| Package | Description |
|---|---|
| icy.action |
Contains all Icy action command classes which are accessible through the search bar
|
| icy.canvas |
Contains base Icy canvas and related classes
|
| icy.common.listener.weak |
Contains common shared weak listener in Icy
|
| icy.file |
Contains all file operation tools and related objects
|
| icy.gui.component |
Contains all custom components related classes (component, UI, renderer, editor...)
|
| icy.gui.component.sequence |
Contains custom UI components for the Icy Sequence object
|
| icy.gui.dialog |
Contains all custom Dialog (modal frame)
|
| icy.gui.frame.sequence |
Contains custom frames for Sequence action / selection...
|
| icy.gui.inspector |
Contains all classes and components related to the Icy inspector
|
| icy.gui.lut |
Contains all graphic components related to the Icy LUT (Look Up Table)
|
| icy.gui.lut.abstract_ | |
| icy.gui.main |
Contains graphic components and objects for the main interface
|
| icy.gui.menu |
Contains graphic components and objects related to the main (Ribbon) menu
|
| icy.gui.sequence |
Contains all Sequence related graphic components and tools
|
| icy.gui.sequence.tools |
Contains all Sequence related graphic components tools
|
| icy.gui.viewer |
Contains all components and classes related to the Icy Viewer
|
| icy.image |
Contains all Image related stuff as the Icy image data structure, ColorModel, ColorSpace, ColorMap, Image tools...
|
| icy.imagej |
Contains all ImageJ related stuff (wrapper, integration...)
|
| icy.main |
Contains the main Icy class, responsible of the Icy application launch process (also contains the Icy version information)
|
| icy.painter |
Contains Icy Overlay / Painter structure definition and basics Overlay helper classes
|
| icy.plugin.abstract_ |
Plugin abstract classes
|
| icy.plugin.interface_ |
All supported plugin interface to specialize plugin in a specific task (Canvas, ROI, file importer...)
|
| icy.roi |
Contains all ROI (Region Of Interest) related classes and tools
|
| icy.sequence |
Contains Icy Sequence structure definition and associated objects / tools.
|
| icy.sequence.edit |
Contains Icy Sequence Edit structure definitions.
|
| icy.util |
Contains common utilities classes (String, XLS, XML, ZIP, JAR, OME, Graphics, Date, Shape, Class...)
|
| icy.vtk |
Contains VTK library related stuff (wrapper, tools)
|
| plugins.kernel.roi.descriptor.intensity |
Contains ROI Descriptor plugins for intensity informations (kernel)
|
| plugins.kernel.roi.descriptor.measure |
Contains ROI Descriptor plugins for basic size measurements (kernel)
|
| plugins.kernel.roi.descriptor.property |
Contains ROI Descriptor plugins for ROI properties (kernel)
|
| plugins.kernel.roi.roi2d |
Contains all 2D ROI classes included in the kernel
|
| plugins.kernel.roi.roi3d |
Contains all 3D ROI classes included in the kernel
|
| plugins.kernel.roi.roi4d |
Contains all 4D ROI classes included in the kernel
|
| plugins.kernel.roi.roi5d |
Contains all 5D ROI classes included in the kernel
|
| plugins.kernel.roi.tool | |
| plugins.tutorial.painter | |
| plugins.tutorial.roi | |
| plugins.tutorial.training | |
| plugins.tutorial.vtk |
| Modifier and Type | Field and Description |
|---|---|
Sequence |
RoiActions.SequenceRoiList.sequence |
| Constructor and Description |
|---|
RoiActions.SequenceRoiList(Sequence sequence,
java.util.List<ROI> rois) |
| Modifier and Type | Method and Description |
|---|---|
Sequence |
IcyCanvas.getRenderedSequence()
Deprecated.
|
Sequence |
IcyCanvas.getRenderedSequence(boolean canvasView)
Deprecated.
|
Sequence |
IcyCanvas.getRenderedSequence(boolean canvasView,
ProgressListener progressListener)
Return a sequence which contains rendered images.
|
Sequence |
IcyCanvas.getRenderedSequence(int imageType,
boolean canvasView)
Deprecated.
use
IcyCanvas.getRenderedSequence(boolean) instead |
Sequence |
IcyCanvas.getSequence() |
| Modifier and Type | Method and Description |
|---|---|
void |
IcyCanvas.sequenceClosed(Sequence sequence) |
| Modifier and Type | Method and Description |
|---|---|
void |
WeakActiveSequenceListener.sequenceActivated(Sequence sequence) |
void |
WeakActiveSequenceListener.sequenceDeactivated(Sequence sequence) |
| Modifier and Type | Method and Description |
|---|---|
static Sequence |
Saver.getCompatibleSequenceForWriter(loci.formats.IFormatWriter writer,
Sequence sequence,
int posT,
int posZ)
Returns a compatible Sequence representing the input sequence so it can be saved with the specified writer.
|
static Sequence |
Loader.internalLoadSingle(SequenceIdImporter importer,
ome.xml.meta.OMEXMLMetadata metadata,
int series,
int resolution,
java.awt.Rectangle region,
int minZ,
int maxZ,
int minT,
int maxT,
int channel,
boolean forceVolatile,
FileFrame loadingFrame)
Internal use only !
|
static Sequence |
Loader.loadSequence(java.io.File file)
Deprecated.
Use
Loader.loadSequence(File, int, boolean) instead. |
static Sequence |
Loader.loadSequence(java.io.File[] files,
int series,
boolean showProgress)
Deprecated.
|
static Sequence |
Loader.loadSequence(java.io.File file,
boolean showProgress)
Deprecated.
Use
Loader.loadSequence(File, int, boolean) instead. |
static Sequence |
Loader.loadSequence(java.io.File file,
int series,
boolean showProgress)
Deprecated.
Use
Loader.loadSequence(String, int, boolean) instead. |
static Sequence |
Loader.loadSequence(java.util.List<?> files)
Load a sequence from the specified list of file and returns it.
|
static Sequence |
Loader.loadSequence(java.util.List<?> files,
boolean showProgress)
Load a sequence from the specified list of file and returns it.
|
static Sequence |
Loader.loadSequence(java.util.List<?> files,
boolean display,
boolean addToRecent)
Deprecated.
|
static Sequence |
Loader.loadSequence(java.util.List<java.lang.String> paths,
int resolution,
java.awt.Rectangle region,
int minZ,
int maxZ,
int minT,
int maxT,
int channel,
boolean directory,
boolean addToRecent,
boolean showProgress)
Load a sequence from the specified list of file and returns it.
|
static Sequence |
Loader.loadSequence(java.util.List<java.lang.String> paths,
int resolution,
java.awt.Rectangle region,
int minZ,
int maxZ,
int minT,
int maxT,
int channel,
boolean forceVolatile,
boolean directory,
boolean addToRecent,
boolean showProgress)
Load a sequence from the specified list of file and returns it.
|
static Sequence |
Loader.loadSequence(SequenceFileImporter importer,
java.util.List<java.lang.String> paths,
boolean showProgress)
Load a sequence from the specified list of file and returns it.
|
static Sequence |
Loader.loadSequence(SequenceFileImporter importer,
java.util.List<java.lang.String> paths,
boolean addToRecent,
boolean showProgress)
Load a sequence from the specified list of file and returns it.
|
static Sequence |
Loader.loadSequence(SequenceFileImporter importer,
java.util.List<java.lang.String> paths,
int resolution,
java.awt.Rectangle region,
int minZ,
int maxZ,
int minT,
int maxT,
int channel,
boolean forceVolatile,
boolean directory,
boolean addToRecent,
boolean showProgress)
Load a sequence from the specified list of file and returns it.
|
static Sequence |
Loader.loadSequence(SequenceFileImporter importer,
java.lang.String path,
int series,
boolean showProgress)
Load a sequence from the specified file.
|
static Sequence |
Loader.loadSequence(SequenceFileImporter importer,
java.lang.String path,
int series,
boolean addToRecent,
boolean showProgress)
Loads the specified image file and return it as a Sequence, it can return
null
if an error occured. |
static Sequence |
Loader.loadSequence(SequenceFileImporter importer,
java.lang.String path,
int series,
int resolution,
java.awt.Rectangle region,
int minZ,
int maxZ,
int minT,
int maxT,
int channel,
boolean addToRecent,
boolean showProgress)
Loads the specified image file and return it as a Sequence, it can return
null
if an error occured. |
static Sequence |
Loader.loadSequence(SequenceFileImporter importer,
java.lang.String path,
int series,
int resolution,
java.awt.Rectangle region,
int minZ,
int maxZ,
int minT,
int maxT,
int channel,
boolean forceVolatile,
boolean addToRecent,
boolean showProgress)
Loads the specified image file and return it as a Sequence, it can return
null
if an error occured. |
static Sequence |
Loader.loadSequence(java.lang.String path,
int series,
boolean showProgress)
Load a sequence from the specified file.
|
static Sequence[] |
Loader.loadSequences(java.io.File[] files,
int[] series,
boolean separate,
boolean autoOrder,
boolean showProgress)
Deprecated.
|
static Sequence[] |
Loader.loadSequences(java.io.File[] files,
int series,
boolean separate,
boolean autoOrder,
boolean showProgress)
Deprecated.
|
static Sequence[] |
Loader.loadSequences(java.io.File file,
int[] series,
boolean showProgress)
Deprecated.
Use
Loader.loadSequence(File, int, boolean) instead. |
| Modifier and Type | Method and Description |
|---|---|
static java.util.List<Sequence> |
Loader.loadSequences(java.io.File file,
java.util.List<java.lang.Integer> series)
Deprecated.
Use
Loader.loadSequences(File, int[], boolean) instead. |
static java.util.List<Sequence> |
Loader.loadSequences(java.io.File file,
java.util.List<java.lang.Integer> series,
boolean showProgress)
Deprecated.
Use
Loader.loadSequences(File, int[], boolean) instead. |
static java.util.List<Sequence> |
Loader.loadSequences(java.io.File file,
java.util.List<java.lang.Integer> series,
boolean display,
boolean addToRecent)
Deprecated.
