Collection of functions that automate many common and essential iPACS queries in VQ.
// iPACS object used for simplifying access to the iPACS for data download/upload
// A Novicki
// Version info
// 1.0: Initial Version
// 1.1 (09/23/14): Added version information, minor bug fixes
// 1.2 (01/14/15):
// Incorporated VQ.dicomBrowserLoad into the getImages function instead of the old method (VQ.downloadImages, dm.openDat).
// Fixed a misspelling in the series sort function.
// Added ROI date filtering to getROIs()
// Added a getWebDisk() method. Returns WebDisk object for this repository
// Changed default path for getROIs/mergeROIs to use the VQ cache instead of the home directory (still tmp.rmha so not making the VQ cache too much larger)
// 1.21 (03/24/15):
// Added study description filter (-descfilter) to getStudies()
// Fixed bug that sometimes occurs on other ipaces with getROIs
//
// 1.22 (02/17/16):
// Added behavior to the getSubjectID, getWeight, getTimePoint, etc functions to return -1 instead of an error if the subject info data point has not been entered
// 1.30 (03/09/17):
// Added a -setId option to getROIs(). Fixed bug in getQuantification
// 1.31 (06/05/17):
// Added in error for when storeData fails
var ipacsversion = '1.31';
function iPACS(){
// Function to standardize thrown errors
// Displays message and quits. Should only be called from catch blocks
this.showError = function(err,fn){
VQ.debug(fn + ' ERROR: ' + err);
VQ.debug(this.serverMode);
if (this.serverMode){
VQ.debug(fn + ' ERROR: ' + err);
VQ.quit();
}
else{
VQ.showMessage(fn + ' ERROR: ' + err);
VQ.abort();
}
}
try{
VQ.debug('ipacs.vqs version: ' + ipacsversion);
if (arguments.length < 1 || arguments.length > 3)
throw "Usage: var repository = new iPACS(address,[project path])";
if (arguments.length == 3){
this.serverMode = arguments[2];
}
var address = arguments[0];
var dcmrep = VQ.dcmRep(address);
var dbgflg = false;
if (!dcmrep.ping())
{
throw "dcmRep ping failed. Check IPACS address";
}
if (address.split(':')[0] == 'folder'){
VQ.debug('Local Data detected');
}
else{
var path = arguments[1];
var projects = dcmrep.getProjectList();
if (!containsstr(path,projects))
{
throw "Project not found. Check Project name.";
}
dcmrep.setProject(path);
}
this.dcmRep = dcmrep;
this.CurrentStudy = '';
this.repository_url = address;
this.project = path;
this.CurrentSeries = '';
Object.defineProperty(this,"CurrentSeries",{writable:true});
Object.defineProperty(this,"dcmRep",{writable:true});
Object.defineProperty(this,"CurrentStudy",{ writable:true});
}
catch(err) {
this.showError(err,'iPACS');
}
// Sets debug flag
// flag == true outputs all debug code
// flag == false supresses all code
this.setDebug = function(flag) {
dbgflg = flag;
return;
}
// Returns a list of all studies found that match nfilt and pidfilt. Follows same rules as VQ.queryStudies, just checks for existence
// accepted arguments: -namefilter, -idfilter, -sort, -datestart,-dateend,-descfilter
// Usage: this.getStudies(argument1,value1,argument2...)
// for sorting method, enter a property to sort for
// defaults: -namefilter *
// -idfilter *
// -descfilter * (This is study description)
// -sort false
// -datestart No filtering
// -dateend No filtering
// -datestart (yyyymmdd) Finds studies from this date on
// -dateend (yyyymmdd) Finds studies up until this date
//
this.getStudies = function() {
try{
if (dbgflg){
VQ.debug(arguments)
for (var i = 0; i<arguments.length; i++){
VQ.debug(arguments[i]);
}
}
if (arguments.length % 2)
throw "Accpeted arguments -namefilter,-idfilter,-descfilter,-sort,-datestart,-dateend"
var idx = 0;
nfilt = '*';
pidfilt = '*';
descfilt = '*';
srt = false;
tdstart = false;
tdend = false;
while (idx < arguments.length){
if (arguments[idx] == '-namefilter'){
nfilt = arguments[idx+1];
}
else if (arguments[idx] == '-idfilter'){
pidfilt = arguments[idx+1];
}
else if (arguments[idx] == '-descfilter'){
descfilt = arguments[idx+1];
}
else if (arguments[idx] == '-sort'){
srt = true;
stype = arguments[idx+1];
}
else if (arguments[idx] == '-datestart'){
if (dbgflg) VQ.debug("Filtering -datestart");
tdstart = true;
dstart = arguments[idx+1];
if (dstart.length != 8) throw "Date must be in the format YYYYMMDD"
}
else if (arguments[idx] == '-dateend'){
tdend = true;
dend = arguments[idx+1]
if (dend.length != 8) throw "Date must be in the format YYYYMMDD"
}
else {
throw "Accepted arguments -namefilter, '-idfilter','-sort','-datestart','-dateend'"
}
// increment by 2
idx = idx +2;
}
var studies = VQ.queryStudies(this.dcmRep,nfilt,pidfilt,'*',descfilt);
if (!studies)
{
