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docs(faq): FAQ and Segmentation Mode Fix for some studies #3762

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merged 13 commits into from
Nov 3, 2023
Merged

docs(faq): FAQ and Segmentation Mode Fix for some studies #3762

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96d8cc9
update docs
sedghi Oct 12, 2023
ed136c3
Merge branch 'master' of github.com:OHIF/Viewers
sedghi Oct 17, 2023
95b1cff
Merge branch 'master' of github.com:OHIF/Viewers
sedghi Oct 24, 2023
121d8c2
Merge branch 'master' of github.com:OHIF/Viewers
sedghi Oct 27, 2023
47c7987
add thumbnail docs
sedghi Oct 27, 2023
cf58c14
fix hp
sedghi Oct 27, 2023
37df8df
upgrade cs3d
sedghi Oct 27, 2023
5361cb1
Merge branch 'master' of github.com:OHIF/Viewers into docs/faq-more
sedghi Oct 30, 2023
0a9353a
add faq for various topics
sedghi Nov 3, 2023
affaa30
update cs3d
sedghi Nov 3, 2023
352572d
Merge branch 'master' of github.com:OHIF/Viewers into docs/faq-more
sedghi Nov 3, 2023
fd9eedc
apply review comments
sedghi Nov 3, 2023
15fceaa
apply review comments
sedghi Nov 3, 2023
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4 changes: 2 additions & 2 deletions extensions/cornerstone-dicom-seg/package.json
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Expand Up @@ -44,8 +44,8 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^1.20.3",
"@cornerstonejs/tools": "^1.20.3",
"@cornerstonejs/adapters": "^1.27.3",
"@cornerstonejs/tools": "^1.27.3",
"@kitware/vtk.js": "27.3.1",
"react-color": "^2.19.3"
}
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8 changes: 4 additions & 4 deletions extensions/cornerstone-dicom-sr/package.json
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Expand Up @@ -36,17 +36,17 @@
"@ohif/extension-cornerstone": "3.8.0-beta.9",
"@ohif/extension-measurement-tracking": "3.8.0-beta.9",
"@ohif/ui": "3.8.0-beta.9",
"dcmjs": "^0.29.11",
"dcmjs": "^0.29.12",
"dicom-parser": "^1.8.9",
"hammerjs": "^2.0.8",
"prop-types": "^15.6.2",
"react": "^17.0.2"
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^1.20.3",
"@cornerstonejs/core": "^1.20.3",
"@cornerstonejs/tools": "^1.20.3",
"@cornerstonejs/adapters": "^1.27.3",
"@cornerstonejs/core": "^1.27.3",
"@cornerstonejs/tools": "^1.27.3",
"classnames": "^2.3.2"
}
}
10 changes: 5 additions & 5 deletions extensions/cornerstone/package.json
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Expand Up @@ -36,7 +36,7 @@
"@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
"@cornerstonejs/codec-openjpeg": "^1.2.2",
"@cornerstonejs/codec-openjph": "^2.4.2",
"@cornerstonejs/dicom-image-loader": "^1.20.3",
"@cornerstonejs/dicom-image-loader": "^1.27.3",
"@ohif/core": "3.8.0-beta.9",
"@ohif/ui": "3.8.0-beta.9",
"dcmjs": "^0.29.11",
Expand All @@ -52,10 +52,10 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^1.20.3",
"@cornerstonejs/core": "^1.20.3",
"@cornerstonejs/streaming-image-volume-loader": "^1.20.3",
"@cornerstonejs/tools": "^1.20.3",
"@cornerstonejs/adapters": "^1.27.3",
"@cornerstonejs/core": "^1.27.3",
"@cornerstonejs/streaming-image-volume-loader": "^1.27.3",
"@cornerstonejs/tools": "^1.27.3",
"@kitware/vtk.js": "27.3.1",
"html2canvas": "^1.4.1",
"lodash.debounce": "4.0.8",
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8 changes: 4 additions & 4 deletions extensions/cornerstone/src/init.tsx
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Expand Up @@ -59,8 +59,8 @@ export default async function init({

await cs3DInit({
rendering: {
preferSizeOverAccuracy: Boolean(appConfig.use16BitDataType),
useNorm16Texture: Boolean(appConfig.use16BitDataType),
preferSizeOverAccuracy: Boolean(appConfig.preferSizeOverAccuracy),
useNorm16Texture: Boolean(appConfig.useNorm16Texture),
},
});