Use
Loader.loadSequences(File, int[], boolean) instead. |
static java.util.List<Sequence> |
Loader.loadSequences(java.util.List<java.io.File> files,
boolean separate)
Deprecated.
|
static java.util.List<Sequence> |
Loader.loadSequences(java.util.List<java.io.File> files,
boolean separate,
boolean showProgress)
Deprecated.
|
static java.util.List<Sequence> |
Loader.loadSequences(java.util.List<java.io.File> files,
boolean separate,
boolean display,
boolean addToRecent)
Deprecated.
|
static java.util.List<Sequence> |
Loader.loadSequences(java.util.List<java.io.File> files,
java.util.List<java.lang.Integer> series)
Deprecated.
|
static java.util.List<Sequence> |
Loader.loadSequences(java.util.List<java.io.File> files,
java.util.List<java.lang.Integer> series,
boolean separate)
Deprecated.
|
static java.util.List<Sequence> |
Loader.loadSequences(java.util.List<java.io.File> files,
java.util.List<java.lang.Integer> series,
boolean separate,
boolean showProgress)
Deprecated.
|
static java.util.List<Sequence> |
Loader.loadSequences(java.util.List<java.io.File> files,
java.util.List<java.lang.Integer> series,
boolean separate,
boolean autoOrder,
boolean showProgress)
Deprecated.
|
static java.util.List<Sequence> |
Loader.loadSequences(java.util.List<java.lang.String> paths,
int series,
boolean separate,
boolean autoOrder,
boolean addToRecent,
boolean showProgress)
Loads a list of sequence from the specified list of file and returns them.
|
static java.util.List<Sequence> |
Loader.loadSequences(SequenceFileImporter importer,
java.util.List<java.lang.String> paths,
int series,
boolean separate,
boolean autoOrder,
boolean addToRecent,
boolean showProgress)
Load a list of sequence from the specified list of file with the given
SequenceFileImporter and returns them. |
static java.util.List<Sequence> |
Loader.loadSequences(SequenceFileImporter importer,
java.util.List<java.lang.String> paths,
int series,
boolean forceVolatile,
boolean separate,
boolean autoOrder,
boolean addToRecent,
boolean showProgress)
Load a list of sequence from the specified list of file with the given
SequenceFileImporter and returns them. |
| Modifier and Type | Method and Description |
|---|---|
static Sequence |
Saver.getCompatibleSequenceForWriter(loci.formats.IFormatWriter writer,
Sequence sequence,
int posT,
int posZ)
Returns a compatible Sequence representing the input sequence so it can be saved with the specified writer.
|
static java.lang.String |
Loader.getSequenceName(Sequence sequence,
java.lang.String path,
boolean multiSerie,
int series) |
static boolean |
Saver.isCompatible(loci.formats.IFormatWriter writer,
Sequence sequence)
Return true if the specified writer is compatible to save the given Sequence.
|
static boolean |
Saver.isCompatible(ImageFileFormat imageFileFormat,
Sequence sequence)
Return true if the specified image file format is compatible to save the given Sequence.
|
static void |
Saver.save(loci.formats.IFormatWriter formatWriter,
Sequence sequence,
java.io.File file,
int fps,
boolean multipleFile,
boolean showProgress,
boolean addToRecent)
Save the specified sequence in the specified file.
|
static void |
Saver.save(loci.formats.IFormatWriter formatWriter,
Sequence sequence,
java.io.File file,
int zMin,
int zMax,
int tMin,
int tMax,
int fps,
boolean multipleFile,
boolean showProgress)
Deprecated.
|
static void |
Saver.save(loci.formats.IFormatWriter formatWriter,
Sequence sequence,
java.io.File file,
int zMin,
int zMax,
int tMin,
int tMax,
int fps,
boolean multipleFile,
boolean showProgress,
boolean addToRecent)
Deprecated.
|
static void |
Saver.save(Sequence sequence,
java.io.File file)
Save the specified sequence in the specified file.
|
static void |
Saver.save(Sequence sequence,
java.io.File file,
boolean multipleFiles)
Deprecated.
Use
Saver.save(Sequence, File, boolean, boolean) instead. |
static void |
Saver.save(Sequence sequence,
java.io.File file,
boolean multipleFiles,
boolean showProgress)
Save the specified sequence in the specified file.
|
static void |
Saver.save(Sequence sequence,
java.io.File file,
int fps,
boolean multipleFile,
boolean showProgress)
Save the specified sequence in the specified file.
|
static void |
Saver.save(Sequence sequence,
java.io.File file,
int zMin,
int zMax,
int tMin,
int tMax,
int fps,
boolean multipleFiles)
Deprecated.
Use
Saver.save(Sequence, File, int, boolean, boolean) instead. |
static void |
Saver.save(Sequence sequence,
java.io.File file,
int zMin,
int zMax,
int tMin,
int tMax,
int fps,
boolean multipleFile,
boolean showProgress)
Deprecated.
Use
Saver.save(Sequence, File, int, boolean, boolean) instead. |
boolean |
SequenceFileExporter.save(Sequence sequence,
java.lang.String path,
FileFrame loadingFrame)
Save the specified sequence in the specified file.
|
static void |
Loader.setupSequence(Sequence sequence,
SequenceIdImporter importer,
boolean multiSerie,
int series,
java.awt.Rectangle region,
int resolution,
int sizeZ,
int sizeT,
int sizeC,
int minZ,
int maxZ,
int minT,
int maxT,
int channel)
Setup the specified sequence object given the different opening informations
|
| Modifier and Type | Method and Description |
|---|---|
void |
AbstractRoisPanel.sequenceActivated(Sequence value) |
void |
AbstractRoisPanel.sequenceDeactivated(Sequence sequence) |
| Modifier and Type | Method and Description |
|---|---|
Sequence |
SequenceChooserPanel.getSelectedSequence() |
Sequence |
SequenceChooser.getSelectedSequence() |
| Modifier and Type | Method and Description |
|---|---|
void |
SequenceChooserPreviewPanel.sequenceChanged(Sequence sequence) |
void |
SequenceChooser.SequenceChooserListener.sequenceChanged(Sequence sequence)
Called when the sequence chooser selection changed for specified sequence.
|
void |
SequenceChooser.sequenceClosed(Sequence sequence) |
void |
SequenceChooser.sequenceOpened(Sequence sequence) |
void |
SequenceChooserPanel.setSelectedSequence(Sequence sequence) |
void |
SequenceChooser.setSelectedSequence(Sequence sequence) |
void |
SequenceChooser.setSequenceSelected(Sequence sequence)
Deprecated.
use
SequenceChooser.setSelectedSequence(Sequence) instead |
| Constructor and Description |
|---|
ImageSaverDialog(Sequence sequence)
Deprecated.
Use
LoaderDialog.AllImagesFileFilter instead. |
ImageSaverDialog(Sequence sequence,
boolean autoSave)
Deprecated.
Use
LoaderDialog.AllImagesFileFilter instead. |
ImageSaverDialog(Sequence sequence,
int defZ,
int defT)
Deprecated.
Use
LoaderDialog.AllImagesFileFilter instead. |
ImageSaverDialog(Sequence sequence,
int defZ,
int defT,
boolean autoSave)
Deprecated.
Use
LoaderDialog.AllImagesFileFilter instead. |
SaverDialog(Sequence sequence)
Saver Dialog
Display a dialog to select the destination file then save the specified sequence. |
SaverDialog(Sequence sequence,
boolean autoSave)
Saver Dialog
Display a dialog to select the destination file then save the specified sequence. |
SaverDialog(Sequence sequence,
int defZ,
int defT)
Deprecated.
Use
SaverDialog.SaverDialog(Sequence) instead |
SaverDialog(Sequence sequence,
int defZ,
int defT,
boolean autoSave)
Deprecated.
Use
SaverDialog.SaverDialog(Sequence, boolean) instead |
| Modifier and Type | Method and Description |
|---|---|
Sequence |
FocusedSequenceActionFrame.getSeqIn()
Deprecated.
|
Sequence |
ActiveSequenceActionFrame.getSeqIn()
Deprecated.
Use
ActiveSequenceActionFrame.getSequence() instead. |
Sequence |
SequenceActionFrame.getSequence() |
Sequence |
ActiveSequenceActionFrame.getSequence() |
| Modifier and Type | Method and Description |
|---|---|
void |
ActiveSequenceActionFrame.sequenceActivated(Sequence sequence) |
void |
SequenceActionFrame.SourceChangeListener.sequenceChanged(Sequence sequence) |
void |
FocusedSequenceActionFrame.sequenceClosed(Sequence sequence)
Deprecated.
|
void |
ActiveSequenceActionFrame.sequenceDeactivated(Sequence sequence) |
void |
FocusedSequenceActionFrame.SourceChangeListener.sourceSequenceChanged(Sequence seq) |
void |
ActiveSequenceActionFrame.SourceChangeListener.sourceSequenceChanged(Sequence seq) |
| Modifier and Type | Method and Description |
|---|---|
void |
UndoManagerPanel.sequenceActivated(Sequence sequence) |
void |
SequencePanel.sequenceActivated(Sequence sequence) |
void |
InspectorPanel.sequenceActivated(Sequence sequence) |
void |
UndoManagerPanel.sequenceDeactivated(Sequence sequence) |
void |
SequencePanel.sequenceDeactivated(Sequence sequence) |
void |
InspectorPanel.sequenceDeactivated(Sequence sequence) |
| Modifier and Type | Method and Description |
|---|---|
Sequence |
LUTViewer.getSequence() |
| Modifier and Type | Method and Description |
|---|---|
void |
ScalerViewer.sequenceClosed(Sequence sequence) |
void |
LUTViewer.sequenceClosed(Sequence sequence) |
| Modifier and Type | Method and Description |
|---|---|
Sequence |
IcyLutViewer.getSequence()
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
Sequence |
MainInterfaceGui.getActiveSequence() |
Sequence |
MainInterfaceBatch.getActiveSequence() |
Sequence |
MainInterface.getActiveSequence()
Returns the current active sequence.
|
Sequence |
MainInterfaceGui.getFirstSequenceContaining(Overlay overlay) |
Sequence |
MainInterfaceBatch.getFirstSequenceContaining(Overlay overlay) |
Sequence |
MainInterface.getFirstSequenceContaining(Overlay overlay)
Returns the first active sequence containing the specified Overlay
|
Sequence |
MainInterfaceGui.getFirstSequenceContaining(Painter painter)
Deprecated.
|
Sequence |
MainInterfaceBatch.getFirstSequenceContaining(Painter painter)
Deprecated.
|
Sequence |
MainInterface.getFirstSequenceContaining(Painter painter)
Deprecated.
