[IDC-1939] Debug Dialog part 1 (#2011)

* WIP debug dialog

* Rename the p10 downloader extension to debugger extension, add button to toolbar. Deactivate it by default.

* Fix unit tests
This commit is contained in:
James Petts authored and GitHub committed 2020-09-03 12:58:04 +02:00
1 parent 6a37a2a661
commit a1dee16a3d
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.debugReportModalHeader {
padding: 10px 0 10px;
color: var(--active-color);
}
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import React from 'react';
import { detect } from 'detect-browser';
import './DebugReportModal.css';
const DubugReportModal = ({
viewports,
studies,
servers,
extensionManager,
}) => {
return (
<div>
<table>
{getAppVersion()}
{getExtensionVersions(extensionManager)}
{getBrowserInfo()}
{getCurrentStudyUrl()}
{getLayout(viewports)}
</table>
</div>
);
};
const getAppVersion = () => {
return (
<React.Fragment>
<tr>
<th className="debugReportModalHeader">App</th>
</tr>
<tr>
<td>Version</td>
<td>{window.version}</td>
</tr>
</React.Fragment>
);
};
const getCurrentStudyUrl = () => {
return (
<React.Fragment>
<tr>
<th className="debugReportModalHeader">App</th>
</tr>
<tr>
<td>URL</td>
<td>{window.location.href}</td>
</tr>
</React.Fragment>
);
};
const getExtensionVersions = extensionManager => {
const { registeredExtensionVesions } = extensionManager;
const lineItems = Object.keys(registeredExtensionVesions).map(extensionId => {
const version = registeredExtensionVesions[extensionId];
return (
<tr>
<td>{extensionId}</td>
<td>{version}</td>
</tr>
);
});
return (
<React.Fragment>
<th className="debugReportModalHeader">Extensions</th>
{lineItems}
</React.Fragment>
);
};
const getLayout = viewports => {
const { numRows, numColumns } = viewports;
return (
<React.Fragment>
<tr>
<th className="debugReportModalHeader">Viewports</th>
</tr>
<tr>
<th>Layout</th>
</tr>
<tr>
<td>Rows</td>
<td>{numRows}</td>
</tr>
<tr>
<td>Columns</td>
<td>{numColumns}</td>
</tr>
<tr>
<th>SeriesInstanceUIDs</th>
</tr>
{getSeriesInstanceUIDsPerRow(viewports)}
</React.Fragment>
);
};
const getBrowserInfo = () => {
const browser = detect();
const { name, os, type, version } = browser;
return (
<React.Fragment>
<tr>
<th className="debugReportModalHeader">Platform</th>
</tr>
<tr>
<td>name</td>
<td>{name}</td>
</tr>
<tr>
<td>os</td>
<td>{os}</td>
</tr>
<tr>
<td>type</td>
<td>{type}</td>
</tr>
<tr>
<td>version</td>
<td>{version}</td>
</tr>
</React.Fragment>
);
};
const getSeriesInstanceUIDsPerRow = viewports => {
const { viewportSpecificData, numColumns } = viewports;
debugger;
// NOTE viewportSpecificData is actually an object with numerical keys.
