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Merge branch 'master' into 1320_ImproveVisualRegression

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Mirna Silva 2020-01-06 19:07:20 -03:00 committed by GitHub
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8
extensions/vtk/CHANGELOG.md
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@ -3,6 +3,14 @@
All notable changes to this project will be documented in this file. All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines. See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [1.2.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.2.4...@ohif/extension-vtk@1.2.5) (2020-01-06)
**Note:** Version bump only for package @ohif/extension-vtk
## [1.2.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.2.3...@ohif/extension-vtk@1.2.4) (2019-12-30) ## [1.2.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.2.3...@ohif/extension-vtk@1.2.4) (2019-12-30)
**Note:** Version bump only for package @ohif/extension-vtk **Note:** Version bump only for package @ohif/extension-vtk

4
extensions/vtk/package.json
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@ -1,6 +1,6 @@
{ {
"name": "@ohif/extension-vtk", "name": "@ohif/extension-vtk",
"version": "1.2.4", "version": "1.2.5",
"description": "OHIF extension for VTK.js", "description": "OHIF extension for VTK.js",
"author": "OHIF", "author": "OHIF",
"license": "MIT", "license": "MIT",
@ -52,7 +52,7 @@
"react-vtkjs-viewport": "^0.3.9" "react-vtkjs-viewport": "^0.3.9"
}, },
"devDependencies": { "devDependencies": {
"@ohif/core": "^2.3.1", "@ohif/core": "^2.3.2",
"@ohif/ui": "^1.1.7", "@ohif/ui": "^1.1.7",
"cornerstone-tools": "^4.9.0", "cornerstone-tools": "^4.9.0",
"cornerstone-wado-image-loader": "^3.0.0", "cornerstone-wado-image-loader": "^3.0.0",

8
platform/core/CHANGELOG.md
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@ -3,6 +3,14 @@
All notable changes to this project will be documented in this file. All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines. See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [2.3.2](https://github.com/OHIF/Viewers/compare/@ohif/core@2.3.1...@ohif/core@2.3.2) (2020-01-06)
**Note:** Version bump only for package @ohif/core
## [2.3.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.3.0...@ohif/core@2.3.1) (2019-12-30) ## [2.3.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.3.0...@ohif/core@2.3.1) (2019-12-30)

2
platform/core/package.json
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@ -1,6 +1,6 @@
{ {
"name": "@ohif/core", "name": "@ohif/core",
"version": "2.3.1", "version": "2.3.2",
"description": "Generic business logic for web-based medical imaging applications", "description": "Generic business logic for web-based medical imaging applications",
"author": "OHIF Core Team", "author": "OHIF Core Team",
"license": "MIT", "license": "MIT",

413
platform/core/src/studies/studyUtils.js
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@ -1,413 +0,0 @@
import DICOMWeb from '../DICOMWeb/';
const WADOProxy = {
convertURL: (url, server) => {
// TODO: Remove all WADOProxy stuff from this file
return url;
},
};
function parseFloatArray(obj) {
const result = [];
if (!obj) {
return result;
}
const objs = obj.split('\\');
for (let i = 0; i < objs.length; i++) {
result.push(parseFloat(objs[i]));
}
return result;
}
/**
* Create a plain JS object that describes a study (a study descriptor object)
* @param {Object} server Object with server configuration parameters
* @param {Object} aSopInstance a SOP Instance from which study information will be added
