feat: Add DICOM SEG support and MPR, referenceLines and StackSync and more (#3015)

* feat: add initial sop class handler for SEG

* feat: move segmentation service

* update segmentation service methods

* fix: viewport data structure

* feat: Add initial render for the DICOM SEG for each displaySet

* fix: various wrong architectural dependencies between services

* feat: initial separate SEG display in each viewport

* feat: refactore viewport action bar

* initial work for SEG hydration

* fix: various bugs regarding drag and dropping different viewports

* fix: rendering issues for multiple seg displaysets

* fix: bugs for thumbnail and hydration

* feat: fix the initial segment color

* update after rebase

* feat: initial design for the segmentation group table

* feat: initial new design for the segmentation panel

* feat: segmentation panel

* feat: make segmentation appear on all related viewports

* fix: segmentation load bug based on functional groups

* initial work for segmentation crosshairs

* fix: various stylings and functionality

* fix: various stylings for the seg panel

* fix: overflow styles

* feat: add more ui components

* feat: added segmentation config

* feat: add jump to segment

* feat: add jump to segment for DICOM SEG viewport

* fix: bugs after rebase

* feat: jump in segmentation viewport

* fix: mpr support for seg

* feat: add more icons

* feat: new icons

* feat: add new side panel

* feat: add segmentation config

* feat: add loading indicator to ohif

* feat: make hanging protocols follow matching rules for viewports

* feat: enhance drag and drop to be hanging protocol aware

* fix: mpr restore previous layout

* fix: crosshairs toggle

* fix: add auth headers to the dicom loader via dicomwebclient

* fix: bug for crosshairs toggle in mpr

* fix: seg viewport reusing old toolGroup

* feat: add loading animation with lottie

* fix: various bugs for Segmentation hydration in mpr

* feat: change outline alpha to outline opacity

* feat: loading indicator for seg viewport

* fix: various segmentation group styles

* fix: local mode for seg

* feat: add animation for the highlight

* fix: loading indicatro to show segment indices

* feat: enhance modality drop down ui

* fix: panels

* fix: download form

* fix: layout shift in loading indicator

* fix: loading indicator to have correct values

* fix: update software number

* fix: image jump between MPR and default

* fix: segmentation cleanup and cine service cleanup

* fix: segmentation toolgroup clena up

* fix: highlight interval should not trigger again

* fix: issue with multiframe sorting

* rename: change onSeriesChange to onArrowsClick

* fix: buttons for tmtv and layout shift

* fix: various bugs wrt crosshairs

* fix: crosshairs re init on reset camera

* fix: middle slice calculation different from cs middle reset camera

* fix: reset camera should reset viewport camera

* fix: loading segments in MPR mode

* fix: tmtv hp back to before

* fix: layout shift

* feat: orientation markers for volume viewport

* fix: capture for volume viewports

* fix: memory leak for back to worklist

* fix: loading bar bg color

* fix: side panel for only one panel

* fix: react select style in production

* fix: various styling for segmentation groups

* fix: various ui styles

* feat: add new segmentation config styles

* fix: hover state for segmentation item

* fix: side panel layout shift

* temp add panels

* try to fix scrollbar for thimbnail

* fix: scroll not appearing for side panels

* feat: changed styles for scrollbar

* feat: add cpu fallback warning

* fix: webworker destroy

* fix: select styles

* fix: orientation marker color and position

* fix: capture screenshot for volume viewports

* fix: hide segment visibility on mpr

* fix: reloading an already loaded seg displayset

* feat: add is equal

* fix: mpr jump to measurements

* apply review comments

* fix: optimization for the segmentation load

* fix: remove unnecessary context menu and hp service reset

* fix: segmentation service wrt brush settings

* feat: initial work for the stack synchronization

* fix: add validateDisplaySetSelectorsForNewDisplaySets to make sure drag and drop can follow requirements

