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First pass at a Hanging Protocol implementation and editor (LT-131)

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Erik Ziegler committed 2016-05-07 12:40:02 +02:00
1 parent dfcb33153f
commit 2e52d9e3c1
157 files changed
+8869 -23585
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Packages/hangingprotocols/server/collections.js
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Meteor.publish('hangingprotocols', function() {
// TODO: filter by availableTo user
return HangingProtocols.find();
});
Meteor.startup(function() {
// Uncomment this next line to reset all your Protocols on every server reset
// HangingProtocols.remove({});
if (HangingProtocols.find().count() === 0) {
console.log('Inserting default protocols');
HangingProtocols.insert(HP.defaultProtocol);
HangingProtocols.insert(HP.testProtocol);
}
});
Packages/hangingprotocols/server/dataDictionary.js
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Packages/hangingprotocols/server/dataSetToJsWithDictionary.js
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/**
* converts an implicit dataSet to a javascript object with the help of a data dictionary
*
* @param dataSet
* @param options
*/
dataSetToJsWithDictionary = function(dataSet, dictionary, options) {
if (!dataSet) {
throw 'dataSetToJsWithDictionary: missing required parameter dataSet';
}
options = options || {
omitPrivateAttibutes: true, // true if private elements should be omitted
maxElementLength: 128 // maximum element length to try and convert to string format
};
// For the purpose of inserting a comma into the tag in order
// to search the dictionary, store a position value
var position = 3;
var result = {};
for (var tag in dataSet.elements) {
var element = dataSet.elements[tag];
// Reformat the tag from x00020010 to "0002,0010" to suit the dictionary
var tagFormatted = tagFormatted.substr(1, position) + ',' + tagFormatted.substr(position);
// Retrieve the tag dictionary entry
var tagDictionaryEntry = dictionary[tagFormatted];
// If there is no tag dictionary entry, or no name
// for this tag, just use the original tag instead
var tagName;
if (!tagDictionaryEntry || !tagDictionaryEntry.name) {
tagName = tag;
} else {
tagName = tagDictionaryEntry.name;
}
// Set the element VR from the dictionary, if necessary and possible
if (!element.vr && tagDictionaryEntry && tagDictionaryEntry.vr) {
element.vr = tagDictionaryEntry.vr;
}
// skip this element if it a private element and our options specify that we should
if (options.omitPrivateAttibutes === true && dicomParser.isPrivateTag(tag)) {
continue;
}
if (element.items) {
// handle sequences
var sequenceItems = [];
for (var i = 0; i < element.items.length; i++) {
sequenceItems.push(dicomParser.dataSetToJsWithDictionary(element.items[i].dataSet, dictionary, options));
}
result[tagName] = sequenceItems;
} else {
var asString;
if (element.length < options.maxElementLength) {
asString = dicomParser.explicitElementToString(dataSet, element);
}
if (asString !== undefined) {
result[tagName] = asString;
} else {
result[tagName] = {
dataOffset: element.dataOffset,
length: element.length
};
}
}
}
return result;
};
Packages/hangingprotocols/server/imageset.js
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DICOMHP.imageSet = function(setNumber, category) {
this.setNumber = setNumber;
this.category = category;
};
DICOMHP.imageSet.prototype.setRelativeTime = function(time) {
this.relativeTime = time;
};
DICOMHP.imageSet.prototype.setTimeUnits = function(units) {
this.timeUnits = units;
};
DICOMHP.imageSet.prototype.setPriorValue = function(priorValue) {
this.priorValue = priorValue;
};
DICOMHP.imageSet.prototype.retrieve = function(studyInstanceId) {
};
Packages/hangingprotocols/server/instanceDataToJsObject.js
