00-Example.vqs

A list of some commonly used functions.

//
// Example VQScript
//
// Please see
//   http://www.davidflanagan.com/javascript5/
// for more details on ECMAScript/JavaScript
//
//
// VQ is a global object
// allowing access to VQ components
//
 
for (var i=0; i<10; i++) {              // Show a simple loop 0-9
    VQ.debug("Simple loop: "+i);        // writes 'Simple loop: 0', ... to log file
}
 
var dm = VQ.dataManager();      // get the Data Manager object:
 
// loadDataLocal(dm);
loadDataRemote(dm);
 
// Examples of how to setup the images
// c.setPal(0, "gold");            // Ref: palette to gold
// c.setRange(0, 0.05, 0.9);       // Ref: range from 5-90%
 
var mainWin = VQ.mainWin();
 
if (0) { preProcessing(); }
if (0) { userInteraction(); }
metaData(dm);
setupMinMax(dm, 0, 0.995);
if (0) { saveImageSeries(); }
bedremoval();
smoothing();
doubleOtsu();
 
VQ.debug( "Value: "+dm.getValue(0,1,2, 0) );
VQ.showMessage("This is a message to the user:\nYou're welcome!");
 
if (0) {
    VQ.writeFile("/tmp/blub.txt",  "Hallo Welt\n");
    VQ.appendFile("/tmp/blub.txt", "Hello World\n");
}
 
 
// storeData("folder:///home/lackas/Users/Desktop/VQScriptOutput");
// VQ.quit();      // and we are done
 
/* FUNCTIONS */
 
function bedremoval() {
    // CT Bed removal
    VQ.triggerAction("Tools|CT|Bed removal");
}
 
function doubleOtsu() {
    // go into 3D ROI mode:
    mainWin.setViewMode("Slice View", "3D ROI Tool");
    VQ.vtkController().setAutoUpdate(false);
 
    // switch page to Segmentation algorithms,
    // not really required, but easier to debug
    VQ.getWidget("tabWidget").setCurrentIndex(3);  
 
    // shortcut:
    var op = VQ.currentOp();
 
    // create ROIs:
    op.addROI("Otsu 1", "red");
    op.addROI("Bone", "peachpuff");
 
    // select Input/Output ROI:
    op.setInputROI(0);
    op.setCurrentROI(1);
 
    // Selecting algorithm:
    VQ.getWidget("MagicSegmentationSelector").setCurrentIndex(3);
    // Would be nice to have: widget.setEditText("Otsu Thresholding");
 
    // Apply algorithm:
    VQ.debug("Setup first otsu");
    VQ.getWidget("MagicApply").click();
 
    // update Input/Output ROI:
    op.setInputROI(1);
    op.setCurrentROI(2);
 
    // Apply again:
    VQ.debug("Setup 2nd otsu");
    VQ.getWidget("MagicApply").click();
 
    // Hide temporary ROI (name, color, immutable, hidden)
    VQ.debug("Double otsu done");
    VQ.vtkController().setAutoUpdate(true);
    op.editROI(1, "Temp", "red", false, true);
}
 
function setupMinMax(dm, id, thres) {// use Min/Max Tool to set percentile based value
    var minMaxTool = VQ.minMaxTool();
    var cutOff = minMaxTool.computePercentileCutoff(id, thres);
    VQ.debug("**** cutOff = "+cutOff);
    var min = dm.getMinCached(id);
    var max = dm.getMaxCached(id);
    VQ.debug("**** min=" +min+", max="+max);
    VQ.sliceViewer().setMinMaxCache(id, min, cutOff);
}
 
function saveImageSeries() {            // saving series of images
    mainWin.setViewMode("Slice View", "3D ROI Tool");
 
    var progress = VQ.progressDialog("Saving Images", "Cancel", 0, dm.getDimX());
 
    for(var x=0; x<dm.getDimX(); x++) {            // set position to third in all three dim
        progress.setValue(x);
        c.setPos(0, x);
        // store an image (type 0=MIP, 1=S, 2=C, 3=T, 4=All, 5=Everything)
        // for each sagittal slice position
        VQ.mainWin().saveImage("out"+VQ.counter(x,3)+".png", 4);    // counter() adds leading 0
    }
    progress.hide();
}
 
function metaData(dm) {
    // print some information, such as dim, vs and patientsname:
    VQ.debug("* Dimensions: " + dm.getDimX() + "x" + dm.getDimY() + "x" + dm.getDimZ() );
    VQ.debug("* Voxel Size: " + dm.voxelSizeXY() + "mm, "+dm.voxelSizeZ() + "mm");
    VQ.debug("* PatientsName:" + dm.getDesc(0, "patientsname"));
 
