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diff --git a/DeconvolutionLab2.config b/DeconvolutionLab2.config
index 67086af..ec0766e 100644
--- a/DeconvolutionLab2.config
+++ b/DeconvolutionLab2.config
@@ -1,58 +1,74 @@
-#DeconvolutionLab2 [Beta 2]
-#DeconvolutionLab2 [Beta 2]
-#Sun Feb 26 14:32:31 CET 2017
-Algorithm.I.gaussian.mean=0.0
-Algorithm.I.gaussian.stdev=1.0
-Algorithm.I.iterations=10
-Algorithm.I.poisson=0.0
-Algorithm.I.reg=0.1
-Algorithm.I.scale=3
-Algorithm.I.step=1.0
-Algorithm.I.wavelets=Haar
-Algorithm.algorithm=Regularized Inverse Filter [RIF | LRIF]
+#DeconvolutionLab2
+#DeconvolutionLab2
+#Fri Apr 21 13:03:50 CEST 2017
+Algorithm.BVLS.iterations=10
+Algorithm.BVLS.step=1.0
+Algorithm.FISTA.iterations=10
+Algorithm.FISTA.reg=0.1
+Algorithm.FISTA.scale=3
+Algorithm.FISTA.step=1.0
+Algorithm.FISTA.wavelets=Haar
+Algorithm.ICTM.iterations=10
+Algorithm.ICTM.reg=0.1
+Algorithm.ICTM.step=1.0
+Algorithm.ISTA.iterations=10
+Algorithm.ISTA.reg=0.1
+Algorithm.ISTA.scale=3
+Algorithm.ISTA.step=1.0
+Algorithm.ISTA.wavelets=Haar
+Algorithm.LW.iterations=10
+Algorithm.LW.step=1.0
+Algorithm.NNLS.iterations=10
+Algorithm.NNLS.step=1.0
+Algorithm.RIF.reg=0.1
+Algorithm.RL.iterations=10
+Algorithm.RLTV.reg=0.1
+Algorithm.SIM.gaussian.mean=0.0
+Algorithm.SIM.gaussian.stdev=1.0
+Algorithm.SIM.poisson=0.0
+Algorithm.TM.iterations=10
+Algorithm.TM.reg=0.1
+Algorithm.TM.step=1.0
+Algorithm.TRIF.reg=0.1
+Algorithm.VC.iterations=10
+Algorithm.VC.step=1.0
+Algorithm.algorithm=Regularized Inverse Filter
Border.apoxy=Uniform
Border.apoz=Uniform
Border.extxy=0
Border.extz=0
Border.padxy=None
Border.padz=None
-Computation.dim=XYZ
+Computation.display=yes
Computation.epsilon=1E-6
Computation.fft=Fastest
+Computation.multithreading=yes
Computation.normalization=1
-Controller.constraint.enable=false
-Controller.constraint.value=no
-Controller.itmax.enable=true
+Computation.system=yes
+Controller.constraint=no
+Controller.monitor=console table
Controller.reference.enable=false
Controller.reference.value=
Controller.residu.enable=false
Controller.residu.value=0.01
+Controller.stats=no
Controller.time.enable=false
Controller.time.value=3600
-DeconvolutionLab.DeconvolutionDialog.location.h=400
-DeconvolutionLab.DeconvolutionDialog.location.w=600
-DeconvolutionLab.DeconvolutionDialog.location.x=802
-DeconvolutionLab.DeconvolutionDialog.location.y=266
+Controller.verbose=log
DeconvolutionLab.MainDialog.location.h=511
DeconvolutionLab.MainDialog.location.w=593
-DeconvolutionLab.MainDialog.location.x=181
-DeconvolutionLab.MainDialog.location.y=298
-Image.image.row0=Cell7.tif;file;/Users/dsage/Desktop/Maria Azevedo/Cell7.tif;
-Image.image.selected=Cell7.tif;file;/Users/dsage/Desktop/Maria Azevedo/Cell7.tif;
+DeconvolutionLab.MainDialog.location.x=108
+DeconvolutionLab.MainDialog.location.y=440
+Image.image.row0=Cell7.tif;file;/Users/dsage/Desktop/Maria Azevedo/Cell7.tif;null
+Image.image.selected=Cell7.tif;file;/Users/dsage/Desktop/Maria Azevedo/Cell7.tif;null
Language.headless=Run (Headless)
Language.job=Job
Language.language=Command line
-PSF.psf.row0=AirySimulated;synthetic;AirySimulated 100.0 0.0 1.0 size 128 128 32 ;
-PSF.psf.selected=AirySimulated;synthetic;AirySimulated 100.0 0.0 1.0 size 128 128 32 ;
+PSF.psf.row0=AirySimulated;synthetic;AirySimulated 100.0 0.0 1.0 size 128 128 32 ;null
+PSF.psf.selected=AirySimulated;synthetic;AirySimulated 100.0 0.0 1.0 size 128 128 32 ;null
+Path.current=Current
+Path.path=/Users/sage/Desktop/worksmlm/deconvolution
Running.Directory=/Users/dsage/git/deconvolution
-Running.Display=yes
Running.Monitor=console table
-Running.Multithreading=yes
Running.Path=current
-Running.Stats=no
-Running.System=yes
Running.Verbose=log
-System.Frame.location.h=313
-System.Frame.location.w=637
-System.Frame.location.x=0
-System.Frame.location.y=23
diff --git a/DeconvolutionLab2/DeconvolutionLab2.config b/DeconvolutionLab2/DeconvolutionLab2.config
index 457d615..ac617a2 100644
--- a/DeconvolutionLab2/DeconvolutionLab2.config
+++ b/DeconvolutionLab2/DeconvolutionLab2.config
@@ -1,93 +1,97 @@
#DeconvolutionLab2
#DeconvolutionLab2
-#Fri Apr 21 11:36:46 CEST 2017
+#Fri Apr 21 17:57:52 CEST 2017
Algorithm.BVLS.iterations=10
Algorithm.BVLS.step=1.0
Algorithm.FISTA.iterations=10
Algorithm.FISTA.reg=0.1
Algorithm.FISTA.scale=3
Algorithm.FISTA.step=1.0
Algorithm.FISTA.wavelets=Haar
Algorithm.ICTM.iterations=10
Algorithm.ICTM.reg=0.4642
Algorithm.ICTM.step=1.0
Algorithm.ISTA.iterations=10
Algorithm.ISTA.reg=0.1
Algorithm.ISTA.scale=3
Algorithm.ISTA.step=1.0
Algorithm.ISTA.wavelets=Haar
Algorithm.LW.iterations=10
Algorithm.LW.step=1.0
Algorithm.NNLS.iterations=10
Algorithm.NNLS.step=1.0
Algorithm.RIF.reg=0.1
Algorithm.RL.iterations=10
Algorithm.RLTV.reg=1.000E-18
Algorithm.SIM.gaussian.mean=0.0
Algorithm.SIM.gaussian.stdev=1.0
Algorithm.SIM.poisson=0.0
Algorithm.TM.iterations=10
Algorithm.TM.reg=0.1
Algorithm.TM.step=1.0
Algorithm.TRIF.reg=0.1
Algorithm.VC.iterations=10
Algorithm.VC.step=1.0
Algorithm.algorithm=Richardson-Lucy Total Variation
Border.apoxy=Uniform
Border.apoz=Uniform
Border.extxy=0
Border.extz=0
Border.padxy=None
Border.padz=None
Computation.display=yes
Computation.epsilon=1E-6
Computation.fft=Fastest
Computation.multithreading=yes
Computation.normalization=1
Computation.system=no
Controller.constraint=no
-Controller.monitor=console
+Controller.monitor=console table
Controller.reference.enable=true
Controller.reference.value=/Users/dsage/Desktop/Screen Shot 2017-04-12 at 22.56.07.png
-Controller.residu.enable=true
+Controller.residu.enable=false
Controller.residu.value=0.01
Controller.stats=show + save
Controller.time.enable=false
Controller.time.value=1
Controller.verbose=log
-DeconvolutionLab.MainDialog.location.h=596
+DeconvolutionLab.DeconvolutionDialog.location.h=400
+DeconvolutionLab.DeconvolutionDialog.location.w=600
+DeconvolutionLab.DeconvolutionDialog.location.x=265
+DeconvolutionLab.DeconvolutionDialog.location.y=516
+DeconvolutionLab.MainDialog.location.h=633
DeconvolutionLab.MainDialog.location.w=500
-DeconvolutionLab.MainDialog.location.x=851
-DeconvolutionLab.MainDialog.location.y=84
+DeconvolutionLab.MainDialog.location.x=1054
+DeconvolutionLab.MainDialog.location.y=111
Image.image.row0=workspace;directory;/Users/dsage/Desktop/workspace;\u232B
Image.image.row10=Screen Shot 2017-04-12 at 22.56.07.png;file;/Users/dsage/Desktop/Screen Shot 2017-04-12 at 22.56.07.png;null
Image.image.row11=RandomLines;synthetic;RandomLines 100.0 size 128 128 32 intensity 255.0 ;\u232B
Image.image.row12=active;platform;active;\u232B
Image.image.row13=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;\u232B
Image.image.row14=Applications;directory;/users/dsage/Applications;\u232B
Image.image.row15=Cube;synthetic;Cube 100.0 0.0 10.0 1.0 size 128 128 32 ;\u232B
Image.image.row16=lib;directory;/Users/dsage/git/deconvolution/DeconvolutionLab2/lib;\u232B
Image.image.row1=CubeSphericalBeads;synthetic;CubeSphericalBeads 3.0 0.5 10.0 5.0 size 128 128 128 intensity 255.0 ;\u232B
Image.image.row2=CubeSphericalBeads;synthetic;CubeSphericalBeads 3.0 0.5 8.0 16.0 size 128 128 32 intensity 255.0 ;\u232B
Image.image.row3=Cube of Spherical Beads;synthetic;Cube of Spherical Beads 3.0 0.5 8.0 8.0 size 128 128 128 intensity 255.0 ;\u232B
Image.image.row4=Screen Shot 2017-04-12 at 22.56.07.png;file;/Users/dsage/Desktop/Screen Shot 2017-04-12 at 22.56.07.png;null
Image.image.row5=20170302_AIDE-MEMOIRE.pdf;file;/Users/dsage/Desktop/20170302_AIDE-MEMOIRE.pdf;null
Image.image.row6=Screen Shot 2017-04-12 at 22.56.07.png;file;/Users/dsage/Desktop/Screen Shot 2017-04-12 at 22.56.07.png;null
Image.image.row7=Screen Shot 2017-04-12 at 22.56.07.png;file;/Users/dsage/Desktop/Screen Shot 2017-04-12 at 22.56.07.png;null
Image.image.row8=20170302_AIDE-MEMOIRE.pdf;file;/Users/dsage/Desktop/20170302_AIDE-MEMOIRE.pdf;null
Image.image.row9=Screen Shot 2017-04-12 at 22.56.07.png;file;/Users/dsage/Desktop/Screen Shot 2017-04-12 at 22.56.07.png;null
-Image.image.selected=workspace;directory;/Users/dsage/Desktop/workspace;\u232B
+Image.image.selected=RandomLines;synthetic;RandomLines 100.0 size 128 128 32 intensity 255.0 ;\u232B
Language.headless=Run (Headless)
Language.job=Job
Language.language=Java
Output.output.row0=mip;MI1;rescaled;;;\u2713;\u2713;\u232B
Output.output.selected=mip;MI1;rescaled;;;\u2713;\u2713;\u232B
PSF.psf.row0=Double-Helix;synthetic;Double-Helix 3.0 30.0 10.0 size 128 128 32 intensity 255.0 ;null
PSF.psf.row1=Sinc;synthetic;Sinc 3.0 3.0 3.0 size 100 128 200 intensity 255.0 ;null
PSF.psf.selected=Double-Helix;synthetic;Double-Helix 3.0 30.0 10.0 size 128 128 32 intensity 255.0 ;null
Path.current=Current
-Path.path=/Users/dsage/git/deconvolution/DeconvolutionLab2
+Path.path=/Users/sage/Desktop/worksmlm/deconvolution/DeconvolutionLab2
Running.Directory=/Users/dsage/git/deconvolution/DeconvolutionLab2
Running.Monitor=table
Running.Path=specify
Running.Verbose=quiet
diff --git a/DeconvolutionLab2/build.xml b/DeconvolutionLab2/build.xml
index 21ed668..0cfdb6a 100644
--- a/DeconvolutionLab2/build.xml
+++ b/DeconvolutionLab2/build.xml
@@ -1,49 +1,48 @@
<?xml version="1.0" encoding="UTF-8"?>
<project name="DeconvolutionLab2" default="build" basedir=".">
<property name="imagej" location="${user.home}/Desktop/ImageJ/plugins" />
<property name="fiji" location="${user.home}/Desktop/Fiji-deconv.app/plugins" />
<property name="matlab" location="/Applications/MATLAB_R2014b.app/java/" />
<property name="doc" location="${user.home}/Desktop/doc/" />
- <property name="javadoc.header" value="&lt;h3&gt;DeconvolutionLab2&lt;/h3&gt;&#09;v1.0" />
- <property name="javadoc.footer" value="&lt;h4&gt;DeconvolutionLab2&lt;/h4&gt;&#09;&lt;script&gt; var tStamp=new Date(); document.write(tStamp.toUTCString()); &lt;/script&gt;" />
- <property name="javadoc.bottom" value='Copyright &amp;copy; &lt;script&gt; var currYear=new Date(); document.write(currYear.getFullYear()); &lt;/script&gt;, Biomedical Imaging Group, EPFL, Lausanne, Switzerland. All rights reserved.' />
+ <property name="javadoc.header" value="&lt;h3&gt;DeconvolutionLab2&lt;/h3&gt;&#09;v1.0" />
+ <property name="javadoc.footer" value="&lt;h4&gt;DeconvolutionLab2&lt;/h4&gt;&#09;&lt;script&gt; var tStamp=new Date(); document.write(tStamp.toUTCString()); &lt;/script&gt;" />
+ <property name="javadoc.bottom" value='Copyright &amp;copy; &lt;script&gt; var currYear=new Date(); document.write(currYear.getFullYear()); &lt;/script&gt;, Biomedical Imaging Group, EPFL, Lausanne, Switzerland. All rights reserved.' />
<target name="build">
<mkdir dir="${doc}" />
<mkdir dir="bin" />
- <copy todir="bin">
- <fileset dir="ij">
- </fileset>
- </copy>
+ <copy todir="bin"><fileset dir="ij"></fileset></copy>
<copy file="plugins.config" toDir="bin" />
-
<zip destfile="../DeconvolutionLab2-src.zip" basedir="src" />
<zip destfile="../DeconvolutionLab2-cls.zip" basedir="bin" />
<jar destfile="../DeconvolutionLab_2.jar" basedir="bin">
<manifest>
<attribute name="Main-Class" value="DeconvolutionLab2" />
<attribute name="Class-Path" value="ij.jar jtransforms.jar" />
</manifest>
</jar>
- <javadoc destdir="${doc}"
- author="true"
- version="true"
- overview="${basedir}/overview.html"
- windowtitle="DeconvolutionLab2">
+ <copy toDir="${fiji}" file="../DeconvolutionLab_2.jar" />
+ <copy toDir="${matlab}" file="../DeconvolutionLab_2.jar" />
+ <copy toDir="${imagej}" file="../DeconvolutionLab_2.jar" />
+
+ <javadoc destdir="${doc}" author="true" version="true" overview="${basedir}/overview.html" windowtitle="DeconvolutionLab2">
<fileset dir="src">
<include name="**/*.java" />
<exclude name="**/fft/**" />
<exclude name="**/jfftw/**" />
</fileset>
- <header><![CDATA[${javadoc.header}]]></header>
- <footer><![CDATA[${javadoc.footer}]]></footer>
- <bottom><![CDATA[${javadoc.bottom}]]></bottom>
+ <header>
+ <![CDATA[${javadoc.header}]]>
+ </header>
+ <footer>
+ <![CDATA[${javadoc.footer}]]>
+ </footer>
+ <bottom>
+ <![CDATA[${javadoc.bottom}]]>
+ </bottom>
</javadoc>
- <copy toDir="${fiji}" file="../DeconvolutionLab_2.jar" />
- <copy toDir="${matlab}" file="../DeconvolutionLab_2.jar" />
- <copy toDir="${imagej}" file="../DeconvolutionLab_2.jar" />
-
</target>
+
</project>
diff --git a/DeconvolutionLab2/src/DeconvolutionLab2.java b/DeconvolutionLab2/src/DeconvolutionLab2.java
index cdfffc5..3034d78 100644
--- a/DeconvolutionLab2/src/DeconvolutionLab2.java
+++ b/DeconvolutionLab2/src/DeconvolutionLab2.java
@@ -1,130 +1,127 @@
/*
* 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/>.