Use
MainInterface.getFirstSequenceContaining(Overlay) instead. |
Sequence |
MainInterfaceGui.getFirstSequenceContaining(ROI roi) |
Sequence |
MainInterfaceBatch.getFirstSequenceContaining(ROI roi) |
Sequence |
MainInterface.getFirstSequenceContaining(ROI roi)
Returns the first active sequence containing the specified ROI
|
Sequence |
MainInterfaceGui.getFirstSequencesContaining(Painter painter)
Deprecated.
|
Sequence |
MainInterfaceBatch.getFirstSequencesContaining(Painter painter)
Deprecated.
|
Sequence |
MainInterface.getFirstSequencesContaining(Painter painter)
Deprecated.
|
Sequence |
MainInterfaceGui.getFirstSequencesContaining(ROI roi)
Deprecated.
|
Sequence |
MainInterfaceBatch.getFirstSequencesContaining(ROI roi) |
Sequence |
MainInterface.getFirstSequencesContaining(ROI roi)
Deprecated.
|
Sequence |
MainInterfaceGui.getFocusedSequence()
Deprecated.
|
Sequence |
MainInterfaceBatch.getFocusedSequence() |
Sequence |
MainInterface.getFocusedSequence()
Deprecated.
Use
MainInterface.getActiveSequence() instead. |
| Modifier and Type | Method and Description |
|---|---|
java.util.ArrayList<Sequence> |
MainInterfaceGui.getSequences() |
java.util.ArrayList<Sequence> |
MainInterfaceBatch.getSequences() |
java.util.ArrayList<Sequence> |
MainInterface.getSequences()
Returns the list of opened sequence (sequence actually displayed in a viewer)
|
java.util.ArrayList<Sequence> |
MainInterfaceGui.getSequences(java.lang.String name) |
java.util.ArrayList<Sequence> |
MainInterfaceBatch.getSequences(java.lang.String name) |
java.util.ArrayList<Sequence> |
MainInterface.getSequences(java.lang.String name)
Returns the list of opened sequence (sequence actually displayed in a viewer) matching the specified name.
|
java.util.List<Sequence> |
MainInterfaceGui.getSequencesContaining(Overlay overlay) |
java.util.ArrayList<Sequence> |
MainInterfaceBatch.getSequencesContaining(Overlay overlay) |
java.util.List<Sequence> |
MainInterface.getSequencesContaining(Overlay overlay)
Returns all active sequence containing the specified Overlay
|
java.util.ArrayList<Sequence> |
MainInterfaceGui.getSequencesContaining(Painter painter)
Deprecated.
|
java.util.ArrayList<Sequence> |
MainInterfaceBatch.getSequencesContaining(Painter painter)
Deprecated.
|
java.util.ArrayList<Sequence> |
MainInterface.getSequencesContaining(Painter painter)
Deprecated.
Use
MainInterface.getSequencesContaining(Overlay) instead. |
java.util.ArrayList<Sequence> |
MainInterfaceGui.getSequencesContaining(ROI roi) |
java.util.ArrayList<Sequence> |
MainInterfaceBatch.getSequencesContaining(ROI roi) |
java.util.ArrayList<Sequence> |
MainInterface.getSequencesContaining(ROI roi)
Returns all active sequence containing the specified ROI
|
| Modifier and Type | Method and Description |
|---|---|
void |
MainInterfaceGui.addSequence(Sequence sequence) |
void |
MainInterfaceBatch.addSequence(Sequence sequence) |
void |
MainInterface.addSequence(Sequence sequence)
Open a viewer for the specified sequence.
|
void |
MainInterfaceGui.closeSequence(Sequence sequence) |
void |
MainInterfaceBatch.closeSequence(Sequence sequence) |
void |
MainInterface.closeSequence(Sequence sequence)
Close all viewers displaying the specified sequence.
|
void |
MainInterfaceGui.closeViewersOfSequence(Sequence sequence)
Deprecated.
|
void |
MainInterfaceBatch.closeViewersOfSequence(Sequence sequence)
Deprecated.
|
void |
MainInterface.closeViewersOfSequence(Sequence sequence)
Deprecated.
Use
MainInterface.closeSequence(Sequence) instead. |
void |
FocusedSequenceListener.focusChanged(Sequence sequence)
Deprecated.
The focus just changed to another sequence.
|
Viewer |
MainInterfaceGui.getFirstViewer(Sequence sequence) |
Viewer |
MainInterfaceBatch.getFirstViewer(Sequence sequence) |
Viewer |
MainInterface.getFirstViewer(Sequence sequence)
Returns first viewer attached to specified sequence
|
java.util.ArrayList<Viewer> |
MainInterfaceGui.getViewers(Sequence sequence) |
java.util.ArrayList<Viewer> |
MainInterfaceBatch.getViewers(Sequence sequence) |
java.util.ArrayList<Viewer> |
MainInterface.getViewers(Sequence sequence)
Returns viewers attached to specified sequence
|
boolean |
MainInterfaceGui.isOpened(Sequence sequence) |
boolean |
MainInterfaceBatch.isOpened(Sequence sequence) |
boolean |
MainInterface.isOpened(Sequence sequence)
Returns true if specified sequence is currently opened (displayed in a viewer)
|
void |
ActiveSequenceListener.sequenceActivated(Sequence sequence)
Sequence just get the active state.
|
void |
GlobalSequenceListener.sequenceClosed(Sequence sequence)
Sequence was just closed (last viewer displaying the sequence just closed)
|
void |
ActiveSequenceListener.sequenceDeactivated(Sequence sequence)
Sequence just lost the active state.
|
void |
GlobalSequenceListener.sequenceOpened(Sequence sequence)
Sequence was just opened (first viewer displaying the sequence just opened)
|
| Modifier and Type | Method and Description |
|---|---|
static IcyCommandToggleMenuButton |
SequenceOperationTask.CopyConvertBand.getConvertButton(Sequence sequence,
DataType dataType,
boolean scaled,
org.pushingpixels.flamingo.api.common.CommandToggleButtonGroup group) |
void |
MainRibbon.sequenceActivated(Sequence sequence) |
void |
MainRibbon.sequenceDeactivated(Sequence sequence) |
| Modifier and Type | Method and Description |
|---|---|
void |
SequenceInfosPanel.sequenceActivated(Sequence sequence) |
void |
SequenceInfosPanel.sequenceDeactivated(Sequence sequence) |
void |
SequencePropertiesPanel.setSequence(Sequence sequence) |
void |
SequenceInfosPanel.updateInfosInternal(Sequence sequence) |
| Constructor and Description |
|---|
SequenceMetadataPanel(Sequence sequence)
Create the panel.
|
SequencePropertiesDialog(Sequence sequence) |
| Modifier and Type | Method and Description |
|---|---|
Sequence |
SequenceDimensionConvertPanel.getSequence() |
Sequence |
SequenceBaseResizePanel.getSequence() |
Sequence[] |
SequenceDimensionMergePanel.getSequences() |
| Constructor and Description |
|---|
SequenceBaseResizePanel(Sequence sequence)
Create the panel.
|
SequenceCanvasResizeFrame(Sequence sequence) |
SequenceCanvasResizePanel(Sequence sequence) |
SequenceDimensionAdjustFrame(Sequence sequence,
DimensionId dim) |
SequenceDimensionConvertFrame(Sequence sequence) |
SequenceDimensionConvertPanel(Sequence sequence) |
SequenceDimensionExtendFrame(Sequence sequence,
DimensionId dim) |
SequenceResizeFrame(Sequence sequence) |
SequenceResizePanel(Sequence sequence) |
| Modifier and Type | Method and Description |
|---|---|
Sequence |
Viewer.getRenderedSequence(boolean canvasView,
ProgressListener progressListener) |
Sequence |
Viewer.getSequence() |
| Modifier and Type | Method and Description |
|---|---|
void |
Viewer.sequenceClosed(Sequence sequence) |
| Constructor and Description |
|---|
Viewer(Sequence sequence) |
Viewer(Sequence sequence,
boolean visible) |
| Modifier and Type | Method and Description |
|---|---|
Sequence |
IcyBufferedImage.getOwnerSequence()
Return the owner sequence (can be null if the image is not owned in any Sequence)
|
| Modifier and Type | Method and Description |
|---|---|
static Sequence |
ImageJUtil.convertToIcySequence(ij.ImagePlus image,
ProgressListener progressListener)
Convert the specified ImageJ
ImagePlus object to Icy Sequence |
| Modifier and Type | Method and Description |
|---|---|
static ij.ImagePlus |
ImageJUtil.convertToImageJImage(Sequence sequence,
boolean useRoiManager,
ProgressListener progressListener)
Convert the specified Icy
Sequence object to ImageJ ImagePlus |
static ij.ImagePlus |
ImageJUtil.convertToImageJImage(Sequence sequence,
ProgressListener progressListener)
Convert the specified Icy
Sequence object to ImageJ ImagePlus |
| Modifier and Type | Method and Description |
|---|---|
static void |
Icy.addSequence(Sequence sequence)
Deprecated.
Uses
Icy.getMainInterface().addSequence(Sequence) instead. |
| Modifier and Type | Method and Description |
|---|---|
java.util.List<Sequence> |
Overlay.getSequences()
Returns all sequences where the overlay is currently attached.
|
java.util.ArrayList<Sequence> |
AbstractPainter.getSequences()
Deprecated.
Returns all sequences where the painter/overlay is currently attached.
|
| Modifier and Type | Method and Description |
|---|---|
void |
Overlay.attachTo(Sequence sequence)
Deprecated.
Use
addOverlay(Overlay) instead. |
void |
AbstractPainter.attachTo(Sequence sequence)
Deprecated.
Use
addPainter(Painter) instead. |
void |
Overlay.detachFrom(Sequence sequence)
Deprecated.
Use
removeOverlay(Overlay) instead. |
void |
AbstractPainter.detachFrom(Sequence sequence)
Deprecated.
Use
removePainter(Painter) instead. |
boolean |
Overlay.isAttached(Sequence sequence)
Returns
true if the overlay is attached to the specified Sequence. |
boolean |
AbstractPainter.isAttached(Sequence sequence)
Deprecated.
