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Re IDC #2765: fix loading of segmentations at first startup (#2768)

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Re IDC #2761: fix loading of segmentations

update dcmjs to 0.19.9
This commit is contained in:
Davide Punzo 2022-04-05 09:39:22 +02:00 committed by GitHub
parent b94d4782d1
commit 32828d9a6e
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
15 changed files with 173 additions and 177 deletions
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2
extensions/cornerstone/package.json
View File

@ -36,7 +36,7 @@
"cornerstone-math": "^0.1.9",
"cornerstone-tools": "^6.0.6",
"cornerstone-wado-image-loader": "^4.1.0",
"dcmjs": "0.19.8",
"dcmjs": "0.19.9",
"dicom-parser": "^1.8.11",
"hammerjs": "^2.0.8",
"prop-types": "^15.6.2",

2
extensions/dicom-html/package.json
View File

@ -29,7 +29,7 @@
},
"peerDependencies": {
"@ohif/core": "^0.50.0",
"dcmjs": "0.19.8",
"dcmjs": "0.19.9",
"prop-types": "^15.6.2",
"react": "^16.8.6",
"react-dom": "^16.8.6"

2
extensions/dicom-rt/package.json
View File

@ -31,7 +31,7 @@
"@ohif/core": "^0.50.0",
"cornerstone-core": "^2.6.1",
"cornerstone-tools": "^6.0.6",
"dcmjs": "0.19.8",
"dcmjs": "0.19.9",
"gl-matrix": "^3.3.0",
"prop-types": "^15.6.2",
"react": "^16.8.6",

2
extensions/dicom-segmentation/package.json
View File

@ -31,7 +31,7 @@
"@ohif/core": "^0.50.0",
"cornerstone-core": "^2.6.1",
"cornerstone-tools": "^6.0.6",
"dcmjs": "0.19.8",
"dcmjs": "0.19.9",
"prop-types": "^15.6.2",
"react": "^16.8.6",
"react-dom": "^16.8.6"

17
extensions/dicom-segmentation/src/components/SegmentationPanel/SegmentationPanel.js
View File

@ -226,7 +226,6 @@ const SegmentationPanel = ({
};
}, [
activeIndex,
updateSegmentationComboBox,
viewports,
]);
@ -234,23 +233,9 @@ const SegmentationPanel = ({
const index = e.detail.activatedLabelmapIndex;
if (index !== -1) {
setState(state => ({ ...state, selectedSegmentation: index }));
} else {
cleanSegmentationComboBox();
}
};
const cleanSegmentationComboBox = () => {
setState(state => ({
...state,
segmentsHidden: [],
segmentNumbers: [],
labelMapList: [],
segmentList: [],
isDisabled: true,
selectedSegmentation: -1,
}));
};
const refreshSegmentations = () => {
const activeViewport = getActiveViewport();
const isDisabled = !activeViewport || !activeViewport.StudyInstanceUID;
@ -709,7 +694,7 @@ const SegmentationPanel = ({
count={state.segmentList.length}
isVisible={
state.segmentsHidden.filter(isHidden => isHidden === true).length <
state.segmentNumbers.length
state.segmentNumbers.length && state.segmentNumbers.length > 0
}
onVisibilityChange={onVisibilityChangeHandler}
>

11
extensions/dicom-segmentation/src/utils/setActiveLabelMap.js
View File

@ -47,14 +47,23 @@ export default async function setActiveLabelmap(
return labelmapIndex;
}
if (!displaySet.isLoaded) {
if (!displaySet.isLoaded && !displaySet.loadError) {
try {
await displaySet.load(referencedDisplaySet, studies);
} catch (error) {
displaySet.isLoaded = false;
displaySet.loadError = true;
displaySet.segLoadErrorMessagge = error.message;
onDisplaySetLoadFailure(error);
/*
* TODO: Improve the way we notify parts of the app
* that depends on derived display sets to be loaded.
* (Implement pubsub for better tracking of derived display sets)
*/
const event = new CustomEvent('segmentationLoadingError');
document.dispatchEvent(event);
return -1;
}
}

2
extensions/dicom-tag-browser/package.json
View File

@ -28,7 +28,7 @@
},
"peerDependencies": {
"@ohif/core": "^2.6.0",
"dcmjs": "0.19.8",
"dcmjs": "0.19.9",
"react": "^16.8.6"
},
"dependencies": {

2
extensions/vtk/package.json
View File

@ -35,7 +35,7 @@
"cornerstone-core": "^2.6.1",
"cornerstone-tools": "^6.0.6",
"cornerstone-wado-image-loader": "^4.1.0",
"dcmjs": "0.19.8",
"dcmjs": "0.19.9",
"dicom-parser": "^1.8.11",
"i18next": "^17.0.3",
"i18next-browser-languagedetector": "^3.0.1",

