[IDC-1129] - DICOM Tag Viewer extension (#2022)

* WIP render top level tags.

* Add drop down to select series.

* Fix errors with type 2 sequences.

* WIP swap instance.

* Fix formatting and make fullscreen.

* Remove debuggers.

* Finish formatting.

* Fix error with double SeriesNumber deconstruction.

* Address reviewer comments.
This commit is contained in:
James Petts 2020-09-10 11:13:24 +01:00 committed by GitHub
parent a7b5f1847a
commit 0ef88e88eb
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GPG Key ID: 4AEE18F83AFDEB23
23 changed files with 612 additions and 7 deletions

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@ -22,11 +22,13 @@ const OHIFDicomHtmlSopClassHandler = {
getDisplaySetFromSeries(series, study, dicomWebClient, authorizationHeaders) {
const instance = series.getFirstInstance();
const metadata = instance.getData().metadata;
const {
SeriesDescription,
SeriesNumber,
SeriesDate,
SeriesTime,
SeriesNumber,
} = instance._instance.metadata;
} = metadata;
return {
plugin: 'html',
@ -37,6 +39,8 @@ const OHIFDicomHtmlSopClassHandler = {
SOPInstanceUID: instance.getSOPInstanceUID(),
SeriesInstanceUID: series.getSeriesInstanceUID(),
StudyInstanceUID: study.getStudyInstanceUID(),
SeriesDescription,
metadata,
SeriesDate,
SeriesTime,
SeriesNumber,

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@ -12,11 +12,13 @@ const DicomMicroscopySopClassHandler = {
getDisplaySetFromSeries(series, study, dicomWebClient) {
const instance = series.getFirstInstance();
const metadata = instance.getData().metadata;
const {
SeriesDescription,
SeriesNumber,
ContentDate,
ContentTime,
SeriesNumber,
} = instance._instance.metadata;
} = metadata;
// Note: We are passing the dicomweb client into each viewport!
@ -28,9 +30,11 @@ const DicomMicroscopySopClassHandler = {
SOPInstanceUID: instance.getSOPInstanceUID(),
SeriesInstanceUID: series.getSeriesInstanceUID(),
StudyInstanceUID: study.getStudyInstanceUID(),
SeriesDescription,
SeriesDate: ContentDate, // Map ContentDate/Time to SeriesTime for series list sorting.
SeriesTime: ContentTime,
SeriesNumber,
metadata,
};
},
};

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@ -12,11 +12,13 @@ const OHIFDicomPDFSopClassHandler = {
getDisplaySetFromSeries(series, study, dicomWebClient, authorizationHeaders) {
const instance = series.getFirstInstance();
const metadata = instance.getData().metadata;
const {
ContentDate,
ContentTime,
SeriesDescription,
SeriesNumber,
} = instance._instance.metadata;
} = metadata;
return {
plugin: 'pdf',
@ -27,9 +29,11 @@ const OHIFDicomPDFSopClassHandler = {
SOPInstanceUID: instance.getSOPInstanceUID(),
SeriesInstanceUID: series.getSeriesInstanceUID(),
StudyInstanceUID: study.getStudyInstanceUID(),
SeriesDescription,
SeriesDate: ContentDate, // Map ContentDate/Time to SeriesTime for series list sorting.
SeriesTime: ContentTime,
SeriesNumber,
metadata,
authorizationHeaders: authorizationHeaders,
};
},

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@ -56,6 +56,7 @@ const OHIFDicomRTStructSopClassHandler = {
SeriesTime,
SeriesNumber,
SeriesDescription,
metadata,
};
if (!metadata.ReferencedSeriesSequence) {

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@ -28,12 +28,12 @@ export default function getSopClassHandlerModule({ servicesManager }) {
const {
SeriesDate,
SeriesTime,
SeriesNumber,
SeriesDescription,
FrameOfReferenceUID,
SOPInstanceUID,
SeriesInstanceUID,
StudyInstanceUID,
SeriesNumber,
} = metadata;
const segDisplaySet = {
@ -55,6 +55,7 @@ export default function getSopClassHandlerModule({ servicesManager }) {
SeriesTime,
SeriesNumber,
SeriesDescription,
metadata,
};
segDisplaySet.getSourceDisplaySet = function(studies) {

