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
1 parent
08c58b0634
commit
83ea228d86
254 files changed
+12856
-3141
No files matched your search
@@ -0,0 +1,312 @@
|
||||
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;
|
||||
Reference in new issue
Block a user