Java IOFunctions.println方法代碼示例

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
public static void removeInconsistentLinks(
		final Collection< Pair< Group< ViewId >, Group< ViewId > > > removedInconsistentPairs,
		final Map< Pair< Group< ViewId >, Group< ViewId > >, ? > stitchingResults )
{
	for ( final Pair< Group< ViewId >, Group< ViewId > > inconsistentPair : removedInconsistentPairs )
	{
		final Pair< Group< ViewId >, Group< ViewId > > reverseInconsistentPair = TransformationTools.reversePair( inconsistentPair );

		if ( stitchingResults.containsKey( inconsistentPair ) )
			stitchingResults.remove( inconsistentPair );
		else if ( stitchingResults.containsKey( reverseInconsistentPair ) )
			stitchingResults.remove( reverseInconsistentPair );
		else
			IOFunctions.println( "ERROR: Could not remove one of the links that was removed by the global optimization. This is not critical, but shouldn't happen." );
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
public MappingFusionParalell( final ViewStructure viewStructure, final ViewStructure referenceViewStructure,
							  final ArrayList<IsolatedPixelWeightenerFactory<?>> isolatedWeightenerFactories,
							  final ArrayList<CombinedPixelWeightenerFactory<?>> combinedWeightenerFactories )
{
	super( viewStructure, referenceViewStructure, isolatedWeightenerFactories, combinedWeightenerFactories );


	if ( viewStructure.getDebugLevel() <= ViewStructure.DEBUG_MAIN )
		IOFunctions.println("(" + new Date(System.currentTimeMillis()) + "): Reserving memory for fused image.");

	final ImageFactory<FloatType> fusedImageFactory = new ImageFactory<FloatType>( new FloatType(), conf.processImageFactory );
	fusedImage = fusedImageFactory.createImage( new int[]{ imgW, imgH, imgD }, "Fused image");

	if (fusedImage == null)
	{
		if ( viewStructure.getDebugLevel() <= ViewStructure.DEBUG_ERRORONLY )
			IOFunctions.println("MappingFusionParalell.constructor: Cannot create output image: " + conf.processImageFactory.getErrorMessage());

		return;
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
public static String saveXML( final SpimData2 data, final String xmlFileName, final String clusterExtension  )
{
	// save the xml
	final XmlIoSpimData2 io = new XmlIoSpimData2( clusterExtension );
	
	final String xml = new File( data.getBasePath(), new File( xmlFileName ).getName() ).getAbsolutePath();
	try 
	{
		io.save( data, xml );
		IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + "): Saved xml '" + io.lastFileName() + "'." );
		return xml;
	}
	catch ( Exception e )
	{
		IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + "): Could not save xml '" + io.lastFileName() + "': " + e );
		e.printStackTrace();
		return null;
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
protected File queryCZIFile()
{
	GenericDialogPlus gd = new GenericDialogPlus( "Define Lightsheet Z.1 Dataset" );

	gd.addFileField( "First_CZI file of the dataset", defaultFirstFile, 50 );

	gd.showDialog();

	if ( gd.wasCanceled() )
		return null;

	final File firstFile = new File( defaultFirstFile = gd.getNextString() );

	if ( !firstFile.exists() )
	{
		IOFunctions.println( "File '" + firstFile.getAbsolutePath() + "' does not exist. Stopping" );
		return null;
	}
	else
	{
		IOFunctions.println( "Investigating file '" + firstFile.getAbsolutePath() + "'." );
		return firstFile;
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
public SPIMImageFusion( ViewStructure viewStructure, ViewStructure referenceViewStructure, 
		 			    ArrayList<IsolatedPixelWeightenerFactory<?>> isolatedWeightenerFactories, 
		 			    ArrayList<CombinedPixelWeightenerFactory<?>> combinedWeightenerFactories )
{
	this.conf = viewStructure.getSPIMConfiguration();
	this.viewStructure = viewStructure;
	this.scale = conf.scale;
	this.isolatedWeightenerFactories = isolatedWeightenerFactories;
	this.combinedWeightenerFactories = combinedWeightenerFactories;
	
	// compute the final image size
	computeFinalImageSize( referenceViewStructure.getViews() );
	
	// compute cropped image size
	initFusion();
	
