Merge branch 'development' into 'polish-rotation-error-determination'

# Conflicts:
#   python/damask/_rotation.py

VERSION

@@ -1 +1 @@
-3.0.0-alpha7-86-g72408f389
+3.0.0-alpha7-91-g584d5b421

python/damask/_colormap.py

@@ -248,7 +248,7 @@ class Colormap(mpl.colors.ListedColormap):
 
         Parameters
         ----------
-        fraction : float or sequence of float
+        fraction : (sequence of) float
             Fractional coordinate(s) to evaluate Colormap at.
 
         Returns

python/damask/_grid.py

@@ -50,7 +50,7 @@ class Grid:
             Coordinates of grid origin in meter. Defaults to [0.0,0.0,0.0].
         initial_conditions : dictionary, optional
             Labels and values of the inital conditions at each material point.
-        comments : str or sequence of str, optional
+        comments : (sequence of) str, optional
             Additional, human-readable information, e.g. history of operations.
 
         """
@@ -427,7 +427,7 @@ class Grid:
         coordinates : str
             Label of the vector column containing the spatial coordinates.
             Need to be ordered (1./x fast, 3./z slow).
-        labels : str or sequence of str
+        labels : (sequence of) str
             Label(s) of the columns containing the material definition.
             Each unique combination of values results in one material ID.
 
@@ -972,15 +972,16 @@ class Grid:
         # materials: 1
 
         """
-        options = ('nearest',False,None)
         orig = tuple(map(np.linspace,self.origin             + self.size/self.cells*.5,
                                      self.origin + self.size - self.size/self.cells*.5,self.cells))
+        interpolator = partial(interpolate.RegularGridInterpolator,
+                               points=orig,method='nearest',bounds_error=False,fill_value=None)
         new = grid_filters.coordinates0_point(cells,self.size,self.origin)
 
-        return Grid(material = interpolate.RegularGridInterpolator(orig,self.material,*options)(new).astype(int),
+        return Grid(material = interpolator(values=self.material)(new).astype(int),
                     size     = self.size,
                     origin   = self.origin,
-                    initial_conditions = {k: interpolate.RegularGridInterpolator(orig,v,*options)(new)
+                    initial_conditions = {k: interpolator(values=v)(new)
                                           for k,v in self.initial_conditions.items()},
                     comments = self.comments+[util.execution_stamp('Grid','scale')],
                    )
@@ -1043,9 +1044,9 @@ class Grid:
 
         Parameters
         ----------
-        from_material : int or sequence of int
+        from_material : (sequence of) int
             Material indices to be substituted.
-        to_material : int or sequence of int
+        to_material : (sequence of) int
             New material indices.
 
         Returns
@@ -1104,7 +1105,7 @@ class Grid:
         distance : float, optional
             Voxel distance checked for presence of other materials.
             Defaults to sqrt(3).
-        selection : int or collection of int, optional
+        selection : (collection of) int, optional
             Material IDs to consider. Defaults to all.
         invert_selection : bool, optional
             Consider all material IDs except those in selection. Defaults to False.
@@ -1179,7 +1180,7 @@ class Grid:
             Center of the primitive.
             If given as integers, cell centers are addressed.
             If given as floats, physical coordinates are addressed.
-        exponent : float or sequence of float, len (3)
+        exponent : (sequence of) float, len (3)
             Exponents for the three axes.
             0 gives octahedron (ǀxǀ^(2^0) + ǀyǀ^(2^0) + ǀzǀ^(2^0) < 1)
             1 gives sphere     (ǀxǀ^(2^1) + ǀyǀ^(2^1) + ǀzǀ^(2^1) < 1)
@@ -1271,7 +1272,7 @@ class Grid:
         offset : int, optional
             Offset (positive or negative) to tag material IDs.
             Defaults to material.max()+1.
-        selection : int or collection of int, optional
+        selection : (collection of) int, optional
             Material IDs that trigger an offset.
             Defaults to any other than own material ID.
         invert_selection : bool, optional

python/damask/_rotation.py

@@ -468,7 +468,7 @@ class Rotation:
 
         Parameters
         ----------
-        shape : int or sequence of ints
+        shape : (sequence of) int
             New shape, number of elements needs to match the original shape.
             If an integer is supplied, then the result will be a 1-D array of that length.
         order : {'C', 'F', 'A'}, optional
@@ -496,7 +496,7 @@ class Rotation:
 
