/*-
* Copyright 2016 Diamond Light Source Ltd.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
* which accompanies this distribution, and is available at
* http://www.eclipse.org/legal/epl-v10.html
*/
package org.dawnsci.surfacescatter;
import java.util.Arrays;
import org.dawnsci.boofcv.BoofCVImageTrackerServiceCreator;
import org.eclipse.dawnsci.analysis.api.image.IImageTracker;
import org.eclipse.dawnsci.analysis.api.image.IImageTracker.TrackerType;
import org.eclipse.january.dataset.Dataset;
import org.eclipse.january.dataset.DatasetFactory;
import org.eclipse.january.dataset.DatasetUtils;
import org.eclipse.january.dataset.DoubleDataset;
import org.eclipse.january.dataset.IDataset;
import org.eclipse.january.dataset.IndexIterator;
import org.eclipse.january.dataset.LinearAlgebra;
import org.eclipse.january.dataset.Maths;
import uk.ac.diamond.scisoft.analysis.fitting.functions.Polynomial2D;
/**
* Cuts out the region of interest and fits it with a 2D polynomial background.
*/
public class TwoDTracking {
private IImageTracker tracker = null;
private Polynomial2D g2;
private double[] location;
private double[] initialLocation;
private Dataset in1;
private int[] len;
private int[] pt;
public IDataset TwoDTracking1(SuperModel sm,
IDataset input,
ExampleModel model,
DataModel dm,
int trackingMarker,
int k,
int selection) {
len = model.getLenPt()[0];
pt = model.getLenPt()[1];
initialLocation = new double[] { (double) pt[1], (double) pt[0], (double) (pt[1] + len[1]), (double) (pt[0]),
(double) pt[1], (double) pt[0] + len[0], (double) (pt[1] + len[1]), (double) (pt[0] + len[0]) };
if (trackingMarker == 3){
model.setInput(null);
trackingMarker = 0;
}
if (trackingMarker == 0) {
if (model.getInput() == null) {
len = model.getLenPt()[0];
pt = model.getLenPt()[1];
// in1 = BoxSlicerRodScanUtilsForDialog.rOIBox(input, len, pt);
tracker = BoofCVImageTrackerServiceCreator.createImageTrackerService();
initialLocation = new double[] { (double) pt[1], (double) pt[0], (double) (pt[1] + len[1]),
(double) (pt[0]), (double) pt[1], (double) pt[0] + len[0], (double) (pt[1] + len[1]),
(double) (pt[0] + len[0]) };
try {
tracker.initialize(input, initialLocation, TrackingMethodology.toTT(model.getTrackerType()));
} catch (Exception e) {
}
model.setTrackerCoordinates(
new double[] { initialLocation[1], initialLocation[0], initialLocation[5], initialLocation[0],
initialLocation[1], initialLocation[2], initialLocation[5], initialLocation[2] });
model.setInput(input);
location = initialLocation;
// sm.addLocationList(k, location);
}
else {
try {
tracker = BoofCVImageTrackerServiceCreator.createImageTrackerService();
tracker.initialize(model.getInput(), model.getTrackerCoordinates(), TrackingMethodology.toTT(model.getTrackerType()));
location = tracker.track(input);
if (location != null) {
model.setTrackerCoordinates(location);
}
int[] len1 = model.getLenPt()[0];
int[] newPt = new int[] { (int) location[0], (int) location[1] };
int[][] newLenPt = new int[2][];
newLenPt[0] = len1;
newLenPt[1] = newPt;
model.setLenPt(newLenPt);
model.setInput(input);
// System.out.println("~~~~~~~~~~~~~~~~~~~success!~~~~~~~~~~~~~~~~~");
} catch (Exception e) {
System.out.println(
"@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@Failed to track");
}
}
}
else if (trackingMarker == 1) {
if (model.getInput() == null) {
len = model.getLenPt()[0];
pt = model.getLenPt()[1];
dm.setInitialDataset(input);
dm.setInitialLenPt(new int[][] {len, pt });
// in1 = BoxSlicerRodScanUtilsForDialog.rOIBox(input, len, pt);
tracker = BoofCVImageTrackerServiceCreator.createImageTrackerService();
initialLocation = new double[] { (double) pt[1], (double) pt[0], (double) (pt[1] + len[1]),
(double) (pt[0]), (double) pt[1], (double) pt[0] + len[0], (double) (pt[1] + len[1]),
(double) (pt[0] + len[0]) };
try {
tracker.initialize(input, initialLocation, TrackingMethodology.toTT(model.getTrackerType()));
} catch (Exception e) {
}
model.setTrackerCoordinates(
new double[] { initialLocation[1], initialLocation[0], initialLocation[5], initialLocation[0],
initialLocation[1], initialLocation[2], initialLocation[5], initialLocation[2] });
model.setInput(input);
location = initialLocation;
}
else {
try {
tracker = BoofCVImageTrackerServiceCreator.createImageTrackerService();
tracker.initialize(model.getInput(), model.getTrackerCoordinates(), TrackingMethodology.toTT(model.getTrackerType()));
location = tracker.track(input);
if (location != null) {
model.setTrackerCoordinates(location);
}
