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chore: fix format
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@lpatiny
lpatiny committed Jun 12, 2024
1 parent 80f699b commit 79c4f3c
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242 changes: 1 addition & 241 deletions src/from/__tests__/__snapshots__/fromVamas.test.js.snap
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Original file line number Diff line number Diff line change
@@ -1,244 +1,4 @@
// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html

exports[`fromVamas > Cellulose with CASA information, regions and components 1`] = `
{
"analyserMode": "FAT",
"analysisSource": {
"beamWidthX": {
"units": "um",
"value": 6000,
},
"beamWidthY": {
"units": "um",
"value": 500,
},
"characteristicEnergy": {
"units": "eV",
"value": 1486.6,
},
"label": "Al Ka, Monochromated",
},
"components": [
{
"area": {
"lowerBound": 1e-20,
"upperBound": 126904.8,
"value": 4830.0138,
},
"assignment": "C 1s 1",
"atomicMass": 12.011,
"bindingEnergy": {
"units": "eV",
"value": 286.7736,
},
"componentID": "C 1s 1",
"fwhm": {
"lowerBound": 0.25,
"upperBound": 6.25,
"value": 1.1057933,
},
"groupIndex": -1,
"kineticEnergy": {
"units": "eV",
"value": 1199.8264,
},
"position": {
"lowerBound": 1199.7,
"upperBound": 1199.87,
"value": 1199.8264,
},
"relativeSensitivityFactor": 0.278,
"shape": {
"kind": "lorentzianAsymmetric",
"options": {
"alpha": 1.4,
"beta": 1.7,
"m": 100,
},
},
"uncorrectedRSF": 0.278,
},
{
"area": {
"constrain": {
"factor": 0.2048,
"linkedComponent": 0,
},
"lowerBound": 0,
"upperBound": 2000,
"value": 989.18682,
},
"assignment": "C 1s 2",
"atomicMass": 12.011,
"bindingEnergy": {
"units": "eV",
"value": 288.1950999999999,
},
"componentID": "C 1s 2",
"fwhm": {
"lowerBound": 0.25,
"upperBound": 6.25,
"value": 1.1121055,
},
"groupIndex": -1,
"kineticEnergy": {
"units": "eV",
"value": 1198.4049,
},
"position": {
"lowerBound": 1198.34,
"upperBound": 1198.74,
"value": 1198.4049,
},
"relativeSensitivityFactor": 0.278,
"shape": {
"kind": "lorentzianAsymmetric",
"options": {
"alpha": 1.4,
"beta": 1.6,
"m": 100,
},
},
"uncorrectedRSF": 0.278,
},
{
"area": {
"lowerBound": 0,
"upperBound": 243,
"value": 56.812945,
},
"assignment": "C 1s degrad",
"atomicMass": 12.011,
"bindingEnergy": {
"units": "eV",
"value": 288.8453999999999,
},
"componentID": "C 1s degrad",
"fwhm": {
"lowerBound": 0.25,
"upperBound": 2,
"value": 0.82920074,
},
"groupIndex": -1,
"kineticEnergy": {
"units": "eV",
"value": 1197.7546,
},
"position": {
"lowerBound": 1197.3546,
"upperBound": 1197.7546,
"value": 1197.7546,
},
"relativeSensitivityFactor": 0.278,
"shape": {
"kind": "gaussianLorentzianProduct",
"options": {
"mixingRatio": 30,
},
},
"uncorrectedRSF": 0.278,
},
{
"area": {
"lowerBound": 1e-20,
"upperBound": 126904.8,
"value": 100.40835,
},
"assignment": "C 1s Adv.C",
"atomicMass": 12.011,
"bindingEnergy": {
"units": "eV",
"value": 284.8711999999998,
},
"componentID": "C 1s Adv.C",
"fwhm": {
"lowerBound": 0.25,
"upperBound": 6.25,
"value": 0.74742285,
},
"groupIndex": -1,
"kineticEnergy": {
"units": "eV",
"value": 1201.7288,
},
"position": {
"lowerBound": 1201.4,
"upperBound": 1201.8,
"value": 1201.7288,
},
"relativeSensitivityFactor": 0.278,
"shape": {
"kind": "gaussianLorentzianProduct",
"options": {
"mixingRatio": 30,
},
},
"uncorrectedRSF": 0.278,
},
],
"energyType": {
"kind": "binding",
"units": "eV",
},
"from": 294.16,
"region": {
"auger": {
"element": null,
"transition": null,
},
"name": "C 1s",
"orbital": {
"angularMomentum": "s",
"element": "C",
"shell": 1,
},
},
"regions": [
{
"background": {
"parameters": {
"averageWidth": 1,
"bindingEnergyEnd": {
"units": "eV",
"value": 283.34839999999986,
},
"bindingEnergyStart": {
"units": "eV",
"value": 293.2871,
},
"crossSection": [
40.442441,
-450,
0,
0,
],
"endOffset": 0,
"kineticEnergyEnd": {
"units": "eV",
"value": 1203.2516,
},
"kineticEnergyStart": {
"units": "eV",
"value": 1193.3129,
},
"relativeSensitivityFactor": 0.278,
"startOffset": 0,
},
"rawParameters": "1193.3129 1203.2516 0.278 2 0 0 40.442441 -450 0 0",
"type": "Shirley",
},
"block": {
"atomicMass": 12.011,
"regionBlockID": "C 1s",
"relativeSensitivityFactor": 0.278,
},
"regionID": "C 1s",
},
],
"speciesLabel": "C",
"to": 282.16,
}
`;
// Jest Snapshot v1, https://goo.gl/fbAQLP

exports[`fromVamas Cellulose with CASA information, regions and components 1`] = `
{
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6 changes: 3 additions & 3 deletions src/utilities/prediction/__tests__/predictUsingHoseCodes.test.js
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ test('predictUsingHoseCodes', async () => {
});
expect(resultSolidRef.peaks[0].x).toBeCloseTo(285.30823, 4);


expect(resultSolidRef.grouped[0].prediction.boxplot.median).not.toBe(resultNoRef.grouped[0].prediction.boxplot.median);

expect(resultSolidRef.grouped[0].prediction.boxplot.median).not.toBe(
resultNoRef.grouped[0].prediction.boxplot.median,
);
});
7 changes: 3 additions & 4 deletions src/utilities/prediction/predictUsingHoseCodes.js
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Original file line number Diff line number Diff line change
Expand Up @@ -71,21 +71,20 @@ export async function predictUsingHoseCodes(molecule, options = {}) {
const xShiftFct = xShiftFcts[energyReference]?.[transition];
if (xShiftFct) {
for (const key of Object.keys(hoseCode.prediction.boxplot)) {
hoseCode.prediction.boxplot[key] = xShiftFct(hoseCode.prediction.boxplot[key]);
hoseCode.prediction.boxplot[key] = xShiftFct(
hoseCode.prediction.boxplot[key],
);
}
}
}



const peaks = values
.filter((value) => value.prediction)
.map((value) => ({
x: value.prediction.boxplot.median,
y: 1,
}));


// todo shift values if required

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Unexpected 'todo' comment: 'todo shift values if required'
const spectrum = generateSpectrum(peaks, spectrumOptions);

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