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@ -0,0 +1,8 @@
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
module.exports = (env, argv) => {
return webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
};

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@ -0,0 +1,38 @@
const merge = require('webpack-merge');
const path = require('path');
const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
const pkg = require('./../package.json');
const ROOT_DIR = path.join(__dirname, './..');
const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
module.exports = (env, argv) => {
const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
return merge(commonConfig, {
devtool: 'source-map',
stats: {
colors: true,
hash: true,
timings: true,
assets: true,
chunks: false,
chunkModules: false,
modules: false,
children: false,
warnings: true,
},
optimization: {
minimize: true,
sideEffects: true,
},
output: {
path: ROOT_DIR,
library: 'OHIFExtDicomP10Downloader',
libraryTarget: 'umd',
libraryExport: 'default',
filename: pkg.main,
},
});
};

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@ -0,0 +1,21 @@
MIT License
Copyright (c) 2018 Open Health Imaging Foundation
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

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@ -0,0 +1 @@
# @ohif/extension-dicom-tag-browser

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@ -0,0 +1,40 @@
{
"name": "@ohif/extension-dicom-tag-browser",
"version": "0.0.1",
"description": "OHIF extension for checking DICOM headers.",
"author": "OHIF",
"license": "MIT",
"repository": "OHIF/Viewers",
"main": "dist/index.umd.js",
"module": "src/index.js",
"publishConfig": {
"access": "public"
},
"engines": {
"node": ">=10",
"npm": ">=6",
"yarn": ">=1.16.0"
},
"files": [
"dist",
"README.md"
],
"scripts": {
"dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo",
"build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
"build:package": "yarn run build",
"prepublishOnly": "yarn run build",
"start": "yarn run dev"
},
"peerDependencies": {
"@ohif/core": "^2.6.0",
"react": "^16.8.6",
"dcmjs": "0.16.0"
},
"dependencies": {
"@babel/runtime": "^7.5.5",
"dicomweb-client": "^0.6.0",
"react-select": "^3.0.8",
"moment": "2.24.0"
}
}

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@ -0,0 +1,58 @@
import React from 'react';
import Select from 'react-select';
const DicomBrowserSelect = ({ value, formatOptionLabel, options }) => (
<Select
value={value}
formatOptionLabel={formatOptionLabel}
styles={dicomBrowserSelectStyles}
options={options}
/>
);
const computedstyle = getComputedStyle(document.body);
const uiGrayDarker = computedstyle.getPropertyValue('--ui-gray-darker');
const activeColor = computedstyle.getPropertyValue('--active-color');
const defaultColor = computedstyle.getPropertyValue('--default-color');
const uiGrayDark = computedstyle.getPropertyValue('--ui-gray-dark');
const dicomBrowserSelectStyles = {
singleValue: (base, state) => ({
...base,
width: '100%',
}),
control: (base, state) => ({
...base,
cursor: 'pointer',
background: uiGrayDarker,
borderRadius: state.isFocused ? '5px 5px 5px 5px' : 5,
borderColor: state.isFocused ? activeColor : defaultColor,
minHeight: '50px',
'&:hover': {
borderColor: activeColor,
},
}),
menu: base => ({
...base,
borderRadius: 5,
background: uiGrayDarker,
}),
option: (base, state) => ({
...base,
cursor: 'pointer',
'&:first-of-type': {
borderTopLeftRadius: 5,
borderTopRightRadius: 5,
},
'&:last-of-type': {
borderBottomLeftRadius: 5,
borderBottomRightRadius: 5,
},
background: state.isSelected ? uiGrayDark : uiGrayDarker,
'&:hover': {
background: uiGrayDark,
},
}),
};
export default DicomBrowserSelect;

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@ -0,0 +1,25 @@
.dcmseg-segmentation-item {
display: flex;
justify-content: start;
margin: 0;
}
.dcmseg-segmentation-item .segmentation-meta {
display: flex;
flex-direction: column;
flex-grow: 1;
overflow: hidden;
}
.dcmseg-segmentation-item .segmentation-meta-title {
text-overflow: ellipsis;
overflow: hidden;
white-space: nowrap;
color: white;
max-width: calc(100% - 30px);
}
.dcmseg-segmentation-item .segmentation-meta-description {
font-size: 12px;
color: var(--text-secondary-color);
}

