add helper and example

Author: rpep

fidimag/common/lib/helper_cython.pyx

@@ -0,0 +1,79 @@
+import numpy as np
+cimport numpy as np
+
+def normalise(a):
+    """
+    normalise the given array a
+    """
+    a.shape = (-1, 3)
+    b = np.sqrt(a[:, 0] ** 2 + a[:, 1] ** 2 + a[:, 2] ** 2)
+    ids = (b == 0)
+    b[ids] = 1.0
+    a[:, 0] /= b
+    a[:, 1] /= b
+    a[:, 2] /= b
+    a.shape = (-1,)
+
+def init_scalar(value, mesh, *args):
+
+    n = mesh.n
+
+    mesh_v = np.zeros(n)
+
+    if isinstance(value, (int, float)):
+        mesh_v[:] = value
+    elif hasattr(value, '__call__'):
+        for i in range(n):
+            mesh_v[i] = value(mesh.coordinates[i], *args)
+
+    elif isinstance(value, np.ndarray):
+        if value.shape == mesh_v.shape:
+            mesh_v[:] = value[:]
+        else:
+            raise ValueError("Array size must match the mesh size")
+
+    return mesh_v
+
+def init_vector(m0, mesh, norm=False, *args):
+
+    n = mesh.n
+
+    spin = np.zeros((n, 3))
+
+    if isinstance(m0, list) or isinstance(m0, tuple):
+        spin[:, :] = m0
+        spin = np.reshape(spin, 3 * n, order='C')
+
+    elif hasattr(m0, '__call__'):
+        v = m0(mesh.coordinates[0], *args)
+        if len(v) != 3:
+            raise Exception(
+                'The length of the value in init_vector method must be 3.')
+        for i in range(n):
+            spin[i, :] = m0(mesh.coordinates[i], *args)
+        spin = np.reshape(spin, 3 * n, order='C')
+
+    elif isinstance(m0, np.ndarray):
+        if m0.shape == (3, ):
+            spin[:] = m0  # broadcasting
+        else:
+            spin.shape = (-1)
+            spin[:] = m0  # overwriting the whole thing
+
+    spin.shape = (-1,)
+
+    if norm:
+        normalise(spin)
+
+    return spin
+
+
+# def init_vector_func_fast(m0, mesh, norm=False, *args):
+#     """
+#     A fast version of init_vector for functions that does
+#     not perform any checking of input arguments.
+#     """
+#     v = m0(mesh.coordinates[0], *args)
+#     for i in range(n):
+#         spin[3*i:] = m0(&mesh, *args)
+#     spin = np.reshape(spin, 3 * n, order='C')

fidimag/user/example.pyx

@@ -7,12 +7,15 @@
 import glob
 import re
 import sys
-
 #if sys.platform == 'darwin':
 #    from distutils import sysconfig
 #    vars = sysconfig.get_config_vars()
 #    vars['LDSHARED'] = vars['LDSHARED'].replace('-bundle', '-dynamiclib')
 
+class BuildError(Exception):
+    pass
+
+
 if 'CC' in os.environ:
     print("Using CC={}".format(os.environ['CC']))
 else:
@@ -66,12 +69,7 @@ def glob_cfiles(path, excludes):
 sources.append(os.path.join(ATOM_DIR, 'clib.pyx'))
 sources += glob_cfiles(ATOM_DIR, excludes=["clib.c"])
 
-user_sources = []
 
-user_cy = glob.glob(os.path.join(USER_DIR, '*.pyx'))
-print("Found user Cython files: {}".format(user_cy))
-user_sources += user_cy
-sources += glob_cfiles(USER_DIR, excludes=user_cy)
 
 common_sources = []
 common_sources.append(os.path.join(COMMON_DIR, 'common_clib.pyx'))
@@ -263,16 +261,30 @@ def glob_cfiles(path, excludes):
               extra_compile_args=com_args,
               extra_link_args=com_link,
               ),
-    Extension("fidimag.extensions.user",
-              sources=user_sources,
-              include_dirs=com_inc,
-              libraries=com_libs,
-              library_dirs=lib_paths, runtime_library_dirs=lib_paths,
-              extra_compile_args=com_args,
-              extra_link_args=com_link,
-              ),
 ]
 
+
+for folder in glob.glob(os.path.join(USER_DIR, '*/')):
+    module_name = folder.split('/')[-2]
+    print(folder.split('/'))
+    print('Found User Module: {}'.format(module_name))
+    user_sources = glob.glob(folder + '/*.pyx')
+    print('\tFound Cython sources: {}'.format(user_sources))
+    if len(user_sources) != 1:
+        raise BuildError("User Modules are only allowed one Cython .pyx file")
+    user_sources += glob_cfiles(folder, excludes=user_sources)
+    ext_modules.append(
+       Extension("fidimag.extensions.user.{}".format(module_name),
+          sources=user_sources,
+          include_dirs=com_inc,
+          libraries=com_libs,
+          library_dirs=lib_paths, runtime_library_dirs=lib_paths,
+          extra_compile_args=com_args,
+          extra_link_args=com_link,
+       ),
+    )
+
+
 setup(
     name='fidimag',
     version=version,