kfb2zarr 0.1.2

Convert KFBio whole slide images (.kfb, .kfbf) to OME-Zarr
Documentation 
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use zune_core::colorspace::ColorSpace;
use zune_core::options::DecoderOptions;
use zune_jpeg::JpegDecoder;

use crate::error::KfbError;

fn decode_jpeg_as(
    data: &[u8],
    colorspace: ColorSpace,
) -> Result<(Vec<u8>, usize, usize), KfbError> {
    let options = DecoderOptions::default()
        .jpeg_set_out_colorspace(colorspace)
        .set_strict_mode(false);
    let mut decoder = JpegDecoder::new_with_options(data, options);
    let pixels = decoder
        .decode()
        .map_err(|e| KfbError::JpegDecode(format!("{e:?}")))?;
    let info = decoder
        .info()
        .ok_or_else(|| KfbError::JpegDecode("no image info after decode".into()))?;
    Ok((pixels, info.width as usize, info.height as usize))
}

/// Decode a JPEG-compressed byte slice into packed RGB pixels.
///
/// Returns a tuple of `(pixels, width, height)` where `pixels` is a `Vec<u8>`
/// of length `width * height * 3` in row-major, interleaved RGB order.
///
/// # Errors
///
/// Returns [`KfbError::JpegDecode`] if the data is not valid JPEG or if image
/// metadata cannot be retrieved after decoding.
pub(crate) fn decode_jpeg(data: &[u8]) -> Result<(Vec<u8>, usize, usize), KfbError> {
    decode_jpeg_as(data, ColorSpace::RGB)
}

pub(crate) fn decode_jpeg_luma(data: &[u8]) -> Result<(Vec<u8>, usize, usize), KfbError> {
    decode_jpeg_as(data, ColorSpace::Luma)
}

