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

This commit is contained in:
Erik Ziegler committed 2016-05-07 12:40:02 +02:00
1 parent dfcb33153f
commit 2e52d9e3c1
157 files changed
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HangingProtocols = new Meteor.Collection('hangingprotocols');
HangingProtocols.allow({
insert: function() {
return true;
},
update: function() {
return true;
}
});
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HP.attributeDefaults = {
abstractPriorValue: 0
};
HP.displaySettings = {
invert: {
id: 'invert',
text: 'Show Grayscale Inverted',
defaultValue: 'NO',
options: ['YES', 'NO']
}
};
HP.studyAttributes = [{
id: 'patientId',
text: '(x00100020) Patient ID'
}, {
id: 'studyInstanceUid',
text: '(x0020000d) Study Instance UID'
}, {
id: 'studyInstanceUid',
text: '(x0020000d) Study Instance UID'
}, {
id: 'studyDate',
text: '(x00080020) Study Date'
}, {
id: 'studyTime',
text: '(x00080030) Study Time'
}, {
id: 'studyDescription',
text: '(x00081030) Study Description'
}, {
id: 'abstractPriorValue',
text: 'Abstract Prior Value'
}];
HP.protocolAttributes = [{
id: 'patientId',
text: '(x00100020) Patient ID'
}, {
id: 'studyInstanceUid',
text: '(x0020000d) Study Instance UID'
}, {
id: 'studyDate',
text: '(x00080020) Study Date'
}, {
id: 'studyTime',
text: '(x00080030) Study Time'
}, {
id: 'studyDescription',
text: '(x00081030) Study Description'
}, {
id: 'anatomicRegion',
text: 'Anatomic Region'
}];
HP.seriesAttributes = [{
id: 'seriesInstanceUid',
text: '(x0020000e) Series Instance UID'
}, {
id: 'modality',
text: '(x00080060) Modality'
}, {
id: 'seriesNumber',
text: '(x00080060) Series Number'
}, {
id: 'seriesDescription',
text: '(x0008103e) Series Description'
}, {
id: 'numImages',
text: 'Number of Images'
}];
HP.instanceAttributes = [{
id: 'sopClassUid',
text: 'SOP Class UID'
}, {
id: 'sopInstanceUid',
text: 'SOP Instance UID'
}, {
id: 'viewPosition',
text: 'View Position'
}, {
id: 'instanceNumber',
text: 'Instance Number'
}, {
id: 'imageType',
text: 'Image Type'
}, {
id: 'frameTime',
text: 'Frame Time'
}, {
id: 'laterality',
text: 'Laterality'
}, {
id: 'index',
text: 'Image Index'
}, {
id: 'photometricInterpretation',
text: 'Photometric Interpretation'
}, {
id: 'sliceThickness',
text: 'Slice Thickness'
}];
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HP = {};
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Router.route('/protocol-export/:_id', function() {
var protocolId = this.params._id;
var protocol = HangingProtocols.findOne({
id: protocolId
});
if (!protocol) {
this.response.writeHead(404);
// This will not actually respond with a 404 because of https://github.com/iron-meteor/iron-router/issues/1055
this.response.end();
return;
}
// Remove the MongoDB _id
delete protocol._id;
var protocolJSON = JSON.stringify(protocol, null, 2),
currentDate = new Date(),
filename = protocol.name + '-' + (currentDate.getTime().toString()) + '.json';
this.response.writeHead(200, {
'Content-Type': 'application/x-download',
'Content-Disposition': 'attachment; filename=' + filename,
'Content-Length': protocolJSON.length
});
this.response.end(protocolJSON);
}, {
where: 'server'
});
Router.route('/protocol-import', {
where: 'server'
}).post(function() {
try {
var toImport = JSON.parse(this.request.body.protocol);
HangingProtocols.insert(toImport);
this.response.writeHead(200);
this.response.end(toImport.id);
} catch(e) {
this.response.writeHead(500);
this.response.end('Failed to parse protocol JSON.');
}
});
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/**
* Removes the first instance of an element from an array, if an equal value exists
*
* @param array
* @param input
*
* @returns {boolean} Whether or not the element was found and removed
*/
function removeFromArray(array, input) {
// If the array is empty, stop here
if (!array ||
!array.length) {
return false;
}
array.forEach(function(value, index) {
if (_.isEqual(value, input)) {
indexToRemove = index;
return false;
}
});
if (indexToRemove === undefined) {
return false;
}
array.splice(indexToRemove, 1);
return true;
}
/**
* This class represents a Hanging Protocol at the highest level
*
* @type {Protocol}
*/
HP.Protocol = class Protocol {
/**
* The Constructor for the Class to create a Protocol with the bare
* minimum information
*
* @param name The desired name for the Protocol
*/
constructor(name) {
// Create a new UUID for this Protocol
this.id = uuid.new();
// Store a value which determines whether or not a Protocol is locked
// This is probably temporary, since we will eventually have role / user
// checks for editing. For now we just need it to prevent changes to the
// default protocols.
