Merge pull request #47 from CellProfiler/features/kirsch-operator

Kirsch operator

.travis.yml

@@ -1,6 +1,7 @@
 addons:
     apt:
         packages:
+            - python-imaging
             - python-matplotlib
             - python-numpy
             - python-scipy

centrosome/kirsch.py

@@ -0,0 +1,21 @@
+import numpy
+import scipy.ndimage.filters
+
+
+def kirsch(image):
+    convolution_mask = [5, -3, -3, -3, -3, -3, 5, 5]
+
+    derivatives = numpy.zeros(image.shape)
+
+    kernel = numpy.zeros((3, 3), image.dtype)
+    kindex = numpy.array([[0,  1, 2],
+                          [7, -1, 3],
+                          [6,  5, 4]])
+    for _ in range(len(convolution_mask)):
+        kernel[kindex >= 0] = numpy.array(convolution_mask)[kindex[kindex >= 0]]
+        derivatives = numpy.maximum(
+            derivatives, scipy.ndimage.filters.convolve(image, kernel))
+
+        convolution_mask = convolution_mask[-1:] + convolution_mask[:-1]
+
+    return derivatives

setup.py

@@ -89,6 +89,7 @@ def run_tests(self):
     ]),
     install_requires=[
         "numpy",
+        "pillow",
         "scikit-image",
         "scipy",
     ],

tests/test_kirsch.py

@@ -0,0 +1,27 @@
+import centrosome.kirsch
+import scipy.misc
+import numpy as np
+import unittest
+
+class TestKirsch(unittest.TestCase):
+    def test_01_01_kirsch(self):
+        #
+        # Test a maximum at all possible orientations
+        #
+        r = np.random.RandomState([ord(_) for _ in "kirsch"])
+        for coords in (((0,  -1), (-1, -1), (-1, 0)),
+                       ((-1, -1), (-1,  0), (-1, 1)),
+                       ((-1,  0), (-1,  1), (0,  1)),
+                       ((-1,  1), ( 0,  1), (1,  1)),
+                       (( 0,  1), ( 1,  1), (1,  0)),
+                       (( 1,  1), ( 1,  0), (1, -1)),
+                       (( 1,  0), ( 1, -1), (0, -1)),
+                       (( 1, -1), ( 0, -1), (-1, -1))):
+            img = r.uniform(size=(3, 3)) * .1
+            expected = -3 * img
+            for ioff, joff in coords:
+                img[ioff + 1, joff + 1] += .5
+                expected[ioff + 1, joff+1] = img[ioff + 1, joff+1] * 5
+            expected[1, 1] = 0
+            result = centrosome.kirsch.kirsch(img)
+            self.assertEqual(result[1, 1], np.sum(expected))