nd2reader/tests/test_raw_metadata.py

import unittest
import six

from nd2reader.artificial import ArtificialND2
from nd2reader.label_map import LabelMap
from nd2reader.raw_metadata import RawMetadata


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(self.metadata._parse_roi_shape(3), 'rectangle')
        self.assertEqual(self.metadata._parse_roi_shape(9), 'circle')
        self.assertIsNone(self.metadata._parse_roi_shape(-1))

    def test_parse_roi_type(self):
        self.assertEqual(self.metadata._parse_roi_type(3), 'reference')
        self.assertEqual(self.metadata._parse_roi_type(2), 'background')
        self.assertEqual(self.metadata._parse_roi_type(4), 'stimulation')
        self.assertIsNone(self.metadata._parse_roi_type(-1))

    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'])