Package loci.plugins.util

Class BFVirtualStack

java.lang.Object

ij.ImageStack

ij.VirtualStack

loci.plugins.util.BFVirtualStack

public class BFVirtualStack
extends VirtualStack

Subclass of VirtualStack that uses Bio-Formats to read planes on demand.

Field Summary

Fields

Modifier and Type	Field	Description
protected loci.formats.cache.Cache	cache
protected String	id
protected ImageProcessorReader	reader

Fields inherited from class ij.ImageStack

cTable

Constructor Summary

Constructors

Constructor	Description
BFVirtualStack(String path, loci.formats.IFormatReader r, boolean colorize, boolean merge, boolean record)

Method Summary

Modifier and Type	Method	Description
loci.formats.cache.Cache	getCache()
int	getHeight()
protected static int	getHeight(loci.formats.IFormatReader r, String path, int series)
List<loci.plugins.util.RecordedImageProcessor.MethodEntry>	getMethodStack()
String	getPath()
ImageProcessor	getProcessor(int n)
ImageProcessorReader	getReader()
RecordedImageProcessor	getRecordedProcessor()
int	getSize()
int	getWidth()
protected static int	getWidth(loci.formats.IFormatReader r, String path, int series)
void	setPlaneIndexes(int[] planeIndexes)

Methods inherited from class ij.VirtualStack

addSlice, addSlice, addSlice, addSlice, deleteLastSlice, deleteSlice, getBitDepth, getDirectory, getFileName, getImageArray, getPixels, getProperties, getSliceLabel, isVirtual, reduce, saveChanges, setBitDepth, 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 java.lang.Object

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

Field Details

reader

protected ImageProcessorReader reader

id

protected String id

cache

protected loci.formats.cache.Cache cache

Constructor Details

BFVirtualStack

public BFVirtualStack(String path,
 loci.formats.IFormatReader r,
 boolean colorize,
 boolean merge,
 boolean record)
               throws loci.formats.FormatException,
IOException,
loci.formats.cache.CacheException

Throws:

loci.formats.FormatException

IOException

loci.formats.cache.CacheException

Method Details

getWidth

protected static int getWidth(loci.formats.IFormatReader r,
 String path,
 int series)
                       throws loci.formats.FormatException,
IOException

Throws:

loci.formats.FormatException

IOException

getHeight

protected static int getHeight(loci.formats.IFormatReader r,
 String path,
 int series)
                        throws loci.formats.FormatException,
IOException

Throws:

loci.formats.FormatException

IOException

getPath

public String getPath()

getReader

public ImageProcessorReader getReader()

getCache

public loci.formats.cache.Cache getCache()

getRecordedProcessor

public RecordedImageProcessor getRecordedProcessor()

getMethodStack

public List<loci.plugins.util.RecordedImageProcessor.MethodEntry> getMethodStack()

setPlaneIndexes

public void setPlaneIndexes(int[] planeIndexes)

getProcessor

public ImageProcessor getProcessor(int n)

Overrides:

getProcessor in class VirtualStack

getWidth

public int getWidth()

Overrides:

getWidth in class ImageStack

getHeight

public int getHeight()

Overrides:

getHeight in class ImageStack

getSize

public int getSize()

Overrides:

getSize in class VirtualStack