nmr-processing 8.7.1 → 9.0.1

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 (16) hide show
  1. package/lib/peaks/peaksToRanges.js +12 -14
  2. package/lib/peaks/peaksToRanges.js.map +1 -1
  3. package/lib/signals/utils/jAnalyzer.js +2 -1
  4. package/lib/signals/utils/jAnalyzer.js.map +1 -1
  5. package/lib/xyz/xyzJResAnalyzer.js +2 -1
  6. package/lib/xyz/xyzJResAnalyzer.js.map +1 -1
  7. package/lib-esm/peaks/peaksToRanges.js +12 -14
  8. package/lib-esm/peaks/peaksToRanges.js.map +1 -1
  9. package/lib-esm/signals/utils/jAnalyzer.js +2 -1
  10. package/lib-esm/signals/utils/jAnalyzer.js.map +1 -1
  11. package/lib-esm/xyz/xyzJResAnalyzer.js +2 -1
  12. package/lib-esm/xyz/xyzJResAnalyzer.js.map +1 -1
  13. package/package.json +2 -2
  14. package/src/peaks/peaksToRanges.ts +12 -16
  15. package/src/signals/utils/jAnalyzer.ts +2 -1
  16. package/src/xyz/xyzJResAnalyzer.ts +2 -1
package/lib/peaks/peaksToRanges.js CHANGED
@@ -23,13 +23,13 @@ const assignSignal = (peak, frequency, nucleus) => {
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  delta: NaN,
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  nbPeaks: 1,
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  kind: 'signal',
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- startX: peak.x - peak.width,
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- stopX: peak.x + peak.width,
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+ startX: peak.x - peak.width / frequency,
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+ stopX: peak.x + peak.width / frequency,
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  observe: frequency,
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  nucleus,
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  integralData: {
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- from: peak.x - peak.width * 3,
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- to: peak.x + peak.width * 3,
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+ from: peak.x - (peak.width * 3) / frequency,
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+ to: peak.x + (peak.width * 3) / frequency,
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  value: 0,
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  },
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  peaks: [
@@ -81,7 +81,7 @@ function peaksToRanges(data, peakList, options = {}) {
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  sum = 0;
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  let peaksO = [];
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  for (let j = signal.maskPattern.length - 1; j >= 0; j--) {
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- sum += computeArea(signal.peaks[j]);
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+ sum += computeArea(signal.peaks[j], frequency);
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  if (!signal.maskPattern[j]) {
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  let peakR = signal.peaks.splice(j, 1)[0];
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  peaksO.push({
@@ -93,7 +93,7 @@ function peaksToRanges(data, peakList, options = {}) {
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  signal.mask2.splice(j, 1);
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  signal.maskPattern.splice(j, 1);
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  signal.nbPeaks--;
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- nHi += computeArea(peakR);
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+ nHi += computeArea(peakR, frequency);
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  }
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  }
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  if (peaksO.length > 0) {
@@ -199,7 +199,7 @@ function detectSignals(data, peakList, options = {}) {
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  signals.push(signal1D);