Expand Down Expand Up @@ -308,8 +308,8 @@ export default async function init({
viewportGridService.subscribe(
viewportGridService.EVENTS.ACTIVE_VIEWPORT_ID_CHANGED,
activeViewportEventListener
);
}
);
}

function CPUModal() {
return (
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3 changes: 2 additions & 1 deletion extensions/cornerstone/src/initWADOImageLoader.js
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Expand Up @@ -49,7 +49,8 @@ export default function initWADOImageLoader(
// Until the default is set to true (which is the case for cornerstone3D),
// we should set this flag to false.
convertFloatPixelDataToInt: false,
use16BitDataType: Boolean(appConfig.use16BitDataType),
use16BitDataType:
Boolean(appConfig.useNorm16Texture) || Boolean(appConfig.preferSizeOverAccuracy),
},
beforeSend: function (xhr) {
//TODO should be removed in the future and request emitted by DicomWebDataSource
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2 changes: 1 addition & 1 deletion extensions/default/package.json
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Expand Up @@ -32,7 +32,7 @@
"peerDependencies": {
"@ohif/core": "3.8.0-beta.9",
"@ohif/i18n": "3.8.0-beta.9",
"dcmjs": "^0.29.11",
"dcmjs": "^0.29.12",
"dicomweb-client": "^0.10.2",
"prop-types": "^15.6.2",
"react": "^17.0.2",
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8 changes: 7 additions & 1 deletion extensions/default/src/init.ts
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Expand Up @@ -51,10 +51,16 @@ export default function init({ servicesManager, configuration = {} }): void {
const handlePETImageMetadata = ({ SeriesInstanceUID, StudyInstanceUID }) => {
const { instances } = DicomMetadataStore.getSeries(StudyInstanceUID, SeriesInstanceUID);

