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.

Source code:

Trac, Gitweb

Author:

Melissa Linkert melissa at glencoesoftware.com

Field Summary

Fields

Modifier and Type	Field and Description
protected Cache	cache
protected java.lang.String	id
protected ImageProcessorReader	reader

Constructor Summary

Constructors

Constructor and Description
BFVirtualStack(java.lang.String path, IFormatReader r, boolean colorize, boolean merge, boolean record)

Method Summary

Methods

Modifier and Type	Method and Description
Cache	getCache()
int	getHeight()
protected static int	getHeight(IFormatReader r, java.lang.String path, int series)
java.util.List<loci.plugins.util.RecordedImageProcessor.MethodEntry>	getMethodStack()
java.lang.String	getPath()
ImageProcessor	getProcessor(int n)
ImageProcessorReader	getReader()
RecordedImageProcessor	getRecordedProcessor()
int	getSize()
int	getWidth()
protected static int	getWidth(IFormatReader r, java.lang.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, getSliceLabel, isVirtual, saveChanges, setBitDepth, setPixels, setSliceLabel, sortDicom, trim

Methods inherited from class ij.ImageStack

addUnsignedShortSlice, getColorModel, getRoi, getShortSliceLabel, getSliceLabels, getVoxel, isHSB, isRGB, setColorModel, setRoi, setVoxel, toString, update

Methods inherited from class java.lang.Object

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

Field Detail

reader

protected ImageProcessorReader reader

id

protected java.lang.String id

cache

protected Cache cache

Constructor Detail

BFVirtualStack

public BFVirtualStack(java.lang.String path,
              IFormatReader r,
              boolean colorize,
              boolean merge,
              boolean record)
               throws FormatException,
                      java.io.IOException,
                      CacheException

Throws:

FormatException

java.io.IOException

CacheException

Method Detail

getWidth

protected static int getWidth(IFormatReader r,
           java.lang.String path,
           int series)
                       throws FormatException,
                              java.io.IOException

Throws:

FormatException

java.io.IOException

getHeight

protected static int getHeight(IFormatReader r,
            java.lang.String path,
            int series)
                        throws FormatException,
                               java.io.IOException

Throws:

FormatException

java.io.IOException

getPath

public java.lang.String getPath()

getReader

public ImageProcessorReader getReader()

getCache

public Cache getCache()

getRecordedProcessor

public RecordedImageProcessor getRecordedProcessor()

getMethodStack

public java.util.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