nd2reader/tests/test_reader.py

import unittest
import numpy as np
import struct

from pims import Frame
from nd2reader.artificial import ArtificialND2
from nd2reader.exceptions import EmptyFileError, InvalidFileType
from nd2reader.reader import ND2Reader
from nd2reader.parser import Parser


class TestReader(unittest.TestCase):
    def test_invalid_file_extension(self):
        self.assertRaises(InvalidFileType, lambda: ND2Reader('test_data/invalid_extension_file.inv'))

    def test_extension(self):
        self.assertTrue('nd2' in ND2Reader.class_exts())

    def test_init_and_init_axes(self):
        with ArtificialND2('test_data/test_nd2_reader.nd2') as artificial:
            with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
                attributes = artificial.data['image_attributes']['SLxImageAttributes']
                self.assertEqual(reader.metadata['width'], attributes['uiWidth'])
                self.assertEqual(reader.metadata['height'], attributes['uiHeight'])

                self.assertEqual(reader.metadata['width'], reader.sizes['x'])
                self.assertEqual(reader.metadata['height'], reader.sizes['y'])

                self.assertEqual(reader.pixel_type, np.float64)
                self.assertEqual(reader.iter_axes, ['t'])

    def test_init_empty_file(self):
        with ArtificialND2('test_data/empty.nd2', skip_blocks=['label_map_marker']):
            with self.assertRaises(EmptyFileError) as exception:
                with ND2Reader('test_data/empty.nd2'):
                    pass
            self.assertEqual(str(exception.exception), "No axes were found for this .nd2 file.")

    def test_get_parser(self):
        with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
            with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
                self.assertIsInstance(reader.parser, Parser)

    def test_get_timesteps(self):
        with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
            with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
                timesteps = reader.timesteps
                self.assertEquals(len(timesteps), 0)

    def test_get_frame_zero(self):
        # Best test we can do for now:
        # test everything up to the actual unpacking of the frame data
        with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
            with ND2Reader('test_data/test_nd2_reader.nd2') as reader:

                with self.assertRaises(struct.error) as exception:
                    frame = reader[0]

                self.assertIn('unpack', str(exception.exception))

    def test_get_frame_2D(self):
        # Best test we can do for now:
        # test everything up to the actual unpacking of the frame data
        with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
            with ND2Reader('test_data/test_nd2_reader.nd2') as reader:

                with self.assertRaises(struct.error) as exception:
                    frame = reader.get_frame_2D(c=0, t=0, z=0, x=0, y=0, v=0)

                self.assertIn('unpack', str(exception.exception))