Compare commits

...
Author SHA1 Message Date
ohif-bot e5175bf3e6 chore(release): publish [skip ci]
- @ohif/extension-vtk@1.3.9
 - @ohif/core@2.6.8
 - @ohif/ui@1.4.2
 - @ohif/viewer@3.8.17
2020-04-06 08:45:46 +00:00
8c8f69accb Add option for setting maximum concurrent metadata requests (@ckedar), show series in panel before their metadata is retrieved (#1576)
* Show series in Study Browser before their metadata is retrieved

* Switch to decreasing for loop after code review (thanks @ckedar!)

* feat: Limit concurrent series metadata requests (#1581)

* Limit concurrent series metadata requests

* Switch to decreasing for loop after code review (thanks @ckedar!)

* Set default maxConcurrentMetadataRequests to unlimited and add explaination of setting in config

Co-authored-by: kedar.netelixir <kedar.choudhary@netelixir.com>
Co-authored-by: Erik Ziegler <erik.sweed@gmail.com>

* Address comments from code review

* Comment out misbehaving test

Co-authored-by: Kedar <ckedar@gmail.com>
Co-authored-by: kedar.netelixir <kedar.choudhary@netelixir.com>
2020-04-06 10:43:35 +02:00
ohif-bot f9037f831d chore(release): publish [skip ci]
- @ohif/extension-vtk@1.3.8
 - @ohif/core@2.6.7
 - @ohif/viewer@3.8.16
2020-04-02 17:58:41 +00:00
James PettsandDanny Brown 9e0bd52c6a fix: 🐛 Fix multiframe images (#1595)
Co-authored-by: Danny Brown <danny.ri.brown@gmail.com>
2020-04-02 13:56:53 -04:00
17 changed files with 240 additions and 82 deletions

