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183 lines
9.8 KiB
183 lines
9.8 KiB
from nd2reader.parser import Nd2Parser
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import unittest
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class MockNd2Parser(object):
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def __init__(self, channels, fields_of_view, z_levels):
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self.channels = channels
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self.fields_of_view = fields_of_view
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self.z_levels = z_levels
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class TestNd2Parser(unittest.TestCase):
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def test_calculate_field_of_view_simple(self):
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""" With a single field of view, the field of view should always be the same number (0). """
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nd2 = MockNd2Parser([''], [0], [0])
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for frame_number in range(1000):
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result = Nd2Parser._calculate_field_of_view(nd2, frame_number)
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self.assertEqual(result, 0)
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def test_calculate_field_of_view_two_channels(self):
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nd2 = MockNd2Parser(['', 'GFP'], [0], [0])
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for frame_number in range(1000):
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result = Nd2Parser._calculate_field_of_view(nd2, frame_number)
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self.assertEqual(result, 0)
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def test_calculate_field_of_view_three_channels(self):
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nd2 = MockNd2Parser(['', 'GFP', 'dsRed'], [0], [0])
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for frame_number in range(1000):
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result = Nd2Parser._calculate_field_of_view(nd2, frame_number)
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self.assertEqual(result, 0)
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def test_calculate_field_of_view_two_fovs(self):
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nd2 = MockNd2Parser([''], [0, 1], [0])
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for frame_number in range(1000):
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result = Nd2Parser._calculate_field_of_view(nd2, frame_number)
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self.assertEqual(result, frame_number % 2)
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def test_calculate_field_of_view_two_fovs_two_zlevels(self):
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nd2 = MockNd2Parser([''], [0, 1], [0, 1])
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 0), 0)
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 1), 0)
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 2), 1)
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 3), 1)
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 4), 0)
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 5), 0)
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 6), 1)
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 7), 1)
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def test_calculate_field_of_view_two_everything(self):
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nd2 = MockNd2Parser(['', 'GFP'], [0, 1], [0, 1])
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 0), 0)
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 1), 0)
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 2), 0)
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 3), 0)
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 4), 1)
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 5), 1)
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 6), 1)
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, 7), 1)
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def test_calculate_field_of_view_7c2f2z(self):
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nd2 = MockNd2Parser(['', 'GFP', 'dsRed', 'dTomato', 'lulzBlue', 'jimbotronPurple', 'orange'], [0, 1], [0, 1])
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for i in range(14):
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, i), 0)
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for i in range(14, 28):
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, i), 1)
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for i in range(28, 42):
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, i), 0)
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for i in range(42, 56):
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, i), 1)
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for i in range(56, 70):
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, i), 0)
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for i in range(70, 84):
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, i), 1)
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def test_calculate_field_of_view_2c3f5z(self):
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""" All prime numbers to elucidate any errors that won't show up when numbers are multiples of each other """
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nd2 = MockNd2Parser(['', 'GFP'], [0, 1, 2], [0, 1, 2, 3, 4])
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for i in range(10):
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, i), 0)
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for i in range(10, 20):
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, i), 1)
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for i in range(20, 30):
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, i), 2)
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for i in range(30, 40):
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, i), 0)
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for i in range(40, 50):
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, i), 1)
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for i in range(50, 60):
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self.assertEqual(Nd2Parser._calculate_field_of_view(nd2, i), 2)
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def test_calculate_channel_simple(self):
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nd2 = MockNd2Parser(['GFP'], [0], [0])
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for i in range(1000):
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self.assertEqual(Nd2Parser._calculate_channel(nd2, i), 'GFP')
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def test_calculate_channel(self):
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nd2 = MockNd2Parser(['', 'GFP', 'dsRed', 'dTomato', 'lulzBlue', 'jimbotronPurple', 'orange'], [0], [0])
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for i in range(1000):
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for n, channel in enumerate(['', 'GFP', 'dsRed', 'dTomato', 'lulzBlue', 'jimbotronPurple', 'orange'], start=i*7):
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self.assertEqual(Nd2Parser._calculate_channel(nd2, n), channel)
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def test_calculate_channel_7c2fov1z(self):
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nd2 = MockNd2Parser(['', 'GFP', 'dsRed', 'dTomato', 'lulzBlue', 'jimbotronPurple', 'orange'], [0, 1], [0])
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for i in range(1000):
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for n, channel in enumerate(['', 'GFP', 'dsRed', 'dTomato', 'lulzBlue', 'jimbotronPurple', 'orange'], start=i*7):
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self.assertEqual(Nd2Parser._calculate_channel(nd2, n), channel)
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def test_calculate_channel_ludicrous_values(self):
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nd2 = MockNd2Parser(['', 'GFP', 'dsRed', 'dTomato', 'lulzBlue', 'jimbotronPurple', 'orange'], list(range(31)), list(range(17)))
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for i in range(10000):
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for n, channel in enumerate(['', 'GFP', 'dsRed', 'dTomato', 'lulzBlue', 'jimbotronPurple', 'orange'], start=i*7):
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self.assertEqual(Nd2Parser._calculate_channel(nd2, n), channel)
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def test_calculate_z_level(self):
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nd2 = MockNd2Parser([''], [0], [0])
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for frame_number in range(1000):
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result = Nd2Parser._calculate_z_level(nd2, frame_number)
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self.assertEqual(result, 0)
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def test_calculate_z_level_1c1f2z(self):
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nd2 = MockNd2Parser([''], [0], [0, 1])
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for frame_number in range(1000):
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result = Nd2Parser._calculate_z_level(nd2, frame_number)
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self.assertEqual(result, frame_number % 2)
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def test_calculate_z_level_31c17f1z(self):
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nd2 = MockNd2Parser(list(range(31)), list(range(17)), [0])
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for frame_number in range(1000):
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result = Nd2Parser._calculate_z_level(nd2, frame_number)
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self.assertEqual(result, 0)
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def test_calculate_z_level_2c1f2z(self):
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nd2 = MockNd2Parser(['', 'GFP'], [0], [0, 1])
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 0), 0)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 1), 0)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 2), 1)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 3), 1)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 4), 0)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 5), 0)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 6), 1)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 7), 1)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 8), 0)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 9), 0)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 10), 1)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 11), 1)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 12), 0)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 13), 0)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 14), 1)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 15), 1)
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def test_calculate_z_level_2c3f5z(self):
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nd2 = MockNd2Parser(['', 'GFP'], [0, 1, 2], [0, 1, 2, 3, 4])
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 0), 0)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 1), 0)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 2), 1)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 3), 1)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 4), 2)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 5), 2)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 6), 3)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 7), 3)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 8), 4)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 9), 4)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 10), 0)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 11), 0)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 12), 1)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 13), 1)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 14), 2)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 15), 2)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 16), 3)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 17), 3)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 18), 4)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 19), 4)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 20), 0)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 21), 0)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 22), 1)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 23), 1)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 24), 2)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 25), 2)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 26), 3)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 27), 3)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 28), 4)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 29), 4)
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self.assertEqual(Nd2Parser._calculate_z_level(nd2, 30), 0)
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