2
platform/core/package.json
View File

@ -39,7 +39,7 @@
"dependencies": {
"@babel/runtime": "^7.5.5",
"ajv": "^6.10.0",
"dcmjs": "0.19.8",
"dcmjs": "0.19.9",
"dicomweb-client": "^0.8.3",
"immer": "9.0.12",
"isomorphic-base64": "^1.0.2",

150
platform/core/src/utils/loadAndCacheDerivedDisplaySets.js
View File

@ -49,7 +49,12 @@ import studyMetadataManager from './studyMetadataManager';
* @param {object} snackbar
* @returns void
*/
async function loadAndCacheDerivedDisplaySets(referencedDisplaySet, studies, logger, snackbar) {
async function loadAndCacheDerivedDisplaySets(
referencedDisplaySet,
studies,
logger,
snackbar
) {
const { StudyInstanceUID, SeriesInstanceUID } = referencedDisplaySet;
const promises = [];
const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
@ -80,60 +85,111 @@ async function loadAndCacheDerivedDisplaySets(referencedDisplaySet, studies, log
});
// For each type, see if any are loaded, if not load the most recent.
await Promise.all(Object.keys(displaySetsPerModality).map(async (key) => {
const displaySets = displaySetsPerModality[key];
await Promise.all(
Object.keys(displaySetsPerModality).map(async key => {
const displaySets = displaySetsPerModality[key];
const isLoaded = displaySets.some(displaySet => displaySet.isLoaded);
if (isLoaded) {
return;
}
if (displaySets.some(displaySet => displaySet.loadError)) {
return;
}
// find most recent and load it.
let recentDateTime = 0;
let recentDisplaySet = displaySets[0];
displaySets.forEach(displaySet => {
const dateTime = Number(
`${displaySet.SeriesDate}${displaySet.SeriesTime}`
);
if (dateTime > recentDateTime) {
recentDateTime = dateTime;
recentDisplaySet = displaySet;
const isLoaded = displaySets.some(displaySet => displaySet.isLoaded);
if (isLoaded) {
return;
}
});
try {
if (recentDisplaySet.hasOwnProperty('getSourceDisplaySet') &&
typeof recentDisplaySet.getSourceDisplaySet === 'function') {
await recentDisplaySet.getSourceDisplaySet(studies);
} else {
await recentDisplaySet.load(referencedDisplaySet, studies);
if (displaySets.some(displaySet => displaySet.loadError)) {
return;
}
} catch (error) {
recentDisplaySet.isLoaded = false;
recentDisplaySet.loadError = true;
logger.error({ error, message: error.message });
snackbar.show({
title: 'Error loading derived display set:',
message: error.message,
type: 'error',
error,
autoClose: false,
// find most recent and load it.
let recentDateTime = 0;
let recentDisplaySet = displaySets[0];
displaySets.forEach(displaySet => {
const dateTime = Number(
`${displaySet.SeriesDate}${displaySet.SeriesTime}`
);
if (dateTime > recentDateTime) {
recentDateTime = dateTime;
recentDisplaySet = displaySet;
}
});
}
}));
try {
if (
recentDisplaySet.hasOwnProperty('getSourceDisplaySet') &&
typeof recentDisplaySet.getSourceDisplaySet === 'function'
) {
if (recentDisplaySet.Modality === 'SEG' && logger) {
const onDisplaySetLoadFailureHandler = error => {
logger.error({ error, message: error.message });
snackbar.show({
title: 'DICOM Segmentation Loader',
message: error.message,
type: 'error',
autoClose: true,
});
};
let activatedLabelmapIndex = -1;
while (activatedLabelmapIndex == -1) {
const {
referencedDisplaySet,
activatedLabelmapPromise,
} = await recentDisplaySet.getSourceDisplaySet(
studies,
true,
onDisplaySetLoadFailureHandler
);
activatedLabelmapIndex = await activatedLabelmapPromise;
const selectionFired = new CustomEvent(
'extensiondicomsegmentationsegselected',
{
detail: { activatedLabelmapIndex: activatedLabelmapIndex },
}
);
document.dispatchEvent(selectionFired);
const lastDateTime = Number(
`${recentDisplaySet.SeriesDate}${recentDisplaySet.SeriesTime}`
);
recentDateTime = 0;
displaySets.forEach(displaySet => {
const dateTime = Number(
`${displaySet.SeriesDate}${displaySet.SeriesTime}`
);
if (dateTime > recentDateTime && dateTime < lastDateTime) {
recentDateTime = dateTime;
recentDisplaySet = displaySet;
}
});
}
} else {
await recentDisplaySet.getSourceDisplaySet(studies);
}
} else {
await recentDisplaySet.load(referencedDisplaySet, studies);
}
} catch (error) {
recentDisplaySet.isLoaded = false;
recentDisplaySet.loadError = true;
logger.error({ error, message: error.message });
snackbar.show({
title: 'Error loading derived display set:',
message: error.message,
type: 'error',
error,
autoClose: false,
});
}
})
);
/*
* TODO: Improve the way we notify parts of the app
* that depends on derived display sets to be loaded.
* (Implement pubsub for better tracking of derived display sets)
*/
* TODO: Improve the way we notify parts of the app
* that depends on derived display sets to be loaded.
* (Implement pubsub for better tracking of derived display sets)
*/
const event = new CustomEvent('deriveddisplaysetsloadedandcached');
document.dispatchEvent(event);
};
}
export default loadAndCacheDerivedDisplaySets;

