npm - nmr-processing - Versions diffs - 6.0.7 → 7.0.1 - Mend

nmr-processing 6.0.7 → 7.0.1

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 (24) hide show

package/lib/peaks/NMRPeak1D.d.ts +5 -2
package/lib/peaks/peaksToRanges.d.ts +3 -1
package/lib/peaks/peaksToRanges.js.map +1 -1
package/lib/peaks/util/jAnalyzer.d.ts +1 -1
package/lib/peaks/util/jAnalyzer.js.map +1 -1
package/lib/prediction/utils/getFilteredIDiaIDs.d.ts +1 -1
package/lib/utilities/resurrectRange.js +12 -16
package/lib/utilities/resurrectRange.js.map +1 -1
package/lib/xy/xyAutoPeaksPicking.d.ts +5 -4
package/lib/xy/xyAutoPeaksPicking.js +14 -23
package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
package/lib-esm/peaks/peaksToRanges.js.map +1 -1
package/lib-esm/peaks/util/jAnalyzer.js.map +1 -1
package/lib-esm/utilities/resurrectRange.js +12 -16
package/lib-esm/utilities/resurrectRange.js.map +1 -1
package/lib-esm/xy/xyAutoPeaksPicking.js +15 -24
package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
package/package.json +11 -12
package/src/{openchemlib.d.ts → openchemlib-utils.d.ts} +0 -1
package/src/peaks/NMRPeak1D.ts +5 -2
package/src/peaks/peaksToRanges.ts +5 -3
package/src/peaks/util/jAnalyzer.ts +3 -1
package/src/utilities/resurrectRange.ts +17 -17
package/src/xy/xyAutoPeaksPicking.ts +25 -36

package/lib/peaks/NMRPeak1D.d.ts CHANGED Viewed

@@ -1,4 +1,7 @@
-import type { Peak1D } from 'ml-gsd';
-export interface NMRPeak1D extends Peak1D {
+import type { PeakXYWidth } from 'cheminfo-types';
+import type { Shape1D } from 'ml-peak-shape-generator';
+export interface NMRPeak1D extends PeakXYWidth {
     kind?: string;
+    fwhm?: number;
+    shape?: Shape1D;
 }

package/lib/peaks/peaksToRanges.d.ts CHANGED Viewed

@@ -54,7 +54,9 @@ export interface OptionsDetectSignals {
     frequency?: number;
     nucleus?: string;
 }
+declare type NMRPeak1DIntern = Omit<NMRPeak1D, 'fwhm' | 'shape'>;
 /**
  * This function clustering peaks and calculate the integration value for each range from the peak list returned from extractPeaks function.
  */
-export declare function peaksToRanges(data: DataXY, peakList: NMRPeak1D[], options?: OptionsPeaksToRanges): NMRRange[];
+export declare function peaksToRanges(data: DataXY, peakList: NMRPeak1DIntern[], options?: OptionsPeaksToRanges): NMRRange[];
+export {};

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

	@@ -1 +1 @@
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package/lib/peaks/util/jAnalyzer.d.ts CHANGED Viewed

@@ -10,7 +10,7 @@ interface IntergralData {
     from: number;
     to: number;
 }
-export declare type Peak1DIntern = Omit<NMRPeak1D, 'y'> & {
+export declare type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape' | 'fwhm'> & {
     intensity: number;
 };
 export interface SignalIntern {

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

	@@ -1 +1 @@
1	- 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package/lib/prediction/utils/getFilteredIDiaIDs.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-/// <reference path="../../../src/openchemlib.d.ts" />
+/// <reference path="../../../src/openchemlib-utils.d.ts" />
 import type { Molecule } from 'openchemlib';
 import type { GroupDiastereotopicAtomIDs } from 'openchemlib-utils';
 export interface GroupDiaIDsWithHose extends GroupDiastereotopicAtomIDs {

