openbnct-core 0.1.1

// SPDX-License-Identifier: Apache-2.0

#![forbid(unsafe_code)]

mod exposure;
mod external_dose;
mod interchange;
mod registration;
mod stats;
mod systematic;

use std::collections::BTreeSet;

use serde::{Deserialize, Serialize};
use thiserror::Error;

pub use exposure::{
    BoundFileReference, EXPOSURE_PLAN_SCHEMA, Exposure, ExposureCovariance, ExposurePlan,
    ExposurePlanError, WeightBasis, accumulate_exposures,
};
pub use external_dose::{
    EXTERNAL_DOSE_SCHEMA, ExternalDoseBundle, ExternalDoseDocument, ExternalDoseError,
    ExternalDoseQuantity, ExternalFractionation, ResampleError, ResampleMethod,
    import_external_dose, resample_trilinear,
};
pub use interchange::{
    COMPONENT_DOSE_INTERCHANGE_SCHEMA, ComponentDoseInterchange, ExternalProducer, ExternalTotal,
    InterchangeError, grid_geometry_equivalent, import_component_dose,
};
pub use registration::{
    LandmarkPair, REGISTRATION_SCHEMA, Registration, RegistrationError, RegistrationMethod,
    RigidTransform, declared_registration, fit_landmark_transform, landmark_registration,
};
pub use stats::{
    dose_covering_percent, equivalent_uniform_dose, masked_values, mean, volume_at_least,
};
pub use systematic::{
    RegionUncertainty, SYSTEMATIC_UNCERTAINTY_QUALIFICATION, SYSTEMATIC_UNCERTAINTY_SCHEMA,
    SourceSummary, SystematicError, SystematicUncertaintyReport, UncertaintySource,
    boron_field_sigma, combine_total_sigma, combine_voxel_sigma, positioning_sigma,
    region_uncertainty, relative_component_sigma, summarize_source,
};

/// A regular patient-coordinate voxel grid.
///
/// `direction` is row-major and maps voxel axes into the patient coordinate
/// frame. Geometry importers must preserve the original DICOM frame of
/// reference outside this numerical representation.
#[derive(Debug, Clone, PartialEq, Serialize, Deserialize)]
#[serde(deny_unknown_fields)]
pub struct GridGeometry {
    pub shape: [u32; 3],
    pub spacing_mm: [f64; 3],
    pub origin_mm: [f64; 3],
    pub direction: [f64; 9],
}

impl GridGeometry {
    pub fn voxel_count(&self) -> Result<usize, ValidationError> {
        if self.shape.contains(&0) {
            return Err(ValidationError::EmptyGrid);
        }
        if self
            .spacing_mm
            .iter()
            .any(|value| !value.is_finite() || *value <= 0.0)
        {
            return Err(ValidationError::InvalidSpacing);
        }
        if self.origin_mm.iter().any(|value| !value.is_finite())
            || self.direction.iter().any(|value| !value.is_finite())
        {
            return Err(ValidationError::NonFiniteGeometry);
        }
        let axes = [
            [self.direction[0], self.direction[3], self.direction[6]],
            [self.direction[1], self.direction[4], self.direction[7]],
            [self.direction[2], self.direction[5], self.direction[8]],
        ];
        let dot = |left: [f64; 3], right: [f64; 3]| {
            left[0].mul_add(right[0], left[1].mul_add(right[1], left[2] * right[2]))
        };
        let determinant = self.direction[0]
            * (self.direction[4] * self.direction[8] - self.direction[5] * self.direction[7])
            - self.direction[1]
                * (self.direction[3] * self.direction[8] - self.direction[5] * self.direction[6])
            + self.direction[2]
                * (self.direction[3] * self.direction[7] - self.direction[4] * self.direction[6]);
        const TOLERANCE: f64 = 1.0e-6;
        if axes
            .iter()
            .any(|axis| (dot(*axis, *axis) - 1.0).abs() > TOLERANCE)
            || dot(axes[0], axes[1]).abs() > TOLERANCE
            || dot(axes[0], axes[2]).abs() > TOLERANCE
            || dot(axes[1], axes[2]).abs() > TOLERANCE
            || (determinant - 1.0).abs() > TOLERANCE
        {
            return Err(ValidationError::InvalidDirection);
        }

        self.shape.iter().try_fold(1_usize, |count, extent| {
            count
                .checked_mul(*extent as usize)
                .ok_or(ValidationError::GridTooLarge)
        })
    }

