Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat: improve manual range picking and fix simulation of diagonal peaks in COSY prediction #3308

Merged
merged 9 commits into from
Feb 20, 2025
Merged

feat: improve manual range picking and fix simulation of diagonal peaks in COSY prediction #3308

Show file tree
Hide file tree
Changes from 7 commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
f72ae25
fix: apply phase correction to the region n reduce critFoundJ to 0.75
jobo322 Dec 3, 2024
1079637
chore: update nmr-processing
jobo322 Dec 3, 2024
16ad07c
fix: improve auto-processing 2D raw data
jobo322 Dec 3, 2024
7caad9b
chore: add 2D processing FID
jobo322 Dec 4, 2024
5f1302e
refactor: use xreimMultipletAnalysis for manual range picking mulitpl…
jobo322 Dec 5, 2024
c1d97f1
chore: fix nmr-processing version
jobo322 Dec 9, 2024
cb53890
chore: update deps
jobo322 Feb 10, 2025
ba11bbd
style: fix 'Multiplet analysis modal' style
hamed-musallam Feb 20, 2025
3739ff8
chore: remove unused code
hamed-musallam Feb 20, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
281 changes: 281 additions & 0 deletions public/data/brukerFolders/hsqcBrukerFilters.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,281 @@
{
"version": 7,
"data": {
"source": {
"entries": [
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/2/acqu"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/2/acqu2"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/2/acqu2s"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/2/acqus"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/2/pdata/1/proc"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/2/pdata/1/proc2"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/2/pdata/1/proc2s"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/2/pdata/1/procs"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/2/ser"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/3/acqu"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/3/acqu2"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/3/acqu2s"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/3/acqus"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/3/pdata/1/proc"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/3/pdata/1/proc2"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/3/pdata/1/proc2s"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/3/pdata/1/procs"
},
{
"baseURL": "", "relativePath": "data/brukerFolders/cosyAndHsqcFid/3/ser"
}
]
},
"spectra": [
{
"id": "1349b256-7a33-4d90-9c7f-cc2e43f3be89",
"meta": {},
"filters": [
{
"name": "apodizationDimension1",
"value": {
"exponential": {
"apply": false,
"options": { "lineBroadening": 0.3 }
},
"sineBell": { "apply": false, "options": { "offset": 0.5 } },
"sineSquare": { "apply": true, "options": { "offset": 0.5 } },
"traf": { "apply": false, "options": { "lineBroadening": 0.3 } },
"gaussian": {
"apply": false,
"options": { "lineBroadening": 0.3, "lineBroadeningCenter": 0 }
}
},
"enabled": true,
"id": "b2567a33-4d90-4c7f-8c2e-43f3be893962"
},
{
"name": "zeroFillingDimension1",
"value": { "nbPoints": 1024 },
"enabled": true,
"id": "567a334d-905c-4fcc-ae43-f3be8939623c"
},
{
"name": "fftDimension1",
"value": {},
"enabled": true,
"id": "7a334d90-5c7f-4c2e-83f3-be8939623c3d"
},
{
"name": "apodizationDimension2",
"value": {
"exponential": {
"apply": false,
"options": { "lineBroadening": 0.3 }
},
"sineBell": { "apply": false, "options": { "offset": 0.5 } },
"sineSquare": { "apply": true, "options": { "offset": 0.5 } },
"traf": { "apply": false, "options": { "lineBroadening": 0.3 } },
"gaussian": {
"apply": false,
"options": { "lineBroadening": 0.3, "lineBroadeningCenter": 0 }
}
},
"enabled": true,
"id": "334d905c-7fcc-4e43-b3be-8939623c3d36"
},
{
"name": "zeroFillingDimension2",
"value": { "nbPoints": 1024 },
"enabled": true,
"id": "4d905c7f-cc2e-43f3-be89-39623c3d3670"
},
{
"name": "fftDimension2",
"value": {},
"enabled": true,
"id": "905c7fcc-2e43-43be-8939-623c3d367007"
},
{
"name": "phaseCorrectionTwoDimensions",
"value": {