package/lib/utilities/resurrectRange.js CHANGED Viewed

@@ -9,16 +9,12 @@ function resurrectRange(part, options = {}) {
     const split = (0, splitParenthesis_1.splitParenthesis)(part);
     if (!split.before)
         return;
-    // before parenthesis there should be only numbers but we will still split with space
-    const beforeParts = split.before
-        .split(/(?: |(?<=[0-9])-)/)
-        .map((part) => Number(part))
-        .filter((part) => !Number.isNaN(part));
-    if (beforeParts.length < 1 || beforeParts.length > 2) {
+    const beforeMatch = /.*?(?<from>-?[0-9.]+)-?(?<to>-?[0-9.]*).*/.exec(split.before);
+    if (!beforeMatch || !beforeMatch.groups)
         return;
-    }
-    const from = beforeParts[0];
-    const to = beforeParts.length > 1 ? beforeParts[1] : beforeParts[0];
+    const isARange = beforeMatch.groups.to !== '';
+    const from = Number(beforeMatch.groups.from);
+    const to = isARange ? Number(beforeMatch.groups.to) : from;
     const insideParts = split.inside.split(/ *, */);
     let signal = { delta: NaN, js: [] };
     let range = { from, to, signals: [signal] };
@@ -30,22 +26,22 @@ function resurrectRange(part, options = {}) {
     if (multiplicityParts.length === 1) {
         const multiplicity = multiplicityParts[0];
         if (multiplicity === 'm') {
-            if (beforeParts.length === 1) {
-                // a complex signal
-                signal.delta = beforeParts[0];
+            if (isARange) {
+                // a real range
+                signal.delta = (from + to) / 2;
                 signal.multiplicity = multiplicity;
             }
             else {
-                // a real range
-                signal.delta = (beforeParts[0] + beforeParts[1]) / 2;
+                // a complex signal
+                signal.delta = from;
                 signal.multiplicity = multiplicity;
             }
         }
         else {
             // looks like a real multiplicity, s, d, dd, etc..
-            if (beforeParts.length === 1) {
+            if (!isARange) {
                 // a complex signal
-                signal.delta = beforeParts[0];
+                signal.delta = from;
                 signal.multiplicity = multiplicity;
             }
         }

package/lib/utilities/resurrectRange.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/xy/xyAutoPeaksPicking.d.ts CHANGED Viewed

@@ -1,13 +1,14 @@
 import { DataXY } from 'cheminfo-types';
-import type { Peak1D, GSDOptions, OptimizePeaksOptions, JoinBroadPeaksOptions } from 'ml-gsd';
-export interface IGetPeakListOptions extends GSDOptions, OptimizePeaksOptions, JoinBroadPeaksOptions {
+import type { GSDOptions, OptimizePeaksOptions, JoinBroadPeaksOptions } from 'ml-gsd';
+import { NMRPeak1D } from '..';
+export interface GetPeakListOptions extends GSDOptions, OptimizePeaksOptions, JoinBroadPeaksOptions {
     /**
      * If it is true, the peaks parameters will be optimized.
      * @default false
      */
     optimize: boolean;
 }
-export interface OptionsXYAutoPeaksPicking extends Partial<IGetPeakListOptions> {
+export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
     /**
      * Low limit value in the x axis to extract a sub set of points from the input data.
      */
@@ -32,4 +33,4 @@ export interface OptionsXYAutoPeaksPicking extends Partial<IGetPeakListOptions>
      */
     useSanPlot?: boolean;
 }
-export declare function xyAutoPeaksPicking(data: DataXY, options?: OptionsXYAutoPeaksPicking): Peak1D[];
+export declare function xyAutoPeaksPicking(data: DataXY, options?: OptionsXYAutoPeaksPicking): NMRPeak1D[];