    /// Return the patient-coordinate center of a voxel in millimetres.
    pub fn voxel_center_lps_mm(&self, voxel: [u32; 3]) -> Result<[f64; 3], ValidationError> {
        self.voxel_count()?;
        if voxel
            .into_iter()
            .zip(self.shape)
            .any(|(index, extent)| index >= extent)
        {
            return Err(ValidationError::VoxelOutOfBounds {
                voxel,
                shape: self.shape,
            });
        }
        let local = [
            f64::from(voxel[0]) * self.spacing_mm[0],
            f64::from(voxel[1]) * self.spacing_mm[1],
            f64::from(voxel[2]) * self.spacing_mm[2],
        ];
        Ok([
            self.origin_mm[0]
                + self.direction[0].mul_add(
                    local[0],
                    self.direction[1].mul_add(local[1], self.direction[2] * local[2]),
                ),
            self.origin_mm[1]
                + self.direction[3].mul_add(
                    local[0],
                    self.direction[4].mul_add(local[1], self.direction[5] * local[2]),
                ),
            self.origin_mm[2]
                + self.direction[6].mul_add(
                    local[0],
                    self.direction[7].mul_add(local[1], self.direction[8] * local[2]),
                ),
        ])
    }

    /// World-axis-aligned bounding box `(minimum, maximum)` of the grid's
    /// voxel extents in LPS millimetres. `origin_mm` is voxel index
    /// `[0,0,0]`'s center, so each face sits half a spacing beyond the
    /// extreme centers along the (possibly rotated) voxel axes.
    pub fn bounding_box_lps_mm(&self) -> Result<([f64; 3], [f64; 3]), ValidationError> {
        self.voxel_count()?;
        let mut minimum = self.origin_mm;
        let mut maximum = self.origin_mm;
        // Axis `axis`'s half-extent in voxel-index units is `shape/2` about
        // the [0,0,0] center; walk the eight extreme-index corners.
        for corner in 0..8 {
            let local = [
                (if corner & 1 == 0 {
                    -0.5
                } else {
                    self.shape[0] as f64 - 0.5
                }) * self.spacing_mm[0],
                (if corner & 2 == 0 {
                    -0.5
                } else {
                    self.shape[1] as f64 - 0.5
                }) * self.spacing_mm[1],
                (if corner & 4 == 0 {
                    -0.5
                } else {
                    self.shape[2] as f64 - 0.5
                }) * self.spacing_mm[2],
            ];
            for axis in 0..3 {
                let value = self.origin_mm[axis]
                    + self.direction[axis * 3].mul_add(
                        local[0],
                        self.direction[axis * 3 + 1]
                            .mul_add(local[1], self.direction[axis * 3 + 2] * local[2]),
                    );
                minimum[axis] = minimum[axis].min(value);
                maximum[axis] = maximum[axis].max(value);
            }
        }
        Ok((minimum, maximum))
    }
}

/// The four physical dose groups retained before biological weighting.
#[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Serialize, Deserialize)]
#[serde(rename_all = "snake_case")]
pub enum DoseComponent {
    Boron,
    Nitrogen,
    Hydrogen,
    Photon,
}

impl DoseComponent {
    pub const REQUIRED: [Self; 4] = [Self::Boron, Self::Nitrogen, Self::Hydrogen, Self::Photon];
}

#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
#[serde(rename_all = "snake_case")]
pub enum DoseUnit {
    Gray,
    GrayPerSourceParticle,
}

/// Immutable identity of a scientific input artifact.
#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
#[serde(deny_unknown_fields)]
pub struct ContentReference {
    pub id: String,
    pub sha256: String,
}

impl ContentReference {
    pub fn validate(&self) -> Result<(), ContentReferenceError> {
        if self.id.trim().is_empty() {
            return Err(ContentReferenceError::EmptyId);
        }
        if !is_canonical_sha256(&self.sha256) {
            return Err(ContentReferenceError::InvalidSha256);
        }
        Ok(())
    }
}

/// Content reference used specifically for the component-definition profile.
pub type ComponentProfileReference = ContentReference;

