Merge pull request #16 from DanielKotik/develop

Merge `develop` into `master`

CITATION.cff

@@ -3,7 +3,7 @@
 cff-version: 1.0.3
 message: If you use this software, please cite it using these metadata.
 title: 'Optical-beams-MEEP'
-doi: 10.5281/zenodo.3691799
+doi: 10.5281/zenodo.2631828 # This DOI represents all versions, and will always resolve to the latest one.
 authors:
 - given-names: Daniel
   family-names: Kotik

optbeam/_2d/beams.pxd

@@ -0,0 +1,46 @@
+from .helpers cimport Beam2d, _complex_quad
+
+# -----------------------------------------------------------------------------
+# declare C functions as "cpdef" to export them to the module
+# -----------------------------------------------------------------------------
+cdef extern from "math.h":
+    cpdef double _exp "exp" (double x) nogil
+    cpdef double _sqrt "sqrt" (double x) nogil
+
+cdef extern from "complex.h":
+    cpdef double complex _cexp "cexp" (double complex z) nogil
+
+# -----------------------------------------------------------------------------
+# function declarations
+# -----------------------------------------------------------------------------
+
+
+# -----------------------------------------------------------------------------
+# class declarations
+# -----------------------------------------------------------------------------
+cdef class Beam2dCartesian(Beam2d):
+    cdef:
+        double _ry, _rz
+
+    cdef double complex spectrum(self, double k_y) nogil
+    cdef double _phase(self, double k_y, double x, double y) nogil
+    cdef double complex _integrand(self, double k_y) nogil
+
+cdef class Gauss2d(Beam2dCartesian):
+    cdef:
+        double _W_y
+        double _norm
+
+    cdef double _f_Gauss(self, double k_y, double W_y) nogil
+    cdef double complex spectrum(self, double k_y) nogil
+
+cdef class IncAiry2d(Beam2dCartesian):
+    cdef:
+        double _W_y
+        double _M
+        double _W
+        double xi
+
+    cdef double _heaviside(self, double x) nogil
+    cdef double complex _f_Airy(self, double k_y, double W_y, double M, double W) nogil
+    cdef double complex spectrum(self, double k_y) nogil

optbeam/_2d/beams.py

@@ -4,20 +4,20 @@
 
 try:
     import cython
+    cython_imported = True
 except ModuleNotFoundError:
-    cython = None
+    cython_imported = False
 
-if not cython or not cython.compiled:
+if not cython_imported or not cython.compiled:
     from math import (exp as _exp,
                       sqrt as _sqrt)
     from cmath import exp as _cexp
+    from .helpers import Beam2d, _complex_quad
 
-if cython and not cython.compiled:
+if cython_imported and not cython.compiled:
     print("\nPlease consider compiling `%s.py` via Cython: "
           "`$ cythonize -3 -i %s.py`\n" % (__name__, __name__))
 
-from .helpers import _complex_quad, Beam2d
-
 
 class Beam2dCartesian(Beam2d):
     """..."""
@@ -39,8 +39,8 @@ def profile(self, r):
         try:
             (result,
              real_tol,
-             imag_tol) = _complex_quad(self if cython
-                                       and cython.compiled else self._integrand,
+             imag_tol) = _complex_quad(self if cython_imported and cython.compiled
+                                       else self._integrand,
                                        -self._k, self._k)
         except Exception as e:
             print(type(e).__name__ + ":", e)

optbeam/_2d/helpers.pxd

@@ -0,0 +1,25 @@
+cimport cython
+from cpython.pycapsule cimport PyCapsule_New
+from cpython cimport bool
+
+
+# -----------------------------------------------------------------------------
+# function declarations
+# -----------------------------------------------------------------------------
+cdef double _imag_1d_func_c(int n, double *arr, void *func_ptr)
+cdef double _real_1d_func_c(int n, double *arr, void *func_ptr)
+
+@cython.locals(real=cython.double, imag=cython.double, real_tol=cython.double,
+               imag_tol=cython.double)
+cpdef (double complex, double, double) _complex_quad(func, double a, double b, dict kwargs=*)
+
+# -----------------------------------------------------------------------------
+# class declarations
+# -----------------------------------------------------------------------------
+cdef class Beam2d:
+    cdef:
+        dict __dict__
+        double x, _k
+        public bool called
+
+    cdef double complex _integrand(self, double x) nogil

