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A

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

B

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

C

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

D

d2s(double) - Method in class org.nanes.slideset.pi.SilentSlicer
 
d2s(double) - Method in class org.nanes.slideset.pi.SilentSlicer
 
data - Variable in class org.nanes.slideset.dm.ColumnBoundReader
 
data - Variable in class org.nanes.slideset.dm.ColumnBoundReader
 
data - Variable in class org.nanes.slideset.dm.ColumnBoundWriter
 
data - Variable in class org.nanes.slideset.dm.ColumnBoundWriter
 
data - Variable in class org.nanes.slideset.ui.NanoHTTPd.Response
Data of the response, may be null.
data - Variable in class org.nanes.slideset.ui.NanoHTTPd.Response
Data of the response, may be null.
data - Variable in class org.nanes.slideset.ui.PluginInputMatcherFrame
 
data - Variable in class org.nanes.slideset.ui.PluginInputMatcherFrame
 
data - Variable in class org.nanes.slideset.ui.SlideSetViewer
 
data - Variable in class org.nanes.slideset.ui.SlideSetViewer
 
DataElement<T> - Class in org.nanes.slideset.dm
Basic element of data stored in SlideSet tables.
DataElement<T> - Class in org.nanes.slideset.dm
Basic element of data stored in SlideSet tables.
DataElement(T) - Constructor for class org.nanes.slideset.dm.DataElement
 
DataElement(T) - Constructor for class org.nanes.slideset.dm.DataElement
 
dataElement - Variable in class org.nanes.slideset.dm.DataTypeIDService.DataElementRecord
dataElement - Variable in class org.nanes.slideset.dm.DataTypeIDService.DataElementRecord
dataElementIndex - Variable in class org.nanes.slideset.dm.DataTypeIDService
Index of available DataElement types
dataElementIndex - Variable in class org.nanes.slideset.dm.DataTypeIDService
Index of available DataElement types
DataElementMetadata - Annotation Type in org.nanes.slideset.dm
Annotation type containing metadata for DataElement classes.
DataElementMetadata - Annotation Type in org.nanes.slideset.dm
Annotation type containing metadata for DataElement classes.
DataElementRecord(Class<? extends DataElement<T>>, String, Class<T>, boolean) - Constructor for class org.nanes.slideset.dm.DataTypeIDService.DataElementRecord
 
DataElementRecord(Class<? extends DataElement<T>>, String, Class<T>, boolean) - Constructor for class org.nanes.slideset.dm.DataTypeIDService.DataElementRecord
 
dataMax - Variable in class org.nanes.slideset.ui.BrightnessContrastRoi
The minimum and maximum values of the data itself.
dataMax - Variable in class org.nanes.slideset.ui.BrightnessContrastRoi
The minimum and maximum values of the data itself.
dataMin - Variable in class org.nanes.slideset.ui.BrightnessContrastRoi
The minimum and maximum values of the data itself.
dataMin - Variable in class org.nanes.slideset.ui.BrightnessContrastRoi
The minimum and maximum values of the data itself.
DatasetToImageFileWriter - Class in org.nanes.slideset.dm.write
 
DatasetToImageFileWriter - Class in org.nanes.slideset.dm.write
 
DatasetToImageFileWriter() - Constructor for class org.nanes.slideset.dm.write.DatasetToImageFileWriter
 
DatasetToImageFileWriter() - Constructor for class org.nanes.slideset.dm.write.DatasetToImageFileWriter
 
DatasetToPngFileWriter - Class in org.nanes.slideset.dm.write
 
DatasetToPngFileWriter - Class in org.nanes.slideset.dm.write
 
DatasetToPngFileWriter() - Constructor for class org.nanes.slideset.dm.write.DatasetToPngFileWriter
 
DatasetToPngFileWriter() - Constructor for class org.nanes.slideset.dm.write.DatasetToPngFileWriter
 
