npm - nmr-processing - Versions diffs - 3.4.1 → 4.0.0 - Mend

nmr-processing 3.4.1 → 4.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (41) hide show

package/CHANGELOG.md +11 -0
package/lib/peaks/peaksFilterImpurities.js +1 -1
package/lib/peaks/peaksFilterImpurities.js.map +1 -1
package/lib/peaks/peaksToRanges.js +11 -17
package/lib/peaks/peaksToRanges.js.map +1 -1
package/lib/peaks/util/determineRealTop.js +3 -2
package/lib/peaks/util/determineRealTop.js.map +1 -1
package/lib/peaks/util/jAnalyzer.js +9 -11
package/lib/peaks/util/jAnalyzer.js.map +1 -1
package/lib/ranges/rangesToXY.d.ts +2 -2
package/lib/ranges/rangesToXY.js.map +1 -1
package/lib/signals/signalsToXY.d.ts +2 -2
package/lib/signals/simulation/simulate1D.d.ts +4 -3
package/lib/signals/simulation/simulate1D.js.map +1 -1
package/lib/types/NMRPeak1D.d.ts +2 -9
package/lib/xy/xyAutoPeaksPicking.d.ts +4 -60
package/lib/xy/xyAutoPeaksPicking.js +3 -3
package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
package/lib-esm/peaks/peaksFilterImpurities.js +1 -1
package/lib-esm/peaks/peaksFilterImpurities.js.map +1 -1
package/lib-esm/peaks/peaksToRanges.js +11 -17
package/lib-esm/peaks/peaksToRanges.js.map +1 -1
package/lib-esm/peaks/util/determineRealTop.js +4 -3
package/lib-esm/peaks/util/determineRealTop.js.map +1 -1
package/lib-esm/peaks/util/jAnalyzer.js +9 -11
package/lib-esm/peaks/util/jAnalyzer.js.map +1 -1
package/lib-esm/ranges/rangesToXY.js.map +1 -1
package/lib-esm/signals/simulation/simulate1D.js.map +1 -1
package/lib-esm/xy/xyAutoPeaksPicking.js +3 -3
package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
package/package.json +4 -4
package/src/peaks/peaksFilterImpurities.ts +1 -1
package/src/peaks/peaksToRanges.ts +11 -17
package/src/peaks/util/determineRealTop.ts +4 -6
package/src/peaks/util/jAnalyzer.ts +10 -12
package/src/ranges/rangesToXY.ts +2 -2
package/src/signals/signalsToXY.ts +2 -2
package/src/signals/simulation/simulate1D.ts +4 -3
package/src/types/NMRPeak1D.ts +3 -9
package/src/xy/xyAutoPeaksPicking.ts +19 -58
package/src/types/ml-gsd/index.d.ts +0 -164

package/lib-esm/peaks/peaksFilterImpurities.js CHANGED Viewed

@@ -29,7 +29,7 @@ function checkImpurity(peakList, impurity, options) {
     while (i--) {
         j = peakList.length;
         while (j--) {
-            tolerance = error + peakList[j].shape.width;
+            tolerance = error + peakList[j].width;
             difference = Math.abs(impurity[i].shift - peakList[j].x);
             if (difference < tolerance) {
                 // && (impurity[i].multiplicity === '' || (impurity[i].multiplicity.indexOf(peakList[j].multiplicity)) { // some impurities has multiplicities like 'bs' but at presents it is unsupported

package/lib-esm/peaks/peaksFilterImpurities.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib-esm/peaks/peaksToRanges.js CHANGED Viewed