this.locked = false;
// Apply the desired name
this.name = name;
// Set the created and modified dates to Now
this.createdDate = new Date();
this.modifiedDate = new Date();
// If we are logged in while creating this Protocol,
// store this information as well
if (Meteor.users && Meteor.userId) {
this.createdBy = Meteor.userId;
this.modifiedBy = Meteor.userId;
}
// Create two empty Sets specifying which roles
// have read and write access to this Protocol
this.availableTo = new Set();
this.editableBy = new Set();
// Define empty arrays for the Protocol matching rules
// and Stages
this.protocolMatchingRules = [];
this.stages = [];
this.numberOfPriorsReferenced = 0;
}
updateNumberOfPriorsReferenced() {
var numPriorsReferenced = 0;
this.stages.forEach(function(stage) {
if (!stage.viewports) {
return;
}
stage.viewports.forEach(function(viewport) {
if (!viewport.studyMatchingRules) {
return;
}
viewport.studyMatchingRules.forEach(function(rule) {
if (rule.attribute === 'abstractPriorValue') {
// TODO: Double check here that the abstractPriorValue is not
// set as zero
numPriorsReferenced++;
} else if (rule.attribute === 'relativeTime') {
numPriorsReferenced++;
}
});
});
});
this.numberOfPriorsReferenced = numPriorsReferenced;
}
/**
* Method to update the modifiedDate when the Protocol
* has been changed
*/
protocolWasModified() {
// If we are logged in while modifying this Protocol,
// store this information as well
if (Meteor.users && Meteor.userId) {
this.modifiedBy = Meteor.userId;
}
this.updateNumberOfPriorsReferenced();
// Update the modifiedDate with the current Date/Time
this.modifiedDate = new Date();
}
/**
* Occasionally the Protocol class needs to be instantiated from a JavaScript Object
* containing the Protocol data. This function fills in a Protocol with the Object
* data.
*
* @param input A Protocol as a JavaScript Object, e.g. retrieved from MongoDB or JSON
*/
fromObject(input) {
// Check if the input already has an ID
// If so, keep it. It not, create a new UUID
this.id = input.id || uuid.new();
// Assign the input name to the Protocol
this.name = input.name;
// Retrieve locked status, use !! to make it truthy
// so that undefined values will be set to false
this.locked = !!input.locked;
// TODO: Check how to regenerate Set from Object
//this.availableTo = new Set(input.availableTo);
//this.editableBy = new Set(input.editableBy);
// If the input contains Protocol matching rules
if (input.protocolMatchingRules) {
input.protocolMatchingRules.forEach(ruleObject => {
// Create new Rules from the stored data
var rule = new HP.ProtocolMatchingRule();
rule.fromObject(ruleObject);
// Add them to the Protocol
this.protocolMatchingRules.push(rule);
});
}
// If the input contains data for various Stages in the
// display set sequence
if (input.stages) {
input.stages.forEach(stageObject => {
// Create Stages from the stored data
var stage = new HP.Stage();
stage.fromObject(stageObject);
// Add them to the Protocol
this.stages.push(stage);
});
}
}
/**
* Creates a clone of the current Protocol with a new name
*
* Note! This method absolutely cannot be renamed 'clone', because
* Minimongo's insert method uses 'clone' internally and this
* somehow causes very bizarre behaviour
*
* @param name
* @returns {Protocol|*}
*/
createClone(name) {
// Create a new JavaScript independent of the current Protocol
var currentProtocol = $.extend({}, this);
// Create a new Protocol to return
var clonedProtocol = new HP.Protocol();
// Apply the desired properties
currentProtocol.id = clonedProtocol.id;
clonedProtocol.fromObject(currentProtocol);
// If we have specified a name, assign it
if (name) {
clonedProtocol.name = name;
}
// Remove any MongoDB ID the current protocol may have had
delete clonedProtocol._id;
// Unlock the clone
clonedProtocol.locked = false;
// Return the cloned Protocol
return clonedProtocol;
}
/**
* Add a Role to the Set of Roles that have access
* to this Protocol
*
* @param role
*/
addAvailableTo(role) {
// Add the role's MongoDB _id to the availableTo Set
this.availableTo.add(role._id);
// Update the modifiedDate and User that last
// modified this Protocol
this.protocolWasModified();
}
/**
* Add a Role to the Set of Roles that have access
* to this Protocol
*
* @param role
*/
addEditableBy(role) {