int[] len1 = model.getLenPt()[0];
int[] newPt = new int[] { (int) location[0], (int) location[1] };
int[][] newLenPt = new int[2][];
newLenPt[0] = len1;
newLenPt[1] = newPt;
model.setLenPt(newLenPt);
model.setInput(input);
// System.out.println("~~~~~~~~~~~~~~~~~~~success!~~~~~~~~~~~~~~~~~");
} catch (Exception e) {
System.out.println(
"@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@Failed to track");
}
}
}
else if (trackingMarker == 2) {
if (model.getInput() == null) {
len = dm.getInitialLenPt()[0];
pt = dm.getInitialLenPt()[1];
tracker =null;
tracker = BoofCVImageTrackerServiceCreator.createImageTrackerService();
initialLocation = new double[] { (double) pt[1], (double) pt[0], (double) (pt[1] + len[1]),
(double) (pt[0]), (double) pt[1], (double) pt[0] + len[0], (double) (pt[1] + len[1]),
(double) (pt[0] + len[0]) };
try {
tracker.initialize(dm.getInitialDataset(), initialLocation, TrackingMethodology.toTT(model.getTrackerType()));
//tracker.initialize(dm.getInitialDataset(), initialLocation, TrackerType.TLD);
location = tracker.track(input);
if (location != null) {
model.setTrackerCoordinates(location);
}
} catch (Exception e) {
e.printStackTrace();
}
// model.setTrackerCoordinates(new double[] { location[1], location[0], location[5], location[0],
// location[1], initialLocation[2], location[5], location[2] });
model.setInput(input);
}
else {
try {
tracker = BoofCVImageTrackerServiceCreator.createImageTrackerService();
tracker.initialize(model.getInput(), model.getTrackerCoordinates(), TrackingMethodology.toTT(model.getTrackerType()));
location = tracker.track(input);
if (location != null) {
model.setTrackerCoordinates(location);
}
int[] len1 = model.getLenPt()[0];
int[] newPt = new int[] { (int) location[0], (int) location[1] };
int[][] newLenPt = new int[2][];
newLenPt[0] = len1;
newLenPt[1] = newPt;
model.setLenPt(newLenPt);
model.setInput(input);
// System.out.println("~~~~~~~~~~~~~~~~~~~success!~~~~~~~~~~~~~~~~~");
} catch (Exception e) {
System.out.println(
"@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@Failed to track");
}
}
}
if (location == null) {
location = model.getTrackerCoordinates();
}
sm.addLocationList(selection, location);
dm.addLocationList(model.getDatImages().getShape()[0], k, location);
len = model.getLenPt()[0];
pt = model.getLenPt()[1];
// in1 = BoxSlicerRodScanUtilsForDialog.rOIHalfBox(input, len, pt);
in1 = BoxSlicerRodScanUtilsForDialog.rOIBox(input, len, pt);
//in1 = (Dataset) PlotSystem2DataSetter.PlotSystem2DataSetter1(model);
if (g2 == null)
g2 = new Polynomial2D(AnalaysisMethodologies.toInt(model.getFitPower()));
if ((int) Math.pow(AnalaysisMethodologies.toInt(model.getFitPower()) + 1, 2) != g2.getNoOfParameters())
g2 = new Polynomial2D(AnalaysisMethodologies.toInt(model.getFitPower()));
Dataset[] fittingBackground = BoxSlicerRodScanUtilsForDialog.LeftRightTopBottomBoxes(input, len, pt,
model.getBoundaryBox());
if(Arrays.equals(fittingBackground[0].getShape(),(new int[] {2,2}))){
return (IDataset) fittingBackground[0];
}
// Dataset offset = DatasetFactory.ones(fittingBackground[2].getShape(), Dataset.FLOAT64);
System.out.println("Tracker position: " + location[0] + " , " + location[1]);
// Dataset intermediateFitTest = Maths.add(offset, fittingBackground[2]);
Dataset matrix = LinearLeastSquaresServicesForDialog.polynomial2DLinearLeastSquaresMatrixGenerator(
AnalaysisMethodologies.toInt(model.getFitPower()), fittingBackground[0], fittingBackground[1]);
DoubleDataset test = (DoubleDataset) LinearAlgebra.solveSVD(matrix, fittingBackground[2]);
double[] params = test.getData();
DoubleDataset in1Background = g2.getOutputValues0(params, len, model.getBoundaryBox(),
AnalaysisMethodologies.toInt(model.getFitPower()));
IndexIterator it = in1Background.getIterator();
while (it.hasNext()) {
double v = in1Background.getElementDoubleAbs(it.index);
if (v < 0)
in1Background.setObjectAbs(it.index, 0.1);
}
dm.addBackgroundDatArray(in1Background);
Dataset pBackgroundSubtracted = Maths.subtract(in1, in1Background, null);
pBackgroundSubtracted.setName("pBackgroundSubtracted");
IndexIterator it1 = pBackgroundSubtracted.getIterator();
while (it1.hasNext()) {
double q = pBackgroundSubtracted.getElementDoubleAbs(it1.index);
if (q < 0)
pBackgroundSubtracted.setObjectAbs(it1.index, 0);
}
Dataset output = DatasetUtils.cast(pBackgroundSubtracted, Dataset.FLOAT64);
output.setName("Region of Interest, polynomial background removed");
return output;
}
public void resetTracker() {
tracker = null;
}
}