Merge branch 'development' into '225-tolerate-non-unit-quaternion'
# Conflicts: # python/damask/_rotation.py # python/tests/test_Rotation.py
This commit is contained in:
Philip Eisenlohr
commit
1f947245bb
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@ -248,7 +248,7 @@ class Colormap(mpl.colors.ListedColormap):
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Parameters
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----------
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fraction : float or sequence of float
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fraction : (sequence of) float
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Fractional coordinate(s) to evaluate Colormap at.
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Returns
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@ -50,7 +50,7 @@ class Grid:
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Coordinates of grid origin in meter. Defaults to [0.0,0.0,0.0].
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initial_conditions : dictionary, optional
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Labels and values of the inital conditions at each material point.
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comments : str or sequence of str, optional
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comments : (sequence of) str, optional
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Additional, human-readable information, e.g. history of operations.
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"""
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@ -427,7 +427,7 @@ class Grid:
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coordinates : str
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Label of the vector column containing the spatial coordinates.
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Need to be ordered (1./x fast, 3./z slow).
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labels : str or sequence of str
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labels : (sequence of) str
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Label(s) of the columns containing the material definition.
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Each unique combination of values results in one material ID.
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@ -972,15 +972,16 @@ class Grid:
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# materials: 1
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"""
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options = ('nearest',False,None)
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orig = tuple(map(np.linspace,self.origin + self.size/self.cells*.5,
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self.origin + self.size - self.size/self.cells*.5,self.cells))
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interpolator = partial(interpolate.RegularGridInterpolator,
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points=orig,method='nearest',bounds_error=False,fill_value=None)
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new = grid_filters.coordinates0_point(cells,self.size,self.origin)
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return Grid(material = interpolate.RegularGridInterpolator(orig,self.material,*options)(new).astype(int),
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return Grid(material = interpolator(values=self.material)(new).astype(int),
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size = self.size,
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origin = self.origin,
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initial_conditions = {k: interpolate.RegularGridInterpolator(orig,v,*options)(new)
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initial_conditions = {k: interpolator(values=v)(new)
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for k,v in self.initial_conditions.items()},
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comments = self.comments+[util.execution_stamp('Grid','scale')],
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)
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@ -1043,9 +1044,9 @@ class Grid:
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Parameters
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----------
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from_material : int or sequence of int
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from_material : (sequence of) int
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Material indices to be substituted.
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to_material : int or sequence of int
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to_material : (sequence of) int
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New material indices.
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Returns
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@ -1104,7 +1105,7 @@ class Grid:
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distance : float, optional
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Voxel distance checked for presence of other materials.
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Defaults to sqrt(3).
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selection : int or collection of int, optional
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selection : (collection of) int, optional
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Material IDs to consider. Defaults to all.
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invert_selection : bool, optional
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Consider all material IDs except those in selection. Defaults to False.
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@ -1179,7 +1180,7 @@ class Grid:
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Center of the primitive.
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If given as integers, cell centers are addressed.
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If given as floats, physical coordinates are addressed.
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exponent : float or sequence of float, len (3)
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exponent : (sequence of) float, len (3)
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Exponents for the three axes.
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0 gives octahedron (ǀxǀ^(2^0) + ǀyǀ^(2^0) + ǀzǀ^(2^0) < 1)
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1 gives sphere (ǀxǀ^(2^1) + ǀyǀ^(2^1) + ǀzǀ^(2^1) < 1)
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@ -1271,7 +1272,7 @@ class Grid:
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offset : int, optional
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Offset (positive or negative) to tag material IDs.
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Defaults to material.max()+1.
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selection : int or collection of int, optional
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selection : (collection of) int, optional
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Material IDs that trigger an offset.
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Defaults to any other than own material ID.
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invert_selection : bool, optional
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@ -468,7 +468,7 @@ class Rotation:
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Parameters
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----------
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shape : int or sequence of ints
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shape : (sequence of) int
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New shape, number of elements needs to match the original shape.
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If an integer is supplied, then the result will be a 1-D array of that length.
