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IJImager.java
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Sat, Aug 24, 21:04

IJImager.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 imagej;
import java.util.HashMap;
import deconvolutionlab.PlatformImager;
import deconvolutionlab.PlatformImager.ContainerImage;
import ij.ImagePlus;
import ij.ImageStack;
import ij.WindowManager;
import ij.io.FileSaver;
import ij.io.Opener;
import ij.process.FloatProcessor;
import ij.process.ImageProcessor;
import signal.ComplexComponent;
import signal.ComplexSignal;
import signal.RealSignal;
public class IJImager extends PlatformImager {
public static RealSignal create(ImagePlus imp) {
int nx = imp.getWidth();
int ny = imp.getHeight();
int nz = imp.getStackSize();
RealSignal signal = new RealSignal(nx, ny, nz);
for (int k = 0; k < nz; k++) {
ImageProcessor ip = imp.getStack().getProcessor(k + 1).convertToFloat();
signal.setXY(k, (float[]) ip.getPixels());
}
return signal;
}
@Override
public RealSignal create() {
return build(WindowManager.getCurrentImage());
}
@Override
public RealSignal create(String name) {
ImagePlus imp = null;
if (name.equalsIgnoreCase("active"))
imp = WindowManager.getCurrentImage();
else
imp = WindowManager.getImage(name);
if (imp == null)
imp = WindowManager.getCurrentImage();
return build(imp);
}
@Override
public RealSignal open(String filename) {
Opener opener = new Opener();
ImagePlus imp = opener.openImage(filename);
return build(imp);
}
@Override
public void show(RealSignal signal, String title) {
show(signal, title, PlatformImager.Type.FLOAT);
}
@Override
public void show(RealSignal signal, String title, PlatformImager.Type type) {
show(signal, title, type, signal.nz / 2);
}
@Override
public void show(RealSignal signal, String title, PlatformImager.Type type, int z) {
ImagePlus imp = build(signal, type);
if (imp != null) {
imp.setTitle(title);
int nz = imp.getStackSize();
imp.show();
imp.setSlice(Math.max(1, Math.min(nz, z)));
imp.getProcessor().resetMinAndMax();
}
}
public ContainerImage createContainer(String title) {
return new ContainerImage();
}
@Override
public void append(ContainerImage container, RealSignal signal, String title) {
append(container, signal, title, PlatformImager.Type.FLOAT);
}
@Override
public void append(ContainerImage container, RealSignal signal, String title, PlatformImager.Type type) { ImagePlus cont = (ImagePlus) container.object;
if (container.object == null) {
ImageStack stack = new ImageStack(signal.nx, signal.ny);
stack.addSlice(build(signal, type).getProcessor());
stack.addSlice(build(signal, type).getProcessor());
container.object = new ImagePlus(title, stack);
((ImagePlus)container.object).show();
}
else {
cont.getStack().addSlice(build(signal, type).getProcessor());
cont.setSlice(cont.getStack().getSize());
cont.updateAndDraw();
cont.getProcessor().resetMinAndMax();
}
}
@Override
public void save(RealSignal signal, String filename) {
save(signal, filename, PlatformImager.Type.FLOAT);
}
@Override
public void save(RealSignal signal, String filename, PlatformImager.Type type) {
ImagePlus imp = build(signal, type);
if (imp != null) {
if (imp.getStackSize() == 1) {
new FileSaver(imp).saveAsTiff(filename);
}
else {
new FileSaver(imp).saveAsTiffStack(filename);
}
}
}
@Override
public void show(ComplexSignal signal, String title) {
show(signal, title, ComplexComponent.MODULE);
}
@Override
public void show(ComplexSignal signal, String title, ComplexComponent complex) {
ImageStack stack = new ImageStack(signal.nx, signal.ny);
for (int k = 0; k < signal.nz; k++) {
float[] plane = null;
switch (complex) {
case REAL:
plane = signal.getRealXY(k);
break;
case IMAGINARY:
plane = signal.getImagXY(k);
break;
case MODULE:
plane = signal.getModuleXY(k);
break;
default:
plane = signal.getModuleXY_dB(k);
}
stack.addSlice(new FloatProcessor(signal.nx, signal.ny, plane));
}
new ImagePlus(title, stack).show();
}
private RealSignal build(ImagePlus imp) {
if (imp == null)
return null;
int nx = imp.getWidth();
int ny = imp.getHeight();
int nz = imp.getStackSize();
RealSignal signal = new RealSignal(nx, ny, nz);
for (int k = 0; k < nz; k++) {
ImageProcessor ip = imp.getStack().getProcessor(k + 1).convertToFloat();
signal.setXY(k, (float[]) ip.getPixels());
}
return signal;
}
private ImagePlus build(RealSignal signal, PlatformImager.Type type) {
if (signal == null)
return null;
ImageStack stack = new ImageStack(signal.nx, signal.ny);
for (int k = 0; k < signal.nz; k++) {
ImageProcessor ip = new FloatProcessor(signal.nx, signal.ny, signal.getXY(k));
switch (type) {
case BYTE:
stack.addSlice(ip.convertToByteProcessor(false));
break;
case SHORT:
stack.addSlice(ip.convertToShortProcessor(false));
break;
case FLOAT:
stack.addSlice(ip);
default:
break;
}
}
return new ImagePlus("", stack);
}
@Override
public String getName() {
return "ImageJ";
}
}

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