diff --git a/.idea/.gitignore b/.idea/.gitignore new file mode 100644 index 0000000..26d3352 --- /dev/null +++ b/.idea/.gitignore @@ -0,0 +1,3 @@ +# Default ignored files +/shelf/ +/workspace.xml diff --git a/.idea/compiler.xml b/.idea/compiler.xml new file mode 100644 index 0000000..d4e6c18 --- /dev/null +++ b/.idea/compiler.xml @@ -0,0 +1,13 @@ + + + + + + + + + + + + + \ No newline at end of file diff --git a/.idea/encodings.xml b/.idea/encodings.xml new file mode 100644 index 0000000..aa00ffa --- /dev/null +++ b/.idea/encodings.xml @@ -0,0 +1,7 @@ + + + + + + + \ No newline at end of file diff --git a/.idea/jarRepositories.xml b/.idea/jarRepositories.xml new file mode 100644 index 0000000..17742c6 --- /dev/null +++ b/.idea/jarRepositories.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/.idea/misc.xml b/.idea/misc.xml new file mode 100644 index 0000000..d5cd614 --- /dev/null +++ b/.idea/misc.xml @@ -0,0 +1,12 @@ + + + + + + + + \ No newline at end of file diff --git a/.idea/uiDesigner.xml b/.idea/uiDesigner.xml new file mode 100644 index 0000000..e96534f --- /dev/null +++ b/.idea/uiDesigner.xml @@ -0,0 +1,124 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/.idea/vcs.xml b/.idea/vcs.xml new file mode 100644 index 0000000..35eb1dd --- /dev/null +++ b/.idea/vcs.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/pom.xml b/pom.xml index 5ec6615..037aec3 100644 --- a/pom.xml +++ b/pom.xml @@ -6,20 +6,26 @@ 4.0.0 - sc.fiji - pom-fiji - 6.1.3 + org.scijava + pom-scijava + 31.1.0 + ch.epfl.big MosaicJ_ 2.0.1-SNAPSHOT - plugins/MosaicJ_.jar - + plugins/ch.epfl.big.MosaicJ_.jar + Performs stitching http://fiji.sc/MosaicJ 2010 + + BIG + http://bigwww.epfl.ch/ + + BIG @@ -42,6 +48,16 @@ + + + Philippe Thevenaz + http://bigwww.epfl.ch/thevenaz/ + + developer + + + + scm:git:git://github.com/fiji/MosaicJ scm:git:git@github.com:fiji/MosaicJ @@ -57,6 +73,11 @@ http://jenkins.imagej.net/job/MosaicJ/ + + BIG + ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, Biomedical Imaging Group (BIG) + + imagej.public @@ -64,6 +85,13 @@ + + + Image.sc Forum + https://forum.image.sc/ + + + diff --git a/src/main/java/MosaicJ_.java b/src/main/java/ch/epfl/big/MosaicJ_.java similarity index 96% rename from src/main/java/MosaicJ_.java rename to src/main/java/ch/epfl/big/MosaicJ_.java index 472d10b..16bfa60 100644 --- a/src/main/java/MosaicJ_.java +++ b/src/main/java/ch/epfl/big/MosaicJ_.java @@ -1,4 +1,4 @@ -/*==================================================================== +package ch.epfl.big;/*==================================================================== | Version: March 13, 2008 \===================================================================*/ @@ -71,10 +71,6 @@ import java.awt.GridLayout; import java.awt.Insets; import java.awt.LayoutManager; -import java.awt.Menu; -import java.awt.MenuBar; -import java.awt.MenuItem; -import java.awt.MenuShortcut; import java.awt.Point; import java.awt.Rectangle; import java.awt.TextArea; @@ -101,23 +97,12 @@ import java.util.Iterator; import java.util.Stack; -import javax.swing.JButton; -import javax.swing.JCheckBox; -import javax.swing.JComponent; -import javax.swing.JDialog; -import javax.swing.JFrame; -import javax.swing.JLabel; -import javax.swing.JOptionPane; -import javax.swing.JPanel; -import javax.swing.JProgressBar; -import javax.swing.JScrollPane; -import javax.swing.JTabbedPane; -import javax.swing.JViewport; +import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; /*==================================================================== -| MosaicJ_ +| ch.epfl.big.MosaicJ_ \===================================================================*/ public class MosaicJ_ extends @@ -127,7 +112,7 @@ public class MosaicJ_ ChangeListener, PlugIn -{ /* begin class MosaicJ_ */ +{ /* begin class ch.epfl.big.MosaicJ_ */ /*.................................................................... private variables @@ -143,50 +128,45 @@ public class MosaicJ_ private final JScrollPane workScrollPane = new JScrollPane(workArea, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS); -private final MenuItem abort = new MenuItem("Abort", - new MenuShortcut(KeyEvent.VK_W)); -private final MenuItem magnification = new MenuItem(""); -private final MenuItem magnify = new MenuItem("Magnify", - new MenuShortcut(KeyEvent.VK_ADD)); -private final MenuItem minify = new MenuItem("Minify", - new MenuShortcut(KeyEvent.VK_SUBTRACT)); -private final MenuItem openFile = new MenuItem("Open Image...", - new MenuShortcut(KeyEvent.VK_O)); -private final MenuItem openImageSequence = new MenuItem( - "Open Image Sequence...", new MenuShortcut(KeyEvent.VK_O, true)); +private final JMenuItem abort = new JMenuItem("Abort"); +private final JMenuItem magnification = new JMenuItem(""); +private final JMenuItem magnify = new JMenuItem("Magnify"); +private final JMenuItem minify = new JMenuItem("Minify"); +private final JMenuItem openFile = new JMenuItem("Open Image..."); +private final JMenuItem openImageSequence = new JMenuItem("Open Image Sequence..."); private int id = 0; -private static MenuItem blending = null; -private static MenuItem createMosaic = null; -private static MenuItem credits = null; -private static MenuItem decolorization = null; -private static MenuItem deselect = null; -private static MenuItem forget = null; -private static MenuItem freeze = null; -private static MenuItem group = null; -private static MenuItem help = null; -private static MenuItem hide = null; -private static MenuItem loadPreMosaic = null; -private static MenuItem maximizeContrast = null; -private static MenuItem nudgeDown = null; -private static MenuItem nudgeLeft = null; -private static MenuItem nudgeRight = null; -private static MenuItem nudgeUp = null; -private static MenuItem outputLog = null; -private static MenuItem quickAndDirty = null; -private static MenuItem replay = null; -private static MenuItem resetContrast = null; -private static MenuItem resetMosaicJ = null; -private static MenuItem revertPreMosaic = null; -private static MenuItem rotation = null; -private static MenuItem savePreMosaic = null; -private static MenuItem selectAll = null; -private static MenuItem sendToBack = null; -private static MenuItem setContrast = null; -private static MenuItem showAll = null; -private static MenuItem status = null; -private static MenuItem stow = null; -private static MenuItem unfreeze = null; -private static MenuItem ungroup = null; +private static JMenuItem blending = null; +private static JMenuItem createMosaic = null; +private static JMenuItem credits = null; +private static JMenuItem decolorization = null; +private static JMenuItem deselect = null; +private static JMenuItem forget = null; +private static JMenuItem freeze = null; +private static JMenuItem group = null; +private static JMenuItem help = null; +private static JMenuItem hide = null; +private static JMenuItem loadPreMosaic = null; +private static JMenuItem maximizeContrast = null; +private static JMenuItem nudgeDown = null; +private static