package GUI;
import AngioTool.AngioTool;import AngioTool.ATPreferences;import AngioTool.MemoryMonitor;import AngioTool.Results;import Batch.Analyzer;import Batch.AnalyzerParameters;import Batch.AnalyzeSkeleton2;import Batch.BatchAnalysisUi;import Batch.BatchUtils;import Batch.Canvas;import Batch.ConvexHull;import Batch.Filters;import Batch.ImageUtils;import Batch.IntVector;import Batch.ISliceRunner;import Batch.Lacunarity2;import Batch.Lee94;import Batch.Outline;import Batch.Particles;import Batch.Rgb;import Batch.SkeletonResult2;import Batch.SpreadsheetWriter;import Batch.Tubeness;import Batch.VesselThickness;import ij.IJ;import ij.ImagePlus;import ij.gui.OvalRoi;import ij.gui.Overlay;import ij.gui.PolygonRoi;import ij.gui.Roi;import ij.gui.ShapeRoi;import ij.measure.Calibration;import ij.process.ByteProcessor;import ij.process.ColorProcessor;import ij.process.ImageProcessor;import java.awt.Color;import java.awt.Cursor;import java.awt.Dimension;import java.awt.Font;import java.awt.Image;import java.awt.Point;import java.awt.event.ActionEvent;import java.awt.event.ActionListener;import java.awt.event.KeyAdapter;import java.awt.event.KeyEvent;import java.awt.event.KeyListener;import java.awt.event.MouseAdapter;import java.awt.event.MouseEvent;import java.awt.event.MouseListener;import java.awt.event.WindowAdapter;import java.awt.event.WindowEvent;import java.io.File;import java.text.DateFormat;import java.util.ArrayList;import java.util.Arrays;import java.util.Collections;import java.util.Date;import java.util.Hashtable;import java.util.Locale;import javax.swing.BorderFactory;import javax.swing.DefaultComboBoxModel;import javax.swing.GroupLayout;import javax.swing.Icon;import javax.swing.ImageIcon;import javax.swing.JButton;import javax.swing.JCheckBox;import javax.swing.JColorChooser;import javax.swing.JComboBox;import javax.swing.JFileChooser;import javax.swing.JFrame;import javax.swing.JLabel;import javax.swing.JOptionPane;import javax.swing.JPanel;import javax.swing.JProgressBar;import javax.swing.JSlider;import javax.swing.JSpinner;import javax.swing.JTabbedPane;import javax.swing.JTextField;import javax.swing.JToggleButton;import javax.swing.SpinnerModel;import javax.swing.SpinnerNumberModel;import javax.swing.SwingUtilities;import javax.swing.SwingWorker;import javax.swing.UIManager;import javax.swing.UnsupportedLookAndFeelException;import javax.swing.WindowConstants;import javax.swing.GroupLayout.Alignment;import javax.swing.border.SoftBevelBorder;import javax.swing.event.ChangeEvent;import javax.swing.event.ChangeListener;import javax.swing.plaf.metal.DefaultMetalTheme;import javax.swing.plaf.metal.MetalLookAndFeel;import javax.swing.plaf.metal.OceanTheme;import kz.swing.markSlider;import org.netbeans.lib.awtextra.AbsoluteConstraints;import org.netbeans.lib.awtextra.AbsoluteLayout;
public class AngioToolGUI extends JFrame implements KeyListener, MouseListener { public static Point ATAboutBoxLoc;
private AnalyzerParameters params; private ISliceRunner sliceRunner = new ISliceRunner.Parallel(Analyzer.threadPool);
private String excelPath; private File currentDir; private Icon lockedIcon; private Icon unlockedIcon; private AngioToolAboutBox aboutBox; private Image imgIcon; private File imageFile; private ImagePlus imageOriginal; private ImagePlus imageResult; private ImagePlus imageThresholded; private ImagePlus imageTubeness; private ImageProcessor ipOriginal; private ImageProcessor ipThresholded; private ImageProcessor tubenessIp; private Tubeness.Scratch tubeness; private int minSigma; private int maxSigma; private double[] firstSigma = new double[]{5.0}; private ArrayList<Double> allSigmas; private ArrayList<Double> currentSigmas; private ArrayList<AngioToolGUI.sigmaImages> sI; private ArrayList<int[]> al; private IntVector convexHull = new IntVector(); private double convexHullArea; private int[] allantoisOverlay; //private Roi outlineRoi; //private PolygonRoi convexHullRoi; //private ArrayList<Roi> skeletonRoi; //private ArrayList<Roi> junctionsRoi; private double averageVesselDiameter; private long thresholdedPixelArea = 0L; private double ElSlope; private double medialELacunarity; private double FlSlope; private double medialFLacunarity; //private int[] lacunarityBoxes; //private ArrayList<Double> Elamdas = new ArrayList<>(); //private ArrayList<Double> Flamdas = new ArrayList<>(); private double meanEl; private double meanFl; private SkeletonResult2 skelResult;
private Results results; private JLabel batchStatusLabel; private JPanel AnalysisTabPanel; private JButton BatchButton; private JButton AnalyzeButton; private JTabbedPane TabbedPane; private JPanel backgroundParticlesPanel; private JButton branchinPointsColorButton; private JLabel branchingPointsLabel; private RoundedPanel branchingPointsRoundedPanel; private JSpinner branchingPointsSpinner; private JButton clearCalibrationButton; private JButton convexHullColorButton; private JLabel convexHullLabel; private RoundedPanel convexHullRoundedPanel; private JSpinner convexHullSizeSpinner; private JLabel distanceInMMLabel; private JNumberTextField distanceInMMNumberTextField; private JLabel distanceInPixelsLabel; private JNumberTextField distanceInPixelsNumberTextField; private JCheckBox fillHolesCheckBox; //private RangeSlider fillHolesRangeSlider; private JSlider fillHolesRangeSliderLow; private JSlider fillHolesRangeSliderHigh; private JSlider fillHolesRangeSlider2; private JSpinner fillHolesSpinner; private JButton helpButton; private JTextField highThresholdTextField; private JComboBox imageResulFormatComboBox; private JTextField lowThresholdTextField; private TransparentTextField memTransparentTextField; private JButton openImageButton; private JButton outlineColorButton; private JLabel outlineLabel; private RoundedPanel outlineRoundedPanel; private JSpinner outlineSpinner; private JPanel overlaySettingsPanel; private static JProgressBar progressBar; private JSpinner removeSmallParticlesSpinner; private JCheckBox resizeImageCheckBox; private JPanel resizeImagePanel; private JLabel resizingFactorLabel; private JSpinner resizingFactorSpinner; private JButton saveImageButton; private JCheckBox saveResultImageCheckBox; private JButton saveResultsToButton; private JTextField saveResultsToTextField; private JPanel savingPreferencesPanel; private JLabel scaleLabel; private JTextField scaleTextField; private JPanel setScalePanel; private JPanel settingsTabPanel; private JCheckBox showBranchingPointsCheckBox; private JCheckBox showConvexHullCheckBox; private JCheckBox showOutlineCheckBox; private JCheckBox showOverlayCheckBox; private JCheckBox showSkeletonCheckBox; private markSlider sigmasMarkSlider; private JSpinner sigmasSpinner; private JButton skeletonColorButton; private RoundedPanel skeletonColorRoundedPanel; private JLabel skeletonLabel; private JSpinner skeletonSpinner; private JCheckBox smallParticlesCheckBox; //private RangeSlider smallParticlesRangeSlider; private JSlider smallParticlesRangeSliderLow; private JSlider smallParticlesRangeSliderHigh; private JSlider smallParticlesRangeSlider2; private JPanel thicknessIntensityPanel; //private RangeSlider thresholdRangeSlider; private JSlider thresholdRangeSliderLow; private JSlider thresholdRangeSliderHigh; private JToggleButton toggleOverlayToggleButton; private JButton unlockButton;
public static int getRangeValueLow(JSlider lowSlider, JSlider highSlider) { return Math.min(lowSlider.getValue(), highSlider.getValue()); }
public static int getRangeValueHigh(JSlider lowSlider, JSlider highSlider) { return Math.max(lowSlider.getValue(), highSlider.getValue()); }
@Override public void keyTyped(KeyEvent e) { }
@Override public void keyPressed(KeyEvent e) { }
@Override public void keyReleased(KeyEvent e) { }
@Override public void mouseClicked(MouseEvent e) { }
@Override public void mousePressed(MouseEvent e) { this.requestFocus(); }
@Override public void mouseReleased(MouseEvent e) { }
@Override public void mouseEntered(MouseEvent e) { }
@Override public void mouseExited(MouseEvent e) { }
public AngioToolGUI(AnalyzerParameters params) { this.params = params; this.initLookAndFeel(); //Utils.NAME = "AngioTool-Batch";
//Utils.checkJavaVersion(1, 7, 0); //Utils.checkImageJVersion(1, 47, "s"); this.setIconImage(AngioTool.ATIcon.getImage()); //ATAboutBoxLoc = (java.awt.Point)ATPreferences.settings.atHelpLoc; this.currentDir = new File(params.defaultPath); this.initComponents(); MemoryMonitor mm = new MemoryMonitor(1000, this.memTransparentTextField); mm.start(); //this.ste = new SaveToExcel(); this.aboutBox = new AngioToolAboutBox(this, false); this.addKeyListener(this); this.addMouseListener(this); this.setFocusable(true); //Utils.isInternetActive = new ReachableTest().test(); }
