tests.test_frames

  1import os
  2
  3import pytest
  4
  5import cv2
  6
  7from csi_images.csi_scans import Scan
  8from csi_images.csi_tiles import Tile
  9from csi_images.csi_frames import Frame
 10
 11if os.environ.get("DEBIAN_FRONTEND") == "noninteractive":
 12    # For Docker testing; do not try to show plots
 13    SHOW_PLOTS = False
 14else:
 15    # Change this to your preference for local testing, but commit as True
 16    SHOW_PLOTS = True
 17
 18
 19@pytest.fixture
 20def scan():
 21    return Scan.load_yaml("tests/data")
 22
 23
 24@pytest.fixture
 25def tile(scan):
 26    return Tile(scan, 100)
 27
 28
 29def test_paths(scan, tile):
 30    frames = Frame.get_frames(tile)
 31    # Check that the paths exist
 32    for frame in frames:
 33        # Manually creating the path
 34        file_path = os.path.join(scan.path, frame.get_file_name())
 35        assert os.path.exists(file_path)
 36        # Using the build-in method
 37        assert os.path.exists(frame.get_file_path())
 38        # Check that the images are "valid"
 39        assert frame.check_image()
 40    # Check that all images are valid
 41    assert Frame.check_all_images(scan)
 42    # Manually set up a frame that shouldn't exist
 43    tile.x = 100
 44    for frame in Frame.get_frames(tile):
 45        assert not frame.check_image()
 46
 47
 48def test_getting_frames(scan, tile):
 49    # Get frames for a single tile
 50    frames = Frame.get_frames(tile)
 51    assert len(frames) == 4
 52
 53    # Get all frames for the scan
 54    frames = Frame.get_all_frames(scan)
 55    assert len(frames) == scan.roi[0].tile_rows * scan.roi[0].tile_cols
 56    assert len(frames[0]) == 4
 57    # Get all frames in a grid
 58    frames = Frame.get_all_frames(scan, as_flat=False)
 59    assert len(frames) == scan.roi[0].tile_rows
 60    assert len(frames[0]) == scan.roi[0].tile_cols
 61    assert len(frames[0][0]) == 4
 62
 63
 64def test_make_rgb(scan, tile):
 65    frames = Frame.get_frames(tile)
 66
 67    if SHOW_PLOTS:
 68        for frame in frames:
 69            cv2.imshow("Frames from a tile", frame.get_image())
 70            cv2.waitKey(0)
 71        cv2.destroyAllWindows()
 72
 73    channel_indices = scan.get_channel_indices(["TRITC", "CY5", "DAPI"])
 74    channels = {
 75        channel_indices[0]: (1.0, 0.0, 0.0),
 76        channel_indices[1]: (0.0, 1.0, 0.0),
 77        channel_indices[2]: (0.0, 0.0, 1.0),
 78    }
 79    image = Frame.make_rgb_image(tile, channels)
 80    real_image_size = scan.get_image_size() + (3,)
 81    assert image.shape == real_image_size
 82
 83    if SHOW_PLOTS:
 84        cv2.imshow("RGB tile", cv2.cvtColor(image, cv2.COLOR_RGB2BGR))
 85        cv2.waitKey(0)
 86        cv2.destroyAllWindows()
 87
 88    # Test with a white channel
 89    channel_indices = scan.get_channel_indices(["TRITC", "CY5", "DAPI", "AF488"])
 90    channels = {
 91        channel_indices[0]: (1.0, 0.0, 0.0),
 92        channel_indices[1]: (0.0, 1.0, 0.0),
 93        channel_indices[2]: (0.0, 0.0, 1.0),
 94        channel_indices[3]: (1.0, 1.0, 1.0),
 95    }
 96    image = Frame.make_rgb_image(tile, channels)
 97    assert image.shape == real_image_size
 98
 99    if SHOW_PLOTS:
100        cv2.imshow("RGBW tile", cv2.cvtColor(image, cv2.COLOR_RGB2BGR))
101        cv2.waitKey(0)
102        cv2.destroyAllWindows()