From 4565a49cfa310f4e8ad39eb12f47b5367aa472ed Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Scho=CC=88nberger?= <jschoenberger@demuc.de>
Date: Thu, 19 Apr 2012 23:37:35 +0200
Subject: [PATCH 01/14] added draw.polygon function with test cases

---
 skimage/draw/_draw.pyx          | 99 +++++++++++++++++++++++++++++++--
 skimage/draw/draw.py            |  2 +-
 skimage/draw/tests/test_draw.py | 78 ++++++++++++++++++++++++--
 3 files changed, 168 insertions(+), 11 deletions(-)

diff --git a/skimage/draw/_draw.pyx b/skimage/draw/_draw.pyx
index a586ae03..df59fadc 100644
--- a/skimage/draw/_draw.pyx
+++ b/skimage/draw/_draw.pyx
@@ -1,16 +1,18 @@
 import numpy as np
+import math
+from libc.stdlib cimport malloc, free
 cimport numpy as np
 cimport cython
 
-cdef extern from "math.h":
-    int abs(int i)
+cdef extern from "../morphology/_pnpoly.h":
+     int pnpoly(int nr_verts, double *xp, double *yp,
+                double x, double y)
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
 def bresenham(int y, int x, int y2, int x2):
-    """
-    Generate line pixel coordinates.
-    
+    """Generate line pixel coordinates.
+
     Parameters
     ----------
     y, x : int
@@ -46,7 +48,7 @@ def bresenham(int y, int x, int y2, int x2):
 
     rr = np.zeros(int(dx) + 1, dtype=np.int32)
     cc = np.zeros(int(dx) + 1, dtype=np.int32)
-    
+
     for i in range(dx):
         if steep:
             rr[i] = x
@@ -64,3 +66,88 @@ def bresenham(int y, int x, int y2, int x2):
     cc[dx] = x2
 
     return rr, cc
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+def _polygon_area(np.ndarray[np.double_t, ndim=1] x, np.ndarray[np.double_t, ndim=1] y):
+    """Calculate area of polygon.
+
+    Parameters
+    ----------
+    x : ndarray
+        X coordinates of polygon
+    y : ndarray
+        Y coordinates of polygon
+
+    Returns
+    -------
+    area : double
+        area of polygon
+    """
+    cdef double area
+    cdef int i
+    cdef int j = x.shape[0]-1
+    for i in xrange(x.shape[0]):
+        area += (x[j]+x[i])*(y[j]-y[i])
+        j = i
+    return abs(0.5*area)
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+def polygon(verts, shape=None):
+    """Generate coordinates of pixels within polygon.
+
+    Parameters
+    ----------
+    verts : Nx2 ndarray
+        (row, col) coordinates
+    shape : tuple, optional
+        image shape which is used to determine maximum extents of output pixel
+        coordinates. This is useful for polygons which exceed the image size,
+        default None
+
+    Returns
+    -------
+    rr, cc : ndarray of int
+        Pixel coordinates of polygon.
+        May be used to directly index into an array, e.g.
+        ``img[rr, cc] = 1``.
+    """
+    cdef int nr_verts = verts.shape[0]
+    cdef int minr = <int>max(0, verts[:,0].min())
+    cdef int maxr = <int>math.ceil(verts[:,0].max())
+    cdef int minc = <int>max(0, verts[:,1].min())
+    cdef int maxc = <int>math.ceil(verts[:,1].max())
+
+    # make sure output coordinates do not exceed image size
+    if shape is not None:
+        maxr = min(shape[0]-1, maxr)
+        maxc = min(shape[1]-1, maxc)
+
+    cdef int r, c
+    cdef int i = 0
+
+    #: make contigous arrays for r, c coordinates
+    verts = verts.astype('double')
+    cdef np.ndarray contiguous_rdata = verts[:,0].copy(order='C')
+    cdef np.ndarray contiguous_cdata = verts[:,1].copy(order='C')
+    cdef np.double_t* rptr = <np.double_t*>contiguous_rdata.data
+    cdef np.double_t* cptr = <np.double_t*>contiguous_cdata.data
+
+    # use area of polygon to determine the rough size of the output arrays
+    cdef double area = _polygon_area(contiguous_cdata, contiguous_rdata)
+
+    #: output coordinate arrays
+    cdef np.ndarray[np.int32_t, ndim=1, mode="c"] rr, cc
+    rr = np.zeros(int(area), dtype=np.int32)
+    cc = np.zeros(int(area), dtype=np.int32)
+
+    for r in range(minr, maxr+1):
+        for c in range(minc, maxc+1):
+            if pnpoly(nr_verts, cptr, rptr, c, r):
+                rr[i] = r
+                cc[i] = c
+                i += 1
+
+    # area >= number of points in polygon, so crop actual points
+    return rr[:i], cc[:i]
diff --git a/skimage/draw/draw.py b/skimage/draw/draw.py
index e66faf1c..5a7f9339 100644
--- a/skimage/draw/draw.py
+++ b/skimage/draw/draw.py
@@ -3,4 +3,4 @@ Methods to draw on arrays.
 
