Second half of acquire-project#125

aliddell · Oct 19, 2023 · 8d7331f · 8d7331f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- Support for [Zarr v3](https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html).
+- Support for
+  the [sharding storage transformer](https://web.archive.org/web/20230213221154/https://zarr-specs.readthedocs.io/en/latest/extensions/storage-transformers/sharding/v1.0.html)
+  in Zarr v3.
 - Ship debug libs for C-Blosc on Linux and Mac.
 
 ### Changed

diff --git a/README.md b/README.md
@@ -13,6 +13,9 @@ This is an Acquire Driver that supports chunked streaming to [zarr][].
 - **Zarr**
 - **ZarrBlosc1ZstdByteShuffle**
 - **ZarrBlosc1Lz4ByteShuffle**
+- **ZarrV3**
+- **ZarrV3Blosc1ZstdByteShuffle**
+- **ZarrV3Blosc1Lz4ByteShuffle**
 
 ## Using the Zarr storage device
 
@@ -24,6 +27,10 @@ Chunking is configured using `storage_properties_set_chunking_props()` when conf
 Multiscale storage can be enabled or disabled by calling `storage_properties_set_enable_multiscale()` when configuring
 the video stream.
 
+For the [Zarr v3] version of each device, you can use the `ZarrV3*` devices.
+**Note:** Zarr v3 is not [yet](https://github.com/ome/ngff/pull/206) supported by the Python OME-Zarr library, so you
+will not be able to read multiscale metadata from the resulting dataset.
+
 ### Configuring chunking
 
 You can configure chunking by calling `storage_properties_set_chunking_props()` on your `StorageProperties` object
@@ -41,21 +48,21 @@ storage_properties_set_chunking_props(struct StorageProperties* out,
 ```
 
 | ![frames](https://github.com/aliddell/acquire-driver-zarr/assets/844464/3510d468-4751-4fa0-b2bf-0e29a5f3ea1c) |
-|:--:|
-| A collection of frames. |
+|:-------------------------------------------------------------------------------------------------------------:|
+|                                            A collection of frames.                                            |
 
 A _tile_ is a contiguous section, or region of interest, of a _frame_.
 
 | ![tiles](https://github.com/aliddell/acquire-driver-zarr/assets/844464/f8d16139-e0ac-44db-855f-2f5ef305c98b) |
-|:--:|
-| A collection of frames, divided into tiles. |
+|:------------------------------------------------------------------------------------------------------------:|
+|                                 A collection of frames, divided into tiles.                                  |
 
 A _chunk_ is nothing more than some number of stacked tiles from subsequent frames, with each tile in a chunk having
 the same ROI in its respective frame.
 
-|  ![chunks](https://github.com/aliddell/acquire-driver-zarr/assets/844464/653e4d82-363e-4e04-9a42-927b052fb6e7) |
-|:--:|
-| A collection of frames, divided into tiles. A single chunk has been highlighted in red. |
+| ![chunks](https://github.com/aliddell/acquire-driver-zarr/assets/844464/653e4d82-363e-4e04-9a42-927b052fb6e7) |
+|:-------------------------------------------------------------------------------------------------------------:|
+|            A collection of frames, divided into tiles. A single chunk has been highlighted in red.            |
 
 You can specify the width and height, in pixels, of each tile, and if your frame size has more than one plane, you can
 specify the number of planes you want per tile as well.
@@ -120,3 +127,5 @@ Then the sequence of levels will have dimensions 1920 x 1080, 960 x 540, 480 x 2
 [Blosc]: https://github.com/Blosc/c-blosc
 
 [Blosc docs]: https://www.blosc.org/
+
+[Zarr v3]: https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -19,6 +19,8 @@ add_library(${tgt} MODULE
         zarr.cpp
         zarr.v2.hh
         zarr.v2.cpp
+        zarr.v3.hh
+        zarr.v3.cpp
         zarr.driver.c
 )
 target_enable_simd(${tgt})

diff --git a/src/zarr.driver.c b/src/zarr.driver.c
@@ -39,6 +39,12 @@ struct Storage*
 compressed_zarr_v2_zstd_init();
 struct Storage*
 compressed_zarr_v2_lz4_init();
+struct Storage*
+zarr_v3_init();
+struct Storage*
+compressed_zarr_v3_zstd_init();
+struct Storage*
+compressed_zarr_v3_lz4_init();
 
 //
 //                  GLOBALS
@@ -49,6 +55,9 @@ enum StorageKind
     Storage_Zarr,
     Storage_ZarrBlosc1ZstdByteShuffle,
     Storage_ZarrBlosc1Lz4ByteShuffle,
+    Storage_ZarrV3,
+    Storage_ZarrV3Blosc1ZstdByteShuffle,
+    Storage_ZarrV3Blosc1Lz4ByteShuffle,
     Storage_Number_Of_Kinds
 };
 
@@ -71,6 +80,9 @@ storage_kind_to_string(const enum StorageKind kind)
         CASE(Storage_Zarr);
         CASE(Storage_ZarrBlosc1ZstdByteShuffle);
         CASE(Storage_ZarrBlosc1Lz4ByteShuffle);
+        CASE(Storage_ZarrV3);
+        CASE(Storage_ZarrV3Blosc1ZstdByteShuffle);
+        CASE(Storage_ZarrV3Blosc1Lz4ByteShuffle);
 #undef CASE
         default:
             return "(unknown)";
@@ -99,6 +111,9 @@ zarr_describe(const struct Driver* driver,
         XXX(Zarr),
         XXX(ZarrBlosc1ZstdByteShuffle),
         XXX(ZarrBlosc1Lz4ByteShuffle),
+        XXX(ZarrV3),
+        XXX(ZarrV3Blosc1ZstdByteShuffle),
+        XXX(ZarrV3Blosc1Lz4ByteShuffle),
     };
     // clang-format on
 #undef XXX
@@ -160,6 +175,10 @@ acquire_driver_init_v0(acquire_reporter_t reporter)
             [Storage_Zarr] = zarr_v2_init,
             [Storage_ZarrBlosc1ZstdByteShuffle] = compressed_zarr_v2_zstd_init,
             [Storage_ZarrBlosc1Lz4ByteShuffle] = compressed_zarr_v2_lz4_init,
+            [Storage_ZarrV3] = zarr_v3_init,
+            [Storage_ZarrV3Blosc1ZstdByteShuffle] =
+              compressed_zarr_v3_zstd_init,
+            [Storage_ZarrV3Blosc1Lz4ByteShuffle] = compressed_zarr_v3_lz4_init,
         };
         memcpy(
           globals.constructors, impls, nbytes); // cppcheck-suppress uninitvar