Cleanup doc files, remove unused package

LDeakin · Mar 11, 2024 · cb09c5e · cb09c5e
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Showing 5 changed files with 17 additions and 30 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git 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
@@ -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
@@ -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 <COMMAND> --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 → docs/ome_zarr.md b/docs/ome.md → 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