Java ViewRegistration.updateModel方法代码示例

import mpicbg.spim.data.registration.ViewRegistration; //导入方法依赖的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; //导入方法依赖的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();
}
 

import mpicbg.spim.data.registration.ViewRegistration; //导入方法依赖的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.ViewRegistration; //导入方法依赖的package包/类
/**
 * Called before the XML is potentially saved
 */
@Override
public boolean cleanUp()
{
	if ( reorientate == 0 || reorientate == 1 )
	{
		// the spimdata registrations were changed
		return true;
	}
	else if ( reorientate == 2 )
	{
		// remove the registrations we added
		if ( viewIdsToApply == null )
		{
			IOFunctions.println( "Something went wrong, the viewIdsToApply list is null." );
		}
		else
		{
			for ( final ViewId viewId : viewIdsToApply )
			{
				final ViewDescription vd = spimData.getSequenceDescription().getViewDescription( viewId );
				
				if ( !vd.isPresent() )
					continue;

				// get the registration
				final ViewRegistration r = spimData.getViewRegistrations().getViewRegistration( viewId );
				final List< ViewTransform > vtl = r.getTransformList();
				vtl.remove( 0 );
				r.updateModel();
			}
		}
	}

	return this.changedSpimDataObject;
}
 

import mpicbg.spim.data.registration.ViewRegistration; //导入方法依赖的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.ViewRegistration; //导入方法依赖的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.ViewRegistration; //导入方法依赖的package包/类
public static <S extends AbstractSequenceDescription< ?,? extends BasicViewDescription<? extends BasicViewSetup>, ?  >>
	List<RandomAccessibleInterval< FloatType >> openVirtuallyFused(
			S sd,
			ViewRegistrations vrs,
			Collection<? extends Collection<ViewId>> views,
			Interval boundingBox,
			double[] downsamplingFactors)
{
	final BasicImgLoader imgLoader = sd.getImgLoader();
	
	final List<RandomAccessibleInterval< FloatType >> openImgs = new ArrayList<>();
	final Interval bbSc = TransformVirtual.scaleBoundingBox( new FinalInterval( boundingBox ), inverse( downsamplingFactors ));
	
	final long[] dim = new long[ bbSc.numDimensions() ];
	bbSc.dimensions( dim );
	
	
	for (Collection<ViewId> viewGroup : views)
	{
		final ArrayList< RandomAccessibleInterval< FloatType > > images = new ArrayList<>();
		final ArrayList< RandomAccessibleInterval< FloatType > > weights = new ArrayList<>();
		
		for ( final ViewId viewId : viewGroup )
		{
			final ViewRegistration vr = vrs.getViewRegistration( viewId );
			vr.updateModel();
			AffineTransform3D model = vr.getModel();

			final float[] blending = Util.getArrayFromValue( FusionTools.defaultBlendingRange, 3 );
			final float[] border = Util.getArrayFromValue( FusionTools.defaultBlendingBorder, 3 );

			model = model.copy();
			TransformVirtual.scaleTransform( model, inverse(downsamplingFactors) );

			final RandomAccessibleInterval inputImg = DownsampleTools.openDownsampled( imgLoader, viewId, model );

			System.out.println( model.inverse() );

			FusionTools.adjustBlending( sd.getViewDescriptions().get( viewId ), blending, border, model );

			images.add( TransformView.transformView( inputImg, model, bbSc, 0, 1 ) );
			weights.add( TransformWeight.transformBlending( inputImg, border, blending, model, bbSc ) );
		}
		
		openImgs.add( new FusedRandomAccessibleInterval( new FinalInterval( dim ), images, weights ) );
		
	}		
	
	return openImgs;
	
}
 

import mpicbg.spim.data.registration.ViewRegistration; //导入方法依赖的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();			
	
}
 

import mpicbg.spim.data.registration.ViewRegistration; //导入方法依赖的package包/类
/**
 * 
 * @param type 0 == before, 1 == replace, 2 == after
 */
protected void pasteSelection( final int type )
{
	if ( cache.size() == 0 )
	{
		JOptionPane.showMessageDialog( table, "Nothing copied so far." );
		return;
	}
	
	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 ViewRegistration vr = tableModel.getViewRegistrations().getViewRegistration( vd );

	// check out where to start inserting
	final int[] selectedRows = table.getSelectedRows();
	Arrays.sort( selectedRows );
	int insertAt;
	
	if ( type == 0 )
	{
		insertAt = selectedRows[ 0 ];
	}
	else if ( type == 1 )
	{
		insertAt = selectedRows[ 0 ];

		// remove the selected entries
		for ( int i = selectedRows[ selectedRows.length - 1 ]; i >= selectedRows[ 0 ]; --i )
			vr.getTransformList().remove( i );
	}
	else
	{
		insertAt = selectedRows[ selectedRows.length - 1 ] + 1;
	}

	// add the new entries
	final ArrayList< ViewTransform > newList = new ArrayList< ViewTransform >();
	
	// add the old entries
	for ( int i = 0; i < insertAt; ++i )
		newList.add( vr.getTransformList().get( i ) );
	
	// add the copied ones
	for ( int i = 0; i < cache.size(); ++i )
		newList.add( duplicate( cache.get( i ) ) );
	