* fix: various react proptypes

* fix: thumbnails for the tmtv and change default props to default params

* feat: make showing loading indicator configurable and add docs

* bump versions and add more docs

* fix demo

* update cornerstone versions

* apply review comments

* feat: add reference lines

* fix build

* fix unit tests

* add reference lines icon

* fix: e2e tests

* fix static wado config

* docs: add segmentation service docs

* fix: docker build

* fix: keep camera and bump versions

* Try re-enabling minification to fix deploy previews

Co-authored-by: Erik Ziegler <erik.sweed@gmail.com>
This commit is contained in:
AlirezaandErik Ziegler authored and GitHub committed 2022-11-16 14:19:52 -05:00
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import vtkMath from '@kitware/vtk.js/Common/Core/Math';
import { utils } from '@ohif/core';
import { SOPClassHandlerId } from './id';
import dcmjs from 'dcmjs';
const { DicomMessage, DicomMetaDictionary } = dcmjs.data;
const sopClassUids = ['1.2.840.10008.5.1.4.1.1.66.4'];
let loadPromises = {};
function _getDisplaySetsFromSeries(
instances,
servicesManager,
extensionManager
) {
const instance = instances[0];
const {
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
SeriesDescription,
SeriesNumber,
SeriesDate,
SOPClassUID,
wadoRoot,
wadoUri,
wadoUriRoot,
} = instance;
const displaySet = {
Modality: 'SEG',
loading: false,
isReconstructable: true, // by default for now since it is a volumetric SEG currently
displaySetInstanceUID: utils.guid(),
SeriesDescription,
SeriesNumber,
SeriesDate,
SOPInstanceUID,
SeriesInstanceUID,
StudyInstanceUID,
SOPClassHandlerId,
SOPClassUID,
referencedImages: null,
referencedSeriesInstanceUID: null,
referencedDisplaySetInstanceUID: null,
isDerivedDisplaySet: true,
isLoaded: false,
isHydrated: false,
segments: {},
sopClassUids,
instance,
wadoRoot,
wadoUriRoot,
wadoUri,
};
const referencedSeriesSequence = instance.ReferencedSeriesSequence;
if (!referencedSeriesSequence) {
throw new Error('ReferencedSeriesSequence is missing for the SEG');
}
const referencedSeries = referencedSeriesSequence[0];
displaySet.referencedImages =
instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
displaySet.getReferenceDisplaySet = () => {
const { DisplaySetService } = servicesManager.services;
const referencedDisplaySets = DisplaySetService.getDisplaySetsForSeries(
displaySet.referencedSeriesInstanceUID
);
if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
throw new Error('Referenced DisplaySet is missing for the SEG');
}
const referencedDisplaySet = referencedDisplaySets[0];
displaySet.referencedDisplaySetInstanceUID =
referencedDisplaySet.displaySetInstanceUID;
// Todo: this needs to be able to work with other reference volumes (other than streaming) such as nifti, etc.
displaySet.referencedVolumeURI = referencedDisplaySet.displaySetInstanceUID;
const referencedVolumeId = `cornerstoneStreamingImageVolume:${displaySet.referencedVolumeURI}`;
displaySet.referencedVolumeId = referencedVolumeId;
return referencedDisplaySet;
};
displaySet.load = async ({ headers }) =>
await _load(displaySet, servicesManager, extensionManager, headers);
return [displaySet];
}
function _load(segDisplaySet, servicesManager, extensionManager, headers) {
const { SOPInstanceUID } = segDisplaySet;
if (
(segDisplaySet.loading || segDisplaySet.isLoaded) &&
loadPromises[SOPInstanceUID]
) {
return loadPromises[SOPInstanceUID];
}
segDisplaySet.loading = true;
// We don't want to fire multiple loads, so we'll wait for the first to finish
// and also return the same promise to any other callers.
loadPromises[SOPInstanceUID] = new Promise(async (resolve, reject) => {
const { SegmentationService } = servicesManager.services;
if (_segmentationExistsInCache(segDisplaySet, SegmentationService)) {
return;
}
if (
!segDisplaySet.segments ||
Object.keys(segDisplaySet.segments).length === 0
) {
const segments = await _loadSegments(
extensionManager,
segDisplaySet,
headers
);
segDisplaySet.segments = segments;
}
const suppressEvents = true;
SegmentationService.createSegmentationForSEGDisplaySet(
segDisplaySet,
null,
suppressEvents
)
.then(() => {
segDisplaySet.loading = false;
resolve();
})
.catch(error => {
segDisplaySet.loading = false;
reject(error);
});
});
return loadPromises[SOPInstanceUID];
}
async function _loadSegments(extensionManager, segDisplaySet, headers) {
const utilityModule = extensionManager.getModuleEntry(
'@ohif/extension-cornerstone.utilityModule.common'
);
const { dicomLoaderService } = utilityModule.exports;
const segArrayBuffer = await dicomLoaderService.findDicomDataPromise(
segDisplaySet,
null,
headers
);
const dicomData = DicomMessage.readFile(segArrayBuffer);
const dataset = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
dataset._meta = DicomMetaDictionary.namifyDataset(dicomData.meta);
if (!Array.isArray(dataset.SegmentSequence)) {
dataset.SegmentSequence = [dataset.SegmentSequence];
}
const segments = _getSegments(dataset);
return segments;
}
function _segmentationExistsInCache(segDisplaySet, SegmentationService) {
// This should be abstracted with the CornerstoneCacheService
const labelmapVolumeId = segDisplaySet.displaySetInstanceUID;
