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Update CornerstoneWADOImageLoader to 0.9.0, tried to get DIMSE + WADO-URI working

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This commit is contained in:
Erik Ziegler 2016-02-09 13:19:11 +01:00
parent da5e752097
commit 8297171f4a
9 changed files with 103 additions and 66 deletions
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2
LesionTracker/defaultSettings.js
View File

@ -1,5 +1,5 @@
Meteor.startup(function() {
if (Meteor.settings) {
if (Object.keys(Meteor.settings).length > 1) {
console.log('Using custom LesionTracker settings');
console.log(Meteor.settings);
return;

2
OHIFViewer/defaultSettings.js
View File

@ -1,5 +1,5 @@
Meteor.startup(function() {
if (Meteor.settings) {
if (Object.keys(Meteor.settings).length > 1) {
console.log('Using custom LesionTracker settings: ');
console.log(Meteor.settings);
return;

126
Packages/cornerstone/client/cornerstoneWADOImageLoader.js
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@ -1,4 +1,4 @@
/*! cornerstone-wado-image-loader - v0.8.1 - 2016-02-07 | (c) 2014 Chris Hafey | https://github.com/chafey/cornerstoneWADOImageLoader */
/*! cornerstone-wado-image-loader - v0.9.0 - 2016-02-08 | (c) 2014 Chris Hafey | https://github.com/chafey/cornerstoneWADOImageLoader */
//
// This is a cornerstone image loader for WADO-URI requests. It has limited support for compressed
// transfer syntaxes, check here to see what is currently supported:
@ -85,10 +85,10 @@ if(typeof cornerstoneWADOImageLoader === 'undefined'){
throw "no color space conversion for photometric interpretation " + photometricInterpretation;
}
deferred.resolve(imageData);
return deferred;
return deferred.promise();
} catch (error) {
deferred.reject(error);
return deferred;
return deferred.promise();
}
}
@ -380,7 +380,7 @@ if(typeof cornerstoneWADOImageLoader === 'undefined'){
}
};
return deferred;
return deferred.promise();
}
function isJPEGBaseline8Bit(dataSet) {
@ -550,6 +550,11 @@ if(typeof cornerstoneWADOImageLoader === 'undefined'){
else if( transferSyntax === "1.2.840.10008.1.2.1") {
return cornerstoneWADOImageLoader.extractUncompressedPixels(dataSet, frame);
}
// Explicit VR Big Endian (retired)
else if ( transferSyntax === "1.2.840.10008.1.2.2" )
{
return cornerstoneWADOImageLoader.extractUncompressedPixels(dataSet, frame, true);
}
// JPEG 2000 Lossless
else if(transferSyntax === "1.2.840.10008.1.2.4.90")
{
@ -599,6 +604,9 @@ if(typeof cornerstoneWADOImageLoader === 'undefined'){
}
else
{
if(console && console.log) {
console.log("Image cannot be decoded due to Unsupported transfer syntax " + transferSyntax);
}
throw "no decoder for transfer syntax " + transferSyntax;
}
}
@ -3288,17 +3296,37 @@ var JpegImage = (function jpegImage() {
(function ($, cornerstone, cornerstoneWADOImageLoader) {
"use strict";
function extractUncompressedPixels(dataSet, frame)
function swap16(val) {
return ((val & 0xFF) << 8)
| ((val >> 8) & 0xFF);
}
function extractUncompressedPixels(dataSet, frame, bigEndian)
{
var pixelFormat = cornerstoneWADOImageLoader.getPixelFormat(dataSet);
var imageFrame = getImageFrame(dataSet, frame, pixelFormat);
// byte swap 16 bit data if bigEndian
if(bigEndian && (pixelFormat === 2 || pixelFormat === 3)) {
for(var i=0; i < imageFrame.length; i++) {
imageFrame[i] = swap16(imageFrame[i]);
}
}
return imageFrame;
}
