bdv

Class BigDataViewer

java.lang.Object

bdv.BigDataViewer

public class BigDataViewer
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
protected VisibilityAndGroupingDialog	activeSourcesDialog
protected BookmarksEditor	bookmarkEditor
protected Bookmarks	bookmarks
protected BrightnessDialog	brightnessDialog
static String	configDir
protected CropDialog	cropDialog
protected JFileChooser	fileChooser
protected HelpDialog	helpDialog
protected ManualTransformation	manualTransformation
protected ManualTransformationEditor	manualTransformationEditor
protected RecordMovieDialog	movieDialog
protected RecordMaxProjectionDialog	movieMaxProjectDialog
protected PreferencesDialog	preferencesDialog
protected File	proposedSettingsFile
protected SetupAssignments	setupAssignments
protected ViewerPanel	viewer
protected ViewerFrame	viewerFrame

Constructor Summary

Constructors

Constructor and Description
BigDataViewer(ArrayList<ConverterSetup> converterSetups, ArrayList<SourceAndConverter<?>> sources, mpicbg.spim.data.generic.AbstractSpimData<?> spimData, int numTimepoints, CacheControl cache, String windowTitle, ProgressWriter progressWriter, ViewerOptions options) Deprecated.
BigDataViewer(List<ConverterSetup> converterSetups, List<SourceAndConverter<?>> sources, mpicbg.spim.data.generic.AbstractSpimData<?> spimData, int numTimepoints, CacheControl cache, String windowTitle, ProgressWriter progressWriter, ViewerOptions options)

Method Summary

Modifier and Type	Method and Description
void	collapseCardPanel()
static ConverterSetup	createConverterSetup(SourceAndConverter<?> soc, int setupId) Create a ConverterSetup for the given SourceAndConverter.
static <T extends net.imglib2.type.numeric.NumericType<T>> net.imglib2.converter.Converter<T,net.imglib2.type.numeric.ARGBType>	createConverterToARGB(T type) Create standard converter from the given type to ARGB: For RealTypes a RealARGBColorConverter is returned.
void	expandAndFocusCardPanel()
AppearanceManager	getAppearanceManager()
ConverterSetups	getConverterSetups()
static org.scijava.ui.behaviour.io.InputTriggerConfig	getInputTriggerConfig(ViewerOptions options) Deprecated. This method is no longer used internally. InputTriggerConfigs are now managed through KeymapManager.
KeymapManager	getKeymapManager()
ManualTransformationEditor	getManualTransformEditor()
SetupAssignments	getSetupAssignments() Deprecated. Instead getViewer().state() returns the ViewerState that can be modified directly.
ViewerPanel	getViewer()
ViewerFrame	getViewerFrame()
void	initGoToBookmark()
void	initGoToBookmarkRotation()
void	initSetBookmark()
static void	initSetups(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, List<ConverterSetup> converterSetups, List<SourceAndConverter<?>> sources)
void	loadSettings()
void	loadSettings(String xmlFilename)
static void	main(String[] args)
static BigDataViewer	open(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, String windowTitle, ProgressWriter progressWriter, ViewerOptions options)
static BigDataViewer	open(ArrayList<ConverterSetup> converterSetups, ArrayList<SourceAndConverter<?>> sources, int numTimepoints, CacheControl cache, String windowTitle, ProgressWriter progressWriter, ViewerOptions options)
static BigDataViewer	open(String xmlFilename, String windowTitle, ProgressWriter progressWriter, ViewerOptions options)
void	saveSettings()
void	saveSettings(String xmlFilename)
void	toggleManualTransformation()
boolean	tryLoadSettings(String xmlFilename)
static <T,V extends net.imglib2.Volatile<T>> SourceAndConverter<T>	wrapWithTransformedSource(SourceAndConverter<T> soc) Decorate source with an extra transformation, that can be edited manually in this viewer.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

configDir

public static String configDir

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

preferencesDialog

protected final PreferencesDialog preferencesDialog

manualTransformationEditor

protected final ManualTransformationEditor manualTransformationEditor

bookmarkEditor

protected final BookmarksEditor bookmarkEditor

fileChooser

protected final JFileChooser fileChooser

proposedSettingsFile

protected File proposedSettingsFile

Constructor Detail

BigDataViewer

@Deprecated
public BigDataViewer(ArrayList<ConverterSetup> converterSetups,
                                 ArrayList<SourceAndConverter<?>> sources,
                                 mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
                                 int numTimepoints,
                                 CacheControl cache,
                                 String windowTitle,
                                 ProgressWriter progressWriter,
                                 ViewerOptions options)

Deprecated.

BigDataViewer

public BigDataViewer(List<ConverterSetup> converterSetups,
                     List<SourceAndConverter<?>> sources,
                     mpicbg.spim.data.generic.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 net.imglib2.type.numeric.NumericType<T>> net.imglib2.converter.Converter<T,net.imglib2.type.numeric.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 net.imglib2.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(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
                              List<ConverterSetup> converterSetups,
                              List<SourceAndConverter<?>> sources)

open

public static BigDataViewer open(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
                                 String windowTitle,
                                 ProgressWriter progressWriter,
                                 ViewerOptions options)

open

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

Throws:

mpicbg.spim.data.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()

getKeymapManager

public KeymapManager getKeymapManager()

getAppearanceManager

public AppearanceManager getAppearanceManager()

tryLoadSettings

public boolean tryLoadSettings(String xmlFilename)

saveSettings

public void saveSettings()

saveSettings

public void saveSettings(String xmlFilename)
                  throws IOException

Throws:

IOException

getInputTriggerConfig

@Deprecated
public static org.scijava.ui.behaviour.io.InputTriggerConfig getInputTriggerConfig(ViewerOptions options)

Deprecated. This method is no longer used internally. InputTriggerConfigs are now managed through KeymapManager.

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").

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)