Skip navigation links
A B C D E F G H I J K L M N O P R S T U V W X Z 

A

a - Variable in class edu.emory.cellbio.ijbat.pi.MathAdd
 
a - Variable in class edu.emory.cellbio.ijbat.pi.MathDiv
 
a - Variable in class edu.emory.cellbio.ijbat.pi.MathMlt
 
a - Variable in class edu.emory.cellbio.ijbat.pi.MathRound
 
a - Variable in class edu.emory.cellbio.ijbat.pi.MathSub
 
AboutPage() - Constructor for class edu.emory.cellbio.ijbat.ui.HttpHelpLoader.AboutPage
 
AbstractOverlaysAlias - Class in edu.emory.cellbio.ijbat.dm
Alias for imagej.data.overlay.AbstractOverlay[]
AbstractOverlaysAlias() - Constructor for class edu.emory.cellbio.ijbat.dm.AbstractOverlaysAlias
 
AbstractOverlaysToRoisetFileWriter - Class in edu.emory.cellbio.ijbat.dm.write
 
AbstractOverlaysToRoisetFileWriter() - Constructor for class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToRoisetFileWriter
 
AbstractOverlaysToSVGFileWriter - Class in edu.emory.cellbio.ijbat.dm.write
 
AbstractOverlaysToSVGFileWriter() - Constructor for class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
 
actionPerformed(ActionEvent) - Method in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
Listener for button actions
actionPerformed(ActionEvent) - Method in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
actionPerformed(ActionEvent) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Action handler
actionPerformed(ActionEvent) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Action handler
actionPerformed(ActionEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
ActionListener implementation
actionPerformed(ActionEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetPropertiesViewer
 
actionPerformed(ActionEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
ActionListener implementation
active - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
 
active - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
active - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
Active flag
active - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Active flag
addAlphabetized(JMenuItem, JMenu, boolean) - Static method in class edu.emory.cellbio.ijbat.ui.UIUtil
Add a menu item to it's proper alphabetized position in the menu.
addChild(SlideSet) - Method in class edu.emory.cellbio.ijbat.SlideSet
Register a SlideSet as the child of this SlideSet
addColumn(LinkedHashMap<String, String>) - Method in class edu.emory.cellbio.ijbat.SlideSet
Add an empty column
addColumn(String, String) - Method in class edu.emory.cellbio.ijbat.SlideSet
Add an empty column with no (null) MIME type.
addColumn(String, Class<? extends DataElement>) - Method in class edu.emory.cellbio.ijbat.SlideSet
Add an empty column with no (null) MIME type.
addColumn(String, String, String) - Method in class edu.emory.cellbio.ijbat.SlideSet
Add an empty column.
addColumn(String, Class<? extends DataElement>, String) - Method in class edu.emory.cellbio.ijbat.SlideSet
Add an empty column.
addColumn(LinkedHashMap<String, String>, ArrayList<DataElement<?>>) - Method in class edu.emory.cellbio.ijbat.SlideSet
Add a column with data
addColumnsForParentFields(ArrayList<Integer>, SlideSet, SlideSet) - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Add columns to the results table for included fields from the input table
addDynamicResource(String, DynamicHelpResource) - Method in class edu.emory.cellbio.ijbat.ui.JarHTTPd
Add mapping for a dynamically generated resource
addFast(Data, ImageDisplayService) - Method in class edu.emory.cellbio.ijbat.ui.FastUpdateImageDisplay
Add Data to the display without rebuilding.
addHeader(String, String) - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.Response
Adds given line to the header.
addInput(String, String[], Object[], String[]) - Method in class edu.emory.cellbio.ijbat.io.CommandSkeletonService.CommandTemplateInputPicker
 
addInput(String, String[], Object[], String[]) - Method in interface edu.emory.cellbio.ijbat.pi.PluginInputPicker
Register a plugin input and the options available for assigning its value.
addInput(String, String[], Object[], String[]) - Method in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
Add an input to the dialog (before display please)
addOutput(String, String[], boolean[], String[], String[], String[]) - Method in class edu.emory.cellbio.ijbat.io.CommandSkeletonService.CommandTemplateOutputPicker
 
addOutput(String, String[], boolean[], String[], String[], String[]) - Method in interface edu.emory.cellbio.ijbat.pi.PluginOutputPicker
Register a plugin output and available options for handling its value.
addOutput(String, String[], boolean[], String[], String[], String[]) - Method in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
addRoiSet - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
addRoiSet - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
addRoot(String) - Method in class edu.emory.cellbio.ijbat.ui.HttpHelpLoader
Add a package for the help server to search when looking for documentation resources.
addRoot(String) - Method in class edu.emory.cellbio.ijbat.ui.JarHTTPd
 
addRow() - Method in class edu.emory.cellbio.ijbat.SlideSet
Add a row with default values
addRow(List<DataElement>) - Method in class edu.emory.cellbio.ijbat.SlideSet
Add a row from a List of DataElements.
addWindowListener(WindowListener) - Method in interface edu.emory.cellbio.ijbat.ui.SlideSetWindow
 
and - Variable in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
 
ao - Variable in class edu.emory.cellbio.ijbat.pi.Test
 
aoutb - Variable in class edu.emory.cellbio.ijbat.pi.ROIOverlap
 
applyDefaultStyles(XMLStreamWriter) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
Default SVG styling attributes for overlays
applyDefaultStyles(XMLStreamWriter) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
Default SVG styling attributes for overlays
arcAsEllipse(String, String, double[], String, Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Attempt to generate an ellipse overlay from an arc path
arcAsEllipse(String, String, double[], String, Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Attempt to generate an ellipse ROI from an arc path
attachKillListener(Window) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Attach a listener to a Window, so that when the Window closes, the ROI Editor will close as well.
autoscaleService - Variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 

B

b - Variable in class edu.emory.cellbio.ijbat.pi.MathAdd
 
b - Variable in class edu.emory.cellbio.ijbat.pi.MathDiv
 
b - Variable in class edu.emory.cellbio.ijbat.pi.MathMlt
 
b - Variable in class edu.emory.cellbio.ijbat.pi.MathRound
 
b - Variable in class edu.emory.cellbio.ijbat.pi.MathSub
 
base - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
The default link prefix field
bcDialog - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
The brightness/contrast dialog
binIDs - Variable in class edu.emory.cellbio.ijbat.pi.BinRegions
 
BinRegions - Class in edu.emory.cellbio.ijbat.pi
Sort one set of ROIs based on a second set of ROIs.
BinRegions() - Constructor for class edu.emory.cellbio.ijbat.pi.BinRegions
 
bins - Variable in class edu.emory.cellbio.ijbat.pi.BinRegions
 
blue - Variable in class edu.emory.cellbio.ijbat.pi.BorderStats
 
blue - Variable in class edu.emory.cellbio.ijbat.pi.RegionStats
 
BooleanElement - Class in edu.emory.cellbio.ijbat.dm
DataElement for storing logical values
BooleanElement() - Constructor for class edu.emory.cellbio.ijbat.dm.BooleanElement
 
BooleanElement(Boolean) - Constructor for class edu.emory.cellbio.ijbat.dm.BooleanElement
 
BooleanToBooleanReader - Class in edu.emory.cellbio.ijbat.dm.read
 
BooleanToBooleanReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.BooleanToBooleanReader
 
BooleanToBooleanWriter - Class in edu.emory.cellbio.ijbat.dm.write
 
BooleanToBooleanWriter() - Constructor for class edu.emory.cellbio.ijbat.dm.write.BooleanToBooleanWriter
 
BooleanToByteReader - Class in edu.emory.cellbio.ijbat.dm.read
 
BooleanToByteReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.BooleanToByteReader
 
BooleanToIntReader - Class in edu.emory.cellbio.ijbat.dm.read
 
BooleanToIntReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.BooleanToIntReader
 
BooleanToShortReader - Class in edu.emory.cellbio.ijbat.dm.read
 
BooleanToShortReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.BooleanToShortReader
 
BorderStats - Class in edu.emory.cellbio.ijbat.pi
Calculate average values for pixels along region of interest borders
BorderStats() - Constructor for class edu.emory.cellbio.ijbat.pi.BorderStats
 
BorderStatsNChan - Class in edu.emory.cellbio.ijbat.pi
Calculate average values for pixels along region of interest borders
BorderStatsNChan() - Constructor for class edu.emory.cellbio.ijbat.pi.BorderStatsNChan
 
bouta - Variable in class edu.emory.cellbio.ijbat.pi.ROIOverlap
 
brightness - Variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
brightnessContrastChanged() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
Called when brightness or contrast changes.
BrightnessContrastRoi<T extends net.imglib2.type.numeric.RealType<T>> - Class in edu.emory.cellbio.ijbat.ui
 
BrightnessContrastRoi() - Constructor for class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
bT - Variable in class edu.emory.cellbio.ijbat.pi.BorderStats
 
bT - Variable in class edu.emory.cellbio.ijbat.pi.RegionStats
 
buildDataElementIndex() - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Set-up the DataElement index
buildElementReaderIndex() - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Set-up the ElementReader index
buildElementTypeMenuTree(String) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Build a JMenu filled with available type codes
buildElementWriterIndex() - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Set-up the ElementWriter index
buildInfo() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Build the info pane
buildLayout() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Build the window
buildLayout() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Build the window
buildLayout() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Build the window
buildLayout() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetPropertiesViewer
 
buildLayout(Component) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Build the window
buildMenuBar() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Build the menu bar
buildMenuBar() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Setup the main menu
buildMenuColP() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Set up the column header popup menu
buildMenuP() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Set up the table pop-up menu
buildMimeReadableIndex() - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Set-up the MIME type index
buildOtherCommandsMenu() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Build the menu listing other ImageJ commands
buildPopupMenu() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Build the popup (right-click) menus
buildSlideSetPluginsMenu() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Build the menu listing SlideSetPlugins
buildTableLayout() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Set up the table itself
buildTree() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Build the tree pane
buildTypeAliasIndex() - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Set-up the TypeAlias index
bundle - Variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
ByteToIntWriter - Class in edu.emory.cellbio.ijbat.dm.write
 
ByteToIntWriter() - Constructor for class edu.emory.cellbio.ijbat.dm.write.ByteToIntWriter
 

C

c - Variable in class edu.emory.cellbio.ijbat.pi.MathAdd
 
c - Variable in class edu.emory.cellbio.ijbat.pi.MathDiv
 
c - Variable in class edu.emory.cellbio.ijbat.pi.MathMlt
 
c - Variable in class edu.emory.cellbio.ijbat.pi.MathSub
 
c - Variable in class edu.emory.cellbio.ijbat.SlideSetIJ2Entry
 
c1 - Variable in class edu.emory.cellbio.ijbat.pi.Correlation
 
c1 - Variable in class edu.emory.cellbio.ijbat.pi.Manders
 
c2 - Variable in class edu.emory.cellbio.ijbat.pi.Correlation
 
c2 - Variable in class edu.emory.cellbio.ijbat.pi.Manders
 
cancelPressed - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
 
cancelPressed - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
canImport(TransferHandler.TransferSupport) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher.DropHandler
 
canImport(TransferHandler.TransferSupport) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer.DropHandler
 
cfr - Variable in class edu.emory.cellbio.ijbat.pi.WekaSegmentationWrapper
 
changeColorMode() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Open the IJ1 channels tool.
changed - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
Changed flag
changed - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Changed flag
changed - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Has the open file been changed?
changeDisplayMode() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Update the color mode
changeLevels - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
changeLevels() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Open the Brightness/Contrast dialog
changeLevels - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
changeLevels() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Open the IJ1 Contrast Adjuster.
channels - Variable in class edu.emory.cellbio.ijbat.pi.OtsuSegmentation
 
chans - Variable in class edu.emory.cellbio.ijbat.pi.BorderStatsNChan
 
chans - Variable in class edu.emory.cellbio.ijbat.pi.RegionStatsNChan
 
checkBounds(int, int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Check validity of an index pair
checkChanged() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Check if the data set has been changed and offer to save it if applicable.
checkColumnBounds(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Check validity of a column index
checkColumnElementConsistency(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Check if all the DataElements in this column are of the same type and have the same MIME type set.
checkColumnLengths() - Method in class edu.emory.cellbio.ijbat.SlideSet
Check to make sure each column is of equal length
checkDataElementCompatibility(int, DataElement<?>) - Method in class edu.emory.cellbio.ijbat.SlideSet
Check if the class and MIME type of a DataElement match those of a column in this table.
checkRowBounds(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Check validity of a row index
checkUnderlyingCompatability(int, Object) - Method in class edu.emory.cellbio.ijbat.SlideSet
Check if an object may be stored in a column directly using a setUnderlying() method (i.e.
checkUpdateSite() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
children - Variable in class edu.emory.cellbio.ijbat.SlideSet
Children of this SlideSet
childWindows - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
List of open child windows
className - Variable in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Command class name
clearOverlaysFast() - Method in class edu.emory.cellbio.ijbat.ui.FastUpdateImageDisplay
Remove all Overlays from the display without rebuilding.
closeChildWindows() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Close any open child windows.
closeFile(XMLStreamWriter) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
End the SVG file and do cleanup
closeFile(XMLStreamWriter) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
End the SVG file and do cleanup
colNames(SlideSet) - Method in class edu.emory.cellbio.ijbat.io.CSVService
 
column - Variable in class edu.emory.cellbio.ijbat.dm.ColumnBoundReader
 
column - Variable in class edu.emory.cellbio.ijbat.dm.ColumnBoundWriter
 
ColumnBoundReader<E extends DataElement,P> - Class in edu.emory.cellbio.ijbat.dm
Binds an ElementReader to a SlideSet table column or to a constant value.
ColumnBoundReader(SlideSet, int, ElementReader<E, P>) - Constructor for class edu.emory.cellbio.ijbat.dm.ColumnBoundReader
Bind an ElementReader to a SlideSet table column.
ColumnBoundReader(E, ElementReader<E, P>, DataTypeIDService) - Constructor for class edu.emory.cellbio.ijbat.dm.ColumnBoundReader
Bind an ElementReader to a constant value.
ColumnBoundWriter<E extends DataElement,P> - Class in edu.emory.cellbio.ijbat.dm
Binds and ElementWriter to a SlideSet table column.
ColumnBoundWriter(SlideSet, int, ElementWriter<E, P>) - Constructor for class edu.emory.cellbio.ijbat.dm.ColumnBoundWriter
Bind an ElementWriter to a SlideSet table column.
columnName - Variable in class edu.emory.cellbio.ijbat.dm.ColumnBoundReader
 
columnProperties - Variable in class edu.emory.cellbio.ijbat.SlideSet
Index of column properties: elementClass - Name of DataElement subclass used mimeType - MIME type used name - Name associated with the column (required) defaultPath - Default relative path for this column (relevant for links only) defaultLinkPrefix - Prefix for generating default links (ex.
columns - Variable in class edu.emory.cellbio.ijbat.SlideSet
Columns in the SlideSet
ColumnTypeException - Exception in edu.emory.cellbio.ijbat.ex
Signals the column types of a table do not match the expected types.
ColumnTypeException() - Constructor for exception edu.emory.cellbio.ijbat.ex.ColumnTypeException
 