const segVolume = SegmentationService.getLabelmapVolume(labelmapVolumeId);
return segVolume !== undefined;
}
function _getPixelData(dataset, segments) {
let frameSize = Math.ceil((dataset.Rows * dataset.Columns) / 8);
let nextOffset = 0;
Object.keys(segments).forEach(segmentKey => {
const segment = segments[segmentKey];
segment.numberOfFrames = segment.functionalGroups.length;
segment.size = segment.numberOfFrames * frameSize;
segment.offset = nextOffset;
nextOffset = segment.offset + segment.size;
const packedSegment = dataset.PixelData[0].slice(
segment.offset,
nextOffset
);
segment.pixelData = dcmjs.data.BitArray.unpack(packedSegment);
segment.geometry = geometryFromFunctionalGroups(
dataset,
segment.functionalGroups
);
});
return segments;
}
function geometryFromFunctionalGroups(dataset, perFrame) {
let pixelMeasures =
dataset.SharedFunctionalGroupsSequence.PixelMeasuresSequence;
let planeOrientation =
dataset.SharedFunctionalGroupsSequence.PlaneOrientationSequence;
let planePosition = perFrame[0].PlanePositionSequence; // TODO: assume sorted frames!
const geometry = {};
// NB: DICOM PixelSpacing is defined as Row then Column,
// unlike ImageOrientationPatient
let spacingBetweenSlices = pixelMeasures.SpacingBetweenSlices;
if (!spacingBetweenSlices) {
if (pixelMeasures.SliceThickness) {
console.log('Using SliceThickness as SpacingBetweenSlices');
spacingBetweenSlices = pixelMeasures.SliceThickness;
}
}
geometry.spacing = [
pixelMeasures.PixelSpacing[1],
pixelMeasures.PixelSpacing[0],
spacingBetweenSlices,
].map(Number);
geometry.dimensions = [dataset.Columns, dataset.Rows, perFrame.length].map(
Number
);
let orientation = planeOrientation.ImageOrientationPatient.map(Number);
const columnStepToPatient = orientation.slice(0, 3);
const rowStepToPatient = orientation.slice(3, 6);
geometry.planeNormal = [];
vtkMath.cross(columnStepToPatient, rowStepToPatient, geometry.planeNormal);
let firstPosition = perFrame[0].PlanePositionSequence.ImagePositionPatient.map(
Number
);
let lastPosition = perFrame[
perFrame.length - 1
].PlanePositionSequence.ImagePositionPatient.map(Number);
geometry.sliceStep = [];
vtkMath.subtract(lastPosition, firstPosition, geometry.sliceStep);
vtkMath.normalize(geometry.sliceStep);
geometry.direction = columnStepToPatient
.concat(rowStepToPatient)
.concat(geometry.sliceStep);
geometry.origin = planePosition.ImagePositionPatient.map(Number);
return geometry;
}
function _getSegments(dataset) {
const segments = {};
dataset.SegmentSequence.forEach(segment => {
const cielab = segment.RecommendedDisplayCIELabValue;
const rgba = dcmjs.data.Colors.dicomlab2RGB(cielab).map(x =>
Math.round(x * 255)
);
rgba.push(255);
const segmentNumber = segment.SegmentNumber;
segments[segmentNumber] = {
color: rgba,
functionalGroups: [],
offset: null,
size: null,
pixelData: null,
label: segment.SegmentLabel,
};
});
// make a list of functional groups per segment
dataset.PerFrameFunctionalGroupsSequence.forEach(functionalGroup => {
const segmentNumber =
functionalGroup.SegmentIdentificationSequence.ReferencedSegmentNumber;
segments[segmentNumber].functionalGroups.push(functionalGroup);
});
return _getPixelData(dataset, segments);
}
function getSopClassHandlerModule({ servicesManager, extensionManager }) {
const getDisplaySetsFromSeries = instances => {
return _getDisplaySetsFromSeries(
instances,
servicesManager,
extensionManager
);
};
return [
{
name: 'dicom-seg',
sopClassUids,
getDisplaySetsFromSeries,
},
];
}
export default getSopClassHandlerModule;
@@ -0,0 +1,7 @@
import packageJson from '../package.json';
const id = packageJson.name;
const SOPClassHandlerName = 'dicom-seg';
const SOPClassHandlerId = `${id}.sopClassHandlerModule.${SOPClassHandlerName}`;
export { id, SOPClassHandlerId, SOPClassHandlerName };
@@ -0,0 +1,93 @@
import { id } from './id';
import React from 'react';
import getSopClassHandlerModule from './getSopClassHandlerModule';
import PanelSegmentation from './panels/PanelSegmentation';
const Component = React.lazy(() => {
return import(
/* webpackPrefetch: true */ './viewports/OHIFCornerstoneSEGViewport'
);
});
const OHIFCornerstoneSEGViewport = props => {
return (
<React.Suspense fallback={<div>Loading...</div>}>
<Component {...props} />
</React.Suspense>
);
};
/**
* You can remove any of the following modules if you don't need them.
*/
const extension = {
/**
* Only required property. Should be a unique value across all extensions.
* You ID can be anything you want, but it should be unique.
*/
id,
/**
* Perform any pre-registration tasks here. This is called before the extension
* is registered. Usually we run tasks such as: configuring the libraries
* (e.g. cornerstone, cornerstoneTools, ...) or registering any services that
* this extension is providing.
*/
preRegistration: ({
servicesManager,
commandsManager,
configuration = {},
}) => {},
/**
* PanelModule should provide a list of panels that will be available in OHIF
* for Modes to consume and render. Each panel is defined by a {name,
* iconName, iconLabel, label, component} object. Example of a panel module
* is the StudyBrowserPanel that is provided by the default extension in OHIF.
*/
