Merge pull request #1123 from stefanv/pnpoly

Expose point_in_poly and move to measure module

bento.info

@@ -37,12 +37,12 @@ Library:
         skimage.io._plugins, skimage.measure, skimage.morphology,
         skimage.scripts, skimage.restoration, skimage.segmentation,
         skimage.transform, skimage.util
-    Extension: skimage.morphology._pnpoly
-        Sources:
-            skimage/morphology/_pnpoly.pyx
     Extension: skimage.io._plugins._colormixer
         Sources:
             skimage/io/_plugins/_colormixer.pyx
+    Extension: skimage.measure._pnpoly
+        Sources:
+            skimage/measure/_pnpoly.pyx
     Extension: skimage.measure._find_contours_cy
         Sources:
             skimage/measure/_find_contours_cy.pyx

doc/logo/scipy_logo.py

@@ -3,11 +3,11 @@ Code used to trace Scipy logo.
 """
 import numpy as np
 import matplotlib.pyplot as plt
-import matplotlib.nxutils as nx
 
 from skimage import io
 from skimage import data
 
+from skimage.measure import points_in_poly
 
 class SymmetricAnchorPoint(object):
     """Anchor point in a parametric curve with symmetric handles
@@ -211,7 +211,7 @@ class ScipyLogo(object):
         y_img, x_img = np.mgrid[:h, :w]
         xy_points = np.column_stack((x_img.flat, y_img.flat))
 
-        mask = nx.points_inside_poly(xy_points, xy_poly)
+        mask = points_in_poly(xy_points, xy_poly)
         return mask.reshape((h, w))
 
 

skimage/measure/__init__.py

@@ -4,6 +4,7 @@ from ._marching_cubes import (marching_cubes, mesh_surface_area,
 from ._regionprops import regionprops, perimeter
 from ._structural_similarity import structural_similarity
 from ._polygon import approximate_polygon, subdivide_polygon
+from ._pnpoly import points_in_poly, grid_points_in_poly
 from ._moments import moments, moments_central, moments_normalized, moments_hu
 from .profile import profile_line
 from .fit import LineModel, CircleModel, EllipseModel, ransac
@@ -30,4 +31,6 @@ __all__ = ['find_contours',
            'mesh_surface_area',
            'correct_mesh_orientation',
            'profile_line',
-           'label']
+           'label',
+           'points_in_poly',
+           'grid_points_in_poly']

skimage/measure/_pnpoly.pyx

@@ -8,7 +8,7 @@ cimport numpy as cnp
 from skimage._shared.geometry cimport point_in_polygon, points_in_polygon
 
 
-def grid_points_inside_poly(shape, verts):
+def grid_points_in_poly(shape, verts):
     """Test whether points on a specified grid are inside a polygon.
 
     For each ``(r, c)`` coordinate on a grid, i.e. ``(0, 0)``, ``(0, 1)`` etc.,
@@ -23,6 +23,10 @@ def grid_points_inside_poly(shape, verts):
         or anti-clockwise.  The first point may (but does not need to be)
         duplicated.
 
+    See Also
+    --------
+    points_in_poly
+
     Returns
     -------
     mask : (M, N) ndarray of bool
@@ -50,7 +54,7 @@ def grid_points_inside_poly(shape, verts):
     return out.view(bool)
 
 
-def points_inside_poly(points, verts):
+def points_in_poly(points, verts):
     """Test whether points lie inside a polygon.
 
     Parameters
@@ -61,6 +65,10 @@ def points_inside_poly(points, verts):
         Vertices of the polygon, sorted either clockwise or anti-clockwise.
         The first point may (but does not need to be) duplicated.
 
