid to be periodic. Defaults to True.
Returns Returns
@ -858,7 +858,7 @@ class Grid:
---------- ----------
cells : sequence of int, len (3) cells : sequence of int, len (3)
Number of cells in x,y,z direction. Number of cells in x,y,z direction.
periodic : Boolean, optional periodic : bool, optional
Assume grid to be periodic. Defaults to True. Assume grid to be periodic. Defaults to True.
Returns Returns
@ -907,7 +907,7 @@ class Grid:
Size of smoothing stencil. Size of smoothing stencil.
selection : sequence of int, optional selection : sequence of int, optional
Field values that can be altered. Defaults to all. Field values that can be altered. Defaults to all.
periodic : Boolean, optional periodic : bool, optional
Assume grid to be periodic. Defaults to True. Assume grid to be periodic. Defaults to True.
Returns Returns
@ -1125,7 +1125,7 @@ class Grid:
trigger : sequence of int, optional trigger : sequence of int, optional
List of material indices that trigger a change. List of material indices that trigger a change.
Defaults to [], meaning that any different neighbor triggers a change. Defaults to [], meaning that any different neighbor triggers a change.
periodic : Boolean, optional periodic : bool, optional
Assume grid to be periodic. Defaults to True. Assume grid to be periodic. Defaults to True.
Returns Returns
@ -1159,7 +1159,7 @@ class Grid:
Parameters Parameters
---------- ----------
periodic : Boolean, optional periodic : bool, optional
Assume grid to be periodic. Defaults to True. Assume grid to be periodic. Defaults to True.
directions : (sequence of) string, optional directions : (sequence of) string, optional
Direction(s) along which the boundaries are determined. Direction(s) along which the boundaries are determined.

12
python/damask/_orientation.py
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@ -393,8 +393,8 @@ class Orientation(Rotation,Crystal):
Returns Returns
------- -------
in : numpy.ndarray of quaternion.shape in : numpy.ndarray of bool, quaternion.shape
Boolean array indicating whether Rodrigues-Frank vector falls into fundamental zone. Whether Rodrigues-Frank vector falls into fundamental zone.
Notes Notes
----- -----
@ -437,8 +437,8 @@ class Orientation(Rotation,Crystal):
Returns Returns
------- -------
in : numpy.ndarray of quaternion.shape in : numpy.ndarray of bool, quaternion.shape
Boolean array indicating whether Rodrigues-Frank vector falls into disorientation FZ. Whether Rodrigues-Frank vector falls into disorientation FZ.
References References
---------- ----------
@ -651,8 +651,8 @@ class Orientation(Rotation,Crystal):
Returns Returns
------- -------
in : numpy.ndarray of shape (...) in : numpy.ndarray, shape (...)
Boolean array indicating whether vector falls into SST. Whether vector falls into SST.
""" """
if not isinstance(vector,np.ndarray) or vector.shape[-1] != 3: if not isinstance(vector,np.ndarray) or vector.shape[-1] != 3:

2
python/damask/_result.py
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@ -1817,7 +1817,7 @@ class Result:
output : (list of) str, optional output : (list of) str, optional
Names of the datasets to export to the file. Names of the datasets to export to the file.
Defaults to '*', in which case all datasets are exported. Defaults to '*', in which case all datasets are exported.
overwrite : boolean, optional overwrite : bool, optional
Overwrite existing configuration files. Overwrite existing configuration files.
Defaults to False. Defaults to False.

