P smlm develop

.gitignore

@@ -12,3 +12,4 @@ nbproject/
 build.properties
 c:/
 dependency-reduced-pom.xml
+/previous_jars/*

README.md

@@ -17,3 +17,7 @@ The modifications were implemented based on [this development version](https://g
 
 ## Getting started
 Install [ImageJ](http://imagej.nih.gov/ij/index.html) and download the latest version of [ThunderSTORM](https://github.com/quantori/prj-thunderstorm/releases/latest). For installation, copy the downloaded file into ImageJ's plugin subdirectory and run ImageJ. See the [Installation guide](https://github.com/zitmen/thunderstorm/wiki/Installation) for more information. To get started using ThunderSTORM, see the [Tutorials](https://github.com/zitmen/thunderstorm/wiki/Tutorials). Example data are provided [here](https://github.com/zitmen/thunderstorm/releases/download/v1.0/example_data.zip).
+
+
+If you use the phasor sub-pixel estimator, please cite this paper (https://doi.org/10.1063/1.5005899):
+* K.J.A. Martens, A.N. Bader, S. Baas, B. Rieger, J. Hohlbein. _Phasor based single-molecule localization microscopy in 3D (pSMLM-3D): an algorithm for MHz localization rates using standard CPUs_ JCP, 2018.

pom.xml

@@ -13,16 +13,48 @@
     </description>
     <url>https://github.com/zitmen/thunderstorm</url>
 
+    <inceptionYear>2013</inceptionYear>
+    <organization>
+        <name>Wageningen University</name>
+        <url>https://wur.nl/</url>
+    </organization>
+
+    <contributors>
+        <contributor>
+            <name>Koen Martens</name>
+            <email>koenjamartens@gmail.com</email>
+            <roles>
+                <role>developer</role>
+            </roles>
+        </contributor>
+    </contributors>
+
+    <mailingLists>
+        <mailingList>
+            <name>Image.sc Forum</name>
+            <archive>https://forum.image.sc/tags/imagej</archive>
+        </mailingList>
+    </mailingLists>
+
+    <parent>
+        <groupId>org.scijava</groupId>
+        <artifactId>pom-scijava</artifactId>
+        <version>36.0.0</version>
+    </parent>
+
     <properties>
         <skipTests>true</skipTests>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <kotlin.version>1.7.10</kotlin.version>
-        <imagej.path>C:\Program Files\ImageJ</imagej.path>
-        <imagej1.version>1.53s</imagej1.version>
-        <maven.compiler.source>1.8</maven.compiler.source>
-        <maven.compiler.target>1.8</maven.compiler.target>
+        <kotlin.version>1.8.0</kotlin.version>
+        <imagej1.version>1.54i</imagej1.version>
+        <maven.compiler.source>21</maven.compiler.source>
+        <maven.compiler.target>21</maven.compiler.target>
+        <imagej.path>C:\Users\gobes001\LocalSoftware\fiji-win64\Fiji.app\jars</imagej.path>
         <lyx.path>C:\Program Files (x86)\LyX 2.1\bin\lyx.exe</lyx.path>
         <help.dir>${basedir}/src/main/resources/resources/help</help.dir>
+        <license.licenseName>GNU GPL 3.0</license.licenseName>
+        <license.copyrightOwners>Zitmen</license.copyrightOwners>
+        <scijava.app.directory>C:\Users\gobes001\LocalSoftware\fiji-win64\Fiji.app</scijava.app.directory>
     </properties>
 
     <profiles>
@@ -48,9 +80,13 @@
 
     <issueManagement>
         <system>GitHub</system>
-        <url>https://github.com/zitmen/thunderstorm/issues</url>
+        <url>https://github.com/HohlbeinLab/prj-thunderstorm/issues</url>
     </issueManagement>
 
