loci.plugins.util

Class BFVirtualStack

java.lang.Object

ij.ImageStack

ij.VirtualStack

loci.plugins.util.BFVirtualStack

public class BFVirtualStack
extends ij.VirtualStack

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

Author:

Melissa Linkert melissa at glencoesoftware.com

Field Summary

Fields

Modifier and Type	Field and Description
protected Cache	cache
private float[]	calibrationTable
private boolean	colorize
private RecordedImageProcessor	currentProcessor
private int	currentSlice
protected String	id
private int[]	len
private boolean	merge
private List<List<RecordedImageProcessor.MethodEntry>>	methodStacks
private int[]	planeIndexes
protected ImageProcessorReader	reader
private boolean	record
private int	series

Constructor Summary

Constructors

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

Method Summary

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

Methods inherited from class ij.ImageStack

addSlice, addUnsignedShortSlice, convertToFloat, create, crop, drawSphere, duplicate, getColorModel, getRoi, getShortSliceLabel, getSliceLabels, getVoxel, getVoxels, getVoxels, isHSB, isRGB, setColorModel, 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 Detail

reader

protected ImageProcessorReader reader

id

protected String id

cache

protected Cache cache

methodStacks

private List<List<RecordedImageProcessor.MethodEntry>> methodStacks

currentSlice

private int currentSlice

currentProcessor

private RecordedImageProcessor currentProcessor

colorize

private boolean colorize

merge

private boolean merge

record

private boolean record

series

private int series

len

private int[] len

planeIndexes

private int[] planeIndexes

calibrationTable

private float[] calibrationTable

Constructor Detail

BFVirtualStack

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

Throws:

FormatException

IOException

CacheException

Method Detail

getWidth

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

Throws:

FormatException

IOException

getHeight

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

Throws:

FormatException

IOException

getPath

public String getPath()

getReader

public ImageProcessorReader getReader()

getCache

public Cache getCache()

getRecordedProcessor

public RecordedImageProcessor getRecordedProcessor()

getMethodStack

public List<RecordedImageProcessor.MethodEntry> getMethodStack()

setPlaneIndexes

public void setPlaneIndexes(int[] planeIndexes)

getProcessor

public ij.process.ImageProcessor getProcessor(int n)

Overrides:

getProcessor 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