if (!instances?.length) {
return;
}

const modality = instances[0].Modality;
if (modality !== 'PT') {

if (!modality || modality !== 'PT') {
return;
}

const imageIds = instances.map(instance => instance.imageId);
const instanceMetadataArray = [];
imageIds.forEach(imageId => {
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2 changes: 1 addition & 1 deletion extensions/dicom-pdf/package.json
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Expand Up @@ -30,7 +30,7 @@
"peerDependencies": {
"@ohif/core": "3.8.0-beta.9",
"@ohif/ui": "3.8.0-beta.9",
"dcmjs": "^0.29.11",
"dcmjs": "^0.29.12",
"dicom-parser": "^1.8.9",
"hammerjs": "^2.0.8",
"prop-types": "^15.6.2",
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2 changes: 1 addition & 1 deletion extensions/dicom-video/package.json
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Expand Up @@ -30,7 +30,7 @@
"peerDependencies": {
"@ohif/core": "3.8.0-beta.9",
"@ohif/ui": "3.8.0-beta.9",
"dcmjs": "^0.29.11",
"dcmjs": "^0.29.12",
"dicom-parser": "^1.8.9",
"hammerjs": "^2.0.8",
"prop-types": "^15.6.2",
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6 changes: 3 additions & 3 deletions extensions/measurement-tracking/package.json
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Expand Up @@ -30,13 +30,13 @@
"start": "yarn run dev"
},
"peerDependencies": {
"@cornerstonejs/core": "^1.20.3",
"@cornerstonejs/tools": "^1.20.3",
"@cornerstonejs/core": "^1.27.3",
"@cornerstonejs/tools": "^1.27.3",
"@ohif/core": "3.8.0-beta.9",
"@ohif/extension-cornerstone-dicom-sr": "3.8.0-beta.9",
"@ohif/ui": "3.8.0-beta.9",
"classnames": "^2.3.2",
"dcmjs": "^0.29.11",
"dcmjs": "^0.29.12",
"lodash.debounce": "^4.17.21",
"prop-types": "^15.6.2",
"react": "^17.0.2",
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2 changes: 1 addition & 1 deletion extensions/tmtv/package.json
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Expand Up @@ -30,7 +30,7 @@
"peerDependencies": {
"@ohif/core": "3.8.0-beta.9",
"@ohif/ui": "3.8.0-beta.9",
"dcmjs": "^0.29.11",
"dcmjs": "^0.29.12",
"dicom-parser": "^1.8.9",
"hammerjs": "^2.0.8",
"prop-types": "^15.6.2",
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11 changes: 9 additions & 2 deletions modes/segmentation/src/index.tsx
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Expand Up @@ -120,9 +120,16 @@ function modeFactory({ modeConfiguration }) {
},
/**
* A boolean return value that indicates whether the mode is valid for the
* modalities of the selected studies. For instance a PET/CT mode should be
* modalities of the selected studies. Currently we don't have stack viewport
* segmentations and we should exclude them
*/
isValidMode: ({ modalities }) => true,
isValidMode: ({ modalities }) => {
if (modalities.length === 1) {
return !['SM', 'US', 'MG', 'OT', 'DOC', 'CR'].includes(modalities[0]);
}

return true;
},
/**
* Mode Routes are used to define the mode's behavior. A list of Mode Route
* that includes the mode's path and the layout to be used. The layout will
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4 changes: 2 additions & 2 deletions platform/app/package.json
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Expand Up @@ -51,7 +51,7 @@
"@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
"@cornerstonejs/codec-openjpeg": "^1.2.2",
"@cornerstonejs/codec-openjph": "^2.4.2",
"@cornerstonejs/dicom-image-loader": "^1.20.3",
"@cornerstonejs/dicom-image-loader": "^1.27.3",
"@ohif/core": "3.8.0-beta.9",
"@ohif/extension-cornerstone": "3.8.0-beta.9",
"@ohif/extension-cornerstone-dicom-rt": "3.8.0-beta.9",
Expand All @@ -72,7 +72,7 @@
"classnames": "^2.3.2",
"core-js": "^3.16.1",
"cornerstone-math": "^0.1.9",
"dcmjs": "^0.29.11",
"dcmjs": "^0.29.12",
"detect-gpu": "^4.0.16",
"dicom-parser": "^1.8.9",
"dotenv-webpack": "^1.7.0",
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2 changes: 1 addition & 1 deletion platform/app/public/config/default_16bit.js
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Expand Up @@ -15,7 +15,7 @@ window.config = {
showWarningMessageForCrossOrigin: false,
showCPUFallbackMessage: true,
showLoadingIndicator: true,
use16BitDataType: true,
useNorm16Texture: true,
useSharedArrayBuffer: 'AUTO',
maxNumRequests: {
interaction: 100,
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4 changes: 2 additions & 2 deletions platform/core/package.json
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Expand Up @@ -35,14 +35,14 @@
"@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
"@cornerstonejs/codec-openjpeg": "^1.2.2",
"@cornerstonejs/codec-openjph": "^2.4.2",
"@cornerstonejs/dicom-image-loader": "^1.20.3",
"@cornerstonejs/dicom-image-loader": "^1.27.3",
"@ohif/ui": "3.8.0-beta.9",
"cornerstone-math": "0.1.9",
"dicom-parser": "^1.8.21"
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"dcmjs": "^0.29.11",
"dcmjs": "^0.29.12",
"dicomweb-client": "^0.10.2",
"gl-matrix": "^3.4.3",
"isomorphic-base64": "^1.0.2",
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8 changes: 4 additions & 4 deletions platform/core/src/services/DisplaySetService/DisplaySetService.ts
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Expand Up @@ -36,7 +36,7 @@ export default class DisplaySetService extends PubSubService {
};