getPanelModule: ({ servicesManager, commandsManager, extensionManager }) => {
const wrappedPanelSegmentation = () => {
return (
<PanelSegmentation
commandsManager={commandsManager}
servicesManager={servicesManager}
extensionManager={extensionManager}
/>
);
};
return [
{
name: 'panelSegmentation',
iconName: 'tab-segmentation',
iconLabel: 'Segmentation',
label: 'Segmentation',
component: wrappedPanelSegmentation,
},
];
},
getViewportModule({ servicesManager, extensionManager }) {
const ExtendedOHIFCornerstoneSEGViewport = props => {
return (
<OHIFCornerstoneSEGViewport
servicesManager={servicesManager}
extensionManager={extensionManager}
{...props}
/>
);
};
return [
{ name: 'dicom-seg', component: ExtendedOHIFCornerstoneSEGViewport },
];
},
/**
* SopClassHandlerModule should provide a list of sop class handlers that will be
* available in OHIF for Modes to consume and use to create displaySets from Series.
* Each sop class handler is defined by a { name, sopClassUids, getDisplaySetsFromSeries}.
* Examples include the default sop class handler provided by the default extension
*/
getSopClassHandlerModule,
};
export default extension;
@@ -0,0 +1,292 @@
import React, { useEffect, useState, useCallback } from 'react';
import PropTypes from 'prop-types';
import { SegmentationGroupTable } from '@ohif/ui';
import callInputDialog from './callInputDialog';
import { useTranslation } from 'react-i18next';
import callColorPickerDialog from './callColorPickerDialog';
export default function PanelSegmentation({
servicesManager,
commandsManager,
}) {
const {
SegmentationService,
UIDialogService,
ViewportGridService,
ToolGroupService,
CornerstoneViewportService,
} = servicesManager.services;
const { t } = useTranslation('PanelSegmentation');
const [selectedSegmentationId, setSelectedSegmentationId] = useState(null);
const [
initialSegmentationConfigurations,
setInitialSegmentationConfigurations,
] = useState(SegmentationService.getConfiguration());
const [segmentations, setSegmentations] = useState(() =>
SegmentationService.getSegmentations()
);
const [isMinimized, setIsMinimized] = useState({});
const onToggleMinimizeSegmentation = useCallback(
id => {
setIsMinimized(prevState => ({
...prevState,
[id]: !prevState[id],
}));
},
[setIsMinimized]
);
// Only expand the last segmentation added to the list and collapse the rest
useEffect(() => {
const lastSegmentationId = segmentations[segmentations.length - 1]?.id;
if (lastSegmentationId) {
setIsMinimized(prevState => ({
...prevState,
[lastSegmentationId]: false,
}));
}
}, [segmentations, setIsMinimized]);
useEffect(() => {
// ~~ Subscription
const added = SegmentationService.EVENTS.SEGMENTATION_ADDED;
const updated = SegmentationService.EVENTS.SEGMENTATION_UPDATED;
const removed = SegmentationService.EVENTS.SEGMENTATION_REMOVED;
const subscriptions = [];
[added, updated, removed].forEach(evt => {
const { unsubscribe } = SegmentationService.subscribe(evt, () => {
const segmentations = SegmentationService.getSegmentations();
setSegmentations(segmentations);
});
subscriptions.push(unsubscribe);
});
return () => {
subscriptions.forEach(unsub => {
unsub();
});
};
}, []);
const onSegmentationClick = (segmentationId: string) => {
SegmentationService.setActiveSegmentationForToolGroup(segmentationId);
};
const onSegmentationDelete = (segmentationId: string) => {
SegmentationService.remove(segmentationId);
};
const getToolGroupIds = segmentationId => {
const toolGroupIds = SegmentationService.getToolGroupIdsWithSegmentation(
segmentationId
);
return toolGroupIds;
};
const onSegmentClick = (segmentationId, segmentIndex) => {
SegmentationService.setActiveSegmentForSegmentation(
segmentationId,
segmentIndex
);
const toolGroupIds = getToolGroupIds(segmentationId);
toolGroupIds.forEach(toolGroupId => {
// const toolGroupId =
SegmentationService.setActiveSegmentationForToolGroup(
segmentationId,
toolGroupId
);
SegmentationService.jumpToSegmentCenter(
segmentationId,
segmentIndex,
toolGroupId
);
});
};
const onSegmentEdit = (segmentationId, segmentIndex) => {
const segmentation = SegmentationService.getSegmentation(segmentationId);
const segment = segmentation.segments[segmentIndex];
const { label } = segment;
callInputDialog(UIDialogService, label, (label, actionId) => {
if (label === '') {
return;
}
SegmentationService.setSegmentLabelForSegmentation(
segmentationId,
segmentIndex,
label
);
});
};
const onSegmentationEdit = segmentationId => {
const segmentation = SegmentationService.getSegmentation(segmentationId);
const { label } = segmentation;
callInputDialog(UIDialogService, label, (label, actionId) => {
if (label === '') {
return;
}
SegmentationService.addOrUpdateSegmentation(
{
id: segmentationId,
label,
},
false, // suppress event
true // notYetUpdatedAtSource
);
});
};
const onSegmentColorClick = (segmentationId, segmentIndex) => {
// Todo: Implement color picker later
return;
};
const onSegmentDelete = (segmentationId, segmentIndex) => {
// SegmentationService.removeSegmentFromSegmentation(
// segmentationId,
// segmentIndex
// );
console.warn('not implemented yet');
};
const onToggleSegmentVisibility = (segmentationId, segmentIndex) => {
const segmentation = SegmentationService.getSegmentation(segmentationId);