 """
 
-from ._draw import bresenham
+from ._draw import bresenham, polygon
diff --git a/skimage/draw/tests/test_draw.py b/skimage/draw/tests/test_draw.py
index ee323d83..80873981 100644
--- a/skimage/draw/tests/test_draw.py
+++ b/skimage/draw/tests/test_draw.py
@@ -1,7 +1,8 @@
 from numpy.testing import assert_array_equal
 import numpy as np
 
-from skimage.draw import bresenham
+from skimage.draw import bresenham, polygon
+
 
 def test_bresenham_horizontal():
     img = np.zeros((10, 10))
@@ -25,7 +26,7 @@ def test_bresenham_vertical():
 
     assert_array_equal(img, img_)
 
-def test_reverse():
+def test_bresenham_reverse():
     img = np.zeros((10, 10))
 
     rr, cc = bresenham(0, 9, 0, 0)
@@ -36,7 +37,7 @@ def test_reverse():
 
     assert_array_equal(img, img_)
 
-def test_diag():
+def test_bresenham_diag():
     img = np.zeros((5, 5))
 
     rr, cc = bresenham(0, 0, 4, 4)
@@ -47,6 +48,75 @@ def test_diag():
     assert_array_equal(img, img_)
 
 
+def test_polygon_rectangle():
+    img = np.zeros((10, 10), 'uint8')
+    poly = np.array(((1, 1), (4, 1), (4, 4), (1, 4), (1, 1)))
+
+    rr, cc = polygon(poly)
+    img[rr,cc] = 1
+
+    img_ = np.zeros((10, 10))
+    img_[1:4,1:4] = 1
+
+    assert_array_equal(img, img_)
+
+def test_polygon_rectangle_angular():
+    img = np.zeros((10, 10), 'uint8')
+    poly = np.array(((0, 3), (4, 7), (7, 4), (3, 0), (0, 3)))
+
+    rr, cc = polygon(poly)
+    img[rr,cc] = 1
+
+    img_ = np.array(
+        [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+         [0, 0, 1, 1, 0, 0, 0, 0, 0, 0],
+         [0, 1, 1, 1, 1, 0, 0, 0, 0, 0],
+         [1, 1, 1, 1, 1, 1, 0, 0, 0, 0],
+         [0, 1, 1, 1, 1, 1, 1, 0, 0, 0],
+         [0, 0, 1, 1, 1, 1, 0, 0, 0, 0],
+         [0, 0, 0, 1, 1, 0, 0, 0, 0, 0],
+         [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+         [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+         [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]
+    )
+
+    assert_array_equal(img, img_)
+
+def test_polygon_parallelogram():
+    img = np.zeros((10, 10), 'uint8')
+    poly = np.array(((1, 1), (5, 1), (7, 6), (3, 6), (1, 1)))
+
+    rr, cc = polygon(poly)
+    img[rr,cc] = 1
+
+    img_ = np.array(
+        [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+         [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+         [0, 1, 1, 1, 0, 0, 0, 0, 0, 0],
+         [0, 1, 1, 1, 1, 1, 0, 0, 0, 0],
+         [0, 1, 1, 1, 1, 1, 0, 0, 0, 0],
+         [0, 1, 1, 1, 1, 1, 0, 0, 0, 0],
+         [0, 0, 0, 0, 1, 1, 0, 0, 0, 0],
+         [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+         [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+         [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]
+    )
+
+    assert_array_equal(img, img_)
+
+def test_polygon_exceed():
+    img = np.zeros((10, 10), 'uint8')
+    poly = np.array(((1, -1), (100, -1), (100, 100), (1, 100), (1, 1)))
+
+    rr, cc = polygon(poly, img.shape)
+    img[rr,cc] = 1
+
+    img_ = np.zeros((10, 10))
+    img_[1:,:] = 1
+
+    assert_array_equal(img, img_)
+
+
 if __name__ == "__main__":
     from numpy.testing import run_module_suite
-    
+    run_module_suite()

From 0aa008712ac83188d9586de54a5137b3f0ce8c0e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Scho=CC=88nberger?= <jschoenberger@demuc.de>
Date: Sat, 21 Apr 2012 16:56:14 +0200
Subject: [PATCH 02/14] replaced fixed output array size with dynamic lists

area of polygon is not suitable to determine the size of the
number of filled pixels for output array
---
 skimage/draw/_draw.pyx | 17 +++++------------
 1 file changed, 5 insertions(+), 12 deletions(-)

diff --git a/skimage/draw/_draw.pyx b/skimage/draw/_draw.pyx
index df59fadc..01b6b17d 100644
--- a/skimage/draw/_draw.pyx
+++ b/skimage/draw/_draw.pyx
@@ -1,6 +1,5 @@
 import numpy as np
 import math
-from libc.stdlib cimport malloc, free
 cimport numpy as np
 cimport cython
 
