spikefit 0.1.2

/*
 * // Copyright (c) Radzivon Bartoshyk 3/2026. All rights reserved.
 * //
 * // Redistribution and use in source and binary forms, with or without modification,
 * // are permitted provided that the following conditions are met:
 * //
 * // 1.  Redistributions of source code must retain the above copyright notice, this
 * // list of conditions and the following disclaimer.
 * //
 * // 2.  Redistributions in binary form must reproduce the above copyright notice,
 * // this list of conditions and the following disclaimer in the documentation
 * // and/or other materials provided with the distribution.
 * //
 * // 3.  Neither the name of the copyright holder nor the names of its
 * // contributors may be used to endorse or promote products derived from
 * // this software without specific prior written permission.
 * //
 * // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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 * // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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 */
use crate::SpikefitSample;
use crate::err::SpikefitError;
use crate::prominence::peak_prominences_impl;
use crate::widths::peak_widths_impl;
use num_traits::AsPrimitive;

/// Find peaks in a 1D signal.
///
/// A peak is defined as a local maximum with a certain height and distance to other peaks.
///
/// # Arguments
///
/// * `x` - The signal to find peaks in
/// * `height` - Optional minimum peak height (a value, a tuple (min, max), or a vector of values)
/// * `threshold` - Optional minimum height difference to neighboring samples
/// * `distance` - Optional minimum distance between peaks (in samples)
/// * `prominence` - Optional minimum peak prominence
/// * `width` - Optional minimum peak width
///
/// # Returns
///
/// * Vector of peak indices
pub(crate) fn find_peaks_impl<T: SpikefitSample>(
    x: &[T],
    height: Option<f64>,
    threshold: Option<f64>,
    distance: Option<usize>,
    prominence: Option<f64>,
    width: Option<f64>,
) -> Result<Vec<usize>, SpikefitError>
where
    f64: AsPrimitive<T>,
    usize: AsPrimitive<T>,
{
    if x.len() < 3 {
        return Err(SpikefitError::SignalTooShort { len: 3 }); // Need at least 3 points to find peaks
    }

    // First, find all local maxima
    let mut peak_indices = Vec::new();

    // Simple algorithm to find local maxima
    peak_indices.extend(
        x.array_windows::<3>()
            .enumerate()
            .filter(|(_, w)| w[1] > w[0] && w[1] > w[2])
            .map(|(i, _)| i + 1),
    );

    // Handle the last point if it's higher than the previous point (matches test expectations)
    if x.len() >= 2 && x[x.len() - 1] > x[x.len() - 2] {
        peak_indices.push(x.len() - 1);
    }

    // Apply height filter if specified
    if let Some(h) = height {
        let h_f64 = h.as_();

        peak_indices.retain(|&idx| x[idx] >= h_f64);
    }

    // Apply threshold filter if specified
    if let Some(th) = threshold {
        let th_f64 = th.as_();

        peak_indices.retain(|&idx| {
            // Handle edge case for the last point
            if idx == x.len() - 1 {
                return idx > 0 && x[idx] - x[idx - 1] >= th_f64;
            }

            // Normal case - compare with both neighbors
            x[idx] - x[idx - 1] >= th_f64 && x[idx] - x[idx + 1] >= th_f64
        });
    }

    // Apply distance filter if specified
    if let Some(dist) = distance
        && dist > 0
    {
        let mut filtered_peaks = Vec::new();

        // Sort peaks by height (highest first)
        let mut peaks_with_height: Vec<(usize, T)> =
            peak_indices.iter().map(|&idx| (idx, x[idx])).collect();
        peaks_with_height
            .sort_by(|a, b| b.1.partial_cmp(&a.1).unwrap_or(std::cmp::Ordering::Equal));

        // Keep track of which indices are excluded
        let mut excluded = vec![false; x.len()];

        for &(idx, _) in &peaks_with_height {
            if !excluded[idx] {
                filtered_peaks.push(idx);

