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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.
"""
from nd2reader import Nd2
import numpy as np
import unittest
class Monocycle1Tests(unittest.TestCase):
def setUp(self):
self.nd2 = Nd2("/var/nd2s/simone1.nd2")
def tearDown(self):
self.nd2.close()
def test_channels(self):
self.assertListEqual(self.nd2.channels, ['Cy3Narrow', 'TxRed-modified', 'FITC', 'DAPI'])
def test_pixel_size(self):
self.assertGreater(self.nd2.pixel_microns, 0.0)
def test_select(self):
manual_images = []
for _, image in zip(range(20), self.nd2):
if image is not None and image.channel == 'FITC':
manual_images.append(image)
filter_images = []
for image in self.nd2.select(channels='FITC'):
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_select_order_all(self):
# If we select every possible image using select(), we should just get every image in order
n = 0
for image in self.nd2.select(channels=['Cy3Narrow', 'DAPI', 'FITC', 'TxRed-modified'],
z_levels=list(range(35)),
fields_of_view=list(range(5))):
while True:
indexed_image = self.nd2[n]
if indexed_image is not None:
break
n += 1
self.assertTrue(np.array_equal(image, indexed_image))
n += 1
if n > 100:
# Quit after the first hundred images just to save time.
# If there's a problem, we'll have seen it by now.
break
def test_select_order_subset(self):
# Test that images are always yielded in increasing order. This guarantees that no matter what subset of images
# we're filtering, we still get them in the chronological order they were acquired
n = -1
for image in self.nd2.select(channels='FITC',
z_levels=[0, 1],
fields_of_view=[1, 2, 4]):
self.assertGreater(image.index, n)
self.assertEqual(image.channel, 'FITC')
self.assertIn(image.field_of_view, (1, 2, 4))
self.assertIn(image.z_level, (0, 1))
n = image.index
if n > 100:
break
class Monocycle2Tests(unittest.TestCase):
def setUp(self):
self.nd2 = Nd2("/var/nd2s/hawkjo.nd2")
def tearDown(self):
self.nd2.close()
def test_pixel_size(self):
self.assertGreater(round(self.nd2.pixel_microns, 2), 0.26)
def test_select(self):
manual_images = []
for _, image in zip(range(20), self.nd2):
if image is not None and image.channel == 'HHQ 500 LP 1':
manual_images.append(image)
filter_images = []
for image in self.nd2.select(channels='HHQ 500 LP 1'):
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_select_order_all(self):
# If we select every possible image using select(), we should just get every image in order
n = 0
for image in self.nd2.select(channels=['HHQ 500 LP 1', 'HHQ 500 LP 2'],
z_levels=[0],
fields_of_view=list(range(100))):
while True:
indexed_image = self.nd2[n]
if indexed_image is not None:
break
n += 1
self.assertTrue(np.array_equal(image, indexed_image))
n += 1
if n > 100:
# Quit after the first hundred images just to save time.
# If there's a problem, we'll have seen it by now.
break
def test_select_order_subset(self):
# Test that images are always yielded in increasing order. This guarantees that no matter what subset of images
# we're filtering, we still get them in the chronological order they were acquired
n = -1
for image in self.nd2.select(channels='HHQ 500 LP 2',
z_levels=[0],
fields_of_view=[1, 2, 4]):
self.assertGreater(image.index, n)
self.assertEqual(image.channel, 'HHQ 500 LP 2')
self.assertIn(image.field_of_view, (1, 2, 4))
self.assertEqual(image.z_level, 0)
n = image.index
if n > 100:
break