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@ -0,0 +1,27 @@
import React from 'react';
import PropTypes from 'prop-types';
import './DicomBrowserSelectItem.css';
const DicomBrowserSelectItem = ({ onClick, title, description }) => {
return (
<li className="dcmseg-segmentation-item" onClick={onClick}>
<div className="segmentation-meta">
<div className="segmentation-meta-title">{title}</div>
<div className="segmentation-meta-description">{description}</div>
</div>
</li>
);
};
DicomBrowserSelectItem.propTypes = {
onClick: PropTypes.func.isRequired,
title: PropTypes.string.isRequired,
description: PropTypes.string.isRequired,
};
DicomBrowserSelectItem.defaultProps = {
description: '',
};
export default DicomBrowserSelectItem;

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@ -0,0 +1,27 @@
.dicom-tag-browser-table {
margin-right: auto;
margin-left: auto;
}
.dicom-tag-browser-table td {
padding-left: 10px;
padding-right: 10px;
color: var(--table-text-primary-color);
border-top: 1px solid #ddd;
white-space: nowrap;
}
.dicom-tag-browser-table td.dicom-tag-browser-table-center {
text-align: center;
}
.dicom-tag-browser-table th {
padding-left: 10px;
padding-right: 10px;
text-align: center;
color: var(--active-color);
}
.dicom-tag-browser-table th.dicom-tag-browser-table-left {
text-align: left;
}

