plugin
CommandLister
run ( )
listCommands ( )
listShortcuts ( )
addShortcutsToVector ( )
showList ( )
LutLoader
defaultDirectory : String
run ( )
showLut ( )
invertLut ( )
fire ( )
grays ( )
primaryColor ( )
ice ( )
spectrum ( )
rgb332 ( )
redGreen ( )
interpolate ( )
openLut ( )
error ( )
openBinaryLut ( )
openTextLut ( )
createImage ( )
ZProjector
AVG_METHOD : int
MAX_METHOD : int
MIN_METHOD : int
SUM_METHOD : int
SD_METHOD : int
MEDIAN_METHOD : int
«JavaArray» METHODS : String
method : int
BYTE_TYPE : int
SHORT_TYPE : int
FLOAT_TYPE : int
lutMessage : String
projImage : ImagePlus
imp : ImagePlus
startSlice : int
stopSlice : int
allTimeFrames : boolean
color : String
isHyperstack : boolean
increment : int
sliceCount : int
/image : ImagePlus
/projection : ImagePlus
ZProjector ( )
ZProjector ( )
run ( )
doRGBProjection ( )
buildControlDialog ( )
doProjection ( )
doHyperStackProjection ( )
getRayFunction ( )
makeOutputImage ( )
projectSlice ( )
makeTitle ( )
doMedianProjection ( )
median ( )
sort ( )
sort ( )
alreadySorted ( )
ScaleBar
«JavaArray» locations : String
UPPER_RIGHT : int
LOWER_RIGHT : int
LOWER_LEFT : int
UPPER_LEFT : int
AT_SELECTION : int
«JavaArray» colors : String
«JavaArray» bcolors : String
«JavaArray» checkboxLabels : String
barWidth : double
defaultBarHeight : int
barHeightInPixels : int
location : String
color : String
bcolor : String
boldText : boolean
hideText : boolean
defaultFontSize : int
fontSize : int
labelAll : boolean
imp : ImagePlus
imageWidth : double
mag : double
xloc : int
yloc : int
barWidthInPixels : int
roiX : int
roiY : int
roiWidth : int
roiHeight : int
serifFont : boolean
«JavaArray» checkboxStates : boolean
run ( )
labelSlices ( )
showDialog ( )
drawScaleBar ( )
updateLocation ( )
updateScalebar ( )
PGM_Reader
width : int
height : int
rawBits : boolean
sixteenBits : boolean
isColor : boolean
isBlackWhite : boolean
maxValue : int
run ( )
openFile ( )
openHeader ( )
openAsciiImage ( )
openRawImage ( )
open16bitRawImage ( )
open16bitAsciiImage ( )
getWord ( )
getInt ( )
MontageMaker
columns : int
rows : int
first : int
last : int
inc : int
borderWidth : int
scale : double
label : boolean
useForegroundColor : boolean
saveID : int
saveStackSize : int
fontSize : int
run ( )
makeMontage ( )
makeMontage ( )
drawBorder ( )
drawLabel ( )
JavaProperties
sb : StringBuffer
run ( )
cores ( )
show ( )
doFullDump ( )
MemoryMonitor
width : int
height : int
fps : long
startTime : long
elapsedTime : long
ip : ImageProcessor
frames : int
ic : ImageCanvas
«JavaArray» mem : double
index : int
value : long
max : double
maxMemory : long
run ( )
showValue ( )
updatePixels ( )
Duplicator
duplicateStack : boolean
duplicateSubstack : boolean
first : int
last : int
checkbox : Checkbox
rangeField : TextField
run ( )
run ( )
duplicateImage ( )
run ( )
showDialog ( )
textValueChanged ( )
TextWriter
run ( )
saveText ( )
Memory
s : String
index1 : int
index2 : int
f : File
fileMissing : boolean
sixtyFourBit : boolean
/memorySetting : long
run ( )
changeMemoryAllocation ( )
showError ( )
getMemorySetting ( )
maxMemory ( )
Commands
run ( )
revert ( )
save ( )
undo ( )
close ( )
closeImage ( )
openStartupMacros ( )
RGBStackConverter
channels1 : int
slices1 : int
frames1 : int
slices2 : int
frames2 : int
width : int
height : int
imageSize : double
keep : boolean
/newDimensions : String
run ( )
compositeToRGB ( )
convertHyperstack ( )
compositeToRGB2 ( )
compositeImageToRGB ( )
