rustdf 0.4.1

use byteorder::{ByteOrder, LittleEndian};
use mscore::timstof::frame::TimsFrame;
use rayon::iter::IntoParallelRefIterator;
use rayon::prelude::*;
use rayon::ThreadPoolBuilder;
use std::io;
use std::io::{Read, Write};

/// Decompresses a ZSTD compressed byte array
///
/// # Arguments
///
/// * `compressed_data` - A byte slice that holds the compressed data
///
/// # Returns
///
/// * `decompressed_data` - A vector of u8 that holds the decompressed data
///
pub fn zstd_decompress(compressed_data: &[u8]) -> io::Result<Vec<u8>> {
    let mut decoder = zstd::Decoder::new(compressed_data)?;
    let mut decompressed_data = Vec::new();
    decoder.read_to_end(&mut decompressed_data)?;
    Ok(decompressed_data)
}

/// Compresses a byte array using ZSTD
///
/// # Arguments
///
/// * `decompressed_data` - A byte slice that holds the decompressed data
///
/// # Returns
///
/// * `compressed_data` - A vector of u8 that holds the compressed data
///
pub fn zstd_compress(decompressed_data: &[u8], compression_level: i32) -> io::Result<Vec<u8>> {
    let mut encoder = zstd::Encoder::new(Vec::new(), compression_level)?;
    encoder.write_all(decompressed_data)?;
    let compressed_data = encoder.finish()?;
    Ok(compressed_data)
}

pub fn reconstruct_compressed_data(
    scans: Vec<u32>,
    mut tofs: Vec<u32>,
    intensities: Vec<u32>,
    total_scans: u32,
    compression_level: i32,
) -> Result<Vec<u8>, Box<dyn std::error::Error>> {
    // Ensuring all vectors have the same length
    assert_eq!(scans.len(), tofs.len());
    assert_eq!(scans.len(), intensities.len());

    // Modify TOFs based on scans
    modify_tofs(&mut tofs, &scans);

    // Get peak counts from total scans and scans
    let peak_cnts = get_peak_cnts(total_scans, &scans);

    // Interleave TOFs and intensities
    let mut interleaved = Vec::new();
    for (&tof, &intensity) in tofs.iter().zip(intensities.iter()) {
        interleaved.push(tof);
        interleaved.push(intensity);
    }

    // Get real data using the custom loop logic
    let real_data = get_realdata(&peak_cnts, &interleaved);

    // Compress real_data using zstd_compress
    let compressed_data = zstd_compress(&real_data, compression_level)?;

    // Final data preparation with compressed data
    let mut final_data = Vec::new();

    // Include the length of the compressed data as a header (4 bytes)
    final_data.extend_from_slice(&(compressed_data.len() as u32 + 8).to_le_bytes());

    // Include total_scans as part of the header
    final_data.extend_from_slice(&total_scans.to_le_bytes());

    // Include the compressed data itself
    final_data.extend_from_slice(&compressed_data);

    Ok(final_data)
}

pub fn compress_collection(
    frames: Vec<TimsFrame>,
    max_scan_count: u32,
    compression_level: i32,
    num_threads: usize,
) -> Vec<Vec<u8>> {
    let pool = ThreadPoolBuilder::new()
        .num_threads(num_threads)
        .build()
        .unwrap();

    let result = pool.install(|| {
        frames
            .par_iter()
            .map(|frame| {
                let compressed_data = reconstruct_compressed_data(
                    frame.scan.iter().map(|&x| x as u32).collect(),
                    frame.tof.iter().map(|&x| x as u32).collect(),
                    frame
                        .ims_frame
                        .intensity
                        .iter()
                        .map(|&x| x as u32)
                        .collect(),
                    max_scan_count,
                    compression_level,
                )
                .unwrap();
                compressed_data
            })
            .collect()
    });
    result
}

/// Parses the decompressed bruker binary data
///
/// # Arguments
///
/// * `decompressed_bytes` - A byte slice that holds the decompressed data
///
/// # Returns
///
/// * `scan_indices` - A vector of u32 that holds the scan indices
/// * `tof_indices` - A vector of u32 that holds the tof indices
/// * `intensities` - A vector of u32 that holds the intensities
///
pub fn parse_decompressed_bruker_binary_data(
    decompressed_bytes: &[u8],
) -> Result<(Vec<u32>, Vec<u32>, Vec<u32>), Box<dyn std::error::Error>> {
    let mut buffer_u32 = Vec::new();

    for i in 0..(decompressed_bytes.len() / 4) {
        let value = LittleEndian::read_u32(&[
            decompressed_bytes[i],
            decompressed_bytes[i + (decompressed_bytes.len() / 4)],
            decompressed_bytes[i + (2 * decompressed_bytes.len() / 4)],
            decompressed_bytes[i + (3 * decompressed_bytes.len() / 4)],
        ]);
        buffer_u32.push(value);
    }

    // get the number of scans
    let scan_count = buffer_u32[0] as usize;

    // get the scan indices
    let mut scan_indices: Vec<u32> = buffer_u32[..scan_count].to_vec();
    for index in &mut scan_indices {
        *index /= 2;
    }

    // first scan index is always 0?
    scan_indices[0] = 0;

    // get the tof indices, which are the first half of the buffer after the scan indices
    let mut tof_indices: Vec<u32> = buffer_u32
        .iter()
        .skip(scan_count)
        .step_by(2)
        .cloned()
        .collect();

