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VA_gtmBrush.java
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VA_gtmBrush.java
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// Grount-Truth marking tool (brush)
// ImageJ-plugin by S.B
import ij.*;
import ij.gui.*;
import ij.io.*;
import ij.plugin.*;
import ij.plugin.tool.PlugInTool;
import ij.process.*;
import java.awt.*;
import java.awt.image.*;
import java.awt.event.*;
import java.io.*;
import java.util.Vector;
public class VA_gtmBrush extends PlugInTool implements Runnable, ImageListener {
private static final String BRUSH_WIDTH_KEY = "roibrushimg.width";
private static final String OVL_OPACITY_KEY = "roibrushimg.dencity";
private static final String EDAUTO_SAVE_KEY = "roibrushimg.autosave";
private static final String LOC_KEY = "roibrushimg.loc";
private static boolean SHAPE_ROI = true; // 'this-time-state choice' between ImageRoi and ShapeRoi
private boolean m_bAutoSave; // do auto-save by [<<] or [>>]
private int m_nWidth; // brush-width 1-100
private int m_nOpaci; // brush-opacity for ImageRoi 1-10
private ImagePlus m_OImp = null; // active frame (with some editable overlay)
private GenericDialog m_GD = null; // control dialog
private Button m_GDbtn1 = null, m_GDbtn2 = null, m_GDbtn3 = null; // control buttons
private String m_sDir = "", m_sName = "", m_sOvlPath = ""; // the files of active frame and coupled overlay
private boolean m_bUpdateRoi = false; // have updates for auto-save
private boolean m_bCurrentImage = false; // set by iCurrentImage; true if "environment_active_frame=OImp'
// services
private String iValidateAttributes() { // validate attributes of active frame
boolean qExists = (new File(m_sOvlPath)).exists();
if (m_GD!=null) {
m_GDbtn3.setEnabled( qExists );
};
return m_sDir+" \n"+m_sName+" ";
}
private String iGetBMPName() { // name.* => name.bmp
int qPosDot = m_sName.lastIndexOf( '.' ); if (qPosDot<0) qPosDot = m_sName.length();
// return m_sName.substring( 0, qPosDot )+".bmp";
return m_sName.substring( 0, qPosDot )+"_GT.bmp";
}
private void iSetAttributes( ImagePlus imp ) { // set attributes of active frame
if (imp!=null) { m_sDir = IJ.getDirectory( "current" ); m_sName = imp.getTitle(); m_sOvlPath = m_sDir+"GT"+File.separator+iGetBMPName(); }
else { m_sDir = m_sName = m_sOvlPath = ""; }
if (m_GD!=null) { MultiLineLabel qLabel = (MultiLineLabel)m_GD.getMessage(); if (qLabel!=null) qLabel.setText( iValidateAttributes() ); };
}
private void iAssignActiveFrame( ImagePlus imp ) { // set attributes and overlay for active frame
if (imp==null) { m_OImp = null; iSetAttributes( null ); }
else { imp.setRoi( (Roi)null ); imp.setOverlay( null );
iSetAttributes( imp ); iSetCurrentOverlay( imp ); imp.draw(); };
}
private ImagePlus iCurrentImage() { // returns environment_active_frame and sets bCurrentImage
ImagePlus qImp = WindowManager.getCurrentImage(); m_bCurrentImage = qImp!=null;
if (m_bCurrentImage && (m_OImp!=qImp)) m_bCurrentImage = false; return qImp;
}
// ImageListener interface
public void imageClosed( ImagePlus imp ) { if (m_sName==imp.getTitle() || m_OImp==imp) iAssignActiveFrame( null ); }
public void imageOpened( ImagePlus imp ) { iAssignActiveFrame( imp ); } // IJ.log( "imageOpened" );
public void imageUpdated( ImagePlus imp ) { /*if (m_OImp==imp) iAssignActiveFrame( imp ); */ } // IJ.log( "imageUpdated" );
// PluginTool services