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

    #[test]
    fn decode_jpeg_returns_rgb_pixels() {
        // Valid 1x1 RGB JPEG (red pixel, generated with Pillow)
        let jpeg: &[u8] = &[
            0xFF, 0xD8, 0xFF, 0xE0, 0x00, 0x10, 0x4A, 0x46, 0x49, 0x46, 0x00, 0x01, 0x01, 0x00,
            0x00, 0x01, 0x00, 0x01, 0x00, 0x00, 0xFF, 0xDB, 0x00, 0x43, 0x00, 0x02, 0x01, 0x01,
            0x01, 0x01, 0x01, 0x02, 0x01, 0x01, 0x01, 0x02, 0x02, 0x02, 0x02, 0x02, 0x04, 0x03,
            0x02, 0x02, 0x02, 0x02, 0x05, 0x04, 0x04, 0x03, 0x04, 0x06, 0x05, 0x06, 0x06, 0x06,
            0x05, 0x06, 0x06, 0x06, 0x07, 0x09, 0x08, 0x06, 0x07, 0x09, 0x07, 0x06, 0x06, 0x08,
            0x0B, 0x08, 0x09, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x06, 0x08, 0x0B, 0x0C, 0x0B, 0x0A,
            0x0C, 0x09, 0x0A, 0x0A, 0x0A, 0xFF, 0xDB, 0x00, 0x43, 0x01, 0x02, 0x02, 0x02, 0x02,
            0x02, 0x02, 0x05, 0x03, 0x03, 0x05, 0x0A, 0x07, 0x06, 0x07, 0x0A, 0x0A, 0x0A, 0x0A,
            0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A,
            0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A,
            0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A,
            0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0xFF, 0xC0, 0x00, 0x11, 0x08, 0x00, 0x01, 0x00, 0x01,
            0x03, 0x01, 0x22, 0x00, 0x02, 0x11, 0x01, 0x03, 0x11, 0x01, 0xFF, 0xC4, 0x00, 0x1F,
            0x00, 0x00, 0x01, 0x05, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x00, 0x00, 0x00, 0x00,
            0x00, 0x00, 0x00, 0x00, 0x01, 0x02, 0x03, 0x04, 0x05, 0x06, 0x07, 0x08, 0x09, 0x0A,
            0x0B, 0xFF, 0xC4, 0x00, 0xB5, 0x10, 0x00, 0x02, 0x01, 0x03, 0x03, 0x02, 0x04, 0x03,
            0x05, 0x05, 0x04, 0x04, 0x00, 0x00, 0x01, 0x7D, 0x01, 0x02, 0x03, 0x00, 0x04, 0x11,
            0x05, 0x12, 0x21, 0x31, 0x41, 0x06, 0x13, 0x51, 0x61, 0x07, 0x22, 0x71, 0x14, 0x32,
            0x81, 0x91, 0xA1, 0x08, 0x23, 0x42, 0xB1, 0xC1, 0x15, 0x52, 0xD1, 0xF0, 0x24, 0x33,
            0x62, 0x72, 0x82, 0x09, 0x0A, 0x16, 0x17, 0x18, 0x19, 0x1A, 0x25, 0x26, 0x27, 0x28,
            0x29, 0x2A, 0x34, 0x35, 0x36, 0x37, 0x38, 0x39, 0x3A, 0x43, 0x44, 0x45, 0x46, 0x47,
            0x48, 0x49, 0x4A, 0x53, 0x54, 0x55, 0x56, 0x57, 0x58, 0x59, 0x5A, 0x63, 0x64, 0x65,
            0x66, 0x67, 0x68, 0x69, 0x6A, 0x73, 0x74, 0x75, 0x76, 0x77, 0x78, 0x79, 0x7A, 0x83,
            0x84, 0x85, 0x86, 0x87, 0x88, 0x89, 0x8A, 0x92, 0x93, 0x94, 0x95, 0x96, 0x97, 0x98,
            0x99, 0x9A, 0xA2, 0xA3, 0xA4, 0xA5, 0xA6, 0xA7, 0xA8, 0xA9, 0xAA, 0xB2, 0xB3, 0xB4,
            0xB5, 0xB6, 0xB7, 0xB8, 0xB9, 0xBA, 0xC2, 0xC3, 0xC4, 0xC5, 0xC6, 0xC7, 0xC8, 0xC9,
            0xCA, 0xD2, 0xD3, 0xD4, 0xD5, 0xD6, 0xD7, 0xD8, 0xD9, 0xDA, 0xE1, 0xE2, 0xE3, 0xE4,
            0xE5, 0xE6, 0xE7, 0xE8, 0xE9, 0xEA, 0xF1, 0xF2, 0xF3, 0xF4, 0xF5, 0xF6, 0xF7, 0xF8,
            0xF9, 0xFA, 0xFF, 0xC4, 0x00, 0x1F, 0x01, 0x00, 0x03, 0x01, 0x01, 0x01, 0x01, 0x01,
            0x01, 0x01, 0x01, 0x01, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x01, 0x02, 0x03, 0x04,
            0x05, 0x06, 0x07, 0x08, 0x09, 0x0A, 0x0B, 0xFF, 0xC4, 0x00, 0xB5, 0x11, 0x00, 0x02,
            0x01, 0x02, 0x04, 0x04, 0x03, 0x04, 0x07, 0x05, 0x04, 0x04, 0x00, 0x01, 0x02, 0x77,
            0x00, 0x01, 0x02, 0x03, 0x11, 0x04, 0x05, 0x21, 0x31, 0x06, 0x12, 0x41, 0x51, 0x07,
            0x61, 0x71, 0x13, 0x22, 0x32, 0x81, 0x08, 0x14, 0x42, 0x91, 0xA1, 0xB1, 0xC1, 0x09,
            0x23, 0x33, 0x52, 0xF0, 0x15, 0x62, 0x72, 0xD1, 0x0A, 0x16, 0x24, 0x34, 0xE1, 0x25,
            0xF1, 0x17, 0x18, 0x19, 0x1A, 0x26, 0x27, 0x28, 0x29, 0x2A, 0x35, 0x36, 0x37, 0x38,
            0x39, 0x3A, 0x43, 0x44, 0x45, 0x46, 0x47, 0x48, 0x49, 0x4A, 0x53, 0x54, 0x55, 0x56,
            0x57, 0x58, 0x59, 0x5A, 0x63, 0x64, 0x65, 0x66, 0x67, 0x68, 0x69, 0x6A, 0x73, 0x74,
            0x75, 0x76, 0x77, 0x78, 0x79, 0x7A, 0x82, 0x83, 0x84, 0x85, 0x86, 0x87, 0x88, 0x89,
            0x8A, 0x92, 0x93, 0x94, 0x95, 0x96, 0x97, 0x98, 0x99, 0x9A, 0xA2, 0xA3, 0xA4, 0xA5,
            0xA6, 0xA7, 0xA8, 0xA9, 0xAA, 0xB2, 0xB3, 0xB4, 0xB5, 0xB6, 0xB7, 0xB8, 0xB9, 0xBA,
            0xC2, 0xC3, 0xC4, 0xC5, 0xC6, 0xC7, 0xC8, 0xC9, 0xCA, 0xD2, 0xD3, 0xD4, 0xD5, 0xD6,
            0xD7, 0xD8, 0xD9, 0xDA, 0xE2, 0xE3, 0xE4, 0xE5, 0xE6, 0xE7, 0xE8, 0xE9, 0xEA, 0xF2,
            0xF3, 0xF4, 0xF5, 0xF6, 0xF7, 0xF8, 0xF9, 0xFA, 0xFF, 0xDA, 0x00, 0x0C, 0x03, 0x01,
            0x00, 0x02, 0x11, 0x03, 0x11, 0x00, 0x3F, 0x00, 0xF8, 0xBE, 0x8A, 0x28, 0xAF, 0xE5,
            0x33, 0xFD, 0xFC, 0x3F, 0xFF, 0xD9,
        ];
        let (pixels, width, height) = decode_jpeg(jpeg).unwrap();
        assert_eq!(width, 1);
        assert_eq!(height, 1);
        assert_eq!(pixels.len(), 3);
    }

