public void hide(boolean refresh) {
container.remove(layout);
if (showMeasurements.isSelected()) {
container.remove(measurements);
showMeasurements.setSelected(false);
}
if (refresh) core.refreshDisplay();
}
public void toggleShowMeasurements() {
if (showMeasurements.isSelected()) {
measurements.setStructures(currentNucId, currentStructureIdx);
measurements.setObjects(list.getSelectedValues());
this.container.add(measurements);
} else this.container.remove(measurements);
core.refreshDisplay();
}
// init also call init from superclass
public void init() {
super.init();
Window w = s.getFullScreenWindow();
w.setFocusTraversalKeysEnabled(false); // just be a tab button, not just jump to next form
w.addKeyListener(this);
mess = "Press escape to exit";
}
private void setSortKeys() {
if (currentChannels != null && currentChannels.length == 1) {
MeasurementKey mkey =
new MeasurementKey(new int[] {currentChannels[0].getIdx()}, MeasurementObject.Number);
System.out.println("Query:" + mkey.toString());
((ObjectManagerLayout) layout).setKeys(Core.getExperiment().getKeys().get(mkey));
} else {
((ObjectManagerLayout) layout).unableSortKeys();
}
}
public void startThreads() {
directTransferThread.start();
persistentQueue.startThreads();
final TimerTask task =
new TimerTask() {
@Override
public void run() {
maybeStartRequests();
}
};
Core.schedule(task, 3000, 3000);
}
public void templateMatching() {
System.loadLibrary(Core.NATIVE_LIBRARY_NAME);
int match_method = 5;
int max_Trackbar = 5;
Mat data = Highgui.imread("images/training_data/1" + "/data (" + 1 + ").jpg");
Mat temp = Highgui.imread("images/template.jpg");
Mat img = data.clone();
int result_cols = img.cols() - temp.cols() + 1;
int result_rows = img.rows() - temp.rows() + 1;
Mat result = new Mat(result_rows, result_cols, CvType.CV_32FC1);
Imgproc.matchTemplate(img, temp, result, match_method);
Core.normalize(result, result, 0, 1, Core.NORM_MINMAX, -1, new Mat());
double minVal;
double maxVal;
Point minLoc;
Point maxLoc;
Point matchLoc;
// minMaxLoc( result, &minVal, &maxVal, &minLoc, &maxLoc, Mat() );
Core.MinMaxLocResult res = Core.minMaxLoc(result);
if (match_method == Imgproc.TM_SQDIFF || match_method == Imgproc.TM_SQDIFF_NORMED) {
matchLoc = res.minLoc;
} else {
matchLoc = res.maxLoc;
}
// / Show me what you got
Core.rectangle(
img,
matchLoc,
new Point(matchLoc.x + temp.cols(), matchLoc.y + temp.rows()),
new Scalar(0, 255, 0));
// Save the visualized detection.
Highgui.imwrite("images/samp.jpg", img);
}
public static Mat getCCH(Mat image) {
ArrayList<MatOfPoint> contours = new ArrayList<MatOfPoint>();
Mat hierarchy = new Mat();
Imgproc.findContours(
image, contours, hierarchy, Imgproc.RETR_EXTERNAL, Imgproc.CHAIN_APPROX_NONE);
Mat chainHistogram = Mat.zeros(1, 8, CvType.CV_32F);
int n = 0;
MatOfPoint2f approxCurve = new MatOfPoint2f();
for (MatOfPoint contour : contours) {
// get the freeman chain code from the contours
int rows = contour.rows();
// System.out.println("\nrows"+rows+"\n"+contour.dump());
int direction = 7;
Mat prevPoint = contours.get(0).row(0);
n += rows - 1;
for (int i = 1; i < rows; i++) {
// get the current point
double x1 = contour.get(i - 1, 0)[1];
double y1 = contour.get(i - 1, 0)[0];
// get the second point
double x2 = contour.get(i, 0)[1];
double y2 = contour.get(i, 0)[0];
if (x2 == x1 && y2 == y1 + 1) direction = 0;
else if (x2 == x1 - 1 && y2 == y1 + 1) direction = 1;
else if (x2 == x1 - 1 && y2 == y1) direction = 2;
else if (x2 == x1 - 1 && y2 == y1 - 1) direction = 3;
else if (x2 == x1 && y2 == y1 - 1) direction = 4;
else if (x2 == x1 + 1 && y2 == y1 - 1) direction = 5;
else if (x2 == x1 + 1 && y2 == y1) direction = 6;
else if (x2 == x1 + 1 && y2 == y1 + 1) direction = 7;
