feat: Add support for Openslide 4.x (#118)

.gitignore

@@ -2,6 +2,8 @@
 # will have compiled files and executables
 /target/
 
+/tests/assets
+
 # These are backup files generated by rustfmt
 **/*.rs.bk
 

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ default_language_version:
     python: python3
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.5.0
     hooks:
     -   id: check-byte-order-marker
     -   id: check-case-conflict
@@ -13,7 +13,7 @@ repos:
     -   id: mixed-line-ending
     -   id: trailing-whitespace
 -   repo: https://github.com/pre-commit/pre-commit
-    rev: v2.13.0
+    rev: v3.5.0
     hooks:
     -   id: validate_manifest
 -   repo: https://github.com/doublify/pre-commit-rust

Cargo.toml

@@ -15,6 +15,7 @@ license = "MIT/Apache-2.0"
 default = ["deepzoom"]
 deepzoom = ["image"]
 image = ["dep:image", "dep:fast_image_resize"]
+openslide4 = []
 
 [dependencies]
 libc = "0.2"

benches/bench_read.rs

@@ -1,5 +1,5 @@
 use bencher::{benchmark_group, benchmark_main, Bencher};
-use openslide_rs::{traits::Slide, Address, DeepZoomGenerator, OpenSlide, Region, Size};
+use openslide_rs::{Address, DeepZoomGenerator, OpenSlide, Region, Size};
 use std::{path::Path, sync::Arc};
 
 fn openslide_read_region_256(bench: &mut Bencher) {
@@ -66,6 +66,26 @@ fn deepzoom_read_image_512(bench: &mut Bencher) {
     bench.iter(|| dz.get_tile_rgb(12, Address { x: 0, y: 0 }));
 }
 
+fn deepzoom_read_image_256_recreate_dz(bench: &mut Bencher) {
+    let slide = OpenSlide::new(Path::new("tests/assets/default.svs")).unwrap();
+
+    bench.iter(|| {
+        let dz: DeepZoomGenerator<OpenSlide, _> =
+            DeepZoomGenerator::new(&slide, 257, 0, false).unwrap();
+        dz.get_tile_rgb(12, Address { x: 0, y: 0 })
+    });
+}
+
+fn deepzoom_read_image_512_recreate_dz(bench: &mut Bencher) {
+    let slide = OpenSlide::new(Path::new("tests/assets/default.svs")).unwrap();
+
+    bench.iter(|| {
+        let dz: DeepZoomGenerator<OpenSlide, _> =
+            DeepZoomGenerator::new(&slide, 511, 0, false).unwrap();
+        dz.get_tile_rgb(12, Address { x: 0, y: 0 })
+    });
+}
+
 fn deepzoom_read_image_256_arc(bench: &mut Bencher) {
     let slide = Arc::new(OpenSlide::new(Path::new("tests/assets/default.svs")).unwrap());
     let dz: DeepZoomGenerator<OpenSlide, _> = DeepZoomGenerator::new(slide, 257, 0, false).unwrap();
@@ -94,6 +114,8 @@ benchmark_group!(
     deepzoom_image,
     deepzoom_read_image_256,
     deepzoom_read_image_512,
+    deepzoom_read_image_256_recreate_dz,
+    deepzoom_read_image_512_recreate_dz,
     deepzoom_read_image_256_arc,
     deepzoom_read_image_512_arc
 );

src/bindings.rs

@@ -11,7 +11,7 @@ use openslide_sys::sys;
 
 /// wrapper around OpenSlideT, this is usefull for implementing Send and Sync
 #[derive(Debug)]
-pub(crate) struct OpenSlideWrapper(pub *mut sys::openslide_t);
+pub(crate) struct OpenSlideWrapper(pub(crate) *mut sys::openslide_t);
 
 impl Deref for OpenSlideWrapper {
     type Target = *mut sys::openslide_t;
@@ -24,6 +24,22 @@ impl Deref for OpenSlideWrapper {
 unsafe impl Send for OpenSlideWrapper {}
 unsafe impl Sync for OpenSlideWrapper {}
 