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  }
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  else {
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- let tmp = peak.x + peak.width;
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+ let tmp = peak.x + peak.width / frequency;
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  signal1D.stopX = Math.max(signal1D.stopX, tmp);
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  signal1D.startX = Math.min(signal1D.startX, tmp);
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  signal1D.nbPeaks++;
@@ -208,8 +208,8 @@ function detectSignals(data, peakList, options = {}) {
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  intensity: peak.y,
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  width: peak.width,
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  });
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- signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.width * 3);
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- signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.width * 3);
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+ signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - (peak.width * 3) / frequency);
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+ signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + (peak.width * 3) / frequency);
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  if (peak.kind)
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  signal1D.kind = peak.kind;
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  }
@@ -221,7 +221,7 @@ function detectSignals(data, peakList, options = {}) {
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  let chemicalShift = 0;
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  let integralPeaks = 0;
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  for (const peak of peaks) {
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- let area = computeArea(peak);
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+ let area = computeArea(peak, frequency);
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  chemicalShift += peak.x * area;
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  integralPeaks += area;
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  }
@@ -249,11 +249,9 @@ function detectSignals(data, peakList, options = {}) {
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  exports.detectSignals = detectSignals;
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  /**
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  * Return the area of a Lorentzian function
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- * @param {object} peak - object with peak information
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- * @return {Number}
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  * @private
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  */
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- function computeArea(peak) {
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- return Math.abs(peak.intensity * peak.width * 1.57); // todo add an option with this value: 1.772453851
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+ function computeArea(peak, frequency) {
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+ return Math.abs(((peak.intensity * peak.width) / frequency) * 1.57); // todo add an option with this value: 1.772453851
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  }
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  //# sourceMappingURL=peaksToRanges.js.map
package/lib/peaks/peaksToRanges.js.map CHANGED
@@ -1 +1 @@
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package/lib/signals/utils/jAnalyzer.js CHANGED
@@ -139,6 +139,7 @@ exports.default = {
139
139
  // Before to return, change the units of peaksComp from Hz to PPM again
