public static double getAverageAnisotropyFactor( final SpimData spimData, final Collection< ? extends ViewId > views ) { final SequenceDescription seq = spimData.getSequenceDescription(); double avgFactor = 0; int count = 0; for ( final ViewId vd : views ) { final ViewSetup vs = seq.getViewSetups().get( vd.getViewSetupId() ); final VoxelDimensions vx = vs.getVoxelSize(); if ( vx != null ) { final double x = vx.dimension( 0 ); final double y = vx.dimension( 1 ); final double z = vx.dimension( 2 ); if ( x == y ) { avgFactor += z / x; ++count; } } } if ( count > 0 ) avgFactor /= (double)count; else avgFactor = 1.0; return avgFactor; }
dog.downsampleXY = DownsampleTools.downsampleFactor( downsampleXYIndex, downsampleZ, vd.getViewSetup().getVoxelSize() ); else dog.downsampleXY = downsampleXYIndex;
public 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 ); }
continue; final VoxelDimensions voxelSize = vd.getViewSetup().getVoxelSize(); unit = vd.getViewSetup().getVoxelSize().unit();
final VoxelDimensions voxelSize = vd.getViewSetup().getVoxelSize(); unit = vd.getViewSetup().getVoxelSize().unit();
downsampleXY = DownsampleTools.downsampleFactor( downsampleXYIndex, downsampleZ, vd.getViewSetup().getVoxelSize() ); else downsampleXY = downsampleXYIndex;
final VoxelDimensions voxelSize = viewDescription.getViewSetup().getVoxelSize();
downsampleXY = DownsampleTools.downsampleFactor( downsampleXYIndex, downsampleZ, viewDescription.getViewSetup().getVoxelSize() ); else downsampleXY = downsampleXYIndex;
final VoxelDimensions voxelSize = vd.getViewSetup().getVoxelSize();
continue; final VoxelDimensions voxelSize = vd.getViewSetup().getVoxelSize();
dom.downsampleXY = DownsampleTools.downsampleFactor( downsampleXYIndex, downsampleZ, vd.getViewSetup().getVoxelSize() ); else dom.downsampleXY = downsampleXYIndex;
vOut.setSize( v.getSize() ); if ( vOut.getVoxelSize() == null && v.getVoxelSize() != null ) vOut.setVoxelSize( v.getVoxelSize() );
final VoxelDimensions voxelSize = viewDescription.getViewSetup().getVoxelSize();
VoxelDimensions voxelSize = setup.getVoxelSize(); final double calX = voxelSize.dimension( 0 ); final double calY = voxelSize.dimension( 1 );