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making all the parameters of biplane calibration algorithm configurab…
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…le by user + new daily build
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@zitmen
zitmen committed Mar 17, 2016
1 parent c2a9903 commit 7f978b7
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Showing 12 changed files with 308 additions and 108 deletions.
2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -4,7 +4,7 @@

<groupId>cz.cuni.lf1.lge</groupId>
<artifactId>ThunderSTORM</artifactId>
<version>dev-2016-03-12-b1</version>
<version>dev-2016-03-17-b1</version>
<packaging>jar</packaging>

<name>ThunderSTORM</name>
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3 changes: 3 additions & 0 deletions src/main/java/cz/cuni/lf1/lge/ThunderSTORM/BiPlaneCalibrationPlugin.java
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Expand Up @@ -25,6 +25,7 @@
public class BiPlaneCalibrationPlugin implements PlugIn {

DefocusFunction defocusModel;
CalibrationConfig calibrationConfig;
IFilterUI selectedFilterUI;
IDetectorUI selectedDetectorUI;
ICalibrationEstimatorUI calibrationEstimatorUI;
Expand Down Expand Up @@ -73,6 +74,7 @@ public void run(String arg) {
if(dialog.showAndGetResult() != JOptionPane.OK_OPTION) {
return;
}
calibrationConfig = dialog.getCalibrationConfig();
selectedFilterUI = dialog.getActiveFilterUI();
selectedDetectorUI = dialog.getActiveDetectorUI();
calibrationEstimatorUI = (ICalibrationEstimatorUI) dialog.getActiveEstimatorUI();
Expand All @@ -94,6 +96,7 @@ public void run(String arg) {

// perform the calibration
final ICalibrationProcess process = CalibrationProcessFactory.create(
calibrationConfig,
selectedFilterUI, selectedDetectorUI, calibrationEstimatorUI,
defocusModel, stageStep, zRangeLimit, imp1, imp2, roi1, roi2);

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6 changes: 2 additions & 4 deletions src/main/java/cz/cuni/lf1/lge/ThunderSTORM/CylindricalLensCalibrationPlugin.java
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Expand Up @@ -2,10 +2,7 @@

import cz.cuni.lf1.lge.ThunderSTORM.UI.AstigmatismCalibrationDialog;
import cz.cuni.lf1.lge.ThunderSTORM.UI.GUI;
import cz.cuni.lf1.lge.ThunderSTORM.calibration.AstigmaticCalibrationProcess;
import cz.cuni.lf1.lge.ThunderSTORM.calibration.CalibrationProcessFactory;
import cz.cuni.lf1.lge.ThunderSTORM.calibration.DefocusFunction;
import cz.cuni.lf1.lge.ThunderSTORM.calibration.NoMoleculesFittedException;
import cz.cuni.lf1.lge.ThunderSTORM.calibration.*;
import cz.cuni.lf1.lge.ThunderSTORM.detectors.ui.IDetectorUI;
import cz.cuni.lf1.lge.ThunderSTORM.estimators.ui.AstigmatismCalibrationEstimatorUI;
import cz.cuni.lf1.lge.ThunderSTORM.estimators.ui.IEstimatorUI;
Expand Down Expand Up @@ -78,6 +75,7 @@ public void run(String arg) {

// perform the calibration
final AstigmaticCalibrationProcess process = (AstigmaticCalibrationProcess) CalibrationProcessFactory.create(
new CalibrationConfig(),
selectedFilterUI, selectedDetectorUI, calibrationEstimatorUI,
defocusModel, stageStep, zRangeLimit, imp, roi);

