From cb09c5ee4550e3dfbafb8df45386e4071613e6da Mon Sep 17 00:00:00 2001 From: Lachlan Deakin Date: Mon, 11 Mar 2024 21:05:40 +1100 Subject: [PATCH] Cleanup doc files, remove unused package --- Cargo.lock | 7 ------- Cargo.toml | 4 ---- README.md | 5 ++--- docs/filter.md | 29 ++++++++++++++--------------- docs/{ome.md => ome_zarr.md} | 2 +- 5 files changed, 17 insertions(+), 30 deletions(-) rename docs/{ome.md => ome_zarr.md} (98%) diff --git a/Cargo.lock b/Cargo.lock index fc21741..8f8b068 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1780,12 +1780,6 @@ version = "0.11.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "5ee073c9e4cd00e28217186dbe12796d692868f432bf2e97ee73bed0c56dfa01" -[[package]] -name = "strum" -version = "0.26.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "723b93e8addf9aa965ebe2d11da6d7540fa2283fcea14b3371ff055f7ba13f5f" - [[package]] name = "syn" version = "1.0.109" @@ -2419,7 +2413,6 @@ dependencies = [ "rayon_iter_concurrent_limit", "serde", "serde_json", - "strum", "sysinfo", "tempfile", "thiserror", diff --git a/Cargo.toml b/Cargo.toml index c91068b..0a6bcfe 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -36,7 +36,6 @@ rayon = "1.8.0" rayon_iter_concurrent_limit = "0.2.0" serde = { version = "1.0.197", features = ["derive"] } serde_json = "1.0.107" -strum = "0.26.1" sysinfo = "0.30.6" tempfile = "3.10.1" thiserror = "1.0.57" @@ -98,8 +97,5 @@ strip = true # zarrs = { path = "../zarrs" } # zarrs = { git = "https://github.com/LDeakin/zarrs.git" } -[dev-dependencies] -tempfile = "3.10.1" - # [profile.release] # debug = 1 diff --git a/README.md b/README.md index 194fd4f..b6b8e50 100644 --- a/README.md +++ b/README.md @@ -13,18 +13,17 @@ Various tools for creating and manipulating [Zarr v3](https://zarr.dev) data wit ## Tools - `zarrs_reencode`: reencode an array. [Example](https://github.com/LDeakin/zarrs_tools/blob/main/docs/reencode_rechunk.md). - Can change the chunk size, shard size, codecs, fill value, chunk key encoding separator, and attributes. - - Outputs OME-Zarr `0.5-dev`. This revision is currently recognised by [Neuroglancer](https://github.com/google/neuroglancer) for Zarr V3. - `zarrs_binary2zarr` (feature `binary`): create an array from piped binary data. [Example](https://github.com/LDeakin/zarrs_tools/blob/main/docs/convert_binary.md). - `zarrs_ncvar2zarr` (feature `ncvar2zarr`): convert a netCDF variable to an array. [Example](https://github.com/LDeakin/zarrs_tools/blob/main/docs/convert_netcdf.md). - Supports multi-file datasets where a variable has been split along a single dimension. > [!WARNING] -> The following tools are experimental and have had limited production testing: +> The following tools are highly experimental and have had limited production testing: - `zarrs_filter` (feature `filter`): apply simple image filters (transformations) to an array. [Example](https://github.com/LDeakin/zarrs_tools/blob/main/docs/filter.md). - Supported filters include: reencode, crop, convert, rescale, clamp, equal, downsample, gradient magnitude. -- `zarrs_ome` (feature `ome`): convert an array to [OME-Zarr](https://ngff.openmicroscopy.org/latest/index.html). [Example](https://github.com/LDeakin/zarrs_tools/blob/main/docs/ome.md). +- `zarrs_ome` (feature `ome`): convert an array to [OME-Zarr](https://ngff.openmicroscopy.org/latest/index.html). [Example](https://github.com/LDeakin/zarrs_tools/blob/main/docs/ome_zarr.md). - Computes a Gaussian image pyramid. ## `zarrs` Benchmarking diff --git a/docs/filter.md b/docs/filter.md index 9426230..98ed831 100644 --- a/docs/filter.md +++ b/docs/filter.md @@ -3,7 +3,7 @@ `zarrs_filter` is a tool supporting several simple image filters (transformations). > [!WARNING] -> `zarrs_filter` is experimental and has had minimal production testing. +> `zarrs_filter` is highly experimental