ome_zarr_metadata 0.3.1

A library for OME-Zarr (previously OME-NGFF) metadata
Documentation 
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//! "labels" and "image-label" metadata.
//!
//! <https://ngff.openmicroscopy.org/0.4/#labels-md>.

use std::{collections::HashSet, path::PathBuf};

use serde::{Deserialize, Serialize};
use validatrix::{Accumulator, Validate};

/// `labels` metadata. A JSON array of paths to the labeled multiscale image(s).
pub type Labels = Vec<String>;

/// `image-label` metadata. Stores information about the display colors, source image, and optionally, further arbitrary properties of a label image.
#[derive(Serialize, Deserialize, Debug, Clone)]
#[serde(deny_unknown_fields)]
pub struct ImageLabel {
    /// The version of the OME-NGFF "image-label" schema.
    pub version: super::ConstrainedVersion,
    /// Describes the color information for the unique label values.
    pub colors: Option<Vec<ImageLabelColor>>,
    /// Arbitrary metadata associated with each unique label (optional).
    #[serde(skip_serializing_if = "Option::is_none")]
    pub properties: Option<Vec<ImageLabelProperties>>,
    /// Information about the original image from which the label image derives (optional).
    #[serde(skip_serializing_if = "Option::is_none")]
    pub source: Option<ImageLabelSource>,
}

impl Validate for ImageLabel {
    fn validate_inner(&self, accum: &mut validatrix::Accumulator) {
        if let Some(c) = self.colors.as_ref() {
            accum.with_key("colors", |a| {
                if c.is_empty() {
                    a.add_failure("empty");
                }
                validate_unique_labels(a, c.iter())
            });
        }

        if let Some(p) = self.properties.as_ref() {
            accum.with_key("properties", |a| {
                if p.is_empty() {
                    a.add_failure("empty");
                }
                validate_unique_labels(a, p.iter());
            });
        }
    }
}

/// [`ImageLabel`] `colors` element metadata. The colour of a unique image label.
#[derive(Serialize, Deserialize, Debug, Clone)]
#[serde(deny_unknown_fields)]
pub struct ImageLabelColor {
    /// Integer label value.
    #[serde(rename = "label-value")]
    pub label_value: u64,
    /// Colour as RGBA array.
    pub rgba: [u8; 4],
}

pub(crate) fn validate_unique_labels<'a, T: HasLabelValue + 'a>(
    accum: &mut Accumulator,
    it: impl IntoIterator<Item = &'a T>,
) {
    let mut set: HashSet<u64> = HashSet::default();
    for (idx, lbl) in it.into_iter().map(HasLabelValue::get_label).enumerate() {
        if !set.insert(lbl) {
            accum.add_failure_at(idx, format!("repeated label {lbl}"));
        }
    }
}

pub(crate) trait HasLabelValue {
    fn get_label(&self) -> u64;
}

impl HasLabelValue for ImageLabelColor {
    fn get_label(&self) -> u64 {
        self.label_value
    }
}

impl HasLabelValue for ImageLabelProperties {
    fn get_label(&self) -> u64 {
        self.label_value
    }
}

/// [`ImageLabel`] `properties` element metadata. Arbitrary metadata of a unique image label.
#[derive(Serialize, Deserialize, Debug, Clone)]
pub struct ImageLabelProperties {
    /// Integer label value.
    #[serde(rename = "label-value")]
    pub label_value: u64,
    /// Arbitrary metadata associated with the label.
    #[serde(flatten)]
    pub properties: serde_json::Map<String, serde_json::Value>,
}

/// [`ImageLabel`] `source` metadata. Information about the source of a label image.
#[derive(Serialize, Deserialize, Debug, Clone)]
pub struct ImageLabelSource {
    /// Relative path to the zarr image group which this group labels.
    pub image: Option<PathBuf>,
}

#[cfg(test)]
mod tests {
    use crate::v0_4::OmeNgffGroupAttributes;

    use super::*;

    #[test]
    fn labels_color_properties() {
        let json = include_str!(concat!(
            env!("CARGO_MANIFEST_DIR"),
            "/ome-zarr/specifications/0.4/examples/label_strict/colors_properties.json"
        ));
        let ome_metadata: OmeNgffGroupAttributes = serde_json::from_str(json).unwrap();
        let _image_label: ImageLabel = ome_metadata.image_label.unwrap();
    }
}