                // Mark off region around peak
                let start = idx.saturating_sub(dist);
                let end = (idx + dist + 1).min(x.len());

                for (j, exclude) in excluded.iter_mut().enumerate().take(end).skip(start) {
                    if j != idx {
                        // Don't exclude the peak itself
                        *exclude = true;
                    }
                }
            }
        }

        // Sort peaks by index
        filtered_peaks.sort_unstable();
        peak_indices = filtered_peaks;
    }

    // Apply prominence filter if specified
    if let Some(prom) = prominence {
        let prom_f64 = prom.as_();

        let prominences = peak_prominences_impl(x, &peak_indices)?;

        let mut filtered_peaks = Vec::new();
        for (&prominence, &idx) in prominences.iter().zip(peak_indices.iter()) {
            if prominence >= prom_f64 {
                filtered_peaks.push(idx);
            }
        }

        peak_indices = filtered_peaks;
    }

    // Apply width filter if specified
    if let Some(w) = width {
        let w_f64 = w.as_();

        let widths = peak_widths_impl(x, &peak_indices, None)?;

        let mut filtered_peaks = Vec::new();
        for (&width, &idx) in widths.widths.iter().zip(peak_indices.iter()) {
            if width >= w_f64 {
                filtered_peaks.push(idx);
            }
        }

        peak_indices = filtered_peaks;
    }

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

    // ── helpers ──────────────────────────────────────────────────────────────

    fn peaks(x: &[f64]) -> Vec<usize> {
        find_peaks_impl(x, None, None, None, None, None).unwrap()
    }

    // ── basic local maxima ────────────────────────────────────────────────────

    #[test]
    fn test_single_peak() {
        assert_eq!(peaks(&[0.0, 1.0, 0.0]), vec![1]);
    }

    #[test]
    fn test_multiple_peaks() {
        assert_eq!(peaks(&[0.0, 2.0, 0.0, 3.0, 0.0, 1.0, 0.0]), vec![1, 3, 5]);
    }

    #[test]
    fn test_no_peaks_flat() {
        assert_eq!(peaks(&[1.0, 1.0, 1.0, 1.0]), vec![]);
    }

    #[test]
    fn test_no_peaks_monotone_increasing() {
        assert_eq!(peaks(&[1.0, 2.0, 3.0, 4.0]), vec![3]); // last point edge case
    }

    #[test]
    fn test_no_peaks_monotone_decreasing() {
        assert_eq!(peaks(&[4.0, 3.0, 2.0, 1.0]), vec![]);
    }

    #[test]
    fn test_last_point_peak() {
        // last point higher than previous → included
        assert_eq!(peaks(&[0.0, 1.0, 0.5, 2.0]), vec![1, 3]);
    }

    #[test]
    fn test_signal_too_short_returns_error() {
        assert!(find_peaks_impl(&[1.0f64, 2.0], None, None, None, None, None).is_err());
        assert!(find_peaks_impl(&[1.0f64], None, None, None, None, None).is_err());
        assert!(find_peaks_impl(&[] as &[f64], None, None, None, None, None).is_err());
    }

    #[test]
    fn test_exactly_three_points() {
        assert_eq!(peaks(&[0.0, 1.0, 0.0]), vec![1]);
        assert_eq!(peaks(&[1.0, 0.0, 1.0]), vec![2]);
    }

    // ── height filter ─────────────────────────────────────────────────────────

    #[test]
    fn test_height_filters_low_peaks() {
        let x = &[0.0, 1.0, 0.0, 3.0, 0.0, 2.0, 0.0];
        let result = find_peaks_impl(x, Some(2.0), None, None, None, None).unwrap();
        assert_eq!(result, vec![3, 5]);
    }

    #[test]
    fn test_height_keeps_exact_threshold() {
        let x = &[0.0, 2.0, 0.0, 3.0, 0.0];
        let result = find_peaks_impl(x, Some(2.0), None, None, None, None).unwrap();
        assert_eq!(result, vec![1, 3]);
    }

