fix(craft): improve multiplet quantitation accuracy

crates/processing/src/craft.rs

@@ -130,7 +130,7 @@ impl CraftParams {
         Self {
             profile: CraftProfile::Conventional,
             regions: Vec::new(),
-            max_components_per_fit_window: 7,
+            max_components_per_fit_window: 15,
             min_amplitude_to_noise: 3.3,
             linewidth_hz: (0.05, 10.0),
             filter_taps: 499,
@@ -329,7 +329,7 @@ pub fn process_craft_cancellable(
         if cancelled() {
             return Err(CraftError::Cancelled);
         }
-        let result = fit_region(input, skip, sw, region, params, cancelled)?;
+        let result = fit_region(input, skip, data.group_delay, sw, region, params, cancelled)?;
         if let Some((kind, message)) = result.warning {
             warnings.push(CraftWarning {
                 kind,
@@ -455,7 +455,10 @@ pub fn process_craft_cancellable(
         .points
         .iter()
         .enumerate()
-        .map(|(index, &sample)| sample - model_at(&components, index as f64 / sw))
+        .map(|(index, &sample)| {
+            let time = (index as f64 - data.group_delay) / sw;
+            sample - model_at(&components, time)
+        })
         .collect();
     let residual_rss: f64 = residual_fid[skip..].iter().map(Complex64::norm_sqr).sum();
     let input_rss: f64 = input.iter().map(Complex64::norm_sqr).sum();
@@ -518,6 +521,7 @@ pub fn process_craft_cancellable(
 fn fit_region(
     input: &[Complex64],
     skipped_points: usize,
+    group_delay_points: f64,
     sw: f64,
     region: HzRegion,
     params: &CraftParams,
@@ -535,7 +539,11 @@ fn fit_region(
         .iter()
         .enumerate()
         .map(|(index, &value)| {
-            let time = (skipped_points + index) as f64 / sw;
+            // Bruker points after the digital-filter transient are already
+            // samples of the FID starting at `ceil(delay) - delay`. Keeping the
+            // raw point number here would reintroduce the removed delay as an
+            // amplitude extrapolation and a first-order phase ramp.
+            let time = (skipped_points as f64 + index as f64 - group_delay_points) / sw;
             value * Complex64::from_polar(1.0, -TAU * center_hz * time)
         })
         .collect();
@@ -568,7 +576,11 @@ fn fit_region(
         .copied()
         .collect();
     let times: Vec<f64> = (0..samples.len())
-        .map(|index| (skipped_points + phase_start + index * decimation) as f64 / sw)
+        .map(|index| {
+            (skipped_points as f64 + phase_start as f64 + (index * decimation) as f64
+                - group_delay_points)
+                / sw
+        })
         .collect();
     if samples.len() < 16 {
         return Ok(RegionResult {

crates/processing/src/craft_tests.rs

@@ -98,6 +98,76 @@ fn ssfp_skip_extrapolates_amplitude_to_time_zero() {
     );
 }
 
+#[test]
+fn group_delay_uses_the_physical_fid_time_origin() {
+    let sw = 2_000.0;
+    let delay = 67.985_885_620_117_2;
+    let expected_amplitude = 5.0;
+    let expected_phase = 0.4;
+    let mut input = data(&[], 4096, sw);
+    input.group_delay = delay;
+    input.points = (0..input.points.len())
+        .map(|index| {
+            let time = (index as f64 - delay) / sw;
+            Complex64::from_polar(
+                expected_amplitude * (-PI * 2.0 * time).exp(),
+                expected_phase + TAU * 100.0 * time,
+            )
+        })
+        .collect();
+    let params = CraftParams {
+        regions: vec![CraftRegion::new(CraftRegionId(1), 0.18, 0.22)],
+        filter_taps: 127,
+        ..CraftParams::default()
+    };
+
+    let result = process_craft_cancellable(
+        &input,
+        &CraftInvocation::acquisition(&input, params),
+        &|| false,
+    )
+    .unwrap();
+
+    assert_eq!(result.components.len(), 1, "{:?}", result.components);
+    let component = &result.components[0];
+    assert!((component.amplitude_t0 - expected_amplitude).abs() < 0.02);
+    let phase_error = (component.phase_rad - expected_phase).sin().abs();
+    assert!(phase_error < 0.01, "phase error was {phase_error}");
+}
+
+#[test]
+fn default_model_limit_resolves_non_lorentzian_multiplet_quantitation() {
+    let mut components = vec![
+        (-108.0, 0.75, 0.3, 0.5),
+        (-100.0, 1.50, 0.3, 0.6),
+        (-92.0, 0.75, 0.3, 0.7),
+    ];
+    for (frequency, amplitude) in [(80.0, 0.25), (88.0, 0.75), (96.0, 0.75), (104.0, 0.25)] {
+        components.push((frequency, amplitude * 0.6, 0.3, 1.0));
+        components.push((frequency + 0.8, amplitude * 0.4, 0.3, 1.8));
+    }
+    let input = data(&components, 4096, 2_000.0);
+    let params = CraftParams {
+        regions: vec![
+            CraftRegion::new(CraftRegionId(0), -0.23, -0.17),
+            CraftRegion::new(CraftRegionId(1), 0.14, 0.23),
+        ],
+        filter_taps: 127,
+        ..CraftParams::default()
+    };
+
+    let result = process_craft_cancellable(
+        &input,
+        &CraftInvocation::acquisition(&input, params),
+        &|| false,
+    )
+    .unwrap();
+
+    assert!(result.diagnostics.fit_windows[1].selected_model_order > 7);
+    let ratio = result.region_ratio.unwrap().value;
+    assert!((ratio - 1.5).abs() < 0.03, "ratio was {ratio}");
+}
+
 #[test]
 fn rejects_frequency_domain_input() {
     let mut input = data(&[], 128, 1000.0);

docs/src/content/docs/guides/craft.md

@@ -60,7 +60,7 @@ profile uses these defaults:
 
 - **Minimum A/N**: 3.3. Lower values retain weaker candidates but increase the
   chance of fitting noise; values below 3.3 are flagged for review.
-- **Max components / fit window**: 7 (allowed range 1–64). Reaching the limit
+- **Max components / fit window**: 15 (allowed range 1–64). Reaching the limit
   is reported as a diagnostic warning.
 - **Linewidth range (Hz)**: 0.05–10 Hz.
 - **Fit window width (Hz)**: 500 Hz. This controls how wide groups are divided

docs/src/content/docs/zh-cn/guides/craft.md

@@ -46,7 +46,7 @@ CRAFT 直接拟合一维 NMR 采集中的原始复数 FID，并报告共振分
 
 - **Minimum A/N**：3.3。较低值会保留更弱的候选分量，但也更容易拟合噪声；低于
   3.3 时会标记为需要复核。
-- **Max components / fit window**：7（允许范围 1–64）。达到上限会在诊断中给出
+- **Max components / fit window**：15（允许范围 1–64）。达到上限会在诊断中给出
   警告。
 - **Linewidth range (Hz)**：0.05–10 Hz。
 - **Fit window width (Hz)**：500 Hz。它只决定宽信号组如何分段计算，不会增加