+#[cfg(feature = "openslide4")]
+#[derive(Debug)]
+pub(crate) struct CacheWrapper(pub(crate) *mut sys::openslide_cache_t);
+
+#[cfg(feature = "openslide4")]
+impl Deref for CacheWrapper {
+    type Target = *mut sys::openslide_cache_t;
+
+    fn deref(&self) -> &Self::Target {
+        &self.0
+    }
+}
+
+#[cfg(feature = "openslide4")]
+unsafe impl Send for CacheWrapper {}
+
 pub fn get_version() -> Result<String> {
     let version = unsafe { sys::openslide_get_version() };
     if !version.is_null() {
@@ -256,3 +272,84 @@ pub fn get_error(osr: *mut sys::openslide_t) -> Result<()> {
     };
     value
 }
+
+#[cfg(feature = "openslide4")]
+pub fn get_icc_profile_size(osr: *mut sys::openslide_t) -> Result<i64> {
+    let size = unsafe { sys::openslide_get_icc_profile_size(osr) };
+    // TODO: check if size == 0 => no ICC profile
+    if size == -1 {
+        get_error(osr)?;
+        return Err(OpenSlideError::CoreError(
+            "Cannot get ICC profile size".to_string(),
+        ));
+    }
+    Ok(size)
+}
+
+#[cfg(feature = "openslide4")]
+pub fn read_icc_profile(osr: *mut sys::openslide_t) -> Result<Vec<u8>> {
+    let size = get_icc_profile_size(osr)?;
+    let mut buffer: Vec<u8> = Vec::with_capacity(size as usize);
+    let p_buffer = buffer.as_mut_ptr() as *mut std::os::raw::c_void;
+    unsafe {
+        sys::openslide_read_icc_profile(osr, p_buffer);
+        get_error(osr)?;
+        buffer.set_len(size as usize);
+    }
+    Ok(buffer)
+}
+
+#[cfg(feature = "openslide4")]
+pub fn get_associated_image_icc_profile_size(
+    osr: *mut sys::openslide_t,
+    name: &str,
+) -> Result<i64> {
+    let c_name = ffi::CString::new(name)?;
+    let size =
+        unsafe { sys::openslide_get_associated_image_icc_profile_size(osr, c_name.as_ptr()) };
+    // TODO: check if size == 0 => no ICC profile
+    if size == -1 {
+        get_error(osr)?;
+        return Err(OpenSlideError::CoreError(
+            "Cannot get ICC profile size".to_string(),
+        ));
+    }
+    Ok(size)
+}
+
+#[cfg(feature = "openslide4")]
+pub fn read_associated_image_icc_profile(
+    osr: *mut sys::openslide_t,
+    name: &str,
+) -> Result<Vec<u8>> {
+    let c_name = ffi::CString::new(name)?;
+    let size = get_associated_image_icc_profile_size(osr, name)?;
+    let mut buffer: Vec<u8> = Vec::with_capacity(size as usize);
+    let p_buffer = buffer.as_mut_ptr() as *mut std::os::raw::c_void;
+    unsafe {
+        sys::openslide_read_associated_image_icc_profile(osr, c_name.as_ptr(), p_buffer);
+        get_error(osr)?;
+        buffer.set_len(size as usize);
+    }
+    Ok(buffer)
+}
+
+#[cfg(feature = "openslide4")]
+pub fn cache_create(capacity: usize) -> Result<*mut sys::openslide_cache_t> {
+    let cache = unsafe { sys::openslide_cache_create(capacity) };
+    if cache.is_null() {
+        Err(OpenSlideError::CoreError("Cannot create cache".to_string()))
+    } else {
+        Ok(cache)
+    }
+}
+
+#[cfg(feature = "openslide4")]
+pub fn set_cache(osr: *mut sys::openslide_t, cache: *mut sys::openslide_cache_t) {
+    unsafe { sys::openslide_set_cache(osr, cache) };
+}
+
+#[cfg(feature = "openslide4")]
+pub fn cache_release(cache: *mut sys::openslide_cache_t) {
+    unsafe { sys::openslide_cache_release(cache) };
+}

src/cache.rs

@@ -0,0 +1,18 @@
+use crate::{bindings, Result};
+
+#[derive(Debug)]
+pub(crate) struct Cache(pub(crate) bindings::CacheWrapper);
+
+impl Drop for Cache {
+    fn drop(&mut self) {
+        bindings::cache_release(*self.0);
+    }
+}
+
+impl Cache {
+    /// Create a new cache with the given capacity
+    pub fn new(capacity: usize) -> Result<Cache> {
+        let cache = bindings::CacheWrapper(bindings::cache_create(capacity)?);
+        Ok(Cache(cache))
+    }
+}

src/lib.rs

@@ -10,6 +10,8 @@ use {
 };
 
 mod bindings;
+#[cfg(feature = "openslide4")]
+mod cache;
 #[cfg(feature = "deepzoom")]
 pub mod deepzoom;
 pub mod errors;

src/properties/openslide.rs

@@ -20,6 +20,7 @@ pub const OPENSLIDE_PROPERTY_NAME_BOUNDS_Y: &str = "openslide.bounds-y";
 pub const OPENSLIDE_PROPERTY_NAME_BOUNDS_WIDTH: &str = "openslide.bounds-width";
 pub const OPENSLIDE_PROPERTY_NAME_BOUNDS_HEIGHT: &str = "openslide.bounds-height";
 pub const OPENSLIDE_PROPERTY_LEVEL_COUNT: &str = "openslide.level-count";
+pub const OPENSLIDE_PROPERTY_NAME_ICC_SIZE: &str = "openslide.icc-size";
 