public activeDisplaySets = [];
public unsuportedSOPClassHandler;
public unsupportedSOPClassHandler;
extensionManager: ExtensionManager;

protected activeDisplaySetsMap = new Map<string, DisplaySet>();
Expand All @@ -47,7 +47,7 @@ export default class DisplaySetService extends PubSubService {

constructor() {
super(EVENTS);
this.unsuportedSOPClassHandler =
this.unsupportedSOPClassHandler =
'@ohif/extension-default.sopClassHandlerModule.not-supported-display-sets-handler';
}

Expand Down Expand Up @@ -81,7 +81,7 @@ export default class DisplaySetService extends PubSubService {
* @param sopClassHandlerUID
*/
public setUnsuportedSOPClassHandler(sopClassHandler) {
this.unsuportedSOPClassHandler = sopClassHandler;
this.unsupportedSOPClassHandler = sopClassHandler;
}

/**
Expand Down Expand Up @@ -384,7 +384,7 @@ export default class DisplaySetService extends PubSubService {
// applying the default sopClassUID handler
if (allDisplaySets.length === 0) {
// applying hp-defined viewport settings to the displaysets
const handler = this.extensionManager.getModuleEntry(this.unsuportedSOPClassHandler);
const handler = this.extensionManager.getModuleEntry(this.unsupportedSOPClassHandler);
const displaySets = handler.getDisplaySetsFromSeries(instances);
if (displaySets?.length) {
displaySets.forEach(ds => {
Expand Down
10 changes: 5 additions & 5 deletions platform/core/src/utils/isDisplaySetReconstructable.js
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Expand Up @@ -14,15 +14,15 @@ export default function isDisplaySetReconstructable(instances) {
if (!instances.length) {
return { value: false };
}

const firstInstance = instances[0];

const Modality = firstInstance.Modality;
const isMultiframe = firstInstance.NumberOfFrames > 1;

if (!constructableModalities.includes(Modality)) {
return { value: false };
}
// This seems to not be a reasonable check. We should just use the geometry
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// const Modality = firstInstance.Modality;
// if (!constructableModalities.includes(Modality)) {
// return { value: false };
// }

// Can't reconstruct if we only have one image.
if (!isMultiframe && instances.length === 1) {
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2 changes: 1 addition & 1 deletion platform/docs/docs/configuration/configurationFiles.md
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Expand Up @@ -179,7 +179,7 @@ if auth headers are used, a preflight request is required.
}
```
- `showLoadingIndicator`: (default to true), if set to false, the loading indicator will not be shown when navigating between studies.
- `use16BitDataType`: (default to false), if set to true, it will use 16 bit data type for the image data wherever possible which has
- `useNorm16Texture`: (default to false), if set to true, it will use 16 bit data type for the image data wherever possible which has
significant impact on reducing the memory usage. However, the 16Bit textures require EXT_texture_norm16 extension in webGL 2.0 (you can check if you have it here https://webglreport.com/?v=2). In addition to the extension, there are reported problems for Intel Macs that might cause the viewer to crash. In summary, it is great a configuration if you have support for it.
- `useSharedArrayBuffer` (default to 'TRUE', options: 'AUTO', 'FALSE', 'TRUE', note that these are strings), for volume loading we use sharedArrayBuffer to be able to
load the volume progressively as the data arrives (each webworker has the shared buffer and can write to it). However, there might be certain environments that do not support sharedArrayBuffer. In that case, you can set this flag to false and the viewer will use the regular arrayBuffer which might be slower for large volume loading.
Expand Down
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