wsi-rs 0.4.0

wsi-rs whole-slide image reader
Documentation
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mod support;

use std::path::PathBuf;
use std::sync::Mutex;

use wsi_rs::{ColorSpace, CpuTile, CpuTileData, CpuTileLayout};

use support::compare::{compare_rgba, tolerance_failure, Tolerance};
use support::corpus::{
    apply_alias_filter, corpus_cache_dir, format_default_extension, parse_manifest,
    public_manifest_path,
};
use support::oracles::{
    is_reference_oracle_unsupported, read_probe, require_reference_tile, sample_buffer_to_rgba,
    top_left_probe, J2kOracle, OpenedSlide, Oracle, ProbeKind, ProbeRequest, ReferenceOracle,
    ReferenceTileError, TileBuffer,
};

static ENV_LOCK: Mutex<()> = Mutex::new(());

const SAMPLE_MANIFEST: &str = r#"
    [[slide]]
    name             = "aperio_svs_brightfield_he_typical"
    alias            = "svs-001"
    path             = ""
    format           = "aperio"
    codecs           = ["jpeg"]
    must_decode      = ["base", "level1", "level2", "label", "macro"]
    source           = "openslide-testdata"
    license          = "CC0-1.0"
    redistributable  = true
    sha256           = "deadbeef"
    citation         = "Goode A. et al. OpenSlide..."
    phi_reviewed     = true
    url              = "https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs"
"#;

#[test]
fn public_prelude_exports_common_reader_types() {
    use wsi_rs::prelude::{
        LevelIdx as PreludeLevelIdx, PlaneIdx as PreludePlaneIdx,
        PlaneSelection as PreludePlaneSelection, RegionRequest as PreludeRegionRequest,
        SceneId as PreludeSceneId, SeriesId as PreludeSeriesId, Slide as PreludeSlide,
        TileOutputPreference as PreludeTileOutputPreference, TilePixels as PreludeTilePixels,
        TileRequest as PreludeTileRequest, WsiError as PreludeWsiError,
    };

    let plane = PreludePlaneSelection::default();
    let region = PreludeRegionRequest::new(
        PreludeSceneId::new(0),
        PreludeSeriesId::new(0),
        PreludeLevelIdx::new(0),
        (0, 0),
        (16, 16),
    )
    .with_plane(PreludePlaneIdx::new(plane));
    let tile = PreludeTileRequest::new(0usize, 0usize, 0u32, 0, 0).with_plane(plane);

    assert_eq!(region.size_px, (16, 16));
    assert_eq!(tile.col, 0);
    let _preference = PreludeTileOutputPreference::cpu();
    let _ = std::any::type_name::<PreludeSlide>();
    let _ = std::any::type_name::<PreludeTilePixels>();
    let _ = std::any::type_name::<PreludeWsiError>();
}

#[test]
fn compare_identical_buffers_pass_with_psnr_inf() {
    let a = vec![10u8, 20, 30, 255, 40, 50, 60, 255];
    let report = compare_rgba(&a, &a, Tolerance::JPEG_TIGHT);

    assert!(report.passed);
    assert_eq!(report.max_abs, 0);
    assert_eq!(report.mean_abs, 0.0);
    assert!(report.psnr_db.is_infinite());
    assert_eq!(report.bytewise_equal_rate, 1.0);
}

#[test]
fn compare_off_by_one_passes_jpeg_tight() {
    let a = vec![10u8; 32];
    let mut b = a.clone();
    b[0] = 11;

    let report = compare_rgba(&a, &b, Tolerance::JPEG_TIGHT);

    assert!(report.passed);
    assert_eq!(report.max_abs, 1);
}

#[test]
fn compare_off_by_two_fails_jpeg_tight_passes_tolerant() {
    let a = vec![10u8, 20, 30, 255, 40, 50, 60, 255];
    let b = vec![12u8, 20, 30, 255, 40, 50, 60, 255];

    let tight = compare_rgba(&a, &b, Tolerance::JPEG_TIGHT);
    let tolerant = compare_rgba(&a, &b, Tolerance::TOLERANT);

    assert!(!tight.passed);
    assert!(tolerant.passed);
}

#[test]
fn compare_tolerance_failure_formats_failed_report() {
    let a = vec![10u8, 20, 30, 255, 40, 50, 60, 255];
    let b = vec![12u8, 20, 30, 255, 40, 50, 60, 255];
    let report = compare_rgba(&a, &b, Tolerance::JPEG_TIGHT);

    let failure = tolerance_failure("svs-001 level=0 j2k-vs-reference", &report)
        .expect("failed report should produce gate failure");

    assert!(failure.contains("svs-001 level=0 j2k-vs-reference"));
    assert!(failure.contains("max_abs=2"));
}

