steinbock.tools
matching
match_masks(mask1, mask2)
Source code in steinbock/tools/matching.py
def match_masks(mask1: np.ndarray, mask2: np.ndarray) -> pd.DataFrame:
nz1 = mask1 != 0
nz2 = mask2 != 0
object_ids1 = []
object_ids2 = []
for object_id1 in np.unique(mask1[nz1]):
for object_id2 in np.unique(mask2[nz2 & (mask1 == object_id1)]):
object_ids1.append(object_id1)
object_ids2.append(object_id2)
for object_id2 in np.unique(mask2[nz2]):
for object_id1 in np.unique(mask1[nz1 & (mask2 == object_id2)]):
object_ids1.append(object_id1)
object_ids2.append(object_id2)
table = pd.DataFrame(data={"Object1": object_ids1, "Object2": object_ids2})
table.drop_duplicates(inplace=True, ignore_index=True)
return table
match_masks_from_disk(mask_files1, mask_files2)
Source code in steinbock/tools/matching.py
def match_masks_from_disk(
mask_files1: Sequence[Union[str, PathLike]],
mask_files2: Sequence[Union[str, PathLike]],
) -> Generator[Tuple[Path, Path, pd.DataFrame], None, None]:
for mask_file1, mask_file2 in zip(mask_files1, mask_files2):
table = match_masks(io.read_mask(mask_file1), io.read_mask(mask_file2))
yield mask_file1, mask_file2, table
del table
mosaics
extract_tiles_from_disk(img_files, tile_size)
Source code in steinbock/tools/mosaics.py
def extract_tiles_from_disk(
img_files: Sequence[Union[str, PathLike]], tile_size: int
) -> Generator[Tuple[Path, int, int, int, int, np.ndarray], None, None]:
for img_file in img_files:
img = io.read_image(img_file, ignore_dtype=True)
for x in range(0, img.shape[2], tile_size):
for y in range(0, img.shape[1], tile_size):
tile = img[:, y : (y + tile_size), x : (x + tile_size)]
yield Path(img_file), x, y, tile.shape[2], tile.shape[1], tile
del tile
del img
stitch_tiles_from_disk(tile_info_groups)
Source code in steinbock/tools/mosaics.py
def stitch_tiles_from_disk(
tile_info_groups: Dict[
str, Sequence[Tuple[Union[str, PathLike], int, int, int, int]]
]
) -> Generator[Tuple[str, np.ndarray], None, None]:
for img_stem_name, tile_info in tile_info_groups.items():
first_tile = io.read_image(tile_info[0][0], ignore_dtype=True)
img_width = max(x + w for _, x, y, w, h in tile_info)
img_height = max(y + h for _, x, y, w, h in tile_info)
img = np.zeros(
(first_tile.shape[0], img_height, img_width),
dtype=first_tile.dtype,
)
for tile_file, x, y, w, h in tile_info:
img[:, y : (y + h), x : (x + w)] = io.read_image(
tile_file, ignore_dtype=True
)
yield img_stem_name, img
del img