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PSFCapsule.java
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Mon, Nov 4, 18:04

PSFCapsule.java
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/*
* DeconvolutionLab2
*
* Conditions of use: You are free to use this software for research or
* educational purposes. In addition, we expect you to include adequate
* citations and acknowledgments whenever you present or publish results that
* are based on it.
*
* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
*/
/*
* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
*
* This file is part of DeconvolutionLab2 (DL2).
*
* DL2 is free software: you can redistribute it and/or modify it under the
* terms of the GNU General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your option) any later
* version.
*
* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with
* DL2. If not, see <http://www.gnu.org/licenses/>.
*/
package deconvolution.capsule;
import java.awt.Dimension;
import javax.swing.JSplitPane;
import bilib.component.PanelImage;
import bilib.table.CustomizedTable;
import bilib.tools.NumFormat;
import deconvolution.Deconvolution;
import deconvolution.Features;
import signal.RealSignal;
import signal.SignalCollector;
/**
* This class is a information module for the PSF source.
*
* @author Daniel Sage
*
*/
public class PSFCapsule extends AbstractCapsule implements Runnable {
private PanelImage pnImage;
private CustomizedTable table;
public PSFCapsule(Deconvolution deconvolution) {
super(deconvolution);
pnImage = new PanelImage();
table = new CustomizedTable(new String[] { "Features", "Values" }, false);
pnImage.setPreferredSize(new Dimension(300, 300));
split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, table.getPane(300, 300), pnImage);
}
@Override
public void update() {
split.setDividerLocation(300);
if (pnImage == null)
return;
if (table == null)
return;
table.removeRows();
table.append(new String[] { "PSF", "Waiting for loading ..." });
Thread thread = new Thread(this);
thread.setPriority(Thread.MIN_PRIORITY);
thread.start();
}
@Override
public String getID() {
return "PSF";
}
@Override
public void run() {
Features features = new Features();
if (deconvolution.image == null) {
startAsynchronousTimer("Open image", 200);
deconvolution.image = deconvolution.openImage();
stopAsynchronousTimer();
}
if (deconvolution.getController().getPadding() == null) {
features.add("Padding", "No valid padding");
return;
}
if (deconvolution.getController().getApodization() == null) {
features.add("Apodization", "No valid apodization");
return;
}
if (deconvolution.psf == null) {
startAsynchronousTimer("Open PSF", 200);
deconvolution.psf = deconvolution.openPSF();
stopAsynchronousTimer();
}
if (deconvolution.psf == null) {
features.add("PSF", "No valid PSF");
return;
}
startAsynchronousTimer("Open PSF", 200);
float stati[] = deconvolution.psf.getStats();
int sizi = deconvolution.psf.nx * deconvolution.psf.ny * deconvolution.psf.nz;
float totali = stati[0] * sizi;
features.add("<html><b>Orignal PSF</b></html>", "");
features.add("Size", deconvolution.psf.dimAsString() + " " + NumFormat.bytes(sizi * 4));
features.add("Mean (stdev)", NumFormat.nice(stati[0]) + " (" + NumFormat.nice(stati[3]) + ")");
features.add("Extrema (min, max)", NumFormat.nice(stati[1]) + ", " + NumFormat.nice(stati[2]));
features.add("Energy (integral)", NumFormat.nice(stati[5]) + " (" + NumFormat.nice(totali) + ")");
table.removeRows();
for (String[] feature : features)
table.append(feature);
RealSignal h;
if (deconvolution.image == null) {
features.add("Image", "No valid input image to resize");
h = deconvolution.psf.duplicate();
}
else
h = deconvolution.psf.changeSizeAs(deconvolution.image);
h.normalize(deconvolution.getController().getNormalizationPSF());
float stats[] = h.getStats();
int sizs = h.nx * h.ny * h.nz;
float totals = stats[0] * sizs;
double incpad = (double)((sizs-sizi)/sizi*100.0);
features.add("<html><b>Working PSF</b></html>", "");
features.add("Size", h.dimAsString() + " " + NumFormat.bytes(sizs * 4));
features.add("Mean (stdev)", NumFormat.nice(stats[0]) + " (" + NumFormat.nice(stats[3]) + ")");
features.add("Extrema (min, max)", NumFormat.nice(stats[1]) + ", " + NumFormat.nice(stats[2]));
features.add("Energy (integral)", NumFormat.nice(stats[5]) + " (" + NumFormat.nice(totals) + ")");
features.add("<html><b>Information</b></html>", "");
features.add("Size increase (image)", NumFormat.nice(incpad) + "%");
features.add("Energy lost", NumFormat.nice((stats[5] - stati[5]) / stati[5] * 100));
SignalCollector.free(h);
table.removeRows();
for (String[] feature : features)
table.append(feature);
pnImage.setImage(deconvolution.psf.preview());
stopAsynchronousTimer();
}
}

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