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fix(segmentation): upgrade cs3d to fix various segmentation bugs (#3885)

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This commit is contained in:
Alireza authored and GitHub committed 2024-01-09 10:15:56 -05:00
1 parent a8a0bdb2df
commit b1efe40aa1
26 files changed
+241 -171
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extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx
+2
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@@ -168,6 +168,8 @@ function OHIFCornerstoneRTViewport(props) {
}, [servicesManager, viewportId, rtDisplaySet, rtIsLoading]);
useEffect(() => {
// I'm not sure what is this, since in RT we support Overlapping segmnets
// via contours
const { unsubscribe } = segmentationService.subscribe(
segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
evt => {
extensions/cornerstone-dicom-seg/package.json
+3 -3
View File
@@ -44,9 +44,9 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^1.40.3",
"@cornerstonejs/tools": "^1.40.3",
"@kitware/vtk.js": "27.3.1",
"@cornerstonejs/adapters": "^1.43.7",
"@cornerstonejs/tools": "^1.43.7",
"@kitware/vtk.js": "29.3.0",
"react-color": "^2.19.3"
}
}
extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js
+9
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@@ -189,6 +189,15 @@ async function _loadSegments({ extensionManager, servicesManager, segDisplaySet,
}
});
if (results.overlappingSegments) {
uiNotificationService.show({
title: 'Overlapping Segments',
message:
'Unsupported overlapping segments detected, segmentation rendering results may be incorrect.',
type: 'warning',
});
}
if (!usedRecommendedDisplayCIELabValue) {
// Display a notification about the non-utilization of RecommendedDisplayCIELabValue
uiNotificationService.show({
extensions/cornerstone-dicom-seg/src/panels/PanelSegmentation.tsx
+1 -1
View File
@@ -1,7 +1,7 @@
import { createReportAsync } from '@ohif/extension-default';
import React, { useEffect, useState, useCallback } from 'react';
import PropTypes from 'prop-types';
import { SegmentationGroupTable, LegacyButtonGroup, LegacyButton } from '@ohif/ui';
import { SegmentationGroupTable } from '@ohif/ui';
import callInputDialog from './callInputDialog';
import callColorPickerDialog from './colorPickerDialog';
extensions/cornerstone-dicom-seg/src/panels/SegmentationToolbox.tsx
+25 -5
View File
@@ -37,7 +37,7 @@ const initialState = {
},
ThresholdBrush: {
brushSize: 15,
thresholdRange: [-500, 500],
thresholdRange: null,
},
activeTool: null,
};
@@ -88,6 +88,8 @@ function SegmentationToolbox({ servicesManager, extensionManager }) {
const setToolActive = useCallback(
toolName => {
initializeThresholdValue(toolName);
toolbarService.recordInteraction({
interactionType: 'tool',
commands: [
@@ -178,6 +180,24 @@ function SegmentationToolbox({ servicesManager, extensionManager }) {
[toolGroupService]
);
function initializeThresholdValue(toolName: any) {
if (state.ThresholdBrush.thresholdRange === null) {
// set the default threshold range from the tool configuration
const toolGroupIds = toolGroupService.getToolGroupIds();
const toolGroupId = toolGroupIds[0];
const toolGroup = toolGroupService.getToolGroup(toolGroupId);
const toolConfig = toolGroup.getToolConfiguration(toolName);
const defaultThresholdRange = toolConfig?.strategySpecificConfiguration?.THRESHOLD?.threshold;
dispatch({
type: ACTIONS.SET_TOOL_CONFIG,
payload: {
tool: 'ThresholdBrush',
config: { thresholdRange: defaultThresholdRange },
},
});
}
}
const onBrushSizeChange = useCallback(
(valueAsStringOrNumber, toolCategory) => {
const value = Number(valueAsStringOrNumber);
@@ -200,8 +220,8 @@ function SegmentationToolbox({ servicesManager, extensionManager }) {
const handleRangeChange = useCallback(
newRange => {
if (
newRange[0] === state.ThresholdBrush.thresholdRange[0] &&
newRange[1] === state.ThresholdBrush.thresholdRange[1]
newRange[0] === state.ThresholdBrush.thresholdRange?.[0] &&
newRange[1] === state.ThresholdBrush.thresholdRange?.[1]
) {
return;
}
@@ -213,7 +233,7 @@ function SegmentationToolbox({ servicesManager, extensionManager }) {
const toolGroup = toolGroupService.getToolGroup(toolGroupId);
toolGroup.setToolConfiguration(toolName, {
strategySpecificConfiguration: {
THRESHOLD_INSIDE_CIRCLE: {
THRESHOLD: {
threshold: newRange,
},
},
@@ -365,7 +385,7 @@ function SegmentationToolbox({ servicesManager, extensionManager }) {
