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OHIF-326, export as CSV. (#1976)

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James Petts 2020-08-19 20:31:25 +01:00 committed by GitHub
parent 68332701ab
commit 42b02a62d3
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GPG Key ID: 4AEE18F83AFDEB23
14 changed files with 211 additions and 50 deletions
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2
extensions/cornerstone/package.json
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@ -33,7 +33,7 @@
"@ohif/ui": "^0.50.0",
"cornerstone-core": "^2.3.0",
"cornerstone-math": "^0.1.8",
"cornerstone-tools": "4.19.1",
"cornerstone-tools": "4.20.1",
"cornerstone-wado-image-loader": "^3.1.2",
"dcmjs": "0.16.1",
"dicom-parser": "^1.8.3",

27
extensions/cornerstone/src/utils/measurementServiceMappings/EllipticalRoi.js
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@ -33,7 +33,9 @@ const EllipticalRoi = {
SeriesInstanceUID
);
const { start, end } = measurementData.handles;
const { cachedStats, handles } = measurementData;
const { start, end } = handles;
const halfXLength = Math.abs(start.x - end.x) / 2;
const halfYLength = Math.abs(start.y - end.y) / 2;
@ -60,6 +62,20 @@ const EllipticalRoi = {
points.push({ x: center.x + halfXLength, y: center.y });
}
let meanSUV;
let stdDevSUV;
if (
cachedStats &&
cachedStats.meanStdDevSUV &&
cachedStats.meanStdDevSUV.mean !== 0
) {
const { meanStdDevSUV } = cachedStats;
meanSUV = meanStdDevSUV.mean;
stdDevSUV = meanStdDevSUV.stdDev;
}
return {
id: measurementData.id,
SOPInstanceUID,
@ -70,10 +86,11 @@ const EllipticalRoi = {
label: measurementData.label,
description: measurementData.description,
unit: measurementData.unit,
area:
measurementData.cachedStats &&
measurementData.cachedStats
.area /* TODO: Add concept names instead (descriptor) */,
area: cachedStats && cachedStats.area,
mean: cachedStats && cachedStats.mean,
stdDev: cachedStats && cachedStats.stdDev,
meanSUV,
stdDevSUV,
type: getValueTypeFromToolType(tool),
points,
};

2
extensions/dicom-rt/package.json
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@ -30,7 +30,7 @@
"peerDependencies": {
"@ohif/core": "^0.50.0",
"cornerstone-core": "^2.2.8",
"cornerstone-tools": "4.19.1",
"cornerstone-tools": "4.20.1",
"dcmjs": "0.16.1",
"prop-types": "^15.6.2",
"react": "^16.8.6",

2
extensions/dicom-segmentation/package.json
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@ -30,7 +30,7 @@
"peerDependencies": {
"@ohif/core": "^0.50.0",
"cornerstone-core": "^2.2.8",
"cornerstone-tools": "4.19.0",
"cornerstone-tools": "4.20.1",
"dcmjs": "0.16.1",
"prop-types": "^15.6.2",
"react": "^16.8.6",

2
extensions/dicom-sr/package.json
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@ -33,7 +33,7 @@
"@ohif/ui": "^0.50.0",
"cornerstone-core": "^2.3.0",
"cornerstone-math": "^0.1.8",
"cornerstone-tools": "4.19.1",
"cornerstone-tools": "4.20.1",
"cornerstone-wado-image-loader": "^3.1.2",
"dcmjs": "0.16.1",
"dicom-parser": "^1.8.3",

2
extensions/measurement-tracking/package.json
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@ -28,7 +28,7 @@
},
"peerDependencies": {
"@ohif/core": "^0.50.0",
"cornerstone-tools": "4.19.0",
"cornerstone-tools": "4.20.1",
"dcmjs": "0.16.1",
"prop-types": "^15.6.2",
"react": "^16.13.1",