 const OPENSLIDE_PROPERTY_LEVEL_DOWNSAMPLE: &str = "downsample";
 const OPENSLIDE_PROPERTY_LEVEL_HEIGHT: &str = "height";
@@ -52,6 +53,7 @@ pub struct OpenSlide {
     pub bounds_y: Option<u32>,
     pub bounds_width: Option<u32>,
     pub bounds_height: Option<u32>,
+    pub icc_profile_size: Option<u32>,
     pub background_color: Option<String>,
     pub levels: Vec<LevelProperties>,
 }
@@ -81,6 +83,7 @@ impl OpenSlide {
             OPENSLIDE_PROPERTY_LEVEL_COUNT => self.level_count = value.parse().ok(),
             OPENSLIDE_PROPERTY_NAME_BOUNDS_X => self.bounds_x = value.parse().ok(),
             OPENSLIDE_PROPERTY_NAME_BOUNDS_Y => self.bounds_y = value.parse().ok(),
+            OPENSLIDE_PROPERTY_NAME_ICC_SIZE => self.icc_profile_size = value.parse().ok(),
             OPENSLIDE_PROPERTY_NAME_BOUNDS_WIDTH => self.bounds_width = value.parse().ok(),
             OPENSLIDE_PROPERTY_NAME_BOUNDS_HEIGHT => self.bounds_height = value.parse().ok(),
             OPENSLIDE_PROPERTY_NAME_BACKGROUND_COLOR => {

src/wrapper.rs

@@ -10,6 +10,9 @@ use {
     image::{RgbImage, RgbaImage},
 };
 
+#[cfg(feature = "openslide4")]
+use crate::cache::Cache;
+
 impl Drop for OpenSlide {
     fn drop(&mut self) {
         bindings::close(*self.osr)
@@ -27,7 +30,8 @@ impl OpenSlide {
     /// This function can be expensive; avoid calling it unnecessarily. For example, a tile server
     /// should not create a new object on every tile request. Instead, it should maintain a cache
     /// of OpenSlide objects and reuse them when possible.
-    pub fn new(path: &Path) -> Result<OpenSlide> {
+    pub fn new<T: AsRef<Path>>(path: T) -> Result<OpenSlide> {
+        let path = path.as_ref();
         if !path.exists() {
             return Err(OpenSlideError::MissingFile(path.display().to_string()));
         }
@@ -53,6 +57,18 @@ impl OpenSlide {
         })
     }
 
+    #[cfg(feature = "openslide4")]
+    pub fn new_with_cache<T: AsRef<Path>>(path: T, capacity: usize) -> Result<OpenSlide> {
+        let osr = OpenSlide::new(path)?;
+        osr.set_cache(Cache::new(capacity)?);
+        Ok(osr)
+    }
+
+    #[cfg(feature = "openslide4")]
+    fn set_cache(&self, cache: Cache) {
+        bindings::set_cache(*self.osr, *cache.0)
+    }
+
     /// Quickly determine whether a whole slide image is recognized.
     pub fn detect_vendor(path: &Path) -> Result<String> {
         if !path.exists() {
@@ -298,6 +314,16 @@ impl OpenSlide {
 
         Ok(image)
     }
+
+    #[cfg(feature = "openslide4")]
+    pub fn icc_profile(&self) -> Result<Vec<u8>> {
+        bindings::read_icc_profile(*self.osr)
+    }
+
+    #[cfg(feature = "openslide4")]
+    pub fn associated_image_icc_profile(&self, name: &str) -> Result<Vec<u8>> {
+        bindings::read_associated_image_icc_profile(*self.osr, name)
+    }
 }
 
 #[cfg(feature = "deepzoom")]

tests/openslide.rs

@@ -3,9 +3,16 @@ use fixture::{boxes_tiff, missing_file, small_svs, unopenable_tiff, unsupported_
 use openslide_rs::{Address, OpenSlide, Region, Size};
 use rstest::rstest;
 use std::path::Path;
+use version_compare::Version;
 
 mod fixture;
 
+#[rstest]
+fn test_version() {
+    let version = OpenSlide::get_version().expect("Failed to get version");
+    Version::from(&version).expect("Failed to parse version");
+}
+
 #[rstest]
 #[should_panic(expected = "MissingFile(\"missing_file\")")]
 #[case(missing_file())]
@@ -259,3 +266,23 @@ fn test_error_thumbnail(#[case] filename: &Path) {
     let size = Size { w: 100, h: 0 };
     slide.thumbnail_rgb(&size).unwrap();
 }
+
+#[rstest]
+#[cfg(feature = "openslide4")]
+#[case(small_svs())]
+fn test_icc_profile(#[case] filename: &Path) {
+    let slide = OpenSlide::new(filename).unwrap();
+
+    let icc_profile = slide.icc_profile().unwrap();
+    assert_eq!(icc_profile.len(), 0);
+}
+
+#[rstest]
+#[cfg(feature = "openslide4")]
+#[case(small_svs())]
+fn test_associated_image_icc_profile(#[case] filename: &Path) {
+    let slide = OpenSlide::new(filename).unwrap();
+
+    let icc_profile = slide.associated_image_icc_profile("thumbnail").unwrap();
+    assert_eq!(icc_profile.len(), 0);
+}