Returns
true if the overlay is attached to the specified Sequence. |
void |
PainterAdapter.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas)
Deprecated.
|
void |
Painter.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas)
Deprecated.
Paint method called to draw the painter.
|
void |
OverlayWrapper.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
void |
Overlay.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas)
Paint method called to draw the overlay.
|
void |
ImageOverlay.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
void |
Anchor3D.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
void |
Anchor2D.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
void |
Anchor3D.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas,
boolean simplified) |
void |
Anchor2D.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas,
boolean simplified) |
| Constructor and Description |
|---|
AbstractPainter(Sequence sequence)
Deprecated.
Uses the
Overlay class instead. |
Anchor2D(Sequence sequence)
Deprecated.
Use
Anchor2D.Anchor2D() instead. |
Anchor2D(Sequence sequence,
double x,
double y)
Deprecated.
Use
Anchor2D.Anchor2D(double, double) instead. |
Anchor2D(Sequence sequence,
double x,
double y,
java.awt.Color color)
Deprecated.
Use
Anchor2D.Anchor2D(double, double, Color, Color) instead. |
Anchor2D(Sequence sequence,
double x,
double y,
java.awt.Color color,
java.awt.Color selectedColor)
Deprecated.
Use
Anchor2D.Anchor2D(double, double, int) instead. |
Anchor2D(Sequence sequence,
double x,
double y,
int ray)
Deprecated.
Use
Anchor2D.Anchor2D(double, double, int) instead. |
Anchor2D(Sequence sequence,
double x,
double y,
int ray,
java.awt.Color color,
java.awt.Color selectedColor)
Deprecated.
Use
Anchor2D.Anchor2D(double, double, int, Color, Color) instead. |
Anchor2D(Sequence sequence,
java.awt.geom.Point2D position)
Deprecated.
Use
Anchor2D.Anchor2D(double, double) instead. |
Anchor2D(Sequence sequence,
java.awt.geom.Point2D position,
java.awt.Color color)
Deprecated.
Use
Anchor2D.Anchor2D(double, double, Color) instead. |
Anchor2D(Sequence sequence,
java.awt.geom.Point2D position,
java.awt.Color color,
java.awt.Color selectedColor)
Deprecated.
Use
Anchor2D.Anchor2D(double, double, Color, Color) instead. |
Anchor2D(Sequence sequence,
java.awt.geom.Point2D position,
int ray)
Deprecated.
Use
Anchor2D.Anchor2D(double, double, int) instead. |
Anchor2D(Sequence sequence,
java.awt.geom.Point2D position,
int ray,
java.awt.Color color)
Deprecated.
Use
Anchor2D.Anchor2D(Point2D, int, Color) instead. |
Anchor2D(Sequence sequence,
java.awt.geom.Point2D position,
int ray,
java.awt.Color color,
java.awt.Color selectedColor)
Deprecated.
Use
Anchor2D.Anchor2D(double, double, int, Color, Color) instead. |
PathAnchor2D(Sequence sequence,
double x1,
double y1,
double x2,
double y2,
double x3,
double y3,
int ray,
java.awt.Color color,
java.awt.Color selectedColor)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
Sequence |
Plugin.getActiveSequence() |
Sequence |
Plugin.getFocusedSequence()
Deprecated.
Use
Plugin.getActiveSequence() instead |
| Modifier and Type | Method and Description |
|---|---|
java.util.ArrayList<Sequence> |
Plugin.getSequences() |
| Modifier and Type | Method and Description |
|---|---|
void |
Plugin.addSequence(Sequence sequence) |
void |
Plugin.removeSequence(Sequence sequence) |
| Modifier and Type | Method and Description |
|---|---|
java.util.Map<ROIDescriptor,java.lang.Object> |
PluginROIDescriptor.compute(ROI roi,
Sequence sequence)
Computes the descriptor(s) (declared in the
PluginROIDescriptor.getDescriptors()) on the specified ROI. |
| Modifier and Type | Method and Description |
|---|---|
static Sequence |
ROIUtil.convertToSequence(java.util.List<ROI> inputRois,
int sizeX,
int sizeY,
int sizeC,
int sizeZ,
int sizeT,
DataType dataType,
boolean label)
Convert a list of ROI into a binary / labeled Sequence.
|
static Sequence |
ROIUtil.convertToSequence(java.util.List<ROI> inputRois,
Sequence sequence,
boolean label)
Convert a list of ROI into a binary / labeled Sequence.
|
static Sequence |
ROIUtil.convertToSequence(ROI inputRoi,
Sequence sequence)
Convert a single ROI into a binary / labeled Sequence.
|
Sequence |
ROI.getFirstSequence()
Return first sequence where ROI is attached
|
| Modifier and Type | Method and Description |
|---|---|
java.util.ArrayList<Sequence> |
ROI.getSequences()
Return sequences where ROI is attached
|
| Modifier and Type | Method and Description |
|---|---|
static ROI |
ROIUtil.adjustToSequence(ROI roi,
Sequence source,
Sequence destination)
Create a copy of the specified ROI coming from source sequence adjusted to the destination sequence.
|
static ROI |
ROIUtil.adjustToSequence(ROI roi,
Sequence source,
Sequence destination,
boolean translate,
boolean scale)
Create a copy of the specified ROI coming from source sequence adjusted to the destination sequence.
|
static ROI |
ROIUtil.adjustToSequence(ROI roi,
Sequence source,
Sequence destination,
boolean translate,
boolean scale,
boolean ignoreErrorOnScale)
Create a copy of the specified ROI coming from source sequence adjusted to the destination sequence.
|
void |
ROI.attachTo(Sequence sequence)
Deprecated.
use
addROI(ROI) instead |
abstract java.lang.Object |
ROIDescriptor.compute(ROI roi,
Sequence sequence)
Computes the descriptor on the specified ROI and return the result.
|
static java.lang.Object |
ROIUtil.computeDescriptor(java.util.Collection<ROIDescriptor> roiDescriptors,
java.lang.String descriptorId,
ROI roi,
Sequence sequence)
Computes the specified descriptor from the input
ROIDescriptor set on given ROI
and returns the result (or null if the descriptor is not found). |
static java.lang.Object |
ROIDescriptor.computeDescriptor(java.util.Collection<ROIDescriptor> roiDescriptors,
java.lang.String descriptorId,
ROI roi,
Sequence sequence)
Computes the specified descriptor from the input
ROIDescriptor set on given ROI
and returns the result (or null if the descriptor is not found). |
static java.lang.Object |
ROIUtil.computeDescriptor(java.util.Set<ROIDescriptor> roiDescriptors,
java.lang.String descriptorId,
ROI roi,
Sequence sequence)
Deprecated.
|
static java.lang.Object |
ROIUtil.computeDescriptor(java.lang.String descriptorId,
ROI roi,
Sequence sequence)
Computes the specified descriptor on given ROI and returns the result (or
null if the descriptor is
not found). |
static java.lang.Object |
ROIDescriptor.computeDescriptor(java.lang.String descriptorId,
ROI roi,
Sequence sequence)
Computes the specified descriptor on given ROI and returns the result (or
null if the descriptor is
not found). |
double |
ROI2D.computePerimeter(Sequence sequence)
Deprecated.
Perimeter computation cannot be cached so directly use #getLength(Sequence) instead.
|
double |
ROI3D.computeSurfaceArea(Sequence sequence)
Compute the surface area in um2 given the pixel size informations from the specified Sequence.
|
static Sequence |
ROIUtil.convertToSequence(java.util.List<ROI> inputRois,
Sequence sequence,
boolean label)
Convert a list of ROI into a binary / labeled Sequence.
|
static Sequence |
ROIUtil.convertToSequence(ROI inputRoi,
Sequence sequence)
Convert a single ROI into a binary / labeled Sequence.
|
static ROI |
ROI.create(java.lang.String className,
Sequence seq,
java.awt.geom.Point2D imagePoint,
boolean creation)
Deprecated.
Use
ROI.create(String, Point5D) instead. |
void |
ROI.detachFrom(Sequence sequence)
Deprecated.
use
removeROI(ROI) instead |
void |
ROI3D.ROI3DPainter.drawName(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas)
Draw the ROI name
|
void |
ROI2D.ROI2DPainter.drawName(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas)
Draw the ROI name
|
abstract void |
ROI3D.ROI3DPainter.drawROI(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas)
Draw the ROI
|
abstract void |
ROI2D.ROI2DPainter.drawROI(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas)
Draw the ROI
|
static java.lang.String |
ROIUtil.getArea(Sequence sequence,
ROI roi)
Deprecated.
Use
ROIAreaDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method instead. |
static java.lang.String |
ROIUtil.getArea(Sequence sequence,
ROI roi,
int roundSignificant)
Deprecated.
Use
ROIAreaDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method instead. |
static java.lang.String |
ROIUtil.getContourSize(Sequence sequence,
double contourPoints,
ROI roi,
int dim,
int roundSignificant)
Deprecated.
Use
ROIContourDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method instead. |
static java.lang.String |
ROIUtil.getContourSize(Sequence sequence,
ROI roi,
int dim)
Deprecated.
Use
ROIContourDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method instead. |
static java.lang.String |
ROIUtil.getContourSize(Sequence sequence,
ROI roi,
int dim,
int roundSignificant)
Deprecated.
Use
ROIContourDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method instead. |
static IntensityInfo |
ROIUtil.getIntensityInfo(Sequence sequence,
ROI roi)
Deprecated.
Use
ROIIntensityDescriptorsPlugin or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
static IntensityInfo |
ROIUtil.getIntensityInfo(Sequence sequence,
ROI roi,
int z,
int t,
int c)
Deprecated.
Use
ROIIntensityDescriptorsPlugin or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
static java.lang.String |
ROIUtil.getInteriorSize(Sequence sequence,
double interiorPoints,
ROI roi,
int dim,
int roundSignificant)
Deprecated.
Use
ROIInteriorDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
static java.lang.String |
ROIUtil.getInteriorSize(Sequence sequence,
ROI roi,
int dim)
Deprecated.
Use
ROIInteriorDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
static java.lang.String |
ROIUtil.getInteriorSize(Sequence sequence,
ROI roi,
int dim,
int roundSignificant)
Deprecated.