throw "No studies found... try new filter";
}
}
catch(err){
this.showError(err,'getStudies()');
}
// Put in date filtering here
if (dbgflg) VQ.debug('Date filtering: ');
if (tdstart)
studies = filtDates(studies,dstart,false);
if (tdend)
studies = filtDates(studies,dend,true);
if (srt)
studies = sortList(studies,stype);
return studies;
}
// Accepts study object or study UID
// Really only used internally
this.setStudy = function(study) {
try{
var studies = VQ.queryStudies(this.dcmRep,'*','*');
for (var i = 0; i < studies.length; i++){
if (studies[i].StudyInstanceUID == study){
if (dbgflg) VQ.debug("Set Current Study: " + this.CurrentStudy.StudyInstanceUID);
this.CurrentStudy = studies[i];
return;
}
if (studies[i].StudyInstanceUID == study.StudyInstanceUID){
this.CurrentStudy = studies[i]
if (dbgflg) VQ.debug("Set Current Study: " + this.CurrentStudy.StudyInstanceUID);
return;
}
}
throw "No matching study found";
}
catch(err){
this.showError(err,'setStudy()');
}
}
// Finds all series within current study
// Automatically sorts list of returned series
// Currently accepted arguments (optional):
// -modality
// -seriesdescription: accepts bash style wildcards (*)
// Example usage repo.getSeries(studies[i],'-modality','CT','-seriesdescription','*focused*')
this.getSeries = function(){
try{
if (dbgflg) VQ.debug(arguments);
sdec = '';
modality = '';
// Odd number of arguments required
if (arguments.length % 2 == 0) throw "Usage: getSeries(study,arguments)";
// Check to make sure first argument is study object
if (arguments[0].StudyInstanceUID){
this.setStudy(arguments[0].StudyInstanceUID);
}
else throw "First argument is not a valid study object";
for (var j = 1; j < arguments.length; j++)
{
if (dbgflg) VQ.debug(arguments[j]);
if (arguments[j] == '-modality') modality = arguments[j+1];
if (arguments[j] == '-seriesdescription') sdec = arguments[j+1];
}
if (this.CurrentStudy == '') throw "No study selected. Have you called setStudy()?";
if (dbgflg){
VQ.debug('modality ' + modality)
VQ.debug('sdec ' + sdec);
VQ.debug("Get Current Study: " + this.CurrentStudy.StudyInstanceUID);
}
var series = VQ.querySeries(this.dcmRep,this.CurrentStudy.StudyInstanceUID);
var oseries = new Array();
for (var i = 0; i < series.length; i++){
if (modality == '' || modality == series[i].Modality)
{
if (sdec == '' || wildcardMatch(series[i].SeriesDescription,sdec)){
oseries.push(series[i])
}
}
}
if ((!series || oseries.length == 0) && dbgflg)
VQ.debug('WARNING: Empty series returned for ' + this.CurrentStudy.PatientsName + ' ' + this.CurrentStudy.PatientID + '. If not intentional please check you filters');
}
catch(err){
this.showError(err,'getSeries()');
}
// Default sorting
// Sorting order of preference: modality, patient id, patient name, series time, series name
oseries.sort(seriesSort);
return oseries;
}
// Sets series as the Current Series. Accepts series object or series UID
// Mainly an internal method
this.setSeries = function(series) {
try{
var tseries = VQ.querySeries(this.dcmRep,this.CurrentStudy.StudyInstanceUID);
for (var i = 0; i < tseries.length; i++) {
if (tseries[i].SeriesInstanceUID == series || tseries[i].SeriesInstanceUID == series.SeriesInstanceUID) {
this.CurrentSeries = tseries[i];
return;
}
}
throw "No matching series found.";
}
catch(err){
this.showError(err,'setSeries()');
}
}
// Downloads images for the the current series, optionally takes a series object as an argument
// Appends the data to the already loaded data
// Argument preceeds current series. Always uses current study
// Also loads the data in vivoquant
// Update: 3rd argument (idx) is now a boolean. True to append, false to load to reference
// Update: now takes optional arguments after the three required arguments:
// -open: boolean on whether to open the images or just download them (only comes into effect if using typefilter)
// -typefilter: filter on ImageType (*RECON* only gets the RECON)
// Note: it filters on the DICOM dump, not the Data Browser response
this.getImages = function() {
try {
var dm = VQ.dataManager();
if (dbgflg) VQ.debug('getImages argument: ' + arguments);
var open = true;
var doFlter = false;
var typefltr = '*';
var isofltr = '*';
switch(arguments.length){
case 0:
case 1:
case 2:
throw "Usage: getImages(study,series,idx,[optional arguments])";
break;
case 3:
this.setStudy(arguments[0]);
this.setSeries(arguments[1]);
idx = arguments[2];
break
default:
this.setStudy(arguments[0]);
this.setSeries(arguments[1]);
idx = arguments[2];
if (arguments.length % 2 == 0)throw "Usage: getImages(study,series,idx,[optional arguments])"