	// compute location of point (0,0,0) in the global coordinate system
	location000 = new Point3f();
	location000.x = cropOffsetX * scale + min.x;
	location000.y = cropOffsetY * scale + min.y;
	location000.z = cropOffsetZ * scale + min.z;
	
	if ( viewStructure.getDebugLevel() <= ViewStructure.DEBUG_MAIN )
		IOFunctions.println( "Location of pixel (0,0,0) in global coordinates is: " + location000 );
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
@Override
public boolean queryParameters( final SpimData2 spimData, final boolean is16bit )
{
	if ( newTimepoints == null || newViewSetups == null )
	{
		IOFunctions.println( "new timepoints and new viewsetup list not set yet ... cannot continue" );
		return false;
	}

	if ( Resave_TIFF.defaultPath == null )
		Resave_TIFF.defaultPath = "";
	
	this.params = Resave_TIFF.getParameters();
	
	if ( this.params == null )
		return false;

	this.saver = new Save3dTIFF( new File( this.params.getXMLFile() ).getParent(), this.params.compress() );
	this.saver.setImgTitler( new XMLTIFFImgTitler( newTimepoints, newViewSetups ) );

	this.spimData = createSpimData2( newTimepoints, newViewSetups, params );

	return true;
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
public PreviewRegistration( final ViewStructure viewStructure )
{
	final OutOfBoundsStrategyValueFactory<FloatType> outsideFactory = new OutOfBoundsStrategyValueFactory<FloatType>( new FloatType(0) );
	final InterpolatorFactory<FloatType> interpolatorFactory = new NearestNeighborInterpolatorFactory<FloatType>( outsideFactory );

	final ArrayList<InverseTransformDescription<FloatType>> list = new ArrayList<InverseTransformDescription<FloatType>>();
	
	for ( final ViewDataBeads view : viewStructure.getViews() )
	{
		if ( view.isConnected() )
		{
			InverseTransformDescription<FloatType> i = new InverseTransformDescription<FloatType>( (AbstractAffineModel3D<?>)view.getTile().getModel(), interpolatorFactory, view.getImage() );
			list.add( i );
		}
	}

	/*
	if ( list.size() > 0 )
		ImageJFunctions.displayAsVirtualStack( list, ImageJFunctions.GRAY32, new int[]{0,1,2}, new int[3] ).show();
	else
		if ( viewStructure.getDebugLevel() <= ViewStructure.DEBUG_ERRORONLY )*/
			IOFunctions.println("PreviewRegistration(): no view is connected to any other view, cannot display.");
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
@Override
public void actionPerformed( final ActionEvent e )
{
	if ( panel == null )
	{
		IOFunctions.println( "Panel not set for " + this.getClass().getSimpleName() );
		return;
	}

	((StitchingExplorerPanel< ?, ? >) panel).togglePreviewMode(false);
	
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
@Override
public void actionPerformed( final ActionEvent e )
{
	if ( panel == null )
	{
		IOFunctions.println( "Panel not set for " + this.getClass().getSimpleName() );
		return;
	}

	new Thread( new Runnable()
	{
		@Override
		public void run()
		{
			// if BDV was closed by the user
			if ( bdv != null && !bdv.getViewerFrame().isVisible() )
				bdv = null;

			if ( bdv == null )
			{

				try
				{
					bdv = createBDV( panel, lo );
				}
				catch (Exception ex)
				{
					IOFunctions.println( "Could not run BigDataViewer: " + ex );
					ex.printStackTrace( System.err );
					bdv = null;
				}
			}
			else
			{
				closeBDV();
			}
		}
	}).start();
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
@Override
public void saveXML()
{
	try
	{
		io.save( data, xml );

		for ( final SelectedViewDescriptionListener< AS > l : listeners )
			l.save();

		if ( SpimData2.class.isInstance( data ) )
		{
			final ViewInterestPoints vip = ( (SpimData2) data ).getViewInterestPoints();

			for ( final ViewInterestPointLists vipl : vip.getViewInterestPoints().values() )
			{
				for ( final String label : vipl.getHashMap().keySet() )
				{
					final InterestPointList ipl = vipl.getInterestPointList( label );
					ipl.saveInterestPoints( false );
					ipl.saveCorrespondingInterestPoints( false );
				}
			}
		}

