Adding phasor as sub-pixel localisation option

README.md

@@ -19,3 +19,6 @@ Install [ImageJ](http://imagej.nih.gov/ij/index.html) and download the latest ve
 ## How to cite ThunderSTORM
 If you use ThunderSTORM to process your data, please, cite our [paper](http://dx.doi.org/10.1093/bioinformatics/btu202):
   * M. Ovesný, P. Křížek, J. Borkovec, Z. Švindrych, G. M. Hagen. _ThunderSTORM: a comprehensive ImageJ plugin for PALM and STORM data analysis and super-resolution imaging._ Bioinformatics 30(16):2389-2390, 2014.
+
+If you use the phasor sub-pixel estimator, please cite this paper in addition (https://doi.org/10.1101/191957):
+  * 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_ bioRxiv, 2017.

pom.xml

@@ -7,15 +7,15 @@
     <version>dev-2016-09-10-b1</version>
     <packaging>jar</packaging>
 
-    <name>ThunderSTORM</name>
+    <name>ThunderSTORM-Phasor_KM</name>
     <description>ThunderSTORM: a comprehensive ImageJ plugin for PALM and STORM data analysis and super-resolution imaging</description>
     <url>https://github.com/zitmen/thunderstorm</url>
 
     <properties>
         <skipTests>true</skipTests>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <kotlin.version>1.0.3</kotlin.version>
-        <imagej.path>C:\Program Files\ImageJ</imagej.path>
+        <imagej.path>C:\Users\Koen Martens\Desktop\Fiji.app</imagej.path>
         <imagej1.version>1.49s</imagej1.version>
         <maven.compiler.source>1.8</maven.compiler.source>
         <maven.compiler.target>1.8</maven.compiler.target>
@@ -270,6 +270,14 @@
             <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>
@@ -311,16 +319,16 @@
             <version>4.11</version>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.bitbucket.pepa_borkovec</groupId>
-            <artifactId>MacroAwareUI</artifactId>
-            <version>889b2b553e96e8493bf6a103acfe2197eb0733ca</version>
-        </dependency>
         <dependency>
             <groupId>commons-io</groupId>
             <artifactId>commons-io</artifactId>
             <version>2.4</version>
             <type>jar</type>
         </dependency>
+        <dependency>
+            <groupId>org.bitbucket.pepa_borkovec</groupId>
+            <artifactId>MacroAwareUI</artifactId>
+            <version>889b2b553e96e8493bf6a103acfe2197eb0733ca</version>
+        </dependency>
     </dependencies>
 </project>

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();

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();
@@ -95,6 +135,7 @@ 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), "");
             }

src/main/java/cz/cuni/lf1/lge/ThunderSTORM/UI/AstigmatismCalibrationDialog.java

@@ -40,7 +40,10 @@ public class AstigmatismCalibrationDialog extends DialogStub implements ActionLi
     ParameterKey.String detectorName;
     ParameterKey.String estimatorName;
     ParameterKey.String defocusName;
+    ParameterKey.String zzeropos;
 
+    protected transient ParameterKey.String ZZEROPOS;
+
     private List<IFilterUI> filters;
     private List<IDetectorUI> detectors;
     private List<IEstimatorUI> estimators;
@@ -60,6 +63,8 @@ public AstigmatismCalibrationDialog(ImagePlus imp, List<IFilterUI> filters, List
         detectorName = params.createStringField("detector", null, detectors.get(0).getName());
         estimatorName = params.createStringField("estimator", null, estimators.get(0).getName());
         defocusName = params.createStringField("defocusing", null, defocusing.get(0).getName());
+
+        zzeropos = params.createStringField("ZzeroPosition", null, "Z=0 at intersection of polynomials");
 
         this.filters = filters;
         this.detectors = detectors;
@@ -77,7 +82,6 @@ protected void layoutComponents() {
         componentConstraints.gridx = 0;
         componentConstraints.fill = GridBagConstraints.BOTH;
         componentConstraints.weightx = 1;
-
         JButton cameraSetup = new JButton("Camera setup");
         cameraSetup.addActionListener(new ActionListener() {
             @Override
@@ -112,6 +116,15 @@ public void actionPerformed(ActionEvent e) {
 