// Since we are here we know that length>3
var i = 3;
while (i < arguments.length){
if (arguments[i] == '-open')
open = arguments[i+1];
if (arguments[i] == '-typefilter'){
typefltr = arguments[i+1];
doFlter = true;
if (dbgflg) VQ.debug('Doing name filtering on images');
}
if (arguments[i] == '-isofilter'){
isofltr = arguments[i+1];
doFilter = true;
if (dbgflg) VQ.debug('Doing isotope filtering on images');
}
i = i+2;
}
break;
}
if (doFlter){
if (idx)
idx_to_load = dm.size();
else
idx_to_load = 0;
if (dbgflg) VQ.debug('Filtering requested. Downloading images before opening');
var quim = VQ.queryImages(this.dcmRep,(this.CurrentStudy).StudyInstanceUID,(this.CurrentSeries).SeriesInstanceUID);
// Do flitering
if (dbgflg) VQ.debug('Query images: ' + quim);
// ImageType seems to be the best one to filter by
var im = [];
for (var i = 0; i < quim.length; i++){
// Query metadata data point
var res = VQ.queryDataPoints(this.dcmRep,'images',quim[i].SOPInstanceUID,'metadata');
if (wildcardMatch(quim[i]['ImageType'],typefltr) && wildcardMatch(res[0]['InjectedDoseIsotope'],isofltr)){
// Download the image if it matches
var tmpim =VQ.downloadImages(this.dcmRep,(this.CurrentStudy).StudyInstanceUID,(this.CurrentSeries).SeriesInstanceUID,quim[i].SOPInstanceUID);
im.push(tmpim);
}
}
if (!im) throw "Image did not download correctly\n" + (this.CurrentStudy).StudyInstanceUID + " " + (this.CurrentSeries).SeriesInstanceUID;
// Open all the images in im, starting at idx
if (dbgflg) VQ.debug('Number of images downloaded: ' + im.length);
if (open){
dm.openDat(idx_to_load,im);
if (dbgflg) VQ.debug('Using openDat to open the downloaded image');
var dispName = this.dcmRep.get('displayedName');
if (dispName && dispName.length) {
dm.setDesc(dm.size()-1,"__repository",dispName);
} else {
dm.setDesc(dm.size()-1,"__repository","VQScriptRep");
}
dm.setDesc(dm.size()-1,"__repository_url",this.repository_url);
dm.setDesc(dm.size()-1,"__project",this.project);
}
}
else {
if (dbgflg) VQ.debug('Using dicomBrowserLoad to open data');
var old_size = dm.size();
VQ.dicomBrowserLoad(this.dcmRep,(this.CurrentStudy).StudyInstanceUID,(this.CurrentSeries).SeriesInstanceUID,idx);
var dispName = this.dcmRep.get('displayedName');
if (dispName && dispName.length) {
dm.setDesc(dm.size()-1,"__repository",dispName);
} else {
dm.setDesc(dm.size()-1,"__repository","VQScriptRep");
}
dm.setDesc(dm.size()-1,"__repository_url",this.repository_url);
dm.setDesc(dm.size()-1,"__project",this.project);
}
}
catch (err){
this.showError(err,'getImages()');
}
return im;
}
// DEPRECIATED: use this.getROIs() for ROI retrevial
// Downloads the latest ROIs from the ipacs (implements commonfuncs.vqs find_latest function). Copied below so commonfuncs doesn not need to be included -- temporary but may change later
// Takes list of ROIs as an argument (mandatory)
// Takes path to save tmp file as second argument (optional)
//
this.getROI = function(){
try{
if (dbgflg) VQ.debug('getROI argument: ' + arguments);
switch (arguments.length){
case 1:
var roilist = arguments[0];
var path = 'roi.rmha';
break;
case 2:
var roilist = arguments[0];
var path = arguments[1];
break;
default:
throw "Usage: getROI(roilist,[temp save path])";
}
var dm = VQ.dataManager();
// Set repository options
var dispName = this.dcmRep.get('displayedName');
if (dispName && dispName.length) {
dm.setDesc(0,"__repository",dispName);
} else {
dm.setDesc(0,"__repository","VQScriptRep");
}
dm.setDesc(0,"__repository_url",this.repository_url);
dm.setDesc(0,"__project",this.project);
var uid = dm.getDesc(0,"sopinstanceuid");
if (dbgflg) VQ.debug('sopinstanceuid ' + uid);
var res = VQ.queryDataPoints(this.dcmRep,"images",uid,"quantification");
if (dbgflg) VQ.debug('res length ' + res.length);
var resfinal = find_latest(res);
var rois_to_use = [];
var rois_to_lose = [];
var wd_idx = [];
if (dbgflg) VQ.debug('resfinal length ' + resfinal.length);
for (r in resfinal){
if (dbgflg) VQ.debug('Final ROIs selected :' + resfinal[r]["name"]);
rois_to_lose.push(parseFloat(resfinal[r]["roiid"]));
if(roilist.indexOf(resfinal[r]["name"]) > -1){
rois_to_use.push(parseFloat(resfinal[r]["roiid"]));
wd_idx.push(parseFloat(r));
}
}
var wd = VQ.webDisk(this.repository_url);
if (dbgflg) VQ.debug('rois_to_use length ' + rois_to_use.length);
for (rt in rois_to_use){
var id = wd_idx[rt];
if (dbgflg) VQ.debug('ROI: ' + resfinal[id]["name"]);
var roifile = resfinal[id]["filename"];
if (dbgflg) VQ.debug('ROIFILE: ' + roifile);
if (!roifile.match("^/")) {
roifile = '/projects' + this.dcmRep.project() + '/' + roifile;
}
if (dbgflg) VQ.debug('ROIFile: ' + roifile);