return Object.keys(viewportSpecificData).map(viewportIndex => {
const vsd = viewportSpecificData[viewportIndex];
const [row, column] = _viewportIndexToViewportPosition(
viewportIndex,
numColumns
);
return (
<tr>
<td>{`[${row},${column}]`}</td>
<td>{vsd.SeriesInstanceUID}</td>
</tr>
);
});
};
const _viewportIndexToViewportPosition = (viewportIndex, numColumns) => {
const row = Math.floor(viewportIndex / numColumns);
const column = viewportIndex % numColumns;
return [row, column];
};
export default DubugReportModal;
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import OHIF from '@ohif/core';
import {
save,
upload,
getDicomWebClientFromContext,
getStudyInstanceUIDFromStudies,
getSOPInstanceReferenceFromActiveViewport,
getSOPInstanceReferencesFromViewports,
} from './utils';
import _downloadAndZip, { downloadInstances } from './downloadAndZip';
import DebugReportModal from './DebugReportModal';
import React from 'react';
const {
utils: { Queue },
} = OHIF;
export function getCommands(context, servicesManager, extensionManager) {
const queue = new Queue(1);
const actions = {
/**
* @example Running this command using Commands Manager
* commandsManager.runCommand(
* 'downloadAndZip',
* {
* listOfUIDs: [...],
* options: {
* progress(status) {
* console.info('Progress:', (status.progress * 100).toFixed(2) + '%');
* }
* }
* },
* 'VIEWER'
* );
*/
downloadAndZip({ servers, dicomWebClient, listOfUIDs, options }) {
return save(
_downloadAndZip(
dicomWebClient || getDicomWebClientFromContext(context, servers),
listOfUIDs,
options
),
listOfUIDs
);
},
downloadAndZipStudy({ servers, studies, progress }) {
const dicomWebClient = getDicomWebClientFromContext(context, servers);
const listOfUIDs = getStudyInstanceUIDFromStudies(studies);
return save(
_downloadAndZip(dicomWebClient, listOfUIDs, { progress }),
listOfUIDs
);
},
downloadAndZipSeriesOnViewports({ servers, viewports, progress }) {
const dicomWebClient = getDicomWebClientFromContext(context, servers);
const listOfUIDs = getSOPInstanceReferencesFromViewports(viewports);
return save(
_downloadAndZip(dicomWebClient, listOfUIDs, { progress }),
listOfUIDs
);
},
downloadAndZipSeriesOnActiveViewport({ servers, viewports, progress }) {
const dicomWebClient = getDicomWebClientFromContext(context, servers);
const listOfUIDs = getSOPInstanceReferenceFromActiveViewport(viewports);
return save(
_downloadAndZip(dicomWebClient, listOfUIDs, { progress }),
listOfUIDs
);
},
downloadAndUploadStudy({ servers, studies, progress, serverConfig }) {
const dicomWebClient = getDicomWebClientFromContext(context, servers);
const listOfUIDs = getStudyInstanceUIDFromStudies(studies);
return upload(
downloadInstances(dicomWebClient, listOfUIDs, { progress }),
/**
* serverConfig is an object with the values used to create a new
* instance of DICOMwebClient.
*
* Basic Structure:
*
* const config = {
* url,
* headers,
* errorInterceptor
* }
*
* const dicomWeb = new api.DICOMwebClient(config);
*/
serverConfig
);
},
openDebugInfoModal({ viewports, studies, servers }) {
const { UIModalService } = servicesManager.services;
const WrappedDebugReportModal = function() {
return (
<DebugReportModal
viewports={viewports}
studies={studies}
servers={servers}
extensionManager={extensionManager}
/>
);
};
UIModalService.show({
content: WrappedDebugReportModal,
title: `Debugging Information`,
});
},
};
const definitions = {
openDebugInfoModal: {
commandFn: actions.openDebugInfoModal,
storeContexts: ['viewports', 'servers', 'studies'],
},
downloadAndZip: {
commandFn: queue.bindSafe(actions.downloadAndZip, error),
storeContexts: ['servers'],
},
downloadAndZipStudy: {
commandFn: queue.bindSafe(actions.downloadAndZipStudy, error),
storeContexts: ['servers', 'studies'],
options: { progress },
},
downloadAndZipSeriesOnViewports: {
commandFn: queue.bindSafe(actions.downloadAndZipSeriesOnViewports, error),
storeContexts: ['servers', 'viewports'],
options: { progress },
},
downloadAndZipSeriesOnActiveViewport: {
commandFn: queue.bindSafe(
actions.downloadAndZipSeriesOnActiveViewport,
error
),
storeContexts: ['servers', 'viewports'],
options: { progress },
},
downloadAndUploadStudy: {
