Java ViewTransformAffine类代码示例

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
public static void setModelToCalibration( final SpimData spimData, final ViewId viewId, final double minResolution )
{
	setModelToIdentity( spimData, viewId );
	
	final ViewRegistrations viewRegistrations = spimData.getViewRegistrations();
	final ViewRegistration r = viewRegistrations.getViewRegistration( viewId );
	
	final ViewDescription viewDescription = spimData.getSequenceDescription().getViewDescription( 
			viewId.getTimePointId(), viewId.getViewSetupId() );

	VoxelDimensions voxelSize = ViewSetupUtils.getVoxelSizeOrLoad( viewDescription.getViewSetup(), viewDescription.getTimePoint(), spimData.getSequenceDescription().getImgLoader() );
	final double calX = voxelSize.dimension( 0 ) / minResolution;
	final double calY = voxelSize.dimension( 1 ) / minResolution;
	final double calZ = voxelSize.dimension( 2 ) / minResolution;
	
	final AffineTransform3D m = new AffineTransform3D();
	m.set( calX, 0.0f, 0.0f, 0.0f, 
		   0.0f, calY, 0.0f, 0.0f,
		   0.0f, 0.0f, calZ, 0.0f );
	final ViewTransform vt = new ViewTransformAffine( "calibration", m );
	r.preconcatenateTransform( vt );
}
 

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
@Override
public < T extends RealType< T > & NativeType< T > > boolean exportImage( final RandomAccessibleInterval<T> img, final BoundingBoxGUI bb, final TimePoint tp, final ViewSetup vs, final double min, final double max )
{
	if ( appendToHdf5 != null )
		return appendToHdf5.exportImage( img, bb, tp, vs, min, max );

	// write the image
	if ( !this.saver.exportImage( img, bb, tp, vs, min, max ) )
		return false;

	// update the registrations
	final ViewRegistration vr = spimData.getViewRegistrations().getViewRegistration( new ViewId( tp.getId(), vs.getId() ) );

	final double scale = bb.getDownSampling();
	final AffineTransform3D m = new AffineTransform3D();
	m.set( scale, 0.0f, 0.0f, bb.min( 0 ),
		   0.0f, scale, 0.0f, bb.min( 1 ),
		   0.0f, 0.0f, scale, bb.min( 2 ) );
	final ViewTransform vt = new ViewTransformAffine( "fusion bounding box", m );

	vr.getTransformList().clear();
	vr.getTransformList().add( vt );

	return true;
}
 

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
@Override
public < T extends RealType< T > & NativeType< T > > boolean exportImage( final RandomAccessibleInterval<T> img, final BoundingBoxGUI bb, final TimePoint tp, final ViewSetup vs, final double min, final double max )
{
	// write the image
	if ( !this.saver.exportImage( img, bb, tp, vs, min, max ) )
		return false;

	// update the registrations
	final ViewRegistration vr = spimData.getViewRegistrations().getViewRegistration( new ViewId( tp.getId(), vs.getId() ) );
	
	final double scale = bb.getDownSampling();
	final AffineTransform3D m = new AffineTransform3D();
	m.set( scale, 0.0f, 0.0f, bb.min( 0 ), 
		   0.0f, scale, 0.0f, bb.min( 1 ),
		   0.0f, 0.0f, scale, bb.min( 2 ) );
	final ViewTransform vt = new ViewTransformAffine( "fusion bounding box", m );

	vr.getTransformList().clear();
	vr.getTransformList().add( vt );
	
	return true;
}
 

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
public static ViewRegistrations createViewRegistrations()
{
	final HashMap< ViewId, ViewRegistration > registrations = new HashMap< ViewId, ViewRegistration >();

	registrations.put( new ViewId( 21, 1 ), new ViewRegistration( 21, 1 ) );