         Parameters
         ----------
-        shape : int or sequence of ints
+        shape : (sequence of) int
             Shape of broadcasted array, needs to be compatible with the original shape.
         mode : str, optional
             Where to preferentially locate missing dimensions.
@@ -773,12 +773,12 @@ class Rotation:
             raise ValueError('P ∉ {-1,1}')
 
         qu[...,1:4] *= -P
+
         if accept_homomorph:
             qu[qu[...,0] < 0.0] *= -1
-        else:
+        elif np.any(qu[...,0] < 0.0):
-            if np.any(qu[...,0] < 0.0):
+            raise ValueError('quaternion with negative first (real) component')
-                raise ValueError('quaternion with negative first (real) component')
+        if not np.allclose(np.linalg.norm(qu,axis=-1), 1.0,rtol=1e-8):
-        if not np.allclose(np.linalg.norm(qu,axis=-1), 1.0,rtol=0.0):
             raise ValueError('quaternion is not of unit length')
 
         return Rotation(qu)
@@ -1022,7 +1022,7 @@ class Rotation:
 
         Parameters
         ----------
-        shape : int or sequence of ints, optional
+        shape : (sequence of) int, optional
             Shape of the returned array. Defaults to None, which gives a scalar.
         rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
             A seed to initialize the BitGenerator.
@@ -1058,7 +1058,7 @@ class Rotation:
             Texture intensity values (probability density or volume fraction) at Euler space grid points.
         phi : numpy.ndarray, shape (n,3)
             Grid coordinates in Euler space at which weights are defined.
-        shape : int or sequence of ints, optional
+        shape : (sequence of) int, optional
             Shape of the returned array. Defaults to None, which gives a scalar.
         degrees : bool, optional
             Euler space grid coordinates are in degrees. Defaults to True.
@@ -1110,7 +1110,7 @@ class Rotation:
             Central rotation.
         sigma : float
             Standard deviation of (Gaussian) misorientation distribution.
-        shape : int or sequence of ints, optional
+        shape : (sequence of) int, optional
             Shape of the returned array. Defaults to None, which gives a scalar.
         degrees : bool, optional
             sigma is given in degrees. Defaults to False.
@@ -1168,7 +1168,7 @@ class Rotation:
         sigma : float, optional
             Standard deviation of (Gaussian) misorientation distribution.
             Defaults to 0.
-        shape : int or sequence of ints, optional
+        shape : (sequence of) int, optional
             Shape of the returned array. Defaults to None, which gives a scalar.
         degrees : bool, optional
             sigma and polar coordinates are given in degrees. Defaults to False.

python/damask/_table.py

@@ -25,7 +25,7 @@ class Table:
             For instance, 'F':(3,3) for a deformation gradient, or 'r':(1,) for a scalar.
         data : numpy.ndarray or pandas.DataFrame, optional
             Data. Existing column labels of a pandas.DataFrame will be replaced.
-        comments : str or iterable of str, optional
+        comments : (iterable of) str, optional
             Additional, human-readable information.
 
         """
@@ -464,9 +464,9 @@ class Table:
 
         Parameters
         ----------
-        label_old : str or iterable of str
+        label_old : (iterable of) str
             Old column label(s).
-        label_new : str or iterable of str
+        label_new : (iterable of) str
             New column label(s).
 
         Returns

python/damask/_vtk.py

@@ -110,7 +110,7 @@ class VTK:
 
         Parameters
         ----------
-        comments : str or sequence of str
+        comments : (sequence of) str
             Comments.
 
         """

python/damask/seeds.py

@@ -118,7 +118,7 @@ def from_grid(grid,
     ----------
     grid : damask.Grid
         Grid from which the material IDs are used as seeds.
-    selection : int or collection of int, optional
+    selection : (collection of) int, optional
         Material IDs to consider.
     invert_selection : bool, optional
         Consider all material IDs except those in selection. Defaults to False.

python/damask/util.py

@@ -46,7 +46,7 @@ def srepr(msg,
 
     Parameters
     ----------
-    msg : object with __repr__ or sequence of objects with __repr__
+    msg : (sequence of) object with __repr__
         Items to join.
     glue : str, optional
         Glue used for joining operation. Defaults to '\n'.
@@ -71,7 +71,7 @@ def emph(msg) -> str:
 
     Parameters
     ----------
-    msg : object with __repr__ or sequence of objects with __repr__
+    msg : (sequence of) object with __repr__
         Message to format.
 
     Returns
@@ -88,7 +88,7 @@ def deemph(msg) -> str:
 
     Parameters
     ----------
-    msg : object with __repr__ or sequence of objects with __repr__
+    msg : (sequence of) object with __repr__
         Message to format.
 
