dspk-synapse 0.0.9

//! Out-of-core streaming spike detection: `RecordingSource` → `PipelineWorkspace` filtering in
//! halo windows → device threshold detection → exact streaming deduplication → device snippet
//! extraction → per-channel templates (`TemplateAccumulator`). No clustering: templates and
//! spike lists are per primary channel.

use cubecl::prelude::Client;
use cubecl::CubeElement;
use dspk_core::compute::{ComputeTarget, ComputeTask};

use dspk_ops::math::execute_channel_noise_std;
use dspk_ops::pipeline::{Pipeline, PipelineWorkspace};
use dspk_core::{ChunkSchedule, DspError, DspResult, HaloWindow, RecordingSource, SampleFormat, WindowLoader};
use crate::io::probe::{precompute_knn_table, SensorLayout};

use crate::core::{DeduplicatedSpike, SortedUnit, SortingOutput, WaveformTemplate};
use crate::detection::{SpikeSpacing, StreamingDedup, detection_heights, execute_detect_spikes_in_vram};
use crate::extraction::{execute_extract_sinc_in_vram, extraction_margin};
use super::accumulator::TemplateAccumulator;
use super::config::StreamingDetectionConfig;
use super::kernels::{execute_reduce_templates_in_vram, execute_snippet_peak_to_peak};
use crate::spatial::localize_spike_center_of_mass;

/// Exponent of the peak-to-peak heights in the centre of mass that locates each spike (1: the
/// heights themselves, as `CenterOfMassLocalizer`'s default).
pub const LOCATION_POWER: f32 = 1.0;

/// Result of running out-of-core threshold spike sorting over a recording.
#[derive(Debug, Clone)]
pub struct StreamingDetectionResult {
    /// Number of channels in the recording.
    pub channels: usize,
    /// Total samples processed across the recording.
    pub total_samples: u64,
    /// Sampling rate in Hz.
    pub sample_rate_hz: f64,
    /// Computed `(left_halo, right_halo)` in samples used during chunked streaming.
    pub halos: (u64, u64),
    /// Calibrated Quiroga MAD noise floor ($\sigma_n$ in $\mu\text{V}$) per channel.
    pub channel_sigmas_uv: Vec<f32>,
    /// Total raw threshold crossings across all channels before spatial deduplication.
    pub total_raw_crossings: u64,
    /// Total spatially deduplicated spikes across the recording.
    pub total_dedup_spikes: u64,
    /// Deduplicated spike count per primary channel.
    pub channel_spike_counts: Vec<u64>,
    /// Online Welford-accumulated waveform template (`mean` $\pm$ `std`) per primary channel.
    pub channel_templates: Vec<Option<WaveformTemplate>>,
    /// Deduplicated spike events with global `sample_index` across the recording.
    pub spikes: Vec<DeduplicatedSpike>,
    /// Location of each spike of `spikes` (µm, centre of mass over its K neighbours); empty when
    /// not located (`StreamingDetectionConfig::locate`).
    pub spike_locations_um: Vec<[f32; 3]>,
}

impl StreamingDetectionResult {
    /// This result as a [`SortingOutput`] with **one unit per primary channel** that has spikes
    /// (a channel-level summary, not a spike sorting: unit metrics describe channels).
    pub fn to_sorting_output(
        &self,
        sorter_name: impl Into<String>,
        probe: Option<SensorLayout>,
    ) -> SortingOutput {
        let mut per_ch_samples: Vec<Vec<u64>> = vec![Vec::new(); self.channels];
        let mut per_ch_amps: Vec<Vec<f32>> = vec![Vec::new(); self.channels];
        let mut per_ch_locs: Vec<Vec<[f32; 3]>> = vec![Vec::new(); self.channels];
        let located = self.spike_locations_um.len() == self.spikes.len();
        for (i, s) in self.spikes.iter().enumerate() {
            if s.primary_channel < self.channels {
                per_ch_samples[s.primary_channel].push(s.sample_index);
                per_ch_amps[s.primary_channel].push(s.peak_amplitude_uv);
                if located {
                    per_ch_locs[s.primary_channel].push(self.spike_locations_um[i]);
                }
            }
        }

        let mut units = Vec::new();
        for ch in 0..self.channels {
            if per_ch_samples[ch].is_empty() {
                continue;
            }
            let template = self.channel_templates.get(ch).and_then(|t| t.clone());
            // No calibrated σ (not expected): NaN rather than an invented noise level
            let noise_sd = self.channel_sigmas_uv.get(ch).copied().unwrap_or(f32::NAN);
            units.push(SortedUnit::from_spikes(
                ch,
                ch,
                std::mem::take(&mut per_ch_samples[ch]),
                std::mem::take(&mut per_ch_amps[ch]),
                std::mem::take(&mut per_ch_locs[ch]),
                template,
                self.sample_rate_hz,
                self.total_samples,
                noise_sd,
            ));
        }