    // access the controler (pos sliders, palette, alpha, int, dim, ...)
    var c = VQ.controler();
    VQ.debug("* Position:" + c.getPos(0) + ":" + c.getPos(1) + ":" + c.getPos(2));
    VQ.debug("* Palette :" + c.getPalname(0));
}
 
function userInteraction() {                        // examples of user interaction
    var item = VQ.getItem("Select View", "View", ["sagittal", "coronal", "transversal"]);
    var i = VQ.getInt("Integer Title", "Integer", 42, 0, 100, 1);
    var d = VQ.getDouble("Double Title", "Double", 3.141, 3, 4, 3);
    var t = VQ.getText("Text Title", "Text", "VQScript rulez!", 0);
    VQ.debug("* item="+item+", i="+i+", d="+d+", t="+t);
}
 
function loadDataRemote(dm) {                        // Testing access to DICOM repositories
    var pwd = '';
    var dcmRepURL = "ipacs://lackas:"+pwd+"@bioscan.ipacs.invicro.com";
    var projectName = "/flectct-segmentation";
    var dcmRep = VQ.dcmRep(dcmRepURL);
    VQ.debug("* ping="+dcmRep.ping());
    VQ.debug("* projects="+dcmRep.getProjectList());
    dcmRep.setProject(projectName);                     // select project
    var studies = VQ.queryStudies(dcmRep, "Mouse*");    // search for patient "Mouse*"
    for (var i=0; i<studies.length; ++i) {
        if (studies[i].PatientsName != "Mouse 15") { continue; }    // skip all but "Mouse 15"
        VQ.debug("* patient["+i+"]: " +studies[i].PatientsName);    // print meta-info
        VQ.debug("* studyuid["+i+"]: "+studies[i].StudyInstanceUID);
        var series = VQ.querySeries(dcmRep, studies[i].StudyInstanceUID);   // fetch series by study id
        for (var j=0; j<series.length; ++j) {
            VQ.debug("  * series["+j+"]: "+series[j].SeriesInstanceUID + ", "+series[j].Modality);
            // // optional print image information
            // var images = VQ.queryImages(dcmRep, studies[i].StudyInstanceUID, 
            //              series[j].SeriesInstanceUID);
            // for (var k=0; k<images.length; ++k) {
            //     VQ.debug("    * image["+k+"]: "+images[k].SOPInstanceUID);
            // }
 
            // download images: 
            var files = VQ.downloadImages(dcmRep, 
                studies[i].StudyInstanceUID, series[j].SeriesInstanceUID);
            dm.openDat(0, files);                           // open data
            dm.setDesc(0, "__repository_url", dcmRepURL);   // set source (to be able to load datapoints,
            dm.setDesc(0, "__project", projectName);        // such as 3D ROIs, annotations, etc...)
        }
    }
    // VQ.abort();  // end script here
} 
 
function loadDataLocal(dm) {
    // define a list with file names (one or multiple for one dataset)
    var list = new Array( "/Users/lackas/Desktop/VQTraining/1.3.6.1.4.1.33793.1.4.0.58478.1299815620.2.dcm" );
    if (!dm.openDat(0, list)) {     // open as reference=0, input1=1, ...
        throw("Could not load data");
    }
}
 
function preProcessing() {      // use a pre-defined protocol to pre-process data
    var protocol = 'autoCrop=true|bedRemoval=true|calibFactor=false|calibFactorValue=CT=1000 Humpf, NM=123.45 kBq|coRegister=true|coRegisterFast=true|coRegisterVersor=false|comment=false|commentText=kBq/ml|convertUnit=false|convertUnitUnit=|qualityControl=false|resample=true|resampleVoxSize=0.3|storeData=false';
    var res = VQ.preProcess(protocol);
    // VQ.showMessage( res );
    VQ.debug( "Pre-Processing: "+res );
    VQ.abort();
}
 
function storeData(repURL) {
    VQ.debug("storeData("+repURL+")");
    var dcmRep = VQ.dcmRep(repURL);
    for (var i=0; i<dm.size(); ++i) {
        VQ.storeData( dcmRep, i );
    }
}
 
function smoothing() {
    mainWin.setViewMode("Slice View", "Filtering");
    VQ.getWidget("cbSelect").setCurrentIndex(4);
    VQ.getWidget("buttonBox").accepted();
}