private void initComponents() { //this.fillHolesRangeSlider = new RangeSlider(); this.fillHolesRangeSliderLow = new JSlider(); this.fillHolesRangeSliderHigh = new JSlider(); //this.smallParticlesRangeSlider = new RangeSlider(); this.smallParticlesRangeSliderLow = new JSlider(); this.smallParticlesRangeSliderHigh = new JSlider(); this.openImageButton = new JButton(); this.BatchButton = new JButton(); this.AnalyzeButton = new JButton(); progressBar = new JProgressBar(); this.TabbedPane = new JTabbedPane(); this.AnalysisTabPanel = new JPanel(); this.thicknessIntensityPanel = new JPanel(); this.sigmasMarkSlider = new markSlider(); this.sigmasSpinner = new JSpinner(); //this.thresholdRangeSlider = new RangeSlider(); this.thresholdRangeSliderLow = new JSlider(); this.thresholdRangeSliderHigh = new JSlider(); this.lowThresholdTextField = new JTextField(); this.highThresholdTextField = new JTextField(); this.backgroundParticlesPanel = new JPanel(); this.smallParticlesCheckBox = new JCheckBox(); this.fillHolesCheckBox = new JCheckBox(); this.fillHolesSpinner = new JSpinner(); this.removeSmallParticlesSpinner = new JSpinner(); this.fillHolesRangeSlider2 = new JSlider(); this.smallParticlesRangeSlider2 = new JSlider(); this.savingPreferencesPanel = new JPanel(); this.saveResultsToButton = new JButton(); this.saveResultsToTextField = new JTextField(); this.saveResultImageCheckBox = new JCheckBox(); this.toggleOverlayToggleButton = new JToggleButton(); this.settingsTabPanel = new JPanel(); this.resizeImagePanel = new JPanel(); this.resizeImageCheckBox = new JCheckBox(); this.resizingFactorLabel = new JLabel(); this.resizingFactorSpinner = new JSpinner(); this.unlockButton = new JButton(); this.setScalePanel = new JPanel(); this.distanceInPixelsLabel = new JLabel(); this.distanceInMMLabel = new JLabel(); this.scaleLabel = new JLabel(); this.scaleTextField = new JTextField(); this.distanceInPixelsNumberTextField = new JNumberTextField(); this.distanceInPixelsNumberTextField.setFormat(2); this.distanceInMMNumberTextField = new JNumberTextField(); this.clearCalibrationButton = new JButton(); this.overlaySettingsPanel = new JPanel(); this.showOutlineCheckBox = new JCheckBox(); this.showBranchingPointsCheckBox = new JCheckBox(); this.showConvexHullCheckBox = new JCheckBox(); this.showSkeletonCheckBox = new JCheckBox(); this.outlineSpinner = new JSpinner(); this.skeletonSpinner = new JSpinner(); this.branchingPointsSpinner = new JSpinner(); this.convexHullSizeSpinner = new JSpinner(); this.outlineColorButton = new JButton(); this.skeletonColorButton = new JButton(); this.branchinPointsColorButton = new JButton(); this.convexHullColorButton = new JButton(); this.branchingPointsLabel = new JLabel(); this.convexHullLabel = new JLabel(); this.skeletonLabel = new JLabel(); this.outlineLabel = new JLabel(); this.skeletonColorRoundedPanel = new RoundedPanel(); this.branchingPointsRoundedPanel = new RoundedPanel(); this.convexHullRoundedPanel = new RoundedPanel(); this.outlineRoundedPanel = new RoundedPanel(); this.showOverlayCheckBox = new JCheckBox(); this.saveImageButton = new JButton(); this.imageResulFormatComboBox = new JComboBox(); //this.ExitButton = new JButton(); this.helpButton = new JButton(); this.memTransparentTextField = new TransparentTextField(); this.fillHolesRangeSliderLow.setPaintLabels(true); this.fillHolesRangeSliderLow.setPaintTicks(true); this.fillHolesRangeSliderLow.setEnabled(false); this.fillHolesRangeSliderLow.setValue(0); this.fillHolesRangeSliderLow.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.fillHolesRangeSliderStateChanged(fillHolesRangeSliderLow, fillHolesRangeSliderHigh); } }); this.fillHolesRangeSliderHigh.setPaintLabels(true); this.fillHolesRangeSliderHigh.setPaintTicks(true); this.fillHolesRangeSliderHigh.setEnabled(false); this.fillHolesRangeSliderHigh.setValue(100); this.fillHolesRangeSliderHigh.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.fillHolesRangeSliderStateChanged(fillHolesRangeSliderLow, fillHolesRangeSliderHigh); } }); this.smallParticlesRangeSliderLow.setPaintLabels(true); this.smallParticlesRangeSliderLow.setPaintTicks(true); this.smallParticlesRangeSliderLow.setEnabled(false); this.smallParticlesRangeSliderLow.setValue(0); this.smallParticlesRangeSliderLow.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.smallParticlesRangeSliderStateChanged(smallParticlesRangeSliderLow, smallParticlesRangeSliderHigh); } }); this.smallParticlesRangeSliderHigh.setPaintLabels(true); this.smallParticlesRangeSliderHigh.setPaintTicks(true); this.smallParticlesRangeSliderHigh.setEnabled(false); this.smallParticlesRangeSliderHigh.setValue(100); this.smallParticlesRangeSliderHigh.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.smallParticlesRangeSliderStateChanged(smallParticlesRangeSliderLow, smallParticlesRangeSliderHigh); } }); this.setDefaultCloseOperation(0); this.addWindowListener(new WindowAdapter() { @Override public void windowClosing(WindowEvent evt) { ExitButtonActionPerformed(null); } }); this.setTitle(AngioTool.VERSION); // Utils.NAME + " " + "0.6a" this.setCursor(new Cursor(0)); this.setMinimumSize(new Dimension(540, 790)); this.setName("mainFrame"); this.setResizable(false); this.getContentPane().setLayout(new AbsoluteLayout()); Font buttonFont = new Font("Tahoma", 1, 11); this.openImageButton.setFont(buttonFont); this.openImageButton.setIcon(AngioTool.ATOpenImage); this.openImageButton.setText("Open Image"); this.openImageButton.setToolTipText("Open Image"); this.openImageButton.setHorizontalTextPosition(0); this.openImageButton.setVerticalTextPosition(3); this.openImageButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.openImageButtonActionPerformed(evt); } }); this.getContentPane().add(this.openImageButton, new AbsoluteConstraints(10, 10, 105, 100)); this.AnalyzeButton.setFont(buttonFont); this.AnalyzeButton.setIcon(AngioTool.ATRunAnalysis); this.AnalyzeButton.setText("Run Analysis"); this.AnalyzeButton.setToolTipText("Run analysis"); this.AnalyzeButton.setEnabled(false); this.AnalyzeButton.setHorizontalTextPosition(0); this.AnalyzeButton.setVerticalTextPosition(3); this.AnalyzeButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.AnalyzeButtonActionPerformed(evt); } }); this.getContentPane().add(this.AnalyzeButton, new AbsoluteConstraints(130, 10, 105, 100)); this.BatchButton.setFont(buttonFont); this.BatchButton.setIcon(AngioTool.ATBatch); this.BatchButton.setText("Batch"); this.BatchButton.setToolTipText("For every image in a folder (recursively), run analysis"); this.BatchButton.setHorizontalTextPosition(0); this.BatchButton.setVerticalTextPosition(3); this.BatchButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.BatchButtonActionPerformed(evt); } }); this.getContentPane().add(this.BatchButton, new AbsoluteConstraints(250, 10, 105, 100)); progressBar.setBorder(new SoftBevelBorder(1)); progressBar.setPreferredSize(new Dimension(152, 20)); this.getContentPane().add(progressBar, new AbsoluteConstraints(125, 730, 400, 21)); this.batchStatusLabel = new JLabel(); this.batchStatusLabel.setFont(new Font("Tahoma", 0, 11)); this.getContentPane().add(batchStatusLabel, new AbsoluteConstraints(16, 115, -1, -1)); this.TabbedPane.setToolTipText("Settings"); this.TabbedPane.setFont(new Font("Tahoma", 0, 14)); this.AnalysisTabPanel.setFont(new Font("Tahoma", 1, 14)); this.AnalysisTabPanel.setLayout(new AbsoluteLayout()); this.thicknessIntensityPanel.setBorder(BorderFactory.createTitledBorder(null, "Vessel diameter and intensity", 0, 0, new Font("Tahoma", 1, 14))); this.thicknessIntensityPanel.setLayout(new AbsoluteLayout()); this.sigmasMarkSlider.addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent evt) { AngioToolGUI.this.sigmasMarkSliderMouseClicked(evt); } }); this.thicknessIntensityPanel.add(this.sigmasMarkSlider, new AbsoluteConstraints(10, 30, 400, -1)); this.sigmasSpinner.setFont(new Font("Tahoma", 0, 14)); this.sigmasSpinner.setModel(new SpinnerNumberModel(0, null, null, 10)); this.sigmasSpinner.setToolTipText("Adjust Maximum Vessel Thickness"); this.sigmasSpinner.setBorder(BorderFactory.createCompoundBorder(null, new SoftBevelBorder(0))); this.sigmasSpinner.setEnabled(false); this.sigmasSpinner.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.sigmasSpinnerStateChanged(evt); } }); this.thicknessIntensityPanel.add(this.sigmasSpinner, new AbsoluteConstraints(420, 20, 56, 49)); this.thresholdRangeSliderLow.setMajorTickSpacing(20); this.thresholdRangeSliderLow.setMaximum(255); this.thresholdRangeSliderLow.setPaintLabels(true); this.thresholdRangeSliderLow.setPaintTicks(true); this.thresholdRangeSliderLow.setEnabled(false); this.thresholdRangeSliderLow.setValue(0); this.thresholdRangeSliderLow.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.thresholdRangeSliderStateChanged(thresholdRangeSliderLow, thresholdRangeSliderHigh); } }); this.thresholdRangeSliderHigh.setMajorTickSpacing(20); this.thresholdRangeSliderHigh.setMaximum(255); this.thresholdRangeSliderHigh.setPaintLabels(true); this.thresholdRangeSliderHigh.setPaintTicks(true); this.thresholdRangeSliderHigh.setEnabled(false); this.thresholdRangeSliderHigh.setValue(255); this.thresholdRangeSliderHigh.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.thresholdRangeSliderStateChanged(thresholdRangeSliderLow, thresholdRangeSliderHigh); } }); this.thicknessIntensityPanel.add(this.thresholdRangeSliderLow, new AbsoluteConstraints(50, 90, 380, 70)); this.thicknessIntensityPanel.add(this.thresholdRangeSliderHigh, new AbsoluteConstraints(50, 160, 380, 70)); this.lowThresholdTextField.setEditable(false); this.lowThresholdTextField.setHorizontalAlignment(0); this.lowThresholdTextField.setText("0"); this.thicknessIntensityPanel.add(this.lowThresholdTextField, new AbsoluteConstraints(10, 110, 25, -1)); this.highThresholdTextField.setEditable(false); this.highThresholdTextField.setHorizontalAlignment(0); this.highThresholdTextField.setText("0"); this.thicknessIntensityPanel.add(this.highThresholdTextField, new AbsoluteConstraints(450, 150, 29, -1)); this.AnalysisTabPanel.add(this.thicknessIntensityPanel, new AbsoluteConstraints(10, 50, 490, 255)); this.backgroundParticlesPanel .setBorder(BorderFactory.createTitledBorder(null, "Eliminate foreground and background small particles", 0, 0, new Font("Tahoma", 1, 14))); this.backgroundParticlesPanel.setToolTipText("Eliminate Background and Foreground small particles"); this.backgroundParticlesPanel.setLayout(new AbsoluteLayout()); this.smallParticlesCheckBox.setFont(new Font("Tahoma", 0, 15)); this.smallParticlesCheckBox.setText("Remove small particles"); this.smallParticlesCheckBox.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.smallParticlesCheckBoxActionPerformed(evt); } }); this.backgroundParticlesPanel.add(this.smallParticlesCheckBox, new AbsoluteConstraints(14, 28, -1, -1)); this.fillHolesCheckBox.setFont(new Font("Tahoma", 0, 15)); this.fillHolesCheckBox.setText("Fill holes"); this.fillHolesCheckBox.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.fillHolesCheckBoxActionPerformed(evt); } }); this.backgroundParticlesPanel.add(this.fillHolesCheckBox, new AbsoluteConstraints(14, 95, -1, -1)); this.fillHolesSpinner.setFont(new Font("Tahoma", 0, 14)); this.fillHolesSpinner.setModel(new SpinnerNumberModel(0, null, null, 10)); this.fillHolesSpinner.setToolTipText("Adjust Maximum Vessel Thickness"); this.fillHolesSpinner.setBorder(BorderFactory.createCompoundBorder(null, new SoftBevelBorder(0))); this.fillHolesSpinner.setEnabled(false); this.fillHolesSpinner.