Use
ROIInteriorDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
double |
ROI3D.getLength(Sequence sequence) |
double |
ROI.getLength(Sequence sequence)
Computes and returns the length/perimeter of the ROI in um given the pixel size informations from the specified
Sequence.
|
static double |
ROIUtil.getMaxIntensity(Sequence sequence,
ROI roi)
Deprecated.
Use
ROIMaxIntensityDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
static double |
ROIUtil.getMaxIntensity(Sequence sequence,
ROI roi,
int z,
int t,
int c)
Deprecated.
Use
ROIMaxIntensityDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
static double |
ROIUtil.getMeanIntensity(Sequence sequence,
ROI roi)
Deprecated.
Use
ROIMeanIntensityDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
static double |
ROIUtil.getMeanIntensity(Sequence sequence,
ROI roi,
int z,
int t,
int c)
Deprecated.
Use
ROIMeanIntensityDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
static double |
ROIUtil.getMinIntensity(Sequence sequence,
ROI roi)
Deprecated.
Use
ROIMinIntensityDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
static double |
ROIUtil.getMinIntensity(Sequence sequence,
ROI roi,
int z,
int t,
int c)
Deprecated.
Use
ROIMinIntensityDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
static long |
ROIUtil.getNumPixel(Sequence sequence,
ROI roi)
Returns the number of sequence pixels contained in the specified ROI.
|
static long |
ROIUtil.getNumPixel(Sequence sequence,
ROI roi,
int z,
int t,
int c)
Returns the number of sequence pixels contained in the specified ROI.
|
double |
ROI2D.getPerimeter(Sequence sequence)
Deprecated.
Use
ROI.getLength(Sequence) instead |
static java.lang.String |
ROIUtil.getPerimeter(Sequence sequence,
ROI roi)
Deprecated.
Use
ROIPerimeterDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
static java.lang.String |
ROIUtil.getPerimeter(Sequence sequence,
ROI roi,
int roundSignificant)
Deprecated.
Use
ROIPerimeterDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
static double |
ROIUtil.getStandardDeviation(Sequence sequence,
ROI roi)
Deprecated.
Use
ROIStandardDeviationDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence)
method instead. |
static double |
ROIUtil.getStandardDeviation(Sequence sequence,
ROI roi,
int z,
int t,
int c)
Deprecated.
Use
ROIStandardDeviationDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence)
method instead. |
static double |
ROIUtil.getSumIntensity(Sequence sequence,
ROI roi)
Deprecated.
Use
ROISumIntensityDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
static double |
ROIUtil.getSumIntensity(Sequence sequence,
ROI roi,
int z,
int t,
int c)
Deprecated.
Use
ROISumIntensityDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
double |
ROI3D.getSurfaceArea(Sequence sequence)
Returns surface area of the 3D ROI in um2 given the pixel size informations from the specified Sequence.
|
static java.lang.String |
ROIUtil.getSurfaceArea(Sequence sequence,
ROI roi)
Deprecated.
Use
ROISurfaceAreaDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
static java.lang.String |
ROIUtil.getSurfaceArea(Sequence sequence,
ROI roi,
int roundSignificant)
Deprecated.
Use
ROISurfaceAreaDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method
instead. |
java.lang.String |
ROIDescriptor.getUnit(Sequence sequence)
Returns the unit of this descriptor (
ex: "px", "mm", "µm2"... |
static java.lang.String |
ROIUtil.getVolume(Sequence sequence,
ROI roi)
Deprecated.
Use
ROIVolumeDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method instead. |
static java.lang.String |
ROIUtil.getVolume(Sequence sequence,
ROI roi,
int roundSignificant)
Deprecated.
Use
ROIVolumeDescriptor or ROIUtil.computeDescriptor(String, ROI, Sequence) method instead. |
boolean |
ROI.isAttached(Sequence sequence)
Return true is this ROI is attached to at least one sequence
|
void |
ROI3D.ROI3DPainter.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
void |
ROI2D.ROI2DPainter.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
void |
ROI.ROIPainter.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
| Modifier and Type | Method and Description |
|---|---|
static Sequence |
SequenceUtil.concatC(Sequence[] sequences)
Create and returns a new sequence by concatenating all given sequences on C dimension.
|
static Sequence |
SequenceUtil.concatC(Sequence[] sequences,
boolean fillEmpty,
boolean rescale)
Create and returns a new sequence by concatenating all given sequences on C dimension.
|
static Sequence |
SequenceUtil.concatC(Sequence[] sequences,
boolean fillEmpty,
boolean rescale,
ProgressListener pl)
Create and returns a new sequence by concatenating all given sequences on C dimension.
|
static Sequence |
SequenceUtil.concatC(Sequence[] sequences,
int[] channels,
boolean fillEmpty,
boolean rescale,
ProgressListener pl)
Create and returns a new sequence by concatenating all given sequences on C dimension.
|
static Sequence |
SequenceUtil.concatT(Sequence[] sequences)
Create and returns a new sequence by concatenating all given sequences on T dimension.
|
static Sequence |
SequenceUtil.concatT(Sequence[] sequences,
boolean interlaced,
boolean fillEmpty,
boolean rescale)
Create and returns a new sequence by concatenating all given sequences on T dimension.
|
static Sequence |
SequenceUtil.concatT(Sequence[] sequences,
boolean interlaced,
boolean fillEmpty,
boolean rescale,
ProgressListener pl)
Create and returns a new sequence by concatenating all given sequences on T dimension.
|
static Sequence |
SequenceUtil.concatZ(Sequence[] sequences)
Create and returns a new sequence by concatenating all given sequences on Z dimension.
|
static Sequence |
SequenceUtil.concatZ(Sequence[] sequences,
boolean interlaced,
boolean fillEmpty,
boolean rescale)
Create and returns a new sequence by concatenating all given sequences on Z dimension.
|
static Sequence |
SequenceUtil.concatZ(Sequence[] sequences,
boolean interlaced,
boolean fillEmpty,
boolean rescale,
ProgressListener pl)
Create and returns a new sequence by concatenating all given sequences on Z dimension.
|
static Sequence |
SequenceUtil.convertColor(Sequence source,
int imageType,
LUT lut)
Do color conversion of the specified
Sequence into the specified type. |
Sequence |
Sequence.convertToType(DataType dataType,
boolean rescale)
Deprecated.
|
Sequence |
Sequence.convertToType(DataType dataType,
Scaler scaler)
Deprecated.
|
Sequence |
Sequence.convertToType(int dataType,
boolean signed,
boolean rescale)
Deprecated.
|
static Sequence |
SequenceUtil.convertToType(Sequence source,
DataType dataType,
boolean rescale)
Converts the source sequence to the specified data type.
|
static Sequence |
SequenceUtil.convertToType(Sequence source,
DataType dataType,
boolean rescale,
boolean useDataBounds)
Converts the source sequence to the specified data type.
|
static Sequence |
SequenceUtil.convertToType(Sequence source,
DataType dataType,
Scaler scaler)
Deprecated.
|
static Sequence |
SequenceUtil.convertType(Sequence source,
DataType dataType,
Scaler[] scalers)
Converts the source sequence to the specified data type.
|
Sequence |
Sequence.extractBand(int bandNumber)
Deprecated.
Use
SequenceUtil.extractChannel(Sequence, int) instead |
Sequence |
Sequence.extractBands(java.util.List<java.lang.Integer> bandNumbers)
Deprecated.
Use
SequenceUtil.extractChannels(Sequence, List) instead |
Sequence |
Sequence.extractChannel(int channelNumber)
Deprecated.
Use
SequenceUtil.extractChannel(Sequence, int) instead. |
static Sequence |
SequenceUtil.extractChannel(Sequence source,
int channel)
Build a new single channel sequence (grey) from the specified channel of the source sequence.
|
Sequence |
Sequence.extractChannels(java.util.List<java.lang.Integer> channelNumbers)
Deprecated.
Use
SequenceUtil.extractChannels(Sequence, List) instead. |
static Sequence |
SequenceUtil.extractChannels(Sequence source,
int... channels)
Build a new sequence by extracting the specified channels from the source sequence.
|
static Sequence |
SequenceUtil.extractChannels(Sequence source,
java.util.List<java.lang.Integer> channels)
Deprecated.
Use
SequenceUtil.extractChannels(Sequence, int...) instead. |
static Sequence |
SequenceUtil.extractFrame(Sequence source,
int t)
Build a new sequence by extracting the specified T frame from the source sequence.
|
static Sequence |
SequenceUtil.extractSlice(Sequence source,
int z)
Build a new sequence by extracting the specified Z slice from the source sequence.
|
Sequence |
Sequence.getCopy()
Deprecated.
Use
SequenceUtil.getCopy(Sequence) instead. |
static Sequence |
SequenceUtil.getCopy(Sequence source)
Creates and return a copy of the sequence.
|
static Sequence |
SequenceUtil.getCopy(Sequence source,
boolean copyROI,
boolean copyOverlay,
boolean nameSuffix)
Creates and return a copy of the sequence.
|
Sequence |
SequenceBuilder.getResult()
Return the output sequence
|
Sequence |
SequenceEvent.getSequence() |
Sequence |
Sequence.getSubSequence(int startX,
int startY,
int startZ,
int startT,
int sizeX,
int sizeY,
int sizeZ,
int sizeT)
Deprecated.
|
static Sequence |
SequenceUtil.getSubSequence(Sequence source,
int startX,
int startY,
int startZ,
int startT,
int sizeX,
int sizeY,
int sizeZ,
int sizeT)
Deprecated.
|
static Sequence |
SequenceUtil.getSubSequence(Sequence source,
int startX,
int startY,
int startC,
int startZ,
int startT,
int sizeX,
int sizeY,
int sizeC,
int sizeZ,
int sizeT)
Deprecated.
|
static Sequence |
SequenceUtil.getSubSequence(Sequence source,
Rectangle5D.Integer region)
Creates a new sequence from the specified region of the source sequence.
|
static Sequence |
SequenceUtil.getSubSequence(Sequence source,
ROI roi)
Creates a new sequence which is a sub part of the source sequence defined by the specified
ROI bounds. |
static Sequence |
SequenceUtil.getSubSequence(Sequence source,
ROI roi,
double nullValue)
Creates a new sequence which is a sub part of the source sequence defined by the specified
ROI
bounds. |
Sequence |
SequenceImporter.load()
Launch the importer.
