feat: cornerstone3D stack and volume viewports (#2787)
* feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: cs3d tools and toolGroups (#20) * add more tools to work with cs3d mode * fix hotkeys * add stack manager usage for stach viewports * add image scrollbar * wip viewport overlay * fix toAnnotation schema for tools * fix the unnecessary size change that triggered resize * hanging protocol improvement to allow unmatched errors * study description matching for hanging protocol * fix the displaysetOptions to work * fix handle the active tool when a new viewport is added * fix separate toolGroups for mode * apply review comments * apply review comments * yarn lock * feat: overlay component (#21) * fix default displayset options * add viewport overlay * apply review comments * feat: loading and orientation indicators (#22) * add loading indicator * add orientation marker initial work * apply review comments * fix: orientation markers (#23) * finished the orientation markers * fix various broken cypress tests * apply review comments * update yarn lock * feat: re-working measurement tracking mode with cornerstone3d (#2805) * feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: Add Measurement tracking mode with cs3D (#2789) * feat: first render for cornerstone3d tracked viewport * make tool active work * wip for SR extension * renamed dicom sr to cornerstone dicom sr * remove cornerstone from dicom pdf and video * move dicom sr logic to sr extension * feat: Add hydration for the length tool * fix SR display tool for length using cs3d * fix default config * fix: various bugs with sr viewport and tracking * fix promptying to continue tracking for when SR is created * feat: add keep trackign of unique identifiers * fix hydration for same imageIds * feat: Add SR toolGroup creation on modeEnter * feat: remove the need for separate mapper for SR hydration * add SR display for ellipse * handle hydration of elliptical ROI tool * remove cornerstone extension * add arrow mapping * feat: Add ArrowAnnotate SR display and hydration * apply review comments * apply review comments * move viewport labels to the viewportData * apply review comments * fix: integration cypress tests with cornerstone3D and add CINE tool (#2795) * fix: integration cypress tests with cornerstone3D * revert to addOrUpdate as it makes more sense * fix local drag and drop * fix tests * move dicomLoaderService to cornerstone extension * fix various import bugs * fix bug for local PT series * fix various unit tests * bump cs3d versions * add angle and magnify tool * bump dependencies to avoid broken peerDeps * feat: add initial work for capture using cs3d * feat: show annotations on the image capture * feat: add svg layer export * feat: Add CINE Tool * feat: remove unnecessary viewport rendering for cine state changes Co-authored-by: Erik Ziegler <erik.sweed@gmail.com> * docs: modify and improve documentation (#2800) * cleanup docs versionings * feat: Add all version explanations * version docs for 3.0 * wip for changing docs * wip for updated docs * add utility module documentation * fix demo with nohoisting of history * add slides and video to resources * apply review comments * fix: drag and drop SR into SR viewport (#2803) * update yarn lock Co-authored-by: Erik <erik.sweed@gmail.com> * update pathnames to match v3-stable * update the e2e pathname * fix: various bugs with regard to tracking workflow (#2811) * fix: various issues with measurement panel * fix: update default tool style for annotations * fix: annotatoin label getting removed * feat: Add backward compatibility for SR hydration with legacy cornerstone * fix: cursors and ellipse ROI max style * fix: ArrowAnnotate SRDisplay * apply review comments * bump package versions * fix: bugin rehydration of SR * fix: e2e tests * fix active viewport thickness and arrowTool ui * add readme for measurement tracking * use uploaded image for readme * add back images * try to fix e2e test * fix: window level presets hotkeys * Update README.md * update yarn lock * feat: volume api and TMTV mode (#2817) * feat: volumeAPI and TMTV