ColumnTypeException(String) - Constructor for exception edu.emory.cellbio.ijbat.ex.ColumnTypeException
 
ColumnTypeException(Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.ColumnTypeException
 
ColumnTypeException(String, Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.ColumnTypeException
 
COLWIDTH - Static variable in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
commandFinderPanel - Variable in class edu.emory.cellbio.ijbat.ui.CommandPicker
 
CommandPicker - Class in edu.emory.cellbio.ijbat.ui
Dialog box to select a recognized ImageJ command
CommandPicker(Context) - Constructor for class edu.emory.cellbio.ijbat.ui.CommandPicker
 
commandService - Variable in class edu.emory.cellbio.ijbat.ui.CommandPicker
 
CommandSkeletonService - Class in edu.emory.cellbio.ijbat.io
Writes CommandTemplate data to an XML file to create a command skeleton and generates CommandTemplates from saved command skeleton XML.
CommandSkeletonService() - Constructor for class edu.emory.cellbio.ijbat.io.CommandSkeletonService
 
CommandSkeletonService.CommandTemplateInputPicker - Class in edu.emory.cellbio.ijbat.io
 
CommandSkeletonService.CommandTemplateOutputPicker - Class in edu.emory.cellbio.ijbat.io
 
CommandTemplate - Class in edu.emory.cellbio.ijbat.dm
Data structure for storing the information needed to create a command skeleton.
CommandTemplate() - Constructor for class edu.emory.cellbio.ijbat.dm.CommandTemplate
 
CommandTemplate(XMLStreamReader) - Constructor for class edu.emory.cellbio.ijbat.dm.CommandTemplate
 
commandTemplate - Variable in class edu.emory.cellbio.ijbat.SlideSet
Command template data
CommandTemplateInputPicker(CommandTemplate) - Constructor for class edu.emory.cellbio.ijbat.io.CommandSkeletonService.CommandTemplateInputPicker
 
CommandTemplateOutputPicker(CommandTemplate) - Constructor for class edu.emory.cellbio.ijbat.io.CommandSkeletonService.CommandTemplateOutputPicker
 
computeBrightnessContrast() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
Computes brightness and contrast from min and max.
computeDataMinMax(RandomAccessibleInterval<? extends RealType<?>>) - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
computeInitialMinMax() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
computeMinMax() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
Computes min and max from brightness and contrast.
concat(double[], double[]) - Method in class edu.emory.cellbio.ijbat.pi.UnmixAbsorbance
Concatenate two vectors
constant - Variable in class edu.emory.cellbio.ijbat.dm.ColumnBoundReader
 
constantValOptions - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
The appropriate values menu buttons
constantVals - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
The constant value fields
context - Variable in class edu.emory.cellbio.ijbat.pi.CreateMask
 
context - Variable in class edu.emory.cellbio.ijbat.pi.UnmixAbsorbance
 
context - Variable in class edu.emory.cellbio.ijbat.ui.CommandPicker
 
contrast - Variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
convertColumn(int, Class<? extends DataElement<?>>, String) - Method in class edu.emory.cellbio.ijbat.SlideSet
Convert the data type stored in a column.
correlate(Float[], Float[]) - Method in class edu.emory.cellbio.ijbat.pi.Correlation
 
Correlation - Class in edu.emory.cellbio.ijbat.pi
 
Correlation() - Constructor for class edu.emory.cellbio.ijbat.pi.Correlation
 
createImageWindow() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Create the image window
CreateMask - Class in edu.emory.cellbio.ijbat.pi
Generate a mask image from an ROI set.
CreateMask() - Constructor for class edu.emory.cellbio.ijbat.pi.CreateMask
 
createRoiSet() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Create a new set of overlays (ROIs)
createRoiSet() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Create a new set of ROIs and add it as a new column in the data table.
creationParams - Variable in class edu.emory.cellbio.ijbat.SlideSet
The input parameters used in the creation of this SlideSet
cs - Variable in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
 
csvs - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
CSVService - Class in edu.emory.cellbio.ijbat.io
Writes SlideSet data as a CSV file.
CSVService() - Constructor for class edu.emory.cellbio.ijbat.io.CSVService
 
ct - Variable in class edu.emory.cellbio.ijbat.io.CommandSkeletonService.CommandTemplateInputPicker
 
ct - Variable in class edu.emory.cellbio.ijbat.io.CommandSkeletonService.CommandTemplateOutputPicker
 
curImage - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
Current image index
curImage - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Current image index
curImageSet - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Current image set index
curRoiSet - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
Current ROI set index
curRoiSet - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Current ROI set index

D

data - Variable in class edu.emory.cellbio.ijbat.dm.ColumnBoundReader
 
data - Variable in class edu.emory.cellbio.ijbat.dm.ColumnBoundWriter
 
data - Variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.Response
Data of the response, may be null.
data - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
 
data - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
DataElement<T> - Class in edu.emory.cellbio.ijbat.dm
Basic element of data stored in SlideSet tables.
DataElement(T) - Constructor for class edu.emory.cellbio.ijbat.dm.DataElement
 
dataElement - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.DataElementRecord
dataElementIndex - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Index of available DataElement types
DataElementMetadata - Annotation Type in edu.emory.cellbio.ijbat.dm
Annotation type containing metadata for DataElement classes.
DataElementRecord(Class<? extends DataElement<T>>, String, Class<T>, boolean) - Constructor for class edu.emory.cellbio.ijbat.dm.DataTypeIDService.DataElementRecord
 
dataMax - Variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
The minimum and maximum values of the data itself.
dataMin - Variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
The minimum and maximum values of the data itself.
DatasetToImageFileWriter - Class in edu.emory.cellbio.ijbat.dm.write
 
DatasetToImageFileWriter() - Constructor for class edu.emory.cellbio.ijbat.dm.write.DatasetToImageFileWriter
 
DataTypeIDService - Class in edu.emory.cellbio.ijbat.dm
Linking Slide Set tables to commands
DataTypeIDService(ImageJ) - Constructor for class edu.emory.cellbio.ijbat.dm.DataTypeIDService
 
DataTypeIDService.DataElementRecord<T> - Class in edu.emory.cellbio.ijbat.dm
 
DataTypeIDService.ReaderRecord<E extends DataElement,P> - Class in edu.emory.cellbio.ijbat.dm
 
DataTypeIDService.WriterRecord<E extends DataElement,P> - Class in edu.emory.cellbio.ijbat.dm
 
decodeHeader(BufferedReader, Properties, Properties, Properties) - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.HTTPSession
Decodes the sent headers and loads the data into java Properties' key - value pairs
decodeMultipartData(String, byte[], BufferedReader, Properties, Properties) - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.HTTPSession
Decodes the Multipart Body data and put it into java Properties' key - value pairs.
decodeParms(String, Properties) - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.HTTPSession
Decodes parameters in percent-encoded URI-format ( e.g.
decodePercent(String) - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.HTTPSession
Decodes the percent encoding scheme.
defaultButton - Variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
DefaultPathNotSetException - Exception in edu.emory.cellbio.ijbat.ex
Indicates that a new link cannot be generated because the default link path is not set in the column properties
DefaultPathNotSetException() - Constructor for exception edu.emory.cellbio.ijbat.ex.DefaultPathNotSetException
Creates a new instance of DefaultPathNotSetException without detail message.
DefaultPathNotSetException(String) - Constructor for exception edu.emory.cellbio.ijbat.ex.DefaultPathNotSetException
Constructs an instance of DefaultPathNotSetException with the specified detail message.
DefaultPathNotSetException(Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.DefaultPathNotSetException
 
DefaultPathNotSetException(String, Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.DefaultPathNotSetException
 
deleteTable() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Delete a table
dialogReturnValue - Variable in class edu.emory.cellbio.ijbat.ui.CommandPicker
 
difw - Variable in class edu.emory.cellbio.ijbat.dm.write.ImageDisplayToImageFileWriter
 
dip - Variable in class edu.emory.cellbio.ijbat.pi.WekaSegmentationWrapper
 
dir - Variable in class edu.emory.cellbio.ijbat.SlideSet
Working directory of this SlideSet
dir - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
The default link directory field
displayMode - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
displayMode - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
distance(double[], double[]) - Static method in class edu.emory.cellbio.ijbat.pi.RoiUtils
Compute the linear distance between two points.
distanceFromLine(double[], double[], double[]) - Static method in class edu.emory.cellbio.ijbat.pi.RoiUtils
Compute the distance of point P from the line defined by points A and B.
distanceFromSegment(double[], double[], double[]) - Static method in class edu.emory.cellbio.ijbat.pi.RoiUtils
Compute the distance of point P from the line segment bounded by points A and B.
distanceSquared(double[], double[]) - Static method in class edu.emory.cellbio.ijbat.pi.RoiUtils
Compute the squared linear distance between two points.
distSquared(double[], double[]) - Static method in class edu.emory.cellbio.ijbat.pi.ROILengths
 
doComponentLayout() - Method in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
Finalize the dialog before display
DoubleElement - Class in edu.emory.cellbio.ijbat.dm
DataElement for storing numeric values
DoubleElement() - Constructor for class edu.emory.cellbio.ijbat.dm.DoubleElement
 
DoubleElement(Double) - Constructor for class edu.emory.cellbio.ijbat.dm.DoubleElement
 
DoubleToDoubleReader - Class in edu.emory.cellbio.ijbat.dm.read
 
DoubleToDoubleReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.DoubleToDoubleReader
 
DoubleToDoubleWriter - Class in edu.emory.cellbio.ijbat.dm.write
 
DoubleToDoubleWriter() - Constructor for class edu.emory.cellbio.ijbat.dm.write.DoubleToDoubleWriter
 
DoubleToFloatReader - Class in edu.emory.cellbio.ijbat.dm.read
 
DoubleToFloatReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.DoubleToFloatReader
 
drawOverlays() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Draw appropriate overlays on the image
drawRois() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Draw ROIs on the image.
DropHandler(SlideSetLauncher) - Constructor for class edu.emory.cellbio.ijbat.ui.SlideSetLauncher.DropHandler
 
DropHandler() - Constructor for class edu.emory.cellbio.ijbat.ui.SlideSetViewer.DropHandler
 
ds - Variable in class edu.emory.cellbio.ijbat.pi.BorderStats
 
ds - Variable in class edu.emory.cellbio.ijbat.pi.BorderStatsNChan
 
ds - Variable in class edu.emory.cellbio.ijbat.pi.Correlation
 
ds - Variable in class edu.emory.cellbio.ijbat.pi.Manders
 
ds - Variable in class edu.emory.cellbio.ijbat.pi.OtsuSegmentation
 
ds - Variable in class edu.emory.cellbio.ijbat.pi.RegionStats
 
ds - Variable in class edu.emory.cellbio.ijbat.pi.RegionStatsNChan
 
ds - Variable in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
 
ds - Variable in class edu.emory.cellbio.ijbat.pi.UnmixAbsorbance
 
ds - Variable in class edu.emory.cellbio.ijbat.pi.WekaSegmentationWrapper
 
dtid - Variable in class edu.emory.cellbio.ijbat.io.XMLService
 
dtid - Variable in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
 
dtid - Variable in class edu.emory.cellbio.ijbat.SlideSet
DataTypeIDService reference
dtid - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
 
dtid - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
dtid - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
dtid - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
dtid - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
dtid - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
DynamicHelpResource - Class in edu.emory.cellbio.ijbat.ui
Dynamically generated resource for the by the documentation server.
DynamicHelpResource() - Constructor for class edu.emory.cellbio.ijbat.ui.DynamicHelpResource
 
DynamicHelpResource.GeneratedResource - Class in edu.emory.cellbio.ijbat.ui
Generated dynamic resource
dynamicPages - Variable in class edu.emory.cellbio.ijbat.ui.JarHTTPd
Mapping of dynamically generated resources, indexed by relative URI

E

edu.emory.cellbio.ijbat - package edu.emory.cellbio.ijbat
Slide Set tables and the ImageJ plugin
edu.emory.cellbio.ijbat.dm - package edu.emory.cellbio.ijbat.dm
Classes implementing the data model
edu.emory.cellbio.ijbat.dm.read - package edu.emory.cellbio.ijbat.dm.read
Readers for converting "underlying" data to "processed" data
edu.emory.cellbio.ijbat.dm.write - package edu.emory.cellbio.ijbat.dm.write
Writers for converting "processed" data to "underlying" data
edu.emory.cellbio.ijbat.ex - package edu.emory.cellbio.ijbat.ex
Error handling
edu.emory.cellbio.ijbat.io - package edu.emory.cellbio.ijbat.io
Read and write data files
edu.emory.cellbio.ijbat.pi - package edu.emory.cellbio.ijbat.pi
Slide Set commands and plugin management
edu.emory.cellbio.ijbat.ui - package edu.emory.cellbio.ijbat.ui
The Slide Set user interface
ElementReader<E extends DataElement,P> - Interface in edu.emory.cellbio.ijbat.dm.read
Converts DataElement "underlying" data to the "processed" data required for command inputs.
elementReaderIndex - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Index of available ElementReaders
ElementReaderMetadata - Annotation Type in edu.emory.cellbio.ijbat.dm.read
Metadata for indexing ElementReaders.
elementType - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.ReaderRecord
DataElement type read by this reader
elementType - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.WriterRecord
DataElement type written by this writer
ElementWriter<E extends DataElement,P> - Interface in edu.emory.cellbio.ijbat.dm.write
Converts "processed" data from command output parameters to "underlying" data that can be stored in a DataElement.
elementWriterIndex - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Index of available ElementWriters
ElementWriterMetadata - Annotation Type in edu.emory.cellbio.ijbat.dm.write
Metadata for indexing ElementWriters.
encodeUri(String) - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
URL-encodes everything between "/"-characters.
errorMessages - Variable in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
 
errorMessages - Variable in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
 
expandAllTreeNodes() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Make sure that all tree nodes are expanded
exportSVG - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
exportSVG() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
exportSVG - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
exportSVG() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Export and SVG file with the current image and ROIs.
ext - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
The default link extension field