optbeam/_3d/beams.pxd

@@ -0,0 +1,70 @@
+from .helpers cimport Beam3d, _complex_dblquad
+
+# -----------------------------------------------------------------------------
+# declare C functions as "cpdef" to export them to the module
+# -----------------------------------------------------------------------------
+# TODO: check why we use cpdef and not cdef
+cdef extern from "stdlib.h":
+    cpdef int _abs "abs" (int n) nogil
+
+cdef extern from "math.h":
+    cpdef double _sin "sin" (double x) nogil
+    cpdef double _cos "cos" (double x) nogil
+    cpdef double _exp "exp" (double x) nogil
+    cpdef double _acos "acos" (double x) nogil
+    cpdef double _atan2 "atan2" (double y, double x) nogil
+
+cdef extern from "complex.h":
+    cpdef double complex _cexp "cexp" (double complex z) nogil
+    cpdef double complex _csqrt "csqrt" (double complex z) nogil
+
+# -----------------------------------------------------------------------------
+# function declarations
+# -----------------------------------------------------------------------------
+
+
+# -----------------------------------------------------------------------------
+# class declarations
+# -----------------------------------------------------------------------------
+cdef class Beam3dSpherical(Beam3d):
+    cdef:
+        double _ry, _rz
+
+    cdef double _phase(self, double sin_theta, double cos_theta, double phi,
+                       double x, double y, double z) nogil
+    # TODO: check if next line is actually needed since we can declared in Beam3d
+    cdef double complex spectrum(self, double sin_theta, double theta, double phi) nogil
+    # TODO: check if next line is actually needed since it is declared in Beam3d
+    cdef double complex _integrand(self, double theta, double phi) nogil
+
+cdef class Beam3dCartesian(Beam3d):
+    cdef:
+        double _ry, _rz
+
+    cdef double _phase(self, double k_y, double k_z, double x, double y, double z) nogil
+    cdef double complex spectrum(self, double k_y, double k_z) nogil
+    cdef double complex _integrand(self, double k_y, double k_z) nogil
+
+cdef class LaguerreGauss3d(Beam3dSpherical):
+    cdef:
+      int _m
+      double _W_y
+      double _norm
+
+    cdef double complex _f_Gauss_spherical(self, double sin_theta, double _W_y, double k) nogil
+    cdef double complex _f_Laguerre_Gauss_spherical(self, double sin_theta, double theta, double phi,
+                                                    double _W_y, double k, int _m) nogil
+    cdef double complex spectrum(self, double sin_theta, double theta, double phi) nogil
+
+cdef class LaguerreGauss3dCartesian(Beam3dCartesian):
+    cdef:
+      int _m
+      double _W_y
+      double _norm
+
+    cdef double _phi(self, double k_y, double k_z) nogil
+    cdef double _theta(self, double k_y, double k_z, double k) nogil
+    cdef double complex _f_Gauss_cartesian(self, double k_y, double k_z, double _W_y) nogil
+    cdef double complex _f_Laguerre_Gauss_cartesian(self, double k_y, double k_z,
+                                                    double _W_y, double k, int _m) nogil
+    cdef double complex spectrum(self, double k_y, double k_z) nogil

optbeam/_3d/beams.py

@@ -4,10 +4,12 @@
 
 try:
     import cython
+    cython_imported = True
 except ModuleNotFoundError:
-    cython = None
+    cython_imported = False
 
-if not cython or not cython.compiled:
+# TODO: check if conditional statement is needed at all
+if not cython_imported or not cython.compiled:
     from math import (sin as _sin,
                       cos as _cos,
                       exp as _exp,
@@ -16,13 +18,13 @@
     from cmath import (exp as _cexp,
                        sqrt as _csqrt)
     from builtins import abs as _abs
+    from .helpers import Beam3d, _complex_dblquad
 
-if cython and not cython.compiled:
+
+if cython_imported and not cython.compiled:
     print("\nPlease consider compiling `%s.py` via Cython: "
           "`$ cythonize -3 -i %s.py`\n" % (__name__, __name__))
 
-from .helpers import _complex_dblquad, Beam3d
-
 
 class Beam3dSpherical(Beam3d):
     """Reference implementaion of a 3d beam in spherical coordinates."""

optbeam/_3d/helpers.pxd

@@ -0,0 +1,27 @@
+cimport cython
+from cpython.pycapsule cimport PyCapsule_New
+from cpython cimport bool
+
+# -----------------------------------------------------------------------------
+# function declarations
+# -----------------------------------------------------------------------------
+cdef double _imag_2d_func_c(int n, double *arr, void *func_ptr)
+cdef double _real_2d_func_c(int n, double *arr, void *func_ptr)
+
+@cython.locals(real=cython.double, imag=cython.double, real_tol=cython.double,
+               imag_tol=cython.double)
+cpdef (double complex, double, double) _complex_dblquad(Beam3d func,
+                                                       double a, double b,
+                                                       double gfun, double hfun,
+                                                       dict kwargs=*)
+
+# -----------------------------------------------------------------------------
+# class declarations
+# -----------------------------------------------------------------------------
+cdef class Beam3d:
+    cdef:
+        dict __dict__
+        double x, _k
+        public bool called
+
+    cdef double complex _integrand(self, double x, double y) nogil

optbeam/_3d/helpers.py

@@ -3,10 +3,11 @@
 
 try:
     import cython
+    cython_imported = True
 except ModuleNotFoundError:
-    cython = None
+    cython_imported = False
 
-if cython:
+if cython_imported:
     if cython.compiled:
         from scipy import LowLevelCallable
     else:
@@ -49,7 +50,7 @@ def _real_2d_func_c(n, arr, func_ptr):
 
 def _complex_dblquad(func, a, b, gfun, hfun, kwargs={}):
     """Integrate real and imaginary part of the given function."""
-    if cython and cython.compiled:
+    if cython_imported and cython.compiled:
         # pure python formulation of: cdef void *f_ptr = <void*>func
         f_ptr = cython.declare(cython.p_void, cython.cast(cython.p_void, func))
 

pyproject.toml

@@ -0,0 +1,2 @@
+[build-system]
+requires = ["setuptools", "wheel", "Cython"]

setup.py

@@ -1,4 +1,5 @@
 from setuptools import setup, find_packages
+from Cython.Build import cythonize
 
 
 with open("README.md") as f:
@@ -23,7 +24,12 @@
     author_email="kotik@physics.org",
     license=license,
     packages=find_packages(exclude=("scripts")),
+    ext_modules=cythonize("optbeam/_2d/*.py",
+                          "optbeam/_3d/*.py",
+                          force=True,
+                          compiler_directives={'language_level': 3}),
+    zip_safe=False,
     include_package_data=True,
-    install_requires=["scipy"],
+    install_requires=["scipy", "cython"],
     extras_require=extras,
 )