	// add the rest
	for ( int i = insertAt; i < vr.getTransformList().size(); ++i )
		newList.add( vr.getTransformList().get( i ) );
	
	vr.getTransformList().clear();
	vr.getTransformList().addAll( newList );
	vr.updateModel();

	// update everything
	tableModel.fireTableDataChanged();
}
 

import mpicbg.spim.data.registration.ViewRegistration; //导入方法依赖的package包/类
/**
 * Creates lists of input points for the registration, based on the current transformation of the views
 * 
 * Note: this always duplicates the location array from the input List> InterestPoint < !!!
 * 
 * @param timepoint
 */
protected HashMap< ViewId, MatchPointList > getInterestPoints( final TimePoint timepoint )
{
	final HashMap< ViewId, MatchPointList > interestPoints = new HashMap< ViewId, MatchPointList >();
	final ViewRegistrations registrations = spimData.getViewRegistrations();
	final ViewInterestPoints interestpoints = spimData.getViewInterestPoints();
	
	for ( final ViewDescription vd : SpimData2.getAllViewIdsForTimePointSorted( spimData, viewIdsToProcess, timepoint) )
	{
		if ( !vd.isPresent() )
			continue;

		final ChannelProcess c = getChannelProcessForChannel( channelsToProcess, vd.getViewSetup().getChannel() );

		// no registration for this viewdescription
		if ( c == null )
			continue;

		final Angle a = vd.getViewSetup().getAngle();
		final Illumination i = vd.getViewSetup().getIllumination();

		// assemble a new list
		final ArrayList< InterestPoint > list = new ArrayList< InterestPoint >();

		// check the existing lists of points
		final ViewInterestPointLists lists = interestpoints.getViewInterestPointLists( vd );

		if ( !lists.contains( c.getLabel() ) )
		{
			IOFunctions.println( "Interest points for label '" + c.getLabel() + "' not found for timepoint: " + timepoint.getId() + " angle: " + 
					a.getId() + " channel: " + c.getChannel().getId() + " illum: " + i.getId() );
			
			continue;
		}
		
		if ( lists.getInterestPointList( c.getLabel() ).getInterestPoints() == null )
		{
			if ( !lists.getInterestPointList( c.getLabel() ).loadInterestPoints() )
			{
				IOFunctions.println( "Interest points for label '" + c.getLabel() + "' could not be loaded for timepoint: " + timepoint.getId() + " angle: " + 
						a.getId() + " channel: " + c.getChannel().getId() + " illum: " + i.getId() );
				
				continue;
			}
		}
		
		final List< InterestPoint > ptList = lists.getInterestPointList( c.getLabel() ).getInterestPoints();
		
		final ViewRegistration r = registrations.getViewRegistration( vd );
		r.updateModel();
		final AffineTransform3D m = r.getModel();
		
		for ( final InterestPoint p : ptList )
		{
			final double[] l = new double[ 3 ];
			m.apply( p.getL(), l );
			
			list.add( new InterestPoint( p.getId(), l ) );
		}
		
		interestPoints.put( vd, new MatchPointList( list, c ) );
	}

	return interestPoints;
}
 

import mpicbg.spim.data.registration.ViewRegistration; //导入方法依赖的package包/类
/**
 * @param spimData
 * @param viewIdsToProcess
 * @param minBB
 * @param maxBB
 * @return - true if the SpimData object was modified, otherwise false
 */
public static boolean computeMaxBoundingBoxDimensions( final SpimData2 spimData, final List< ViewId > viewIdsToProcess, final double[] minBB, final double[] maxBB )
{
	for ( int d = 0; d < minBB.length; ++d )
	{
		minBB[ d ] = Double.MAX_VALUE;
		maxBB[ d ] = -Double.MAX_VALUE;
	}

	boolean changed = false;
	IOFunctions.println( new Date( System.currentTimeMillis() ) + ": Estimating Bounding Box for Fusion. If size of images is not known (they were never opened before), some of them need to be opened once to determine their size.");

	for ( final ViewId viewId : viewIdsToProcess )
	{
		final ViewDescription viewDescription = spimData.getSequenceDescription().getViewDescription( 
				viewId.getTimePointId(), viewId.getViewSetupId() );

		if ( !viewDescription.isPresent() )
			continue;

		if ( !viewDescription.getViewSetup().hasSize() )
			changed = true;

		final Dimensions size = ViewSetupUtils.getSizeOrLoad( viewDescription.getViewSetup(), viewDescription.getTimePoint(), spimData.getSequenceDescription().getImgLoader() );
		final double[] min = new double[]{ 0, 0, 0 };
		final double[] max = new double[]{
				size.dimension( 0 ) - 1,
				size.dimension( 1 ) - 1,
				size.dimension( 2 ) - 1 };
		
		final ViewRegistration r = spimData.getViewRegistrations().getViewRegistration( viewId );
		r.updateModel();
		final FinalRealInterval interval = r.getModel().estimateBounds( new FinalRealInterval( min, max ) );
		
		for ( int d = 0; d < minBB.length; ++d )
		{
			minBB[ d ] = Math.min( minBB[ d ], interval.realMin( d ) );
			maxBB[ d ] = Math.max( maxBB[ d ], interval.realMax( d ) );
		}
	}

	return changed;
}