DataTypeIDService - Class in org.nanes.slideset.dm
Linking Slide Set tables to commands
DataTypeIDService - Class in org.nanes.slideset.dm
Linking Slide Set tables to commands
DataTypeIDService(ImageJ) - Constructor for class org.nanes.slideset.dm.DataTypeIDService
 
DataTypeIDService(ImageJ) - Constructor for class org.nanes.slideset.dm.DataTypeIDService
 
DataTypeIDService.DataElementRecord<T> - Class in org.nanes.slideset.dm
 
DataTypeIDService.DataElementRecord<T> - Class in org.nanes.slideset.dm
 
DataTypeIDService.ReaderRecord<E extends DataElement,P> - Class in org.nanes.slideset.dm
 
DataTypeIDService.ReaderRecord<E extends DataElement,P> - Class in org.nanes.slideset.dm
 
DataTypeIDService.WriterRecord<E extends DataElement,P> - Class in org.nanes.slideset.dm
 
DataTypeIDService.WriterRecord<E extends DataElement,P> - Class in org.nanes.slideset.dm
 
decodeHeader(BufferedReader, Properties, Properties, Properties) - Method in class org.nanes.slideset.ui.NanoHTTPd.HTTPSession
Decodes the sent headers and loads the data into java Properties' key - value pairs
decodeHeader(BufferedReader, Properties, Properties, Properties) - Method in class org.nanes.slideset.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 org.nanes.slideset.ui.NanoHTTPd.HTTPSession
Decodes the Multipart Body data and put it into java Properties' key - value pairs.
decodeMultipartData(String, byte[], BufferedReader, Properties, Properties) - Method in class org.nanes.slideset.ui.NanoHTTPd.HTTPSession
Decodes the Multipart Body data and put it into java Properties' key - value pairs.
decodeParms(String, Properties) - Method in class org.nanes.slideset.ui.NanoHTTPd.HTTPSession
Decodes parameters in percent-encoded URI-format ( e.g.
decodeParms(String, Properties) - Method in class org.nanes.slideset.ui.NanoHTTPd.HTTPSession
Decodes parameters in percent-encoded URI-format ( e.g.
decodePercent(String) - Method in class org.nanes.slideset.ui.NanoHTTPd.HTTPSession
Decodes the percent encoding scheme.
decodePercent(String) - Method in class org.nanes.slideset.ui.NanoHTTPd.HTTPSession
Decodes the percent encoding scheme.
defaultButton - Variable in class org.nanes.slideset.ui.BrightnessContrastRoi
 
defaultButton - Variable in class org.nanes.slideset.ui.BrightnessContrastRoi
 
DefaultPathNotSetException - Exception in org.nanes.slideset.ex
Indicates that a new link cannot be generated because the default link path is not set in the column properties
DefaultPathNotSetException - Exception in org.nanes.slideset.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 org.nanes.slideset.ex.DefaultPathNotSetException
Creates a new instance of DefaultPathNotSetException without detail message.
DefaultPathNotSetException(String) - Constructor for exception org.nanes.slideset.ex.DefaultPathNotSetException
Constructs an instance of DefaultPathNotSetException with the specified detail message.
DefaultPathNotSetException(Throwable) - Constructor for exception org.nanes.slideset.ex.DefaultPathNotSetException
 
DefaultPathNotSetException(String, Throwable) - Constructor for exception org.nanes.slideset.ex.DefaultPathNotSetException
 
DefaultPathNotSetException() - Constructor for exception org.nanes.slideset.ex.DefaultPathNotSetException
Creates a new instance of DefaultPathNotSetException without detail message.
DefaultPathNotSetException(String) - Constructor for exception org.nanes.slideset.ex.DefaultPathNotSetException
Constructs an instance of DefaultPathNotSetException with the specified detail message.
DefaultPathNotSetException(Throwable) - Constructor for exception org.nanes.slideset.ex.DefaultPathNotSetException
 