package/lib/xy/xyAutoPeaksPicking.js CHANGED Viewed

@@ -4,19 +4,21 @@ exports.xyAutoPeaksPicking = void 0;
 const ml_gsd_1 = require("ml-gsd");
 const ml_spectra_processing_1 = require("ml-spectra-processing");
 function xyAutoPeaksPicking(data, options = {}) {
-    const { from, to, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorWidth = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, lookNegative = false, sgOptions = { windowSize: 9, polynomial: 3 }, } = options;
+    const { from, to, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorLimits = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, sgOptions = {}, lookNegative = false, } = options;
+    const { windowSize = 9, polynomial = 3 } = sgOptions;
     if (from !== undefined && to !== undefined) {
         data = (0, ml_spectra_processing_1.xyExtract)(data, { zones: [{ from, to }] });
     }
-    if (data.x.length < sgOptions.windowSize)
+    if (data.x.length < windowSize)
         return [];
     const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
     let getPeakOptions = {
         shape,
         broadWidth,
         optimize,
-        factorWidth,
-        sgOptions,
+        factorLimits,
+        maxCriteria: true,
+        sgOptions: { windowSize, polynomial },
         minMaxRatio,
         broadRatio,
         noiseLevel: cutOff.positive,
@@ -27,23 +29,24 @@ function xyAutoPeaksPicking(data, options = {}) {
     let peaks = getPeakList(data, getPeakOptions);
     if (lookNegative) {
         getPeakOptions.noiseLevel = cutOff.negative;
-        peaks.push(...getNegativePeaks(data, getPeakOptions));
+        getPeakOptions.maxCriteria = false;
+        peaks.push(...getPeakList(data, getPeakOptions));
     }
     return peaks;
 }
 exports.xyAutoPeaksPicking = xyAutoPeaksPicking;
 function getPeakList(data, options) {
-    const { shape, broadWidth, optimize, factorWidth, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
+    const { shape, broadWidth, optimize, maxCriteria, factorLimits, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
     let peakList = (0, ml_gsd_1.gsd)(data, {
-        shape,
         sgOptions,
+        maxCriteria,
         minMaxRatio,
         noiseLevel,
         smoothY,
         realTopDetection,
     });
     if (broadWidth) {
-        peakList = (0, ml_gsd_1.joinBroadPeaks)(data, peakList, {
+        peakList = (0, ml_gsd_1.joinBroadPeaks)(peakList, {
             broadRatio,
             broadWidth,
             shape,
@@ -51,25 +54,13 @@ function getPeakList(data, options) {
         });
     }
     if (optimize) {
-        peakList = (0, ml_gsd_1.optimizePeaks)(data, peakList, {
+        return (0, ml_gsd_1.optimizePeaks)(data, peakList, {
             shape,
-            factorWidth,
+            factorLimits,
             optimization,
         });
     }
-    return peakList;
-}
-function getNegativePeaks(data, options) {
-    let { x, y } = data;
-    let negativeDataY = new Float64Array(data.y.length);
-    for (let i = 0; i < negativeDataY.length; i++) {
-        negativeDataY[i] = -1 * y[i];
-    }
-    let peakList = getPeakList({ x, y: negativeDataY }, options);
-    for (const peak of peakList) {
-        peak.y *= -1;
-    }
-    return peakList;
+    return (0, ml_gsd_1.appendShapeAndFWHM)(peakList, { shape });
 }
 function getCutOff(data, options) {
     const { noiseLevel, useSanPlot, thresholdFactor } = options;

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

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

	@@ -1 +1 @@
1	- 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package/lib-esm/utilities/resurrectRange.js CHANGED Viewed

@@ -6,16 +6,12 @@ export function resurrectRange(part, options = {}) {
     const split = splitParenthesis(part);
     if (!split.before)
         return;
-    // before parenthesis there should be only numbers but we will still split with space
-    const beforeParts = split.before
-        .split(/(?: |(?<=[0-9])-)/)
-        .map((part) => Number(part))
-        .filter((part) => !Number.isNaN(part));
-    if (beforeParts.length < 1 || beforeParts.length > 2) {
+    const beforeMatch = /.*?(?<from>-?[0-9.]+)-?(?<to>-?[0-9.]*).*/.exec(split.before);
+    if (!beforeMatch || !beforeMatch.groups)
         return;
-    }
-    const from = beforeParts[0];
-    const to = beforeParts.length > 1 ? beforeParts[1] : beforeParts[0];
+    const isARange = beforeMatch.groups.to !== '';
+    const from = Number(beforeMatch.groups.from);
+    const to = isARange ? Number(beforeMatch.groups.to) : from;
     const insideParts = split.inside.split(/ *, */);
     let signal = { delta: NaN, js: [] };
     let range = { from, to, signals: [signal] };
@@ -27,22 +23,22 @@ export function resurrectRange(part, options = {}) {
     if (multiplicityParts.length === 1) {
         const multiplicity = multiplicityParts[0];
         if (multiplicity === 'm') {
-            if (beforeParts.length === 1) {
-                // a complex signal
-                signal.delta = beforeParts[0];
+            if (isARange) {
+                // a real range
+                signal.delta = (from + to) / 2;
                 signal.multiplicity = multiplicity;
             }
             else {
-                // a real range
-                signal.delta = (beforeParts[0] + beforeParts[1]) / 2;
+                // a complex signal
+                signal.delta = from;
                 signal.multiplicity = multiplicity;
             }
         }
         else {
             // looks like a real multiplicity, s, d, dd, etc..
-            if (beforeParts.length === 1) {
+            if (!isARange) {
                 // a complex signal
-                signal.delta = beforeParts[0];
+                signal.delta = from;
                 signal.multiplicity = multiplicity;
             }
         }