|
static Sequence |
SequenceUtil.rotate(Sequence source,
double angle)
Return a rotated version of the source Sequence with specified parameters.
|
static Sequence |
SequenceUtil.rotate(Sequence source,
double xOrigin,
double yOrigin,
double angle,
IcyBufferedImageUtil.FilterType filterType)
Return a rotated version of the source sequence with specified parameters.
|
static Sequence |
SequenceUtil.rotate(Sequence source,
double angle,
IcyBufferedImageUtil.FilterType filterType)
Return a rotated version of the source Sequence with specified parameters.
|
static Sequence |
SequenceUtil.scale(Sequence source,
int width,
int height)
Return a copy of the sequence with specified size.
|
static Sequence |
SequenceUtil.scale(Sequence source,
int width,
int height,
boolean resizeContent,
int xAlign,
int yAlign)
Return a copy of the sequence with specified size.
|
static Sequence |
SequenceUtil.scale(Sequence source,
int width,
int height,
boolean resizeContent,
int xAlign,
int yAlign,
IcyBufferedImageUtil.FilterType filterType)
Return a copy of the source sequence with specified size, alignment rules and filter type.
|
static Sequence |
SequenceUtil.scale(Sequence source,
int width,
int height,
IcyBufferedImageUtil.FilterType filterType)
Return a copy of the sequence with specified size.
|
static Sequence |
SequenceUtil.toARGB(Sequence source)
Convert the specified sequence to ARGB sequence (4 channels)
|
static Sequence |
SequenceUtil.toGray(Sequence source)
Convert the specified sequence to gray sequence (single channel)
|
static Sequence |
SequenceUtil.toRGB(Sequence source)
Convert the specified sequence to RGB sequence (3 channels)
|
| Modifier and Type | Method and Description |
|---|---|
static void |
SequenceUtil.addT(Sequence sequence,
int num)
Add one or severals frames at position t.
|
static void |
SequenceUtil.addT(Sequence sequence,
int num,
boolean copyLast)
Add one or severals frames at position t.
|
static void |
SequenceUtil.addT(Sequence sequence,
int t,
int num)
Add one or severals frames at position t.
|
static void |
SequenceUtil.addT(Sequence sequence,
int t,
int num,
int copyLast)
Add one or severals frames at position t.
|
static void |
SequenceUtil.addZ(Sequence sequence,
int num)
Add one or severals slices at position z.
|
static void |
SequenceUtil.addZ(Sequence sequence,
int num,
boolean copyLast)
Add one or severals slices at position z.
|
static void |
SequenceUtil.addZ(Sequence sequence,
int z,
int num)
Add one or severals slices at position z.
|
static void |
SequenceUtil.addZ(Sequence sequence,
int z,
int num,
int copyLast)
Add one or severals slices at position z.
|
static void |
SequenceUtil.adjustZT(Sequence sequence,
int newSizeZ,
int newSizeT,
boolean reverseOrder)
Adjust Z and T dimension of the sequence.
|
static Sequence |
SequenceUtil.concatC(Sequence[] sequences)
Create and returns a new sequence by concatenating all given sequences on C dimension.
|
static Sequence |
SequenceUtil.concatC(Sequence[] sequences,
boolean fillEmpty,
boolean rescale)
Create and returns a new sequence by concatenating all given sequences on C dimension.
|
static Sequence |
SequenceUtil.concatC(Sequence[] sequences,
boolean fillEmpty,
boolean rescale,
ProgressListener pl)
Create and returns a new sequence by concatenating all given sequences on C dimension.
|
static Sequence |
SequenceUtil.concatC(Sequence[] sequences,
int[] channels,
boolean fillEmpty,
boolean rescale,
ProgressListener pl)
Create and returns a new sequence by concatenating all given sequences on C dimension.
|
static Sequence |
SequenceUtil.concatT(Sequence[] sequences)
Create and returns a new sequence by concatenating all given sequences on T dimension.
|
static Sequence |
SequenceUtil.concatT(Sequence[] sequences,
boolean interlaced,
boolean fillEmpty,
boolean rescale)
Create and returns a new sequence by concatenating all given sequences on T dimension.
|
static Sequence |
SequenceUtil.concatT(Sequence[] sequences,
boolean interlaced,
boolean fillEmpty,
boolean rescale,
ProgressListener pl)
Create and returns a new sequence by concatenating all given sequences on T dimension.
|
static Sequence |
SequenceUtil.concatZ(Sequence[] sequences)
Create and returns a new sequence by concatenating all given sequences on Z dimension.
|
static Sequence |
SequenceUtil.concatZ(Sequence[] sequences,
boolean interlaced,
boolean fillEmpty,
boolean rescale)
Create and returns a new sequence by concatenating all given sequences on Z dimension.
|
static Sequence |
SequenceUtil.concatZ(Sequence[] sequences,
boolean interlaced,
boolean fillEmpty,
boolean rescale,
ProgressListener pl)
Create and returns a new sequence by concatenating all given sequences on Z dimension.
|
static Sequence |
SequenceUtil.convertColor(Sequence source,
int imageType,
LUT lut)
Do color conversion of the specified
Sequence into the specified type. |
static java.awt.geom.Point2D |
SequenceUtil.convertPoint(java.awt.geom.Point2D pt,
Sequence source,
Sequence destination)
|
static Point3D |
SequenceUtil.convertPoint(Point3D pt,
Sequence source,
Sequence destination)
|
static java.awt.geom.Rectangle2D |
SequenceUtil.convertRectangle(java.awt.geom.Rectangle2D rect,
Sequence source,
Sequence destination)
|
static Rectangle3D |
SequenceUtil.convertRectangle(Rectangle3D rect,
Sequence source,
Sequence destination)
|
static void |
SequenceUtil.convertToStack(Sequence sequence)
Set all images of the sequence in Z dimension.
|
static void |
SequenceUtil.convertToTime(Sequence sequence)
Set all images of the sequence in T dimension.
|
static Sequence |
SequenceUtil.convertToType(Sequence source,
DataType dataType,
boolean rescale)
Converts the source sequence to the specified data type.
|
static Sequence |
SequenceUtil.convertToType(Sequence source,
DataType dataType,
boolean rescale,
boolean useDataBounds)
Converts the source sequence to the specified data type.
|
static Sequence |
SequenceUtil.convertToType(Sequence source,
DataType dataType,
Scaler scaler)
Deprecated.
|
static void |
SequenceUtil.convertToVolume(Sequence sequence)
Deprecated.
Use
SequenceUtil.convertToStack(Sequence) instead. |
static Sequence |
SequenceUtil.convertType(Sequence source,
DataType dataType,
Scaler[] scalers)
Converts the source sequence to the specified data type.
|
void |
Sequence.copyDataFrom(Sequence source)
Copy data from the specified Sequence
|
void |
Sequence.copyFrom(Sequence source,
boolean copyName)
Copy data and metadata from the specified Sequence
|
void |
Sequence.copyMetaDataFrom(Sequence source,
boolean copyName)
Copy metadata from the specified Sequence
|
static Sequence |
SequenceUtil.extractChannel(Sequence source,
int channel)
Build a new single channel sequence (grey) from the specified channel of the source sequence.
|
static Sequence |
SequenceUtil.extractChannels(Sequence source,
int... channels)
Build a new sequence by extracting the specified channels from the source sequence.
|
static Sequence |
SequenceUtil.extractChannels(Sequence source,
java.util.List<java.lang.Integer> channels)
Deprecated.
Use
SequenceUtil.extractChannels(Sequence, int...) instead. |
static Sequence |
SequenceUtil.extractFrame(Sequence source,
int t)
Build a new sequence by extracting the specified T frame from the source sequence.
|
static Sequence |
SequenceUtil.extractSlice(Sequence source,
int z)
Build a new sequence by extracting the specified Z slice from the source sequence.
|
static ome.xml.meta.OMEXMLMetadata |
MetaDataUtil.generateMetaData(Sequence sequence,
boolean separateChannel)
Generates Meta Data for the given Sequence.
|
static ome.xml.meta.OMEXMLMetadata |
MetaDataUtil.generateMetaData(Sequence sequence,
boolean useZ,
boolean useT,
boolean separateChannel)
Deprecated.
Use
MetaDataUtil.generateMetaData(Sequence, boolean) instead. |
static ome.xml.meta.OMEXMLMetadata |
MetaDataUtil.generateMetaData(Sequence sequence,
int sizeZ,
int sizeT,
boolean separateChannel)
Deprecated.
Use
MetaDataUtil.generateMetaData(Sequence, boolean) instead. |
static Sequence |
SequenceUtil.getCopy(Sequence source)
Creates and return a copy of the sequence.
|
static Sequence |
SequenceUtil.getCopy(Sequence source,
boolean copyROI,
boolean copyOverlay,
boolean nameSuffix)
Creates and return a copy of the sequence.
|
static IcyBufferedImage |
SequenceUtil.AddZHelper.getExtendedImage(Sequence sequence,
int t,
int z,
int insertPosition,
int numInsert,
int copyLast) |
static IcyBufferedImage |
SequenceUtil.AddTHelper.getExtendedImage(Sequence sequence,
int t,
int z,
int insertPosition,
int numInsert,
int copyLast) |
static IcyBufferedImage |
SequenceUtil.MergeCHelper.getImage(Sequence[] sequences,
int[] channels,
int sizeX,
int sizeY,
int t,
int z,
boolean fillEmpty,
boolean rescale) |
static IcyBufferedImage |
SequenceUtil.MergeZHelper.getImage(Sequence[] sequences,
int sizeX,
int sizeY,
int sizeC,
int t,
int z,
boolean interlaced,
boolean fillEmpty,
boolean rescale) |
static IcyBufferedImage |
SequenceUtil.MergeTHelper.getImage(Sequence[] sequences,
int sizeX,
int sizeY,
int sizeC,
int t,
int z,
boolean interlaced,
boolean fillEmpty,
boolean rescale) |
static IcyBufferedImage |
SequenceUtil.AdjustZTHelper.getImage(Sequence sequence,
int t,
int z,
int newSizeZ,
int newSizeT,
boolean reverseOrder) |
static int |
SequenceUtil.getMaxDim(Sequence[] sequences,
DimensionId dim)
Returns the max size of specified dimension for the given sequences.