*/
import java.io.File;
import deconvolution.Command;
import deconvolution.Deconvolution;
import deconvolutionlab.Constants;
import deconvolutionlab.Imager;
import deconvolutionlab.Imager.Platform;
import deconvolutionlab.Lab;
import deconvolutionlab.LabDialog;
import deconvolutionlab.monitor.Monitors;
public class DeconvolutionLab2 {
public static String ack = Constants.name + " " + Constants.version + " " + Constants.copyright;
public static void main(String arg[]) {
-
- System.out.println(ack);
Lab.init(Platform.STANDALONE);
-
if (arg.length == 0) {
System.out.println("Starting lab");
lab(arg);
return;
}
String flag = arg[0].trim().toLowerCase();
if (flag.equalsIgnoreCase("help")) {
System.out.println("Starting help");
help();
return;
}
else if (flag.equalsIgnoreCase("lab")) {
System.out.println("Starting lab");
lab(arg);
}
else if (flag.equalsIgnoreCase("fft")) {
System.out.println("Starting fft");
Lab.checkFFT(Monitors.createDefaultMonitor());
}
else if (flag.equalsIgnoreCase("run")) {
System.out.println("Starting run");
String cmd = "";
for (int i = 1; i < arg.length; i++)
cmd += arg[i] + " ";
new Deconvolution("Run", cmd, Deconvolution.Finish.KILL).deconvolve();
}
else if (flag.equalsIgnoreCase("launch")) {
System.out.println("Starting launch");
String cmd = "";
for (int i = 1; i < arg.length; i++)
cmd += arg[i] + " ";
new Deconvolution("Launch", cmd, Deconvolution.Finish.KILL).launch();
}
else
System.out.println("" + flag + " command not found");
}
private static void lab(String arg[]) {
String config = System.getProperty("user.dir") + File.separator + "DeconvolutionLab2.config";
if (arg.length >= 2) {
String filename = arg[1].trim();
File file = new File(filename);
if (file.exists())
if (file.isFile())
if (file.canRead())
config = filename;
}
Lab.init(Platform.STANDALONE, config);
LabDialog dialog = new LabDialog();
dialog.setVisible(true);
}
public static void help() {
System.out.println("More info:" + Constants.url);
System.out.println("Syntax:");
System.out.println("java -jar DeconvolutionLab_2.jar lab");
System.out.println("java -jar DeconvolutionLab_2.jar run {command} ...");
System.out.println("java -jar DeconvolutionLab_2.jar launch {command} ...");
System.out.println("java -jar DeconvolutionLab_2.jar fft");
System.out.println("java -jar DeconvolutionLab_2.jar info");
System.out.println("java -jar DeconvolutionLab_2.jar help");
System.out.println("{command} is the full command line for running a deconvolution");
System.out.println("Keywords of {command}: ");
for (String keyword : Command.keywords)
System.out.println("\t" + keyword);
}
public DeconvolutionLab2(String cmd) {
System.out.println("cmd: " + cmd);
Lab.init(Imager.Platform.STANDALONE, System.getProperty("user.dir") + File.separator + "DeconvolutionLab2.config");
new Deconvolution("CommandLine", cmd).deconvolve();
}
}
diff --git a/DeconvolutionLab2/src/deconvolution/Deconvolution.java b/DeconvolutionLab2/src/deconvolution/Deconvolution.java
index d80e9e4..e263ea8 100644
--- a/DeconvolutionLab2/src/deconvolution/Deconvolution.java
+++ b/DeconvolutionLab2/src/deconvolution/Deconvolution.java
@@ -1,387 +1,398 @@
/*
* 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;
import java.io.File;
import bilib.tools.NumFormat;
import deconvolution.algorithm.AbstractAlgorithm;
import deconvolution.algorithm.Controller;
import deconvolutionlab.Lab;
import deconvolutionlab.Output;
import deconvolutionlab.monitor.AbstractMonitor;
import deconvolutionlab.monitor.Monitors;
import deconvolutionlab.monitor.StatusMonitor;
import deconvolutionlab.monitor.TableMonitor;
import signal.RealSignal;
import signal.SignalCollector;
/**
* This class is the main class to run deconvolution with or without user interface.
*
* All the parameters are given in the command line (String variable command).
*
* @author Daniel Sage
*
*/
public class Deconvolution implements Runnable {
public enum Finish {
DIE, ALIVE, KILL
};
private AbstractAlgorithm algo = null;
private Controller controller = new Controller();
private String command = "";
private Features report = new Features();
private String name = "";
public RealSignal image;
public RealSignal psf;
private RealSignal deconvolvedImage;
private Finish finish = Finish.DIE;
private DeconvolutionDialog dialog;
+ private boolean embeddedStats = false;
+
public Deconvolution(String name, String command) {
this.name = name;
this.finish = Finish.DIE;
setCommand(command);
}
public Deconvolution(String name, String command, Finish finish) {
this.name = name;
this.finish = finish;
setCommand(command);
}
public void setCommand(String command) {
this.command = command;
controller = Command.decodeController(command);
algo = Command.decodeAlgorithm(command);
algo.setController(controller);
this.command = command;
if (name.equals("") && algo != null)
name = algo.getShortnames()[0];
}
public RealSignal deconvolve() {
return deconvolve(image, psf);
}
public RealSignal deconvolve(RealSignal image, RealSignal psf) {
this.image = image;
this.psf = psf;
for(AbstractMonitor monitor : controller.getMonitors())
if (monitor instanceof TableMonitor)
Lab.setVisible(((TableMonitor)monitor).getPanel(), "Monitor of " + name, 10, 10);
if (controller.getFFT() == null) {
run();
return deconvolvedImage;
}
if (!controller.getFFT().isMultithreadable()) {
run();
return deconvolvedImage;
}
if (controller.isMultithreading()) {
Thread thread = new Thread(this);
thread.setPriority(Thread.MIN_PRIORITY);
thread.start();
}
else {
run();
}
return deconvolvedImage;
}
/**
* This method runs the deconvolution with a graphical user interface.
*/
public void launch() {
- TableMonitor tableMonitor = null;
- for(AbstractMonitor monitor : controller.getMonitors())
- if (monitor instanceof TableMonitor)
- tableMonitor = (TableMonitor)monitor;
-
- dialog = new DeconvolutionDialog(DeconvolutionDialog.Module.ALL, this, tableMonitor, controller.getStats());
+ embeddedStats = true;
+ dialog = new DeconvolutionDialog(DeconvolutionDialog.Module.ALL, this);
controller.getMonitors().add(new StatusMonitor(dialog.getProgressBar()));
Lab.setVisible(dialog, false);
}
@Override
public void run() {
double chrono = System.nanoTime();
Monitors monitors = controller.getMonitors();
report.add("Path", controller.toStringPath());
if (image == null)
image = openImage();
if (image == null) {
monitors.error("Image: Not valid " + command);
report.add("Image", "Not valid");
if (finish == Finish.KILL)
System.exit(-101);
return;
}
report.add("Image", image.dimAsString());
monitors.log("Image: " + image.dimAsString());
psf = openPSF();
if (psf == null) {
monitors.error("PSF: not valid");
report.add("PSF", "Not valid");
if (finish == Finish.KILL)
System.exit(-102);
return;
}
report.add("PSF", psf.dimAsString());
if (algo == null) {
monitors.error("Algorithm: not valid");
if (finish == Finish.KILL)
System.exit(-103);
return;
}
report.add("FFT", controller.getFFT().getName());
report.add("Algorithm", algo.getName());
+ if (embeddedStats) {
+ TableMonitor tableMonitor = null;
+ for(AbstractMonitor monitor : controller.getMonitors())
+ if (monitor instanceof TableMonitor)
+ tableMonitor = (TableMonitor)monitor;
+ if (controller.getStats().getMode() == Stats.Mode.SHOW || controller.getStats().getMode() == Stats.Mode.SHOWSAVE) {
+ controller.getStats().setEmbeddedInFrame(embeddedStats);
+ dialog.addStats(controller.getStats());
+ }
+ if (tableMonitor != null) {
+ dialog.addMonitor(tableMonitor);
+ }
+ }
algo.setController(controller);
deconvolvedImage = algo.run(image, psf, controller.getStats());
report.add("End", NumFormat.time(System.nanoTime() - chrono));
if (finish == Finish.KILL) {
System.out.println("End");
System.exit(0);
}
if (finish == Finish.DIE)
die();
}
public void close() {
if (dialog != null)
dialog.dispose();
SignalCollector.free(image);
SignalCollector.free(psf);
SignalCollector.free(deconvolvedImage);
algo = null;
image = null;
psf = null;
deconvolvedImage = null;
System.gc();
}
public void die() {
SignalCollector.free(image);
SignalCollector.free(psf);
}
/**
* This methods make a recap of the deconvolution. Useful before starting
* the processing.
*
* @return list of messages to print
*/
public Features recap() {
Features features = new Features();
Token image = Command.extract(command, "-image");
features.add("Image", image == null ? "keyword -image not found" : image.parameters);
double norm = controller.getNormalizationPSF();
String normf = (norm < 0 ? " (no normalization)" : " (normalization to " + norm + ")");
Token psf = Command.extract(command, "-psf");
features.add("PSF", psf == null ? "keyword -psf not found" : psf.parameters + " norm:" + normf);
if (algo == null) {
features.add("Algorithm", "not valid>");
}
else {
Controller controller = algo.getController();
features.add("Algorithm", algo.toString());
features.add("Stopping Criteria", controller.getStoppingCriteriaAsString(algo));
features.add("Reference", controller.getReference());
features.add("Constraint", controller.getConstraintAsString());
features.add("Padding", controller.getPadding().toString());
features.add("Apodization", controller.getApodization().toString());
features.add("FFT", controller.getFFT() == null ? "null" : controller.getFFT().getName());
}
features.add("Path", controller.getPath());
features.add("Monitor", controller.toStringMonitor());
if (controller.getStats() != null)
features.add("Stats", controller.getStats().toStringStats());
features.add("Running", controller.toStringRunning());
for (Output out : controller.getOuts())
features.add("Output " + out.getName(), out.toString());
return features;
}
public Features checkOutput() {
Features features = new Features();
if (deconvolvedImage == null) {
features.add("Image", "No valid output image");
return features;
}
float stati[] = deconvolvedImage.getStats();
int sizi = deconvolvedImage.nx * deconvolvedImage.ny * deconvolvedImage.nz;
float totali = stati[0] * sizi;
features.add("<html><b>Deconvolved Image</b></html>", "");
features.add("Size", deconvolvedImage.dimAsString() + " " + NumFormat.bytes(sizi * 4));
features.add("Mean (stdev)", NumFormat.nice(stati[0]) + " (" + NumFormat.nice(stati[3]) + ")");
features.add("Min ... Max", NumFormat.nice(stati[1]) + " ... " + NumFormat.nice(stati[2]));
features.add("Energy (int)", NumFormat.nice(stati[5]) + " (" + NumFormat.nice(totali) + ")");
return features;
}
public void abort() {
algo.getController().abort();
}
public RealSignal openImage() {
Token token = Command.extract(command, "-image");
if (token == null)
return null;
if (token.parameters.startsWith(">>>"))
return null;
String arg = token.option.trim();
String cmd = token.parameters.substring(arg.length(), token.parameters.length()).trim();
image = createRealSignal(controller.getMonitors(), arg, cmd, controller.getPath());
return image;
}
public RealSignal openPSF() {
Token token = Command.extract(command, "-psf");
if (token == null)
return null;
if (token.parameters.startsWith(">>>"))
return null;
String arg = token.option.trim();
String cmd = token.parameters.substring(arg.length(), token.parameters.length()).trim();
psf = createRealSignal(controller.getMonitors(), arg, cmd, controller.getPath());
return psf;
}
private static RealSignal createRealSignal(Monitors monitors, String arg, String cmd, String path) {
RealSignal signal = null;
if (arg.equalsIgnoreCase("synthetic")) {
signal = Lab.createSynthetic(monitors, cmd);
}
if (arg.equalsIgnoreCase("platform")) {
signal = Lab.getImage(monitors, cmd);
}
if (arg.equalsIgnoreCase("file")) {
File file = new File(path + File.separator + cmd);
if (file != null) {
if (file.isFile())
signal = Lab.openFile(monitors, path + File.separator + cmd);
}
if (signal == null) {
File local = new File(cmd);
if (local != null) {
if (local.isFile())
signal = Lab.openFile(monitors, cmd);
}
}
}
if (arg.equalsIgnoreCase("dir") || arg.equalsIgnoreCase("directory")) {
File file = new File(path + File.separator + cmd);
if (file != null) {
if (file.isDirectory())
signal = Lab.openDir(monitors, path + File.separator + cmd);
}
if (signal == null) {
File local = new File(cmd);
if (local != null) {
if (local.isDirectory())
signal = Lab.openDir(monitors, cmd);
}
}
}
return signal;
}
public void setAlgorithm(AbstractAlgorithm algo) {
this.algo = algo;
}
public AbstractAlgorithm getAlgorithm() {
return algo;
}
public void setController(Controller controller) {
this.controller = controller;
}
public Controller getController() {
return controller;
}
public RealSignal getOutput() {
return deconvolvedImage;
}
public RealSignal getImage() {
return image;
}
public RealSignal getPSF() {
return psf;
}
public Features getDeconvolutionReports() {
return report;
}
public String getName() {
return name;
}
public Monitors getMonitors() {
return controller.getMonitors();
}
public String getCommand() {
return command;
}
}
diff --git a/DeconvolutionLab2/src/deconvolution/DeconvolutionDialog.java b/DeconvolutionLab2/src/deconvolution/DeconvolutionDialog.java
index 86340c8..b848d0e 100644
--- a/DeconvolutionLab2/src/deconvolution/DeconvolutionDialog.java
+++ b/DeconvolutionLab2/src/deconvolution/DeconvolutionDialog.java
@@ -1,374 +1,374 @@
/*
* 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;
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.GridLayout;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.WindowEvent;
import java.awt.event.WindowListener;
import javax.swing.BorderFactory;
import javax.swing.BoxLayout;
import javax.swing.JButton;
import javax.swing.JDialog;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JProgressBar;
import javax.swing.JToolBar;
import bilib.component.BorderToggledButton;
import bilib.component.PanelImage;
import deconvolution.capsule.AlgorithmCapsule;
import deconvolution.capsule.ImageCapsule;
import deconvolution.capsule.PSFCapsule;