package/lib-esm/utilities/resurrectRange.js.map CHANGED Viewed

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

@@ -1,19 +1,21 @@
-import { gsd, joinBroadPeaks, optimizePeaks } from 'ml-gsd';
+import { gsd, optimizePeaks, joinBroadPeaks, appendShapeAndFWHM } from 'ml-gsd';
 import { xyExtract, xNoiseSanPlot, xAbsoluteMedian, } from 'ml-spectra-processing';
 export function xyAutoPeaksPicking(data, options = {}) {
-    const { from, to, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorWidth = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, lookNegative = false, sgOptions = { windowSize: 9, polynomial: 3 }, } = options;
+    const { from, to, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorLimits = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, sgOptions = {}, lookNegative = false, } = options;
+    const { windowSize = 9, polynomial = 3 } = sgOptions;
     if (from !== undefined && to !== undefined) {
         data = xyExtract(data, { zones: [{ from, to }] });
     }
-    if (data.x.length < sgOptions.windowSize)
+    if (data.x.length < windowSize)
         return [];
     const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
     let getPeakOptions = {
         shape,
         broadWidth,
         optimize,
-        factorWidth,
-        sgOptions,
+        factorLimits,
+        maxCriteria: true,
+        sgOptions: { windowSize, polynomial },
         minMaxRatio,
         broadRatio,
         noiseLevel: cutOff.positive,
@@ -24,22 +26,23 @@ export function xyAutoPeaksPicking(data, options = {}) {
     let peaks = getPeakList(data, getPeakOptions);
     if (lookNegative) {
         getPeakOptions.noiseLevel = cutOff.negative;
-        peaks.push(...getNegativePeaks(data, getPeakOptions));
+        getPeakOptions.maxCriteria = false;
+        peaks.push(...getPeakList(data, getPeakOptions));
     }
     return peaks;
 }
 function getPeakList(data, options) {
-    const { shape, broadWidth, optimize, factorWidth, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
+    const { shape, broadWidth, optimize, maxCriteria, factorLimits, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
     let peakList = gsd(data, {
-        shape,
         sgOptions,
+        maxCriteria,
         minMaxRatio,
         noiseLevel,
         smoothY,
         realTopDetection,
     });
     if (broadWidth) {
-        peakList = joinBroadPeaks(data, peakList, {
+        peakList = joinBroadPeaks(peakList, {
             broadRatio,
             broadWidth,
             shape,
@@ -47,25 +50,13 @@ function getPeakList(data, options) {
         });
     }
     if (optimize) {
-        peakList = optimizePeaks(data, peakList, {
+        return optimizePeaks(data, peakList, {
             shape,
-            factorWidth,
+            factorLimits,
             optimization,
         });
     }
-    return peakList;
-}
-function getNegativePeaks(data, options) {
-    let { x, y } = data;
-    let negativeDataY = new Float64Array(data.y.length);
-    for (let i = 0; i < negativeDataY.length; i++) {
-        negativeDataY[i] = -1 * y[i];
-    }
-    let peakList = getPeakList({ x, y: negativeDataY }, options);
-    for (const peak of peakList) {
-        peak.y *= -1;
-    }
-    return peakList;
+    return appendShapeAndFWHM(peakList, { shape });
 }
 function getCutOff(data, options) {
     const { noiseLevel, useSanPlot, thresholdFactor } = options;

