Merge c651a48 into c52fdc7

vanvalenlab · Jun 2, 2022 · c6f2013 · c6f2013
2 parents c52fdc7 + c651a48
commit c6f2013
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Showing 2 changed files with 26 additions and 18 deletions.
diff --git a/deepcell_spots/image_alignment.py b/deepcell_spots/image_alignment.py
@@ -150,21 +150,17 @@ def align_images(image_dict, reference_dict):
 
         keypoints1, descriptors1 = orb.detectAndCompute(im1, None)
 
-        # Match features.
+        # Match features
         matcher = cv2.DescriptorMatcher_create(cv2.DESCRIPTOR_MATCHER_BRUTEFORCE_HAMMING)
         matches = matcher.match(descriptors1, descriptors2, None)
 
         # Sort matches by score
-        matches.sort(key=lambda x: x.distance, reverse=False)
+        matches = sorted(matches, key=lambda x: x.distance, reverse=False)
 
         # Remove not so good matches
         numGoodMatches = int(len(matches) * GOOD_MATCH_PERCENT)
         matches = matches[:numGoodMatches]
 
-        # Draw top matches
-        imMatches = cv2.drawMatches(reference_im, keypoints2, im1, keypoints1, matches, None)
-        cv2.imwrite("matches.jpg", imMatches)
-
         # Extract location of good matches
         points1 = np.zeros((len(matches), 2), dtype=np.float32)
         points2 = np.zeros((len(matches), 2), dtype=np.float32)

diff --git a/deepcell_spots/image_alignment_test.py b/deepcell_spots/image_alignment_test.py
@@ -29,21 +29,33 @@
 import numpy as np
 from tensorflow.python.platform import test
 
-from deepcell_spots.image_alignment import crop_images
+from deepcell_spots.image_alignment import crop_images, align_images
+
+
+def pad_with(vector, pad_width, iaxis, kwargs):
+    pad_value = kwargs.get('padder', 0)
+    vector[:pad_width[0]] = pad_value
+    vector[-pad_width[1]:] = pad_value
 
 
 class TestImageAlignment(test.TestCase):
-    # def test_align_images(self):
-    #     im = np.random.random((1, 10, 10, 1)) > 0.9
-    #     im = im*65535
-    #     im_dict = {}
-    #     ref_dict = {}
-    #     for i in range(10):
-    #         im_dict[i] = im
-    #         ref_dict[i] = im
-    #     aligned_dict = align_images(im_dict, ref_dict)
-
-    #     self.assertEqual(np.shape(im_dict.values()), np.shape(aligned_dict.values()))
+    def test_align_images(self):
+        im_size = 100
+        shift = 5
+
+        im_dict = {}
+        ref_dict = {}
+        for i in range(10):
+            im = np.random.random((1, im_size, im_size, 1)) * 65535
+            shift_im = np.expand_dims(np.pad(im[0, ..., 0],
+                                      shift,
+                                      pad_with)[:im_size, :im_size], axis=[0, -1])
+
+            im_dict[i] = im
+            ref_dict[i] = shift_im
+        aligned_dict = align_images(im_dict, ref_dict)
+
+        self.assertEqual(np.shape(im_dict.values()), np.shape(aligned_dict.values()))
 
     def test_crop_images(self):
         # With padding