import deconvolution.capsule.RecapCapsule;
import deconvolution.capsule.ReportCapsule;
import deconvolutionlab.Config;
import deconvolutionlab.Constants;
import deconvolutionlab.Lab;
import deconvolutionlab.monitor.StatusMonitor;
import deconvolutionlab.monitor.TableMonitor;
public class DeconvolutionDialog extends JDialog implements WindowListener, ActionListener, Runnable {
public enum State {
NOTDEFINED, READY, RUN, FINISH
};
public enum Module {
- ALL, RECAP, IMAGE, PSF, ALGO
+ ALL, RECAP, IMAGE, PSF, ALGO, RUN
};
private JButton bnStart = new JButton("Run");
private JButton bnStop = new JButton("Stop");
private JButton bnReset = new JButton("Reset");
private JButton bnHelp = new JButton("Help");
private JButton bnQuit = new JButton("Quit");
private BorderToggledButton bnRecap = new BorderToggledButton("Recap");
private BorderToggledButton bnImage = new BorderToggledButton("Image");
private BorderToggledButton bnPSF = new BorderToggledButton("PSF");
private BorderToggledButton bnAlgo = new BorderToggledButton("Algorithm");
private BorderToggledButton bnReport = new BorderToggledButton("Report");
private BorderToggledButton bnMonitor = new BorderToggledButton("Monitor");
private BorderToggledButton bnStats = new BorderToggledButton("Stats");
+ JToolBar tool = new JToolBar();
private Thread thread = null;
private Deconvolution deconvolution;
private JProgressBar progress = new JProgressBar();
public static Point location = new Point(0, 0);
private JPanel cards = new JPanel(new CardLayout());
private boolean flagMonitor = false;
private boolean flagStats = false;
private ImageCapsule image;
private PSFCapsule psf;
private RecapCapsule recap;
private AlgorithmCapsule algorithm;
private ReportCapsule report;
- private TableMonitor tableMonitor;
-
- public DeconvolutionDialog(Module module, Deconvolution deconvolution, TableMonitor tableMonitor, Stats stats) {
+ public DeconvolutionDialog(Module module, Deconvolution deconvolution) {
super(new JFrame(), deconvolution.getName());
this.deconvolution = deconvolution;
- this.tableMonitor = tableMonitor;
image = new ImageCapsule(deconvolution);
psf = new PSFCapsule(deconvolution);
recap = new RecapCapsule(deconvolution);
algorithm = new AlgorithmCapsule(deconvolution);
report = new ReportCapsule(deconvolution);
// Panel status bar on bottom
progress.setAlignmentX(JLabel.CENTER_ALIGNMENT);
progress.setBorder(BorderFactory.createLoweredBevelBorder());
JToolBar statusBar = new JToolBar();
statusBar.setBorder(BorderFactory.createLoweredBevelBorder());
statusBar.setFloatable(false);
statusBar.setLayout(new BorderLayout());
statusBar.add(bnHelp, BorderLayout.WEST);
statusBar.add(progress, BorderLayout.CENTER);
statusBar.add(bnQuit, BorderLayout.EAST);
// Panel bottom
JPanel bottom = new JPanel();
bottom.setLayout(new BoxLayout(bottom, BoxLayout.PAGE_AXIS));
// Panel buttons
if (module == Module.ALL) {
PanelImage buttons = new PanelImage("celegans.jpg");
buttons.setLayout(new FlowLayout());
buttons.setBorder(BorderFactory.createEtchedBorder());
buttons.add(bnReset);
buttons.add(bnStop);
buttons.add(bnStart);
bottom.add(buttons);
}
bottom.add(statusBar);
// Panel Image
cards.add(recap.getName(), recap.getPane());
cards.add(image.getName(), image.getPane());
cards.add(psf.getName(), psf.getPane());
cards.add(algorithm.getName(), algorithm.getPane());
cards.add(report.getName(), report.getPane());
- if (tableMonitor != null)
- cards.add("Monitor", tableMonitor.getPanel());
- if (stats != null)
- cards.add("Stats", stats.getPanel());
// Panel Main
JPanel panel = new JPanel();
panel.setLayout(new BorderLayout());
panel.add(cards, BorderLayout.CENTER);
panel.add(bottom, BorderLayout.SOUTH);
// Panel tool with all buttons
if (module == Module.ALL) {
- JToolBar tool = new JToolBar();
tool.setFloatable(false);
tool.setLayout(new GridLayout(1, 6));
tool.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 0));
tool.add(bnRecap);
tool.add(bnImage);
tool.add(bnPSF);
tool.add(bnAlgo);
- if (tableMonitor != null)
- tool.add(bnMonitor);
- if (stats != null)
- tool.add(bnStats);
tool.add(bnReport);
panel.add(tool, BorderLayout.NORTH);
}
add(panel);
bnReset.addActionListener(this);
bnQuit.addActionListener(this);
bnStart.addActionListener(this);
bnStop.addActionListener(this);
bnHelp.addActionListener(this);
bnImage.addActionListener(this);
bnPSF.addActionListener(this);
bnAlgo.addActionListener(this);
bnRecap.addActionListener(this);
- if (tableMonitor != null)
- bnMonitor.addActionListener(this);
- if (stats != null)
- bnStats.addActionListener(this);
bnReport.addActionListener(this);
this.addWindowListener(this);
setMinimumSize(new Dimension(Constants.widthGUI, 400));
setPreferredSize(new Dimension(Constants.widthGUI, 400));
pack();
Config.registerFrame("DeconvolutionLab", "DeconvolutionDialog", this);
Rectangle rect = Config.getDialog("DeconvolutionLab.DeconvolutionDialog");
if (rect.x > 0 && rect.y > 0)
setLocation(rect.x, rect.y);
bnStop.setEnabled(false);
if (module == Module.ALL) {
toggle(bnRecap);
recap.update();
}
if (module == Module.IMAGE) {
toggle(bnImage);
deconvolution.getMonitors().add(new StatusMonitor(getProgressBar()));
image.update();
}
if (module == Module.PSF) {
toggle(bnPSF);
deconvolution.getMonitors().add(new StatusMonitor(getProgressBar()));
psf.update();
}
if (module == Module.ALGO) {
toggle(bnAlgo);
deconvolution.getMonitors().add(new StatusMonitor(getProgressBar()));
algorithm.update();
}
if (module == Module.RECAP) {
toggle(bnRecap);
recap.update();
}
}
@Override
public void actionPerformed(ActionEvent e) {
if (e.getSource() == bnStart) {
if (flagMonitor)
toggle(bnMonitor);
else if (flagStats)
toggle(bnStats);
if (thread == null) {
thread = new Thread(this);
thread.setPriority(Thread.MIN_PRIORITY);
thread.start();
}
}
else if (e.getSource() == bnStop) {
toggle(bnReport);
if (deconvolution != null)
deconvolution.abort();
}
else if (e.getSource() == bnImage) {
toggle(bnImage);
image.update();
}
else if (e.getSource() == bnPSF) {
toggle(bnPSF);
psf.update();
}
else if (e.getSource() == bnAlgo) {
toggle(bnAlgo);
algorithm.update();
}
else if (e.getSource() == bnRecap) {
toggle(bnRecap);
recap.update();
}
else if (e.getSource() == bnReport) {
toggle(bnReport);
report.update();
}
else if (e.getSource() == bnReset) {
toggle(bnRecap);
- if (tableMonitor != null)
- tableMonitor.clear();
-
bnStart.setEnabled(true);
}
else if (e.getSource() == bnQuit) {
deconvolution.close();
deconvolution = null;
dispose();
}
else if (e.getSource() == bnHelp)
Lab.help();
else if (e.getSource() == bnMonitor)
toggle(bnMonitor);
else if (e.getSource() == bnStats)
toggle(bnStats);
}
@Override
public void run() {
bnRecap.setEnabled(false);
bnImage.setEnabled(false);
bnPSF.setEnabled(false);
bnAlgo.setEnabled(false);
bnStart.setEnabled(false);
bnStop.setEnabled(true);
deconvolution.setCommand(recap.getCommand());
deconvolution.run();
toggle(bnReport);
bnStop.setEnabled(false);
report.update();
bnRecap.setEnabled(true);
bnAlgo.setEnabled(true);
bnPSF.setEnabled(true);
bnImage.setEnabled(true);
thread = null;
}
+ public void addStats(Stats stats) {
+ if (stats != null) {
+ cards.add("Stats", stats.getPanel());
+ tool.add(bnStats);
+ pack();
+ bnStats.addActionListener(this);
+ }
+ }
+
+ public void addMonitor(TableMonitor tableMonitor) {
+ if (tableMonitor != null) {
+ cards.add("Monitor", tableMonitor.getPanel());
+ tool.add(bnMonitor);
+ pack();
+ bnMonitor.addActionListener(this);
+ }
+ }
+
public static void setLocationLaunch(Point l) {
location = l;
}
private void toggle(BorderToggledButton bn) {
((CardLayout) (cards.getLayout())).show(cards, bn.getText());
bnRecap.setSelected(false);
bnImage.setSelected(false);
bnPSF.setSelected(false);
bnAlgo.setSelected(false);
bnMonitor.setSelected(false);
bnStats.setSelected(false);
bnReport.setSelected(false);
bn.setSelected(true);
}
@Override
public void windowOpened(WindowEvent e) {
}
@Override
public void windowClosing(WindowEvent e) {
deconvolution.close();
deconvolution = null;
dispose();
}
@Override
public void windowClosed(WindowEvent e) {
}
@Override
public void windowIconified(WindowEvent e) {
}
@Override
public void windowDeiconified(WindowEvent e) {
}
@Override
public void windowActivated(WindowEvent e) {
}
@Override
public void windowDeactivated(WindowEvent e) {
}
public JProgressBar getProgressBar() {
return progress;
}
}
diff --git a/DeconvolutionLab2/src/deconvolution/Stats.java b/DeconvolutionLab2/src/deconvolution/Stats.java
index a753b08..c1ca4c1 100644
--- a/DeconvolutionLab2/src/deconvolution/Stats.java
+++ b/DeconvolutionLab2/src/deconvolution/Stats.java
@@ -1,159 +1,170 @@
/*
* 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;
import java.awt.BorderLayout;
import java.awt.Dimension;
import java.io.File;
import java.util.ArrayList;
import javax.swing.BorderFactory;
import javax.swing.JFrame;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import bilib.table.CustomizedColumn;
import bilib.table.CustomizedTable;
import bilib.tools.NumFormat;
import deconvolutionlab.Constants;
import deconvolutionlab.Lab;
import deconvolutionlab.monitor.Monitors;
import deconvolutionlab.system.SystemUsage;
import signal.RealSignal;
import signal.SignalCollector;
public class Stats {
public enum Mode {NO, SHOW, SAVE, SHOWSAVE};
private CustomizedTable table;
private float[] statsInput;
private Mode mode;
+ private boolean embedded = false;
+
public Stats(Mode mode) {
this.mode = mode;
ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
columns.add(new CustomizedColumn("Iterations", String.class, 100, false));
columns.add(new CustomizedColumn("Mean", String.class, 100, false));
columns.add(new CustomizedColumn("Minimum", String.class, 100, false));
columns.add(new CustomizedColumn("Maximum", String.class, 100, false));
columns.add(new CustomizedColumn("Stdev", String.class, 100, false));
columns.add(new CustomizedColumn("Energy", String.class, 100, false));
columns.add(new CustomizedColumn("Time", String.class, 100, false));
columns.add(new CustomizedColumn("Memory", String.class, 100, false));
columns.add(new CustomizedColumn("Signal", String.class, 100, false));
columns.add(new CustomizedColumn("PSNR", String.class, 100, false));
columns.add(new CustomizedColumn("SNR", String.class, 100, false));
columns.add(new CustomizedColumn("Residu", String.class, 100, false));
table = new CustomizedTable(columns, true);
}
+ public void setEmbeddedInFrame(boolean embedded) {
+ this.embedded = embedded;
+ }
+
+ /**
+ * Show the stats table in a frame if it is not yet embedded in another frame.
+ */
public void show() {
+ if (embedded)
+ return;
if (mode == Mode.SHOW || mode == Mode.SHOWSAVE) {
JFrame frame = new JFrame("Stats");
frame.getContentPane().add(getPanel());
frame.pack();
Lab.setVisible(frame);
}
}
public void save(Monitors monitors, String path) {
if (mode == Mode.SAVE || mode == Mode.SHOWSAVE) {
String filename = path + File.separator + "stats.csv";
monitors.log("Stats save " + filename);
table.saveCSV(filename);
}
}
public void addInput(RealSignal x) {
statsInput = x.getStats();
table.append(compute(x, 0, "", "", "", ""));
}
public void add(RealSignal x, int iterations) {
table.append(compute(x, iterations, "", "", "", ""));
}
public void add(RealSignal x, int iterations, String time, String psnr, String snr, String residu) {
table.append(compute(x, iterations, time, psnr, snr, residu));
}
public String[] compute(RealSignal x, int iterations, String time, String psnr, String snr, String residu) {
float params[] = null;
if (x != null)
params = x.getStats();
String[] row = new String[12];
row[0] = "" + iterations;
row[1] = (params == null ? "-" : "" + params[0]);
row[2] = (params == null ? "-" : "" + params[1]);
row[3] = (params == null ? "-" : "" + params[2]);
row[4] = (params == null ? "-" : "" + params[3]);
row[5] = (params == null ? "-" : "" + params[5]);
row[6] = time;
row[7] = NumFormat.bytes(SystemUsage.getHeapUsed());
row[8] = SignalCollector.sumarize();
row[9] = psnr;
row[10] = snr;
row[11] = residu;
return row;
}
public JPanel getPanel() {
JScrollPane scroll = new JScrollPane(table);
scroll.setPreferredSize(new Dimension(Constants.widthGUI, 400));
JPanel panel = new JPanel(new BorderLayout());
panel = new JPanel(new BorderLayout());
panel.add(scroll);
panel.setBorder(BorderFactory.createEtchedBorder());
return panel;
}
public String toStringStats() {
if (mode == Mode.SHOW)
return "show";
if (mode == Mode.SAVE)
return "save";
if (mode == Mode.SHOWSAVE)
return "show and save";
return "no";
}
public Mode getMode() {
return mode;
}
public float[] getStatsInput() {
return statsInput;
}
}
diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java b/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java
index 5a8026b..699f287 100644
--- a/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java
+++ b/DeconvolutionLab2/src/deconvolution/algorithm/AbstractAlgorithm.java
@@ -1,408 +1,409 @@
/*
* 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.algorithm;
import java.util.ArrayList;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
+import signal.Constraint;
+import signal.RealSignal;
+import signal.SignalCollector;
+import signal.apodization.Apodization;
+import signal.padding.Padding;
import bilib.tools.NumFormat;
+import deconvolution.DeconvolutionDialog;
import deconvolution.Stats;
import deconvolutionlab.Lab;
import deconvolutionlab.Output;
import deconvolutionlab.monitor.Monitors;
import deconvolutionlab.monitor.Verbose;
import deconvolutionlab.system.SystemInfo;
import fft.AbstractFFT;
import fft.FFT;
-import signal.Constraint;
-import signal.RealSignal;
-import signal.SignalCollector;
-import signal.apodization.Apodization;
-import signal.padding.Padding;
/**
* This class is the common part of every algorithm of deconvolution.