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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "6.0.7",
+  "version": "7.0.1",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -38,16 +38,16 @@
   },
   "homepage": "https://github.com/cheminfo/nmr-processing#readme",
   "devDependencies": {
-    "@types/jest": "^27.4.0",
+    "@types/jest": "^27.4.1",
     "cheminfo-build": "^1.1.11",
-    "cheminfo-types": "^0.9.1",
-    "eslint": "^8.8.0",
+    "cheminfo-types": "^1.0.0",
+    "eslint": "^8.9.0",
     "eslint-config-cheminfo-typescript": "^10.3.0",
-    "jest": "^27.4.7",
+    "jest": "^27.5.1",
     "jest-matcher-deep-close-to": "^3.0.2",
     "md5": "^2.3.0",
     "ml-array-median": "^1.1.6",
-    "nmr-xy-testdata": "^0.5.0",
+    "nmr-xy-testdata": "^0.5.1",
     "openchemlib": "^7.4.3",
     "prettier": "^2.5.1",
     "rimraf": "^3.0.2",
@@ -55,7 +55,6 @@
     "typescript": "^4.5.5"
   },
   "dependencies": {
-    "assign-deep": "^1.0.1",
     "binary-search": "^1.3.6",
     "cross-fetch": "^3.1.5",
     "form-data": "^4.0.0",
@@ -64,18 +63,18 @@
     "ml-array-rescale": "^1.3.7",
     "ml-array-sequential-fill": "^1.1.8",
     "ml-array-sum": "^1.1.6",
-    "ml-gsd": "^9.1.0",
+    "ml-gsd": "^10.1.1",
     "ml-hclust": "^3.1.0",
     "ml-levenberg-marquardt": "^4.0.0",
     "ml-matrix": "^6.8.2",
     "ml-matrix-convolution": "^1.0.0",
     "ml-matrix-peaks-finder": "^1.0.0",
-    "ml-peak-shape-generator": "^4.0.2",
+    "ml-peak-shape-generator": "^4.1.1",
     "ml-simple-clustering": "^0.1.0",
     "ml-sparse-matrix": "^2.1.0",
-    "ml-spectra-processing": "^9.0.0",
+    "ml-spectra-processing": "^11.0.0",
     "ml-tree-set": "^0.1.1",
-    "openchemlib-utils": "^1.8.0",
-    "spectrum-generator": "^6.0.2"
+    "openchemlib-utils": "^1.9.0",
+    "spectrum-generator": "^7.0.1"
   }
 }

package/src/{openchemlib.d.ts → openchemlib-utils.d.ts} RENAMED Viewed

@@ -11,7 +11,6 @@ declare module 'openchemlib-utils' {
   function getGroupedDiastereotopicAtomIDs(
     molecule: Molecule,
   ): GroupedDiastereotopicAtomIDs;
   interface GetHoseCodesForAtomOptions {
     minSphereSize?: number;
     maxSphereSize?: number;

package/src/peaks/NMRPeak1D.ts CHANGED Viewed

@@ -1,5 +1,8 @@
-import type { Peak1D } from 'ml-gsd';
+import type { PeakXYWidth } from 'cheminfo-types';
+import type { Shape1D } from 'ml-peak-shape-generator';
-export interface NMRPeak1D extends Peak1D {
+export interface NMRPeak1D extends PeakXYWidth {
   kind?: string;
+  fwhm?: number;
+  shape?: Shape1D;
 }

package/src/peaks/peaksToRanges.ts CHANGED Viewed

@@ -70,6 +70,8 @@ type SignalInternMandatory = MakeMandatory<
   'symRank' | 'mask' | 'peaksComp' | 'mask2' | 'maskPattern'
 >;
+type NMRPeak1DIntern = Omit<NMRPeak1D, 'fwhm' | 'shape'>;
 function checkSignalAfterCompilePattern(
   signal: SignalIntern,
 ): asserts signal is SignalInternMandatory {
@@ -83,7 +85,7 @@ function checkSignalAfterCompilePattern(
 }
 const assignSignal = (
-  peak: NMRPeak1D,
+  peak: NMRPeak1DIntern,
   frequency: number,
   nucleus: string,
 ): SignalIntern => {
@@ -115,7 +117,7 @@ const assignSignal = (
 export function peaksToRanges(
   data: DataXY,
-  peakList: NMRPeak1D[],
+  peakList: NMRPeak1DIntern[],
   options: OptionsPeaksToRanges = {},
 ): NMRRange[] {
   let {
@@ -280,7 +282,7 @@ export function peaksToRanges(
 function detectSignals(
   data: DataXY,
-  peakList: NMRPeak1D[],
+  peakList: NMRPeak1DIntern[],
   options: OptionsDetectSignals = {},
 ): SignalIntern[] {
   let {

