ohif-viewer/Packages/hangingprotocols/client/protocolEngine.js
2016-07-22 11:03:01 +02:00

686 lines
24 KiB
JavaScript

// Define a global variable that will be used to refer to the Protocol Engine
// It must be populated by HP.setEngine when the Viewer is initialized and a ProtocolEngine
// is instantiated on top of the LayoutManager. If the global ProtocolEngine variable remains
// undefined, none of the HangingProtocol functions will operate.
ProtocolEngine = undefined;
/**
* Sets the ProtocolEngine global given an instantiated ProtocolEngine. This is done so that
* The functions in the package can depend on a ProtocolEngine variable, but this variable does
* not have to be exported from the application level.
*
* (There may be a better way to do this, but for now this works with no real downside)
*
* @param protocolEngine An instantiated ProtocolEngine linked to a LayoutManager from the
* Viewerbase package
*/
HP.setEngine = function(protocolEngine) {
ProtocolEngine = protocolEngine;
};
// Define an empty object to store callbacks that are used to retrieve custom attributes
// The simplest example for a custom attribute is the Timepoint type (i.e. baseline or follow-up)
// used in the LesionTracker application.
//
// Timepoint type can be obtained given a studyId, and this is done through a custom callback.
// Developers can define attributes (i.e. attributeId = timepointType) with a name ('Timepoint Type')
// and a callback function that is used to calculate them.
//
// The input to the callback, which is called during viewport-image matching rule evaluation
// is the set of attributes that contains the specified attribute. In our example, timepointType is
// linked to the study attributes, and so the inputs to the callback is an object containing
// the study attributes.
HP.CustomAttributeRetrievalCallbacks = {};
/**
* Adds a custom attribute to be used in the HangingProtocol UI and matching rules, including a
* callback that will be used to calculate the attribute value.
*
* @param attributeId The ID used to refer to the attribute (e.g. 'timepointType')
* @param attributeName The name of the attribute to be displayed (e.g. 'Timepoint Type')
* @param callback The function used to calculate the attribute value from the other attributes at its level (e.g. study/series/image)
*/
HP.addCustomAttribute = function(attributeId, attributeName, callback) {
HP.CustomAttributeRetrievalCallbacks[attributeId] = {
name: attributeName,
callback: callback
};
};
// Define an empty object to store callbacks that are used to apply custom viewport settings
// after a viewport is rendered.
HP.CustomViewportSettings = {};
/**
* Adds a custom setting that can be chosen in the HangingProtocol UI and applied to a Viewport
*
* @param settingId The ID used to refer to the setting (e.g. 'displayCADMarkers')
* @param settingName The name of the setting to be displayed (e.g. 'Display CAD Markers')
* @param options
* @param callback A function to be run after a viewport is rendered with a series
*/
HP.addCustomViewportSetting = function(settingId, settingName, options, callback) {
HP.CustomViewportSettings[settingId] = {
id: settingId,
text: settingName,
options: options,
callback: callback
};
};
Meteor.startup(function() {
HP.addCustomViewportSetting('wlPreset', 'Window/Level Preset', Object.keys(OHIF.viewer.wlPresets), function(element, optionValue) {
if (OHIF.viewer.wlPresets.hasOwnProperty(optionValue)) {
applyWLPreset(optionValue, element);
}
});
});
// Log decisions regarding matching
HP.match = function(attributes, rules) {
var options = {
format: 'grouped'
};
var score = 0;
var details = {
passed: [],
failed: []
};
var requiredFailed = false;
rules.forEach(rule => {
var attribute = rule.attribute;
// If the attributes we are testing (e.g. study, series, or instance attributes) do
// not contain the attribute specified in the rule, check whether or not they have been
// defined in the CustomAttributeRetrievalCallbacks Object.
// TODO: Investigate why attributes.hasOwnProperty(attribute) doesn't work?
if (attributes[attribute] === undefined &&
HP.CustomAttributeRetrievalCallbacks.hasOwnProperty(attribute)) {
var customAttribute = HP.CustomAttributeRetrievalCallbacks[attribute];
attributes[attribute] = customAttribute.callback(attributes);
}
// Format the constraint as required by Validate.js
var testConstraint = {};
testConstraint[attribute] = rule.constraint;
// Use Validate.js to evaluate the constraints on the specified attributes
var errorMessages = validate(attributes, testConstraint, [options]);
if (!errorMessages) {
// If no errorMessages were returned, then validation passed.