DefaultPathNotSetException(String, Throwable) - Constructor for exception org.nanes.slideset.ex.DefaultPathNotSetException
 
deleteTable() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Delete a table
deleteTable() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Delete a table
dialogReturnValue - Variable in class org.nanes.slideset.ui.CommandPicker
 
dialogReturnValue - Variable in class org.nanes.slideset.ui.CommandPicker
 
difw - Variable in class org.nanes.slideset.dm.write.ImageDisplayToImageFileWriter
 
difw - Variable in class org.nanes.slideset.dm.write.ImageDisplayToImageFileWriter
 
dil - Variable in class org.nanes.slideset.pi.CountIntersections
 
dil - Variable in class org.nanes.slideset.pi.CountIntersections
 
dir - Variable in class org.nanes.slideset.SlideSet
Working directory of this SlideSet
dir - Variable in class org.nanes.slideset.SlideSet
Working directory of this SlideSet
dir - Variable in class org.nanes.slideset.ui.PluginOutputMatcherFrame
The default link directory field
dir - Variable in class org.nanes.slideset.ui.PluginOutputMatcherFrame
The default link directory field
displayMode - Variable in class org.nanes.slideset.ui.RoiEditor
 
displayMode - Variable in class org.nanes.slideset.ui.RoiEditor
 
displayMode - Variable in class org.nanes.slideset.ui.RoiEditorIJ1
 
displayMode - Variable in class org.nanes.slideset.ui.RoiEditorIJ1
 
distance(double[], double[]) - Static method in class org.nanes.slideset.pi.RoiUtils
Compute the linear distance between two points.
distance(double[], double[]) - Static method in class org.nanes.slideset.pi.RoiUtils
Compute the linear distance between two points.
distanceFromLine(double[], double[], double[]) - Static method in class org.nanes.slideset.pi.RoiUtils
Compute the distance of point P from the line defined by points A and B.
distanceFromLine(double[], double[], double[]) - Static method in class org.nanes.slideset.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 org.nanes.slideset.pi.RoiUtils
Compute the distance of point P from the line segment bounded by points A and B.
distanceFromSegment(double[], double[], double[]) - Static method in class org.nanes.slideset.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 org.nanes.slideset.pi.RoiUtils
Compute the squared linear distance between two points.
distanceSquared(double[], double[]) - Static method in class org.nanes.slideset.pi.RoiUtils
Compute the squared linear distance between two points.
distSquared(double[], double[]) - Static method in class org.nanes.slideset.pi.ROILengths
 
distSquared(double[], double[]) - Static method in class org.nanes.slideset.pi.ROILengths
 
doComponentLayout() - Method in class org.nanes.slideset.ui.PluginInputMatcherFrame
Finalize the dialog before display
doComponentLayout() - Method in class org.nanes.slideset.ui.PluginInputMatcherFrame
Finalize the dialog before display
doIrregularSetup(Roi) - Method in class org.nanes.slideset.pi.SilentSlicer
 
doIrregularSetup(Roi) - Method in class org.nanes.slideset.pi.SilentSlicer
 
DoubleElement - Class in org.nanes.slideset.dm
DataElement for storing numeric values
DoubleElement - Class in org.nanes.slideset.dm
DataElement for storing numeric values
DoubleElement() - Constructor for class org.nanes.slideset.dm.DoubleElement
 
DoubleElement(Double) - Constructor for class org.nanes.slideset.dm.DoubleElement
 
DoubleElement() - Constructor for class org.nanes.slideset.dm.DoubleElement
 
DoubleElement(Double) - Constructor for class org.nanes.slideset.dm.DoubleElement
 
DoubleToDoubleReader - Class in org.nanes.slideset.dm.read
 
DoubleToDoubleReader - Class in org.nanes.slideset.dm.read
 
DoubleToDoubleReader() - Constructor for class org.nanes.slideset.dm.read.DoubleToDoubleReader
 
DoubleToDoubleReader() - Constructor for class org.nanes.slideset.dm.read.DoubleToDoubleReader
 
DoubleToDoubleWriter - Class in org.nanes.slideset.dm.write
 
DoubleToDoubleWriter - Class in org.nanes.slideset.dm.write
 
DoubleToDoubleWriter() - Constructor for class org.nanes.slideset.dm.write.DoubleToDoubleWriter
 