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

@@ -29,7 +29,9 @@ interface IntergralData {
   to: number;
 }
-export type Peak1DIntern = Omit<NMRPeak1D, 'y'> & { intensity: number };
+export type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape' | 'fwhm'> & {
+  intensity: number;
+};
 export interface SignalIntern {
   delta: number;

package/src/utilities/resurrectRange.ts CHANGED Viewed

@@ -9,17 +9,17 @@ export function resurrectRange(part: string, options: any = {}) {
   const { nucleus = '1h', frequency = 400 } = options;
   const split = splitParenthesis(part);
   if (!split.before) return;
-  // before parenthesis there should be only numbers but we will still split with space
-  const beforeParts = split.before
-    .split(/(?: |(?<=[0-9])-)/)
-    .map((part: string) => Number(part))
-    .filter((part: number) => !Number.isNaN(part));
-  if (beforeParts.length < 1 || beforeParts.length > 2) {
-    return;
-  }
-  const from = beforeParts[0];
-  const to = beforeParts.length > 1 ? beforeParts[1] : beforeParts[0];
+  const beforeMatch = /.*?(?<from>-?[0-9.]+)-?(?<to>-?[0-9.]*).*/.exec(
+    split.before,
+  );
+  if (!beforeMatch || !beforeMatch.groups) return;
+  const isARange = beforeMatch.groups.to !== '';
+  const from = Number(beforeMatch.groups.from);
+  const to = isARange ? Number(beforeMatch.groups.to) : from;
   const insideParts = split.inside.split(/ *, */);
   let signal: NMRSignal1D = { delta: NaN, js: [] };
   let range: NMRRange = { from, to, signals: [signal] };
@@ -37,20 +37,20 @@ export function resurrectRange(part: string, options: any = {}) {
   if (multiplicityParts.length === 1) {
     const multiplicity = multiplicityParts[0];
     if (multiplicity === 'm') {
-      if (beforeParts.length === 1) {
-        // a complex signal
-        signal.delta = beforeParts[0];
+      if (isARange) {
+        // a real range
+        signal.delta = (from + to) / 2;
         signal.multiplicity = multiplicity;
       } else {
-        // a real range
-        signal.delta = (beforeParts[0] + beforeParts[1]) / 2;
+        // a complex signal
+        signal.delta = from;
         signal.multiplicity = multiplicity;
       }
     } else {
       // looks like a real multiplicity, s, d, dd, etc..
-      if (beforeParts.length === 1) {
+      if (!isARange) {
         // a complex signal
-        signal.delta = beforeParts[0];
+        signal.delta = from;
         signal.multiplicity = multiplicity;
       }
     }