@@ -17,22 +17,20 @@ const assignSignal = (peak, frequency, nucleus) => {
         delta: NaN,
         nbPeaks: 1,
         kind: 'signal',
-        startX: peak.x - peak.shape.width,
-        stopX: peak.x + peak.shape.width,
+        startX: peak.x - peak.width,
+        stopX: peak.x + peak.width,
         observe: frequency,
         nucleus,
         integralData: {
-            from: peak.x - peak.shape.width * 3,
-            to: peak.x + peak.shape.width * 3,
+            from: peak.x - peak.width * 3,
+            to: peak.x + peak.width * 3,
             value: 0,
         },
         peaks: [
             {
                 x: peak.x,
                 intensity: peak.y,
-                shape: {
-                    width: peak.shape.width,
-                },
+                width: peak.width,
             },
         ],
     };
@@ -81,9 +79,7 @@ export function peaksToRanges(data, peakList, options = {}) {
                         peaksO.push({
                             x: peakR.x,
                             y: peakR.intensity,
-                            shape: {
-                                width: peakR.shape.width,
-                            },
+                            width: peakR.width,
                         });
                         signal.mask.splice(j, 1);
                         signal.mask2.splice(j, 1);
@@ -194,19 +190,17 @@ function detectSignals(data, peakList, options = {}) {
             signals.push(signal1D);
         }
         else {
-            let tmp = peak.x + peak.shape.width;
+            let tmp = peak.x + peak.width;
             signal1D.stopX = Math.max(signal1D.stopX, tmp);
             signal1D.startX = Math.min(signal1D.startX, tmp);
             signal1D.nbPeaks++;
             signal1D.peaks.push({
                 x: peak.x,
                 intensity: peak.y,
-                shape: {
-                    width: peak.shape.width,
-                },
+                width: peak.width,
             });
-            signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.shape.width * 3);
-            signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.shape.width * 3);
+            signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.width * 3);
+            signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.width * 3);
             if (peak.kind)
                 signal1D.kind = peak.kind;
         }
@@ -250,6 +244,6 @@ function detectSignals(data, peakList, options = {}) {
  * @private
  */
 function computeArea(peak) {
-    return Math.abs(peak.intensity * peak.shape.width * 1.57); // todo add an option with this value: 1.772453851
+    return Math.abs(peak.intensity * peak.width * 1.57); // todo add an option with this value: 1.772453851
 }
 //# sourceMappingURL=peaksToRanges.js.map

package/lib-esm/peaks/peaksToRanges.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib-esm/peaks/util/determineRealTop.js CHANGED Viewed

@@ -1,6 +1,5 @@
 import LM from 'ml-levenberg-marquardt';
-import { gaussian2D } from 'ml-peak-shape-generator';
-const { fct: gaussian2DFct } = gaussian2D;
+import { Gaussian2D } from 'ml-peak-shape-generator';
 const direction8X = [-1, -1, -1, 0, 0, 1, 1, 1];
 const direction8Y = [-1, 0, 1, -1, 1, -1, 0, 1];
 const direction16X = [-2, -2, -2, -2, -2, -1, -1, 0, 0, 1, 1, 2, 2, 2, 2, 2];
@@ -106,6 +105,7 @@ function fitGaussian(data, options) {
     };
 }
 function paramGaussian2D(intervalX, intervalY, nCols) {
+    const gaussian2D = new Gaussian2D();
     return (p) => {
         return (t) => {
             let nL = p.length / 5;
@@ -113,9 +113,10 @@ function paramGaussian2D(intervalX, intervalY, nCols) {
             let xIndex = t % nCols;
             let yIndex = (t - xIndex) / nCols;
             for (let i = 0; i < nL; i++) {
+                gaussian2D.fwhm = { x: p[i + 3 * nL], y: p[i + 4 * nL] };
                 result +=
                     p[i + 2 * nL] *
-                        gaussian2DFct((xIndex - p[i]) * intervalX, (yIndex - p[i + nL]) * intervalY, p[i + 3 * nL], p[i + 4 * nL]);
+                        gaussian2D.fct((xIndex - p[i]) * intervalX, (yIndex - p[i + nL]) * intervalY);
             }
             return result;
         };

package/lib-esm/peaks/util/determineRealTop.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib-esm/peaks/util/jAnalyzer.js CHANGED Viewed