@@ -125,7 +124,6 @@ def polygon(verts, shape=None):
         maxc = min(shape[1]-1, maxc)
 
     cdef int r, c
-    cdef int i = 0
 
     #: make contigous arrays for r, c coordinates
     verts = verts.astype('double')
@@ -134,20 +132,15 @@ def polygon(verts, shape=None):
     cdef np.double_t* rptr = <np.double_t*>contiguous_rdata.data
     cdef np.double_t* cptr = <np.double_t*>contiguous_cdata.data
 
-    # use area of polygon to determine the rough size of the output arrays
-    cdef double area = _polygon_area(contiguous_cdata, contiguous_rdata)
-
     #: output coordinate arrays
-    cdef np.ndarray[np.int32_t, ndim=1, mode="c"] rr, cc
-    rr = np.zeros(int(area), dtype=np.int32)
-    cc = np.zeros(int(area), dtype=np.int32)
+    rr = list()
+    cc = list()
 
     for r in range(minr, maxr+1):
         for c in range(minc, maxc+1):
             if pnpoly(nr_verts, cptr, rptr, c, r):
-                rr[i] = r
-                cc[i] = c
-                i += 1
+                rr.append(r)
+                cc.append(c)
 
     # area >= number of points in polygon, so crop actual points
-    return rr[:i], cc[:i]
+    return np.array(rr), np.array(cc)

From 649d912071d82d0622ef4be86c41ed9270f349ef Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Scho=CC=88nberger?= <jschoenberger@demuc.de>
Date: Sat, 21 Apr 2012 16:59:29 +0200
Subject: [PATCH 03/14] improved doc string

---
 skimage/draw/_draw.pyx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/skimage/draw/_draw.pyx b/skimage/draw/_draw.pyx
index 01b6b17d..efe1897d 100644
--- a/skimage/draw/_draw.pyx
+++ b/skimage/draw/_draw.pyx
@@ -102,8 +102,8 @@ def polygon(verts, shape=None):
         (row, col) coordinates
     shape : tuple, optional
         image shape which is used to determine maximum extents of output pixel
-        coordinates. This is useful for polygons which exceed the image size,
-        default None
+        coordinates. This is useful for polygons which exceed the image size.
+        By default the full extents of the polygon are used.
 
     Returns
     -------

From 0db612724da4c24acdb73e7d4cf5e643e488cd0c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Scho=CC=88nberger?= <jschoenberger@demuc.de>
Date: Sun, 22 Apr 2012 10:46:37 +0200
Subject: [PATCH 04/14] removed area function and removed old comment

---
 skimage/draw/_draw.pyx | 29 +++--------------------------
 1 file changed, 3 insertions(+), 26 deletions(-)

diff --git a/skimage/draw/_draw.pyx b/skimage/draw/_draw.pyx
index efe1897d..44bfea55 100644
--- a/skimage/draw/_draw.pyx
+++ b/skimage/draw/_draw.pyx
@@ -3,10 +3,12 @@ import math
 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)
 
+
 @cython.boundscheck(False)
 @cython.wraparound(False)
 def bresenham(int y, int x, int y2, int x2):
@@ -68,31 +70,7 @@ def bresenham(int y, int x, int y2, int x2):
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
-def _polygon_area(np.ndarray[np.double_t, ndim=1] x, np.ndarray[np.double_t, ndim=1] y):
-    """Calculate area of polygon.
-
-    Parameters
-    ----------
-    x : ndarray
-        X coordinates of polygon
-    y : ndarray
-        Y coordinates of polygon
-
-    Returns
-    -------
-    area : double
-        area of polygon
-    """
-    cdef double area
-    cdef int i
-    cdef int j = x.shape[0]-1
-    for i in xrange(x.shape[0]):
-        area += (x[j]+x[i])*(y[j]-y[i])
-        j = i
-    return abs(0.5*area)
-
-@cython.boundscheck(False)
-@cython.wraparound(False)
+@cython.nonecheck(False)
 def polygon(verts, shape=None):
     """Generate coordinates of pixels within polygon.
 
@@ -142,5 +120,4 @@ def polygon(verts, shape=None):
                 rr.append(r)
                 cc.append(c)
 
-    # area >= number of points in polygon, so crop actual points
     return np.array(rr), np.array(cc)

From 4834d7eb4d4d61487dde9f4d68c885d8355e5d0e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Scho=CC=88nberger?= <jschoenberger@demuc.de>
Date: Mon, 23 Apr 2012 15:37:07 +0200
Subject: [PATCH 05/14] added example script for draw.polygon function