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2 changes: 1 addition & 1 deletion src/main/java/cz/cuni/lf1/lge/ThunderSTORM/ThunderSTORM.java
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Expand Up @@ -2,7 +2,7 @@

public class ThunderSTORM {

public static final String VERSION = "dev-2016-03-12-b1";
public static final String VERSION = "dev-2016-03-17-b1";
public static final String URL_DAILY = "https://googledrive.com/host/0BzOGc-xMFyDYR1JaelZYQmJsaUE/builds/daily";
public static final String URL_STABLE = "https://googledrive.com/host/0BzOGc-xMFyDYR1JaelZYQmJsaUE/builds/stable";
public static final String FILE_NAME = "Thunder_STORM";
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169 changes: 156 additions & 13 deletions src/main/java/cz/cuni/lf1/lge/ThunderSTORM/UI/BiplaneCalibrationDialog.java
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@@ -1,6 +1,7 @@
package cz.cuni.lf1.lge.ThunderSTORM.UI;

import cz.cuni.lf1.lge.ThunderSTORM.ModuleLoader;
import cz.cuni.lf1.lge.ThunderSTORM.calibration.CalibrationConfig;
import cz.cuni.lf1.lge.ThunderSTORM.calibration.DefocusFunction;
import cz.cuni.lf1.lge.ThunderSTORM.detectors.ui.IDetectorUI;
import cz.cuni.lf1.lge.ThunderSTORM.estimators.ui.IEstimatorUI;
Expand All @@ -11,6 +12,7 @@
import cz.cuni.lf1.lge.ThunderSTORM.util.MacroUI.ParameterKey;
import cz.cuni.lf1.lge.ThunderSTORM.util.MacroUI.ParameterTracker;
import cz.cuni.lf1.lge.ThunderSTORM.util.MacroUI.validators.DoubleValidatorFactory;
import cz.cuni.lf1.lge.ThunderSTORM.util.MacroUI.validators.IntegerValidatorFactory;
import cz.cuni.lf1.lge.ThunderSTORM.util.PluginCommands;
import ij.IJ;
import ij.ImagePlus;
Expand Down Expand Up @@ -44,7 +46,27 @@ public class BiplaneCalibrationDialog extends DialogStub implements ActionListen
private List<IDetectorUI> detectors;
private List<IEstimatorUI> estimators;
private List<DefocusFunction> defocusing;
ExecutorService previewThreadRunner = Executors.newSingleThreadExecutor();

ParameterKey.Double dist2thrZStackMatching;
ParameterKey.Integer minimumFitsCount;
ParameterKey.Integer polyFitMaxIters;
ParameterKey.Integer finalPolyFitMaxIters;
ParameterKey.Integer minFitsInZRange;
ParameterKey.Integer movingAverageLag;
ParameterKey.Boolean checkIfDefocusIsInRange;
ParameterKey.Integer inlierFittingMaxIters;
ParameterKey.Double inlierFittingInlierFraction;
ParameterKey.Boolean showResultsTable;

ParameterKey.Integer rtfIterNum;
ParameterKey.Double rtfThDist;
ParameterKey.Double rtfThInlr;

ParameterKey.Integer hIterNum;
ParameterKey.Double hThDist;
ParameterKey.Double hThInlr;
ParameterKey.Double hThPairDist;
ParameterKey.Double hThAllowedTransformChange;

public BiplaneCalibrationDialog(List<IFilterUI> filters, List<IDetectorUI> detectors, List<IEstimatorUI> estimators, List<DefocusFunction> defocusing) {
super(new ParameterTracker("thunderstorm.calibration"), IJ.getInstance(), "Calibration options");
Expand All @@ -60,6 +82,28 @@ public BiplaneCalibrationDialog(List<IFilterUI> filters, List<IDetectorUI> detec
rawImage1Stack = params.createStringField("raw_image1_stack", null, "");
rawImage2Stack = params.createStringField("raw_image2_stack", null, "");