22
python/damask/_rotation.py
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@ -671,7 +671,7 @@ class Rotation:
---------- ----------
q : numpy.ndarray of shape (...,4) q : numpy.ndarray of shape (...,4)
Unit quaternion (q_0, q_1, q_2, q_3) in positive real hemisphere, i.e. ǀqǀ = 1, q_0 ≥ 0. Unit quaternion (q_0, q_1, q_2, q_3) in positive real hemisphere, i.e. ǀqǀ = 1, q_0 ≥ 0.
accept_homomorph : boolean, optional accept_homomorph : bool, optional
Allow homomorphic variants, i.e. q_0 < 0 (negative real hemisphere). Allow homomorphic variants, i.e. q_0 < 0 (negative real hemisphere).
Defaults to False. Defaults to False.
P : int ∈ {-1,1}, optional P : int ∈ {-1,1}, optional
@ -706,7 +706,7 @@ class Rotation:
phi : numpy.ndarray of shape (...,3) phi : numpy.ndarray of shape (...,3)
Euler angles (φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π]) Euler angles (φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π])
or (φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360]) if degrees == True. or (φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360]) if degrees == True.
degrees : boolean, optional degrees : bool, optional
Euler angles are given in degrees. Defaults to False. Euler angles are given in degrees. Defaults to False.
Notes Notes
@ -737,9 +737,9 @@ class Rotation:
axis_angle : numpy.ndarray of shape (...,4) axis_angle : numpy.ndarray of shape (...,4)
Axis and angle (n_1, n_2, n_3, ω) with ǀnǀ = 1 and ω ∈ [0,π] Axis and angle (n_1, n_2, n_3, ω) with ǀnǀ = 1 and ω ∈ [0,π]
or ω ∈ [0,180] if degrees == True. or ω ∈ [0,180] if degrees == True.
degrees : boolean, optional degrees : bool, optional
Angle ω is given in degrees. Defaults to False. Angle ω is given in degrees. Defaults to False.
normalize: boolean, optional normalize: bool, optional
Allow ǀnǀ ≠ 1. Defaults to False. Allow ǀnǀ ≠ 1. Defaults to False.
P : int ∈ {-1,1}, optional P : int ∈ {-1,1}, optional
Sign convention. Defaults to -1. Sign convention. Defaults to -1.
@ -773,9 +773,9 @@ class Rotation:
---------- ----------
basis : numpy.ndarray of shape (...,3,3) basis : numpy.ndarray of shape (...,3,3)
Three three-dimensional lattice basis vectors. Three three-dimensional lattice basis vectors.
orthonormal : boolean, optional orthonormal : bool, optional
Basis is strictly orthonormal, i.e. is free of stretch components. Defaults to True. Basis is strictly orthonormal, i.e. is free of stretch components. Defaults to True.
reciprocal : boolean, optional reciprocal : bool, optional
Basis vectors are given in reciprocal (instead of real) space. Defaults to False. Basis vectors are given in reciprocal (instead of real) space. Defaults to False.
""" """
@ -851,7 +851,7 @@ class Rotation:
---------- ----------
rho : numpy.ndarray of shape (...,4) rho : numpy.ndarray of shape (...,4)
Rodrigues–Frank vector (n_1, n_2, n_3, tan(ω/2)) with ǀnǀ = 1 and ω ∈ [0,π]. Rodrigues–Frank vector (n_1, n_2, n_3, tan(ω/2)) with ǀnǀ = 1 and ω ∈ [0,π].
normalize : boolean, optional normalize : bool, optional
Allow ǀnǀ ≠ 1. Defaults to False. Allow ǀnǀ ≠ 1. Defaults to False.
P : int ∈ {-1,1}, optional P : int ∈ {-1,1}, optional
Sign convention. Defaults to -1. Sign convention. Defaults to -1.
@ -977,9 +977,9 @@ class Rotation:
N : integer, optional N : integer, optional
Number of discrete orientations to be sampled from the given ODF. Number of discrete orientations to be sampled from the given ODF.
Defaults to 500. Defaults to 500.
degrees : boolean, optional degrees : bool, optional
Euler space grid coordinates are in degrees. Defaults to True. Euler space grid coordinates are in degrees. Defaults to True.
fractions : boolean, optional fractions : bool, optional
ODF values correspond to volume fractions, not probability densities. ODF values correspond to volume fractions, not probability densities.
Defaults to True. Defaults to True.
rng_seed: {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional rng_seed: {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
@ -1033,7 +1033,7 @@ class Rotation:
Standard deviation of (Gaussian) misorientation distribution. Standard deviation of (Gaussian) misorientation distribution.
N : int, optional N : int, optional
Number of samples. Defaults to 500. Number of samples. Defaults to 500.
degrees : boolean, optional degrees : bool, optional
sigma is given in degrees. Defaults to True. sigma is given in degrees. Defaults to True.
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator. A seed to initialize the BitGenerator.
@ -1072,7 +1072,7 @@ class Rotation:
Defaults to 0. Defaults to 0.
N : int, optional N : int, optional
Number of samples. Defaults to 500. Number of samples. Defaults to 500.
degrees : boolean, optional degrees : bool, optional
sigma, alpha, and beta are given in degrees. sigma, alpha, and beta are given in degrees.
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator. A seed to initialize the BitGenerator.