#[derive(Debug, Clone, PartialEq, Serialize, Deserialize)]
#[serde(deny_unknown_fields)]
pub struct DoseVolume {
    pub component: DoseComponent,
    pub unit: DoseUnit,
    pub values: Vec<f64>,
    /// One-sigma absolute standard uncertainty in the same unit as `values`.
    pub absolute_standard_uncertainty: Option<Vec<f64>>,
}

impl DoseVolume {
    /// Derive relative uncertainty for one voxel.
    ///
    /// Relative uncertainty is deliberately absent when no absolute
    /// uncertainty exists or when the mean is zero.
    pub fn relative_standard_uncertainty(
        &self,
        voxel_index: usize,
    ) -> Result<Option<f64>, ValidationError> {
        let mean = self
            .values
            .get(voxel_index)
            .ok_or(ValidationError::DoseIndexOutOfBounds {
                index: voxel_index,
                length: self.values.len(),
            })?;
        let Some(uncertainty) = &self.absolute_standard_uncertainty else {
            return Ok(None);
        };
        let absolute = uncertainty
            .get(voxel_index)
            .ok_or(ValidationError::UncertaintyLength {
                component: self.component,
                expected: self.values.len(),
                actual: uncertainty.len(),
            })?;
        if *mean == 0.0 {
            Ok(None)
        } else {
            Ok(Some(*absolute / *mean))
        }
    }
}

#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
#[serde(rename_all = "snake_case")]
pub enum TotalUncertaintyMethod {
    /// Uncertainty comes from a dedicated physical-total estimator.
    DedicatedEstimator,
    /// Uncertainty was calculated from batch-level component covariance.
    BatchCovariance,
    /// No defensible total uncertainty is available.
    Unavailable,
}

#[derive(Debug, Clone, PartialEq, Serialize, Deserialize)]
#[serde(deny_unknown_fields)]
pub struct PhysicalTotalDoseVolume {
    pub unit: DoseUnit,
    pub values: Vec<f64>,
    pub absolute_standard_uncertainty: Option<Vec<f64>>,
    pub uncertainty_method: TotalUncertaintyMethod,
}

/// Named voxel mask in grid order (`i + nx*j + nx*ny*k`).
#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
#[serde(deny_unknown_fields)]
pub struct RegionMask {
    pub name: String,
    pub voxels: Vec<bool>,
}

impl RegionMask {
    /// Number of voxels included in the mask.
    #[must_use]
    pub fn included_voxel_count(&self) -> usize {
        self.voxels.iter().filter(|voxel| **voxel).count()
    }

    /// `self` minus `other`, under `name`.
    ///
    /// Both masks must describe the same voxel count — masks do not carry
    /// their grid, so the caller binds them to a shared case geometry. The
    /// result must select at least one voxel.
    pub fn subtract(
        &self,
        other: &RegionMask,
        name: impl Into<String>,
    ) -> Result<RegionMask, ValidationError> {
        self.combine(other, name, |a, b| a && !b)
    }

    /// Union of `self` and `other`, under `name`.
    pub fn union(
        &self,
        other: &RegionMask,
        name: impl Into<String>,
    ) -> Result<RegionMask, ValidationError> {
        self.combine(other, name, |a, b| a || b)
    }

    /// Intersection of `self` and `other`, under `name`.
    pub fn intersection(
        &self,
        other: &RegionMask,
        name: impl Into<String>,
    ) -> Result<RegionMask, ValidationError> {
        self.combine(other, name, |a, b| a && b)
    }

    fn combine(
        &self,
        other: &RegionMask,
        name: impl Into<String>,
        op: impl Fn(bool, bool) -> bool,
    ) -> Result<RegionMask, ValidationError> {
        if self.voxels.len() != other.voxels.len() {
            return Err(ValidationError::MaskVoxelCountMismatch {
                name: self.name.clone(),
                other: other.name.clone(),
                expected: self.voxels.len(),
                actual: other.voxels.len(),
            });
        }
        let voxels = self
            .voxels
            .iter()
            .copied()
            .zip(other.voxels.iter().copied())
            .map(|(a, b)| op(a, b))
            .collect::<Vec<_>>();
        let mask = RegionMask {
            name: name.into(),
            voxels,
        };
        if mask.included_voxel_count() == 0 {
            return Err(ValidationError::EmptyMask(mask.name));
        }
        Ok(mask)
    }

