12 releases

0.4.0 Nov 21, 2022
0.3.9 Nov 10, 2020
0.3.7 Oct 26, 2020
0.3.4 Jul 20, 2020
0.2.0 Oct 24, 2018

#809 in Command line utilities

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n5gest Build Status

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.


    -h, --help       Prints help information
    -V, --version    Prints version information

    -t, --threads <threads>    Number of threads for parallel processing. By default, the number of CPU
 cores is used.

    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 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:


Version bumping (including changelog release section versioning) is handled by cargo-release, e.g.:

cargo release --dev-version minor


Licensed under either of

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.


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