nmr-processing 9.0.0 → 9.0.2-pre.1660221022

package/src/xy/xyAutoPeaksPicking.ts

@@ -189,15 +189,16 @@ function getPeakList(data: DataXY, options: GetPeakListOptions) {
     });
   }
 
-  if (optimize) {
-    return optimizePeaks(data, peakList, {
-      shape,
-      factorLimits,
-      optimization,
-    });
-  }
-
-  return convertWidthToHz(peakList, frequency);
+  return convertWidthToHz(
+    optimize
+      ? optimizePeaks(data, peakList, {
+          shape,
+          factorLimits,
+          optimization,
+        })
+      : peakList,
+    { frequency },
+  );
 }
 
 function getCutOff(data: number[] | Float64Array, options: OptionsGetCutOff) {

package/src/xy/xyPeaksOptimization.ts

@@ -1,10 +1,25 @@
 import { DataXY, PeakXYWidth } from 'cheminfo-types';
 import { optimizePeaks, OptimizePeaksOptions } from 'ml-gsd';
 
+import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
+import { convertWidthToPPM } from '../peaks/util/convertWidthToPPM';
+
+export interface XYPeaksOptimizationOptions extends OptimizePeaksOptions {
+  /**
+   * frequency to convert width and fwhm to ppm.
+   */
+  frequency: number;
+}
 export function xyPeaksOptimization(
   data: DataXY,
   peaks: PeakXYWidth[],
-  options: OptimizePeaksOptions,
+  options: XYPeaksOptimizationOptions,
 ) {
-  return optimizePeaks(data, peaks, options);
+  const { frequency } = options;
+  const newPeaks = convertWidthToPPM(peaks, { frequency });
+  const optimizedPeaks = optimizePeaks(data, newPeaks, options);
+  return convertWidthToHz(optimizedPeaks, {
+    frequency,
+    output: optimizedPeaks,
+  });
 }

package/src/xyz/xyzJResAnalyzer.ts

@@ -88,6 +88,7 @@ function compilePattern(
     dy: signals[0].y.resolution,
   };
 
+  const defaultWidth = 0.02 * observedFrequencies[0];
   const newSignals = JSON.parse(JSON.stringify(signals));
   //adapt to 1D jAnalyzer
   for (const signal of newSignals) {
@@ -102,7 +103,7 @@ function compilePattern(
       to: Number.MIN_SAFE_INTEGER,
     };
     for (const peak of peaks) {
-      if (!peak.width) peak.width = 0.02;
+      if (!peak.width) peak.width = defaultWidth;
     }
     peaks.sort((a: Peak2D, b: Peak2D) => a.y - b.y);
   }