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@ -0,0 +1,228 @@
import React, { useState } from 'react';
import { classes } from '@ohif/core';
import dcmjs from 'dcmjs';
import DicomBrowserSelect from './DicomBrowserSelect';
import moment from 'moment';
import './DicomTagBrowser.css';
import DicomBrowserSelectItem from './DicomBrowserSelectItem';
const { ImageSet } = classes;
const { DicomMetaDictionary } = dcmjs.data;
const { nameMap } = DicomMetaDictionary;
const DicomTagBrowser = ({ displaySets, displaySetInstanceUID }) => {
const [
activeDisplaySetInstanceUID,
setActiveDisplaySetInstanceUID,
] = useState(displaySetInstanceUID);
const [activeInstance, setActiveInstance] = useState(0);
const activeDisplaySet = displaySets.find(
ds => ds.displaySetInstanceUID === activeDisplaySetInstanceUID
);
const displaySetList = displaySets.map(displaySet => {
const {
displaySetInstanceUID,
SeriesDate,
SeriesTime,
SeriesNumber,
SeriesDescription,
Modality,
} = displaySet;
/* Map to display representation */
const dateStr = `${SeriesDate}:${SeriesTime}`.split('.')[0];
const date = moment(dateStr, 'YYYYMMDD:HHmmss');
const displayDate = date.format('ddd, MMM Do YYYY');
return {
value: displaySetInstanceUID,
title: `${SeriesNumber} (${Modality}): ${SeriesDescription}`,
description: displayDate,
onClick: () => {
setActiveDisplaySetInstanceUID(displaySetInstanceUID);
setActiveInstance(0);
},
};
});
let metadata;
const isImageStack = activeDisplaySet instanceof ImageSet;
let selectedInstanceValue;
let instanceList;
if (isImageStack) {
const { images } = activeDisplaySet;
const image = images[activeInstance];
instanceList = images.map((image, index) => {
const metadata = image.getData().metadata;
const { InstanceNumber } = metadata;
return {
value: index,
title: `Instance Number: ${InstanceNumber}`,
description: '',
onClick: () => {
setActiveInstance(index);
},
};
});
selectedInstanceValue = instanceList[activeInstance];
metadata = image.getData().metadata;
} else {
metadata = activeDisplaySet.metadata;
}
const selectedDisplaySetValue = displaySetList.find(
ds => ds.value === activeDisplaySetInstanceUID
);
return (
<div>
<DicomBrowserSelect
value={selectedDisplaySetValue}
formatOptionLabel={DicomBrowserSelectItem}
options={displaySetList}
/>
{isImageStack ? (
<DicomBrowserSelect
value={selectedInstanceValue}
formatOptionLabel={DicomBrowserSelectItem}
options={instanceList}
/>
) : null}
<DicomTagTable instanceMetadata={metadata}></DicomTagTable>
</div>
);
};
function DicomTagTable({ instanceMetadata }) {
const rows = getRows(instanceMetadata);
return (
<div>
<table className="dicom-tag-browser-table">
<tr>
<th className="dicom-tag-browser-table-left">Tag</th>
<th className="dicom-tag-browser-table-left">Value Representation</th>
<th className="dicom-tag-browser-table-left">Keyword</th>
<th className="dicom-tag-browser-table-left">Value</th>
</tr>
{rows.map(row => (
<tr>
<td>{row[0]}</td>
<td>{row[1]}</td>
<td>{row[2]}</td>
<td>{row[3]}</td>
</tr>
))}
</table>
</div>
);
}
function getRows(metadata, depth = 0) {
// Tag, Type, Value, Keyword
const keywords = Object.keys(metadata);
let tagIndent = '';
for (let i = 0; i < depth; i++) {
tagIndent += '>';
}
const rows = [];
for (let i = 0; i < keywords.length; i++) {
let keyword = keywords[i];
if (keyword === '_vrMap') {
continue;
}
const tagInfo = nameMap[keyword];
let value = metadata[keyword];
if (tagInfo && tagInfo.vr === 'SQ') {
const sequenceAsArray = toArray(value);
// Push line defining the sequence
rows.push([`${tagIndent}${tagInfo.tag}`, tagInfo.vr, keyword, '']);
if (value === null) {
// Type 2 Sequence
continue;
}
sequenceAsArray.forEach(item => {
const sequenceRows = getRows(item, depth + 1);
sequenceRows.forEach(row => {
rows.push(row);
});
});
continue;
}
if (Array.isArray(value)) {
value = value.join('\\');
}
if (typeof value === 'number') {
value = value.toString();
}
if (typeof value !== 'string') {
if (value === null) {
value = ' ';
} else {
if (typeof value === 'object') {
if (value.InlineBinary) {
value = 'Inline Binary';
} else if (value.BulkDataURI) {
value = `Bulk Data URI`; //: ${value.BulkDataURI}`;
} else if (value.Alphabetic) {
value = value.Alphabetic;
} else {
console.error('Unrecognised Value for element:');
console.error(value);
value = ' ';
}
} else {
console.error('Unrecognised Value for element:');
console.error(value);
value = ' ';
}
}
}
// Remove retired tags
keyword = keyword.replace('RETIRED_', '');
if (tagInfo) {
rows.push([`${tagIndent}${tagInfo.tag}`, tagInfo.vr, keyword, value]);
} else {
// Private tag
const tag = `(${keyword.substring(0, 4)},${keyword.substring(4, 8)})`;
rows.push([`${tagIndent}${tag}`, '', 'Private Tag', value]);
}
}
return rows;
}
function toArray(objectOrArray) {
return Array.isArray(objectOrArray) ? objectOrArray : [objectOrArray];
}
export default DicomTagBrowser;

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@ -0,0 +1,52 @@
import { utils } from '@ohif/core';
import React from 'react';
import DicomTagBrowser from './components/DicomTagBrowser';
const { studyMetadataManager } = utils;
export default function getCommandsModule(servicesManager) {
const actions = {
openDICOMTagViewer({ viewports }) {
const { activeViewportIndex, viewportSpecificData } = viewports;
const activeViewportSpecificData =
viewportSpecificData[activeViewportIndex];
const {
StudyInstanceUID,
displaySetInstanceUID,
} = activeViewportSpecificData;
const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
const displaySets = studyMetadata.getDisplaySets();
const { UIModalService } = servicesManager.services;
const WrappedDicomTagBrowser = function() {
return (
<DicomTagBrowser
displaySets={displaySets}
displaySetInstanceUID={displaySetInstanceUID}
/>
);
};
UIModalService.show({
content: WrappedDicomTagBrowser,
title: `DICOM Tag Browser`,
fullscreen: true,
});
},
};
const definitions = {
openDICOMTagViewer: {
commandFn: actions.openDICOMTagViewer,
storeContexts: ['servers', 'viewports'],
},
};
return {
actions,
definitions,
};
}

