examples.loading_scan_images

 1#!/usr/bin/env python
 2
 3import os
 4from csi_images.csi_scans import Scan
 5from csi_images.csi_tiles import Tile
 6from csi_images.csi_frames import Frame
 7
 8
 9# Create a basic DatabaseHandler
10def load_in_images():
11    repository_path = os.path.dirname(os.path.dirname(__file__))
12    test_data_path = os.path.join(repository_path, "tests", "data")
13
14    # First, let's load in a scan's metadata
15    scan = Scan.load_yaml(test_data_path)
16
17    # Using that metadata, we can load in a tile or a ton of tiles
18    tile = Tile(scan, 0)
19    tiles = Tile.get_tiles(scan)
20
21    # By default, these will load in a single list
22    assert len(tiles) == scan.roi[0].tile_rows * scan.roi[0].tile_cols
23
24    # But we can also load them in as a grid
25    tiles = Tile.get_tiles(scan, as_flat=False)
26    assert len(tiles) == scan.roi[0].tile_rows
27    assert len(tiles[0]) == scan.roi[0].tile_cols
28
29    # We can also load in frames for a tile or a ton of tiles
30    frames = Frame.get_frames(tile)
31    all_frames = Frame.get_all_frames(scan)
32    assert len(all_frames) == scan.roi[0].tile_rows * scan.roi[0].tile_cols
33    assert len(all_frames[0]) == 4
34    all_frames = Frame.get_all_frames(scan, as_flat=False)
35    assert len(all_frames) == scan.roi[0].tile_rows
36    assert len(all_frames[0]) == scan.roi[0].tile_cols
37    assert len(all_frames[0][0]) == 4
38
39    # And for each frame, we can load the actual image
40    # First element is the image array, second element is the file path it came from
41    image = frames[0].get_image()
42    assert image.shape == scan.get_image_size()
43
44
45if __name__ == "__main__":
46    load_in_images()