Add integrate function to shared package

skimage/_shared/setup.py

@@ -14,9 +14,12 @@ def configuration(parent_package='', top_path=None):
     config.add_data_dir('tests')
 
     cython(['interpolation.pyx'], working_path=base_path)
+    cython(['transform.pyx'], working_path=base_path)
 
     config.add_extension('interpolation', sources=['interpolation.c'],
                          include_dirs=[get_numpy_include_dirs()])
+    config.add_extension('transform', sources=['transform.c'],
+                         include_dirs=[get_numpy_include_dirs()])
 
     return config
 

skimage/_shared/transform.pxd

@@ -0,0 +1,6 @@
+cimport numpy as cnp
+import numpy as np
+
+
+cdef float integrate(cnp.ndarray[float, ndim=2,  mode="c"] sat,
+                     int r0, int c0, int r1, int c1)

skimage/_shared/transform.pyx

@@ -0,0 +1,45 @@
+#cython: cdivison=True
+#cython: boundscheck=False
+#cython: nonecheck=False
+#cython: wraparound=False
+cimport numpy as cnp
+import numpy as np
+
+
+cdef float integrate(cnp.ndarray[float, ndim=2,  mode="c"] sat,
+                     int r0, int c0, int r1, int c1):
+    """
+    Using a summed area table / integral image, calculate the sum
+    over a given window.
+
+    This function is the same as the `integrate` function in
+    `skimage.transform.integrate`, but this Cython version significantly
+    speeds up the code.
+
+    Parameters
+    ----------
+    sat : ndarray of float
+        Summed area table / integral image.
+    r0, c0 : int
+        Top-left corner of block to be summed.
+    r1, c1 : int
+        Bottom-right corner of block to be summed.
+
+    Returns
+    -------
+    S : int
+        Sum over the given window.
+    """
+    cdef float S = 0
+
+    S += sat[r1, c1]
+
+    if (r0 - 1 >= 0) and (c0 - 1 >= 0):
+        S += sat[r0 - 1, c0 - 1]
+
+    if (r0 - 1 >= 0):
+        S -= sat[r0 - 1, c1]
+
+    if (c0 - 1 >= 0):
+        S -= sat[r1, c0 - 1]
+    return S

skimage/feature/_template.pyx

@@ -35,51 +35,8 @@ cimport numpy as np
 import numpy as np
 from scipy.signal import fftconvolve
 from skimage.transform import integral
-
-
-cdef extern from "math.h":
-    float sqrt(float x)
-    float fabs(float x)
-
-
-@cython.boundscheck(False)
-cdef float integrate(np.ndarray[float, ndim=2,  mode="c"] sat,
-        int r0, int c0, int r1, int c1):
-    """
-    Using a summed area table / integral image, calculate the sum
-    over a given window.
-
-    This function is the same as the `integrate` function in
-    `skimage.transform.integrate`, but this Cython version significantly
-    speeds up the code.
-
-    Parameters
-    ----------
-    sat : ndarray of float
-        Summed area table / integral image.
-    r0, c0 : int
-        Top-left corner of block to be summed.
-    r1, c1 : int
-        Bottom-right corner of block to be summed.
-
-    Returns
-    -------
-    S : int
-        Sum over the given window.
-    """
-    cdef float S = 0
-
-    S += sat[r1, c1]
-
-    if (r0 - 1 >= 0) and (c0 - 1 >= 0):
-        S += sat[r0 - 1, c0 - 1]
-
-    if (r0 - 1 >= 0):
-        S -= sat[r0 - 1, c1]
-
-    if (c0 - 1 >= 0):
-        S -= sat[r1, c0 - 1]
-    return S
+from libc.math cimport sqrt, fabs
+from skimage._shared.transform cimport integrate
 
 
 @cython.boundscheck(False)

skimage/feature/setup.py

@@ -16,10 +16,9 @@ def configuration(parent_package='', top_path=None):
     cython(['_template.pyx'], working_path=base_path)
 
     config.add_extension('_texture', sources=['_texture.c'],
-                         include_dirs=[get_numpy_include_dirs(),
-                                       '../transform'])
+                         include_dirs=[get_numpy_include_dirs(), '../_shared'])
     config.add_extension('_template', sources=['_template.c'],
-                         include_dirs=[get_numpy_include_dirs()])
+                         include_dirs=[get_numpy_include_dirs(), '../_shared'])
 
     return config