2
platform/viewer/package.json
View File

@ -66,7 +66,7 @@
"cornerstone-math": "^0.1.9",
"cornerstone-tools": "^6.0.6",
"cornerstone-wado-image-loader": "^4.1.0",
"dcmjs": "0.19.8",
"dcmjs": "0.19.9",
"dicom-parser": "^1.8.11",
"dicomweb-client": "^0.8.3",
"hammerjs": "^2.0.8",

131
platform/viewer/src/connectedComponents/Viewer.js
View File

@ -105,6 +105,11 @@ class Viewer extends Component {
if (this.props.dialog) {
this.props.dialog.dismissAll();
}
document.removeEventListener(
'segmentationLoadingError',
this._updateThumbnails
);
}
retrieveTimepoints = filter => {
@ -212,6 +217,12 @@ class Viewer extends Component {
),
});
}
document.addEventListener(
'segmentationLoadingError',
this._updateThumbnails.bind(this),
false
);
}
componentDidUpdate(prevProps) {
@ -255,6 +266,20 @@ class Viewer extends Component {
}
}
_updateThumbnails() {
const { studies, activeViewportIndex, viewports } = this.props;
const activeViewport = viewports[activeViewportIndex];
const activeDisplaySetInstanceUID = activeViewport
? activeViewport.displaySetInstanceUID
: undefined;
this.setState({
thumbnails: _mapStudiesToThumbnails(studies, activeDisplaySetInstanceUID),
activeDisplaySetInstanceUID,
});
}
_getActiveViewport() {
return this.props.viewports[this.props.activeViewportIndex];
}
@ -461,9 +486,7 @@ const _checkForDerivedDisplaySets = async function(displaySet, study) {
/**
* Async function to check if there are any inconsistences in the series.
*
* For segmentation checks that the geometry is consistent with the source images:
* 1) no frames out of plane;
* 2) have the same width and height.
* For segmentation returns any error during loading.
*
* For reconstructable 3D volume:
* 1) Is series multiframe?
@ -477,10 +500,7 @@ const _checkForDerivedDisplaySets = async function(displaySet, study) {
* @param {*object} displaySet
* @returns {[string]} an array of strings containing the warnings
*/
const _checkForSeriesInconsistencesWarnings = async function(
displaySet,
studies
) {
const _checkForSeriesInconsistencesWarnings = async function(displaySet) {
if (displaySet.inconsistencyWarnings) {
// warnings already checked and cached in displaySet
return displaySet.inconsistencyWarnings;
@ -546,98 +566,14 @@ const _checkForSeriesInconsistencesWarnings = async function(
if (displaySet.isModalitySupported === false) {
inconsistencyWarnings.push('The datasets modality is not supported.');
}
displaySet.inconsistencyWarnings = inconsistencyWarnings;
} else {
const segMetadata = displaySet.metadata;
if (!segMetadata) {
return inconsistencyWarnings;
}
const { referencedDisplaySet } = displaySet.getSourceDisplaySet(
studies,
false
);
if (!referencedDisplaySet) {
return inconsistencyWarnings;
}
const imageIds = referencedDisplaySet.images.map(image =>
image.getImageId()
);
if (!imageIds || imageIds.length === 0) {
return inconsistencyWarnings;
}
for (
let i = 0,
groupsLen = segMetadata.PerFrameFunctionalGroupsSequence.length;
i < groupsLen;
++i
) {
const PerFrameFunctionalGroups =
segMetadata.PerFrameFunctionalGroupsSequence[i];
if (!PerFrameFunctionalGroups) {
continue;
}
let SourceImageSequence = undefined;
if (segMetadata.SourceImageSequence) {
SourceImageSequence = segMetadata.SourceImageSequence[i];
} else if (PerFrameFunctionalGroups.DerivationImageSequence) {
SourceImageSequence =
PerFrameFunctionalGroups.DerivationImageSequence.SourceImageSequence;
}
if (!SourceImageSequence) {
if (inconsistencyWarnings.length === 0) {
const warningMessage =
'The segmentation ' +
'has frames out of plane respect to the source images.';
inconsistencyWarnings.push(warningMessage);
}
continue;
}
const { ReferencedSOPInstanceUID } = SourceImageSequence;
const imageId = imageIds.find(imageId => {
const sopCommonModule = cornerstone.metaData.get(
'sopCommonModule',
imageId
);
if (!sopCommonModule) {
return;
}
return sopCommonModule.sopInstanceUID === ReferencedSOPInstanceUID;
});
if (!imageId) {
continue;
}
const sourceImageMetadata = cornerstone.metaData.get('instance', imageId);
if (
segMetadata.Rows !== sourceImageMetadata.Rows ||
segMetadata.Columns !== sourceImageMetadata.Columns
) {
const warningMessage =
'The segmentation ' +
'has frames with different geometry ' +
'dimensions (Rows and Columns) respect to the source images.';
inconsistencyWarnings.push(warningMessage);
break;
}
}
if (inconsistencyWarnings.length !== 0) {
const warningMessage =
'The segmentation format is not supported yet. ' +
'The segmentation data (segments) could not be loaded.';
inconsistencyWarnings.push(warningMessage);
if (displaySet.loadError) {
inconsistencyWarnings.push(displaySet.segLoadErrorMessagge);
displaySet.inconsistencyWarnings = inconsistencyWarnings;
}
}
// cache the warnings
displaySet.inconsistencyWarnings = inconsistencyWarnings;
return inconsistencyWarnings;
};
@ -736,10 +672,7 @@ const _mapStudiesToThumbnails = function(studies, activeDisplaySetInstanceUID) {
altImageText = displaySet.Modality ? displaySet.Modality : 'UN';
}
const hasWarnings = _checkForSeriesInconsistencesWarnings(
displaySet,
studies
);
const hasWarnings = _checkForSeriesInconsistencesWarnings(displaySet);
const hasDerivedDisplaySets = _checkForDerivedDisplaySets(
displaySet,

