CLI utilities for working with N5 files.
Written in Rust using the Rust N5 crate.
$ cargo install n5gest
$ n5gest -h
n5gest = "0.4.0"
Andrew Champion <andrew.champion@gmail.com>
Utilities for N5 files.
USAGE:
n5gest [OPTIONS] <SUBCOMMAND>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
-t, --threads <threads> Number of threads for parallel processing. By default, the number of CPU
cores is used.
SUBCOMMANDS:
bench-read Benchmark reading an entire dataset.
cast Cast an existing dataset into a new dataset with a given data type.
crop-blocks Crop wrongly sized blocks to match dataset dimensions at the end of a given axis.
delete-uniform-blocks
Delete blocks uniformly filled with a given value, such as empty blocks.
export Export a sequence of image files from a series of z-sections.
help Prints this message or the help of the given subcommand(s)
import Import a sequence of image files as a series of z-sections into a 3D N5 dataset.
import-tiff Import a single file TIFF stack as a series of z-sections into a 3D N5 dataset
ls List all datasets under an N5 root.
map Run simple math expressions mapping values to new datasets. For example, to clip
values in a dataset: `map example.n5 dataset_in example.n5 dataset_out "min(128, x)"`
Note that this converts back and forth to `f64` for the calculation.
map-fold Run simple math expressions as folds over blocks. For example, to find the
maximum value in a positive dataset: `map-fold example.n5 dataset 0 "max(acc, x)"`
recompress Recompress an existing dataset into a new dataset with a given compression.
slice-img Export a 2D subslice of an ND dataset to an image file. For exporting sequences of
images see `export`
stat Retrieve metadata about the number of blocks that exists and their timestamps.
validate-blocks Report malformed blocks.Installation options:
- Compile and install using cargo:
cargo install n5gest - Download a precompiled binary from the latest GitHub releases
- Install a precompiled binary using cargo-binstall:
cargo binstall n5gest
Version bumping (including changelog release section versioning) is handled by cargo-release, e.g.:
cargo release --dev-version minor
Licensed under either of
- Apache License, Version 2.0, (LICENSE-APACHE or http://www.apache.org/licenses/LICENSE-2.0)
- MIT license (LICENSE-MIT or http://opensource.org/licenses/MIT)
at your option.
Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.