Sequence

java.lang.Object
- icy.sequence.Sequence

All Implemented Interfaces:

ChangeListener, IcyColorModelListener, IcyBufferedImageListener, OverlayListener, ROIListener, SequenceModel, java.util.EventListener
```
public class Sequence
extends java.lang.Object
implements SequenceModel, IcyColorModelListener, IcyBufferedImageListener, ChangeListener, ROIListener, OverlayListener
```
Image sequence object.
A Sequence is basically a 5 dimension (XYCZT) image where :
XY dimension = planar image
C dimension = channel
Z dimension = depth
T dimension = time

The XYC dimensions are bounded into the IcyBufferedImage object so Sequence define a list of IcyBufferedImage where each image is associated to a Z and T information.

Author:

Fabrice de Chaumont & Stephane

Nested Class Summary
- Nested classes/interfaces inherited from interface icy.sequence.SequenceModel
  SequenceModel.SequenceModelListener

Field Summary

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`DEFAULT_NAME`
`static java.lang.String`	`ID_CHANNEL_NAME`
`static java.lang.String`	`ID_NAME`
`static java.lang.String`	`ID_PIXEL_SIZE_X`
`static java.lang.String`	`ID_PIXEL_SIZE_Y`
`static java.lang.String`	`ID_PIXEL_SIZE_Z`
`static java.lang.String`	`ID_POSITION_T`
`static java.lang.String`	`ID_POSITION_T_OFFSET`
`static java.lang.String`	`ID_POSITION_X`
`static java.lang.String`	`ID_POSITION_Y`
`static java.lang.String`	`ID_POSITION_Z`
`static java.lang.String`	`ID_TIME_INTERVAL`
`static java.lang.String`	`ID_VIRTUAL`
`static int`	`TYPE_BYTE` Deprecated.
`static int`	`TYPE_DOUBLE` Deprecated.
`static int`	`TYPE_FLOAT` Deprecated.
`static int`	`TYPE_INT` Deprecated.
`static int`	`TYPE_SHORT` Deprecated.
`static int`	`TYPE_UNDEFINED` Deprecated.

Constructor Summary

Constructors
Constructor and Description
`Sequence()` Creates an empty sequence.
`Sequence(java.awt.image.BufferedImage image)` Creates a sequence containing the specified image.
`Sequence(IcyBufferedImage image)` Creates a sequence containing the specified image.
`Sequence(ome.xml.meta.OMEXMLMetadata meta)` Creates a new empty sequence with specified metadata.
`Sequence(loci.formats.ome.OMEXMLMetadataImpl meta)` Deprecated. Use `Sequence(OMEXMLMetadata)` instead.
`Sequence(loci.formats.ome.OMEXMLMetadataImpl meta, java.lang.String name)` Deprecated. Use `Sequence(OMEXMLMetadata, String)` instead.
`Sequence(ome.xml.meta.OMEXMLMetadata meta, java.lang.String name)` Creates a new empty sequence with specified meta data object and name.
`Sequence(java.lang.String name)` Creates an empty sequence with specified name.
`Sequence(java.lang.String name, java.awt.image.BufferedImage image)` Creates a sequence with specified name and containing the specified image
`Sequence(java.lang.String name, IcyBufferedImage image)` Creates a sequence with specified name and containing the specified image