const segmentInfo = segmentation.segments[segmentIndex];
const isVisible = !segmentInfo.isVisible;
const toolGroupIds = getToolGroupIds(segmentationId);
// Todo: right now we apply the visibility to all tool groups
toolGroupIds.forEach(toolGroupId => {
SegmentationService.setSegmentVisibility(
segmentationId,
segmentIndex,
isVisible,
toolGroupId
);
});
};
const onToggleSegmentationVisibility = segmentationId => {
SegmentationService.toggleSegmentationVisibility(segmentationId);
};
const setSegmentationConfiguration = useCallback(
(segmentationId, key, value) => {
SegmentationService.setConfiguration({
segmentationId,
[key]: value,
});
},
[SegmentationService]
);
return (
<div className="flex flex-col justify-between mt-1">
{/* show segmentation table */}
{segmentations?.length ? (
<SegmentationGroupTable
title={t('Segmentations')}
showAddSegmentation={false}
segmentations={segmentations}
isMinimized={isMinimized}
activeSegmentationId={selectedSegmentationId}
onSegmentationClick={onSegmentationClick}
onSegmentationDelete={onSegmentationDelete}
onSegmentationEdit={onSegmentationEdit}
onSegmentClick={onSegmentClick}
onSegmentEdit={onSegmentEdit}
onSegmentColorClick={onSegmentColorClick}
onSegmentDelete={onSegmentDelete}
onToggleSegmentVisibility={onToggleSegmentVisibility}
onToggleSegmentationVisibility={onToggleSegmentationVisibility}
onToggleMinimizeSegmentation={onToggleMinimizeSegmentation}
segmentationConfig={{
initialConfig: initialSegmentationConfigurations,
usePercentage: true,
}}
setRenderOutline={value =>
setSegmentationConfiguration(
selectedSegmentationId,
'renderOutline',
value
)
}
setOutlineOpacityActive={value =>
setSegmentationConfiguration(
selectedSegmentationId,
'outlineOpacity',
value
)
}
setRenderFill={value =>
setSegmentationConfiguration(
selectedSegmentationId,
'renderFill',
value
)
}
setRenderInactiveSegmentations={value =>
setSegmentationConfiguration(
selectedSegmentationId,
'renderInactiveSegmentations',
value
)
}
setOutlineWidthActive={value =>
setSegmentationConfiguration(
selectedSegmentationId,
'outlineWidthActive',
value
)
}
setFillAlpha={value =>
setSegmentationConfiguration(
selectedSegmentationId,
'fillAlpha',
value
)
}
setFillAlphaInactive={value =>
setSegmentationConfiguration(
selectedSegmentationId,
'fillAlphaInactive',
value
)
}
/>
) : null}
</div>
);
}
PanelSegmentation.propTypes = {
commandsManager: PropTypes.shape({
runCommand: PropTypes.func.isRequired,
}),
servicesManager: PropTypes.shape({
services: PropTypes.shape({
SegmentationService: PropTypes.shape({
getSegmentation: PropTypes.func.isRequired,
getSegmentations: PropTypes.func.isRequired,
toggleSegmentationVisibility: PropTypes.func.isRequired,
subscribe: PropTypes.func.isRequired,
EVENTS: PropTypes.object.isRequired,
}).isRequired,
}).isRequired,
}).isRequired,
};
@@ -0,0 +1,63 @@
import React from 'react';
import { Input, Dialog } from '@ohif/ui';
function callInputDialog(UIDialogService, label, callback) {
const dialogId = 'enter-segment-label';
const onSubmitHandler = ({ action, value }) => {
switch (action.id) {
case 'save':
callback(value.label, action.id);
break;
case 'cancel':
callback('', action.id);
break;
}
UIDialogService.dismiss({ id: dialogId });
};
if (UIDialogService) {
UIDialogService.create({
id: dialogId,
centralize: true,
isDraggable: false,
showOverlay: true,
content: Dialog,
contentProps: {
title: 'Enter Segment Label',
value: { label },
noCloseButton: true,
onClose: () => UIDialogService.dismiss({ id: dialogId }),
actions: [
{ id: 'cancel', text: 'Cancel', type: 'primary' },
{ id: 'save', text: 'Confirm', type: 'secondary' },
],
onSubmit: onSubmitHandler,
body: ({ value, setValue }) => {
return (
<div className="p-4 bg-primary-dark">
<Input
autoFocus
className="mt-2 bg-black border-primary-main"
type="text"
containerClassName="mr-2"
value={value.label}
onChange={event => {
event.persist();
setValue(value => ({ ...value, label: event.target.value }));
}}
onKeyPress={event => {
if (event.key === 'Enter') {
onSubmitHandler({ value, action: { id: 'save' } });
}
}}
/>
</div>
);
},
},
});
}
}
export default callInputDialog;
@@ -0,0 +1,35 @@
import React, { useReducer } from 'react';
// Todo: use defaults in cs3d
const initialState = {
renderOutline: true,
renderFill: true,
outlineOpacity: 0.9,
outlineWidth: 3,
fillOpacity: 0.9,
fillOpacityInactive: 0.8,
renderInactiveSegmentations: true,
};
const reducer = (state, action) => {
switch (action.type) {
case 'RENDER_OUTLINE':
return { ...state, renderOutline: action.payload.value };
case 'RENDER_FILL':
return { ...state, renderFill: action.payload.value };
case 'SET_OUTLINE_OPACITY':
return { ...state, outlineOpacity: action.payload.value };
case 'SET_OUTLINE_WIDTH':
return { ...state, outlineWidth: action.payload.value };
case 'SET_FILL_OPACITY':
return { ...state, fillOpacity: action.payload.value };
case 'SET_FILL_OPACITY_INACTIVE':
return { ...state, fillOpacityInactive: action.payload.value };
case 'RENDER_INACTIVE_SEGMENTATIONS':
return { ...state, renderInactiveSegmentations: action.payload.value };
default:
return state;
}
};
export { initialState, reducer };
@@ -0,0 +1,71 @@
async function _hydrateSEGDisplaySet({