---
 doc/examples/plot_polygon.py | 39 ++++++++++++++++++++++++++++++++++++
 skimage/setup.py             |  1 +
 2 files changed, 40 insertions(+)
 create mode 100644 doc/examples/plot_polygon.py

diff --git a/doc/examples/plot_polygon.py b/doc/examples/plot_polygon.py
new file mode 100644
index 00000000..6fa58906
--- /dev/null
+++ b/doc/examples/plot_polygon.py
@@ -0,0 +1,39 @@
+"""
+============
+Fill polygon
+============
+
+This example shows how to fill polygons in images.
+"""
+
+import matplotlib.pyplot as plt
+
+from skimage.draw import polygon
+import numpy as np
+
+
+img = np.zeros((500, 500), 'uint8')
+polygon1 = np.array((
+    (50, 50),
+    (150, 30),
+    (400, 100),
+    (300, 200),
+    (480, 400),
+    (100, 420),
+    (50, 50),
+))
+polygon2 = np.array((
+    (300, 300),
+    (480, 320),
+    (380, 430),
+    (220, 590),
+    (300, 300),
+))
+rr, cc = polygon(polygon1, img.shape)
+img[rr,cc] = 127
+rr, cc = polygon(polygon2, img.shape)
+img[rr,cc] = 255
+
+plt.gray()
+plt.imshow(img)
+plt.show()
\ No newline at end of file
diff --git a/skimage/setup.py b/skimage/setup.py
index c26014f8..f555c89a 100644
--- a/skimage/setup.py
+++ b/skimage/setup.py
@@ -16,6 +16,7 @@ def configuration(parent_package='', top_path=None):
     config.add_subpackage('draw')
     config.add_subpackage('feature')
     config.add_subpackage('measure')
+    config.add_subpackage('geometry')
 
     def add_test_directories(arg, dirname, fnames):
         if dirname.split(os.path.sep)[-1] == 'tests':

From 7191eaf05897cdd8f3276dea97df5bfb7cb35d41 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Scho=CC=88nberger?= <jschoenberger@demuc.de>
Date: Mon, 23 Apr 2012 15:39:26 +0200
Subject: [PATCH 06/14] removed geometry package from setup script

---
 skimage/setup.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/skimage/setup.py b/skimage/setup.py
index f555c89a..c26014f8 100644
--- a/skimage/setup.py
+++ b/skimage/setup.py
@@ -16,7 +16,6 @@ def configuration(parent_package='', top_path=None):
     config.add_subpackage('draw')
     config.add_subpackage('feature')
     config.add_subpackage('measure')
-    config.add_subpackage('geometry')
 
     def add_test_directories(arg, dirname, fnames):
         if dirname.split(os.path.sep)[-1] == 'tests':

From de8369be50208f94db5f90ebe33474ebafd7a8e6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Scho=CC=88nberger?= <jschoenberger@demuc.de>
Date: Mon, 23 Apr 2012 16:20:49 +0200
Subject: [PATCH 07/14] added draw circle and ellipse functions

---
 skimage/draw/_draw.pyx          | 65 +++++++++++++++++++++++++++++++++
 skimage/draw/draw.py            |  2 +-
 skimage/draw/tests/test_draw.py | 54 ++++++++++++++++++++++++++-
 3 files changed, 119 insertions(+), 2 deletions(-)

diff --git a/skimage/draw/_draw.pyx b/skimage/draw/_draw.pyx
index 44bfea55..6f6c955f 100644
--- a/skimage/draw/_draw.pyx
+++ b/skimage/draw/_draw.pyx
@@ -1,5 +1,6 @@
 import numpy as np
 import math
+from libc.math cimport sqrt
 cimport numpy as np
 cimport cython
 
@@ -121,3 +122,67 @@ def polygon(verts, shape=None):
                 cc.append(c)
 
     return np.array(rr), np.array(cc)
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+@cython.nonecheck(False)
+@cython.cdivision(True)
+def ellipse(double cy, double cx, double b, double a, shape=None):
+    """Generate coordinates of pixels within ellipse.
+
+    Parameters
+    ----------
+    cy, cx : double
+        centre coordinate of ellipse
+    b, a: double
+        minor and major semi-axes. (x/a)**2 + (y/b)**2 = 1
+
+    Returns
+    -------
+    rr, cc : ndarray of int
+        Pixel coordinates of ellipse.
+        May be used to directly index into an array, e.g.
+        ``img[rr, cc] = 1``.
+    """
+    cdef int minr = <int>max(0, cy-b)
+    cdef int maxr = <int>math.ceil(cy+b)
+    cdef int minc = <int>max(0, cx-a)
+    cdef int maxc = <int>math.ceil(cx+a)
+
+    # make sure output coordinates do not exceed image size
+    if shape is not None:
+        maxr = min(shape[0]-1, maxr)
+        maxc = min(shape[1]-1, maxc)
+
+    cdef int r, c
+
+    #: output coordinate arrays
+    rr = list()
+    cc = list()
+
+    for r in range(minr, maxr+1):
+        for c in range(minc, maxc+1):
+            if sqrt(((r - cy)/b)**2 + ((c - cx)/a)**2) < 1:
+                rr.append(r)
+                cc.append(c)
+
+    return np.array(rr), np.array(cc)
+
+def circle(double cy, double cx, double radius, shape=None):
+    """Generate coordinates of pixels within circle.
+
+    Parameters
+    ----------
+    cy, cx : double
+        centre coordinate of circle
+    radius: double
+        radius of circle
+
+    Returns
+    -------
+    rr, cc : ndarray of int
+        Pixel coordinates of ellipse.
+        May be used to directly index into an array, e.g.
+        ``img[rr, cc] = 1``.
+    """
+    return ellipse(cy, cx, radius, radius, shape)
diff --git a/skimage/draw/draw.py b/skimage/draw/draw.py
index 5a7f9339..a18cdeb6 100644
--- a/skimage/draw/draw.py
+++ b/skimage/draw/draw.py
@@ -3,4 +3,4 @@ Methods to draw on arrays.
 
