fix: shift spectrum 2D (#2744)

* chore: remove unused dependency * fix: twice shift [X|Y] * chore: shift spectra to match 1D and COSY * chore: fix eslint
cheminfo · Nov 9, 2023 · bd77ab4 · bd77ab4
1 parent 64d89b9
commit bd77ab4
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Showing 5 changed files with 100 additions and 49 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -73,7 +73,6 @@
     "immer": "^10.0.3",
     "jszip": "^3.10.1",
     "lodash": "^4.17.21",
-    "ml-airpls": "^1.0.2",
     "ml-array-max": "^1.2.4",
     "ml-array-mean": "^1.1.6",
     "ml-array-median": "^1.1.6",

diff --git a/public/data/oxfordInstruments/oxfordCosy.json b/public/data/oxfordInstruments/oxfordCosy.json
@@ -17,13 +17,19 @@
         },
         "filters": [
           {
+            "id": "a10b030f-a565-42a4-84b1-b9e9087a3ec9",
             "name": "blpDimension1",
             "label": "Backward-LP Dimension 1",
-            "value": {},
-            "flag": true,
-            "isDeleteAllow": true
+            "value": {
+              "nbCoefficients": 15,
+              "nbPoints": -2,
+              "nbInputs": 1024
+            },
+            "isDeleteAllow": true,
+            "flag": true
           },
           {
+            "id": "0b030fa5-6552-4484-b1b9-e9087a3ec927",
             "name": "apodizationDimension1",
             "label": "Apodization on Dimension 1",
             "value": {
@@ -39,34 +45,43 @@
                     }
                   }
                 ]
-              },
-              "apply": true
+              }
             },
-            "flag": true,
-            "isDeleteAllow": true
+            "isDeleteAllow": true,
+            "flag": true
           },
           {
-            "name": "fftDimension1",
-            "label": "FFT Dimension 1",
+            "id": "030fa565-52a4-44b1-b9e9-087a3ec92779",
+            "name": "zeroFillingDimension1",
+            "label": "Zero filling on Dimension 1",
             "value": {
-              "phaseCorrection": {
-                "mode": "mc"
-              },
-              "zeroFilling": {
-                "nbPoints": 2048
-              }
+              "nbPoints": 2048
             },
-            "flag": true,
-            "isDeleteAllow": true
+            "isDeleteAllow": true,
+            "flag": true
           },
           {
-            "name": "flpDimension2",
-            "label": "Forward-LP Dimension 2",
+            "id": "0fa56552-a484-41b9-a908-7a3ec9277962",
+            "name": "fftDimension1",
+            "label": "FFT Dimension 1",
             "value": {},
-            "flag": true,
-            "isDeleteAllow": true
+            "isDeleteAllow": true,
+            "flag": true
+          },
+          {
+            "id": "a56552a4-84b1-49e9-887a-3ec927796285",
+            "name": "flpDimension2",
+            "label": "Fordward-LP Dimension 2",
+            "value": {
+              "nbCoefficients": 15,
+              "nbPoints": 0,
+              "nbInputs": 113
+            },
+            "isDeleteAllow": true,
+            "flag": true
           },
           {
+            "id": "6552a484-b1b9-4908-ba3e-c9277962857d",
             "name": "apodizationDimension2",
             "label": "Apodization on Dimension 2",
             "value": {
@@ -82,30 +97,54 @@
                     }
                   }
                 ]
-              },
-              "apply": true
+              }
             },
-            "flag": true,
-            "isDeleteAllow": true
+            "isDeleteAllow": true,
+            "flag": true
+          },
+          {
+            "id": "52a484b1-b9e9-487a-bec9-277962857d88",
+            "name": "zeroFillingDimension2",
+            "label": "Zero filling on Dimension 2",
+            "value": {
+              "nbPoints": 2048
+            },
+            "isDeleteAllow": true,
+            "flag": true
           },
           {
+            "id": "84b1b9e9-087a-4ec9-a779-62857d888202",
             "name": "fftDimension2",
             "label": "FFT Dimension 2",
+            "value": {},
+            "isDeleteAllow": true,
+            "flag": true
+          },
+          {
+            "id": "a484b1b9-e908-4a3e-8927-7962857d8882",
+            "name": "symmetrizeCosyLike",
+            "label": "symmetrize COSY-like",
+            "value": {},
+            "isDeleteAllow": true,
+            "flag": true
+          },
+          {
+            "name": "shift2DX",
+            "label": "Shift 2D X",
             "value": {
-              "phaseCorrection": {
-                "mode": "mc"
-              },
-              "zeroFilling": {
-                "nbPoints": 2048
-              }
+              "shift": 0.07471201832594754
             },
+            "id": "c788ea09-165e-49ba-afba-1e2e362f7eb5",
             "flag": true,
             "isDeleteAllow": true
           },
           {
-            "name": "symmetrizeCosyLike",
-            "label": "symmetrize COSY-like",
-            "value": {},
+            "name": "shift2DY",
+            "label": "Shift 2D Y",
+            "value": {
+              "shift": 0.06849902778751127
+            },
+            "id": "09165ee9-ba6f-4a1e-ae36-2f7eb5385f7f",
             "flag": true,
             "isDeleteAllow": true
           }
@@ -158,11 +197,22 @@
             "name": "phaseCorrection",
             "label": "Phase correction",
             "value": {
-              "ph0": -126,
+              "ph0": -128.9,
               "ph1": 0,
               "absolute": false
             },
             "flag": true,
+            "isDeleteAllow": true,
+            "id": "6ae7ba0d-db09-486c-9cbf-2ac7e57dbc3d"
+          },
+          {
+            "name": "shiftX",
+            "label": "Shift X",
+            "value": {
+              "shift": -0.10005791743496187
+            },
+            "id": "f86c9cbf-2ac7-457d-bc3d-9465b326c07b",
+            "flag": true,
             "isDeleteAllow": true
           }
         ]

