fix: skipped cycle handling (temporary)

Author: jspaezp

rust/timscentroid/src/indexing.rs

@@ -14,7 +14,10 @@ use timsrust::{
     FramePeaks,
     Metadata,
 };
-use tracing::instrument;
+use tracing::{
+    instrument,
+    warn,
+};
 
 use crate::rt_mapping::{
     CycleToRTMapping,
@@ -669,14 +672,29 @@ impl<T: RTIndex> IndexedPeakGroup<T> {
     ) -> Vec<(usize, u32, u32)> {
         let mut out = Vec::new();
         let mut cycle_index = 0;
+        let mut last_pushed_cycle = None;
 
         for (i, meta) in frame_reader.frame_metas.iter().enumerate() {
             if matches!(meta.ms_level, timsrust::MSLevel::MS1) {
                 cycle_index += 1;
             }
             if filter(meta) {
+                if let Some(last_cycle) = last_pushed_cycle
+                    && last_cycle == cycle_index
+                {
+                    warn!(
+                        "Found multiple frames in the same cycle,
+                        skipping the non-first ones (cycle: {}, rt: {})
+                        this might point to an error when collecting the data
+                        (missing ms1 frame)
+                        ",
+                        last_cycle, meta.rt_in_seconds,
+                    );
+                    continue;
+                }
                 let rt_ms = (meta.rt_in_seconds * 1000.0).round() as u32;
                 out.push((i, cycle_index, rt_ms));
+                last_pushed_cycle = Some(cycle_index);
             }
         }
         // TODO: check that cycle indices are continuous AND without replicates
@@ -685,11 +703,21 @@ impl<T: RTIndex> IndexedPeakGroup<T> {
             // Note: These are assertions instead of errors because
             // they are invariants I am checking, not recoverable errors, none of the logic
             // after this point would make sense if this is not true.
+            //
+            // This checks that whatever filter is used returns only a single frame within each
+            // cycle ...
             assert!(
                 w[0].1 < w[1].1,
-                "Cycle indices should be strictly increasing"
+                "Cycle indices should be strictly increasing, {:?} vs {:?}",
+                w[0],
+                w[1],
+            );
+            assert!(
+                w[0].2 <= w[1].2,
+                "Retention times should be non-decreasing, {:?} vs {:?}",
+                w[0],
+                w[1],
             );
-            assert!(w[0].2 <= w[1].2, "Retention times should be non-decreasing");
             assert!(
                 w[1].1 - w[0].1 == 1,
                 "Cycle indices should be continuous without gaps, found gap between {} and {}",

rust/timsquery/src/models/aggregators/spectrum_agg.rs

@@ -167,4 +167,3 @@ impl Add for MzMobilityStatsCollector {
         }
     }
 }
-

rust/timsquery/src/models/indexed_data.rs

@@ -455,7 +455,9 @@ impl<FH: KeyLike> QueriableData<ChromatogramCollector<FH, f32>> for IndexedPeaks
     }
 }
 
-impl<FH: KeyLike> QueriableData<SpectralCollector<FH, MzMobilityStatsCollector>> for IndexedPeaksHandle {
+impl<FH: KeyLike> QueriableData<SpectralCollector<FH, MzMobilityStatsCollector>>
+    for IndexedPeaksHandle
+{
     fn add_query(
         &self,
         aggregator: &mut SpectralCollector<FH, MzMobilityStatsCollector>,

rust/timsquery_viewer/src/app.rs

@@ -310,9 +310,7 @@ impl ViewerApp {
                     for &pane in ALL_PANES {
                         if dock_state.find_tab(&pane).is_none() {
                             tracing::info!("Adding missing pane {:?} to saved layout", pane);
-                            dock_state
-                                .main_surface_mut()
-                                .push_to_first_leaf(pane);
+                            dock_state.main_surface_mut().push_to_first_leaf(pane);
                         }
                     }
 
@@ -603,7 +601,13 @@ impl ViewerApp {
             return Err("Computation cancelled".to_string());
         }
 
-        Ok((output, collector, expected_intensities, selected_idx as u64, elution_group))
+        Ok((
+            output,
+            collector,
+            expected_intensities,
+            selected_idx as u64,
+            elution_group,
+        ))
     }
 
     /// Check if background chromatogram computation completed
@@ -1296,10 +1300,7 @@ impl ViewerApp {
 }
 
 /// Encode an egui ColorImage as PNG and write to disk
-fn save_color_image_as_png(
-    image: &egui::ColorImage,
-    path: &std::path::Path,
-) -> Result<(), String> {
+fn save_color_image_as_png(image: &egui::ColorImage, path: &std::path::Path) -> Result<(), String> {
     let width = image.width() as u32;
     let height = image.height() as u32;
     let pixels: Vec<u8> = image
@@ -1442,7 +1443,7 @@ impl<'a> AppTabViewer<'a> {
         let action = ConfigPanel::render_export_section(
             ui,
             self.screenshot_delay_secs,
-            &self.screenshot_state,
+            self.screenshot_state,
         );
         match action {
             ScreenshotAction::None => {}

rust/timsquery_viewer/src/computed_state.rs

@@ -544,7 +544,10 @@ impl ComputedState {
                 return false;
             };
             (
-                result.elution_group.clone().with_rt_seconds(rt_seconds as f32),
+                result
+                    .elution_group
+                    .clone()
+                    .with_rt_seconds(rt_seconds as f32),
                 result.output.mobility_ook0 as f64,
             )
         };
@@ -567,9 +570,7 @@ impl ComputedState {
 
         let to_range = |r: OptionallyRestricted<TupleRange<f32>>| -> (f64, f64) {
             match r {
-                OptionallyRestricted::Restricted(tr) => {
-                    (tr.start() as f64, tr.end() as f64)
-                }
+                OptionallyRestricted::Restricted(tr) => (tr.start() as f64, tr.end() as f64),
                 OptionallyRestricted::Unrestricted => (0.0, 2.0),
             }
         };

rust/timsquery_viewer/src/ui/panels/config_panel.rs

@@ -13,8 +13,10 @@ const SECTION_SPACING: f32 = 12.0;
 const INTERNAL_SPACING: f32 = 8.0;
 
 /// Screenshot capture lifecycle
+#[derive(Default)]
 pub enum ScreenshotState {
     /// Nothing happening
+    #[default]
     Idle,
     /// Timer running, show remaining seconds overlay
     Countdown { deadline: Instant },
@@ -24,12 +26,6 @@ pub enum ScreenshotState {
     Saving(Arc<egui::ColorImage>),
 }
 
-impl Default for ScreenshotState {
-    fn default() -> Self {
-        Self::Idle
-    }
-}
-
 /// Actions the export UI can request
 pub enum ScreenshotAction {
     None,
@@ -243,9 +239,10 @@ impl ConfigPanel {
                             .as_secs_f32()
                             .ceil() as u32;
                         ui.horizontal(|ui| {
-                            ui.add_enabled(false, egui::Button::new(
-                                format!("Capturing in {}s...", remaining),
-                            ));
+                            ui.add_enabled(
+                                false,
+                                egui::Button::new(format!("Capturing in {}s...", remaining)),
+                            );
                             if ui.button("Cancel").clicked() {
                                 action = ScreenshotAction::Cancel;
                             }

rust/timsquery_viewer/src/ui/panels/mobility_panel.rs

@@ -20,7 +20,7 @@ pub struct MobilityPanel;
 
 impl MobilityPanel {
     pub fn new() -> Self {
-        Self::default()
+        Self
     }
 
     pub fn title(&self) -> &str {