 """
 
-from ._draw import bresenham, polygon
+from ._draw import bresenham, polygon, ellipse, circle
diff --git a/skimage/draw/tests/test_draw.py b/skimage/draw/tests/test_draw.py
index 80873981..ed309cf6 100644
--- a/skimage/draw/tests/test_draw.py
+++ b/skimage/draw/tests/test_draw.py
@@ -1,7 +1,7 @@
 from numpy.testing import assert_array_equal
 import numpy as np
 
-from skimage.draw import bresenham, polygon
+from skimage.draw import bresenham, polygon, circle, ellipse
 
 
 def test_bresenham_horizontal():
@@ -116,6 +116,58 @@ def test_polygon_exceed():
 
     assert_array_equal(img, img_)
 
+def test_circle():
+    img = np.zeros((15, 15), 'uint8')
+
+    rr, cc = circle(7, 7, 6)
+    img[rr,cc] = 1
+
+    img_ = np.array(
+      [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0],
+       [0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0],
+       [0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
+       [0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
+       [0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
+       [0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
+       [0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
+       [0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
+       [0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
+       [0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0],
+       [0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]
+    )
+
+    assert_array_equal(img, img_)
+
+def test_ellipse():
+    img = np.zeros((15, 15), 'uint8')
+
+    rr, cc = ellipse(7, 7, 3, 7)
+    img[rr,cc] = 1
+
+    img_ = np.array(
+      [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+       [0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
+       [0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
+       [0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
+       [0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
+       [0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
+       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]
+    )
+
+    assert_array_equal(img, img_)
+
 
 if __name__ == "__main__":
     from numpy.testing import run_module_suite

From d83592cc055c5fcc76243ecc199b00e70daed393 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Scho=CC=88nberger?= <jschoenberger@demuc.de>
Date: Mon, 23 Apr 2012 16:22:37 +0200
Subject: [PATCH 08/14] improved doc string

---
 skimage/draw/_draw.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skimage/draw/_draw.pyx b/skimage/draw/_draw.pyx
index 6f6c955f..38e8f941 100644
--- a/skimage/draw/_draw.pyx
+++ b/skimage/draw/_draw.pyx
@@ -78,7 +78,7 @@ def polygon(verts, shape=None):
     Parameters
     ----------
     verts : Nx2 ndarray
-        (row, col) coordinates
+        (row, col) vertices of polygon
     shape : tuple, optional
         image shape which is used to determine maximum extents of output pixel
         coordinates. This is useful for polygons which exceed the image size.

From 53ac34a8d000bec2fc24c9c7b5c5dd8ab31a094b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Scho=CC=88nberger?= <jschoenberger@demuc.de>
Date: Mon, 23 Apr 2012 17:07:27 +0200
Subject: [PATCH 09/14] renamed function bresenham to line

---
 skimage/draw/_draw.pyx          |  2 +-
 skimage/draw/draw.py            |  2 +-
 skimage/draw/tests/test_draw.py | 18 +++++++++---------
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/skimage/draw/_draw.pyx b/skimage/draw/_draw.pyx
index 38e8f941..ac4b078c 100644
--- a/skimage/draw/_draw.pyx
+++ b/skimage/draw/_draw.pyx
@@ -12,7 +12,7 @@ cdef extern from "../morphology/_pnpoly.h":
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
-def bresenham(int y, int x, int y2, int x2):
+def line(int y, int x, int y2, int x2):
     """Generate line pixel coordinates.
 
     Parameters
diff --git a/skimage/draw/draw.py b/skimage/draw/draw.py
index a18cdeb6..b7bb5b88 100644
--- a/skimage/draw/draw.py
+++ b/skimage/draw/draw.py
@@ -3,4 +3,4 @@ Methods to draw on arrays.
 
