Update coordinate convention, inline matplotlib clip_to_bbox

The `clip_to_bbox` function is only available in later versions of Matplotlib,
so for now inline it so that we remain compatible with v1.1.

TODO.txt

@@ -1,9 +1,10 @@
 Remember to list any API changes below in `doc/source/api_changes.txt`.
 
 
-
 Version 0.14
 ------------
+* In `skimage._shared._geometry`, remove `clip_to_bbox` and replace with
+  `poly.clip_to_bbox`, if our dependency on Matplotlib is now >= 1.2.
 * Remove deprecated ``ntiles_*` kwargs in ``equalize_adapthist``.
 * Remove deprecated ``skimage.restoration.nl_means_denoising``.
 * Remove deprecated ``skimage.filters.gaussian_filter``.

skimage/_shared/_geometry.py

@@ -3,19 +3,19 @@ __all__ = ['polygon_clip', 'polygon_area']
 import numpy as np
 
 
-def polygon_clip(yp, xp, r0, c0, r1, c1):
+def polygon_clip(rp, cp, r0, c0, r1, c1):
     """Clip a polygon to the given bounding box.
 
     Parameters
     ----------
-    yp, xp : (N,) ndarray of double
+    rp, cp : (N,) ndarray of double
         Row and column coordinates of the polygon.
     (r0, c0), (r1, c1) : double
         Top-left and bottom-right coordinates of the bounding box.
 
     Returns
     -------
-    y_clipped, x_clipped : (M,) ndarray of double
+    r_clipped, c_clipped : (M,) ndarray of double
         Coordinates of clipped polygon.
 
     Notes
@@ -24,29 +24,36 @@ def polygon_clip(yp, xp, r0, c0, r1, c1):
     AGG 2.4 and exposed in Matplotlib.
 
     """
-    from matplotlib import path, transforms
+    from matplotlib import _path, path, transforms
 
-    poly = path.Path(np.vstack((yp, xp)).T, closed=True)
+    # `clip_to_bbox` is included directly from Matplotlib
+    # since it was only included after v1.1
+    def clip_to_bbox(poly_path, bbox, inside=True):
+        verts = _path.clip_path_to_rect(poly_path, bbox, inside)
+        paths = [path.Path(poly) for poly in verts]
+        return poly_path.make_compound_path(*paths)
+
+    poly = path.Path(np.vstack((rp, cp)).T, closed=True)
     clip_rect = transforms.Bbox([[r0, c0], [r1, c1]])
 
-    poly_clipped = poly.clip_to_bbox(clip_rect).to_polygons()[0]
+    poly_clipped = clip_to_bbox(poly, clip_rect).to_polygons()[0]
 
     return poly_clipped[:, 0], poly_clipped[:, 1]
 
 
-def polygon_area(py, px):
+def polygon_area(pr, pc):
     """Compute the area of a polygon.
 
     Parameters
     ----------
-    py, px : (N,) array of float
-        Polygon coordinates.
+    pr, pc : (N,) array of float
+        Polygon row and column coordinates.
 
     Returns
     -------
     a : float
         Area of the polygon.
     """
-    py = np.asarray(py)
-    px = np.asarray(px)
-    return 0.5 * np.abs(np.sum((px[:-1] * py[1:]) - (px[1:] * py[:-1])))
+    pr = np.asarray(pr)
+    pc = np.asarray(pc)
+    return 0.5 * np.abs(np.sum((pc[:-1] * pr[1:]) - (pc[1:] * pr[:-1])))