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addImage(java.awt.image.BufferedImage image)` Add an image (image is added in Z dimension).
`void`	`addImage(int t, java.awt.image.BufferedImage image)` Add an image at specified T position.
`void`	`addListener(SequenceListener listener)` Add the specified listener to listeners list
`boolean`	`addOverlay(Overlay overlay)` Add an overlay to the sequence.
`boolean`	`addPainter(Painter painter)` Deprecated. Use `addOverlay(Overlay)` instead.
`boolean`	`addROI(ROI roi)` Add the specified ROI to the sequence.
`boolean`	`addROI(ROI roi, boolean canUndo)` Add the specified ROI to the sequence.
`boolean`	`addROIs(java.util.Collection<? extends ROI> rois, boolean canUndo)` Add the specified collection of ROI to the sequence.
`void`	`addSequenceModelListener(SequenceModel.SequenceModelListener listener)` Add the specified `SequenceModel.SequenceModelListener` to listeners list
`boolean`	`addUndoableEdit(IcyUndoableEdit edit)` Add an Undoable edit to the Sequence UndoManager
`VolumetricImage`	`addVolumetricImage()` Add an empty volumetricImage at last index + 1
`VolumetricImage`	`addVolumetricImage(int t, VolumetricImage volImg)` Add a volumetricImage at t position It actually create a new volumetricImage and add it to the sequence The new created volumetricImage is returned
`void`	`beginUpdate()`
`double`	`calculateSize(double pixelNumber, int dimCompute, int dimResult)` Returns the size in �m for the specified amount of sample/pixel value in the specified dimension order.
`java.lang.String`	`calculateSize(double pixelNumber, int dimCompute, int dimResult, int significantDigit)` Returns the size and appropriate unit in form of String for specified amount of sample/pixel value in the specified dimension order.
`double`	`calculateSizeBestUnit(double pixelNumber, int dimCompute, int dimResult)` Returns the size converted in the best unit (see `getBestPixelSizeUnit(int, int)` for the specified amount of sample/pixel value in the specified dimension order.
`void`	`clearUndoManager()` Clear all undo operations from the `UndoManager`.
`void`	`close()` This method close all attached viewers
`void`	`closed()` Called when sequence has been closed (all viewers displaying it closed).
`void`	`colorModelChanged(IcyColorModelEvent e)`
`boolean`	`contains(Overlay overlay)` Returns true if the sequence contains the specified overlay
`boolean`	`contains(Painter painter)` Deprecated. Use `contains(Overlay)` instead.
`boolean`	`contains(ROI roi)` Returns true if the sequence contains the specified ROI
`Sequence`	`convertToType(DataType dataType, boolean rescale)` Deprecated. Use `SequenceUtil.convertToType(Sequence, DataType, boolean)` instead.
`Sequence`	`convertToType(DataType dataType, Scaler scaler)` Deprecated. Use `SequenceUtil.convertType(Sequence, DataType, Scaler[])` instead.
`Sequence`	`convertToType(int dataType, boolean signed, boolean rescale)` Deprecated. Use `SequenceUtil.convertToType(Sequence, DataType, boolean)` instead
`void`	`copyDataFrom(Sequence source)` Copy data from the specified Sequence
`void`	`copyFrom(Sequence source, boolean copyName)` Copy data and metadata from the specified Sequence
`void`	`copyMetaDataFrom(Sequence source, boolean copyName)` Copy metadata from the specified Sequence
`LUT`	`createCompatibleLUT()` Creates and returns the default LUT for this sequence.
`boolean`	`createUndoDataPoint(java.lang.String name)` Create a restore point for sequence data.
`boolean`	`createUndoMetadataPoint(java.lang.String name)` Create a restore point for sequence metadata.
`boolean`	`createUndoPoint(java.lang.String name)` Create a complete restore point for this sequence.
`void`	`dataChanged()` Data has changed (global change) Be careful, this implies all component bounds are recalculated, can be heavy !
`void`	`endUpdate()`
`Sequence`	`extractBand(int bandNumber)` Deprecated. Use `SequenceUtil.extractChannel(Sequence, int)` instead
`Sequence`	`extractBands(java.util.List<java.lang.Integer> bandNumbers)` Deprecated. Use `SequenceUtil.extractChannels(Sequence, List)` instead
`Sequence`	`extractChannel(int channelNumber)` Deprecated. Use `SequenceUtil.extractChannel(Sequence, int)` instead.
`Sequence`	`extractChannels(java.util.List<java.lang.Integer> channelNumbers)` Deprecated. Use `SequenceUtil.extractChannels(Sequence, List)` instead.
`void`	`fireModelDimensionChangedEvent()` fire model dimension changed event
`void`	`fireModelImageChangedEvent()` fire model image changed event
`java.util.ArrayList<IcyBufferedImage>`	`getAllImage()` Returns all images of sequence in [ZT] order: T=0 Z=0 T=0 Z=1 T=0 Z=2 ...
`java.util.ArrayList<VolumetricImage>`	`getAllVolumetricImage()` Returns all VolumetricImage
`boolean`	`getAutoUpdateChannelBounds()`
`UnitUtil.UnitPrefix`	`getBestPixelSizeUnit(int dimCompute, int dimResult)` Returns the best pixel size unit for the specified dimension order given the sequence's pixel size informations.
`java.awt.Rectangle`	`getBounds()` Deprecated. Use `getBounds2D()` instead
`java.awt.Rectangle`	`getBounds2D()` Returns 2D bounds of sequence {0, 0, sizeX, sizeY}
`Rectangle5D.Integer`	`getBounds5D()` Returns 5D bounds of sequence {0, 0, 0, 0, 0, sizeX, sizeY, sizeZ, sizeT, sizeC}
`double[]`	`getChannelBounds(int channel)` Get bounds (min and max values) in the whole sequence for the specified channel.
`double`	`getChannelMax(int channel)` Get maximum value in the whole sequence for the specified channel.
`double`	`getChannelMin(int channel)` Get the minimum value in the whole sequence for the specified channel.
`java.lang.String`	`getChannelName(int index)` Get name for specified channel
`double[][]`	`getChannelsBounds()` Get bounds (min and max values) in the whole sequence for all channels.
`double[]`	`getChannelsGlobalBounds()` Get global bounds (min and max values) in the whole sequence for all channels.
`double[]`	`getChannelsGlobalTypeBounds()` Get the global preferred data type bounds (min and max values) for all channels.
`double[][]`	`getChannelsTypeBounds()` Get the preferred data type bounds (min and max values) in the whole sequence for all channels.
`double[]`	`getChannelTypeBounds(int channel)` Get the preferred data type bounds (min and max values) in the whole sequence for the specified channel.
`double[]`	`getChannelTypeGlobalBounds()` Deprecated. Use `getChannelsGlobalTypeBounds()` instead
`double`	`getChannelTypeMax(int channel)` Get the preferred data type maximum value in the whole sequence for the specified channel.
`double`	`getChannelTypeMin(int channel)` Get the preferred data type minimum value in the whole sequence for the specified channel.
`IcyColorMap`	`getColorMap(int channel)` Get the user colormap for the specified channel.
`IcyColorModel`	`getColorModel()` Returns the colorModel
`double[]`	`getComponentAbsBounds(int component)` Deprecated. Use `getChannelTypeBounds(int)` instead.
`double`	`getComponentAbsMaxValue(int component)` Deprecated. Use `getChannelTypeMax(int)` instead.
`double`	`getComponentAbsMinValue(int component)` Deprecated. Use `getChannelTypeMin(int)` instead.
`double[][]`	`getComponentsAbsBounds()` Deprecated. Use `getChannelsTypeBounds()` instead.
`double[][]`	`getComponentsUserBounds()` Deprecated. Use `getChannelsBounds()` instead.
`double[]`	`getComponentUserBounds(int component)` Deprecated. Use `getChannelBounds(int)` instead.
`double`	`getComponentUserMaxValue(int component)` Deprecated. Use `getChannelMax(int)` instead.
`double`	`getComponentUserMinValue(int component)` Deprecated. Use `getChannelMin(int)` instead.
`Sequence`	`getCopy()` Deprecated. Use `SequenceUtil.getCopy(Sequence)` instead.
`double`	`getData(int t, int z, int c, int y, int x)` Returns the data value located at position (t, z, c, y, x) as double.
`java.lang.Object`	`getDataCopyC(int t, int z, int x, int y)` Returns a 1D array data copy [C] of specified t, z, x, y
`java.lang.Object`	`getDataCopyC(int t, int z, int x, int y, java.lang.Object out, int off)` Returns a 1D array data copy [C] of specified t, z, x, y If (out !
`byte[]`	`getDataCopyCAsByte(int t, int z, int x, int y)` Returns a 1D array data copy [C] of specified t, z, x, y
`byte[]`	`getDataCopyCAsByte(int t, int z, int x, int y, byte[] out, int off)` Returns a 1D array data copy [C] of specified t, z, x, y If (out !
`double[]`	`getDataCopyCAsDouble(int t, int z, int x, int y)` Returns a 1D array data copy [C] of specified t, z, x, y
`double[]`	`getDataCopyCAsDouble(int t, int z, int x, int y, double[] out, int off)` Returns a 1D array data copy [C] of specified t, z, x, y If (out !
`float[]`	`getDataCopyCAsFloat(int t, int z, int x, int y)` Returns a 1D array data copy [C] of specified t, z, x, y
`float[]`	`getDataCopyCAsFloat(int t, int z, int x, int y, float[] out, int off)` Returns a 1D array data copy [C] of specified t, z, x, y If (out !
`int[]`	`getDataCopyCAsInt(int t, int z, int x, int y)` Returns a 1D array data copy [C] of specified t, z, x, y
`int[]`	`getDataCopyCAsInt(int t, int z, int x, int y, int[] out, int off)` Returns a 1D array data copy [C] of specified t, z, x, y If (out !
`short[]`	`getDataCopyCAsShort(int t, int z, int x, int y)` Returns a 1D array data copy [C] of specified t, z, x, y
`short[]`	`getDataCopyCAsShort(int t, int z, int x, int y, short[] out, int off)` Returns a 1D array data copy [C] of specified t, z, x, y If (out !
`java.lang.Object`	`getDataCopyCXY(int t, int z)` Returns a 1D array data copy [CXY] of internal 2D array data [C][XY] for specified t, z
`java.lang.Object`	`getDataCopyCXY(int t, int z, java.lang.Object out, int off)` Returns a 1D array data copy [CXY] of internal 2D array data [C][XY] for specified t, z If (out !
`byte[]`	`getDataCopyCXYAsByte(int t, int z)` Returns a 1D array data copy [CXY] of internal 2D array data [C][XY] for specified t, z
`byte[]`	`getDataCopyCXYAsByte(int t, int z, byte[] out, int off)` Returns a 1D array data copy [CXY] of internal 2D array data [C][XY] for specified t, z If (out !
`double[]`	`getDataCopyCXYAsDouble(int t, int z)` Returns a 1D array data copy [CXY] of internal 2D array data [C][XY] for specified t, z
`double[]`	`getDataCopyCXYAsDouble(int t, int z, double[] out, int off)` Returns a 1D array data copy [CXY] of internal 2D array data [C][XY] for specified t, z If (out !
`float[]`	`getDataCopyCXYAsFloat(int t, int z)` Returns a 1D array data copy [CXY] of internal 2D array data [C][XY] for specified t, z
`float[]`	`getDataCopyCXYAsFloat(int t, int z, float[] out, int off)` Returns a 1D array data copy [CXY] of internal 2D array data [C][XY] for specified t, z If (out !
`int[]`	`getDataCopyCXYAsInt(int t, int z)` Returns a 1D array data copy [CXY] of internal 2D array data [C][XY] for specified t, z
`int[]`	`getDataCopyCXYAsInt(int t, int z, int[] out, int off)` Returns a 1D array data copy [CXY] of internal 2D array data [C][XY] for specified t, z If (out !
`short[]`	`getDataCopyCXYAsShort(int t, int z)` Returns a 1D array data copy [CXY] of internal 2D array data [C][XY] for specified t, z
`short[]`	`getDataCopyCXYAsShort(int t, int z, short[] out, int off)` Returns a 1D array data copy [CXY] of internal 2D array data [C][XY] for specified t, z If (out !
`java.lang.Object`	`getDataCopyCXYZ(int t)` Returns a 1D array data copy [CXYZ] of internal 3D array data [Z][C][XY] for specified t
`java.lang.Object`	`getDataCopyCXYZ(int t, java.lang.Object out, int off)` Returns a 1D array data copy [CXYZ] of internal 3D array data [Z][C][XY] for specified t If (out !
`byte[]`	`getDataCopyCXYZAsByte(int t)` Returns a 1D array data copy [CXYZ] of internal 3D array data [Z][C][XY] for specified t
`byte[]`	`getDataCopyCXYZAsByte(int t, byte[] out, int off)` Returns a 1D array data copy [CXYZ] of internal 3D array data [Z][C][XY] for specified t If (out !
`double[]`	`getDataCopyCXYZAsDouble(int t)` Returns a 1D array data copy [CXYZ] of internal 3D array data [Z][C][XY] for specified t
`double[]`	`getDataCopyCXYZAsDouble(int t, double[] out, int off)` Returns a 1D array data copy [CXYZ] of internal 3D array data [Z][C][XY] for specified t If (out !
`float[]`	`getDataCopyCXYZAsFloat(int t)` Returns a 1D array data copy [CXYZ] of internal 3D array data [Z][C][XY] for specified t
`float[]`	`getDataCopyCXYZAsFloat(int t, float[] out, int off)` Returns a 1D array data copy [CXYZ] of internal 3D array data [Z][C][XY] for specified t If (out !
`int[]`	`getDataCopyCXYZAsInt(int t)` Returns a 1D array data copy [CXYZ] of internal 3D array data [Z][C][XY] for specified t