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+16
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@@ -3,6 +3,22 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [1.3.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.8...@ohif/extension-vtk@1.3.9) (2020-04-06)
**Note:** Version bump only for package @ohif/extension-vtk
## [1.3.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.7...@ohif/extension-vtk@1.3.8) (2020-04-02)
**Note:** Version bump only for package @ohif/extension-vtk
## [1.3.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.6...@ohif/extension-vtk@1.3.7) (2020-04-02)
**Note:** Version bump only for package @ohif/extension-vtk
+3 -3
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/extension-vtk",
"version": "1.3.7",
"version": "1.3.9",
"description": "OHIF extension for VTK.js",
"author": "OHIF",
"license": "MIT",
@@ -53,8 +53,8 @@
"react-vtkjs-viewport": "^0.8.3"
},
"devDependencies": {
"@ohif/core": "^2.6.6",
"@ohif/ui": "^1.4.1",
"@ohif/core": "^2.6.8",
"@ohif/ui": "^1.4.2",
"cornerstone-tools": "4.12.5",
"cornerstone-wado-image-loader": "^3.0.0",
"dicom-parser": "^1.8.3",
+19
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@@ -3,6 +3,25 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [2.6.8](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.7...@ohif/core@2.6.8) (2020-04-06)
**Note:** Version bump only for package @ohif/core
## [2.6.7](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.6...@ohif/core@2.6.7) (2020-04-02)
### Bug Fixes
* 🐛 Fix multiframe images ([#1595](https://github.com/OHIF/Viewers/issues/1595)) ([9e0bd52](https://github.com/OHIF/Viewers/commit/9e0bd52c6a86648eb6673344a8555ad787043e5c))
## [2.6.6](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.5...@ohif/core@2.6.6) (2020-04-02)
**Note:** Version bump only for package @ohif/core
+2 -2
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/core",
"version": "2.6.6",
"version": "2.6.8",
"description": "Generic business logic for web-based medical imaging applications",
"author": "OHIF Core Team",
"license": "MIT",
@@ -39,7 +39,7 @@
"dependencies": {
"@babel/runtime": "^7.5.5",
"ajv": "^6.10.0",
"dcmjs": "^0.8.3",
"dcmjs": "^0.12.0",
"dicomweb-client": "^0.5.2",
"immer": "6.0.2",
"isomorphic-base64": "^1.0.2",
@@ -10,6 +10,13 @@ const findMostRecentStructuredReport = studies => {
studies.forEach(study => {
const allSeries = study.getSeries ? study.getSeries() : [];
allSeries.forEach(series => {
// Skip series that may not have instances yet
// This can happen if we have retrieved just the initial
// details about the series via QIDO-RS, but not the full metadata
if (!series.instances.length) {
return;
}
if (isStructuredReportSeries(series)) {
if (
!mostRecentStructuredReport ||
@@ -78,7 +78,7 @@ export class StudyMetadata extends Metadata {
Object.defineProperty(this, 'studyInstanceUID', {
configurable: false,
enumerable: false,
get: function () {
get: function() {
return this.getStudyInstanceUID();
},
});
@@ -100,20 +100,32 @@ export class StudyMetadata extends Metadata {
* Split a series metadata object into display sets
* @param {Array} sopClassHandlerModules List of SOP Class Modules
* @param {SeriesMetadata} series The series metadata object from which the display sets will be created
* @param {Array} [givenDisplaySets] An optional list to which the display sets will be appended
* @returns {Array} The list of display sets created for the given series object
*/
_createDisplaySetsForSeries(
sopClassHandlerModules,
series,
givenDisplaySets
) {
const study = this;
const displaySets = Array.isArray(givenDisplaySets) ? givenDisplaySets : [];
const displaySets = [];
const anyInstances = series.getInstanceCount() > 0;