"horizontal": { "ph0": 33.84521484375, "ph1": -5.625 },
"vertical": { "ph0": -15.28564453125, "ph1": 33.75 }
},
"enabled": true,
"id": "5c7fcc2e-43f3-4e89-b962-3c3d36700728"
}
],
"info": {},
"display": {
"isPositiveVisible": true,
"isNegativeVisible": true,
"isVisible": true,
"contourOptions": {
"positive": { "contourLevels": [47, 100], "numberOfLayers": 10 },
"negative": { "contourLevels": [47, 100], "numberOfLayers": 10 }
},
"dimension": 2,
"negativeColor": "yellow",
"positiveColor": "black"
},
"data": {},
"sourceSelector": {
"files": [
"data/brukerFolders/cosyAndHsqcFid/3/acqu2s",
"data/brukerFolders/cosyAndHsqcFid/3/acqus",
"data/brukerFolders/cosyAndHsqcFid/3/ser",
"data/brukerFolders/cosyAndHsqcFid/3/pdata/1/procs",
"data/brukerFolders/cosyAndHsqcFid/3/pdata/1/proc2s"
]
},
"zones": {
"values": [],
"options": { "isSumConstant": true, "sumAuto": true }
},
"customInfo": {}
},
{
"id": "7b9a1a5f-da6e-4dc9-88f1-18972ad0f7e7",
"meta": {},
"sourceSelector": {
"files": [
"data/brukerFolders/cosyAndHsqcFid/2/acqu2s",
"data/brukerFolders/cosyAndHsqcFid/2/acqus",
"data/brukerFolders/cosyAndHsqcFid/2/ser",
"data/brukerFolders/cosyAndHsqcFid/2/pdata/1/procs",
"data/brukerFolders/cosyAndHsqcFid/2/pdata/1/proc2s"
]
},
"filters": [
{
"name": "apodizationDimension1",
"value": {
"exponential": {
"apply": false,
"options": { "lineBroadening": 0.3 }
},
"sineBell": {
"apply": true,
"options": { "offset": 0, "exponent": 1 }
},
"sineSquare": { "apply": false, "options": { "offset": 0 } },
"traf": { "apply": false, "options": { "lineBroadening": 0.3 } },
"gaussian": {
"apply": false,
"options": { "lineBroadening": 0.3, "lineBroadeningCenter": 0 }
}
},
"enabled": true,
"id": "1a5fda6e-9dc9-48f1-9897-2ad0f7e70197"
},
{
"name": "zeroFillingDimension1",
"value": { "nbPoints": 1024 },
"enabled": true,
"id": "5fda6e9d-c948-4118-972a-d0f7e70197ad"
},
{
"name": "fftDimension1",
"value": {},
"enabled": true,
"id": "da6e9dc9-48f1-4897-aad0-f7e70197ad07"
},
{
"name": "apodizationDimension2",
"value": {
"exponential": {
"apply": false,
"options": { "lineBroadening": 0.3 }
},
"sineBell": {
"apply": true,
"options": { "offset": 0, "exponent": 1 }
},
"sineSquare": { "apply": false, "options": { "offset": 0 } },
"traf": { "apply": false, "options": { "lineBroadening": 0.3 } },
"gaussian": {
"apply": false,
"options": { "lineBroadening": 0.3, "lineBroadeningCenter": 0 }
}
},
"enabled": true,
"id": "6e9dc948-f118-472a-90f7-e70197ad075d"
},
{
"name": "zeroFillingDimension2",
"value": { "nbPoints": 1024 },
"enabled": true,
"id": "9dc948f1-1897-4ad0-b7e7-0197ad075d90"
},
{
"name": "fftDimension2",
"value": {},
"enabled": true,
"id": "c948f118-972a-40f7-a701-97ad075d90f1"
},
{
"name": "phaseCorrectionTwoDimensions",
"value": {},
"enabled": true,
"id": "48f11897-2ad0-47e7-8197-ad075d90f11e",
"error": "Phase correction is not applicable to raw data"
},
{
"name": "symmetrizeCosyLike",
"value": {},
"enabled": false,
"id": "f118972a-d0f7-4701-97ad-075d90f11e9a"
}
],
"info": {},
"display": {
"isPositiveVisible": true,
"isNegativeVisible": true,
"isVisible": true,
"contourOptions": {
"positive": { "contourLevels": [51, 100], "numberOfLayers": 10 },
"negative": { "contourLevels": [51, 100], "numberOfLayers": 10 }
},
"dimension": 2,
"negativeColor": "blue",
"positiveColor": "darkblue"
},
"data": {},
"zones": {
"values": [],
"options": { "isSumConstant": true, "sumAuto": true }
},
"customInfo": {}
}
]
}
}
81 changes: 29 additions & 52 deletions src/component/modal/MultipletAnalysisModal.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,52 +1,15 @@
import { Dialog } from '@blueprintjs/core';
/** @jsxImportSource @emotion/react */
import { Dialog, DialogBody } from '@blueprintjs/core';
import styled from '@emotion/styled';
import { xGetFromToIndex, xyToXYObject } from 'ml-spectra-processing';
import { analyseMultiplet } from 'multiplet-analysis';
import type { ActiveSpectrum } from 'nmr-load-save';
import { xreimMultipletAnalysis } from 'nmr-processing';
import { useEffect, useState } from 'react';
import { Axis, LineSeries, Plot } from 'react-plot';