	final AffineTransform3D t00 = new AffineTransform3D();
	t00.set( 1, 0, 0, 1.3, 0, 1, 0, 1.3, 0, 0, 1, 2.3 );
	registrations.put( new ViewId( 1, 0 ), new ViewRegistration( 0, 0, t00 ) );

	final ArrayList< ViewTransform > list = new ArrayList< ViewTransform >();
	list.add( new ViewTransformAffine( null, t00 ) );
	list.add( new ViewTransformAffine( "identity", new AffineTransform3D() ) );
	registrations.put( new ViewId( 41, 1 ), new ViewRegistration( 41, 1, list ) );

	final ViewRegistrations viewRegistrations = new ViewRegistrations( registrations );
	return viewRegistrations;
}
 

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
public static void preConcatenateTransform( final SpimData spimData, final ViewId viewId, final AffineTransform3D model, final String name )
{
	final ViewRegistrations viewRegistrations = spimData.getViewRegistrations();

	// update the view registration
	final ViewRegistration vr = viewRegistrations.getViewRegistration( viewId );
	final ViewTransform vt = new ViewTransformAffine( name, model );
	vr.preconcatenateTransform( vt );
}
 

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
/**
 * Assembles the {@link ViewRegistration} object consisting of a list of {@link ViewRegistration}s for all {@link ViewDescription}s that are present
 * 
 * @param viewDescriptionList
 * @param minResolution - the smallest resolution in any dimension (distance between two pixels in the output image will be that wide)
 * @return
 */
protected static ViewRegistrations createViewRegistrations( final Map< ViewId, ViewDescription > viewDescriptionList, final double minResolution )
{
	final HashMap< ViewId, ViewRegistration > viewRegistrationList = new HashMap< ViewId, ViewRegistration >();
	
	for ( final ViewDescription viewDescription : viewDescriptionList.values() )
		if ( viewDescription.isPresent() )
		{
			final ViewRegistration viewRegistration = new ViewRegistration( viewDescription.getTimePointId(), viewDescription.getViewSetupId() );
			
			final VoxelDimensions voxelSize = viewDescription.getViewSetup().getVoxelSize(); 

			final double calX = voxelSize.dimension( 0 ) / minResolution;
			final double calY = voxelSize.dimension( 1 ) / minResolution;
			final double calZ = voxelSize.dimension( 2 ) / minResolution;
			
			final AffineTransform3D m = new AffineTransform3D();
			m.set( calX, 0.0f, 0.0f, 0.0f, 
				   0.0f, calY, 0.0f, 0.0f,
				   0.0f, 0.0f, calZ, 0.0f );
			final ViewTransform vt = new ViewTransformAffine( "calibration", m );
			viewRegistration.preconcatenateTransform( vt );
			
			viewRegistrationList.put( viewRegistration, viewRegistration );
		}
	
	return new ViewRegistrations( viewRegistrationList );
}
 

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
protected static ViewTransform duplicate( final ViewTransform vt )
{
	final AffineTransform3D t = new AffineTransform3D();
	t.set( vt.asAffine3D().getRowPackedCopy() );
	
	return new ViewTransformAffine( vt.getName(), t );
}
 

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
protected static ViewTransform newName( final ViewTransform vt, final String name )
{
	final AffineTransform3D t = new AffineTransform3D();
	t.set( vt.asAffine3D().getRowPackedCopy() );
	
	return new ViewTransformAffine( name, t );
}
 

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
protected static ViewTransform newMatrixEntry( final ViewTransform vt, final double value, final int index )
{
	final AffineTransform3D t = new AffineTransform3D();
	final double[] m = vt.asAffine3D().getRowPackedCopy();
	m[ index ] = value;
	t.set( m );
	
	return new ViewTransformAffine( vt.getName(), t );
}
 

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
protected void delete()
{
	if ( table.getSelectedRowCount() == 0 )
	{
		JOptionPane.showMessageDialog( table, "Nothing selected." );
		return;
	}

	final BasicViewDescription< ? > vd = tableModel.getCurrentViewDescription();

