edu.stanford.rsl.konrad.io
Class Nrrd_Reader

java.lang.Object
  extended by ij.ImagePlus
      extended by edu.stanford.rsl.konrad.io.Nrrd_Reader
All Implemented Interfaces:
ij.measure.Measurements, ij.plugin.PlugIn, java.awt.image.ImageObserver

public class Nrrd_Reader
extends ij.ImagePlus
implements ij.plugin.PlugIn

ImageJ plugin to read a file in Gordon Kindlmann's NRRD or 'nearly raw raster data' format, a simple format which handles coordinate systems and data types in a very general way. See http://teem.sourceforge.net/nrrd and http://flybrain.stanford.edu/nrrd


Field Summary
 java.lang.String headerPath
           
 java.lang.String imageName
           
 java.lang.String imagePath
           
 java.lang.String int16Types
           
 java.lang.String int32Types
           
 java.lang.String uint16Types
           
 java.lang.String uint32Types
           
 java.lang.String uint8Types
           
 
Fields inherited from class ij.ImagePlus
changes, COLOR_256, COLOR_RGB, GRAY16, GRAY32, GRAY8
 
Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Fields inherited from interface ij.measure.Measurements
AREA, AREA_FRACTION, CENTER_OF_MASS, CENTROID, CIRCULARITY, ELLIPSE, FERET, INTEGRATED_DENSITY, INVERT_Y, KURTOSIS, LABELS, LIMIT, MAX_STANDARDS, MEAN, MEDIAN, MIN_MAX, MODE, PERIMETER, RECT, SCIENTIFIC_NOTATION, SHAPE_DESCRIPTORS, SKEWNESS, SLICE, STACK_POSITION, STD_DEV
 
Constructor Summary
Nrrd_Reader()
           
 
Method Summary
 NrrdFileInfo getHeaderInfo(java.lang.String directory, java.lang.String fileName)
           
 ij.ImagePlus load(java.lang.String directory, java.lang.String fileName)
           
 void run(java.lang.String arg)
           
 
Methods inherited from class ij.ImagePlus
addImageListener, close, convertIndexToPosition, copy, copyScale, createEmptyStack, createHyperStack, createImagePlus, createLut, createNewRoi, draw, draw, flatten, flush, getBitDepth, getBufferedImage, getBytesPerPixel, getCalibration, getCanvas, getChannel, getChannelProcessor, getClipboard, getCurrentSlice, getDefault16bitRange, getDimensions, getDisplayRangeMax, getDisplayRangeMin, getFileInfo, getFrame, getGlobalCalibration, getHeight, getHideOverlay, getID, getImage, getImageStack, getImageStackSize, getLocalCalibration, getLocationAsString, getLuts, getMask, getNChannels, getNDimensions, getNFrames, getNSlices, getOpenAsHyperStack, getOriginalFileInfo, getOverlay, getPixel, getProcessor, getProperties, getProperty, getRoi, getShortTitle, getSlice, getStack, getStackIndex, getStackSize, getStartTime, getStatistics, getStatistics, getStatistics, getStatistics, getTitle, getType, getWidth, getWindow, hide, imageUpdate, isComposite, isDisplayedHyperStack, isHyperStack, isInvertedLut, isLocked, isProcessor, isVisible, killRoi, killStack, lock, lockSilently, mouseMoved, paste, removeImageListener, repaintWindow, resetClipboard, resetDisplayRange, resetStack, restoreRoi, revert, saveRoi, setActivated, setCalibration, setColor, setDefault16bitRange, setDimensions, setDisplayRange, setDisplayRange, setFileInfo, setGlobalCalibration, setHideOverlay, setIgnoreFlush, setImage, setOpenAsHyperStack, setOverlay, setOverlay, setOverlay, setPosition, setPosition, setPositionWithoutUpdate, setProcessor, setProcessor, setProperty, setRoi, setRoi, setRoi, setRoi, setSlice, setSliceWithoutUpdate, setStack, setStack, setStack, setTitle, setWindow, show, show, startTiming, toString, trimProcessor, unlock, updateAndDraw, updateAndRepaintWindow, updateChannelAndDraw, updateImage, updatePosition, updateStatusbarValue
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

uint8Types

public final java.lang.String uint8Types
See Also:
Constant Field Values

int16Types

public final java.lang.String int16Types
See Also:
Constant Field Values

uint16Types

public final java.lang.String uint16Types
See Also:
Constant Field Values

int32Types

public final java.lang.String int32Types
See Also:
Constant Field Values

uint32Types

public final java.lang.String uint32Types
See Also:
Constant Field Values

headerPath

public java.lang.String headerPath

imagePath

public java.lang.String imagePath

imageName

public java.lang.String imageName
Constructor Detail

Nrrd_Reader

public Nrrd_Reader()
Method Detail

run

public void run(java.lang.String arg)
Specified by:
run in interface ij.plugin.PlugIn

load

public ij.ImagePlus load(java.lang.String directory,
                         java.lang.String fileName)

getHeaderInfo

public NrrdFileInfo getHeaderInfo(java.lang.String directory,
                                  java.lang.String fileName)
                           throws java.io.IOException
Throws:
java.io.IOException