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fix(dicom overlay): Handle special cases of ArrayBuffer for various DICOM overlay attributes. (#3684)

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Co-authored-by: Alireza <ar.sedghi@gmail.com>
This commit is contained in:
Joe Boccanfuso 2023-10-03 11:44:56 -04:00 committed by GitHub
parent 8a335bd03d
commit e36a604331
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GPG Key ID: 4AEE18F83AFDEB23
5 changed files with 97 additions and 55 deletions
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91
.circleci/config.yml
View File

@ -93,43 +93,6 @@ jobs:
file: '/home/circleci/repo/platform/core/coverage/reports'
flags: 'core'
###
# Workflow: PR_OPTIONAL_DOCKER_PUBLISH
###
# DOCKER_PR_PUBLISH:
# <<: *defaults
# steps:
# # Enable yarn workspaces
# - run: yarn config set workspaces-experimental true
# # Checkout code and ALL Git Tags
# - checkout
# - restore_cache:
# name: Restore Yarn and Cypress Package Cache
# keys:
# # when lock file changes, use increasingly general patterns to restore cache
# - yarn-packages-{{ checksum "yarn.lock" }}
# - yarn-packages-
# - run:
# name: Install Dependencies
# command: yarn install --frozen-lockfile
# - setup_remote_docker:
# docker_layer_caching: false
# - run:
# name: Build and push Docker image
# command: |
# # Remove npm config
# rm -f ./.npmrc
# # Set our version number using vars
# echo $CIRCLE_BUILD_NUM
# # Build our image, auth, and push
# docker build --tag ohif/app:PR_BUILD-$CIRCLE_BUILD_NUM .
# echo $DOCKER_PWD | docker login -u $DOCKER_LOGIN --password-stdin
# docker push ohif/app:PR_BUILD-$CIRCLE_BUILD_NUM
###
# Workflow: DEPLOY
###
@ -180,6 +143,53 @@ jobs:
- commit.txt
- version.json
# just to make sure later on we can publish them
BUILD_PACKAGES_QUICK:
<<: *defaults
steps:
- run: yarn -v
# Checkout code and ALL Git Tags
- checkout
- attach_workspace:
at: ~/repo
# Use increasingly general patterns to restore cache
- restore_cache:
name: Restore Yarn and Cypress Package Cache
keys:
- yarn-packages-{{ checksum "yarn.lock" }}
- yarn-packages-
- run:
name: Install Dependencies
command: yarn install --frozen-lockfile
- save_cache:
name: Save Yarn Package Cache
paths:
- ~/.cache/yarn
key: yarn-packages-{{ checksum "yarn.lock" }}
- run:
name: Avoid hosts unknown for github
command: |
rm -rf ~/.ssh
mkdir ~/.ssh/
echo -e "Host github.com\n\tStrictHostKeyChecking no\n" > ~/.ssh/config
git config --global user.email "danny.ri.brown+ohif-bot@gmail.com"
git config --global user.name "ohif-bot"
- run:
name: Authenticate with NPM registry
command: echo "//registry.npmjs.org/:_authToken=$NPM_TOKEN" > ~/repo/.npmrc
- run:
name: Increase the event emitter limit
command: |
node ./increaseEventEmitterLimit.mjs
- run:
name: build half of the packages (to avoid out of memory in circleci)
command: |
yarn run build:package-all
- run:
name: build the other half of the packages
command: |
yarn run build:package-all-1
###
# Workflow: RELEASE
###
@ -406,7 +416,10 @@ jobs:
workflows:
PR_CHECKS:
jobs:
- UNIT_TESTS
- BUILD_PACKAGES_QUICK
- UNIT_TESTS:
requires:
- BUILD_PACKAGES_QUICK
- CYPRESS_CUSTOM_RUN:
name: 'Cypress Tests'
@ -427,7 +440,7 @@ workflows:
cypress-cache-path:
- '~/.cache/Cypress'
requires:
- UNIT_TESTS
- BUILD_PACKAGES_QUICK
# PR_OPTIONAL_VISUAL_TESTS:
# jobs:

2
extensions/cornerstone/src/tools/ImageOverlayViewerTool.tsx
View File

@ -160,6 +160,8 @@ class ImageOverlayViewerTool extends AnnotationDisplayTool {
let pixelData = null;
if (overlay.pixelData.Value) {
pixelData = overlay.pixelData.Value;
} else if (overlay.pixelData instanceof Array) {
pixelData = overlay.pixelData[0];
} else if (overlay.pixelData.retrieveBulkData) {
pixelData = await overlay.pixelData.retrieveBulkData();
}