F

f - Static variable in class edu.emory.cellbio.ijbat.dm.read.BooleanToByteReader
 
f - Static variable in class edu.emory.cellbio.ijbat.dm.read.BooleanToShortReader
 
FastUpdateImageDisplay - Class in edu.emory.cellbio.ijbat.ui
Performance improvements to DefaultImageDisplay
FastUpdateImageDisplay() - Constructor for class edu.emory.cellbio.ijbat.ui.FastUpdateImageDisplay
 
fields - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
The combo boxes
FileLink - Interface in edu.emory.cellbio.ijbat.dm
 
FileLinkElement - Class in edu.emory.cellbio.ijbat.dm
DataElement for storing file references
FileLinkElement() - Constructor for class edu.emory.cellbio.ijbat.dm.FileLinkElement
 
FileLinkElement(String) - Constructor for class edu.emory.cellbio.ijbat.dm.FileLinkElement
 
fillServices(Module, Iterable<ModuleItem<?>>) - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Prefill service inputs
filtered - Variable in class edu.emory.cellbio.ijbat.pi.FilterRegions
 
FilterRegions - Class in edu.emory.cellbio.ijbat.pi
Filter one set of ROIs using another set of ROIs as a mask
FilterRegions() - Constructor for class edu.emory.cellbio.ijbat.pi.FilterRegions
 
fis - Variable in class edu.emory.cellbio.ijbat.io.CommandSkeletonService
 
fis - Variable in class edu.emory.cellbio.ijbat.io.XMLService
 
flagOverlayChanges(ObjectEvent) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Check to see if an ROI change should set the changed flag
FloatToDoubleWriter - Class in edu.emory.cellbio.ijbat.dm.write
 
FloatToDoubleWriter() - Constructor for class edu.emory.cellbio.ijbat.dm.write.FloatToDoubleWriter
 
fos - Variable in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
 
fos - Variable in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
 
fos - Variable in class edu.emory.cellbio.ijbat.io.CommandSkeletonService
 
fos - Variable in class edu.emory.cellbio.ijbat.io.CSVService
 
fos - Variable in class edu.emory.cellbio.ijbat.io.XMLService
 

G

gap - Static variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
Padding
gap - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
Padding
generateDefaultLinkPath(int, int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Generate a default link path for a specified cell.
GeneratedResource(InputStream, int, String) - Constructor for class edu.emory.cellbio.ijbat.ui.DynamicHelpResource.GeneratedResource
 
generateResource(String) - Method in class edu.emory.cellbio.ijbat.ui.DynamicHelpResource
Generate the dynamic resource
generateResource(String) - Method in class edu.emory.cellbio.ijbat.ui.HttpHelpLoader.AboutPage
 
getBoundaryPositions(byte[], byte[]) - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.HTTPSession
Find the byte positions where multipart boundaries start.
getBrightness() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
getChildren() - Method in class edu.emory.cellbio.ijbat.SlideSet
Get a list of this SlideSet's children
getColumnClass(int) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetTableModel
 
getColumnCount() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetTableModel
 
getColumnDefaultPath(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the default relative path associated with the column.
getColumnElementClass(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
 
getColumnElementType(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the DataElement type used in a column.
getColumnFromHeaderEvent(ActionEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Find out which column header triggered a popup menu
getColumnIndex(String) - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the index of the first column with a matching name, or -1 if no such column
getColumnMimeType(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the column MIME type
getColumnName() - Method in class edu.emory.cellbio.ijbat.dm.ColumnBoundReader
Get the human-readable label for the column
getColumnName(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the name of a column
getColumnName(int) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetTableModel
 
getColumnNum() - Method in class edu.emory.cellbio.ijbat.dm.ColumnBoundReader
Get the column index
getColumnNum() - Method in class edu.emory.cellbio.ijbat.dm.ColumnBoundWriter
Get the column index
getColumnProperties(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the properties of a column
getColumnReadWritePairs(Class<?>, SlideSet, ArrayList<ColumnBoundReader>, ArrayList<ColumnBoundWriter>) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Get ColumnBoundReaderColumnBoundWriter pairs that can be used to read and write the specified type to a column in the provided SlideSet table.
getColumnTypeName() - Method in class edu.emory.cellbio.ijbat.dm.ColumnBoundReader
Get a human-readable label for the column type
getColumnTypeName(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Get a human-readable name for the data type of a column.
getColumnUnderlyingType(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the underlying type used to store data in a column.
getCommandClass() - Method in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Get the command class name
getCommandTemplate() - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the command template data for this SlideSet
getCompatableColumnReaders(Class<?>, SlideSet) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Get a list of ColumnBoundReaders that will read data from the given table that are assignment-compatible with the specified class.
getCompatableReaders(Class<?>, ArrayList<Class<? extends ElementReader>>, ArrayList<String>, boolean) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Get the list of ElementReaders that will read to the specified type.
getCompatableWriters(Class<?>, ArrayList<Class<? extends ElementWriter>>, ArrayList<String>, ArrayList<String>) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Get a list of ElementWriters compatible with a class.
getContext() - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the SciJava application Context
getContrast() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
getCreationParams() - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the creation parameters of this SlideSet
getDataElement(int, int) - Method in class edu.emory.cellbio.ijbat.SlideSet
getDefaultLinkCount(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the counter for default links for a column.
getDefaultLinkExtension(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the default link extension for a column.
getDefaultLinkPrefix(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the prefix for default links for a column.
getElementTypes(boolean) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Get a list of DataElement types in the index.
getFirstPathInstructionEnd(String) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Get the end index of the first path data instruction in pathData.
getFirstPathInstructionEnd(String) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Get the end index of the first path data instruction in pathData.
getFirstTransformEnd(String) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Get the index of the end of the first transform string in a transform attribute list.
getFirstTransformEnd(String) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Get the index of the end of the first transform string in a transform attribute list.
getHelp(String) - Method in interface edu.emory.cellbio.ijbat.ui.HelpLoader
 
getHelp() - Method in interface edu.emory.cellbio.ijbat.ui.HelpLoader
 
getHelp(String) - Method in class edu.emory.cellbio.ijbat.ui.HttpHelpLoader
Open a documentation page.
getHelp() - Method in class edu.emory.cellbio.ijbat.ui.HttpHelpLoader
 
getHelp - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
Button to view the relevant documentation, if applicable
getHelp(String) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Load documentation in a web browser.
getImageNames() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Get the short names of image files to put in the list, prefixed by the row number to avoid name duplications which cause problems with DefaultComboBoxModel.
getImageNames() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Get the short names of image files to put in the list, prefixed by the row number to avoid name duplications which cause problems with DefaultComboBoxModel.
getImageSetNames() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Get the names of available image sets to put in the list, prefixed by the row number to avoid name duplications which cause problems with DefaultComboBoxModel.
getInputChoices(ArrayList<Integer>, ArrayList<Object>) - Method in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Get the command input choice parameters.
getInputChoices(ArrayList<Integer>, ArrayList<Object>) - Method in class edu.emory.cellbio.ijbat.io.CommandSkeletonService.CommandTemplateInputPicker
 
getInputChoices(ArrayList<Integer>, ArrayList<Object>) - Method in interface edu.emory.cellbio.ijbat.pi.PluginInputPicker
Get chosen options for assignment of each plugin input value.
getInputChoices(ArrayList<Integer>, ArrayList<Object>) - Method in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
 
getItemText(int, int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Get a text representation of an item, i.e.
getMaximum() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
getMimeReadableName(String) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Get the human-readable name of an MIME type, if it is registered in the index.
getMimeType() - Method in class edu.emory.cellbio.ijbat.dm.DataElement
Get the MIME type of this element
getMimeTypes() - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Get a list of MIME types from the index
getMinimum() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
getMyJarPath() - Method in class edu.emory.cellbio.ijbat.ui.HttpHelpLoader.AboutPage
 
getName() - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the name of this SlideSet
getNeighbors(long[], int, int) - Method in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
Get the 4-connected neighborhood in the x-y plane
getNewColumnElement(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Generate a new DataElement appropriate for the selected column.
getNextPoint(long[], ArrayList<long[][]>) - Method in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
Find the edge in set with one point matching p.
getNumCols() - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the number of columns
getNumResults(Map<String, Object>) - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Checks to make sure that all results are either length 1 (i.e.
getNumRows() - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the number of rows
getOutputChoices(ArrayList<Integer>, ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Method in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Set the command output choices.
getOutputChoices(ArrayList<Integer>, ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Method in class edu.emory.cellbio.ijbat.io.CommandSkeletonService.CommandTemplateOutputPicker
 
getOutputChoices(ArrayList<Integer>, ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Method in interface edu.emory.cellbio.ijbat.pi.PluginOutputPicker
Get chosen options for handling of each plugin output value, as well as fields from the parent table that should be copied to the results table.
getOutputChoices(ArrayList<Integer>, ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Method in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
getOwner() - Method in class edu.emory.cellbio.ijbat.dm.DataElement
Get the SlideSet table which owns this element
getParent() - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the parent of this SlideSet
getPath() - Method in class edu.emory.cellbio.ijbat.pi.WekaClassifierFile
 
getPlanarAxes(AbstractOverlay, int[]) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
Get the X and Y axis indeces for an overlay
getPluginInfo() - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Get a list of available SlideSetPlugins
getPluginMenuPaths() - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Get a list of the plugin paths, i.e.
getPort() - Method in class edu.emory.cellbio.ijbat.ui.JarHTTPd
Get the port on which the server is listening.
getPrimitiveWrapper(Class<?>) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Returns the wrapper class for a primitive type.
getReadableElementType(Class<? extends DataElement>, String) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Get a human-readable name for a DataElement type— MIME type pair
getReaderElementType(Class<? extends ElementReader>) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Get the DataElement type read by an ElementReader type.
getReaderMimeTypes(Class<? extends ElementReader>) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Get the list of MIME types that can be read by an ElementReader type.
getReaders(Iterable<ModuleItem<?>>, SlideSet, PluginInputPicker, String, CommandTemplate) - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Create a list of ColumnBoundReaders for each input
getReaderUnderlyingType(Class<? extends ElementReader>) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Get the underlying type read by an ElementReader type.
getRealType() - Method in class edu.emory.cellbio.ijbat.dm.AbstractOverlaysAlias
 
getRealType() - Method in class edu.emory.cellbio.ijbat.dm.RoisAlias
 
getRealType() - Method in interface edu.emory.cellbio.ijbat.dm.TypeAlias
The real type referenced by this alias type
getRoiLenth(AbstractOverlay) - Static method in class edu.emory.cellbio.ijbat.pi.ROILengths
Calculate the length, in pixels, of an AbstractOverlay border.
getRoiSetNames() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Get the names of available ROI sets to put in the list, prefixed by the row number to avoid name duplications which cause problems with DefaultComboBoxModel.
getRoiSetNames() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Get the names of available ROI sets to put in the list, prefixed by the row number to avoid name duplications which cause problems with DefaultComboBoxModel.
getRowCount() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetTableModel
 
getSelectedCommand() - Method in class edu.emory.cellbio.ijbat.ui.CommandPicker
 
getSelectedSlideSets() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Get a list of the SlideSets selected in the tree
getTableForWriters(ArrayList<String>, ArrayList<Class<? extends ElementWriter>>, SlideSet, ArrayList<ColumnBoundWriter>) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Create a table with column types matching the specified list of ElementWriter classes.
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetTreeRenderer
 
getTreeRoot() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Get the SlideSet at the root of the tree
getTypeAlias(Class<?>) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Replace a TypeAlias type with it's 'real' type.
getUnderlying() - Method in class edu.emory.cellbio.ijbat.dm.DataElement
Get this element's "underlying" value
getUnderlying(int, int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Get an item as the underlying data object, i.e.
getUnderlyingText() - Method in class edu.emory.cellbio.ijbat.dm.BooleanElement
 
getUnderlyingText() - Method in class edu.emory.cellbio.ijbat.dm.DataElement
Get a String representation of this element's "underlying" value
getUnderlyingText() - Method in class edu.emory.cellbio.ijbat.dm.DoubleElement
 
getUnderlyingText() - Method in class edu.emory.cellbio.ijbat.dm.FileLinkElement
 
getUnderlyingText() - Method in class edu.emory.cellbio.ijbat.dm.IntegerElement
 
getUnderlyingText() - Method in class edu.emory.cellbio.ijbat.dm.StringElement
 
getUnfilledInputs(Module, Iterable<ModuleItem<?>>) - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Get a list of inputs that have not been filled
getValueAt(int, int) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetTableModel
 
getView() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
getWorkingDirectory() - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the working directory of this SlideSet
getWriter() - Method in class edu.emory.cellbio.ijbat.dm.ColumnBoundWriter
Get the bound writer
getWriterElementType(Class<? extends ElementWriter>) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Get the DataElement type written by an ElementWriter type.
getWriters(ArrayList<ModuleItem<?>>, boolean, PluginOutputPicker, ArrayList<ColumnBoundWriter>, SlideSet, String[], ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>, CommandTemplate) - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Prepare for plugin results be creating a results table and appropriate ColumnBoundWriters to write the results to it
GIF - Static variable in class edu.emory.cellbio.ijbat.dm.MIME
 
