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@ -7,6 +7,7 @@ from nd2reader import Nd2 |
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import numpy as np |
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from datetime import datetime |
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import unittest |
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import six |
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class FunctionalTests(unittest.TestCase): |
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@ -108,18 +109,57 @@ class FunctionalTests(unittest.TestCase): |
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self.assertTupleEqual((self.nd2[54].z_level, self.nd2[54].channel), (0, 'BF')) |
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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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self.assertIsNone(image) |
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def test_fast_filter(self): |
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def test_index(self): |
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# Do indexes get added to images properly? |
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for n, image in enumerate(self.nd2): |
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if image is not None: |
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self.assertEqual(n, image.index) |
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if n > 50: |
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break |
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def test_filter(self): |
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# If we take the first 20 GFP images, they should be identical to the first 20 items iterated from filter() |
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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(200), self.nd2): |
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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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manual_images.append(image) |
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filter_images = [] |
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for image in self.nd2.filter(channels=['GFP']): |
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for image in self.nd2.filter(channels='GFP'): |
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filter_images.append(image) |
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if len(filter_images) == len(manual_images): |
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break |
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for a, b in zip(manual_images, filter_images): |
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self.assertTrue(np.array_equal(a, b)) |
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def test_filter_order_all(self): |
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# If we select every possible image using filter(), we should just get every image in order |
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n = 0 |
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for image in self.nd2.filter(channels=['BF', '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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break |
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n += 1 |
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self.assertTrue(np.array_equal(image, indexed_image)) |
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n += 1 |
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if n > 100: |
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break |
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def test_filter_order_subset(self): |
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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.filter(channels='BF', 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.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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if n > 100: |
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break |