@@ -150,13 +150,13 @@ function updateSignal(signal, jCouplings) {
     // Update the limits of the signal
     let peaks = signal.peaksComp; // Always in Hz
     let nbPeaks = peaks.length;
-    signal.startX = peaks[0].x / signal.observe - peaks[0].shape.width;
+    signal.startX = peaks[0].x / signal.observe - peaks[0].width;
     signal.stopX =
-        peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].shape.width;
+        peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width;
     signal.integralData.from =
-        peaks[0].x / signal.observe - peaks[0].shape.width * 3;
+        peaks[0].x / signal.observe - peaks[0].width * 3;
     signal.integralData.to =
-        peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].shape.width * 3;
+        peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width * 3;
     // Compile the pattern and format the constant couplings
     signal.maskPattern = signal.mask2;
     signal.multiplicity = abstractPattern(signal, jCouplings);
@@ -375,9 +375,7 @@ function symmetrize(signalInput, maxError, iteration, key) {
         peaks[i] = {
             x: peak[jAxis] * newSignal.observe,
             intensity: peak[intensity],
-            shape: {
-                width: peak.shape.width,
-            },
+            width: peak.width,
         };
     }
     // Join the peaks that are closer than 0.25 Hz
@@ -389,7 +387,7 @@ function symmetrize(signalInput, maxError, iteration, key) {
             peaks[i].intensity = peaks[i].intensity + peaks[i + 1].intensity;
             peaks[i].x /= peaks[i].intensity;
             peaks[i].intensity /= 2;
-            peaks[i].shape.width += peaks[i + 1].shape.width;
+            peaks[i].width += peaks[i + 1].width;
             peaks.splice(i + 1, 1);
         }
     }
@@ -437,9 +435,9 @@ function symmetrize(signalInput, maxError, iteration, key) {
                 let diffR = Math.abs(peaks[right].x - cs);
                 if (Math.abs(diffL - diffR) < maxError) {
                     avg = Math.min(peaks[left].intensity, peaks[right].intensity);
-                    avgWidth = Math.min(peaks[left].shape.width, peaks[right].shape.width);
+                    avgWidth = Math.min(peaks[left].width, peaks[right].width);
                     peaks[left].intensity = peaks[right].intensity = avg;
-                    peaks[left].shape.width = peaks[right].shape.width = avgWidth;
+                    peaks[left].width = peaks[right].width = avgWidth;
                     middle = [
                         middle[0] + (peaks[right].x + peaks[left].x) / 2,
                         middle[1] + 1,
@@ -616,6 +614,6 @@ function chemicalShift(peaks, mask = []) {
  * @private
  */
 function getArea(peak) {
-    return Math.abs(peak.intensity * peak.shape.width * 1.57); // 1.772453851);
+    return Math.abs(peak.intensity * peak.width * 1.57); // 1.772453851);
 }
 //# sourceMappingURL=jAnalyzer.js.map

package/lib-esm/peaks/util/jAnalyzer.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib-esm/xy/xyAutoPeaksPicking.js CHANGED Viewed

@@ -32,14 +32,14 @@ function getPeakList(data, options) {
         shape,
         sgOptions,
         minMaxRatio,
-        broadRatio,
         noiseLevel,
         smoothY,
         realTopDetection,
     });
     if (broadWidth) {
-        peakList = joinBroadPeaks(peakList, {
-            width: broadWidth,
+        peakList = joinBroadPeaks(data, peakList, {
+            broadRatio,
+            broadWidth,
             shape,
             optimization,
         });

package/lib-esm/xy/xyAutoPeaksPicking.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "3.4.1",
+  "version": "4.0.0",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -73,18 +73,18 @@
     "ml-array-rescale": "^1.3.6",
     "ml-array-sequential-fill": "^1.1.7",
     "ml-array-sum": "^1.1.5",
-    "ml-gsd": "^7.0.1",
+    "ml-gsd": "^9.0.1",
     "ml-hclust": "^3.1.0",
     "ml-levenberg-marquardt": "^3.1.1",
     "ml-matrix": "^6.8.0",
     "ml-matrix-convolution": "^1.0.0",
     "ml-matrix-peaks-finder": "^1.0.0",
-    "ml-peak-shape-generator": "^2.0.2",
+    "ml-peak-shape-generator": "^3.0.3",
     "ml-simple-clustering": "^0.1.0",
     "ml-sparse-matrix": "^2.1.0",
     "ml-spectra-processing": "^6.8.0",
     "ml-tree-set": "^0.1.1",
     "openchemlib-utils": "^1.5.1",
-    "spectrum-generator": "^5.4.1"
+    "spectrum-generator": "^6.0.1"
   }
 }

package/src/peaks/peaksFilterImpurities.ts CHANGED Viewed

@@ -66,7 +66,7 @@ function checkImpurity(
   while (i--) {
     j = peakList.length;
     while (j--) {
-      tolerance = error + peakList[j].shape.width;
+      tolerance = error + peakList[j].width;
       difference = Math.abs(impurity[i].shift - peakList[j].x);
       if (difference < tolerance) {
         // && (impurity[i].multiplicity === '' || (impurity[i].multiplicity.indexOf(peakList[j].multiplicity)) { // some impurities has multiplicities like 'bs' but at presents it is unsupported