+    <ciManagement>
+        <system>None</system>
+    </ciManagement>
+
     <licenses>
         <license>
             <name>GNU GPL v3</name>
@@ -157,25 +193,6 @@
                     </execution>
                 </executions>
             </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-antrun-plugin</artifactId>
-                <executions>
-                    <execution>
-                        <id>copytoplugins</id>
-                        <phase>install</phase>
-                        <goals>
-                            <goal>run</goal>
-                        </goals>
-                        <configuration>
-                            <tasks>
-                                <copy tofile="${imagej.path}/plugins/Thunder_STORM.jar"
-                                      file="target/Thunder_STORM.jar"/>
-                            </tasks>
-                        </configuration>
-                    </execution>
-                </executions>
-            </plugin>
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>exec-maven-plugin</artifactId>
@@ -218,12 +235,18 @@
             </plugin>
         </plugins>
     </build>
+
     <repositories>
+        <repository>
+            <id>scijava.public</id>
+            <url>https://maven.scijava.org/content/groups/public</url>
+        </repository>
         <repository>
             <id>jitpack.io</id>
             <url>https://jitpack.io</url>
         </repository>
     </repositories>
+
     <dependencies>
         <dependency>
             <groupId>org.jetbrains.kotlin</groupId>
@@ -264,14 +287,20 @@
         <dependency>
             <groupId>net.imagej</groupId>
             <artifactId>ij</artifactId>
-            <version>${imagej1.version}</version>
-            <scope>provided</scope>
         </dependency>
         <dependency>
             <groupId>net.sf.cssbox</groupId>
             <artifactId>swingbox</artifactId>
             <version>1.1</version>
         </dependency>
+                <!--Added by KM-->
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+            <version>1.7.25</version>
+            <scope>provided</scope>
+        </dependency>
+        <!--End Added by KM-->
         <dependency>
             <groupId>net.java.balloontip</groupId>
             <artifactId>balloontip</artifactId>

previous_jars/maven-archiver/pom.properties

@@ -0,0 +1,5 @@
+#Generated by Maven
+#Thu Apr 04 16:11:10 CEST 2024
+artifactId=ThunderSTORM
+groupId=cz.cuni.lf1.lge
+version=optimization-release-v1.0

src/main/java/cz/cuni/lf1/lge/ThunderSTORM/AnalysisPlugIn.java

@@ -24,6 +24,7 @@
 import cz.cuni.lf1.lge.ThunderSTORM.util.Point;
 import cz.cuni.lf1.lge.ThunderSTORM.util.VectorMath;
 import ij.IJ;
+import ij.ImageJ;
 import ij.ImagePlus;
 import ij.gui.Roi;
 import ij.plugin.filter.ExtendedPlugInFilter;
@@ -64,7 +65,8 @@ public final class AnalysisPlugIn implements ExtendedPlugInFilter {
     private RenderingQueue renderingQueue;
     private Roi roi;
     private AnalysisOptionsDialog dialog;
-
+
+
     /**
      * Returns flags specifying capabilities of the plugin.
      *
@@ -144,12 +146,9 @@ public int showDialog(final ImagePlus imp, final String command, PlugInFilterRun
             } else {
                 // Create and show the dialog
                 try {
-                    SwingUtilities.invokeAndWait(new Runnable() {
-                        @Override
-                        public void run() {
-                            dialog = new AnalysisOptionsDialog(imp, command, allFilters, allDetectors, allEstimators, allRenderers);
-                            dialog.setVisible(true);
-                        }
+                    SwingUtilities.invokeAndWait(() -> {
+                        dialog = new AnalysisOptionsDialog(imp, command, allFilters, allDetectors, allEstimators, allRenderers);
+                        dialog.setVisible(true);
                     });
                 } catch(InvocationTargetException e) {
                     throw e.getCause();
@@ -310,4 +309,26 @@ synchronized public void showResults() {
             renderingQueue.repaintLater();
         }
     }
+
+
+    // Only run from the IDE
+    public static void main(String[] args) throws Exception {
+        Class<?> clazz = AnalysisPlugIn.class;
+        java.net.URL url = clazz.getProtectionDomain().getCodeSource().getLocation();
+        java.io.File file = new java.io.File(url.toURI());
+        System.setProperty("plugins.dir", file.getAbsolutePath());
+        //System.setProperty("plugins.dir", "C:\\Users\\gobes001\\source\\repos\\thunderstorm-prj\\target");
+        // start ImageJ
+        ImageJ imagej = new ImageJ();
+
+        // open the Clown sample
+        ImagePlus image = IJ.openImage("C:\\Users\\gobes001\\source\\repos\\thunderstorm-prj\\Substack.tif");
+        image.show();
+
+        // run the plugin
+        IJ.runPlugIn(clazz.getName(), "");
+
+        //IJ.run("Run Analysis");
+        //new AnalysisPlugIn("runAnalysis");
+    }
 }

src/main/java/cz/cuni/lf1/lge/ThunderSTORM/BiPlaneCalibrationPlugin.java

@@ -32,6 +32,7 @@ public class BiPlaneCalibrationPlugin implements PlugIn {
     String savePath;
     double stageStep;
     double zRangeLimit;//in nm
+    double zzeropos;//in nm
     ImagePlus imp1, imp2;
     Roi roi1, roi2;
 