function getImageFrame(dataSet, frame, pixelFormat) {
// Note - we may want to sanity check the rows * columns * bitsAllocated * samplesPerPixel against the buffer size
var pixelDataElement = dataSet.elements.x7fe00010;
var height = dataSet.uint16('x00280010');
var width = dataSet.uint16('x00280011');
var samplesPerPixel = dataSet.uint16('x00280002');
var pixelDataOffset = pixelDataElement.dataOffset;
var numPixels = width * height * samplesPerPixel;
// Note - we may want to sanity check the rows * columns * bitsAllocated * samplesPerPixel against the buffer size
if (!numPixels) {
throw "Sanity check failed when calculating the number of pixels";
}
var frameOffset = 0;
if(pixelFormat === 1) {
frameOffset = pixelDataOffset + frame * numPixels;
@ -3307,11 +3335,13 @@ var JpegImage = (function jpegImage() {
else if(pixelFormat === 2) {
frameOffset = pixelDataOffset + frame * numPixels * 2;
return new Uint16Array(dataSet.byteArray.buffer, frameOffset, numPixels);
return imageFrame;
}
else if(pixelFormat === 3) {
frameOffset = pixelDataOffset + frame * numPixels * 2;
return new Int16Array(dataSet.byteArray.buffer, frameOffset, numPixels);
}
throw "Unknown pixel format";
}
cornerstoneWADOImageLoader.extractUncompressedPixels = extractUncompressedPixels;
@ -3373,26 +3403,28 @@ var JpegImage = (function jpegImage() {
"use strict";
function getPixelSpacing(dataSet)
{
// NOTE - these are not required for all SOP Classes
// so we return them as undefined. We also do not
// deal with the complexity associated with projection
// radiographs here and leave that to a higher layer
var pixelSpacing = dataSet.string('x00280030');
if(pixelSpacing && pixelSpacing.length > 0) {
var split = pixelSpacing.split('\\');
return {
row: parseFloat(split[0]),
column: parseFloat(split[1])
};
}
else {
return {
row: undefined,
column: undefined
};
function getPixelSpacing(dataSet) {
// NOTE - these are not required for all SOP Classes
// so we return them as undefined. We also do not
// deal with the complexity associated with projection
// radiographs here and leave that to a higher layer
var pixelSpacing = dataSet.string('x00280030');
if (pixelSpacing && pixelSpacing.length > 0) {
var split = pixelSpacing.split('\\');
// Make sure that neither pixel spacing value is 0 or undefined
if (parseFloat(split[0]) && parseFloat(split[1])) {
return {
row: parseFloat(split[0]),
column: parseFloat(split[1])
};
}
}
return {
row: undefined,
column: undefined
};
}
// module exports
cornerstoneWADOImageLoader.getPixelSpacing = getPixelSpacing;
@ -3411,8 +3443,8 @@ var JpegImage = (function jpegImage() {
};
if(dataSet.elements.x00281052 && dataSet.elements.x00281053) {
result.intercept = dataSet.floatString('x00281052');
result.slope = dataSet.floatString('x00281053');
result.intercept = dataSet.floatString('x00281052') || result.intercept;
result.slope = dataSet.floatString('x00281053') || result.slope;
}
return result;
@ -3480,14 +3512,14 @@ var JpegImage = (function jpegImage() {
}, function(error) {
deferred.reject(error);
});
return deferred;
return deferred.promise();
}
var fileIndex = parseInt(url);
var file = cornerstoneWADOImageLoader.fileManager.get(fileIndex);
if(file === undefined) {
deferred.reject('unknown file index ' + url);
return deferred;
return deferred.promise();
}
@ -3508,19 +3540,19 @@ var JpegImage = (function jpegImage() {