         JPanel aditionalOptions = new JPanel(new GridBagLayout());
         aditionalOptions.setBorder(BorderFactory.createTitledBorder("Additional options"));
+
+
+        ButtonGroup btnGroup = new ButtonGroup();
+        JRadioButton intersectionRadioButton = new JRadioButton("Z=0 at intersection of polynomials");
+        JRadioButton middleStackRadioButton = new JRadioButton("Z=0 at middle of image stack");
+        btnGroup.add(intersectionRadioButton);
+        btnGroup.add(middleStackRadioButton);
+        zzeropos.registerComponent(btnGroup);
+
         aditionalOptions.add(new JLabel("Z stage step [nm]:"), GridBagHelper.leftCol());
         JTextField stageStepTextField = new JTextField("", 20);
         stageStep.registerComponent(stageStepTextField);
@@ -130,7 +143,10 @@ public void actionPerformed(ActionEvent e) {
         gbc.fill = GridBagConstraints.HORIZONTAL;
         aditionalOptions.add(calibrationPanel, gbc);
         pane.add(aditionalOptions, componentConstraints);
-
+        aditionalOptions.add(new JLabel("Z calibration: "), GridBagHelper.leftCol());
+        aditionalOptions.add(intersectionRadioButton, GridBagHelper.rightCol());
+        aditionalOptions.add(middleStackRadioButton, GridBagHelper.rightCol());
+
         JButton defaults = new JButton("Defaults");
         JButton preview = new JButton("Preview");
         JButton ok = new JButton("OK");
@@ -295,6 +311,11 @@ public double getZRangeLimit() {
         return zRangeLimit.getValue();
     }
 
+    public double getZZeroPos() {
+        if (zzeropos.getValue()=="Z=0 at middle of image stack"){return 1;}
+        else {return 0;}
+    }
+
     @Override
     public void dispose() {
         super.dispose();

src/main/java/cz/cuni/lf1/lge/ThunderSTORM/UI/HelpButton.java

@@ -123,7 +123,7 @@ private void showInTextWindow() throws IOException {
         //set page shown in browser
         if(url != null && !url.equals(htmlBrowser.getPage())) {
             try {
-                htmlBrowser.setPage(url);
+                htmlBrowser.setPage(url.toString());
             } catch(Exception e) {
                 htmlBrowser.setText("Could not load help file");
             }

src/main/java/cz/cuni/lf1/lge/ThunderSTORM/calibration/AbstractCalibrationProcess.java

@@ -40,6 +40,7 @@ abstract class AbstractCalibrationProcess implements ICalibrationProcess {
     protected DefocusFunction defocusModel;
     protected double stageStep;
     protected double zRange;
+    protected double zzeropos;
 
     // results
     protected double angle = 0.0;
@@ -53,14 +54,15 @@ abstract class AbstractCalibrationProcess implements ICalibrationProcess {
     protected double[] allSigma1s;
     protected double[] allSigma2s;
 
-    public AbstractCalibrationProcess(CalibrationConfig config, IFilterUI selectedFilterUI, IDetectorUI selectedDetectorUI, ICalibrationEstimatorUI calibrationEstimatorUI, DefocusFunction defocusModel, double stageStep, double zRangeLimit) {
+    public AbstractCalibrationProcess(CalibrationConfig config, IFilterUI selectedFilterUI, IDetectorUI selectedDetectorUI, ICalibrationEstimatorUI calibrationEstimatorUI, DefocusFunction defocusModel, double stageStep, double zRangeLimit, double zzeropos) {
         this.config = config;
         this.selectedFilterUI = selectedFilterUI;
         this.selectedDetectorUI = selectedDetectorUI;
         this.calibrationEstimatorUI = calibrationEstimatorUI;
         this.defocusModel = defocusModel;
         this.stageStep = stageStep;
         this.zRange = zRangeLimit;
+        this.zzeropos = zzeropos;
     }
 
     /**
@@ -123,7 +125,7 @@ public void run(int i) {
         return MathProxy.atan2(sin, cos) / 4;
     }
 
-    protected void fitQuadraticPolynomials(Collection<PSFSeparator.Position> positions) {
+    protected void fitQuadraticPolynomials(ImagePlus imp, Collection<PSFSeparator.Position> positions) {
         // fit a quadratic polynomial to sigma1 = f(zpos) and sigma1 = f(zpos) for each bead
         IterativeFitting polynomialFitter = new IterativeFitting(config.inlierFittingMaxIters, config.inlierFittingInlierFraction);
         allPolynomsS1 = new ArrayList<DefocusFunction>();
@@ -144,7 +146,7 @@ protected void fitQuadraticPolynomials(Collection<PSFSeparator.Position> positio
                 if(p.getSize() < config.minimumFitsCount) {
                     continue;
                 }
-                double z0guess = guessZ0(p);
+                double z0guess = guessZ0(imp, p);
                 p.discardFitsByFrameRange(z0guess - zRange/stageStep, z0guess + zRange/stageStep);
 