segDisplaySet,
viewportIndex,
toolGroupId,
servicesManager,
}) {
const {
SegmentationService,
HangingProtocolService,
ViewportGridService,
} = servicesManager.services;
const displaySetInstanceUID = segDisplaySet.referencedDisplaySetInstanceUID;
let segmentationId = null;
// We need the hydration to notify panels about the new segmentation added
const suppressEvents = false;
segmentationId = await SegmentationService.createSegmentationForSEGDisplaySet(
segDisplaySet,
segmentationId,
suppressEvents
);
SegmentationService.hydrateSegmentation(segDisplaySet.displaySetInstanceUID);
const { viewports } = ViewportGridService.getState();
const updatedViewports = HangingProtocolService.getViewportsRequireUpdate(
viewportIndex,
displaySetInstanceUID
);
ViewportGridService.setDisplaySetsForViewports(updatedViewports);
// Todo: fix this after we have a better way for stack viewport segmentations
// check every viewport in the viewports to see if the displaySetInstanceUID
// is being displayed, if so we need to update the viewport to use volume viewport
// (if already is not using it) since Cornerstone3D currently only supports
// volume viewport for segmentation
viewports.forEach((viewport, index) => {
if (index === viewportIndex) {
return;
}
const shouldDisplaySeg = SegmentationService.shouldRenderSegmentation(
viewport.displaySetInstanceUIDs,
segDisplaySet.displaySetInstanceUID
);
if (shouldDisplaySeg) {
ViewportGridService.setDisplaySetsForViewport({
viewportIndex: index,
displaySetInstanceUIDs: viewport.displaySetInstanceUIDs,
viewportOptions: {
viewportType: 'volume',
toolGroupId,
initialImageOptions: {
preset: 'middle',
},
},
});
}
});
return true;
}
export default _hydrateSEGDisplaySet;
@@ -0,0 +1,34 @@
function createSEGToolGroupAndAddTools(
ToolGroupService,
toolGroupId,
extensionManager
) {
const utilityModule = extensionManager.getModuleEntry(
'@ohif/extension-cornerstone.utilityModule.tools'
);
const { toolNames, Enums } = utilityModule.exports;
const tools = {
active: [
{
toolName: toolNames.WindowLevel,
bindings: [{ mouseButton: Enums.MouseBindings.Primary }],
},
{
toolName: toolNames.Pan,
bindings: [{ mouseButton: Enums.MouseBindings.Auxiliary }],
},
{
toolName: toolNames.Zoom,
bindings: [{ mouseButton: Enums.MouseBindings.Secondary }],
},
{ toolName: toolNames.StackScrollMouseWheel, bindings: [] },
],
enabled: [{ toolName: toolNames.SegmentationDisplay }],
};
return ToolGroupService.createToolGroupAndAddTools(toolGroupId, tools, {});
}
export default createSEGToolGroupAndAddTools;
@@ -0,0 +1,70 @@
import hydrateSEGDisplaySet from './_hydrateSEG';
const RESPONSE = {
NO_NEVER: -1,
CANCEL: 0,
HYDRATE_SEG: 5,
};
function promptHydrateSEG({
servicesManager,
segDisplaySet,
viewportIndex,
toolGroupId = 'default',
}) {
const { UIViewportDialogService } = servicesManager.services;
return new Promise(async function(resolve, reject) {
const promptResult = await _askHydrate(
UIViewportDialogService,
viewportIndex
);
if (promptResult === RESPONSE.HYDRATE_SEG) {
const isHydrated = await hydrateSEGDisplaySet({
segDisplaySet,
viewportIndex,
toolGroupId,
servicesManager,
});
resolve(isHydrated);
}
});
}
function _askHydrate(UIViewportDialogService, viewportIndex) {
return new Promise(function(resolve, reject) {
const message = 'Do you want to open this Segmentation?';
const actions = [
{
type: 'secondary',
text: 'No',
value: RESPONSE.CANCEL,
},
{
type: 'primary',
text: 'Yes',
value: RESPONSE.HYDRATE_SEG,
},
];
const onSubmit = result => {
UIViewportDialogService.hide();
resolve(result);
};
UIViewportDialogService.show({
viewportIndex,
type: 'info',
message,
actions,
onSubmit,
onOutsideClick: () => {
UIViewportDialogService.hide();
resolve(RESPONSE.CANCEL);
},
});
});
}
export default promptHydrateSEG;
@@ -0,0 +1,424 @@
import React, { useCallback, useEffect, useRef, useState } from 'react';
import PropTypes from 'prop-types';
import OHIF, { utils } from '@ohif/core';
import {
Notification,
ViewportActionBar,
useViewportGrid,
useViewportDialog,
LoadingIndicatorProgress,
} from '@ohif/ui';
import { useTranslation } from 'react-i18next';
import createSEGToolGroupAndAddTools from '../utils/initSEGToolGroup';
import _hydrateSEGDisplaySet from '../utils/_hydrateSEG';
import promptHydrateSEG from '../utils/promptHydrateSEG';
import _getStatusComponent from './_getStatusComponent';
const { formatDate } = utils;
const SEG_TOOLGROUP_BASE_NAME = 'SEGToolGroup';
function OHIFCornerstoneSEGViewport(props) {
const {
children,
displaySets,
viewportOptions,
viewportIndex,
viewportLabel,
servicesManager,
extensionManager,
} = props;
const { t } = useTranslation('SEGViewport');
const {
DisplaySetService,
ToolGroupService,
SegmentationService,
} = servicesManager.services;
const toolGroupId = `${SEG_TOOLGROUP_BASE_NAME}-${viewportIndex}`;
// SEG viewport will always have a single display set
if (displaySets.length > 1) {
throw new Error('SEG viewport should only have a single display set');
}
const segDisplaySet = displaySets[0];
const [viewportGrid, viewportGridService] = useViewportGrid();
const [viewportDialogState, viewportDialogApi] = useViewportDialog();
// States
const [isToolGroupCreated, setToolGroupCreated] = useState(false);
