linumpy.mosaic.discovery#

Discover OCT tile files in a directory and extract mosaic metadata.

Attributes#

DEFAULT_TILE_FILE_PATTERN

Functions#

get_largest_cc(segmentation)

Get the largest connected component in a binary image.

get_tiles_ids(directory[, z])

Analyzes a directory and detects all the tiles in contains.

get_tiles_ids_from_list(tiles_list[, file_pattern])

Extract tile (x, y, z) grid positions from a sorted list of tile paths.

get_mosaic_info(directory, z[, overlap_fraction, ...])

Return mosaic metadata for all tiles at a given z slice.

Module Contents#

linumpy.mosaic.discovery.get_largest_cc(segmentation)[source]#

Get the largest connected component in a binary image.

Parameters:

segmentation (np.ndarray) – The binary image to process.

Returns:

The largest connected component.

Return type:

np.ndarray

linumpy.mosaic.discovery.DEFAULT_TILE_FILE_PATTERN = 'tile_x(?P<x>\\d+)_y(?P<y>\\d+)_z(?P<z>\\d+)'[source]#
linumpy.mosaic.discovery.get_tiles_ids(directory, z=None)[source]#

Analyzes a directory and detects all the tiles in contains.

Parameters:
Return type:

tuple[list, list]

linumpy.mosaic.discovery.get_tiles_ids_from_list(tiles_list, file_pattern=DEFAULT_TILE_FILE_PATTERN)[source]#

Extract tile (x, y, z) grid positions from a sorted list of tile paths.

Parameters:

  • tiles_list (list)

  • file_pattern (str)

Return type:

list

linumpy.mosaic.discovery.get_mosaic_info(directory, z, overlap_fraction=0.2, use_stage_positions=False)[source]#

Return mosaic metadata for all tiles at a given z slice.

Parameters:
Return type:

dict