}, function(error) {
deferred.reject(error);
});
return deferred;
return deferred.promise();
}
var imagePromise = cornerstoneWADOImageLoader.createImageObject(dataSet, imageId, frame);
imagePromise.then(function(image) {
deferred.resolve(image);
}, function() {
deferred.reject();
}, function(error) {
deferred.reject(error);
});
};
fileReader.readAsArrayBuffer(file);
return deferred;
return deferred.promise();
}
// registery dicomweb and wadouri image loader prefixes
@ -3697,7 +3729,7 @@ var JpegImage = (function jpegImage() {
};
xhr.send();
return deferred;
return deferred.promise();
};
}(cornerstoneWADOImageLoader));
/**
@ -3746,7 +3778,7 @@ var JpegImage = (function jpegImage() {
var image = cornerstoneWADOImageLoader.imageManager.get(index);
if(image === undefined) {
deferred.reject('unknown imageId');
return deferred;
return deferred.promise();
}
var mediaType;// = 'image/dicom+jp2';
@ -3781,7 +3813,7 @@ var JpegImage = (function jpegImage() {
deferred.reject(reason);
});
return deferred;
return deferred.promise();
}
// registery dicomweb and wadouri image loader prefixes
@ -4044,7 +4076,7 @@ var JpegImage = (function jpegImage() {
}
catch(err) {
deferred.reject(err);
return deferred;
return deferred.promise();
}
imageDataPromise.then(function(imageData) {
@ -4095,7 +4127,8 @@ var JpegImage = (function jpegImage() {
sharedCacheKey: sharedCacheKey
};
if(image.windowCenter === undefined) {
if(image.windowCenter === undefined || isNaN(image.windowCenter) ||
image.windowWidth === undefined || isNaN(image.windowWidth)) {
image.windowWidth = 255;
image.windowCenter = 128;
}
@ -4104,7 +4137,7 @@ var JpegImage = (function jpegImage() {
deferred.reject(error);
});
return deferred;
return deferred.promise();
}
// module exports
@ -4171,7 +4204,7 @@ var JpegImage = (function jpegImage() {
bytesPerPixel = getBytesPerPixel(dataSet);
} catch(error) {
deferred.reject(error);
return deferred;
return deferred.promise();
}
var numPixels = rows * columns;
@ -4188,7 +4221,7 @@ var JpegImage = (function jpegImage() {
}
catch(err) {
deferred.reject(err);
return deferred;
return deferred.promise();
}
var minMax = cornerstoneWADOImageLoader.getMinMax(storedPixelData);
@ -4241,7 +4274,8 @@ var JpegImage = (function jpegImage() {
// TODO: deal with pixel padding and all of the various issues by setting it to min pixel value (or lower)
// TODO: Mask out overlays embedded in pixel data above high bit
if(image.windowCenter === undefined) {
if(image.windowCenter === undefined || isNaN(image.windowCenter) ||
image.windowWidth === undefined || isNaN(image.windowWidth)) {
var maxVoi = image.maxPixelValue * image.slope + image.intercept;
var minVoi = image.minPixelValue * image.slope + image.intercept;
image.windowWidth = maxVoi - minVoi;
@ -4249,7 +4283,7 @@ var JpegImage = (function jpegImage() {
}
deferred.resolve(image);
return deferred;
return deferred.promise();
}
// module exports
@ -4260,7 +4294,7 @@ var JpegImage = (function jpegImage() {
"use strict";
// module exports
cornerstoneWADOImageLoader.version = '0.8.1';
cornerstoneWADOImageLoader.version = '0.9.0';
}(cornerstoneWADOImageLoader));
(function ($, cornerstone, cornerstoneWADOImageLoader) {
@ -4316,7 +4350,7 @@ var JpegImage = (function jpegImage() {
xhr.send();
return deferred;
return deferred.promise();
}
cornerstoneWADOImageLoader.internal.xhrRequest = xhrRequest;

