Geom.load_ASCII now auto-shifts material indices
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commit
cb22c34db2
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@ -247,7 +247,7 @@ class Geom:
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raise TypeError(f'Invalid file: expected {grid.prod()} entries, found {i}')
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raise TypeError(f'Invalid file: expected {grid.prod()} entries, found {i}')
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if not np.any(np.mod(material,1) != 0.0): # no float present
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if not np.any(np.mod(material,1) != 0.0): # no float present
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material = material.astype('int')
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material = material.astype('int') - (1 if material.min() > 0 else 0)
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return Geom(material.reshape(grid,order='F'),size,origin,comments)
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return Geom(material.reshape(grid,order='F'),size,origin,comments)
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@ -802,7 +802,7 @@ class Orientation(Rotation):
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return np.all(components >= 0.0,axis=-1)
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return np.all(components >= 0.0,axis=-1)
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def IPF_color(self,vector,proper=False):
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def IPF_color(self,vector,in_SST=True,proper=False):
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"""
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"""
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Map vector to RGB color within standard stereographic triangle of own symmetry.
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Map vector to RGB color within standard stereographic triangle of own symmetry.
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@ -810,6 +810,9 @@ class Orientation(Rotation):
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----------
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----------
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vector : numpy.ndarray of shape (...,3)
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vector : numpy.ndarray of shape (...,3)
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Vector to colorize.
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Vector to colorize.
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in_SST : bool, optional
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Consider symmetrically equivalent orientations such that poles are located in SST.
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Defaults to True.
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proper : bool, optional
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proper : bool, optional
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Consider only vectors with z >= 0, hence combine two neighboring SSTs (with mirrored colors).
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Consider only vectors with z >= 0, hence combine two neighboring SSTs (with mirrored colors).
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Defaults to False.
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Defaults to False.
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@ -824,7 +827,7 @@ class Orientation(Rotation):
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Inverse pole figure color of the e_3 direction for a crystal in "Cube" orientation with cubic symmetry:
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Inverse pole figure color of the e_3 direction for a crystal in "Cube" orientation with cubic symmetry:
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>>> o = damask.Orientation(lattice='cubic')
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>>> o = damask.Orientation(lattice='cubic')
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>>> o.IPF_color(o.to_SST([0,0,1]))
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>>> o.IPF_color([0,0,1])
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array([1., 0., 0.])
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array([1., 0., 0.])
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References
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References
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@ -847,10 +850,13 @@ class Orientation(Rotation):
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... }
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... }
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"""
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"""
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vector_ = np.array(vector)
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if np.array(vector).shape[-1] != 3:
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if vector_.shape[-1] != 3:
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raise ValueError('Input is not a field of three-dimensional vectors.')
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raise ValueError('Input is not a field of three-dimensional vectors.')
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vector_ = self.to_SST(vector,proper) if in_SST else \
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self @ np.broadcast_to(vector,self.shape+(3,))
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if self.family == 'cubic':
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if self.family == 'cubic':
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basis = {'improper':np.array([ [-1. , 0. , 1. ],
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basis = {'improper':np.array([ [-1. , 0. , 1. ],
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[ np.sqrt(2.) , -np.sqrt(2.) , 0. ],
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[ np.sqrt(2.) , -np.sqrt(2.) , 0. ],
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@ -1076,7 +1082,7 @@ class Orientation(Rotation):
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@classmethod
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@classmethod
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def Bravais_to_Miller(cls,uvtw=None,hkil=None):
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def Bravais_to_Miller(cls,*,uvtw=None,hkil=None):
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"""
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"""
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Transform 4 Miller–Bravais indices to 3 Miller indices of crystal direction [uvw] or plane normal (hkl).
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Transform 4 Miller–Bravais indices to 3 Miller indices of crystal direction [uvw] or plane normal (hkl).
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@ -1104,7 +1110,7 @@ class Orientation(Rotation):
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@classmethod
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@classmethod
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def Miller_to_Bravais(cls,uvw=None,hkl=None):
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def Miller_to_Bravais(cls,*,uvw=None,hkl=None):
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"""
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"""
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Transform 3 Miller indices to 4 Miller–Bravais indices of crystal direction [uvtw] or plane normal (hkil).
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Transform 3 Miller indices to 4 Miller–Bravais indices of crystal direction [uvtw] or plane normal (hkil).
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@ -1133,7 +1139,7 @@ class Orientation(Rotation):
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return np.einsum('il,...l->...i',basis,axis)
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return np.einsum('il,...l->...i',basis,axis)
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def to_lattice(self,direction=None,plane=None):
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def to_lattice(self,*,direction=None,plane=None):
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"""
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"""
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Calculate lattice vector corresponding to crystal frame direction or plane normal.
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Calculate lattice vector corresponding to crystal frame direction or plane normal.
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@ -1157,7 +1163,7 @@ class Orientation(Rotation):
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return np.einsum('il,...l->...i',basis,axis)
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return np.einsum('il,...l->...i',basis,axis)
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def to_frame(self,uvw=None,hkl=None,with_symmetry=False):
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def to_frame(self,*,uvw=None,hkl=None,with_symmetry=False):
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"""
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"""
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Calculate crystal frame vector along lattice direction [uvw] or plane normal (hkl).
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Calculate crystal frame vector along lattice direction [uvw] or plane normal (hkl).