*
* @author Daniel Sage
*
*/
public abstract class AbstractAlgorithm implements Callable<RealSignal> {
/** y is the input signal of the deconvolution. */
protected RealSignal y;
/** h is the PSF signal for the deconvolution. */
protected RealSignal h;
protected boolean threaded;
/** Optimized implementation in term of memory footprint */
protected boolean optimizedMemoryFootprint;
protected int iterMax = 0;
protected AbstractFFT fft;
protected Controller controller;
public AbstractAlgorithm() {
setController(new Controller());
optimizedMemoryFootprint = true;
threaded = true;
fft = FFT.getFastestFFT().getDefaultFFT();
}
public AbstractAlgorithm(Controller controller) {
this.controller = controller;
optimizedMemoryFootprint = true;
threaded = true;
fft = FFT.getFastestFFT().getDefaultFFT();
}
public void setOptimizedMemoryFootprint(boolean optimizedMemoryFootprint) {
this.optimizedMemoryFootprint = optimizedMemoryFootprint;
}
public abstract String getName();
public abstract String[] getShortnames();
public abstract double getMemoryFootprintRatio();
public abstract int getComplexityNumberofFFT();
public abstract boolean isRegularized();
public abstract boolean isStepControllable();
public abstract boolean isIterative();
public abstract boolean isWaveletsBased();
public abstract void setParameters(double[] params);
public abstract double getRegularizationFactor();
public abstract double getStepFactor();
public abstract double[] getParameters();
public abstract double[] getDefaultParameters();
public RealSignal run(RealSignal image, RealSignal psf) {
return run(image, psf, new Stats(Stats.Mode.NO));
}
public RealSignal run(RealSignal image, RealSignal psf, Stats stats) {
if (controller.isSystem())
SystemInfo.activate();
Padding pad = controller.getPadding();
Apodization apo = controller.getApodization();
double norm = controller.getNormalizationPSF();
fft = controller.getFFT();
controller.setIterationsMax(iterMax);
if (image == null)
return null;
if (psf == null)
return null;
// Prepare the controller and the outputs
Monitors monitors = controller.getMonitors();
monitors.setVerbose(controller.getVerbose());
monitors.log("Path: " + controller.toStringPath());
monitors.log("Algorithm: " + getName());
// Prepare the signal and the PSF
y = pad.pad(monitors, image);
y.setName("y");
apo.apodize(monitors, y);
monitors.log("Input: " + y.dimAsString());
h = psf.changeSizeAs(y);
h.setName("h");
h.normalize(norm);
monitors.log("PSF: " + h.dimAsString() + " normalized " + (norm <= 0 ? "no" : norm));
String iterations = (isIterative() ? iterMax + " iterations" : "direct");
controller.setIterationsMax(iterMax);
monitors.log(getShortnames()[0] + " is starting (" + iterations + ")");
controller.setMonitors(monitors);
-
+
controller.start(y, stats);
h.circular();
// FFT
fft.init(monitors, y.nx, y.ny, y.nz);
controller.setFFT(fft);
monitors.log(getShortnames()[0] + " data ready");
double params[] = getParameters();
if (params != null) {
if (params.length > 0) {
String s = " ";
for (double param : params)
s += "" + param + " ";
monitors.log(getShortnames()[0] + s);
}
}
RealSignal x = null;
try {
if (threaded == true) {
ExecutorService pool = Executors.newSingleThreadExecutor();
Future<RealSignal> future = pool.submit(this);
x = future.get();
}
else {
x = call();
}
}
catch (InterruptedException ex) {
ex.printStackTrace();
x = y.duplicate();
}
catch (ExecutionException ex) {
ex.printStackTrace();
x = y.duplicate();
}
catch (Exception e) {
e.printStackTrace();
x = y.duplicate();
}
SignalCollector.free(y);
SignalCollector.free(h);
x.setName("x");
RealSignal result = pad.crop(monitors, x);
controller.finish(result);
monitors.log(getName() + " is finished");
SignalCollector.free(x);
if (controller.isDisplayFinal())
Lab.show(monitors, result, "Final Display of " + getShortnames()[0]);
result.setName("Output of " + this.getShortnames()[0]);
return result;
}
public void setController(Controller controller) {
this.controller = controller;
}
public Controller getController() {
return controller;
}
public int getIterationsMax() {
return iterMax;
}
public int getIterations() {
return controller.getIterations();
}
public double getTime() {
return controller.getTimeNano();
}
public double getMemory() {
return controller.getMemory();
}
public void setWavelets(String waveletsName) {
}
@Override
public String toString() {
String s = "";
s += getName();
s += (isIterative() ? ", " + iterMax + " iterations" : " (direct)");
s += (isRegularized() ? ", &lambda=" + NumFormat.nice(getRegularizationFactor()) : "");
s += (isStepControllable() ? ", &gamma=" + NumFormat.nice(getStepFactor()) : "");
return s;
}
public String getParametersAsString() {
double p[] = getParameters();
String param = "";
for (int i = 0; i < p.length; i++)
if (i == p.length - 1)
param += p[i];
else
param += p[i] + ", ";
return param;
}
public AbstractFFT getFFT() {
return controller.getFFT();
}
public void setFFT(AbstractFFT fft) {
this.fft = fft;
controller.setFFT(fft);
}
public String getPath() {
return controller.getPath();
}
public void setPath(String path) {
controller.setPath(path);
}
public boolean isSystem() {
return controller.isSystem();
}
public void setSystem(boolean system) {
controller.setSystem(system);
}
public boolean isMultithreading() {
return controller.isMultithreading();
}
public void setMultithreading(boolean multithreading) {
controller.setMultithreading(multithreading);
}
public boolean isDisplayFinal() {
return controller.isDisplayFinal();
}
public void setDisplayFinal(boolean displayFinal) {
controller.setDisplayFinal(displayFinal);
}
public double getNormalizationPSF() {
return controller.getNormalizationPSF();
}
public void setNormalizationPSF(double normalizationPSF) {
controller.setNormalizationPSF(normalizationPSF);
}
public double getEpsilon() {
return controller.getEpsilon();
}
public void setEpsilon(double epsilon) {
controller.setEpsilon(epsilon);
}
public Padding getPadding() {
return controller.getPadding();
}
public void setPadding(Padding padding) {
controller.setPadding(padding);
}
public Apodization getApodization() {
return controller.getApodization();
}
public void setApodization(Apodization apodization) {
controller.setApodization(apodization);
}
public Monitors getMonitors() {
return controller.getMonitors();
}
public void setMonitors(Monitors monitors) {
controller.setMonitors(monitors);
}
public Verbose getVerbose() {
return controller.getVerbose();
}
public void setVerbose(Verbose verbose) {
controller.setVerbose(verbose);
}
public Constraint.Mode getConstraint() {
return controller.getConstraint();
}
public void setConstraint(Constraint.Mode constraint) {
controller.setConstraint(constraint);
}
public Stats getStats() {
return controller.getStats();
}
public void setStats(Stats stats) {
controller.setStats(stats);
}
public double getResiduMin() {
return controller.getResiduMin();
}
public void setResiduMin(double residuMin) {
controller.setResiduMin(residuMin);
}
public double getTimeLimit() {
return controller.getTimeLimit();
}
public void setTimeLimit(double timeLimit) {
controller.setTimeLimit(timeLimit);
}
public String getReference() {
return controller.getReference();
}
public void setReference(String reference) {
controller.setReference(reference);
}
public ArrayList<Output> getOuts() {
return controller.getOuts();
}
public void setOuts(ArrayList<Output> outs) {
controller.setOuts(outs);
}
public void addOutput(Output out) {
controller.addOutput(out);
}
}
diff --git a/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java b/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java
index 5701561..0e2b292 100644
--- a/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java
+++ b/DeconvolutionLab2/src/deconvolution/algorithm/Controller.java
@@ -1,638 +1,631 @@
/*
* 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.algorithm;
import java.io.File;
import java.util.ArrayList;
import java.util.Timer;
import java.util.TimerTask;
+import signal.Assessment;
+import signal.ComplexSignal;
+import signal.Constraint;
+import signal.RealSignal;
+import signal.apodization.Apodization;
+import signal.padding.Padding;
import bilib.tools.NumFormat;
import deconvolution.Deconvolution;
import deconvolution.Stats;
import deconvolutionlab.Constants;
import deconvolutionlab.Output;
import deconvolutionlab.monitor.AbstractMonitor;
import deconvolutionlab.monitor.ConsoleMonitor;
import deconvolutionlab.monitor.Monitors;
import deconvolutionlab.monitor.TableMonitor;
import deconvolutionlab.monitor.Verbose;
import deconvolutionlab.system.SystemUsage;
import fft.AbstractFFT;
import fft.FFT;
-import signal.Assessment;
-import signal.ComplexSignal;
-import signal.Constraint;
-import signal.RealSignal;
-import signal.apodization.Apodization;
-import signal.padding.Padding;
/**
* This is an important class to manage all the common task of the algorithm.
* The method start() is called before at the starting of the algorithm. The
* method ends() is called at the end of every iterations for the iterative
* algorithm. It returns true if one the stopping criteria is true. The method
* finish() is called when the algorithm is completely terminated.
*
* @author Daniel Sage
*
*/
public class Controller {
private String path;
private boolean system;
private boolean multithreading;
private boolean displayFinal;
private double normalizationPSF;
private double epsilon;
private Padding padding;
private Apodization apodization;
private ArrayList<Output> outs;
private Stats stats;
private Constraint.Mode constraintMode;
private double residuMin;
private double timeLimit;
private String reference;
private Monitors monitors;
private Verbose verbose;
private AbstractFFT fft;
private int iterationsMax = 100;
private boolean doResidu = false;
private boolean doTime = false;
private boolean doReference = false;
private boolean doConstraint = false;
private boolean abort = false;
private double timeStarting = 0;
private double memoryStarting = 0;
private double residu = Double.MAX_VALUE;
private int iterations = 0;
private double memoryPeak = 0;
private double snr = 0;
private double psnr = 0;
private RealSignal refImage;
private RealSignal prevImage;
private RealSignal x;
private Timer timer;
public Controller() {
doResidu = false;
doTime = false;
doReference = false;
doConstraint = false;
timeStarting = System.nanoTime();
setPath(System.getProperty("user.dir"));
setSystem(true);
setMultithreading(true);
setDisplayFinal(true);
setFFT(FFT.getFastestFFT().getDefaultFFT());
setNormalizationPSF(1);
setEpsilon(1e-6);
setPadding(new Padding());
setApodization(new Apodization());
monitors = new Monitors();
monitors.add(new ConsoleMonitor());
monitors.add(new TableMonitor("Monitor", Constants.widthGUI, 240));
setVerbose(Verbose.Log);
setStats(new Stats(Stats.Mode.NO));
setConstraint(Constraint.Mode.NO);
setResiduMin(-1);
setTimeLimit(-1);
setReference("");
setOuts(new ArrayList<Output>());
}
public void setFFT(AbstractFFT fft) {
this.fft = fft;
}
public void abort() {
this.abort = true;
}
public void setIterationsMax(int iterationsMax) {
this.iterationsMax = iterationsMax;
}
public boolean needSpatialComputation() {
return doConstraint || doResidu || doReference;
}
/**
* Call one time at the beginning of the algorithms
*
* @param x
* the input signal
*/
public void start(RealSignal x, Stats stats) {
this.x = x;
this.stats = stats;
stats.show();
stats.addInput(x);
iterations = 0;
timer = new Timer();
timer.schedule(new Updater(), 0, 100);
timeStarting = System.nanoTime();
memoryStarting = SystemUsage.getHeapUsed();
if (doConstraint && x != null)
Constraint.setModel(x);
if (doReference) {
refImage = new Deconvolution("Reference", "-image file " + reference).openImage();
if (refImage == null)
monitors.error("Impossible to load the reference image " + reference);
else
monitors.log("Reference image loaded");
}
for (Output out : outs)
out.executeStarting(monitors, x, this);
this.prevImage = x;
}
public boolean ends(ComplexSignal X) {
boolean out = false;
for (Output output : outs)
out = out | output.is(iterations);
if (doConstraint || doResidu || doReference || out) {
if (fft == null)
fft = FFT.createDefaultFFT(monitors, X.nx, X.ny, X.nz);
x = fft.inverse(X, x);
return ends(x);
}
return ends((RealSignal) null);
}
public boolean ends(RealSignal x) {
this.x = x;
if (doConstraint || doResidu || doReference)
compute(iterations, x, doConstraint, doResidu, doReference);
for (Output out : outs)
out.executeIterative(monitors, x, this, iterations);
iterations++;
double p = iterations * 100.0 / iterationsMax;
monitors.progress("Iterative " + iterations + "/" + iterationsMax, p);
double timeElapsed = getTimeSecond();
boolean stopIter = (iterations >= iterationsMax);
boolean stopTime = doTime && (timeElapsed >= timeLimit);
boolean stopResd = doResidu && (residu <= residuMin);
monitors.log("@" + iterations + " Time: " + NumFormat.seconds(timeElapsed));
addStats();
String prefix = "Stopped>> by ";
if (abort)
monitors.log(prefix + "abort");
if (stopIter)
monitors.log(prefix + "iteration " + iterations + " > " + iterationsMax);
if (stopTime)
monitors.log(prefix + "time " + timeElapsed + " > " + timeLimit);
if (stopResd)
monitors.log(prefix + "residu " + NumFormat.nice(residu) + " < " + NumFormat.nice(residuMin));
return abort | stopIter | stopTime | stopResd;
}
public void finish(RealSignal x) {
this.x = x;
boolean ref = doReference;
boolean con = doConstraint;
boolean res = doResidu;
if (con || res || ref)
compute(iterations, x, con, res, ref);
addStats();
stats.save(monitors, path);
for (Output out : outs)
out.executeFinal(monitors, x, this);
monitors.log("Time: " + NumFormat.seconds(getTimeNano()) + " Peak:" + getMemoryAsString());
if (timer != null)
timer.cancel();
}
private void compute(int iterations, RealSignal x, boolean con, boolean res, boolean ref) {
if (x == null)
return;
if (con && constraintMode != null)
new Constraint(monitors).apply(x, constraintMode);
if (ref && refImage != null) {
String s = "";
psnr = Assessment.psnr(x, refImage);
snr = Assessment.snr(x, refImage);
s += " PSNR: " + NumFormat.nice(psnr);
s += " SNR: " + NumFormat.nice(snr);
monitors.log("@" + iterations + " " + s);
}
residu = Double.MAX_VALUE;
if (res && prevImage != null) {
residu = Assessment.relativeResidu(x, prevImage);
prevImage = x.duplicate();
monitors.log("@" + iterations + " Residu: " + NumFormat.nice(residu));
}
}
private void addStats() {
String pnsrText = doReference ? NumFormat.nice(psnr) : "n/a";
String snrText = doReference ? NumFormat.nice(snr) : "n/a";
String residuText = doResidu ? NumFormat.nice(residu) : "n/a";
stats.add(x, iterations, NumFormat.seconds(getTimeNano()), pnsrText, snrText, residuText);
}
public double getTimeNano() {
return (System.nanoTime() - timeStarting);
}
public double getTimeSecond() {
return (System.nanoTime() - timeStarting) * 1e-9;
}
public String getConstraintAsString() {
if (!doConstraint)
return "no";
if (constraintMode == null)
return "null";
return constraintMode.name().toLowerCase();
}
public String getStoppingCriteriaAsString(AbstractAlgorithm algo) {
String stop = algo.isIterative() ? "iterations limit=" + algo.getIterationsMax() + ", " : "direct, ";
stop += doTime ? ", time limit=" + NumFormat.nice(timeLimit * 1e-9) : " no time limit" + ", ";
stop += doResidu ? ", residu limit=" + NumFormat.nice(residuMin) : " no residu limit";
return stop;
}
public double getMemory() {
return memoryPeak - memoryStarting;
}
public String getMemoryAsString() {
return NumFormat.bytes(getMemory());
}
public int getIterations() {
return iterations;
}
private void update() {
memoryPeak = Math.max(memoryPeak, SystemUsage.getHeapUsed());
}
public AbstractFFT getFFT() {
return fft;
}
/**
* @return the path
*/
public String getPath() {
return path;
}
/**
* @param path
* the path to set
*/
public void setPath(String path) {
this.path = path;
}
/**
* @return the system
*/
public boolean isSystem() {
return system;
}
/**
* @param system
* the system to set
*/
public void setSystem(boolean system) {
this.system = system;
}
/**
* @return the multithreading
*/
public boolean isMultithreading() {
return multithreading;
}
/**
* @param multithreading
* the multithreading to set
*/
public void setMultithreading(boolean multithreading) {
this.multithreading = multithreading;
}
/**
* @return the displayFinal
*/
public boolean isDisplayFinal() {
return displayFinal;
}
/**
* @param displayFinal
* the displayFinal to set
*/
public void setDisplayFinal(boolean displayFinal) {
this.displayFinal = displayFinal;
}
/**
* @return the normalizationPSF
*/
public double getNormalizationPSF() {
return normalizationPSF;
}
/**
* @param normalizationPSF
* the normalizationPSF to set
*/
public void setNormalizationPSF(double normalizationPSF) {
this.normalizationPSF = normalizationPSF;
}
/**
* @return the epsilon
*/
public double getEpsilon() {
return epsilon;
}
/**
* @param epsilon
* the epsilon to set
*/
public void setEpsilon(double epsilon) {
this.epsilon = epsilon;
}
/**
* @return the padding
*/
public Padding getPadding() {
return padding;
}
/**
* @param padding
* the padding to set
*/
public void setPadding(Padding padding) {
this.padding = padding;
}
/**
* @return the apodization
*/
public Apodization getApodization() {
return apodization;
}
/**
* @param apodization
* the apodization to set
*/
public void setApodization(Apodization apodization) {
this.apodization = apodization;
}
/**
* @return the monitors
*/
public Monitors getMonitors() {
return monitors;
}
/**
* @param monitors
* the monitors to set
*/
public void setMonitors(Monitors monitors) {
this.monitors = monitors;
}
/**
* @return the verbose
*/
public Verbose getVerbose() {
return verbose;
}
/**
* @param verbose
* the verbose to set
*/
public void setVerbose(Verbose verbose) {
this.verbose = verbose;
}
public Constraint.Mode getConstraint() {
return constraintMode;
}
public void setConstraint(Constraint.Mode constraintMode) {
doConstraint = constraintMode != Constraint.Mode.NO;
this.constraintMode = constraintMode;
}
/**
* @return the stats
*/
public Stats getStats() {
return stats;
}
/**
* @param stats
* the stats to set
*/
public void setStats(Stats stats) {
this.stats = stats;
}
/**
* @return the residuMin
*/
public double getResiduMin() {
return residuMin;
}
/**
* @param residuMin
* the residuMin to set
*/
public void setResiduMin(double residuMin) {
doResidu = residuMin > 0;
this.residuMin = residuMin;
}
/**
* @return the timeLimit
*/
public double getTimeLimit() {
return timeLimit;
}
/**
* @param timeLimit
* the timeLimit to set
*/
public void setTimeLimit(double timeLimit) {
doTime = timeLimit > 0;
this.timeLimit = timeLimit;
}
/**
* @return the reference
*/
public String getReference() {
return reference;
}
/**
* @param reference
* the reference to set
*/
public void setReference(String reference) {
doReference = false;
if (reference == null)
return;
if (reference.equals(""))
return;
doReference = true;
this.reference = reference;
}
/**
* @return the outs
*/
public ArrayList<Output> getOuts() {
return outs;
}
/**
* @param outs
* the outs to set
*/
public void setOuts(ArrayList<Output> outs) {
this.outs = outs;
}
public void addOutput(Output out) {
this.outs.add(out);
}
public String toStringMonitor() {
String s = "[" + verbose.name().toLowerCase() + "] ";
for (AbstractMonitor monitor : monitors) {
s += "" + monitor.getName() + " ";
}
return s;
}
- /**
- * @return the stats
- */
public Stats.Mode getStatsMode() {
return stats.getMode();
}
- /**
- * @param stats
- * the stats to set
- */
public void setStatsMode(Stats.Mode mode) {
this.stats = new Stats(mode);
}
public String toStringRunning() {
String s = "";
s += "system " + (system ? "shown" : "hidden ");
s += ", multithreading " + (multithreading ? "on" : "off ");
s += ", display final " + (displayFinal ? "on " : "off ");
return s;
}
public String toStringPath() {
File dir = new File(path);
if (dir.exists()) {
if (dir.isDirectory()) {
if (dir.canWrite())
return path + " (writable)";
else
return path + " (non-writable)";
}
else {
return path + " (non-directory)";
}
}
else {
return path + " (not-valid)";
}
}
private class Updater extends TimerTask {
@Override
public void run() {
update();
}
}
}
diff --git a/DeconvolutionLab2/src/deconvolutionlab/Lab.java b/DeconvolutionLab2/src/deconvolutionlab/Lab.java
index 71510bd..4bd3f9d 100644
--- a/DeconvolutionLab2/src/deconvolutionlab/Lab.java
+++ b/DeconvolutionLab2/src/deconvolutionlab/Lab.java
@@ -1,526 +1,524 @@
/*
* 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 deconvolutionlab;
import java.io.File;
import java.util.ArrayList;
import java.util.regex.Pattern;
import javax.swing.JDialog;
import javax.swing.JFrame;
import javax.swing.JPanel;
import bilib.tools.NumFormat;
import bilib.tools.WebBrowser;
import deconvolutionlab.Imager.ContainerImage;
import deconvolutionlab.monitor.Monitors;
import fft.AbstractFFT;
import fft.AbstractFFTLibrary;
import fft.FFT;
import imagej.IJImager;
import plugins.sage.deconvolutionlab.IcyImager;
import signal.ComplexComponent;
import signal.ComplexSignal;
import signal.RealSignal;
import signal.factory.SignalFactory;
import signal.factory.Sphere;
/**
* This class contains a collection of useful static methods to manage all the
* peripherical aspects of the deconvolution, such as load, display, or save an
* image.