GLOBAL - Static variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
gmtFrmt - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
GMT date formatter
goImageBack - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
goImageBack - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
goImageNext - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
goImageNext - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
green - Variable in class edu.emory.cellbio.ijbat.pi.BorderStats
 
green - Variable in class edu.emory.cellbio.ijbat.pi.RegionStats
 
gT - Variable in class edu.emory.cellbio.ijbat.pi.BorderStats
 
gT - Variable in class edu.emory.cellbio.ijbat.pi.RegionStats
 

H

handleActionEvent(ActionEvent) - Method in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
handleActionEvent(ActionEvent) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Handle an ActionEvent
handleActionEvent(ActionEvent) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Handle an ActionEvent
handleActionEvent(ActionEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Handle an action event
handleActionEvent(ActionEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Handle an action event
handleError(Exception) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
handleError(Exception) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Handle an exception
handleError(Exception) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Record an error
handleMouseEvent(MouseEvent, String) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Handle a mouse event
handleMouseEvent(MouseEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Handle a mouse event
header - Variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.Response
Headers for the HTTP response.
headLable - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
Header labels
headLink - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
headType - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
HelpLoader - Interface in edu.emory.cellbio.ijbat.ui
GUI-agnostic interface for a documentation system.
helpLoader - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
HelpPath - Annotation Type in edu.emory.cellbio.ijbat.pi
Annotate a SlideSetPlugin with this annotation type to set an associated documentation page.
hidden - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.DataElementRecord
Is this a hidden element type?
hidden - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.ReaderRecord
Is this a hidden reader?
hl - Variable in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
 
HTTP_BADREQUEST - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Some HTTP response status codes
HTTP_FORBIDDEN - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Some HTTP response status codes
HTTP_INTERNALERROR - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Some HTTP response status codes
HTTP_NOTFOUND - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Some HTTP response status codes
HTTP_NOTIMPLEMENTED - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Some HTTP response status codes
HTTP_OK - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Some HTTP response status codes
HTTP_REDIRECT - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Some HTTP response status codes
HttpHelpLoader - Class in edu.emory.cellbio.ijbat.ui
Load and display documentation in the system-default web browser.
HttpHelpLoader(ImageJ) - Constructor for class edu.emory.cellbio.ijbat.ui.HttpHelpLoader
 
HttpHelpLoader.AboutPage - Class in edu.emory.cellbio.ijbat.ui
 
HTTPSession(Socket) - Constructor for class edu.emory.cellbio.ijbat.ui.NanoHTTPd.HTTPSession
 

I

i - Variable in class edu.emory.cellbio.ijbat.pi.MathDiv
 
i - Variable in class edu.emory.cellbio.ijbat.pi.Test
 
ij - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
 
ij - Variable in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
 
ij - Variable in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
 
ij - Variable in class edu.emory.cellbio.ijbat.io.XMLService
 
ij - Variable in class edu.emory.cellbio.ijbat.pi.OtsuSegmentation
 
ij - Variable in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
 
ij - Variable in class edu.emory.cellbio.ijbat.pi.Test
 
ij - Variable in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
 
ij - Variable in class edu.emory.cellbio.ijbat.pi.WekaSegmentationWrapper
 
ij - Variable in class edu.emory.cellbio.ijbat.SlideSet
ImageJ context reference
ij - Variable in class edu.emory.cellbio.ijbat.SlideSetIJ2Entry
 
ij - Variable in class edu.emory.cellbio.ijbat.ui.HttpHelpLoader
 
ij - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
 
ij - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
ij - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
ij - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
ij - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
ij - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
IJ1ROIsToSVGFileWriter - Class in edu.emory.cellbio.ijbat.dm.write
Write ImageJ1-style ROIs as SVG files.
IJ1ROIsToSVGFileWriter() - Constructor for class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
 
IMAGE - Static variable in class edu.emory.cellbio.ijbat.dm.MIME
Image of unknown format
imageDisplay - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
The image display
ImageDisplayToImageFileWriter - Class in edu.emory.cellbio.ijbat.dm.write
 
ImageDisplayToImageFileWriter() - Constructor for class edu.emory.cellbio.ijbat.dm.write.ImageDisplayToImageFileWriter
 
ImageFileToDatasetReader - Class in edu.emory.cellbio.ijbat.dm.read
 
ImageFileToDatasetReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.ImageFileToDatasetReader
 
ImageFileToImageDisplayReader - Class in edu.emory.cellbio.ijbat.dm.read
 
ImageFileToImageDisplayReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.ImageFileToImageDisplayReader
 
ImageFileToImageWindowReader - Class in edu.emory.cellbio.ijbat.dm.read
 
ImageFileToImageWindowReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.ImageFileToImageWindowReader
 
imageList - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
imageList - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
imageReaders - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
images - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
imageSetList - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
imageSetNames - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Names of the image sets
imageWindow - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
The image window
imageWindow - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
The image display
imgIDs - Variable in class edu.emory.cellbio.ijbat.pi.BinRegions
 
ImgLinkException - Exception in edu.emory.cellbio.ijbat.ex
Signals a problem with a link to an image.
ImgLinkException() - Constructor for exception edu.emory.cellbio.ijbat.ex.ImgLinkException
Creates a new instance of ImgLinkException without detail message.
ImgLinkException(String) - Constructor for exception edu.emory.cellbio.ijbat.ex.ImgLinkException
Constructs an instance of ImgLinkException with the specified detail message.
ImgLinkException(Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.ImgLinkException
 
ImgLinkException(String, Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.ImgLinkException
 
importData(TransferHandler.TransferSupport) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher.DropHandler
 
importData(TransferHandler.TransferSupport) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer.DropHandler
 
inBounds(double[], long[]) - Method in class edu.emory.cellbio.ijbat.pi.BorderStats
Check if a point is within the image dimensions
inBounds(double[], long[]) - Method in class edu.emory.cellbio.ijbat.pi.BorderStatsNChan
Check if a point is within the image dimensions
inBounds(double[], long[]) - Method in class edu.emory.cellbio.ijbat.pi.CreateMask
 
inBounds(double[], long[]) - Method in class edu.emory.cellbio.ijbat.pi.RegionStats
 
inBounds(double[], long[]) - Method in class edu.emory.cellbio.ijbat.pi.RegionStatsNChan
 
inBounds(long[], long[]) - Method in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
 
includeTree - Variable in class edu.emory.cellbio.ijbat.io.XMLService
 
ind(int) - Method in class edu.emory.cellbio.ijbat.io.XMLService
Generate an indent for "pretty" XML
index - Variable in class edu.emory.cellbio.ijbat.pi.ROILengths
 
info - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
initialized - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
 
initialized - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
initialMax - Variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
The initial minimum and maximum values of the data view.
initialMin - Variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
The initial minimum and maximum values of the data view.
initValues() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
inputChoices - Variable in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Input choices
inputConstants - Variable in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Input constants as strings
inputNames - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
List of the input names
inputs - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
Include inputs in output check boxes
inputsMenu - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
Include inputs in output menu
IntegerElement - Class in edu.emory.cellbio.ijbat.dm
DataElement for storing integer values
IntegerElement() - Constructor for class edu.emory.cellbio.ijbat.dm.IntegerElement
 
IntegerElement(Integer) - Constructor for class edu.emory.cellbio.ijbat.dm.IntegerElement
 
IntToByteReader - Class in edu.emory.cellbio.ijbat.dm.read
 
IntToByteReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.IntToByteReader
 
IntToDoubleReader - Class in edu.emory.cellbio.ijbat.dm.read
 
IntToDoubleReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.IntToDoubleReader
 
IntToFloatReader - Class in edu.emory.cellbio.ijbat.dm.read
 
IntToFloatReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.IntToFloatReader
 
IntToIntReader - Class in edu.emory.cellbio.ijbat.dm.read
 
IntToIntReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.IntToIntReader
 
IntToIntWriter - Class in edu.emory.cellbio.ijbat.dm.write
 
IntToIntWriter() - Constructor for class edu.emory.cellbio.ijbat.dm.write.IntToIntWriter
 
IntToLongReader - Class in edu.emory.cellbio.ijbat.dm.read
 
IntToLongReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.IntToLongReader
 
IntToShortReader - Class in edu.emory.cellbio.ijbat.dm.read
 
IntToShortReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.IntToShortReader
 
inv - Variable in class edu.emory.cellbio.ijbat.pi.BorderStats
 
inv - Variable in class edu.emory.cellbio.ijbat.pi.BorderStatsNChan
 
inv - Variable in class edu.emory.cellbio.ijbat.pi.RegionStats
 
inv - Variable in class edu.emory.cellbio.ijbat.pi.RegionStatsNChan
 
ipd - Variable in class edu.emory.cellbio.ijbat.pi.WekaSegmentationWrapper
 
isAbreastSegment(double[], double[], double[]) - Static method in class edu.emory.cellbio.ijbat.pi.RoiUtils
Is a point next to a line segment? I.e.
isCellEditable(int, int) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLockedTableModel
 
isCellEditable(int, int) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetTableModel
 
isLocked() - Method in class edu.emory.cellbio.ijbat.SlideSet
Is the read-only flag set on this SlideSet?
isNearBorder(double[], AbstractOverlay, double) - Static method in class edu.emory.cellbio.ijbat.pi.RoiUtils
Determine if a point is near a border defined by an set of vertices.
isNearBorder(double[], PolygonOverlay, double) - Static method in class edu.emory.cellbio.ijbat.pi.RoiUtils
Handler for PolygonOverlays
isNearBorder(double[], LineOverlay, double) - Static method in class edu.emory.cellbio.ijbat.pi.RoiUtils
Handler for LineOverlays
isNearBorder(double[], GeneralPathOverlay, double) - Static method in class edu.emory.cellbio.ijbat.pi.RoiUtils
Handler for GeneralPathOverlays
isNearBorder(double[], double[][], double, boolean) - Static method in class edu.emory.cellbio.ijbat.pi.RoiUtils
Determine if a point is near a border defined by an set of vertices.
isOptionLink - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
Index of which TypeCode options represent file references
isPrimativeWrapper(Class<?>) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Is the type a wrapper class for a java primitive?
itdr - Variable in class edu.emory.cellbio.ijbat.dm.read.ImageFileToImageDisplayReader
 

J

JarHTTPd - Class in edu.emory.cellbio.ijbat.ui
HTTP server for displaying user documentation pages from within the Slide Set JAR file.
JarHTTPd(int) - Constructor for class edu.emory.cellbio.ijbat.ui.JarHTTPd
 
JPG - Static variable in class edu.emory.cellbio.ijbat.dm.MIME
 

K

keep - Variable in class edu.emory.cellbio.ijbat.pi.FilterRegions
 
kill() - Method in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
 
kill() - Method in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
kill() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Clean up and close the editor
kill() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Clean up and close the editor
kill() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
kill() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
kill() - Method in interface edu.emory.cellbio.ijbat.ui.SlideSetWindow
Perform any clean-up functions necessary to close the window.

L

labels - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
The parameter labels
labels - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
The result labels
lastPopupPoint - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Location where the last popup menu was triggered
launcher - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher.DropHandler
 
layoutHeaders() - Method in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
length - Variable in class edu.emory.cellbio.ijbat.pi.BorderStats
 
length - Variable in class edu.emory.cellbio.ijbat.pi.BorderStatsNChan
 
length - Variable in class edu.emory.cellbio.ijbat.pi.ROILengths
 
length - Variable in class edu.emory.cellbio.ijbat.ui.DynamicHelpResource.GeneratedResource
Number of bytes in the resource stream
lh - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
 
LICENCE - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
The distribution licence
linkDirDefault - Static variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
linkDirDefaults - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
Default link directories for each field and option
LinkException - Exception in edu.emory.cellbio.ijbat.ex
Signals a problem with a data table file reference
LinkException() - Constructor for exception edu.emory.cellbio.ijbat.ex.LinkException
Creates a new instance of LinkException without detail message.
LinkException(String) - Constructor for exception edu.emory.cellbio.ijbat.ex.LinkException
Constructs an instance of LinkException with the specified detail message.
LinkException(Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.LinkException
 
LinkException(String, Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.LinkException
 
linkExt - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.WriterRecord
For file links, the default file extension to use with this writer
linkExtDefault - Static variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
linkExtDefaults - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
Default link file prefixes for each field and option
LinkNotFoundException - Exception in edu.emory.cellbio.ijbat.ex
Indicates a link points to a file that does not exist.
LinkNotFoundException() - Constructor for exception edu.emory.cellbio.ijbat.ex.LinkNotFoundException
Creates a new instance of LinkNotFoundException without detail message.
LinkNotFoundException(String) - Constructor for exception edu.emory.cellbio.ijbat.ex.LinkNotFoundException
Constructs an instance of LinkNotFoundException with the specified detail message.
LinkNotFoundException(Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.LinkNotFoundException
 