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.fillHolesSpinnerStateChanged(evt); } }); this.backgroundParticlesPanel.add(this.fillHolesSpinner, new AbsoluteConstraints(400, 120, 75, 35)); this.removeSmallParticlesSpinner.setFont(new Font("Tahoma", 0, 14)); this.removeSmallParticlesSpinner.setModel(new SpinnerNumberModel(0, null, null, 10)); this.removeSmallParticlesSpinner.setToolTipText("Adjust Maximum Vessel Thickness"); this.removeSmallParticlesSpinner.setBorder(BorderFactory.createCompoundBorder(null, new SoftBevelBorder(0))); this.removeSmallParticlesSpinner.setEnabled(false); this.removeSmallParticlesSpinner.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.removeSmallParticlesSpinnerStateChanged(evt); } }); this.backgroundParticlesPanel.add(this.removeSmallParticlesSpinner, new AbsoluteConstraints(400, 55, 75, 35)); this.fillHolesRangeSlider2.setPaintLabels(true); this.fillHolesRangeSlider2.setPaintTicks(true); this.fillHolesRangeSlider2.setValue(0); this.fillHolesRangeSlider2.setEnabled(false); this.fillHolesRangeSlider2.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.fillHolesRangeSlider2StateChanged(evt); } }); this.backgroundParticlesPanel.add(this.fillHolesRangeSlider2, new AbsoluteConstraints(50, 117, 340, 50)); this.smallParticlesRangeSlider2.setPaintLabels(true); this.smallParticlesRangeSlider2.setPaintTicks(true); this.smallParticlesRangeSlider2.setValue(0); this.smallParticlesRangeSlider2.setEnabled(false); this.smallParticlesRangeSlider2.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.smallParticlesRangeSlider2StateChanged(evt); } }); this.backgroundParticlesPanel.add(this.smallParticlesRangeSlider2, new AbsoluteConstraints(50, 50, 340, 50)); this.AnalysisTabPanel.add(this.backgroundParticlesPanel, new AbsoluteConstraints(10, 310, 490, 170)); this.toggleOverlayToggleButton.setSelected(!params.shouldShowOverlayOrGallery); this.toggleOverlayToggleButton.setText(params.shouldShowOverlayOrGallery ? "Hide Overlay" : "Show Overlay"); this.toggleOverlayToggleButton.setEnabled(false); this.toggleOverlayToggleButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.toggleOverlayToggleButtonActionPerformed(evt); } }); this.AnalysisTabPanel.add(this.toggleOverlayToggleButton, new AbsoluteConstraints(400, 10, -1, -1)); this.TabbedPane.addTab("Analysis", this.AnalysisTabPanel); this.settingsTabPanel.setFont(new Font("Tahoma", 1, 14)); this.settingsTabPanel.setLayout(new AbsoluteLayout()); this.resizeImagePanel.setBorder(BorderFactory.createTitledBorder(null, "Resize Image", 0, 0, new Font("Tahoma", 1, 14))); this.resizeImagePanel.setLayout(new AbsoluteLayout()); this.resizeImageCheckBox.setFont(new Font("Tahoma", 0, 14)); this.resizeImageCheckBox.setText("Resize image"); this.resizeImageCheckBox.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.resizeImageCheckBoxActionPerformed(evt); } }); this.resizeImagePanel.add(this.resizeImageCheckBox, new AbsoluteConstraints(50, 40, 131, -1)); this.resizingFactorLabel.setFont(new Font("Tahoma", 0, 14)); this.resizingFactorLabel.setText("Resizing factor"); this.resizingFactorLabel.setEnabled(false); this.resizeImagePanel.add(this.resizingFactorLabel, new AbsoluteConstraints(190, 45, -1, -1)); this.resizingFactorSpinner.setModel(new SpinnerNumberModel(1.0, 1.0, 10.0, 0.5)); this.resizingFactorSpinner.setToolTipText("Set resizing factor"); this.resizingFactorSpinner.setEnabled(false); setSpinnerValue(this.resizingFactorSpinner, 1.0); // must be a Double this.resizingFactorSpinner.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.resizingFactorSpinnerStateChanged(evt); } }); this.resizeImagePanel.add(this.resizingFactorSpinner, new AbsoluteConstraints(290, 40, 52, 30)); this.unlockButton.setFont(buttonFont); this.unlockButton.setIcon(new ImageIcon(this.getClass().getResource("/images/unlocked.png"))); this.unlockButton.setText("Lock"); this.unlockButton.setHorizontalTextPosition(0); this.unlockButton.setPressedIcon(new ImageIcon(this.getClass().getResource("/images/unlocked.png"))); this.unlockButton.setVerticalTextPosition(3); this.unlockButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.unlockButtonActionPerformed(evt); } }); this.resizeImagePanel.add(this.unlockButton, new AbsoluteConstraints(395, 25, 70, -1)); this.settingsTabPanel.add(this.resizeImagePanel, new AbsoluteConstraints(10, 11, 490, 100)); this.setScalePanel.setBorder(BorderFactory.createTitledBorder(null, "Calibration", 0, 0, new Font("Tahoma", 1, 14))); this.setScalePanel.setLayout(new AbsoluteLayout()); this.distanceInPixelsLabel.setFont(new Font("Tahoma", 0, 14)); this.distanceInPixelsLabel.setText("Distance in pixels"); this.setScalePanel.add(this.distanceInPixelsLabel, new AbsoluteConstraints(15, 30, -1, -1)); this.distanceInMMLabel.setFont(new Font("Tahoma", 0, 14)); this.distanceInMMLabel.setText("Distance in mm"); this.setScalePanel.add(this.distanceInMMLabel, new AbsoluteConstraints(280, 30, -1, -1)); this.scaleLabel.setFont(new Font("Tahoma", 0, 14)); this.scaleLabel.setText("Scale"); this.setScalePanel.add(this.scaleLabel, new AbsoluteConstraints(120, 70, -1, -1)); this.scaleTextField.setEditable(false); this.scaleTextField.setFont(new Font("Tahoma", 1, 12)); this.scaleTextField.setHorizontalAlignment(0); this.scaleTextField.setToolTipText("Scale"); this.scaleTextField.setBorder(null); this.setScalePanel.add(this.scaleTextField, new AbsoluteConstraints(160, 73, 180, -1)); this.distanceInPixelsNumberTextField.setHorizontalAlignment(0); this.distanceInPixelsNumberTextField.addKeyListener(new KeyAdapter() { @Override public void keyReleased(KeyEvent evt) { AngioToolGUI.this.distanceInPixelsNumberTextFieldKeyReleased(evt); } }); this.setScalePanel.add(this.distanceInPixelsNumberTextField, new AbsoluteConstraints(125, 30, 120, -1)); this.distanceInMMNumberTextField.setHorizontalAlignment(0); this.distanceInMMNumberTextField.addKeyListener(new KeyAdapter() { @Override public void keyReleased(KeyEvent evt) { AngioToolGUI.this.distanceInMMNumberTextFieldKeyReleased(evt); } }); this.setScalePanel.add(this.distanceInMMNumberTextField, new AbsoluteConstraints(380, 30, 60, -1)); this.clearCalibrationButton.setText("Clear Calibration"); this.clearCalibrationButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.clearCalibrationButtonActionPerformed(evt); } }); this.setScalePanel.add(this.clearCalibrationButton, new AbsoluteConstraints(350, 70, -1, -1)); this.settingsTabPanel.add(this.setScalePanel, new AbsoluteConstraints(10, 120, 490, 107)); this.overlaySettingsPanel.setBorder(BorderFactory.createTitledBorder(null, "Overlay Settings", 0, 0, new Font("Tahoma", 1, 14))); this.overlaySettingsPanel.setLayout(new AbsoluteLayout()); this.showOutlineCheckBox.setFont(new Font("Tahoma", 0, 14)); this.showOutlineCheckBox.setSelected(true); this.showOutlineCheckBox.setText("Show outline"); this.showOutlineCheckBox.setToolTipText("Show outline"); this.showOutlineCheckBox.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.showOutlineCheckBoxActionPerformed(evt); } }); this.overlaySettingsPanel.add(this.showOutlineCheckBox, new AbsoluteConstraints(20, 60, -1, -1)); this.showBranchingPointsCheckBox.setFont(new Font("Tahoma", 0, 14)); this.showBranchingPointsCheckBox.setSelected(true); this.showBranchingPointsCheckBox.setText("Branching points"); this.showBranchingPointsCheckBox.setToolTipText("Show branching points"); this.showBranchingPointsCheckBox.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.showBranchingPointsCheckBoxActionPerformed(evt); } }); this.overlaySettingsPanel.add(this.showBranchingPointsCheckBox, new AbsoluteConstraints(240, 60, -1, -1)); this.showConvexHullCheckBox.setFont(new Font("Tahoma", 0, 14)); this.showConvexHullCheckBox.setSelected(true); this.showConvexHullCheckBox.setText("Show boundary"); this.showConvexHullCheckBox.setToolTipText("Show boundary"); this.showConvexHullCheckBox.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.showConvexHullCheckBoxActionPerformed(evt); } }); this.overlaySettingsPanel.add(this.showConvexHullCheckBox, new AbsoluteConstraints(240, 90, -1, -1)); this.showSkeletonCheckBox.setFont(new Font("Tahoma", 0, 14)); this.showSkeletonCheckBox.setSelected(true); this.showSkeletonCheckBox.setText("Show skeleton"); this.showSkeletonCheckBox.setToolTipText("Show skeleton"); this.showSkeletonCheckBox.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.showSkeletonCheckBoxActionPerformed(evt); } }); this.overlaySettingsPanel.add(this.showSkeletonCheckBox, new AbsoluteConstraints(20, 90, -1, -1)); this.outlineSpinner.setModel(new SpinnerNumberModel(1, 1, null, 1)); setSpinnerValue(this.outlineSpinner, params.outlineSize); this.outlineSpinner.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.outlineSpinnerStateChanged(evt); } }); this.overlaySettingsPanel.add(this.outlineSpinner, new AbsoluteConstraints(180, 60, 50, 23)); this.skeletonSpinner.setModel(new SpinnerNumberModel(1, 1, null, 1)); setSpinnerValue(this.skeletonSpinner, params.skeletonSize); this.skeletonSpinner.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.skeletonSpinnerStateChanged(evt); } }); this.overlaySettingsPanel.add(this.skeletonSpinner, new AbsoluteConstraints(180, 90, 50, 23)); this.branchingPointsSpinner.setModel(new SpinnerNumberModel(1, 1, null, 1)); setSpinnerValue(this.branchingPointsSpinner, params.branchingPointsSize); this.branchingPointsSpinner.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.branchingPointsSpinnerStateChanged(evt); } }); this.overlaySettingsPanel.add(this.branchingPointsSpinner, new AbsoluteConstraints(420, 60, 50, 23)); this.convexHullSizeSpinner.setModel(new SpinnerNumberModel(1, 1, null, 1)); setSpinnerValue(this.convexHullSizeSpinner, params.convexHullSize); this.convexHullSizeSpinner.