    /// Mean and maximum of a per-voxel quantity inside this mask.
    ///
    /// `values` must be laid out on the same voxel count as the mask.
    pub fn summarize(&self, values: &[f64]) -> Result<MaskDoseSummary, ValidationError> {
        if values.len() != self.voxels.len() {
            return Err(ValidationError::MaskValuesLength {
                mask: self.name.clone(),
                mask_voxels: self.voxels.len(),
                values: values.len(),
            });
        }
        let included = self
            .voxels
            .iter()
            .copied()
            .zip(values.iter().copied())
            .filter_map(|(inside, value)| inside.then_some(value));
        let mut sum = 0.0;
        let mut maximum = f64::NEG_INFINITY;
        let mut count = 0_usize;
        for value in included {
            if !value.is_finite() {
                return Err(ValidationError::NonFiniteMaskValue {
                    mask: self.name.clone(),
                });
            }
            sum += value;
            maximum = maximum.max(value);
            count += 1;
        }
        if count == 0 {
            return Err(ValidationError::EmptyMask(self.name.clone()));
        }
        Ok(MaskDoseSummary {
            voxel_count: count,
            mean: sum / count as f64,
            maximum,
        })
    }

    /// Centroid of the included voxels' centers in LPS millimetres.
    ///
    /// `geometry` must describe the grid this mask indexes; the mask must
    /// select at least one voxel.
    pub fn centroid_lps_mm(&self, geometry: &GridGeometry) -> Result<[f64; 3], ValidationError> {
        let total = geometry.voxel_count()?;
        if self.voxels.len() != total {
            return Err(ValidationError::MaskVoxelCountMismatch {
                name: self.name.clone(),
                other: "geometry".into(),
                expected: total,
                actual: self.voxels.len(),
            });
        }
        let nx = geometry.shape[0] as usize;
        let ny = geometry.shape[1] as usize;
        let mut centroid = [0.0_f64; 3];
        let mut count = 0_usize;
        for (index, inside) in self.voxels.iter().copied().enumerate() {
            if !inside {
                continue;
            }
            let voxel = [
                (index % nx) as u32,
                ((index % (nx * ny)) / nx) as u32,
                (index / (nx * ny)) as u32,
            ];
            let center = geometry.voxel_center_lps_mm(voxel)?;
            for axis in 0..3 {
                centroid[axis] += center[axis];
            }
            count += 1;
        }
        if count == 0 {
            return Err(ValidationError::EmptyMask(self.name.clone()));
        }
        for axis in &mut centroid {
            *axis /= count as f64;
        }
        Ok(centroid)
    }
}

/// Mean and maximum of a per-voxel quantity inside a `RegionMask`.
#[derive(Debug, Clone, Copy, PartialEq)]
pub struct MaskDoseSummary {
    pub voxel_count: usize,
    pub mean: f64,
    pub maximum: f64,
}

/// Contract-id namespace emitted by current artifacts.
pub const SCHEMA_PREFIX: &str = "openbnct.";

/// Contract-id namespace used by artifacts written before the project was
/// renamed from NCTForge to OpenBNCT. Such artifacts remain valid inputs and
/// are normalized on read; new artifacts always emit [`SCHEMA_PREFIX`].
pub const LEGACY_SCHEMA_PREFIX: &str = "nctforge.";

/// Hyphenated tool/method-id namespace of the same pre-rename era (e.g.
/// `nctforge-openmc-data-inspector/0.3.0`).
pub const LEGACY_TOOL_PREFIX: &str = "nctforge-";

/// Returns `id` with a legacy `nctforge.`/`nctforge-` contract or tool
/// namespace replaced by the current `openbnct.`/`openbnct-` namespace. Ids
/// without a legacy prefix are returned unchanged.
pub fn normalize_contract_id(id: &str) -> String {
    if let Some(rest) = id.strip_prefix(LEGACY_SCHEMA_PREFIX) {
        return format!("{SCHEMA_PREFIX}{rest}");
    }
    if let Some(rest) = id.strip_prefix(LEGACY_TOOL_PREFIX) {
        return format!("openbnct-{rest}");
    }
    id.to_string()
}

