IO Module
SCOUT’s IO module is for reading and writing different volumetric image formats and preparing chunked arrays for processing. SCOUT makes use of TIFF and Zarr file formats throughout the analysis pipeline, and the this module is meant to consolidate these side-effecting IO operations.
- scout.io.imread(path)
Reads TIFF file into a numpy array in memory.
- Parameters
path (str) – Path to TIFF image to open
- Returns
image – Image array
- Return type
ndarray
- scout.io.imread_folder(path, nb_workers)
Finds all TIFF images in a folder and loads them into a single array.
Note: all images must be the same shape to be able to stack them.
- Parameters
path (str) – Path to directory with TIFF images in alphabetical order
nb_workers (int) – Number of parallel processes to use in reading images
- Returns
data – Image array
- Return type
ndarray
- scout.io.imread_parallel(paths, nb_workers)
Reads TIFF files into a numpy array in memory.
- Parameters
paths (list) – A list of TIFF paths to read (order is preserved)
nb_workers (int) – Number of parallel processes to use in reading images
- Returns
data – Image data
- Return type
ndarray
- scout.io.imsave(path, data, compress=1)
Saves numpy array as a TIFF image.
- Parameters
path (str) – Path to TIFF image to create / overwrite
data (ndarray) – Image data array
compress (int) – Level of lossless TIFF compression (0-9)
- scout.io.new_zarr(path, shape, chunks, dtype, in_memory=False, **kwargs)
Create new Zarr NestedDirectoryStore at path.
NOTE: Persistent Zarr arrays are stored on disk. To avoid data loss, be careful when calling new_zarr on a path with an existing array.
- Parameters
path (str) – Path to new zarr array
shape (tuple) – Overall shape of the zarr array
chunks (tuple) – Shape of each chunk for the zarr array
dtype (str) – Data type of for the zarr array
kwargs (dict) – Keyword args to passs to zarr.open()
- Returns
arr – Reference to open zarr array
- Return type
zarr Array
- scout.io.new_zarr_like(path, arr, **kwargs)
Creates a new zarr array like arr.
- Parameters
path (str) – Path to new zarr array
arr (zarr Array) – Reference to template zarr array
kwargs (dict) – Keyword args to passs to zarr.open()
- Returns
new_arr – Reference to new zarr array
- Return type
zarr Array
- scout.io.open(path, nested=True, mode='a')
Opens a persistent Zarr array or NestedDirectoryStore located at path.
- Parameters
path (str) – Path to Zarr array or NestedDirectoryStore
nested (bool) – Flag to indicate if path is for flat Zarr array or NestedDirectoryStore
mode (str) – Read / write permissions mode
- Returns
arr – Reference to open Zarr array
- Return type
zarr Array