6
python/damask/_vtk.py
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@ -28,8 +28,8 @@ class VTK:
---------- ----------
vtk_data : subclass of vtk.vtkDataSet vtk_data : subclass of vtk.vtkDataSet
Description of geometry and topology, optionally with attached data. Description of geometry and topology, optionally with attached data.
Valid types are vtk.vtkRectilinearGrid, vtk.vtkUnstructuredGrid, Valid types are vtk.vtkImageData, vtk.vtkUnstructuredGrid,
or vtk.vtkPolyData. vtk.vtkPolyData, and vtk.vtkRectilinearGrid.
""" """
self.vtk_data = vtk_data self.vtk_data = vtk_data
@ -242,7 +242,7 @@ class VTK:
---------- ----------
fname : str or pathlib.Path fname : str or pathlib.Path
Filename for writing. Filename for writing.
parallel : boolean, optional parallel : bool, optional
Write data in parallel background process. Defaults to True. Write data in parallel background process. Defaults to True.
compress : bool, optional compress : bool, optional
Compress with zlib algorithm. Defaults to True. Compress with zlib algorithm. Defaults to True.

14
python/damask/seeds.py
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@ -61,7 +61,7 @@ def from_Poisson_disc(size: _FloatSequence, N_seeds: int, N_candidates: int, dis
Number of candidates to consider for finding best candidate. Number of candidates to consider for finding best candidate.
distance : float distance : float
Minimum acceptable distance to other seeds. Minimum acceptable distance to other seeds.
periodic : boolean, optional periodic : bool, optional
Calculate minimum distance for periodically repeated grid. Calculate minimum distance for periodically repeated grid.
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator. Defaults to None. A seed to initialize the BitGenerator. Defaults to None.
@ -99,8 +99,8 @@ def from_Poisson_disc(size: _FloatSequence, N_seeds: int, N_candidates: int, dis
return coords return coords
def from_grid(grid, selection: _IntSequence = None, def from_grid(grid, selection: _IntSequence = None, invert_selection: bool = False,
invert: bool = False, average: bool = False, periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]: average: bool = False, periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]:
""" """
Create seeds from grid description. Create seeds from grid description.
@ -110,11 +110,11 @@ def from_grid(grid, selection: _IntSequence = None,
Grid from which the material IDs are used as seeds. Grid from which the material IDs are used as seeds.
selection : sequence of int, optional selection : sequence of int, optional
Material IDs to consider. Material IDs to consider.
invert : boolean, false invert_selection : bool, optional
Consider all material IDs except those in selection. Defaults to False. Consider all material IDs except those in selection. Defaults to False.
average : boolean, optional average : bool, optional
Seed corresponds to center of gravity of material ID cloud. Seed corresponds to center of gravity of material ID cloud.
periodic : boolean, optional periodic : bool, optional
Center of gravity accounts for periodic boundaries. Center of gravity accounts for periodic boundaries.
Returns Returns
@ -125,7 +125,7 @@ def from_grid(grid, selection: _IntSequence = None,
""" """
material = grid.material.reshape((-1,1),order='F') material = grid.material.reshape((-1,1),order='F')
mask = _np.full(grid.cells.prod(),True,dtype=bool) if selection is None else \ mask = _np.full(grid.cells.prod(),True,dtype=bool) if selection is None else \
_np.isin(material,selection,invert=invert).flatten() _np.isin(material,selection,invert=invert_selection).flatten()
coords = _grid_filters.coordinates0_point(grid.cells,grid.size).reshape(-1,3,order='F') coords = _grid_filters.coordinates0_point(grid.cells,grid.size).reshape(-1,3,order='F')
if not average: if not average:

2
python/tests/test_seeds.py
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@ -67,5 +67,5 @@ class TestSeeds:
coords = seeds.from_random(size,N_seeds,cells) coords = seeds.from_random(size,N_seeds,cells)
grid = Grid.from_Voronoi_tessellation(cells,size,coords) grid = Grid.from_Voronoi_tessellation(cells,size,coords)
selection=np.random.randint(N_seeds)+1 selection=np.random.randint(N_seeds)+1
coords,material = seeds.from_grid(grid,average=average,periodic=periodic,invert=invert,selection=[selection]) coords,material = seeds.from_grid(grid,average=average,periodic=periodic,invert_selection=invert,selection=[selection])
assert selection not in material if invert else (selection==material).all() assert selection not in material if invert else (selection==material).all()