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Feat/cs3d planar freehand sr (#268)
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* freehand and probe tool and reformat

* Generalise the CS3D dcmjs controller to be able to save and encode annotations onto multiple referenced series from one SR.

* Remove debugger

* Add erronously added data

* Make changes based on Alireza's feedback
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@JamesAPetts
JamesAPetts committed May 19, 2022
1 parent cef28a9 commit 7da0083
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Showing 10 changed files with 573 additions and 192 deletions.
1 change: 1 addition & 0 deletions packages/adapters/src/adapters/Cornerstone/MeasurementReport.js
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Original file line number Diff line number Diff line change
Expand Up @@ -238,6 +238,7 @@ export default class MeasurementReport {
derivationSourceDataset._vrMap = _vrMap;

const report = new StructuredReport([derivationSourceDataset]);

const contentItem = MeasurementReport.contentItem(
derivationSourceDataset
);
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50 changes: 30 additions & 20 deletions packages/adapters/src/adapters/Cornerstone3D/ArrowAnnotate.js
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Original file line number Diff line number Diff line change
Expand Up @@ -4,44 +4,54 @@ import CORNERSTONE_3D_TAG from "./cornerstone3DTag";
import CodingScheme from "./CodingScheme";

const ARROW_ANNOTATE = "ArrowAnnotate";
const trackingIdentifierTextValue = "Cornerstone3DTools@^0.1.0:ArrowAnnotate";
const trackingIdentifierTextValue = `${CORNERSTONE_3D_TAG}:${ARROW_ANNOTATE}`;

const { codeValues, CodingSchemeDesignator } = CodingScheme;

class ArrowAnnotate {
constructor() {}

static getMeasurementData(MeasurementGroup, imageId, imageToWorldCoords) {
static getMeasurementData(
MeasurementGroup,
sopInstanceUIDToImageIdMap,
imageToWorldCoords,
metadata
) {
const {
defaultState,
SCOORDGroup,
findingGroup
} = MeasurementReport.getSetupMeasurementData(MeasurementGroup);
SCOORDGroup
} = MeasurementReport.getSetupMeasurementData(
MeasurementGroup,
sopInstanceUIDToImageIdMap,
metadata,
ArrowAnnotate.toolType
);

const text = findingGroup.ConceptCodeSequence.CodeMeaning;
const referencedImageId =
defaultState.annotation.metadata.referencedImageId;

const text = defaultState.metadata.label;

const { GraphicData } = SCOORDGroup;

const worldCoords = [];
for (let i = 0; i < GraphicData.length; i += 2) {
const point = imageToWorldCoords(imageId, [
const point = imageToWorldCoords(referencedImageId, [
GraphicData[i],
GraphicData[i + 1]
]);
worldCoords.push(point);
}

const state = {
...defaultState,
toolType: ArrowAnnotate.toolType,
data: {
text,
handles: {
points: [worldCoords[0], worldCoords[1]],
activeHandleIndex: 0,
textBox: {
hasMoved: false
}
const state = defaultState;

state.annotation.data = {
text,
handles: {
points: [worldCoords[0], worldCoords[1]],
activeHandleIndex: 0,
textBox: {
hasMoved: false
}
}
};
Expand Down Expand Up @@ -99,9 +109,9 @@ ArrowAnnotate.isValidCornerstoneTrackingIdentifier = TrackingIdentifier => {
return false;
}

const [cornerstone4Tag, toolType] = TrackingIdentifier.split(":");
const [cornerstone3DTag, toolType] = TrackingIdentifier.split(":");

if (cornerstone4Tag !== CORNERSTONE_3D_TAG) {
if (cornerstone3DTag !== CORNERSTONE_3D_TAG) {
return false;
}

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79 changes: 36 additions & 43 deletions packages/adapters/src/adapters/Cornerstone3D/Bidirectional.js
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Original file line number Diff line number Diff line change
Expand Up @@ -9,24 +9,27 @@ const LONG_AXIS = "Long Axis";
const SHORT_AXIS = "Short Axis";
const FINDING = "121071";
const FINDING_SITE = "G-C0E3";
const trackingIdentifierTextValue = "Cornerstone3DTools@^0.1.0:Bidirectional";
const trackingIdentifierTextValue = `${CORNERSTONE_3D_TAG}:${BIDIRECTIONAL}`;

class Bidirectional {
constructor() {}

static getMeasurementData(MeasurementGroup, imageId, imageToWorldCoords) {
static getMeasurementData(
MeasurementGroup,
sopInstanceUIDToImageIdMap,
imageToWorldCoords,
metadata
) {
const { defaultState } = MeasurementReport.getSetupMeasurementData(
MeasurementGroup
);
const { ContentSequence } = MeasurementGroup;

const findingGroup = toArray(ContentSequence).find(
group => group.ConceptNameCodeSequence.CodeValue === FINDING
MeasurementGroup,
sopInstanceUIDToImageIdMap,
metadata,
Bidirectional.toolType
);

const findingSiteGroups = toArray(ContentSequence).filter(
group => group.ConceptNameCodeSequence.CodeValue === FINDING_SITE
);
const referencedImageId =
defaultState.annotation.metadata.referencedImageId;
const { ContentSequence } = MeasurementGroup;