		IOFunctions.println( "Saved XML '" + xml + "'." );
	}
	catch ( SpimDataException e )
	{
		IOFunctions.println( "Failed to save XML '" + xml + "': " + e );
		e.printStackTrace();
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
public boolean saveCorrespondingInterestPoints()
{
	final List< CorrespondingInterestPoints > list = getCorrespondingInterestPoints();
	
	if ( list == null )
		return false;
	
	try
	{
		final File dir = new File( getBaseDir(), getFile().getParent() );
		
		if ( !dir.exists() )
		{
			IOFunctions.println( "Creating directory: " + dir );
			dir.mkdirs();
		}
		
		PrintWriter out = TextFileAccess.openFileWriteEx( new File( getBaseDir(), getFile().toString() + getCorrespondencesExt() ) );
		
		// header
		out.println( "id" + "\t" + "corresponding_timepoint_id" + "\t" + "corresponding_viewsetup_id" + "\t" + "corresponding_label" + "\t" + "corresponding_id" );
		
		// id of the interestpoint from this List && for the corresponding interestpoint viewid(timepointId, viewsetupId), label, and id
		for ( final CorrespondingInterestPoints p : list )
			out.println( p.getDetectionId() + "\t" + p.getCorrespondingViewId().getTimePointId() + "\t" + p.getCorrespondingViewId().getViewSetupId() + "\t" + p.getCorrespodingLabel() + "\t" + p.getCorrespondingDetectionId() );
					
		out.close();
		
		return true;
	}
	catch ( final IOException e )
	{
		IOFunctions.println( "InterestPointList.saveCorrespondingInterestPoints(): " + e );
		e.printStackTrace();
		return false;
	}				
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
@Override
public void actionPerformed( final ActionEvent arg0 )
{
	final Roi roi = imp.getRoi();

	if ( roi == null )
	{
		IOFunctions.println( "No ROI selected in max projection image." );
	}
	else
	{
		int count = ipList.size();

		for ( int i = ipList.size() - 1; i >= 0; --i )
		{
			final double[] l = ipList.get( i ).getL();

			final boolean contains = roi.contains( (int)Math.round( l[ xDim ] ), (int)Math.round( l[ yDim ] ) );
			
			if ( inside && contains || !inside && !contains )
				ipList.remove( i );
		}

		drawProjectedInterestPoints( imp, ipList, projectionDim );

		IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + ": " + ipList.size() + " points remaining, removed " + (count - ipList.size()) + " points ... " );
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
@Override
public void actionPerformed( final ActionEvent e )
{
	if ( panel == null )
	{
		IOFunctions.println( "Panel not set for " + this.getClass().getSimpleName() );
		return;
	}

	if ( !SpimData2.class.isInstance( panel.getSpimData() ) )
	{
		IOFunctions.println( "Only supported for SpimData2 objects: " + this.getClass().getSimpleName() );
		return;
	}

	new Thread( new Runnable()
	{
		@Override
		public void run()
		{
			if ( new Interest_Point_Registration().register( (SpimData2)panel.getSpimData(), panel.selectedRowsViewId() ) )
			{
				panel.updateContent(); // update interestpoint and registration panel if available
				ViewSetupExplorerPanel.bdvPopup().updateBDV();
			}
		}
	} ).start();
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
public double getViewSpecificError ( final ViewDataBeads otherView )
{
	boolean foundView = false;
	
	for( ViewErrorPairWise viewError : connectedViews )
		if ( viewError.getView() == otherView )
			return viewError.getAvgError();

	if ( !foundView && view.getViewStructure().getDebugLevel() <= ViewStructure.DEBUG_ERRORONLY )
		IOFunctions.println( "ViewErrorStatistics.getViewSpecificError(): Warning! " + otherView + " is not part of the structure of my view " + view );
	
	return -1;
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
public static void concatenateAxialScaling( final ArrayList<ViewDataBeads> views, final int debugLevel )
{
	if ( debugLevel <= ViewStructure.DEBUG_ALL )
		IOFunctions.println("----------------------Scaling corrected-------------------");
	
	//
	// update target registration
	//
	for ( final ViewDataBeads view : views)
		concatenateAxialScaling( view, debugLevel );		
}