/// True when `actual` identifies the same contract as `expected`, tolerating
/// the legacy `nctforge.` namespace on either side. Use this wherever an
/// externally supplied artifact's `schema_version` is checked, so committed
/// `nctforge.*` evidence remains readable.
pub fn schema_matches(actual: &str, expected: &str) -> bool {
    normalize_contract_id(actual) == normalize_contract_id(expected)
}

/// Serde `deserialize_with` for `schema_version` fields: accepts the legacy
/// `nctforge.` namespace and normalizes it to `openbnct.` in memory, so
/// pre-rename artifacts load into current contracts transparently.
pub fn deserialize_contract_id<'de, D>(deserializer: D) -> Result<String, D::Error>
where
    D: serde::Deserializer<'de>,
{
    Ok(normalize_contract_id(&String::deserialize(deserializer)?))
}

/// Schema identifier carried by every `PhysicalDoseBundle`.
pub const PHYSICAL_DOSE_BUNDLE_SCHEMA: &str = "openbnct.physical-dose-bundle/0.2.0";

#[derive(Debug, Clone, PartialEq, Serialize, Deserialize)]
#[serde(deny_unknown_fields)]
pub struct PhysicalDoseBundle {
    #[serde(deserialize_with = "crate::deserialize_contract_id")]
    pub schema_version: String,
    pub case_id: String,
    pub frame_of_reference_uid: Option<String>,
    pub geometry: GridGeometry,
    pub component_profile: ComponentProfileReference,
    /// Material- and nuclear-data-specific neutron response curves.
    pub response_set: ContentReference,
    pub components: Vec<DoseVolume>,
    /// A dedicated physical total, retained separately from component means.
    pub physical_total: PhysicalTotalDoseVolume,
    /// Identifier of the run manifest that binds inputs, engine, data, and logs.
    pub provenance_id: String,
}

impl PhysicalDoseBundle {
    pub fn validate(&self) -> Result<(), ValidationError> {
        let voxel_count = self.geometry.voxel_count()?;
        for (label, value) in [
            ("schema_version", self.schema_version.as_str()),
            ("case_id", self.case_id.as_str()),
            ("provenance_id", self.provenance_id.as_str()),
        ] {
            if value.trim().is_empty() {
                return Err(ValidationError::EmptyIdentifier(label));
            }
        }
        self.component_profile
            .validate()
            .map_err(|_| ValidationError::InvalidContentReference("component_profile"))?;
        self.response_set
            .validate()
            .map_err(|_| ValidationError::InvalidContentReference("response_set"))?;

        let mut observed = BTreeSet::new();

        for volume in &self.components {
            if !observed.insert(volume.component) {
                return Err(ValidationError::DuplicateComponent(volume.component));
            }
            if volume.values.len() != voxel_count {
                return Err(ValidationError::DoseLength {
                    component: volume.component,
                    expected: voxel_count,
                    actual: volume.values.len(),
                });
            }
            if volume
                .values
                .iter()
                .any(|value| !value.is_finite() || *value < 0.0)
            {
                return Err(ValidationError::InvalidDose(volume.component));
            }
            if volume.unit != self.physical_total.unit {
                return Err(ValidationError::DoseUnitMismatch {
                    component: volume.component,
                    component_unit: volume.unit,
                    total_unit: self.physical_total.unit,
                });
            }
            if let Some(uncertainty) = &volume.absolute_standard_uncertainty {
                if uncertainty.len() != voxel_count {
                    return Err(ValidationError::UncertaintyLength {
                        component: volume.component,
                        expected: voxel_count,
                        actual: uncertainty.len(),
                    });
                }
                if uncertainty
                    .iter()
                    .any(|value| !value.is_finite() || *value < 0.0)
                {
                    return Err(ValidationError::InvalidUncertainty(volume.component));
                }
            }
        }

        for required in DoseComponent::REQUIRED {
            if !observed.contains(&required) {
                return Err(ValidationError::MissingComponent(required));
            }
        }

