hdf5-reader 0.6.1

pub mod deflate;
pub mod fletcher32;
#[cfg(feature = "lz4")]
pub mod lz4;
pub mod nbit;
pub mod scaleoffset;
pub mod shuffle;

use std::collections::HashMap;

use crate::error::{Error, Result};
use crate::messages::filter_pipeline::FilterDescription;

/// Standard HDF5 filter IDs.
pub const FILTER_DEFLATE: u16 = 1;
pub const FILTER_SHUFFLE: u16 = 2;
pub const FILTER_FLETCHER32: u16 = 3;
pub const FILTER_SZIP: u16 = 4;
pub const FILTER_NBIT: u16 = 5;
pub const FILTER_SCALEOFFSET: u16 = 6;
/// HDF5 registered LZ4 filter.
pub const FILTER_LZ4: u16 = 32004;

/// A user-supplied filter function.
///
/// Takes the filter description, input data, and element size, then returns
/// the decoded output.
pub type FilterFn = Box<dyn Fn(&FilterDescription, &[u8], usize) -> Result<Vec<u8>> + Send + Sync>;

enum FilterImplementation {
    Builtin,
    Custom(FilterFn),
}

/// A registry of filter implementations.
///
/// Comes pre-loaded with deflate, shuffle, and fletcher32. Users can register
/// additional filters (e.g., Blosc, LZ4, ZFP) before reading datasets.
pub struct FilterRegistry {
    filters: HashMap<u16, FilterImplementation>,
}

impl FilterRegistry {
    /// Create a new registry with the built-in filters pre-registered.
    pub fn new() -> Self {
        let mut registry = FilterRegistry {
            filters: HashMap::new(),
        };
        registry.register_builtin(FILTER_DEFLATE);
        registry.register_builtin(FILTER_SHUFFLE);
        registry.register_builtin(FILTER_FLETCHER32);
        registry.register_builtin(FILTER_NBIT);
        registry.register_builtin(FILTER_SCALEOFFSET);
        #[cfg(feature = "lz4")]
        registry.register_builtin(FILTER_LZ4);
        registry
    }

    fn register_builtin(&mut self, id: u16) {
        self.filters.insert(id, FilterImplementation::Builtin);
    }

    /// Register a custom filter implementation for the given filter ID.
    ///
    /// Overwrites any previously registered filter with the same ID.
    pub fn register(&mut self, id: u16, f: FilterFn) {
        self.filters.insert(id, FilterImplementation::Custom(f));
    }

    /// Apply a single filter by ID.
    pub fn apply(
        &self,
        filter: &FilterDescription,
        data: &[u8],
        element_size: usize,
    ) -> Result<Vec<u8>> {
        self.apply_with_limit(filter, data, element_size, None)
    }

    /// Apply a single filter by ID, passing a maximum decoded output length to
    /// built-in filters that can enforce it while decoding.
    pub fn apply_with_limit(
        &self,
        filter: &FilterDescription,
        data: &[u8],
        element_size: usize,
        max_output_len: Option<usize>,
    ) -> Result<Vec<u8>> {
        match self.filters.get(&filter.id) {
            Some(FilterImplementation::Builtin) => {
                apply_builtin_filter_with_limit(filter, data, element_size, max_output_len)
            }
            Some(FilterImplementation::Custom(f)) => f(filter, data, element_size),
            None => Err(Error::UnsupportedFilter(format!("filter id {}", filter.id))),
        }
    }
}

impl Default for FilterRegistry {
    fn default() -> Self {
        Self::new()
    }
}

/// Apply the filter pipeline in reverse (decompression direction) to a chunk.
///
/// HDF5 stores filters in the order they were applied during writing.
/// On read, we apply them in reverse order.
///
/// If `registry` is `None`, the built-in filter set is used.
///
/// `filter_mask` is a bitmask where bit N being set means filter N should be skipped.
pub fn apply_pipeline(
    data: &[u8],
    filters: &[FilterDescription],
    filter_mask: u32,
    element_size: usize,
    registry: Option<&FilterRegistry>,
) -> Result<Vec<u8>> {
    apply_pipeline_with_limit(data, filters, filter_mask, element_size, registry, None)
}

/// Apply the filter pipeline in reverse (decompression direction) to a chunk,
/// passing a maximum decoded output length to built-in filters that support
/// bounded decompression.
pub fn apply_pipeline_with_limit(
    data: &[u8],
    filters: &[FilterDescription],
    filter_mask: u32,
    element_size: usize,
    registry: Option<&FilterRegistry>,
    max_output_len: Option<usize>,
) -> Result<Vec<u8>> {
    // Count active filters so an all-skipped pipeline can avoid the loop.
    let active_count = filters
        .iter()
        .enumerate()
        .rev()
        .filter(|(i, _)| filter_mask & (1 << i) == 0)
        .count();

    if active_count == 0 {
        validate_output_limit("filter pipeline", data.len(), max_output_len)?;
        return Ok(data.to_vec());
    }

    // For a single active filter, avoid the double-buffer loop overhead.
    if active_count == 1 {
        for (i, filter) in filters.iter().enumerate().rev() {
            if filter_mask & (1 << i) != 0 {
                continue;
            }
            let output = if let Some(reg) = registry {
                reg.apply_with_limit(filter, data, element_size, max_output_len)?
            } else {
                apply_builtin_filter_with_limit(filter, data, element_size, max_output_len)?
            };
            validate_output_limit("filter pipeline", output.len(), max_output_len)?;
            return Ok(output);
        }
    }

