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