 """
 
-from ._draw import bresenham, polygon, ellipse, circle
+from ._draw import line, polygon, ellipse, circle
diff --git a/skimage/draw/tests/test_draw.py b/skimage/draw/tests/test_draw.py
index ed309cf6..42bbafc9 100644
--- a/skimage/draw/tests/test_draw.py
+++ b/skimage/draw/tests/test_draw.py
@@ -1,13 +1,13 @@
 from numpy.testing import assert_array_equal
 import numpy as np
 
-from skimage.draw import bresenham, polygon, circle, ellipse
+from skimage.draw import line, polygon, circle, ellipse
 
 
-def test_bresenham_horizontal():
+def test_line_horizontal():
     img = np.zeros((10, 10))
 
-    rr, cc = bresenham(0, 0, 0, 9)
+    rr, cc = line(0, 0, 0, 9)
     img[rr, cc] = 1
 
     img_ = np.zeros((10, 10))
@@ -15,10 +15,10 @@ def test_bresenham_horizontal():
 
     assert_array_equal(img, img_)
 
-def test_bresenham_vertical():
+def test_line_vertical():
     img = np.zeros((10, 10))
 
-    rr, cc = bresenham(0, 0, 9, 0)
+    rr, cc = line(0, 0, 9, 0)
     img[rr, cc] = 1
 
     img_ = np.zeros((10, 10))
@@ -26,10 +26,10 @@ def test_bresenham_vertical():
 
     assert_array_equal(img, img_)
 
-def test_bresenham_reverse():
+def test_line_reverse():
     img = np.zeros((10, 10))
 
-    rr, cc = bresenham(0, 9, 0, 0)
+    rr, cc = line(0, 9, 0, 0)
     img[rr, cc] = 1
 
     img_ = np.zeros((10, 10))
@@ -37,10 +37,10 @@ def test_bresenham_reverse():
 
     assert_array_equal(img, img_)
 
-def test_bresenham_diag():
+def test_line_diag():
     img = np.zeros((5, 5))
 
-    rr, cc = bresenham(0, 0, 4, 4)
+    rr, cc = line(0, 0, 4, 4)
     img[rr, cc] = 1
 
     img_ = np.eye(5)

From 48328cda8afb954f647355d616d00813efc0006c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Scho=CC=88nberger?= <jschoenberger@demuc.de>
Date: Mon, 23 Apr 2012 17:07:36 +0200
Subject: [PATCH 10/14] combined all draw functions in one example script

---
 doc/examples/plot_polygon.py | 39 -----------------------------
 doc/examples/plot_shapes.py  | 48 ++++++++++++++++++++++++++++++++++++
 2 files changed, 48 insertions(+), 39 deletions(-)
 delete mode 100644 doc/examples/plot_polygon.py
 create mode 100644 doc/examples/plot_shapes.py

diff --git a/doc/examples/plot_polygon.py b/doc/examples/plot_polygon.py
deleted file mode 100644
index 6fa58906..00000000
--- a/doc/examples/plot_polygon.py
+++ /dev/null
@@ -1,39 +0,0 @@
-"""
-============
-Fill polygon
-============
-
-This example shows how to fill polygons in images.
-"""
-
-import matplotlib.pyplot as plt
-
-from skimage.draw import polygon
-import numpy as np
-
-
-img = np.zeros((500, 500), 'uint8')
-polygon1 = np.array((
-    (50, 50),
-    (150, 30),
-    (400, 100),
-    (300, 200),
-    (480, 400),
-    (100, 420),
-    (50, 50),
-))
-polygon2 = np.array((
-    (300, 300),
-    (480, 320),
-    (380, 430),
-    (220, 590),
-    (300, 300),
-))
-rr, cc = polygon(polygon1, img.shape)
-img[rr,cc] = 127
-rr, cc = polygon(polygon2, img.shape)
-img[rr,cc] = 255
-
-plt.gray()
-plt.imshow(img)
-plt.show()
\ No newline at end of file
diff --git a/doc/examples/plot_shapes.py b/doc/examples/plot_shapes.py
new file mode 100644
index 00000000..806049ad
--- /dev/null
+++ b/doc/examples/plot_shapes.py
@@ -0,0 +1,48 @@
+"""
+===========
+Fill shapes
+===========
+
+This example shows how to fill several different shapes:
+* line
+* polygon
+* circle
+* ellipse
+
+"""
+
+import matplotlib.pyplot as plt
+
+from skimage.draw import line, polygon, circle, ellipse
+import numpy as np
+
+
+img = np.zeros((500, 500, 3), 'uint8')
+
+#: draw line
+rr, cc = line(120, 123, 20, 400)
+img[rr,cc,0] = 255
+
+#: fill polygon
+poly = np.array((
+    (300, 300),
+    (480, 320),
+    (380, 430),
+    (220, 590),
+    (300, 300),
+))
+rr, cc = polygon(poly, img.shape)
+img[rr,cc,1] = 255
+
+#: fill circle
+rr, cc = circle(200, 200, 100, img.shape)
+img[rr,cc,0] = 255
+rr, cc = circle(200, 200, 100, img.shape)
+img[rr,cc,1] = 255
+
+#: fill ellipse
+rr, cc = ellipse(300, 300, 100, 200, img.shape)
+img[rr,cc,2] = 255
+
+plt.imshow(img)
+plt.show()
\ No newline at end of file

