Java ViewRegistration类代码示例

import mpicbg.spim.data.registration.ViewRegistration; //导入依赖的package包/类
/**
 * 
 * @param vr the ViewRegistration to decompose
 * @param is2d true or false
 * @param dsCorrectionT downsampling correction 
 * @return (1) the ViewRegistration without Translation part and the translation, with the inverse of (1) and dsCorrection applied
 */
public static Pair<AffineGet, TranslationGet> getInitialTransforms( final ViewRegistration vr, final boolean is2d, final AffineTransform3D dsCorrectionT )
{
	AffineTransform3D model = vr.getModel().copy();
	
	// get model without translation (last column set to 0)
	AffineTransform3D modelWithoutTranslation = model.copy();
	modelWithoutTranslation.set( 0, 0, 3 );
	modelWithoutTranslation.set( 0, 1, 3 );
	modelWithoutTranslation.set( 0, 2, 3 );
	
	// the translation with inverse of other part of model applied
	final double[] target = model.getTranslation();
	modelWithoutTranslation.applyInverse( target, target );
	
	// we go from big to downsampled, thats why the inverse
	dsCorrectionT.applyInverse( target, target );
	
	
	if ( is2d )
		return new ValuePair<>(modelWithoutTranslation, new Translation2D( target[ 0 ], target[ 1 ] ));
	else
		return new ValuePair<>(modelWithoutTranslation, new Translation3D( target[ 0 ], target[ 1 ], target[ 2 ] ));
}
 

import mpicbg.spim.data.registration.ViewRegistration; //导入依赖的package包/类
public FusionResult(
		final String filepath,
		final String filepattern,
		final TimePoints timepoints,
		final int numSlices,
		final double sliceValueMin,
		final double sliceValueMax,
		final Map< Integer, AffineTransform3D > perTimePointFusionTransforms )
{
	final HashMap< Integer, Integer > setupIdToChannelId = new HashMap<>();
	setupIdToChannelId.put( 0, 0 );
	final ImgLoader fusionLoader = new FusionImageLoader<>( filepath +"/" + filepattern, setupIdToChannelId, numSlices, new FusionImageLoader.Gray32ImagePlusLoader(), sliceValueMin, sliceValueMax );
	final int setupId = 0;
	final String name = "fused";
	final int timepointId = timepoints.getTimePointsOrdered().get( 0 ).getId();
	final Dimensions size = fusionLoader.getSetupImgLoader( setupId ).getImageSize( timepointId );
	final VoxelDimensions voxelSize = fusionLoader.getSetupImgLoader( setupId ).getVoxelSize( timepointId );
	final BasicViewSetup setup = new BasicViewSetup( setupId, name, size, voxelSize );
	desc = new SequenceDescriptionMinimal( timepoints, Entity.idMap( Arrays.asList( setup ) ), fusionLoader, null );
	final ArrayList< ViewRegistration > registrations = new ArrayList<>();
	for ( final TimePoint timepoint : timepoints.getTimePointsOrdered() )
		registrations.add( new ViewRegistration( timepoint.getId(), 0, perTimePointFusionTransforms.get( timepoint.getId() ) ) );
	regs = new ViewRegistrations( registrations );
}
 

import mpicbg.spim.data.registration.ViewRegistration; //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.ViewRegistration; //导入依赖的package包/类
@Override
public Object getValueAt( final int row, final int column )
{
	if ( currentVD == null )
		return column == 0 ? "No View Description selected" : "";

	final ViewRegistration vr = viewRegistrations.getViewRegistration( currentVD );
	
	if ( vr.getTransformList().isEmpty() )
	{
		return column == 0 ? "No transformations present" : "";
	}
	else
	{
		if ( column == 0 )
			return vr.getTransformList().get( row ).getName();
		else
			return vr.getTransformList().get( row ).asAffine3D().getRowPackedCopy()[ column - 1 ];
	}
}
 

import mpicbg.spim.data.registration.ViewRegistration; //导入依赖的package包/类
protected Pair< Integer, Integer > numReorientated()
{
	final ViewRegistrations vrs = spimData.getViewRegistrations();

	int isReorientated = 0;
	int sumViews = 0;

	for ( final ViewId viewId : viewIdsToProcess )
	{
		final ViewDescription vd = spimData.getSequenceDescription().getViewDescription( viewId );
		
		if ( !vd.isPresent() )
			continue;

		final ViewRegistration vr = vrs.getViewRegistration( viewId );
		final ViewTransform vt = vr.getTransformList().get( 0 );