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@ -1185,7 +1191,7 @@ class Orientation(Rotation):
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np.einsum('il,...l->...i',basis,axis))
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np.einsum('il,...l->...i',basis,axis))
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def to_pole(self,uvw=None,hkl=None,with_symmetry=False):
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def to_pole(self,*,uvw=None,hkl=None,with_symmetry=False):
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"""
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"""
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Calculate lab frame vector along lattice direction [uvw] or plane normal (hkl).
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Calculate lab frame vector along lattice direction [uvw] or plane normal (hkl).
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@ -746,7 +746,7 @@ class Result:
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'hex':'hP'}[q['meta']['Lattice']])
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'hex':'hP'}[q['meta']['Lattice']])
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return {
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return {
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'data': np.uint8(o.IPF_color(o.to_SST(l))*255),
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'data': np.uint8(o.IPF_color(l)*255),
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'label': 'IPFcolor_[{} {} {}]'.format(*m),
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'label': 'IPFcolor_[{} {} {}]'.format(*m),
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'meta' : {
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'meta' : {
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'Unit': '8-bit RGB',
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'Unit': '8-bit RGB',
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@ -74,6 +74,7 @@ class TestGeom:
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def test_save_load_ASCII(self,default,tmp_path):
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def test_save_load_ASCII(self,default,tmp_path):
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default.save_ASCII(tmp_path/'ASCII')
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default.save_ASCII(tmp_path/'ASCII')
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default.material -= 1
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assert geom_equal(Geom.load_ASCII(tmp_path/'ASCII'),default)
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assert geom_equal(Geom.load_ASCII(tmp_path/'ASCII'),default)
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def test_invalid_origin(self,default):
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def test_invalid_origin(self,default):
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@ -231,11 +231,11 @@ class TestOrientation:
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@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
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@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
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@pytest.mark.parametrize('vector',np.array([[1,0,0],[1,2,3],[-1,1,-1]]))
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@pytest.mark.parametrize('vector',np.array([[1,0,0],[1,2,3],[-1,1,-1]]))
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@pytest.mark.parametrize('proper',[True,False])
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@pytest.mark.parametrize('proper',[True,False])
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def test_IPF_color_vectorization(self,lattice,shape,vector,proper):
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@pytest.mark.parametrize('in_SST',[True,False])
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def test_IPF_color_vectorization(self,lattice,shape,vector,proper,in_SST):
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o = Orientation.from_random(lattice=lattice,shape=shape)
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o = Orientation.from_random(lattice=lattice,shape=shape)
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poles = o.to_SST(vector=vector,proper=proper)
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for r, theO in zip(o.IPF_color(vector,in_SST=in_SST,proper=proper).reshape((-1,3)),o.flatten()):
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for r, theO in zip(o.IPF_color(poles,proper=proper).reshape((-1,3)),o.flatten()):
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assert np.allclose(r,theO.IPF_color(vector,in_SST=in_SST,proper=proper))
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assert np.allclose(r,theO.IPF_color(theO.to_SST(vector=vector,proper=proper),proper=proper))
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@pytest.mark.parametrize('lattice',Orientation.crystal_families)
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@pytest.mark.parametrize('lattice',Orientation.crystal_families)
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@pytest.mark.parametrize('a,b',[
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@pytest.mark.parametrize('a,b',[
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@ -263,14 +263,14 @@ class TestOrientation:
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cube = Orientation(lattice='cubic')
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cube = Orientation(lattice='cubic')
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for direction in set(permutations(np.array(color['direction']))):
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for direction in set(permutations(np.array(color['direction']))):
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assert np.allclose(np.array(color['RGB']),
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assert np.allclose(np.array(color['RGB']),
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cube.IPF_color(cube.to_SST(vector=np.array(direction),proper=proper),proper=proper))
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cube.IPF_color(vector=np.array(direction),proper=proper))
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@pytest.mark.parametrize('lattice',Orientation.crystal_families)
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@pytest.mark.parametrize('lattice',Orientation.crystal_families)
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@pytest.mark.parametrize('proper',[True,False])
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@pytest.mark.parametrize('proper',[True,False])
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def test_IPF_equivalent(self,set_of_quaternions,lattice,proper):
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def test_IPF_equivalent(self,set_of_quaternions,lattice,proper):
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direction = np.random.random(3)*2.0-1.0
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direction = np.random.random(3)*2.0-1.0
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o = Orientation(rotation=set_of_quaternions,lattice=lattice).equivalent
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o = Orientation(rotation=set_of_quaternions,lattice=lattice).equivalent
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color = o.IPF_color(o.to_SST(vector=direction,proper=proper),proper=proper)
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color = o.IPF_color(vector=direction,proper=proper)
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assert np.allclose(np.broadcast_to(color[0,...],color.shape),color)
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assert np.allclose(np.broadcast_to(color[0,...],color.shape),color)
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@pytest.mark.parametrize('lattice',Orientation.crystal_families)
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@pytest.mark.parametrize('lattice',Orientation.crystal_families)
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@ -177,7 +177,7 @@ class TestResult:
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lattice={'fcc':'cF',
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lattice={'fcc':'cF',
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'bcc':'cI',
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'bcc':'cI',
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'hex':'hP'}[crystal_structure])
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'hex':'hP'}[crystal_structure])
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in_memory = np.uint8(c.IPF_color(c.to_SST(np.array(d)))*255)
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in_memory = np.uint8(c.IPF_color(np.array(d))*255)
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in_file = default.read_dataset(loc['color'])
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in_file = default.read_dataset(loc['color'])
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assert np.allclose(in_memory,in_file)
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assert np.allclose(in_memory,in_file)
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