`int[]`	`getDataCopyCXYZAsInt(int t, int[] out, int off)` Returns a 1D array data copy [CXYZ] of internal 3D array data [Z][C][XY] for specified t If (out !
`short[]`	`getDataCopyCXYZAsShort(int t)` Returns a 1D array data copy [CXYZ] of internal 3D array data [Z][C][XY] for specified t
`short[]`	`getDataCopyCXYZAsShort(int t, short[] out, int off)` Returns a 1D array data copy [CXYZ] of internal 3D array data [Z][C][XY] for specified t If (out !
`java.lang.Object`	`getDataCopyCXYZT()` Returns a 1D array data copy [CXYZT] of internal 4D array data [T][Z][C][XY]
`java.lang.Object`	`getDataCopyCXYZT(java.lang.Object out, int off)` Returns a 1D array data copy [CXYZT] of internal 4D array data [T][Z][C][XY] If (out !
`byte[]`	`getDataCopyCXYZTAsByte()` Returns a 1D array data copy [CXYZT] of internal 4D array data [T][Z][C][XY]
`byte[]`	`getDataCopyCXYZTAsByte(byte[] out, int off)` Returns a 1D array data copy [CXYZT] of internal 4D array data [T][Z][C][XY] If (out !
`double[]`	`getDataCopyCXYZTAsDouble()` Returns a 1D array data copy [CXYZT] of internal 4D array data [T][Z][C][XY]
`double[]`	`getDataCopyCXYZTAsDouble(double[] out, int off)` Returns a 1D array data copy [CXYZT] of internal 4D array data [T][Z][C][XY] If (out !
`float[]`	`getDataCopyCXYZTAsFloat()` Returns a 1D array data copy [CXYZT] of internal 4D array data [T][Z][C][XY]
`float[]`	`getDataCopyCXYZTAsFloat(float[] out, int off)` Returns a 1D array data copy [CXYZT] of internal 4D array data [T][Z][C][XY] If (out !
`int[]`	`getDataCopyCXYZTAsInt()` Returns a 1D array data copy [CXYZT] of internal 4D array data [T][Z][C][XY]
`int[]`	`getDataCopyCXYZTAsInt(int[] out, int off)` Returns a 1D array data copy [CXYZT] of internal 4D array data [T][Z][C][XY] If (out !
`short[]`	`getDataCopyCXYZTAsShort()` Returns a 1D array data copy [CXYZT] of internal 4D array data [T][Z][C][XY]
`short[]`	`getDataCopyCXYZTAsShort(short[] out, int off)` Returns a 1D array data copy [CXYZT] of internal 4D array data [T][Z][C][XY] If (out !
`java.lang.Object`	`getDataCopyXY(int t, int z, int c)` Returns a 1D array data copy [XY] of internal 1D array data [XY] for specified t, z, c
`java.lang.Object`	`getDataCopyXY(int t, int z, int c, java.lang.Object out, int off)` Returns a 1D array data copy [XY] of internal 1D array data [XY] for specified t, z, c If (out !
`byte[]`	`getDataCopyXYAsByte(int t, int z, int c)` Returns a 1D array data copy [XY] of internal 1D array data [XY] for specified t, z, c
`byte[]`	`getDataCopyXYAsByte(int t, int z, int c, byte[] out, int off)` Returns a 1D array data copy [XY] of internal 1D array data [XY] for specified t, z, c If (out !
`double[]`	`getDataCopyXYAsDouble(int t, int z, int c)` Returns a 1D array data copy [XY] of internal 1D array data [XY] for specified t, z, c
`double[]`	`getDataCopyXYAsDouble(int t, int z, int c, double[] out, int off)` Returns a 1D array data copy [XY] of internal 1D array data [XY] for specified t, z, c If (out !
`float[]`	`getDataCopyXYAsFloat(int t, int z, int c)` Returns a 1D array data copy [XY] of internal 1D array data [XY] for specified t, z, c
`float[]`	`getDataCopyXYAsFloat(int t, int z, int c, float[] out, int off)` Returns a 1D array data copy [XY] of internal 1D array data [XY] for specified t, z, c If (out !
`int[]`	`getDataCopyXYAsInt(int t, int z, int c)` Returns a 1D array data copy [XY] of internal 1D array data [XY] for specified t, z, c
`int[]`	`getDataCopyXYAsInt(int t, int z, int c, int[] out, int off)` Returns a 1D array data copy [XY] of internal 1D array data [XY] for specified t, z, c If (out !
`short[]`	`getDataCopyXYAsShort(int t, int z, int c)` Returns a 1D array data copy [XY] of internal 1D array data [XY] for specified t, z, c
`short[]`	`getDataCopyXYAsShort(int t, int z, int c, short[] out, int off)` Returns a 1D array data copy [XY] of internal 1D array data [XY] for specified t, z, c If (out !
`java.lang.Object`	`getDataCopyXYC(int t, int z)` Returns a 1D array data copy [XYC] of internal 2D array data [C][XY] for specified t, z
`java.lang.Object`	`getDataCopyXYC(int t, int z, java.lang.Object out, int off)` Returns a 1D array data copy [XYC] of internal 2D array data [C][XY] for specified t, z If (out !
`byte[]`	`getDataCopyXYCAsByte(int t, int z)` Returns a 1D array data copy [XYC] of internal 2D array data [C][XY] for specified t, z
`byte[]`	`getDataCopyXYCAsByte(int t, int z, byte[] out, int off)` Returns a 1D array data copy [XYC] of internal 2D array data [C][XY] for specified t, z If (out !
`double[]`	`getDataCopyXYCAsDouble(int t, int z)` Returns a 1D array data copy [XYC] of internal 2D array data [C][XY] for specified t, z
`double[]`	`getDataCopyXYCAsDouble(int t, int z, double[] out, int off)` Returns a 1D array data copy [XYC] of internal 2D array data [C][XY] for specified t, z If (out !
`float[]`	`getDataCopyXYCAsFloat(int t, int z)` Returns a 1D array data copy [XYC] of internal 2D array data [C][XY] for specified t, z
`float[]`	`getDataCopyXYCAsFloat(int t, int z, float[] out, int off)` Returns a 1D array data copy [XYC] of internal 2D array data [C][XY] for specified t, z If (out !
`int[]`	`getDataCopyXYCAsInt(int t, int z)` Returns a 1D array data copy [XYC] of internal 2D array data [C][XY] for specified t, z
`int[]`	`getDataCopyXYCAsInt(int t, int z, int[] out, int off)` Returns a 1D array data copy [XYC] of internal 2D array data [C][XY] for specified t, z If (out !
`short[]`	`getDataCopyXYCAsShort(int t, int z)` Returns a 1D array data copy [XYC] of internal 2D array data [C][XY] for specified t, z
`short[]`	`getDataCopyXYCAsShort(int t, int z, short[] out, int off)` Returns a 1D array data copy [XYC] of internal 2D array data [C][XY] for specified t, z If (out !
`java.lang.Object`	`getDataCopyXYCZ(int t)` Returns a 1D array data copy [XYCZ] of internal 3D array data [Z][C][XY] for specified t
`java.lang.Object`	`getDataCopyXYCZ(int t, java.lang.Object out, int off)` Returns a 1D array data copy [XYCZ] of internal 3D array data [Z][C][XY] for specified t If (out !
`byte[]`	`getDataCopyXYCZAsByte(int t)` Returns a 1D array data copy [XYCZ] of internal 3D array data [Z][C][XY] for specified t
`byte[]`	`getDataCopyXYCZAsByte(int t, byte[] out, int off)` Returns a 1D array data copy [XYCZ] of internal 3D array data [Z][C][XY] for specified t If (out !
`double[]`	`getDataCopyXYCZAsDouble(int t)` Returns a 1D array data copy [XYCZ] of internal 3D array data [Z][C][XY] for specified t
`double[]`	`getDataCopyXYCZAsDouble(int t, double[] out, int off)` Returns a 1D array data copy [XYCZ] of internal 3D array data [Z][C][XY] for specified t If (out !
`float[]`	`getDataCopyXYCZAsFloat(int t)` Returns a 1D array data copy [XYCZ] of internal 3D array data [Z][C][XY] for specified t
`float[]`	`getDataCopyXYCZAsFloat(int t, float[] out, int off)` Returns a 1D array data copy [XYCZ] of internal 3D array data [Z][C][XY] for specified t If (out !
`int[]`	`getDataCopyXYCZAsInt(int t)` Returns a 1D array data copy [XYCZ] of internal 3D array data [Z][C][XY] for specified t
`int[]`	`getDataCopyXYCZAsInt(int t, int[] out, int off)` Returns a 1D array data copy [XYCZ] of internal 3D array data [Z][C][XY] for specified t If (out !
`short[]`	`getDataCopyXYCZAsShort(int t)` Returns a 1D array data copy [XYCZ] of internal 3D array data [Z][C][XY] for specified t
`short[]`	`getDataCopyXYCZAsShort(int t, short[] out, int off)` Returns a 1D array data copy [XYCZ] of internal 3D array data [Z][C][XY] for specified t If (out !
`java.lang.Object`	`getDataCopyXYCZT()` Returns a 1D array data copy [XYCZT] of internal 4D array data [T][Z][C][XY]
`java.lang.Object`	`getDataCopyXYCZT(java.lang.Object out, int off)` Returns a 1D array data copy [XYCZT] of internal 4D array data [T][Z][C][XY] If (out !
`byte[]`	`getDataCopyXYCZTAsByte()` Returns a 1D array data copy [XYCZT] of internal 4D array data [T][Z][C][XY]
`byte[]`	`getDataCopyXYCZTAsByte(byte[] out, int off)` Returns a 1D array data copy [XYCZT] of internal 4D array data [T][Z][C][XY] If (out !
`double[]`	`getDataCopyXYCZTAsDouble()` Returns a 1D array data copy [XYCZT] of internal 4D array data [T][Z][C][XY]
`double[]`	`getDataCopyXYCZTAsDouble(double[] out, int off)` Returns a 1D array data copy [XYCZT] of internal 4D array data [T][Z][C][XY] If (out !
`float[]`	`getDataCopyXYCZTAsFloat()` Returns a 1D array data copy [XYCZT] of internal 4D array data [T][Z][C][XY]
`float[]`	`getDataCopyXYCZTAsFloat(float[] out, int off)` Returns a 1D array data copy [XYCZT] of internal 4D array data [T][Z][C][XY] If (out !
`int[]`	`getDataCopyXYCZTAsInt()` Returns a 1D array data copy [XYCZT] of internal 4D array data [T][Z][C][XY]
`int[]`	`getDataCopyXYCZTAsInt(int[] out, int off)` Returns a 1D array data copy [XYCZT] of internal 4D array data [T][Z][C][XY] If (out !
`short[]`	`getDataCopyXYCZTAsShort()` Returns a 1D array data copy [XYCZT] of internal 4D array data [T][Z][C][XY]
`short[]`	`getDataCopyXYCZTAsShort(short[] out, int off)` Returns a 1D array data copy [XYCZT] of internal 4D array data [T][Z][C][XY] If (out !
`java.lang.Object`	`getDataCopyXYZ(int t, int c)` Returns a 1D array data copy [XYZ] of internal 2D array data [Z][XY] for specified t, c
`java.lang.Object`	`getDataCopyXYZ(int t, int c, java.lang.Object out, int off)` Returns a 1D array data copy [XYZ] of internal 2D array data [Z][XY] for specified t, c If (out !
`byte[]`	`getDataCopyXYZAsByte(int t, int c)` Returns a 1D array data copy [XYZ] of internal 2D array data [Z][XY] for specified t, c
`byte[]`	`getDataCopyXYZAsByte(int t, int c, byte[] out, int off)` Returns a 1D array data copy [XYZ] of internal 2D array data [Z][XY] for specified t, c If (out !
`double[]`	`getDataCopyXYZAsDouble(int t, int c)` Returns a 1D array data copy [XYZ] of internal 2D array data [Z][XY] for specified t, c
`double[]`	`getDataCopyXYZAsDouble(int t, int c, double[] out, int off)` Returns a 1D array data copy [XYZ] of internal 2D array data [Z][XY] for specified t, c If (out !
`float[]`	`getDataCopyXYZAsFloat(int t, int c)` Returns a 1D array data copy [XYZ] of internal 2D array data [Z][XY] for specified t, c
`float[]`	`getDataCopyXYZAsFloat(int t, int c, float[] out, int off)` Returns a 1D array data copy [XYZ] of internal 2D array data [Z][XY] for specified t, c If (out !
`int[]`	`getDataCopyXYZAsInt(int t, int c)` Returns a 1D array data copy [XYZ] of internal 2D array data [Z][XY] for specified t, c
`int[]`	`getDataCopyXYZAsInt(int t, int c, int[] out, int off)` Returns a 1D array data copy [XYZ] of internal 2D array data [Z][XY] for specified t, c If (out !
`short[]`	`getDataCopyXYZAsShort(int t, int c)` Returns a 1D array data copy [XYZ] of internal 2D array data [Z][XY] for specified t, c
`short[]`	`getDataCopyXYZAsShort(int t, int c, short[] out, int off)` Returns a 1D array data copy [XYZ] of internal 2D array data [Z][XY] for specified t, c If (out !
`java.lang.Object`	`getDataCopyXYZT(int c)` Returns a 1D array data copy [XYZT] of internal 3D array data [T][Z][XY] for specified c
`java.lang.Object`	`getDataCopyXYZT(int c, java.lang.Object out, int off)` Returns a 1D array data copy [XYZT] of internal 3D array data [T][Z][XY] for specified c If (out !
`byte[]`	`getDataCopyXYZTAsByte(int c)` Returns a 1D array data copy [XYZT] of internal 3D array data [T][Z][XY] for specified c
`byte[]`	`getDataCopyXYZTAsByte(int c, byte[] out, int off)` Returns a 1D array data copy [XYZT] of internal 3D array data [T][Z][XY] for specified c If (out !
`double[]`	`getDataCopyXYZTAsDouble(int c)` Returns a 1D array data copy [XYZT] of internal 3D array data [T][Z][XY] for specified c
`double[]`	`getDataCopyXYZTAsDouble(int c, double[] out, int off)` Returns a 1D array data copy [XYZT] of internal 3D array data [T][Z][XY] for specified c If (out !
`float[]`	`getDataCopyXYZTAsFloat(int c)` Returns a 1D array data copy [XYZT] of internal 3D array data [T][Z][XY] for specified c
`float[]`	`getDataCopyXYZTAsFloat(int c, float[] out, int off)` Returns a 1D array data copy [XYZT] of internal 3D array data [T][Z][XY] for specified c If (out !
`int[]`	`getDataCopyXYZTAsInt(int c)` Returns a 1D array data copy [XYZT] of internal 3D array data [T][Z][XY] for specified c
`int[]`	`getDataCopyXYZTAsInt(int c, int[] out, int off)` Returns a 1D array data copy [XYZT] of internal 3D array data [T][Z][XY] for specified c If (out !
`short[]`	`getDataCopyXYZTAsShort(int c)` Returns a 1D array data copy [XYZT] of internal 3D array data [T][Z][XY] for specified c
`short[]`	`getDataCopyXYZTAsShort(int c, short[] out, int off)` Returns a 1D array data copy [XYZT] of internal 3D array data [T][Z][XY] for specified c If (out !