JMenuItem nudgeLeft = null; +private static JMenuItem nudgeRight = null; +private static JMenuItem nudgeUp = null; +private static JMenuItem outputLog = null; +private static JMenuItem quickAndDirty = null; +private static JMenuItem replay = null; +private static JMenuItem resetContrast = null; +private static JMenuItem resetMosaicJ = null; +private static JMenuItem revertPreMosaic = null; +private static JMenuItem rotation = null; +private static JMenuItem savePreMosaic = null; +private static JMenuItem selectAll = null; +private static JMenuItem sendToBack = null; +private static JMenuItem setContrast = null; +private static JMenuItem showAll = null; +private static JMenuItem status = null; +private static JMenuItem stow = null; +private static JMenuItem unfreeze = null; +private static JMenuItem ungroup = null; private static boolean blend = true; private static boolean createOutputLog = false; private static boolean hidden = false; @@ -268,7 +248,7 @@ public void actionPerformed ( if (e.getSource() == magnify) { updateScale(reductionFactor / 2); magnify.setEnabled(1 < reductionFactor); - magnification.setLabel(getMagnificationAsString()); + magnification.setText(getMagnificationAsString()); } if (e.getSource() == maximizeContrast) { playField.maximizeContrastSelectedThumbs(); @@ -276,7 +256,7 @@ public void actionPerformed ( if (e.getSource() == minify) { updateScale(2 * reductionFactor); magnify.setEnabled(true); - magnification.setLabel(getMagnificationAsString()); + magnification.setText(getMagnificationAsString()); } if (e.getSource() == nudgeDown) { playField.translateSelectedThumbs(0, 1); @@ -448,77 +428,110 @@ public void stateChanged ( public void run ( final String arg ) { + abort.setMnemonic(KeyEvent.VK_W); + magnify.setMnemonic(KeyEvent.VK_ADD); + minify.setMnemonic(KeyEvent.VK_SUBTRACT); + openFile.setMnemonic(KeyEvent.VK_O); + openImageSequence.setMnemonic(KeyEvent.VK_Q); // Previous shortcut to (O,true) + setTitle("MosaicJ " + getMagnificationAsString()); hidden = false; - blending = new MenuItem((blend) + blending = new JMenuItem((blend) ? ("Deactivate Blending") : ("Activate Blending")); - createMosaic = new MenuItem( - "Create Mosaic", new MenuShortcut(KeyEvent.VK_S)); - credits = new MenuItem( - "Credits"); - decolorization = new MenuItem((smartDecolorization) + + createMosaic = new JMenuItem("Create Mosaic"); + createMosaic.setMnemonic(KeyEvent.VK_M); // Previous shortcut to S + + credits = new JMenuItem("Credits"); + + decolorization = new JMenuItem((smartDecolorization) ? ("Deactivate Smart Color Conversion") : ("ActivateSmart Color Conversion")); - deselect = new MenuItem( - "Deselect", new MenuShortcut(KeyEvent.VK_D)); - forget = new MenuItem( - "Forget", new MenuShortcut(KeyEvent.VK_X)); - freeze = new MenuItem( - "Freeze", new MenuShortcut(KeyEvent.VK_F)); - group = new MenuItem( - "Group", new MenuShortcut(KeyEvent.VK_G)); - help = new MenuItem( - "Help"); - hide = new MenuItem( - "Hide", new MenuShortcut(KeyEvent.VK_H, true)); - loadPreMosaic = new MenuItem( - "Load Pre-Mosaic...", new MenuShortcut(KeyEvent.VK_R, true)); - maximizeContrast = new MenuItem( - "Maximize Contrast", new MenuShortcut(KeyEvent.VK_L, true)); - nudgeDown = new MenuItem( - "Nudge Down", new MenuShortcut(KeyEvent.VK_DOWN)); - nudgeLeft = new MenuItem( - "Nudge Left", new MenuShortcut(KeyEvent.VK_LEFT)); - nudgeRight = new MenuItem( - "Nudge Right", new MenuShortcut(KeyEvent.VK_RIGHT)); - nudgeUp = new MenuItem( - "Nudge Up", new MenuShortcut(KeyEvent.VK_UP)); - outputLog = new MenuItem((createOutputLog) + + deselect = new JMenuItem("Deselect"); + deselect.setMnemonic(KeyEvent.VK_D); + + forget = new JMenuItem("Forget"); + forget.setMnemonic(KeyEvent.VK_X); + + freeze = new JMenuItem("Freeze"); + freeze.setMnemonic(KeyEvent.VK_F); + + group = new JMenuItem("Group"); + group.setMnemonic(KeyEvent.VK_G); + + help = new JMenuItem("Help"); + + hide = new JMenuItem("Hide"); + hide.setMnemonic(KeyEvent.VK_H); + + loadPreMosaic = new JMenuItem("Load Pre-Mosaic..."); + loadPreMosaic.setMnemonic(KeyEvent.VK_R); + + maximizeContrast = new JMenuItem("Maximize Contrast"); + maximizeContrast.setMnemonic(KeyEvent.VK_L); + + nudgeDown = new JMenuItem("Nudge Down"); + nudgeDown.setMnemonic(KeyEvent.VK_DOWN); + + nudgeLeft = new JMenuItem("Nudge Left"); + nudgeLeft.setMnemonic(KeyEvent.VK_LEFT); + + nudgeRight = new JMenuItem("Nudge Right"); + nudgeRight.setMnemonic(KeyEvent.VK_RIGHT); + + nudgeUp = new JMenuItem("Nudge Up"); + nudgeUp.setMnemonic(KeyEvent.VK_UP); + + outputLog = new JMenuItem((createOutputLog) ? ("Deactivate Log File") : ("Activate Log File")); - quickAndDirty = new MenuItem((quickAndDirtyScaling) + + quickAndDirty = new JMenuItem((quickAndDirtyScaling) ? ("Deactivate Quick&Dirty Scaling") : ("Activate Quick&Dirty Scaling")); - replay = new MenuItem( - "Replay from Log..."); - resetMosaicJ = new MenuItem( - "Reset MosaicJ"); - resetContrast = new MenuItem( - "Reset Contrast", new MenuShortcut(KeyEvent.VK_R)); - revertPreMosaic = new MenuItem( - "Previous Pre-Mosaic...", new MenuShortcut(KeyEvent.VK_Z)); - rotation = new MenuItem((rotate) + + replay = new JMenuItem("Replay from Log..."); + + resetMosaicJ = new JMenuItem("Reset MosaicJ"); + + resetContrast = new JMenuItem("Reset Contrast"); + resetContrast.setMnemonic(KeyEvent.VK_C); // Previous shortcut to R + + revertPreMosaic = new JMenuItem("Previous Pre-Mosaic..."); + revertPreMosaic.setMnemonic(KeyEvent.VK_Z); + + rotation = new JMenuItem((rotate) ? ("Deactivate Rotation") : ("Activate Rotation")); - savePreMosaic = new MenuItem( - "Save Pre-Mosaic...", new MenuShortcut(KeyEvent.VK_S, true)); - selectAll = new MenuItem( - "Select All", new MenuShortcut(KeyEvent.VK_A)); - sendToBack = new MenuItem( - "Send to Back", new MenuShortcut(KeyEvent.VK_B)); - setContrast = new MenuItem( - "Set Contrast...", new MenuShortcut(KeyEvent.VK_L)); - showAll = new MenuItem( - "Show All", new MenuShortcut(KeyEvent.VK_A, true)); - status = new MenuItem( - "Status"); - stow = new MenuItem( - "Stow", new MenuShortcut(KeyEvent.VK_T)); - unfreeze = new MenuItem( - "Unfreeze", new MenuShortcut(KeyEvent.VK_F, true)); - ungroup = new MenuItem( - "Ungroup", new MenuShortcut(KeyEvent.VK_U)); + + savePreMosaic = new JMenuItem("Save Pre-Mosaic..."); + savePreMosaic.setMnemonic(KeyEvent.VK_S); + + selectAll = new JMenuItem("Select All"); + selectAll.setMnemonic(KeyEvent.VK_A); + + sendToBack = new JMenuItem("Send to Back"); + sendToBack.setMnemonic(KeyEvent.VK_B); + + setContrast = new JMenuItem("Set Contrast..."); + setContrast.setMnemonic(KeyEvent.VK_K); // Previous shortcut to L + + showAll = new JMenuItem("Show All"); + showAll.setMnemonic(KeyEvent.VK_E); // Previous shortcut to A + + status = new JMenuItem("Status"); + + stow = new JMenuItem("Stow"); + stow.setMnemonic(KeyEvent.VK_T); + + unfreeze = new JMenuItem("Unfreeze"); + unfreeze.setMnemonic(KeyEvent.VK_N); // Previous shortcut to F + + ungroup = new JMenuItem("Ungroup"); + ungroup.setMnemonic(KeyEvent.VK_U); + if ((SCREEN_WIDTH < 640) || (SCREEN_HEIGHT < 480)) { IJ.error("Screen too small to proceed."); return; @@ -546,7 +559,6 @@ public void run ( getContentPane().setLayout(new BorderLayout(0, 0)); getContentPane().add(workScrollPane, BorderLayout.CENTER); getContentPane().add(thumbnailScrollPane, BorderLayout.SOUTH); - setVisible(true); playField = new MosaicJPlayField(workArea.getWidth(), workArea.getHeight(), workScrollPane, reductionFactor); @@ -558,7 +570,7 @@ public void run ( getContentPane().remove(progressBar); getContentPane().validate(); - final Menu fileMenu = new Menu("File"); + final JMenu fileMenu = new JMenu("File"); openFile.addActionListener(this); fileMenu.add(openFile); openImageSequence.addActionListener(this); @@ -591,7 +603,7 @@ public void run ( abort.addActionListener(this); fileMenu.add(abort); - final Menu editMenu = new Menu("Edit"); + final JMenu editMenu = new JMenu("Edit"); selectAll.addActionListener(this); editMenu.add(selectAll); deselect.addActionListener(this); @@ -611,7 +623,7 @@ public void run ( nudgeDown.addActionListener(this); editMenu.add(nudgeDown); - final Menu objectMenu = new Menu("Object"); + final JMenu objectMenu = new JMenu("Object"); sendToBack.addActionListener(this); objectMenu.add(sendToBack); objectMenu.addSeparator(); @@ -636,7 +648,7 @@ public void run ( resetContrast.addActionListener(this); objectMenu.add(resetContrast); - final Menu scaleMenu = new Menu("Scale"); + final JMenu scaleMenu = new JMenu("Scale"); minify.addActionListener(this); scaleMenu.add(minify); magnify.setEnabled(1 < reductionFactor); @@ -649,7 +661,7 @@ public void run ( magnification.setEnabled(false); scaleMenu.add(magnification); - final Menu helpMenu = new Menu("Help"); + final JMenu helpMenu = new JMenu("Help"); help.addActionListener(this); //@ helpMenu.add(help); credits.addActionListener(this); @@ -657,16 +669,18 @@ public void run ( status.addActionListener(this); helpMenu.add(status); - final MenuBar menuBar = new MenuBar(); + final JMenuBar menuBar = new JMenuBar(); menuBar.add(fileMenu); menuBar.add(editMenu); menuBar.add(objectMenu); menuBar.add(scaleMenu); menuBar.add(helpMenu); - setMenuBar(menuBar); + setJMenuBar(menuBar); loadPreMosaic(IJ.getDirectory("temp") + "MosaicJPreMosaic", false); setActivatedMenus(true, true, true, false, false); + + setVisible(true); } /* end run */ /*.................................................................... @@ -1347,10 +1361,10 @@ private void savePreMosaic ( } } /* savePreMosaic */ -} /* end class MosaicJ_ */ +} /* end class ch.epfl.big.MosaicJ_ */ /*==================================================================== -| MosaicJCredits +| ch.epfl.big.MosaicJCredits \===================================================================*/ class MosaicJCredits extends @@ -1358,7 +1372,7 @@ class MosaicJCredits implements ActionListener -{ /* begin class MosaicJCredits */ +{ /* begin class ch.epfl.big.MosaicJCredits */ /*.................................................................... ActionListener methods @@ -1418,18 +1432,18 @@ public MosaicJCredits ( pack(); GUI.center(this); setVisible(true); -} /* end MosaicJCredits */ +} /* end ch.epfl.big.MosaicJCredits */ -} /* end class MosaicJCredits */ +} /* end class ch.epfl.big.MosaicJCredits */ /*==================================================================== -| MosaicJEdge +| ch.epfl.big.MosaicJEdge \===================================================================*/ class MosaicJEdge implements Comparable -{ /* begin class