var resGet = wd.get(roifile,path);
if (!resGet) throw "Download of ROI failed\nDo you have write access at " + path + "?";
}
VQ.mainWin().setViewMode("Slice View","3D ROI Tool");
VQ.currentOp().loadROI(path);
}
catch(error){
this.showError(error,'getROI()');
}
}
// Updated function for ROI retreval. Now takes 3 optional arguments
// -names: list of ROI names (all must be found for a file to load)
// -creator: string of the creator of the ROI datapoint
// -savepath: path to where you want to save the temporary roi file (ex C:\tmp\tmp.rmha)
// -datestart: oldest date to grab an ROI. Format: yyyymmdd
// -dateend: most recent to grab ROI, format: yyyymmdd. See getStudies for more detailed useage
// -setid: [GREEDY] downloads and opens the ROI that matches the setid. Ignores all other options except savepath
// Example usage: repo.getROIs('-creator','anovicki','-names',['Heart','Muscle'],'-savepath','C:\tmp.rmha'
// All arguments are optional and order does not matter
this.getROIs = function(){
try{
if (arguments.length % 2) throw "Must have even number of arguments: accepted options: -names, -creator, -savepath, -datestart, -datestart"
var idx = 0;
// Default argument values
var path = VQ.getCache() + '/tmp.rmha';
var fltnames = false;
var fltcreator = false;
var tdstart = false;
var tdend = false;
var dstart = '20000101';
var dend = '20281231';
var doSetID = false;
var setId = '{}';
while (idx < arguments.length)
{
if (dbgflg) VQ.debug('idx: ' + idx);
if (arguments[idx] == '-names'){
fltnames = true;
roilist = arguments[idx+1];
}
else if (arguments[idx] == '-creator'){
fltcreator = true;
cname = arguments[idx+1];
}
else if (arguments[idx] == '-savepath'){
path = arguments[idx+1];
}
else if (arguments[idx] == '-datestart'){
tdstart = true;
dstart = arguments[idx+1];
if (dstart.length != 8) throw "Date must be in the format YYYYMMDD"
}
else if (arguments[idx] == '-dateend'){
tdend = true;
dend = arguments[idx+1];
if (dend.length != 8) throw "Date must be in the format YYYYMMDD"
}
else if (arguments[idx] == '-setid'){
doSetID = true;
setId = arguments[idx+1];
}
else{
throw "Improper usage, accepted arguments are -names, -creator, -savepath"
}
idx = idx + 2;
}
// Begin getROIs script
//
var dm = VQ.dataManager();
// Set repository options
var dispName = this.dcmRep.get('displayedName');
if (dispName && dispName.length) {
dm.setDesc(0,"__repository",dispName);
} else {
dm.setDesc(0,"__repository","VQScriptRep");
}
dm.setDesc(0,"__repository_url",this.repository_url);
dm.setDesc(0,"__project",this.project);
// Get data points
var uid = dm.getDesc(0,"sopinstanceuid");
if (dbgflg) VQ.debug('sopinstanceuid ' + uid);
var res = VQ.queryDataPoints(this.dcmRep,"images",uid,"quantification");
if (dbgflg) VQ.debug('res length ' + res.length);
fnames = new Array()
// Make array of filenames
for (var i=0; i < res.length; i++){
fnames.push(res[i].filename);
}
// Find unique filenames
ufnames = unique(fnames);
rlist = new Array(ufnames.length)
// Make array of roi objects - construct with roi filename
for (var i = 0; i < rlist.length; i ++){
rlist[i] = new roi_obj(ufnames[i]);
}
// Populate roi object list
//
// Add elements to object array (can be cleaned up)
for (var i=0; i < res.length; i++){
for (var j =0; j < rlist.length; j++){
if (res[i].filename == rlist[j].filename){
// Add creator if none existed
if (!rlist[j].creator)
rlist[j].creator = res[i].creator;
// Add timestamp -- timestamp might be different from DP to DP, but there shouldn't be overlap from one roi file to the next (aka they should all be within 2 mins of each other)
if (!rlist[j].timestamp)
rlist[j].timestamp = res[i].timestamp;
if (rlist[j].setid == '{}')
rlist[j].setid = "" + res[i].setid;
// Add roi name append list already there
(rlist[j].names).push(res[i].name);
}
}
}
// Apply filters:
//
if (doSetID){
for (var i = 0 ;i < rlist.length; i++){
if (rlist[i].setid == setId || rlist[i].setid == '{' + setId + '}'){
rlist = rlist.splice(i,1);
break
}
}
}
else{
if (fltnames)
rlist = filterName(rlist,roilist);
if (fltcreator)
rlist = filterCreator(rlist,cname);
// Put in date filtering here
if (dbgflg && (tdstart || tdend)) VQ.debug('Date filtering: ');
if (tdstart)
rlist = filtDates_roi(rlist,dstart,false);
if (tdend)
rlist = filtDates_roi(rlist,dend,true);
}
// Get most recent roi
var curr_roi = find_latest_roi(rlist);
if (!curr_roi){
if (dbgflg) VQ.debug('Error: No ROI found that matches the filters');
return false;
}
// Okay now download roi and load it into VQ
var wd = VQ.webDisk(this.repository_url);
var roifile = curr_roi["filename"];