    // Multi-filter pipeline: the first stage reads from the borrowed input
    // slice (avoiding a copy), subsequent stages consume the previous output.
    // Each filter stage necessarily allocates (output sizes are unpredictable),
    // but we avoid the initial data.to_vec() copy.
    let mut owned: Option<Vec<u8>> = None;

    for (i, filter) in filters.iter().enumerate().rev() {
        if filter_mask & (1 << i) != 0 {
            continue;
        }

        let input: &[u8] = match &owned {
            Some(buf) => buf,
            None => data,
        };

        owned = Some(if let Some(reg) = registry {
            reg.apply_with_limit(filter, input, element_size, max_output_len)?
        } else {
            apply_builtin_filter_with_limit(filter, input, element_size, max_output_len)?
        });
    }

    let output = owned.unwrap_or_else(|| data.to_vec());
    validate_output_limit("filter pipeline", output.len(), max_output_len)?;
    Ok(output)
}

fn apply_builtin_filter_with_limit(
    filter: &FilterDescription,
    data: &[u8],
    element_size: usize,
    max_output_len: Option<usize>,
) -> Result<Vec<u8>> {
    match filter.id {
        FILTER_DEFLATE => match max_output_len {
            Some(max_output_len) => deflate::decompress_with_limit(data, max_output_len),
            None => deflate::decompress(data),
        },
        FILTER_SHUFFLE => Ok(shuffle::unshuffle(data, element_size)),
        FILTER_FLETCHER32 => fletcher32::verify_and_strip(data),
        FILTER_SZIP => Err(Error::UnsupportedFilter("szip".into())),
        FILTER_NBIT => match max_output_len {
            Some(max_output_len) => {
                nbit::decompress_with_limit(data, &filter.client_data, max_output_len)
            }
            None => nbit::decompress(data, &filter.client_data),
        },
        FILTER_SCALEOFFSET => match max_output_len {
            Some(max_output_len) => {
                scaleoffset::decompress_with_limit(data, &filter.client_data, max_output_len)
            }
            None => scaleoffset::decompress(data, &filter.client_data),
        },
        #[cfg(feature = "lz4")]
        FILTER_LZ4 => match max_output_len {
            Some(max_output_len) => lz4::decompress_with_limit(data, max_output_len),
            None => lz4::decompress(data),
        },
        id => Err(Error::UnsupportedFilter(format!("filter id {}", id))),
    }
}

fn validate_output_limit(context: &str, len: usize, max_output_len: Option<usize>) -> Result<()> {
    if let Some(max_output_len) = max_output_len {
        if len > max_output_len {
            return Err(Error::DecompressionError(format!(
                "{context} decoded to {len} bytes, limit {max_output_len}"
            )));
        }
    }
    Ok(())
}

#[cfg(test)]
mod tests {
    use super::*;
    use flate2::write::ZlibEncoder;
    use flate2::Compression;
    use std::io::Write;

    #[test]
    fn filter_registry_default() {
        let registry = FilterRegistry::new();
        // Built-in filters should be registered
        assert!(registry.filters.contains_key(&FILTER_DEFLATE));
        assert!(registry.filters.contains_key(&FILTER_SHUFFLE));
        assert!(registry.filters.contains_key(&FILTER_FLETCHER32));
        assert!(registry.filters.contains_key(&FILTER_NBIT));
        assert!(registry.filters.contains_key(&FILTER_SCALEOFFSET));
    }

    #[test]
    fn filter_registry_custom() {
        let mut registry = FilterRegistry::new();
        // Register a no-op custom filter
        registry.register(32000, Box::new(|_, data, _| Ok(data.to_vec())));
        let filter = FilterDescription {
            id: 32000,
            name: None,
            client_data: Vec::new(),
        };
        let result = registry.apply(&filter, &[1, 2, 3], 1).unwrap();
        assert_eq!(result, vec![1, 2, 3]);
    }

    #[test]
    fn filter_registry_unknown() {
        let registry = FilterRegistry::new();
        let filter = FilterDescription {
            id: 9999,
            name: None,
            client_data: Vec::new(),
        };
        let err = registry.apply(&filter, &[1, 2, 3], 1).unwrap_err();
        assert!(matches!(err, Error::UnsupportedFilter(_)));
    }

    #[test]
    fn apply_pipeline_with_limit_caps_registry_deflate_output() {
        let original = vec![0u8; 4096];
        let mut encoder = ZlibEncoder::new(Vec::new(), Compression::default());
        encoder.write_all(&original).unwrap();
        let compressed = encoder.finish().unwrap();
        let filter = FilterDescription {
            id: FILTER_DEFLATE,
            name: None,
            client_data: vec![6],
        };
        let registry = FilterRegistry::new();

        let decoded =
            apply_pipeline_with_limit(&compressed, &[filter], 0, 1, Some(&registry), Some(65))
                .unwrap();

        assert_eq!(decoded.len(), 65);
        assert_eq!(decoded, original[..65]);
    }

    #[test]
    fn apply_pipeline_with_limit_rejects_oversized_final_output() {
        let filter = FilterDescription {
            id: FILTER_SHUFFLE,
            name: None,
            client_data: Vec::new(),
        };

        let err =
            apply_pipeline_with_limit(&[1, 2, 3, 4], &[filter], 0, 1, None, Some(3)).unwrap_err();

        assert!(err.to_string().contains("limit 3"));
    }
}