nd2reader/functional_tests/FYLM141111001.py

"""
These tests require that you have a specific ND2 file created by the developer of nd2reader. You will never need to
run them unless you're Jim Rybarski.

"""
from nd2reader import Nd2
from skimage import io
import numpy as np
from datetime import datetime
import unittest
import time


class FYLM141111Tests(unittest.TestCase):
    def setUp(self):
        self.nd2 = Nd2("/var/nd2s/FYLM-141111-001.nd2")

    def tearDown(self):
        self.nd2.close()

    def test_shape(self):
        self.assertEqual(self.nd2.height, 1280)
        self.assertEqual(self.nd2.width, 800)

    def test_date(self):
        self.assertEqual(self.nd2.date, datetime(2014, 11, 11, 15, 59, 19))

    @unittest.skip("This will fail until we address issue #59")
    def test_length(self):
        self.assertEqual(len(self.nd2), 17808)

    def test_frames(self):
        self.assertEqual(len(self.nd2.frames), 636)

    def test_fovs(self):
        self.assertEqual(len(self.nd2.fields_of_view), 8)

    def test_channels(self):
        self.assertTupleEqual(tuple(sorted(self.nd2.channels)), ('', 'GFP'))

    def test_z_levels(self):
        self.assertTupleEqual(tuple(self.nd2.z_levels), (0, 1, 2))

    def test_pixel_size(self):
        self.assertGreater(self.nd2.pixel_microns, 0.0)

    def test_image(self):
        image = self.nd2[14]
        self.assertEqual(image.field_of_view, 2)
        self.assertEqual(image.frame_number, 0)
        self.assertAlmostEqual(image.timestamp, 19.0340758)
        self.assertEqual(image.channel, '')
        self.assertEqual(image.z_level, 1)
        self.assertEqual(image.height, self.nd2.height)
        self.assertEqual(image.width, self.nd2.width)

    def test_last_image(self):
        image = self.nd2[30526]
        self.assertEqual(image.frame_number, 635)

    def test_bad_image(self):
        image = self.nd2[13]
        self.assertIsNone(image)

    def test_iteration(self):
        images = [image for image in self.nd2[:10]]
        self.assertEqual(len(images), 10)

    def test_iteration_step(self):
        images = [image for image in self.nd2[:10:2]]
        self.assertEqual(len(images), 5)

    def test_iteration_backwards(self):
        images = [image for image in self.nd2[:10:-1]]
        self.assertEqual(len(images), 10)

    def test_get_image_by_attribute_ok(self):
        image = self.nd2.get_image(4, 0, 'GFP', 1)
        self.assertIsNotNone(image)
        image = self.nd2.get_image(4, 0, '', 0)
        self.assertIsNotNone(image)
        image = self.nd2.get_image(4, 0, '', 1)
        self.assertIsNotNone(image)

    def test_images(self):
        self.assertTupleEqual((self.nd2[0].z_level, self.nd2[0].channel), (0, ''))
        self.assertIsNone(self.nd2[1])
        self.assertTupleEqual((self.nd2[2].z_level, self.nd2[2].channel), (1, ''))
        self.assertTupleEqual((self.nd2[3].z_level, self.nd2[3].channel), (1, 'GFP'))
        self.assertTupleEqual((self.nd2[4].z_level, self.nd2[4].channel), (2, ''))
        self.assertIsNone(self.nd2[5])
        self.assertTupleEqual((self.nd2[6].z_level, self.nd2[6].channel), (0, ''))
        self.assertIsNone(self.nd2[7])
        self.assertTupleEqual((self.nd2[8].z_level, self.nd2[8].channel), (1, ''))
        self.assertTupleEqual((self.nd2[9].z_level, self.nd2[9].channel), (1, 'GFP'))
        self.assertTupleEqual((self.nd2[10].z_level, self.nd2[10].channel), (2, ''))
        self.assertIsNone(self.nd2[11])
        self.assertTupleEqual((self.nd2[12].z_level, self.nd2[12].channel), (0, ''))
        self.assertIsNone(self.nd2[13])
        self.assertTupleEqual((self.nd2[14].z_level, self.nd2[14].channel), (1, ''))
        self.assertTupleEqual((self.nd2[15].z_level, self.nd2[15].channel), (1, 'GFP'))
        self.assertTupleEqual((self.nd2[16].z_level, self.nd2[16].channel), (2, ''))
        self.assertIsNone(self.nd2[17])
        self.assertTupleEqual((self.nd2[18].z_level, self.nd2[18].channel), (0, ''))
        self.assertIsNone(self.nd2[19])
        self.assertIsNone(self.nd2[47])
        self.assertTupleEqual((self.nd2[48].z_level, self.nd2[48].channel), (0, ''))
        self.assertIsNone(self.nd2[49])
        self.assertTupleEqual((self.nd2[50].z_level, self.nd2[50].channel), (1, ''))
        self.assertIsNone(self.nd2[51])
        self.assertTupleEqual((self.nd2[52].z_level, self.nd2[52].channel), (2, ''))
        self.assertIsNone(self.nd2[53])
        self.assertTupleEqual((self.nd2[54].z_level, self.nd2[54].channel), (0, ''))