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent evt) { AngioToolGUI.this.convexHullSizeSpinnerStateChanged(evt); } }); this.overlaySettingsPanel.add(this.convexHullSizeSpinner, new AbsoluteConstraints(420, 90, 50, 23)); this.outlineColorButton.setContentAreaFilled(false); //this.outlineColorButton.setBackground(OutlineColor); this.outlineColorButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.outlineColorButtonActionPerformed(evt); } }); this.overlaySettingsPanel.add(this.outlineColorButton, new AbsoluteConstraints(150, 60, 26, 23)); this.skeletonColorButton.setToolTipText("Skeleton Color"); this.skeletonColorButton.setContentAreaFilled(false); //this.skeletonColorButton.setBackground(SkeletonColor); this.skeletonColorButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.skeletonColorButtonActionPerformed(evt); } }); this.overlaySettingsPanel.add(this.skeletonColorButton, new AbsoluteConstraints(150, 90, 26, 23)); this.branchinPointsColorButton.setContentAreaFilled(false); //this.branchinPointsColorButton.setBackground(BranchingPointColor); this.branchinPointsColorButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.branchinPointsColorButtonActionPerformed(evt); } }); this.overlaySettingsPanel.add(this.branchinPointsColorButton, new AbsoluteConstraints(390, 60, 26, 23)); this.convexHullColorButton.setContentAreaFilled(false); //this.convexHullColorButton.setBackground(ConvexHullColor); this.convexHullColorButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.convexHullColorButtonActionPerformed(evt); } }); this.overlaySettingsPanel.add(this.convexHullColorButton, new AbsoluteConstraints(390, 90, 26, 23)); /* this.branchingPointsLabel.setFont(new Font("Tahoma", 0, 14)); this.branchingPointsLabel.setText("Width"); this.overlaySettingsPanel.add(this.branchingPointsLabel, new AbsoluteConstraints(320, 120, -1, -1)); this.convexHullLabel.setFont(new Font("Tahoma", 0, 14)); this.convexHullLabel.setText("Width"); this.overlaySettingsPanel.add(this.convexHullLabel, new AbsoluteConstraints(320, 150, -1, -1)); this.skeletonLabel.setFont(new Font("Tahoma", 0, 14)); this.skeletonLabel.setText("Width"); this.overlaySettingsPanel.add(this.skeletonLabel, new AbsoluteConstraints(320, 90, -1, -1)); this.outlineLabel.setFont(new Font("Tahoma", 0, 14)); this.outlineLabel.setText("Width"); this.overlaySettingsPanel.add(this.outlineLabel, new AbsoluteConstraints(320, 60, -1, -1)); */ this.skeletonColorRoundedPanel.setBackground(params.skeletonColor.toColor()); this.skeletonColorRoundedPanel.setCornerRadius(7); GroupLayout skeletonColorRoundedPanelLayout = new GroupLayout(this.skeletonColorRoundedPanel); this.skeletonColorRoundedPanel.setLayout(skeletonColorRoundedPanelLayout); skeletonColorRoundedPanelLayout.setHorizontalGroup(skeletonColorRoundedPanelLayout.createParallelGroup(Alignment.LEADING).addGap(0, 30, 32767)); skeletonColorRoundedPanelLayout.setVerticalGroup(skeletonColorRoundedPanelLayout.createParallelGroup(Alignment.LEADING).addGap(0, 23, 32767)); this.overlaySettingsPanel.add(this.skeletonColorRoundedPanel, new AbsoluteConstraints(148, 90, 30, 23)); this.branchingPointsRoundedPanel.setBackground(params.branchingPointsColor.toColor()); this.branchingPointsRoundedPanel.setCornerRadius(7); GroupLayout branchingPointsRoundedPanelLayout = new GroupLayout(this.branchingPointsRoundedPanel); this.branchingPointsRoundedPanel.setLayout(branchingPointsRoundedPanelLayout); branchingPointsRoundedPanelLayout.setHorizontalGroup(branchingPointsRoundedPanelLayout.createParallelGroup(Alignment.LEADING).addGap(0, 30, 32767)); branchingPointsRoundedPanelLayout.setVerticalGroup(branchingPointsRoundedPanelLayout.createParallelGroup(Alignment.LEADING).addGap(0, 23, 32767)); this.overlaySettingsPanel.add(this.branchingPointsRoundedPanel, new AbsoluteConstraints(388, 60, 30, 23)); this.convexHullRoundedPanel.setBackground(params.convexHullColor.toColor()); this.convexHullRoundedPanel.setCornerRadius(7); GroupLayout convexHullRoundedPanelLayout = new GroupLayout(this.convexHullRoundedPanel); this.convexHullRoundedPanel.setLayout(convexHullRoundedPanelLayout); convexHullRoundedPanelLayout.setHorizontalGroup(convexHullRoundedPanelLayout.createParallelGroup(Alignment.LEADING).addGap(0, 30, 32767)); convexHullRoundedPanelLayout.setVerticalGroup(convexHullRoundedPanelLayout.createParallelGroup(Alignment.LEADING).addGap(0, 23, 32767)); this.overlaySettingsPanel.add(this.convexHullRoundedPanel, new AbsoluteConstraints(388, 90, 30, 23)); this.outlineRoundedPanel.setBackground(params.outlineColor.toColor()); this.outlineRoundedPanel.setCornerRadius(7); GroupLayout outlineRoundedPanelLayout = new GroupLayout(this.outlineRoundedPanel); this.outlineRoundedPanel.setLayout(outlineRoundedPanelLayout); outlineRoundedPanelLayout.setHorizontalGroup(outlineRoundedPanelLayout.createParallelGroup(Alignment.LEADING).addGap(0, 30, 32767)); outlineRoundedPanelLayout.setVerticalGroup(outlineRoundedPanelLayout.createParallelGroup(Alignment.LEADING).addGap(0, 23, 32767)); this.overlaySettingsPanel.add(this.outlineRoundedPanel, new AbsoluteConstraints(148, 60, 30, 23)); this.showOverlayCheckBox.setFont(new Font("Tahoma", 0, 14)); this.showOverlayCheckBox.setSelected(params.shouldShowOverlayOrGallery); this.showOverlayCheckBox.setText("Show overlay"); this.showOverlayCheckBox.setToolTipText("Show overlay"); this.showOverlayCheckBox.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.showOverlayCheckBoxActionPerformed(evt); } }); this.overlaySettingsPanel.add(this.showOverlayCheckBox, new AbsoluteConstraints(10, 30, -1, -1)); this.saveImageButton.setFont(new Font("Tahoma", 1, 14)); this.saveImageButton.setText("Save Image"); this.saveImageButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.saveImageButtonActionPerformed(evt); } }); this.overlaySettingsPanel.add(this.saveImageButton, new AbsoluteConstraints(170, 130, 125, 25)); this.imageResulFormatComboBox.setModel(new DefaultComboBoxModel<>(new String[]{"jpg", "tiff", "png", "bmp"})); this.imageResulFormatComboBox.setSelectedItem(params.resultImageFormat); this.imageResulFormatComboBox.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.imageResulFormatComboBoxActionPerformed(evt); } }); this.overlaySettingsPanel.add(this.imageResulFormatComboBox, new AbsoluteConstraints(310, 130, 50, 25)); this.settingsTabPanel.add(this.overlaySettingsPanel, new AbsoluteConstraints(10, 230, 490, 170)); this.savingPreferencesPanel.setBorder(BorderFactory.createTitledBorder(null, "Saving Preferences", 0, 0, new Font("Tahoma", 1, 14))); this.savingPreferencesPanel.setLayout(new AbsoluteLayout()); this.saveResultsToButton.setFont(buttonFont); this.saveResultsToButton.setIcon(AngioTool.ATExcel); this.saveResultsToButton.setText("Save To"); this.saveResultsToButton.setToolTipText("Save To"); this.saveResultsToButton.setHorizontalTextPosition(0); this.saveResultsToButton.setVerticalTextPosition(3); this.saveResultsToButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.saveResultsToButtonActionPerformed(evt); } }); this.savingPreferencesPanel.add(this.saveResultsToButton, new AbsoluteConstraints(10, 30, -1, 100)); this.saveResultsToTextField.setFont(new Font("Tahoma", 0, 14)); this.savingPreferencesPanel.add(this.saveResultsToTextField, new AbsoluteConstraints(120, 50, 360, 28)); this.saveResultImageCheckBox.setFont(new Font("Tahoma", 0, 14)); this.saveResultImageCheckBox.setSelected(true); this.saveResultImageCheckBox.setText("Save result image"); this.saveResultImageCheckBox.setToolTipText("Save the result Image"); this.savingPreferencesPanel.add(this.saveResultImageCheckBox, new AbsoluteConstraints(190, 90, -1, 37)); this.settingsTabPanel.add(this.savingPreferencesPanel, new AbsoluteConstraints(10, 405, 490, 140)); this.TabbedPane.addTab("Settings", this.settingsTabPanel); this.getContentPane().add(this.TabbedPane, new AbsoluteConstraints(10, 129, 515, 590)); /* this.ExitButton.setFont(buttonFont); this.ExitButton.setIcon(Utils.ATExit); this.ExitButton.setText("Exit"); this.ExitButton.setToolTipText("Exit"); this.ExitButton.setHorizontalTextPosition(0); this.ExitButton.setVerticalTextPosition(3); this.ExitButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.ExitButtonActionPerformed(evt); } }); this.getContentPane().add(this.ExitButton, new AbsoluteConstraints(370, 10, 105, 100)); */ this.helpButton.setFont(buttonFont); this.helpButton.setIcon(AngioTool.ATHelp); this.helpButton.setText("Help"); this.helpButton.setHorizontalTextPosition(0); this.helpButton.setVerticalTextPosition(3); this.helpButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { AngioToolGUI.this.helpButtonActionPerformed(evt); } }); this.getContentPane().add(this.helpButton, new AbsoluteConstraints(420, 10, 105, 100)); this.memTransparentTextField.setBorder(new SoftBevelBorder(1)); this.memTransparentTextField.setEditable(false); this.memTransparentTextField.setHorizontalAlignment(0); this.memTransparentTextField.setFont(buttonFont); this.getContentPane().add(this.memTransparentTextField, new AbsoluteConstraints(10, 730, 100, 20)); this.pack(); }
private void openImageButtonActionPerformed(ActionEvent evt) { JFileChooser fc = new JFileChooser(); fc.setPreferredSize(new Dimension(1000, 600)); fc.setFileView(new ImageFileView()); fc.setAccessory(new ImagePreview(fc)); fc.setMultiSelectionEnabled(false); fc.setCurrentDirectory(this.currentDir); fc.setFileFilter(new ImageFilter()); int returnVal = fc.showOpenDialog(this); if (returnVal == 0) { this.initVariables(); this.imageFile = fc.getSelectedFile(); this.currentDir = fc.getCurrentDirectory(); if (this.imageFile != null) { this.results.image = this.imageFile; this.imageOriginal = this.openImageAndIsolateDominantChannel(this.imageFile.getAbsolutePath());
if (this.resizeImageCheckBox.isSelected()) { ImageProcessor resized = this.imageOriginal.getProcessor().resize((int)((double)this.imageOriginal.getWidth() / params.resizingFactor)); this.imageOriginal.setProcessor(resized); }
this.resizeImageCheckBox.setEnabled(false); this.resizingFactorSpinner.setEnabled(false); this.resizingFactorLabel.setEnabled(false); this.unlockButton.setText(this.resizeImageCheckBox.isEnabled() ? "Lock" : "Unlock"); this.unlockButton.setSelected(true); this.AnalyzeButton.setEnabled(true); this.imageResult.setProcessor(this.imageOriginal.getProcessor().duplicate()); this.ipOriginal = this.imageOriginal.getProcessor().convertToByte(params.shouldScalePixelValues); this.imageResult.show(); this.imageResult.getWindow().setLocation(this.getX() + this.getWidth(), this.getY()); this.imageResult.getWindow().setIconImage(this.imgIcon); this.initControls(); this.computeFirstOutline(this.firstSigma); this.updateOverlay(); } } }
private void thresholdRangeSliderStateChanged(JSlider lowSlider, JSlider highSlider) { if (!lowSlider.getValueIsAdjusting() && !highSlider.getValueIsAdjusting()) { int lowValue = lowSlider.getValue(); int highValue = highSlider.getValue(); this.lowThresholdTextField.setText("" + lowValue); this.highThresholdTextField.setText("" + highValue); this.updateOutline(null); } }