`double`	`getDataInterpolated(int t, double z, int c, double y, double x)` Returns the data value located at position (t, z, c, y, x) as double.
`DataType`	`getDataType_()` Returns the data type of sequence
`int`	`getDataType()` Deprecated. use `getDataType_()` instead
`double[]`	`getDataTypeBounds()` Get data type bounds (min and max values).
`double`	`getDataTypeMax()` Get the data type maximum value.
`double`	`getDataTypeMin()` Get the data type minimum value.
`java.lang.Object`	`getDataXY(int t, int z, int c)` Returns a direct reference to 1D array data [XY] for specified t, z, c
`byte[]`	`getDataXYAsByte(int t, int z, int c)` Returns a direct reference to 1D byte array data [XY] for specified t, z, c
`double[]`	`getDataXYAsDouble(int t, int z, int c)` Returns a direct reference to 1D byte array data [XY] for specified t, z, c
`float[]`	`getDataXYAsFloat(int t, int z, int c)` Returns a direct reference to 1D byte array data [XY] for specified t, z, c
`int[]`	`getDataXYAsInt(int t, int z, int c)` Returns a direct reference to 1D byte array data [XY] for specified t, z, c
`short[]`	`getDataXYAsShort(int t, int z, int c)` Returns a direct reference to 1D byte array data [XY] for specified t, z, c
`java.lang.Object`	`getDataXYC(int t, int z)` Returns a direct reference to 2D array data [C][XY] for specified t, z
`byte[][]`	`getDataXYCAsByte(int t, int z)` Returns a direct reference to 2D byte array data [C][XY] for specified t, z
`double[][]`	`getDataXYCAsDouble(int t, int z)` Returns a direct reference to 2D byte array data [C][XY] for specified t, z
`float[][]`	`getDataXYCAsFloat(int t, int z)` Returns a direct reference to 2D byte array data [C][XY] for specified t, z
`int[][]`	`getDataXYCAsInt(int t, int z)` Returns a direct reference to 2D byte array data [C][XY] for specified t, z
`short[][]`	`getDataXYCAsShort(int t, int z)` Returns a direct reference to 2D byte array data [C][XY] for specified t, z
`java.lang.Object`	`getDataXYCZ(int t)` Returns a direct reference to 3D array data [Z][C][XY] for specified t
`byte[][][]`	`getDataXYCZAsByte(int t)` Returns a direct reference to 3D byte array data [Z][C][XY] for specified t
`double[][][]`	`getDataXYCZAsDouble(int t)` Returns a direct reference to 3D byte array data [Z][C][XY] for specified t
`float[][][]`	`getDataXYCZAsFloat(int t)` Returns a direct reference to 3D byte array data [Z][C][XY] for specified t
`int[][][]`	`getDataXYCZAsInt(int t)` Returns a direct reference to 3D byte array data [Z][C][XY] for specified t
`short[][][]`	`getDataXYCZAsShort(int t)` Returns a direct reference to 3D byte array data [Z][C][XY] for specified t
`java.lang.Object`	`getDataXYCZT()` Returns a direct reference to 4D array data [T][Z][C][XY]
`byte[][][][]`	`getDataXYCZTAsByte()` Returns a direct reference to 4D byte array data [T][Z][C][XY]
`double[][][][]`	`getDataXYCZTAsDouble()` Returns a direct reference to 4D byte array data [T][Z][C][XY]
`float[][][][]`	`getDataXYCZTAsFloat()` Returns a direct reference to 4D byte array data [T][Z][C][XY]
`int[][][][]`	`getDataXYCZTAsInt()` Returns a direct reference to 4D byte array data [T][Z][C][XY]
`short[][][][]`	`getDataXYCZTAsShort()` Returns a direct reference to 4D byte array data [T][Z][C][XY]
`java.lang.Object`	`getDataXYZ(int t, int c)` Returns a direct reference to 2D byte array data [Z][XY] for specified t, c
`byte[][]`	`getDataXYZAsByte(int t, int c)` Returns a direct reference to 2D byte array data [Z][XY] for specified t, c
`double[][]`	`getDataXYZAsDouble(int t, int c)` Returns a direct reference to 2D byte array data [Z][XY] for specified t, c
`float[][]`	`getDataXYZAsFloat(int t, int c)` Returns a direct reference to 2D byte array data [Z][XY] for specified t, c
`int[][]`	`getDataXYZAsInt(int t, int c)` Returns a direct reference to 2D byte array data [Z][XY] for specified t, c
`short[][]`	`getDataXYZAsShort(int t, int c)` Returns a direct reference to 2D byte array data [Z][XY] for specified t, c
`java.lang.Object`	`getDataXYZT(int c)` Returns a direct reference to 3D byte array data [T][Z][XY] for specified c
`byte[][][]`	`getDataXYZTAsByte(int c)` Returns a direct reference to 3D byte array data [T][Z][XY] for specified c
`double[][][]`	`getDataXYZTAsDouble(int c)` Returns a direct reference to 3D byte array data [T][Z][XY] for specified c
`float[][][]`	`getDataXYZTAsFloat(int c)` Returns a direct reference to 3D byte array data [T][Z][XY] for specified c
`int[][][]`	`getDataXYZTAsInt(int c)` Returns a direct reference to 3D byte array data [T][Z][XY] for specified c
`short[][][]`	`getDataXYZTAsShort(int c)` Returns a direct reference to 3D byte array data [T][Z][XY] for specified c
`java.lang.String`	`getDefaultChannelName(int index)` Get default name for specified channel
`IcyColorMap`	`getDefaultColorMap(int channel)` Get the default colormap for the specified channel
`LUT`	`getDefaultLUT()` Same as `createCompatibleLUT()`
`int`	`getDepth()` Deprecated.
`java.awt.Dimension`	`getDimension()` Deprecated. Use `getDimension2D()` instead.
`java.awt.Dimension`	`getDimension2D()` Returns 2D dimension of sequence {sizeX, sizeY}
`Dimension5D.Integer`	`getDimension5D()` Returns 5D dimension of sequence {sizeX, sizeY, sizeZ, sizeT, sizeC}
`java.lang.String`	`getFilename()` Returns the origin filename (from/to which the sequence has been loaded/saved).
`IcyBufferedImage`	`getFirstImage()` Returns the first image of first VolumetricImage
`IcyBufferedImage`	`getFirstNonNullImage()` Returns the first non null image if exist
`Viewer`	`getFirstViewer()` Returns first viewer attached to this sequence
`ROI`	`getFocusedROI()` Returns the current focused ROI (null if no ROI focused)
`double[]`	`getGlobalChannelTypeBounds()` Deprecated. Use `getChannelTypeGlobalBounds()` instead.
`double[]`	`getGlobalComponentAbsBounds()` Deprecated. Use `getChannelsGlobalTypeBounds()` instead.
`int`	`getHeight()` Same as `getSizeY()`
`int`	`getId()` get sequence id (this id is unique during an ICY session)
`IcyBufferedImage`	`getImage(int t, int z)` Returns image at time t and depth z
`IcyBufferedImage`	`getImage(int t, int z, boolean loadData)` Returns image at time t and depth z.
`IcyBufferedImage`	`getImage(int t, int z, int c)` Returns a single component image corresponding to the component c of the image at time t and depth z.
`ImageProvider`	`getImageProvider()` Returns the `ImageProvider` used to load the sequence data.
`java.util.ArrayList<IcyBufferedImage>`	`getImages(int t)` Returns all images at specified t position
`IcyBufferedImage`	`getLastImage()` Returns the last image of last VolumetricImage
`IcyBufferedImage`	`getLastImage(int t)` Returns the last image of VolumetricImage[t]
`int`	`getLength()` Deprecated.
`SequenceListener[]`	`getListeners()` Get listeners list
`loci.formats.ome.OMEXMLMetadataImpl`	`getMetadata()` Deprecated. Use `getOMEXMLMetadata()` instead.
`java.lang.String`	`getName()`
`org.w3c.dom.Node`	`getNode(java.lang.String name)` Get XML data node identified by specified name.
`int`	`getNumComponents()` Deprecated.
`int`	`getNumImage()` return the number of loaded image
`int`	`getNumSample()` Returns the number of sample.
`ome.xml.meta.OMEXMLMetadata`	`getOMEXMLMetadata()` Returns meta data object
`int`	`getOriginChannel()` Returns the channel position from original image if this image is a single channel extraction of the original image.
`int`	`getOriginResolution()` Returns the resolution level from the origin image (defined by `getFilename()`).
`int`	`getOriginTMax()` Returns the T range maximum from original image if this image is a crop in T of the original image.
`int`	`getOriginTMin()` Returns the T range minimum from original image if this image is a crop in T of the original image.
`java.awt.Rectangle`	`getOriginXYRegion()` Returns the region (X,Y) from original image if this image is a crop of the original image (in original image resolution).
`int`	`getOriginZMax()` Returns the Z range maximum from original image if this image is a crop in Z of the original image.
`int`	`getOriginZMin()` Returns the Z range minimum from original image if this image is a crop in Z of the original image.
`java.lang.String`	`getOutputBaseName(java.lang.String folderExt)` Returns the output base filename.
`java.lang.String`	`getOutputExtension()` Returns the output filename extension (not the file extension, just extension from base name).
`java.lang.String`	`getOutputFilename(boolean withExtension)` Return the desired output filename for this Sequence.
`java.util.List<Overlay>`	`getOverlays()` Returns all overlays attached to this sequence
`<T extends Overlay> java.util.List<T>`	`getOverlays(java.lang.Class<T> overlayClass)` Returns overlays of specified class attached to this sequence
`java.util.Set<Overlay>`	`getOverlaySet()` Returns all overlays attached to this sequence (HashSet form)
`java.util.ArrayList<Painter>`	`getPainters()` Deprecated. Use `getOverlays()` instead.
`java.util.List<Painter>`	`getPainters(java.lang.Class<? extends Painter> painterClass)` Deprecated. Use `getOverlays(Class)` instead.
`java.util.HashSet<Painter>`	`getPainterSet()` Deprecated. Use `getOverlaySet()` instead.
`double[]`	`getPixelSize()` Returns pixel size for [X,Y,Z] dimension (in �m to be OME compatible)
`double`	`getPixelSizeScaling(int dimCompute, int dimResult)` Returns the pixel size scaling factor to convert a number of pixel/voxel unit into `�m` For instance to get the scale ration for 2D distance: `valueMicroMeter = pixelNum * getPixelSizeScaling(2, 1)` For a 2D surface: `valueMicroMeter2 = pixelNum * getPixelSizeScaling(2, 2)` For a 3D volume: `valueMicroMeter3 = pixelNum * getPixelSizeScaling(3, 3)`
`double`	`getPixelSizeX()` Returns X pixel size (in �m to be OME compatible)
`double`	`getPixelSizeY()` Returns Y pixel size (in �m to be OME compatible)
`double`	`getPixelSizeZ()` Returns Z pixel size (in �m to be OME compatible)
`double[]`	`getPosition()` Returns the physical position [X,Y,Z] (in �m) of the image represented by this Sequence.
`long`	`getPositionT()` Same as `getTimeStamp()`
`double`	`getPositionTOffset(int t, int z, int c)` Returns the time position offset (in second for OME compatibility) relative to first image for the image at specified (T,Z,C) position.
`double`	`getPositionX()` Returns the X physical position / offset (in �m) of the image represented by this Sequence.
`double`	`getPositionY()` Returns the Y physical position / offset (in �m) of the image represented by this Sequence.
`double`	`getPositionZ()` Returns the Z physical position / offset (in �m) of the image represented by this Sequence.
`java.util.ArrayList<ROI2D>`	`getROI2Ds()` Returns all 2D ROIs attached to this sequence.
`java.util.List<ROI2D>`	`getROI2Ds(boolean sorted)` Returns all 2D ROIs attached to this sequence.
`java.util.ArrayList<ROI3D>`	`getROI3Ds()` Returns all 3D ROIs attached to this sequence.
`java.util.List<ROI3D>`	`getROI3Ds(boolean sorted)` Returns all 3D ROIs attached to this sequence.
`int`	`getROICount(java.lang.Class<? extends ROI> roiClass)` Returns the number of ROI of specified ROI class attached to the sequence.
`java.util.ArrayList<ROI>`	`getROIs()` Returns all ROIs attached to this sequence.
`java.util.List<ROI>`	`getROIs(boolean sorted)` Returns all ROIs attached to this sequence.
`java.util.List<ROI>`	`getROIs(java.lang.Class<? extends ROI> roiClass)` Deprecated. Use `getROIs(Class, boolean)` instead
`<T extends ROI> java.util.List<T>`	`getROIs(java.lang.Class<T> roiClass, boolean sorted)` Returns ROIs of specified class attached to this sequence
`java.util.HashSet<ROI>`	`getROISet()` Returns all ROIs attached to this sequence (HashSet form)
`ROI`	`getSelectedROI()` Returns the first selected ROI found (null if no ROI selected)
`ROI2D`	`getSelectedROI2D()` Returns the first selected 2D ROI found (null if no 2D ROI selected)
`java.util.ArrayList<ROI2D>`	`getSelectedROI2Ds()` Returns all selected 2D ROI
`ROI3D`	`getSelectedROI3D()` Returns the first selected 3D ROI found (null if no 3D ROI selected)
`java.util.ArrayList<ROI3D>`	`getSelectedROI3Ds()` Returns all selected 3D ROI
`java.util.ArrayList<ROI>`	`getSelectedROIs()` Returns all selected ROI
`java.util.List<ROI>`	`getSelectedROIs(java.lang.Class<? extends ROI> roiClass, boolean wantReadOnly)` Returns all selected ROI of given class.
`<T extends ROI> java.util.List<T>`	`getSelectedROIs(java.lang.Class<T> roiClass, boolean sorted, boolean wantReadOnly)` Returns all selected ROI of given class.
`java.util.Set<ROI>`	`getSelectedROISet()` Returns all selected ROI (Set format).