CalibrationConfig defaultConfig = new CalibrationConfig();
dist2thrZStackMatching = params.createDoubleField("dist2thrZStackMatching", DoubleValidatorFactory.positive(), defaultConfig.dist2thrZStackMatching);
minimumFitsCount = params.createIntField("minimumFitsCount", IntegerValidatorFactory.positive(), defaultConfig.minimumFitsCount);
polyFitMaxIters = params.createIntField("polyFitMaxIters", IntegerValidatorFactory.positive(), defaultConfig.polyFitMaxIters);
finalPolyFitMaxIters = params.createIntField("finalPolyFitMaxIters", IntegerValidatorFactory.positive(), defaultConfig.finalPolyFitMaxIters);
minFitsInZRange = params.createIntField("minFitsInZRange", IntegerValidatorFactory.positive(), defaultConfig.minFitsInZRange);
movingAverageLag = params.createIntField("movingAverageLag", IntegerValidatorFactory.positive(), defaultConfig.movingAverageLag);
checkIfDefocusIsInRange = params.createBooleanField("checkIfDefocusIsInRange", null, defaultConfig.checkIfDefocusIsInRange);
inlierFittingMaxIters = params.createIntField("inlierFittingMaxIters", IntegerValidatorFactory.positive(), defaultConfig.inlierFittingMaxIters);
inlierFittingInlierFraction = params.createDoubleField("inlierFittingInlierFraction", DoubleValidatorFactory.rangeInclusive(0.0, 1.0), defaultConfig.inlierFittingInlierFraction);
showResultsTable = params.createBooleanField("showResultsTable", null, defaultConfig.showResultsTable);

rtfIterNum = params.createIntField("rtfIterNum", IntegerValidatorFactory.positive(), defaultConfig.ransacTranslationAndFlip.iterNum);
rtfThDist = params.createDoubleField("rtfThDist", DoubleValidatorFactory.positive(), defaultConfig.ransacTranslationAndFlip.thDist);
rtfThInlr = params.createDoubleField("rtfThInlr", DoubleValidatorFactory.rangeInclusive(0.0, 1.0), defaultConfig.ransacTranslationAndFlip.thInlr);

hIterNum = params.createIntField("hIterNum", IntegerValidatorFactory.positive(), defaultConfig.ransacHomography.iterNum);
hThDist = params.createDoubleField("hThDist", DoubleValidatorFactory.positive(), defaultConfig.ransacHomography.thDist);
hThInlr = params.createDoubleField("hThInlr", DoubleValidatorFactory.rangeInclusive(0.0, 1.0), defaultConfig.ransacHomography.thInlr);
hThPairDist = params.createDoubleField("hThPairDist", DoubleValidatorFactory.positive(), defaultConfig.ransacHomography.thPairDist);
hThAllowedTransformChange = params.createDoubleField("hThAllowedTransformChange", DoubleValidatorFactory.positive(), defaultConfig.ransacHomography.thAllowedTransformChange);

this.filters = filters;
this.detectors = detectors;
this.estimators = estimators;
Expand All @@ -68,7 +112,7 @@ public BiplaneCalibrationDialog(List<IFilterUI> filters, List<IDetectorUI> detec

@Override
protected void layoutComponents() {
Container pane = getContentPane();
JPanel pane = new JPanel();
//
pane.setLayout(new GridBagLayout());
GridBagConstraints componentConstraints = new GridBagConstraints();
Expand Down Expand Up @@ -150,25 +194,115 @@ public void actionPerformed(ActionEvent e) {
additionalOptions.add(calibrationPanel, gbc);
pane.add(additionalOptions, componentConstraints);