140
140
  for (let peakComp of signal.peaksComp) {
141
141
  peakComp.x /= signal.observe;
142
+ peakComp.width *= signal.observe;
142
143
  }
143
144
  return signal;
144
145
  },
@@ -377,7 +378,7 @@ function symmetrize(signalInput, maxError, iteration, key) {
377
378
  peaks[i] = {
378
379
  x: peak[jAxis] * newSignal.observe,
379
380
  intensity: peak[intensity],
380
- width: peak.width,
381
+ width: peak.width / newSignal.observe,
381
382
  };
382
383
  }
383
384
  // Join the peaks that are closer than 0.25 Hz
package/lib/signals/utils/jAnalyzer.js.map CHANGED
@@ -1 +1 @@
1
- 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package/lib/xyz/xyzJResAnalyzer.js CHANGED
@@ -37,6 +37,7 @@ function compilePattern(signals, options) {
37
37
  dx: signals[0].x.resolution,
38
38
  dy: signals[0].y.resolution,
39
39
  };
40
+ const defaultWidth = 0.02 * observedFrequencies[0];
40
41
  const newSignals = JSON.parse(JSON.stringify(signals));
41
42
  //adapt to 1D jAnalyzer
42
43
  for (const signal of newSignals) {
@@ -52,7 +53,7 @@ function compilePattern(signals, options) {
52
53
  };
53
54
  for (const peak of peaks) {
54
55
  if (!peak.width)
55
- peak.width = 0.02;
56
+ peak.width = defaultWidth;
56
57
  }
57
58
  peaks.sort((a, b) => a.y - b.y);
58
59
  }
package/lib/xyz/xyzJResAnalyzer.js.map CHANGED
@@ -1 +1 @@
1
- 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package/lib-esm/peaks/peaksToRanges.js CHANGED
@@ -17,13 +17,13 @@ const assignSignal = (peak, frequency, nucleus) => {
17
17
  delta: NaN,
18
18
  nbPeaks: 1,
19
19
  kind: 'signal',
20
- startX: peak.x - peak.width,
21
- stopX: peak.x + peak.width,
20
+ startX: peak.x - peak.width / frequency,
21
+ stopX: peak.x + peak.width / frequency,
22
22
  observe: frequency,
23
23
  nucleus,
24
24
  integralData: {
25
- from: peak.x - peak.width * 3,
26
- to: peak.x + peak.width * 3,
25
+ from: peak.x - (peak.width * 3) / frequency,
26
+ to: peak.x + (peak.width * 3) / frequency,
27
27
  value: 0,
28
28
  },
29
29
  peaks: [
@@ -75,7 +75,7 @@ export function peaksToRanges(data, peakList, options = {}) {
75
75
  sum = 0;
76
76
  let peaksO = [];
77
77
  for (let j = signal.maskPattern.length - 1; j >= 0; j--) {
78
- sum += computeArea(signal.peaks[j]);
78
+ sum += computeArea(signal.peaks[j], frequency);
79
79
  if (!signal.maskPattern[j]) {
80
80
  let peakR = signal.peaks.splice(j, 1)[0];
81
81
  peaksO.push({
@@ -87,7 +87,7 @@ export function peaksToRanges(data, peakList, options = {}) {
87
87
  signal.mask2.splice(j, 1);
88
88
  signal.maskPattern.splice(j, 1);
89
89
  signal.nbPeaks--;
90
- nHi += computeArea(peakR);
90
+ nHi += computeArea(peakR, frequency);
91
91
  }
92
92
  }
93
93
  if (peaksO.length > 0) {
@@ -192,7 +192,7 @@ export function detectSignals(data, peakList, options = {}) {
192
192
  signals.push(signal1D);
193
193
  }
194
194
  else {
195
- let tmp = peak.x + peak.width;
195
+ let tmp = peak.x + peak.width / frequency;
196
196
  signal1D.stopX = Math.max(signal1D.stopX, tmp);
197
197
  signal1D.startX = Math.min(signal1D.startX, tmp);
198
198
  signal1D.nbPeaks++;
@@ -201,8 +201,8 @@ export function detectSignals(data, peakList, options = {}) {
201
201
  intensity: peak.y,
202
202
  width: peak.width,
203
203
  });
204
- signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.width * 3);
205
- signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.width * 3);
204
+ signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - (peak.width * 3) / frequency);
205
+ signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + (peak.width * 3) / frequency);
206
206
  if (peak.kind)
207
207
  signal1D.kind = peak.kind;
208
208
  }
@@ -214,7 +214,7 @@ export function detectSignals(data, peakList, options = {}) {
214
214
  let chemicalShift = 0;
215
215
  let integralPeaks = 0;
216
216
  for (const peak of peaks) {
217
- let area = computeArea(peak);
217
