fix: phase correction 2D slices (#2748)

* fix: phase correction 2D slices * refactor: slicing function --------- Co-authored-by: hamed musallam <[email protected]>
cheminfo · Nov 13, 2023 · 110998a · 110998a
1 parent a2736cf
commit 110998a
Showing 1 changed file with 69 additions and 39 deletions.
diff --git a/src/data/data2d/Spectrum2D/getSlice.ts b/src/data/data2d/Spectrum2D/getSlice.ts
@@ -1,6 +1,12 @@
-import type { NmrData1D, NmrData2DFid, NmrData2DFt } from 'cheminfo-types';
+import type {
+  NmrData1D,
+  NmrData2D,
+  NmrData2DFid,
+  NmrData2DFt,
+} from 'cheminfo-types';
 import { zoneToX } from 'ml-spectra-processing';
 import type { Spectrum1D, Spectrum2D } from 'nmr-load-save';
+import { Info2D } from 'nmr-processing';
 
 import { TraceDirection } from '../../../component/reducer/Reducer';
 import { initiateDatum1D } from '../../data1d/Spectrum1D';
@@ -15,6 +21,12 @@ interface SlicePosition {
   y: number;
 }
 
+const BASE_INFO = {
+  isFid: false,
+  isComplex: false, // if isComplex is true that mean it contains real/ imaginary  x set, if not hid re/im button .
+  dimension: 1,
+};
+
 interface SliceOptions {
   sliceType?: 'real' | 'imaginary' | 'both';
 }
@@ -26,73 +38,91 @@ export function getSlice(
 ): Record<TraceDirection, Spectrum1D> | undefined {
   const { sliceType = 'real' } = options;
   const { data: spectraData, info } = spectrum;
-  const realData = info.isFid
-    ? (spectraData as NmrData2DFid).re
-    : (spectraData as NmrData2DFt).rr;
-  const imaginaryData = info.isFid
-    ? (spectraData as NmrData2DFid).im
-    : (spectraData as NmrData2DFt).ir;
 
-  const xLength = realData.z[0].length;
-  const yLength = realData.z.length;
+  const real = getRealData(spectraData, info);
+  const imaginary = getImaginaryData(spectraData, info);
+
+  const xLength = real.z[0].length;
+  const yLength = real.z.length;
 
-  const xStep = (realData.maxX - realData.minX) / (xLength - 1);
-  const yStep = (realData.maxY - realData.minY) / (yLength - 1);
-  const xIndex = Math.floor((position.x - realData.minX) / xStep);
-  const yIndex = Math.floor((position.y - realData.minY) / yStep);
+  const xStep = (real.maxX - real.minX) / (xLength - 1);
+  const yStep = (real.maxY - real.minY) / (yLength - 1);
+  const xIndex = Math.floor((position.x - real.minX) / xStep);
+  const yIndex = Math.floor((position.y - real.minY) / yStep);
 
-  if (xIndex < 0 || xIndex >= realData.z[0].length) return;
-  if (yIndex < 0 || yIndex >= realData.z.length) return;
+  if (xIndex < 0 || xIndex >= real.z[0].length) return;
+  if (yIndex < 0 || yIndex >= real.z.length) return;
 
   const infoX = {
     nucleus: info.nucleus[0], // 1H, 13C, 19F, ...
-    isFid: false,
-    isComplex: false, // if isComplex is true that mean it contains real/ imaginary  x set, if not hid re/im button .
-    dimension: 1,
+    ...BASE_INFO,
   };
 
   const infoY = {
     nucleus: info.nucleus[1], // 1H, 13C, 19F, ...
-    isFid: false,
-    isComplex: false, // if isComplex is true that mean it contains real/ imaginary  x set, if not hid re/im button .
-    dimension: 1,
-  };
-
-  const dataX: NmrData1D = {
-    x: zoneToX({ from: realData.minX, to: realData.maxX }, xLength),
-    re: new Float64Array(xLength),
+    ...BASE_INFO,
   };
 
-  const dataY: NmrData1D = {
-    x: zoneToX({ from: realData.minY, to: realData.maxY }, yLength),
-    re: new Float64Array(yLength),
-  };
+  const dataX = initiateData(real.minX, real.maxX, xLength);
+  const dataY = initiateData(real.minY, real.maxY, yLength);
 
   if (['real', 'both'].includes(sliceType)) {
     for (let i = 0; i < xLength; i++) {
-      dataX.re[i] += realData.z[yIndex][i];
+      dataX.re[i] += real.z[yIndex][i];
     }
     for (let i = 0; i < yLength; i++) {
-      dataY.re[i] += realData.z[i][xIndex];
+      dataY.re[i] += real.z[i][xIndex];
     }
   }
 
-  if (imaginaryData && ['imaginary', 'both'].includes(sliceType)) {
+  if (imaginary && ['imaginary', 'both'].includes(sliceType)) {
     infoX.isComplex = true;
-    infoY.isComplex = true;
     dataX.im = new Float64Array(xLength);
-    dataY.im = new Float64Array(yLength);
-
     for (let i = 0; i < xLength; i++) {
-      dataX.im[i] += imaginaryData.z[yIndex][i];
+      dataX.im[i] += imaginary.z[yIndex][i];
     }
 
-    for (let i = 0; i < yLength; i++) {
-      dataY.im[i] += imaginaryData.z[i][xIndex];
+    //FT spectra vertical slicing should use ri instead of ir
+    const imaginaryVerticalData = getImaginaryData(spectraData, info, {
+      ftObjectKey: 'ri',
+    });
+
+    if (imaginaryVerticalData) {
+      infoY.isComplex = true;
+      for (let i = 0; i < yLength; i++) {
+        dataY.im = new Float64Array(yLength);
+        dataY.im[i] += imaginaryVerticalData.z[i][xIndex];
+      }
     }
   }
 
   const horizontal = initiateDatum1D({ info: infoX, data: dataX });
   const vertical = initiateDatum1D({ info: infoY, data: dataY });
   return { horizontal, vertical };
 }
+
+function initiateData(from: number, to: number, length: number): NmrData1D {
+  return {
+    x: zoneToX({ from, to }, length),
+    re: new Float64Array(length),
+  };
+}
+
+function getRealData(data: NmrData2D, info: Info2D) {
+  if (info.isFid) {
+    return (data as NmrData2DFid).re;
+  }
+  return (data as NmrData2DFt).rr;
+}
+function getImaginaryData(
+  data: NmrData2D,
+  info: Info2D,
+  options: { ftObjectKey?: 'ir' | 'ri' } = {},
+) {
+  if (info.isFid) {
+    return (data as NmrData2DFid).im;
+  }
+  const { ftObjectKey = 'ir' } = options;
+
+  return (data as NmrData2DFt)?.[ftObjectKey];
+}