const longAxisNUMGroup = toArray(ContentSequence).find(
group => group.ConceptNameCodeSequence.CodeMeaning === LONG_AXIS
Expand All @@ -49,43 +52,33 @@ class Bidirectional {
[longAxisSCOORDGroup, shortAxisSCOORDGroup].forEach(group => {
const { GraphicData } = group;
for (let i = 0; i < GraphicData.length; i += 2) {
const point = imageToWorldCoords(imageId, [
const point = imageToWorldCoords(referencedImageId, [
GraphicData[i],
GraphicData[i + 1]
]);
worldCoords.push(point);
}
});

const state = {
...defaultState,
finding: findingGroup
? findingGroup.ConceptCodeSequence
: undefined,
findingSites: findingSiteGroups.map(fsg => {
return { ...fsg.ConceptCodeSequence };
}),
toolType: Bidirectional.toolType,
data: {
handles: {
points: [
worldCoords[0],
worldCoords[1],
worldCoords[2],
worldCoords[3]
],
activeHandleIndex: 0,
textBox: {
hasMoved: false
}
},
cachedStats: {
[`imageId:${imageId}`]: {
length:
longAxisNUMGroup.MeasuredValueSequence.NumericValue,
width:
shortAxisNUMGroup.MeasuredValueSequence.NumericValue
}
const state = defaultState;

state.annotation.data = {
handles: {
points: [
worldCoords[0],
worldCoords[1],
worldCoords[2],
worldCoords[3]
],
activeHandleIndex: 0,
textBox: {
hasMoved: false
}
},
cachedStats: {
[`imageId:${referencedImageId}`]: {
length: longAxisNUMGroup.MeasuredValueSequence.NumericValue,
width: shortAxisNUMGroup.MeasuredValueSequence.NumericValue
}
}
};
Expand Down Expand Up @@ -189,9 +182,9 @@ Bidirectional.isValidCornerstoneTrackingIdentifier = TrackingIdentifier => {
return false;
}

const [cornerstone4Tag, toolType] = TrackingIdentifier.split(":");
const [cornerstone3DTag, toolType] = TrackingIdentifier.split(":");

if (cornerstone4Tag !== CORNERSTONE_3D_TAG) {
if (cornerstone3DTag !== CORNERSTONE_3D_TAG) {
return false;
}

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54 changes: 32 additions & 22 deletions packages/adapters/src/adapters/Cornerstone3D/EllipticalROI.js
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Original file line number Diff line number Diff line change
Expand Up @@ -8,22 +8,30 @@ const FINDING = "121071";
const FINDING_SITE = "G-C0E3";
const EPSILON = 1e-4;

const trackingIdentifierTextValue = "Cornerstone3DTools@^0.1.0:EllipticalROI";
const trackingIdentifierTextValue = `${CORNERSTONE_3D_TAG}:${ELLIPTICALROI}`;

class EllipticalROI {
constructor() {}

static getMeasurementData(
MeasurementGroup,
imageId,
sopInstanceUIDToImageIdMap,
imageToWorldCoords,
metadata
) {
const {
defaultState,
NUMGroup,
SCOORDGroup
} = MeasurementReport.getSetupMeasurementData(MeasurementGroup);
} = MeasurementReport.getSetupMeasurementData(
MeasurementGroup,
sopInstanceUIDToImageIdMap,
metadata,
EllipticalROI.toolType
);

const referencedImageId =
defaultState.annotation.metadata.referencedImageId;

const { GraphicData } = SCOORDGroup;

Expand All @@ -33,7 +41,7 @@ class EllipticalROI {
// in the image plane and then choose the correct points to use for the ellipse.
const pointsWorld = [];
for (let i = 0; i < GraphicData.length; i += 2) {
const worldPos = imageToWorldCoords(imageId, [
const worldPos = imageToWorldCoords(referencedImageId, [
GraphicData[i],
GraphicData[i + 1]
]);
Expand All @@ -56,7 +64,10 @@ class EllipticalROI {
vec3.sub(minorAxisVec, minorAxisEnd, minorAxisStart);
vec3.normalize(minorAxisVec, minorAxisVec);

const imagePlaneModule = metadata.get("imagePlaneModule", imageId);
const imagePlaneModule = metadata.get(
"imagePlaneModule",
referencedImageId
);

if (!imagePlaneModule) {
throw new Error("imageId does not have imagePlaneModule metadata");
Expand Down Expand Up @@ -99,24 +110,23 @@ class EllipticalROI {
console.warn("OBLIQUE ELLIPSE NOT YET SUPPORTED");
}

const state = {
...defaultState,
toolType: EllipticalROI.toolType,
data: {
handles: {
points: [...ellipsePoints],
activeHandleIndex: 0,
textBox: {
hasMoved: false
}
},
cachedStats: {
[`imageId:${imageId}`]: {
area: NUMGroup.MeasuredValueSequence.NumericValue
}
const state = defaultState;

state.annotation.data = {
handles: {
points: [...ellipsePoints],
activeHandleIndex: 0,
textBox: {
hasMoved: false
}
},
cachedStats: {
[`imageId:${referencedImageId}`]: {
area: NUMGroup.MeasuredValueSequence.NumericValue
}
}
};

return state;
}

Expand Down Expand Up @@ -180,9 +190,9 @@ EllipticalROI.isValidCornerstoneTrackingIdentifier = TrackingIdentifier => {
return false;
}

const [cornerstone4Tag, toolType] = TrackingIdentifier.split(":");
const [cornerstone3DTag, toolType] = TrackingIdentifier.split(":");

if (cornerstone4Tag !== CORNERSTONE_3D_TAG) {
if (cornerstone3DTag !== CORNERSTONE_3D_TAG) {
return false;
}

Expand Down
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