164
extensions/measurement-tracking/src/_shared/downloadCSVReport.js Normal file
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@ -0,0 +1,164 @@
import { DicomMetadataStore } from '@ohif/core';
export default function downloadCSVReport(
measurementData,
StudyInstanceUID,
referencedSeriesInstanceUIDs,
MeasurementService
) {
const { VALUE_TYPES } = MeasurementService;
if (measurementData.length === 0) {
// Prevent download of report with no measurements.
return;
}
const seriesMetadataMap = {};
referencedSeriesInstanceUIDs.forEach(SeriesInstanceUID => {
seriesMetadataMap[SeriesInstanceUID] = DicomMetadataStore.getSeries(
StudyInstanceUID,
SeriesInstanceUID
);
});
const rows = [
[
'Patient ID',
'Patient Name',
'Study UID',
'Series UID',
'SOP Instance UID',
'Label',
'Long Axis (mm)',
'Short Axis (mm)',
'Length (mm)',
'Area (mmˆ2)',
'Mean',
'StDev',
'Units',
],
];
measurementData.forEach(measurement => {
switch (measurement.type) {
case VALUE_TYPES.BIDIRECTIONAL:
rows.push(_getBidirectionalRow(measurement, seriesMetadataMap));
break;
case VALUE_TYPES.ELLIPSE:
rows.push(_getEllipseRow(measurement, seriesMetadataMap));
break;
case VALUE_TYPES.POINT:
rows.push(_getAdditionalFindingRow(measurement, seriesMetadataMap));
break;
case VALUE_TYPES.POLYLINE:
rows.push(_getLengthRow(measurement, seriesMetadataMap));
}
});
let csvContent =
'data:text/csv;charset=utf-8,' + rows.map(row => row.join(',')).join('\n');
_createAndDownloadFile(csvContent);
}
function _getBidirectionalRow(measurement, seriesMetadataMap) {
const commonRowItems = _getCommonRowItems(measurement, seriesMetadataMap);
return [
...commonRowItems,
measurement.longestDiameter, // Long Axis (mm)
measurement.shortestDiameter, // Short Axis (mm)
];
}
function _getCommonRowItems(measurement, seriesMetadataMap) {
const seriesMetadata = seriesMetadataMap[measurement.referenceSeriesUID];
const firstInstance = seriesMetadata.instances[0];
const row = [
firstInstance.PatientID, // Patient ID
firstInstance.PatientName.Alphabetic, // PatientName
measurement.referenceStudyUID, // StudyInstanceUID
measurement.referenceSeriesUID, // SeriesInstanceUID
measurement.SOPInstanceUID, // SOPInstanceUID
measurement.label || '', // Label
];
return row;
}
function _getAdditionalFindingRow(measurement, seriesMetadataMap) {
const commonRowItems = _getCommonRowItems(measurement, seriesMetadataMap);
return [...commonRowItems];
}
function _getEllipseRow(measurement, seriesMetadataMap) {
const commonRowItems = _getCommonRowItems(measurement, seriesMetadataMap);
const blankColumns = ['', '', ''];
const { area, mean, stdDev, unit } = _getEllipseStatsWithUnits(
measurement,
seriesMetadataMap
);
return [
...commonRowItems,
...blankColumns,
area, // Area (mmˆ2)
mean, // Mean
stdDev, // StDev
unit,
];
}
function _getEllipseStatsWithUnits(measurement, seriesMetadataMap) {
const seriesMetadata = seriesMetadataMap[measurement.referenceSeriesUID];
const firstInstance = seriesMetadata.instances[0];
const modality = firstInstance.Modality;
switch (modality) {
case 'CT':
return {
mean: `${measurement.mean.toFixed(1)}`,
stdDev: `${measurement.stdDev.toFixed(1)}`,
area: measurement.area.toFixed(1),
unit: 'HU',
};
case 'PT':
if (measurement.meanSUV) {
return {
mean: `${measurement.meanSUV.toFixed(1)}`,
stdDev: `${measurement.stdDevSUV.toFixed(1)}`,
area: measurement.area.toFixed(1),
unit: 'SUV',
};
}
// If no SUV calculation then fallback to default.
default:
return {
mean: `${measurement.mean.toFixed(1)}`,
stdDev: `${measurement.stdDev.toFixed(1)}`,
area: measurement.area.toFixed(1),
unit: 'Pixel Values',
};
}
}
function _getLengthRow(measurement, seriesMetadataMap) {
const commonRowItems = _getCommonRowItems(measurement, seriesMetadataMap);
const blankColumns = ['', ''];
return [...commonRowItems, ...blankColumns, measurement.length.toFixed(1)];
}
function _createAndDownloadFile(csvContent) {
const encodedUri = encodeURI(csvContent);
const link = document.createElement('a');
link.setAttribute('href', encodedUri);
link.setAttribute('download', 'MeasurementReport.csv');
document.body.appendChild(link);
link.click();
}

12
extensions/measurement-tracking/src/panels/PanelMeasurementTableTracking/ActionButtons.jsx
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@ -6,15 +6,9 @@ function ActionButtons({ onExportClick, onCreateReportClick }) {
return (
<React.Fragment>
<ButtonGroup color="black" size="inherit">
<Button className="text-base px-2 py-2" onClick={onExportClick}>Export</Button>
<IconButton
className="px-2"
color="black"
size="initial"
variant="outlined"
>
<Icon name="arrow-down" />
</IconButton>
<Button className="text-base px-2 py-2" onClick={onExportClick}>
Export
</Button>
</ButtonGroup>
<Button
className="ml-2 text-base"

24
extensions/measurement-tracking/src/panels/PanelMeasurementTableTracking/index.js
View File