mode * feat: use cs3d cache service to obtain viewportData * wip for volume api * wip: fusion viewport * feat: add blend mode option * wip for image scrollbar * fix drag and drop thumbnail * wip for image scrollbar for voluems * fix: element mismatch bug for scroll * feat: Add image scrollbar to volumes * feat: add syncGroups to volume api * feat: add tmtv mode initial setup * feat: add initial image options for the stack viewports * feat: Add custom load strategy for volume viewports via HP * apply review comments fix: Jump presets cs3d (#2812) * feat: Add JumpPreset to OHIF for Cornerstone3D * fix: accessing viewport service from servicesManager feat: volume API and TMTV mode (#2814) * fix: do not display overlays on mip viewports * feat: add optional disableCommands for toggle buttons * fix: toggleCrossharis * feat: config the crosshairs * feat: add PetSUV Panel for changing metadata * feat: initial work for the rectangleROIThreshold panel * wip: measurement service * roi threshold working * feat: Add displayText to segmentations * feat: add remove segmentation * feat: add csv export * feat: add RT export for annotations in tmtv mode * fix: fusion to use pt in tmtv mode and measuremet mappings * fix: various bugs * apply review comments * apply review comments * feat: add fusion color maps * add readme to tmtv mode * Update README.md * fix: try to fix build * fix unit tests * Update README.md * feat: add about to the panel * fix: changing strategy in roi panel * apply review comments * update package versions * wip for stackPrefetch * fix: cornerstone3d hydration and renaming (#2818) * update readme * renamed cornerstone extension * wip for renaming cornerstone3D variables * wip for renaming cornerstone3D variables * wip for fixing bugs for SR viewport * fix: jumpToMeasurement and initial label after hydration * fix: fileName capitalization * feat: use the new prefetch stack in the cs3d (#2820) * feat: use the new prefetch stack in the cs3d * use viewport scroll api for stack viewport * fix cine stop when scrollbar changes * feat: use new prefetch events * fix loading state to not show repeatedly * fix: various bugs for tmtv mode thresholding and new icons (#2823) * feat: make tmtv mode available in worklist * feat: add new icons for tmtv mode * feat: add fusion color icon * fix: parallel scale calculation * fix: bump Cornerstone to get large image support working * fix: Fix issues with CPU viewport flipping, including config files * fix: bump cornerstone to fix magnify tool * fix: Bump Cornerstone version to fix resetCamera issue in StackViewport * ci: Add _headers file to enable CORS headers for Netlify Drag/Drop deploys * fix: WADO-URI was not working. PET Metadata was coming from the wrong place. Fixed some minor React errors * feat(OHIF):Allow modes and extensions to be added after commpile time. (#2838) Also works with the compile time add that the existing cli uses, so that both build types work. Eric and I agreed this doesn't change existing functionality, but is almost entirely build issues/fixes. * bump: dependency versions to fix hydration bugs (#2848) * bump: dcmjs version to fix hydration bugs * try to fix tests * bump dependency versions Co-authored-by: Alireza <ar.sedghi@gmail.com> Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
This commit is contained in:
668 files changed
+41669
-13410
No files matched your search
@@ -0,0 +1,155 @@
|
||||
import { Types } from '@cornerstonejs/core';
|
||||
import { utilities } from '@cornerstonejs/tools';
|
||||
import { vec3 } from 'gl-matrix';
|
||||
|
||||
type AnnotationsForThresholding = {
|
||||
data: {
|
||||
handles: {
|
||||
points: Types.Point3[];
|
||||
};
|
||||
cachedStats?: {
|
||||
projectionPoints?: Types.Point3[][];
|
||||
};
|
||||
};
|
||||
};
|
||||
|
||||
/**
|
||||
* This method calculates the SUV peak on a segmented ROI from a reference PET
|
||||
* volume. If a rectangle annotation is provided, the peak is calculated within that
|
||||
* rectangle. Otherwise, the calculation is performed on the entire volume which
|
||||
* will be slower but same result.