+    See Also
+    --------
+    grid_points_in_poly
+
     Returns
     -------
     mask : (N,) array of bool

skimage/measure/setup.py

@@ -16,6 +16,7 @@ def configuration(parent_package='', top_path=None):
     cython(['_find_contours_cy.pyx'], working_path=base_path)
     cython(['_moments.pyx'], working_path=base_path)
     cython(['_marching_cubes_cy.pyx'], working_path=base_path)
+    cython(['_pnpoly.pyx'], working_path=base_path)
 
     config.add_extension('_ccomp', sources=['_ccomp.c'],
                          include_dirs=[get_numpy_include_dirs()])
@@ -26,6 +27,8 @@ def configuration(parent_package='', top_path=None):
     config.add_extension('_marching_cubes_cy',
                          sources=['_marching_cubes_cy.c'],
                          include_dirs=[get_numpy_include_dirs()])
+    config.add_extension('_pnpoly', sources=['_pnpoly.c'],
+                         include_dirs=[get_numpy_include_dirs(), '../_shared'])
 
     return config
 

skimage/measure/tests/test_pnpoly.py

@@ -1,8 +1,7 @@
 import numpy as np
 from numpy.testing import assert_array_equal
 
-from skimage.morphology._pnpoly import points_inside_poly, \
-                                       grid_points_inside_poly
+from skimage.measure import points_in_poly, grid_points_in_poly
 
 
 class test_npnpoly():
@@ -11,29 +10,29 @@ class test_npnpoly():
                       [0, 1],
                       [1, 1],
                       [1, 0]])
-        assert(points_inside_poly([[0.5, 0.5]], v)[0])
-        assert(not points_inside_poly([[-0.1, 0.1]], v)[0])
+        assert(points_in_poly([[0.5, 0.5]], v)[0])
+        assert(not points_in_poly([[-0.1, 0.1]], v)[0])
 
     def test_triangle(self):
         v = np.array([[0, 0],
                       [1, 0],
                       [0.5, 0.75]])
-        assert(points_inside_poly([[0.5, 0.7]], v)[0])
-        assert(not points_inside_poly([[0.5, 0.76]], v)[0])
-        assert(not points_inside_poly([[0.7, 0.5]], v)[0])
+        assert(points_in_poly([[0.5, 0.7]], v)[0])
+        assert(not points_in_poly([[0.5, 0.76]], v)[0])
+        assert(not points_in_poly([[0.7, 0.5]], v)[0])
 
     def test_type(self):
-        assert(points_inside_poly([[0, 0]], [[0, 0]]).dtype == np.bool)
+        assert(points_in_poly([[0, 0]], [[0, 0]]).dtype == np.bool)
 
 
-def test_grid_points_inside_poly():
+def test_grid_points_in_poly():
     v = np.array([[0, 0],
                   [5, 0],
                   [5, 5]])
 
     expected = np.tril(np.ones((5, 5), dtype=bool))
 
-    assert_array_equal(grid_points_inside_poly((5, 5), v),
+    assert_array_equal(grid_points_in_poly((5, 5), v),
                        expected)
 
 if __name__ == "__main__":

skimage/morphology/convex_hull.py

@@ -1,7 +1,7 @@
 __all__ = ['convex_hull_image', 'convex_hull_object']
 
 import numpy as np
-from ._pnpoly import grid_points_inside_poly
+from ..measure import grid_points_in_poly
 from ._convex_hull import possible_hull
 from ..measure._label import label
 from skimage.util import unique_rows
@@ -72,7 +72,7 @@ def convex_hull_image(image):
 
     # For each pixel coordinate, check whether that pixel
     # lies inside the convex hull
-    mask = grid_points_inside_poly(image.shape[:2], v)
+    mask = grid_points_in_poly(image.shape[:2], v)
 
     return mask
 

skimage/morphology/setup.py

@@ -15,7 +15,6 @@ def configuration(parent_package='', top_path=None):
     cython(['cmorph.pyx'], working_path=base_path)
     cython(['_watershed.pyx'], working_path=base_path)
     cython(['_skeletonize_cy.pyx'], working_path=base_path)
-    cython(['_pnpoly.pyx'], working_path=base_path)
     cython(['_convex_hull.pyx'], working_path=base_path)
     cython(['_greyreconstruct.pyx'], working_path=base_path)
 
@@ -25,8 +24,6 @@ def configuration(parent_package='', top_path=None):
                          include_dirs=[get_numpy_include_dirs()])
     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(), '../_shared'])
     config.add_extension('_convex_hull', sources=['_convex_hull.c'],
                          include_dirs=[get_numpy_include_dirs()])
     config.add_extension('_greyreconstruct', sources=['_greyreconstruct.c'],