JPanel advancedOptions = new JPanel(new GridBagLayout());
advancedOptions.setBorder(BorderFactory.createTitledBorder("Advanced calibration settings"));
advancedOptions.add(new JLabel("Squared dist thr for z-stack matching:"), GridBagHelper.leftCol());
JTextField dist2thrZStackMatchingTextField = new JTextField("", 20);
dist2thrZStackMatching.registerComponent(dist2thrZStackMatchingTextField);
advancedOptions.add(dist2thrZStackMatchingTextField, GridBagHelper.rightCol());
advancedOptions.add(new JLabel("Minimum fits count:"), GridBagHelper.leftCol());
JTextField minimumFitsCountTextField = new JTextField("", 20);
minimumFitsCount.registerComponent(minimumFitsCountTextField);
advancedOptions.add(minimumFitsCountTextField, GridBagHelper.rightCol());
advancedOptions.add(new JLabel("Poly fit max iters:"), GridBagHelper.leftCol());
JTextField polyFitMaxItersTextField = new JTextField("", 20);
polyFitMaxIters.registerComponent(polyFitMaxItersTextField);
advancedOptions.add(polyFitMaxItersTextField, GridBagHelper.rightCol());
advancedOptions.add(new JLabel("Final poly fit max iters:"), GridBagHelper.leftCol());
JTextField finalPolyFitMaxItersTextField = new JTextField("", 20);
finalPolyFitMaxIters.registerComponent(finalPolyFitMaxItersTextField);
advancedOptions.add(finalPolyFitMaxItersTextField, GridBagHelper.rightCol());
advancedOptions.add(new JLabel("Min fits in z-range:"), GridBagHelper.leftCol());
JTextField minFitsInZRangeTextField = new JTextField("", 20);
minFitsInZRange.registerComponent(minFitsInZRangeTextField);
advancedOptions.add(minFitsInZRangeTextField, GridBagHelper.rightCol());
advancedOptions.add(new JLabel("Moving average lag:"), GridBagHelper.leftCol());
JTextField movingAverageLagTextField = new JTextField("", 20);
movingAverageLag.registerComponent(movingAverageLagTextField);
advancedOptions.add(movingAverageLagTextField, GridBagHelper.rightCol());
advancedOptions.add(new JLabel("Check if defocus is in range:"), GridBagHelper.leftCol());
JCheckBox checkIfDefocusIsInRangeCheckBox = new JCheckBox();
checkIfDefocusIsInRange.registerComponent(checkIfDefocusIsInRangeCheckBox);
advancedOptions.add(checkIfDefocusIsInRangeCheckBox, GridBagHelper.rightCol());
advancedOptions.add(new JLabel("Inlier fitting max iters:"), GridBagHelper.leftCol());
JTextField inlierFittingMaxItersTextField = new JTextField("", 20);
inlierFittingMaxIters.registerComponent(inlierFittingMaxItersTextField);
advancedOptions.add(inlierFittingMaxItersTextField, GridBagHelper.rightCol());
advancedOptions.add(new JLabel("Inliers fraction:"), GridBagHelper.leftCol());
JTextField inlierFittingInlierFractionTextField = new JTextField("", 20);
inlierFittingInlierFraction.registerComponent(inlierFittingInlierFractionTextField);
advancedOptions.add(inlierFittingInlierFractionTextField, GridBagHelper.rightCol());
advancedOptions.add(new JLabel("Show results table:"), GridBagHelper.leftCol());
JCheckBox showResultsTableCheckBox = new JCheckBox();
showResultsTable.registerComponent(showResultsTableCheckBox);
advancedOptions.add(showResultsTableCheckBox, GridBagHelper.rightCol());

JPanel rtfRansacOptions = new JPanel(new GridBagLayout());
rtfRansacOptions.setBorder(BorderFactory.createTitledBorder("RANSAC: rough translation and flip estimate"));
rtfRansacOptions.add(new JLabel("Iterations:"), GridBagHelper.leftCol());
JTextField rtfIterNumTextField = new JTextField("", 20);
rtfIterNum.registerComponent(rtfIterNumTextField);
rtfRansacOptions.add(rtfIterNumTextField, GridBagHelper.rightCol());
rtfRansacOptions.add(new JLabel("Inlier distance threshold:"), GridBagHelper.leftCol());
JTextField rtfThDistTextField = new JTextField("", 20);
rtfThDist.registerComponent(rtfThDistTextField);
rtfRansacOptions.add(rtfThDistTextField, GridBagHelper.rightCol());
rtfRansacOptions.add(new JLabel("Inliers portion threshold:"), GridBagHelper.leftCol());
JTextField rtfThInlrTextField = new JTextField("", 20);
rtfThInlr.registerComponent(rtfThInlrTextField);
rtfRansacOptions.add(rtfThInlrTextField, GridBagHelper.rightCol());
advancedOptions.add(rtfRansacOptions, GridBagHelper.twoCols());