sixteenBitsToRGB ( )
showDialog ( )
dialogItemChanged ( )
Concatenator
imp1 : ImagePlus
imp2 : ImagePlus
keep : boolean
title : String
run ( )
concatenate ( )
showDialog ( )
error ( )
ImagesToStack
rgb : int
COPY_CENTER : int
COPY_TOP_LEFT : int
SCALE_SMALL : int
SCALE_LARGE : int
«JavaArray» methods : String
method : int
bicubic : boolean
keep : boolean
titlesAsLabels : boolean
filter : String
width : int
height : int
maxWidth : int
maxHeight : int
minWidth : int
minHeight : int
minSize : int
maxSize : int
cal2 : Calibration
stackType : int
«JavaArray» image : ImagePlus
name : String
run ( )
convertImagesToStack ( )
findMinMaxSize ( )
exclude ( )
CommandFinder
multiClickInterval : int
lastClickTime : long
lastClickedItem : String
d : JFrame
prompt : JTextField
completions : JList
scrollPane : JScrollPane
completionsModel : DefaultListModel
runButton : JButton
closeButton : JButton
exportButton : JButton
fullInfoCheckBox : JCheckBox
closeCheckBox : JCheckBox
commandsHash : Hashtable
«JavaArray» commands : String
listLabelToCommand : Hashtable
closeWhenRunning : boolean
CommandFinder ( )
makeListLabel ( )
populateList ( )
actionPerformed ( )
itemStateChanged ( )
mouseClicked ( )
mousePressed ( )
mouseReleased ( )
mouseEntered ( )
mouseExited ( )
export ( )
runFromLabel ( )
keyPressed ( )
keyReleased ( )
keyTyped ( )
parseMenu ( )
findAllMenuItems ( )
run ( )
windowClosing ( )
windowActivated ( )
windowDeactivated ( )
windowClosed ( )
windowOpened ( )
windowIconified ( )
windowDeiconified ( )
MacroInstaller
MAX_SIZE : int
MAX_MACROS : int
XINC : int
YINC : int
commandPrefix : char
commandPrefixS : String
MACROS_MENU_COMMANDS : int
«JavaArray» macroStarts : int
«JavaArray» macroNames : String
mb : MenuBar
nMacros : int
pgm : Program
firstEvent : boolean
shortcutsInUse : String
inUseCount : int
nShortcuts : int
toolCount : int
text : String
anonymousName : String
macrosMenu : Menu
autoRunCount : int
autoRunAndHideCount : int
openingStartupMacrosInEditor : boolean
defaultDir : String
fileName : String
instance : MacroInstaller
listener : MacroInstaller
/macroCount : int
/program : Program
/autoRunAndHide : boolean
run ( )
install ( )
install ( )
install ( )
installFile ( )
installLibrary ( )
installFromIJJar ( )
installPopupMenu ( )
removeShortcuts ( )
addShortcut ( )
showDialog ( )
open ( )
openFromIJJar ( )
runMacroTool ( )
runMenuTool ( )
runMacroCommand ( )
runMacroShortcut ( )
runMacro ( )
runMacro ( )
actionPerformed ( )
Slicer
«JavaArray» starts : String
startAt : String
rotate : boolean
flip : boolean
nointerpolate : boolean
inputZSpacing : double
outputZSpacing : double
outputSlices : int
noRoi : boolean
rgb : boolean
notFloat : boolean
fields : Vector
checkboxes : Vector
message : Label
imp : ImagePlus
gx1 : double
gy1 : double
gx2 : double
gy2 : double
gLength : double
n : int
«JavaArray» x : double
«JavaArray» y : double
xbase : int
ybase : int
length : double
«JavaArray» segmentLengths : double
«JavaArray» dx : double
«JavaArray» dy : double
/availableMemory : int
run ( )
reslice ( )
resliceHyperstack ( )
showDialog ( )
d2s ( )
saveLineInfo ( )
resliceRectOrLine ( )
createOutputStack ( )
getSlice ( )
putRow ( )
putColumn ( )
getIrregularProfile ( )
doIrregularSetup ( )
getLine ( )
getOrthoLine ( )
drawLine ( )
textValueChanged ( )
itemStateChanged ( )
updateSize ( )
getSize ( )
makePolygon ( )
getOutputStackSize ( )
RGBStackMerge
createComposite : boolean