    def test_get_image_by_attribute_none(self):
        # Should handle missing images without an exception
        image = self.nd2.get_image(4, 0, 'GFP', 0)
        self.assertIsNone(image)

    def test_index(self):
        # Do indexes get added to images properly?
        for n, image in enumerate(self.nd2):
            if image is not None:
                self.assertEqual(n, image.index)
            if n > 50:
                break

    def test_select(self):
        # If we take the first 20 GFP images, they should be identical to the first 20 items iterated from select()
        # if we set our criteria to just 'GFP'
        manual_images = []
        for _, image in zip(range(20), self.nd2):
            if image is not None and image.channel == 'GFP':
                manual_images.append(image)

        filter_images = []
        for image in self.nd2.select(channels='GFP'):
            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=['', 'GFP'], z_levels=[0, 1, 2], fields_of_view=list(range(8))):
            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:
                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='', z_levels=[0, 1], fields_of_view=[1, 2, 4]):
            self.assertGreater(image.index, n)
            self.assertEqual(image.channel, '')
            self.assertIn(image.field_of_view, (1, 2, 4))
            self.assertIn(image.z_level, (0, 1))
            n = image.index
            if n > 100:
                break

    def test_select_start(self):
        count = 0
        for _ in self.nd2.select(channels='GFP', start=29000):
            count += 1
        self.assertEqual(127, count)

    def test_select_stop(self):
        count = 0
        for _ in self.nd2.select(channels='GFP', stop=20):
            count += 1
        self.assertEqual(count, 3)

    def test_select_start_stop(self):
        count = 0
        for _ in self.nd2.select(channels='GFP', start=10, stop=20):
            count += 1
        self.assertEqual(count, 1)

    def test_select_start_stop_brightfield(self):
        count = 0
        for _ in self.nd2.select(channels='', start=10, stop=20):
            count += 1
        self.assertEqual(count, 5)

    def test_select_faster(self):
        select_count = 0
        select_start = time.time()
        for i in self.nd2.select(channels='GFP', start=10, stop=50):
            if i is not None and i.channel == 'GFP':
                select_count += 1
        select_duration = time.time() - select_start

        direct_count = 0
        direct_start = time.time()
        for i in self.nd2[10:50]:
            if i is not None and i.channel == 'GFP':
                direct_count += 1
        direct_duration = time.time() - direct_start
        self.assertEqual(select_count, direct_count)
        self.assertGreater(direct_duration, select_duration)

    def test_pixel_microns(self):
        self.assertEqual(round(self.nd2.pixel_microns, 2), 0.22)

    def test_numpy_operations(self):
        # just to make sure we can do this kind of thing and get scalars
        self.assertTrue(0 < np.mean(self.nd2[0]) < np.sum(self.nd2[0]))

    def test_numpy_mean(self):
        # make sure we get the right value and type
        expected_mean = 17513.053581054686
        mean = np.mean(self.nd2[0])
        self.assertEqual(type(mean), np.float64)
        self.assertAlmostEqual(expected_mean, mean)

    def test_subtract_images(self):
        # just to prove we can really treat Image like an array
        diff = self.nd2[0] - self.nd2[2]
        self.assertTrue(np.any(diff))

    def test_show(self):
        io.imshow(self.nd2[0])
        io.show()
        self.assertTrue(True)