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@ -34,7 +34,7 @@ class FunctionalTests(unittest.TestCase): |
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self.assertEqual(len(self.nd2.fields_of_view), 8) |
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def test_channels(self): |
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self.assertTupleEqual(tuple(sorted(self.nd2.channels)), ('BF', 'GFP')) |
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self.assertTupleEqual(tuple(sorted(self.nd2.channels)), ('', 'GFP')) |
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def test_z_levels(self): |
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self.assertTupleEqual(tuple(self.nd2.z_levels), (0, 1, 2)) |
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@ -44,7 +44,7 @@ class FunctionalTests(unittest.TestCase): |
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self.assertEqual(image.field_of_view, 2) |
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self.assertEqual(image.frame_number, 0) |
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self.assertAlmostEqual(image.timestamp, 19.0340758) |
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self.assertEqual(image.channel, 'BF') |
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self.assertEqual(image.channel, '') |
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self.assertEqual(image.z_level, 1) |
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self.assertEqual(image.height, self.nd2.height) |
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self.assertEqual(image.width, self.nd2.width) |
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@ -70,46 +70,46 @@ class FunctionalTests(unittest.TestCase): |
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self.assertEqual(len(images), 10) |
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def test_get_image_by_attribute_ok(self): |
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image = self.nd2.get_image(4, 0, "GFP", 1) |
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image = self.nd2.get_image(4, 0, 'GFP', 1) |
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self.assertIsNotNone(image) |
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image = self.nd2.get_image(4, 0, "BF", 0) |
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image = self.nd2.get_image(4, 0, '', 0) |
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self.assertIsNotNone(image) |
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image = self.nd2.get_image(4, 0, "BF", 1) |
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image = self.nd2.get_image(4, 0, '', 1) |
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self.assertIsNotNone(image) |
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def test_images(self): |
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self.assertTupleEqual((self.nd2[0].z_level, self.nd2[0].channel), (0, 'BF')) |
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self.assertTupleEqual((self.nd2[0].z_level, self.nd2[0].channel), (0, '')) |
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self.assertIsNone(self.nd2[1]) |
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self.assertTupleEqual((self.nd2[2].z_level, self.nd2[2].channel), (1, 'BF')) |
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self.assertTupleEqual((self.nd2[2].z_level, self.nd2[2].channel), (1, '')) |
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self.assertTupleEqual((self.nd2[3].z_level, self.nd2[3].channel), (1, 'GFP')) |
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self.assertTupleEqual((self.nd2[4].z_level, self.nd2[4].channel), (2, 'BF')) |
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self.assertTupleEqual((self.nd2[4].z_level, self.nd2[4].channel), (2, '')) |
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self.assertIsNone(self.nd2[5]) |
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self.assertTupleEqual((self.nd2[6].z_level, self.nd2[6].channel), (0, 'BF')) |
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self.assertTupleEqual((self.nd2[6].z_level, self.nd2[6].channel), (0, '')) |
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self.assertIsNone(self.nd2[7]) |
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self.assertTupleEqual((self.nd2[8].z_level, self.nd2[8].channel), (1, 'BF')) |
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self.assertTupleEqual((self.nd2[8].z_level, self.nd2[8].channel), (1, '')) |
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self.assertTupleEqual((self.nd2[9].z_level, self.nd2[9].channel), (1, 'GFP')) |
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self.assertTupleEqual((self.nd2[10].z_level, self.nd2[10].channel), (2, 'BF')) |
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self.assertTupleEqual((self.nd2[10].z_level, self.nd2[10].channel), (2, '')) |
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self.assertIsNone(self.nd2[11]) |
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self.assertTupleEqual((self.nd2[12].z_level, self.nd2[12].channel), (0, 'BF')) |
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self.assertTupleEqual((self.nd2[12].z_level, self.nd2[12].channel), (0, '')) |
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self.assertIsNone(self.nd2[13]) |
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self.assertTupleEqual((self.nd2[14].z_level, self.nd2[14].channel), (1, 'BF')) |
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self.assertTupleEqual((self.nd2[14].z_level, self.nd2[14].channel), (1, '')) |
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self.assertTupleEqual((self.nd2[15].z_level, self.nd2[15].channel), (1, 'GFP')) |