                 // retrieve values again after filtering out fits not in range
@@ -321,7 +323,8 @@ protected static void drawOverlay(ImagePlus imp, Roi roi, List<Molecule> allFits
     /**
      * guess z0 of molecule
      */
-    protected double guessZ0(PSFSeparator.Position p) {
+    protected double guessZ0(ImagePlus imp, PSFSeparator.Position p) {
+        final ImageStack stack = imp.getStack();
         double[] sigma1AsArray = p.getAsArray(LABEL_SIGMA1);
         double[] sigma2AsArray = p.getAsArray(LABEL_SIGMA2);
         double[] intensityAsArray = p.getAsArray(LABEL_INTENSITY);
@@ -341,7 +344,11 @@ protected double guessZ0(PSFSeparator.Position p) {
             }
         }
 
-        return p.fits.get(minIdx).getParam(LABEL_FRAME);
+        double stackSize = stack.getSize();
+        if (zzeropos==1){//If zero is at middle of image stack -KM
+            return (stackSize/2);
+        }else{//If zero is a polynomial crossover -KM
+            return p.fits.get(minIdx).getParam(LABEL_FRAME);}
     }
 
     private static double[] flattenListOfArrays(List<double[]> list) {

src/main/java/cz/cuni/lf1/lge/ThunderSTORM/calibration/AstigmaticBiplaneCalibrationProcess.java

@@ -45,8 +45,8 @@ public class AstigmaticBiplaneCalibrationProcess extends AbstractCalibrationProc
 
     public AstigmaticBiplaneCalibrationProcess(CalibrationConfig config, IFilterUI selectedFilterUI, IDetectorUI selectedDetectorUI,
                                                AstigmaticBiplaneCalibrationEstimatorUI calibrationEstimatorUI, DefocusFunction defocusModel,
-                                               double stageStep, double zRangeLimit, ImagePlus imp1, ImagePlus imp2, Roi roi1, Roi roi2) {
-        super(config, selectedFilterUI, selectedDetectorUI, calibrationEstimatorUI, defocusModel, stageStep, zRangeLimit);
+                                               double stageStep, double zRangeLimit, ImagePlus imp1, ImagePlus imp2, Roi roi1, Roi roi2, double zzeropos) {
+        super(config, selectedFilterUI, selectedDetectorUI, calibrationEstimatorUI, defocusModel, stageStep, zRangeLimit, zzeropos);
         this.imp1 = imp1;
         this.imp2 = imp2;
         this.roi1 = roi1;
@@ -60,7 +60,7 @@ public void runCalibration() {
         IJ.log("angle2 = " + angle2);
         IJ.log("Homography transformation matrix: " + transformationMatrix.toString());
 
-        fitQuadraticPolynomials(pos12.keySet());
+        fitQuadraticPolynomials(imp1, pos12.keySet());
         polyS11 = polynomS1Final;
         polyS12 = polynomS2Final;
         allPolyS11 = allPolynomsS1;
@@ -71,7 +71,7 @@ public void runCalibration() {
         IJ.log("s11 = " + polynomS1Final.toString());
         IJ.log("s12 = " + polynomS2Final.toString());
 
-        fitQuadraticPolynomials(pos12.values());
+        fitQuadraticPolynomials(imp1, pos12.values());
         polyS21 = polynomS1Final;
         polyS22 = polynomS2Final;
         allPolyS21 = allPolynomsS1;
@@ -155,7 +155,7 @@ public void drawSigmaPlots() {
     }
 
     @Override
-    protected double guessZ0(PSFSeparator.Position p) {
+    protected double guessZ0(ImagePlus imp, PSFSeparator.Position p) {
         double[] sigma1AsArray = p.getAsArray(LABEL_SIGMA1);
         double[] sigma2AsArray = p.getAsArray(LABEL_SIGMA2);
         double[] sigma3AsArray = p.getAsArray(LABEL_SIGMA3);