*/
function createStudy(server, aSopInstance) {
// TODO: Pass a reference ID to the server instead of including the URLs here
return {
seriesList: [],
seriesMap: Object.create(null),
seriesLoader: null,
wadoUriRoot: server.wadoUriRoot,
wadoRoot: server.wadoRoot,
qidoRoot: server.qidoRoot,
patientName: DICOMWeb.getName(aSopInstance['00100010']),
patientId: DICOMWeb.getString(aSopInstance['00100020']),
patientAge: DICOMWeb.getNumber(aSopInstance['00101010']),
patientSize: DICOMWeb.getNumber(aSopInstance['00101020']),
patientWeight: DICOMWeb.getNumber(aSopInstance['00101030']),
accessionNumber: DICOMWeb.getString(aSopInstance['00080050']),
studyDate: DICOMWeb.getString(aSopInstance['00080020']),
modalities: DICOMWeb.getString(aSopInstance['00080061']),
studyDescription: DICOMWeb.getString(aSopInstance['00081030']),
imageCount: DICOMWeb.getString(aSopInstance['00201208']),
studyInstanceUid: DICOMWeb.getString(aSopInstance['0020000D']),
institutionName: DICOMWeb.getString(aSopInstance['00080080']),
};
}
/** Returns a WADO url for an instance
*
* @param studyInstanceUid
* @param seriesInstanceUid
* @param sopInstanceUid
* @returns {string}
*/
function buildInstanceWadoUrl(
server,
studyInstanceUid,
seriesInstanceUid,
sopInstanceUid
) {
// TODO: This can be removed, since DICOMWebClient has the same function. Not urgent, though
const params = [];
params.push('requestType=WADO');
params.push(`studyUID=${studyInstanceUid}`);
params.push(`seriesUID=${seriesInstanceUid}`);
params.push(`objectUID=${sopInstanceUid}`);
params.push('contentType=application/dicom');
params.push('transferSyntax=*');
const paramString = params.join('&');
return `${server.wadoUriRoot}?${paramString}`;
}
function buildInstanceWadoRsUri(
server,
studyInstanceUid,
seriesInstanceUid,
sopInstanceUid
) {
return `${server.wadoRoot}/studies/${studyInstanceUid}/series/${seriesInstanceUid}/instances/${sopInstanceUid}`;
}
function buildInstanceFrameWadoRsUri(
server,
studyInstanceUid,
seriesInstanceUid,
sopInstanceUid,
frame
) {
const baseWadoRsUri = buildInstanceWadoRsUri(
server,
studyInstanceUid,
seriesInstanceUid,
sopInstanceUid
);
frame = frame != null || 1;
return `${baseWadoRsUri}/frames/${frame}`;
}
function getFrameIncrementPointer(element) {
const frameIncrementPointerNames = {
'00181065': 'frameTimeVector',
'00181063': 'frameTime',
};
if (!element || !element.Value || !element.Value.length) {
return;
}
const value = element.Value[0];
return frameIncrementPointerNames[value];
}
function getRadiopharmaceuticalInfo(instance) {
const modality = DICOMWeb.getString(instance['00080060']);
if (modality !== 'PT') {
return;
}
const radiopharmaceuticalInfo = instance['00540016'];
if (
radiopharmaceuticalInfo === undefined ||
!radiopharmaceuticalInfo.Value ||
!radiopharmaceuticalInfo.Value.length
) {
return;
}
const firstPetRadiopharmaceuticalInfo = radiopharmaceuticalInfo.Value[0];
return {
radiopharmaceuticalStartTime: DICOMWeb.getString(
firstPetRadiopharmaceuticalInfo['00181072']
),
radionuclideTotalDose: DICOMWeb.getNumber(
firstPetRadiopharmaceuticalInfo['00181074']
),
radionuclideHalfLife: DICOMWeb.getNumber(
firstPetRadiopharmaceuticalInfo['00181075']
),
};
}
/**
* Parses the SourceImageSequence, if it exists, in order
* to return a ReferenceSOPInstanceUID. The ReferenceSOPInstanceUID
* is used to refer to this image in any accompanying DICOM-SR documents.
*
* @param instance
* @returns {String} The ReferenceSOPInstanceUID
*/
function getSourceImageInstanceUid(instance) {
// TODO= Parse the whole Source Image Sequence
// This is a really poor workaround for now.