if (dbgflg) VQ.debug('ROIFILE: ' + roifile);
//if (!roifile.match("^/")) {
if (roifile.slice(0,1) != '/'){
roifile = '/projects' + this.dcmRep.project() + '/' + roifile;
}
if (dbgflg) VQ.debug('ROIFile: ' + roifile);
var resGet = wd.get(roifile,path);
if (!resGet) throw "Download of ROI failed\nDo you have write access at " + path + "?";
VQ.mainWin().setViewMode("Slice View","3D ROI Tool");
VQ.currentOp().loadROI(path);
} // End try block
catch(error){
this.showError(error,'getROIs');
}
return curr_roi;
} // End function
// Function to merge ROIs from different ROI files on the iPACS. ROIlist is required
// Downloads the most recent version of each ROI found in array supplied by -names argument
// and merges them together
//
// Required arguments -names
// Optional arguments -creator,
// -savepath (default: tmp.rmha)
// -exactlist (default: true) If true, deletes all Rois not in ROI list
this.mergeROIs = function(){
try{
if (arguments.length % 2) throw "Must have even number of arguments: accepted options: -names, -creator, -savepath, -exactlist"
var idx = 0;
// Default argument values
path = VQ.getCache() + '/tmp.rmha';
fltnames = false;
fltcreator = false;
exactlist = true;
while (idx < arguments.length)
{
VQ.debug('idx: ' + idx);
if (arguments[idx] == '-names'){
fltnames = true;
roilist = arguments[idx+1];
}
else if (arguments[idx] == '-creator'){
fltcreator = true;
cname = arguments[idx+1];
}
else if (arguments[idx] == '-savepath'){
path = arguments[idx+1];
}
else if (arguments[idx] == '-exactlist'){
exactlist = arguments[idx+1];
}
else{
throw "Improper usage, accepted arguments are -names, -creator, -savepath, -exactlist"
}
idx = idx + 2;
}
// Names is required
if (!fltnames){
throw "-names argument is required"
}
// Begin getROIs script
//
var dm = VQ.dataManager();
// Set repository options
var dispName = this.dcmRep.get('displayedName');
if (dispName && dispName.length) {
dm.setDesc(0,"__repository",dispName);
} else {
dm.setDesc(0,"__repository","VQScriptRep");
}
dm.setDesc(0,"__repository_url",this.repository_url);
dm.setDesc(0,"__project",this.project);
// Get data points
var uid = dm.getDesc(0,"sopinstanceuid");
if (dbgflg) VQ.debug('sopinstanceuid ' + uid);
var res = VQ.queryDataPoints(this.dcmRep,"images",uid,"quantification");
if (dbgflg) VQ.debug('res length ' + res.length);
fnames = new Array()
// Make array of filenames
for (var i=0; i < res.length; i++){
fnames.push(res[i].filename);
}
// Find unique filenames
ufnames = unique(fnames);
rlist = new Array(ufnames.length)
// Make array of roi objects - construct with roi filename
for (var i = 0; i < rlist.length; i ++){
rlist[i] = new roi_obj(ufnames[i]);
}
// Populate roi object list
//
// Add elements to object array (can be cleaned up)
for (var i=0; i < res.length; i++){
for (var j =0; j < rlist.length; j++){
if (res[i].filename == rlist[j].filename){
// Add creator if none existed
if (!rlist[j].creator)
rlist[j].creator = res[i].creator;
// Add timestamp -- timestamp might be different from DP to DP, but there shouldn't be overlap from one roi file to the next (aka they should all be within 2 mins of each other)
if (!rlist[j].timestamp)
rlist[j].timestamp = res[i].timestamp;
// Add roi name append list already there
(rlist[j].names).push(res[i].name);
}
}
}
if (dbgflg){
VQ.debug('rlist:');
/////// PRINT OUT
for (var i=0; i < rlist.length;i++){
VQ.debug(rlist[i].filename + '**__**' + rlist[i].names);
}
/////////////////
}
// Put in meat of the merge script here
if (fltcreator)
rlist = filterCreator(rlist,cname);
// Filter names is a little more involved here
frois = new Array();
froilist = new Array();
for (var i=0; i < roilist.length; i++){
// Need to slice because 2nd argument needs to be an array
tmp_rlist = filterName(rlist,roilist.slice(i,i+1));
if (dbgflg) VQ.debug(roilist[i] + ' ' + tmp_rlist[0].filename)
// tmp_rlist should now only be the roi_obj that have roilist[i] in it
tmp_latest = find_latest_roi(tmp_rlist);
edit = false;
for (var j =0; j < frois.length; j++){
if (tmp_latest.filename == frois[j].filename)
{
froilist[j].push(roilist[i])
edit = true;
}
}
if (!edit){
frois.push(tmp_latest);
tmp = new Array();
tmp.push(roilist[i]);
froilist.push(tmp);
}
if (frois.length != froilist.length)
VQ.suspend('Something happened....');
}
// Print
if (dbgflg){
VQ.debug('froilist[i]')
VQ.debug('frois[i].filename');
for (var i = 0; i < frois.length; i++){
VQ.debug(froilist[i])
VQ.debug(frois[i].filename)
}
}
// Assuming the filter worked, we now hoave arrays of filenames to download, with associated ROIs to keep
VQ.mainWin().setViewMode('Slice View','3D ROI Tool');