JPanel hRansacOptions = new JPanel(new GridBagLayout());
hRansacOptions.setBorder(BorderFactory.createTitledBorder("RANSAC: fine homography estimate"));
hRansacOptions.add(new JLabel("Iterations:"), GridBagHelper.leftCol());
JTextField hIterNumTextField = new JTextField("", 20);
hIterNum.registerComponent(hIterNumTextField);
hRansacOptions.add(hIterNumTextField, GridBagHelper.rightCol());
hRansacOptions.add(new JLabel("Inlier distance threshold:"), GridBagHelper.leftCol());
JTextField hThDistTextField = new JTextField("", 20);
hThDist.registerComponent(hThDistTextField);
hRansacOptions.add(hThDistTextField, GridBagHelper.rightCol());
hRansacOptions.add(new JLabel("Inliers portion threshold:"), GridBagHelper.leftCol());
JTextField hThInlrTextField = new JTextField("", 20);
hThInlr.registerComponent(hThInlrTextField);
hRansacOptions.add(hThInlrTextField, GridBagHelper.rightCol());
hRansacOptions.add(new JLabel("Pair distance threshold:"), GridBagHelper.leftCol());
JTextField hThPairDistTextField = new JTextField("", 20);
hThPairDist.registerComponent(hThPairDistTextField);
hRansacOptions.add(hThPairDistTextField, GridBagHelper.rightCol());
hRansacOptions.add(new JLabel("Allowed transform change:"), GridBagHelper.leftCol());
JTextField hThAllowedTransformChangeTextField = new JTextField("", 20);
hThAllowedTransformChange.registerComponent(hThAllowedTransformChangeTextField);
hRansacOptions.add(hThAllowedTransformChangeTextField, GridBagHelper.rightCol());
advancedOptions.add(hRansacOptions, GridBagHelper.twoCols());

pane.add(advancedOptions, componentConstraints);

JButton defaults = new JButton("Defaults");
JButton ok = new JButton("OK");
JButton cancel = new JButton("Cancel");

defaults.addActionListener(this);
ok.addActionListener(this);
cancel.addActionListener(this);
//

JPanel buttons = new JPanel();
buttons.add(defaults);
buttons.add(Box.createHorizontalStrut(30));
buttons.add(ok);
buttons.add(cancel);
pane.add(buttons, componentConstraints);
pane.setBorder(BorderFactory.createEmptyBorder(10, 20, 10, 20));

setResizable(true);
setLayout(new BorderLayout());
JScrollPane scrollPane = new JScrollPane(pane, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
scrollPane.setBorder(BorderFactory.createEmptyBorder());
add(scrollPane);

getRootPane().setDefaultButton(ok);
getRootPane().setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
setResizable(false);
params.loadPrefs();
pack();
}

@Override
Expand Down Expand Up @@ -214,7 +348,12 @@ public int showAndGetResult() {

return JOptionPane.OK_OPTION;
} else {
return super.showAndGetResult();
int result = super.showAndGetResult();
int maxScreenHeight = GraphicsEnvironment.getLocalGraphicsEnvironment().getMaximumWindowBounds().height;
if(getHeight() > maxScreenHeight) {
setSize(getWidth(), maxScreenHeight);
}
return result;
}
}

Expand Down Expand Up @@ -254,11 +393,15 @@ public ImagePlus getSecondPlaneStack() {
return WindowManager.getImage(rawImage2Stack.getValue());
}

@Override
public void dispose() {
super.dispose();
if(previewThreadRunner != null) {
previewThreadRunner.shutdownNow();
}
public CalibrationConfig getCalibrationConfig() {
return new CalibrationConfig(dist2thrZStackMatching.getValue(), minimumFitsCount.getValue(),
polyFitMaxIters.getValue(), finalPolyFitMaxIters.getValue(), minFitsInZRange.getValue(),
movingAverageLag.getValue(), checkIfDefocusIsInRange.getValue(), inlierFittingMaxIters.getValue(),
inlierFittingInlierFraction.getValue(), showResultsTable.getValue(),
CalibrationConfig.RansacConfig.createTranslationAndFlipConfig(
rtfIterNum.getValue(), rtfThDist.getValue(), rtfThInlr.getValue()),
CalibrationConfig.RansacConfig.createHomographyConfig(
hIterNum.getValue(), hThDist.getValue(), hThInlr.getValue(),
hThPairDist.getValue(), hThAllowedTransformChange.getValue()));
}
}
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