feat!: improve appendCalibration and rename after / before

src/parser/casa/__tests__/appendCalibration.test.js

@@ -16,22 +16,22 @@ Calib M = 1.1 A = 5.1 ADD`;
   expect(calibrations).toHaveLength(3);
   expect(calibrations).toStrictEqual([
     {
-      after: 20.1,
-      before: 10.1,
+      referenced: 20.1,
+      measured: 10.1,
       bindingEnergyShift: 10.000000000000002,
       kind: 'bindingEnergy',
       kineticEnergyShift: -10.000000000000002,
     },
     {
-      after: 40.2,
-      before: 20.2,
+      referenced: 40.2,
+      measured: 20.2,
       bindingEnergyShift: 20.000000000000004,
       kind: 'bindingEnergy',
       kineticEnergyShift: -20.000000000000004,
     },
     {
-      after: 5.1,
-      before: 1.1,
+      referenced: 5.1,
+      measured: 1.1,
       bindingEnergyShift: -3.9999999999999996,
       kind: 'kineticEnergy',
       kineticEnergyShift: 3.9999999999999996,

src/parser/casa/appendCalibration.js

@@ -1,10 +1,21 @@
+/**
+ * Referencing: (energy calibration, typically performed on the binding energy scale)
+" Calib M = 0 A = 3.111 ADD"
+ * means that the block should be shifted in binding energy by adding the difference A - M = 3.111 eV. M is not necessarily 0.
+ * If the line contains BE, it means that the operation should be done on the BE scale,
+ * alternatively, simply change the sign of the difference, here it would be -3,111, to be added to the data in the binding energy scale.
+ * @param {object} calibrations 
+ * @param {string} line 
+ */
+
+
 export function appendCalibration(calibrations, line) {
   let calibration = {};
   // Calib M = 281.1700 A = 284.8 BE ADD
   // calibration may be present on many lines
 
   let fields = line.match(
-    /Calib M = (?<before>.*) A = (?<after>[^ ]*) (?<rest>.*)/,
+    /Calib M = (?<measured>.*) A = (?<referenced>[^ ]*) (?<rest>.*)/,
   );
   if (!fields) {
     throw new Error(`appendCalibration fails on: ${line}`);
@@ -14,13 +25,13 @@ export function appendCalibration(calibrations, line) {
       `appendCalibration fails because line does not contain ADD: ${line}`,
     );
   }
-  calibration.before = Number(fields.groups.before);
-  calibration.after = Number(fields.groups.after);
+  calibration.measured = Number(fields.groups.measured);
+  calibration.referenced = Number(fields.groups.referenced);
   if (fields.groups.rest.includes('BE')) {
-    calibration.bindingEnergyShift = calibration.after - calibration.before;
+    calibration.bindingEnergyShift = calibration.referenced - calibration.measured;
     calibration.kind = 'bindingEnergy';
   } else {
-    calibration.bindingEnergyShift = calibration.before - calibration.after;
+    calibration.bindingEnergyShift = calibration.measured - calibration.referenced;
     calibration.kind = 'kineticEnergy';
   }
   calibration.kineticEnergyShift = -calibration.bindingEnergyShift;