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@ -0,0 +1,26 @@
import getCommandsModule from './getCommandsModule';
import toolbarModule from './toolbarModule';
/**
* Constants
*/
/**
* Extension
*/
export default {
/**
* Only required property. Should be a unique value across all extensions.
*/
id: 'dicom-tag-browser',
/**
* MODULE GETTERS
*/
getCommandsModule({ servicesManager }) {
return getCommandsModule(servicesManager);
},
getToolbarModule() {
return toolbarModule;
},
};

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@ -0,0 +1,20 @@
const TOOLBAR_BUTTON_TYPES = {
COMMAND: 'command',
};
const definitions = [
{
id: 'TagBrowser',
label: 'Tag Browser',
icon: 'list',
//
type: TOOLBAR_BUTTON_TYPES.COMMAND,
commandName: 'openDICOMTagViewer',
context: 'VIEWER',
},
];
export default {
definitions,
defaultContext: 'VIEWER',
};

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@ -38,6 +38,7 @@ function _show({
onClose = null,
closeButton = true,
title = null,
fullscreen = false,
customClassName = null,
}) {
return serviceImplementation._show({
@ -48,6 +49,7 @@ function _show({
onClose,
closeButton,
title,
fullscreen,
customClassName,
});
}

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@ -22,6 +22,7 @@ const OHIFModal = ({
closeButton,
shouldCloseOnEsc,
isOpen,
fullscreen,
title,
onClose,
children,
@ -41,9 +42,13 @@ const OHIFModal = ({
);
};
const classes = fullscreen
? classNames('OHIFModal', className, 'OHIFModal-fullscreen')
: classNames('OHIFModal', className);
return (
<Modal
className={classNames('OHIFModal', className)}
className={classes}
data-cy="modal"
shouldCloseOnEsc={shouldCloseOnEsc}
isOpen={isOpen}

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@ -18,9 +18,17 @@
@media (min-width: 768px)
width: 600px
&.OHIFModal-fullscreen
width: 95%
@media (min-width: 992px)
width: 900px
&.OHIFModal-fullscreen
width: 95%
&__content
padding: 20px
max-height: 90vh;

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@ -36,6 +36,7 @@ const ModalProvider = ({ children, modal: Modal, service }) => {
closeButton: true,
title: null,
customClassName: '',
fullscreen: false,
};
const [options, setOptions] = useState(DEFAULT_OPTIONS);
@ -78,6 +79,7 @@ const ModalProvider = ({ children, modal: Modal, service }) => {
title,
customClassName,
shouldCloseOnEsc,
fullscreen,
closeButton,
} = options;
@ -89,6 +91,7 @@ const ModalProvider = ({ children, modal: Modal, service }) => {
shouldCloseOnEsc={shouldCloseOnEsc}
isOpen={isOpen}
title={title}
fullscreen={fullscreen}
closeButton={closeButton}
onClose={() => {
if (onClose) {

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@ -29,6 +29,7 @@ import OHIFDicomSegmentationExtension from '@ohif/extension-dicom-segmentation';
import OHIFDicomRtExtension from '@ohif/extension-dicom-rt';
import OHIFDicomMicroscopyExtension from '@ohif/extension-dicom-microscopy';
import OHIFDicomPDFExtension from '@ohif/extension-dicom-pdf';
import OHIFDicomTagBrowserExtension from '@ohif/extension-dicom-tag-browser';
// Add this for Debugging purposes:
//import OHIFDebuggingExtension from '@ohif/extension-debugging';
import { version } from '../package.json';
@ -53,6 +54,7 @@ const appProps = {
OHIFDicomPDFExtension,
OHIFDicomSegmentationExtension,
OHIFDicomRtExtension,
OHIFDicomTagBrowserExtension,
//OHIFDebuggingExtension,
],
};