package/src/xy/xyAutoPeaksPicking.ts CHANGED Viewed

@@ -1,7 +1,6 @@
 import { DataXY } from 'cheminfo-types';
-import { gsd, joinBroadPeaks, optimizePeaks } from 'ml-gsd';
+import { gsd, optimizePeaks, joinBroadPeaks, appendShapeAndFWHM } from 'ml-gsd';
 import type {
-  Peak1D,
   GSDOptions,
   OptimizePeaksOptions,
   JoinBroadPeaksOptions,
@@ -12,6 +11,8 @@ import {
   xAbsoluteMedian,
 } from 'ml-spectra-processing';
+import { NMRPeak1D } from '..';
 /**
  * Implementation of the peak picking method described by Cobas in:
  * A new approach to improving automated analysis of proton NMR spectra
@@ -25,7 +26,7 @@ interface OptionsGetCutOff {
   thresholdFactor: number;
 }
-export interface IGetPeakListOptions
+export interface GetPeakListOptions
   extends GSDOptions,
     OptimizePeaksOptions,
     JoinBroadPeaksOptions {
@@ -35,9 +36,7 @@ export interface IGetPeakListOptions
    */
   optimize: boolean;
 }
-export interface OptionsXYAutoPeaksPicking
-  extends Partial<IGetPeakListOptions> {
+export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
   /**
    * Low limit value in the x axis to extract a sub set of points from the input data.
    */
@@ -66,7 +65,7 @@ export interface OptionsXYAutoPeaksPicking
 export function xyAutoPeaksPicking(
   data: DataXY,
   options: OptionsXYAutoPeaksPicking = {},
-): Peak1D[] {
+): NMRPeak1D[] {
   const {
     from,
     to,
@@ -77,28 +76,31 @@ export function xyAutoPeaksPicking(
     useSanPlot = false,
     smoothY = true,
     optimize = false,
-    factorWidth = 4,
+    factorLimits = 4,
     realTopDetection = true,
     shape = { kind: 'gaussian' },
     optimization = { kind: 'lm' },
     broadWidth = 0.25,
+    sgOptions = {},
     lookNegative = false,
-    sgOptions = { windowSize: 9, polynomial: 3 },
   } = options;
+  const { windowSize = 9, polynomial = 3 } = sgOptions;
   if (from !== undefined && to !== undefined) {
     data = xyExtract(data, { zones: [{ from, to }] });
   }
-  if (data.x.length < sgOptions.windowSize) return [];
+  if (data.x.length < windowSize) return [];
   const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
-  let getPeakOptions: IGetPeakListOptions = {
+  let getPeakOptions: GetPeakListOptions = {
     shape,
     broadWidth,
     optimize,
-    factorWidth,
-    sgOptions,
+    factorLimits,
+    maxCriteria: true,
+    sgOptions: { windowSize, polynomial },
     minMaxRatio,
     broadRatio,
     noiseLevel: cutOff.positive,
@@ -111,17 +113,19 @@ export function xyAutoPeaksPicking(
   if (lookNegative) {
     getPeakOptions.noiseLevel = cutOff.negative;
-    peaks.push(...getNegativePeaks(data, getPeakOptions));
+    getPeakOptions.maxCriteria = false;
+    peaks.push(...getPeakList(data, getPeakOptions));
   }
   return peaks;
 }
-function getPeakList(data: DataXY, options: IGetPeakListOptions) {
+function getPeakList(data: DataXY, options: GetPeakListOptions) {
   const {
     shape,
     broadWidth,
     optimize,
-    factorWidth,
+    maxCriteria,
+    factorLimits,
     sgOptions,
     minMaxRatio,
     broadRatio,
@@ -132,8 +136,8 @@ function getPeakList(data: DataXY, options: IGetPeakListOptions) {
   } = options;
   let peakList = gsd(data, {
-    shape,
     sgOptions,
+    maxCriteria,
     minMaxRatio,
     noiseLevel,
     smoothY,
@@ -141,7 +145,7 @@ function getPeakList(data: DataXY, options: IGetPeakListOptions) {
   });
   if (broadWidth) {
-    peakList = joinBroadPeaks(data, peakList, {
+    peakList = joinBroadPeaks(peakList, {
       broadRatio,
       broadWidth,
       shape,
@@ -150,29 +154,14 @@ function getPeakList(data: DataXY, options: IGetPeakListOptions) {
   }
   if (optimize) {
-    peakList = optimizePeaks(data, peakList, {
+    return optimizePeaks(data, peakList, {
       shape,
-      factorWidth,
+      factorLimits,
       optimization,
     });
   }
-  return peakList;
-}
-function getNegativePeaks(data: DataXY, options: IGetPeakListOptions) {
-  let { x, y } = data;
-  let negativeDataY = new Float64Array(data.y.length);
-  for (let i = 0; i < negativeDataY.length; i++) {
-    negativeDataY[i] = -1 * y[i];
-  }
-  let peakList = getPeakList({ x, y: negativeDataY }, options);
-  for (const peak of peakList) {
-    peak.y *= -1;
-  }
-  return peakList;
+  return appendShapeAndFWHM(peakList, { shape });
 }
 function getCutOff(data: number[] | Float64Array, options: OptionsGetCutOff) {