DoubleToDoubleWriter() - Constructor for class org.nanes.slideset.dm.write.DoubleToDoubleWriter
 
DoubleToFloatReader - Class in org.nanes.slideset.dm.read
 
DoubleToFloatReader - Class in org.nanes.slideset.dm.read
 
DoubleToFloatReader() - Constructor for class org.nanes.slideset.dm.read.DoubleToFloatReader
 
DoubleToFloatReader() - Constructor for class org.nanes.slideset.dm.read.DoubleToFloatReader
 
drawLine(double, double, double, double, ImagePlus) - Method in class org.nanes.slideset.pi.SilentSlicer
 
drawLine(double, double, double, double, ImagePlus) - Method in class org.nanes.slideset.pi.SilentSlicer
 
drawOverlays() - Method in class org.nanes.slideset.ui.RoiEditor
Draw appropriate overlays on the image
drawOverlays() - Method in class org.nanes.slideset.ui.RoiEditor
Draw appropriate overlays on the image
drawRois() - Method in class org.nanes.slideset.ui.RoiEditorIJ1
Draw ROIs on the image.
drawRois() - Method in class org.nanes.slideset.ui.RoiEditorIJ1
Draw ROIs on the image.
DropHandler(SlideSetLauncher) - Constructor for class org.nanes.slideset.ui.SlideSetLauncher.DropHandler
 
DropHandler(SlideSetLauncher) - Constructor for class org.nanes.slideset.ui.SlideSetLauncher.DropHandler
 
DropHandler() - Constructor for class org.nanes.slideset.ui.SlideSetViewer.DropHandler
 
DropHandler() - Constructor for class org.nanes.slideset.ui.SlideSetViewer.DropHandler
 
ds - Variable in class org.nanes.slideset.pi.BorderStats
 
ds - Variable in class org.nanes.slideset.pi.BorderStats
 
ds - Variable in class org.nanes.slideset.pi.BorderStatsNChan
 
ds - Variable in class org.nanes.slideset.pi.BorderStatsNChan
 
ds - Variable in class org.nanes.slideset.pi.Correlation
 
ds - Variable in class org.nanes.slideset.pi.Correlation
 
ds - Variable in class org.nanes.slideset.pi.Manders
 
ds - Variable in class org.nanes.slideset.pi.Manders
 
ds - Variable in class org.nanes.slideset.pi.OtsuSegmentation
 
ds - Variable in class org.nanes.slideset.pi.OtsuSegmentation
 
ds - Variable in class org.nanes.slideset.pi.RegionStats
 
ds - Variable in class org.nanes.slideset.pi.RegionStats
 
ds - Variable in class org.nanes.slideset.pi.RegionStatsNChan
 
ds - Variable in class org.nanes.slideset.pi.RegionStatsNChan
 
ds - Variable in class org.nanes.slideset.pi.RegionStatsNChanExclusion
 
ds - Variable in class org.nanes.slideset.pi.RegionStatsNChanExclusion
 
ds - Variable in class org.nanes.slideset.pi.ThresholdSegmentation
 
ds - Variable in class org.nanes.slideset.pi.ThresholdSegmentation
 
ds - Variable in class org.nanes.slideset.pi.UnmixAbsorbance
 
ds - Variable in class org.nanes.slideset.pi.UnmixAbsorbance
 
dtid - Variable in class org.nanes.slideset.io.XMLService
 
dtid - Variable in class org.nanes.slideset.io.XMLService
 
dtid - Variable in class org.nanes.slideset.pi.SlideSetPluginLoader
 
dtid - Variable in class org.nanes.slideset.pi.SlideSetPluginLoader
 
dtid - Variable in class org.nanes.slideset.SlideSet
DataTypeIDService reference
dtid - Variable in class org.nanes.slideset.SlideSet
DataTypeIDService reference
dtid - Variable in class org.nanes.slideset.ui.PluginInputMatcherFrame
 