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var valueRepresentationTypes = {
number: [
'SH',
'LO'
]
};
/**
* converts an WADO instance to a javascript object with the help of a data dictionary
*
* @param instance
* @param options
*/
instanceDataToJsObject = function(instance, dictionary) {
if (!instance) {
throw 'instanceDataToJsObject: missing required parameter dataSet';
}
var result = {};
// The comma is always inserted after the first four digits
var position = 4;
Object.keys(instance).forEach(function(tag) {
var item = instance[tag];
// Reformat the tag from 00020010 to "(0002,0010)" to suit the dictionary
var tagFormatted = '(' + tag.substr(0, position) + ',' + tag.substr(position) + ')';
// Retrieve the tag dictionary entry
var tagDictionaryEntry = dictionary[tagFormatted];
console.log(tagDictionaryEntry);
// If there is no tag dictionary entry, or no name
// for this tag, just use the original tag instead
var tagName;
if (!tagDictionaryEntry || !tagDictionaryEntry.name) {
tagName = tag;
} else {
tagName = tagDictionaryEntry.name;
}
if (item.Value && item.Value.length > 1) {
// handle sequences
var sequenceItems = [];
item.Value.forEach(function(instance) {
sequenceItems.push(instanceDataToJsObject(instance, dictionary));
});
result[tagName] = sequenceItems;
} else if (!item.Value || !item.Value.length) {
// Handle empty arrays
result[tagName] = undefined;
} else {
// Handle single valued cases
if (item.vr === 'PN') {
// Patient Name
result[tagName] = DICOMWeb.getName(item);
} else if (valueRepresentationTypes.number.indexOf(item.vr) > 0) {
// Number type
result[tagName] = DICOMWeb.getNumber(item);
} else {
// Everything else
result[tagName] = DICOMWeb.getString(item);
}
}
});
console.log(result);
return result;
};
Packages/hangingprotocols/server/match.js
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var tags = {
sopClassUid: '00080016'
};
var tagValues = {
HangingProtocolStorage: '1.2.840.10008.5.1.4.38.1'
};
/**
* Finds appropriate hanging protocols given a studyInstanceUid
*
* This function retrieves all hanging protocols in storage
* in order to find those that match the parameters of the given study
*
* @param studyInstanceUID
* @returns {Array} An array of matching hanging protocols
*/
DICOMHP.match = function(studyInstanceUID) {
// First, retrieve the metaData from the given study
var studyInstance = Services.WADO.retrieveMetadata(studyInstanceUID);
if (!studyInstance) {
return;
}
// Note: It turns out Orthanc doesn't support hanging protocol storage yet,
// so I will just stop here.
var studyData = instanceDataToJsObject(studyInstance, TAG_DICT);
/*var searchParameters = {
tags['sopClassUid']: tagValues['HangingProtocolStorage']
};
var modalities = studyData.ModalitiesInStudy;
var modalityMatch;
if (modalities) {
modalityMatch = [];
modalities.split('\\').forEach(function(modality){
if (modality && modality != 'SC') {
modalityMatch.push(modality);
}
});
}
var firstInstance = Services.WADO..retrieveMetadata(studyInstanceUID, null, null, {limit : 1}),
lateralityMatch;
if (firstInstance.length > 0) {
lateralityMatch = firstInstance[0]["00200060"].Value[0];
}
// since orthanc doesn't support sequence matching
var allProtocols = Services.WADO..searchForInstances(null, null, params);
if (allProtocols.length < 1) {
return [];
}
var matchedProtocols = [];
allProtocols.forEach(function(protocol) {
var definitionSequence = protocol["0072000C"].Value;
definitionSequence.forEach(function(definition){
var defModality = definition["00080060"].Value[0];
if (defModality && modalityMatch && modalityMatch.indexOf(defModality) != -1) {
matchedProtocols.push(protocol);
return;
}
var defLaterality = definition["00200060"].Value[0];
if (defLaterality && (defLaterality == lateralityMatch)) {
matchedProtocols.push(protocol);
}
});
});
return matchedProtocols;*/