    #[test]
    fn decode_jpeg_luma_returns_single_channel_pixels() {
        // Same 1x1 RGB JPEG as above, decoded to luminance.
        let jpeg: &[u8] = &[
            0xFF, 0xD8, 0xFF, 0xE0, 0x00, 0x10, 0x4A, 0x46, 0x49, 0x46, 0x00, 0x01, 0x01, 0x00,
            0x00, 0x01, 0x00, 0x01, 0x00, 0x00, 0xFF, 0xDB, 0x00, 0x43, 0x00, 0x02, 0x01, 0x01,
            0x01, 0x01, 0x01, 0x02, 0x01, 0x01, 0x01, 0x02, 0x02, 0x02, 0x02, 0x02, 0x04, 0x03,
            0x02, 0x02, 0x02, 0x02, 0x05, 0x04, 0x04, 0x03, 0x04, 0x06, 0x05, 0x06, 0x06, 0x06,
            0x05, 0x06, 0x06, 0x06, 0x07, 0x09, 0x08, 0x06, 0x07, 0x09, 0x07, 0x06, 0x06, 0x08,
            0x0B, 0x08, 0x09, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x06, 0x08, 0x0B, 0x0C, 0x0B, 0x0A,
            0x0C, 0x09, 0x0A, 0x0A, 0x0A, 0xFF, 0xDB, 0x00, 0x43, 0x01, 0x02, 0x02, 0x02, 0x02,
            0x02, 0x02, 0x05, 0x03, 0x03, 0x05, 0x0A, 0x07, 0x06, 0x07, 0x0A, 0x0A, 0x0A, 0x0A,
            0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A,
            0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A,
            0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0x0A,
            0x0A, 0x0A, 0x0A, 0x0A, 0x0A, 0xFF, 0xC0, 0x00, 0x11, 0x08, 0x00, 0x01, 0x00, 0x01,
            0x03, 0x01, 0x22, 0x00, 0x02, 0x11, 0x01, 0x03, 0x11, 0x01, 0xFF, 0xC4, 0x00, 0x1F,
            0x00, 0x00, 0x01, 0x05, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x00, 0x00, 0x00, 0x00,
            0x00, 0x00, 0x00, 0x00, 0x01, 0x02, 0x03, 0x04, 0x05, 0x06, 0x07, 0x08, 0x09, 0x0A,
            0x0B, 0xFF, 0xC4, 0x00, 0xB5, 0x10, 0x00, 0x02, 0x01, 0x03, 0x03, 0x02, 0x04, 0x03,
            0x05, 0x05, 0x04, 0x04, 0x00, 0x00, 0x01, 0x7D, 0x01, 0x02, 0x03, 0x00, 0x04, 0x11,
            0x05, 0x12, 0x21, 0x31, 0x41, 0x06, 0x13, 0x51, 0x61, 0x07, 0x22, 0x71, 0x14, 0x32,
            0x81, 0x91, 0xA1, 0x08, 0x23, 0x42, 0xB1, 0xC1, 0x15, 0x52, 0xD1, 0xF0, 0x24, 0x33,
            0x62, 0x72, 0x82, 0x09, 0x0A, 0x16, 0x17, 0x18, 0x19, 0x1A, 0x25, 0x26, 0x27, 0x28,
            0x29, 0x2A, 0x34, 0x35, 0x36, 0x37, 0x38, 0x39, 0x3A, 0x43, 0x44, 0x45, 0x46, 0x47,
            0x48, 0x49, 0x4A, 0x53, 0x54, 0x55, 0x56, 0x57, 0x58, 0x59, 0x5A, 0x63, 0x64, 0x65,
            0x66, 0x67, 0x68, 0x69, 0x6A, 0x73, 0x74, 0x75, 0x76, 0x77, 0x78, 0x79, 0x7A, 0x83,