	if ( vd == null )
	{
		JOptionPane.showMessageDialog( table, "No active viewdescription." );
		return;
	}

	final int[] selectedRows = table.getSelectedRows();
	Arrays.sort( selectedRows );

	final ViewRegistration vr = tableModel.getViewRegistrations().getViewRegistration( vd );

	for ( int i = selectedRows[ selectedRows.length - 1 ]; i >= selectedRows[ 0 ]; --i )
		vr.getTransformList().remove( i );

	if  ( vr.getTransformList().isEmpty() )
		vr.getTransformList().add( new ViewTransformAffine( null, new AffineTransform3D() ) );

	vr.updateModel();

	// update everything
	tableModel.fireTableDataChanged();
}
 

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
@SuppressWarnings({ "rawtypes", "unchecked" })
@Override
public < T extends RealType< T > & NativeType< T > > boolean exportImage( RandomAccessibleInterval< T > img, BoundingBoxGUI bb, TimePoint tp, ViewSetup vs, double min, double max )
{
	System.out.println( "exportImage2()" );

	// write the image
	final RandomAccessibleInterval< UnsignedShortType > ushortimg;
	if ( ! UnsignedShortType.class.isInstance( Util.getTypeFromInterval( img ) ) )
		ushortimg = convert( img, params );
	else
		ushortimg = ( RandomAccessibleInterval ) img;
	final Partition partition = viewIdToPartition.get( new ViewId( tp.getId(), vs.getId() ) );
	final ExportMipmapInfo mipmapInfo = perSetupExportMipmapInfo.get( vs.getId() );
	final boolean writeMipmapInfo = true; // TODO: remember whether we already wrote it and write only once
	final boolean deflate = params.getDeflate();
	final ProgressWriter progressWriter = new SubTaskProgressWriter( this.progressWriter, 0.0, 1.0 ); // TODO
	final int numThreads = Math.max( 1, Runtime.getRuntime().availableProcessors() - 2 );
	WriteSequenceToHdf5.writeViewToHdf5PartitionFile( ushortimg, partition, tp.getId(), vs.getId(), mipmapInfo, writeMipmapInfo, deflate, null, null, numThreads, progressWriter );

	// update the registrations
	final ViewRegistration vr = spimData.getViewRegistrations().getViewRegistration( new ViewId( tp.getId(), vs.getId() ) );

	final double scale = bb.getDownSampling();
	final AffineTransform3D m = new AffineTransform3D();
	m.set( scale, 0.0f, 0.0f, bb.min( 0 ),
		   0.0f, scale, 0.0f, bb.min( 1 ),
		   0.0f, 0.0f, scale, bb.min( 2 ) );
	final ViewTransform vt = new ViewTransformAffine( "fusion bounding box", m );

	vr.getTransformList().clear();
	vr.getTransformList().add( vt );

	return true;
}
 

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
@SuppressWarnings( { "unchecked", "rawtypes" } )
@Override
public < T extends RealType< T > & NativeType< T > > boolean exportImage( RandomAccessibleInterval< T > img, BoundingBoxGUI bb, TimePoint tp, ViewSetup vs, double min, double max )
{
	System.out.println( "exportImage2()" );

	// write the image
	final RandomAccessibleInterval< UnsignedShortType > ushortimg;
	if ( ! UnsignedShortType.class.isInstance( Util.getTypeFromInterval( img ) ) )
		ushortimg = ExportSpimData2HDF5.convert( img, params );
	else
		ushortimg = ( RandomAccessibleInterval ) img;

	final Partition partition = viewIdToPartition.get( new ViewId( tp.getId(), vs.getId() ) );
	final ExportMipmapInfo mipmapInfo = perSetupExportMipmapInfo.get( vs.getId() );
	final boolean writeMipmapInfo = true; // TODO: remember whether we already wrote it and write only once
	final boolean deflate = params.getDeflate();
	final ProgressWriter progressWriter = new SubTaskProgressWriter( this.progressWriter, 0.0, 1.0 ); // TODO
	final int numThreads = Math.max( 1, Runtime.getRuntime().availableProcessors() - 2 );
	WriteSequenceToHdf5.writeViewToHdf5PartitionFile( ushortimg, partition, tp.getId(), vs.getId(), mipmapInfo, writeMipmapInfo, deflate, null, null, numThreads, progressWriter );