commandFn: queue.bindSafe(actions.downloadAndUploadStudy, error),
storeContexts: ['servers', 'studies'],
options: { progress },
},
};
return {
actions,
definitions,
};
}
/**
* Utils
*/
function progress(status) {
OHIF.log.info(
'Download and Zip Progress:',
(status.progress * 100.0).toFixed(2) + '%'
);
}
function error(e) {
if (e.message === 'Queue limit reached') {
OHIF.log.warn('A download is already in progress, please wait.');
} else {
OHIF.log.error(e);
}
}
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import OHIF from '@ohif/core';
import { api } from 'dicomweb-client';
import dicomParser from 'dicom-parser';
import JSZip from 'jszip';
/**
* Constants
*/
const {
utils: {
isDicomUid,
hierarchicalListUtils,
progressTrackingUtils: progressUtils,
},
} = OHIF;
/**
* Public Methods
*/
/**
* Download and Zip all DICOM P10 instances from specified DICOM Web Client
* based on an hierarchical list of UIDs;
*
* @param {DICOMwebClient} dicomWebClient A DICOMwebClient instance through
* which the referenced instances will be retrieved;
* @param {Array} listOfUIDs The hierarchical list of UIDs from the instances
* that should be retrieved:
* A hierarchical list of UIDs is a regular JS Array where the type of the UID
* (study, series, instance) is determined by its nasting lavel. For example:
* @ The following list instructs the library to download all the instances
* from both studies "A" and "B":
*
* ['studyUIDFromA', 'studyUIDFromB']
*
* @ In the previous example both UIDs are treated as STUDY UIDs because both
* of them are listed in the same (top) level of the list. If, on the other
* hand, only instances from series "I" and "J" from the study "B"
* are to be downloaded, the expected hierarchical list would be:
*
* ['studyUIDFromA', ['studyUIDFromB', ['seriesUIDFromI', 'seriesUIDFromJ']]]
*
* @ Which, when prettified, reads like this:
*
* [
* 'studyUIDFromA',
* ['studyUIDFromB', [
* 'seriesUIDFromI',
* 'seriesUIDFromJ'
* ]]
* ]
*
* @ Furthermore, if only instances "X", "Y" and "Z" from series "J" need to
* be downloaded (instead of all the instances from that series), the list
* could be changed to:
*
* [
* 'studyUIDFromA',
* ['studyUIDFromB', [
* 'seriesUIDFromI',
* ['seriesUIDFromJ', [
* 'instanceUIDFromX',
* 'instanceUIDFromY',
* 'instanceUIDFromZ'
* ]]
* ]]
* ]
*
* Please refer to hierarchicalListUtils.js for more information and utilities;
*
* @param {Object} options A plain object with options;
* @param {function} options.progress A callback to retrieve notifications
* @returns {Promise} A promise that resolves to an URL from which the ZIP file
* can be downloaded;
*/
async function downloadAndZip(dicomWebClient, listOfUIDs, options) {
if (dicomWebClient instanceof api.DICOMwebClient) {
const settings = buildSettings(listOfUIDs, options);
const { compression } = settings.tasks;
const buffers = await downloadBuffers(settings, dicomWebClient);
compression.deferred.resolve(zipAll(buffers, settings));
const url = await compression.deferred.promise;
return url;
}
throw new Error('A valid DICOM Web Client instance is expected');
}
async function downloadInstances(dicomWebClient, listOfUIDs, options) {
if (dicomWebClient instanceof api.DICOMwebClient) {
const settings = buildSettings(listOfUIDs, options);
const buffers = await downloadBuffers(settings, dicomWebClient);
return buffers;
}
throw new Error('A valid DICOM Web Client instance is expected');
}
async function downloadBuffers(settings, dicomWebClient) {
const { compression } = settings.tasks;
// Register user-provided progress handler as a task list observer
progressUtils.addObserver(settings.taskList, settings.options.progress);
const buffers = await downloadAll(dicomWebClient, settings).catch(error => {
// Reject promise from compression task on download failure
compression.deferred.reject(error);
throw error;
});
return buffers;
}
/**
* Utils
*/
async function zipAll(buffers, settings) {
const zip = new JSZip();
OHIF.log.info('Adding DICOM P10 files to archive:', buffers.length);
buffers.forEach((buffer, i) => {
const path = buildPath(buffer) || `${i}.dcm`;
zip.file(path, buffer);
});
// Set compression task progress to 50%
