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142 lines
5.5 KiB
142 lines
5.5 KiB
"""
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Tests on ND2s that have 1 or 2 cycles only. This is unlike the ND2s I work with typically, which are all done over very long periods of time.
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"""
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from nd2reader import Nd2
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import numpy as np
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import unittest
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class Monocycle1Tests(unittest.TestCase):
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def setUp(self):
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self.nd2 = Nd2("/var/nd2s/simone1.nd2")
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def tearDown(self):
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self.nd2.close()
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def test_channels(self):
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self.assertListEqual(self.nd2.channels, ['Cy3Narrow', 'TxRed-modified', 'FITC', 'DAPI'])
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def test_pixel_size(self):
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self.assertGreater(self.nd2.pixel_microns, 0.0)
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def test_select(self):
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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 == 'FITC':
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manual_images.append(image)
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filter_images = []
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for image in self.nd2.select(channels='FITC'):
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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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self.assertEqual(len(manual_images), len(filter_images))
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self.assertGreater(len(manual_images), 0)
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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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self.assertEqual(a.index, b.index)
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self.assertEqual(a.field_of_view, b.field_of_view)
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self.assertEqual(a.channel, b.channel)
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def test_select_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=['Cy3Narrow', 'DAPI', 'FITC', 'TxRed-modified'],
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z_levels=list(range(35)),
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fields_of_view=list(range(5))):
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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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# Quit after the first hundred images just to save time.
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# If there's a problem, we'll have seen it by now.
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break
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def test_select_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.select(channels='FITC',
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z_levels=[0, 1],
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fields_of_view=[1, 2, 4]):
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self.assertGreater(image.index, n)
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self.assertEqual(image.channel, 'FITC')
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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
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class Monocycle2Tests(unittest.TestCase):
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def setUp(self):
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self.nd2 = Nd2("/var/nd2s/hawkjo.nd2")
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def tearDown(self):
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self.nd2.close()
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@unittest.skip('missing file')
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def test_pixel_size(self):
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self.assertGreater(self.nd2.pixel_microns, 0.0)
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@unittest.skip('missing file')
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def test_select(self):
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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 == 'HHQ 500 LP 1':
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manual_images.append(image)
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filter_images = []
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for image in self.nd2.select(channels='HHQ 500 LP 1'):
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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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self.assertEqual(len(manual_images), len(filter_images))
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self.assertGreater(len(manual_images), 0)
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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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self.assertEqual(a.index, b.index)
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self.assertEqual(a.field_of_view, b.field_of_view)
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self.assertEqual(a.channel, b.channel)
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@unittest.skip('missing file')
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def test_select_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=['HHQ 500 LP 1', 'HHQ 500 LP 2'],
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z_levels=[0],
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fields_of_view=list(range(100))):
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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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# Quit after the first hundred images just to save time.
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# If there's a problem, we'll have seen it by now.
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break
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@unittest.skip('missing file')
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def test_select_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.select(channels='HHQ 500 LP 2',
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z_levels=[0],
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fields_of_view=[1, 2, 4]):
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self.assertGreater(image.index, n)
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self.assertEqual(image.channel, 'HHQ 500 LP 2')
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self.assertIn(image.field_of_view, (1, 2, 4))
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self.assertEqual(image.z_level, 0)
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n = image.index
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if n > 100:
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break
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