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240 lines
9.1 KiB
240 lines
9.1 KiB
"""
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These tests require that you have a specific ND2 file created by the developer of nd2reader. You will never need to
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run them unless you're Jim Rybarski.
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"""
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from nd2reader import Nd2
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from skimage import io
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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 time
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class FYLM141111Tests(unittest.TestCase):
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def setUp(self):
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self.nd2 = Nd2("/var/nd2s/FYLM-141111-001.nd2")
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def tearDown(self):
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self.nd2.close()
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def test_shape(self):
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self.assertEqual(self.nd2.height, 1280)
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self.assertEqual(self.nd2.width, 800)
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def test_date(self):
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self.assertEqual(self.nd2.date, datetime(2014, 11, 11, 15, 59, 19))
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@unittest.skip("This will fail until we address issue #59")
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def test_length(self):
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self.assertEqual(len(self.nd2), 17808)
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def test_frames(self):
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self.assertEqual(len(self.nd2.frames), 636)
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def test_fovs(self):
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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)), ('', '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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def test_pixel_size(self):
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self.assertGreater(self.nd2.pixel_microns, 0.0)
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def test_image(self):
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image = self.nd2[14]
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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, '')
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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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def test_last_image(self):
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image = self.nd2[30526]
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self.assertEqual(image.frame_number, 635)
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def test_bad_image(self):
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image = self.nd2[13]
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self.assertIsNone(image)
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def test_iteration(self):
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images = [image for image in self.nd2[:10]]
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self.assertEqual(len(images), 10)
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def test_iteration_step(self):
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images = [image for image in self.nd2[:10:2]]
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self.assertEqual(len(images), 5)
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def test_iteration_backwards(self):
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images = [image for image in self.nd2[:10:-1]]
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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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self.assertIsNotNone(image)
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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, '', 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, ''))
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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, ''))
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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, ''))
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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, ''))
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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, ''))
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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, ''))
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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, ''))
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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, ''))
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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, ''))
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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, ''))
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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, ''))
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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, ''))
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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, ''))
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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, ''))
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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_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_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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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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manual_images.append(image)
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filter_images = []
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for image in self.nd2.select(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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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=['', '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_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='', 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, '')
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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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def test_select_start(self):
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count = 0
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for _ in self.nd2.select(channels='GFP', start=29000):
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count += 1
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self.assertEqual(127, count)
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def test_select_stop(self):
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count = 0
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for _ in self.nd2.select(channels='GFP', stop=20):
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count += 1
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self.assertEqual(count, 3)
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def test_select_start_stop(self):
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count = 0
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for _ in self.nd2.select(channels='GFP', start=10, stop=20):
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count += 1
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self.assertEqual(count, 1)
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def test_select_start_stop_brightfield(self):
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count = 0
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for _ in self.nd2.select(channels='', start=10, stop=20):
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count += 1
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self.assertEqual(count, 5)
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def test_select_faster(self):
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select_count = 0
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select_start = time.time()
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for i in self.nd2.select(channels='GFP', start=10, stop=50):
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if i is not None and i.channel == 'GFP':
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select_count += 1
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select_duration = time.time() - select_start
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direct_count = 0
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direct_start = time.time()
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for i in self.nd2[10:50]:
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if i is not None and i.channel == 'GFP':
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direct_count += 1
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direct_duration = time.time() - direct_start
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self.assertEqual(select_count, direct_count)
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self.assertGreater(direct_duration, select_duration)
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def test_pixel_microns(self):
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self.assertEqual(round(self.nd2.pixel_microns, 2), 0.22)
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def test_numpy_operations(self):
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# just to make sure we can do this kind of thing and get scalars
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self.assertTrue(0 < np.mean(self.nd2[0]) < np.sum(self.nd2[0]))
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def test_numpy_mean(self):
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# make sure we get the right value and type
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expected_mean = 17513.053581054686
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mean = np.mean(self.nd2[0])
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self.assertEqual(type(mean), np.float64)
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self.assertAlmostEqual(expected_mean, mean)
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def test_subtract_images(self):
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# just to prove we can really treat Image like an array
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diff = self.nd2[0] - self.nd2[2]
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self.assertTrue(np.any(diff))
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def test_show(self):
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io.imshow(self.nd2[0])
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io.show()
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self.assertTrue(True)
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