else System.out.print("err");
double counter = chainHistogram.get(0, direction)[0];
chainHistogram.put(0, direction, ++counter);
System.out.print(direction);
}
}
System.out.println("\n" + chainHistogram.dump());
Scalar alpha = new Scalar(n); // the factor
Core.divide(chainHistogram, alpha, chainHistogram);
System.out.println("\nrows=" + n + " " + chainHistogram.dump());
return chainHistogram;
}
private void sort(String key, Object3DGui[] objectsGui, int structureIdx) {
Object3DGui.setAscendingOrger(((ObjectManagerLayout) layout).getAscendingOrder());
HashMap<Integer, BasicDBObject> objects =
Core.getExperiment().getConnector().getObjects(currentNucId, structureIdx);
boolean notFound = false;
for (Object3DGui o : objectsGui) {
BasicDBObject dbo = objects.get(o.getLabel());
if (dbo != null) {
if (dbo.containsField(key)) o.setValue(dbo.getDouble(key));
else {
o.setValue(-1);
notFound = true;
}
}
}
if (notFound)
ij.IJ.log("Warning measurement: " + key + " not found for one or several objects");
Arrays.sort(objectsGui);
}
public void show(boolean refresh) {
container.add(layout);
if (refresh) core.refreshDisplay();
}
@Override
public void startElement(String namespaceURI, String localName, String qName, Attributes atts) {
state = findState(qName);
String at;
if (state != XmlState.BDN && !valid) {
logger.error("BDN tag missing");
}
txt = null;
switch (state) {
case UNKNOWN:
logger.error("Unknown tag " + qName + "\n");
break;
case BDN:
if (valid) {
logger.error("BDN must be used only once");
} else {
valid = true;
}
break;
case NAME:
at = atts.getValue("Title");
if (at != null) {
title = at;
logger.trace("Title: " + title + "\n");
}
break;
case LANGUAGE:
at = atts.getValue("Code");
if (at != null) {
language = at;
logger.trace("Language: " + language + "\n");
}
break;
case FORMAT:
at = atts.getValue("FrameRate");
if (at != null) {
fps = SubtitleUtils.getFps(at);
fpsXml = XmlFps(fps);
logger.trace("fps: " + ToolBox.formatDouble(fps) + "\n");
}
at = atts.getValue("VideoFormat");
if (at != null) {
String res = at;
for (Resolution r : Resolution.values()) {
if (res.length() == 4
&& res.charAt(0) != '7') { // hack to rename 480p/576p to 480i/576i
res = res.replace('p', 'i');
}
if (r.getResolutionNameForXml().equalsIgnoreCase(res)) {
resolution = r;
logger.trace("Language: " + r.getResolutionNameForXml() + "\n");
break;
}
}
}
break;
case EVENTS:
at = atts.getValue("NumberofEvents");
if (at != null) {
int n = ToolBox.getInt(at);
if (n > 0) {
/* number of subtitles read from the xml */
Core.setProgressMax(n);
}
}
break;
case EVENT:
pic = new SubPictureXml();
subPictures.add(pic);
int num = subPictures.size();
logger.info("#" + num + "\n");
Core.setProgress(num);
at = atts.getValue("InTC");
if (at != null) {
pic.setStartTime(timeStrXmlToPTS(at, fpsXml));
if (pic.getStartTime() == -1) {
pic.setStartTime(0);
logger.warn("Invalid start time " + at + "\n");
}
}
at = atts.getValue("OutTC");
if (at != null) {
pic.setEndTime(timeStrXmlToPTS(at, fpsXml));
if (pic.getEndTime() == -1) {
pic.setEndTime(0);
logger.warn("Invalid end time " + at + "\n");
}
}
if (fps != fpsXml) {
pic.setStartTime((pic.getStartTime() * 1001 + 500) / 1000);
pic.setEndTime((pic.getEndTime() * 1001 + 500) / 1000);
}
at = atts.getValue("Forced");
pic.setForced(at != null && at.equalsIgnoreCase("true"));
if (pic.isForced()) {
numForcedFrames++;
}
int dim[] = resolution.getDimensions();
pic.setWidth(dim[0]);
pic.setHeight(dim[1]);
break;
case GRAPHIC:
pic.setImageWidth(ToolBox.getInt(atts.getValue("Width")));
pic.setImageHeight(ToolBox.getInt(atts.getValue("Height")));
pic.setOfsX(ToolBox.getInt(atts.getValue("X")));
pic.setOfsY(ToolBox.getInt(atts.getValue("Y")));
pic.storeOriginalOffsets();
txt = new StringBuffer();
break;
}
}