imp : ImagePlus
«JavaArray» blank : byte
run ( )
mergeStacks ( )
mergeHyperstacks ( )
createComposite ( )
mergeStacks ( )
getPixels ( )
invert ( )
error ( )
Hotkeys
TITLE : String
command : String
shortcut : String
«JavaArray» /allCommands : String
«JavaArray» /installedCommands : String
run ( )
installHotkey ( )
removeHotkey ( )
deletePlugin ( )
ContrastEnhancer
max : int
range : int
classicEqualization : boolean
stackSize : int
updateSelectionOnly : boolean
equalize : boolean
normalize : boolean
processStack : boolean
useStackHistogram : boolean
entireImage : boolean
saturated : double
gEqualize : boolean
gNormalize : boolean
run ( )
showDialog ( )
stretchHistogram ( )
stretchHistogram ( )
stretchHistogram ( )
stretchCompositeImageHistogram ( )
getMinAndMax ( )
normalize ( )
applyTable ( )
normalizeFloat ( )
equalize ( )
equalize ( )
getWeightedValue ( )
FileInfoVirtualStack
«JavaArray» info : FileInfo
nImages : int
/size : int
/width : int
/height : int
FileInfoVirtualStack ( )
FileInfoVirtualStack ( )
run ( )
open ( )
getInt ( )
getNumber ( )
getBoolean ( )
deleteSlice ( )
getProcessor ( )
getSliceLabel ( )
Timer
j : int
startTime : long
nullLoopTime : long
numLoops : int
run ( )
showTime ( )
WandToolOptions
«JavaArray» modes : String
mode : String
tolerance : double
run ( )
DICOM_Sorter
MAX_DIGITS : int
run ( )
sort ( )
sortStack ( )
getSortStrings ( )
toString ( )
isDicomStack ( )
getSeriesNumber ( )
getNumericTag ( )
getTag ( )
LUT_Editor
imp : ImagePlus
openButton : Button
saveButton : Button
resizeButton : Button
invertButton : Button
colorPanel
bitDepth : int
run ( )
save ( )
actionPerformed ( )
BatchProcesser
MACRO_FILE_NAME : String
«JavaArray» formats : String
format : String
«JavaArray» code : String
macro : String
testImage : int
input : Button
output : Button
open : Button
save : Button
test : Button
inputDir : TextField
outputDir : TextField
gd : GenericDialog
thread : Thread
virtualStack : ImagePlus
/virtualStackImage : ImagePlus
/folderImage : ImagePlus
/dirAndName : String
run ( )
showDialog ( )
processVirtualStack ( )
pad ( )
processFolder ( )
addSeparator ( )
validateFormat ( )
addPanels ( )
addButtons ( )
itemStateChanged ( )
actionPerformed ( )
open ( )
save ( )
error ( )
run ( )
AVI_Reader
FOURCC_RIFF : int
FOURCC_AVI : int
FOURCC_LIST : int
FOURCC_hdrl : int
FOURCC_avih : int
FOURCC_strl : int
FOURCC_strh : int
FOURCC_strf : int
FOURCC_movi : int
FOURCC_rec : int
FOURCC_JUNK : int
FOURCC_vids : int
FOURCC_00db : int
FOURCC_00dc : int
NO_COMPRESSION : int
NO_COMPRESSION_RGB : int
NO_COMPRESSION_RAW : int
NO_COMPRESSION_Y800 : int
NO_COMPRESSION_Y8 : int
NO_COMPRESSION_GREY : int
NO_COMPRESSION_Y16 : int
NO_COMPRESSION_MIL : int
AYUV_COMPRESSION : int
UYVY_COMPRESSION : int
Y422_COMPRESSION : int
UYNV_COMPRESSION : int
CYUV_COMPRESSION : int
V422_COMPRESSION : int
YUY2_COMPRESSION : int
YUNV_COMPRESSION : int
YUYV_COMPRESSION : int
YVYU_COMPRESSION : int
JPEG_COMPRESSION : int
JPEG_COMPRESSION2 : int
JPEG_COMPRESSION3 : int
MJPG_COMPRESSION : int
PNG_COMPRESSION : int
PNG_COMPRESSION2 : int
PNG_COMPRESSION3 : int
BITMASK24 : int
SIZE_MASK : long
firstFrameNumber : int
lastFrameNumber : int
convertToGray : boolean
flipVertical : boolean
isVirtual : boolean
raFile : RandomAccessFile
raFilePath : String
headerOK : boolean
streamNumber : int
fileSize : long
paddingGranularity : int
dataCompression : int
scanLineSize : int
dataTopDown : boolean