`java.util.Set<ROI>`	`getSelectedROISet(java.lang.Class<? extends ROI> roiClass, boolean wantReadOnly)` Returns all selected ROI of given class (Set format).
`<T extends ROI> java.util.Set<T>`	`getSelectedROISet(java.lang.Class<T> roiClass)` Returns all selected ROI of given class (Set format).
`int`	`getSerieIndex()` Deprecated. Use `getSeries()` instead
`int`	`getSeries()` Returns series index if the Sequence comes from a multi serie image.
`int`	`getSize(DimensionId dim)` Returns the size of the specified dimension
`int`	`getSizeC()` Returns the number of component/channel/band per image
`int`	`getSizeT()` return the number of volumetricImage in the sequence
`int`	`getSizeX()` Returns the width of the sequence (0 if the sequence contains no image).
`int`	`getSizeY()` Returns the height of the sequence (0 if the sequence contains no image).
`int`	`getSizeZ()` Returns the global number of z stack in the sequence.
`int`	`getSizeZ(int t)` Returns the number of z stack for the volumetricImage[t].
`Sequence`	`getSubSequence(int startX, int startY, int startZ, int startT, int sizeX, int sizeY, int sizeZ, int sizeT)` Deprecated. Uses `SequenceUtil.getSubSequence(Sequence, int, int, int, int, int, int, int, int)` instead.
`double`	`getTimeInterval()` Returns T time interval (in second for OME compatibility)
`long`	`getTimeStamp()` Returns the timestamp (elapsed milliseconds from the Java epoch of 1970-01-01 T00:00:00Z) of the image represented by this Sequence.
`IcyUndoManager`	`getUndoManager()` Get the Undo manager of this sequence
`LUT`	`getUserLUT()` Returns the users LUT.
`java.util.ArrayList<Viewer>`	`getViewers()` Returns viewers attached to this sequence
`VolumetricImage`	`getVolumetricImage(int t)` Returns the VolumetricImage at position t
`java.util.TreeMap<java.lang.Integer,VolumetricImage>`	`getVolumetricImages()` Returns all VolumetricImage as TreeMap (contains t position)
`int`	`getWidth()` Same as `getSizeX()`
`boolean`	`hasOverlay()` Returns true if the sequence contains at least one Overlay.
`boolean`	`hasOverlay(java.lang.Class<? extends Overlay> overlayClass)` Returns true if the sequence contains Overlay of specified Overlay class.
`boolean`	`hasPainter()` Deprecated. Use `hasOverlay()` instead.
`boolean`	`hasROI()` Returns true if the sequence contains at least one ROI.
`boolean`	`hasROI(java.lang.Class<? extends ROI> roiClass)` Returns true if the sequence contains ROI of specified ROI class.
`boolean`	`hasSelectedROI()` Returns true if the sequence contains at least one selected ROI.
`boolean`	`hasUserLUT()` Returns `true` if a user LUT has be defined for this sequence.
`void`	`imageChanged(IcyBufferedImageEvent e)`
`boolean`	`isAWTDispatching()` Deprecated. Don't use it, events should stay on current thread
`boolean`	`isCompatible(IcyBufferedImage image)` Test if the specified image is compatible with current loaded images in sequence
`boolean`	`isCompatible(IcyColorModel cm)` Test if the specified colorModel is compatible with sequence colorModel
`boolean`	`isComponentAbsBoundsAutoUpdate()` Deprecated. Use `getAutoUpdateChannelBounds()` instead.
`boolean`	`isComponentUserBoundsAutoUpdate()` Deprecated. Use `getAutoUpdateChannelBounds()` instead.
`boolean`	`isDefaultChannelName(int index)` Returns true is the specified channel uses default attributed name
`boolean`	`isDefaultName()` Returns true if the sequence uses default attributed name
`boolean`	`isEmpty()` return true if no image in sequence
`boolean`	`isFloatDataType()` Returns true if this is a float data type sequence
`boolean`	`isLutCompatible(LUT lut)` Returns true if specified LUT is compatible with sequence LUT
`org.w3c.dom.Node`	`isNodeExisting(java.lang.String name)` Returns true if the specified XML data node exist
`boolean`	`isSignedDataType()` Returns true if this is a signed data type sequence
`boolean`	`isUpdating()`
`boolean`	`isVirtual()` Same as `isVolatile()`
`boolean`	`isVolatile()` Returns true if this sequence contains volatile image (see `IcyBufferedImage.isVolatile()`).
`void`	`loadAllData()` Force all image data to be loaded (so channels bounds can be correctly computed).
`boolean`	`loadXMLData()` Load XML persistent data from file.
`void`	`metaChanged(java.lang.String metaName)` sequence meta has changed
`void`	`metaChanged(java.lang.String metaName, int param)` sequence meta has changed
`void`	`onChanged(CollapsibleEvent e)` process on sequence change
`void`	`onImageAdded(IcyBufferedImage image)` Do common job on "image add" here
`void`	`onImageRemoved(IcyBufferedImage image)` Do common job on "image remove" here
`void`	`onImageReplaced(IcyBufferedImage oldImage, IcyBufferedImage newImage)` Do common job on "image replaced" here
`void`	`overlayChanged(Overlay overlay)` Notify specified painter of overlay has changed (the sequence should contains the specified Overlay)
`void`	`overlayChanged(OverlayEvent event)` Called when an overlay has changed (internal method).
`void`	`packImageList()` Remove empty element of image list
`void`	`painterChanged(Painter painter)` Deprecated. Use `overlayChanged(Overlay)` instead.
`boolean`	`redo()` Redo the next Undoable change set in the Sequence `UndoManager`
`void`	`refreshXMLData()` Synchronize XML data with sequence data : This function refresh all the meta data and ROIs of the sequence and put it in the current XML document.
`void`	`removeAllImage()` Deprecated. Use `removeAllImages()` instead.
`boolean`	`removeAllImage(int t)` Deprecated. Use `removeAllImages(int)` instead.
`void`	`removeAllImages()` Remove all images
`boolean`	`removeAllImages(int t)` Remove all images at position `t`
`void`	`removeAllROI()` Remove all ROI from the sequence.
`void`	`removeAllROI(boolean canUndo)` Remove all ROI from the sequence.
`boolean`	`removeImage(int t, int z)` Remove the image at the specified position.
`void`	`removeListener(SequenceListener listener)` Remove the specified listener from listeners list
`boolean`	`removeOverlay(Overlay overlay)` Remove an overlay from the sequence.
`boolean`	`removePainter(Painter painter)` Deprecated. Use `removeOverlay(Overlay)` instead.
`boolean`	`removeROI(ROI roi)` Remove the specified ROI from the sequence.
`boolean`	`removeROI(ROI roi, boolean canUndo)` Remove the specified ROI from the sequence.
`boolean`	`removeROIs(java.util.Collection<? extends ROI> rois, boolean canUndo)` Remove the specified collection of ROI from the sequence.
`boolean`	`removeSelectedROIs(boolean removeReadOnly)` Remove all selected ROI from the sequence.
`boolean`	`removeSelectedROIs(boolean removeReadOnly, boolean canUndo)` Remove all selected ROI from the sequence.
`void`	`removeSequenceModelListener(SequenceModel.SequenceModelListener listener)` Remove the specified `SequenceModel.SequenceModelListener` from listeners list
`boolean`	`removeVolumetricImage(int t)` Deprecated. Use `removeAllImages(int)` instead.
`void`	`resetOriginInformation()` Reset origin information (used after saved operation normally, internal use only).
`void`	`roiChanged()` Deprecated. Use `roiChanged(ROI)` method instead.
`void`	`roiChanged(ROI roi)` Notify specified roi has changed (the sequence should contains the specified ROI)
`void`	`roiChanged(ROIEvent event)`
`boolean`	`saveXMLData()` Save attached XML data.
`void`	`setAutoUpdateChannelBounds(boolean value)` If set to `true` (default) then channel bounds will be automatically recalculated when sequence data is modified.
`void`	`setAWTDispatching(boolean value)` Deprecated. Don't use it, events should stay on current thread
`void`	`setChannelName(int index, java.lang.String value)` Set name for specified channel
`void`	`setColormap(int channel, IcyColorMap map)` Set the user colormap for the specified channel.
`void`	`setColormap(int channel, IcyColorMap map, boolean setAlpha)` Set the user colormap for the specified channel.
`void`	`setComponentAbsBoundsAutoUpdate(boolean value)` Deprecated. Use `setAutoUpdateChannelBounds(boolean)` instead.
`void`	`setComponentUserBoundsAutoUpdate(boolean value)` Deprecated. Use `setAutoUpdateChannelBounds(boolean)` instead.
`void`	`setDataXY(int t, int z, int c, java.lang.Object value)` Sets 1D array data [XY] for specified t, z, c
`void`	`setDefaultColormap(int channel, IcyColorMap map)` Set the default colormap for the specified channel
`void`	`setDefaultColormap(int channel, IcyColorMap map, boolean setAlpha)` Set the default colormap for the specified channel
`void`	`setFilename(java.lang.String filename)` Set the origin filename (from/to which the sequence has been loaded/saved).
`boolean`	`setFocusedROI(ROI roi)` Set the focused ROI
`void`	`setImage(int t, int z, java.awt.image.BufferedImage image)` Set an image at the specified position.
`void`	`setImageProvider(ImageProvider value)` Set the `ImageProvider` used to load the sequence data.
`void`	`setMetaData(ome.xml.meta.OMEXMLMetadata metaData)` Set the meta data object
`void`	`setMetaData(loci.formats.ome.OMEXMLMetadataImpl metaData)` Deprecated. Use `setMetaData(OMEXMLMetadata)` instead.
`void`	`setName(java.lang.String value)` Sequence name
`org.w3c.dom.Node`	`setNode(java.lang.String name)` Deprecated. Use `getNode(String)` instead.
`void`	`setOriginChannel(int value)` Internal use only, you should not directly use this method.
`void`	`setOriginResolution(int value)` Internal use only, you should not directly use this method.
`void`	`setOriginTMax(int value)` Internal use only, you should not directly use this method.
`void`	`setOriginTMin(int value)` Internal use only, you should not directly use this method.
`void`	`setOriginXYRegion(java.awt.Rectangle value)` Internal use only, you should not directly use this method.
`void`	`setOriginZMax(int value)` Internal use only, you should not directly use this method.
`void`	`setOriginZMin(int value)` Internal use only, you should not directly use this method.
`void`	`setPixelSizeX(double value)` Set X pixel size (in �m to be OME compatible)
`void`	`setPixelSizeY(double value)` Set Y pixel size (in �m to be OME compatible)
`void`	`setPixelSizeZ(double value)` Set Z pixel size (in �m to be OME compatible)
`void`	`setPositionT(long value)` Same as `setTimeStamp(long)`
`void`	`setPositionTOffset(int t, int z, int c, double value)` Sets the time position / offset (in second for OME compatibility) relative to first image for the image at specified (T,Z,C) position.
`void`	`setPositionX(double value)` Sets the X physical position / offset (in �m) of the image represented by this Sequence.
`void`	`setPositionY(double value)` Sets the X physical position / offset (in �m) of the image represented by this Sequence.
`void`	`setPositionZ(double value)` Sets the X physical position / offset (in �m) of the image represented by this Sequence.
`boolean`	`setSelectedROI(ROI roi)` Set the selected ROI (exclusive selection).
`boolean`	`setSelectedROI(ROI roi, boolean exclusive)` Deprecated. Use `setSelectedROI(ROI)` instead.
`void`	`setSelectedROIs(java.util.ArrayList<ROI> selected)` Deprecated. Use `setSelectedROIs(List)` instead.
`void`	`setSelectedROIs(java.util.List<? extends ROI> selected)` Set selected ROI (unselected all others)
`void`	`setSeries(int value)` Set series index if the Sequence comes from a multi serie image (internal use only).
`void`	`setT(int t)` Deprecated. Use this piece of code instead : `for(Viewer v: Icy.getMainInterface().getViewers(sequence))` `v.setT(...)`
`void`	`setTimeInterval(double value)` Set T time resolution (in second to be OME compatible)
`void`	`setTimeStamp(long value)` Sets the timestamp (elapsed milliseconds from the Java epoch of 1970-01-01 T00:00:00Z) for the image represented by this Sequence.
`void`	`setUserLUT(LUT lut)` Sets the user LUT (saved in XML persistent metadata).
`void`	`setVirtual(boolean value)` Same as `setVolatile(boolean)`
`void`	`setVolatile(boolean value)` Set the volatile state for this Sequence (see `IcyBufferedImage.setVolatile(boolean)`).
`java.lang.String`	`toString()`
`boolean`	`undo()` Undo to the last Undoable change set in the Sequence `UndoManager`
`void`	`updateChannelsBounds()` Update channels bounds (min and max values).
`void`	`updateChannelsBounds(boolean forceRecalculation)` Update channels bounds (min and max values).
`void`	`updateComponentsBounds()` Deprecated. Use `updateChannelsBounds(boolean)` instead.
`void`	`updateComponentsBounds(boolean forceRecalculation)` Deprecated. Use `updateChannelsBounds(boolean)` instead.
`void`	`updateComponentsBounds(boolean forceRecalculation, boolean adjustByteToo)` Deprecated. Use `updateChannelsBounds(boolean)` instead.