const [selectedSegment, setSelectedSegment] = useState(1);
// Hydration means that the SEG is opened and segments are loaded into the
// segmentation panel, and SEG is also rendered on any viewport that is in the
// same frameOfReferenceUID as the referencedSeriesUID of the SEG. However,
// loading basically means SEG loading over network and bit unpacking of the
// SEG data.
const [isHydrated, setIsHydrated] = useState(segDisplaySet.isHydrated);
const [segIsLoading, setSegIsLoading] = useState(!segDisplaySet.isLoaded);
const [element, setElement] = useState(null);
const [processingProgress, setProcessingProgress] = useState({
segmentIndex: 1,
totalSegments: null,
});
// refs
const referencedDisplaySetRef = useRef(null);
const { viewports, activeViewportIndex } = viewportGrid;
const referencedDisplaySet = segDisplaySet.getReferenceDisplaySet();
const referencedDisplaySetMetadata = _getReferencedDisplaySetMetadata(
referencedDisplaySet
);
referencedDisplaySetRef.current = {
displaySet: referencedDisplaySet,
metadata: referencedDisplaySetMetadata,
};
/**
* OnElementEnabled callback which is called after the cornerstoneExtension
* has enabled the element. Note: we delegate all the image rendering to
* cornerstoneExtension, so we don't need to do anything here regarding
* the image rendering, element enabling etc.
*/
const onElementEnabled = evt => {
setElement(evt.detail.element);
};
const onElementDisabled = () => {
setElement(null);
};
const getCornerstoneViewport = useCallback(() => {
const { component: Component } = extensionManager.getModuleEntry(
'@ohif/extension-cornerstone.viewportModule.cornerstone'
);
const {
displaySet: referencedDisplaySet,
} = referencedDisplaySetRef.current;
// Todo: jump to the center of the first segment
return (
<Component
{...props}
displaySets={[referencedDisplaySet, segDisplaySet]}
viewportOptions={{
viewportType: 'volume',
toolGroupId: toolGroupId,
orientation: viewportOptions.orientation,
}}
onElementEnabled={onElementEnabled}
onElementDisabled={onElementDisabled}
// initialImageIndex={initialImageIndex}
></Component>
);
}, [viewportIndex, segDisplaySet, toolGroupId]);
const onSegmentChange = useCallback(
direction => {
direction = direction === 'left' ? -1 : 1;
const segmentationId = segDisplaySet.displaySetInstanceUID;
const segmentation = SegmentationService.getSegmentation(segmentationId);
const { segments } = segmentation;
const numberOfSegments = Object.keys(segments).length;
let newSelectedSegmentIndex = selectedSegment + direction;
if (newSelectedSegmentIndex > numberOfSegments - 1) {
newSelectedSegmentIndex = 1;
} else if (newSelectedSegmentIndex === 0) {
newSelectedSegmentIndex = numberOfSegments - 1;
}
SegmentationService.jumpToSegmentCenter(
segmentationId,
newSelectedSegmentIndex,
toolGroupId
);
setSelectedSegment(newSelectedSegmentIndex);
},
[selectedSegment]
);
useEffect(() => {
if (segIsLoading) {
return;
}
promptHydrateSEG({
servicesManager,
viewportIndex,
segDisplaySet,
}).then(isHydrated => {
if (isHydrated) {
setIsHydrated(true);
}
});
}, [servicesManager, viewportIndex, segDisplaySet, segIsLoading]);
useEffect(() => {
const { unsubscribe } = SegmentationService.subscribe(
SegmentationService.EVENTS.SEGMENTATION_PIXEL_DATA_CREATED,
evt => {
if (
evt.segDisplaySet.displaySetInstanceUID ===
segDisplaySet.displaySetInstanceUID
) {
setSegIsLoading(false);
}
}
);
return () => {
unsubscribe();
};
}, [segDisplaySet]);
useEffect(() => {
const { unsubscribe } = SegmentationService.subscribe(
SegmentationService.EVENTS.SEGMENT_PIXEL_DATA_CREATED,
({ segmentIndex, numSegments }) => {
setProcessingProgress({
segmentIndex,
totalSegments: numSegments,
});
}
);
return () => {
unsubscribe();
};
}, [segDisplaySet]);
/**
Cleanup the SEG viewport when the viewport is destroyed
*/
useEffect(() => {
const onDisplaySetsRemovedSubscription = DisplaySetService.subscribe(
DisplaySetService.EVENTS.DISPLAY_SETS_REMOVED,
({ displaySetInstanceUIDs }) => {
const activeViewport = viewports[activeViewportIndex];
if (
displaySetInstanceUIDs.includes(activeViewport.displaySetInstanceUID)
) {
viewportGridService.setDisplaySetsForViewport({
viewportIndex: activeViewportIndex,
displaySetInstanceUIDs: [],
});
}
}
);
return () => {
onDisplaySetsRemovedSubscription.unsubscribe();
};
}, []);
useEffect(() => {
let toolGroup = ToolGroupService.getToolGroup(toolGroupId);
if (toolGroup) {
return;
}
toolGroup = createSEGToolGroupAndAddTools(
ToolGroupService,
toolGroupId,
extensionManager
);
setToolGroupCreated(true);
return () => {
// remove the segmentation representations if seg displayset changed
SegmentationService.removeSegmentationRepresentationFromToolGroup(
toolGroupId
);
ToolGroupService.destroyToolGroup(toolGroupId);
};
}, []);
useEffect(() => {
setIsHydrated(segDisplaySet.isHydrated);
return () => {
// remove the segmentation representations if seg displayset changed
SegmentationService.removeSegmentationRepresentationFromToolGroup(
toolGroupId
);
referencedDisplaySetRef.current = null;
};
}, [segDisplaySet]);
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
let childrenWithProps = null;
if (
!referencedDisplaySetRef.current ||