// Add the role's MongoDB _id to the editableBy Set
this.editableBy.add(role._id);
// Update the modifiedDate and User that last
// modified this Protocol
this.protocolWasModified();
}
/**
* Adds a Stage to this Protocol's display set sequence
*
* @param stage
*/
addStage(stage) {
this.stages.push(stage);
// Update the modifiedDate and User that last
// modified this Protocol
this.protocolWasModified();
}
/**
* Adds a Rule to this Protocol's array of matching rules
*
* @param rule
*/
addProtocolMatchingRule(rule) {
this.protocolMatchingRules.push(rule);
// Update the modifiedDate and User that last
// modified this Protocol
this.protocolWasModified();
}
/**
* Removes a Rule from this Protocol's array of matching rules
*
* @param rule
*/
removeProtocolMatchingRule(rule) {
var wasRemoved = removeFromArray(this.protocolMatchingRules, rule);
// Update the modifiedDate and User that last
// modified this Protocol
if (wasRemoved) {
this.protocolWasModified();
}
}
};
/**
* This Class represents a Rule to be evaluated given a set of attributes
* Rules have:
* - An attribute (e.g. 'seriesDescription')
* - A constraint Object, in the form required by Validate.js:
*
* rule.constraint = {
* contains: {
* value: 'T-1'
* }
* };
*
* Note: In this example we use the 'contains' Validator, which is a custom Validator defined in Viewerbase
*
* - A value for whether or not they are Required to be matched (default: False)
* - A value for their relative weighting during Protocol or Image matching (default: 1)
*/
class Rule {
/**
* The Constructor for the Class to create a Rule with the bare
* minimum information
*
* @param name The desired name for the Rule
*/
constructor(attribute, constraint, required, weight) {
// Create a new UUID for this Rule
this.id = uuid.new();
// Set the Rule's weight (defaults to 1)
this.weight = weight || 1;
// If an attribute is specified, assign it
if (attribute) {
this.attribute = attribute;
}
// If a constraint is specified, assign it
if (constraint) {
this.constraint = constraint;
}
// If a value for 'required' is specified, assign it
if (required === undefined) {
// If no value was specified, default to False
this.required = false;
} else {
this.required = required;
}
}
/**
* Occasionally the Rule class needs to be instantiated from a JavaScript Object.
* This function fills in a Protocol with the Object data.
*
* @param input A Rule as a JavaScript Object, e.g. retrieved from MongoDB or JSON
*/
fromObject(input) {
// Check if the input already has an ID
// If so, keep it. It not, create a new UUID
this.id = input.id || uuid.new();
// Assign the specified input data to the Rule
this.required = input.required;
this.weight = input.weight;
this.attribute = input.attribute;
this.constraint = input.constraint;
}
}
/**
* The ProtocolMatchingRule Class extends the Rule Class.
*
* At present it does not add any new methods or attributes
* @type {ProtocolMatchingRule}
*/
HP.ProtocolMatchingRule = class ProtocolMatchingRule extends Rule {};
/**
* A Stage is one step in the Display Set Sequence for a Hanging Protocol
*
* Stages are defined as a ViewportStructure and an array of Viewports
*
* @type {Stage}
*/
HP.Stage = class Stage {
constructor(ViewportStructure, name) {
// Create a new UUID for this Stage
this.id = uuid.new();
// Assign the name and ViewportStructure provided
this.name = name;
this.viewportStructure = ViewportStructure;
// Create an empty array for the Viewports
this.viewports = [];
// Set the created date to Now
this.createdDate = new Date();
}
/**
* Creates a clone of the current Stage with a new name
*
* Note! This method absolutely cannot be renamed 'clone', because
* Minimongo's insert method uses 'clone' internally and this
* somehow causes very bizarre behaviour
*
* @param name
* @returns {Stage|*}
*/
createClone(name) {
// Create a new JavaScript independent of the current Protocol
var currentStage = $.extend({}, this);
// Create a new Stage to return
var clonedStage = new HP.Stage();
// Assign the desired properties
currentStage.id = clonedStage.id;
clonedStage.fromObject(currentStage);
// If we have specified a name, assign it
if (name) {
clonedStage.name = name;
}
// Return the cloned Stage
return clonedStage;
}
/**
* Occasionally the Stage class needs to be instantiated from a JavaScript Object.