import { isSpectrum2D } from '../../data/data2d/Spectrum2D/index.js';
import { useChartData } from '../context/ChartContext.js';
import { useScaleChecked } from '../context/ScaleContext.js';
import { StyledDialogBody } from '../elements/StyledDialogBody.js';

const DialogBody = styled(StyledDialogBody)`
button:focus {
outline: none;
}

.header {
color: #464646;
font-size: 15px;
height: 20px;
}

.container {
padding: 10px;
max-height: 500px;
overflow-y: auto;

.row {
outline: none;
display: flex !important;
flex-direction: row;
margin: 0;

.multiplicity {
flex: 2;
display: flex;
align-items: center;
justify-content: center;
padding: 0 20px;
}
}

.row:nth-child(odd) {
background: #fafafa;
}
}
`;

const LoaderContainer = styled.div`
display: flex;
Expand Down Expand Up @@ -138,7 +101,7 @@
}

const {
data: { x, re },
data: { x, re, im },
info,
} = spectrum;

Expand All @@ -149,26 +112,40 @@
from,
to,
});

const analysesProps = {
x: x.slice(fromIndex, toIndex),
y: re.slice(fromIndex, toIndex),
re: re.slice(fromIndex, toIndex),
im: im?.slice(fromIndex, toIndex),
};
// console.log(
// 'hola',
// JSON.stringify(analysesProps, (key, value) =>
// ArrayBuffer.isView(value) ? Array.from(value as any) : value,
// ),
// );
try {
const result = analyseMultiplet(analysesProps, {
frequency: info.originFrequency,
minimalResolution: 0.1,
maxTestedJ: 17,
takeBestPartMultiplet: true,
correctVerticalOffset: true,
symmetrizeEachStep: true,
decreasingJvalues: true,
makeShortCutForSpeed: true,
debug: true,
const result = xreimMultipletAnalysis(analysesProps, {
autoPhase: false,
analyzer: {
frequency: info.originFrequency,
minimalResolution: 0.1,
critFoundJ: 0.75,
maxTestedJ: 17,
minTestedJ: 1,
checkSymmetryFirst: false,
takeBestPartMultiplet: true,
correctVerticalOffset: true,
symmetrizeEachStep: false,
decreasingJvalues: true,
makeShortCutForSpeed: true,
debug: true,
},
});
setCalcFinished(true);
setAnalysisData(result);
} catch (error) {
// TODO: handle error

Check warning on line 148 in src/component/modal/MultipletAnalysisModal.tsx

View workflow job for this annotation

GitHub Actions / nodejs / lint-eslint 

Unexpected 'todo' comment: 'TODO: handle error'
reportError(error);
}
}
Expand Down
Loading
Loading