        SortingOutput::new(
            sorter_name,
            self.sample_rate_hz,
            self.total_samples,
            probe,
            units,
            None,
        )
    }
}

/// Out-of-core streaming spike detector with per-channel templates (see the module docs).
pub struct StreamingDetector {
    config: StreamingDetectionConfig,
}

impl StreamingDetector {
    pub fn new(config: StreamingDetectionConfig) -> Self {
        Self { config }
    }

    /// Streams `source` out-of-core on `target`.
    ///
    /// # Errors
    ///
    /// [`DspError::ComputeError`] when `target` is not available; otherwise as [`Self::run_on`].
    pub fn run_with(
        &self,
        target: ComputeTarget,
        source: &dyn RecordingSource,
        pipeline: &Pipeline,
        probe: &SensorLayout,
    ) -> DspResult<StreamingDetectionResult> {
        struct Task<'a> {
            runner: &'a StreamingDetector,
            source: &'a dyn RecordingSource,
            pipeline: &'a Pipeline,
            probe: &'a SensorLayout,
        }
        impl ComputeTask for Task<'_> {
            type Output = DspResult<StreamingDetectionResult>;
            fn run(self, client: Client) -> Self::Output {
                self.runner.run_on(client, self.source, self.pipeline, self.probe)
            }
        }
        target
            .run(Task { runner: self, source, pipeline, probe })
            .map_err(|e| DspError::ComputeError(e.to_string()))?
    }

    /// Streams `source` out-of-core in halo-padded batches using double-buffered I/O prefetching
    /// and a persistent `PipelineWorkspace` on `client`'s runtime, returning global spikes and
    /// per-channel templates.
    ///
    /// # Errors
    ///
    /// When the pipeline is invalid at the recording's rate, or reading `source` fails.
    pub fn run_on(
        &self,
        client: Client,
        source: &dyn RecordingSource,
        pipeline: &Pipeline,
        probe: &SensorLayout,
    ) -> DspResult<StreamingDetectionResult> {
        let info = source.info();
        let channels = info.channel_count();
        let total_samples = info.samples;
        let fs = info.sample_rate_hz();

        let (left_halo, right_halo) = self.config.compute_halos(fs, pipeline)?;
        let batch_samples = self.config.batch_samples(fs);
        let refrac_samples = self.config.refractory_samples(fs);
        let pre_samples = self.config.pre_samples(fs);
        let post_samples = self.config.post_samples(fs);
        let snippet_samples = pre_samples + post_samples;
        let k_neighbors = self.config.k_neighbors.clamp(1, channels.max(1));

        let schedule = ChunkSchedule::full_recording(
            total_samples,
            batch_samples,
            left_halo,
            right_halo,
        );

        let mut workspace = PipelineWorkspace::new(
            client,
            pipeline.clone(),
            channels,
            schedule.max_read_samples().max(1),
            fs,
        )
        .map_err(|e| dspk_core::DspError::InvalidConfig(e.to_string()))?;

        // Phase 1: Calibrate fixed per-channel noise floor (sigma_n) from chunks spread over the recording
        let channel_sigmas_uv =
            calibrate_noise(source, &mut workspace, &self.config, (left_halo, right_halo))?;

        // Pre-upload per-channel detection heights and K-nearest neighbor table to VRAM once
        let heights = detection_heights(&channel_sigmas_uv, self.config.threshold_factor);
        let heights_handle = workspace.client().create_from_slice(f32::as_bytes(&heights));
        let spacing = SpikeSpacing { refractory_samples: refrac_samples, rule: self.config.distance_rule };
        let knn_table = precompute_knn_table(probe, channels, k_neighbors);
        let knn_handle = workspace
            .client()
            .create_from_slice(u32::as_bytes(&knn_table));