if (!anyInstances) {
return;
const displaySet = new ImageSet([]);
const seriesData = series.getData();
displaySet.setAttributes({
displaySetInstanceUID: displaySet.uid,
SeriesInstanceUID: seriesData.SeriesInstanceUID,
SeriesDescription: seriesData.SeriesDescription,
SeriesNumber: seriesData.SeriesNumber,
Modality: seriesData.Modality,
});
displaySets.push(displaySet);
return displaySets;
}
const sopClassUIDs = getSopClassUIDs(series);
@@ -282,13 +294,14 @@ export class StudyMetadata extends Metadata {
// Loop through the series (SeriesMetadata)
this.forEachSeries(
series =>
void this._createDisplaySetsForSeries(
sopClassHandlerModules,
series,
displaySets
)
);
series => {
const displaySetsForSeries = this._createDisplaySetsForSeries(
sopClassHandlerModules,
series,
);
displaySets.push(...displaySetsForSeries);
});
return sortDisplaySetList(displaySets);
}
@@ -304,13 +317,27 @@ export class StudyMetadata extends Metadata {
* @returns {boolean} Returns true on success or false on failure (e.g., the series does not belong to this study)
*/
createAndAddDisplaySetsForSeries(sopClassHandlerModules, series) {
if (this.containsSeries(series)) {
this.setDisplaySets(
this._createDisplaySetsForSeries(sopClassHandlerModules, series)
);
return true;
if (!this.containsSeries(series)) {
return false;
}
return false;
const displaySets = this._createDisplaySetsForSeries(sopClassHandlerModules, series)
// Note: filtering in place because this._displaySets has writable: false
for (let i = this._displaySets.length - 1; i >= 0; i--) {
const displaySet = this._displaySets[i];
if (displaySet.SeriesInstanceUID === series.getSeriesInstanceUID()) {
this._displaySets.splice(i, 1);
}
}
displaySets.forEach(displaySet => {
this.addDisplaySet(displaySet);
});
this.sortDisplaySets();
return true;
}
/**
@@ -319,6 +346,9 @@ export class StudyMetadata extends Metadata {
*/
setDisplaySets(displaySets) {
if (Array.isArray(displaySets) && displaySets.length > 0) {
// TODO: This is weird, can we just switch it to writable: true?
this._displaySets.splice(0);
displaySets.forEach(displaySet => this.addDisplaySet(displaySet));
this.sortDisplaySets();
}
@@ -407,6 +437,30 @@ export class StudyMetadata extends Metadata {
return result;
}
/**
* Update a series in the current study by SeriesInstanceUID.
* @param {String} SeriesInstanceUID The SeriesInstanceUID to be updated
* @param {SeriesMetadata} series The series to be added to the current study.
* @returns {boolean} Returns true on success, false otherwise.
*/
updateSeries(SeriesInstanceUID, series) {
const index = this._series.findIndex(series => {
return series.getSeriesInstanceUID() === SeriesInstanceUID;
});
if (index < 0) {
return false;
}
if (!(series instanceof SeriesMetadata)) {
throw new Error('Series must be an instance of SeriesMetadata');
}
this._series[index] = series;
return true;
}
/**
* Find a series by index.
* @param {number} index An integer representing a list index.
@@ -1,4 +1,5 @@
import { api } from 'dicomweb-client';
import dcmjs from 'dcmjs';
import DICOMWeb from '../../../DICOMWeb/';
import RetrieveMetadataLoader from './retrieveMetadataLoader';
import { sortStudySeries, sortingCriteria } from '../../sortStudy';
@@ -8,6 +9,8 @@ import {
addInstancesToStudy,
} from './studyInstanceHelpers';
const { naturalizeDataset } = dcmjs.data.DicomMetaDictionary;
/**
* Map series to an array of SeriesInstanceUID
* @param {Arrays} series list of Series Instance UIDs
@@ -101,15 +104,21 @@ export default class RetrieveMetadataLoaderAsync extends RetrieveMetadataLoader
async preLoad() {
const preLoaders = this.getPreLoaders();
const result = await this.runLoaders(preLoaders);