progressUtils.update(settings.tasks.compression.task, 0.5);
const blob = await zip.generateAsync({ type: 'blob' });
return URL.createObjectURL(blob);
}
function buildSettings(listOfUIDs, options) {
const taskList = progressUtils.createList();
const compression = progressUtils.addDeferred(taskList);
const downloads = [];
// Build downloads list
hierarchicalListUtils.forEach(
listOfUIDs,
(StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID) => {
if (isDicomUid(StudyInstanceUID)) {
downloads.push({
tracking: progressUtils.addDeferred(taskList),
parameters: [StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID],
});
}
}
);
// Print tree of hierarchical references
OHIF.log.info('Downloading DICOM P10 files for references:');
OHIF.log.info(hierarchicalListUtils.print(listOfUIDs));
return {
options: Object(options),
taskList,
tasks: {
downloads,
compression,
},
};
}
function buildPath(buffer) {
let path;
try {
const byteArray = new Uint8Array(buffer);
const dataSet = dicomParser.parseDicom(byteArray, {
// Stop parsing after SeriesInstanceUID is found
untilTag: 'x0020000e',
});
const StudyInstanceUID = dataSet.string('x0020000d');
const SeriesInstanceUID = dataSet.string('x0020000e');
const SOPInstanceUID = dataSet.string('x00080018');
if (StudyInstanceUID && SeriesInstanceUID && SOPInstanceUID) {
path = `${StudyInstanceUID}/${SeriesInstanceUID}/${SOPInstanceUID}.dcm`;
}
} catch (e) {
OHIF.log.error('Error parsing downloaded DICOM P10 file...', e);
}
return path;
}
async function downloadAll(dicomWebClient, settings) {
const { downloads } = settings.tasks;
// Make sure at least one download was initiated
if (downloads.length < 1) {
throw new Error('No valid reference to be downloaded');
}
const promises = downloads.map(item => {
const {
parameters,
tracking: { deferred, task },
} = item;
deferred.resolve(download(task, dicomWebClient, ...parameters));
return deferred.promise;
});
// Wait on created download promises
return Promise.all(promises).then(results => {
const buffers = [];
// The "results" array may directly contain buffers (ArrayBuffer instances)
// or arrays of buffers, depending on the type of downloads initiated on the
// previous step (retrieveStudy, retrieveSeries or retrieveinstance). Ex:
// results = [buf1, [buf2, buf3], buf4, [buf5], ...];
results.forEach(
function select(nesting, result) {
if (result instanceof ArrayBuffer) {
buffers.push(result);
} else if (nesting && Array.isArray(result)) {
// "nesting" argument is important to make sure only two levels
// of arrays are visited. For example, "bufX" should not be visited:
// [buf1, [buf2, buf3, [bufX]], buf4, [buf5], ...];
result.forEach(select.bind(null, false));
}
}.bind(null, true)
);
return buffers;
});
}
async function download(
task,
dicomWebClient,
studyInstanceUID,
seriesInstanceUID,
sopInstanceUID
) {
// Strict DICOM-formatted variable names COULDN'T be used here because the
// DICOM Web client interface expects them in this specific format.
// @TODO: Add support for download progress handler which will use the
// currently not use "task" param
if (!isDicomUid(studyInstanceUID)) {
throw new Error('Download requires at least a "StudyInstanceUID" property');
}
if (!isDicomUid(seriesInstanceUID)) {
// Download entire study
return dicomWebClient.retrieveStudy({
studyInstanceUID,
});
}
if (!isDicomUid(sopInstanceUID)) {
// Download entire series
return dicomWebClient.retrieveSeries({
studyInstanceUID,
seriesInstanceUID,
});
}
// Download specific instance
return dicomWebClient.retrieveInstance({
studyInstanceUID,
seriesInstanceUID,
sopInstanceUID,
});
}
/**
* Exports
*/
export { downloadAndZip as default, downloadAndZip, downloadInstances };
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import { getDicomWebClientFromConfig } from './utils';
import { getCommands } from './commandsModule';
import { version } from '../package.json';
import toolbarModule from './toolbarModule';
/**
* Constants
*/
/**
* Globals
*/
const sharedContext = {
dicomWebClient: null,
};
/**
* Extension
*/
export default {
/**
* Only required property. Should be a unique value across all extensions.