// Add the rule's weight to the total score
score += rule.weight;
// Log that this rule passed in the matching details object
details.passed.push({
rule: rule
});
} else {
// If errorMessages were present, then validation failed
// If the rule that failed validation was Required, then
// mark that a required Rule has failed
if (rule.required) {
requiredFailed = true;
}
// Log that this rule failed in the matching details object
// and include any error messages
details.failed.push({
rule: rule,
errorMessages: errorMessages
});
}
});
// If a required Rule has failed Validation, set the matching score to zero
if (requiredFailed) {
score = 0;
}
return {
score: score,
details: details
};
};
var sortByScore = function(arr) {
arr.sort(function(a, b) {
return b.score - a.score;
});
};
HP.ProtocolEngine = class ProtocolEngine {
constructor(LayoutManager, studies) {
this.LayoutManager = LayoutManager;
this.studies = studies;
this.reset();
// Create an array for new stage ids to be stored
// while editing a stage
this.newStageIds = [];
}
/**
* Resets the ProtocolEngine to the best match
*/
reset() {
var protocol = this.getBestMatch();
this.setHangingProtocol(protocol);
}
/**
* Retrieves the current Stage from the current Protocol and stage index
*
* @returns {*} The Stage model for the currently displayed Stage
*/
getCurrentStageModel() {
return this.protocol.stages[this.stage];
}
findMatchByStudy(study) {
var matched = [];
HangingProtocols.find().forEach(protocol => {
// Clone the protocol's protocolMatchingRules array
// We clone it so that we don't accidentally add the
// numberOfPriorsReferenced rule to the Protocol itself.
var rules = protocol.protocolMatchingRules.slice(0);
if (!rules) {
return;
}
study.numberOfPriorsReferenced = this.getNumberOfAvailablePriors(study);
var rule = new HP.ProtocolMatchingRule('numberOfPriorsReferenced', {
numericality: {
greaterThanOrEqualTo: protocol.numberOfPriorsReferenced
}
});
rules.push(rule);
var matchedDetails = HP.match(study, rules);
if (matchedDetails.score > 0) {
matched.push({
score: matchedDetails.score,
protocol: protocol
});
}
});
if (!matched.length) {
var defaultProtocol = HangingProtocols.findOne({
id: 'defaultProtocol'
});
return [{
score: 1,
protocol: defaultProtocol
}];
}
sortByScore(matched);
return matched;
}
/**
* Populates the MatchedProtocols Collection by running the matching procedure
*/
updateMatches() {
// Clear all data from the MatchedProtocols Collection
MatchedProtocols.remove({});
// For each study, find the matching protocols
this.studies.forEach(study => {
var matched = this.findMatchByStudy(study);
// For each matched protocol, check if it is already in MatchedProtocols
matched.forEach(function(matchedDetail) {
var protocol = matchedDetail.protocol;
var protocolInCollection = MatchedProtocols.findOne({
id: protocol.id
});
// If it is not already in the MatchedProtocols Collection, insert it
if (!protocolInCollection) {
MatchedProtocols.insert(protocol);
}
});
});
}
/**
* Return the best matched Protocol to the current study or set of studies
* @returns {*}
*/
getBestMatch() {
// Run the matching to populate the MatchedProtocols Collection
this.updateMatches();
// Retrieve the highest scoring Protocol
var sorted = MatchedProtocols.find({}, {
sort: {
score: -1
},
limit: 1
}).fetch();
// Return the highest scoring Protocol
return sorted[0];
}
/**
* Calculates the number of previous studies in the cached Worklist that
* have the same patientId and an earlier study date
*
* @param study The input study
* @returns {any|*} The number of available prior studies with the same patientId
*/
getNumberOfAvailablePriors(study) {
var studies = WorklistStudies.find({
patientId: study.patientId,
studyDate: {
$lt: study.studyDate
}
});
return studies.count();
}
findRelatedStudies(protocol, study) {
if (!protocol.protocolMatchingRules) {
return;
}
var studies = WorklistStudies.find({
patientId: study.patientId,
studyDate: {
$lt: study.studyDate
}
}, {
sort: {
studyDate: -1
}
});
var related = [];
var currentDate = moment(study.studyDate, 'YYYYMMDD');
studies.forEach(function(priorStudy, priorIndex) {
// Calculate an abstract prior value for the study in question
if (priorIndex === (studies.length - 1)) {
priorStudy.abstractPriorValue = -1;
} else {
// Abstract prior index starts from 1 in the DICOM standard
priorStudy.abstractPriorValue = priorIndex + 1;
}
// Calculate the relative time using Moment.js
var priorDate = moment(priorStudy.studyDate, 'YYYYMMDD');
priorStudy.relativeTime = currentDate.diff(priorDate);
var details = HP.match(priorStudy, protocol.protocolMatchingRules);
if (details.score) {
related.push({
score: details.score,
study: priorStudy
});
}
});
sortByScore(related);
return related.map(function(v) {
return v.study;
});
}
// Match images given a list of Studies and a Viewport's image matching reqs
matchImages(viewport) {
var studyMatchingRules = viewport.studyMatchingRules;
var seriesMatchingRules = viewport.seriesMatchingRules;
var instanceMatchingRules = viewport.imageMatchingRules;
var highestStudyMatchingScore = 0;
var highestSeriesMatchingScore = 0;
var highestImageMatchingScore = 0;
var matchingScores = [];
var bestMatch;
var currentStudy = this.studies[0];
currentStudy.abstractPriorValue = 0;
studyMatchingRules.forEach(rule => {
if (rule.attribute === 'abstractPriorValue') {
var validatorType = Object.keys(rule.constraint)[0];
var validator = Object.keys(rule.constraint[validatorType])[0];
var abstractPriorValue = rule.constraint[validatorType][validator];
abstractPriorValue = parseInt(abstractPriorValue, 10);
// TODO: Restrict or clarify validators for abstractPriorValue?