and has had limited production testing. The filters currently supported are: - **reencode**: Reencode (change encoding, data type, etc.) @@ -23,23 +23,22 @@ zarrs_filter --help ``` # Examples (CLI) -`array.zarr` is a $1243\times1403\times1510$ `int16` array. ```bash cargo install --features=filter --path . export ENCODE_ARGS="--shard-shape 256,256,256 --chunk-shape 32,32,32" -zarrs_filter reencode data/array.zarr data/filter/array_reencode.zarr ${ENCODE_ARGS} -zarrs_filter reencode data/array.zarr data/filter/array_reencode_int32.zarr ${ENCODE_ARGS} --data-type int32 -zarrs_filter reencode data/array.zarr data/filter/array_reencode_float32.zarr ${ENCODE_ARGS} --data-type float32 -zarrs_filter crop data/array.zarr data/filter/array_crop.zarr ${ENCODE_ARGS} --data-type float32 256,256,256 768,768,768 -zarrs_filter rescale data/array.zarr data/filter/array_rescale.zarr ${ENCODE_ARGS} --data-type float32 2.0 1.0 --fill-value 1.0 -zarrs_filter clamp data/array.zarr data/filter/array_clamp.zarr ${ENCODE_ARGS} --data-type float32 5 255 --fill-value 5.0 -zarrs_filter equal data/array.zarr data/filter/array_equal_bool.zarr ${ENCODE_ARGS} --data-type bool 1 --fill-value true -zarrs_filter equal data/array.zarr data/filter/array_equal_uint8.zarr ${ENCODE_ARGS} --data-type uint8 1 --fill-value 1 -zarrs_filter downsample data/array.zarr data/filter/array_downsample.zarr ${ENCODE_ARGS} --data-type float32 2,2,2 -zarrs_filter downsample data/filter/array_equal_uint8.zarr data/filter/array_downsample_discrete.zarr ${ENCODE_ARGS} --data-type uint8 2,2,2 --discrete -zarrs_filter gradient-magnitude data/array.zarr data/filter/array_gradient_magnitude.zarr ${ENCODE_ARGS} --data-type float32 -zarrs_filter gaussian data/array.zarr data/filter/array_gaussian.zarr ${ENCODE_ARGS} --data-type float32 1.0,1.0,1.0 3,3,3 -zarrs_filter summed-area-table data/array.zarr data/filter/array_sat.zarr ${ENCODE_ARGS} --data-type int64 +zarrs_filter reencode array.zarr array_reencode.zarr ${ENCODE_ARGS} +zarrs_filter reencode array.zarr array_reencode_int32.zarr ${ENCODE_ARGS} --data-type int32 +zarrs_filter reencode array.zarr array_reencode_float32.zarr ${ENCODE_ARGS} --data-type float32 +zarrs_filter crop array.zarr array_crop.zarr ${ENCODE_ARGS} --data-type float32 256,256,256 768,768,768 +zarrs_filter rescale array.zarr array_rescale.zarr ${ENCODE_ARGS} --data-type float32 2.0 1.0 --fill-value 1.0 +zarrs_filter clamp array.zarr array_clamp.zarr ${ENCODE_ARGS} --data-type float32 5 255 --fill-value 5.0 +zarrs_filter equal array.zarr array_equal_bool.zarr ${ENCODE_ARGS} --data-type bool 1 --fill-value true +zarrs_filter equal array.zarr array_eq_u8.zarr ${ENCODE_ARGS} --data-type uint8 1 --fill-value 1 +zarrs_filter downsample array.zarr array_downsample.zarr ${ENCODE_ARGS} --data-type float32 2,2,2 +zarrs_filter downsample array_eq_u8.zarr array_downsample_discrete.zarr ${ENCODE_ARGS} --data-type uint8 2,2,2 --discrete +zarrs_filter gradient-magnitude array.zarr array_gradient_magnitude.zarr ${ENCODE_ARGS} --data-type float32 +zarrs_filter gaussian array.zarr array_gaussian.zarr ${ENCODE_ARGS} --data-type float32 1.0,1.0,1.0 3,3,3 +zarrs_filter summed-area-table array.zarr array_sat.zarr ${ENCODE_ARGS} --data-type int64 ``` # Examples (Config) diff --git a/docs/ome.md b/docs/ome_zarr.md similarity index 98% rename from docs/ome.md rename to docs/ome_zarr.md index 56ba46d..abbbe2d 100644 --- a/docs/ome.md +++ b/docs/ome_zarr.md @@ -3,7 +3,7 @@ Convert a Zarr V3 array to [OME-Zarr](https://ngff.openmicroscopy.org/latest/index.html) (0.5-dev). > [!WARNING] -> `zarrs_ome` is experimental and has had minimal production testing. +> `zarrs_ome` is highly experimental and has had limited production testing. `zarrs_ome` creates a multi-resolution Zarr V3 array through various methods: - Gaussian image pyramid