report fixed wavelength in emission spec

dist/helpers/chem.js

@@ -783,6 +783,9 @@ const ExtractJcamp = source => {
   //   : ((Format.isXRDLayout(layout) || Format.isCyclicVoltaLayout(layout))
   //     ? extrFeaturesXrd(jcamp, layout, peakUp) : extrFeaturesNi(jcamp, layout, peakUp, spectra));
 
+  if (layout === _list_layout.LIST_LAYOUT.EMISSIONS) {
+    _format.default.extractFixedWavelength(source);
+  }
   return {
     spectra,
     features,

dist/helpers/format.js

@@ -1,9 +1,11 @@
 "use strict";
 
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = void 0;
+var _jcampconverter = _interopRequireDefault(require("jcampconverter"));
 var _converter = require("./converter");
 var _list_layout = require("../constants/list_layout");
 var _multiplicity_calc = require("./multiplicity_calc");
@@ -58,6 +60,18 @@ const toPeakStr = peaks => {
   const str = arr.join('#');
   return str;
 };
+let fixedWavelength = null;
+const extractFixedWavelength = source => {
+  const jcamp = _jcampconverter.default.convert(source, {
+    xy: true,
+    keepRecordsRegExp: /(CSAUTOMETADATA)/
+  });
+  // eslint-disable-next-line prefer-destructuring
+  fixedWavelength = jcamp.info.$CSAUTOMETADATA.match(/FIXEDWAVELENGTH=([\d.]+)/)[1];
+  return {
+    fixedWavelength
+  };
+};
 const spectraOps = {
   [_list_layout.LIST_LAYOUT.PLAIN]: {
     head: '',
@@ -127,10 +141,6 @@ const spectraOps = {
     head: 'SIZE EXCLUSION CHROMATOGRAPHY',
     tail: '.'
   },
-  [_list_layout.LIST_LAYOUT.EMISSIONS]: {
-    head: 'EMISSION',
-    tail: '.'
-  },
   [_list_layout.LIST_LAYOUT.DLS_INTENSITY]: {
     head: 'DLS',
     tail: '.'
@@ -259,7 +269,7 @@ const formatedEmissions = function (peaks, maxY) {
     x: k,
     y: ordered[k]
   }));
-  return ordered.map(o => `${o.x} nm (${fixDigit(o.y, 2)} a.u.)`).join(', ');
+  return ordered.map(o => `${o.x}`).join(', ');
 };
 const formatedDLSIntensity = function (peaks, maxY) {
   let decimal = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : 2;
@@ -402,6 +412,12 @@ const peaksWrapper = function (layout, shift) {
       tail: ''
     };
   }
+  if (layout === _list_layout.LIST_LAYOUT.EMISSIONS) {
+    return {
+      head: `EMISSION: λex = ${fixedWavelength} nm,  λem = `,
+      tail: ' nm'
+    };
+  }
   const ops = spectraOps[layout];
   return {
     head: `${ops.head}${solvTxt} = `,
@@ -526,7 +542,8 @@ const Format = {
   hasMultiCurves,
   isAIFLayout,
   isDLSACFLayout,
-  strNumberFixedDecimal
+  strNumberFixedDecimal,
+  extractFixedWavelength
 };
 var _default = Format;
 exports.default = _default;

src/__tests__/fixtures/emissions_jcamp.js

@@ -1,10 +1,12 @@
 const emissionsJcamp = `
-##TITLE=
+##TITLE=Example of fluorescence measurement (4).1_bagit
 ##JCAMP-DX=5.0
 ##DATA TYPE=LINK
 ##BLOCKS=1
+
+
 $$ === CHEMSPECTRA SPECTRUM ORIG ===
-##TITLE=
+##TITLE=Example of fluorescence measurement (4).1_bagit
 ##JCAMP-DX=5.00
 ##DATA TYPE=Emissions
 ##DATA CLASS=XYDATA
@@ -826,6 +828,7 @@ $$ === CHEMSPECTRA SPECTRUM ORIG ===
 800.0, 0.0258263
 $$ === CHEMSPECTRA INTEGRALS AND MULTIPLETS ===
 ##$OBSERVEDINTEGRALS= (X Y Z)
+
 ##$OBSERVEDMULTIPLETS=
 ##$OBSERVEDMULTIPLETSPEAKS=
 $$ === CHEMSPECTRA SIMULATION ===
@@ -834,12 +837,12 @@ $$ === CHEMSPECTRA SIMULATION ===
 
 
 $$ === CHEMSPECTRA PEAK TABLE EDIT ===
-##TITLE=
+##TITLE=Example of fluorescence measurement (4).1_bagit
 ##JCAMP-DX=5.00
 ##DATA TYPE=EmissionsPEAKTABLE
 ##DATA CLASS=PEAKTABLE
 ##$CSCATEGORY=EDIT_PEAK
-##$CSTHRESHOLD=0.05
+##$CSTHRESHOLD=0.5
 ##MAXX=800.0
 ##MAXY=295.575
 ##MINX=400.0
@@ -853,12 +856,12 @@ $$ === CHEMSPECTRA PEAK TABLE EDIT ===
 
 
 $$ === CHEMSPECTRA PEAK TABLE AUTO ===
-##TITLE=
+##TITLE=Example of fluorescence measurement (4).1_bagit
 ##JCAMP-DX=5.00
 ##DATA TYPE=EmissionsPEAKTABLE
 ##DATA CLASS=PEAKTABLE
 ##$CSCATEGORY=AUTO_PEAK
-##$CSTHRESHOLD=0.05
+##$CSTHRESHOLD=0.5
 ##MAXX=800.0
 ##MAXY=295.575
 ##MINX=400.0
@@ -871,7 +874,16 @@ $$ === CHEMSPECTRA PEAK TABLE AUTO ===
 484.5, 190.807
 ##END=
 