private ImageRoi iGetImageRoi( Overlay ovl ) { // returns ImageRoi looking like 'native one from this module'
if (ovl==null || ovl.size()<1) return null;
Roi qRoi = ovl.get(0); if (!(qRoi instanceof ImageRoi)) return null;
return (ImageRoi)qRoi;
}
private void iSetCurrentOverlay( ImagePlus imp ) { // assign
m_OImp = imp; m_bUpdateRoi = false;
if (SHAPE_ROI) { // ShapeRoi
Roi qRoi = m_OImp.getRoi();
if (qRoi==null || !(qRoi instanceof ShapeRoi)) {
ImagePlus qOImp = (new Opener()).openImage( m_sOvlPath );
if (qOImp!=null) {
BinaryProcessor qIP = new BinaryProcessor( (ByteProcessor)qOImp.getProcessor() );
qIP.invert(); qOImp.setProcessor( qIP );
IJ.run( qOImp, "Create Selection", "" ); // it might take long time
m_OImp.setRoi( qOImp.getRoi() );
};
};
} // ShapeRoi
else { // ImageRoi
ImageRoi qOImageRoi = iGetImageRoi( m_OImp.getOverlay() );
if (qOImageRoi==null) {
ColorProcessor qOIPc = new ColorProcessor( m_OImp.getWidth(), m_OImp.getHeight() );
ImagePlus qOImp = (new Opener()).openImage( m_sOvlPath );
if (qOImp!=null) {
ByteProcessor qIP = qOImp.getProcessor().convertToByteProcessor();
qOIPc.setChannel( 1, qIP ); qOIPc.setChannel( 2, qIP ); // IJ.log( "- Overlay load for "+ m_sPath+m_sName );
};
qOImageRoi = new ImageRoi( 0, 0, qOIPc ); qOImageRoi.setOpacity( m_nOpaci/10.0 ); qOImageRoi.setZeroTransparent( true );
m_OImp.setOverlay( new Overlay(qOImageRoi) );
};
}; // ImageRoi
// m_OImageRoi.setOpacity( 1.0-m_nTrnsp/100.0 );
// qOImageRoiN.setStrokeColor( Color.yellow );
//m_OImageRoi.setStrokeWidth( 1 );
}
private void iUpdateROI( ImagePlus imp, MouseEvent e, boolean fromPressed ) {
if (SHAPE_ROI) { // ShapeRoi
ImageCanvas qIC = imp.getCanvas();
int qx = qIC.offScreenX(e.getX()), qy = qIC.offScreenY(e.getY());
ShapeRoi qBrushRoi = new ShapeRoi( new OvalRoi(qx-m_nWidth/2,qy-m_nWidth/2,m_nWidth,m_nWidth) );
Roi qRoi = imp.getRoi();
if (e.isAltDown()) {
if (qRoi!=null) {
IJ.showStatus( m_sName+" -" );
if (!(qRoi instanceof ShapeRoi)) qRoi = new ShapeRoi( qRoi );
((ShapeRoi)qRoi).not( qBrushRoi );
};
}
else {
IJ.showStatus( m_sName+" +" );
if (qRoi!=null) { if (!(qRoi instanceof ShapeRoi)) qRoi = new ShapeRoi( qRoi );
((ShapeRoi)qRoi).or( qBrushRoi ); }
else qRoi = qBrushRoi;
};
if (qRoi!=null) {
// qRoi.setStrokeWidth( 1 ); qRoi.setFillColor( Color.blue );
imp.setRoi( qRoi );
};
} // ShapeRoi
else { // ImageRoi
ImageRoi qImageRoi = iGetImageRoi( imp.getOverlay() ) ;
ImageProcessor qOIP = qImageRoi.getProcessor();
if (fromPressed) {
if (e.isAltDown()) { IJ.showStatus( m_sName+" -" ); qOIP.setColor( 0 ); }
else { IJ.showStatus( m_sName+" +" ); qOIP.setColor( Color.yellow ); };
};
ImageCanvas qIC = imp.getCanvas();
int qx = qIC.offScreenX(e.getX()), qy = qIC.offScreenY(e.getY());
qOIP.setLineWidth( m_nWidth ); if (fromPressed) qOIP.moveTo( qx, qy ); qOIP.lineTo( qx, qy );
qImageRoi.setProcessor( qOIP ); imp.draw();
}; // ImageRoi
}
// PluginTool interface
public void run( String AArg ) {
m_nWidth = Prefs.getInt( BRUSH_WIDTH_KEY, 10 );
m_nOpaci = Prefs.getInt( OVL_OPACITY_KEY, 5 );
m_bAutoSave = Prefs.getBoolean( EDAUTO_SAVE_KEY, true );
Toolbar.addPlugInTool( this );
}
public void mousePressed( ImagePlus imp, MouseEvent e ) { iSetAttributes( imp ); iSetCurrentOverlay( imp ); iUpdateROI( imp, e, true ); }
public void mouseDragged( ImagePlus imp, MouseEvent e ) { m_bUpdateRoi = true; iUpdateROI( imp, e, false ); }
public void mouseReleased( ImagePlus imp, MouseEvent e ) { }
public String getToolName() { return "gtmBrush"; }