referencedDisplaySet.displaySetInstanceUID !==
referencedDisplaySetRef.current.displaySet.displaySetInstanceUID
) {
return null;
}
if (children && children.length) {
childrenWithProps = children.map((child, index) => {
return (
child &&
React.cloneElement(child, {
viewportIndex,
key: index,
})
);
});
}
const {
PatientID,
PatientName,
PatientSex,
PatientAge,
SliceThickness,
ManufacturerModelName,
StudyDate,
SeriesDescription,
SpacingBetweenSlices,
SeriesNumber,
} = referencedDisplaySetRef.current.metadata;
const onPillClick = () => {
promptHydrateSEG({
servicesManager,
viewportIndex,
segDisplaySet,
}).then(isHydrated => {
if (isHydrated) {
setIsHydrated(true);
}
});
};
return (
<>
<ViewportActionBar
onDoubleClick={evt => {
evt.stopPropagation();
evt.preventDefault();
}}
onArrowsClick={onSegmentChange}
getStatusComponent={() => {
return _getStatusComponent({
isHydrated,
onPillClick,
});
}}
studyData={{
label: viewportLabel,
useAltStyling: true,
studyDate: formatDate(StudyDate),
currentSeries: SeriesNumber,
seriesDescription: `SEG Viewport ${SeriesDescription}`,
patientInformation: {
patientName: PatientName
? OHIF.utils.formatPN(PatientName.Alphabetic)
: '',
patientSex: PatientSex || '',
patientAge: PatientAge || '',
MRN: PatientID || '',
thickness: SliceThickness ? `${SliceThickness.toFixed(2)}mm` : '',
spacing:
SpacingBetweenSlices !== undefined
? `${SpacingBetweenSlices.toFixed(2)}mm`
: '',
scanner: ManufacturerModelName || '',
},
}}
/>
<div className="relative flex flex-row w-full h-full overflow-hidden">
{segIsLoading && (
<LoadingIndicatorProgress
className="w-full h-full"
progress={
processingProgress.totalSegments !== null
? ((processingProgress.segmentIndex + 1) /
processingProgress.totalSegments) *
100
: null
}
textBlock={
!processingProgress.totalSegments ? (
<span className="text-white text-sm">Loading SEG ...</span>
) : (
<span className="text-white text-sm flex items-baseline space-x-2">
<div>Loading Segment</div>
<div className="w-3">{`${processingProgress.segmentIndex}`}</div>
<div>/</div>
<div>{`${processingProgress.totalSegments}`}</div>
</span>
)
}
/>
)}
{getCornerstoneViewport()}
<div className="absolute w-full">
{viewportDialogState.viewportIndex === viewportIndex && (
<Notification
id="viewport-notification"
message={viewportDialogState.message}
type={viewportDialogState.type}
actions={viewportDialogState.actions}
onSubmit={viewportDialogState.onSubmit}
onOutsideClick={viewportDialogState.onOutsideClick}
/>
)}
</div>
{childrenWithProps}
</div>
</>
);
}
OHIFCornerstoneSEGViewport.propTypes = {
displaySets: PropTypes.arrayOf(PropTypes.object),
viewportIndex: PropTypes.number.isRequired,
dataSource: PropTypes.object,
children: PropTypes.node,
customProps: PropTypes.object,
};
OHIFCornerstoneSEGViewport.defaultProps = {
customProps: {},
};
function _getReferencedDisplaySetMetadata(referencedDisplaySet) {
const image0 = referencedDisplaySet.images[0];
const referencedDisplaySetMetadata = {
PatientID: image0.PatientID,
PatientName: image0.PatientName,
PatientSex: image0.PatientSex,
PatientAge: image0.PatientAge,
SliceThickness: image0.SliceThickness,
StudyDate: image0.StudyDate,
SeriesDescription: image0.SeriesDescription,
SeriesInstanceUID: image0.SeriesInstanceUID,
SeriesNumber: image0.SeriesNumber,
ManufacturerModelName: image0.ManufacturerModelName,
SpacingBetweenSlices: image0.SpacingBetweenSlices,
};
return referencedDisplaySetMetadata;
}
export default OHIFCornerstoneSEGViewport;
@@ -0,0 +1,92 @@
import React from 'react';
import classNames from 'classnames';
import { Icon, Tooltip } from '@ohif/ui';
import _hydrateSEGDisplaySet from '../utils/_hydrateSEG';
export default function _getStatusComponent({ isHydrated, onPillClick }) {
let ToolTipMessage = null;
let StatusIcon = null;
switch (isHydrated) {
case true:
StatusIcon = () => (
<div
className="flex items-center justify-center -mr-1 rounded-full"
style={{
width: '18px',
height: '18px',
backgroundColor: '#98e5c1',
border: 'solid 1.5px #000000',
}}
>
<Icon
name="exclamation"
style={{ color: '#000', width: '12px', height: '12px' }}
/>
</div>
);
ToolTipMessage = () => (
<div>This Segmentation is loaded in the segmentation panel</div>
);
break;
case false:
StatusIcon = () => (
<div
className="flex items-center justify-center -mr-1 bg-white rounded-full group-hover:bg-customblue-200"
style={{
width: '18px',
height: '18px',
border: 'solid 1.5px #000000',
}}
>
<Icon
name="arrow-left"
style={{ color: '#000', width: '14px', height: '14px' }}
/>
</div>
);
ToolTipMessage = () => <div>Click to load segmentation.</div>;
}
const StatusPill = () => (
<div
className={classNames(
'group relative flex items-center justify-center px-8 rounded-full cursor-default bg-customgreen-100',
{
'hover:bg-customblue-100': !isHydrated,
'cursor-pointer': !isHydrated,
}
)}
style={{
height: '24px',
width: '55px',
}}
onClick={() => {
if (!isHydrated) {
if (onPillClick) {
onPillClick();
}
}
}}
>
<div className="pr-1 text-base font-medium leading-none text-black">
SEG
</div>
<StatusIcon />
</div>
);
return (
<>
{ToolTipMessage && (
<Tooltip content={<ToolTipMessage />} position="bottom-left">
<StatusPill />
</Tooltip>
)}
{!ToolTipMessage && <StatusPill />}
</>
);
}