var roi = VQ.currentOp();
// Start off by removing all rois
while (roi.numROIs() > 1)
roi.deleteROI(1,0);
var wd = VQ.webDisk(this.repository_url)
// Time to get started
for (var i = 0 ; i< frois.length; i++){
var roifile = frois[i].filename;
if (dbgflg) VQ.debug(roifile);
//if (!roifile.match("^/")){
if (roifile.slice(0,1) != '/'){
roifile = '/projects' + this.dcmRep.project() + '/' + roifile;
}
var resGet = wd.get(roifile,path);
// Ignore the background so total number of ROIs will beour starting point
var curridx = roi.numROIs();
roi.mergeROIs(path);
// This should increase the number of rois
roi_names_we_want = froilist[i];
if (exactlist) {
// Okay now we remove the extras
while (curridx < roi.numROIs()){
// Simplified form-- if the name exists, in the string, keep it. Else delete
stats = roi.getROIDetails(curridx);
if (hasstr(stats[0],roi_names_we_want)){
curridx++;
}
else {
roi.deleteROI(curridx,0);
}
}
}
}
// End merge script
}
catch (error){
this.showError(error,'mergeROIs()')
}
}
// Returns webdisk object for current directory
this.getWebDisk = function(){
return VQ.webDisk(this.repository_url);
}
// Note: inputs have to be turned on in order for the ROIs to be submitted
this.submitROIs = function(){
try{
var dm = VQ.dataManager();
var mw = VQ.mainWin();
mw.setViewMode("Slice View",'3D ROI Tool');
var roi = VQ.currentOp();
// Set repository
// Will upload for all inputs in the datamanager
var i = 0;
while(dm.hasData(i)){
var dispName = this.dcmRep.get('displayedName');
if (dispName && dispName.length) {
dm.setDesc(i,"__repository",dispName);
} else {
dm.setDesc(i,"__repository","VQScriptRep");
}
dm.setDesc(i,"__repository_url",this.repository_url);
dm.setDesc(i,"__project",this.project);
i++;
}
roi.submitROI(true);
}
catch(error){
this.showError(error,'submitROIs');
}
}
// Submits the image at id to the ipacs repository
this.submitData = function(id){
try{
var dm = VQ.dataManager();
if (!dm.hasData(id)) throw "No image is loaded at index " + id + '.';
var dispName = this.dcmRep.get('displayedName');
if (dispName && dispName.length) {
dm.setDesc(id,"__repository",dispName);
} else {
dm.setDesc(id,"__repository","VQScriptRep");
}
dm.setDesc(id,"__repository_url",this.repository_url);
dm.setDesc(id,"__project",this.output_p);
var res = VQ.storeData(this.dcmRep,id);
if (res != 0) throw "submitData has failed with error " + res + " (" + this.dcmRep.takeError() + ").";
}
catch(error){
this.showError(error,'submitData');
}
}
// Function to get injectedDose from the iPACS subject information data point
this.getInjectedDose = function(id){
try{
var dm = VQ.dataManager();
if (!dm.hasData(id)) throw "No image is loaded at index " + id + '.';
// Query data point subject information
var uid = dm.getDesc(id,'seriesinstanceuid');
var res = VQ.queryDataPoints(this.dcmRep,'series',uid,'SubjectInformation');
if (res.length < 1) return -1;
inj = res[0]['injecteddose'];
if (inj == undefined) {
if (dbgflg) VQ.debug("injected dose datapoint not entered");
return -1;
}
// find the tail
tail = res[0]['tailUptake'];
if (tail == undefined || tail == '')
tail=0;
else
tail = parseFloat(tail);
if (dbgflg) VQ.debug('Subtracting a tail uptake of ' + tail + ' uCi from the injected dose uptake of ' + inj + ' uCi.');
return inj-tail;
}
catch(error){
this.showError(error,'getInjectedDose')
}
}
// Function to get time point from the iPACS subject information data point
this.getTimePoint = function(id){
try{
var dm = VQ.dataManager();
if (!dm.hasData(id)) throw "No image is loaded at index " + id + '.';
// Query data point subject information
var uid = dm.getDesc(id,'seriesinstanceuid');
var res = VQ.queryDataPoints(this.dcmRep,'series',uid,'SubjectInformation');
if (res.length < 1) return -1;
tm = res[0]['Timepoint'];
if (tm == undefined) {
if (dbgflg) VQ.debug("time point datapoint not entered");
return -1;
}
return tm;
}
catch(error){
this.showError(error,'getTimePoint')
}
}
// Function to get SubjectID from the iPACS subject information data point
this.getSubjectID = function(id){
try{
var dm = VQ.dataManager();
if (!dm.hasData(id)) throw "No image is loaded at index " + id + '.';
// Query data point subject information
var uid = dm.getDesc(id,'seriesinstanceuid');
var res = VQ.queryDataPoints(this.dcmRep,'series',uid,'SubjectInformation');
if (res.length < 1) return -1;
id = res[0]['SubjectID'];
if (id == undefined) {
if (dbgflg) VQ.debug("Subject ID datapoint not entered");
return -1;
}
return id;
}
catch(error){
this.showError(error,'getSubjectID')
}
}
// Function to get Group from the iPACS subject information data point