public String getToolIcon() { return "Cff0O11ffCcc1V66ff"; }
public void showPopupMenu( java.awt.event.MouseEvent e, Toolbar tb ) { // IJ.log( "showPopupMenu "+Toolbar.getToolName() );
ImagePlus qImp = iCurrentImage(); iAssignActiveFrame( qImp );
if (qImp!=null) showOptionsDialog();
else
if (m_GD!=null)
IJ.showMessage( "gtmBrush", "Close Control Options' dialog to preset Opacity" );
else {
GenericDialog qGD = new GenericDialog( "gtmBrush preset Opacity" );
qGD.addNumericField( "0:'ShapeRoi', 1-10:'ImageRoi'", SHAPE_ROI?0:m_nOpaci, 0 ); qGD.showDialog();
if (!qGD.wasCanceled()) {
int qOpaci = (int)qGD.getNextNumber();
if (!qGD.invalidNumber())
if (qOpaci<1 || qOpaci>10) SHAPE_ROI = true;
else { SHAPE_ROI = false; m_nOpaci = qOpaci; Prefs.set( OVL_OPACITY_KEY, m_nOpaci ); }
};
};
}
// modeless dialog
public void run() { new Options( this ); } // called by showOptionsDialog
public void showOptionsDialog() {
Thread qT = new Thread( this, "gtmBrush Control Options" ); qT.setPriority( Thread.MIN_PRIORITY ); qT.start();
}
class Options implements DialogListener {
private VA_gtmBrush m_Owner; // the owner
Options( VA_gtmBrush AOwner ) { m_Owner = AOwner; if (m_GD!=null) m_GD.toFront(); else showDialog(); }
private void iSaveCurrent( boolean AExplicit ) { // saves coupled overlay
m_bUpdateRoi = false;
int qPosFSep = m_sOvlPath.lastIndexOf( File.separator );
if (qPosFSep<0 || m_OImp==null) { if (AExplicit) IJ.error( "Nothing to save" ); }
else { // attributes are Ok
File qNewDir = new File( m_sOvlPath.substring(0,qPosFSep+1) );
if (!qNewDir.exists() && !qNewDir.mkdirs()) IJ.error( "Can't create "+qNewDir.getName() );
else { // couple-directory is Ok
ImageProcessor qIP;
if (SHAPE_ROI) { // ShapeRoi
qIP = new ByteProcessor( m_OImp.getWidth(), m_OImp.getHeight() );
ShapeRoi qRoi = (ShapeRoi)m_OImp.getRoi();
if (qRoi!=null) { Rectangle qB = qRoi.getBounds(); qIP.copyBits( qRoi.getMask(), qB.x, qB.y, Blitter.COPY ); }
else IJ.log( "WRN: save empty BMP for ShapeRoi=null" );
} // ShapeRoi
else { // ImageRoi
qIP = iGetImageRoi( m_OImp.getOverlay() ).getProcessor().convertToByteProcessor();
qIP.threshold( 1 );
}; // ImageRoi
ImagePlus qImp = new ImagePlus( m_Owner.iGetBMPName(), qIP );
FileSaver qFS = new FileSaver( qImp ); // qImp.show();
if (!qFS.saveAsBmp( m_sOvlPath )) IJ.error( "Can't save "+m_sOvlPath ); // IJ.log( "Save "+qS ); //???
else iSetAttributes( null );
}; // couple-directory is Ok
}; // attributes are Ok
}
public void showDialog() {
m_GD = new NonBlockingGenericDialog( "gtmBrush Control Options" );
m_GDbtn1 = new Button( "Reload" );
m_GDbtn1.addActionListener( new ActionListener(){ public void actionPerformed( ActionEvent e ) {
m_OImp.setRoi( (Roi)null ); m_OImp.setOverlay( null ); iAssignActiveFrame( m_OImp );
}; } ); // btn1.Listener
m_GDbtn2 = new Button( " Save " );
m_GDbtn2.addActionListener( new ActionListener(){ public void actionPerformed( ActionEvent e ) {
iSaveCurrent( true );
}; } ); // btn2.Listener
m_GDbtn3 = new Button( "Delete" );
m_GDbtn3.addActionListener( new ActionListener(){ public void actionPerformed( ActionEvent e ) {
if (!(new File(m_sOvlPath)).delete()) IJ.error( "can't delete "+m_sOvlPath );
else { m_OImp.setRoi( (Roi)null ); m_OImp.setOverlay( null ); iAssignActiveFrame( m_OImp ); };
}; } ); // btn3.Listener
Button qBtn4 = new Button( " << " );
qBtn4.addActionListener( new ActionListener(){ public void actionPerformed( ActionEvent e ) {