3
Packages/dimseservice/server/DIMSE.js
View File

@ -167,7 +167,7 @@ DIMSE.retrieveInstances = function(studyInstanceUID, seriesInstanceUID, params)
0x0008103E: '',
0x00200011: '',
0x00080016: '',
0x00080018: '',
0x00080018: '', // sopInstanceUid. This is missing from the results?
0x00200013: '',
0x00280010: '',
0x00280011: '',
@ -181,6 +181,7 @@ DIMSE.retrieveInstances = function(studyInstanceUID, seriesInstanceUID, params)
var instances = [];
result.on('result', function(msg) {
console.log(msg);
instances.push(msg);
});

2
Packages/lesiontracker/client/components/studyDateList/studyDateList.js
View File

@ -17,7 +17,7 @@ Template.studyDateList.helpers({
patientId: currentStudyInBrowser.patientId
}, {
sort: {
studyDate: 1
studyDate: -1
}
});

13
Packages/viewerbase/server/methods/getStudyMetadata.js
View File

@ -10,10 +10,13 @@ Meteor.methods({
throw 'No properly configured server was available over DICOMWeb';
}
// Get the server data. This is user-defined in the
// config.json files used to run the Meteor server
var server = Meteor.settings.dicomWeb.endpoints[0];
return Services.WADO.RetrieveMetadata(server, studyInstanceUid);
if (Meteor.settings.dicomWeb && Meteor.settings.defaultServiceType === 'dicomWeb') {
// Get the server data. This is user-defined in the
// config.json files used to run the Meteor server
var server = Meteor.settings.dicomWeb.endpoints[0];
return Services.WADO.RetrieveMetadata(server, studyInstanceUid);
} else if (Meteor.settings.dimse && Meteor.settings.defaultServiceType === 'dimse') {
return Services.DIMSE.RetrieveMetadata(studyInstanceUid);
}
}
});

2
Packages/viewerbase/server/services/dimse/instances.js
View File

@ -37,7 +37,7 @@ function resultDataToStudyMetadata(resultData) {
var serverRoot = host + ':' + port;
log.info('INSTANCE');
log.info(instance);
//log.info(instance);
var sopInstanceUid = instance[0x00080018];
var uri = serverRoot + '/studies/' + studyInstanceUid + '/series/' + seriesInstanceUid + '/instances/' + sopInstanceUid + '/frames/1';

17
Packages/viewerbase/server/services/dimse/retrieveMetadata.js
View File

@ -26,6 +26,7 @@ function getSourceImageInstanceUid(instance) {
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
*/
function resultDataToStudyMetadata(studyInstanceUid, resultData) {
console.log('resultDataToStudyMetadata');
var seriesMap = {};
var seriesList = [];
@ -69,7 +70,8 @@ function resultDataToStudyMetadata(studyInstanceUid, resultData) {
var sopInstanceUid = instance[0x00080018];
log.info('instance');
log.info(instance);
//console.log('instance');
//console.log(instance);
var instanceSummary = {
imageType: instance[0x00080008],
sopClassUid: instance[0x00080016],
@ -99,12 +101,9 @@ function resultDataToStudyMetadata(studyInstanceUid, resultData) {
frameRate: parseFloat(instance[0x00181063])
};
var host = Meteor.settings.dimse.host,
port = Meteor.settings.dimse.port;
var serverRoot = host + ':' + port;
instanceSummary.wadorsuri = serverRoot + '/studies/' + studyInstanceUid + '/series/' + seriesInstanceUid + '/instances/' + sopInstanceUid + '/frames/1';
// Retrieve the actual data over WADO-URI
var server = Meteor.settings.dicomWeb.endpoints[0];
instanceSummary.wadouri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + "&contentType=application%2Fdicom";
series.instances.push(instanceSummary);
});
@ -156,7 +155,7 @@ Services.DIMSE.RetrieveMetadata = function(studyInstanceUid) {
study.studyInstanceUid = studyInstanceUid;
console.log(study);
console.log(study.seriesList[0].instances[0]);
//console.log(study);
//console.log(study.seriesList[0].instances[0]);
return study;
};

2
config/dockerDCM4CHE.json
View File

@ -6,7 +6,7 @@
"wadoUriRootNOTE" : "either this uri is not correct for wado-uri or wado-uri is not configured on orthanc currently",
"wadoUriRoot" : "http://192.168.99.100:8080/dcm4chee-arc/aets/DCM4CHEE/wado",
"qidoRoot": "http://192.168.99.100:8080/dcm4chee-arc/aets/DCM4CHEE/rs",
"wadoRoot": "http://192.168.99.100:8080/dcm4chee-arc/aets/DCM4CHEE/wado",
"wadoRoot": "http://192.168.99.100:8080/dcm4chee-arc/aets/DCM4CHEE/rs/wado/DCM4CHEE",
"qidoSupportsIncludeField": true,
"imageRendering" : "wadouri",
"requestOptions" : {