Field Detail

• viewerFrame

  protected final ViewerFrame viewerFrame

• viewer

  protected final ViewerPanel viewer

• setupAssignments

  protected final SetupAssignments setupAssignments

• manualTransformation

  protected final ManualTransformation manualTransformation

• bookmarks

  protected final Bookmarks bookmarks

• brightnessDialog

  protected final BrightnessDialog brightnessDialog

• cropDialog

  protected final CropDialog cropDialog

• movieDialog

  protected final RecordMovieDialog movieDialog

• movieMaxProjectDialog

  protected final RecordMaxProjectionDialog movieMaxProjectDialog

• activeSourcesDialog

  protected final VisibilityAndGroupingDialog activeSourcesDialog

• helpDialog

  protected final HelpDialog helpDialog

• manualTransformationEditor

  protected final ManualTransformationEditor manualTransformationEditor

• bookmarkEditor

  protected final BookmarksEditor bookmarkEditor

• fileChooser

  protected final JFileChooser fileChooser

• proposedSettingsFile

  protected File proposedSettingsFile

Constructor Detail

• BigDataViewer

  public BigDataViewer(ArrayList<ConverterSetup> converterSetups,
                       ArrayList<SourceAndConverter<?>> sources,
                       AbstractSpimData<?> spimData,
                       int numTimepoints,
                       CacheControl cache,
                       String windowTitle,
                       ProgressWriter progressWriter,
                       ViewerOptions options)

  Parameters:

  converterSetups - list of ConverterSetup that control min/max and color of sources.

  sources - list of pairs of source of some type and converter from that type to ARGB.

  spimData - may be null. The AbstractSpimData of the dataset (if there is one). If it exists, it is used to set up a "Crop" dialog.

  numTimepoints - the number of timepoints in the dataset.

  cache - handle to cache. This is used to control io timing.

  windowTitle - title of the viewer window.

  progressWriter - a ProgressWriter to which BDV may report progress (currently only used in the "Record Movie" dialog).

  options - optional parameters.

Method Detail

• toggleManualTransformation

  public void toggleManualTransformation()

• initSetBookmark

  public void initSetBookmark()

• initGoToBookmark

  public void initGoToBookmark()

• initGoToBookmarkRotation

  public void initGoToBookmarkRotation()

• createConverterToARGB

  public static <T extends NumericType<T>> Converter<T,ARGBType> createConverterToARGB(T type)

  Create standard converter from the given type to ARGB:

  • For RealTypes a RealARGBColorConverter is returned.
  • For ARGBTypes a ScaledARGBConverter.ARGB is returned.
  • For VolatileARGBTypes a ScaledARGBConverter.VolatileARGB is returned.

• createConverterSetup

  public static ConverterSetup createConverterSetup(SourceAndConverter<?> soc,
                                                    int setupId)

  Create a ConverterSetup for the given SourceAndConverter. Nested volatile SourceAndConverter are added to the ConverterSetup if present. If SourceAndConverter does not comprise a ColorConverter, returns null.

  Parameters:

  soc - SourceAndConverter for which to create a ConverterSetup

  setupId - setupId of the created ConverterSetup

  Returns:

  a new ConverterSetup or null

• wrapWithTransformedSource

  public static <T,V extends Volatile<T>> SourceAndConverter<T> wrapWithTransformedSource(SourceAndConverter<T> soc)

  Decorate source with an extra transformation, that can be edited manually in this viewer. Nested volatile SourceAndConverter are wrapped as well, if present.

• initSetups

  public static void initSetups(AbstractSpimData<?> spimData,
                                List<ConverterSetup> converterSetups,
                                List<SourceAndConverter<?>> sources)

• open

  public static BigDataViewer open(AbstractSpimData<?> spimData,
                                   String windowTitle,
                                   ProgressWriter progressWriter,
                                   ViewerOptions options)

• open

  public static BigDataViewer open(String xmlFilename,
                                   String windowTitle,
                                   ProgressWriter progressWriter,
                                   ViewerOptions options)
                            throws SpimDataException

  Throws:

  SpimDataException

• open

  public static BigDataViewer open(ArrayList<ConverterSetup> converterSetups,
                                   ArrayList<SourceAndConverter<?>> sources,
                                   int numTimepoints,
                                   CacheControl cache,
                                   String windowTitle,
                                   ProgressWriter progressWriter,
                                   ViewerOptions options)

• getViewer

  public ViewerPanel getViewer()

• getViewerFrame

  public ViewerFrame getViewerFrame()

• getConverterSetups

  public ConverterSetups getConverterSetups()

• getSetupAssignments

  @Deprecated
  public SetupAssignments getSetupAssignments()

  Deprecated. Instead getViewer().state() returns the ViewerState that can be modified directly.

• getManualTransformEditor

  public ManualTransformationEditor getManualTransformEditor()

• tryLoadSettings

  public boolean tryLoadSettings(String xmlFilename)

• saveSettings

  public void saveSettings()

• saveSettings

  public void saveSettings(String xmlFilename)
                    throws IOException

  Throws:

  IOException

• getInputTriggerConfig

  public static InputTriggerConfig getInputTriggerConfig(ViewerOptions options)

  If options doesn't define a InputTriggerConfig, try to load it from files in this order:

  1. "bdvkeyconfig.yaml" in the current directory.
  2. ".bdv/bdvkeyconfig.yaml" in the user's home directory.
  3. legacy "bigdataviewer.keys.properties" in current directory (will be also written to "bdvkeyconfig.yaml").

  Parameters:

  options -

  Returns:

• loadSettings

  public void loadSettings()

• loadSettings

  public void loadSettings(String xmlFilename)
                    throws IOException,
                           org.jdom2.JDOMException

  Throws:

  IOException

  org.jdom2.JDOMException

• expandAndFocusCardPanel

  public void expandAndFocusCardPanel()

• collapseCardPanel

  public void collapseCardPanel()

• main

  public static void main(String[] args)