cm : ColorModel
variableLength : boolean
frameInfos : Vector
stack : ImageStack
imp : ImagePlus
verbose : boolean
startTime : long
dwMicroSecPerFrame : int
dwMaxBytesPerSec : int
dwReserved1 : int
dwFlags : int
dwTotalFrames : int
dwInitialFrames : int
dwStreams : int
dwSuggestedBufferSize : int
dwWidth : int
dwHeight : int
fccStreamHandler : int
dwStreamFlags : int
dwPriorityLanguage : int
dwStreamInitialFrames : int
dwStreamScale : int
dwStreamRate : int
dwStreamStart : int
dwStreamLength : int
dwStreamSuggestedBufferSize : int
dwStreamQuality : int
dwStreamSampleSize : int
biSize : int
biWidth : int
biHeight : int
biPlanes : short
biBitCount : short
biCompression : int
biSizeImage : int
biXPelsPerMeter : int
biYPelsPerMeter : int
biClrUsed : int
biClrImportant : int
/imagePlus : ImagePlus
/width : int
/height : int
/size : int
/framesPerSecond : ImagePlus
run ( )
makeStack ( )
getProcessor ( )
getSliceLabel ( )
deleteSlice ( )
showDialog ( )
readAVI ( )
openAndReadHeader ( )
findFourccAndRead ( )
readContents ( )
readAviHeader ( )
readStreamHeader ( )
readBitMapInfo ( )
readMovieData ( )
readFrame ( )
readCompressedFrame ( )
readFixedLengthFrame ( )
unpack8bit ( )
unpackGray ( )
unpackShort ( )
unpack ( )
writeRGBfromYUV ( )
readInt ( )
readShort ( )
readType ( )
frameLabel ( )
posSizeString ( )
posSizeString ( )
timeString ( )
fourccString ( )
exceptionMessage ( )
updateProgress ( )
TextReader
words : int
chars : int
lines : int
width : int
directory : String
name : String
path : String
hideErrorMessages : boolean
run ( )
showDialog ( )
open ( )
open ( )
hideErrorMessages ( )
countLines ( )
read ( )
Zoom
run ( )
zoomToSelection ( )
setZoom ( )
«interface»
PlugIn
run ( )
Animator
animationRate : double
firstFrame : int
lastFrame : int
imp : ImagePlus
swin : StackWindow
slice : int
nSlices : int
/frameRate : double
run ( )
stopAnimation ( )
startAnimation ( )
doOptions ( )
nextSlice ( )
previousSlice ( )
setSlice ( )
Colors
«JavaArray» colors : String
fchoice : Choice
bchoice : Choice
schoice : Choice
fc2 : Color
bc2 : Color
sc2 : Color
run ( )
showDialog ( )
getColorName ( )
getColor ( )
decode ( )
hexToColor ( )
colorToString ( )
parseHex ( )
itemStateChanged ( )
pointToolOptions ( )
FITS_Writer
run ( )
createHeader ( )
writeCard ( )
s2ch ( )
appendFile ( )
writeData ( )
getHeader ( )
eighty ( )
copyHeader ( )
AboutBox
SMALL_FONT : int
LARGE_FONT : int
run ( )
x ( )
StackWriter
«JavaArray» choices : String
fileType : String
ndigits : int
useLabels : boolean
firstTime : boolean
startAt : int
hyperstack : boolean
«JavaArray» dim : int
run ( )
getDigits ( )
BatchConverter
«JavaArray» formats : String
format : String
scale : double
interpolationMethod : int
«JavaArray» methods : String
input : Button
output : Button
inputDir : TextField
outputDir : TextField
gd : GenericDialog
run ( )
showDialog ( )
addPanels ( )
actionPerformed ( )
Orthogonal_Views
win : ImageWindow
imp : ImagePlus
canvas : ImageCanvas
H_ROI : int
H_ZOOM : int
xz_image : ImagePlus
yz_image : ImagePlus
xzID : int
yzID : int
fp1 : ImageProcessor
fp2 : ImageProcessor
ax : double
ay : double
az : double
rotate : boolean
sticky : boolean
xyX : int
xyY : int
cal : Calibration
cal_xz : Calibration
cal_yz : Calibration
magnification : double
color : Color
instance : Orthogonal_Views
updater : Updater
min : double
max : double
screen : Dimension
flipXZ : boolean
syncZoom : boolean
crossLoc : Point
firstTime : boolean
