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fix: 🐛 IDC2733: find segmentations reference source image Ids (#253)
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@Punzo
Punzo committed Mar 14, 2022
1 parent abced98 commit f3e7101
Showing 1 changed file with 130 additions and 125 deletions.
255 changes: 130 additions & 125 deletions packages/adapters/src/adapters/Cornerstone/Segmentation_4X.js
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Original file line number Diff line number Diff line change
Expand Up @@ -378,7 +378,6 @@ function generateToolState(
throw new Error(
"Segmentations orthogonal to the acquisition plane of the source data are not yet supported."
);
break;
case "Oblique":
throw new Error(
"Segmentations oblique to the acquisition plane of the source data are not yet supported."
Expand Down Expand Up @@ -571,18 +570,6 @@ function getCorners(imagePlaneModule) {
columnLength * rowCosines[2]
];

// console.log(
// `entireRowVector: ${(entireRowVector[0],
// entireRowVector[1],
// entireRowVector[2])}`
// );

// console.log(
// `entireColumnVector: ${(entireColumnVector[0],
// entireColumnVector[1],
// entireColumnVector[2])}`
// );

const topLeft = [ipp[0], ipp[1], ipp[2]];
const topRight = [
topLeft[0] + entireRowVector[0],
Expand All @@ -606,62 +593,71 @@ function getCorners(imagePlaneModule) {

/**
* Find the reference frame of the segmentation frame in the source data.
* @returns {string} Returns the imageId
*
* @param {Object} multiframe dicom metadata
* @param {Int} frameSegment frame dicom index
* @param {String[]} imageIds A list of imageIds.
* @param {Object} metadataProvider A Cornerstone metadataProvider to query
* metadata from imageIds.
* @param {Float} tolerance The tolerance parameter
*
* @returns {String} Returns the imageId
*/
function findReferenceSourceImageId(
SourceImageSequence,
multiframe,
frameSegment,
imageIds,
metadataProvider,
PerFrameFunctionalGroups,
frameOfReferenceUID,
tolerance
) {
const imageId = getImageIdOfSourceImage(
const {
FrameOfReferenceUID,
PerFrameFunctionalGroupsSequence,
SourceImageSequence,
imageIds,
metadataProvider
);

if (!imageId) {
/** not found, we can do a check with the PlanePositionSequence.
* (WARNING!) However, if more than a source series is present,
* this logic can find the wrong frame
* (i.e. two source series, with the same frameOfReferenceUID,
* that have each a frame with the same ImagePositionPatient of PlanePositionSequence).
*/
if (
PerFrameFunctionalGroups.PlanePositionSequence !== undefined &&
PerFrameFunctionalGroups.PlanePositionSequence[0] !== undefined &&
PerFrameFunctionalGroups.PlanePositionSequence[0]
.ImagePositionPatient !== undefined
) {
for (let i = 0; i < imageIds.length; ++i) {
const sourceImageMetadata = cornerstone.metaData.get(
"instance",
imageIds[i]
);

if (
sourceImageMetadata === undefined ||
sourceImageMetadata.ImagePositionPatient === undefined ||
sourceImageMetadata.FrameOfReferenceUID !==
frameOfReferenceUID
) {
continue;
}
ReferencedSeriesSequence
} = multiframe;
const PerFrameFunctionalGroup =
PerFrameFunctionalGroupsSequence[frameSegment];
let imageId = undefined;

if (ReferencedSeriesSequence) {
const referencedSeriesSequence = Array.isArray(ReferencedSeriesSequence)
? ReferencedSeriesSequence[0]
: ReferencedSeriesSequence;
const ReferencedSeriesInstanceUID =
referencedSeriesSequence.SeriesInstanceUID;

imageId = getImageIdOfSourceImagebyGeometry(
ReferencedSeriesInstanceUID,
FrameOfReferenceUID,
PerFrameFunctionalGroup,
imageIds,
tolerance
);
}

if (
compareArrays(
PerFrameFunctionalGroups.PlanePositionSequence[0]
.ImagePositionPatient,
sourceImageMetadata.ImagePositionPatient,
tolerance
)
) {
return imageIds[i];
}
}
if (imageId === undefined) {
let sourceImageSequence;
if (SourceImageSequence) {
sourceImageSequence = multiframe.SourceImageSequence[frameSegment];
} else if (PerFrameFunctionalGroup.DerivationImageSequence) {
let DerivationImageSequence =
PerFrameFunctionalGroup.DerivationImageSequence;
DerivationImageSequence = Array.isArray(DerivationImageSequence)
? DerivationImageSequence[0]
: DerivationImageSequence;

sourceImageSequence = DerivationImageSequence.SourceImageSequence;
sourceImageSequence = Array.isArray(sourceImageSequence)
? sourceImageSequence[0]
: sourceImageSequence;
}

imageId = getImageIdOfSourceImagebySourceImageSequence(
sourceImageSequence,
imageIds,
metadataProvider
);
}

return imageId;
Expand Down Expand Up @@ -721,29 +717,11 @@ function checkSEGsOverlapping(
continue;
}

let SourceImageSequence;

if (multiframe.SourceImageSequence) {
SourceImageSequence = multiframe.SourceImageSequence[frameSegment];
} else {
SourceImageSequence =
PerFrameFunctionalGroups.DerivationImageSequence
.SourceImageSequence;
}

if (!SourceImageSequence) {
console.warn(
"Source Image Sequence information missing: individual SEG frames are out of plane, this is not yet supported, skipping this frame."
);
continue;
}

const imageId = findReferenceSourceImageId(
SourceImageSequence,
multiframe,
frameSegment,
imageIds,
metadataProvider,
PerFrameFunctionalGroups,
multiframe.FrameOfReferenceUID,
tolerance
);