|
||||
* @param viewport Viewport to use for the calculation
|
||||
* @param labelmap Labelmap from which the mask is taken
|
||||
* @param referenceVolume PET volume to use for SUV calculation
|
||||
* @param toolData [Optional] list of toolData to use for SUV calculation
|
||||
* @param segmentIndex The index of the segment to use for masking
|
||||
* @returns
|
||||
*/
|
||||
function calculateSuvPeak(
|
||||
labelmap: Types.IImageVolume,
|
||||
referenceVolume: Types.IImageVolume,
|
||||
annotations?: AnnotationsForThresholding[],
|
||||
segmentIndex = 1
|
||||
): {
|
||||
max: number;
|
||||
maxIJK: Types.Point3;
|
||||
maxLPS: Types.Point3;
|
||||
mean: number;
|
||||
} {
|
||||
if (referenceVolume.metadata.Modality !== 'PT') {
|
||||
return;
|
||||
}
|
||||
|
||||
if (labelmap.scalarData.length !== referenceVolume.scalarData.length) {
|
||||
throw new Error(
|
||||
'labelmap and referenceVolume must have the same number of pixels'
|
||||
);
|
||||
}
|
||||
|
||||
const {
|
||||
scalarData: labelmapData,
|
||||
dimensions,
|
||||
imageData: labelmapImageData,
|
||||
} = labelmap;
|
||||
|
||||
const {
|
||||
scalarData: referenceVolumeData,
|
||||
imageData: referenceVolumeImageData,
|
||||
} = referenceVolume;
|
||||
|
||||
let boundsIJK;
|
||||
// Todo: using the first annotation for now
|
||||
if (annotations && annotations[0].data?.cachedStats) {
|
||||
const { projectionPoints } = annotations[0].data.cachedStats;
|
||||
const pointsToUse = [].concat(...projectionPoints); // cannot use flat() because of typescript compiler right now
|
||||
|
||||
const rectangleCornersIJK = pointsToUse.map(world => {
|
||||
const ijk = vec3.fromValues(0, 0, 0);
|
||||
referenceVolumeImageData.worldToIndex(world, ijk);
|
||||
return ijk as Types.Point3;
|
||||
});
|
||||
|
||||
boundsIJK = utilities.boundingBox.getBoundingBoxAroundShape(
|
||||
rectangleCornersIJK,
|
||||
dimensions
|
||||
);
|
||||
}
|
||||
|
||||
let max = 0;
|
||||
let maxIJK = [0, 0, 0];
|
||||
let maxLPS = [0, 0, 0];
|
||||
|
||||
const callback = ({ pointIJK, pointLPS }) => {
|
||||
const offset = referenceVolumeImageData.computeOffsetIndex(pointIJK);
|
||||
const value = labelmapData[offset];
|
||||
|
||||
if (value !== segmentIndex) {
|
||||
return;
|
||||
}
|
||||
|
||||
const referenceValue = referenceVolumeData[offset];
|
||||
|
||||
if (referenceValue > max) {
|
||||
max = referenceValue;
|
||||
maxIJK = pointIJK;
|
||||
maxLPS = pointLPS;
|
||||
}
|
||||
};
|
||||
|
||||
utilities.pointInShapeCallback(
|
||||
labelmapImageData,
|
||||
() => true,
|
||||
callback,
|
||||
boundsIJK
|
||||
);
|
||||
|
||||
const direction = labelmapImageData
|
||||
.getDirection()
|
||||
.slice(0, 3) as Types.Point3;
|
||||
|
||||
/**
|
||||
* 2. Find the bottom and top of the great circle for the second sphere (1cc sphere)
|
||||
* V = (4/3)πr3
|
||||
*/
|
||||
const radius = Math.pow(1 / ((4 / 3) * Math.PI), 1 / 3) * 10;
|
||||
const diameter = radius * 2;
|
||||
|
||||
const secondaryCircleWorld = vec3.create();
|
||||
const bottomWorld = vec3.create();
|
||||
const topWorld = vec3.create();
|
||||
referenceVolumeImageData.indexToWorld(<vec3>maxIJK, secondaryCircleWorld);
|
||||
vec3.scaleAndAdd(bottomWorld, secondaryCircleWorld, direction, -diameter / 2);
|
||||
vec3.scaleAndAdd(topWorld, secondaryCircleWorld, direction, diameter / 2);
|
||||
const suvPeakCirclePoints = [bottomWorld, topWorld] as [
|
||||
Types.Point3,
|
||||
Types.Point3
|
||||
];
|
||||
|
||||
/**
|
||||
* 3. Find the Mean and Max of the 1cc sphere centered on the suv Max of the previous
|
||||
* sphere
|
||||
*/
|
||||
let count = 0;
|
||||
let acc = 0;
|
||||
const suvPeakMeanCallback = ({ value }) => {
|
||||
acc += value;
|
||||
count += 1;
|
||||
};
|
||||
|
||||
utilities.pointInSurroundingSphereCallback(
|
||||
referenceVolumeImageData,
|
||||
suvPeakCirclePoints,
|
||||
suvPeakMeanCallback
|
||||
);
|
||||
|
||||
const mean = acc / count;
|
||||
|
||||
return {
|
||||
max,
|
||||
maxIJK,
|
||||
maxLPS,
|
||||
mean,
|
||||
};
|
||||
}
|
||||
|
||||
export default calculateSuvPeak;
|
||||
Reference in new issue
Block a user