private void fillHolesCheckBoxActionPerformed(ActionEvent evt) { params.shouldFillHoles = !params.shouldFillHoles; this.fillHolesRangeSlider2.setEnabled(params.shouldFillHoles); this.fillHolesSpinner.setEnabled(params.shouldFillHoles); this.updateOutline(null); }
private void fillHolesRangeSliderStateChanged(JSlider lowSlider, JSlider highSlider) { if (params.shouldFillHoles) { if (!lowSlider.getValueIsAdjusting() && !highSlider.getValueIsAdjusting()) { this.updateOutline(null); } } }
private void sigmasMarkSliderMouseClicked(MouseEvent evt) { markSlider ms = (markSlider)evt.getSource(); double[] s = getSigmaMarks();
try { this.updateSigmas(s); } catch (OutOfMemoryError var5) { if (JOptionPane.showConfirmDialog(null, "Your system has run out of memory\n Reinitializing all variables...", "AngioTool", 0, 0, null) == 0) { this.initVariables(); } }
this.updateOutline(s); }
private void smallParticlesCheckBoxActionPerformed(ActionEvent evt) { params.shouldRemoveSmallParticles = !params.shouldRemoveSmallParticles; this.smallParticlesRangeSlider2.setEnabled(params.shouldRemoveSmallParticles); this.removeSmallParticlesSpinner.setEnabled(params.shouldRemoveSmallParticles); this.updateOutline(null); }
private void smallParticlesRangeSliderStateChanged(JSlider lowSlider, JSlider highSlider) { if (params.shouldRemoveSmallParticles) { if (!lowSlider.getValueIsAdjusting() && !highSlider.getValueIsAdjusting()) { this.updateOutline(null); } } }
private void BatchButtonActionPerformed(ActionEvent evt) { new BatchAnalysisUi(this, getBatchAnalyzerSettings()).showDialog(); }
private void AnalyzeButtonActionPerformed(ActionEvent evt) { new AngioToolGUI.AngioToolWorker().execute(); }
private void resizeImageCheckBoxActionPerformed(ActionEvent evt) { this.resizingFactorSpinner.setEnabled(this.resizeImageCheckBox.isSelected()); this.resizingFactorLabel.setEnabled(this.resizeImageCheckBox.isSelected()); }
private void toggleOverlayToggleButtonActionPerformed(ActionEvent evt) { params.shouldShowOverlayOrGallery = !params.shouldShowOverlayOrGallery; String title = params.shouldShowOverlayOrGallery ? "Hide Overlay" : "Show Overlay"; this.toggleOverlayToggleButton.setText(title); this.showOverlayCheckBox.setSelected(params.shouldShowOverlayOrGallery); this.updateOverlay(); }
static int getSpinnerValueInt(JSpinner spinner) { SpinnerModel model = spinner.getModel(); if (model instanceof SpinnerNumberModel) return ((SpinnerNumberModel)model).getNumber().intValue();
try { return (int)model.getValue(); } catch (Throwable t1) { try { return (int)((double)model.getValue()); } catch (Throwable t2) { try { return Integer.parseInt(model.getValue().toString()); } catch (Throwable t3) { return 0; } } } }
static double getSpinnerValueDouble(JSpinner spinner) { SpinnerModel model = spinner.getModel(); if (model instanceof SpinnerNumberModel) return ((SpinnerNumberModel)model).getNumber().doubleValue();
try { return (double)model.getValue(); } catch (Throwable t1) { try { return (double)((int)model.getValue()); } catch (Throwable t2) { try { return Double.parseDouble(model.getValue().toString()); } catch (Throwable t3) { return 0.0; } } } }
static void setSpinnerValue(JSpinner spinner, Number value) { Object existing = spinner.getValue(); if (existing instanceof Integer) { int valueInt = value == null ? 0 : (value instanceof Integer ? (int)value : (int)((double)value)); spinner.setValue(valueInt); } else if (existing instanceof Double) { double valueDbl = value == null ? 0.0 : (value instanceof Integer ? (double)((int)value) : (double)value); spinner.setValue(valueDbl); } else if (value == null) { spinner.setValue(0); } else if (value instanceof Integer) { try { spinner.setValue((int)value); } catch (Throwable t) { spinner.setValue((double)((int)value)); } } else { try { spinner.setValue((double)value); } catch (Throwable t) { spinner.setValue((int)((double)value)); } } }
private void sigmasSpinnerStateChanged(ChangeEvent evt) { int curValue = getSpinnerValueInt(sigmasSpinner); if (curValue <= 0) { setSpinnerValue(this.sigmasSpinner, 0); curValue = 0; }
this.sigmasMarkSlider.setMaximum(curValue); }
private void saveResultsToButtonActionPerformed(ActionEvent evt) { JFileChooser fc = new JFileChooser(); fc.setDialogTitle("Save As"); fc.setDialogType(1); fc.setApproveButtonToolTipText("Set the Excel file name where the data will be saved"); fc.setCurrentDirectory(this.currentDir); fc.setFileFilter(new ExcelFilter()); int returnVal = fc.showOpenDialog(this); if (returnVal == 0) { File resultsFile = fc.getSelectedFile(); String extension = null; extension = BatchUtils.getExtension(resultsFile); if (extension != null) { if (!extension.equals("xls") && !extension.equals("xlsx")) { this.saveResultsToTextField.setText(resultsFile.getPath() + ".xls"); } else { this.saveResultsToTextField.setText(resultsFile.getPath()); } } else { this.saveResultsToTextField.setText(resultsFile.getPath() + ".xls"); }
this.excelPath = resultsFile.getPath(); //this.ste = new SaveToExcel(resultsFile.getPath(), true); } }
private void resizingFactorSpinnerStateChanged(ChangeEvent evt) { params.resizingFactor = getSpinnerValueDouble(this.resizingFactorSpinner); }
private void skeletonColorButtonActionPerformed(ActionEvent evt) { JButton button = (JButton)evt.getSource(); Color background = JColorChooser.showDialog(null, button.getToolTipText(), params.skeletonColor.toColor()); if (background != null) { params.skeletonColor = new Rgb(background); this.skeletonColorRoundedPanel.setBackground(background); this.updateOverlay(); } }
private void branchinPointsColorButtonActionPerformed(ActionEvent evt) { JButton button = (JButton)evt.getSource(); Color background = JColorChooser.showDialog(null, button.getToolTipText(), params.branchingPointsColor.toColor()); if (background != null) { params.branchingPointsColor = new Rgb(background); this.branchingPointsRoundedPanel.setBackground(background); this.updateOverlay(); } }
private void convexHullColorButtonActionPerformed(ActionEvent evt) { JButton button = (JButton)evt.getSource(); Color background = JColorChooser.showDialog(null, button.getToolTipText(), params.convexHullColor.toColor()); if (background != null) { params.convexHullColor = new Rgb(background); this.convexHullRoundedPanel.setBackground(background); this.updateOverlay(); } }
private void outlineColorButtonActionPerformed(ActionEvent evt) { JButton button = (JButton)evt.getSource(); Color background = JColorChooser.showDialog(null, button.getToolTipText(), params.outlineColor.toColor()); if (background != null) { params.outlineColor = new Rgb(background); this.outlineRoundedPanel.setBackground(background); this.updateOverlay(); } }
private void distanceInPixelsNumberTextFieldKeyReleased(KeyEvent evt) { if (!this.distanceInMMNumberTextField.getText().equals("") && !this.distanceInPixelsNumberTextField.getText().equals("")) { this.scaleTextField.setText("" + (double)this.distanceInPixelsNumberTextField.getInt() / this.distanceInMMNumberTextField.getDouble() + " pixels/mm"); } }
private void distanceInMMNumberTextFieldKeyReleased(KeyEvent evt) { if (!this.distanceInMMNumberTextField.getText().equals("") && !this.distanceInPixelsNumberTextField.getText().equals("")) { this.scaleTextField.setText("" + (double)this.distanceInPixelsNumberTextField.getInt() / this.distanceInMMNumberTextField.getDouble() + " pixels/mm"); } }
private void fillHolesSpinnerStateChanged(ChangeEvent evt) { int curValue = getSpinnerValueInt(this.fillHolesSpinner); if (curValue <= 0) { setSpinnerValue(this.fillHolesSpinner, 0); curValue = 0; }
this.fillHolesRangeSlider2.setMaximum(curValue); this.fillHolesRangeSlider2.setMajorTickSpacing(this.fillHolesRangeSlider2.getMaximum() / 10); Hashtable h = this.fillHolesRangeSlider2.createStandardLabels(this.fillHolesRangeSlider2.getMaximum() / 10); this.fillHolesRangeSlider2.setLabelTable(h); }
private void removeSmallParticlesSpinnerStateChanged(ChangeEvent evt) { int curValue = getSpinnerValueInt(this.removeSmallParticlesSpinner); if (curValue <= 0) { setSpinnerValue(this.removeSmallParticlesSpinner, 0); curValue = 0; }
this.smallParticlesRangeSlider2.setMaximum(curValue); this.smallParticlesRangeSlider2.setMajorTickSpacing(this.smallParticlesRangeSlider2.getMaximum() / 10); Hashtable h = this.smallParticlesRangeSlider2.createStandardLabels(this.smallParticlesRangeSlider2.getMaximum() / 10); this.smallParticlesRangeSlider2.setLabelTable(h); }
private void ExitButtonActionPerformed(ActionEvent evt) { /* if (JOptionPane.showConfirmDialog(null, "Do you really want to exit AngioTool?", "AngioTool", 0, 3, null) != 0) return; */
if (this.imageResult != null) { this.imageResult.close(); }
this.setVisible(false); this.exit(); System.exit(0); }
private void showConvexHullCheckBoxActionPerformed(ActionEvent evt) { this.updateOverlay(); }
private void showSkeletonCheckBoxActionPerformed(ActionEvent evt) { this.updateOverlay(); }
private void skeletonSpinnerStateChanged(ChangeEvent evt) { this.updateOverlay(); }
private void outlineSpinnerStateChanged(ChangeEvent evt) { this.updateOverlay(); }
private void branchingPointsSpinnerStateChanged(ChangeEvent evt) { this.updateOverlay(); }
private void convexHullSizeSpinnerStateChanged(ChangeEvent evt) { this.updateOverlay(); }
private void showOutlineCheckBoxActionPerformed(ActionEvent evt) { this.updateOverlay(); }
private void showBranchingPointsCheckBoxActionPerformed(ActionEvent evt) { this.updateOverlay(); }
private void showOverlayCheckBoxActionPerformed(ActionEvent evt) { if (this.imageResult != null) { this.updateOverlay(); String title = !this.showOverlayCheckBox.isSelected() ? "Show Overlay" : "Hide Overlay"; this.toggleOverlayToggleButton.setText(title); this.toggleOverlayToggleButton.setSelected(!this.showOverlayCheckBox.isSelected()); } }
private void saveImageButtonActionPerformed(ActionEvent evt) { if (this.imageResult != null) { ImagePlus imageResultFlattenen = this.imageResult.flatten(); IJ.saveAs(imageResultFlattenen, params.resultImageFormat, this.imageFile.getAbsolutePath() + " result." + params.resultImageFormat); } else if (JOptionPane.showConfirmDialog(null, "No image to save", "AngioTool", -1, 2, null) == 0) { System.gc(); } }