this.getGroup= function(id){
try{
var dm = VQ.dataManager();
if (!dm.hasData(id)) throw "No image is loaded at index " + id + '.';
// Query data point subject information
var uid = dm.getDesc(id,'seriesinstanceuid');
var res = VQ.queryDataPoints(this.dcmRep,'series',uid,'SubjectInformation');
if (res.length < 1) return -1;
id = res[0]['Group'];
if (id == undefined) {
if (dbgflg) VQ.debug("Group datapoint not entered");
return -1;
}
return id;
}
catch(error){
this.showError(error,'getGroup')
}
}
// Function to get Weight (g) from the iPACS subject information data point
this.getWeight= function(id){
try{
var dm = VQ.dataManager();
if (!dm.hasData(id)) throw "No image is loaded at index " + id + '.';
// Query data point subject information
var uid = dm.getDesc(id,'seriesinstanceuid');
var res = VQ.queryDataPoints(this.dcmRep,'series',uid,'SubjectInformation');
if (res.length < 1) return -1;
id = res[0]['weight'];
if (id == undefined) {
if (dbgflg) VQ.debug("weight datapoint not entered");
return -1;
}
return id;
}
catch(error){
this.showError(error,'getWeight')
}
}
// Function to get all quantification datapoints for a given dataManager index
this.getQuantification = function(){
try{
if (arguments.length ==0)
var id = 0;
else
var id = arguments[0];
var dm = VQ.dataManager();
if (!dm.hasData(id)) throw "No image is loaded at index " + id + '.';
var uid = dm.getDesc(id,'sopinstanceuid');
var res = VQ.queryDataPoints(this.dcmRep,'images',uid,'quantification');
return res
}
catch(error){
this.showError(error,'getQuantification');
}
}
// End of ipacs object
}
// Helper funcions
//
//
// Function to emulate bash style * wildcard
function wildcardMatch(str,pattern){
// Break the pattern up by '*'
pat = pattern.split('*');
//VQ.debug('pat: ' + pat);
var idx = 0;
for (var i = 0; i < pat.length; i++){
// If the first character is *
if (pat[i] == '')
continue;
var tmp = str.indexOf(pat[i]);
// tmp must be 0 on the first run if we didn't start with a *
if (i == 0 && tmp != 0)
return false;
// tmp is found where we want
if (tmp >= idx)
{
idx = tmp + pat[i].length;
}
// tmp not found
else
return false;
}
// Last character has to be a *, or we need to get all the way to the end of the string
if (pat[pat.length-1] == '' || idx == str.length)
return true;
else
return false;
}
// String matching function
// Returns true if str matches any element of strlist (array)
function containsstr(str,strlist){
for (var i = 0; i < strlist.length; i++){
if (str == strlist[i]){
return true;
}
}
return false;
}
// Same as containsstr, but doesn't need to match exactly
function hasstr(str,strlist){
for (var i = 0; i < strlist.length; i++){
if (strlist[i].indexOf(str) > -1)
return true;
}
return false;
}
function findLastInput(dataman){
var idx = 0;
while (dataman.hasData(idx)){
idx ++;
}
return idx;
}
// This is depreciated for find_latest_roi
function find_latest(res) { //find the latest timestamp for each unique roi
var ids = []
for (r in res) {
ids.push(res[r]["roiid"]);
}
var uids = unique(ids);
var resfinal = [];
var ts = new Date();
for (u in uids) {
ts.setFullYear(2000,0,0);
for (r in res) {
if (res[r]["roiid"] == uids[u]){
var timestamp = convert_date(res[r]["timestamp"]);
if (timestamp > ts){
var ts = timestamp;
resfinal.push(res[r]);
}
}
}
}
return resfinal;
}
// Returns all unique elements in an array
function unique(origArr) {
var newArr = [],
origLen = origArr.length,
found,
x, y;
for ( x = 0; x < origLen; x++ ) {
found = undefined;
for ( y = 0; y < newArr.length; y++ ) {
if ( origArr[x] === newArr[y] ) {
found = true;
break;
}
}
if ( !found) newArr.push( origArr[x] );
}
return newArr;
}
// Keep this
function convert_date(stamp){ //convert the timestamp, stored as a str in the iPACS, into a JS date obj
if (stamp.indexOf('T') > -1)
var datetime = stamp.split("T");
else
var datetime = stamp.split(" ");
var fulldate = datetime[0].split("-");
var fulltime = datetime[1].split(":");
var d = new Date(
fulldate[0],
parseFloat(fulldate[1])-1,
fulldate[2],
fulltime[0],
fulltime[1],
fulltime[2]);
return d;
}
// Gabe's sort functions used for sorting incoming data
/**
* Convenience sort function for strings
*/
function stringSort(a, b) {
if (a < b) {
return -1;
} else if (a > b) {
return 1;
} else {
return 0;
}
}
// Function to filter out dates either older or newer than fdate. Takes array of studies
// if older, returns studies before date
// if !older, returns studies after date
function filtDates(studies,fdate,older){
// fdate is a string YYYYMMDD (guraranteed in parent fn)
yr = fdate.slice(0,4);
mo = parseFloat(fdate.slice(4,6))-1;