	// update the registrations
	final ViewRegistration vr = spimData.getViewRegistrations().getViewRegistration( new ViewId( tp.getId(), vs.getId() ) );

	final double scale = bb.getDownSampling();
	final AffineTransform3D m = new AffineTransform3D();
	m.set( scale, 0.0f, 0.0f, bb.min( 0 ),
		   0.0f, scale, 0.0f, bb.min( 1 ),
		   0.0f, 0.0f, scale, bb.min( 2 ) );
	final ViewTransform vt = new ViewTransformAffine( "fusion bounding box", m );

	vr.getTransformList().clear();
	vr.getTransformList().add( vt );

	return true;
}
 

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
public static SpimData twoAngles()
{
	final ArrayList< ViewSetup > setups = new ArrayList< ViewSetup >();
	final ArrayList< ViewRegistration > registrations = new ArrayList< ViewRegistration >();

	final Channel c0 = new Channel( 0, "test" );
	final Angle a0 = new Angle( 0 );
	final Angle a1 = new Angle( 1 );
	final Illumination i0 = new Illumination( 0 );

	final Dimensions d0 = new FinalDimensions( 512l, 512l, 86l );
	final VoxelDimensions vd0 = new FinalVoxelDimensions( "px", 0.4566360, 0.4566360, 2.0000000 );

	setups.add( new ViewSetup( 0, "setup 0", d0, vd0, c0, a0, i0 ) );
	setups.add( new ViewSetup( 1, "setup 1", d0, vd0, c0, a1, i0 ) );

	final ArrayList< TimePoint > t = new ArrayList< TimePoint >();
	t.add( new TimePoint( 0 ) );
	final TimePoints timepoints = new TimePoints( t );

	final ArrayList< ViewId > missing = new ArrayList< ViewId >();
	final MissingViews missingViews = new MissingViews( missing );

	final ImgLoader imgLoader = new ImgLoader()
	{
		@Override
		public SetupImgLoader< ? > getSetupImgLoader( int setupId )
		{
			return new MySetupImgLoader( setupId );
		}
	};

	for ( final ViewSetup vs : setups )
	{
		final ViewRegistration vr = new ViewRegistration( t.get( 0 ).getId(), vs.getId() );

		final double minResolution = Math.min( Math.min( vs.getVoxelSize().dimension( 0 ), vs.getVoxelSize().dimension( 1 ) ), vs.getVoxelSize().dimension( 2 ) );
		
		final double calX = vs.getVoxelSize().dimension( 0 ) / minResolution;
		final double calY = vs.getVoxelSize().dimension( 1 ) / minResolution;
		final double calZ = vs.getVoxelSize().dimension( 2 ) / minResolution;
		
		final AffineTransform3D m = new AffineTransform3D();
		m.set( calX, 0.0f, 0.0f, 0.0f, 
			   0.0f, calY, 0.0f, 0.0f,
			   0.0f, 0.0f, calZ, 0.0f );
		final ViewTransform vt = new ViewTransformAffine( "Calibration", m );
		vr.preconcatenateTransform( vt );

		vr.updateModel();		
		
		registrations.add( vr );
	}

	final SequenceDescription sd = new SequenceDescription( timepoints, setups, imgLoader, missingViews );
	final SpimData data = new SpimData( new File( "" ), sd, new ViewRegistrations( registrations ) );

