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79 lines
3.3 KiB
79 lines
3.3 KiB
import unittest
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import numpy as np
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import struct
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from pims import Frame
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from zolfa.nd2reader.artificial import ArtificialND2
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from zolfa.nd2reader.exceptions import EmptyFileError, InvalidFileType
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from zolfa.nd2reader.reader import ND2Reader
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from zolfa.nd2reader.parser import Parser
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class TestReader(unittest.TestCase):
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def test_invalid_file_extension(self):
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self.assertRaises(InvalidFileType, lambda: ND2Reader('test_data/invalid_extension_file.inv'))
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def test_extension(self):
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self.assertTrue('nd2' in ND2Reader.class_exts())
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def cmp_two_readers(self, r1, r2):
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attributes = r1.data['image_attributes']['SLxImageAttributes']
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self.assertEqual(r2.metadata['width'], attributes['uiWidth'])
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self.assertEqual(r2.metadata['height'], attributes['uiHeight'])
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self.assertEqual(r2.metadata['width'], r2.sizes['x'])
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self.assertEqual(r2.metadata['height'], r2.sizes['y'])
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self.assertEqual(r2.pixel_type, np.float64)
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self.assertEqual(r2.iter_axes, ['t'])
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def test_init_and_init_axes(self):
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with ArtificialND2('test_data/test_nd2_reader.nd2') as artificial:
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with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
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self.cmp_two_readers(artificial, reader)
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def test_init_from_handler(self):
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with ArtificialND2('test_data/test_nd2_reader.nd2') as artificial:
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with open('test_data/test_nd2_reader.nd2', "rb") as FH:
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with ND2Reader(FH) as reader:
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self.cmp_two_readers(artificial, reader)
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def test_init_empty_file(self):
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with ArtificialND2('test_data/empty.nd2', skip_blocks=['label_map_marker']):
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with self.assertRaises(EmptyFileError) as exception:
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with ND2Reader('test_data/empty.nd2'):
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pass
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self.assertEqual(str(exception.exception), "No axes were found for this .nd2 file.")
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def test_get_parser(self):
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with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
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with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
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self.assertIsInstance(reader.parser, Parser)
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def test_get_timesteps(self):
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with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
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with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
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timesteps = reader.timesteps
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self.assertEquals(len(timesteps), 0)
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def test_get_frame_zero(self):
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# Best test we can do for now:
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# test everything up to the actual unpacking of the frame data
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with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
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with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
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with self.assertRaises(struct.error) as exception:
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frame = reader[0]
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self.assertIn('unpack', str(exception.exception))
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def test_get_frame_2D(self):
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# Best test we can do for now:
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# test everything up to the actual unpacking of the frame data
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with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
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with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
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with self.assertRaises(struct.error) as exception:
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frame = reader.get_frame_2D(c=0, t=0, z=0, x=0, y=0, v=0)
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self.assertIn('unpack', str(exception.exception))
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