var studies = WorklistStudies.find({
patientId: currentStudy.patientId,
studyDate: {
$lt: currentStudy.studyDate
}
}, {
sort: {
studyDate: -1
}
}).fetch();
// TODO: Revisit this later: What about two studies with the same
// study date?
var priorStudy;
if (abstractPriorValue === -1) {
priorStudy = studies[studies.length - 1];
} else {
var studyIndex = Math.max(abstractPriorValue - 1, 0);
priorStudy = studies[studyIndex];
}
if (!priorStudy) {
return;
}
var alreadyLoaded = ViewerStudies.findOne({
studyInstanceUid: priorStudy.studyInstanceUid
});
if (!alreadyLoaded) {
getStudyMetadata(priorStudy.studyInstanceUid, study => {
study.abstractPriorValue = abstractPriorValue;
ViewerStudies.insert(study);
this.studies.push(study);
this.matchImages(viewport);
this.updateViewports();
});
}
}
// TODO: Add relative Date / time
});
var lastStudyIndex = this.studies.length - 1;
this.studies.forEach(function(study) {
var studyMatchDetails = HP.match(study, studyMatchingRules);
if ((studyMatchingRules.length && !studyMatchDetails.score) ||
studyMatchDetails.score < highestStudyMatchingScore) {
return;
}
highestStudyMatchingScore = studyMatchDetails.score;
study.seriesList.forEach(function(series) {
var seriesMatchDetails = HP.match(series, seriesMatchingRules);
if ((seriesMatchingRules.length && !seriesMatchDetails.score) ||
seriesMatchDetails.score < highestSeriesMatchingScore) {
return;
}
highestSeriesMatchingScore = seriesMatchDetails.score;
series.instances.forEach(function(instance, index) {
// This tests to make sure there is actually image data in this instance
// TODO: Change this when we add PDF and MPEG support
// See https://ohiforg.atlassian.net/browse/LT-227
if (!instance.rows || !instance.columns) {
return;
}
var instanceMatchDetails = HP.match(instance, instanceMatchingRules);
var matchDetails = {
passed: [],
failed: []
};
matchDetails.passed = matchDetails.passed.concat(instanceMatchDetails.details.passed);
matchDetails.passed = matchDetails.passed.concat(seriesMatchDetails.details.passed);
matchDetails.passed = matchDetails.passed.concat(studyMatchDetails.details.passed);
matchDetails.failed = matchDetails.failed.concat(instanceMatchDetails.details.failed);
matchDetails.failed = matchDetails.failed.concat(seriesMatchDetails.details.failed);
matchDetails.failed = matchDetails.failed.concat(studyMatchDetails.details.failed);
var totalMatchScore = instanceMatchDetails.score + seriesMatchDetails.score + studyMatchDetails.score;
var imageDetails = {
studyInstanceUid: study.studyInstanceUid,
seriesInstanceUid: series.seriesInstanceUid,
sopInstanceUid: instance.sopInstanceUid,
currentImageIdIndex: index,
matchingScore: totalMatchScore,
matchDetails: matchDetails
};
if ((totalMatchScore > highestImageMatchingScore) || !bestMatch) {
highestImageMatchingScore = totalMatchScore;
bestMatch = imageDetails;
}
matchingScores.push(imageDetails);
});
});
});
return {
bestMatch: bestMatch,
matchingScores: matchingScores
};
}
/**
* Rerenders viewports that are part of the current ProtocolEngine's LayoutManager
* using the matching rules internal to each viewport.
*
* If this function is provided the index of a viewport, only the specified viewport
* is rerendered.