// Later we should probably parse the whole sequence.
var SourceImageSequence = instance['00082112'];
if (
SourceImageSequence &&
SourceImageSequence.Value &&
SourceImageSequence.Value.length &&
SourceImageSequence.Value[0]['00081155'].Value
) {
return SourceImageSequence.Value[0]['00081155'].Value[0];
}
}
async function makeSOPInstance(server, study, instance) {
const { studyInstanceUid } = study;
const seriesInstanceUid = DICOMWeb.getString(instance['0020000E']);
let series = study.seriesMap[seriesInstanceUid];
if (!series) {
series = {
seriesInstanceUid,
seriesDescription: DICOMWeb.getString(instance['0008103E']),
modality: DICOMWeb.getString(instance['00080060']),
seriesNumber: DICOMWeb.getNumber(instance['00200011']),
seriesDate: DICOMWeb.getString(instance['00080021']),
seriesTime: DICOMWeb.getString(instance['00080031']),
instances: [],
};
study.seriesMap[seriesInstanceUid] = series;
study.seriesList.push(series);
}
const sopInstanceUid = DICOMWeb.getString(instance['00080018']);
const wadouri = buildInstanceWadoUrl(
server,
studyInstanceUid,
seriesInstanceUid,
sopInstanceUid
);
const baseWadoRsUri = buildInstanceWadoRsUri(
server,
studyInstanceUid,
seriesInstanceUid,
sopInstanceUid
);
const wadorsuri = buildInstanceFrameWadoRsUri(
server,
studyInstanceUid,
seriesInstanceUid,
sopInstanceUid
);
const sopInstance = {
imageType: DICOMWeb.getString(instance['00080008']),
sopClassUid: DICOMWeb.getString(instance['00080016']),
modality: DICOMWeb.getString(instance['00080060']),
sopInstanceUid,
instanceNumber: DICOMWeb.getNumber(instance['00200013']),
imagePositionPatient: DICOMWeb.getString(instance['00200032']),
imageOrientationPatient: DICOMWeb.getString(instance['00200037']),
frameOfReferenceUID: DICOMWeb.getString(instance['00200052']),
sliceLocation: DICOMWeb.getNumber(instance['00201041']),
samplesPerPixel: DICOMWeb.getNumber(instance['00280002']),
photometricInterpretation: DICOMWeb.getString(instance['00280004']),
planarConfiguration: DICOMWeb.getNumber(instance['00280006']),
rows: DICOMWeb.getNumber(instance['00280010']),
columns: DICOMWeb.getNumber(instance['00280011']),
pixelSpacing: DICOMWeb.getString(instance['00280030']),
pixelAspectRatio: DICOMWeb.getString(instance['00280034']),
bitsAllocated: DICOMWeb.getNumber(instance['00280100']),
bitsStored: DICOMWeb.getNumber(instance['00280101']),
highBit: DICOMWeb.getNumber(instance['00280102']),
pixelRepresentation: DICOMWeb.getNumber(instance['00280103']),
smallestPixelValue: DICOMWeb.getNumber(instance['00280106']),
largestPixelValue: DICOMWeb.getNumber(instance['00280107']),
windowCenter: DICOMWeb.getString(instance['00281050']),
windowWidth: DICOMWeb.getString(instance['00281051']),
rescaleIntercept: DICOMWeb.getNumber(instance['00281052']),
rescaleSlope: DICOMWeb.getNumber(instance['00281053']),
rescaleType: DICOMWeb.getNumber(instance['00281054']),
sourceImageInstanceUid: getSourceImageInstanceUid(instance),
laterality: DICOMWeb.getString(instance['00200062']),
viewPosition: DICOMWeb.getString(instance['00185101']),
acquisitionDateTime: DICOMWeb.getString(instance['0008002A']),
numberOfFrames: DICOMWeb.getNumber(instance['00280008']),
frameIncrementPointer: getFrameIncrementPointer(instance['00280009']),
frameTime: DICOMWeb.getNumber(instance['00181063']),