+
+$$ === CHEMSPECTRA AUTO METADATA ===
+##$CSAUTOMETADATA=
+DATA CLASS=XYPOINTS
+DATA TYPE=Emissions
+XUNITS=wavelength (nm)
+YUNITS=Intensity
+FIXEDWAVELENGTH=380.0
 ##END=
 
+##END=
 `;
 export default emissionsJcamp;

src/__tests__/units/helpers/format.test.tsx

@@ -137,7 +137,7 @@ describe('Test format helper', () => {
       it('Get peaks for Emission layout', () => {
         params.layout = LIST_LAYOUT.EMISSIONS
         const body = Format.peaksBody(params)
-        expect(body).toEqual('2.0 nm (2.00 a.u.), 1.0 nm (1.00 a.u.)')
+        expect(body).toEqual('2.0, 1.0')
       })
 
 

src/helpers/chem.js

@@ -751,6 +751,10 @@ const ExtractJcamp = (source) => {
   //   : ((Format.isXRDLayout(layout) || Format.isCyclicVoltaLayout(layout))
   //     ? extrFeaturesXrd(jcamp, layout, peakUp) : extrFeaturesNi(jcamp, layout, peakUp, spectra));
 
+  if (layout === LIST_LAYOUT.EMISSIONS) {
+    Format.extractFixedWavelength(source);
+  }
+
   return { spectra, features, layout };
 };
 

src/helpers/format.js

@@ -1,5 +1,6 @@
 /* eslint-disable no-mixed-operators, prefer-object-spread,
 function-paren-newline, no-unused-vars, default-param-last */
+import Jcampconverter from 'jcampconverter';
 import { ToXY, IsSame } from './converter';
 import { LIST_LAYOUT } from '../constants/list_layout';
 import { calcMpyCenter } from './multiplicity_calc';
@@ -51,6 +52,22 @@ const toPeakStr = (peaks) => {
   return str;
 };
 
+let fixedWavelength = null;
+
+const extractFixedWavelength = (source) => {
+  const jcamp = Jcampconverter.convert(
+    source,
+    {
+      xy: true,
+      keepRecordsRegExp: /(CSAUTOMETADATA)/,
+    },
+  );
+  // eslint-disable-next-line prefer-destructuring
+  fixedWavelength = jcamp.info.$CSAUTOMETADATA.match(/FIXEDWAVELENGTH=([\d.]+)/)[1];
+
+  return { fixedWavelength };
+};
+
 const spectraOps = {
   [LIST_LAYOUT.PLAIN]: { head: '', tail: '.' },
   [LIST_LAYOUT.H1]: { head: '1H', tail: '.' },
@@ -69,7 +86,6 @@ const spectraOps = {
   [LIST_LAYOUT.CYCLIC_VOLTAMMETRY]: { head: 'CYCLIC VOLTAMMETRY', tail: '.' },
   [LIST_LAYOUT.CDS]: { head: 'CIRCULAR DICHROISM SPECTROSCOPY', tail: '.' },
   [LIST_LAYOUT.SEC]: { head: 'SIZE EXCLUSION CHROMATOGRAPHY', tail: '.' },
-  [LIST_LAYOUT.EMISSIONS]: { head: 'EMISSION', tail: '.' },
   [LIST_LAYOUT.DLS_INTENSITY]: { head: 'DLS', tail: '.' },
 };
 
@@ -189,7 +205,7 @@ const formatedEmissions = (
 
   ordered = Object.keys(ordered).sort(sortFunc)
     .map((k) => ({ x: k, y: ordered[k] }));
-  return ordered.map((o) => `${o.x} nm (${fixDigit(o.y, 2)} a.u.)`).join(', ');
+  return ordered.map((o) => `${o.x}`).join(', ');
 };
 
 const formatedDLSIntensity = (
@@ -324,6 +340,9 @@ const peaksWrapper = (layout, shift, atIndex = 0) => {
     return { head: '', tail: '' };
   }
 
+  if (layout === LIST_LAYOUT.EMISSIONS) {
+    return { head: `EMISSION: λex = ${fixedWavelength} nm,  λem = `, tail: ' nm' };
+  }
   const ops = spectraOps[layout];
   return { head: `${ops.head}${solvTxt} = `, tail: ops.tail };
 };
@@ -459,6 +478,7 @@ const Format = {
   isAIFLayout,
   isDLSACFLayout,
   strNumberFixedDecimal,
+  extractFixedWavelength,
 };
 
 export default Format;