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order : {'C', 'F', 'A'}, optional
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@ -496,7 +496,7 @@ class Rotation:
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Parameters
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----------
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shape : int or sequence of ints
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shape : (sequence of) int
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Shape of broadcasted array, needs to be compatible with the original shape.
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mode : str, optional
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Where to preferentially locate missing dimensions.
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@ -1028,7 +1028,7 @@ class Rotation:
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Parameters
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----------
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shape : int or sequence of ints, optional
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shape : (sequence of) int, optional
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Shape of the returned array. Defaults to None, which gives a scalar.
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rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
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A seed to initialize the BitGenerator.
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@ -1064,7 +1064,7 @@ class Rotation:
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Texture intensity values (probability density or volume fraction) at Euler space grid points.
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phi : numpy.ndarray, shape (n,3)
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Grid coordinates in Euler space at which weights are defined.
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shape : int or sequence of ints, optional
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shape : (sequence of) int, optional
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Shape of the returned array. Defaults to None, which gives a scalar.
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degrees : bool, optional
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Euler space grid coordinates are in degrees. Defaults to True.
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@ -1116,7 +1116,7 @@ class Rotation:
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Central rotation.
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sigma : float
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Standard deviation of (Gaussian) misorientation distribution.
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shape : int or sequence of ints, optional
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shape : (sequence of) int, optional
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Shape of the returned array. Defaults to None, which gives a scalar.
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degrees : bool, optional
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sigma is given in degrees. Defaults to False.
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@ -1174,7 +1174,7 @@ class Rotation:
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sigma : float, optional
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Standard deviation of (Gaussian) misorientation distribution.
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Defaults to 0.
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shape : int or sequence of ints, optional
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shape : (sequence of) int, optional
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Shape of the returned array. Defaults to None, which gives a scalar.
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degrees : bool, optional
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sigma and polar coordinates are given in degrees. Defaults to False.
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@ -25,7 +25,7 @@ class Table:
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For instance, 'F':(3,3) for a deformation gradient, or 'r':(1,) for a scalar.
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data : numpy.ndarray or pandas.DataFrame, optional
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Data. Existing column labels of a pandas.DataFrame will be replaced.
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comments : str or iterable of str, optional
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comments : (iterable of) str, optional
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Additional, human-readable information.
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"""
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@ -464,9 +464,9 @@ class Table:
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Parameters
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----------
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label_old : str or iterable of str
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label_old : (iterable of) str
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Old column label(s).
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label_new : str or iterable of str
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label_new : (iterable of) str
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New column label(s).
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Returns
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@ -110,7 +110,7 @@ class VTK:
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Parameters
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----------
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comments : str or sequence of str
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comments : (sequence of) str
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Comments.
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"""
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@ -118,7 +118,7 @@ def from_grid(grid,
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----------
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grid : damask.Grid
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Grid from which the material IDs are used as seeds.
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selection : int or collection of int, optional
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selection : (collection of) int, optional
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Material IDs to consider.
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invert_selection : bool, optional
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Consider all material IDs except those in selection. Defaults to False.
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@ -46,7 +46,7 @@ def srepr(msg,
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Parameters
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----------
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msg : object with __repr__ or sequence of objects with __repr__
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msg : (sequence of) object with __repr__
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Items to join.
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glue : str, optional
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Glue used for joining operation. Defaults to '\n'.
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@ -71,7 +71,7 @@ def emph(msg) -> str:
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Parameters
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----------
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msg : object with __repr__ or sequence of objects with __repr__
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msg : (sequence of) object with __repr__
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Message to format.
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Returns
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@ -88,7 +88,7 @@ def deemph(msg) -> str:
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Parameters
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----------
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msg : object with __repr__ or sequence of objects with __repr__
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msg : (sequence of) object with __repr__
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Message to format.
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Returns
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@ -105,7 +105,7 @@ def warn(msg) -> str:
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Parameters
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----------
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msg : object with __repr__ or sequence of objects with __repr__
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msg : (sequence of) object with __repr__
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Message to format.