private void unlockButtonActionPerformed(ActionEvent evt) { this.resizeImageCheckBox.setEnabled(!this.resizeImageCheckBox.isEnabled()); this.resizingFactorLabel.setEnabled(this.resizeImageCheckBox.isSelected() && this.resizeImageCheckBox.isEnabled()); this.resizingFactorSpinner.setEnabled(this.resizeImageCheckBox.isSelected() && this.resizeImageCheckBox.isEnabled()); this.unlockButton.setText(this.resizeImageCheckBox.isEnabled() ? "Lock" : "Unlock"); this.unlockButton.setSelected(!this.resizeImageCheckBox.isEnabled()); }
private void helpButtonActionPerformed(ActionEvent evt) { this.aboutBox.setLocation(new Point(200, 50)); this.aboutBox.setVisible(true); }
private void fillHolesRangeSlider2StateChanged(ChangeEvent evt) { if (params.shouldFillHoles) { JSlider source = (JSlider)evt.getSource(); if (!source.getValueIsAdjusting()) { this.updateOutline(null); } } }
private void smallParticlesRangeSlider2StateChanged(ChangeEvent evt) { if (params.shouldRemoveSmallParticles) { JSlider source = (JSlider)evt.getSource(); if (!source.getValueIsAdjusting()) { this.updateOutline(null); } } }
private void imageResulFormatComboBoxActionPerformed(ActionEvent evt) { params.resultImageFormat = (String)this.imageResulFormatComboBox.getSelectedItem(); }
private void clearCalibrationButtonActionPerformed(ActionEvent evt) { this.distanceInMMNumberTextField.setText(""); this.distanceInPixelsNumberTextField.setText(""); this.scaleTextField.setText(""); }
private double[] getSigmaMarks() { ArrayList<Integer> intMarks = this.sigmasMarkSlider.getMarks(); if (intMarks == null || intMarks.isEmpty()) return new double[] {this.firstSigma[0]};
double[] marks = new double[intMarks.size()]; for (int i = 0; i < marks.length; i++) marks[i] = (double)intMarks.get(i);
return marks; }
private void reallocateTubeness() { if (this.tubeness == null) this.tubeness = new Tubeness.Scratch();
int width = this.ipOriginal.getWidth(); int height = this.ipOriginal.getHeight(); if (tubeness.image == null || tubeness.image.length < width * height) tubeness.useBuffers( new float[width * height], new float[width * height], new float[width * height], new float[width * height] ); }
private void reallocateSkeletonResult() { if (this.skelResult == null) this.skelResult = new SkeletonResult2();
int width = this.ipOriginal.getWidth(); int height = this.ipOriginal.getHeight(); if (skelResult.imageInfo == null || skelResult.imageInfo.length < width * height) skelResult.useBuffers( new int[width * height], new int[width * height], new int[width * height], new int[width * height], new int[width * height] ); }
private void populateResults() { double areaScalingFactor = 1.0; if (!this.distanceInMMNumberTextField.getText().equals("") && !this.distanceInPixelsNumberTextField.getText().equals("")) { params.linearScalingFactor = this.distanceInMMNumberTextField.getDouble() / (double)this.distanceInPixelsNumberTextField.getInt(); } if (params.linearScalingFactor == 0.0) params.linearScalingFactor = 1.0;
areaScalingFactor = params.linearScalingFactor * params.linearScalingFactor;
this.results.image = this.imageFile; this.results.thresholdLow = this.thresholdRangeSliderLow.getValue(); this.results.thresholdHigh = this.thresholdRangeSliderHigh.getValue(); this.results.sigmas = getSigmaMarks(); this.results.removeSmallParticles = (int)this.smallParticlesRangeSlider2.getValue(); this.results.fillHoles = (int)this.fillHolesRangeSlider2.getValue(); this.results.LinearScalingFactor = params.linearScalingFactor; this.results.AreaScalingFactor = areaScalingFactor; this.results.allantoisPixelsArea = this.convexHullArea; this.results.allantoisMMArea = this.convexHullArea * areaScalingFactor; this.results.totalNJunctions = this.skelResult.isolatedJunctions.size; this.results.JunctionsPerArea = (double)this.skelResult.isolatedJunctions.size / this.convexHullArea; this.results.JunctionsPerScaledArea = (double)this.skelResult.isolatedJunctions.size / this.results.allantoisMMArea; this.results.vesselMMArea = (double)this.results.vesselPixelArea * areaScalingFactor; this.results.vesselPercentageArea = this.results.vesselMMArea * 100.0 / this.results.allantoisMMArea; if (params.shouldComputeThickness) { this.results.averageVesselDiameter = this.averageVesselDiameter; }
double totalLength = 0.0; int nTrees = this.skelResult.treeCount; for (int i = 0; i < nTrees; i++) totalLength += (double)this.skelResult.totalBranchLengths[i];
double averageLength = 0.0; if (nTrees > 0) averageLength = totalLength / (double)nTrees * params.linearScalingFactor;
this.results.totalLength = totalLength * params.linearScalingFactor; this.results.averageBranchLength = averageLength; this.results.totalNEndPoints = this.skelResult.endPoints.size / 3;
try { this.writeResultsToExcel(this.excelPath, this.results); } catch (Exception ex) { // ... }
if (this.saveResultImageCheckBox.isSelected()) { ImagePlus imageResultFlattenen = this.imageResult.flatten(); IJ.saveAs(imageResultFlattenen, "jpg", this.imageFile.getAbsolutePath() + " result.jpg"); } }
private void writeResultsToExcel(String path, Results res) throws Exception { Locale locale = new Locale("en", "US"); Date today = new Date(); SpreadsheetWriter writer = SpreadsheetWriter.fromExistingXlsx(path); writer.writeRow( "Image Name", "Date", "Time", "Image Location", "Low Threshold", "High Threshold", "Vessel Thickness", "Small Particles", "Fill Holes", "Scaling factor", "", "Explant area", "Vessels area", "Vessels percentage area", "Total Number of Junctions", "Junctions density", "Total Vessels Length", "Average Vessels Length", "Total Number of End Points", "Average Vessel diameter", "Elacunarity", "Elacunarity Slope", "Flacunarity", "Flacunarity Slope", "Mean F Lacunarity", "Mean E Lacunarity" ); writer.writeRow( results.image.getName(), DateFormat.getDateInstance(2, locale).format(today), DateFormat.getTimeInstance(2, locale).format(today), results.image.getAbsolutePath(), results.thresholdLow, results.thresholdHigh, results.getSigmas(), results.removeSmallParticles, results.fillHoles, results.LinearScalingFactor, "", results.allantoisMMArea, results.vesselMMArea, results.vesselPercentageArea, results.totalNJunctions, results.JunctionsPerScaledArea, results.totalLength, results.averageBranchLength, results.totalNEndPoints, results.averageVesselDiameter, results.ELacunarity, results.ELacunaritySlope, results.FLacuanrity, results.FLacunaritySlope, results.meanFl, results.meanEl ); }
public static void updateStatus(final int i, final String s) { Runnable doSetProgressBarValue = new Runnable() { @Override public void run() { AngioToolGUI.progressBar.setValue(i); AngioToolGUI.progressBar.setString(s + " " + i + "%"); } }; SwingUtilities.invokeLater(doSetProgressBarValue); }
public void updateOverlay() { if (this.imageResult != null) { int width = this.imageResult.getWidth(); int height = this.imageResult.getHeight();
//Arrays.fill(this.allantoisOverlay, 0); /* if (this.allantoisOverlay == null || this.allantoisOverlay.length < width * height) this.allantoisOverlay = new int[width * height]; */
params.shouldShowOverlayOrGallery = this.showOverlayCheckBox.isSelected(); params.shouldDrawOutline = this.showOutlineCheckBox.isSelected(); params.shouldDrawSkeleton = this.showSkeletonCheckBox.isSelected(); params.shouldDrawBranchPoints = this.showBranchingPointsCheckBox.isSelected(); params.shouldDrawConvexHull = this.showConvexHullCheckBox.isSelected(); params.outlineColor = new Rgb(this.outlineRoundedPanel.getBackground()); params.skeletonColor = new Rgb(this.skeletonColorRoundedPanel.getBackground()); params.branchingPointsColor = new Rgb(this.branchingPointsRoundedPanel.getBackground()); params.convexHullColor = new Rgb(this.convexHullRoundedPanel.getBackground());
if (params.shouldShowOverlayOrGallery) { if (this.skelResult != null) {
if (params.shouldDrawSkeleton) { params.skeletonSize = getSpinnerValueInt(this.skeletonSpinner); int skelColor = params.skeletonColor.getARGB();
Canvas.drawCircles( allantoisOverlay, width, height, null, this.skelResult.slabList.buf, this.skelResult.slabList.size, 3, skelColor, params.skeletonSize ); Canvas.drawCircles( allantoisOverlay, width, height, this.skelResult.removedJunctions.buf, this.skelResult.junctionVoxels.buf, this.skelResult.removedJunctions.size, 3, skelColor, params.skeletonSize ); }
if (params.shouldDrawBranchPoints) { int branchingPointsSize = getSpinnerValueInt(this.branchingPointsSpinner); Canvas.drawCircles( allantoisOverlay, width, height, this.skelResult.isolatedJunctions.buf, this.skelResult.junctionVoxels.buf, this.skelResult.isolatedJunctions.size, 3, params.branchingPointsColor.getARGB(), branchingPointsSize ); } }
if (params.shouldDrawConvexHull) { params.convexHullSize = getSpinnerValueInt(convexHullSizeSpinner); Canvas.drawLines( allantoisOverlay, width, height, null, this.convexHull.buf, this.convexHull.size, 2, params.convexHullColor.getARGB(), params.convexHullSize ); } }
applyOverlayToResult(this.imageResult, this.imageOriginal, this.allantoisOverlay); this.imageResult.updateAndDraw(); } }
private void updateOutline(double[] sigmas) { if (this.tubenessIp == null) return;
if (sigmas != null) { ImageProcessor ip = new ByteProcessor(this.tubenessIp.getWidth(), this.tubenessIp.getHeight());
for(int i = 0; i < this.currentSigmas.size(); ++i) { double s = this.currentSigmas.get(i);
for(int si = 0; si < this.sI.size(); ++si) { AngioToolGUI.sigmaImages siTemp = this.sI.get(si); if (siTemp.sigma == s) { ImageProcessor tempIp = siTemp.tubenessImage.duplicate(); tempIp.copyBits(ip, 0, 0, 13); ip = tempIp; break; } } }
this.tubenessIp = ip.duplicate(); }
ImageProcessor temp = this.tubenessIp.duplicate(); temp = temp.convertToByte(true); this.imageThresholded.setProcessor(temp);
int width = this.imageThresholded.getWidth(); int height = this.imageThresholded.getHeight();
BatchUtils.thresholdFlexible( (byte[])this.imageThresholded.getProcessor().getPixels(), width, height, this.thresholdRangeSliderLow.getValue(), this.thresholdRangeSliderHigh.getValue() );
temp.setThreshold(255.0, 255.0, 2); //ImageProcessor check = this.imageThresholded.getProcessor().duplicate();
byte[] thresholdedPixels = (byte[])this.imageThresholded.getProcessor().getPixels(); byte[] tempImage = new byte[width * height];
Filters.filterMax(tempImage, thresholdedPixels, width, height); Filters.filterMax(thresholdedPixels, tempImage, width, height); Filters.filterMin(tempImage, thresholdedPixels, width, height); Filters.filterMin(thresholdedPixels, tempImage, width, height);