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - DEFAULT_NAME
```
public static final java.lang.String DEFAULT_NAME
```
    See Also:
    Constant Field Values
  - TYPE_BYTE
```
@Deprecated
public static final int TYPE_BYTE
```
    Deprecated.
    
    See Also:
    Constant Field Values
  - TYPE_DOUBLE
```
@Deprecated
public static final int TYPE_DOUBLE
```
    Deprecated.
    
    See Also:
    Constant Field Values
  - TYPE_FLOAT
```
@Deprecated
public static final int TYPE_FLOAT
```
    Deprecated.
    
    See Also:
    Constant Field Values
  - TYPE_INT
```
@Deprecated
public static final int TYPE_INT
```
    Deprecated.
    
    See Also:
    Constant Field Values
  - TYPE_SHORT
```
@Deprecated
public static final int TYPE_SHORT
```
    Deprecated.
    
    See Also:
    Constant Field Values
  - TYPE_UNDEFINED
```
@Deprecated
public static final int TYPE_UNDEFINED
```
    Deprecated.
    
    See Also:
    Constant Field Values
  - ID_NAME
```
public static final java.lang.String ID_NAME
```
    See Also:
    Constant Field Values
  - ID_POSITION_X
```
public static final java.lang.String ID_POSITION_X
```
    See Also:
    Constant Field Values
  - ID_POSITION_Y
```
public static final java.lang.String ID_POSITION_Y
```
    See Also:
    Constant Field Values
  - ID_POSITION_Z
```
public static final java.lang.String ID_POSITION_Z
```
    See Also:
    Constant Field Values
  - ID_POSITION_T
```
public static final java.lang.String ID_POSITION_T
```
    See Also:
    Constant Field Values
  - ID_POSITION_T_OFFSET
```
public static final java.lang.String ID_POSITION_T_OFFSET
```
    See Also:
    Constant Field Values
  - ID_PIXEL_SIZE_X
```
public static final java.lang.String ID_PIXEL_SIZE_X
```
    See Also:
    Constant Field Values
  - ID_PIXEL_SIZE_Y
```
public static final java.lang.String ID_PIXEL_SIZE_Y
```
    See Also:
    Constant Field Values
  - ID_PIXEL_SIZE_Z
```
public static final java.lang.String ID_PIXEL_SIZE_Z
```
    See Also:
    Constant Field Values
  - ID_TIME_INTERVAL
```
public static final java.lang.String ID_TIME_INTERVAL
```
    See Also:
    Constant Field Values
  - ID_CHANNEL_NAME
```
public static final java.lang.String ID_CHANNEL_NAME
```
    See Also:
    Constant Field Values
  - ID_VIRTUAL
```
public static final java.lang.String ID_VIRTUAL
```
    See Also:
    Constant Field Values
- Constructor Detail
  - Sequence
```
public Sequence(ome.xml.meta.OMEXMLMetadata meta,
        java.lang.String name)
```
    Creates a new empty sequence with specified meta data object and name.
  - Sequence
```
@Deprecated
public Sequence(loci.formats.ome.OMEXMLMetadataImpl meta,
                   java.lang.String name)
```
    Deprecated. Use Sequence(OMEXMLMetadata, String) instead.
  - Sequence
```
public Sequence(java.lang.String name,
        IcyBufferedImage image)
```
    Creates a sequence with specified name and containing the specified image
  - Sequence
```
public Sequence(java.lang.String name,
        java.awt.image.BufferedImage image)
```
    Creates a sequence with specified name and containing the specified image
  - Sequence
```
@Deprecated
public Sequence(loci.formats.ome.OMEXMLMetadataImpl meta)
```
    Deprecated. Use Sequence(OMEXMLMetadata) instead.
  - Sequence
```
public Sequence(ome.xml.meta.OMEXMLMetadata meta)
```
    Creates a new empty sequence with specified metadata.
  - Sequence
```
public Sequence(IcyBufferedImage image)
```
    Creates a sequence containing the specified image.
  - Sequence
```
public Sequence(java.awt.image.BufferedImage image)
```
    Creates a sequence containing the specified image.
  - Sequence
```
public Sequence(java.lang.String name)
```
    Creates an empty sequence with specified name.
  - Sequence
```
public Sequence()
```
    Creates an empty sequence.
- Method Detail
  - close
```
public void close()
```
    This method close all attached viewers
  - closed
```
public void closed()
```
    Called when sequence has been closed (all viewers displaying it closed).
    Used internally, you should not call it this method directly !
  - copyFrom
```
public void copyFrom(Sequence source,
            boolean copyName)
```
    Copy data and metadata from the specified Sequence
    
    Parameters:
    source - the source sequence to copy data from
    copyName - if set to true it will also copy the name from the source sequence
  - copyDataFrom
```
public void copyDataFrom(Sequence source)
```
    Copy data from the specified Sequence
  - copyMetaDataFrom
```
public void copyMetaDataFrom(Sequence source,
                    boolean copyName)
```
    Copy metadata from the specified Sequence
    
    Parameters:
    source - the source sequence to copy metadata from
    copyName - if set to true it will also copy the name from the source sequence
  - createUndoPoint
```
public boolean createUndoPoint(java.lang.String name)
```
    Create a complete restore point for this sequence.
    