/image : ImagePlus
run ( )
addListeners ( )
calibrate ( )
updateMagnification ( )
updateViews ( )
arrangeWindows ( )
createProcessors ( )
updateXZView ( )
updateYZView ( )
updateZYView ( )
drawCross ( )
dispose ( )
mouseClicked ( )
mouseEntered ( )
mouseExited ( )
mousePressed ( )
mouseReleased ( )
update ( )
exec ( )
updateCrosses ( )
mouseDragged ( )
mouseMoved ( )
keyPressed ( )
keyReleased ( )
keyTyped ( )
actionPerformed ( )
imageClosed ( )
imageOpened ( )
imageUpdated ( )
commandExecuting ( )
windowActivated ( )
windowClosed ( )
windowClosing ( )
windowDeactivated ( )
windowDeiconified ( )
windowIconified ( )
windowOpened ( )
adjustmentValueChanged ( )
mouseWheelMoved ( )
focusGained ( )
focusLost ( )
BMP_Writer
BITMAPFILEHEADER_SIZE : int
BITMAPINFOHEADER_SIZE : int
«JavaArray» bitmapFileHeader : byte
«JavaArray» bfType : byte
bfSize : int
bfReserved1 : int
bfReserved2 : int
bfOffBits : int
«JavaArray» bitmapInfoHeader : byte
biSize : int
biWidth : int
padWidth : int
biHeight : int
biPlanes : int
biBitCount : int
biCompression : int
biSizeImage : int
biXPelsPerMeter : int
biYPelsPerMeter : int
biClrUsed : int
biClrImportant : int
«JavaArray» intBitmap : int
«JavaArray» byteBitmap : byte
fo : FileOutputStream
bfo : BufferedOutputStream
imp : ImagePlus
run ( )
writeImage ( )
saveBitmap ( )
save ( )
writeBitmapPalette ( )
convertImage ( )
writeBitmap ( )
writeBitmapFileHeader ( )
writeBitmapInfoHeader ( )
intToWord ( )
intToDWord ( )
HyperStackReducer
imp : ImagePlus
channels1 : int
slices1 : int
frames1 : int
channels2 : int
slices2 : int
frames2 : int
imageSize : double
keep : boolean
/newDimensions : String
HyperStackReducer ( )
HyperStackReducer ( )
run ( )
reduce ( )
showDialog ( )
dialogItemChanged ( )
StackCombiner
imp1 : ImagePlus
imp2 : ImagePlus
vertical : boolean
run ( )
combineHorizontally ( )
combineVertically ( )
showDialog ( )
error ( )
Resizer
IN_PLACE : int
SCALE_T : int
newWidth : int
newHeight : int
constrain : boolean
interpolationMethod : int
«JavaArray» methods : String
fields : Vector
checkboxes : Vector
origWidth : double
origHeight : double
sizeToHeight : boolean
run ( )
zScale ( )
zScaleHyperstack ( )
shrinkHyperstack ( )
shrinkZ ( )
resizeZ ( )
textValueChanged ( )
updateFields ( )
itemStateChanged ( )
PNM_Writer
run ( )
URLOpener
url : String
run ( )
noExtension ( )
openTextFile ( )
CanvasResizer
zeroFill : boolean
run ( )
expandStack ( )
expandImage ( )
SpecifyROI
xRoi : double
yRoi : double
width : double
height : double
oval : boolean
centered : boolean
scaledUnits : boolean
prevRoi : Rectangle
prevPixelWidth : double
iSlice : int
bAbort : boolean
imp : ImagePlus
fields : Vector
checkboxes : Vector
stackSize : int
run ( )
validDialogValues ( )
showDialog ( )
drawRoi ( )
dialogItemChanged ( )
FITS_Reader
run ( )
NewPlugin
MACRO : int
JAVASCRIPT : int
PLUGIN : int
PLUGIN_FILTER : int
PLUGIN_FRAME : int
TEXT_FILE : int
TABLE : int
rows : int
columns : int
tableWidth : int
tableHeight : int
type : int
name : String
monospaced : boolean
menuBar : boolean
ed : Editor
/editor : Editor
run ( )
createMacro ( )
createTable ( )
createPlugin ( )
showDialog ( )
CompositeConverter
run ( )
convertRGBToCompositeImage ( )
convertRGBToCompositeStack ( )
BMP_Reader
run ( )
HyperStackConverter
C : int
Z : int
T : int
CZT : int
CTZ : int
ZCT : int
ZTC : int
TCZ : int
TZC : int
«JavaArray» orders : String
order : int
splitRGB : boolean
run ( )
convertStackToHS ( )