Particles.Scratch particles = new Particles.Scratch(); int[] shapeRegions = new int[width * height]; Particles.computeShapes(particles, shapeRegions, thresholdedPixels, width, height); Particles.removeVesselVoids(particles, shapeRegions, thresholdedPixels, width, height);
if (this.smallParticlesCheckBox.isSelected()) { Particles.fillShapes(particles, shapeRegions, thresholdedPixels, width, height, (int)this.smallParticlesRangeSlider2.getValue(), true); }
if (this.fillHolesCheckBox.isSelected()) { Particles.fillShapes(particles, shapeRegions, thresholdedPixels, width, height, (int)this.fillHolesRangeSlider2.getValue(), false); }
if (this.allantoisOverlay == null || this.allantoisOverlay.length < width * height) this.allantoisOverlay = new int[width * height]; else Arrays.fill(this.allantoisOverlay, 0);
if (params.shouldDrawOutline) { Outline.drawOutline( this.allantoisOverlay, new int[width * height], new int[width * height], 0xff000000 | this.outlineRoundedPanel.getBackground().getRGB(), getSpinnerValueDouble(this.outlineSpinner), particles.shapes, shapeRegions, thresholdedPixels, width, height ); }
applyOverlayToResult(this.imageResult, this.imageOriginal, this.allantoisOverlay); this.imageResult.updateAndDraw();
/* ImagePlus iplus = new ImagePlus("tubenessIp", this.imageThresholded.getProcessor()); this.outlineRoi = Utils.thresholdToSelection(iplus); this.outlineRoi.setStrokeWidth((float)getSpinnerValueDouble(this.outlineSpinner)); this.allantoisOverlay.clear(); this.allantoisOverlay.add(this.outlineRoi); this.allantoisOverlay.setStrokeColor(this.outlineRoundedPanel.getBackground()); this.imageResult.setOverlay(this.allantoisOverlay); */ }
private void initVariables() { if (this.imageFile != null) { this.imageFile = null; this.imageFile = new File(""); }
this.sigmasMarkSlider.resetAll(); this.sigmasMarkSlider.setMaximum(100); this.sigmasMarkSlider.setEnabled(false); setSpinnerValue(this.sigmasSpinner, 100); this.minSigma = Integer.MAX_VALUE; this.maxSigma = Integer.MIN_VALUE; this.allSigmas = new ArrayList<>(); this.currentSigmas = new ArrayList<>(); this.thresholdRangeSliderLow.setEnabled(false); this.thresholdRangeSliderHigh.setEnabled(false); this.thresholdRangeSliderLow.setValue(15); this.thresholdRangeSliderHigh.setValue(255); this.fillHolesCheckBox.setSelected(params.shouldFillHoles); this.smallParticlesCheckBox.setSelected(params.shouldRemoveSmallParticles); if (this.imageResult != null) { this.imageResult.close(); this.imageResult.flush(); }
this.imageResult = new ImagePlus(); this.imageResult.setTitle("Result"); if (this.imageThresholded != null) { this.imageThresholded.close(); this.imageThresholded.flush(); }
this.imageThresholded = new ImagePlus(); this.imageThresholded.setTitle("Thresholded"); if (this.imageTubeness != null) { this.imageTubeness.close(); this.imageTubeness.flush(); }
this.imageTubeness = new ImagePlus(); this.imageTubeness.setTitle("Tubeness"); this.sI = new ArrayList<>(); //this.allantoisOverlay = new Overlay(); this.results = new Results(); this.results.computeLacunarity = params.shouldComputeLacunarity; this.results.computeThickness = params.shouldComputeThickness;
for(int i = 0; i < 10; ++i) { System.gc(); } }
/* private void smoothROIs(int fraction) { ShapeRoi sr = (ShapeRoi)Utils.thresholdToSelection(this.imageThresholded); ShapeRoi tempSr = ComputeShapeRoiSplines.computeSplines(Analyzer.threadPool, 8, sr, 5); this.imageThresholded.getProcessor().setColor(Color.black); this.imageThresholded.getProcessor().fill(); Utils.selectionToThreshold(tempSr, this.imageThresholded); this.outlineRoi = Utils.thresholdToSelection(this.imageThresholded); this.allantoisOverlay.clear(); this.allantoisOverlay.add(tempSr); this.allantoisOverlay.setStrokeColor(Color.yellow); this.imageThresholded.setOverlay(this.allantoisOverlay); this.imageResult.setOverlay(this.allantoisOverlay); } */
public void computeLacunarity(ImagePlus iplus, int numBoxes, int minBoxSize, int slideXY) { Lacunarity2.Statistics l = new Lacunarity2.Statistics(); Lacunarity2.computeLacunarity(l, (byte[])iplus.getProcessor().getPixels(), iplus.getWidth(), iplus.getHeight(), numBoxes, minBoxSize, slideXY); this.ElSlope = l.elCurve; this.FlSlope = l.flCurve; this.medialELacunarity = l.elMedial; this.meanEl = l.elMean; this.medialFLacunarity = l.flMedial; this.meanFl = l.flMean; }
private ArrayList<Roi> computeSkeletonRoi(int size) { ArrayList<Roi> list = new ArrayList<>();
for (int i = 0; i < this.skelResult.slabList.size; i += 3) { int x = this.skelResult.slabList.buf[i]; int y = this.skelResult.slabList.buf[i+1];
OvalRoi r = new OvalRoi( x - size / 2, y - size / 2, size, size ); list.add(r); }
return list; }
private ArrayList<Roi> computeJunctionsRoi(int size) { ArrayList<Roi> list = new ArrayList<>();
for (int i = 0; i < this.skelResult.isolatedJunctions.size; i++) { int idx = this.skelResult.isolatedJunctions.buf[i]; int x = this.skelResult.junctionVoxels.buf[idx]; int y = this.skelResult.junctionVoxels.buf[idx+1];
Roi r = new OvalRoi( x - size / 2, y - size / 2, size, size ); list.add(r); }
return list; }
private Object updateSigmas(double[] s) { this.upateAllSigmas(s); this.updateCurrentSimgas(s); return ""; }
private void upateAllSigmas(double[] s) { if (this.ipOriginal == null) return;
reallocateTubeness();
for(int i = 0; i < s.length; ++i) { double sigma = s[i]; if (!this.allSigmas.contains(sigma)) { this.allSigmas.add(sigma); double[] sigmaDouble = new double[]{sigma}; this.imageTubeness = new ImagePlus("", this.ipOriginal); Tubeness.computeTubenessImage( this.tubeness, sliceRunner, (byte[])this.imageTubeness.getProcessor().getPixels(), (byte[])this.ipOriginal.getPixels(), this.imageTubeness.getWidth(), this.imageTubeness.getHeight(), sigmaDouble, 1 ); this.sI.add(new AngioToolGUI.sigmaImages(sigma, this.imageTubeness.getProcessor())); }
updateStatus(i / s.length * 100, "computing outline... "); } }
private void updateCurrentSimgas(double[] s) { if (this.currentSigmas == null) this.currentSigmas = new ArrayList<>(); else this.currentSigmas.clear();
for(int i = 0; i < s.length; ++i) { this.currentSigmas.add(s[i]); } }
private void updateSigmas(int low, int high) { this.upateAllSigmas(low, high); this.updateCurrentSimgas(low, high); }
private void upateAllSigmas(int low, int high) { if (this.ipOriginal == null) return;
reallocateTubeness();
if (!this.allSigmas.contains((double)low)) { this.allSigmas.add((double)low); double[] s = new double[]{(double)low}; this.imageTubeness = new ImagePlus("", this.ipOriginal); Tubeness.computeTubenessImage( this.tubeness, sliceRunner, (byte[])this.imageTubeness.getProcessor().getPixels(), (byte[])this.ipOriginal.getPixels(), this.imageTubeness.getWidth(), this.imageTubeness.getHeight(), s, 1 ); this.sI.add(new AngioToolGUI.sigmaImages((double)low, this.imageTubeness.getProcessor())); }
if (!this.allSigmas.contains((double)high)) { this.allSigmas.add((double)high); double[] s = new double[]{(double)high}; this.imageTubeness = new ImagePlus("", this.ipOriginal); Tubeness.computeTubenessImage( this.tubeness, sliceRunner, (byte[])this.imageTubeness.getProcessor().getPixels(), (byte[])this.ipOriginal.getPixels(), this.imageTubeness.getWidth(), this.imageTubeness.getHeight(), s, 1 ); this.sI.add(new AngioToolGUI.sigmaImages((double)high, this.imageTubeness.getProcessor())); }
Collections.sort(this.allSigmas); }
private void updateCurrentSimgas(int low, int high) { if (this.currentSigmas == null) this.currentSigmas = new ArrayList<>(); else this.currentSigmas.clear();
for(int i = 0; i < this.allSigmas.size(); ++i) { double s = this.allSigmas.get(i); if (s >= (double)low && s <= (double)high && !this.currentSigmas.contains(s)) { this.currentSigmas.add(s); } } }
private void preCompute() { this.initControls(); this.computeFirstOutline(this.firstSigma); }
private void initControls() { if (this.ipOriginal != null) { int width = this.ipOriginal.getWidth(); int height = this.ipOriginal.getHeight(); this.minSigma = 1; this.maxSigma = (int)Math.sqrt((double)(width * width + height * height)) / 70; this.maxSigma = BatchUtils.roundIntegerToNearestUpperTenth(this.maxSigma); } else { this.minSigma = 1; this.maxSigma = 50; } this.sigmasMarkSlider.setEnabled(true); this.sigmasMarkSlider.resetAll(); this.sigmasMarkSlider.setMaximum(this.minSigma); this.sigmasMarkSlider.setMaximum(this.maxSigma); this.sigmasSpinner.setEnabled(true); setSpinnerValue(this.sigmasSpinner, this.maxSigma); this.thresholdRangeSliderLow.setEnabled(true); this.thresholdRangeSliderHigh.setEnabled(true); this.thresholdRangeSliderLow.setValue(15); this.lowThresholdTextField.setText("" + this.thresholdRangeSliderLow.getValue()); this.highThresholdTextField.setText("" + this.thresholdRangeSliderHigh.getValue()); this.fillHolesCheckBox.setEnabled(true); this.fillHolesCheckBox.setSelected(false); this.fillHolesRangeSlider2.setEnabled(this.fillHolesCheckBox.isSelected()); this.fillHolesRangeSlider2.setMinimum(this.minSigma - 1); this.fillHolesRangeSlider2.setMaximum(30 * this.maxSigma); this.fillHolesRangeSlider2.setMajorTickSpacing(30 * this.maxSigma / 10); this.fillHolesSpinner.setEnabled(this.fillHolesCheckBox.isSelected()); setSpinnerValue(this.fillHolesSpinner, 30 * this.maxSigma); this.smallParticlesCheckBox.setEnabled(true); this.smallParticlesCheckBox.setSelected(false); this.smallParticlesRangeSlider2.setEnabled(this.smallParticlesCheckBox.isSelected()); this.smallParticlesRangeSlider2.setMinimum(this.minSigma - 1); this.smallParticlesRangeSlider2.setMaximum(40 * this.maxSigma); this.smallParticlesRangeSlider2.setMajorTickSpacing(40 * this.maxSigma / 10); this.removeSmallParticlesSpinner.setEnabled(this.smallParticlesCheckBox.isSelected()); setSpinnerValue(this.removeSmallParticlesSpinner, 40 * this.maxSigma / 10); this.firstSigma[0] = (double)Math.round((float)(this.maxSigma / 4)); this.toggleOverlayToggleButton.setEnabled(true); setSpinnerValue(this.outlineSpinner, 1); setSpinnerValue(this.skeletonSpinner, this.maxSigma / 8); setSpinnerValue(this.branchingPointsSpinner, this.maxSigma / 5); setSpinnerValue(this.convexHullSizeSpinner, 1); }