    Parameters:
    name - restore point name (visible in the History panel)
    
    Returns:
    false if for some reason the operation failed (out of memory for instance)
    See Also:
    undo()
  - createUndoDataPoint
```
public boolean createUndoDataPoint(java.lang.String name)
```
    Create a restore point for sequence data.
    
    Parameters:
    name - restore point name (visible in the History panel)
    
    Returns:
    false if for some reason the operation failed (out of memory for instance)
    See Also:
    undo()
  - createUndoMetadataPoint
```
public boolean createUndoMetadataPoint(java.lang.String name)
```
    Create a restore point for sequence metadata.
    
    Parameters:
    name - restore point name (visible in the History panel)
    
    Returns:
    false if for some reason the operation failed (out of memory for instance)
    See Also:
    undo()
  - addUndoableEdit
```
public boolean addUndoableEdit(IcyUndoableEdit edit)
```
    Add an Undoable edit to the Sequence UndoManager
    
    Parameters:
    edit - the undoable edit to add
    
    Returns:
    false if the operation failed
  - undo
```
public boolean undo()
```
    Undo to the last Undoable change set in the Sequence UndoManager
    
    Returns:
    true if the operation succeed
    See Also:
    createUndoPoint(String), UndoManager.undo()
  - redo
```
public boolean redo()
```
    Redo the next Undoable change set in the Sequence UndoManager
    
    Returns:
    true if the operation succeed
    See Also:
    createUndoPoint(String), UndoManager.redo()
  - clearUndoManager
```
public void clearUndoManager()
```
    Clear all undo operations from the UndoManager.
    You should use this method after you modified the sequence without providing any undo support.
  - convertToType
```
@Deprecated
public Sequence convertToType(DataType dataType,
                                boolean rescale)
```
    Deprecated. Use SequenceUtil.convertToType(Sequence, DataType, boolean) instead.
  - convertToType
```
@Deprecated
public Sequence convertToType(DataType dataType,
                                Scaler scaler)
```
    Deprecated. Use SequenceUtil.convertType(Sequence, DataType, Scaler[]) instead.
  - convertToType
```
@Deprecated
public Sequence convertToType(int dataType,
                                boolean signed,
                                boolean rescale)
```
    Deprecated. Use SequenceUtil.convertToType(Sequence, DataType, boolean) instead
  - extractChannel
```
@Deprecated
public Sequence extractChannel(int channelNumber)
```
    Deprecated. Use SequenceUtil.extractChannel(Sequence, int) instead.
  - extractChannels
```
@Deprecated
public Sequence extractChannels(java.util.List<java.lang.Integer> channelNumbers)
```
    Deprecated. Use SequenceUtil.extractChannels(Sequence, List) instead.
  - extractBand
```
@Deprecated
public Sequence extractBand(int bandNumber)
```
    Deprecated. Use SequenceUtil.extractChannel(Sequence, int) instead
  - extractBands
```
@Deprecated
public Sequence extractBands(java.util.List<java.lang.Integer> bandNumbers)
```
    Deprecated. Use SequenceUtil.extractChannels(Sequence, List) instead
  - getVolumetricImages
```
public java.util.TreeMap<java.lang.Integer,VolumetricImage> getVolumetricImages()
```
    Returns all VolumetricImage as TreeMap (contains t position)
  - getAllVolumetricImage
```
public java.util.ArrayList<VolumetricImage> getAllVolumetricImage()
```
    Returns all VolumetricImage
  - getFirstViewer
```
public Viewer getFirstViewer()
```
    Returns first viewer attached to this sequence
  - getViewers
```
public java.util.ArrayList<Viewer> getViewers()
```
    Returns viewers attached to this sequence
  - setVolatile
```
public void setVolatile(boolean value)
                 throws java.lang.OutOfMemoryError,
                        java.lang.UnsupportedOperationException
```
    Set the volatile state for this Sequence (see IcyBufferedImage.setVolatile(boolean)).
    
    Throws:
    
    java.lang.OutOfMemoryError - if there is not enough memory available to store image data when setting back to non volatile state
    
    java.lang.UnsupportedOperationException - if cache engine is not initialized (error at initialization).
  - setVirtual
```
public void setVirtual(boolean value)
                throws java.lang.OutOfMemoryError,
                       java.lang.UnsupportedOperationException
```
    Same as setVolatile(boolean)
    
    Throws:
    
    java.lang.OutOfMemoryError - if there is not enough memory available to store image data when setting back to non volatile state
    
    java.lang.UnsupportedOperationException - if cache engine is not initialized (error at initialization).
  - isVolatile
```
public boolean isVolatile()
```
    Returns true if this sequence contains volatile image (see IcyBufferedImage.isVolatile()).
  - isVirtual
```
public boolean isVirtual()
```
    Same as isVolatile()
  - getId
```
public int getId()
```
    get sequence id (this id is unique during an ICY session)
  - setName
```
public void setName(java.lang.String value)
```
    Sequence name
  - getName
```
public java.lang.String getName()
```
  - getFilename
```
public java.lang.String getFilename()
```
    Returns the origin filename (from/to which the sequence has been loaded/saved).
    This filename information is also used to store the XML persistent data.
    null / empty --> no file attachment
    image file --> single file attachment directory or metadata file --> multiples files attachment
    
    Returns:
    the origin filename
  - setFilename
```
public void setFilename(java.lang.String filename)
```
    Set the origin filename (from/to which the sequence has been loaded/saved).
    When you set the filename you need to ensure that "sub part" information are correctly reset (setOriginXXX(...) methods) as this filename will be used to generate the XML persistent data file name.
    null / empty --> no file attachment
    image file --> single file attachment directory or metadata file --> multiples files attachment
    
    Parameters:
    filename - the filename to set
  - getImageProvider
```
public ImageProvider getImageProvider()
```
    Returns the ImageProvider used to load the sequence data.
    It can return null if the Sequence was not loaded from a specific resource or if it was saved in between.
    
    Returns:
    the ImageProvider used to load the Sequence
  - setImageProvider
```
public void setImageProvider(ImageProvider value)
```
    Set the ImageProvider used to load the sequence data.
    When you set the ImageProvider you need to ensure we can use it (should be opened for SequenceIdImporter).
    Also "sub part" informations has to be correctly set (setOriginXXX(...) methods) as we may use it to retrieve sequence data from the ImageProvider.
  - getOutputBaseName
```
public java.lang.String getOutputBaseName(java.lang.String folderExt)
```
    Returns the output base filename.
    This function is supposed to be used internally only.
    
    Parameters:
    folderExt - If the filename of this sequence refer a folder then we extend it with 'folderExt' to build the base name.
    See Also:
    getOutputExtension()
  - getOutputExtension
```
public java.lang.String getOutputExtension()
```
    Returns the output filename extension (not the file extension, just extension from base name).
    The extension is based on some internals informations as serie index and resolution level.
    This function is supposed to be used internally only.
    
    See Also:
    getOutputBaseName(String)
  - getOutputFilename
```
public java.lang.String getOutputFilename(boolean withExtension)
```
    Return the desired output filename for this Sequence.
    It uses the origin filename and add a specific extension depending some internals properties.
    
    Parameters:
    withExtension - Add the original file extension is set to true
    See Also:
    getFilename(), getOutputBaseName(String), getOutputExtension()
  - getOriginResolution
```
public int getOriginResolution()
```
    Returns the resolution level from the origin image (defined by getFilename()).
    By default it returns 0 if this sequence corresponds to the full resolution of the original image.
    1 --> original resolution / 2
    2 --> original resolution / 4
    3 --> original resolution / 8
    ...
  - setOriginResolution
```
public void setOriginResolution(int value)
```
    Internal use only, you should not directly use this method.
    
    See Also:
    getOriginResolution()
  - getOriginXYRegion
```
public java.awt.Rectangle getOriginXYRegion()
```
    Returns the region (X,Y) from original image if this image is a crop of the original image (in original image resolution).
    Default value is null (full size).
  - setOriginXYRegion
```
public void setOriginXYRegion(java.awt.Rectangle value)
```
    Internal use only, you should not directly use this method.
    
    See Also:
    getOriginXYRegion()
  - getOriginZMin
```
public int getOriginZMin()
```
    Returns the Z range minimum from original image if this image is a crop in Z of the original image.
    Default value is -1 which mean we have the whole Z range.
  - setOriginZMin
```
public void setOriginZMin(int value)
```
    Internal use only, you should not directly use this method.
    
    See Also:
    getOriginZMin()
  - getOriginZMax
```
public int getOriginZMax()
```
    Returns the Z range maximum from original image if this image is a crop in Z of the original image.
    Default value is -1 which mean we have the whole Z range.
  - setOriginZMax
```
public void setOriginZMax(int value)
```
    Internal use only, you should not directly use this method.
    
    See Also:
    getOriginZMax()
  - getOriginTMin
```
public int getOriginTMin()
```
    Returns the T range minimum from original image if this image is a crop in T of the original image.
    Default value is -1 which mean we have the whole T range.
  - setOriginTMin
```
public void setOriginTMin(int value)
```
    Internal use only, you should not directly use this method.
    
    See Also:
    getOriginTMin()
  - getOriginTMax
```
public int getOriginTMax()
```
    Returns the T range maximum from original image if this image is a crop in T of the original image.
    Default value is -1 which mean we have the whole T range.
  - setOriginTMax
```
public void setOriginTMax(int value)
```
    Internal use only, you should not directly use this method.
    
    See Also:
    getOriginTMax()
  - getOriginChannel
```
public int getOriginChannel()
```
    Returns the channel position from original image if this image is a single channel extraction of the original image.
    Default value is -1 which mean that all channels were preserved.
  - setOriginChannel
```
public void setOriginChannel(int value)
```
    Internal use only, you should not directly use this method.
    