* This function fills in a Protocol with the Object data.
*
* @param input A Stage as a JavaScript Object, e.g. retrieved from MongoDB or JSON
*/
fromObject(input) {
// Check if the input already has an ID
// If so, keep it. It not, create a new UUID
this.id = input.id || uuid.new();
// Assign the input name to the Stage
this.name = input.name;
// If a ViewportStructure is present in the input, add it from the
// input data
this.viewportStructure = new HP.ViewportStructure();
this.viewportStructure.fromObject(input.viewportStructure);
// If any viewports are present in the input object
if (input.viewports) {
input.viewports.forEach(viewportObject => {
// Create a new Viewport with their data
var viewport = new HP.Viewport();
viewport.fromObject(viewportObject);
// Add it to the viewports array
this.viewports.push(viewport);
});
}
}
};
/**
* The ViewportStructure class represents the layout and layout properties that
* Viewports are displayed in. ViewportStructure has a type, which corresponds to
* a layout template, and a set of properties, which depend on the type.
*
* @type {ViewportStructure}
*/
HP.ViewportStructure = class ViewportStructure {
constructor(type, properties) {
this.type = type;
this.properties = properties;
}
/**
* Occasionally the ViewportStructure class needs to be instantiated from a JavaScript Object.
* This function fills in a ViewportStructure with the Object data.
*
* @param input The ViewportStructure as a JavaScript Object, e.g. retrieved from MongoDB or JSON
*/
fromObject(input) {
this.type = input.type;
this.properties = input.properties;
}
/**
* Retrieve the layout template name based on the layout type
*
* @returns {string}
*/
getLayoutTemplateName() {
// Viewport structure can be updated later when we build more complex display layouts
switch (this.type) {
case 'grid':
return 'gridLayout';
}
}
/**
* Retrieve the number of Viewports required for this layout
* given the layout type and properties
*
* @returns {string}
*/
getNumViewports() {
// Viewport structure can be updated later when we build more complex display layouts
switch (this.type) {
case 'grid':
// For the typical grid layout, we only need to multiply rows by columns to
// obtain the number of viewports
return this.properties.rows * this.properties.columns;
}
}
};
/**
* This Class defines a Viewport in the Hanging Protocol Stage. A Viewport contains
* arrays of Rules that are matched in the ProtocolEngine in order to determine which
* images should be hung.
*
* @type {Viewport}
*/
HP.Viewport = class Viewport {
constructor() {
this.viewportSettings = {};
this.imageMatchingRules = [];
this.seriesMatchingRules = [];
this.studyMatchingRules = [];
}
/**
* Occasionally the Viewport class needs to be instantiated from a JavaScript Object.
* This function fills in a Viewport with the Object data.
*
* @param input The Viewport as a JavaScript Object, e.g. retrieved from MongoDB or JSON
*/
fromObject(input) {
// If ImageMatchingRules exist, create them from the Object data
// and add them to the Viewport's imageMatchingRules array
if (input.imageMatchingRules) {
input.imageMatchingRules.forEach(ruleObject => {
var rule = new HP.ImageMatchingRule();
rule.fromObject(ruleObject);
this.imageMatchingRules.push(rule);
});
}
// If SeriesMatchingRules exist, create them from the Object data
// and add them to the Viewport's seriesMatchingRules array
if (input.seriesMatchingRules) {
input.seriesMatchingRules.forEach(ruleObject => {
var rule = new HP.SeriesMatchingRule();
rule.fromObject(ruleObject);
this.seriesMatchingRules.push(rule);
});
}
// If StudyMatchingRules exist, create them from the Object data
// and add them to the Viewport's studyMatchingRules array
if (input.studyMatchingRules) {
input.studyMatchingRules.forEach(ruleObject => {
var rule = new HP.StudyMatchingRule();
rule.fromObject(ruleObject);
this.studyMatchingRules.push(rule);
});
}
// If ViewportSettings exist, add them to the current protocol
if (input.viewportSettings) {
this.viewportSettings = input.viewportSettings;
}
}
/**
* Finds and removes a rule from whichever array it exists in.