da = fdate.slice(6);
//VQ.debug('yr:' + yr + ' mo:' + mo + ' da:' + da);
d = new Date(yr,mo,da,0,0,0,0);
var studies_out = new Array();
for (var i = 0; i < studies.length; i++){
sdate = studies[i].StudyDate;
yr = sdate.slice(0,4);
mo = parseFloat(sdate.slice(4,6))-1;
da = sdate.slice(6);
d2 = new Date(yr,mo,da,0,0,0,0);
//VQ.debug('yr:' + yr + ' mo:' + mo + ' da:' + da);
if (d2 > d && !older) // Its more recent
studies_out.push(studies[i]);
else if (d2 < d && older) // Its older
studies_out.push(studies[i]);
}
return studies_out;
}
// Function to filter out dates either older or newer than fdate. Takes array of studies
// if older, returns studies before date
// if !older, returns studies after date
function filtDates_roi(studies,fdate,older){
// fdate is a string YYYYMMDD (guraranteed in parent fn)
yr = fdate.slice(0,4);
mo = parseFloat(fdate.slice(4,6))-1;
da = fdate.slice(6);
//VQ.debug('yr:' + yr + ' mo:' + mo + ' da:' + da);
d = new Date(yr,mo,da,0,0,0,0);
var studies_out = new Array();
for (var i = 0; i < studies.length; i++){
sdate = studies[i].timestamp;
yr = sdate.slice(0,4);
mo = parseFloat(sdate.slice(4,6))-1;
da = sdate.slice(6);
d2 = new Date(yr,mo,da,0,0,0,0);
//VQ.debug('yr:' + yr + ' mo:' + mo + ' da:' + da);
if (d2 > d && !older) // Its more recent
studies_out.push(studies[i]);
else if (d2 < d && older) // Its older
studies_out.push(studies[i]);
}
return studies_out;
}
// Custom sort function that calls a specific sort function. Useful becuase of how javascripts sort() method works-- the input is specific
function sortList(list,prop){
switch (prop) {
case "PatientsName":
list.sort(nameSort);
break
case "PatientID":
list.sort(idSort);
break;
case "StudyDate":
list.sort(timeSort);
break;
case "StudyTime":
list.sort(timeSort);
break;
default:
list.sort(seriesSort);
}
return list;
}
// Sort by patients name
function nameSort(a,b){
var idA = a['PatientsName'];
var idB = b['PatientsName'];
return stringSort(idA,idB);
}
// Sort by patient id
function idSort(a,b){
var idA = a['PatientID'];
var idB = b['PatientID'];
return stringSort(idA,idB);
}
// Sort by series description
function descSort(a,b){
var idA = a['SeriesDescription'];
var idB = b['SeriesDescription'];
return stringSort(idA,idB);
}
// Sort by time
function timeSort(a,b){
var ta = a.StudyDate + a.StudyTime;
var tb = b.StudyDate + b.StudyTime;
return stringSort(ta,tb);
}
/**
* Convenience sort function for iPACS data
* Sorts series by default
*/
function seriesSort(a, b) {
// Modality
var modPriority = [ "CT", "MR", "NM", "PT", "AT" ];
var idA = modPriority.indexOf(a.Modality);
var idB = modPriority.indexOf(b.Modality);
if (idA !== idB) {
return idA - idB;
}
// Patient ID
if (a.PatientID !== b.PatientID) {
return stringSort(a.PatientID, b.PatientID);
}
// Patient Name
if (a.PatientsName !== b.PatientsName) {
return stringSort(a.PatientsName, b.PatientsName);
}
// Series time
var timeA = a.SeriesDate + a.SeriesTime;
var timeB = b.SeriesDate + b.SeriesTime;
if (timeA !== timeB) {
return stringSort(timeA, timeB);
}
// Series name
if (a.SeriesDescription !== b.SeriesDescription) {
return stringSort(a.SeriesDescription, b.SeriesDescription);
}
}
// get ROI helper methods
// Given a list of roi objects, filter out all ones that don't contain AT LEAST all elements in roilist (list of roi names)
function filterName(rlist,roilist){
var rlist_final = new Array();
for (var i = 0; i < rlist.length ; i ++){
var nlist = rlist[i].names;
var found_roi = true;
for (var j = 0 ; j < roilist.length; j ++){
if (nlist.indexOf(roilist[j]) > -1)
continue;
else
found_roi = false;
}
if (found_roi)
rlist_final.push(rlist[i]);
}
return rlist_final;
}
// Given a list of roi objects, filter out all ones that weren't created by cname
function filterCreator(rlist,cname){
var rlist_final = new Array();
for (var i = 0; i < rlist.length; i++){
if (wildcardMatch(rlist[i].creator,cname))
rlist_final.push(rlist[i]);
}
return rlist_final;
}
function find_latest_roi(res) { //find the latest timestamp for each unique roi
var resfinal = res[0];
var ts = new Date();
ts.setFullYear(2000,0,0);
for (r in res) {
var timestamp = convert_date(res[r]["timestamp"]);
if (timestamp > ts){
var ts = timestamp;
resfinal = res[r];
}
}
return resfinal;
}
// Helper declaration to create an roi object
// Not sure if this is overkill, but prefer it this way
// Possibly have constructor take filename as argument -- should be unique for each roi object
function roi_obj(filename){
this.creator = '';
this.timestamp = '';
this.filename = filename;
this.names = [];
this.setid = '{}';
}
// End of file