    See Also:
    getOriginChannel()
  - resetOriginInformation
```
public void resetOriginInformation()
```
    Reset origin information (used after saved operation normally, internal use only).
  - getSeries
```
public int getSeries()
```
    Returns series index if the Sequence comes from a multi serie image.
    By default it returns 0 if the sequence comes from a single serie image or if this is the first series image.
  - setSeries
```
public void setSeries(int value)
```
    Set series index if the Sequence comes from a multi serie image (internal use only).
  - getSerieIndex
```
@Deprecated
public int getSerieIndex()
```
    Deprecated. Use getSeries() instead
  - getOMEXMLMetadata
```
public ome.xml.meta.OMEXMLMetadata getOMEXMLMetadata()
```
    Returns meta data object
  - setMetaData
```
public void setMetaData(ome.xml.meta.OMEXMLMetadata metaData)
```
    Set the meta data object
  - getMetadata
```
@Deprecated
public loci.formats.ome.OMEXMLMetadataImpl getMetadata()
```
    Deprecated. Use getOMEXMLMetadata() instead.
  - setMetaData
```
@Deprecated
public void setMetaData(loci.formats.ome.OMEXMLMetadataImpl metaData)
```
    Deprecated. Use setMetaData(OMEXMLMetadata) instead.
  - getPosition
```
public double[] getPosition()
```
    Returns the physical position [X,Y,Z] (in �m) of the image represented by this Sequence. This information can be used to represent the position of the image in the original sample (microscope information) or the position of a sub image from the original image (crop operation).
    Note that OME store this information at Plane level (each Z,T,C), here we just use value from Plane(0,0,0) then we use the pixels size and time interval information to compute other positions.
  - getPositionX
```
public double getPositionX()
```
    Returns the X physical position / offset (in �m) of the image represented by this Sequence.
    This information can be used to represent the position of the image in the original sample (microscope information) or the position of a sub image the original image (crop operation).
    Note that OME store this information at Plane level (each Z,T,C), here we just use value from Plane(0,0,0) then we use the pixels size and time interval information to compute other positions.
  - getPositionY
```
public double getPositionY()
```
    Returns the Y physical position / offset (in �m) of the image represented by this Sequence.
    This information can be used to represent the position of the image in the original sample (microscope information) or the position of a sub image the original image (crop operation).
    Note that OME store this information at Plane level (each Z,T,C), here we just use value from Plane(0,0,0) then we use the pixels size and time interval information to compute other positions.
  - getPositionZ
```
public double getPositionZ()
```
    Returns the Z physical position / offset (in �m) of the image represented by this Sequence.
    This information can be used to represent the position of the image in the original sample (microscope information) or the position of a sub image the original image (crop operation).
    Note that OME store this information at Plane level (each Z,T,C), here we just use value from Plane(0,0,0) then we use the pixels size and time interval information to compute other positions.
  - getPositionT
```
public long getPositionT()
```
    Same as getTimeStamp()
  - getTimeStamp
```
public long getTimeStamp()
```
    Returns the timestamp (elapsed milliseconds from the Java epoch of 1970-01-01 T00:00:00Z) of the image represented by this Sequence.
    
    See Also:
    getPositionTOffset(int, int, int), getTimeInterval()
  - getPositionTOffset
```
public double getPositionTOffset(int t,
                        int z,
                        int c)
```
    Returns the time position offset (in second for OME compatibility) relative to first image for the image at specified (T,Z,C) position.
    
    See Also:
    getTimeInterval(), getTimeStamp()
  - setPositionX
```
public void setPositionX(double value)
```
    Sets the X physical position / offset (in �m) of the image represented by this Sequence.
    This information can be used to represent the position of the image in the original sample (microscope information) or the position of a sub image the original image (crop operation).
    Note that OME store this information at Plane level (each Z,T,C), here we always use value from Plane(0,0,0)
  - setPositionY
```
public void setPositionY(double value)
```
    Sets the X physical position / offset (in �m) of the image represented by this Sequence.
    This information can be used to represent the position of the image in the original sample (microscope information) or the position of a sub image the original image (crop operation).
    Note that OME store this information at Plane level (each Z,T,C), here we always use value from Plane(0,0,0)
  - setPositionZ
```
public void setPositionZ(double value)
```
    Sets the X physical position / offset (in �m) of the image represented by this Sequence.
    This information can be used to represent the position of the image in the original sample (microscope information) or the position of a sub image the original image (crop operation).
    Note that OME store this information at Plane level (each Z,T,C), here we always use value from Plane(0,0,0)
  - setPositionT
```
public void setPositionT(long value)
```
    Same as setTimeStamp(long)
  - setTimeStamp
```
public void setTimeStamp(long value)
```
    Sets the timestamp (elapsed milliseconds from the Java epoch of 1970-01-01 T00:00:00Z) for the image represented by this Sequence.
    
    See Also:
    setPositionTOffset(int, int, int, double), setTimeInterval(double)
  - setPositionTOffset
```
public void setPositionTOffset(int t,
                      int z,
                      int c,
                      double value)
```
    Sets the time position / offset (in second for OME compatibility) relative to first image for the image at specified (T,Z,C) position.
    
    See Also:
    setTimeInterval(double), setTimeStamp(long)
  - getPixelSize
```
public double[] getPixelSize()
```
    Returns pixel size for [X,Y,Z] dimension (in �m to be OME compatible)
  - getPixelSizeX
```
public double getPixelSizeX()
```
    Returns X pixel size (in �m to be OME compatible)
  - getPixelSizeY
```
public double getPixelSizeY()
```
    Returns Y pixel size (in �m to be OME compatible)
  - getPixelSizeZ
```
public double getPixelSizeZ()
```
    Returns Z pixel size (in �m to be OME compatible)
  - getTimeInterval
```
public double getTimeInterval()
```
    Returns T time interval (in second for OME compatibility)
    
    See Also:
    getPositionTOffset(int, int, int)
  - setPixelSizeX
```
public void setPixelSizeX(double value)
```
    Set X pixel size (in �m to be OME compatible)
  - setPixelSizeY
```
public void setPixelSizeY(double value)
```
    Set Y pixel size (in �m to be OME compatible)
  - setPixelSizeZ
```
public void setPixelSizeZ(double value)
```
    Set Z pixel size (in �m to be OME compatible)
  - setTimeInterval
```
public void setTimeInterval(double value)
```
    Set T time resolution (in second to be OME compatible)
    
    See Also:
    setPositionTOffset(int, int, int, double)
  - getPixelSizeScaling
```
public double getPixelSizeScaling(int dimCompute,
                         int dimResult)
```
    Returns the pixel size scaling factor to convert a number of pixel/voxel unit into �m
    
    For instance to get the scale ration for 2D distance:
    valueMicroMeter = pixelNum * getPixelSizeScaling(2, 1)
    For a 2D surface:
    valueMicroMeter2 = pixelNum * getPixelSizeScaling(2, 2)
    For a 3D volume:
    valueMicroMeter3 = pixelNum * getPixelSizeScaling(3, 3)
    
    Parameters:
    dimCompute - dimension order for size calculation
    
    1 --> pixel size X used for conversion
    
    2 --> pixel size X and Y used for conversion
    
    3 or above --> pixel size X, Y and Z used for conversion
    
    dimResult - dimension order for the result (unit)
    
    1 --> distance
    
    2 --> area
    
    3 or above --> volume
  - getBestPixelSizeUnit
```
public UnitUtil.UnitPrefix getBestPixelSizeUnit(int dimCompute,
                                       int dimResult)
```
    Returns the best pixel size unit for the specified dimension order given the sequence's pixel size informations.
  - Compute a 2D distance:
  - Compute a 2D surface:
  - Compute a 3D volume:

Parameters:: dimCompute - dimension order for size calculation

1 --> pixel size X used for conversion

2 --> pixel size X and Y used for conversion

3 or above --> pixel size X, Y and Z used for conversion; dimResult - dimension order for the result (unit)

1 --> distance

2 --> area

3 or above --> volume
See Also:: calculateSizeBestUnit(double, int, int)

calculateSize
```
public double calculateSize(double pixelNumber,
                   int dimCompute,
                   int dimResult)
```
Returns the size in �m for the specified amount of sample/pixel value in the specified dimension order.

For the perimeter in �m:
perimeter = calculateSize(contourInPixel, 2, 1)
For a 2D surface in �m2:
surface = calculateSize(interiorInPixel, 2, 2)
For a 2D surface area in �m2:
volume = calculateSize(contourInPixel, 3, 2)
For a 3D volume in �m3:
volume = calculateSize(interiorInPixel, 3, 3)

Parameters:
pixelNumber - number of pixel
dimCompute - dimension order for size calculation

1 --> pixel size X used for conversion

2 --> pixel size X and Y used for conversion

3 or above --> pixel size X, Y and Z used for conversion

dimResult - dimension order for the result (unit)

1 --> distance

2 --> area

3 or above --> volume

See Also:
calculateSizeBestUnit(double, int, int)

calculateSizeBestUnit
```
public double calculateSizeBestUnit(double pixelNumber,
                           int dimCompute,
                           int dimResult)
```
Returns the size converted in the best unit (see getBestPixelSizeUnit(int, int) for the specified amount of sample/pixel value in the specified dimension order.
Compute a 2D distance:

 dimCompute = 2;
 dimUnit = 1;
 valueBestUnit = calculateSizeBestUnit(pixelNum, dimCompute, dimUnit);
 bestUnit = getBestPixelSizeUnit(dimCompute, dimUnit);
 valueString = Double.toString(valueBestUnit) + " " + bestUnit.toString() + "m";

Compute a 2D surface:

 dimCompute = 2;
 dimUnit = 2;
 valueBestUnit = calculateSizeBestUnit(pixelNum, dimCompute, dimUnit);
 bestUnit = getBestPixelSizeUnit(dimCompute, dimUnit);
 valueString = Double.toString(valueBestUnit) + " " + bestUnit.toString() + "m2";

Compute a 3D volume:

 dimCompute = 3;
 dimUnit = 3;
 valueBestUnit = calculateSizeBestUnit(pixelNum, dimCompute, dimUnit);
 bestUnit = getBestPixelSizeUnit(dimCompute, dimUnit);
 valueString = Double.toString(valueBestUnit) + " " + bestUnit.toString() + "m3";

Class Sequence

Nested Class Summary

Nested classes/interfaces inherited from interface icy.sequence.SequenceModel

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_NAME

TYPE_BYTE

TYPE_DOUBLE

TYPE_FLOAT

TYPE_INT

TYPE_SHORT

TYPE_UNDEFINED

ID_NAME

ID_POSITION_X

ID_POSITION_Y

ID_POSITION_Z

ID_POSITION_T

ID_POSITION_T_OFFSET

ID_PIXEL_SIZE_X

ID_PIXEL_SIZE_Y

ID_PIXEL_SIZE_Z

ID_TIME_INTERVAL

ID_CHANNEL_NAME

ID_VIRTUAL

Constructor Detail

Sequence

Sequence

Sequence

Sequence

Sequence

Sequence

Sequence

Sequence

Sequence

Sequence

Method Detail

close

closed

copyFrom

copyDataFrom

copyMetaDataFrom

createUndoPoint

createUndoDataPoint

createUndoMetadataPoint

addUndoableEdit

undo

redo

clearUndoManager

convertToType

convertToType

convertToType

extractChannel

extractChannels

extractBand

extractBands

getVolumetricImages

getAllVolumetricImage

getFirstViewer

getViewers

setVolatile

setVirtual

isVolatile

isVirtual

getId

setName

getName

getFilename

setFilename

getImageProvider

setImageProvider

getOutputBaseName

getOutputExtension

getOutputFilename

getOriginResolution

setOriginResolution

getOriginXYRegion

setOriginXYRegion