@@ -81,6 +82,7 @@ public void run(String arg) {
             savePath = dialog.getSavePath();
             stageStep = dialog.getStageStep();
             zRangeLimit = dialog.getZRangeLimit();
+            zzeropos = 0;
             defocusModel = dialog.getActiveDefocusFunction();
 
             if (!isStack(imp1 = dialog.getFirstPlaneStack())) return;
@@ -98,7 +100,7 @@ public void run(String arg) {
             final ICalibrationProcess process = CalibrationProcessFactory.create(
                     calibrationConfig,
                     selectedFilterUI, selectedDetectorUI, calibrationEstimatorUI,
-                    defocusModel, stageStep, zRangeLimit, imp1, imp2, roi1, roi2);
+                    defocusModel, stageStep, zRangeLimit, imp1, imp2, roi1, roi2, zzeropos);
 
             try {
                 process.runCalibration();
@@ -127,4 +129,4 @@ public void run(String arg) {
             IJ.handleException(ex);
         }
     }
-}
+}

src/main/java/cz/cuni/lf1/lge/ThunderSTORM/CylindricalLensCalibrationPlugin.java

@@ -1,5 +1,6 @@
 package cz.cuni.lf1.lge.ThunderSTORM;
 
+import cz.cuni.lf1.lge.ThunderSTORM.estimators.ui.PhasorAstigmatismCalibrationEstimatorUI;
 import cz.cuni.lf1.lge.ThunderSTORM.UI.AstigmatismCalibrationDialog;
 import cz.cuni.lf1.lge.ThunderSTORM.UI.GUI;
 import cz.cuni.lf1.lge.ThunderSTORM.calibration.*;
@@ -24,10 +25,13 @@ public class CylindricalLensCalibrationPlugin implements PlugIn {
     DefocusFunction defocusModel;
     IFilterUI selectedFilterUI;
     IDetectorUI selectedDetectorUI;
+    IEstimatorUI selectedEstimatorUI;
+    PhasorAstigmatismCalibrationEstimatorUI phasorCalibrationEstimatorUI;
     AstigmatismCalibrationEstimatorUI calibrationEstimatorUI;
     String savePath;
     double stageStep;
     double zRangeLimit;//in nm
+    double zzeropos;
     ImagePlus imp;
     Roi roi;
 
@@ -47,9 +51,10 @@ public void run(String arg) {
         try {
             //load modules
             calibrationEstimatorUI = new AstigmatismCalibrationEstimatorUI();
+            phasorCalibrationEstimatorUI = new PhasorAstigmatismCalibrationEstimatorUI();
             List<IFilterUI> filters = ModuleLoader.getUIModules(IFilterUI.class);
             List<IDetectorUI> detectors = ModuleLoader.getUIModules(IDetectorUI.class);
-            List<IEstimatorUI> estimators = Arrays.asList(new IEstimatorUI[]{calibrationEstimatorUI}); // only one estimator can be used
+            List<IEstimatorUI> estimators = Arrays.asList(new IEstimatorUI[]{calibrationEstimatorUI, phasorCalibrationEstimatorUI}); 
             List<DefocusFunction> defocusFunctions = ModuleLoader.getUIModules(DefocusFunction.class);
             Thresholder.loadFilters(filters);
 