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Returns
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@ -122,7 +122,7 @@ def strikeout(msg) -> str:
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Parameters
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----------
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msg : object with __repr__ or iterable of objects with __repr__
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msg : (iterable of) object with __repr__
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Message to format.
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Returns
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@ -738,7 +738,7 @@ def tail_repack(extended: _Union[str, _Sequence[str]],
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Parameters
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----------
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extended : str or list of str
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extended : (list of) str
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Extended string list with potentially autosplitted tailing string relative to `existing`.
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existing : list of str
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Base string list.
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@ -767,7 +767,7 @@ def aslist(arg: _Union[_IntCollection, int, None]) -> _List:
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Parameters
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----------
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arg : int or collection of int or None
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arg : (collection of) int or None
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Entity to transform into list.
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Returns
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@ -708,6 +708,7 @@ class TestRotation:
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@pytest.mark.parametrize('degrees',[True,False])
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def test_axis_angle(self,set_of_rotations,degrees,normalize,P):
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c = np.array([P*-1,P*-1,P*-1,1.])
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c[:3] *= 0.9 if normalize else 1.0
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for rot in set_of_rotations:
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m = rot.as_Euler_angles()
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o = Rotation.from_axis_angle(rot.as_axis_angle(degrees)*c,degrees,normalize,P).as_Euler_angles()
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@ -730,16 +731,30 @@ class TestRotation:
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assert ok and np.isclose(np.linalg.norm(o[:3]),1.0) \
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and o[3]<=np.pi+1.e-9, f'{m},{o},{rot.as_quaternion()}'
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def test_parallel(self,set_of_rotations):
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a = np.array([[1.0,0.0,0.0],
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[0.0,1.0,0.0]])
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for rot in set_of_rotations:
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assert rot.allclose(Rotation.from_parallel(a,rot.broadcast_to((2,))@a))
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@pytest.mark.parametrize('P',[1,-1])
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@pytest.mark.parametrize('normalize',[True,False])
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def test_Rodrigues(self,set_of_rotations,normalize,P):
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c = np.array([P*-1,P*-1,P*-1,1.])
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c[:3] *= 0.9 if normalize else 1.0
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for rot in set_of_rotations:
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m = rot.as_matrix()
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o = Rotation.from_Rodrigues_vector(rot.as_Rodrigues_vector()*c,normalize,P).as_matrix()
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ok = np.allclose(m,o,atol=atol)
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assert ok and np.isclose(np.linalg.det(o),1.0), f'{m},{o}'
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def test_Rodrigues_compact(self,set_of_rotations):
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for rot in set_of_rotations:
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c = rot.as_Rodrigues_vector(compact=True)
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r = rot.as_Rodrigues_vector(compact=False)
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assert np.allclose(r[:3]*r[3], c, equal_nan=True)
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@pytest.mark.parametrize('P',[1,-1])
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def test_homochoric(self,set_of_rotations,P):
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cutoff = np.tan(np.pi*.5*(1.-1e-4))
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@ -890,6 +905,15 @@ class TestRotation:
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with pytest.raises(ValueError):
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fr(eval(f'R.{to}()'),P=-30)
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def test_invalid_multiplication(self):
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rot = Rotation.from_random()
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with pytest.raises(TypeError):
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rot@Rotation.from_random()
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with pytest.raises(TypeError):
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rot@[1,2,3,4]
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@pytest.mark.parametrize('shape',[None,(3,),(4,2)])
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def test_broadcast(self,shape):
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rot = Rotation.from_random(shape)
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@ -900,7 +924,7 @@ class TestRotation:
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assert np.allclose(rot_broadcast.quaternion[...,i,:], rot.quaternion)
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@pytest.mark.parametrize('function,invalid',[(Rotation.from_quaternion, np.array([-1,0,0,0])),
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@pytest.mark.parametrize('function,invalid',[(Rotation.from_quaternion, np.array([-1,0,0,0])),
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(Rotation.from_quaternion, np.array([1,1,1,0])),
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(Rotation.from_Euler_angles, np.array([1,4,0])),
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(Rotation.from_axis_angle, np.array([1,0,0,4])),
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