acquifer.ij

Class VirtualImageSeries

Object

ij.ImageStack

ij.VirtualStack

acquifer.ij.VirtualImageSeries

public class VirtualImageSeries
extends ij.VirtualStack

Custom VirtualStack for ImageSeries.
The VirtualStack is a 1D-version of the ImageSeries, flattened in c,z,t order. .
Images are loaded on the fly, and if no ImagePlane is available for a given c,z,t a black ImagePlane is returned.

Constructor Summary

Constructors

Constructor and Description
VirtualImageSeries(acquifer.core.ImageSeries imageSeries)

Method Summary

Modifier and Type	Method and Description
void	deleteSlice(int n) Remove IamgePlane at 1-based index n, from the VirtualSeries and move following planes "to the left" in the array of IamgePlanes.
int	getBitDepth()
String	getDirectory()
String	getFileName(int n)
int	getHeight()
acquifer.core.im.ImagePlane	getImagePlane(int n) Return the ImagePlane (or null if missing) at index n (1-based).
ij.process.ImageProcessor	getProcessor(int n) Return the ImageProcessor for the index n (1-based) or a black ImageProcessor if no ImagePlane is available.
int	getSize()
String	getSliceLabel(int n) Return the slice label for the slice at 1-based index n.
int	getWidth()
void	setBitDepth(int bitDepth)

Methods inherited from class ij.VirtualStack

addSlice, addSlice, addSlice, addSlice, deleteLastSlice, getImageArray, getPixels, getProperties, isVirtual, saveChanges, setIndexes, setPixels, setSliceLabel, size, sortDicom, translate, trim

Methods inherited from class ij.ImageStack

addSlice, addUnsignedShortSlice, convertToFloat, create, create, crop, drawSphere, duplicate, getColorModel, getRoi, getShortSliceLabel, getShortSliceLabel, getSliceLabels, getVoxel, getVoxels, getVoxels, isHSB, isHSB32, isLab, isRGB, setColorModel, setOptions, setProcessor, setRoi, setVoxel, setVoxels, setVoxels, toString, update

Methods inherited from class Object

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

Constructor Detail

VirtualImageSeries

public VirtualImageSeries(acquifer.core.ImageSeries imageSeries)
                   throws IOException

Throws:

IOException

Method Detail

getDirectory

public String getDirectory()

Overrides:

getDirectory in class ij.VirtualStack

getWidth

public int getWidth()

Overrides:

getWidth in class ij.ImageStack

getHeight

public int getHeight()

Overrides:

getHeight in class ij.ImageStack

getSize

public int getSize()

Overrides:

getSize in class ij.VirtualStack

getBitDepth

public int getBitDepth()

Overrides:

getBitDepth in class ij.VirtualStack

setBitDepth

public void setBitDepth(int bitDepth)

Overrides:

setBitDepth in class ij.VirtualStack

getImagePlane

public acquifer.core.im.ImagePlane getImagePlane(int n)

Return the ImagePlane (or null if missing) at index n (1-based).

getSliceLabel

public String getSliceLabel(int n)

Return the slice label for the slice at 1-based index n.
Return "Missing image file" if there is no ImagePlane available for the given position.

Overrides:

getSliceLabel in class ij.VirtualStack

getFileName

public String getFileName(int n)

Overrides:

getFileName in class ij.VirtualStack

getProcessor

public ij.process.ImageProcessor getProcessor(int n)

Return the ImageProcessor for the index n (1-based) or a black ImageProcessor if no ImagePlane is available.
VirtualStack are originally 1D and ordered by CZT.
For VirtualImageSeries a 1D index is not meaningful since we use a n-dimensional data-storage.
This method is thus here only for compatibility with the rest of the ImageJ API.

Overrides:

getProcessor in class ij.VirtualStack

deleteSlice

public void deleteSlice(int n)

Remove IamgePlane at 1-based index n, from the VirtualSeries and move following planes "to the left" in the array of IamgePlanes.
Rarely used (StackCombiner makes use of it).

Overrides:

deleteSlice in class ij.VirtualStack