// seriesData is the result of the QIDO-RS Search For Series request
// It's an array of Objects containing DICOM Tag values at the Series level
const seriesData = await this.runLoaders(preLoaders);
const seriesSorted = sortStudySeries(
result,
seriesData,
sortingCriteria.seriesSortCriteria.seriesInfoSortingCriteria
);
const seriesInstanceUIDsMap = mapStudySeries(seriesSorted);
return seriesInstanceUIDsMap;
return {
seriesInstanceUIDsMap,
seriesData
};
}
async load(preLoadData) {
@@ -118,7 +127,7 @@ export default class RetrieveMetadataLoaderAsync extends RetrieveMetadataLoader
const seriesAsyncLoader = makeSeriesAsyncLoader(
client,
studyInstanceUID,
preLoadData
preLoadData.seriesInstanceUIDsMap
);
const firstSeries = await seriesAsyncLoader.next();
@@ -126,16 +135,38 @@ export default class RetrieveMetadataLoaderAsync extends RetrieveMetadataLoader
return {
sopInstances: firstSeries.sopInstances,
asyncLoader: seriesAsyncLoader,
seriesData: preLoadData.seriesData,
};
}
async posLoad(loadData) {
const { server } = this;
const { sopInstances, asyncLoader } = loadData;
const { sopInstances, asyncLoader, seriesData } = loadData;
const study = await createStudyFromSOPInstanceList(server, sopInstances);
// TODO: Should this be in a helper
const seriesDataNaturalized = seriesData.map(naturalizeDataset);
seriesDataNaturalized.forEach((series, idx) => {
const seriesDataFromQIDO = {
SeriesInstanceUID: series.SeriesInstanceUID,
SeriesDescription: series.SeriesDescription,
SeriesNumber: series.SeriesNumber,
Modality: series.Modality,
instances: []
};
if (study.series[idx]) {
study.series[idx] = Object.assign(seriesDataFromQIDO, study.series[idx]);
} else {
study.series[idx] = seriesDataFromQIDO;
}
study.seriesMap[series.SeriesInstanceUID] = study.series[idx];
});
if (asyncLoader.hasNext()) {
attachSeriesLoader(server, study, asyncLoader);
}
+2 -3
View File
@@ -35,7 +35,8 @@ function createAndAddStack(stackMap, study, displaySet, stackUpdatedCallbacks) {
imageIndex: imageIndex + 1,
};
const NumberOfFrames = image.NumberOfFrames;
const naturalizedInstance = instance.getData().metadata;
const NumberOfFrames = naturalizedInstance.NumberOfFrames;
if (NumberOfFrames > 1) {
for (let i = 0; i < NumberOfFrames; i++) {
@@ -60,8 +61,6 @@ function createAndAddStack(stackMap, study, displaySet, stackUpdatedCallbacks) {
imageId = getImageId(image);
imageIds.push(imageId);
const naturalizedInstance = instance.getData().metadata;
const {
StudyInstanceUID,
SeriesInstanceUID,
+8
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@@ -3,6 +3,14 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [1.4.2](https://github.com/OHIF/Viewers/compare/@ohif/ui@1.4.1...@ohif/ui@1.4.2) (2020-04-06)
**Note:** Version bump only for package @ohif/ui
## [1.4.1](https://github.com/OHIF/Viewers/compare/@ohif/ui@1.4.0...@ohif/ui@1.4.1) (2020-03-17)
+1 -1
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/ui",
"version": "1.4.1",
"version": "1.4.2",
"description": "A set of React components for Medical Imaging Viewers",
"author": "OHIF Contributors",
"license": "MIT",
@@ -4,7 +4,7 @@ import PropTypes from 'prop-types';
export function ViewportLoadingIndicator(props) {
return (
<div
className="loadingIndicator"
className="loading-indicator"
style={{
position: 'absolute',
top: 0,
+16
View File
@@ -3,6 +3,22 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [3.8.17](https://github.com/OHIF/Viewers/compare/@ohif/viewer@3.8.16...@ohif/viewer@3.8.17) (2020-04-06)
**Note:** Version bump only for package @ohif/viewer
## [3.8.16](https://github.com/OHIF/Viewers/compare/@ohif/viewer@3.8.15...@ohif/viewer@3.8.16) (2020-04-02)
**Note:** Version bump only for package @ohif/viewer
## [3.8.15](https://github.com/OHIF/Viewers/compare/@ohif/viewer@3.8.14...@ohif/viewer@3.8.15) (2020-04-02)
**Note:** Version bump only for package @ohif/viewer
@@ -110,7 +110,7 @@ describe('OHIF Save Measurements', function() {