LinkNotFoundException(String, Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.LinkNotFoundException
 
linkPreDefault - Static variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
linkPreDefaults - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
Default link file prefixes for each field and option
listeners - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLog
 
listPathInstructions(String) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Make a path data String into a convenient List!
listPathInstructions(String) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Make a path data String into a convenient List!
lman - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
The layout manager
lman - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
The layout manager
loadData() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Load the internal data
loadDocument(File) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Load the DOM from an SVG file
loadDocument(File) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Load the DOM from an SVG file
loadImage(int) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Load and display the selected image
loadImage(int) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Load and display the selected image.
loadImageData() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Load the index of images
loadingImage - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
Busy loading an image flag
loadingImage - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Busy loading an image flag
loadOverlays() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Load overlay data from disk
loadPlugins() - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Because the CommandService is persnickety when launched through Fiji, we'll do this manually.
loadRois() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Load the ROI data
lock() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Activate read-only mode and prevent changes to ROIs
lock() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Activate read-only mode and prevent changes to ROIs
locked - Variable in class edu.emory.cellbio.ijbat.SlideSet
Is this SlideSet locked?
locked - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
Read-only mode
locked - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Read-only mode flag
locked - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Read-only mode
lockedTables - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Data tables that are in use (locked) and the threads using them
lockSlideSet(SlideSet) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Check-out a SlideSet for use.
log - Variable in class edu.emory.cellbio.ijbat.pi.BorderStats
 
log - Variable in class edu.emory.cellbio.ijbat.pi.BorderStatsNChan
 
log - Variable in class edu.emory.cellbio.ijbat.pi.MathDiv
 
log - Variable in class edu.emory.cellbio.ijbat.pi.MathRound
 
log - Variable in class edu.emory.cellbio.ijbat.pi.ROILengths
 
log - Variable in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
 
log - Variable in class edu.emory.cellbio.ijbat.pi.UnmixAbsorbance
 
log - Variable in class edu.emory.cellbio.ijbat.pi.WekaSegmentationWrapper
 
log - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
The log
log - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
The log
log - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
log - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
LogListener - Interface in edu.emory.cellbio.ijbat.ui
Interface for receiving messages sent from the SlideSetLog.
logMessage(String) - Method in interface edu.emory.cellbio.ijbat.ui.LogListener
Receive a message from the log.
logMessage(String) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
LongToIntWriter - Class in edu.emory.cellbio.ijbat.dm.write
 
LongToIntWriter() - Constructor for class edu.emory.cellbio.ijbat.dm.write.LongToIntWriter
 

M

m1 - Variable in class edu.emory.cellbio.ijbat.pi.Manders
 
m2 - Variable in class edu.emory.cellbio.ijbat.pi.Manders
 
main(String...) - Static method in class edu.emory.cellbio.ijbat.SlideSetIJ1Entry
 
main(String[]) - Static method in class edu.emory.cellbio.ijbat.TestMain
 
makeColumnBoundConstantReader(Class<? extends ElementReader>, Object, SlideSet) - Method in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Create a ColumnBoundReader that will always read from a constant DataElement.
makeDefaultLink(int, int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Set a cell to an auto-generated link
makeEllipseOverlay(double, double, double, double, Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from parsed ellipse data
makeEllipseOverlay(double, double, double, double, Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from parsed ellipse data
makeParameterOptionsMenu(String[], JFormattedTextField) - Method in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
Create a button and menu to list appropriate values for an input parameter
makePathRelative(String, String) - Static method in class edu.emory.cellbio.ijbat.io.Util
Make path relative to workingDirectory, if possible
Manders - Class in edu.emory.cellbio.ijbat.pi
SlideSet command for measuring Manders' Colocalization Coefficients within regions of interest.
Manders() - Constructor for class edu.emory.cellbio.ijbat.pi.Manders
 
maps - Variable in class edu.emory.cellbio.ijbat.pi.OtsuSegmentation
 
mask - Variable in class edu.emory.cellbio.ijbat.pi.CreateMask
 
mask - Variable in class edu.emory.cellbio.ijbat.pi.FilterRegions
 
MathAdd - Class in edu.emory.cellbio.ijbat.pi
 
MathAdd() - Constructor for class edu.emory.cellbio.ijbat.pi.MathAdd
 
MathDiv - Class in edu.emory.cellbio.ijbat.pi
 
MathDiv() - Constructor for class edu.emory.cellbio.ijbat.pi.MathDiv
 
MathMlt - Class in edu.emory.cellbio.ijbat.pi
 
MathMlt() - Constructor for class edu.emory.cellbio.ijbat.pi.MathMlt
 
MathRound - Class in edu.emory.cellbio.ijbat.pi
Round a double to an int
MathRound() - Constructor for class edu.emory.cellbio.ijbat.pi.MathRound
 
MathSub - Class in edu.emory.cellbio.ijbat.pi
 
MathSub() - Constructor for class edu.emory.cellbio.ijbat.pi.MathSub
 
max - Variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
MAX_POWER - Static variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
The exponential power used for computing contrast.
maxSize - Variable in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
 
means - Variable in class edu.emory.cellbio.ijbat.pi.BorderStatsNChan
 
means - Variable in class edu.emory.cellbio.ijbat.pi.RegionStatsNChan
 
menuBar - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
menuBar - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
menuColP - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Column header popup menu
menuP - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Table popup menu
MIME - Class in edu.emory.cellbio.ijbat.dm
MIME type constants
MIME() - Constructor for class edu.emory.cellbio.ijbat.dm.MIME
 
mime - Variable in class edu.emory.cellbio.ijbat.ui.DynamicHelpResource.GeneratedResource
MIME type of the resource stream
mime - Static variable in class edu.emory.cellbio.ijbat.ui.HttpHelpLoader.AboutPage
 
MIME_DEFAULT_BINARY - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Common mime types for dynamic content
MIME_HTML - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Common mime types for dynamic content
MIME_PLAINTEXT - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Common mime types for dynamic content
MIME_XML - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Common mime types for dynamic content
mimeReadableIndex - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Index associating MIME types with human-readable names: <MIME type, readable name>
mimeType - Variable in class edu.emory.cellbio.ijbat.dm.DataElement
 
mimeType - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.WriterRecord
MIME type written by this writer
mimeType - Variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.Response
MIME type of content, e.g.
mimeTypes - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.ReaderRecord
MIME types compatible with this reader
min - Variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
minMaxChanged() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
Called when min or max changes.
minSize - Variable in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
 
mouseClicked(MouseEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
MouseListener implementation
mouseClicked(MouseEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
MouseListener implementation
mouseEntered(MouseEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
MouseListener implementation
mouseEntered(MouseEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
mouseExited(MouseEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
MouseListener implementation
mouseExited(MouseEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
mousePressed(MouseEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
MouseListener implementation
mousePressed(MouseEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
mouseReleased(MouseEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
MouseListener implementation
mouseReleased(MouseEvent) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
MultipleResults - Interface in edu.emory.cellbio.ijbat.pi
SlideSetPlugins which report multiple results as arrays or Lists should implement this interface.
myServerSocket - Variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
 
mySocket - Variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.HTTPSession
 
myTcpPort - Variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
 
myThread - Variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
 

N

name - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.DataElementRecord
Element human-readable name
name - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.ReaderRecord
Human-readable name for the reader
name - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.WriterRecord
Human-readable name for the writer
name - Variable in class edu.emory.cellbio.ijbat.SlideSet
Name of this SlideSet
NanoHTTPd - Class in edu.emory.cellbio.ijbat.ui
A simple, tiny, nicely embeddable HTTP 1.0 server in Java

NanoHTTPd(int) - Constructor for class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Starts a HTTP server to given port.
NanoHTTPd.HTTPSession - Class in edu.emory.cellbio.ijbat.ui
Handles one session, i.e.
NanoHTTPd.Response - Class in edu.emory.cellbio.ijbat.ui
HTTP response.
newFile() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Start a new file
nil - Static variable in class edu.emory.cellbio.ijbat.pi.CreateMask
 
NoPluginInputSourceException - Exception in edu.emory.cellbio.ijbat.ex
Signals that a command cannot be run on a table one of the plugin inputs requires a type which cannot be read from the table or entered as a constant.
NoPluginInputSourceException() - Constructor for exception edu.emory.cellbio.ijbat.ex.NoPluginInputSourceException
Creates a new instance of NoPluginInputSourceException without detail message.
NoPluginInputSourceException(String) - Constructor for exception edu.emory.cellbio.ijbat.ex.NoPluginInputSourceException
Constructs an instance of NoPluginInputSourceException with the specified detail message.
NoPluginInputSourceException(Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.NoPluginInputSourceException
 
NoPluginInputSourceException(String, Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.NoPluginInputSourceException
 
numRows - Variable in class edu.emory.cellbio.ijbat.SlideSet
Number of rows in the SlideSet

O

offsetBottomRightEdges(PolygonRegionOfInterest, int, int) - Method in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
Offset the bottom and right edges of an ROI outlining pixels as a workaround for issues with the contains() method.
okPressed - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
 
okPressed - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
onEvent(OverlayUpdatedEvent) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Check to see if one of the ROIs has been changed
onEvent(OverlayRestructuredEvent) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Check to see if one of the ROIs has been restructured
onEvent(OverlayCreatedEvent) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Handle an ROI creation
onEvent(OverlayDeletedEvent) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Handle an ROI deletion
openPath - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Path to the currently open file
openROIManager - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
openROIManager() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Open the ImageJ overlay manager window
openROIManager() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Open the IJ1 ROI Manager and line it up below the ROI Editor pane.
openXML() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Open a new file selected using a dialog - do not run on event thread
openXML(File) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Open a specified file
OperationCanceledException - Exception in edu.emory.cellbio.ijbat.ex
Thrown when a SlideSet operation has been canceled.
OperationCanceledException() - Constructor for exception edu.emory.cellbio.ijbat.ex.OperationCanceledException
Creates a new instance of OperationCanceledException without detail message.
OperationCanceledException(String) - Constructor for exception edu.emory.cellbio.ijbat.ex.OperationCanceledException
Constructs an instance of OperationCanceledException with the specified detail message.
OperationCanceledException(Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.OperationCanceledException
 
OperationCanceledException(String, Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.OperationCanceledException
 
optionIndex - Variable in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
An index to match choices in each combo box to the appropriate SlideSet column index
optionIndex - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
Index of TypeCode options
os - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
OtsuSegmentation - Class in edu.emory.cellbio.ijbat.pi
Segment an image using Otsu's method.
OtsuSegmentation() - Constructor for class edu.emory.cellbio.ijbat.pi.OtsuSegmentation
 
out - Variable in class edu.emory.cellbio.ijbat.pi.WekaSegmentationWrapper
 
outputChoices - Variable in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Output choices
outputDirs - Variable in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Output directories
outputExts - Variable in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Output file extensions
outputPres - Variable in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Output file prefixes
outputSanityChecks() - Method in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
overlap - Variable in class edu.emory.cellbio.ijbat.pi.ROIOverlap
 
overlay - Variable in class edu.emory.cellbio.ijbat.pi.ROILengths
 
owner - Variable in class edu.emory.cellbio.ijbat.dm.DataElement
 

P

p1ds - Variable in class edu.emory.cellbio.ijbat.pi.UnmixAbsorbance
 
p2ds - Variable in class edu.emory.cellbio.ijbat.pi.UnmixAbsorbance
 
pageIndex - Variable in class edu.emory.cellbio.ijbat.ui.HttpHelpLoader
 
pane - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
parent - Variable in class edu.emory.cellbio.ijbat.SlideSet
Parent of this SlideSet
parentFields - Variable in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Parent fields to copy
parseCircle(Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a circle element
parseCircle(Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a circle element
parseDocument(Document) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Get the list of overlays that can be created from the DOM
parseDocument(Document) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Get the list of ROIs that can be created from the DOM
parseEllipse(Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from an ellipse element
parseEllipse(Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from an ellipse element
parseLength(String) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Parse an SVG length String (possibly with units), and convert to pixels
parseLength(String) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Parse an SVG length String (possibly with units), and convert to pixels
parseLine(Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a line element.
parseLine(Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a line element.
parseListOfNumbers(String) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Parse a list of numbers, possibly with units
parseListOfNumbers(String) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Parse a list of numbers, possibly with units
parseListOfPoints(String) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Parse a list of points, as used in polygon and polyline elements
parseListOfPoints(String) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Parse a list of points, as used in polygon and polyline elements
parseNode(Node) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from an SVG node
parseNode(Node) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Generate an overlay from an SVG node
parsePath(Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a path element
parsePath(Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a path element May return a different type of ROI, depending on the data:
parsePolygon(Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a polygon element
parsePolygon(Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a polygon element
parsePolyline(Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a polyline element
parsePolyline(Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a polyline element
parseRect(Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a rect element
parseRect(Element) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a rect element
parseRecursiveMenuAdd(String[], String, JMenu) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Deprecated.
Use UIUtil.parseRecursiveMenuAdd(java.lang.String[], java.lang.String, javax.swing.JMenu, java.awt.event.ActionListener) instead

Add a menu item to a menu tree, along with sub-menu nodes if needed

parseRecursiveMenuAdd(String[], String, JMenu, ActionListener) - Static method in class edu.emory.cellbio.ijbat.ui.UIUtil
Add a menu item to a menu tree, along with sub-menu nodes if needed
parseRGBtoPigment(String, int) - Method in class edu.emory.cellbio.ijbat.pi.UnmixAbsorbance
Parse a whitespace-separated RGB string to an array of absorbance values
parseTransform(double[], String) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Transform a coordinate pair
parseTransform(double[], String) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Transform a coordinate pair
path - Variable in class edu.emory.cellbio.ijbat.pi.WekaClassifierFile
 
pickAndRunCommand() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Launch a CommandPicker dialog, and run the selected ImageJ Command.
pigmentOne - Variable in class edu.emory.cellbio.ijbat.pi.UnmixAbsorbance
 
pigmentTwo - Variable in class edu.emory.cellbio.ijbat.pi.UnmixAbsorbance
 
PLANE - Static variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
PluginInputMatcherFrame - Class in edu.emory.cellbio.ijbat.ui
GUI for assigning SlideSet columns to plugin inputs
PluginInputMatcherFrame(SlideSet, ImageJ, DataTypeIDService) - Constructor for class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
 
PluginInputPicker - Interface in edu.emory.cellbio.ijbat.pi
Scheme for selecting among available options for assigning plugin input parameter values.
PluginOutputMatcherFrame - Class in edu.emory.cellbio.ijbat.ui
GUI for selecting options for handling plugin outputs.
PluginOutputMatcherFrame(ImageJ, DataTypeIDService) - Constructor for class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
PluginOutputPicker - Interface in edu.emory.cellbio.ijbat.pi
Scheme for selecting among available options for handling plugin output values.
plugins - Variable in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
 
