@SuppressWarnings({ "unchecked", "rawtypes" }) public static < T extends RealType< T > > RandomAccessibleInterval< T > getImage( final T type, ImgLoader imgLoader, final ViewId view, final boolean normalize ) { if ( (RealType)type instanceof FloatType ) return (RandomAccessibleInterval)imgLoader.getSetupImgLoader( view.getViewSetupId() ).getFloatImage( view.getTimePointId(), normalize, LOAD_COMPLETELY ); else if ( (RealType)type instanceof UnsignedShortType ) return (RandomAccessibleInterval)imgLoader.getSetupImgLoader( view.getViewSetupId() ).getImage( view.getTimePointId(), LOAD_COMPLETELY ); else return null; }
@Override public VoxelDimensions getVoxelSize(int timepointId) { return wrappedImgLoader.getSetupImgLoader( setupId ).getVoxelSize( timepointId ); }
@Override public int compare( final ViewId o1, final ViewId o2 ) { return sd.getViewDescription( o1 ).getViewSetup().getChannel().getId() - sd.getViewDescription( o2 ).getViewSetup().getChannel().getId(); } } );
public static ArrayList< ViewDescription > getAllViewIdsForChannelTimePointSorted( final SpimData data, final Collection< ? extends ViewId > viewIds, final Channel channel, final TimePoint timePoint ) { final ArrayList< ViewDescription > views = new ArrayList< ViewDescription >(); for ( final ViewId id : viewIds ) { final ViewDescription vd = data.getSequenceDescription().getViewDescription( id ); if ( vd.isPresent() && vd.getViewSetup().getChannel().getId() == channel.getId() && id.getTimePointId() == timePoint.getId() ) views.add( vd ); } Collections.sort( views ); return views; }
/** * find ViewSetup index corresponding to given (angle, illumination, * channel) triple. * * @return setup index or -1 if no corresponding setup was found. */ protected static int getViewSetupId( final ArrayList< ViewSetup > setups, final int angle, final int illumination, final int channel ) { for ( final ViewSetup s : setups ) if ( s.getAngle().getId() == angle && s.getIllumination().getId() == illumination && s.getChannel().getId() == channel ) return s.getId(); return -1; }
public static ViewSetup getViewSetup( final List< ? extends ViewSetup > list, final Channel c, final Angle a, final Illumination i, final Tile x ) { for ( final ViewSetup viewSetup : list ) { if ( viewSetup.getAngle().getId() == a.getId() && viewSetup.getChannel().getId() == c.getId() && viewSetup.getIllumination().getId() == i.getId() && viewSetup.getTile().getId() == x.getId() ) { return viewSetup; } } return null; }
protected String nameForGroup( final Group< ViewDescription > group ) { final ViewDescription vd1 = group.iterator().next(); String name = "TP=" + vd1.getTimePointId() + " Angle=" + vd1.getViewSetup().getAngle().getName() + " Channel=" + vd1.getViewSetup().getChannel().getName(); if ( !groupIllums ) name += " Illum=" + vd1.getViewSetup().getChannel().getName(); if ( !groupTiles ) name += " Tile=" + vd1.getViewSetup().getTile().getName(); return name; }
public static int inputBytePerPixel( final ViewId viewId, final SpimData2 spimData ) { SetupImgLoader< ? > loader = spimData.getSequenceDescription().getImgLoader().getSetupImgLoader( viewId.getViewSetupId() ); Object type = loader.getImageType(); if ( UnsignedByteType.class.isInstance( type ) ) return 1; else if ( UnsignedShortType.class.isInstance( type ) ) return 2; else return 4; } }
public static TimePoints createTimepoints() { final ArrayList< TimePoint > timepointList = new ArrayList< TimePoint >(); timepointList.add( new TimePoint( 0 ) ); return new TimePoints( timepointList ); }
public String dialogName() { String s = ""; s += ( ts.size() > 1 ) ? "all_timepoints" : "timepoint_" + ts.iterator().next().getName(); s += ( cs.size() > 1 ) ? "_all_channels" : "_channel_" + cs.iterator().next().getName(); s += ( is.size() > 1 ) ? "_all_illuminations" : "_illumination_" + is.iterator().next().getName(); s += ( as.size() > 1 ) ? "_all_angles" : "_angle_" + as.iterator().next().getName(); return s; } /*
@Override public VoxelDimensions getVoxelSize(int timepointId) { return wrappedImgLoader.getSetupImgLoader( setupId ).getVoxelSize( timepointId ); } }
@Override public Dimensions getImageSize(int timepointId) { return wrappedImgLoader.getSetupImgLoader( setupId ).getImageSize( timepointId ); }
@Override public T getImageType() { @SuppressWarnings("unchecked") final T res = (T) wrappedImgLoader.getSetupImgLoader( setupId ).getImageType(); return res; }
@Override public boolean inRange( final V view1, final V view2 ) { // if one of the views is a reference timepoint or if they are from the same timepoint (fixed views are discarded later) if ( view1.getTimePointId() == referenceTimepoint || view2.getTimePointId() == referenceTimepoint || view1.getTimePointId() == view2.getTimePointId() ) return true; else return false; }
@Override public Dimensions getImageSize(int timepointId) { return wrappedImgLoader.getSetupImgLoader( setupId ).getImageSize( timepointId ); }
@Override public AffineTransform3D[] getMipmapTransforms() { return wrappedImgLoader.getSetupImgLoader( setupId ).getMipmapTransforms(); }
@Override public T getImageType() { @SuppressWarnings("unchecked") T res = (T) wrappedImgLoader.getSetupImgLoader( setupId ).getImageType(); return res; }
@Override public double[][] getMipmapResolutions() { return wrappedImgLoader.getSetupImgLoader( setupId ).getMipmapResolutions(); }
@Override public int numMipmapLevels() { return wrappedImgLoader.getSetupImgLoader( setupId ).numMipmapLevels(); }
@Override public Dimensions getImageSize(int timepointId, int level) { return wrappedImgLoader.getSetupImgLoader( setupId ).getImageSize( timepointId, level ); }