		++sumViews;

		if ( vt.hasName() && vt.getName().startsWith( reorientationDescription ) )
				++isReorientated;
	}

	return new ValuePair< Integer, Integer >( isReorientated, sumViews );
}
 

import mpicbg.spim.data.registration.ViewRegistration; //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.ViewRegistration; //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.ViewRegistration; //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.ViewRegistration; //导入依赖的package包/类
public static boolean nonTranslationsEqual(final ViewRegistration vr1, final ViewRegistration vr2)
{
	final int n = vr1.getModel().numDimensions();
	final AffineTransform3D dsTransform = new AffineTransform3D();
	
	final Pair< AffineGet, TranslationGet > initialTransforms1 = getInitialTransforms( vr1, n == 2, dsTransform );
	final Pair< AffineGet, TranslationGet > initialTransforms2 = getInitialTransforms( vr2, n == 2, dsTransform );
	
	return allAlmostEqual( initialTransforms1.getA().getRowPackedCopy(), initialTransforms2.getA().getRowPackedCopy(), 0.01 );
}
 

import mpicbg.spim.data.registration.ViewRegistration; //导入依赖的package包/类
public static AffineTransform3D getAccumulativeTransformForRawDataTransform(ViewRegistration viewRegistration,
		AffineGet rawTransform)
{
	final AffineTransform3D vrModel = viewRegistration.getModel();
	final AffineTransform3D result = vrModel.inverse().copy();
	result.preConcatenate( rawTransform ).preConcatenate( vrModel );
	return result;
}
 

import mpicbg.spim.data.registration.ViewRegistration; //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.ViewRegistration; //导入依赖的package包/类
public static HashMap< String, Integer > assembleRegistrationNames( final SpimData data, final List< ViewId > viewIds )
{
	final ViewRegistrations vr = data.getViewRegistrations();
	final SequenceDescription sd = data.getSequenceDescription();

	final HashMap< String, Integer > names = new HashMap< String, Integer >();

	for ( final ViewId viewId: viewIds )
	{
		final ViewDescription vd = sd.getViewDescription( viewId );

		if ( !vd.isPresent() )
			continue;

		final ViewRegistration r = vr.getViewRegistration( vd );
		final String rName = r.getTransformList().get( 0 ).getName();

		if ( rName != null )
		{
			if ( names.containsKey( rName ) )
				names.put( rName, names.get( rName ) + 1 );
			else
				names.put( rName, 1 );
		}
	}

	return names;
}
 

import mpicbg.spim.data.registration.ViewRegistration; //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.ViewRegistration; //导入依赖的package包/类
@Override
public void getLocalToGlobalTransform( final int timepointIndex, final AffineTransform3D transform )
{
	if ( currentVD != null )
	{
		final ViewRegistration vr = panel.viewSetupExplorer.getSpimData().getViewRegistrations().getViewRegistration( currentVD );
		vr.updateModel();
		transform.set( vr.getModel() );
	}
}
 

import mpicbg.spim.data.registration.ViewRegistration; //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;
	}

	//final AbstractSpimData< ? > data = (AbstractSpimData< ? >)panel.getSpimData();
	final List< ViewId > viewIds = panel.selectedRowsViewId();

	final ViewRegistrations vr = panel.getSpimData().getViewRegistrations();
	for ( final ViewId viewId : viewIds )
	{
		final ViewRegistration v = vr.getViewRegistrations().get( viewId );
		
		if ( index == 0 )
			v.getTransformList().remove( 0 );
		else
			v.getTransformList().remove( v.getTransformList().size() - 1 );

		v.updateModel();
	}

	panel.updateContent();
	ViewSetupExplorerPanel.bdvPopup().updateBDV();
}