        if self.physical_total.values.len() != voxel_count {
            return Err(ValidationError::TotalDoseLength {
                expected: voxel_count,
                actual: self.physical_total.values.len(),
            });
        }
        if self
            .physical_total
            .values
            .iter()
            .any(|value| !value.is_finite() || *value < 0.0)
        {
            return Err(ValidationError::InvalidTotalDose);
        }
        if let Some(uncertainty) = &self.physical_total.absolute_standard_uncertainty {
            if uncertainty.len() != voxel_count {
                return Err(ValidationError::TotalUncertaintyLength {
                    expected: voxel_count,
                    actual: uncertainty.len(),
                });
            }
            if uncertainty
                .iter()
                .any(|value| !value.is_finite() || *value < 0.0)
            {
                return Err(ValidationError::InvalidTotalUncertainty);
            }
        }
        match (
            self.physical_total.absolute_standard_uncertainty.is_some(),
            self.physical_total.uncertainty_method,
        ) {
            (false, TotalUncertaintyMethod::Unavailable)
            | (true, TotalUncertaintyMethod::DedicatedEstimator)
            | (true, TotalUncertaintyMethod::BatchCovariance) => {}
            _ => return Err(ValidationError::InconsistentTotalUncertainty),
        }

        Ok(())
    }
}

fn is_canonical_sha256(value: &str) -> bool {
    value.len() == 64
        && value
            .bytes()
            .all(|byte| byte.is_ascii_digit() || (b'a'..=b'f').contains(&byte))
}

#[derive(Debug, Error, PartialEq)]
pub enum ValidationError {
    #[error("voxel grid contains an empty dimension")]
    EmptyGrid,
    #[error("voxel spacing must be finite and greater than zero")]
    InvalidSpacing,
    #[error("voxel geometry contains a non-finite value")]
    NonFiniteGeometry,
    #[error("voxel direction matrix must be right-handed and orthonormal")]
    InvalidDirection,
    #[error("voxel count overflows the addressable platform size")]
    GridTooLarge,
    #[error("voxel {voxel:?} is outside grid shape {shape:?}")]
    VoxelOutOfBounds { voxel: [u32; 3], shape: [u32; 3] },
    #[error("physical dose component {0:?} is missing")]
    MissingComponent(DoseComponent),
    #[error("physical dose component {0:?} occurs more than once")]
    DuplicateComponent(DoseComponent),
    #[error("{component:?} has {actual} dose values; expected {expected}")]
    DoseLength {
        component: DoseComponent,
        expected: usize,
        actual: usize,
    },
    #[error("{0:?} contains a negative or non-finite physical dose")]
    InvalidDose(DoseComponent),
    #[error("{component:?} has {actual} uncertainty values; expected {expected}")]
    UncertaintyLength {
        component: DoseComponent,
        expected: usize,
        actual: usize,
    },
    #[error("{0:?} contains a negative or non-finite uncertainty")]
    InvalidUncertainty(DoseComponent),
    #[error("dose index {index} is outside volume length {length}")]
    DoseIndexOutOfBounds { index: usize, length: usize },
    #[error("required identifier {0} is empty")]
    EmptyIdentifier(&'static str),
    #[error("{0} must have a nonempty ID and canonical lowercase SHA-256 digest")]
    InvalidContentReference(&'static str),
    #[error("{component:?} uses {component_unit:?}, but the physical total uses {total_unit:?}")]
    DoseUnitMismatch {
        component: DoseComponent,
        component_unit: DoseUnit,
        total_unit: DoseUnit,
    },
    #[error("physical total has {actual} dose values; expected {expected}")]
    TotalDoseLength { expected: usize, actual: usize },
    #[error("physical total contains a negative or non-finite dose")]
    InvalidTotalDose,
    #[error("physical total has {actual} uncertainty values; expected {expected}")]
    TotalUncertaintyLength { expected: usize, actual: usize },
    #[error("physical total contains a negative or non-finite uncertainty")]
    InvalidTotalUncertainty,
    #[error("physical-total uncertainty and its method are inconsistent")]
    InconsistentTotalUncertainty,
    #[error(
        "mask {name:?} has {actual} voxels but mask {other:?} has {expected}; masks must share one voxel count"
    )]
    MaskVoxelCountMismatch {
        name: String,
        other: String,
        expected: usize,
        actual: usize,
    },
    #[error("mask {0:?} selects no voxels")]
    EmptyMask(String),
    #[error("threshold window [{minimum}, {maximum}] must be finite with minimum <= maximum")]
    InvalidThresholdWindow { minimum: f64, maximum: f64 },
    #[error("mask {mask:?} covers {mask_voxels} voxels but the values array has {values} entries")]
    MaskValuesLength {
        mask: String,
        mask_voxels: usize,
        values: usize,
    },
    #[error("mask {mask:?} contains a non-finite value")]
    NonFiniteMaskValue { mask: String },
    #[error("dose selection {mask:?} contains a negative or non-finite value at voxel {index}")]
    InvalidMaskedDose { mask: String, index: usize },
    #[error("dose statistic {name} is invalid: {reason}")]
    InvalidStatistic { name: &'static str, reason: String },
}