if (m_bAutoSave && m_bUpdateRoi) iSaveCurrent( false );
(new NextImageOpener()).run( "backwardsc" ); iAssignActiveFrame( iCurrentImage() );
}; } ); // btn4.Listener
Button qBtn5 = new Button( " >> " );
qBtn5.addActionListener( new ActionListener(){ public void actionPerformed( ActionEvent e ) {
if (m_bAutoSave && m_bUpdateRoi) iSaveCurrent( false );
(new NextImageOpener()).run( "forwardsc" ); iAssignActiveFrame( iCurrentImage() );
}; } ); // btn5.Listener
// non-functional layout just for for interior
final Panel qBtnPan = new Panel();
GridBagLayout qGBL = new GridBagLayout(); qBtnPan.setLayout( qGBL );
GridBagConstraints qGBC = new GridBagConstraints(); qGBC.anchor = GridBagConstraints.WEST;
qGBC.insets = new Insets(0,0,0, 5); qGBL.setConstraints( m_GDbtn1, qGBC ); qBtnPan.add( m_GDbtn1 );
qGBC.insets = new Insets(0,0,0, 5); qGBL.setConstraints( m_GDbtn2, qGBC ); qBtnPan.add( m_GDbtn2 );
qGBC.insets = new Insets(0,0,0,15); qGBL.setConstraints( m_GDbtn3, qGBC ); qBtnPan.add( m_GDbtn3 );
qGBC.insets = new Insets(0,0,0, 5); qGBL.setConstraints( qBtn4, qGBC ); qBtnPan.add( qBtn4 );
qGBC.insets = new Insets(0,0,0, 5); qGBL.setConstraints( qBtn5, qGBC ); qBtnPan.add( qBtn5 );
m_GD.addPanel( qBtnPan, GridBagConstraints.WEST, new Insets(0,0,0,0) );
qGBL = (GridBagLayout)m_GD.getLayout();
qGBC = qGBL.getConstraints( qBtnPan ); qGBC.gridx = 1;
qGBL.setConstraints( qBtnPan, qGBC );
// sliders
m_GD.addCheckbox( "Auto-save", m_bAutoSave );
m_GD.addSlider( "Width", 1, 100, m_nWidth );
if (!SHAPE_ROI) m_GD.addSlider( "Opacity", 1, 10, m_nOpaci ); // for ImageRoi
// standard buttons
m_GD.setInsets( 10, 10, 0 ); m_GD.addMessage( iValidateAttributes(), null, Color.darkGray );
m_GD.hideCancelButton(); m_GD.setOKLabel( "Close" );
m_GD.addHelp(
"<html><h2>ground-truth marking Brush</h2><font size=-1>"+
"This brush draws (erases when key 'ALT' is pressed) an 'overlay' associated with './GT/CurrentImage.bmp'<br>"+
"'CurrentImage.ext' remains unchanged. Do not operate with 'overlays' manually when this tool is active.<br>"+
"<font color=blue>[Reload]</font> reloads 'overlay'<br>"+
"<font color=blue>[Save]</font> saves 'overlay'<br>"+
"<font color=red>[Delete]</font> deletes 'overlay'<br>"+
"<font color=blue>[<<]</font> open Previous'<br>"+
"<font color=blue>[>>]</font> open Next'<br>"+
"</font>" );
// show the dialog
//iSetAttributes( null );
m_GD.addDialogListener( this );
Point qLoc = Prefs.getLocation( LOC_KEY );
if (qLoc!=null) { m_GD.centerDialog( false ); m_GD.setLocation( qLoc ); }
ImagePlus.addImageListener( m_Owner );
m_GD.showDialog();
ImagePlus.removeImageListener( m_Owner );
Prefs.saveLocation( LOC_KEY, m_GD.getLocation() );
m_GDbtn1 = m_GDbtn2 = m_GDbtn3 = null; m_GD = null;
iAssignActiveFrame( null );
}
public boolean dialogItemChanged( GenericDialog m_GD, AWTEvent e ) {
m_nWidth = (int)m_GD.getNextNumber(); if (m_GD.invalidNumber() || m_nWidth<1 || m_nWidth>100) m_nWidth = 10;
Prefs.set( BRUSH_WIDTH_KEY, m_nWidth );
if (!SHAPE_ROI) { // for ImageRoi
int qOpaci = (int)m_GD.getNextNumber(); if (m_GD.invalidNumber() || qOpaci<1 || qOpaci>10) qOpaci = 5;
if (m_nOpaci!=qOpaci) { m_nOpaci = qOpaci;
ImagePlus qImp = iCurrentImage();
if (m_bCurrentImage) { iGetImageRoi(qImp.getOverlay()).setOpacity( m_nOpaci/10.0 ); qImp.draw(); };
};
};
m_bAutoSave = m_GD.getNextBoolean(); Prefs.set( EDAUTO_SAVE_KEY, m_bAutoSave );
return true;
}
} // of modeless dialog
} // end of public class VA_gtmBrush