Merge pull request #134 from jimrybarski/133-index-error

fixes #133. The index assigned to images produced by `select` was wrong.

functional_tests/FYLM141111001.py

@@ -133,8 +133,13 @@ class FunctionalTests(unittest.TestCase):
             filter_images.append(image)
             if len(filter_images) == len(manual_images):
                 break
+        self.assertEqual(len(manual_images), len(filter_images))
+        self.assertGreater(len(manual_images), 0)
         for a, b in zip(manual_images, filter_images):
             self.assertTrue(np.array_equal(a, b))
+            self.assertEqual(a.index, b.index)
+            self.assertEqual(a.field_of_view, b.field_of_view)
+            self.assertEqual(a.channel, b.channel)
 
     def test_filter_order_all(self):
         # If we select every possible image using select(), we should just get every image in order

nd2reader/driver/v3.py

@@ -24,6 +24,12 @@ class V3Driver(object):
         self._label_map = label_map
         self._file_handle = file_handle
 
+    def calculate_image_properties(self, index):
+        field_of_view = self._calculate_field_of_view(index)
+        channel = self._calculate_channel(index)
+        z_level = self._calculate_z_level(index)
+        return field_of_view, channel, z_level
+
     def get_image(self, index):
         """
         Creates an Image object and adds its metadata, based on the index (which is simply the order in which the image was acquired). May return None if the ND2 contains
@@ -35,10 +41,8 @@ class V3Driver(object):
         :rtype:    Image or None
 
         """
+        field_of_view, channel, z_level = self.calculate_image_properties(index)
         channel_offset = index % len(self._metadata.channels)
-        field_of_view = self._calculate_field_of_view(index)
-        channel = self._calculate_channel(index)
-        z_level = self._calculate_z_level(index)
         image_group_number = int(index / len(self._metadata.channels))
         frame_number = self._calculate_frame_number(image_group_number, field_of_view, z_level)
         try:

nd2reader/interface.py

@@ -77,12 +77,11 @@ class Nd2(object):
         z_levels = self._to_list(z_levels, self.z_levels)
 
         for frame in self.frames:
-            for f in fields_of_view:
-                for z in z_levels:
-                    for c in channels:
-                        image = self.get_image(frame, f, c, z)
-                        if image is not None:
-                            yield image
+            field_of_view, channel, z_level = self._parser.driver.calculate_image_properties(frame)
+            if field_of_view in fields_of_view and channel in channels and z_level in z_levels:
+                image = self._parser.driver.get_image(frame)
+                if image is not None:
+                    yield image
 
     @property
     def height(self):