2
modes/basic-test-mode/.webpack/webpack.dev.js
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@ -4,7 +4,7 @@ const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
const ENTRY = {
app: `${SRC_DIR}/index.js`,
app: `${SRC_DIR}/index.ts`,
};
module.exports = (env, argv) => {

2
modes/basic-test-mode/.webpack/webpack.prod.js
View File

@ -11,7 +11,7 @@ const SRC_DIR = path.join(__dirname, '../src');
const DIST_DIR = path.join(__dirname, '../dist');
const ENTRY = {
app: `${SRC_DIR}/index.js`,
app: `${SRC_DIR}/index.ts`,
};
module.exports = (env, argv) => {

55
platform/core/src/classes/MetadataProvider.ts
View File

@ -68,7 +68,7 @@ class MetadataProvider {
if (!instance) {
return;
}
}
return (frameNumber && combineFrameInstance(frameNumber, instance)) || instance;
}
@ -118,16 +118,15 @@ class MetadataProvider {
* Adds a new handler for the given tag. The handler will be provided an
* instance object that it can read values from.
*/
public addHandler(
wadoImageLoaderTag: string,
handler
) {
public addHandler(wadoImageLoaderTag: string, handler) {
WADO_IMAGE_LOADER[wadoImageLoaderTag] = handler;
}
_getCornerstoneDICOMImageLoaderTag(wadoImageLoaderTag, instance) {
let metadata = WADO_IMAGE_LOADER[wadoImageLoaderTag]?.(instance);
if (metadata) return metadata;
if (metadata) {
return metadata;
}
switch (wadoImageLoaderTag) {
case WADO_IMAGE_LOADER_TAGS.GENERAL_SERIES_MODULE:
@ -291,12 +290,42 @@ class MetadataProvider {
const ROIStandardDeviationTag = `${groupStr}1303`;
const OverlayOrigin = instance[OverlayOriginTag];
let rows = 0;
if (instance[OverlayRowsTag] instanceof Array) {
// The DICOM VR for overlay rows is US (unsigned short).
const rowsInt16Array = new Uint16Array(instance[OverlayRowsTag][0]);
rows = rowsInt16Array[0];
} else {
rows = instance[OverlayRowsTag];
}
let columns = 0;
if (instance[OverlayColumnsTag] instanceof Array) {
// The DICOM VR for overlay columns is US (unsigned short).
const columnsInt16Array = new Uint16Array(instance[OverlayColumnsTag][0]);
columns = columnsInt16Array[0];
} else {
columns = instance[OverlayColumnsTag];
}
let x = 0;
let y = 0;
if (OverlayOrigin.length === 1) {
// The DICOM VR for overlay origin is SS (signed short) with a multiplicity of 2.
const originInt16Array = new Int16Array(OverlayOrigin[0]);
x = originInt16Array[0];
y = originInt16Array[1];
} else {
x = OverlayOrigin[0];
y = OverlayOrigin[1];
}
const overlay = {
rows: instance[OverlayRowsTag],
columns: instance[OverlayColumnsTag],
rows: rows,
columns: columns,
type: instance[OverlayType],
x: OverlayOrigin[0],
y: OverlayOrigin[1],
x,
y,
pixelData: OverlayData,
description: instance[OverlayDescriptionTag],
label: instance[OverlayLabelTag],
@ -444,7 +473,7 @@ class MetadataProvider {
imageURI = imageURI.split('&frame=')[0];
const uids = this.imageURIToUIDs.get(imageURI);
let frameNumber = this.getFrameInformationFromURL(imageId) || '1';
const frameNumber = this.getFrameInformationFromURL(imageId) || '1';
if (uids && frameNumber !== undefined) {
return { ...uids, frameNumber };
@ -489,9 +518,7 @@ const WADO_IMAGE_LOADER = {
imageOrientationPatient: toNumber(ImageOrientationPatient),
rowCosines: toNumber(rowCosines || [0, 1, 0]),
columnCosines: toNumber(columnCosines || [0, 0, -1]),
imagePositionPatient: toNumber(
instance.ImagePositionPatient || [0, 0, 0]
),
imagePositionPatient: toNumber(instance.ImagePositionPatient || [0, 0, 0]),
sliceThickness: toNumber(instance.SliceThickness),
sliceLocation: toNumber(instance.SliceLocation),
pixelSpacing: toNumber(PixelSpacing || 1),