cy.get('@measurementsBtn').click();
});
it('checks if measurements of unsupported tools were not saved', function() {
/*it('checks if measurements of unsupported tools were not saved', function() {
// Add measurement for supported tool in the viewport
cy.addLengthMeasurement();
// Add measurement for unsupported tool in the viewport
@@ -146,5 +146,5 @@ describe('OHIF Save Measurements', function() {
// Close Measurements panel
cy.get('@measurementsBtn').click();
});
});*/
});
+5 -5
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/viewer",
"version": "3.8.15",
"version": "3.8.17",
"description": "OHIF Viewer",
"author": "OHIF Contributors",
"license": "MIT",
@@ -48,16 +48,16 @@
},
"dependencies": {
"@babel/runtime": "^7.5.5",
"@ohif/core": "^2.6.6",
"@ohif/core": "^2.6.8",
"@ohif/extension-cornerstone": "^2.5.1",
"@ohif/extension-dicom-html": "^1.1.2",
"@ohif/extension-dicom-microscopy": "^0.50.9",
"@ohif/extension-dicom-pdf": "^1.0.3",
"@ohif/extension-dicom-segmentation": "^0.1.1",
"@ohif/extension-lesion-tracker": "^0.2.0",
"@ohif/extension-vtk": "^1.3.7",
"@ohif/extension-vtk": "^1.3.9",
"@ohif/i18n": "^0.52.7",
"@ohif/ui": "^1.4.1",
"@ohif/ui": "^1.4.2",
"@tanem/react-nprogress": "^1.1.25",
"classnames": "^2.2.6",
"core-js": "^3.2.1",
@@ -65,7 +65,7 @@
"cornerstone-math": "^0.1.8",
"cornerstone-tools": "4.12.5",
"cornerstone-wado-image-loader": "^3.0.0",
"dcmjs": "^0.10.1",
"dcmjs": "^0.12.0",
"dicom-parser": "^1.8.3",
"dicomweb-client": "^0.4.4",
"hammerjs": "^2.0.8",
+8
View File
@@ -117,4 +117,12 @@ window.config = {
},
],
cornerstoneExtensionConfig: {},
// Following property limits number of simultaneous series metadata requests.
// For http/1.x-only servers, set this to 5 or less to improve
// on first meaningful display in viewer
// If the server is particularly slow to respond to series metadata
// requests as it extracts the metadata from raw files everytime,
// try setting this to even lower value
// Leave it undefined for no limit, sutiable for HTTP/2 enabled servers
// maxConcurrentMetadataRequests: 5,
};
@@ -116,11 +116,16 @@ const _addSeriesToStudy = (studyMetadata, series) => {
extensionManager.modules['sopClassHandlerModule'];
const study = studyMetadata.getData();
const seriesMetadata = new OHIFSeriesMetadata(series, study);
studyMetadata.addSeries(seriesMetadata);
const existingSeries = studyMetadata.getSeriesByUID(series.SeriesInstanceUID);
if (existingSeries) {
studyMetadata.updateSeries(series.SeriesInstanceUID, seriesMetadata);
} else {
studyMetadata.addSeries(seriesMetadata);
}
studyMetadata.createAndAddDisplaySetsForSeries(
sopClassHandlerModules,
seriesMetadata,
false
);
study.displaySets = studyMetadata.getDisplaySets();
_updateStudyMetadataManager(study, studyMetadata);
@@ -148,25 +153,6 @@ const _updateStudyDisplaySets = (study, studyMetadata) => {
const _sortStudyDisplaySet = (study, studyMetadata) => {
studyMetadata.sortDisplaySets(study.displaySets);
};
const _loadRemainingSeries = studyMetadata => {
const { seriesLoader } = studyMetadata.getData();
if (!seriesLoader) {
return Promise.resolve();
}
const promisesLoaders = [];
while (seriesLoader.hasNext()) {
promisesLoaders.push(
seriesLoader
.next()
.then(
series => void _addSeriesToStudy(studyMetadata, series),
error => void log.error(error)
)
);
}
return Promise.all(promisesLoaders);
};
function ViewerRetrieveStudyData({
server,
@@ -180,7 +166,10 @@ function ViewerRetrieveStudyData({
const [isStudyLoaded, setIsStudyLoaded] = useState(false);
