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

# Conflicts:
#   python/damask/_rotation.py
This commit is contained in:
Philip Eisenlohr 2022-11-16 18:05:36 +00:00
parent 740965df7c 5d656d9c76
commit 25979fcd77
9 changed files with 61 additions and 35 deletions
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2
VERSION
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@ -1 +1 @@
3.0.0-alpha7-86-g72408f389
3.0.0-alpha7-91-g584d5b421

2
python/damask/_colormap.py
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@ -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

21
python/damask/_grid.py
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@ -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

20
python/damask/_rotation.py
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@ -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:
if np.any(qu[...,0] < 0.0):
raise ValueError('quaternion with negative first (real) component')
if not np.allclose(np.linalg.norm(qu,axis=-1), 1.0,rtol=0.0):
elif np.any(qu[...,0] < 0.0):
raise ValueError('quaternion with negative first (real) component')
if not np.allclose(np.linalg.norm(qu,axis=-1), 1.0,rtol=1e-8):
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.

6
python/damask/_table.py
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@ -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

2
python/damask/_vtk.py
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@ -110,7 +110,7 @@ class VTK:
Parameters
----------
comments : str or sequence of str
comments : (sequence of) str
Comments.
"""

2
python/damask/seeds.py
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@ -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.

14
python/damask/util.py
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@ -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

27
python/tests/test_Rotation.py
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@ -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)