Breakout Zarr v2 files from #125 (#136)

First half of #125.

Supersedes #113. Supersedes #117.
Closes #112. Closes #114. Closes #115.

## Changes

### Added

- Ship debug libs for C-Blosc on Linux and Mac.

### Changed

- Upgrades C-Blosc from v1.21.4 to v1.21.5.

### Fixed

- A bug where enabling multiscale without specifying the tile size would
cause an error.
- Exceptions thrown off the main thread are now caught and logged, and
Zarr throws an error in `append`.

CHANGELOG.md

@@ -7,9 +7,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Unreleased
 
+### Added
+
+- Ship debug libs for C-Blosc on Linux and Mac.
+
+### Changed
+
+- Upgrades C-Blosc from v1.21.4 to v1.21.5.
+
 ### Fixed
 
 - A bug where enabling multiscale without specifying the tile size would cause an error.
+- Exceptions thrown off the main thread are now caught and logged, and Zarr throws an error in `append`.
 
 ## [0.1.4](https://github.com/acquire-project/acquire-driver-zarr/compare/v0.1.3...v0.1.4) - 2023-08-11
 

src/3rdParty/cblosc/CMakeLists.txt

@@ -7,10 +7,10 @@ if(WIN32)
     set(libd "${pwd}/lib/win64/libblosc-debug.lib")
 elseif(APPLE)
     set(lib "${pwd}/lib/osx/libblosc.a")
-    set(libd ${lib})
+    set(libd "${pwd}/lib/osx/libblosc-debug.a")
 elseif(LINUX)
     set(lib "${pwd}/lib/linux-amd64/libblosc.a")
-    set(libd ${lib})
+    set(libd "${pwd}/lib/linux-amd64/libblosc-debug.a")
 endif()
 
 message(STATUS "C-Blosc: ${pwd}")

src/3rdParty/cblosc/lib/osx/README.md

@@ -1,6 +1,6 @@
 The library here was built as follows.
 
-Against v1.21.4 (2c2f9bd) of the c-blosc source hosted at:
+Against v1.21.5 (d306135) of the c-blosc source hosted at:
 https://github.com/Blosc/c-blosc
 
 It's a universal binary compiled for `arm64` and `x86_64`.

src/CMakeLists.txt

@@ -1,26 +1,24 @@
 add_subdirectory(3rdParty)
 
-if(NOT TARGET acquire-core-logger)
-        add_subdirectory(acquire-core-libs)
-endif()
+if (NOT TARGET acquire-core-logger)
+    add_subdirectory(acquire-core-libs)
+endif ()
 
 set(tgt acquire-driver-zarr)
 add_library(${tgt} MODULE
         prelude.h
-        tiled.frame.hh
-        tiled.frame.cpp
-        chunk.writer.hh
-        chunk.writer.cpp
-        frame.scaler.hh
-        frame.scaler.cpp
+        common.hh
+        common.cpp
+        writers/writer.hh
+        writers/writer.cpp
+        writers/chunk.writer.hh
+        writers/chunk.writer.cpp
+        writers/blosc.compressor.hh
+        writers/blosc.compressor.cpp
         zarr.hh
         zarr.cpp
-        zarr.encoder.hh
-        zarr.encoder.cpp
-        zarr.raw.hh
-        zarr.raw.cpp
-        zarr.blosc.hh
-        zarr.blosc.cpp
+        zarr.v2.hh
+        zarr.v2.cpp
         zarr.driver.c
 )
 target_enable_simd(${tgt})

src/README.md

@@ -0,0 +1,42 @@
+# The Zarr Storage device
+
+## Components
+
+### The `StorageInterface` class.
+
+Defines the interface that all Acquire `Storage` devices must implement, namely
+
+- `set`: Set the storage properties.
+- `get`: Get the storage properties.
+- `get_meta`: Get metadata for the storage properties.
+- `start`: Signal to the `Storage` device that it should start accepting frames.
+- `stop`: Signal to the `Storage` device that it should stop accepting frames.
+- `append`: Write incoming frames to the filesystem or other storage layer.
+- `reserve_image_shape`: Set the image shape for allocating chunk writers.
+
+### The `Zarr` class
+
+An abstract class that implements the `StorageInterface`.
+Zarr is "[a file storage format for chunked, compressed, N-dimensional arrays based on an open-source specification.](https://zarr.readthedocs.io/en/stable/index.html)"
+
+### The `ZarrV2` class
+
+Subclass of the `Zarr` class.
+Implements abstract methods for writer allocation and metadata.
+Specifically, `ZarrV2` allocates one writer of type `ChunkWriter` for each multiscale level-of-detail
+and writes metadata in the format specified by the [Zarr V2 spec](https://zarr.readthedocs.io/en/stable/spec/v2.html).
+
+### The `Writer` class
+
+An abstract class that writes frames to the filesystem or other storage layer.
+In general, frames are chunked and potentially compressed.
+The `Writer` handles chunking, chunk compression, and writing.
+
+### The `ChunkWriter` class
+
+Subclass of the `Writer` class.
+Implements abstract methods relating to writing and flushing chunk buffers.
+
+### The `BloscCompressionParams` struct
+
+Stores parameters for compression using [C-Blosc](https://github.com/Blosc/c-blosc).