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self.assertTupleEqual((self.nd2[16].z_level, self.nd2[16].channel), (2, 'BF')) |
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self.assertTupleEqual((self.nd2[16].z_level, self.nd2[16].channel), (2, '')) |
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self.assertIsNone(self.nd2[17]) |
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self.assertTupleEqual((self.nd2[18].z_level, self.nd2[18].channel), (0, 'BF')) |
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self.assertTupleEqual((self.nd2[18].z_level, self.nd2[18].channel), (0, '')) |
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self.assertIsNone(self.nd2[19]) |
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self.assertIsNone(self.nd2[47]) |
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self.assertTupleEqual((self.nd2[48].z_level, self.nd2[48].channel), (0, 'BF')) |
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self.assertTupleEqual((self.nd2[48].z_level, self.nd2[48].channel), (0, '')) |
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self.assertIsNone(self.nd2[49]) |
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self.assertTupleEqual((self.nd2[50].z_level, self.nd2[50].channel), (1, 'BF')) |
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self.assertTupleEqual((self.nd2[50].z_level, self.nd2[50].channel), (1, '')) |
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self.assertIsNone(self.nd2[51]) |
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self.assertTupleEqual((self.nd2[52].z_level, self.nd2[52].channel), (2, 'BF')) |
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self.assertTupleEqual((self.nd2[52].z_level, self.nd2[52].channel), (2, '')) |
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self.assertIsNone(self.nd2[53]) |
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self.assertTupleEqual((self.nd2[54].z_level, self.nd2[54].channel), (0, 'BF')) |
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self.assertTupleEqual((self.nd2[54].z_level, self.nd2[54].channel), (0, '')) |
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def test_get_image_by_attribute_none(self): |
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# Should handle missing images without an exception |
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image = self.nd2.get_image(4, 0, "GFP", 0) |
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image = self.nd2.get_image(4, 0, 'GFP', 0) |
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self.assertIsNone(image) |
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def test_index(self): |
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@ -122,7 +122,7 @@ class FunctionalTests(unittest.TestCase): |
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def test_select(self): |
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# If we take the first 20 GFP images, they should be identical to the first 20 items iterated from select() |
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# if we set our criteria to just "GFP" |
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# if we set our criteria to just 'GFP' |
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manual_images = [] |
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for _, image in zip(range(20), self.nd2): |
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if image is not None and image.channel == 'GFP': |
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@ -144,7 +144,7 @@ class FunctionalTests(unittest.TestCase): |
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def test_filter_order_all(self): |
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# If we select every possible image using select(), we should just get every image in order |
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n = 0 |
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for image in self.nd2.select(channels=['BF', 'GFP'], z_levels=[0, 1, 2], fields_of_view=list(range(8))): |
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for image in self.nd2.select(channels=['', 'GFP'], z_levels=[0, 1, 2], fields_of_view=list(range(8))): |
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while True: |
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indexed_image = self.nd2[n] |
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if indexed_image is not None: |
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@ -159,9 +159,9 @@ class FunctionalTests(unittest.TestCase): |
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# Test that images are always yielded in increasing order. This guarantees that no matter what subset of images |
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# we're filtering, we still get them in the chronological order they were acquired |
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n = -1 |
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for image in self.nd2.select(channels='BF', z_levels=[0, 1], fields_of_view=[1, 2, 4]): |
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for image in self.nd2.select(channels='', z_levels=[0, 1], fields_of_view=[1, 2, 4]): |
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self.assertGreater(image.index, n) |
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self.assertEqual(image.channel, 'BF') |
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self.assertEqual(image.channel, '') |
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self.assertIn(image.field_of_view, (1, 2, 4)) |
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self.assertIn(image.z_level, (0, 1)) |
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n = image.index |
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Jim Rybarski
9 years ago