PNG - Static variable in class edu.emory.cellbio.ijbat.dm.MIME
 
populateText() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetPropertiesViewer
 
populateTree(DefaultMutableTreeNode, SlideSet) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Iteratively populate the tree pane
popupMenuHash - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Index specifying popup menus associated with various components
popupMenus - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
port - Variable in class edu.emory.cellbio.ijbat.ui.HttpHelpLoader
 
pre - Static variable in class edu.emory.cellbio.ijbat.ui.HttpHelpLoader
 
print(String) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLog
Relay a message to the log listeners.
println(String) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLog
Relay a message (with newline character appended) to the log listeners.
printLogHead() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Print a header message to the info window
prob - Variable in class edu.emory.cellbio.ijbat.pi.WekaSegmentationWrapper
 
processedType - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.ReaderRecord
Type returned by this reader's read() method
processedType - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.WriterRecord
Type accepted by this writer's write() method
ps - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
 
ps - Variable in class edu.emory.cellbio.ijbat.io.XMLService
 
pw - Variable in class edu.emory.cellbio.ijbat.io.CSVService
 

R

r - Variable in class edu.emory.cellbio.ijbat.pi.Correlation
 
rangeChoice - Variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
rds - Variable in class edu.emory.cellbio.ijbat.pi.UnmixAbsorbance
 
read(int) - Method in class edu.emory.cellbio.ijbat.dm.ColumnBoundReader
Read data from the specified row
read(BooleanElement) - Method in class edu.emory.cellbio.ijbat.dm.read.BooleanToBooleanReader
 
read(BooleanElement) - Method in class edu.emory.cellbio.ijbat.dm.read.BooleanToByteReader
 
read(BooleanElement) - Method in class edu.emory.cellbio.ijbat.dm.read.BooleanToIntReader
 
read(BooleanElement) - Method in class edu.emory.cellbio.ijbat.dm.read.BooleanToShortReader
 
read(DoubleElement) - Method in class edu.emory.cellbio.ijbat.dm.read.DoubleToDoubleReader
 
read(DoubleElement) - Method in class edu.emory.cellbio.ijbat.dm.read.DoubleToFloatReader
 
read(E) - Method in interface edu.emory.cellbio.ijbat.dm.read.ElementReader
Convert "underlying" data to "processed" data.
read(FileLinkElement) - Method in class edu.emory.cellbio.ijbat.dm.read.ImageFileToDatasetReader
 
read(FileLinkElement) - Method in class edu.emory.cellbio.ijbat.dm.read.ImageFileToImageDisplayReader
 
read(FileLinkElement) - Method in class edu.emory.cellbio.ijbat.dm.read.ImageFileToImageWindowReader
 
read(IntegerElement) - Method in class edu.emory.cellbio.ijbat.dm.read.IntToByteReader
 
read(IntegerElement) - Method in class edu.emory.cellbio.ijbat.dm.read.IntToDoubleReader
 
read(IntegerElement) - Method in class edu.emory.cellbio.ijbat.dm.read.IntToFloatReader
 
read(IntegerElement) - Method in class edu.emory.cellbio.ijbat.dm.read.IntToIntReader
 
read(IntegerElement) - Method in class edu.emory.cellbio.ijbat.dm.read.IntToLongReader
 
read(IntegerElement) - Method in class edu.emory.cellbio.ijbat.dm.read.IntToShortReader
 
read(FileLinkElement) - Method in class edu.emory.cellbio.ijbat.dm.read.RoisetFileToAbstractOverlayReader
 
read(StringElement) - Method in class edu.emory.cellbio.ijbat.dm.read.StringToStringReader
 
read(FileLinkElement) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
 
read(FileLinkElement) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
 
read(FileLinkElement) - Method in class edu.emory.cellbio.ijbat.dm.read.WekaClassifierReader
 
read(File, ArrayList<CommandTemplate>, ArrayList<String>) - Method in class edu.emory.cellbio.ijbat.io.CommandSkeletonService
Read a command skeleton from an XML file.
read(File) - Method in class edu.emory.cellbio.ijbat.io.XMLService
Read SlideSet data from an XML file
reader - Variable in class edu.emory.cellbio.ijbat.dm.ColumnBoundReader
 
reader - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.ReaderRecord
ReaderRecord(String, String, Class<P>, Class<E>, String[], boolean) - Constructor for class edu.emory.cellbio.ijbat.dm.DataTypeIDService.ReaderRecord
 
readTable() - Method in class edu.emory.cellbio.ijbat.io.XMLService
Nestable utility function to read one SlideSet
readXML(XMLStreamReader) - Method in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Populate these properties from an XML stream.
rebuildNow() - Method in class edu.emory.cellbio.ijbat.ui.FastUpdateImageDisplay
Trigger a call to rebuild().
red - Variable in class edu.emory.cellbio.ijbat.pi.BorderStats
 
red - Variable in class edu.emory.cellbio.ijbat.pi.RegionStats
 
reduce(Object, int) - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Get element result from an output Object which may or may not be an array or a List.
reduceClass(Class<?>) - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
If a class is an array or a List, returns the class of the array or list element.
reflect(double[], double[]) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Point a reflected about point b
reflect(double[], double[]) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Point a reflected about point b
refreshList() - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Redo the search for plugins
refreshTree() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Refresh the tree in case any changes have been made to the tables
regions - Variable in class edu.emory.cellbio.ijbat.pi.CreateMask
 
regions - Variable in class edu.emory.cellbio.ijbat.pi.FilterRegions
 
RegionStats - Class in edu.emory.cellbio.ijbat.pi
 
RegionStats() - Constructor for class edu.emory.cellbio.ijbat.pi.RegionStats
 
RegionStatsNChan - Class in edu.emory.cellbio.ijbat.pi
 
RegionStatsNChan() - Constructor for class edu.emory.cellbio.ijbat.pi.RegionStatsNChan
 
registerBrightnessContrast(BrightnessContrastRoi) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Register a Brightness/Contrast dialog
registerChildWindow(SlideSetWindow) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Keep track of a child window
registerListener(LogListener) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLog
Register a LogListener to receive messages.
releaseSlideSet(SlideSet) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Release a previously locked SlideSet for further use.
removeChild(SlideSet) - Method in class edu.emory.cellbio.ijbat.SlideSet
Remove a SlideSet as a child of this SlideSet
removeColumn(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Remove a column
removeRow(int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Remove a row
renameTable() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Rename a table
renameTable() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Rename this table
resetLog() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Get user confirmation to clear the log
resolvePath(String) - Method in class edu.emory.cellbio.ijbat.SlideSet
Resolve a possibly abstract path using this SlideSet's working directory.
Response() - Constructor for class edu.emory.cellbio.ijbat.ui.NanoHTTPd.Response
Default constructor: response = HTTP_OK, data = mime = 'null'
Response(String, String, InputStream) - Constructor for class edu.emory.cellbio.ijbat.ui.NanoHTTPd.Response
Basic constructor.
Response(String, String, String) - Constructor for class edu.emory.cellbio.ijbat.ui.NanoHTTPd.Response
Convenience method that makes an InputStream out of given text.
revertOverlays() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
With user confirmation, revert overlays to last saved version.
revertRois() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
With user confirmation, revert overlays to last saved version.
roi - Variable in class edu.emory.cellbio.ijbat.pi.BorderStats
 
roi - Variable in class edu.emory.cellbio.ijbat.pi.BorderStatsNChan
 
roi - Variable in class edu.emory.cellbio.ijbat.pi.Correlation
 
roi - Variable in class edu.emory.cellbio.ijbat.pi.Manders
 
roi - Variable in class edu.emory.cellbio.ijbat.pi.RegionStats
 
roi - Variable in class edu.emory.cellbio.ijbat.pi.RegionStatsNChan
 
ROI2 - Static variable in class edu.emory.cellbio.ijbat.dm.MIME
 
roia - Variable in class edu.emory.cellbio.ijbat.pi.ROIOverlap
 
roib - Variable in class edu.emory.cellbio.ijbat.pi.ROIOverlap
 
roiEditor - Variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
RoiEditor - Class in edu.emory.cellbio.ijbat.ui
Editor for ROI set files.
RoiEditor(SlideSet, DataTypeIDService, ImageJ, SlideSetLog) - Constructor for class edu.emory.cellbio.ijbat.ui.RoiEditor
 
RoiEditorIJ1 - Class in edu.emory.cellbio.ijbat.ui
ROI Set Editor using the ImageJ1 user interface
RoiEditorIJ1(SlideSet, DataTypeIDService, ImageJ, SlideSetLog) - Constructor for class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
ROILengths - Class in edu.emory.cellbio.ijbat.pi
 
ROILengths() - Constructor for class edu.emory.cellbio.ijbat.pi.ROILengths
 
RoiLinkException - Exception in edu.emory.cellbio.ijbat.ex
Signals a problem with a link to an ROI set.
RoiLinkException() - Constructor for exception edu.emory.cellbio.ijbat.ex.RoiLinkException
Creates a new instance of RoiLinkException without detail message.
RoiLinkException(String) - Constructor for exception edu.emory.cellbio.ijbat.ex.RoiLinkException
Constructs an instance of RoiLinkException with the specified detail message.
RoiLinkException(Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.RoiLinkException
 
RoiLinkException(String, Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.RoiLinkException
 
roiManager - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
The ROI manager
roiManager() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Get the ROI manager
roiModified(ImagePlus, int) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Automatically add ROIs to the ROI manager.
ROIOverlap - Class in edu.emory.cellbio.ijbat.pi
Count overlapping pixels in two sets of ROIs.
ROIOverlap() - Constructor for class edu.emory.cellbio.ijbat.pi.ROIOverlap
 
roiReaders - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
roiReaders - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
rois - Variable in class edu.emory.cellbio.ijbat.pi.BinRegions
 
RoisAlias - Class in edu.emory.cellbio.ijbat.dm
Alias for ij.gui.Roi[]
RoisAlias() - Constructor for class edu.emory.cellbio.ijbat.dm.RoisAlias
 
RoisetFileToAbstractOverlayReader - Class in edu.emory.cellbio.ijbat.dm.read
 
RoisetFileToAbstractOverlayReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.RoisetFileToAbstractOverlayReader
 
roiSetList - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
roiSetList - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
roiSetNames - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
Names of the ROI sets
roiSetNames - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Names of the ROI sets
roiSets - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
ROI sets AbstractOverlay[image#][Roi#]
roiSets - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
ROI sets AbstractOverlay[image#][Roi#]
RoiUtils - Class in edu.emory.cellbio.ijbat.pi
Utility functions for working with regions of interest
RoiUtils() - Constructor for class edu.emory.cellbio.ijbat.pi.RoiUtils
 
roiWriters - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
roiWriters - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
roots - Variable in class edu.emory.cellbio.ijbat.ui.HttpHelpLoader
 
roots - Variable in class edu.emory.cellbio.ijbat.ui.JarHTTPd
List of packages within which to search for resources to serve
row(SlideSet, int) - Method in class edu.emory.cellbio.ijbat.io.CSVService
 
rT - Variable in class edu.emory.cellbio.ijbat.pi.BorderStats
 
rT - Variable in class edu.emory.cellbio.ijbat.pi.RegionStats
 
run() - Method in class edu.emory.cellbio.ijbat.pi.BinRegions
 
run() - Method in class edu.emory.cellbio.ijbat.pi.BorderStats
 
run() - Method in class edu.emory.cellbio.ijbat.pi.BorderStatsNChan
 
run() - Method in class edu.emory.cellbio.ijbat.pi.Correlation
 
run() - Method in class edu.emory.cellbio.ijbat.pi.CreateMask
 
run() - Method in class edu.emory.cellbio.ijbat.pi.FilterRegions
 
run() - Method in class edu.emory.cellbio.ijbat.pi.Manders
 
run() - Method in class edu.emory.cellbio.ijbat.pi.MathAdd
 
run() - Method in class edu.emory.cellbio.ijbat.pi.MathDiv
 
run() - Method in class edu.emory.cellbio.ijbat.pi.MathMlt
 
run() - Method in class edu.emory.cellbio.ijbat.pi.MathRound
 
run() - Method in class edu.emory.cellbio.ijbat.pi.MathSub
 
run() - Method in class edu.emory.cellbio.ijbat.pi.OtsuSegmentation
 
run() - Method in class edu.emory.cellbio.ijbat.pi.RegionStats
 
run() - Method in class edu.emory.cellbio.ijbat.pi.RegionStatsNChan
 
run() - Method in class edu.emory.cellbio.ijbat.pi.ROILengths
 
run() - Method in class edu.emory.cellbio.ijbat.pi.ROIOverlap
 
run() - Method in class edu.emory.cellbio.ijbat.pi.Test
 
run() - Method in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
 
run() - Method in class edu.emory.cellbio.ijbat.pi.UnmixAbsorbance
 
run() - Method in class edu.emory.cellbio.ijbat.pi.WekaSegmentationWrapper
 
run(String) - Method in class edu.emory.cellbio.ijbat.SlideSetIJ1Entry
 
run() - Method in class edu.emory.cellbio.ijbat.SlideSetIJ2Entry
 
run() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
run() - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.HTTPSession
 
runCommandSkeleton() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Run a command skeleton
runCount - Variable in class edu.emory.cellbio.ijbat.pi.BinRegions
 
runPlugin(String, SlideSet, PluginInputPicker, PluginOutputPicker) - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Run a SlideSetPlugin
runPlugin(CommandInfo, SlideSet, PluginInputPicker, PluginOutputPicker) - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Run a SlideSetPlugin
runSkeleton(List<CommandTemplate>, List<String>, SlideSet, SlideSetPluginLoader, boolean) - Method in class edu.emory.cellbio.ijbat.io.CommandSkeletonService
Run a command skeleton on a data table.
runSspl(String) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Run a SlideSet plugin command
runSspl(CommandInfo) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Run an ImageJ Command