dtid - Variable in class org.nanes.slideset.ui.PluginInputMatcherFrame
 
dtid - Variable in class org.nanes.slideset.ui.PluginOutputMatcherFrame
 
dtid - Variable in class org.nanes.slideset.ui.PluginOutputMatcherFrame
 
dtid - Variable in class org.nanes.slideset.ui.RoiEditor
 
dtid - Variable in class org.nanes.slideset.ui.RoiEditor
 
dtid - Variable in class org.nanes.slideset.ui.RoiEditorIJ1
 
dtid - Variable in class org.nanes.slideset.ui.RoiEditorIJ1
 
dtid - Variable in class org.nanes.slideset.ui.SlideSetLauncher
 
dtid - Variable in class org.nanes.slideset.ui.SlideSetLauncher
 
dtid - Variable in class org.nanes.slideset.ui.SlideSetViewer
 
dtid - Variable in class org.nanes.slideset.ui.SlideSetViewer
 
dtids - Variable in class org.nanes.slideset.script.SlideSetScript
 
dtids - Variable in class org.nanes.slideset.script.SlideSetScript
 
dx - Variable in class org.nanes.slideset.pi.SilentSlicer
 
dx - Variable in class org.nanes.slideset.pi.SilentSlicer
 
dy - Variable in class org.nanes.slideset.pi.SilentSlicer
 
dy - Variable in class org.nanes.slideset.pi.SilentSlicer
 
DynamicHelpResource - Class in org.nanes.slideset.ui
Dynamically generated resource for the by the documentation server.
DynamicHelpResource - Class in org.nanes.slideset.ui
Dynamically generated resource for the by the documentation server.
DynamicHelpResource() - Constructor for class org.nanes.slideset.ui.DynamicHelpResource
 
DynamicHelpResource() - Constructor for class org.nanes.slideset.ui.DynamicHelpResource
 
DynamicHelpResource.GeneratedResource - Class in org.nanes.slideset.ui
Generated dynamic resource
DynamicHelpResource.GeneratedResource - Class in org.nanes.slideset.ui
Generated dynamic resource
dynamicPages - Variable in class org.nanes.slideset.ui.JarHTTPd
Mapping of dynamically generated resources, indexed by relative URI
dynamicPages - Variable in class org.nanes.slideset.ui.JarHTTPd
Mapping of dynamically generated resources, indexed by relative URI

E

ElementReader<E extends DataElement,P> - Interface in org.nanes.slideset.dm.read
Converts DataElement "underlying" data to the "processed" data required for command inputs.
ElementReader<E extends DataElement,P> - Interface in org.nanes.slideset.dm.read
Converts DataElement "underlying" data to the "processed" data required for command inputs.
elementReaderIndex - Variable in class org.nanes.slideset.dm.DataTypeIDService
Index of available ElementReaders
elementReaderIndex - Variable in class org.nanes.slideset.dm.DataTypeIDService
Index of available ElementReaders
ElementReaderMetadata - Annotation Type in org.nanes.slideset.dm.read
Metadata for indexing ElementReaders.
ElementReaderMetadata - Annotation Type in org.nanes.slideset.dm.read
Metadata for indexing ElementReaders.
elementType - Variable in class org.nanes.slideset.dm.DataTypeIDService.ReaderRecord
DataElement type read by this reader
elementType - Variable in class org.nanes.slideset.dm.DataTypeIDService.ReaderRecord
DataElement type read by this reader
elementType - Variable in class org.nanes.slideset.dm.DataTypeIDService.WriterRecord
DataElement type written by this writer
elementType - Variable in class org.nanes.slideset.dm.DataTypeIDService.WriterRecord
DataElement type written by this writer
ElementWriter<E extends DataElement,P> - Interface in org.nanes.slideset.dm.write
Converts "processed" data from command output parameters to "underlying" data that can be stored in a DataElement.
ElementWriter<E extends DataElement,P> - Interface in org.nanes.slideset.dm.write
Converts "processed" data from command output parameters to "underlying" data that can be stored in a DataElement.
elementWriterIndex - Variable in class org.nanes.slideset.dm.DataTypeIDService
Index of available ElementWriters
elementWriterIndex - Variable in class org.nanes.slideset.dm.DataTypeIDService
Index of available ElementWriters
ElementWriterMetadata - Annotation Type in org.nanes.slideset.dm.write
Metadata for indexing ElementWriters.
ElementWriterMetadata - Annotation Type in org.nanes.slideset.dm.write
Metadata for indexing ElementWriters.
encodeUri(String) - Method in class org.nanes.slideset.ui.NanoHTTPd
URL-encodes everything between "/"-characters.
encodeUri(String) - Method in class org.nanes.slideset.ui.NanoHTTPd
URL-encodes everything between "/"-characters.
errorMessages - Variable in class org.nanes.slideset.dm.write.AbstractOverlaysToSVGFileWriter
 