	return data;
}
 

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
public static void applyToData(Map<ViewId, Translation3D> locations, boolean pixelUnits, boolean keepRotation,
		AbstractSpimData< ? > data)
{
	if (data == null)
		return;
	final Map< ViewId, Translation3D > transformsForData = getTransformsForData( locations, pixelUnits, data );
	final Collection< BasicViewDescription< ? > > vds = (Collection< BasicViewDescription< ? > >) data.getSequenceDescription().getViewDescriptions().values();

	for ( BasicViewDescription< ? > vd : vds )
	{
		if (!vd.isPresent())
			continue;

		if (!transformsForData.containsKey( vd ))
			continue;

		final ViewRegistration vr = data.getViewRegistrations().getViewRegistration( vd );

		final ViewTransform vtCalib = vr.getTransformList().get( vr.getTransformList().size() - 1 );
		final AffineTransform3D calib = new AffineTransform3D();
		calib.set( vr.getTransformList().get( vr.getTransformList().size() - 1 ).asAffine3D().getRowPackedCopy() );

		vr.getTransformList().clear();
		vr.preconcatenateTransform( vtCalib );

		final AffineTransform3D tr = new AffineTransform3D();
		tr.set( transformsForData.get( vd ).getRowPackedCopy() );
		ViewTransformAffine vtTC = new ViewTransformAffine( "Translation from Tile Configuration", tr );
		vr.preconcatenateTransform( vtTC );

		if (keepRotation)
		{
			AffineTransform3D rotation = new AffineTransform3D();
			Pair< Double, Integer > rotAngleAndAxis = RegularTranformHelpers.getRoatationFromMetadata( vd.getViewSetup().getAttribute( Angle.class ) );
			if (rotAngleAndAxis != null)
			{
				rotation.rotate( rotAngleAndAxis.getB(), rotAngleAndAxis.getA() );
				vr.preconcatenateTransform( new ViewTransformAffine( "Rotation from Metadata", rotation.copy() ));
			}
		}
		vr.updateModel();
	}
}
 

import mpicbg.spim.data.registration.ViewTransformAffine; //导入依赖的package包/类
@Override
public void actionPerformed( final ActionEvent e )
{
	if ( panel == null )
	{
		IOFunctions.println( "Panel not set for " + this.getClass().getSimpleName() );
		return;
	}

	BigDataViewer bdv = panel.bdvPopup().getBDV();
	
	if (bdv == null)
	{
		IOFunctions.println( "BigDataViewer is not open. Please start it to access this functionality." );
		return;
	}			
	
	
	for (int i = 0; i < bdv.getViewer().getVisibilityAndGrouping().numSources(); ++i)
	{
		Integer tpId = bdv.getViewer().getState().getCurrentTimepoint();
		SourceState<?> s = bdv.getViewer().getVisibilityAndGrouping().getSources().get( i );
		
		// get manual transform
		AffineTransform3D tAffine = new AffineTransform3D();
		((TransformedSource< ? >)s.getSpimSource()).getFixedTransform( tAffine );
		
		// get old transform
		ViewRegistration vr = panel.getSpimData().getViewRegistrations().getViewRegistration( new ViewId(tpId, i ));
		AffineGet old = vr.getTransformList().get( 1 ).asAffine3D();
		
		// update transform in ViewRegistrations
		AffineTransform3D newTransform = new AffineTransform3D();
		newTransform.set( old.get( 0, 3 ) + tAffine.get( 0, 3 ), 0, 3 );
		newTransform.set( old.get( 1, 3 ) + tAffine.get( 1, 3 ), 1, 3 );
		newTransform.set( old.get( 2, 3 ) + tAffine.get( 2, 3 ), 2, 3 );
		
		ViewTransform newVt = new ViewTransformAffine( "Translation", newTransform );				
		vr.getTransformList().set( 1, newVt );
		vr.updateModel();
		
		// reset manual transform
		((TransformedSource< ? >)s.getSpimSource()).setFixedTransform( new AffineTransform3D() );
		bdv.getViewer().requestRepaint();
	}
	
	panel.bdvPopup().updateBDV();			
	
}