Merge branch 'master' of https://github.com/jonwright/ImageD11

Author: jonwright

ImageD11/forward_model/grainmaps.py

@@ -1081,6 +1081,8 @@ def to_tsl(symmetry):
 
     def symmetry_operators(self, use_miller_bravais=False):
         """Define the equivalent crystal symmetries.
+        Note that it takes the highest symmetry in each of the 7 crystal systems
+        This may not be quite right if a specific point group with less symmetry is desired
 
         Those come from Randle & Engler, 2000. For instance in the cubic
         crystal struture, for instance there are 24 equivalent cube orientations.
@@ -1144,12 +1146,21 @@ def symmetry_operators(self, use_miller_bravais=False):
               sym[8] = np.array([[-0.5, s60, 0.], [s60, 0.5, 0.], [0., 0., -1.]])
               sym[9] = np.array([[-1., 0., 0.], [0., 1., 0.], [0., 0., -1.]])
               sym[10] = np.array([[-0.5, -s60, 0.], [-s60, 0.5, 0.], [0., 0., -1.]])
-              sym[11] = np.array([[0.5, -s60, 0.], [-s60, -0.5, 0.], [0., 0., -1.]])
+              sym[11] = np.array([[0.5, -s60, 0.], [-s60, -0.5, 0.], [0., 0., -1.]])               
+        elif self is Symmetry.trigonal:
+              sym = np.zeros((6, 3, 3), dtype=float)
+              s60 = np.sin(60 * np.pi / 180)
+              sym[0] = np.array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]])
+              sym[1] = np.array([[-0.5, -s60, 0.], [s60, -0.5, 0.], [0., 0., 1.]])
+              sym[2] = np.array([[-0.5, s60, 0.], [-s60, -0.5, 0.], [0., 0., 1.]])
+              sym[3] = np.array([[1., 0., 0.], [0., -1., 0.], [0., 0., -1.]])    
+              sym[4] = np.array([[-0.5, s60, 0.], [s60, 0.5, 0.], [0., 0., -1.]])
+              sym[5] = np.array([[-0.5, -s60, 0.], [-s60, 0.5, 0.], [0., 0., -1.]])
         elif self is Symmetry.orthorhombic:
             sym = np.zeros((4, 3, 3), dtype=float)
             sym[0] = np.array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]])
             sym[1] = np.array([[1., 0., 0.], [0., -1., 0.], [0., 0., -1.]])
-            sym[2] = np.array([[-1., 0., -1.], [0., 1., 0.], [0., 0., -1.]])
+            sym[2] = np.array([[-1., 0., 0.], [0., 1., 0.], [0., 0., -1.]])
             sym[3] = np.array([[-1., 0., 0.], [0., -1., 0.], [0., 0., 1.]])
         elif self is Symmetry.tetragonal:
             sym = np.zeros((8, 3, 3), dtype=float)
@@ -1161,6 +1172,10 @@ def symmetry_operators(self, use_miller_bravais=False):
             sym[5] = np.array([[-1., 0., 0.], [0., 1., 0.], [0., 0., -1.]])
             sym[6] = np.array([[0., 1., 0.], [1., 0., 0.], [0., 0., -1.]])
             sym[7] = np.array([[0., -1., 0.], [-1., 0., 0.], [0., 0., -1.]])
+        elif self is Symmetry.monoclinic:
+            sym = np.zeros((2, 3, 3), dtype=float)
+            sym[0] = np.array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]])
+            sym[1] = np.array([[-1., 0., 0.], [0., -1., 0.], [0., 0., 1.]])
         elif self is Symmetry.triclinic:
             sym = np.zeros((1, 3, 3), dtype=float)
             sym[0] = np.array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]])
@@ -1448,8 +1463,14 @@ def disorientation(ori1, ori2, crystal_structure=Symmetry.triclinic):
         oi_list = np.einsum('nij,jk->nik', symmetries, ori2)
 
         # Compute all combinations of symmetrized ori1 and ori2
-        oj_list_T = np.transpose(oj_list, axes=(0, 2, 1))
-        delta_list = np.einsum('bij,bjk->bik', oi_list, oj_list_T)
+        delta_list_AB = np.einsum('aij,bkj->abik', oi_list, oj_list)
+        delta_list_BA = np.einsum('aij,bkj->abik', oj_list, oi_list)
+        
+        # Flatten (2*Nsymmetry*Nsymmetry, 3, 3)
+        delta_list = np.concatenate([
+            delta_list_AB.reshape(-1, 3, 3),
+            delta_list_BA.reshape(-1, 3, 3)
+        ])
 
         # Calculate misorientation angles for all delta matrices
         mis_angles = np.array([misorientation_angle_from_delta(delta) for delta in delta_list])

setup.py

@@ -78,15 +78,14 @@ def build_extension(self, ext):
         c = self.compiler.compiler_type
         CF = [] ; LF=[]
         if "CFLAGS" in os.environ:
-            CF = os.environ.get("CFLAGS").split(" ")
+            CF = os.environ.get("CFLAGS").split()
         if "LDFLAGS" in os.environ:
-            LF = os.environ.get("LDFLAGS").split(" ")
-        for e in self.extensions:
-            if c in copt:
-               e.extra_compile_args = copt[ c ] + CF
-               e.extra_link_args = lopt[ c ] + LF
-        print("Customised compiler",c,e.extra_compile_args,
-                    e.extra_link_args)
+            LF = os.environ.get("LDFLAGS").split()
+        if c in copt:
+            ext.extra_compile_args = copt[ c ] + CF
+            ext.extra_link_args = lopt[ c ] + LF
+        print("Customised compiler",c,ext.extra_compile_args,
+                    ext.extra_link_args)
         if ext.sources[0].endswith('.pyf'):
             name = ext.sources[0]
             # generate wrappers
@@ -105,7 +104,7 @@ def build_extension(self, ext):
 
 csources = [os.path.join('src',c) for c in cnames.split()]
 
-extension = Extension( "_cImageD11",  csources,
+extension = Extension( "ImageD11._cImageD11",  csources,
                 include_dirs = [ 'src',numpy.get_include(), numpy.f2py.get_include() ])
 
 ################################################################################
@@ -211,7 +210,6 @@ def build_extension(self, ext):
       description='ImageD11',
       license = "GPL",
 #      python_requires='<3.12',  # Numba still not working for 3.12
-      ext_package = "ImageD11",   # Puts extensions in the ImageD11 directory
       ext_modules = [extension,],
       setup_requires = minimal,   # to compile
       install_requires = minimal + useful,