        // Spikes are detected where a full snippet (plus sinc taps) can be cut from the recording.
        let margin = extraction_margin(self.config.apply_sinc_shift);
        let detect_range = self.config.detection_range(fs, total_samples);

        // Phase 2: Stream HaloWindows with double-buffered prefetching and zero-readback VRAM kernels
        let mut accumulators: Vec<TemplateAccumulator> = (0..channels)
            .map(|ch| {
                let ids = knn_table[ch * k_neighbors..(ch + 1) * k_neighbors].iter().map(|&c| c as usize).collect();
                TemplateAccumulator::new(ids, snippet_samples)
            })
            .collect();
        let mut channel_spike_counts = vec![0u64; channels];
        let mut total_raw_crossings = 0u64;
        let mut total_dedup_spikes = 0u64;
        let mut global_spikes = Vec::new();
        let mut global_locations: Vec<[f32; 3]> = Vec::new();
        let locate = self.config.locate;
        let elems_per_spike = k_neighbors * snippet_samples;
        let mut dedup = StreamingDedup::new(probe, self.config.spatial_radius_um, refrac_samples as u64);
        // Detection looks `spacing.distance()` samples past each window's own range (exact
        // streaming with `DistanceRule::LocallyExclusive`); the halos cover it
        debug_assert!(left_halo as usize >= refrac_samples + pre_samples + margin);
        debug_assert!(right_halo as usize >= spacing.distance());

        // Integer recordings upload their stored values and are scaled on the device
        let stored = matches!(info.format, SampleFormat::I8 | SampleFormat::I16 | SampleFormat::U16 | SampleFormat::I32)
            && total_samples > 0
            && source.read_stored(&[0], 0..1, &mut vec![0u8; info.format.bytes()]).is_ok();
        if stored {
            let gains: Vec<f32> = info.channels.iter().map(|c| c.gain).collect();
            let offsets: Vec<f32> = info.channels.iter().map(|c| c.offset).collect();
            workspace.set_stored_scaling(&gains, &offsets);
        }
        let client = workspace.client().clone();

        let mut process = |win: &HaloWindow, filt_handle: cubecl::server::Handle| -> DspResult<()> {
            let n_read = win.read_len();
            let read_start = win.read_global.start;

            // 2. Detect crossings in this window's share of the detection range (spacing decided
            //    with the neighbouring samples of the halo)
            let det_start = win.valid_global.start.max(detect_range.start);
            let det_end = win.valid_global.end.min(detect_range.end);
            if det_start < det_end {
                let local = |g: u64| (g - read_start) as usize;
                let crossings = execute_detect_spikes_in_vram(
                    &client,
                    &filt_handle,
                    &heights_handle,
                    channels,
                    n_read,
                    local(det_start)..local(det_end),
                    read_start,
                    self.config.polarity,
                    spacing,
                );
                total_raw_crossings += crossings.len() as u64;
                dedup.push(&crossings);
            }

            // 3. Spatial deduplication of every crossing whose ±refractory neighbourhood is complete
            let finalized = if win.valid_global.end >= total_samples {
                dedup.finish()
            } else {
                dedup.finalize_before(win.valid_global.end)
            };
            total_dedup_spikes += finalized.len() as u64;
            if finalized.is_empty() {
                return Ok(());
            }
            let local: Vec<DeduplicatedSpike> = finalized
                .iter()
                .map(|d| DeduplicatedSpike { sample_index: d.sample_index - read_start, ..d.clone() })
                .collect();

            // 4. Extract Blackman-Harris sinc-realigned snippets and reduce moments directly in VRAM
            //    (and locate each spike from its snippet's heights; unknown, NaN, if not extracted)
            let mut locations = vec![[f32::NAN; 3]; if locate { finalized.len() } else { 0 }];
            if let Some(extracted) = execute_extract_sinc_in_vram::<f32>(
                &client,
                &filt_handle,
                &knn_handle,
                channels,
                n_read,
                &local,
                k_neighbors,
                pre_samples,
                post_samples,
                self.config.apply_sinc_shift,
            ) {
                debug_assert_eq!(extracted.dropped, 0, "finalized spikes lie inside the window");
                if locate {
                    let ptp = execute_snippet_peak_to_peak(&client, &extracted.snippets, extracted.kept.len(), k_neighbors, snippet_samples);
                    for (row, (&spike, &primary)) in extracted.kept.iter().zip(&extracted.primaries).enumerate() {
                        let p = primary as usize;
                        let ids: Vec<usize> = knn_table[p * k_neighbors..(p + 1) * k_neighbors].iter().map(|&c| c as usize).collect();
                        locations[spike] = localize_spike_center_of_mass(&ids, &ptp[row * k_neighbors..(row + 1) * k_neighbors], probe, LOCATION_POWER);
                    }
                }
                let batch_stats = execute_reduce_templates_in_vram(
                    &client,
                    &extracted.snippets,
                    &extracted.primaries,
                    channels,
                    k_neighbors,
                    snippet_samples,
                );