15
platform/viewer/src/connectedComponents/ViewerMain.js
View File

@ -154,12 +154,25 @@ class ViewerMain extends Component {
});
};
const { referencedDisplaySet } = displaySet.getSourceDisplaySet(
const {
referencedDisplaySet,
activatedLabelmapPromise,
} = displaySet.getSourceDisplaySet(
this.props.studies,
true,
onDisplaySetLoadFailureHandler
);
displaySet = referencedDisplaySet;
activatedLabelmapPromise.then(activatedLabelmapIndex => {
const selectionFired = new CustomEvent(
'extensiondicomsegmentationsegselected',
{
detail: { activatedLabelmapIndex: activatedLabelmapIndex },
}
);
document.dispatchEvent(selectionFired);
});
} else {
displaySet = displaySet.getSourceDisplaySet(this.props.studies);
}

2
platform/viewer/src/googleCloud/DicomStorePickerModal.js
View File

@ -36,7 +36,7 @@ function DicomStorePickerModal({
user,
url,
},
onClose
onClose,
});
}
};

8
yarn.lock
View File

@ -5449,10 +5449,10 @@ dateformat@^3.0.0:
resolved "https://registry.yarnpkg.com/dateformat/-/dateformat-3.0.3.tgz#a6e37499a4d9a9cf85ef5872044d62901c9889ae"
integrity sha512-jyCETtSl3VMZMWeRo7iY1FL19ges1t55hMo5yaam4Jrsm5EPL89UQkoQRyiI+Yf4k8r2ZpdngkV8hr1lIdjb3Q==
dcmjs@0.19.8:
version "0.19.8"
resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.19.8.tgz#9be7471f8f2e20d4e09489b5f0c51dfa56621ec1"
integrity sha512-po/GWh7pXF+diO/umpqOfpF0Kk7MzAmhFlscOR+KchCIZbN0pmt2npFT3p8jMii/FBre++k+8PIvFa/LKh0P2A==
dcmjs@0.19.9:
version "0.19.9"
resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.19.9.tgz#be500101b1f75a28ea9eb7ef845a8ed197355e76"
integrity sha512-V+0tND+SPX5e7WFeLzeoooaTsZbiKmEP2i3AyERsojaXXfaDV5E+pta5IqId4Ok1yfRT5qfTFwLGstGT6nLplA==
dependencies:
"@babel/polyfill" "^7.8.3"
"@babel/runtime" "^7.8.4"