    // get the intensities, which are the second half of the buffer
    let intensities: Vec<u32> = buffer_u32
        .iter()
        .skip(scan_count + 1)
        .step_by(2)
        .cloned()
        .collect();

    // calculate the last scan before moving scan indices
    let last_scan = intensities.len() as u32 - scan_indices[1..].iter().sum::<u32>();

    // shift the scan indices to the right
    for i in 0..(scan_indices.len() - 1) {
        scan_indices[i] = scan_indices[i + 1];
    }

    // set the last scan index
    let len = scan_indices.len();
    scan_indices[len - 1] = last_scan;

    // convert the tof indices to cumulative sums
    let mut index = 0;
    for &size in &scan_indices {
        let mut current_sum = 0;
        for _ in 0..size {
            current_sum += tof_indices[index];
            tof_indices[index] = current_sum;
            index += 1;
        }
    }

    // adjust the tof indices to be zero-indexed
    let adjusted_tof_indices: Vec<u32> = tof_indices.iter().map(|&val| val - 1).collect();
    Ok((scan_indices, adjusted_tof_indices, intensities))
}

pub fn get_peak_cnts(total_scans: u32, scans: &[u32]) -> Vec<u32> {
    let mut peak_cnts = vec![total_scans];
    let mut ii = 0;
    for scan_id in 1..total_scans {
        let mut counter = 0;
        while ii < scans.len() && scans[ii] < scan_id {
            ii += 1;
            counter += 1;
        }
        peak_cnts.push(counter * 2);
    }
    peak_cnts
}

pub fn modify_tofs(tofs: &mut [u32], scans: &[u32]) {
    let mut last_tof = -1i32; // Using i32 to allow -1
    let mut last_scan = 0;
    for ii in 0..tofs.len() {
        if last_scan != scans[ii] {
            last_tof = -1;
            last_scan = scans[ii];
        }
        let val = tofs[ii] as i32; // Cast to i32 for calculation
        tofs[ii] = (val - last_tof) as u32; // Cast back to u32
        last_tof = val;
    }
}

pub fn get_realdata(peak_cnts: &[u32], interleaved: &[u32]) -> Vec<u8> {
    let mut back_data = Vec::new();

    // Convert peak counts to bytes and add to back_data
    for &cnt in peak_cnts {
        back_data.extend_from_slice(&cnt.to_le_bytes());
    }

    // Convert interleaved data to bytes and add to back_data
    for &value in interleaved {
        back_data.extend_from_slice(&value.to_le_bytes());
    }

    // Call get_realdata_loop for data rearrangement
    get_realdata_loop(&back_data)
}

pub fn get_realdata_loop(back_data: &[u8]) -> Vec<u8> {
    let mut real_data = vec![0u8; back_data.len()];
    let mut reminder = 0;
    let mut bd_idx = 0;
    for rd_idx in 0..back_data.len() {
        if bd_idx >= back_data.len() {
            reminder += 1;
            bd_idx = reminder;
        }
        real_data[rd_idx] = back_data[bd_idx];
        bd_idx += 4;
    }
    real_data
}

pub fn get_data_for_compression(
    tofs: &Vec<u32>,
    scans: &Vec<u32>,
    intensities: &Vec<u32>,
    max_scans: u32,
) -> Vec<u8> {
    let mut tof_copy = tofs.clone();
    modify_tofs(&mut tof_copy, &scans);
    let peak_cnts = get_peak_cnts(max_scans, &scans);
    let interleaved: Vec<u32> = tofs
        .iter()
        .zip(intensities.iter())
        .flat_map(|(tof, intensity)| vec![*tof, *intensity])
        .collect();

    get_realdata(&peak_cnts, &interleaved)
}

pub fn get_data_for_compression_par(
    tofs: Vec<Vec<u32>>,
    scans: Vec<Vec<u32>>,
    intensities: Vec<Vec<u32>>,
    max_scans: u32,
    num_threads: usize,
) -> Vec<Vec<u8>> {
    let pool = ThreadPoolBuilder::new()
        .num_threads(num_threads)
        .build()
        .unwrap();

    let result = pool.install(|| {
        tofs.par_iter()
            .zip(scans.par_iter())
            .zip(intensities.par_iter())
            .map(|((tof, scan), intensity)| {
                get_data_for_compression(tof, scan, intensity, max_scans)
            })
            .collect()
    });

    result
}

pub fn flatten_scan_values(scan: &Vec<u32>, zero_indexed: bool) -> Vec<u32> {
    let add = if zero_indexed { 0 } else { 1 };
    scan.iter()
        .enumerate()
        .flat_map(|(index, &count)| vec![(index + add) as u32; count as usize].into_iter())
        .collect()
}

// Merge and sort inclusive integer ranges like [(3,7), (8,12), (20,25)].
pub fn merge_ranges(mut ranges: Vec<(usize, usize)>) -> Vec<(usize, usize)> {
    if ranges.is_empty() { return ranges; }
    ranges.sort_unstable_by_key(|x| x.0);
    let mut out: Vec<(usize, usize)> = Vec::with_capacity(ranges.len());
    let mut cur = ranges[0];
    for (l, r) in ranges.into_iter().skip(1) {
        if l <= cur.1 + 1 {
            cur.1 = cur.1.max(r);
        } else {
            out.push(cur);
            cur = (l, r);
        }
    }
    out.push(cur);
    out
}