* <p>
* At the construction of the class, the config is loaded. In practice, any
* deconvolution program has to start with Lab.init(Platform).
*
* @author Daniel Sage
*
*/
public class Lab {
private static Imager imaging;
private static ArrayList<JFrame> frames;
private static ArrayList<JDialog> dialogs;
static {
frames = new ArrayList<JFrame>();
dialogs = new ArrayList<JDialog>();
imaging = new IJImager();
Config.init(System.getProperty("user.dir") + File.separator + "DeconvolutionLab2.config");
}
/**
* Initializes the Lab with a give platform.
*
* @param platform
* The platform is ImageJ, ICY, or Matlab.
*/
public static void init(Imager.Platform platform) {
init(platform, System.getProperty("user.dir") + File.separator + "DeconvolutionLab2.config");
}
/**
* Initializes the Lab with a give platform and a given configuration file
*
* @param platform
* @param configFilename
*/
public static void init(Imager.Platform platform, String configFilename) {
switch (platform) {
case IMAGEJ:
imaging = new IJImager();
break;
case ICY:
imaging = new IcyImager();
break;
default:
imaging = new IJImager();
break;
}
Config.init(configFilename);
}
/**
* Returns the platform.
*
* @return
*/
public static Imager.Platform getPlatform() {
return imaging.getPlatform();
}
/**
* Open a web page on the DeconvolutionLab2.
*/
public static void help() {
WebBrowser.open(Constants.url);
}
/**
* Checks the installed FFT libraries on a small (40, 30, 20) signal.
*
* @param monitors
*/
public static void checkFFT(Monitors monitors) {
ArrayList<AbstractFFTLibrary> libraries = FFT.getInstalledLibraries();
for (AbstractFFTLibrary library : libraries) {
RealSignal y = new Sphere(3, 1).generate(40, 30, 20);
double chrono = System.nanoTime();
AbstractFFT fft = library.getDefaultFFT();
fft.init(monitors, y.nx, y.ny, y.nz);
RealSignal x = fft.inverse(fft.transform(y));
chrono = System.nanoTime() - chrono;
double residu = y.getEnergy() - x.getEnergy();
monitors.log("\t residu of reconstruction: " + residu);
monitors.log("\t computation time (" + x.nx + "x" + x.ny + "x" + x.nz + ") " + NumFormat.time(chrono));
}
}
public static ContainerImage createContainer(Monitors monitors, String title) {
monitors.log("Create Live Real Signal " + title);
return imaging.createContainer(title);
}
public static void append(Monitors monitors, ContainerImage container, RealSignal signal, String title) {
imaging.append(container, signal, title, Imager.Type.FLOAT);
monitors.log("Add Live Real Signal " + title);
}
public static void append(Monitors monitors, ContainerImage container, RealSignal signal, String title, Imager.Type type) {
imaging.append(container, signal, title, type);
monitors.log("Add Live Real Signal " + title);
}
/**
* Displays a the module of complex signal.
*
* @param monitors
* @param signal
* @param title
*/
public static void show(Monitors monitors, ComplexSignal signal, String title) {
if (signal == null) {
monitors.error("Show " + title + " this image does not exist.");
return;
}
monitors.log("Show Real Signal " + title);
imaging.show(signal, title, ComplexComponent.MODULE);
}
/**
* Displays a real 3D signal a z-stack of images.
*
* @param signal
*/
public static void show(RealSignal signal) {
if (signal == null) {
return;
}
imaging.show(signal, signal.name, Imager.Type.FLOAT, signal.nz / 2);
}
/**
* Displays a real 3D signal a z-stack of images.
*
* @param monitors
* @param signal
*/
public static void show(Monitors monitors, RealSignal signal) {
if (signal == null) {
monitors.error("This image does not exist.");
return;
}
monitors.log("Show Real Signal " + signal.name);
imaging.show(signal, signal.name, Imager.Type.FLOAT, signal.nz / 2);
}
/**
* Displays a real 3D signal a z-stack of images.
*
* @param monitors
* @param signal
* @param title
*/
public static void show(Monitors monitors, RealSignal signal, String title) {
if (signal == null) {
monitors.error("Show " + title + " this image does not exist.");
return;
}
monitors.log("Show Real Signal " + title);
imaging.show(signal, title, Imager.Type.FLOAT, signal.nz / 2);
}
/**
* Displays a real 3D signal a z-stack of images using a given type.
*
* @param monitors
* @param signal
* @param title
* @param type
*/
public static void show(Monitors monitors, RealSignal signal, String title, Imager.Type type) {
if (signal == null) {
monitors.error("Show " + title + " this image does not exist.");
return;
}
monitors.log("Show Real Signal " + title);
imaging.show(signal, title, type, signal.nz / 2);
}
/**
* Displays a real 3D signal a z-stack of images using a given type and
* shows the slice number z.
*
* @param monitors
* @param signal
* @param title
* @param type
* @param z
*/
public static void show(Monitors monitors, RealSignal signal, String title, Imager.Type type, int z) {
if (signal == null) {
monitors.error("Show " + title + " this image does not exist.");
return;
}
monitors.log("Show Real Signal " + title);
imaging.show(signal, title, type, z);
}
public static void save(Monitors monitors, RealSignal signal, String filename) {
imaging.save(signal, filename, Imager.Type.FLOAT);
monitors.log("Save Real Signal " + filename);
}
public static void save(Monitors monitors, RealSignal signal, String filename, Imager.Type type) {
imaging.save(signal, filename, type);
monitors.log("Save Real Signal " + filename);
}
public static RealSignal createSynthetic(Monitors monitors, String cmd) {
RealSignal signal = SignalFactory.createFromCommand(cmd);
if (signal == null)
monitors.error("Unable to create " + cmd);
else
monitors.log("Create " + cmd);
return signal;
}
/**
* Return the active image.
*
- * @param monitors
* @return
*/
public static RealSignal getImage() {
return getImager().getActiveImage();
}
/**
* Return an image from the platform with a specified name.
*
- * @param monitors
+ * @param name
* @return
*/
public static RealSignal getImage(String name) {
return getImager().getImageByName(name);
}
/**
* Return an image from the platform with a specified name.
*
* @param monitors
* @param name
* @return
*/
public static RealSignal getImage(Monitors monitors, String name) {
RealSignal signal = getImager().getImageByName(name);
if (signal == null)
monitors.error("Unable to get " + name);
else
monitors.log("Load " + name);
return signal;
}
/**
* Open an image from the disk.
*
- * @param monitors
* @param filename
* @return
*/
public static RealSignal openFile(String filename) {
return imaging.open(filename);
}
/**
* Open an image from the disk.
*
* @param monitors
* @param filename
* @return
*/
public static RealSignal openFile(Monitors monitors, String filename) {
RealSignal signal = imaging.open(filename);
if (signal == null)
monitors.error("Unable to open " + filename);
else
monitors.log("Load " + filename);
return signal;
}
/**
* Open a series of image from a directory.
*
* @param path
* @return
*/
public static RealSignal openDir(String path) {
return openDir(Monitors.createDefaultMonitor(), path);
}
/**
* Open a series of image from a directory.
*
* @param monitors
* @param path
* @return
*/
public static RealSignal openDir(Monitors monitors, String path) {
String parts[] = path.split(" pattern ");
String dirname = path;
String regex = "";
if (parts.length == 2) {
dirname = parts[0].trim();
regex = parts[1].trim();
}
File file = new File(dirname + File.separator);
if (!file.isDirectory()) {
monitors.error("Dir " + dirname + " is not a directory.");
return null;
}
String[] list = file.list();
ArrayList<RealSignal> slices = new ArrayList<RealSignal>();
int nx = 0;
int ny = 0;
Pattern pattern = Pattern.compile(regex);
for (String filename : list) {
if (pattern.matcher(filename).find()) {
RealSignal slice = imaging.open(dirname + File.separator + filename);
if (slice != null) {
slices.add(slice);
nx = Math.max(nx, slice.nx);
ny = Math.max(ny, slice.ny);
monitors.log("Image " + path + File.separator + filename + " is loaded.");
}
}
else {
monitors.error("Error in loading image " + path + File.separator + filename);
}
}
int nz = slices.size();
if (nz <= 0) {
monitors.error("Dir " + path + " do no contain valid images.");
return null;
}
RealSignal signal = new RealSignal(file.getName(), nx, ny, nz);
for (int z = 0; z < slices.size(); z++)
signal.setSlice(z, slices.get(z));
return signal;
}
public static void showOrthoview(RealSignal signal, String title, int hx, int hy, int hz) {
if (signal == null) {
return;
}
imaging.show(signal.createOrthoview(hx, hy, hz), title, Imager.Type.FLOAT, 0);
}
public static void showOrthoview(Monitors monitors, RealSignal signal, String title, int hx, int hy, int hz) {
if (signal == null) {
monitors.error("Show Orthoview " + title + " this image does not exist.");
return;
}
imaging.show(signal.createOrthoview(hx, hy, hz), title, Imager.Type.FLOAT, 0);
}
public static void showOrthoview(RealSignal signal) {
if (signal == null) {
return;
}
int hx = signal.nx / 2;
int hy = signal.ny / 2;
int hz = signal.nz / 2;
imaging.show(signal.createOrthoview(hx, hy, hz), signal.name, Imager.Type.FLOAT, 0);
}
public static void showOrthoview(Monitors monitors, RealSignal signal, String title) {
if (signal == null) {
monitors.error("Show Orthoview " + title + " this image does not exist.");
return;
}
int hx = signal.nx / 2;
int hy = signal.ny / 2;
int hz = signal.nz / 2;
imaging.show(signal.createOrthoview(hx, hy, hz), title, Imager.Type.FLOAT, 0);
}
public static void showMIP(RealSignal signal) {
if (signal == null) {
return;
}
imaging.show(signal.createMIP(), signal.name, Imager.Type.FLOAT, 0);
}
public static void showMIP(Monitors monitors, RealSignal signal, String title) {
if (signal == null) {
monitors.error("Show MIP " + title + " this image does not exist.");
return;
}
imaging.show(signal.createMIP(), title, Imager.Type.FLOAT, 0);
}
public static void showPlanar(RealSignal signal) {
if (signal == null) {
return;
}
imaging.show(signal.createMontage(), signal.name, Imager.Type.FLOAT, 0);
}
public static void showPlanar(Monitors monitors, RealSignal signal, String title) {
if (signal == null) {
monitors.error("Show Planar " + title + " this image does not exist.");
return;
}
imaging.show(signal.createMontage(), title, Imager.Type.FLOAT, 0);
}
/*
public static RealSignal create(Monitors monitors, String name) {
RealSignal signal = imaging.create(name);
if (signal != null)
monitors.log("Created the real signal " + name + " " + signal.toString());
else
monitors.error("Impossible to create the real signal " + name);
return signal;
}
public static RealSignal create(Monitors monitors) {
RealSignal signal = imaging.create();
if (signal != null)
monitors.log("Created the real signal from the active window " + signal.toString());
else
monitors.error("Impossible to create the real signal from the active window");
return signal;
}
*/
public static Imager getImager() {
return imaging;
}
public static String getActiveImage() {
if (imaging.isSelectable())
return imaging.getSelectedImage();
return "";
}
public static void setVisible(JDialog dialog, boolean modal) {
if (dialog == null)
return;
dialogs.add(dialog);
imaging.setVisible(dialog, modal);
}
public static void setVisible(JPanel panel, String name, int x, int y) {
JFrame frame = new JFrame(name);
frame.getContentPane().add(panel);
frame.pack();
frame.setLocation(x, y);
frame.setVisible(true);
frames.add(frame);
}
public static void setVisible(JFrame frame) {
frames.add(frame);
frame.setVisible(true);
}
public static void close() {
for (JFrame frame : frames)
if (frame != null)
frame.dispose();
for (JDialog dialog : dialogs)
if (dialog != null)
dialog.dispose();
}
}
diff --git a/DeconvolutionLab2/src/deconvolutionlab/Output.java b/DeconvolutionLab2/src/deconvolutionlab/Output.java
index eb6a621..e89ab05 100644
--- a/DeconvolutionLab2/src/deconvolutionlab/Output.java
+++ b/DeconvolutionLab2/src/deconvolutionlab/Output.java
@@ -1,368 +1,371 @@
/*
* 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 deconvolutionlab;
import java.io.File;
import bilib.tools.NumFormat;
import deconvolution.algorithm.Controller;
import deconvolutionlab.Imager.ContainerImage;
import deconvolutionlab.monitor.Monitors;
import signal.Constraint;
import signal.RealSignal;
public class Output {
public enum View {
STACK, SERIES, ORTHO, MIP, PLANAR, FIGURE
};
public enum Dynamic {
INTACT, RESCALED, NORMALIZED, CLIPPED
};
private ContainerImage container = null;
private int px = 0;
private int py = 0;
private int pz = 0;
private boolean center = true;
private String name = "";
private boolean save = true;
private boolean show = true;
private View view = View.STACK;
private Imager.Type type = Imager.Type.FLOAT;
private Dynamic dynamic = Dynamic.INTACT;
private int frequency = 0;
public Output(View view, int frequency, String param) {
String[] tokens = param.trim().split(" ");
this.view = view;
this.frequency = frequency;
this.name = "";
this.center = true;
this.save = true;
this.show = true;
this.container = Lab.createContainer(Monitors.createDefaultMonitor(), "");
for (int i = 0; i < tokens.length; i++) {
boolean found = false;
String p = tokens[i].trim().toLowerCase();
if (p.startsWith("@")) {
found = true;
}
if (p.startsWith("noshow")) {
show = false;
found = true;
}
if (p.startsWith("nosave")) {
save = false;
found = true;
}
for (Dynamic d : Dynamic.values()) {
if (p.toLowerCase().equals(d.name().toLowerCase())) {
dynamic = d;
found = true;
}
}
for (View v : View.values()) {
if (p.toLowerCase().equals(v.name().toLowerCase())) {
view = v;
found = true;
}
}
for (Imager.Type t : Imager.Type.values()) {
if (p.toLowerCase().equals(t.name().toLowerCase())) {
type = t;
found = true;
}
}
if (p.startsWith("(") && p.endsWith(")")) {
double pos[] = NumFormat.parseNumbers(p);
if (pos.length > 0)
px = (int) Math.round(pos[0]);
if (pos.length > 1)
py = (int) Math.round(pos[1]);
if (pos.length > 2)
pz = (int) Math.round(pos[2]);
found = true;
center = false;
}
if (!found)
name += tokens[i] + " ";
name = name.trim();
}
}
public Output(View view, boolean show, boolean save, int frequency, String name, Dynamic dynamic, Imager.Type type, boolean center) {
this.name = name;
this.show = show;
this.save = save;
this.view = view;
this.type = type;
this.dynamic = dynamic;
this.center = center;
this.frequency = frequency;
}
public Output(View view, boolean show, boolean save, int frequency, String name, Dynamic dynamic, Imager.Type type, int px, int py, int pz) {
this.name = name;
this.show = show;
this.save = save;
this.view = view;
this.type = type;
this.dynamic = dynamic;
this.center = false;
this.px = px;
this.py = py;
this.pz = pz;
this.frequency = frequency;
}
public boolean is(int iterations) {
if (frequency == 0)
return false;
return iterations % frequency == 0;
}
public View getView() {
return view;
}
public String getName() {
return name;
}
public int extractFrequency(String param) {
String line = param.trim();
if (!line.startsWith("@"))
line = "@0 " + line;
String parts[] = line.split(" ");
if (parts.length >= 1) {
return (int) Math.round(NumFormat.parseNumber(parts[0], 0));
}
return 0;
}
public void setKeypoint(int px, int py, int pz) {
this.px = px;
this.py = py;
this.pz = pz;
this.center = false;
}
public String[] getAsString() {
String t = (type == Imager.Type.FLOAT ? "" : type.name().toLowerCase());
String d = (dynamic == Dynamic.INTACT ? "" : dynamic.name().toLowerCase());
String k = "";
if (!center)
k = " (" + px + "," + py + "," + pz + ")";
else