+ let area = computeArea(peak, frequency);
218
218
  chemicalShift += peak.x * area;
219
219
  integralPeaks += area;
220
220
  }
@@ -241,11 +241,9 @@ export function detectSignals(data, peakList, options = {}) {
241
241
  }
242
242
  /**
243
243
  * Return the area of a Lorentzian function
244
- * @param {object} peak - object with peak information
245
- * @return {Number}
246
244
  * @private
247
245
  */
248
- function computeArea(peak) {
249
- return Math.abs(peak.intensity * peak.width * 1.57); // todo add an option with this value: 1.772453851
246
+ function computeArea(peak, frequency) {
247
+ return Math.abs(((peak.intensity * peak.width) / frequency) * 1.57); // todo add an option with this value: 1.772453851
250
248
  }
251
249
  //# sourceMappingURL=peaksToRanges.js.map
package/lib-esm/peaks/peaksToRanges.js.map CHANGED
@@ -1 +1 @@
1
- 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package/lib-esm/signals/utils/jAnalyzer.js CHANGED
@@ -137,6 +137,7 @@ export default {
137
137
  // Before to return, change the units of peaksComp from Hz to PPM again
138
138
  for (let peakComp of signal.peaksComp) {
139
139
  peakComp.x /= signal.observe;
140
+ peakComp.width *= signal.observe;
140
141
  }
141
142
  return signal;
142
143
  },
@@ -375,7 +376,7 @@ function symmetrize(signalInput, maxError, iteration, key) {
375
376
  peaks[i] = {
376
377
  x: peak[jAxis] * newSignal.observe,
377
378
  intensity: peak[intensity],
378
- width: peak.width,
379
+ width: peak.width / newSignal.observe,
379
380
  };
380
381
  }
381
382
  // Join the peaks that are closer than 0.25 Hz
package/lib-esm/signals/utils/jAnalyzer.js.map CHANGED
@@ -1 +1 @@
1
- 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package/lib-esm/xyz/xyzJResAnalyzer.js CHANGED
@@ -30,6 +30,7 @@ function compilePattern(signals, options) {
30
30
  dx: signals[0].x.resolution,
31
31
  dy: signals[0].y.resolution,
32
32
  };
33
+ const defaultWidth = 0.02 * observedFrequencies[0];
33
34
  const newSignals = JSON.parse(JSON.stringify(signals));
34
35
  //adapt to 1D jAnalyzer
35
36
  for (const signal of newSignals) {
@@ -45,7 +46,7 @@ function compilePattern(signals, options) {
45
46
  };
46
47
  for (const peak of peaks) {
47
48
  if (!peak.width)
48
- peak.width = 0.02;
49
+ peak.width = defaultWidth;
49
50
  }
50
51
  peaks.sort((a, b) => a.y - b.y);
51
52
  }
package/lib-esm/xyz/xyzJResAnalyzer.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "nmr-processing",
3
- "version": "8.7.1",
3
+ "version": "9.0.1",
4
4
  "description": "Pure functions allowing to process NMR spectra.",
5
5
  "main": "./lib/index.js",
6
6
  "module": "./lib-esm/index.js",
@@ -69,7 +69,7 @@
69
69
  "ml-matrix": "^6.10.2",
70
70
  "ml-matrix-convolution": "^1.0.0",
71
71
  "ml-matrix-peaks-finder": "^1.0.0",
72
- "ml-peak-shape-generator": "^4.1.1",
72
+ "ml-peak-shape-generator": "^4.1.2",
73
73
  "ml-simple-clustering": "^0.1.0",
74
74
  "ml-sparse-matrix": "^2.1.0",
75
75
  "ml-spectra-processing": "^11.12.0",
package/src/peaks/peaksToRanges.ts CHANGED
@@ -93,13 +93,13 @@ const assignSignal = (
93
93
  delta: NaN,
94
94
  nbPeaks: 1,
95
95
  kind: 'signal',
96
- startX: peak.x - peak.width,
97
- stopX: peak.x + peak.width,
96
+ startX: peak.x - peak.width / frequency,
97
+ stopX: peak.x + peak.width / frequency,
98
98
  observe: frequency,
99
99
  nucleus,
100
100
  integralData: {
101
- from: peak.x - peak.width * 3,
102
- to: peak.x + peak.width * 3,
101
+ from: peak.x - (peak.width * 3) / frequency,
102
+ to: peak.x + (peak.width * 3) / frequency,
103
103
  value: 0,
104
104
  },
105
105
  peaks: [
@@ -148,7 +148,6 @@ export function peaksToRanges(
148
148
  }
149
149
 
150
150
  let signals = detectSignals(data, peakList, signalOptions);
151
-
152
151
  if (clean) {
153
152
  for (let i = 0; i < signals.length; i++) {
154
153
  if (Math.abs(signals[i].integralData.value) < clean) {
@@ -173,7 +172,7 @@ export function peaksToRanges(