frameTimeVector: parseFloatArray(DICOMWeb.getString(instance['00181065'])),
sliceThickness: DICOMWeb.getNumber(instance['00180050']),
spacingBetweenSlices: DICOMWeb.getString(instance['00180088']),
lossyImageCompression: DICOMWeb.getString(instance['00282110']),
derivationDescription: DICOMWeb.getString(instance['00282111']),
lossyImageCompressionRatio: DICOMWeb.getString(instance['00282112']),
lossyImageCompressionMethod: DICOMWeb.getString(instance['00282114']),
echoNumber: DICOMWeb.getString(instance['00180086']),
contrastBolusAgent: DICOMWeb.getString(instance['00180010']),
radiopharmaceuticalInfo: getRadiopharmaceuticalInfo(instance),
baseWadoRsUri: baseWadoRsUri,
wadouri: WADOProxy.convertURL(wadouri, server),
wadorsuri: WADOProxy.convertURL(wadorsuri, server),
wadoRoot: server.wadoRoot,
imageRendering: server.imageRendering,
thumbnailRendering: server.thumbnailRendering,
};
// Get additional information if the instance uses "PALETTE COLOR" photometric interpretation
if (sopInstance.photometricInterpretation === 'PALETTE COLOR') {
const redPaletteColorLookupTableDescriptor = parseFloatArray(
DICOMWeb.getString(instance['00281101'])
);
const greenPaletteColorLookupTableDescriptor = parseFloatArray(
DICOMWeb.getString(instance['00281102'])
);
const bluePaletteColorLookupTableDescriptor = parseFloatArray(
DICOMWeb.getString(instance['00281103'])
);
const palettes = await getPaletteColors(
server,
instance,
redPaletteColorLookupTableDescriptor
);
if (palettes) {
if (palettes.uid) {
sopInstance.paletteColorLookupTableUID = palettes.uid;
}
sopInstance.redPaletteColorLookupTableData = palettes.red;
sopInstance.greenPaletteColorLookupTableData = palettes.green;
sopInstance.bluePaletteColorLookupTableData = palettes.blue;
sopInstance.redPaletteColorLookupTableDescriptor = redPaletteColorLookupTableDescriptor;
sopInstance.greenPaletteColorLookupTableDescriptor = greenPaletteColorLookupTableDescriptor;
sopInstance.bluePaletteColorLookupTableDescriptor = bluePaletteColorLookupTableDescriptor;
}
}
series.instances.push(sopInstance);
return sopInstance;
}
function getPaletteColor(server, instance, tag, lutDescriptor) {
const numLutEntries = lutDescriptor[0];
const bits = lutDescriptor[2];
let uri = WADOProxy.convertURL(instance[tag].BulkDataURI, server);
// TODO: Workaround for dcm4chee behind SSL-terminating proxy returning
// incorrect bulk data URIs
if (server.wadoRoot.indexOf('https') === 0 && !uri.includes('https')) {
uri = uri.replace('http', 'https');
}
const config = {
url: server.wadoRoot, //BulkDataURI is absolute, so this isn't used
headers: DICOMWeb.getAuthorizationHeader(server),
};
const dicomWeb = new api.DICOMwebClient(config);
const options = {
BulkDataURI: uri,
};
const readUInt16 = (byteArray, position) => {
return byteArray[position] + byteArray[position + 1] * 256;
};
const arrayBufferToPaletteColorLUT = result => {
const arraybuffer = result[0];
const byteArray = new Uint8Array(arraybuffer);
const lut = [];
for (let i = 0; i < numLutEntries; i++) {
if (bits === 16) {
lut[i] = readUInt16(byteArray, i * 2);
} else {
lut[i] = byteArray[i];
}
}
return lut;
};
return dicomWeb.retrieveBulkData(options).then(arrayBufferToPaletteColorLUT);
}
/**
* Fetch palette colors for instances with "PALETTE COLOR" photometricInterpretation.