*
* @param viewportIndex
*/
updateViewports(viewportIndex) {
// Make sure we have an active protocol with a non-empty array of display sets
if (!this.protocol || !this.protocol.stages || !this.protocol.stages.length) {
return;
}
// Retrieve the current display set in the display set sequence
var stageModel = this.getCurrentStageModel();
// If the current display set does not fulfill the requirements to be displayed,
// stop here.
if (!stageModel ||
!stageModel.viewportStructure ||
!stageModel.viewports ||
!stageModel.viewports.length) {
return;
}
// Retrieve the layoutTemplate associated with the current display set's viewport structure
// If no such template name exists, stop here.
var layoutTemplateName = stageModel.viewportStructure.getLayoutTemplateName();
if (!layoutTemplateName) {
return;
}
// Retrieve the properties associated with the current display set's viewport structure template
// If no such layout properties exist, stop here.
var layoutProps = stageModel.viewportStructure.properties;
if (!layoutProps) {
return;
}
// Create an empty array to store the output viewportData
var viewportData = [];
// Empty the matchDetails associated with the ProtocolEngine.
// This will be used to store the pass/fail details and score
// for each of the viewport matching procedures
this.matchDetails = [];
// Loop through each viewport
stageModel.viewports.forEach((viewport, viewportIndex) => {
var details = this.matchImages(viewport);
this.matchDetails[viewportIndex] = details;
// Convert any YES/NO values into true/false for Cornerstone
var cornerstoneViewportParams = {};
Object.keys(viewport.viewportSettings).forEach(function(key) {
var value = viewport.viewportSettings[key];
if (value === 'YES') {
value = true;
} else if (value === 'NO') {
value = false;
}
cornerstoneViewportParams[key] = value;
});
// imageViewerViewports occasionally needs relevant layout data in order to set
// the element style of the viewport in question
var currentViewportData = $.extend({
viewportIndex: viewportIndex,
viewport: cornerstoneViewportParams
}, layoutProps);
var customSettings = [];
Object.keys(viewport.viewportSettings).forEach(id => {
var setting = HP.CustomViewportSettings[id];
if (!setting) {
return;
}
customSettings.push({
id: id,
value: viewport.viewportSettings[id]
});
});
currentViewportData.renderedCallback = function(element) {
console.log('renderedCallback for ' + element.id);
customSettings.forEach(function(customSetting) {
console.log('Applying custom setting: ' + customSetting.id);
console.log('with value: ' + customSetting.value);
var setting = HP.CustomViewportSettings[customSetting.id];
setting.callback(element, customSetting.value);
});
};
if (details.bestMatch) {
currentViewportData.studyInstanceUid = details.bestMatch.studyInstanceUid;
currentViewportData.seriesInstanceUid = details.bestMatch.seriesInstanceUid;
currentViewportData.sopInstanceUid = details.bestMatch.sopInstanceUid;
currentViewportData.currentImageIdIndex = details.bestMatch.currentImageIdIndex;
}
viewportData.push(currentViewportData);
});
this.LayoutManager.layoutTemplateName = layoutTemplateName;
this.LayoutManager.layoutProps = layoutProps;
this.LayoutManager.viewportData = viewportData;
if (viewportIndex !== undefined && viewportData[viewportIndex]) {
this.LayoutManager.rerenderViewportWithNewSeries(viewportIndex, viewportData[viewportIndex]);
} else {
this.LayoutManager.updateViewports();
}
}
/**
* Sets the current Hanging Protocol to the specified Protocol
* An optional argument can also be used to prevent the updating of the Viewports
*
* @param newProtocol
* @param updateViewports
*/
setHangingProtocol(newProtocol, updateViewports=true) {
// Reset the array of newStageIds
this.newStageIds = [];
if (HP.Protocol.prototype.isPrototypeOf(newProtocol)) {
this.protocol = newProtocol;
} else {
this.protocol = new HP.Protocol();
this.protocol.fromObject(newProtocol);
}
this.stage = 0;
// Update viewports by default
if (updateViewports) {
this.updateViewports();
}
MatchedProtocols.update({}, {
$set: {
selected: false
}
}, {
multi: true
});
MatchedProtocols.update({
id: this.protocol.id
}, {
$set: {
selected: true
}
});
}
/**
* Changes the current stage to a new stage index in the display set sequence
*
* @param stage An integer value specifying the index of the desired Stage
*/
setCurrentProtocolStage(stage) {
if (!this.protocol || !this.protocol.stages || !this.protocol.stages.length) {
return;
}
if (stage >= this.protocol.stages.length) {
return;
}
this.stage = stage;
this.updateViewports();
}
/**
* Retrieves the number of Stages in the current Protocol
*/
getNumProtocolStages() {
if (!this.protocol || !this.protocol.stages || !this.protocol.stages.length) {
return;
}
return this.protocol.stages.length;
}
/**
* Switches to the next protocol stage in the display set sequence
*/
nextProtocolStage() {
this.setCurrentProtocolStage(++this.stage);
}
/**
* Switches to the previous protocol stage in the display set sequence
*/
previousProtocolStage() {
this.setCurrentProtocolStage(--this.stage);
}
};