#[test]
fn corpus_parses_minimal_manifest() {
    let manifest = parse_manifest(SAMPLE_MANIFEST).expect("parse");
    let slide = manifest.slides.first().expect("slide");

    assert_eq!(manifest.slides.len(), 1);
    assert_eq!(slide.alias, "svs-001");
    assert_eq!(slide.format, "aperio");
    assert!(slide.redistributable);
    assert_eq!(slide.codecs, vec!["jpeg"]);
    assert_eq!(slide.must_decode.len(), 5);
}

#[test]
fn corpus_unknown_format_extension_returns_none() {
    assert!(format_default_extension("nonsense").is_none());
    assert_eq!(format_default_extension("aperio"), Some("svs"));
}

#[test]
fn corpus_cache_dir_respects_env() {
    let _guard = ENV_LOCK.lock().unwrap();
    let _env = EnvGuard::set("WSI_RS_PARITY_CORPUS_CACHE", "/tmp/sv-corpus-test");

    let path = corpus_cache_dir();

    assert_eq!(path, PathBuf::from("/tmp/sv-corpus-test"));
}

#[test]
fn corpus_public_manifest_parses() {
    let path = public_manifest_path();
    let text = std::fs::read_to_string(&path).expect("read public manifest");
    let manifest = parse_manifest(&text).expect("parse public manifest");

    assert!(!manifest.slides.is_empty(), "public manifest has no slides");
    for slide in &manifest.slides {
        assert!(
            slide.redistributable,
            "public entry {} not redistributable",
            slide.alias
        );
        assert!(!slide.alias.is_empty());
        assert!(!slide.format.is_empty());
        assert!(!slide.codecs.is_empty());
    }
}

#[test]
fn corpus_must_decode_level_matches_base_and_numbered_levels() {
    let mut manifest = parse_manifest(SAMPLE_MANIFEST).expect("parse");
    let entry = manifest.slides.first_mut().expect("slide");
    entry.must_decode = vec!["base".into(), "level1".into(), "level12".into()];

    assert!(entry.must_decode_level(0));
    assert!(entry.must_decode_level(1));
    assert!(entry.must_decode_level(12));
    assert!(!entry.must_decode_level(2));
    assert!(!entry.must_decode_level(10));
}

#[test]
fn corpus_expected_failure_matches_pair_and_level_aliases() {
    let mut manifest = parse_manifest(SAMPLE_MANIFEST).expect("parse");
    let entry = manifest.slides.first_mut().expect("slide");
    entry.expected_failures = vec![
        "j2k-vs-reference:base".into(),
        "reference-vs-openslide:level2".into(),
    ];

    assert!(entry.expected_failure("j2k-vs-reference", 0));
    assert!(entry.expected_failure("reference-vs-openslide", 2));
    assert!(!entry.expected_failure("j2k-vs-reference", 1));
    assert!(!entry.expected_failure("j2k-vs-openslide", 0));
}

#[test]
fn corpus_alias_filter_keeps_requested_manifest_entries() {
    let mut manifest = parse_manifest(SAMPLE_MANIFEST).expect("parse");
    let second = manifest.slides[0].clone();
    manifest.slides.push(support::corpus::CorpusEntry {
        alias: "ndpi-001".into(),
        format: "ndpi".into(),
        name: "hamamatsu_ndpi".into(),
        ..second
    });

    apply_alias_filter(&mut manifest, Some("ndpi-001,missing-001"));

    assert_eq!(manifest.slides.len(), 1);
    assert_eq!(manifest.slides[0].alias, "ndpi-001");
}

