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81 lines
3.5 KiB
81 lines
3.5 KiB
import unittest
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import six
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from zolfa.nd2reader.artificial import ArtificialND2
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from zolfa.nd2reader.label_map import LabelMap
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from zolfa.nd2reader.raw_metadata import RawMetadata
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from zolfa.nd2reader.common_raw_metadata import parse_roi_shape, parse_roi_type, parse_dimension_text_line
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class TestRawMetadata(unittest.TestCase):
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def setUp(self):
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self.nd2 = ArtificialND2('test_data/test_nd2_raw_metadata001.nd2')
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self.raw_text, self.locations, self.file_data = self.nd2.raw_text, self.nd2.locations, self.nd2.data
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self.label_map = LabelMap(self.raw_text)
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self.metadata = RawMetadata(self.nd2.file_handle, self.label_map)
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def test_parse_roi_shape(self):
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self.assertEqual(parse_roi_shape(3), 'rectangle')
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self.assertEqual(parse_roi_shape(9), 'circle')
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self.assertIsNone(parse_roi_shape(-1))
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def test_parse_roi_type(self):
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self.assertEqual(parse_roi_type(3), 'reference')
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self.assertEqual(parse_roi_type(2), 'background')
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self.assertEqual(parse_roi_type(4), 'stimulation')
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self.assertIsNone(parse_roi_type(-1))
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def test_parse_dimension_text(self):
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line = six.b('Metadata:\r\nDimensions: T(443) x \xce\xbb(1)\r\nCamera Name: Andor Zyla VSC-01537')
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self.assertEqual(parse_dimension_text_line(line), six.b('Dimensions: T(443) x \xce\xbb(1)'))
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self.assertIsNone(parse_dimension_text_line(six.b('Dim: nothing')))
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def test_parse_z_levels(self):
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# smokescreen test to check if the fallback to z_coordinates is working
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# for details, see RawMetadata._parse_z_levels()
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dimension_text = self.metadata._parse_dimension_text()
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z_levels = self.metadata._parse_dimension(r""".*?Z\((\d+)\).*?""", dimension_text)
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z_coords = self.metadata._parse_z_coordinates()
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self.assertEqual(len(dimension_text), 0)
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self.assertEqual(len(z_levels), 0)
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self.assertEqual(len(self.metadata._parse_z_levels()), len(z_coords))
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def test_dict(self):
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self.assertTrue(type(self.metadata.__dict__) is dict)
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def test_parsed_metadata_has_all_keys(self):
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metadata = self.metadata.get_parsed_metadata()
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self.assertTrue(type(metadata) is dict)
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required_keys = ["height", "width", "date", "fields_of_view", "frames", "z_levels", "total_images_per_channel",
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"channels", "pixel_microns"]
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for required in required_keys:
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self.assertTrue(required in metadata)
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def test_cached_metadata(self):
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metadata_one = self.metadata.get_parsed_metadata()
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metadata_two = self.metadata.get_parsed_metadata()
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self.assertEqual(metadata_one, metadata_two)
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def test_pfs_status(self):
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self.assertEqual(self.file_data['pfs_status'], self.metadata.pfs_status[0])
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def _assert_dicts_equal(self, parsed_dict, original_dict):
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for attribute in original_dict.keys():
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parsed_key = six.b(attribute)
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self.assertIn(parsed_key, parsed_dict.keys())
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if isinstance(parsed_dict[parsed_key], dict):
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self._assert_dicts_equal(parsed_dict[parsed_key], original_dict[attribute])
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else:
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self.assertEqual(parsed_dict[parsed_key], original_dict[attribute])
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def test_image_attributes(self):
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parsed_dict = self.metadata.image_attributes
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self._assert_dicts_equal(parsed_dict, self.file_data['image_attributes'])
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def test_color_channels(self):
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parsed_channels = self.metadata.get_parsed_metadata()['channels']
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self.assertEquals(parsed_channels, ['TRITC'])
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