S

S_MAX - Static variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
S_MIN - Static variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
saveChanges - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
saveChanges - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
saveCommandSkeleton() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Export command skeleton data
saveCSV() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Export table data as a CSV file
saveLogText() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Write the log window text to a file
saveOverlays() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Save overlays drawn on the current image to memory, not to disk.
saveResults(Module, ArrayList<ModuleItem<?>>, boolean, ArrayList<ColumnBoundWriter>, ArrayList<Integer>, SlideSet, SlideSet, int) - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Save results from a command execution
saveRois() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Save ROIs from the ROI manager (to memory, not to disk).
saveTmpFile(byte[], int, int) - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.HTTPSession
Retrieves the content of a sent file and saves it to a temporary file.
saveXML(boolean) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Save a file
segs - Variable in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
 
sendError(String, String) - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.HTTPSession
Returns an error message as a HTTP response and throws InterruptedException to stop further request processing.
sendResponse(String, String, Properties, InputStream) - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.HTTPSession
Sends given response to the socket.
serve(String, String, Properties, Properties, Properties) - Method in class edu.emory.cellbio.ijbat.ui.JarHTTPd
Override of NanoHTTPd See serveJar
serve(String, String, Properties, Properties, Properties) - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Override this to customize the server.
serveFile(String, Properties, File, boolean) - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Serves file from homeDir and its' subdirectories (only).
serveJar(String, Properties) - Method in class edu.emory.cellbio.ijbat.ui.JarHTTPd
Search for a JVM resource
server - Variable in class edu.emory.cellbio.ijbat.ui.HttpHelpLoader
 
serveStream(InputStream, Properties, int, String) - Method in class edu.emory.cellbio.ijbat.ui.JarHTTPd
Serve data from a stream.
setActionListeners() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Set action listeners for the controls
setActionListeners() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Set action listeners for the controls
setBrightness(int) - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
setColumnDefaultPath(int, String) - Method in class edu.emory.cellbio.ijbat.SlideSet
Set the default relative path associated with the column.
setColumnMimeType(int, String) - Method in class edu.emory.cellbio.ijbat.SlideSet
Set the column MIME type
setColumnName(int, String) - Method in class edu.emory.cellbio.ijbat.SlideSet
Set the name of a column
setCommandClass(String) - Method in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Set the command class name
setCommandTemplate(CommandTemplate) - Method in class edu.emory.cellbio.ijbat.SlideSet
Set the command template data for this SlideSet
setContrast(int) - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
setCreationParams(LinkedHashMap) - Method in class edu.emory.cellbio.ijbat.SlideSet
Set the creation parameters of this SlideSet
setDefault() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
setDefaultLinkCount(int, int) - Method in class edu.emory.cellbio.ijbat.SlideSet
Set the counter for default links for a column.
setDefaultLinkExtension(int, String) - Method in class edu.emory.cellbio.ijbat.SlideSet
Set the default link extension for a column.
setDefaultLinkPrefix(int, String) - Method in class edu.emory.cellbio.ijbat.SlideSet
Set the prefix for default links for a column.
setFromSequence() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
Set values of selected cells using a sequence
setHelpPath(String, HelpLoader) - Method in class edu.emory.cellbio.ijbat.io.CommandSkeletonService.CommandTemplateInputPicker
 
setHelpPath(String, HelpLoader) - Method in interface edu.emory.cellbio.ijbat.pi.PluginInputPicker
Register the documentation path for this plugin.
setHelpPath(String, HelpLoader) - Method in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
 
setImage(int) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Change display to the image with the given index in the list.
setImage(int) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Open the indexed image, with wrap-around correction for out of range indeces.
setImageSet(int) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Open the currently-selected image from the indexed image set.
setInputChoices(ArrayList<Integer>, ArrayList<Object>) - Method in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Set the command input choice parameters.
setLock(boolean) - Method in class edu.emory.cellbio.ijbat.SlideSet
Set the read-only flag for this SlideSet.
setMaximum(double) - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
setMimeType(String) - Method in class edu.emory.cellbio.ijbat.dm.DataElement
Set the MIME type of this element
setMinimum(double) - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
setName(String) - Method in class edu.emory.cellbio.ijbat.SlideSet
Set the name of this SlideSet
setOutputChoices(ArrayList<Integer>, ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Method in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Set the command output choices.
setOwner(SlideSet) - Method in class edu.emory.cellbio.ijbat.dm.DataElement
Set the SlideSet table which owns this element
setParent(SlideSet) - Method in class edu.emory.cellbio.ijbat.SlideSet
Register a SlideSet as the parent of this SlideSet
setParentFieldLabels(String[]) - Method in class edu.emory.cellbio.ijbat.io.CommandSkeletonService.CommandTemplateOutputPicker
 
setParentFieldLabels(String[]) - Method in interface edu.emory.cellbio.ijbat.pi.PluginOutputPicker
Register fields from the parent table that are available for copying to the results table.
setParentFieldLabels(String[]) - Method in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
Add a popup menu to allow selection of parent fields that should be included in the results table.
setPath(SlideSet, String) - Static method in class edu.emory.cellbio.ijbat.io.Util
 
setPath(String) - Method in class edu.emory.cellbio.ijbat.pi.WekaClassifierFile
 
setPathForTree(SlideSet, String) - Static method in class edu.emory.cellbio.ijbat.io.Util
Set the working directory for a SlideSet, along with all of its relatives
setROISet(int) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Load the selected ROI set into the display.
setRoiSet(int) - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Load the indexed ROI set into the display.
setUnderlying(T) - Method in class edu.emory.cellbio.ijbat.dm.DataElement
Set this element's "underlying" value
setUnderlying(int, int, Object) - Method in class edu.emory.cellbio.ijbat.SlideSet
Change the underlying table-stored value of an item.
setUnderlyingText(String) - Method in class edu.emory.cellbio.ijbat.dm.BooleanElement
 
setUnderlyingText(String) - Method in class edu.emory.cellbio.ijbat.dm.DataElement
Set this element's "underlying" value based on a String
setUnderlyingText(String) - Method in class edu.emory.cellbio.ijbat.dm.DoubleElement
 
setUnderlyingText(String) - Method in class edu.emory.cellbio.ijbat.dm.FileLinkElement
 
setUnderlyingText(String) - Method in class edu.emory.cellbio.ijbat.dm.IntegerElement
 
setUnderlyingText(String) - Method in class edu.emory.cellbio.ijbat.dm.StringElement
 
setupFile(String, int, int, String) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
Start the SVG file
setupFile(String, int, int, String) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
Start the SVG file
setupFileLinkColumns(SlideSet, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Method in class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
Generate default path links as needed
setValueAt(Object, int, int) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLockedTableModel
 
setValueAt(Object, int, int) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetTableModel
 
setView(DatasetView) - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
setVisible(boolean) - Method in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
 
setVisible(boolean) - Method in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
Control dialog visibility.
setVisible(boolean) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
setWorkingDirectory(String) - Method in class edu.emory.cellbio.ijbat.SlideSet
Set the working directory of this SlideSet
ShortToIntWriter - Class in edu.emory.cellbio.ijbat.dm.write
 
ShortToIntWriter() - Constructor for class edu.emory.cellbio.ijbat.dm.write.ShortToIntWriter
 
show() - Method in class edu.emory.cellbio.ijbat.ui.CommandPicker
Show the command picker dialog.
showAndWait() - Method in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
Show the dialog and wait for a user response
showAndWait() - Method in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
Show the dialog and wait for a user response
showAndWait() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Run the ROI editor.
showAndWait() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Run the ROI editor.
size - Variable in class edu.emory.cellbio.ijbat.pi.BorderStats
 
size - Variable in class edu.emory.cellbio.ijbat.pi.BorderStatsNChan
 
size - Variable in class edu.emory.cellbio.ijbat.pi.RegionStats
 
size - Variable in class edu.emory.cellbio.ijbat.pi.RegionStatsNChan
 
SLIDER_MAX - Static variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
SLIDER_MIN - Static variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
SlideSet - Class in edu.emory.cellbio.ijbat
Slide Set API documentation
SlideSet(ImageJ, DataTypeIDService) - Constructor for class edu.emory.cellbio.ijbat.SlideSet
 
slideSet - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
slideSet - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
slideSet - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetTableModel
The underlying data
SlideSetException - Exception in edu.emory.cellbio.ijbat.ex
Signals a potentially recoverable SlideSet exception.
SlideSetException() - Constructor for exception edu.emory.cellbio.ijbat.ex.SlideSetException
Creates a new instance of SlideSetException without detail message.
SlideSetException(String) - Constructor for exception edu.emory.cellbio.ijbat.ex.SlideSetException
Constructs an instance of SlideSetException with the specified detail message.
SlideSetException(Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.SlideSetException
 
SlideSetException(String, Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.SlideSetException
 
SlideSetIJ1Entry - Class in edu.emory.cellbio.ijbat
Note: This plugin is probably no longer necessary, as Fiji recognizes IJ2 plugins Entry point for ImageJ1 / Fiji
SlideSetIJ1Entry() - Constructor for class edu.emory.cellbio.ijbat.SlideSetIJ1Entry
 
SlideSetIJ2Entry - Class in edu.emory.cellbio.ijbat
Entry point for ImageJ2/Fiji
SlideSetIJ2Entry() - Constructor for class edu.emory.cellbio.ijbat.SlideSetIJ2Entry
 
SlideSetLauncher - Class in edu.emory.cellbio.ijbat.ui
Main SlideSet user interface.
SlideSetLauncher(ImageJ, DataTypeIDService, XMLService, CSVService, SlideSetLog) - Constructor for class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
SlideSetLauncher.DropHandler - Class in edu.emory.cellbio.ijbat.ui
Drop handler for the main view pains
SlideSetLockedTableModel - Class in edu.emory.cellbio.ijbat.ui
An un-editable TableModel for the SlideSet class.
SlideSetLockedTableModel(SlideSet) - Constructor for class edu.emory.cellbio.ijbat.ui.SlideSetLockedTableModel
 
SlideSetLog - Class in edu.emory.cellbio.ijbat.ui
Utility for passing log messages between Slide Set components.
SlideSetLog() - Constructor for class edu.emory.cellbio.ijbat.ui.SlideSetLog
 
SlideSetPlugin - Class in edu.emory.cellbio.ijbat.pi
Slide Set commands
SlideSetPlugin() - Constructor for class edu.emory.cellbio.ijbat.pi.SlideSetPlugin
 
SlideSetPluginLoader - Class in edu.emory.cellbio.ijbat.pi
Managing command execution
SlideSetPluginLoader(ImageJ, DataTypeIDService, SlideSetLog, HelpLoader) - Constructor for class edu.emory.cellbio.ijbat.pi.SlideSetPluginLoader
 
SlideSetPropertiesViewer - Class in edu.emory.cellbio.ijbat.ui
View the properties of a SlideSet table
SlideSetPropertiesViewer(Frame, SlideSet) - Constructor for class edu.emory.cellbio.ijbat.ui.SlideSetPropertiesViewer
 
SlideSetTableModel - Class in edu.emory.cellbio.ijbat.ui
Swing TableModel for the SlideSet class.
SlideSetTableModel(SlideSet) - Constructor for class edu.emory.cellbio.ijbat.ui.SlideSetTableModel
 
SlideSetTreeRenderer - Class in edu.emory.cellbio.ijbat.ui
TreeCellRenderer that will change the display style of a locked table in the tree.
SlideSetTreeRenderer() - Constructor for class edu.emory.cellbio.ijbat.ui.SlideSetTreeRenderer
 
SlideSetViewer - Class in edu.emory.cellbio.ijbat.ui
View and edit a SlideSet
SlideSetViewer(SlideSet, ImageJ, DataTypeIDService, SlideSetLog, boolean) - Constructor for class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
SlideSetViewer(SlideSet, ImageJ, DataTypeIDService, SlideSetLog, boolean, Component) - Constructor for class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
SlideSetViewer.DropHandler - Class in edu.emory.cellbio.ijbat.ui
Drop handler for the table header
SlideSetWindow - Interface in edu.emory.cellbio.ijbat.ui
Interface for SlideSet window management functions
sspl - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
start() - Method in class edu.emory.cellbio.ijbat.ui.HttpHelpLoader
 
status - Variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.Response
HTTP status code after processing, e.g.
stop() - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Stops the server.
stream - Variable in class edu.emory.cellbio.ijbat.ui.DynamicHelpResource.GeneratedResource
Resource stream
StringElement - Class in edu.emory.cellbio.ijbat.dm
DataElement for storing text values
StringElement() - Constructor for class edu.emory.cellbio.ijbat.dm.StringElement
 
StringElement(String) - Constructor for class edu.emory.cellbio.ijbat.dm.StringElement
 
StringToStringReader - Class in edu.emory.cellbio.ijbat.dm.read
 
StringToStringReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.StringToStringReader
 
StringToStringWriter - Class in edu.emory.cellbio.ijbat.dm.write
 
StringToStringWriter() - Constructor for class edu.emory.cellbio.ijbat.dm.write.StringToStringWriter
 
stripMultipartHeaders(byte[], int) - Method in class edu.emory.cellbio.ijbat.ui.NanoHTTPd.HTTPSession
It returns the offset separating multipart file headers from the file's data.
SVG - Static variable in class edu.emory.cellbio.ijbat.dm.MIME
 
SVGFileToAbstractOverlayReader - Class in edu.emory.cellbio.ijbat.dm.read
 
SVGFileToAbstractOverlayReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
 
SVGFileToIJ1ROIReader - Class in edu.emory.cellbio.ijbat.dm.read
Read ImageJ1-style ROIs from an SVG file.
SVGFileToIJ1ROIReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
 
SVGParseException - Exception in edu.emory.cellbio.ijbat.ex
Signals an error parsing an SVG file
SVGParseException() - Constructor for exception edu.emory.cellbio.ijbat.ex.SVGParseException
 
SVGParseException(String) - Constructor for exception edu.emory.cellbio.ijbat.ex.SVGParseException
 
SVGParseException(Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.SVGParseException
 
SVGParseException(String, Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.SVGParseException
 

T

t - Static variable in class edu.emory.cellbio.ijbat.dm.read.BooleanToByteReader
 
t - Static variable in class edu.emory.cellbio.ijbat.dm.read.BooleanToShortReader
 
t1 - Variable in class edu.emory.cellbio.ijbat.pi.Manders
 
t2 - Variable in class edu.emory.cellbio.ijbat.pi.Manders
 
table - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetPropertiesViewer
 
table - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
 
template - Variable in class edu.emory.cellbio.ijbat.pi.CreateMask
 
Test - Class in edu.emory.cellbio.ijbat.pi
Test SlideSet compatible plugin
Test() - Constructor for class edu.emory.cellbio.ijbat.pi.Test
 