k = "";
String sa = save ? "\u2713" : "";
String sh = show ? "\u2713" : "";
String fr = frequency > 0 ? " @" + frequency : "";
return new String[] { view.name().toLowerCase() + fr, name, d, t, k, sh, sa, "\u232B" };
}
public void executeStarting(Monitors monitors, RealSignal signal, Controller controller) {
if (signal == null)
return;
execute(monitors, signal, controller, true, false, false, 0);
}
public void executeFinal(Monitors monitors, RealSignal signal, Controller controller) {
if (signal == null)
return;
execute(monitors, signal, controller, false, false, true, 0);
}
public void executeIterative(Monitors monitors, RealSignal signal, Controller controller, int iter) {
if (signal == null)
return;
execute(monitors, signal, controller, false, true, false, iter);
}
private void execute(Monitors monitors, RealSignal signal, Controller controller, boolean start, boolean live, boolean finish, int iter) {
String title = name;
if (live)
if (!is(iter))
return;
if (controller != null && live) {
if (controller.getIterations() > 0) {
title += "@" + controller.getIterations();
}
}
RealSignal x = null;
Constraint constraint = new Constraint(monitors);
switch (dynamic) {
case RESCALED:
x = signal.duplicate();
constraint.rescaled(x, 0, 255);
break;
case CLIPPED:
x = signal.duplicate();
float[] stats = controller.getStats().getStatsInput();
if (stats != null)
constraint.clipped(x, stats[1], stats[2]);
break;
case NORMALIZED:
x = signal.duplicate();
float[] stats1 = controller.getStats().getStatsInput();
if (stats1 != null)
constraint.normalized(x, stats1[0], stats1[3]);
break;
default:
x = signal;
}
String filename = controller.getPath() + File.separator + title + ".tif";
switch (view) {
case STACK:
if (show && !live)
Lab.show(monitors, x, title, type, (center ? x.nz / 2 : pz));
if (save && !live)
Lab.save(monitors, x, filename, type);
break;
case SERIES:
for (int k = 0; k < x.nz; k++) {
RealSignal slice = x.getSlice(k);
+ String z = "-z" + String.format("%06d", k) ;
if (show && !live)
- Lab.show(monitors, slice, title, type);
- if (save && !live)
- Lab.save(monitors, slice, filename, type);
+ Lab.show(monitors, slice, title + z, type);
+ if (save && !live) {
+ String zfilename = controller.getPath() + File.separator + title + z + ".tif";
+ Lab.save(monitors, slice, zfilename, type);
+ }
}
break;
case ORTHO:
if (!start)
orthoview(monitors, x, title, filename, live);
break;
case FIGURE:
if (!start)
figure(monitors, x, title, filename, live);
break;
case MIP:
if (!start)
mip(monitors, x, title, filename, live);
break;
case PLANAR:
if (!start)
planar(monitors, x, title, filename, live);
break;
default:
break;
}
}
private void mip(Monitors monitors, RealSignal signal, String title, String filename, boolean live) {
RealSignal plane = signal.createMIP();
if (show && live) {
Lab.append(monitors, container, plane, title, type);
}
if (show && !live)
Lab.show(monitors, plane, title, type);
if (save)
Lab.save(monitors, plane, filename, type);
}
private void orthoview(Monitors monitors, RealSignal signal, String title, String filename, boolean live) {
int cx = px;
int cy = py;
int cz = pz;
if (center) {
cx = signal.nx / 2;
cy = signal.ny / 2;
cz = signal.nz / 2;
}
RealSignal plane = signal.createOrthoview(cx, cy, cz);
if (show && live) {
if (container == null)
container = Lab.createContainer(monitors, title);
Lab.append(monitors, container, plane, title, type);
}
if (show && !live)
Lab.show(monitors, plane, title, type);
if (save)
Lab.save(monitors, plane, filename, type);
}
private void figure(Monitors monitors, RealSignal signal, String title, String filename, boolean live) {
int cx = px;
int cy = py;
int cz = pz;
if (center) {
cx = signal.nx / 2;
cy = signal.ny / 2;
cz = signal.nz / 2;
}
RealSignal plane = signal.createFigure(cx, cy, cz);
if (show && live) {
if (container == null)
container = Lab.createContainer(monitors, title);
Lab.append(monitors, container, plane, title, type);
}
if (show && !live)
Lab.show(monitors, plane, title, type);
if (save)
Lab.save(monitors, plane, filename, type);
}
private void planar(Monitors monitors, RealSignal signal, String title, String filename, boolean live) {
RealSignal plane = signal.createMontage();
if (show && live) {
if (container == null)
container = Lab.createContainer(monitors, title);
Lab.append(monitors, container, plane, title, type);
}
if (show && !live)
Lab.show(monitors, plane, title, type);
if (save)
Lab.save(monitors, plane, filename, type);
}
@Override
public String toString() {
String t = type.name().toLowerCase();
String v = view.name().toLowerCase();
String d = dynamic.name().toLowerCase();
String f = frequency > 0 ? " every " + frequency + " iterations" : "";
String k = (center ? "" : " keypoint = (" + px + "," + py + "," + pz + ")");
return v + " " + name + " format = (" + d + ", " + t + ") " + k + f;
}
}
diff --git a/DeconvolutionLab2/src/deconvolutionlab/module/AlgorithmModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/AlgorithmModule.java
index 70a6d4e..659c79e 100644
--- a/DeconvolutionLab2/src/deconvolutionlab/module/AlgorithmModule.java
+++ b/DeconvolutionLab2/src/deconvolutionlab/module/AlgorithmModule.java
@@ -1,169 +1,170 @@
/*
* 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 deconvolutionlab.module;
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.ArrayList;
import javax.swing.BorderFactory;
import javax.swing.BoxLayout;
import javax.swing.JComboBox;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.border.Border;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import bilib.component.HTMLPane;
import deconvolution.Command;
import deconvolution.Deconvolution;
import deconvolution.DeconvolutionDialog;
import deconvolution.algorithm.AbstractAlgorithmPanel;
import deconvolution.algorithm.Algorithm;
import deconvolutionlab.Config;
import deconvolutionlab.Lab;
public class AlgorithmModule extends AbstractModule implements ActionListener, ChangeListener {
private JComboBox<String> cmb;
private HTMLPane doc;
private JPanel cards;
private JLabel shortname;
public AlgorithmModule(boolean expanded) {
super("Algorithm", "-algorithm", "", "Check", expanded);
ArrayList<AbstractAlgorithmPanel> deconv = Algorithm.getAvailableAlgorithms();
for (AbstractAlgorithmPanel panel : deconv)
cmb.addItem(panel.getName());
cmb.addActionListener(this);
}
@Override
public String getCommand() {
String name = (String) cmb.getSelectedItem();
AbstractAlgorithmPanel algo = Algorithm.getPanel(name);
String cmd = "-algorithm " + algo.getShortnames()[0] + " " + algo.getCommand();
String synopsis = algo.getShortnames()[0] + " " + algo.getCommand();
setSynopsis(synopsis);
setCommand(cmd);
return cmd;
}
@Override
public JPanel buildExpandedPanel() {
shortname = new JLabel("-------");
Border bl1 = BorderFactory.createEtchedBorder();
Border bl2 = BorderFactory.createEmptyBorder(0, 10, 0, 10);
shortname.setBorder(BorderFactory.createCompoundBorder(bl1, bl2));
cmb = new JComboBox<String>();
JPanel pnc = new JPanel();
pnc.add(cmb);
doc = new HTMLPane(100, 1000);
cards = new JPanel(new CardLayout());
ArrayList<AbstractAlgorithmPanel> panels = Algorithm.getAvailableAlgorithms();
for (AbstractAlgorithmPanel panel : panels) {
JScrollPane scroll = new JScrollPane(panel.getPanelParameters());
scroll.setBorder(BorderFactory.createEmptyBorder());
scroll.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
scroll.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
cards.add(panel.getName(), scroll);
}
cmb.setMaximumRowCount(panels.size());
JPanel top = new JPanel(new BorderLayout());
top.add(cmb, BorderLayout.CENTER);
top.add(shortname, BorderLayout.EAST);
JPanel control = new JPanel();
control.setLayout(new BoxLayout(control, BoxLayout.PAGE_AXIS));
Border b1 = BorderFactory.createEtchedBorder();
Border b2 = BorderFactory.createEmptyBorder(10, 10, 10, 10);
control.setBorder(BorderFactory.createCompoundBorder(b1, b2));
cards.setBorder(BorderFactory.createEtchedBorder());
control.add(top);
control.add(cards);
doc.append("h1", "Documentation");
JPanel panel = new JPanel(new BorderLayout());
panel.add(control, BorderLayout.NORTH);
panel.add(doc.getPane(), BorderLayout.CENTER);
// cmb.addActionListener(this);
getAction2Button().setToolTipText("Human readable of the command line");
getAction2Button().addActionListener(this);
Config.register(getName(), "algorithm", cmb, Algorithm.getDefaultAlgorithm());
panel.setBorder(BorderFactory.createEtchedBorder());
+
return panel;
}
@Override
public void actionPerformed(ActionEvent e) {
super.actionPerformed(e);
if (e.getSource() == cmb) {
doc.clear();
String name = (String) cmb.getSelectedItem();
AbstractAlgorithmPanel algo = Algorithm.getPanel(name);
doc.append(algo.getDocumentation());
CardLayout cl = (CardLayout) (cards.getLayout());
cl.show(cards, name);
String s = "<html><b><p style =\"font-family:georgia\">";
for(int i=0; i<algo.getShortnames().length; i++)
s += (i==0 ? "" : " | ") + algo.getShortnames()[i] ;
shortname.setText(s + "</b></html>");
}
if (e.getSource() == getAction2Button()) {
Deconvolution deconvolution = new Deconvolution("Check Algorithm", Command.command());
- DeconvolutionDialog d = new DeconvolutionDialog(DeconvolutionDialog.Module.ALGO, deconvolution, null, null);
+ DeconvolutionDialog d = new DeconvolutionDialog(DeconvolutionDialog.Module.ALGO, deconvolution);
Lab.setVisible(d, false);
}
setSynopsis((String) cmb.getSelectedItem());
setCommand(getCommand());
Command.command();
}
@Override
public void stateChanged(ChangeEvent e) {
setSynopsis((String) cmb.getSelectedItem());
setCommand(getCommand());
Command.command();
}
@Override
public void close() {
}
}
diff --git a/DeconvolutionLab2/src/deconvolutionlab/module/BatchModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/BatchModule.java
index 47cfaab..578a1a2 100644
--- a/DeconvolutionLab2/src/deconvolutionlab/module/BatchModule.java
+++ b/DeconvolutionLab2/src/deconvolutionlab/module/BatchModule.java
@@ -1,169 +1,170 @@
/*
* 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 deconvolutionlab.module;
import java.awt.BorderLayout;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.util.ArrayList;
import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JPanel;
import javax.swing.JToolBar;
import javax.swing.ListSelectionModel;
import bilib.table.CustomizedColumn;
import bilib.table.CustomizedTable;
import deconvolution.Deconvolution;
import deconvolutionlab.Constants;
public class BatchModule extends AbstractModule implements MouseListener, ActionListener {
private CustomizedTable table;
private JButton bnRun;
private JButton bnLaunch;
public BatchModule(boolean expanded) {
super("Batch", "", "", "", expanded);
}
@Override
public String getCommand() {
return "";
}
@Override
public JPanel buildExpandedPanel() {
bnRun = new JButton("Run Jobs");
bnLaunch = new JButton("Launch Jobs");
ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
columns.add(new CustomizedColumn("Job", String.class, 120, false));
columns.add(new CustomizedColumn("Command", String.class, Constants.widthGUI, false));
columns.add(new CustomizedColumn("", String.class, 30, "\u232B", "Delete this job"));
table = new CustomizedTable(columns, true);
table.getColumnModel().getColumn(2).setMaxWidth(30);
table.getColumnModel().getColumn(2).setMinWidth(30);
table.addMouseListener(this);
table.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
JToolBar pn = new JToolBar("Controls Batch");
pn.setBorder(BorderFactory.createEmptyBorder());
pn.setLayout(new GridLayout(1, 2));
pn.setFloatable(false);
pn.add(bnRun);
pn.add(bnLaunch);
JPanel panel = new JPanel(new BorderLayout());
panel.add(table.getPane(100, 100), BorderLayout.CENTER);
panel.add(pn, BorderLayout.SOUTH);
getAction1Button().addActionListener(this);
bnRun.addActionListener(this);
bnLaunch.addActionListener(this);
return panel;
}
@Override
public void actionPerformed(ActionEvent e) {
super.actionPerformed(e);
if (e.getSource() == bnRun) {
if (table.getSelectedRows().length == 0)
table.setColumnSelectionInterval(0, table.getRowCount());
int rows[] = table.getSelectedRows();
for (int row : rows)
new Deconvolution("Batch" + table.getCell(row, 0), table.getCell(row, 1)).deconvolve();
}
else if (e.getSource() == bnLaunch) {
if (table.getSelectedRows().length == 0)
table.setColumnSelectionInterval(0, table.getRowCount());
int rows[] = table.getSelectedRows();
for (int row : rows)
new Deconvolution("Batch " + table.getCell(row, 0), table.getCell(row, 1)).launch();
}
+ update();
}
private void update() {
setSynopsis("" + table.getRowCount() + " jobs");
}
public int getCountJob() {
return table.getRowCount();
}
public void addJob(String name, String command) {
table.append(new String[] { name, command, "" });
update();
}
@Override
public void mouseClicked(MouseEvent e) {
if (e.getSource() == table) {
int row = table.getSelectedRow();
if (row < 0)
return;
if (table.getSelectedColumn() == 2) {
table.removeRow(row);
if (table.getRowCount() > 0)
table.setRowSelectionInterval(0, 0);
}
}
update();
}
@Override
public void mousePressed(MouseEvent e) {
}
@Override
public void mouseReleased(MouseEvent e) {
}
@Override
public void mouseEntered(MouseEvent e) {
}
@Override
public void mouseExited(MouseEvent e) {
}
@Override
public void close() {
getAction1Button().removeActionListener(this);
}
}
diff --git a/DeconvolutionLab2/src/deconvolutionlab/module/CommandModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/CommandModule.java
index abc1941..8c0b2ea 100644
--- a/DeconvolutionLab2/src/deconvolutionlab/module/CommandModule.java
+++ b/DeconvolutionLab2/src/deconvolutionlab/module/CommandModule.java
@@ -1,92 +1,92 @@
/*
* 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 deconvolutionlab.module;
import java.awt.BorderLayout;
import java.awt.event.ActionEvent;
import javax.swing.JPanel;
import bilib.component.HTMLPane;
import deconvolution.Command;
import deconvolution.Deconvolution;
import deconvolution.DeconvolutionDialog;
import deconvolutionlab.Lab;
public class CommandModule extends AbstractModule {
private HTMLPane window;
public CommandModule() {
super("Command", "", "", "Check", true);
}
public HTMLPane getPane() {
return window;
}
@Override
public JPanel buildExpandedPanel() {
window = new HTMLPane("Monaco", 100, 100);
JPanel panel = new JPanel(new BorderLayout());
panel.add(window.getPane(), BorderLayout.CENTER);
getAction2Button().setToolTipText("Human readable of the command line");
getAction2Button().addActionListener(this);
return panel;
}
@Override
public void actionPerformed(ActionEvent e) {
super.actionPerformed(e);
if (e.getSource() == getAction2Button()) {
Deconvolution deconvolution = new Deconvolution("Check Command", Command.command());
- DeconvolutionDialog d = new DeconvolutionDialog(DeconvolutionDialog.Module.RECAP, deconvolution, null, null);
+ DeconvolutionDialog d = new DeconvolutionDialog(DeconvolutionDialog.Module.RECAP, deconvolution);
Lab.setVisible(d, false);
}
}
@Override
public void close() {
}
@Override
public void setCommand(String command) {
window.clear();
window.append("p", command);
}
@Override
public String getCommand() {
return window.getText();
}
}
diff --git a/DeconvolutionLab2/src/deconvolutionlab/module/ControllerModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/ControllerModule.java
index e66b396..aa8b097 100644
--- a/DeconvolutionLab2/src/deconvolutionlab/module/ControllerModule.java
