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Refactor pnpoly function in Cython and add to shared package

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This commit is contained in:
Johannes Schönberger
2012-08-21 15:43:26 +02:00
parent a08779e06a
commit c471d475eb
8 changed files with 45 additions and 92 deletions
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skimage/_shared/geometry.pxd
+7
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@@ -0,0 +1,7 @@
cdef inline unsigned char point_in_polygon(int nr_verts, double *xp, double *yp,
double x, double y)
cdef void points_in_polygon(int nr_verts, double *xp, double *yp,
int nr_points, double *x, double *y,
unsigned char *result)
skimage/_shared/geometry.pyx
+27
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@@ -0,0 +1,27 @@
#cython: cdivison=True
#cython: boundscheck=False
#cython: nonecheck=False
#cython: wraparound=False
cdef inline unsigned char point_in_polygon(int nr_verts, double *xp, double *yp,
double x, double y):
cdef int i
cdef unsigned char c = 0
cdef int j = nr_verts - 1
for i in range(nr_verts):
if (
(((yp[i] <= y) and (y < yp[j])) or
((yp[j] <= y) and (y < yp[i])))
and (x < (xp[j] - xp[i]) * (y - yp[i]) / (yp[j] - yp[i]) + xp[i])
):
c = not c
j = i
return c
cdef void points_in_polygon(int nr_verts, double *xp, double *yp,
int nr_points, double *x, double *y,
unsigned char *result):
cdef int n
for n in range(nr_points):
result[n] = point_in_polygon(nr_verts, xp, yp, x[n], y[n])
skimage/_shared/setup.py
+2
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@@ -13,9 +13,11 @@ def configuration(parent_package='', top_path=None):
config = Configuration('_shared', parent_package, top_path)
config.add_data_dir('tests')
cython(['geometry.pyx'], working_path=base_path)
cython(['interpolation.pyx'], working_path=base_path)
cython(['transform.pyx'], working_path=base_path)
config.add_extension('geometry', sources=['geometry.c'])
config.add_extension('interpolation', sources=['interpolation.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('transform', sources=['transform.c'],
skimage/draw/_draw.pyx
+2 -6
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@@ -3,11 +3,7 @@ import math
from libc.math cimport sqrt
cimport numpy as np
cimport cython
cdef extern from "../morphology/_pnpoly.h":
int pnpoly(int nr_verts, double *xp, double *yp,
double x, double y)
from skimage._shared.geometry cimport point_in_polygon
@cython.boundscheck(False)
@@ -119,7 +115,7 @@ def polygon(y, x, shape=None):
for r in range(minr, maxr+1):
for c in range(minc, maxc+1):
if pnpoly(nr_verts, cptr, rptr, c, r):
if point_in_polygon(nr_verts, cptr, rptr, c, r):
rr.append(r)
cc.append(c)
skimage/draw/setup.py
+1 -1
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@@ -15,7 +15,7 @@ def configuration(parent_package='', top_path=None):
cython(['_draw.pyx'], working_path=base_path)
config.add_extension('_draw', sources=['_draw.c'],
include_dirs=[get_numpy_include_dirs()])
include_dirs=[get_numpy_include_dirs(), '../shared'])
return config
skimage/morphology/_pnpoly.h
-72
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@@ -1,72 +0,0 @@
/* `pnpoly` is from
http://www.ecse.rpi.edu/Homepages/wrf/Research/Short_Notes/pnpoly.html
Copyright (c) 1970-2003, Wm. Randolph Franklin
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use, copy,
modify, merge, publish, distribute, sublicense, and/or sell copies
of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimers.
2. Redistributions in binary form must reproduce the above
copyright notice in the documentation and/or other materials
provided with the distribution.
3. The name of W. Randolph Franklin may not be used to endorse or
promote products derived from this Software without specific
prior written permission.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE. */
#ifdef __cplusplus
extern "C" {
#endif
unsigned char pnpoly(int nr_verts, double *xp, double *yp, double x, double y)
{
int i, j;
unsigned char c = 0;
for (i = 0, j = nr_verts-1; i < nr_verts; j = i++) {
if ((((yp[i]<=y) && (y<yp[j])) ||
((yp[j]<=y) && (y<yp[i]))) &&
(x < (xp[j] - xp[i]) * (y - yp[i]) / (yp[j] - yp[i]) + xp[i]))
c = !c;
}
return c;
}
void npnpoly(int nr_verts, double *xp, double *yp,
int nr_points, double *x, double *y,
unsigned char *result)
/*
* For N provided points, calculate whether they are in
* the polygon defined by vertices *xp, *yp.
*
* nr_verts : number of vertices
* *xp, *yp : x and y coordinates of vertices
* nr_points : number of data points provided
* *x, *y : data points
*/
{
unsigned char n = 0;
for (n = 0; n < nr_points; n++) {
result[n] = pnpoly(nr_verts, xp, yp, x[n], y[n]);
}
}
#ifdef __cplusplus
}
#endif
skimage/morphology/_pnpoly.pyx
+5 -12
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@@ -2,14 +2,7 @@
cimport numpy as np
import numpy as np
cdef extern from "_pnpoly.h":
int pnpoly(int nr_verts, double *xp, double *yp,
double x, double y)
void npnpoly(int nr_verts, double *xp, double *yp,
int nr_points, double *x, double *y,
unsigned char *result)
from skimage._shared.geometry cimport point_in_polygon, points_in_polygon
def grid_points_inside_poly(shape, verts):
@@ -49,10 +42,10 @@ def grid_points_inside_poly(shape, verts):
for m in range(M):
for n in range(N):
out[m, n] = pnpoly(V, <double*>vx.data, <double*>vy.data, m, n)
out[m, n] = point_in_polygon(V, <double*>vx.data, <double*>vy.data, m, n)
return out.view(bool)
def points_inside_poly(points, verts):
"""Test whether points lie inside a polygon.
@@ -84,8 +77,8 @@ def points_inside_poly(points, verts):
cdef np.ndarray[np.uint8_t, ndim=1] out = \
np.zeros(x.shape[0], dtype=np.uint8)
npnpoly(vx.shape[0], <double*>vx.data, <double*>vy.data,
points_in_polygon(vx.shape[0], <double*>vx.data, <double*>vy.data,
x.shape[0], <double*>x.data, <double*>y.data,
<unsigned char*>out.data)
skimage/morphology/setup.py
+1 -1
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@@ -28,7 +28,7 @@ def configuration(parent_package='', top_path=None):
config.add_extension('_skeletonize_cy', sources=['_skeletonize_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_pnpoly', sources=['_pnpoly.c'],
include_dirs=[get_numpy_include_dirs()])
include_dirs=[get_numpy_include_dirs(), '../shared'])
config.add_extension('_convex_hull', sources=['_convex_hull.c'],
include_dirs=[get_numpy_include_dirs()])