private void computeFirstOutline(double[] sigmas) { this.imageTubeness = new ImagePlus("imageTubeness", this.ipOriginal); this.tubenessIp = this.imageTubeness.getProcessor(); Calibration c = this.imageTubeness.getCalibration(); reallocateTubeness(); Tubeness.computeTubenessImage( this.tubeness, sliceRunner, (byte[])this.tubenessIp.getPixels(), (byte[])this.ipOriginal.getPixels(), this.imageTubeness.getWidth(), this.imageTubeness.getHeight(), params.sigmas, params.sigmas.length ); this.sI.add(new AngioToolGUI.sigmaImages(sigmas[0], this.tubenessIp)); this.sigmasMarkSlider.addMark((int)sigmas[0]); this.allSigmas.add(sigmas[0]); this.currentSigmas.add(sigmas[0]); this.ipThresholded = this.tubenessIp.duplicate(); this.ipThresholded = this.ipThresholded.convertToByte(params.shouldScalePixelValues); this.imageThresholded.setProcessor(this.ipThresholded); BatchUtils.thresholdFlexible((byte[])this.ipThresholded.getPixels(), this.imageThresholded.getWidth(), this.imageThresholded.getHeight(), this.thresholdRangeSliderLow.getValue(), this.thresholdRangeSliderHigh.getValue()); this.ipThresholded.setThreshold(255.0, 255.0, 2); this.updateOutline(null); }
private void initLookAndFeel() { String lookAndFeel = null; if ("System" != null) { if ("System".equals("Metal")) { lookAndFeel = UIManager.getCrossPlatformLookAndFeelClassName(); } else if ("System".equals("System")) { lookAndFeel = UIManager.getSystemLookAndFeelClassName(); } else if ("System".equals("Motif")) { lookAndFeel = "com.sun.java.swing.plaf.motif.MotifLookAndFeel"; } else if ("System".equals("GTK")) { lookAndFeel = "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"; } else if ("System".equals("Nimbus")) { lookAndFeel = "javax.swing.plaf.nimbus.NimbusLookAndFeel"; } else { lookAndFeel = UIManager.getCrossPlatformLookAndFeelClassName(); }
try { UIManager.setLookAndFeel(lookAndFeel); if ("System".equals("Metal")) { if ("Test".equals("DefaultMetal")) { MetalLookAndFeel.setCurrentTheme(new DefaultMetalTheme()); } else if ("Test".equals("Ocean")) { MetalLookAndFeel.setCurrentTheme(new OceanTheme()); }
UIManager.setLookAndFeel(new MetalLookAndFeel()); } } catch (ClassNotFoundException var3) { var3.printStackTrace(); } catch (UnsupportedLookAndFeelException var4) { var4.printStackTrace(); } catch (Exception var5) { var5.printStackTrace(); } }
SwingUtilities.updateComponentTreeUI(this); }
private void exit() { //this.updatePreferences(); ATPreferences.savePreferences(params, AngioTool.PREFS_TXT); }
private AnalyzerParameters getBatchAnalyzerSettings() { try { return ATPreferences.load(this, AngioTool.BATCH_TXT); } catch (Exception ex) { // pass }
double scale = 1.0; if (!this.distanceInMMNumberTextField.getText().equals("") && !AngioToolGUI.this.distanceInPixelsNumberTextField.getText().equals("")) { int pixelDistance = Math.max(AngioToolGUI.this.distanceInPixelsNumberTextField.getInt(), 1); scale = this.distanceInMMNumberTextField.getDouble() / (double)pixelDistance; }
return new AnalyzerParameters( this.currentDir.getAbsolutePath(), null, "", this.saveResultImageCheckBox.isSelected(), false, "", params.resultImageFormat, this.resizeImageCheckBox.isSelected(), params.resizingFactor, params.shouldRemoveSmallParticles, (int)this.smallParticlesRangeSlider2.getValue(), params.shouldFillHoles, (int)this.fillHolesRangeSlider2.getValue(), getSigmaMarks(), this.thresholdRangeSliderHigh.getValue(), this.thresholdRangeSliderLow.getValue(), params.shouldUseFastSkeletonizer, true, scale, params.shouldShowOverlayOrGallery, this.showOutlineCheckBox.isSelected(), new Rgb(this.outlineRoundedPanel.getBackground()), getSpinnerValueDouble(this.outlineSpinner), this.showSkeletonCheckBox.isSelected(), new Rgb(this.skeletonColorRoundedPanel.getBackground()), getSpinnerValueDouble(this.skeletonSpinner), this.showBranchingPointsCheckBox.isSelected(), new Rgb(this.branchingPointsRoundedPanel.getBackground()), getSpinnerValueDouble(this.branchingPointsSpinner), this.showConvexHullCheckBox.isSelected(), new Rgb(this.convexHullRoundedPanel.getBackground()), getSpinnerValueDouble(this.convexHullSizeSpinner), params.shouldScalePixelValues, params.shouldComputeLacunarity, params.shouldComputeThickness ); }
private String doSingleAnalysis() { int progress = 0; progressBar.setMinimum(0); progressBar.setMaximum(100); progressBar.setStringPainted(true); updateStatus(progress, ""); this.updateOutline(null); int fraction = 1;
/* int splineIterations = 0; for(int i = 0; i < splineIterations; ++i) { this.smoothROIs(fraction); progress += 11; updateStatus(progress, "smooth ROIs"); } */
this.results.vesselPixelArea = BatchUtils.countForegroundPixels((byte[])this.imageThresholded.getProcessor().getPixels(), this.imageThresholded.getWidth(), this.imageThresholded.getHeight()); if (params.shouldComputeLacunarity) { updateStatus(progress, "Computing lacunarity..."); ImageProcessor ipTemp = this.imageThresholded.getProcessor().duplicate(); ImagePlus iplusTemp = new ImagePlus("iplusTemp", ipTemp); /* if (!Utils.isReleaseVersion) { IJ.saveAs(iplusTemp, "tiff", this.imageFile.getAbsolutePath() + " lacunarity.tif"); } */
this.computeLacunarity(iplusTemp, 10, 10, 5); this.results.ELacunaritySlope = this.ElSlope; this.results.ELacunarity = this.medialELacunarity; this.results.FLacunaritySlope = this.FlSlope; this.results.FLacuanrity = this.medialFLacunarity; this.results.meanEl = this.meanEl; this.results.meanFl = this.meanFl; /* if (!Utils.isReleaseVersion) { for(int i = 0; i < this.lacunarityBoxes.length; ++i) { System.out.println(this.lacunarityBoxes[i] + "\t" + this.Elamdas.get(i) + "\t" + this.Flamdas.get(i)); }
System.out.println( "ElSlope = " + this.ElSlope + "\tFlSlope = " + this.FlSlope + "\tmedialELacuanrity = " + this.medialELacunarity + "\tmeanEl= " + this.meanEl + "\tmeanFl= " + this.meanFl ); } */ }
this.convexHullArea = ConvexHull.findConvexHull( this.convexHull, (byte[])this.imageThresholded.getProcessor().getPixels(), this.imageThresholded.getWidth(), this.imageThresholded.getHeight() ); //this.convexHullRoi = new PolygonRoi(this.convexHull.polygon(), 2);
progress += 5; updateStatus(progress, "Analyzing skeleton... "); updateStatus(progress, "Skeletonize");
this.ipThresholded = this.imageThresholded.getProcessor(); ImagePlus iplusSkeleton = this.imageThresholded.duplicate(); iplusSkeleton.setTitle("iplusSkeleton");
int skelWidth = iplusSkeleton.getWidth(); int skelHeight = iplusSkeleton.getHeight(); byte[] skelImage = new byte[skelWidth * skelHeight]; Object[] skelLayers = new Object[1]; skelLayers[0] = iplusSkeleton.getProcessor().getPixels();
Lee94.skeletonize( new Lee94.Scratch(), skelImage, sliceRunner, Analyzer.MAX_WORKERS, skelLayers, skelWidth, skelHeight, iplusSkeleton.getBitDepth() );
progress += 33; updateStatus(progress, "Computing convex hull... "); reallocateSkeletonResult(); AnalyzeSkeleton2.analyze( this.skelResult, skelImage, skelWidth, skelHeight, 1 );
if (params.shouldComputeThickness) { int area = skelWidth * skelHeight; int[] thicknessScratch = new int[area]; this.averageVesselDiameter = params.linearScalingFactor * VesselThickness.computeMedianVesselThickness( sliceRunner, Analyzer.MAX_WORKERS, this.skelResult.slabList.buf, this.skelResult.slabList.size, 3, thicknessScratch, skelImage, skelWidth, skelHeight ); }
//this.skeletonRoi = this.computeSkeletonRoi(getSpinnerValueInt(this.skeletonSpinner)); //this.junctionsRoi = this.computeJunctionsRoi(getSpinnerValueInt(this.branchingPointsSpinner)); this.updateOverlay(); updateStatus(95, " Saving result image... "); updateStatus(100, "Done... "); return "Good"; }
ImagePlus openImageAndIsolateDominantChannel(String absPath) { ImagePlus image = IJ.openImage(absPath); if (image != null) { int width = image.getWidth(); int height = image.getHeight(); int area = width * height; if (image.getType() == ImagePlus.COLOR_RGB) { int[] rgbPixels = (int[])((ColorProcessor)image.getProcessor()).getPixels(); long redTally = 0; long greenTally = 0; long blueTally = 0; for (int i = 0; i < area; i++) { int r = (rgbPixels[i] >> 16) & 0xff; int g = (rgbPixels[i] >> 8) & 0xff; int b = rgbPixels[i] & 0xff; redTally += r; greenTally += g; blueTally += b; }
int mask; if (redTally >= greenTally && redTally >= blueTally) mask = 0xffff0000; else if (greenTally >= blueTally) mask = 0xff00ff00; else mask = 0xff0000ff;
for (int i = 0; i < area; i++) rgbPixels[i] &= mask; } else { byte[] pixels = (byte[])image.getProcessor().convertToByte(true).getPixels(); int[] rgbPixels = new int[area]; for (int i = 0; i < area; i++) { int p = pixels[i] & 0xff; rgbPixels[i] = (p << 24) | (p << 8); } image.setProcessor(new ColorProcessor(width, height, rgbPixels)); } } return image; }
void applyOverlayToResult(ImagePlus result, ImagePlus original, int[] overlay) { int width = result.getWidth(); int height = result.getHeight();
int[] output = (int[])result.getProcessor().getPixels(); int[] input = (int[])original.getProcessor().getPixels();
int area = width * height; for (int i = 0; i < area; i++) { double a1 = (double)((overlay[i] >> 24) & 0xff) / 255.0; double r1 = (double)((overlay[i] >> 16) & 0xff) / 255.0; double g1 = (double)((overlay[i] >> 8) & 0xff) / 255.0; double b1 = (double)(overlay[i] & 0xff) / 255.0;
double a2 = (double)((input[i] >> 24) & 0xff) / 255.0; double r2 = (double)((input[i] >> 16) & 0xff) / 255.0; double g2 = (double)((input[i] >> 8) & 0xff) / 255.0; double b2 = (double)(input[i] & 0xff) / 255.0;
output[i] = ((int)(255.0 * (1.0 - ((1.0 - a1) * (1.0 - a2)))) << 24 & 0xff000000) | ((int)(255.0 * ((1.0 - a1) * r2 + a1 * r1)) << 16 & 0xff0000) | ((int)(255.0 * ((1.0 - a1) * g2 + a1 * g1)) << 8 & 0xff00) | ((int)(255.0 * ((1.0 - a1) * b2 + a1 * b1)) & 0xff); } }
class AngioToolWorker extends SwingWorker<Object, Object> {
@Override public Object doInBackground() { return doSingleAnalysis(); }
@Override protected void done() { try { AngioToolGUI.this.populateResults(); } catch (Exception var2) { } } }
private class sigmaImages { double sigma; ImageProcessor tubenessImage;
public sigmaImages(double sigma, ImageProcessor tubenessImage) { this.sigma = sigma; this.tubenessImage = tubenessImage; }
public void showImage() { ImagePlus iplus = new ImagePlus("sigma " + this.sigma, this.tubenessImage); iplus.show(); }
@Override public String toString() { return "sigma " + this.sigma + " tubenessIamge= " + this.tubenessImage; } }}