                // 5. Merge batch moments into online Welford/Chan accumulators in O(1) memory
                for (ch, acc) in accumulators.iter_mut().enumerate() {
                    let count = batch_stats.counts.get(ch).copied().unwrap_or(0) as u64;
                    if count > 0 {
                        let start = ch * elems_per_spike;
                        let end = start + elems_per_spike;
                        acc.merge_batch(
                            count,
                            &batch_stats.mean[start..end],
                            &batch_stats.m2[start..end],
                        );
                    }
                }
            }

            // 6. Record global spike timestamps (and locations)
            global_locations.extend(locations);
            for d in finalized {
                if d.primary_channel < channels {
                    channel_spike_counts[d.primary_channel] += 1;
                }
                global_spikes.push(d);
            }

            Ok(())
        };

        // 1. Filter each padded chunk in VRAM (persistent ping-pong buffers, no host readback)
        let loader = WindowLoader::new(source);
        if stored {
            loader.stream_stored(schedule.windows(), |win, bytes| {
                let filt_handle = workspace.process_stored_chunk_in_vram(bytes, info.format, win.read_len())?;
                process(win, filt_handle)
            })?;
        } else {
            loader.stream(schedule.windows(), |win, raw_padded| {
                let filt_handle = workspace.process_chunk_in_vram(raw_padded, win.read_len());
                process(win, filt_handle)
            })?;
        }

        let channel_templates = accumulators.iter().map(|a| a.finalize()).collect();

        Ok(StreamingDetectionResult {
            channels,
            total_samples,
            sample_rate_hz: fs,
            halos: (left_halo, right_halo),
            channel_sigmas_uv,
            total_raw_crossings,
            total_dedup_spikes,
            channel_spike_counts,
            channel_templates,
            spikes: global_spikes,
            spike_locations_um: global_locations,
        })
    }
}

/// Per-channel noise floor σ (Quiroga MAD) as the median over `config.calibration_chunks` chunks
/// spread evenly across the recording (total `config.calibration_duration_sec`). Each chunk is
/// filtered with `halos` of context so its interior is settled. Independent of the batch size.
///
/// # Errors
///
/// When reading `source` fails.
pub fn calibrate_noise(
    source: &dyn RecordingSource,
    workspace: &mut PipelineWorkspace,
    config: &StreamingDetectionConfig,
    halos: (u64, u64),
) -> DspResult<Vec<f32>> {
    let info = source.info();
    let (channels, total, fs) = (info.channel_count(), info.samples, info.sample_rate_hz());
    let mut per_chunk: Vec<Vec<f32>> = vec![Vec::new(); channels];
    let windows: Vec<HaloWindow> = config
        .calibration_chunks(fs, total)
        .into_iter()
        .enumerate()
        .map(|(index, chunk)| HaloWindow::around(index, chunk, halos.0, halos.1, total))
        .collect();
    WindowLoader::new(source).stream(&windows, |window, raw| {
        // Filtered chunk stays on the device; only one σ per channel is downloaded
        let filt = workspace.process_chunk_in_vram(raw, window.read_len());
        let sigmas = execute_channel_noise_std::<f32>(
            workspace.client(),
            &filt,
            channels,
            window.read_len(),
            window.valid_local.clone(),
        );
        for (acc, sigma) in per_chunk.iter_mut().zip(sigmas) {
            acc.push(sigma as f32);
        }
        Ok(())
    })?;

    Ok(per_chunk
        .into_iter()
        .map(|mut v| {
            if v.is_empty() {
                return 0.0;
            }
            v.sort_by(f32::total_cmp);
            let m = v.len() / 2;
            if v.len() % 2 == 1 { v[m] } else { 0.5 * (v[m - 1] + v[m]) }
        })
        .collect())
}