#[derive(Debug, Error, PartialEq, Eq)]
pub enum ContentReferenceError {
    #[error("content reference ID is empty")]
    EmptyId,
    #[error("content reference SHA-256 must be 64 lowercase hexadecimal characters")]
    InvalidSha256,
}

#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn legacy_nctforge_contract_ids_match_current_schemas() {
        assert!(schema_matches(
            "nctforge.physical-dose-bundle/0.2.0",
            PHYSICAL_DOSE_BUNDLE_SCHEMA
        ));
        assert!(schema_matches(
            PHYSICAL_DOSE_BUNDLE_SCHEMA,
            "nctforge.physical-dose-bundle/0.2.0"
        ));
        assert!(!schema_matches(
            "nctforge.physical-dose-bundle/0.1.0",
            PHYSICAL_DOSE_BUNDLE_SCHEMA
        ));
        assert!(!schema_matches(
            "other.physical-dose-bundle/0.2.0",
            PHYSICAL_DOSE_BUNDLE_SCHEMA
        ));
        assert_eq!(
            normalize_contract_id("nctforge.registration/0.1.0"),
            "openbnct.registration/0.1.0"
        );
        assert_eq!(
            normalize_contract_id("openbnct.registration/0.1.0"),
            "openbnct.registration/0.1.0"
        );
    }

    #[test]
    fn legacy_schema_version_is_accepted_on_read() {
        let mut bundle = valid_bundle();
        bundle.schema_version = "nctforge.physical-dose-bundle/0.2.0".into();
        assert!(bundle.validate().is_ok());
    }

    fn geometry() -> GridGeometry {
        GridGeometry {
            shape: [2, 2, 1],
            spacing_mm: [1.0, 1.0, 2.0],
            origin_mm: [0.0; 3],
            direction: [1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0],
        }
    }

    fn volume(component: DoseComponent) -> DoseVolume {
        DoseVolume {
            component,
            unit: DoseUnit::GrayPerSourceParticle,
            values: vec![1.0; 4],
            absolute_standard_uncertainty: Some(vec![0.1; 4]),
        }
    }

    fn valid_bundle() -> PhysicalDoseBundle {
        PhysicalDoseBundle {
            schema_version: PHYSICAL_DOSE_BUNDLE_SCHEMA.into(),
            case_id: "synthetic".into(),
            frame_of_reference_uid: None,
            geometry: geometry(),
            component_profile: ComponentProfileReference {
                id: "openbnct.macroscopic-absorbed-dose.v1".into(),
                sha256: "a".repeat(64),
            },
            response_set: ContentReference {
                id: "openbnct.synthetic-response-set.v1".into(),
                sha256: "b".repeat(64),
            },
            components: DoseComponent::REQUIRED.into_iter().map(volume).collect(),
            physical_total: PhysicalTotalDoseVolume {
                unit: DoseUnit::GrayPerSourceParticle,
                values: vec![4.0; 4],
                absolute_standard_uncertainty: Some(vec![0.2; 4]),
                uncertainty_method: TotalUncertaintyMethod::DedicatedEstimator,
            },
            provenance_id: "manifest-sha256:synthetic".into(),
        }
    }

    #[test]
    fn rejects_incomplete_component_bundle() {
        let mut bundle = valid_bundle();
        bundle.components.clear();

        assert_eq!(
            bundle.validate(),
            Err(ValidationError::MissingComponent(DoseComponent::Boron))
        );
    }

    #[test]
    fn rejects_non_orthonormal_grid_direction() {
        let mut invalid = geometry();
        invalid.direction[4] = 2.0;
        assert_eq!(
            invalid.voxel_count(),
            Err(ValidationError::InvalidDirection)
        );
    }