*/
id: 'dicom-p10-downloader',
version,
/**
* LIFECYCLE HOOKS
*/
preRegistration({ appConfig }) {
const dicomWebClient = getDicomWebClientFromConfig(appConfig);
if (dicomWebClient) {
sharedContext.dicomWebClient = dicomWebClient;
}
},
/**
* MODULE GETTERS
*/
getCommandsModule({ servicesManager, extensionManager }) {
return getCommands(sharedContext, servicesManager, extensionManager);
},
getToolbarModule() {
return toolbarModule;
},
};
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const TOOLBAR_BUTTON_TYPES = {
COMMAND: 'command',
};
const definitions = [
{
id: 'Debug Info',
label: 'Debug Info',
icon: 'cog',
//
type: TOOLBAR_BUTTON_TYPES.COMMAND,
commandName: 'openDebugInfoModal',
context: 'VIEWER',
},
];
export default {
definitions,
defaultContext: 'VIEWER',
};
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import OHIF from '@ohif/core';
import { api } from 'dicomweb-client';
import { saveAs } from 'file-saver';
const {
utils: { isDicomUid, resolveObjectPath, hierarchicalListUtils },
DICOMWeb,
} = OHIF;
function validDicomUid(subject) {
if (isDicomUid(subject)) {
return subject;
}
}
function getActiveServerFromServersStore(store) {
const servers = resolveObjectPath(store, 'servers');
if (Array.isArray(servers) && servers.length > 0) {
return servers.find(server => resolveObjectPath(server, 'active') === true);
}
}
function getDicomWebClientFromConfig(config) {
const servers = resolveObjectPath(config, 'servers.dicomWeb');
if (Array.isArray(servers) && servers.length > 0) {
const server = servers[0];
return new api.DICOMwebClient({
url: server.wadoRoot,
headers: DICOMWeb.getAuthorizationHeader(server),
});
}
}
function getDicomWebClientFromContext(context, store) {
const activeServer = getActiveServerFromServersStore(store);
if (activeServer) {
return new api.DICOMwebClient({
url: activeServer.wadoRoot,
headers: DICOMWeb.getAuthorizationHeader(activeServer),
});
} else if (context.dicomWebClient instanceof api.DICOMwebClient) {
return context.dicomWebClient;
}
}
function getSOPInstanceReference(viewports, index) {
if (index >= 0) {
const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = Object(
resolveObjectPath(viewports, `viewportSpecificData.${index}`)
);
return Object.freeze(
hierarchicalListUtils.addToList(
[],
validDicomUid(StudyInstanceUID),
validDicomUid(SeriesInstanceUID),
validDicomUid(SOPInstanceUID)
)
);
}
}
function getSOPInstanceReferenceFromActiveViewport(viewports) {
return getSOPInstanceReference(
viewports,
resolveObjectPath(viewports, 'activeViewportIndex')
);
}
function getSOPInstanceReferencesFromViewports(viewports) {
const list = [];
const viewportSpecificData = resolveObjectPath(
viewports,
'viewportSpecificData'
);
Object.keys(viewportSpecificData).forEach(index => {
const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = Object(
viewportSpecificData[index]
);
hierarchicalListUtils.addToList(
list,
validDicomUid(StudyInstanceUID),
validDicomUid(SeriesInstanceUID),
validDicomUid(SOPInstanceUID)
);
});
return list;
}
function save(promise, listOfUIDs) {
return Promise.resolve(promise)
.then(url => {
OHIF.log.info('Files successfully compressed:', url);
const StudyInstanceUID = hierarchicalListUtils.getItem(listOfUIDs, 0);
saveAs(url, `${StudyInstanceUID}.zip`);
return url;
})
.catch(error => {
OHIF.log.error('Failed to create Zip file...', error);
return null;
});
}
function upload(promise, serverConfig) {
return Promise.resolve(promise)
.then(async instances => {
const instancesAmount = instances.length;
OHIF.log.info(`Uploading study to ${serverConfig.url}`);
OHIF.log.info(
`${instancesAmount} instances are being uploaded. Don't close your browser.`
);
try {
const dicomWeb = new api.DICOMwebClient(serverConfig);
let progress = 0;
const getProgress = () => {
return ((progress * 100) / instancesAmount).toFixed();
};
for (const instance of instances) {
const options = {
datasets: [instance],
};
await dicomWeb.storeInstances(options);
progress++;
OHIF.log.info(`Progress: ${getProgress()}%`);
}
OHIF.log.info('Successfully uploaded!');
} catch (error) {
OHIF.log.error(`Failed to upload: ${error}`);
}
return instances;
})
.catch(error => {
OHIF.log.error(`Failed to upload: ${error}`);
return null;
});
}
function getStudyInstanceUIDFromStudies(studies) {
return Object.keys(Object(Object(studies).studyData)).slice(0, 1);
}
export {
save,
upload,
validDicomUid,
getDicomWebClientFromConfig,
getDicomWebClientFromContext,
getStudyInstanceUIDFromStudies,
getSOPInstanceReferenceFromActiveViewport,
getSOPInstanceReferencesFromViewports,
};