package/src/peaks/peaksToRanges.ts CHANGED Viewed

@@ -91,22 +91,20 @@ const assignSignal = (
     delta: NaN,
     nbPeaks: 1,
     kind: 'signal',
-    startX: peak.x - peak.shape.width,
-    stopX: peak.x + peak.shape.width,
+    startX: peak.x - peak.width,
+    stopX: peak.x + peak.width,
     observe: frequency,
     nucleus,
     integralData: {
-      from: peak.x - peak.shape.width * 3,
-      to: peak.x + peak.shape.width * 3,
+      from: peak.x - peak.width * 3,
+      to: peak.x + peak.width * 3,
       value: 0,
     },
     peaks: [
       {
         x: peak.x,
         intensity: peak.y,
-        shape: {
-          width: peak.shape.width,
-        },
+        width: peak.width,
       },
     ],
   };
@@ -177,9 +175,7 @@ export function peaksToRanges(
             peaksO.push({
               x: peakR.x,
               y: peakR.intensity,
-              shape: {
-                width: peakR.shape.width,
-              },
+              width: peakR.width,
             });
             signal.mask.splice(j, 1);
             signal.mask2.splice(j, 1);
@@ -306,24 +302,22 @@ function detectSignals(
       if (peak.kind) signal1D.kind = peak.kind;
       signals.push(signal1D);
     } else {
-      let tmp = peak.x + peak.shape.width;
+      let tmp = peak.x + peak.width;
       signal1D.stopX = Math.max(signal1D.stopX, tmp);
       signal1D.startX = Math.min(signal1D.startX, tmp);
       signal1D.nbPeaks++;
       signal1D.peaks.push({
         x: peak.x,
         intensity: peak.y,
-        shape: {
-          width: peak.shape.width,
-        },
+        width: peak.width,
       });
       signal1D.integralData.from = Math.min(
         signal1D.integralData.from,
-        peak.x - peak.shape.width * 3,
+        peak.x - peak.width * 3,
       );
       signal1D.integralData.to = Math.max(
         signal1D.integralData.to,
-        peak.x + peak.shape.width * 3,
+        peak.x + peak.width * 3,
       );
       if (peak.kind) signal1D.kind = peak.kind;
     }
@@ -371,5 +365,5 @@ function detectSignals(
  * @private
  */
 function computeArea(peak: Peak1DIntern) {
-  return Math.abs(peak.intensity * peak.shape.width * 1.57); // todo add an option with this value: 1.772453851
+  return Math.abs(peak.intensity * peak.width * 1.57); // todo add an option with this value: 1.772453851
 }

package/src/peaks/util/determineRealTop.ts CHANGED Viewed

@@ -1,10 +1,8 @@
 import LM from 'ml-levenberg-marquardt';
-import { gaussian2D } from 'ml-peak-shape-generator';
+import { Gaussian2D } from 'ml-peak-shape-generator';
 import type { MPFPeak } from '../../types/MPFPeak';
-const { fct: gaussian2DFct } = gaussian2D;
 const direction8X = [-1, -1, -1, 0, 0, 1, 1, 1];
 const direction8Y = [-1, 0, 1, -1, 1, -1, 0, 1];
 const direction16X = [-2, -2, -2, -2, -2, -1, -1, 0, 0, 1, 1, 2, 2, 2, 2, 2];
@@ -142,6 +140,7 @@ function fitGaussian(
 }
 function paramGaussian2D(intervalX: number, intervalY: number, nCols: number) {
+  const gaussian2D = new Gaussian2D();
   return (p: number[]) => {
     return (t: number) => {
       let nL = p.length / 5;
@@ -149,13 +148,12 @@ function paramGaussian2D(intervalX: number, intervalY: number, nCols: number) {
       let xIndex = t % nCols;
       let yIndex = (t - xIndex) / nCols;
       for (let i = 0; i < nL; i++) {
+        gaussian2D.fwhm = {x: p[i + 3 * nL], y: p[i + 4 * nL]};
         result +=
           p[i + 2 * nL] *
-          gaussian2DFct(
+          gaussian2D.fct(
             (xIndex - p[i]) * intervalX,
             (yIndex - p[i + nL]) * intervalY,
-            p[i + 3 * nL],
-            p[i + 4 * nL],
           );
       }
       return result;