|
static java.awt.Point |
SequenceUtil.getOriginPoint(java.awt.Point pt,
Sequence source)
Convert the given Point coordinate from the source Sequence into the original image coordinate (pixel)
This method use the getOriginResolution() and getOriginXYRegion() informations
to compute the original image position. |
static java.awt.Rectangle |
SequenceUtil.getOriginRectangle(java.awt.Rectangle rect,
Sequence source)
Convert the given Rectangle region from the source Sequence into the original image region coordinates
(pixel)
This method use the getOriginResolution() and getOriginXYRegion() informations
to compute the original image region coordinates. |
static Sequence |
SequenceUtil.getSubSequence(Sequence source,
int startX,
int startY,
int startZ,
int startT,
int sizeX,
int sizeY,
int sizeZ,
int sizeT)
Deprecated.
|
static Sequence |
SequenceUtil.getSubSequence(Sequence source,
int startX,
int startY,
int startC,
int startZ,
int startT,
int sizeX,
int sizeY,
int sizeC,
int sizeZ,
int sizeT)
Deprecated.
|
static Sequence |
SequenceUtil.getSubSequence(Sequence source,
Rectangle5D.Integer region)
Creates a new sequence from the specified region of the source sequence.
|
static Sequence |
SequenceUtil.getSubSequence(Sequence source,
ROI roi)
Creates a new sequence which is a sub part of the source sequence defined by the specified
ROI bounds. |
static Sequence |
SequenceUtil.getSubSequence(Sequence source,
ROI roi,
double nullValue)
Creates a new sequence which is a sub part of the source sequence defined by the specified
ROI
bounds. |
static void |
SequenceUtil.moveT(Sequence sequence,
int t,
int newT)
Modify frame position.
|
static void |
SequenceUtil.moveT(Sequence sequence,
int from,
int to,
int offset)
Modify T position of a range of frame by the specified offset
|
static void |
SequenceUtil.moveZ(Sequence sequence,
int z,
int newZ)
Modify slice position.
|
static void |
SequenceUtil.moveZ(Sequence sequence,
int from,
int to,
int offset)
Modify Z position of a range of slice by the specified offset
|
static void |
SequenceUtil.removeChannel(Sequence source,
int channel)
Remove the specified channel from the source sequence.
|
static void |
SequenceUtil.removeT(Sequence sequence,
int t)
Remove a frame at position t.
|
static void |
SequenceUtil.removeTAndShift(Sequence sequence,
int t)
Remove a frame at position t and shift all the further t by -1.
|
static void |
SequenceUtil.removeZ(Sequence sequence,
int z)
Remove a slice at position Z.
|
static void |
SequenceUtil.removeZAndShift(Sequence sequence,
int z)
Remove a slice at position t and shift all the further t by -1.
|
static void |
SequenceUtil.reverseT(Sequence sequence)
Reverse T frames order.
|
static void |
SequenceUtil.reverseZ(Sequence sequence)
Reverse Z slices order.
|
static Sequence |
SequenceUtil.rotate(Sequence source,
double angle)
Return a rotated version of the source Sequence with specified parameters.
|
static Sequence |
SequenceUtil.rotate(Sequence source,
double xOrigin,
double yOrigin,
double angle,
IcyBufferedImageUtil.FilterType filterType)
Return a rotated version of the source sequence with specified parameters.
|
static Sequence |
SequenceUtil.rotate(Sequence source,
double angle,
IcyBufferedImageUtil.FilterType filterType)
Return a rotated version of the source Sequence with specified parameters.
|
boolean |
SequenceExporter.save(Sequence sequence)
Launch the exporter and save the specified Sequence.
|
static Sequence |
SequenceUtil.scale(Sequence source,
int width,
int height)
Return a copy of the sequence with specified size.
|
static Sequence |
SequenceUtil.scale(Sequence source,
int width,
int height,
boolean resizeContent,
int xAlign,
int yAlign)
Return a copy of the sequence with specified size.
|
static Sequence |
SequenceUtil.scale(Sequence source,
int width,
int height,
boolean resizeContent,
int xAlign,
int yAlign,
IcyBufferedImageUtil.FilterType filterType)
Return a copy of the source sequence with specified size, alignment rules and filter type.
|
static Sequence |
SequenceUtil.scale(Sequence source,
int width,
int height,
IcyBufferedImageUtil.FilterType filterType)
Return a copy of the sequence with specified size.
|
void |
WeakSequenceListener.sequenceClosed(Sequence sequence) |
void |
SequenceListener.sequenceClosed(Sequence sequence)
Called when sequence has been closed (all viewers displaying it closed).
|
void |
SequenceAdapter.sequenceClosed(Sequence sequence) |
static void |
SequenceUtil.swapT(Sequence sequence,
int t1,
int t2)
Exchange 2 frames position on the sequence.
|
static void |
SequenceUtil.swapZ(Sequence sequence,
int z1,
int z2)
Exchange 2 slices position on the sequence.
|
static Sequence |
SequenceUtil.toARGB(Sequence source)
Convert the specified sequence to ARGB sequence (4 channels)
|
static Sequence |
SequenceUtil.toGray(Sequence source)
Convert the specified sequence to gray sequence (single channel)
|
static Sequence |
SequenceUtil.toRGB(Sequence source)
Convert the specified sequence to RGB sequence (3 channels)
|
| Constructor and Description |
|---|
SequenceBuilder(int sizeX,
int sizeY,
int sizeZ,
int sizeT,
int sizeC,
DataType dataType,
Sequence target)
If non-null, the 'target' argument will be used to store the result of the
sequence building process, and no new sequence will be created.
|
SequenceDataIterator(Sequence sequence)
Create a new SequenceData iterator to iterate all data.
|
SequenceDataIterator(Sequence sequence,
int z,
int t,
int c)
Create a new SequenceData iterator to iterate data of specified channel.
|
SequenceDataIterator(Sequence sequence,
int startX,
int endX,
int startY,
int endY,
int c,
int z,
int t)
Deprecated.
|
SequenceDataIterator(Sequence sequence,
int startX,
int endX,
int startY,
int endY,
int startC,
int endC,
int startZ,
int endZ,
int startT,
int endT)
Deprecated.
|
SequenceDataIterator(Sequence sequence,
Rectangle5D.Integer bounds5D)
Create a new SequenceData iterator to iterate data through the specified 5D region
(inclusive).
|
SequenceDataIterator(Sequence sequence,
java.awt.Rectangle XYBounds,
int z,
int t,
int c)
Create a new SequenceData iterator to iterate data through the specified dimensions
(inclusive).
|
SequenceDataIterator(Sequence sequence,
ROI roi)
Create a new SequenceData iterator to iterate data through the specified ROI.
|
SequenceDataIterator(Sequence sequence,
ROI roi,
boolean inclusive)
Create a new SequenceData iterator to iterate data through the specified ROI.
|
SequenceDataIterator(Sequence sequence,
ROI roi,
boolean inclusive,
int z,
int t,
int c)
Create a new SequenceData iterator to iterate data through the specified ROI.
|
SequenceEvent(Sequence sequence,
SequenceEvent.SequenceEventSourceType sourceType) |
SequenceEvent(Sequence sequence,
SequenceEvent.SequenceEventSourceType sourceType,
java.lang.Object source) |
SequenceEvent(Sequence sequence,
SequenceEvent.SequenceEventSourceType sourceType,
java.lang.Object source,
int param) |
SequenceEvent(Sequence sequence,
SequenceEvent.SequenceEventSourceType sourceType,
java.lang.Object source,
SequenceEvent.SequenceEventType type) |
SequenceEvent(Sequence sequence,
SequenceEvent.SequenceEventSourceType sourceType,
java.lang.Object source,
SequenceEvent.SequenceEventType type,
int param) |
SequenceEvent(Sequence sequence,
SequenceEvent.SequenceEventSourceType sourceType,
SequenceEvent.SequenceEventType type) |
SequencePersistent(Sequence sequence) |
VolumetricImage(Sequence seq) |
| Modifier and Type | Method and Description |
|---|---|
Sequence |
AbstractSequenceEdit.getSequence() |
| Constructor and Description |
|---|
AbstractROISequenceEdit(Sequence sequence,
ROI roi) |
AbstractROISequenceEdit(Sequence sequence,
ROI roi,
java.lang.String name) |
AbstractROISequenceEdit(Sequence sequence,
ROI roi,
java.lang.String name,
java.awt.Image icon) |
AbstractROIsSequenceEdit(Sequence sequence,
java.util.Collection<ROI> rois) |
AbstractROIsSequenceEdit(Sequence sequence,
java.util.Collection<ROI> rois,
java.lang.String name) |
AbstractROIsSequenceEdit(Sequence sequence,
java.util.Collection<ROI> rois,
java.lang.String name,
java.awt.Image icon) |
AbstractSequenceEdit(Sequence sequence) |
AbstractSequenceEdit(Sequence sequence,
java.awt.Image icon) |
AbstractSequenceEdit(Sequence sequence,
java.lang.String name) |
AbstractSequenceEdit(Sequence sequence,
java.lang.String name,
java.awt.Image icon) |
DataSequenceEdit(Sequence previous,
Sequence sequence) |
DataSequenceEdit(Sequence previous,
Sequence sequence,
java.awt.Image icon) |
DataSequenceEdit(Sequence previous,
Sequence sequence,
java.lang.String name) |
DataSequenceEdit(Sequence previous,
Sequence sequence,
java.lang.String name,
java.awt.Image icon) |
DefaultSequenceEdit(Sequence previous,
Sequence sequence) |
DefaultSequenceEdit(Sequence previous,
Sequence sequence,
java.awt.Image icon) |
MetadataSequenceEdit(ome.xml.meta.OMEXMLMetadata previous,
Sequence sequence) |
MetadataSequenceEdit(ome.xml.meta.OMEXMLMetadata previous,
Sequence sequence,
java.awt.Image icon) |
MetadataSequenceEdit(ome.xml.meta.OMEXMLMetadata previous,
Sequence sequence,
java.lang.String name) |
MetadataSequenceEdit(ome.xml.meta.OMEXMLMetadata previous,
Sequence sequence,
java.lang.String name,
java.awt.Image icon) |
ROIAddSequenceEdit(Sequence sequence,
ROI source) |
ROIAddSequenceEdit(Sequence sequence,
ROI source,
java.lang.String name) |
ROIAddsSequenceEdit(Sequence sequence,
java.util.Collection<ROI> rois) |
ROIAddsSequenceEdit(Sequence sequence,
java.util.Collection<ROI> rois,
java.lang.String name) |
ROIRemoveSequenceEdit(Sequence sequence,
ROI source) |
ROIRemovesSequenceEdit(Sequence sequence,
java.util.Collection<ROI> rois) |
ROIReplaceSequenceEdit(Sequence sequence,
ROI oldRoi,
ROI newRoi) |
ROIReplaceSequenceEdit(Sequence sequence,
ROI oldRoi,
ROI newRoi,
java.lang.String name) |
ROIReplacesSequenceEdit(Sequence sequence,
java.util.Collection<ROI> oldRois,
java.util.Collection<ROI> newRois) |
ROIReplacesSequenceEdit(Sequence sequence,
java.util.Collection<ROI> oldRois,
java.util.Collection<ROI> newRois,
java.lang.String name) |
| Modifier and Type | Method and Description |
|---|---|
static ome.xml.meta.OMEXMLMetadata |
OMEUtil.generateMetaData(Sequence sequence,
boolean separateChannel)
Deprecated.