#[test]
fn oracle_names_are_stable() {
    assert_eq!(J2kOracle.name(), "j2k");
    assert_eq!(ReferenceOracle.name(), "reference");
}

#[test]
fn oracle_reference_unsupported_decode_is_an_error() {
    let err = require_reference_tile(
        Err(ReferenceTileError::unsupported(
            "fixture format is not TIFF JPEG",
        )),
        "fixture level=0 tile=(0,0)",
    )
    .expect_err("unsupported reference decode must not fall back to production");

    assert!(err.contains("reference oracle unsupported"));
    assert!(err.contains("fixture format is not TIFF JPEG"));
    assert!(is_reference_oracle_unsupported(&err));
}

#[test]
fn oracle_sample_buffer_to_rgba_respects_planar_rgb_layout() {
    let tile = CpuTile::new(
        2,
        1,
        3,
        ColorSpace::Rgb,
        CpuTileLayout::Planar,
        CpuTileData::u8(vec![10, 40, 20, 50, 30, 60]),
    )
    .expect("valid planar RGB tile");

    let out = sample_buffer_to_rgba(tile).expect("convert");

    assert_eq!(out.pixels_rgba, vec![10, 20, 30, 255, 40, 50, 60, 255]);
}

#[test]
fn oracle_top_left_probe_falls_back_to_region_for_irregular_layout() {
    let slide = OpenedSlide {
        path: PathBuf::from("fixture.bif"),
        oracle_name: "fixture",
        level_count: 1,
        level_dimensions: vec![(123, 45)],
        tile_sizes: vec![None],
        probe_regions: vec![None],
        reader: Box::new(|_, _, _, _, _| Err("tile reader should not be used".into())),
        region_reader: Box::new(|level, x, y, width, height| {
            assert_eq!(level, 0);
            assert_eq!((x, y), (0, 0));
            assert_eq!((width, height), (123, 45));
            Ok(TileBuffer {
                pixels_rgba: vec![0; width as usize * height as usize * 4],
                width,
                height,
            })
        }),
    };

    let probe = top_left_probe(&slide, 0).expect("probe");

    assert_eq!(probe.kind, ProbeKind::Region);
    assert_eq!((probe.width, probe.height), (123, 45));
    let tile = read_probe(&slide, probe).expect("read probe");
    assert_eq!((tile.width, tile.height), (123, 45));
}

#[test]
fn oracle_top_left_probe_prefers_sparse_layout_probe_when_available() {
    let slide = OpenedSlide {
        path: PathBuf::from("fixture.mrxs"),
        oracle_name: "fixture",
        level_count: 1,
        level_dimensions: vec![(1000, 1000)],
        tile_sizes: vec![None],
        probe_regions: vec![Some(ProbeRequest {
            level: 0,
            x: 320,
            y: 448,
            width: 128,
            height: 96,
            kind: ProbeKind::Region,
        })],
        reader: Box::new(|_, _, _, _, _| Err("tile reader should not be used".into())),
        region_reader: Box::new(|level, x, y, width, height| {
            assert_eq!(level, 0);
            assert_eq!((x, y), (320, 448));
            assert_eq!((width, height), (128, 96));
            Ok(TileBuffer {
                pixels_rgba: vec![0; width as usize * height as usize * 4],
                width,
                height,
            })
        }),
    };

    let probe = top_left_probe(&slide, 0).expect("probe");

    assert_eq!(probe.kind, ProbeKind::Region);
    assert_eq!((probe.x, probe.y), (320, 448));
    let tile = read_probe(&slide, probe).expect("read probe");
    assert_eq!((tile.width, tile.height), (128, 96));
}