<InputDoubleRange
values={state.ThresholdBrush.thresholdRange}
onChange={handleRangeChange}
minValue={-1000}
minValue={-1000} // Todo: these should be configurable
maxValue={1000}
step={1}
showLabel={true}
extensions/cornerstone-dicom-seg/src/viewports/OHIFCornerstoneSEGViewport.tsx
-8
View File
@@ -172,14 +172,6 @@ function OHIFCornerstoneSEGViewport(props) {
if (evt.segDisplaySet.displaySetInstanceUID === segDisplaySet.displaySetInstanceUID) {
setSegIsLoading(false);
}
if (evt.overlappingSegments) {
uiNotificationService.show({
title: 'Overlapping Segments',
message: 'Overlapping segments detected which is not currently supported',
type: 'warning',
});
}
}
);
extensions/cornerstone-dicom-sr/package.json
+3 -3
View File
@@ -44,9 +44,9 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^1.40.3",
"@cornerstonejs/core": "^1.40.3",
"@cornerstonejs/tools": "^1.40.3",
"@cornerstonejs/adapters": "^1.43.7",
"@cornerstonejs/core": "^1.43.7",
"@cornerstonejs/tools": "^1.43.7",
"classnames": "^2.3.2"
}
}
extensions/cornerstone/package.json
+6 -6
View File
@@ -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": "^1.40.3",
"@cornerstonejs/dicom-image-loader": "^1.43.7",
"@ohif/core": "3.8.0-beta.42",
"@ohif/ui": "3.8.0-beta.42",
"dcmjs": "^0.29.12",
@@ -52,11 +52,11 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^1.40.3",
"@cornerstonejs/core": "^1.40.3",
"@cornerstonejs/streaming-image-volume-loader": "^1.40.3",
"@cornerstonejs/tools": "^1.40.3",
"@kitware/vtk.js": "27.3.1",
"@cornerstonejs/adapters": "^1.43.7",
"@cornerstonejs/core": "^1.43.7",
"@cornerstonejs/streaming-image-volume-loader": "^1.43.7",
"@cornerstonejs/tools": "^1.43.7",
"@kitware/vtk.js": "29.3.01",
"html2canvas": "^1.4.1",
"lodash.debounce": "4.0.8",
"lodash.merge": "^4.6.2",
extensions/cornerstone/src/init.tsx
+3 -3
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@@ -253,10 +253,10 @@ export default async function init({
/**
* Runs error handler for failed requests.
* @param event
* @param event
*/
const imageLoadFailedHandler = ({ detail }) => {
const handler = errorHandler.getHTTPErrorHandler()
const handler = errorHandler.getHTTPErrorHandler();
handler(detail.error);
};
@@ -290,7 +290,7 @@ export default async function init({
});
eventTarget.addEventListener(EVENTS.IMAGE_LOAD_FAILED, imageLoadFailedHandler);
eventTarget.addEventListener(EVENTS.IMAGE_LOAD_ERROR, imageLoadFailedHandler);
function elementEnabledHandler(evt) {
const { element } = evt.detail;
extensions/cornerstone/src/services/SegmentationService/SegmentationService.ts
-40
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@@ -1,5 +1,3 @@
import cloneDeep from 'lodash.clonedeep';
import { Types as OhifTypes, ServicesManager, PubSubService } from '@ohif/core';
import {
cache,
@@ -11,7 +9,6 @@ import {
volumeLoader,
} from '@cornerstonejs/core';
import {
CONSTANTS as cstConstants,
Enums as csToolsEnums,
segmentation as cstSegmentation,
Types as cstTypes,
@@ -23,7 +20,6 @@ import { easeInOutBell, reverseEaseInOutBell } from '../../utils/transitions';
import { Segment, Segmentation, SegmentationConfig } from './SegmentationServiceTypes';
import { mapROIContoursToRTStructData } from './RTSTRUCT/mapROIContoursToRTStructData';
const { COLOR_LUT } = cstConstants;
const LABELMAP = csToolsEnums.SegmentationRepresentations.Labelmap;
const CONTOUR = csToolsEnums.SegmentationRepresentations.Contour;
@@ -465,15 +461,6 @@ class SegmentationService extends PubSubService {
},
]);
// if first segmentation, we can use the default colorLUT, otherwise
// we need to generate a new one and use a new colorLUT
const colorLUTIndex = 0;
if (Object.keys(this.segmentations).length !== 0) {
const newColorLUT = this.generateNewColorLUT();
const colorLUTIndex = this.getNextColorLUTIndex();
cstSegmentation.config.color.addColorLUT(newColorLUT, colorLUTIndex);
}
this.segmentations[segmentationId] = {
...segmentation,
label: segmentation.label || '',
@@ -482,7 +469,6 @@ class SegmentationService extends PubSubService {
segmentCount: segmentation.segmentCount ?? 0,
isActive: false,
isVisible: true,
colorLUTIndex,
};
cachedSegmentation = this.segmentations[segmentationId];
@@ -1037,8 +1023,6 @@ class SegmentationService extends PubSubService {
segmentation.hydrated = true;
}
const { colorLUTIndex } = segmentation;
// Based on the segmentationId, set the colorLUTIndex.