Use
MetaDataUtil.generateMetaData(Sequence, boolean) instead. |
static ome.xml.meta.OMEXMLMetadata |
OMEUtil.generateMetaData(Sequence sequence,
boolean useZ,
boolean useT,
boolean separateChannel)
Deprecated.
Use
MetaDataUtil.generateMetaData(Sequence, boolean) instead. |
static ome.xml.meta.OMEXMLMetadata |
OMEUtil.generateMetaData(Sequence sequence,
int sizeZ,
int sizeT,
boolean separateChannel)
Deprecated.
Use
MetaDataUtil.generateMetaData(Sequence, boolean) instead. |
| Modifier and Type | Method and Description |
|---|---|
static vtk.vtkImageData |
VtkUtil.getImageData(Sequence sequence,
int posT,
int posC)
Build and return volume image data from given Sequence object.
|
| Modifier and Type | Method and Description |
|---|---|
java.lang.Object |
ROISumIntensityDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIStandardDeviationDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIMinIntensityDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIMeanIntensityDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIMaxIntensityDescriptor.compute(ROI roi,
Sequence sequence) |
java.util.Map<ROIDescriptor,java.lang.Object> |
ROIIntensityDescriptorsPlugin.compute(ROI roi,
Sequence sequence) |
static ROIIntensityDescriptorsPlugin.IntensityDescriptorInfos |
ROIIntensityDescriptorsPlugin.computeIntensityDescriptors(ROI roi,
Sequence sequence,
boolean allowMultiChannel)
Returns the pixel intensity information for the specified ROI and Sequence.
|
static double |
ROIMaxIntensityDescriptor.computeMaxIntensity(ROI roi,
Sequence sequence)
Computes and returns the maximum intensity for the specified ROI on given sequence.
|
static double |
ROIMeanIntensityDescriptor.computeMeanIntensity(ROI roi,
Sequence sequence)
Computes and returns the mean intensity for the specified ROI on given sequence.
|
static double |
ROIMinIntensityDescriptor.computeMinIntensity(ROI roi,
Sequence sequence)
Computes and returns the minimum intensity for the specified ROI on given sequence.
|
static double |
ROIStandardDeviationDescriptor.computeStandardDeviation(ROI roi,
Sequence sequence)
Computes and returns the compute standard deviation for the specified ROI on given sequence.
|
static double |
ROISumIntensityDescriptor.computeSumIntensity(ROI roi,
Sequence sequence)
Computes and returns the intensity sum for the specified ROI on given sequence.
|
| Modifier and Type | Method and Description |
|---|---|
java.lang.Object |
ROIVolumeDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROISurfaceAreaDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIPerimeterDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIMassCenterZDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIMassCenterYDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIMassCenterXDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIMassCenterTDescriptor.compute(ROI roi,
Sequence sequence) |
java.util.Map<ROIDescriptor,java.lang.Object> |
ROIMassCenterDescriptorsPlugin.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIMassCenterCDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIInteriorDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIContourDescriptor.compute(ROI roi,
Sequence sequence) |
java.util.Map<ROIDescriptor,java.lang.Object> |
ROIBasicMeasureDescriptorsPlugin.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIAreaDescriptor.compute(ROI roi,
Sequence sequence) |
static double |
ROIAreaDescriptor.computeArea(double interiorPoints,
ROI roi,
Sequence sequence)
Computes and returns the surface area from a given number of contour points expressed in the
unit of the descriptor (see
ROIAreaDescriptor.getUnit(Sequence)) for the specified sequence and ROI. |
static double |
ROIAreaDescriptor.computeArea(ROI roi,
Sequence sequence)
Computes and returns the area expressed in the unit of the descriptor (see
ROIAreaDescriptor.getUnit(Sequence)) for the
specified ROI. |
static double |
ROIInteriorDescriptor.computeInterior(double interiorPoints,
ROI roi,
Sequence sequence,
int dim)
Returns the interior size from a given number of interior points in the best unit (see
getBestPixelSizeUnit(int, int)) for the specified sequence and dimension. |
static double |
ROIPerimeterDescriptor.computePerimeter(ROI roi,
Sequence sequence)
Computes and returns the perimeter expressed in the unit of the descriptor (see
ROIPerimeterDescriptor.getUnit(Sequence)) for
the specified ROI. |
static double |
ROISurfaceAreaDescriptor.computeSurfaceArea(ROI roi,
Sequence sequence)
Computes and returns the surface area expressed in the unit of the descriptor (see
ROISurfaceAreaDescriptor.getUnit(Sequence))
for the specified ROI. |
static double |
ROIVolumeDescriptor.computeVolume(double interiorPoints,
ROI roi,
Sequence sequence)
Computes and returns the volume from a given number of interior points expressed in the
unit of the descriptor (see
ROIVolumeDescriptor.getUnit(Sequence)) for the specified sequence and ROI. |
static double |
ROIVolumeDescriptor.computeVolume(ROI roi,
Sequence sequence)
Computes and returns the volume expressed in the unit of the descriptor (see
ROIVolumeDescriptor.getUnit(Sequence)) for the
specified ROI. |
static double |
ROIBasicMeasureDescriptorsPlugin.getMultiplierFactor(Sequence sequence,
ROI roi,
int dim)
Calculate the multiplier factor depending the wanted dimension information.
|
java.lang.String |
ROIVolumeDescriptor.getUnit(Sequence sequence) |
java.lang.String |
ROISurfaceAreaDescriptor.getUnit(Sequence sequence) |
java.lang.String |
ROIPerimeterDescriptor.getUnit(Sequence sequence) |
java.lang.String |
ROIInteriorDescriptor.getUnit(Sequence sequence) |
java.lang.String |
ROIContourDescriptor.getUnit(Sequence sequence) |
java.lang.String |
ROIAreaDescriptor.getUnit(Sequence sequence) |
| Modifier and Type | Method and Description |
|---|---|
java.lang.Object |
ROISizeZDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROISizeYDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROISizeXDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROISizeTDescriptor.compute(ROI roi,
Sequence sequence) |
java.util.Map<ROIDescriptor,java.lang.Object> |
ROISizeDescriptorsPlugin.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROISizeCDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIReadOnlyDescriptor.compute(ROI roi,
Sequence sequence) |
java.util.Map<ROIDescriptor,java.lang.Object> |
ROIPropertyDescriptorsPlugin.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIPositionZDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIPositionYDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIPositionXDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIPositionTDescriptor.compute(ROI roi,
Sequence sequence) |
java.util.Map<ROIDescriptor,java.lang.Object> |
ROIPositionDescriptorsPlugin.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIPositionCDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIOpacityDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROINameDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIIconDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIGroupIdDescriptor.compute(ROI roi,
Sequence sequence) |
java.lang.Object |
ROIColorDescriptor.compute(ROI roi,
Sequence sequence) |
| Modifier and Type | Method and Description |
|---|---|
void |
ROI2DShape.ROI2DShapePainter.drawROI(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas)
Draw the ROI
|
void |
ROI2DPoint.ROI2DPointPainter.drawROI(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
void |
ROI2DArea.ROI2DAreaPainter.drawROI(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas)
Draw the ROI itself
|
double |
ROI2DShape.getLength(Sequence sequence) |
double |
ROI2DEllipse.getLength(Sequence sequence) |
void |
ROI2DArea.ROI2DAreaPainter.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
| Modifier and Type | Method and Description |
|---|---|
double |
ROI3DStack.computeSurfaceArea(Sequence sequence) |
double |
ROI3DShape.computeSurfaceArea(Sequence sequence) |
void |
ROI3DStack.ROI3DStackPainter.drawROI(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
void |
ROI3DShape.ROI3DShapePainter.drawROI(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas)
Draw the ROI
|
void |
ROI3DPolyLine.ROI3DPolyLinePainter.drawROI(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
void |
ROI3DPoint.ROI3DPointPainter.drawROI(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
void |
ROI3DLine.ROI3DLinePainter.drawROI(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
double |
ROI3DShape.getLength(Sequence sequence) |
void |
ROI3DStackShape.ROI3DStackShapePainter.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
void |
ROI3DStack.ROI3DStackPainter.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
void |
ROI3DArea.ROI3DAreaPainter.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
| Modifier and Type | Method and Description |
|---|---|
void |
ROI4DStack.ROI4DStackPainter.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
| Modifier and Type | Method and Description |
|---|---|
void |
ROI5DStack.ROI5DStackPainter.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
ROILineCutter.splitOverlappedROIs(java.util.List<Sequence> sequences)
This is a special function of this ROI, it cuts all overlapped ROI from given Sequences based on the current ROI
shape (line).
|
| Modifier and Type | Method and Description |
|---|---|
void |
AnimatedOverlay.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
| Modifier and Type | Method and Description |
|---|---|
void |
IntensityOverRoiPainter.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
void |
ProcessingFromROI.sequenceClosed(Sequence sequence) |
| Modifier and Type | Method and Description |
|---|---|
void |
OverlayPlugin1.SimpleCrossOverlay.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |
| Modifier and Type | Method and Description |
|---|---|
void |
VtkLabelPainter.paint(java.awt.Graphics2D g,
Sequence sequence,
IcyCanvas canvas) |