     Returns
@@ -105,7 +105,7 @@ def warn(msg) -> str:
 
     Parameters
     ----------
-    msg : object with __repr__ or sequence of objects with __repr__
+    msg : (sequence of) object with __repr__
         Message to format.
 
     Returns
@@ -122,7 +122,7 @@ def strikeout(msg) -> str:
 
     Parameters
     ----------
-    msg : object with __repr__ or iterable of objects with __repr__
+    msg : (iterable of) object with __repr__
         Message to format.
 
     Returns
@@ -738,7 +738,7 @@ def tail_repack(extended: _Union[str, _Sequence[str]],
 
     Parameters
     ----------
-    extended : str or list of str
+    extended : (list of) str
         Extended string list with potentially autosplitted tailing string relative to `existing`.
     existing : list of str
         Base string list.
@@ -767,7 +767,7 @@ def aslist(arg: _Union[_IntCollection, int, None]) -> _List:
 
     Parameters
     ----------
-    arg : int or collection of int or None
+    arg : (collection of) int or None
         Entity to transform into list.
 
     Returns

python/tests/test_Rotation.py

@@ -708,6 +708,7 @@ class TestRotation:
     @pytest.mark.parametrize('degrees',[True,False])
     def test_axis_angle(self,set_of_rotations,degrees,normalize,P):
         c = np.array([P*-1,P*-1,P*-1,1.])
+        c[:3] *= 0.9 if normalize else 1.0
         for rot in set_of_rotations:
             m = rot.as_Euler_angles()
             o = Rotation.from_axis_angle(rot.as_axis_angle(degrees)*c,degrees,normalize,P).as_Euler_angles()
@@ -730,16 +731,30 @@ class TestRotation:
             assert ok and np.isclose(np.linalg.norm(o[:3]),1.0) \
                       and o[3]<=np.pi+1.e-9, f'{m},{o},{rot.as_quaternion()}'
 
+    def test_parallel(self,set_of_rotations):
+        a = np.array([[1.0,0.0,0.0],
+                      [0.0,1.0,0.0]])
+        for rot in set_of_rotations:
+            assert rot.allclose(Rotation.from_parallel(a,rot.broadcast_to((2,))@a))
+
     @pytest.mark.parametrize('P',[1,-1])
     @pytest.mark.parametrize('normalize',[True,False])
     def test_Rodrigues(self,set_of_rotations,normalize,P):
         c = np.array([P*-1,P*-1,P*-1,1.])
+        c[:3] *= 0.9 if normalize else 1.0
         for rot in set_of_rotations:
             m = rot.as_matrix()
             o = Rotation.from_Rodrigues_vector(rot.as_Rodrigues_vector()*c,normalize,P).as_matrix()
             ok = np.allclose(m,o,atol=atol)
             assert ok and np.isclose(np.linalg.det(o),1.0), f'{m},{o}'
 
+    def test_Rodrigues_compact(self,set_of_rotations):
+        for rot in set_of_rotations:
+            c = rot.as_Rodrigues_vector(compact=True)
+            r = rot.as_Rodrigues_vector(compact=False)
+            assert np.allclose(r[:3]*r[3], c, equal_nan=True)
+
+
     @pytest.mark.parametrize('P',[1,-1])
     def test_homochoric(self,set_of_rotations,P):
         cutoff = np.tan(np.pi*.5*(1.-1e-4))
@@ -760,8 +775,9 @@ class TestRotation:
 
     @pytest.mark.parametrize('P',[1,-1])
     @pytest.mark.parametrize('accept_homomorph',[True,False])
+    # @pytest.mark.parametrize('normalize',[True,False])
     def test_quaternion(self,set_of_rotations,P,accept_homomorph):
-        c = np.array([1,P*-1,P*-1,P*-1]) * (-1 if accept_homomorph else 1)
+        c = np.array([1,P*-1,P*-1,P*-1]) * (-1 if accept_homomorph else 1) #* (0.9 if normalize else 1.0)
         for rot in set_of_rotations:
             m = rot.as_cubochoric()
             o = Rotation.from_quaternion(rot.as_quaternion()*c,accept_homomorph,P).as_cubochoric()
@@ -889,6 +905,15 @@ class TestRotation:
         with pytest.raises(ValueError):
             fr(eval(f'R.{to}()'),P=-30)
 
+
+    def test_invalid_multiplication(self):
+        rot = Rotation.from_random()
+        with pytest.raises(TypeError):
+            rot@Rotation.from_random()
+        with pytest.raises(TypeError):
+            rot@[1,2,3,4]
+
+
     @pytest.mark.parametrize('shape',[None,(3,),(4,2)])
     def test_broadcast(self,shape):
         rot = Rotation.from_random(shape)