shuffle ( )
convertHSToStack ( )
newHyperStack ( )
ThreadLister
run ( )
print_thread_info ( )
list_group ( )
listAllThreads ( )
DragAndDrop
iterator : Iterator
convertToRGB : boolean
virtualStack : boolean
openAsVirtualStack : boolean
run ( )
drop ( )
fixLinuxString ( )
parseHTML ( )
dragEnter ( )
dragOver ( )
dragExit ( )
dropActionChanged ( )
run ( )
openURL ( )
openFile ( )
openDirectory ( )
JpegWriter
DEFAULT_QUALITY : int
/quality : int
run ( )
save ( )
saveAsJpeg ( )
Options
run ( )
miscOptions ( )
lineWidth ( )
io ( )
conversions ( )
appearance ( )
invertLuts ( )
Distribution
parameter : String
autoBinning : boolean
showStats : boolean
nBins : int
range : String
checkbox : Checkbox
nBinsField : TextField
rangeField : TextField
defaultNBins : String
defaultRange : String
run ( )
getIndex ( )
textValueChanged ( )
stats ( )
FolderOpener
convertToGrayscale : boolean
convertToRGB : boolean
sortFileNames : boolean
virtualStack : boolean
scale : double
n : int
start : int
increment : int
filter : String
isRegex : boolean
fi : FileInfo
info1 : String
run ( )
showDialog ( )
trimFileList ( )
sortFileList ( )
FFT
displayFFT : boolean
displayRawPS : boolean
displayFHT : boolean
displayComplex : boolean
fileName : String
imp : ImagePlus
padded : boolean
originalWidth : int
originalHeight : int
stackSize : int
slice : int
doFFT : boolean
run ( )
doInverseTransform ( )
doForewardTransform ( )
newFHT ( )
pad ( )
showStatus ( )
doMasking ( )
changeValuesAndSymmetrize ( )
smooth ( )
redisplayPowerSpectrum ( )
swapQuadrants ( )
showDialog ( )
doFHTInverseTransform ( )
doComplexInverseTransform ( )
unpad ( )
c2c2DFFT ( )
cplxFHT ( )
ImageCalculator
«JavaArray» operators : String
«JavaArray» lcOperators : String
operator : int
title1 : String
title2 : String
createWindow : boolean
floatResult : boolean
processStack : boolean
/blitterMode : int
run ( )
run ( )
calculate ( )
getOperator ( )
calculate ( )
doStackOperation ( )
doOperation ( )
createNewImage ( )
duplicateStack ( )
NextImageOpener
forward : boolean
closeCurrent : boolean
imp0 : ImagePlus
run ( )
getName ( )
open ( )
getNext ( )
ControlPanel
pluginsPath : String
pcpVersion : String
fileSeparator : String
sep : char
jvmversion : String
jvmversionMajor : String
ij : ImageJ
panels : Hashtable
visiblePanels : Vector
expandedNodes : Vector
defaultArg : String
currentArg : String
pcpProperties : Properties
pcpPropsFile : File
savePropsUponClose : boolean
propertiesChanged : boolean
closeChildPanelOnExpand : boolean
requireDoubleClick : boolean
quitting : boolean
menus : Vector
allMenus : Vector
«JavaArray» installableMenuLabels : String
commands : Hashtable
menuCommands : Hashtable
«JavaArray» pluginsArray : String
treeCommands : Hashtable
argLength : int
path : String
root : DefaultMutableTreeNode
reloadMI : MenuItem
/doubleClick : boolean
/version : String
/visiblePanelsCount : int
/expandedStateProperty : String
/panelShowingProperty : String
ControlPanel ( )
run ( )
load ( )
buildTree ( )
doRoot ( )
doRootFromMenus ( )
recurseSubMenu ( )
populateNode ( )
populateNode ( )
buildTreePath ( )
buildTreePath ( )
newPanel ( )
newPanel ( )
newPanel ( )
requiresDoubleClick ( )
hasPanelForNode ( )
getPanelForNode ( )
hasVisiblePanels ( )
registerPanel ( )
loadProperties ( )
saveProperties ( )
hasExpandedStateProperty ( )
unsetExpandedStateProperty ( )
unsetPanelShowingProperty ( )
hasPanelShowingProperty ( )
restoreVisiblePanels ( )