};
Packages/hangingprotocols/server/methods.js
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/*DICOMTags = new Meteor.Collection(null);
Object.keys(HP.tagDescriptions).forEach(function(key) {
var value = HP.tagDescriptions[key];
DICOMTags.insert({
id: key,
name: '(' + key + ') ' + value
});
});
Meteor.methods({
dicomTagSearch: function(partialName) {
check(partialName, String);
var results = DICOMTags.find({
name: {
$regex: partialName,
$options: 'i'
}
}, {
limit: 20,
fields: {
id: 1,
name: 1
}
}).fetch();
return {
results: results
};
}
}); */
Meteor.methods({
removeHangingProtocol: function(id) {
HangingProtocols.remove(id);
},
removeHangingProtocolByID: function(id) {
HangingProtocols.remove({
id: id
});
}
});
Packages/hangingprotocols/server/namespace.js
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DICOMHP = {};
Packages/hangingprotocols/server/select.js
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DICOMHP.select = function(hpInstance) {
var imageSetsSequence = hpInstance['00720020'].Value;
if (!imageSetsSequence) {
return [];
}
var matchedImageSets = [];
imageSetsSequence.forEach(function(imageSet) {
var selectorSequence = imageSet['00720022'].Value;
selectorSequence.forEach(function(selector) {
var usageFlag = selector['00720024'].Value[0],
selectorAttribute = selector['00720026'].Value[0],
selectorAttributeVR = selector['00720050'].Value[0],
selectorAttributeValue = null;
if (selectorAttributeVR == 'SQ') {
return;
} else if (selectorAttributeVR == 'AT') {
selectorAttributeValue = selector['00720060'].Value[0];
} else if (selectorAttributeVR == 'CS') {
selectorAttributeValue = selector['00720062'].Value[0];
} else if (selectorAttributeVR == 'IS') {
selectorAttributeValue = selector['00720064'].Value[0];
} else if (selectorAttributeVR == 'LO') {
selectorAttributeValue = selector['00720066'].Value[0];
} else if (selectorAttributeVR == 'LT') {
selectorAttributeValue = selector['00720068'].Value[0];
} else if (selectorAttributeVR == 'PN') {
selectorAttributeValue = selector['0072006A'].Value[0];
} else if (selectorAttributeVR == 'SH') {
selectorAttributeValue = selector['0072006C'].Value[0];
} else if (selectorAttributeVR == 'ST') {
selectorAttributeValue = selector['0072006E'].Value[0];
} else if (selectorAttributeVR == 'UT') {
selectorAttributeValue = selector['00720070'].Value[0];
} else if (selectorAttributeVR == 'DS') {
selectorAttributeValue = selector['00720072'].Value[0];
} else if (selectorAttributeVR == 'FD') {
selectorAttributeValue = selector['00720074'].Value[0];
} else if (selectorAttributeVR == 'FL') {
selectorAttributeValue = selector['00720076'].Value[0];
} else if (selectorAttributeVR == 'UL') {
selectorAttributeValue = selector['00720078'].Value[0];
} else if (selectorAttributeVR == 'US') {
selectorAttributeValue = selector['0072007A'].Value[0];
} else if (selectorAttributeVR == 'SL') {
selectorAttributeValue = selector['0072007C'].Value[0];
} else if (selectorAttributeVR == 'SS') {
selectorAttributeValue = selector['0072007E'].Value[0];
}
if (selectorAttributeValue !== null) {
}
});
var timeBasedImageSetsSequence = imageSet['00720030'].Value;
timeBasedImageSetsSequence.forEach(function(timeImageSet) {
var setNumber = timeImageSet['00720032'].Value[0], selectorCategory = timeImageSet['00720034'].Value[0];
var mImageSet = new DICOMHP.imageSet(setNumber, selectorCategory);
if (selectorCategory == 'RELATIVE_TIME') {
var relativeTime = timeImageSet['00720038'].Value[0], timeUnits = timeImageSet['0072003A'].Value[0];
mImageSet.setRelativeTime(relativeTime);
mImageSet.setTimeUnits(timeUnits);
} else if (selectorCategory == 'ABSTRACT_PRIOR') {
var priorValue = timeImageSet['0072003C'].Value[0];
mImageSet.setPriorValue(priorValue);
}
matchedImageSets.push(mImageSet);
});
});
return matchedImageSets;
};