@ -7,12 +7,13 @@ import {
Input,
useViewportGrid,
} from '@ohif/ui';
import { DicomMetadataStore, DICOMSR, utils } from '@ohif/core';
import { DicomMetadataStore, utils } from '@ohif/core';
import { useDebounce } from '@hooks';
import ActionButtons from './ActionButtons';
import { useTrackedMeasurements } from '../../getContextModule';
import createReportDialogPrompt from '../../_shared/createReportDialogPrompt';
import RESPONSES from '../../_shared/PROMPT_RESPONSES';
import downloadCSVReport from '../../_shared/downloadCSVReport';
const { formatDate } = utils;
@ -144,21 +145,12 @@ function PanelMeasurementTableTracking({ servicesManager, extensionManager }) {
trackedSeries.includes(m.referenceSeriesUID)
);
const promptResult = await createReportDialogPrompt(UIDialogService);
if (promptResult.action === RESPONSES.CREATE_REPORT) {
const additionalFindings = ['ArrowAnnotate'];
const SeriesDescription =
// isUndefinedOrEmpty
promptResult.value === undefined || promptResult.value === ''
? 'Research Derived Series' // default
: promptResult.value; // provided value
DICOMSR.downloadReport(trackedMeasurements, additionalFindings, {
SeriesDescription,
});
}
downloadCSVReport(
trackedMeasurements,
trackedStudy,
trackedSeries,
MeasurementService
);
}
const jumpToImage = ({ id, isActive }) => {

2
extensions/vtk/package.json
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@ -57,7 +57,7 @@
"@ohif/core": "^2.9.6",
"@ohif/ui": "^2.0.0",
"cornerstone-core": "^2.3.0",
"cornerstone-tools": "4.19.0",
"cornerstone-tools": "4.20.1",
"cornerstone-wado-image-loader": "^3.1.2",
"dicom-parser": "^1.8.3",
"gh-pages": "^2.0.1",

2
platform/core/package.json
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@ -31,7 +31,7 @@
},
"peerDependencies": {
"cornerstone-core": "^2.3.0",
"cornerstone-tools": "4.19.1",
"cornerstone-tools": "4.20.1",
"cornerstone-wado-image-loader": "^3.1.2",
"dicom-parser": "^1.8.3"
},

2
platform/core/src/services/MeasurementService/MeasurementService.js
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@ -40,6 +40,8 @@ const MEASUREMENT_SCHEMA_KEYS = [
'type',
'unit',
'area', // TODO: Add concept names instead (descriptor)
'mean',
'stdDev',
'length',
'shortestDiameter',
'longestDiameter',

2
platform/viewer/package.json
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@ -68,7 +68,7 @@
"classnames": "^2.2.6",
"core-js": "^3.2.1",
"cornerstone-math": "^0.1.8",
"cornerstone-tools": "4.19.1",
"cornerstone-tools": "4.20.1",
"cornerstone-wado-image-loader": "^3.1.2",
"dcmjs": "0.16.1",
"dicom-parser": "^1.8.3",

16
yarn.lock
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@ -7921,18 +7921,10 @@ cornerstone-math@^0.1.8:
resolved "https://registry.yarnpkg.com/cornerstone-math/-/cornerstone-math-0.1.8.tgz#68ab1f9e4fdcd7c5cb23a0d2eb4263f9f894f1c5"
integrity sha512-x7NEQHBtVG7j1yeyj/aRoKTpXv1Vh2/H9zNLMyqYJDtJkNng8C4Q8M3CgZ1qer0Yr7eVq2x+Ynmj6kfOm5jXKw==
cornerstone-tools@4.19.0:
version "4.19.0"
resolved "https://registry.yarnpkg.com/cornerstone-tools/-/cornerstone-tools-4.19.0.tgz#4c1cb0729fdf5ba5f3c2b83172395738dc8a972b"
integrity sha512-Q8fgx4eN9F0TG84UXprMWjU4YpF/Vhs7ux67b0nV/E5SbyCip7yple4SfDbABB8oxVqzOdKpBnICMNTZNAyyKg==
dependencies:
"@babel/runtime" "7.1.2"
cornerstone-math "0.1.7"
cornerstone-tools@4.19.1:
version "4.19.1"
resolved "https://registry.yarnpkg.com/cornerstone-tools/-/cornerstone-tools-4.19.1.tgz#8a3e9473495b83e9f88dcbad99ac79eae65a81d4"
integrity sha512-ltobIAUEgnPswhWLSAm05HRP7pw99m07RNBYuoN4NInDD2ctvk3HxAjM1CAV2GO1zv8yMwKOaE/j2m70Na12mQ==
cornerstone-tools@4.20.1:
version "4.20.1"
resolved "https://registry.yarnpkg.com/cornerstone-tools/-/cornerstone-tools-4.20.1.tgz#90f6c28356622eac037683b19f9175f85d33dff7"
integrity sha512-SyQsrg3bnGHUvWGZpUq7ia7/gj12S9zQFK2VMhpyAYxK9pWz+PRv8HBi0eEe/fWGAo/Vc62IRkdP3uF9MJlqiQ==
dependencies:
"@babel/runtime" "7.1.2"
cornerstone-math "0.1.7"