+++ b/DeconvolutionLab2/src/deconvolutionlab/module/ControllerModule.java
@@ -1,266 +1,265 @@
/*
* 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 deconvolutionlab.module;
import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.io.File;
import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextField;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import bilib.component.GridPanel;
import bilib.tools.Files;
import deconvolution.Command;
import deconvolutionlab.Config;
import signal.Constraint;
public class ControllerModule extends AbstractModule implements ActionListener, ChangeListener, KeyListener {
private JButton bnBrowse;
private JTextField txtReference;
private JTextField txtResidu;
private JTextField txtTime;
private JTextField txtIterations;
private JComboBox<String> cmbConstraint;
private JComboBox<String> cmbStats;
private JComboBox<String> cmbMonitor;
private JComboBox<String> cmbVerbose;
private JCheckBox chkResidu;
private JCheckBox chkReference;
private JCheckBox chkTime;
public ControllerModule(boolean expanded) {
super("Controller", "", "Default", "", expanded);
}
@Override
public String getCommand() {
String cmd = "";
if (cmbMonitor.getSelectedIndex() != 0)
cmd += "-monitor " + cmbMonitor.getSelectedItem() + " ";
if (cmbVerbose.getSelectedIndex() != 0)
cmd += "-verbose " + cmbVerbose.getSelectedItem() + " ";
if (cmbStats.getSelectedIndex() != 0)
cmd += "-stats " + cmbStats.getSelectedItem() + " ";
if (cmbConstraint.getSelectedIndex() != 0)
cmd += "-constraint " + cmbConstraint.getSelectedItem() + " ";
if (chkReference.isSelected())
cmd += "-reference " + txtReference.getText() + " ";
if (chkResidu.isSelected())
cmd += "-residu " + txtResidu.getText() + " ";
if (chkTime.isSelected())
cmd += "-time " + txtTime.getText() + " ";
return cmd;
}
@Override
public JPanel buildExpandedPanel() {
chkTime = new JCheckBox("");
chkResidu = new JCheckBox("");
chkReference = new JCheckBox("");
bnBrowse = new JButton("Browse");
txtReference = new JTextField("");
txtResidu = new JTextField("0.01");
txtTime = new JTextField("3600");
txtIterations = new JTextField("Iteration max (mandatory)");
txtIterations.setEditable(false);
cmbMonitor = new JComboBox<String>(new String[] {"console table", "console", "table", "no" });
cmbVerbose = new JComboBox<String>(new String[] {"log", "quiet", "mute", "prolix" });
cmbConstraint = new JComboBox<String>(Constraint.getContraintsAsArray());
cmbStats = new JComboBox<String>(new String[] {"no", "show", "show + save", "save"});
txtReference.setPreferredSize(new Dimension(200, 20));
GridPanel pn = new GridPanel(true, 2);
pn.place(0, 0, "monitor");
pn.place(0, 2, cmbMonitor);
pn.place(0, 3, "Monitoring message");
pn.place(1, 0, "verbose");
pn.place(1, 2, cmbVerbose);
pn.place(1, 3, "");
pn.place(3, 0, "stats");
pn.place(3, 2, cmbStats);
pn.place(3, 3, "Signal's statistics");
pn.place(4, 0, "constraint");
pn.place(4, 2, cmbConstraint);
pn.place(4, 3, "Additional constraint");
pn.place(5, 0, "residu");
pn.place(5, 1, chkResidu);
pn.place(5, 2, txtResidu);
pn.place(5, 3, "Additional stopping criteria");
pn.place(6, 0, "time");
pn.place(6, 1, chkTime);
pn.place(6, 2, txtTime);
pn.place(6, 3, "Additional stopping criteria");
pn.place(7, 0, "reference");
pn.place(7, 1, chkReference);
pn.place(7, 2, 2, 1, txtReference);
pn.place(8, 2, bnBrowse);
pn.place(8, 3, 1, 1, "Ground-truth file");
JScrollPane scroll = new JScrollPane(pn);
scroll.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
scroll.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
JPanel panel = new JPanel(new BorderLayout());
- panel.setBorder(BorderFactory.createEtchedBorder());
panel.add(scroll, BorderLayout.CENTER);
Config.register(getName(), "residu.enable", chkResidu, false);
Config.register(getName(), "reference.enable", chkReference, false);
Config.register(getName(), "time.enable", chkTime, false);
Config.register(getName(), "reference.value", txtReference, "");
Config.register(getName(), "residu.value", txtResidu, "0.01");
Config.register(getName(), "time.value", txtTime, "3600");
Config.register(getName(), "constraint", cmbConstraint, cmbConstraint.getItemAt(0));
Config.register(getName(), "stats", cmbStats, cmbStats.getItemAt(0));
Config.register(getName(), "monitor", cmbMonitor, cmbMonitor.getItemAt(0));
Config.register(getName(), "verbose", cmbVerbose, cmbVerbose.getItemAt(0));
bnBrowse.addActionListener(this);
chkResidu.addChangeListener(this);
chkReference.addChangeListener(this);
chkTime.addChangeListener(this);
txtResidu.addKeyListener(this);
txtReference.addKeyListener(this);
txtTime.addKeyListener(this);
cmbConstraint.addActionListener(this);
cmbMonitor.addActionListener(this);
cmbVerbose.addActionListener(this);
getAction1Button().addActionListener(this);
return panel;
}
private void update() {
setCommand(getCommand());
int count = 0;
count += (chkResidu.isSelected() ? 1 : 0);
count += (chkTime.isSelected() ? 1 : 0);
count += (chkReference.isSelected() ? 1 : 0);
setSynopsis("" + count + " controls");
Command.command();
}
@Override
public void actionPerformed(ActionEvent e) {
super.actionPerformed(e);
if (e.getSource() == bnBrowse) {
File file = Files.browseFile(Command.getPath());
if (file != null)
txtReference.setText(file.getAbsolutePath());
}
if (e.getSource() == getAction1Button()) {
chkResidu.removeChangeListener(this);
chkReference.removeChangeListener(this);
chkTime.removeChangeListener(this);
chkResidu.setSelected(false);
chkReference.setSelected(false);
chkTime.setSelected(false);
txtReference.setText("");
txtResidu.setText("0.01");
txtTime.setText("3600");
cmbConstraint.setSelectedIndex(0);
cmbStats.setSelectedIndex(0);
cmbMonitor.setSelectedIndex(0);
cmbVerbose.setSelectedIndex(0);
chkResidu.addChangeListener(this);
chkReference.addChangeListener(this);
chkTime.addChangeListener(this);
}
update();
}
@Override
public void stateChanged(ChangeEvent e) {
update();
}
@Override
public void keyTyped(KeyEvent e) {
}
@Override
public void keyPressed(KeyEvent e) {
}
@Override
public void keyReleased(KeyEvent e) {
update();
}
@Override
public void close() {
bnBrowse.removeActionListener(this);
chkReference.removeChangeListener(this);
chkResidu.removeChangeListener(this);
cmbVerbose.removeActionListener(this);
cmbMonitor.removeActionListener(this);
cmbConstraint.removeActionListener(this);
chkTime.removeChangeListener(this);
getAction1Button().removeChangeListener(this);
}
}
diff --git a/DeconvolutionLab2/src/deconvolutionlab/module/ImageModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/ImageModule.java
index 0e11e00..7439be2 100644
--- a/DeconvolutionLab2/src/deconvolutionlab/module/ImageModule.java
+++ b/DeconvolutionLab2/src/deconvolutionlab/module/ImageModule.java
@@ -1,362 +1,362 @@
/*
* 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 deconvolutionlab.module;
import java.awt.BorderLayout;
import java.awt.GridLayout;
import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.Transferable;
import java.awt.datatransfer.UnsupportedFlavorException;
import java.awt.dnd.DnDConstants;
import java.awt.dnd.DropTarget;
import java.awt.dnd.DropTargetDropEvent;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JPanel;
import javax.swing.JToolBar;
import bilib.table.CustomizedColumn;
import bilib.table.CustomizedTable;
import bilib.tools.Files;
import deconvolution.Command;
import deconvolution.Deconvolution;
import deconvolution.DeconvolutionDialog;
import deconvolutionlab.Config;
import deconvolutionlab.Constants;
import deconvolutionlab.Imager;
import deconvolutionlab.Lab;
import deconvolutionlab.dialog.PatternDialog;
import deconvolutionlab.dialog.SyntheticDialog;
import deconvolutionlab.monitor.Monitors;
import signal.RealSignal;
import signal.factory.SignalFactory;
public class ImageModule extends AbstractModule implements ActionListener, MouseListener {
private CustomizedTable table;
private JButton bnFile;
private JButton bnDirectory;
private JButton bnSynthetic;
private JButton bnPlatform;
public ImageModule(boolean expanded) {
super("Image", "-image", (Lab.getPlatform() == Imager.Platform.IMAGEJ ? "Active" : ""), "Check", expanded);
}
@Override
public String getCommand() {
int row = table.getSelectedRow();
if (row < 0)
return "";
return "-image " + table.getCell(row, 1) + " " + table.getCell(row, 2);
}
@Override
public JPanel buildExpandedPanel() {
ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
columns.add(new CustomizedColumn("Name", String.class, 100, false));
columns.add(new CustomizedColumn("Source", String.class, 100, false));
columns.add(new CustomizedColumn("Command", String.class, Constants.widthGUI - 200, true));
columns.add(new CustomizedColumn("", String.class, 30, "\u232B", "Delete this image source"));
table = new CustomizedTable(columns, true);
table.getColumnModel().getColumn(3).setMaxWidth(30);
table.getColumnModel().getColumn(3).setMinWidth(30);
table.addMouseListener(this);
bnFile = new JButton("\u2295 file");
bnDirectory = new JButton("\u2295 directory");
bnSynthetic = new JButton("\u2295 synthetic");
bnPlatform = new JButton("\u2295 platform");
JToolBar pn = new JToolBar("Controls Image");
pn.setBorder(BorderFactory.createEmptyBorder());
pn.setLayout(new GridLayout(1, 4));
pn.setFloatable(false);
pn.add(bnFile);
pn.add(bnDirectory);
pn.add(bnSynthetic);
if (Lab.getPlatform() == Imager.Platform.IMAGEJ)
pn.add(bnPlatform);
JPanel panel = new JPanel();
panel.setBorder(BorderFactory.createEtchedBorder());
panel.setLayout(new BorderLayout());
panel.add(pn, BorderLayout.SOUTH);
panel.add(table.getMinimumPane(100, 100), BorderLayout.CENTER);
// Add drop area
table.setDropTarget(new LocalDropTarget());
getCollapsedPanel().setDropTarget(new LocalDropTarget());
bnTitle.setDropTarget(new LocalDropTarget());
bnSynopsis.setDropTarget(new LocalDropTarget());
bnExpand.setDropTarget(new LocalDropTarget());
bnFile.addActionListener(this);
bnDirectory.addActionListener(this);
bnSynthetic.addActionListener(this);
bnPlatform.addActionListener(this);
getAction1Button().addActionListener(this);
getAction2Button().addActionListener(this);
bnFile.setToolTipText("Add a new source read from a single file (3D z-stack)");
bnDirectory.setToolTipText("Add a new source read from the 2D images from a directory");
bnSynthetic.setToolTipText("Add a new source artificially created");
bnPlatform.setToolTipText("Add a new source from a list of images of the platform");
getAction2Button().setToolTipText("Click to have a preview, Shift-click or Ctrl-click to show the complete stack");
getAction1Button().setToolTipText("Select the active window from the running platform");
Config.registerTable(getName(), "image", table);
return panel;
}
public void update() {
int row = table.getSelectedRow();
if (row >= 0) {
setCommand(getCommand());
setSynopsis(table.getCell(row, 0));
Command.command();
}
else {
setSynopsis("");
setCommand("Drag your image file, here");
}
getAction2Button().setEnabled(table.getRowCount() > 0);
}
@Override
public void actionPerformed(ActionEvent e) {
super.actionPerformed(e);
if (e.getSource() == bnFile)
file(Command.getPath());
else if (e.getSource() == bnDirectory)
dir(Command.getPath());
else if (e.getSource() == bnSynthetic)
synthetic(false);
else if (e.getSource() == bnPlatform)
platform();
else if (e.getSource() == getAction1Button()) {
int row = -1;
for(int i=0; i<table.getRowCount(); i++) {
if (table.getCell(i, 0).equalsIgnoreCase("active"))
if (table.getCell(i, 1).equalsIgnoreCase("platform"))
if (table.getCell(i, 2).equalsIgnoreCase("active"))
row = i;
}
if (row < 0)
table.insert(new String[] { "active", "platform", "active", "\u232B" });
else
table.setRowSelectionInterval(row, row);
}
else if (e.getSource() == getAction2Button()) {
boolean s = (e.getModifiers() & ActionEvent.SHIFT_MASK) == ActionEvent.SHIFT_MASK;
boolean c = (e.getModifiers() & ActionEvent.CTRL_MASK) == ActionEvent.CTRL_MASK;
display(s | c);
}
update();
}
public void platform() {
String name = Lab.getActiveImage();
if (name != "")
table.insert(new String[] { name, "platform", name, "\u232B" });
}
private void file(String path) {
File file = Files.browseFile(path);
if (file == null)
return;
table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "\u232B" });
}
private void dir(String path) {
File file = Files.browseDirectory(path);
if (file == null)
return;
PatternDialog dlg = new PatternDialog(file);
Lab.setVisible(dlg, true);
if (dlg.wasCancel())
return;
table.insert(new String[] { dlg.getDirName(), "directory", dlg.getCommand(), "\u232B" });
}
private void synthetic(boolean edit) {
ArrayList<SignalFactory> list = SignalFactory.getImages();
SyntheticDialog dlg = new SyntheticDialog(list);
if (edit) {
int row = table.getSelectedRow();
if (row >= 0) {
dlg.setParameters(table.getCell(row, 0), table.getCell(row, 2));
}
}
Lab.setVisible(dlg, true);
if (dlg.wasCancel())
return;
if (edit) {
int row = table.getSelectedRow();
if (row <= 0)
table.removeRow(row);
}
table.insert(new String[] { dlg.getShapeName(), "synthetic", dlg.getCommand(), "\u232B" });
}
private void edit() {
int row = table.getSelectedRow();
if (row < 0)
return;
String name = table.getCell(row, 0).trim();
for (SignalFactory factory : SignalFactory.getAll()) {
System.out.println(">>edit>> " + name + " == " + factory.getName().trim());
if (name.equals(factory.getName().trim())) {
synthetic(true);
return;
}
}
String filename = table.getCell(row, 1).trim();
File file = new File(filename);
if (!file.exists())
return;
if (file.isFile())
file(table.getCell(row, 21));
else
dir(table.getCell(row, 1));
}
private void display(boolean stack) {
int row = table.getSelectedRow();
if (row < 0)
return;
Deconvolution deconvolution = new Deconvolution("Check Image", Command.command());
deconvolution.openImage();
if (stack) {
RealSignal x = deconvolution.getImage();
if (x != null)
Lab.show(Monitors.createDefaultMonitor(), x, table.getCell(row, 0));
}
else {
- DeconvolutionDialog d = new DeconvolutionDialog(DeconvolutionDialog.Module.IMAGE, deconvolution, null, null);
+ DeconvolutionDialog d = new DeconvolutionDialog(DeconvolutionDialog.Module.IMAGE, deconvolution);
Lab.setVisible(d, false);
}
}
@Override
public void mouseClicked(MouseEvent e) {
if (e.getSource() == table) {
int row = table.getSelectedRow();
if (row < 0)
return;
if (table.getSelectedColumn() == 3) {
table.removeRow(row);
if (table.getRowCount() > 0)
table.setRowSelectionInterval(0, 0);
}
update();
if (e.getClickCount() == 2) {
edit();
}
}
}
@Override
public void mousePressed(MouseEvent e) {
}
@Override
public void mouseReleased(MouseEvent e) {
}
@Override
public void mouseEntered(MouseEvent e) {
}
@Override
public void mouseExited(MouseEvent e) {
}
@Override
public void close() {
bnFile.removeActionListener(this);
bnDirectory.removeActionListener(this);
bnSynthetic.removeActionListener(this);
bnPlatform.removeActionListener(this);
}
public class LocalDropTarget extends DropTarget {
@Override
public void drop(DropTargetDropEvent e) {
e.acceptDrop(DnDConstants.ACTION_COPY);
e.getTransferable().getTransferDataFlavors();
Transferable transferable = e.getTransferable();
DataFlavor[] flavors = transferable.getTransferDataFlavors();
for (DataFlavor flavor : flavors) {
if (flavor.isFlavorJavaFileListType()) {
try {
List<File> files = (List<File>) transferable.getTransferData(flavor);
for (File file : files) {
if (file.isDirectory()) {