TestMain - Class in edu.emory.cellbio.ijbat
Test class to run IJ2
TestMain() - Constructor for class edu.emory.cellbio.ijbat.TestMain
 
textArea - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetPropertiesViewer
 
theMimeTypes - Static variable in class edu.emory.cellbio.ijbat.ui.NanoHTTPd
Hashtable mapping (String)FILENAME_EXTENSION -> (String)MIME_TYPE BN: Changed from 'private' to 'protected'
thresholds - Variable in class edu.emory.cellbio.ijbat.pi.OtsuSegmentation
 
ThresholdSegmentation - Class in edu.emory.cellbio.ijbat.pi
Segment an image into 4-neighborhood regions based on threshold values.
ThresholdSegmentation() - Constructor for class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
 
TIFF - Static variable in class edu.emory.cellbio.ijbat.dm.MIME
 
toString() - Method in class edu.emory.cellbio.ijbat.SlideSet
Get the name of this SlideSet
transformMatrix(double[], double[]) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Apply a matrix transformation.
transformMatrix(double[], double[]) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Apply a matrix transformation.
transformRotate(double[], double) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Apply a rotation about the origin
transformRotate(double[], double, double, double) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Apply a rotation about center point {cx,cy}
transformRotate(double[], double) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Apply a rotation about the origin
transformRotate(double[], double, double, double) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Apply a rotation about center point {cx,cy}
transformScale(double[], double, double) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Apply a scale
transformScale(double[], double, double) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Apply a scale
transformSkewX(double[], double) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Skew along the x-axis
transformSkewX(double[], double) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Skew along the x-axis
transformSkewY(double[], double) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Skew along the y-axis
transformSkewY(double[], double) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Skew along the y-axis
transformToDocumentSpace(double[], Node) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Transform a point ({x,y}) to document space by recursively looking for transform attributes in the given nodes and all parent nodes.
transformToDocumentSpace(double[], Node) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Transform a point ({x,y}) to document space by recursively looking for transform attributes in the given nodes and all parent nodes.
transformTranslate(double[], double, double) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Apply a translation
transformTranslate(double[], double, double) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Apply a translation
tree - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
triangleAltitude(double, double) - Static method in class edu.emory.cellbio.ijbat.pi.RoiUtils
Compute the altitude of a triangle.
ts - Variable in class edu.emory.cellbio.ijbat.pi.BorderStatsNChan
 
ts - Variable in class edu.emory.cellbio.ijbat.pi.RegionStatsNChan
 
ts - Variable in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
 
TXT - Static variable in class edu.emory.cellbio.ijbat.dm.MIME
 
TypeAlias<T> - Interface in edu.emory.cellbio.ijbat.dm
Work-around for inability to create annotation fields with array types.
typeAliasIndex - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService
Index of aliased types: <real type, alias type>
TypeAliasMetadata - Annotation Type in edu.emory.cellbio.ijbat.dm
In order to be discoverable at run-time, TypeAliases should be marked with this annotation type.
typeName - Variable in class edu.emory.cellbio.ijbat.dm.ColumnBoundReader
 
types - Variable in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
The result type combo box

U

ui - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
UIUtil - Class in edu.emory.cellbio.ijbat.ui
Utility functions related to the UI
UIUtil() - Constructor for class edu.emory.cellbio.ijbat.ui.UIUtil
 
underlying - Variable in class edu.emory.cellbio.ijbat.dm.DataElement
 
underlyingClass - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.DataElementRecord
Underlying type used by the element
undoChanges - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditor
 
undoChanges - Variable in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
 
unlockTable() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Clear a read-only flag on a DataSet table
unmix(Dataset, double[], double[]) - Method in class edu.emory.cellbio.ijbat.pi.UnmixAbsorbance
Separate an RGB image into two absorbance components.
UnmixAbsorbance - Class in edu.emory.cellbio.ijbat.pi
Separate RGB images into two absorbance components.
UnmixAbsorbance() - Constructor for class edu.emory.cellbio.ijbat.pi.UnmixAbsorbance
 
UnsupportedOverlayException - Exception in edu.emory.cellbio.ijbat.ex
Signal that an Overlay type is not supported.
UnsupportedOverlayException() - Constructor for exception edu.emory.cellbio.ijbat.ex.UnsupportedOverlayException
 
UnsupportedOverlayException(String) - Constructor for exception edu.emory.cellbio.ijbat.ex.UnsupportedOverlayException
 
UnsupportedOverlayException(Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.UnsupportedOverlayException
 
UnsupportedOverlayException(String, Throwable) - Constructor for exception edu.emory.cellbio.ijbat.ex.UnsupportedOverlayException
 
updateControls() - Method in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
 
updateControls() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Update the state of the controls Do NOT call from the event dispatch thread.
updateControls() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Update the state of the controls
updateControlState(int) - Method in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
updateControlStates() - Method in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
 
updateDisplay() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
Updates the displayed min/max range to match min and max values.
Util - Class in edu.emory.cellbio.ijbat.io
Utility methods related to IO
Util() - Constructor for class edu.emory.cellbio.ijbat.io.Util
 

V

v - Variable in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
 
vectorAdd(double[], double[]) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Vectorized add function
vectorAdd(double[], double[]) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Vectorized add function
vectorEquals(long[], long[]) - Method in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
 
vectorNegate(double[]) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
Multiply a vector by -I
vectorNegate(double[]) - Method in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
Multiply a vector by -I
ver - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Application version
view - Variable in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
 
viewChanged() - Method in class edu.emory.cellbio.ijbat.ui.BrightnessContrastRoi
Called when view changes.
viewRois(int) - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
Launch the RoiEditor
viewTable() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
View a SlideSet
viewTableProperties() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
View table properties
viewTableProperties() - Method in class edu.emory.cellbio.ijbat.ui.SlideSetViewer
View this table's properties
vTemp - Variable in class edu.emory.cellbio.ijbat.pi.ThresholdSegmentation
 

W

w - Variable in class edu.emory.cellbio.ijbat.pi.BorderStats
 
w - Variable in class edu.emory.cellbio.ijbat.pi.BorderStatsNChan
 
w - Variable in class edu.emory.cellbio.ijbat.pi.Manders
 
warningMessage - Variable in class edu.emory.cellbio.ijbat.dm.read.SVGFileToAbstractOverlayReader
 
warningMessage - Variable in class edu.emory.cellbio.ijbat.dm.read.SVGFileToIJ1ROIReader
 
wasCanceled() - Method in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
Did the user press Cancel?
wasOKd() - Method in class edu.emory.cellbio.ijbat.ui.CommandPicker
 
wasOKed() - Method in class edu.emory.cellbio.ijbat.ui.PluginInputMatcherFrame
Did the user press OK?
wasOKed() - Method in class edu.emory.cellbio.ijbat.ui.PluginOutputMatcherFrame
Did the user press OK?
WEKA - Static variable in class edu.emory.cellbio.ijbat.dm.MIME
 
WekaClassifierFile - Class in edu.emory.cellbio.ijbat.pi
 
WekaClassifierFile(String) - Constructor for class edu.emory.cellbio.ijbat.pi.WekaClassifierFile
 
WekaClassifierReader - Class in edu.emory.cellbio.ijbat.dm.read
 
WekaClassifierReader() - Constructor for class edu.emory.cellbio.ijbat.dm.read.WekaClassifierReader
 
WekaSegmentationWrapper - Class in edu.emory.cellbio.ijbat.pi
Wrapper to access the Trainable Weka Segmentation plugin
WekaSegmentationWrapper() - Constructor for class edu.emory.cellbio.ijbat.pi.WekaSegmentationWrapper
 
wildcards - Variable in class edu.emory.cellbio.ijbat.ui.HttpHelpLoader.AboutPage
 
write(P, int) - Method in class edu.emory.cellbio.ijbat.dm.ColumnBoundWriter
Write data to the table
write(AbstractOverlay[], FileLinkElement) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToRoisetFileWriter
 
write(AbstractOverlay[], FileLinkElement) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
 
write(AbstractOverlay[], String) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
 
write(AbstractOverlay[], String, int, int) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
 
write(AbstractOverlay[], String, int, int, String) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
 
write(Boolean, BooleanElement) - Method in class edu.emory.cellbio.ijbat.dm.write.BooleanToBooleanWriter
 
write(Byte, IntegerElement) - Method in class edu.emory.cellbio.ijbat.dm.write.ByteToIntWriter
 
write(Dataset, FileLinkElement) - Method in class edu.emory.cellbio.ijbat.dm.write.DatasetToImageFileWriter
 
write(Double, DoubleElement) - Method in class edu.emory.cellbio.ijbat.dm.write.DoubleToDoubleWriter
 
write(P, E) - Method in interface edu.emory.cellbio.ijbat.dm.write.ElementWriter
Convert "processed" data to "underlying" data.
write(Float, DoubleElement) - Method in class edu.emory.cellbio.ijbat.dm.write.FloatToDoubleWriter
 
write(Roi[], FileLinkElement) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
 
write(Roi[], String) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
 
write(Roi[], String, int, int) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
 
write(Roi[], String, int, int, String) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
 
write(ImageDisplay, FileLinkElement) - Method in class edu.emory.cellbio.ijbat.dm.write.ImageDisplayToImageFileWriter
 
write(Integer, IntegerElement) - Method in class edu.emory.cellbio.ijbat.dm.write.IntToIntWriter
 
write(Long, IntegerElement) - Method in class edu.emory.cellbio.ijbat.dm.write.LongToIntWriter
 
write(Short, IntegerElement) - Method in class edu.emory.cellbio.ijbat.dm.write.ShortToIntWriter
 
write(String, StringElement) - Method in class edu.emory.cellbio.ijbat.dm.write.StringToStringWriter
 
write(ArrayDeque<CommandTemplate>, List<String>, File) - Method in class edu.emory.cellbio.ijbat.io.CommandSkeletonService
Write a command skeleton to an XML file.
write(SlideSet, File) - Method in class edu.emory.cellbio.ijbat.io.CommandSkeletonService
Write a command skeleton to an XML file.
write(SlideSet, File) - Method in class edu.emory.cellbio.ijbat.io.CSVService
Write a SlideSet to a CSV file
write(SlideSet, File, boolean) - Method in class edu.emory.cellbio.ijbat.io.CSVService
 
write(SlideSet, File) - Method in class edu.emory.cellbio.ijbat.io.XMLService
Write SlideSet data to an XML file.
writeEllipseOverlay(XMLStreamWriter, EllipseOverlay) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
Write an ellipse overlay
writeFile(String, AbstractOverlay[], int, int, String) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
Write the SVG file to path
writeFile(String, Roi[], int, int, String) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
Write the SVG file to path
writeGeneralPathOverlay(XMLStreamWriter, GeneralPathOverlay) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
Write a general path overlay
writeLine(XMLStreamWriter, Line) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
Write a Line ROI
writeLineOverlay(XMLStreamWriter, LineOverlay) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
Write a line overlay
writeOvalRoi(XMLStreamWriter, OvalRoi) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
Write an OvalRoi
writeOverlay(XMLStreamWriter, AbstractOverlay) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
Write an overlay, if supported
writeOverlay(XMLStreamWriter, Roi) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
Write an overlay, if supported
writeOverlays() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditor
Save all overlays to disk
writePointOverlay(XMLStreamWriter, PointOverlay) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
Write a point overlay.
writePointRoi(XMLStreamWriter, PointRoi) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
Write a PointRoi
writePolygonOverlay(XMLStreamWriter, PolygonOverlay) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
Write a polygon overlay
writePolygonRoi(XMLStreamWriter, PolygonRoi) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
Write a PolygonRoi
writer - Variable in class edu.emory.cellbio.ijbat.dm.ColumnBoundWriter
 
writer - Variable in class edu.emory.cellbio.ijbat.dm.DataTypeIDService.WriterRecord
writeRectangle(XMLStreamWriter, Roi) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
Write a rectangular Roi
writeRectangleOverlay(XMLStreamWriter, RectangleOverlay) - Method in class edu.emory.cellbio.ijbat.dm.write.AbstractOverlaysToSVGFileWriter
Write a rectangle overlay
writeRois() - Method in class edu.emory.cellbio.ijbat.ui.RoiEditorIJ1
Save all the ROIs to disk.
writeRoiSetFile(Roi[], File) - Static method in class edu.emory.cellbio.ijbat.io.Util
Utility function to write an ROI set file.
WriterRecord(String, String, Class<P>, Class<E>, String, String) - Constructor for class edu.emory.cellbio.ijbat.dm.DataTypeIDService.WriterRecord
 
writeShapeRoi(XMLStreamWriter, ShapeRoi) - Method in class edu.emory.cellbio.ijbat.dm.write.IJ1ROIsToSVGFileWriter
Write a ShapeRoi
writeTable(SlideSet, int) - Method in class edu.emory.cellbio.ijbat.io.XMLService
Nestable utility function to write one SlideSet
writeXML(XMLStreamWriter, String) - Method in class edu.emory.cellbio.ijbat.dm.CommandTemplate
Write these properties to an XML stream.

X

XML - Static variable in class edu.emory.cellbio.ijbat.dm.MIME
 
xmls - Variable in class edu.emory.cellbio.ijbat.ui.SlideSetLauncher
 
XMLService - Class in edu.emory.cellbio.ijbat.io
Writes SlideSet data as an XML file and generates a SlideSet from saved XML data.
XMLService(ImageJ, DataTypeIDService) - Constructor for class edu.emory.cellbio.ijbat.io.XMLService
 
xsr - Variable in class edu.emory.cellbio.ijbat.io.CommandSkeletonService
 
xsr - Variable in class edu.emory.cellbio.ijbat.io.XMLService
 
xsw - Variable in class edu.emory.cellbio.ijbat.io.CommandSkeletonService
 
xsw - Variable in class edu.emory.cellbio.ijbat.io.XMLService
 

Z

ZIP - Static variable in class edu.emory.cellbio.ijbat.dm.MIME
 
A B C D E F G H I J K L M N O P R S T U V W X Z 
Skip navigation links

Copyright © 2019. All rights reserved.