173
172
  sum = 0;
174
173
  let peaksO = [];
175
174
  for (let j = signal.maskPattern.length - 1; j >= 0; j--) {
176
- sum += computeArea(signal.peaks[j]);
175
+ sum += computeArea(signal.peaks[j], frequency);
177
176
  if (!signal.maskPattern[j]) {
178
177
  let peakR = signal.peaks.splice(j, 1)[0];
179
178
  peaksO.push({
@@ -185,7 +184,7 @@ export function peaksToRanges(
185
184
  signal.mask2.splice(j, 1);
186
185
  signal.maskPattern.splice(j, 1);
187
186
  signal.nbPeaks--;
188
- nHi += computeArea(peakR);
187
+ nHi += computeArea(peakR, frequency);
189
188
  }
190
189
  }
191
190
  if (peaksO.length > 0) {
@@ -229,7 +228,6 @@ export function peaksToRanges(
229
228
  }
230
229
  }
231
230
  }
232
-
233
231
  let ranges: NMRRange[] = [];
234
232
  for (let i = 0; i < signals.length; i++) {
235
233
  let signal = signals[i];
@@ -306,7 +304,7 @@ export function detectSignals(
306
304
  if (peak.kind) signal1D.kind = peak.kind;
307
305
  signals.push(signal1D);
308
306
  } else {
309
- let tmp = peak.x + peak.width;
307
+ let tmp = peak.x + peak.width / frequency;
310
308
  signal1D.stopX = Math.max(signal1D.stopX, tmp);
311
309
  signal1D.startX = Math.min(signal1D.startX, tmp);
312
310
  signal1D.nbPeaks++;
@@ -317,11 +315,11 @@ export function detectSignals(
317
315
  });
318
316
  signal1D.integralData.from = Math.min(
319
317
  signal1D.integralData.from,
320
- peak.x - peak.width * 3,
318
+ peak.x - (peak.width * 3) / frequency,
321
319
  );
322
320
  signal1D.integralData.to = Math.max(
323
321
  signal1D.integralData.to,
324
- peak.x + peak.width * 3,
322
+ peak.x + (peak.width * 3) / frequency,
325
323
  );
326
324
  if (peak.kind) signal1D.kind = peak.kind;
327
325
  }
@@ -334,7 +332,7 @@ export function detectSignals(
334
332
  let integralPeaks = 0;
335
333
 
336
334
  for (const peak of peaks) {
337
- let area = computeArea(peak);
335
+ let area = computeArea(peak, frequency);
338
336
  chemicalShift += peak.x * area;
339
337
  integralPeaks += area;
340
338
  }
@@ -364,10 +362,8 @@ export function detectSignals(
364
362
 
365
363
  /**
366
364
  * Return the area of a Lorentzian function
367
- * @param {object} peak - object with peak information
368
- * @return {Number}
369
365
  * @private
370
366
  */
371
- function computeArea(peak: Peak1DIntern) {
372
- return Math.abs(peak.intensity * peak.width * 1.57); // todo add an option with this value: 1.772453851
367
+ function computeArea(peak: Peak1DIntern, frequency: number) {
368
+ return Math.abs(((peak.intensity * peak.width) / frequency) * 1.57); // todo add an option with this value: 1.772453851
373
369
  }
package/src/signals/utils/jAnalyzer.ts CHANGED
@@ -210,6 +210,7 @@ export default {
210
210
  // Before to return, change the units of peaksComp from Hz to PPM again
211
211
  for (let peakComp of signal.peaksComp) {
212
212
  peakComp.x /= signal.observe;
213
+ peakComp.width *= signal.observe;
213
214
  }
214
215
  return signal;
215
216
  },
@@ -471,7 +472,7 @@ function symmetrize(
471
472
  peaks[i] = {
472
473
  x: peak[jAxis] * newSignal.observe,
473
474
  intensity: peak[intensity],
474
- width: peak.width,
475
+ width: peak.width / newSignal.observe,
475
476
  };
476
477
  }
477
478
  // Join the peaks that are closer than 0.25 Hz
package/src/xyz/xyzJResAnalyzer.ts CHANGED
@@ -88,6 +88,7 @@ function compilePattern(
88
88
  dy: signals[0].y.resolution,
89
89
  };
90
90
 
91
+ const defaultWidth = 0.02 * observedFrequencies[0];
91
92
  const newSignals = JSON.parse(JSON.stringify(signals));
92
93
  //adapt to 1D jAnalyzer
93
94
  for (const signal of newSignals) {
@@ -102,7 +103,7 @@ function compilePattern(
102
103
  to: Number.MIN_SAFE_INTEGER,
103
104
  };
104
105
  for (const peak of peaks) {
105
- if (!peak.width) peak.width = 0.02;
106
+ if (!peak.width) peak.width = defaultWidth;
106
107
  }
107
108
  peaks.sort((a: Peak2D, b: Peak2D) => a.y - b.y);
108
109
  }