diff --git a/public/data/oxfordInstruments/oxfordInstruments.json b/public/data/oxfordInstruments/oxfordInstruments.json
@@ -66,11 +66,22 @@
             "name": "phaseCorrection",
             "label": "Phase correction",
             "value": {
-              "ph0": -126,
+              "ph0": -128.9,
               "ph1": 0,
               "absolute": false
             },
             "flag": true,
+            "isDeleteAllow": true,
+            "id": "6ae7ba0d-db09-486c-9cbf-2ac7e57dbc3d"
+          },
+          {
+            "name": "shiftX",
+            "label": "Shift X",
+            "value": {
+              "shift": -0.10005791743496187
+            },
+            "id": "f86c9cbf-2ac7-457d-bc3d-9465b326c07b",
+            "flag": true,
             "isDeleteAllow": true
           }
         ]

diff --git a/src/component/2d/ft/Contours.tsx b/src/component/2d/ft/Contours.tsx
@@ -3,7 +3,6 @@ import get from 'lodash/get';
 import { Spectrum2D } from 'nmr-load-save';
 import { memo, useMemo, useRef } from 'react';
 
-import { getShift } from '../../../data/data2d/Spectrum2D';
 import {
   drawContours,
   getDefaultContoursLevel,
@@ -36,22 +35,15 @@ function usePath(
 ) {
   const scaleX = useScale2DX();
   const scaleY = useScale2DY();
-  const shift = getShift(spectrum);
 
   const pathBuilder = new PathBuilder();
   for (const element of contours) {
     if (element.lines) {
       const lines = element.lines;
       if (lines.length < 1e6) {
         for (let i = 0; i < lines.length; i += 4) {
-          pathBuilder.moveTo(
-            scaleX(lines[i] + shift.x),
-            scaleY(lines[i + 1] + shift.y),
-          );
-          pathBuilder.lineTo(
-            scaleX(lines[i + 2] + shift.x),
-            scaleY(lines[i + 3] + shift.y),
-          );
+          pathBuilder.moveTo(scaleX(lines[i]), scaleY(lines[i + 1]));
+          pathBuilder.lineTo(scaleX(lines[i + 2]), scaleY(lines[i + 3]));
         }
       }
     }