table.insert(new String[] { file.getName(), "directory", file.getAbsolutePath(), "\u232B" });
table.setRowSelectionInterval(0, 0);
update();
}
if (file.isFile()) {
table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "\u232B" });
update();
}
}
}
catch (UnsupportedFlavorException ex) {
ex.printStackTrace();
}
catch (IOException ex) {
ex.printStackTrace();
}
}
}
e.dropComplete(true);
super.drop(e);
}
}
}
diff --git a/DeconvolutionLab2/src/deconvolutionlab/module/OutputModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/OutputModule.java
index 01bf3fe..7fbad60 100644
--- a/DeconvolutionLab2/src/deconvolutionlab/module/OutputModule.java
+++ b/DeconvolutionLab2/src/deconvolutionlab/module/OutputModule.java
@@ -1,236 +1,236 @@
/*
* 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 deconvolutionlab.module;
import java.awt.BorderLayout;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.util.ArrayList;
import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JPanel;
import javax.swing.JToolBar;
import bilib.table.CustomizedColumn;
import bilib.table.CustomizedTable;
import deconvolution.Command;
import deconvolutionlab.Config;
import deconvolutionlab.Constants;
import deconvolutionlab.Lab;
import deconvolutionlab.Output;
import deconvolutionlab.Output.View;
import deconvolutionlab.dialog.OutputDialog;
public class OutputModule extends AbstractModule implements ActionListener, MouseListener {
private CustomizedTable table;
private JButton bnStack;
private JButton bnSeries;
private JButton bnMIP;
private JButton bnOrtho;
private JButton bnPlanar;
private JButton bnFigure;
public OutputModule(boolean expanded) {
- super("Output", "", "", "Default", expanded);
+ super("Output", "", "Clear", "", expanded);
}
@Override
public String getCommand() {
String cmd = " ";
if (table == null)
return cmd;
for (int i = 0; i < table.getRowCount(); i++) {
String[] values = new String[table.getColumnCount()];
for(int c=0; c<table.getColumnCount(); c++)
values[c] = table.getCell(i, c) == null ? "" : table.getCell(i, c).trim();
cmd += " -out " + values[0] + " " + values[1] + " " + values[2] + " " + values[3] + " " + values[4];
if (values[5].equals(""))
cmd += " noshow";
if (values[6].equals(""))
cmd += " nosave";
}
return cmd;
}
public void update() {
setCommand(getCommand());
setSynopsis(table.getRowCount() + " output" + (table.getRowCount() > 1 ? "s" : ""));
Command.command();
getAction1Button().setEnabled(table.getRowCount() > 0);
}
@Override
public JPanel buildExpandedPanel() {
String[] dynamics = { "intact", "rescaled", "normalized", "clipped" };
String[] types = { "float", "short", "byte" };
ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
columns.add(new CustomizedColumn("Mode", String.class, 80, false));
columns.add(new CustomizedColumn("Name", String.class, Constants.widthGUI, true));
columns.add(new CustomizedColumn("Dynamic", String.class, 100, dynamics, "Select the dynamic range"));
columns.add(new CustomizedColumn("Type", String.class, 100, types, "Select the type"));
columns.add(new CustomizedColumn("Keypoint", String.class, 120, false));
columns.add(new CustomizedColumn("Show", String.class, 50, false));
columns.add(new CustomizedColumn("Save", String.class, 50, false));
columns.add(new CustomizedColumn("Del", String.class, 30, "\u232B", "Delete this image source"));
table = new CustomizedTable(columns, true);
table.getColumnModel().getColumn(5).setMaxWidth(50);
table.getColumnModel().getColumn(6).setMaxWidth(50);
table.getColumnModel().getColumn(7).setMaxWidth(30);
table.getColumnModel().getColumn(0).setMaxWidth(100);
table.getColumnModel().getColumn(2).setMaxWidth(100);
table.getColumnModel().getColumn(3).setMaxWidth(100);
table.addMouseListener(this);
bnStack = new JButton("\u2295 stack");
bnSeries = new JButton("\u2295 series");
bnMIP = new JButton("\u2295 mip");
bnOrtho = new JButton("\u2295 ortho");
bnPlanar = new JButton("\u2295 planar");
bnFigure = new JButton("\u2295 figure");
JToolBar pn = new JToolBar("Controls Image");
pn.setBorder(BorderFactory.createEmptyBorder());
pn.setLayout(new GridLayout(1, 6));
pn.setFloatable(false);
pn.add(bnStack);
pn.add(bnSeries);
pn.add(bnMIP);
pn.add(bnOrtho);
pn.add(bnPlanar);
pn.add(bnFigure);
JToolBar tool = new JToolBar("Path");
tool.setBorder(BorderFactory.createEmptyBorder());
tool.setLayout(new BorderLayout());
tool.setFloatable(false);
JPanel panel = new JPanel();
panel.setBorder(BorderFactory.createEtchedBorder());
panel.setLayout(new BorderLayout());
panel.add(tool, BorderLayout.NORTH);
panel.add(pn, BorderLayout.SOUTH);
panel.add(table.getMinimumPane(100, 100), BorderLayout.CENTER);
bnStack.addActionListener(this);
bnSeries.addActionListener(this);
bnMIP.addActionListener(this);
bnOrtho.addActionListener(this);
bnPlanar.addActionListener(this);
bnFigure.addActionListener(this);
getAction1Button().addActionListener(this);
Config.registerTable(getName(), "output", table);
return panel;
}
@Override
public void actionPerformed(ActionEvent e) {
super.actionPerformed(e);
View view = null;
if (e.getSource() == bnStack)
view = View.STACK;
else if (e.getSource() == bnSeries)
view = View.SERIES;
else if (e.getSource() == bnMIP)
view = View.MIP;
else if (e.getSource() == bnOrtho)
view = View.ORTHO;
else if (e.getSource() == bnPlanar)
view = View.PLANAR;
else if (e.getSource() == bnFigure)
view = View.FIGURE;
if (view != null) {
OutputDialog dlg = new OutputDialog(view);
Lab.setVisible(dlg, true);
if (dlg.wasCancel())
return;
Output out = dlg.getOut();
if (out != null)
table.insert(out.getAsString());
//Lab.setVisible(new OutputPanel(view), "panel", 30, 30);
update();
}
if (e.getSource() == getAction1Button()) {
table.removeRows();
}
}
@Override
public void mouseClicked(MouseEvent e) {
int row = table.getSelectedRow();
if (table.getSelectedColumn() == 7) {
table.removeRow(row);
if (table.getRowCount() > 0)
table.setRowSelectionInterval(0, 0);
}
update();
Command.command();
}
@Override
public void mousePressed(MouseEvent e) {
}
@Override
public void mouseReleased(MouseEvent e) {
}
@Override
public void mouseEntered(MouseEvent e) {
}
@Override
public void mouseExited(MouseEvent e) {
}
@Override
public void close() {
bnStack.removeActionListener(this);
bnSeries.removeActionListener(this);
bnMIP.removeActionListener(this);
bnOrtho.removeActionListener(this);
bnPlanar.removeActionListener(this);
bnFigure.removeActionListener(this);
getAction1Button().removeActionListener(this);
getAction2Button().removeActionListener(this);
}
}
diff --git a/DeconvolutionLab2/src/deconvolutionlab/module/PSFModule.java b/DeconvolutionLab2/src/deconvolutionlab/module/PSFModule.java
index 3019f59..637a7ce 100644
--- a/DeconvolutionLab2/src/deconvolutionlab/module/PSFModule.java
+++ b/DeconvolutionLab2/src/deconvolutionlab/module/PSFModule.java
@@ -1,350 +1,350 @@
/*
* 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 deconvolutionlab.module;
import java.awt.BorderLayout;
import java.awt.GridLayout;
import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.Transferable;
import java.awt.datatransfer.UnsupportedFlavorException;
import java.awt.dnd.DnDConstants;
import java.awt.dnd.DropTarget;
import java.awt.dnd.DropTargetDropEvent;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JPanel;
import javax.swing.JToolBar;
import bilib.table.CustomizedColumn;
import bilib.table.CustomizedTable;
import bilib.tools.Files;
import deconvolution.Command;
import deconvolution.Deconvolution;
import deconvolution.DeconvolutionDialog;
import deconvolutionlab.Config;
import deconvolutionlab.Constants;
import deconvolutionlab.Imager;
import deconvolutionlab.Lab;
import deconvolutionlab.dialog.PatternDialog;
import deconvolutionlab.dialog.SyntheticDialog;
import deconvolutionlab.monitor.Monitors;
import signal.RealSignal;
import signal.factory.SignalFactory;
public class PSFModule extends AbstractModule implements ActionListener, MouseListener {
private CustomizedTable table;
private JButton bnFile;
private JButton bnDirectory;
private JButton bnSynthetic;
private JButton bnPlatform;
public PSFModule(boolean expanded) {
super("PSF", "-psf", "", "Check", expanded);
}
@Override
public String getCommand() {
int row = table.getSelectedRow();
if (row < 0)
return "";
return "-psf " + table.getCell(row, 1) + " " + table.getCell(row, 2);
}
@Override
public JPanel buildExpandedPanel() {
ArrayList<CustomizedColumn> columns = new ArrayList<CustomizedColumn>();
columns.add(new CustomizedColumn("Name", String.class, 100, false));
columns.add(new CustomizedColumn("Source", String.class, 100, false));
columns.add(new CustomizedColumn("Command", String.class, Constants.widthGUI - 200, true));
columns.add(new CustomizedColumn("", String.class, 30, "\u232B", "Delete this PSF source"));
table = new CustomizedTable(columns, true);
table.getColumnModel().getColumn(3).setMaxWidth(30);
table.getColumnModel().getColumn(3).setMinWidth(30);
table.addMouseListener(this);
bnFile = new JButton("\u2295 file");
bnDirectory = new JButton("\u2295 directory");
bnSynthetic = new JButton("\u2295 synthetic");
bnPlatform = new JButton("\u2295 platform");
JToolBar pn = new JToolBar("Controls PSF");
pn.setBorder(BorderFactory.createEmptyBorder());
pn.setLayout(new GridLayout(1, 5));
pn.setFloatable(false);
pn.add(bnFile);
pn.add(bnDirectory);
pn.add(bnSynthetic);
if (Lab.getPlatform() == Imager.Platform.IMAGEJ)
pn.add(bnPlatform);
JPanel panel = new JPanel();
panel.setBorder(BorderFactory.createEtchedBorder());
panel.setLayout(new BorderLayout());
panel.add(pn, BorderLayout.SOUTH);
panel.add(table.getMinimumPane(100, 100), BorderLayout.CENTER);
// Add drop area
table.setDropTarget(new LocalDropTarget());
getCollapsedPanel().setDropTarget(new LocalDropTarget());
bnTitle.setDropTarget(new LocalDropTarget());
bnSynopsis.setDropTarget(new LocalDropTarget());
bnExpand.setDropTarget(new LocalDropTarget());
bnFile.addActionListener(this);
bnDirectory.addActionListener(this);
bnSynthetic.addActionListener(this);
bnPlatform.addActionListener(this);
getAction1Button().addActionListener(this);
getAction2Button().addActionListener(this);
bnFile.setToolTipText("Add a new source read from a single file (3D z-stack)");
bnDirectory.setToolTipText("Add a new source read from the 2D images from a directory");
bnSynthetic.setToolTipText("Add a new source artificially created");
bnPlatform.setToolTipText("Add a new source from a list of images of the platform");
getAction2Button().setToolTipText("Click to have a preview, Shift-click or Ctrl-click to show the complete stack");
getAction1Button().setToolTipText("Select the active window");
Config.registerTable(getName(), "psf", table);
return panel;
}
public void update() {
int row = table.getSelectedRow();
if (row >= 0) {
setCommand(getCommand());
setSynopsis(table.getCell(row, 0));
Command.command();
}
else {
setSynopsis("");
setCommand("Drag your image file, here");
}
getAction2Button().setEnabled(table.getRowCount() > 0);
}
@Override
public void actionPerformed(ActionEvent e) {
super.actionPerformed(e);
if (e.getSource() == bnFile)
file(Command.getPath());
else if (e.getSource() == bnDirectory)
dir(Command.getPath());
else if (e.getSource() == bnSynthetic)
synthetic(false);
else if (e.getSource() == bnPlatform)
platform();
else if (e.getSource() == getAction1Button())
platform();
else if (e.getSource() == getAction2Button()) {
boolean s = (e.getModifiers() & ActionEvent.SHIFT_MASK) == ActionEvent.SHIFT_MASK;
boolean c = (e.getModifiers() & ActionEvent.CTRL_MASK) == ActionEvent.CTRL_MASK;
display(s | c);
}
update();
}
public void platform() {
String name = Lab.getActiveImage();
if (name != "")
table.insert(new String[] {name, "platform", name, "\u232B" });
}
private void file(String path) {
File file = Files.browseFile(path);
if (file == null)
return;
table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "\u232B" });
}
private void dir(String path) {
File file = Files.browseDirectory(path);
if (file == null)
return;
PatternDialog dlg = new PatternDialog(file);
Lab.setVisible(dlg, true);
if (dlg.wasCancel())
return;
table.insert(new String[] { dlg.getDirName(), "directory", dlg.getCommand(), "\u232B" });
}
private void synthetic(boolean edit) {
ArrayList<SignalFactory> list = SignalFactory.getPSF();
SyntheticDialog dlg = new SyntheticDialog(list);
if (edit) {
int row = table.getSelectedRow();
if (row >= 0) {
dlg.setParameters(table.getCell(row, 0), table.getCell(row, 2));
}
}
Lab.setVisible(dlg, true);
if (dlg.wasCancel())
return;
if (edit) {
int row = table.getSelectedRow();
if (row <= 0)
table.removeRow(row);
}
table.insert(new String[] { dlg.getShapeName(), "synthetic", dlg.getCommand(), "" });
}
private void edit() {
int row = table.getSelectedRow();
if (row < 0)
return;
String name = table.getCell(row, 0).trim();
for(SignalFactory factory : SignalFactory.getAll()) {
if (name.equals(factory.getName().trim())) {
synthetic(true);
return;
}
}
String filename = table.getCell(row, 1).trim();
File file = new File(filename);
if (!file.exists())
return;
if (file.isFile())
file(table.getCell(row, 21));
else
dir(table.getCell(row, 1));
}
private void display(boolean stack) {
int row = table.getSelectedRow();
if (row < 0)
return;
Deconvolution deconvolution = new Deconvolution("Check PSF", Command.command());
deconvolution.openPSF();
if (stack) {
RealSignal x = deconvolution.getPSF();
if (x != null)
Lab.show(Monitors.createDefaultMonitor(), x, table.getCell(row, 0));
}
else {
- DeconvolutionDialog d = new DeconvolutionDialog(DeconvolutionDialog.Module.PSF, deconvolution, null, null);
+ DeconvolutionDialog d = new DeconvolutionDialog(DeconvolutionDialog.Module.PSF, deconvolution);
Lab.setVisible(d, false);
}
}
@Override
public void mouseClicked(MouseEvent e) {
if (e.getSource() == table) {
int row = table.getSelectedRow();
if (row < 0)
return;
if (table.getSelectedColumn() == 3) {
table.removeRow(row);
if (table.getRowCount() > 0)
table.setRowSelectionInterval(0, 0);
}
update();
if (e.getClickCount() == 2) {
edit();
}
}
}
@Override
public void mousePressed(MouseEvent e) {
}
@Override
public void mouseReleased(MouseEvent e) {
}
@Override
public void mouseEntered(MouseEvent e) {
}
@Override
public void mouseExited(MouseEvent e) {
}
@Override
public void close() {
bnFile.removeActionListener(this);
bnDirectory.removeActionListener(this);
bnSynthetic.removeActionListener(this);
bnPlatform.removeActionListener(this);
}
public class LocalDropTarget extends DropTarget {
@Override
public void drop(DropTargetDropEvent e) {
e.acceptDrop(DnDConstants.ACTION_COPY);
e.getTransferable().getTransferDataFlavors();
Transferable transferable = e.getTransferable();
DataFlavor[] flavors = transferable.getTransferDataFlavors();
for (DataFlavor flavor : flavors) {
if (flavor.isFlavorJavaFileListType()) {
try {
List<File> files = (List<File>) transferable.getTransferData(flavor);
for (File file : files) {
if (file.isDirectory()) {
table.insert(new String[] { file.getName(), "directory", file.getAbsolutePath(), "\u232B" });
table.setRowSelectionInterval(0, 0);
update();
}
if (file.isFile()) {
table.insert(new String[] { file.getName(), "file", file.getAbsolutePath(), "\u232B" });
update();
}
}
}
catch (UnsupportedFlavorException ex) {
ex.printStackTrace();
}
catch (IOException ex) {
ex.printStackTrace();
}
}
}
e.dropComplete(true);
super.drop(e);
}
}
}

Event Timeline

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