recordGeometry ( )
restoreGeometry ( )
closeAll ( )
verifyQuit ( )
showHelp ( )
pStr2Key ( )
key2pStr ( )
s2ints ( )
SurfacePlotter
fontSize : int
plotWidth : int
polygonMultiplier : int
oneToOne : boolean
firstTime : boolean
showWireframe : boolean
showGrayscale : boolean
showAxis : boolean
whiteBackground : boolean
blackFill : boolean
smooth : boolean
img : ImagePlus
«JavaArray» x : int
«JavaArray» y : int
invertedLut : boolean
angleInDegrees : double
angle : double
angle2InDegrees : double
angle2 : double
yinc2 : double
p1x : double
p1y : double
p2x : double
p2y : double
p3x : double
p3y : double
lut : LookUpTable
run ( )
showDialog ( )
makeSurfacePlot ( )
drawAndLabelAxis ( )
drawAxis ( )
drawString ( )
clearAboveProfile ( )
trimPlot ( )
fixLut ( )
GifWriter
transparentIndex : int
run ( )
XYCoordinates
processStack : boolean
invertY : boolean
suppress : boolean
run ( )
FFTMath
CONJUGATE_MULTIPLY : int
MULTIPLY : int
DIVIDE : int
«JavaArray» ops : String
index1 : int
index2 : int
operation : int
doInverse : boolean
title : String
imp1 : ImagePlus
imp2 : ImagePlus
run ( )
showDialog ( )
doMath ( )
BatchMeasure
run ( )
Histogram
nBins : int
useImageMinAndMax : boolean
xMin : double
xMax : double
yMax : String
stackHistogram : boolean
imageID : int
checkbox : Checkbox
minField : TextField
maxField : TextField
defaultMin : String
defaultMax : String
run ( )
showDialog ( )
textValueChanged ( )
setupDialog ( )
BrowserLauncher
mrjFileUtilsClass : Class
openURL : Method
error : boolean
run ( )
openURL ( )
loadClasses ( )
SimpleCommands
searchArg : String
«JavaArray» choices : String
choiceIndex : int
run ( )
reset ( )
unlock ( )
resetClipboard ( )
resetUndo ( )
rename ( )
search ( )
installation ( )
aboutPluginsHelp ( )
StackReverser
run ( )
flipStack ( )
OverlayCommands
overlay2 : Overlay
createImageRoi : boolean
run ( )
addSelection ( )
addImage ( )
hide ( )
show ( )
remove ( )
flatten ( )
fromRoiManager ( )
toRoiManager ( )
Scaler
imp : ImagePlus
xstr : String
ystr : String
zstr : String
newWidth : int
newHeight : int
newDepth : int
newWindow : boolean
interpolationMethod : int
«JavaArray» methods : String
fillWithBackground : boolean
processStack : boolean
xscale : double
yscale : double
zscale : double
title : String
fields : Vector
bgValue : double
constainAspectRatio : boolean
xField : TextField
yField : TextField
zField : TextField
widthField : TextField
heightField : TextField
depthField : TextField
r : Rectangle
fieldWithFocus
oldDepth : int
run ( )
createNewStack ( )
scale ( )
showDialog ( )
textValueChanged ( )
focusGained ( )
focusLost ( )
PNG_Writer
imp : ImagePlus
run ( )
writeImage ( )
writeImageWithTransparency ( )
write16gs ( )
Installer
«JavaArray» menus : String
TITLE : String
command : String
shortcut : String
defaultPlugin : String
menuStr : String
«JavaArray» /plugins : String
run ( )
installPlugin ( )
installAbout ( )
getSubdirectoryPlugins ( )
TextFileReader
run ( )
Selection
imp : ImagePlus
«JavaArray» kernel : float
«JavaArray» kernel3 : float
angle : String
enlarge : String
bandSize : String
nonScalable : boolean
linec : Color
fillc : Color
lineWidth : int
run ( )
runMacro ( )
fitSpline ( )
getUncalibratedLength ( )
trimPolygon ( )
rodbard ( )
smooth ( )
getCurvature ( )
drawEllipse ( )
convexHull ( )
findFirstPoint ( )
createMask ( )
createMaskFromThreshold ( )
createSelectionFromMask ( )
invert ( )
addToRoiManager ( )
createOverlay ( )