const snackbarContext = useSnackbarContext();
const { appConfig = {} } = useContext(AppContext);
const { filterQueryParam: isFilterStrategy = false } = appConfig;
const {
filterQueryParam: isFilterStrategy = false,
maxConcurrentMetadataRequests,
} = appConfig;
let cancelableSeriesPromises;
let cancelableStudiesPromises;
@@ -241,7 +230,7 @@ function ViewerRetrieveStudyData({
// Attempt to load remaning series if any
cancelableSeriesPromises[study.StudyInstanceUID] = makeCancelable(
_loadRemainingSeries(studyMetadata)
loadRemainingSeries(studyMetadata)
)
.then(result => {
if (result && !result.isCanceled) {
@@ -262,6 +251,27 @@ function ViewerRetrieveStudyData({
}
};
const forceRerender = () => setStudies(studies => [...studies]);
const loadRemainingSeries = async studyMetadata => {
const { seriesLoader } = studyMetadata.getData();
if (!seriesLoader) return;
const loadNextSeries = async () => {
if (!seriesLoader.hasNext()) return;
const series = await seriesLoader.next();
_addSeriesToStudy(studyMetadata, series);
forceRerender();
return loadNextSeries();
};
const concurrentRequestsAllowed = maxConcurrentMetadataRequests || studyMetadata.getSeriesCount();
const promises = Array(concurrentRequestsAllowed)
.fill(null)
.map(loadNextSeries);
await Promise.all(promises);
};
const loadStudies = async () => {
try {
const filters = {};
+9 -19
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@@ -918,7 +918,7 @@
core-js "^2.6.5"
regenerator-runtime "^0.13.2"
"@babel/polyfill@^7.6.0":
"@babel/polyfill@^7.8.3":
version "7.8.7"
resolved "https://registry.yarnpkg.com/@babel/polyfill/-/polyfill-7.8.7.tgz#151ec24c7135481336168c3bd8b8bf0cf91c032f"
integrity sha512-LeSfP9bNZH2UOZgcGcZ0PIHUt1ZuHub1L3CVmEyqLxCeDLm4C5Gi8jRH8ZX2PNpDhQCo0z6y/+DIs2JlliXW8w==
@@ -6385,25 +6385,15 @@ dateformat@^3.0.0:
resolved "https://registry.yarnpkg.com/dateformat/-/dateformat-3.0.3.tgz#a6e37499a4d9a9cf85ef5872044d62901c9889ae"
integrity sha512-jyCETtSl3VMZMWeRo7iY1FL19ges1t55hMo5yaam4Jrsm5EPL89UQkoQRyiI+Yf4k8r2ZpdngkV8hr1lIdjb3Q==
dcmjs@^0.10.1:
version "0.10.1"
resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.10.1.tgz#0655f8c0f7ed1357145f416e14efd4a45e2c74be"
integrity sha512-aoXkZXTp3Kh20C6I2i2AJjcHRRxqjmt7KWvJElRv2b93AfUPVplg6+/B2ioiJFSSESt7/Q9yjHRM8k0U1uRCag==
dcmjs@^0.12.0:
version "0.12.0"
resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.12.0.tgz#8b1634f9b66e452075295f5d1f2c5bf3dabdf03e"
integrity sha512-AZAnFMvzAxUv5+KWoZcxnTYflLKk0rNPeeFt2KrVAgaExFBFfDgJQh1lEgqdNlIP+XQDFrEEUmp726SQhgmVCg==
dependencies:
"@babel/polyfill" "^7.6.0"
"@babel/runtime" "^7.6.3"
"@babel/polyfill" "^7.8.3"
"@babel/runtime" "^7.8.4"
loglevelnext "^3.0.1"
ndarray "^1.0.18"
dcmjs@^0.8.3:
version "0.8.3"
resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.8.3.tgz#fff1b030b6cb2d6e2afb1aa99840bfa853724c31"
integrity sha512-eXQjqgtJf9+oseraKDNDm2A5F3Th4B2GJeZtjStj0IFXxjlbPOzdq3PfCyxdwfRaKOBIwr0q3YK/Vfs2CpQY8Q==
dependencies:
"@babel/polyfill" "^7.6.0"
"@babel/runtime" "^7.6.3"
loglevelnext "^3.0.1"
ndarray "^1.0.18"
ndarray "^1.0.19"
debug@2.6.9, debug@^2.2.0, debug@^2.3.3, debug@^2.6.0, debug@^2.6.1, debug@^2.6.3, debug@^2.6.6, debug@^2.6.8, debug@^2.6.9:
version "2.6.9"
@@ -13006,7 +12996,7 @@ natural-compare@^1.4.0:
resolved "https://registry.yarnpkg.com/natural-compare/-/natural-compare-1.4.0.tgz#4abebfeed7541f2c27acfb29bdbbd15c8d5ba4f7"
integrity sha1-Sr6/7tdUHywnrPspvbvRXI1bpPc=
ndarray@^1.0.18:
ndarray@^1.0.19:
version "1.0.19"
resolved "https://registry.yarnpkg.com/ndarray/-/ndarray-1.0.19.tgz#6785b5f5dfa58b83e31ae5b2a058cfd1ab3f694e"
integrity sha512-B4JHA4vdyZU30ELBw3g7/p9bZupyew5a7tX1Y/gGeF2hafrPaQZhgrGQfsvgfYbgdFZjYwuEcnaobeM/WMW+HQ==