From 5b854d9b3c425cf104e1ab20bac78b738aa8ab57 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Scho=CC=88nberger?= <jschoenberger@demuc.de>
Date: Mon, 23 Apr 2012 18:38:20 +0200
Subject: [PATCH 11/14] changed interface of draw.polygon function for a more
 consistent usage

---
 doc/examples/plot_shapes.py     |  2 +-
 skimage/draw/_draw.pyx          | 32 +++++++++++++++++++++-----------
 skimage/draw/tests/test_draw.py |  8 ++++----
 3 files changed, 26 insertions(+), 16 deletions(-)

diff --git a/doc/examples/plot_shapes.py b/doc/examples/plot_shapes.py
index 806049ad..55569016 100644
--- a/doc/examples/plot_shapes.py
+++ b/doc/examples/plot_shapes.py
@@ -31,7 +31,7 @@ poly = np.array((
     (220, 590),
     (300, 300),
 ))
-rr, cc = polygon(poly, img.shape)
+rr, cc = polygon(poly[:,0], poly[:,1], img.shape)
 img[rr,cc,1] = 255
 
 #: fill circle
diff --git a/skimage/draw/_draw.pyx b/skimage/draw/_draw.pyx
index ac4b078c..d124f75d 100644
--- a/skimage/draw/_draw.pyx
+++ b/skimage/draw/_draw.pyx
@@ -72,13 +72,15 @@ def line(int y, int x, int y2, int x2):
 @cython.boundscheck(False)
 @cython.wraparound(False)
 @cython.nonecheck(False)
-def polygon(verts, shape=None):
+def polygon(y, x, shape=None):
     """Generate coordinates of pixels within polygon.
 
     Parameters
     ----------
-    verts : Nx2 ndarray
-        (row, col) vertices of polygon
+    y : (N,) ndarray
+        y coordinates of vertices of polygon
+    x : (N,) ndarray
+        x coordinates of vertices of polygon
     shape : tuple, optional
         image shape which is used to determine maximum extents of output pixel
         coordinates. This is useful for polygons which exceed the image size.
@@ -91,11 +93,11 @@ def polygon(verts, shape=None):
         May be used to directly index into an array, e.g.
         ``img[rr, cc] = 1``.
     """
-    cdef int nr_verts = verts.shape[0]
-    cdef int minr = <int>max(0, verts[:,0].min())
-    cdef int maxr = <int>math.ceil(verts[:,0].max())
-    cdef int minc = <int>max(0, verts[:,1].min())
-    cdef int maxc = <int>math.ceil(verts[:,1].max())
+    cdef int nr_verts = x.shape[0]
+    cdef int minr = <int>max(0, y.min())
+    cdef int maxr = <int>math.ceil(y.max())
+    cdef int minc = <int>max(0, x.min())
+    cdef int maxc = <int>math.ceil(x.max())
 
     # make sure output coordinates do not exceed image size
     if shape is not None:
@@ -105,9 +107,17 @@ def polygon(verts, shape=None):
     cdef int r, c
 
     #: make contigous arrays for r, c coordinates
-    verts = verts.astype('double')
-    cdef np.ndarray contiguous_rdata = verts[:,0].copy(order='C')
-    cdef np.ndarray contiguous_cdata = verts[:,1].copy(order='C')
+    y = y.astype('double')
+    x = x.astype('double')
+    cdef np.ndarray contiguous_rdata, contiguous_cdata
+    if not y.flags['C_CONTIGUOUS']:
+        contiguous_rdata = y.copy(order='C')
+    else:
+        contiguous_rdata = y
+    if not y.flags['C_CONTIGUOUS']:
+        contiguous_cdata = x.copy(order='C')
+    else:
+        contiguous_cdata = x
     cdef np.double_t* rptr = <np.double_t*>contiguous_rdata.data
     cdef np.double_t* cptr = <np.double_t*>contiguous_cdata.data
 
diff --git a/skimage/draw/tests/test_draw.py b/skimage/draw/tests/test_draw.py
index 42bbafc9..dd1c81e2 100644
--- a/skimage/draw/tests/test_draw.py
+++ b/skimage/draw/tests/test_draw.py
@@ -52,7 +52,7 @@ def test_polygon_rectangle():
     img = np.zeros((10, 10), 'uint8')
     poly = np.array(((1, 1), (4, 1), (4, 4), (1, 4), (1, 1)))
 
-    rr, cc = polygon(poly)
+    rr, cc = polygon(poly[:,0], poly[:,1])
     img[rr,cc] = 1
 
     img_ = np.zeros((10, 10))
@@ -64,7 +64,7 @@ def test_polygon_rectangle_angular():
     img = np.zeros((10, 10), 'uint8')
     poly = np.array(((0, 3), (4, 7), (7, 4), (3, 0), (0, 3)))
 