setProperties ( )
GelAnalyzer
GEL : String
OD : int
PERCENT : int
OUTLINE : int
INVERT : int
saveID : int
nLanes : int
saveNLanes : int
firstRect : Rectangle
MAX_LANES : int
«JavaArray» x : int
plotsCanvas
ipLanes : ImageProcessor
gel : ImagePlus
plotHeight : int
options : int
uncalibratedOD : boolean
labelWithPercentages : boolean
outlineLanes : boolean
invertPeaks : boolean
overlay : Overlay
invertedLut : boolean
imp : ImagePlus
f : Font
odMin : double
odMax : double
isVertical : boolean
showLaneDialog : boolean
/customLut : ImageProcessor
run ( )
showDialog ( )
selectFirstLane ( )
selectNextLane ( )
updateRoiList ( )
plotLanes ( )
od ( )
outlineLanes ( )
show ( )
savePreferences ( )
StackEditor
imp : ImagePlus
nSlices : int
width : int
height : int
deleteFrames : boolean
run ( )
addSlice ( )
deleteSlice ( )
deleteHyperstackSliceOrFrame ( )
convertImagesToStack ( )
convertStackToImages ( )
getTitle ( )
Clipboard
clipboard : Clipboard
«JavaArray» /transferDataFlavors : DataFlavor
/qTJavaInstalled : boolean
run ( )
copy ( )
paste ( )
setup ( )
copyToSystem ( )
showSystemClipboard ( )
isDataFlavorSupported ( )
getTransferData ( )
showInternalClipboard ( )
displayMacImage ( )
getMacImage ( )
getImageFromPictStream ( )
ListVirtualStack
virtual : boolean
«JavaArray» list : String
«JavaArray» labels : String
nImages : int
imageWidth : int
imageHeight : int
/size : int
/width : int
/height : int
run ( )
showDialog ( )
convertToRealStack ( )
open ( )
deleteSlice ( )
getProcessor ( )
getSliceLabel ( )
WindowOrganizer
XSTART : int
YSTART : int
XOFFSET : int
YOFFSET : int
MAXSTEP : int
GAP : int
titlebarHeight : int
run ( )
tileWindows ( )
getWindow ( )
cascadeWindows ( )
showAll ( )
Converter
newWindowCreated : boolean
imp : ImagePlus
/number : int
run ( )
convert ( )
unsupportedConversion ( )
MeasurementsWriter
run ( )
save ( )
Raw
defaultDirectory : String
run ( )
Straightener
processStack : boolean
run ( )
straighten ( )
straightenStack ( )
straightenLine ( )
rotateLine ( )
straightenRGB ( )
straightenComposite ( )
RoiReader
polygon : int
rect : int
oval : int
line : int
freeLine : int
segLine : int
noRoi : int
freehand : int
traced : int
run ( )
openRoi ( )
ProxySettings
props : Properties
proxyhost : String
proxyport : int
proxyuser : String
proxypass : String
authenticate : boolean
run ( )
showDialog ( )
ScreenGrabber
run ( )
captureScreen ( )
captureImage ( )
ArrowToolOptions
colorName : String
gd : GenericDialog
run ( )
arrowToolOptions ( )
dialogItemChanged ( )
ClassChecker
«JavaArray» paths : String
«JavaArray» names : String
run ( )
deleteDuplicates ( )
delete ( )
write ( )
getPathsAndNames ( )
getSubdirectoryFiles ( )
Macro_Runner
run ( )
runMacroFromJar ( )
runMacroFile ( )
runMacro ( )
runMacroFromIJJar ( )
runJavaScript ( )
ImageJ_Updater
/upgradeVersion : String
/mac : boolean
run ( )
showDialog ( )
openUrlAsString ( )
getJar ( )
saveJar ( )
openUrlAsList ( )
version ( )
error ( )
updateMenus ( )
Thresholder
minThreshold : double
maxThreshold : double
autoThreshold : boolean
skipDialog : boolean
fill1 : boolean
fill2 : boolean
useBW : boolean
useLocal : boolean
convertToMask : boolean
/invertedLut : ImagePlus
run ( )
convertStack ( )
applyThreshold ( )
applyShortOrFloatThreshold ( )
convertStackToBinary ( )
convertToByte ( )
autoThreshold ( )
DICOM
showErrors : boolean
inputStream : BufferedInputStream
DICOM ( )
DICOM ( )
DICOM ( )
run ( )
open ( )
convertToUnsigned ( )