private ForDeprecatedConstructors(
final AbstractSpimData<?> spimData,
final String windowTitle,
final ProgressWriter progressWriter) {
this.windowTitle = windowTitle;
this.progressWriter = progressWriter;
this.spimData = spimData;
windowWidth = 800;
windowHeight = 600;
if (WrapBasicImgLoader.wrapImgLoaderIfNecessary(spimData)) {
System.err.println(
"WARNING:\nOpening <SpimData> dataset that is not suited for interactive browsing.\nConsider resaving as HDF5 for better performance.");
}
converterSetups = new ArrayList<ConverterSetup>();
sources = new ArrayList<SourceAndConverter<?>>();
initSetups(spimData, converterSetups, sources);
final AbstractSequenceDescription<?, ?, ?> seq = spimData.getSequenceDescription();
numTimepoints = seq.getTimePoints().size();
cache = ((ViewerImgLoader<?, ?>) seq.getImgLoader()).getCache();
WrapBasicImgLoader.removeWrapperIfPresent(spimData);
}
private static void initSetupsARGBType(
final AbstractSpimData<?> spimData,
final ARGBType type,
final List<ConverterSetup> converterSetups,
final List<SourceAndConverter<?>> sources) {
if (spimData.getSequenceDescription().getImgLoader() instanceof WrapBasicImgLoader) {
initSetupsARGBTypeNonVolatile(spimData, type, converterSetups, sources);
return;
}
final AbstractSequenceDescription<?, ?, ?> seq = spimData.getSequenceDescription();
for (final BasicViewSetup setup : seq.getViewSetupsOrdered()) {
final ScaledARGBConverter.VolatileARGB vconverter =
new ScaledARGBConverter.VolatileARGB(0, 255);
final ScaledARGBConverter.ARGB converter = new ScaledARGBConverter.ARGB(0, 255);
final int setupId = setup.getId();
final String setupName = createSetupName(setup);
final VolatileSpimSource<ARGBType, VolatileARGBType> vs =
new VolatileSpimSource<ARGBType, VolatileARGBType>(spimData, setupId, setupName);
final SpimSource<ARGBType> s = vs.nonVolatile();
// Decorate each source with an extra transformation, that can be
// edited manually in this viewer.
final TransformedSource<VolatileARGBType> tvs = new TransformedSource<VolatileARGBType>(vs);
final TransformedSource<ARGBType> ts = new TransformedSource<ARGBType>(s, tvs);
final SourceAndConverter<VolatileARGBType> vsoc =
new SourceAndConverter<VolatileARGBType>(tvs, vconverter);
final SourceAndConverter<ARGBType> soc =
new SourceAndConverter<ARGBType>(ts, converter, vsoc);
sources.add(soc);
converterSetups.add(new RealARGBColorConverterSetup(setupId, converter, vconverter));
}
}
private static <T extends RealType<T>> void initSetupsRealTypeNonVolatile(
final AbstractSpimData<?> spimData,
final T type,
final List<ConverterSetup> converterSetups,
final List<SourceAndConverter<?>> sources) {
final double typeMin = type.getMinValue();
final double typeMax = type.getMaxValue();
final AbstractSequenceDescription<?, ?, ?> seq = spimData.getSequenceDescription();
for (final BasicViewSetup setup : seq.getViewSetupsOrdered()) {
final RealARGBColorConverter<T> converter =
new RealARGBColorConverter.Imp1<T>(typeMin, typeMax);
converter.setColor(new ARGBType(0xffffffff));
final int setupId = setup.getId();
final String setupName = createSetupName(setup);
final SpimSource<T> s = new SpimSource<T>(spimData, setupId, setupName);
// Decorate each source with an extra transformation, that can be
// edited manually in this viewer.
final TransformedSource<T> ts = new TransformedSource<T>(s);
final SourceAndConverter<T> soc = new SourceAndConverter<T>(ts, converter);
sources.add(soc);
converterSetups.add(new RealARGBColorConverterSetup(setupId, converter));
}
}
@SuppressWarnings("unchecked")
public SpimSource(final AbstractSpimData<?> spimData, final int setup, final String name) {
super(spimData, setup, name);
final AbstractSequenceDescription<?, ?, ?> seq = spimData.getSequenceDescription();
imgLoader = (ViewerImgLoader<T, ?>) seq.getImgLoader();
loadTimepoint(0);
}
private static <T extends RealType<T>, V extends Volatile<T> & RealType<V>>
void initSetupsRealType(
final AbstractSpimData<?> spimData,
final T type,
final List<ConverterSetup> converterSetups,
final List<SourceAndConverter<?>> sources) {
if (spimData.getSequenceDescription().getImgLoader() instanceof WrapBasicImgLoader) {
initSetupsRealTypeNonVolatile(spimData, type, converterSetups, sources);
return;
}
final double typeMin = Math.max(0, Math.min(type.getMinValue(), 65535));
final double typeMax = Math.max(0, Math.min(type.getMaxValue(), 65535));
final AbstractSequenceDescription<?, ?, ?> seq = spimData.getSequenceDescription();
for (final BasicViewSetup setup : seq.getViewSetupsOrdered()) {
final RealARGBColorConverter<V> vconverter =
new RealARGBColorConverter.Imp0<V>(typeMin, typeMax);
vconverter.setColor(new ARGBType(0xffffffff));
final RealARGBColorConverter<T> converter =
new RealARGBColorConverter.Imp1<T>(typeMin, typeMax);
converter.setColor(new ARGBType(0xffffffff));
final int setupId = setup.getId();
final String setupName = createSetupName(setup);
final VolatileSpimSource<T, V> vs =
new VolatileSpimSource<T, V>(spimData, setupId, setupName);
final SpimSource<T> s = vs.nonVolatile();
// Decorate each source with an extra transformation, that can be
// edited manually in this viewer.
final TransformedSource<V> tvs = new TransformedSource<V>(vs);
final TransformedSource<T> ts = new TransformedSource<T>(s, tvs);
final SourceAndConverter<V> vsoc = new SourceAndConverter<V>(tvs, vconverter);
final SourceAndConverter<T> soc = new SourceAndConverter<T>(ts, converter, vsoc);
sources.add(soc);
converterSetups.add(new RealARGBColorConverterSetup(setupId, converter, vconverter));
}
}
public static BigDataViewer open(
final AbstractSpimData<?> spimData,
final String windowTitle,
final ProgressWriter progressWriter) {
final int width = 800;
final int height = 600;
if (WrapBasicImgLoader.wrapImgLoaderIfNecessary(spimData)) {
System.err.println(
"WARNING:\nOpening <SpimData> dataset that is not suited for interactive browsing.\nConsider resaving as HDF5 for better performance.");
}
final ArrayList<ConverterSetup> converterSetups = new ArrayList<ConverterSetup>();
final ArrayList<SourceAndConverter<?>> sources = new ArrayList<SourceAndConverter<?>>();
initSetups(spimData, converterSetups, sources);
final AbstractSequenceDescription<?, ?, ?> seq = spimData.getSequenceDescription();
final int numTimepoints = seq.getTimePoints().size();
final Cache cache = ((ViewerImgLoader<?, ?>) seq.getImgLoader()).getCache();
final BigDataViewer bdv =
new BigDataViewer(
converterSetups,
sources,
spimData,
numTimepoints,
cache,
windowTitle,
width,
height,
progressWriter);
WrapBasicImgLoader.removeWrapperIfPresent(spimData);
bdv.viewerFrame.setVisible(true);
InitializeViewerState.initTransform(bdv.viewer);
return bdv;
}