            0x84, 0x85, 0x86, 0x87, 0x88, 0x89, 0x8A, 0x92, 0x93, 0x94, 0x95, 0x96, 0x97, 0x98,
            0x99, 0x9A, 0xA2, 0xA3, 0xA4, 0xA5, 0xA6, 0xA7, 0xA8, 0xA9, 0xAA, 0xB2, 0xB3, 0xB4,
            0xB5, 0xB6, 0xB7, 0xB8, 0xB9, 0xBA, 0xC2, 0xC3, 0xC4, 0xC5, 0xC6, 0xC7, 0xC8, 0xC9,
            0xCA, 0xD2, 0xD3, 0xD4, 0xD5, 0xD6, 0xD7, 0xD8, 0xD9, 0xDA, 0xE1, 0xE2, 0xE3, 0xE4,
            0xE5, 0xE6, 0xE7, 0xE8, 0xE9, 0xEA, 0xF1, 0xF2, 0xF3, 0xF4, 0xF5, 0xF6, 0xF7, 0xF8,
            0xF9, 0xFA, 0xFF, 0xC4, 0x00, 0x1F, 0x01, 0x00, 0x03, 0x01, 0x01, 0x01, 0x01, 0x01,
            0x01, 0x01, 0x01, 0x01, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x01, 0x02, 0x03, 0x04,
            0x05, 0x06, 0x07, 0x08, 0x09, 0x0A, 0x0B, 0xFF, 0xC4, 0x00, 0xB5, 0x11, 0x00, 0x02,
            0x01, 0x02, 0x04, 0x04, 0x03, 0x04, 0x07, 0x05, 0x04, 0x04, 0x00, 0x01, 0x02, 0x77,
            0x00, 0x01, 0x02, 0x03, 0x11, 0x04, 0x05, 0x21, 0x31, 0x06, 0x12, 0x41, 0x51, 0x07,
            0x61, 0x71, 0x13, 0x22, 0x32, 0x81, 0x08, 0x14, 0x42, 0x91, 0xA1, 0xB1, 0xC1, 0x09,
            0x23, 0x33, 0x52, 0xF0, 0x15, 0x62, 0x72, 0xD1, 0x0A, 0x16, 0x24, 0x34, 0xE1, 0x25,
            0xF1, 0x17, 0x18, 0x19, 0x1A, 0x26, 0x27, 0x28, 0x29, 0x2A, 0x35, 0x36, 0x37, 0x38,
            0x39, 0x3A, 0x43, 0x44, 0x45, 0x46, 0x47, 0x48, 0x49, 0x4A, 0x53, 0x54, 0x55, 0x56,
            0x57, 0x58, 0x59, 0x5A, 0x63, 0x64, 0x65, 0x66, 0x67, 0x68, 0x69, 0x6A, 0x73, 0x74,
            0x75, 0x76, 0x77, 0x78, 0x79, 0x7A, 0x82, 0x83, 0x84, 0x85, 0x86, 0x87, 0x88, 0x89,
            0x8A, 0x92, 0x93, 0x94, 0x95, 0x96, 0x97, 0x98, 0x99, 0x9A, 0xA2, 0xA3, 0xA4, 0xA5,
            0xA6, 0xA7, 0xA8, 0xA9, 0xAA, 0xB2, 0xB3, 0xB4, 0xB5, 0xB6, 0xB7, 0xB8, 0xB9, 0xBA,
            0xC2, 0xC3, 0xC4, 0xC5, 0xC6, 0xC7, 0xC8, 0xC9, 0xCA, 0xD2, 0xD3, 0xD4, 0xD5, 0xD6,
            0xD7, 0xD8, 0xD9, 0xDA, 0xE2, 0xE3, 0xE4, 0xE5, 0xE6, 0xE7, 0xE8, 0xE9, 0xEA, 0xF2,
            0xF3, 0xF4, 0xF5, 0xF6, 0xF7, 0xF8, 0xF9, 0xFA, 0xFF, 0xDA, 0x00, 0x0C, 0x03, 0x01,
            0x00, 0x02, 0x11, 0x03, 0x11, 0x00, 0x3F, 0x00, 0xF8, 0xBE, 0x8A, 0x28, 0xAF, 0xE5,
            0x33, 0xFD, 0xFC, 0x3F, 0xFF, 0xD9,
        ];
        let (pixels, width, height) = decode_jpeg_luma(jpeg).unwrap();
        assert_eq!(width, 1);
        assert_eq!(height, 1);
        assert_eq!(pixels.len(), 1);
    }
}