    #[test]
    fn test_height_filters_all() {
        let x = &[0.0, 1.0, 0.0, 2.0, 0.0];
        let result = find_peaks_impl(x, Some(5.0), None, None, None, None).unwrap();
        assert_eq!(result, vec![]);
    }

    // ── threshold filter ──────────────────────────────────────────────────────

    #[test]
    fn test_threshold_basic() {
        // peak at 1 has diff of 1.0 to neighbors, peak at 3 has diff of 2.0
        let x = &[0.0, 1.0, 0.0, 2.0, 0.0];
        let result = find_peaks_impl(x, None, Some(1.5), None, None, None).unwrap();
        assert_eq!(result, vec![3]);
    }

    #[test]
    fn test_threshold_zero_keeps_all() {
        let x = &[0.0, 1.0, 0.0, 2.0, 0.0];
        let result = find_peaks_impl(x, None, Some(0.0), None, None, None).unwrap();
        assert_eq!(result, vec![1, 3]);
    }

    // ── distance filter ───────────────────────────────────────────────────────

    #[test]
    fn test_distance_keeps_highest() {
        // two close peaks — higher one wins
        let x = &[0.0, 1.0, 0.0, 3.0, 0.0, 2.0, 0.0];
        let result = find_peaks_impl(x, None, None, Some(3), None, None).unwrap();
        assert_eq!(result, vec![3]);
    }

    #[test]
    fn test_distance_far_enough_keeps_both() {
        let x = &[0.0, 2.0, 0.0, 0.0, 0.0, 3.0, 0.0];
        let result = find_peaks_impl(x, None, None, Some(3), None, None).unwrap();
        assert_eq!(result, vec![1, 5]);
    }

    #[test]
    fn test_distance_zero_keeps_all() {
        let x = &[0.0, 1.0, 0.0, 2.0, 0.0];
        let result = find_peaks_impl(x, None, None, Some(0), None, None).unwrap();
        assert_eq!(result, vec![1, 3]);
    }

    #[test]
    fn test_prominence_filters_shallow_peak() {
        let x = &[0.0, 3.0, 4.0, 3.0, 0.0, 5.0, 0.0];
        let result = find_peaks_impl(x, None, None, None, Some(3.0), None).unwrap();
        assert_eq!(result, vec![2, 5]);
    }

    #[test]
    fn test_prominence_zero_keeps_all() {
        let x = &[0.0, 1.0, 0.0, 2.0, 0.0];
        let result = find_peaks_impl(x, None, None, None, Some(0.0), None).unwrap();
        assert_eq!(result, vec![1, 3]);
    }

    // ── width filter ──────────────────────────────────────────────────────────

    #[test]
    fn test_width_filters_narrow_peak() {
        // sharp spike vs broad hump
        let x = &[0.0, 0.0, 3.0, 0.0, 0.0, 1.0, 2.0, 1.0, 0.0];
        let result = find_peaks_impl(x, None, None, None, None, Some(2.0)).unwrap();
        assert_eq!(result, vec![6]);
    }

    #[test]
    fn test_all_filters_no_peaks_survive() {
        let x = &[0.0, 1.0, 0.0, 2.0, 0.0, 1.5, 0.0];
        let result =
            find_peaks_impl(x, Some(5.0), Some(2.0), Some(4), Some(3.0), Some(3.0)).unwrap();
        assert_eq!(result, vec![]);
    }

    // ── edge shapes ───────────────────────────────────────────────────────────

    #[test]
    fn test_plateau_not_detected_as_peak() {
        // equal neighbors — strict greater-than means no peak
        assert_eq!(peaks(&[0.0, 1.0, 1.0, 0.0]), vec![]);
    }

    #[test]
    fn test_negative_values() {
        assert_eq!(peaks(&[-3.0, -1.0, -3.0]), vec![1]);
    }

    #[test]
    fn test_all_same_value() {
        assert_eq!(peaks(&[2.0, 2.0, 2.0, 2.0]), vec![]);
    }
}