MosaicJEdge */ +{ /* begin class ch.epfl.big.MosaicJEdge */ /*.................................................................... private variables @@ -1454,7 +1468,7 @@ public MosaicJEdge ( this.source = source; this.target = target; this.edgeWeight = edgeWeight; -} /* end MosaicJEdge */ +} /* end ch.epfl.big.MosaicJEdge */ /*.................................................................... Comparable methods @@ -1567,16 +1581,16 @@ public void swap ( targetPoints = p; } /* end swap */ -} /* end class MosaicJEdge */ +} /* end class ch.epfl.big.MosaicJEdge */ /*==================================================================== -| MosaicJHierarchy +| ch.epfl.big.MosaicJHierarchy \===================================================================*/ class MosaicJHierarchy extends Component -{ /* begin class MosaicJHierarchy */ +{ /* begin class ch.epfl.big.MosaicJHierarchy */ /*.................................................................... private variables @@ -1600,7 +1614,7 @@ public MosaicJHierarchy ( final int reductionFactor ) { this.reductionFactor = reductionFactor; -} /* end MosaicJHierarchy */ +} /* end ch.epfl.big.MosaicJHierarchy */ /*------------------------------------------------------------------*/ public MosaicJHierarchy ( @@ -1616,7 +1630,7 @@ public MosaicJHierarchy ( thumb.getLocation().y * reductionFactor); thumb.setTrueLocation(trueLocation); createOutline(); -} /* end MosaicJHierarchy */ +} /* end ch.epfl.big.MosaicJHierarchy */ /*.................................................................... Component methods @@ -1892,10 +1906,10 @@ private boolean overlapContains ( return(inside); } /* end overlapContains */ -} /* end class MosaicJHierarchy */ +} /* end class ch.epfl.big.MosaicJHierarchy */ /*==================================================================== -| MosaicJPlayField +| ch.epfl.big.MosaicJPlayField \===================================================================*/ class MosaicJPlayField extends @@ -1905,7 +1919,7 @@ class MosaicJPlayField MouseListener, MouseMotionListener -{ /* begin class MosaicJPlayField */ +{ /* begin class ch.epfl.big.MosaicJPlayField */ /*.................................................................... private variables @@ -1939,7 +1953,7 @@ public MosaicJPlayField ( setLayout(this); addMouseListener(this); addMouseMotionListener(this); -} /* end MosaicJPlayField */ +} /* end ch.epfl.big.MosaicJPlayField */ /*.................................................................... Component methods @@ -2706,10 +2720,10 @@ private void select ( repaint(bounds.x, bounds.y, bounds.width, bounds.height); } /* end select */ -} /* end class MosaicJPlayField */ +} /* end class ch.epfl.big.MosaicJPlayField */ /*==================================================================== -| MosaicJStatus +| ch.epfl.big.MosaicJStatus \===================================================================*/ class MosaicJStatus extends @@ -2717,7 +2731,7 @@ class MosaicJStatus implements ActionListener -{ /* begin class MosaicJStatus */ +{ /* begin class ch.epfl.big.MosaicJStatus */ /*.................................................................... private variables @@ -2783,7 +2797,7 @@ public MosaicJStatus ( GUI.center(this); setResizable(false); setVisible(true); -} /* end MosaicJStatus */ +} /* end ch.epfl.big.MosaicJStatus */ /*.................................................................... Subclasses @@ -2961,10 +2975,10 @@ private ImportPanel ( } /* end subclass ImportPanel */ -} /* end class MosaicJStatus */ +} /* end class ch.epfl.big.MosaicJStatus */ /*==================================================================== -| MosaicJThumb +| ch.epfl.big.MosaicJThumb \===================================================================*/ class MosaicJThumb extends @@ -2972,7 +2986,7 @@ class MosaicJThumb implements MouseListener -{ /* begin class MosaicJThumb */ +{ /* begin class ch.epfl.big.MosaicJThumb */ /*.................................................................... public variables @@ -3075,7 +3089,7 @@ public MosaicJThumb ( thumbnailArea.add(this); incrementScrollWidth(width); thumbnailArea.repaint(); -} /* end MosaicJThumb */ +} /* end ch.epfl.big.MosaicJThumb */ /*------------------------------------------------------------------*/ public MosaicJThumb ( @@ -3118,7 +3132,7 @@ public MosaicJThumb ( thumbnailArea.add(this); incrementScrollWidth(width); thumbnailArea.repaint(); -} /* end MosaicJThumb */ +} /* end ch.epfl.big.MosaicJThumb */ /*------------------------------------------------------------------*/ public MosaicJThumb ( @@ -3144,7 +3158,7 @@ public MosaicJThumb ( new ImageConverter(imp).convertRGBStackToRGB(); } final FloatProcessor fp = getGray32Processor(imp, slice, false); -} /* end MosaicJThumb */ +} /* end ch.epfl.big.MosaicJThumb */ /*.................................................................... JComponent methods @@ -4625,14 +4639,14 @@ private void symmetricFirMirrorOffBounds1D ( } } /* end symmetricFirMirrorOffBounds1D */ -} /* end class MosaicJThumb */ +} /* end class ch.epfl.big.MosaicJThumb */ /*==================================================================== -| MosaicJTree +| ch.epfl.big.MosaicJTree \===================================================================*/ class MosaicJTree -{ /*begin class MosaicJTree */ +{ /*begin class ch.epfl.big.MosaicJTree */ /*.................................................................... static public methods @@ -5629,5 +5643,4 @@ static private boolean pathExists ( } return(false); } /* end pathExists */ - -} /* end class MosaicJTree */ \ No newline at end of file +} /* end class ch.epfl.big.MosaicJTree */ \ No newline at end of file diff --git a/src/main/resources/plugins.config b/src/main/resources/plugins.config index b4cc76d..3c9d371 100644 --- a/src/main/resources/plugins.config +++ b/src/main/resources/plugins.config @@ -5,4 +5,4 @@ # P. Thevenaz, M. Unser # User-Friendly Semiautomated Assembly of Accurate Image Mosaics in Microscopy -Plugins>Stitching, "MosaicJ", MosaicJ_ +Plugins>Stitching, "MosaicJ", ch.epfl.big.MosaicJ_ diff --git a/src/test/java/ch/epfl/big/SimpleIJLaunch.java b/src/test/java/ch/epfl/big/SimpleIJLaunch.java new file mode 100644 index 0000000..e2ba0be --- /dev/null +++ b/src/test/java/ch/epfl/big/SimpleIJLaunch.java @@ -0,0 +1,26 @@ +package ch.epfl.big; + +import ij.IJ; +import ij.ImageJ; + + +/** + * + * To launch the plugin (for the layout bug) + * - Comment the lines 546-552 where the check of TurboReg is done + */ +public class SimpleIJLaunch { + public static void main(String[] args) { + + // set the plugins.dir property to make the plugin appear in the Plugins menu + Class clazz = MosaicJ_.class; + String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString(); + String pluginsDir = url.substring("file:".length(), url.length() - clazz.getName().length() - ".class".length()); + System.setProperty("plugins.dir", pluginsDir); + + // start ImageJ + new ImageJ(); + IJ.runPlugIn(clazz.getName(),""); + } + +}