#[cfg(feature = "parity-openslide")]
#[test]
fn openslide_shim_missing_env_path_does_not_panic() {
    let _guard = ENV_LOCK.lock().unwrap();
    let _env = EnvGuard::set(
        "OPENSLIDE_LIB_PATH",
        "/definitely/does/not/exist/libopenslide.dylib",
    );

    let result = support::openslide_shim::try_load();

    let _ = result;
}

#[cfg(feature = "parity-openslide")]
#[test]
fn openslide_shim_bounds_parser_reads_canvas_origin() {
    let props = [
        ("openslide.bounds-x", "10778"),
        ("openslide.bounds-y", "35096"),
        ("openslide.bounds-width", "36832"),
        ("openslide.bounds-height", "38432"),
    ];

    let bounds = support::openslide_shim::parse_bounds_from_properties(|name| {
        props
            .iter()
            .find(|(key, _)| *key == name)
            .map(|(_, value)| (*value).to_string())
    })
    .expect("bounds");

    assert_eq!(bounds.x, 10778);
    assert_eq!(bounds.y, 35096);
    assert_eq!(bounds.width, 36832);
    assert_eq!(bounds.height, 38432);
}

#[cfg(feature = "parity-openslide")]
#[test]
fn openslide_shim_bounds_parser_rejects_missing_or_empty_bounds() {
    assert!(support::openslide_shim::parse_bounds_from_properties(|_| None).is_none());

    let props = [
        ("openslide.bounds-x", "0"),
        ("openslide.bounds-y", "0"),
        ("openslide.bounds-width", "0"),
        ("openslide.bounds-height", "100"),
    ];

    assert!(
        support::openslide_shim::parse_bounds_from_properties(|name| {
            props
                .iter()
                .find(|(key, _)| *key == name)
                .map(|(_, value)| (*value).to_string())
        })
        .is_none()
    );
}

#[cfg(feature = "parity-openslide")]
#[test]
fn openslide_oracle_dimensions_use_bounds_canvas_when_smaller_than_full_canvas() {
    let full_canvas_dims = [(53130, 153470), (13283, 38368), (3321, 9592)];
    let bounds = support::openslide_shim::OpenSlideBounds {
        x: 10778,
        y: 35096,
        width: 36832,
        height: 38432,
    };

    let dims =
        support::oracles::comparable_openslide_level_dimensions(&full_canvas_dims, Some(bounds));

    assert_eq!(dims, vec![(36832, 38432), (9208, 9608), (2302, 2402)]);
    assert!(support::oracles::openslide_level_dimensions_match(
        (2302, 2402),
        full_canvas_dims[2],
        &full_canvas_dims,
        Some(bounds),
    ));
    assert!(!support::oracles::openslide_level_dimensions_match(
        (36832, 38432),
        full_canvas_dims[0],
        &full_canvas_dims,
        None,
    ));
}

#[cfg(feature = "parity-openslide")]
#[test]
fn openslide_oracle_maps_level_coordinates_to_level_zero_world_coordinates() {
    let full_canvas_dims = [(53130, 153470), (13283, 38368), (3321, 9592)];
    let bounds = support::openslide_shim::OpenSlideBounds {
        x: 10778,
        y: 35096,
        width: 36832,
        height: 38432,
    };

    let world = support::oracles::openslide_world_origin_for_probe(
        &full_canvas_dims,
        Some(bounds),
        1,
        256,
        512,
    );

    assert_eq!(world, (11802, 37144));
}

#[cfg(feature = "parity-openslide")]
#[test]
fn openslide_oracle_bounds_canvas_policy_is_vendor_specific() {
    let bounds = support::openslide_shim::OpenSlideBounds {
        x: 10778,
        y: 35096,
        width: 36832,
        height: 38432,
    };

    assert_eq!(
        support::oracles::openslide_comparison_bounds(Some("leica"), Some(bounds)),
        Some(bounds)
    );
    assert_eq!(
        support::oracles::openslide_comparison_bounds(Some("mirax"), Some(bounds)),
        None
    );
    assert_eq!(
        support::oracles::openslide_comparison_bounds(None, Some(bounds)),
        None
    );
}

struct EnvGuard {
    key: &'static str,
    prev: Option<std::ffi::OsString>,
}

impl EnvGuard {
    fn set(key: &'static str, value: &str) -> Self {
        let prev = std::env::var_os(key);
        std::env::set_var(key, value);
        Self { key, prev }
    }
}

impl Drop for EnvGuard {
    fn drop(&mut self) {
        if let Some(value) = &self.prev {
            std::env::set_var(self.key, value);
        } else {
            std::env::remove_var(self.key);
        }
    }
}