-    rr, cc = polygon(poly)
+    rr, cc = polygon(poly[:,0], poly[:,1])
     img[rr,cc] = 1
 
     img_ = np.array(
@@ -86,7 +86,7 @@ def test_polygon_parallelogram():
     img = np.zeros((10, 10), 'uint8')
     poly = np.array(((1, 1), (5, 1), (7, 6), (3, 6), (1, 1)))
 
-    rr, cc = polygon(poly)
+    rr, cc = polygon(poly[:,0], poly[:,1])
     img[rr,cc] = 1
 
     img_ = np.array(
@@ -108,7 +108,7 @@ def test_polygon_exceed():
     img = np.zeros((10, 10), 'uint8')
     poly = np.array(((1, -1), (100, -1), (100, 100), (1, 100), (1, 1)))
 
-    rr, cc = polygon(poly, img.shape)
+    rr, cc = polygon(poly[:,0], poly[:,1], img.shape)
     img[rr,cc] = 1
 
     img_ = np.zeros((10, 10))

From af345f1a3238797d61aeefb24585b39b4cd9ebe8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Scho=CC=88nberger?= <jschoenberger@demuc.de>
Date: Mon, 23 Apr 2012 18:45:11 +0200
Subject: [PATCH 12/14] improved color assignment of circle in shapes example
 script

---
 doc/examples/plot_shapes.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/doc/examples/plot_shapes.py b/doc/examples/plot_shapes.py
index 55569016..8107fc80 100644
--- a/doc/examples/plot_shapes.py
+++ b/doc/examples/plot_shapes.py
@@ -36,9 +36,7 @@ img[rr,cc,1] = 255
 
 #: fill circle
 rr, cc = circle(200, 200, 100, img.shape)
-img[rr,cc,0] = 255
-rr, cc = circle(200, 200, 100, img.shape)
-img[rr,cc,1] = 255
+img[rr,cc,:] = (255, 255, 0)
 
 #: fill ellipse
 rr, cc = ellipse(300, 300, 100, 200, img.shape)

From 9fdfdc9708d43c3ad65fbb7c608fb1850039058f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Scho=CC=88nberger?= <jschoenberger@demuc.de>
Date: Mon, 23 Apr 2012 22:06:26 +0200
Subject: [PATCH 13/14] added explicit cython list type and changed creation of
 contiguous arrays

---
 skimage/draw/_draw.pyx | 20 ++++++--------------
 1 file changed, 6 insertions(+), 14 deletions(-)

diff --git a/skimage/draw/_draw.pyx b/skimage/draw/_draw.pyx
index d124f75d..9dc1d307 100644
--- a/skimage/draw/_draw.pyx
+++ b/skimage/draw/_draw.pyx
@@ -107,23 +107,15 @@ def polygon(y, x, shape=None):
     cdef int r, c
 
     #: make contigous arrays for r, c coordinates
-    y = y.astype('double')
-    x = x.astype('double')
     cdef np.ndarray contiguous_rdata, contiguous_cdata
-    if not y.flags['C_CONTIGUOUS']:
-        contiguous_rdata = y.copy(order='C')
-    else:
-        contiguous_rdata = y
-    if not y.flags['C_CONTIGUOUS']:
-        contiguous_cdata = x.copy(order='C')
-    else:
-        contiguous_cdata = x
+    contiguous_rdata = np.ascontiguousarray(y, 'double')
+    contiguous_cdata = np.ascontiguousarray(x, 'double')
     cdef np.double_t* rptr = <np.double_t*>contiguous_rdata.data
     cdef np.double_t* cptr = <np.double_t*>contiguous_cdata.data
 
     #: output coordinate arrays
-    rr = list()
-    cc = list()
+    cdef list rr = list()
+    cdef list cc = list()
 
     for r in range(minr, maxr+1):
         for c in range(minc, maxc+1):
@@ -167,8 +159,8 @@ def ellipse(double cy, double cx, double b, double a, shape=None):
     cdef int r, c
 
     #: output coordinate arrays
-    rr = list()
-    cc = list()
+    cdef list rr = list()
+    cdef list cc = list()
 
     for r in range(minr, maxr+1):
         for c in range(minc, maxc+1):

From c7d06951a8191598bbd0bc677b13156b7bc4a575 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20Scho=CC=88nberger?= <jschoenberger@demuc.de>
Date: Mon, 23 Apr 2012 22:16:59 +0200
Subject: [PATCH 14/14] DOC: update contributors

---
 CONTRIBUTORS.txt | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CONTRIBUTORS.txt b/CONTRIBUTORS.txt
index 5082c508..8258eada 100644
--- a/CONTRIBUTORS.txt
+++ b/CONTRIBUTORS.txt
@@ -98,3 +98,6 @@
 
 - Nicolas Poilvert
   Shape views: ``util.shape.view_as_windows`` and ``util.shape.view_as_blocks``
+
+- Johannes Schönberger
+  Polygon, circle and ellipse drawing functions