Expand Down Expand Up @@ -912,28 +890,11 @@ function insertOverlappingPixelDataPlanar(
);
}

let SourceImageSequence = undefined;
if (multiframe.SourceImageSequence) {
SourceImageSequence = multiframe.SourceImageSequence[i];
} else {
SourceImageSequence =
PerFrameFunctionalGroups.DerivationImageSequence
.SourceImageSequence;
}

if (!SourceImageSequence) {
throw new Error(
"Source Image Sequence information missing: individual SEG frames are out of plane. " +
"This is not yet supported. Aborting segmentation loading."
);
}

const imageId = findReferenceSourceImageId(
SourceImageSequence,
multiframe,
i,
imageIds,
metadataProvider,
PerFrameFunctionalGroups,
multiframe.FrameOfReferenceUID,
tolerance
);

Expand Down Expand Up @@ -1103,28 +1064,11 @@ function insertPixelDataPlanar(
);
}

let SourceImageSequence = undefined;
if (multiframe.SourceImageSequence) {
SourceImageSequence = multiframe.SourceImageSequence[i];
} else {
SourceImageSequence =
PerFrameFunctionalGroups.DerivationImageSequence
.SourceImageSequence;
}

if (!SourceImageSequence) {
throw new Error(
"Source Image Sequence information missing: individual SEG frames are out of plane. " +
"This is not yet supported. Aborting segmentation loading."
);
}

const imageId = findReferenceSourceImageId(
SourceImageSequence,
multiframe,
i,
imageIds,
metadataProvider,
PerFrameFunctionalGroups,
multiframe.FrameOfReferenceUID,
tolerance
);

Expand Down Expand Up @@ -1293,15 +1237,15 @@ function unpackPixelData(multiframe) {
}

/**
* getImageIdOfSourceImage - Returns the Cornerstone imageId of the source image.
* getImageIdOfSourceImagebySourceImageSequence - Returns the Cornerstone imageId of the source image.
*
* @param {Object} SourceImageSequence Sequence describing the source image.
* @param {String[]} imageIds A list of imageIds.
* @param {Object} metadataProvider A Cornerstone metadataProvider to query
* metadata from imageIds.
* @return {String} The corresponding imageId.
* @param {Object} SourceImageSequence Sequence describing the source image.
* @param {String[]} imageIds A list of imageIds.
* @param {Object} metadataProvider A Cornerstone metadataProvider to query
* metadata from imageIds.
* @return {String} The corresponding imageId.
*/
function getImageIdOfSourceImage(
function getImageIdOfSourceImagebySourceImageSequence(
SourceImageSequence,
imageIds,
metadataProvider
Expand All @@ -1325,6 +1269,67 @@ function getImageIdOfSourceImage(
);
}

/**
* getImageIdOfSourceImagebyGeometry - Returns the Cornerstone imageId of the source image.
*
* @param {String} ReferencedSeriesInstanceUID Referenced series of the source image.
* @param {String} FrameOfReferenceUID Frame of reference.
* @param {Object} PerFrameFunctionalGroup Sequence describing segmentation reference attributes per frame.
* @param {String[]} imageIds A list of imageIds.
* @param {Float} tolerance The tolerance parameter
*
* @return {String} The corresponding imageId.
*/
function getImageIdOfSourceImagebyGeometry(
ReferencedSeriesInstanceUID,
FrameOfReferenceUID,
PerFrameFunctionalGroup,
imageIds,
tolerance
) {
if (
ReferencedSeriesInstanceUID === undefined ||
PerFrameFunctionalGroup.PlanePositionSequence === undefined ||
PerFrameFunctionalGroup.PlanePositionSequence[0] === undefined ||
PerFrameFunctionalGroup.PlanePositionSequence[0]
.ImagePositionPatient === undefined
) {
return undefined;
}

for (
let imageIdsIndexc = 0;
imageIdsIndexc < imageIds.length;
++imageIdsIndexc
) {
const sourceImageMetadata = cornerstone.metaData.get(
"instance",
imageIds[imageIdsIndexc]
);

if (
sourceImageMetadata === undefined ||
sourceImageMetadata.ImagePositionPatient === undefined ||
sourceImageMetadata.FrameOfReferenceUID !== FrameOfReferenceUID ||
sourceImageMetadata.SeriesInstanceUID !==
ReferencedSeriesInstanceUID
) {
continue;
}

if (
compareArrays(
PerFrameFunctionalGroup.PlanePositionSequence[0]
.ImagePositionPatient,
sourceImageMetadata.ImagePositionPatient,
tolerance
)
) {
return imageIds[imageIdsIndexc];
}
}
}

/**
* getImageIdOfReferencedSingleFramedSOPInstance - Returns the imageId
* corresponding to the specified sopInstanceUid for single-frame images.
Expand Down

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