* It is not required to specify if it exists in studyMatchingRules,
* seriesMatchingRules, or imageMatchingRules
*
* @param rule
*/
removeRule(rule) {
var array;
if (rule instanceof HP.StudyMatchingRule) {
array = this.studyMatchingRules;
} else if (rule instanceof HP.SeriesMatchingRule) {
array = this.seriesMatchingRules;
} else if (rule instanceof HP.ImageMatchingRule) {
array = this.imageMatchingRules;
}
removeFromArray(array, rule);
}
};
/**
* The ImageMatchingRule class extends the Rule Class.
*
* At present it does not add any new methods or attributes
* @type {ImageMatchingRule}
*/
HP.ImageMatchingRule = class ImageMatchingRule extends Rule {};
/**
* The SeriesMatchingRule Class extends the Rule Class.
*
* At present it does not add any new methods or attributes
* @type {SeriesMatchingRule}
*/
HP.SeriesMatchingRule = class SeriesMatchingRule extends Rule {};
/**
* The StudyMatchingRule Class extends the Rule Class.
*
* At present it does not add any new methods or attributes
* @type {StudyMatchingRule}
*/
HP.StudyMatchingRule = class StudyMatchingRule extends Rule {};
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function getDefaultProtocol() {
var protocol = new HP.Protocol('Default');
protocol.id = 'defaultProtocol';
protocol.locked = true;
var oneByOne = new HP.ViewportStructure('grid', {
rows: 1,
columns: 1
});
var viewport = new HP.Viewport();
var first = new HP.Stage(oneByOne, 'oneByOne');
first.viewports.push(viewport);
protocol.stages.push(first);
HP.defaultProtocol = protocol;
return HP.defaultProtocol;
}
function getMRTwoByTwoTest() {
var proto = new HP.Protocol('MR_TwoByTwo');
proto.locked = true;
// Use http://localhost:3000/viewer/1.2.840.113619.2.5.1762583153.215519.978957063.78
var studyInstanceUid = new HP.ProtocolMatchingRule('studyInstanceUid', {
equals: {
value: '1.2.840.113619.2.5.1762583153.215519.978957063.78'
}
}, true);
proto.addProtocolMatchingRule(studyInstanceUid);
var oneByTwo = new HP.ViewportStructure('grid', {
rows: 1,
columns: 2
});
// Stage 1
var left = new HP.Viewport();
var right = new HP.Viewport();
var firstSeries = new HP.SeriesMatchingRule('seriesNumber', {
equals: {
value: 1
}
});
var secondSeries = new HP.SeriesMatchingRule('seriesNumber', {
equals: {
value: 2
}
});
var thirdImage = new HP.ImageMatchingRule('instanceNumber', {
equals: {
value: 3
}
});
left.seriesMatchingRules.push(firstSeries);
left.imageMatchingRules.push(thirdImage);
right.seriesMatchingRules.push(secondSeries);
right.imageMatchingRules.push(thirdImage);
var first = new HP.Stage(oneByTwo, 'oneByTwo');
first.viewports.push(left);
first.viewports.push(right);
proto.stages.push(first);
// Stage 2
var twoByOne = new HP.ViewportStructure('grid', {
rows: 2,
columns: 1
});
var left2 = new HP.Viewport();
var right2 = new HP.Viewport();
var fourthSeries = new HP.SeriesMatchingRule('seriesNumber', {
equals: {
value: 4
}
});
var fifthSeries = new HP.SeriesMatchingRule('seriesNumber', {
equals: {
value: 5
}
});
left2.seriesMatchingRules.push(fourthSeries);
left2.imageMatchingRules.push(thirdImage);
right2.seriesMatchingRules.push(fifthSeries);
right2.imageMatchingRules.push(thirdImage);
var second = new HP.Stage(twoByOne, 'twoByOne');
second.viewports.push(left2);
second.viewports.push(right2);
proto.stages.push(second);
HP.testProtocol = proto;
return HP.testProtocol;
}
getDefaultProtocol();
getMRTwoByTwoTest();