    #[test]
    fn validates_complete_physical_dose_contract() {
        assert_eq!(valid_bundle().validate(), Ok(()));
    }

    #[test]
    fn serializes_only_canonical_component_names() {
        assert_eq!(
            serde_json::to_string(&DoseComponent::Hydrogen).unwrap(),
            "\"hydrogen\""
        );
        assert!(serde_json::from_str::<DoseComponent>("\"hydrogen_recoil\"").is_err());
    }

    #[test]
    fn derives_relative_uncertainty_but_not_for_zero_mean() {
        let volume = DoseVolume {
            component: DoseComponent::Boron,
            unit: DoseUnit::Gray,
            values: vec![0.0, 2.0],
            absolute_standard_uncertainty: Some(vec![0.1, 0.2]),
        };

        assert_eq!(volume.relative_standard_uncertainty(0), Ok(None));
        let relative = volume.relative_standard_uncertainty(1).unwrap().unwrap();
        assert!((relative - 0.1).abs() < f64::EPSILON);
    }

    #[test]
    fn rejects_mixed_component_and_total_units() {
        let mut bundle = valid_bundle();
        bundle.components[0].unit = DoseUnit::Gray;

        assert_eq!(
            bundle.validate(),
            Err(ValidationError::DoseUnitMismatch {
                component: DoseComponent::Boron,
                component_unit: DoseUnit::Gray,
                total_unit: DoseUnit::GrayPerSourceParticle,
            })
        );
    }

    #[test]
    fn requires_consistent_total_uncertainty_state() {
        let mut bundle = valid_bundle();
        bundle.physical_total.uncertainty_method = TotalUncertaintyMethod::Unavailable;

        assert_eq!(
            bundle.validate(),
            Err(ValidationError::InconsistentTotalUncertainty)
        );
    }

    #[test]
    fn rejects_noncanonical_component_profile_hash() {
        let mut bundle = valid_bundle();
        bundle.component_profile.sha256 = "A".repeat(64);

        assert_eq!(
            bundle.validate(),
            Err(ValidationError::InvalidContentReference(
                "component_profile"
            ))
        );
    }

    #[test]
    fn rejects_noncanonical_response_set_hash() {
        let mut bundle = valid_bundle();
        bundle.response_set.sha256 = "B".repeat(64);

        assert_eq!(
            bundle.validate(),
            Err(ValidationError::InvalidContentReference("response_set"))
        );
    }

    fn mask(name: &str, voxels: &[bool]) -> RegionMask {
        RegionMask {
            name: name.into(),
            voxels: voxels.to_vec(),
        }
    }

    #[test]
    fn mask_subtract_removes_shared_voxels() {
        let organ = mask("ORGAN", &[true, true, true, true]);
        let tumor = mask("TUMOR", &[false, true, true, false]);

        let limited = organ.subtract(&tumor, "ORGAN-T").unwrap();

        assert_eq!(limited.name, "ORGAN-T");
        assert_eq!(limited.voxels, vec![true, false, false, true]);
        assert_eq!(limited.included_voxel_count(), 2);
    }

    #[test]
    fn mask_union_and_intersection() {
        let a = mask("A", &[true, true, false, false]);
        let b = mask("B", &[false, true, true, false]);

        assert_eq!(
            a.union(&b, "U").unwrap().voxels,
            vec![true, true, true, false]
        );
        assert_eq!(
            a.intersection(&b, "I").unwrap().voxels,
            vec![false, true, false, false]
        );
    }

    #[test]
    fn mask_ops_reject_frame_mismatch() {
        let a = mask("A", &[true; 4]);
        let b = mask("B", &[true; 8]);

        assert_eq!(
            a.union(&b, "U"),
            Err(ValidationError::MaskVoxelCountMismatch {
                name: "A".into(),
                other: "B".into(),
                expected: 4,
                actual: 8,
            })
        );
    }

    #[test]
    fn mask_ops_reject_empty_result() {
        let a = mask("A", &[true, true, false, false]);
        let b = mask("B", &[false, false, true, true]);

        assert_eq!(
            a.intersection(&b, "I"),
            Err(ValidationError::EmptyMask("I".into()))
        );
        assert_eq!(
            a.subtract(&a.clone(), "E"),
            Err(ValidationError::EmptyMask("E".into()))
        );
    }
}