*
* @param server {Object} Current server;
* @param instance {Object} The retrieved instance metadata;
* @returns {String} The ReferenceSOPInstanceUID
*/
async function getPaletteColors(server, instance, lutDescriptor) {
let paletteUID = DICOMWeb.getString(instance['00281199']);
return new Promise((resolve, reject) => {
let entry;
if (paletteColorCache.isValidUID(paletteUID)) {
entry = paletteColorCache.get(paletteUID);
if (entry) {
return resolve(entry);
}
}
// no entry in cache... Fetch remote data.
const r = getPaletteColor(server, instance, '00281201', lutDescriptor);
const g = getPaletteColor(server, instance, '00281202', lutDescriptor);
const b = getPaletteColor(server, instance, '00281203', lutDescriptor);
const promises = [r, g, b];
Promise.all(promises).then(args => {
entry = {
red: args[0],
green: args[1],
blue: args[2],
};
// when paletteUID is present, the entry can be cached...
entry.uid = paletteUID;
paletteColorCache.add(entry);
resolve(entry);
});
});
}
/**
* Add a list of SOP Instances to a given study object descriptor
* @param {Object} server Object with server configuration parameters
* @param {Object} study The study descriptor to which the given SOP instances will be added
* @param {Array} sopInstanceList A list of SOP instance objects
*/
async function addInstancesToStudy(server, study, sopInstanceList) {
return Promise.all(
sopInstanceList.map(function(sopInstance) {
return makeSOPInstance(server, study, sopInstance);
})
);
}
const createStudyFromSOPInstanceList = async (server, sopInstanceList) => {
if (Array.isArray(sopInstanceList) && sopInstanceList.length > 0) {
const firstSopInstance = sopInstanceList[0];
const study = createStudy(server, firstSopInstance);
await addInstancesToStudy(server, study, sopInstanceList);
return study;
}
throw new Error('Failed to create study out of provided SOP instance list');
};
export { createStudyFromSOPInstanceList, addInstancesToStudy };

8
platform/viewer/CHANGELOG.md
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@ -3,6 +3,14 @@
All notable changes to this project will be documented in this file. All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines. See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [3.3.5](https://github.com/OHIF/Viewers/compare/@ohif/viewer@3.3.4...@ohif/viewer@3.3.5) (2020-01-06)
**Note:** Version bump only for package @ohif/viewer
## [3.3.4](https://github.com/OHIF/Viewers/compare/@ohif/viewer@3.3.3...@ohif/viewer@3.3.4) (2019-12-30) ## [3.3.4](https://github.com/OHIF/Viewers/compare/@ohif/viewer@3.3.3...@ohif/viewer@3.3.4) (2019-12-30)
**Note:** Version bump only for package @ohif/viewer **Note:** Version bump only for package @ohif/viewer

6
platform/viewer/package.json
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@ -1,6 +1,6 @@
{ {
"name": "@ohif/viewer", "name": "@ohif/viewer",
"version": "3.3.4", "version": "3.3.5",
"description": "OHIF Viewer", "description": "OHIF Viewer",
"author": "OHIF Contributors", "author": "OHIF Contributors",
"license": "MIT", "license": "MIT",
@ -45,12 +45,12 @@
}, },
"dependencies": { "dependencies": {
"@babel/runtime": "^7.5.5", "@babel/runtime": "^7.5.5",
"@ohif/core": "^2.3.1", "@ohif/core": "^2.3.2",
"@ohif/extension-cornerstone": "^2.2.1", "@ohif/extension-cornerstone": "^2.2.1",
"@ohif/extension-dicom-html": "^1.1.0", "@ohif/extension-dicom-html": "^1.1.0",
"@ohif/extension-dicom-microscopy": "^0.50.6", "@ohif/extension-dicom-microscopy": "^0.50.6",
"@ohif/extension-dicom-pdf": "^1.0.1", "@ohif/extension-dicom-pdf": "^1.0.1",
"@ohif/extension-vtk": "^1.2.4", "@ohif/extension-vtk": "^1.2.5",
"@ohif/i18n": "^0.52.4", "@ohif/i18n": "^0.52.4",
"@ohif/ui": "^1.1.7", "@ohif/ui": "^1.1.7",
"@tanem/react-nprogress": "^1.1.25", "@tanem/react-nprogress": "^1.1.25",