@@ -60,24 +65,59 @@ public void run(String arg) {
                 IJ.handleException(e);
             }
             AstigmatismCalibrationDialog dialog;
+
             dialog = new AstigmatismCalibrationDialog(imp, filters, detectors, estimators, defocusFunctions);
             if(dialog.showAndGetResult() != JOptionPane.OK_OPTION) {
                 return;
             }
             selectedFilterUI = dialog.getActiveFilterUI();
             selectedDetectorUI = dialog.getActiveDetectorUI();
+            selectedEstimatorUI = dialog.getActiveEstimatorUI();
             savePath = dialog.getSavePath();
             stageStep = dialog.getStageStep();
             zRangeLimit = dialog.getZRangeLimit();
             defocusModel = dialog.getActiveDefocusFunction();
-
+			//zzeropos is  boolean indicator for setting z=0 at intersection of defocus curves, or at middle of calibration stack - KM
+            zzeropos = dialog.getZZeroPos();
+
+            String activeEstimator = ""+selectedEstimatorUI;
+            String subStringGauss = "ui.AstigmatismCalibrationEstimatorUI";
+            String subStringPhasor = "ui.PhasorAstigmatismCalibrationEstimatorUI";
+            //IJ.log(activeEstimator);
             roi = imp.getRoi() != null ? imp.getRoi() : new Roi(0, 0, imp.getWidth(), imp.getHeight());
 
             // perform the calibration
+			//if Phasor is selected - KM
+            if (activeEstimator.toLowerCase().contains(subStringPhasor.toLowerCase())){
+            final PhasorAstigmaticCalibrationProcess process = (PhasorAstigmaticCalibrationProcess) PhasorCalibrationProcessFactory.create(
+                    new CalibrationConfig(),
+                    selectedFilterUI, selectedDetectorUI, phasorCalibrationEstimatorUI,
+                    defocusModel, stageStep, zRangeLimit, imp, roi, zzeropos);
+
+            try {
+                process.runCalibration();
+            } catch(NoMoleculesFittedException ex) {
+                // if no beads were succesfully fitted, draw localizations anyway
+                process.drawOverlay();
+                IJ.handleException(ex);
+                return;
+            }
+            process.drawOverlay();
+            process.drawSigmaPlots();
+
+            try {
+                process.getCalibration(defocusModel).saveToFile(savePath);
+            } catch(IOException ex) {
+                UI.showAnotherLocationDialog(ex, process.getCalibration(defocusModel));
+            }
+            } else 
+			//If Gauss is selected, do the standard calibration -KM
+			{
+			//The boolean zzeropos is added to differentiate between zero at intersection or middle of calibration stack -KM
             final AstigmaticCalibrationProcess process = (AstigmaticCalibrationProcess) CalibrationProcessFactory.create(
                     new CalibrationConfig(),
                     selectedFilterUI, selectedDetectorUI, calibrationEstimatorUI,
-                    defocusModel, stageStep, zRangeLimit, imp, roi);
+                    defocusModel, stageStep, zRangeLimit, imp, roi, zzeropos);
 
             try {
                 process.runCalibration();
@@ -95,8 +135,9 @@ public void run(String arg) {
             } catch(IOException ex) {
                 UI.showAnotherLocationDialog(ex, process.getCalibration(defocusModel));
             }
+			}
         } catch(Exception ex) {
             IJ.handleException(ex);
         }
     }
-}
+}

src/main/java/cz/cuni/lf1/lge/ThunderSTORM/ImportExportPlugIn.java

@@ -353,11 +353,11 @@ public ImportDialog(Window owner, boolean groundTruth) {
             assert moduleNames != null && moduleNames.length > 0;
             fileFormat = fileParams.createStringField("fileFormat", StringValidatorFactory.isMember(moduleNames), moduleNames[0]);
             filePath = fileParams.createStringField("filePath", StringValidatorFactory.fileExists(), "");
-            detectMeasurementProtocol = fileParams.createBooleanField("detectMeasurementProtocol", null, true);
             startingFrame = params.createIntField("startingFrame", IntegerValidatorFactory.positiveNonZero(), 1);
             append = params.createBooleanField("append", null, false);
             this.groundTruth = groundTruth;
             if(!groundTruth) {
+                detectMeasurementProtocol = fileParams.createBooleanField("detectMeasurementProtocol", null, true);
                 showPreview = params.createBooleanField("livePreview", null, true);
                 rawImageStack = params.createStringField("rawImageStack", StringValidatorFactory.openImages(true), "");
             }
@@ -671,4 +671,4 @@ public void run() {
             }
         };
     }
-}
+}