const segmentationRepresentationUIDs = await cstSegmentation.addSegmentationRepresentations(
toolGroupId,
@@ -1057,12 +1041,6 @@ class SegmentationService extends PubSubService {
segmentationRepresentationUIDs[0]
);
cstSegmentation.config.color.setColorLUT(
toolGroupId,
segmentationRepresentationUIDs[0],
colorLUTIndex
);
// add the segmentation segments properly
for (const segment of segmentation.segments) {
if (segment === null || segment === undefined) {
@@ -1530,7 +1508,6 @@ class SegmentationService extends PubSubService {
segments: [],
isVisible: true,
isActive: false,
colorLUTIndex: 0,
};
}
@@ -2124,23 +2101,6 @@ class SegmentationService extends PubSubService {
return viewportInfo.getToolGroupId();
};
private getNextColorLUTIndex = (): number => {
let i = 0;
while (true) {
if (cstSegmentation.state.getColorLUT(i) === undefined) {
return i;
}
i++;
}
};
private generateNewColorLUT() {
const newColorLUT = cloneDeep(COLOR_LUT);
return newColorLUT;
}
/**
* Converts object of objects to array.
*
extensions/cornerstone/src/services/ViewportService/Viewport.ts
+4 -4
View File
@@ -1,5 +1,5 @@
import { Types, Enums } from '@cornerstonejs/core';
import { Types as UITypes } from '@ohif/ui';
import { Types as CoreTypes } from '@ohif/core';
import { StackViewportData, VolumeViewportData } from '../../types/CornerstoneCacheService';
import getCornerstoneBlendMode from '../../utils/getCornerstoneBlendMode';
import getCornerstoneOrientation from '../../utils/getCornerstoneOrientation';
@@ -18,7 +18,7 @@ export type ViewportOptions = {
toolGroupId: string;
viewportId: string;
// Presentation ID to store/load presentation state from
presentationIds?: UITypes.PresentationIds;
presentationIds?: CoreTypes.PresentationIds;
orientation?: Enums.OrientationAxis;
background?: Types.Point3;
displayArea?: Types.DisplayArea;
@@ -36,7 +36,7 @@ export type PublicViewportOptions = {
id?: string;
viewportType?: string;
toolGroupId?: string;
presentationIds?: UITypes.PresentationIds;
presentationIds?: CoreTypes.PresentationIds;
viewportId?: string;
orientation?: Enums.OrientationAxis;
background?: Types.Point3;
@@ -71,7 +71,7 @@ export type DisplaySetOptions = {
voiInverted: boolean;
blendMode?: Enums.BlendModes;
slabThickness?: number;
colormap?: { name: string, opacity?: number };
colormap?: { name: string; opacity?: number };
displayPreset?: string;
};
extensions/cornerstone/src/types/Presentation.ts
+2 -2
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@@ -1,12 +1,12 @@
/** Store presentation data for either stack viewports or volume viewports */
import { Types } from '@cornerstonejs/core';
import { Types as UITypes } from '@ohif/ui';
import { Types as CoreTypes } from '@ohif/core';
/**
* Has information on the presentation of the viewport.
*/
export interface Presentation extends Types.StackViewportProperties {
presentationIds: UITypes.PresentationIds;
presentationIds: CoreTypes.PresentationIds;
viewportType: string;
initialImageIndex: number;
camera: Types.ICamera;
extensions/measurement-tracking/package.json
+2 -2
View File
@@ -30,8 +30,8 @@
"start": "yarn run dev"
},
"peerDependencies": {
"@cornerstonejs/core": "^1.40.3",
"@cornerstonejs/tools": "^1.40.3",
"@cornerstonejs/core": "^1.43.7",
"@cornerstonejs/tools": "^1.43.7",
"@ohif/core": "3.8.0-beta.42",
"@ohif/extension-cornerstone-dicom-sr": "3.8.0-beta.42",
"@ohif/ui": "3.8.0-beta.42",