errorMessages - Variable in class org.nanes.slideset.dm.write.AbstractOverlaysToSVGFileWriter
 
errorMessages - Variable in class org.nanes.slideset.dm.write.IJ1ROIsToSVGFileWriter
 
errorMessages - Variable in class org.nanes.slideset.dm.write.IJ1ROIsToSVGFileWriter
 
exclEdges - Variable in class org.nanes.slideset.pi.FindMaxima
 
exclEdges - Variable in class org.nanes.slideset.pi.FindMaxima
 
expandAllTreeNodes() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Make sure that all tree nodes are expanded
expandAllTreeNodes() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Make sure that all tree nodes are expanded
exportSVG - Variable in class org.nanes.slideset.ui.RoiEditor
 
exportSVG() - Method in class org.nanes.slideset.ui.RoiEditor
 
exportSVG - Variable in class org.nanes.slideset.ui.RoiEditor
 
exportSVG() - Method in class org.nanes.slideset.ui.RoiEditor
 
exportSVG - Variable in class org.nanes.slideset.ui.RoiEditorIJ1
 
exportSVG() - Method in class org.nanes.slideset.ui.RoiEditorIJ1
Export and SVG file with the current image and ROIs.
exportSVG - Variable in class org.nanes.slideset.ui.RoiEditorIJ1
 
exportSVG() - Method in class org.nanes.slideset.ui.RoiEditorIJ1
Export and SVG file with the current image and ROIs.
ext - Variable in class org.nanes.slideset.ui.PluginOutputMatcherFrame
The default link extension field
ext - Variable in class org.nanes.slideset.ui.PluginOutputMatcherFrame
The default link extension field

F

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

G

gap - Static variable in class org.nanes.slideset.ui.PluginInputMatcherFrame
Padding
gap - Static variable in class org.nanes.slideset.ui.PluginInputMatcherFrame
Padding
gap - Variable in class org.nanes.slideset.ui.PluginOutputMatcherFrame
Padding
gap - Variable in class org.nanes.slideset.ui.PluginOutputMatcherFrame
Padding
generateDefaultLinkPath(int, int) - Method in class org.nanes.slideset.SlideSet
Generate a default link path for a specified cell.
generateDefaultLinkPath(int, int) - Method in class org.nanes.slideset.SlideSet
Generate a default link path for a specified cell.
GeneratedResource(InputStream, int, String) - Constructor for class org.nanes.slideset.ui.DynamicHelpResource.GeneratedResource
 
GeneratedResource(InputStream, int, String) - Constructor for class org.nanes.slideset.ui.DynamicHelpResource.GeneratedResource
 
generateResource(String) - Method in class org.nanes.slideset.ui.DynamicHelpResource
Generate the dynamic resource
generateResource(String) - Method in class org.nanes.slideset.ui.DynamicHelpResource
Generate the dynamic resource
generateResource(String) - Method in class org.nanes.slideset.ui.HttpHelpLoader.AboutPage
 
generateResource(String) - Method in class org.nanes.slideset.ui.HttpHelpLoader.AboutPage
 
getAvailableMemory() - Method in class org.nanes.slideset.pi.SilentSlicer
 
getAvailableMemory() - Method in class org.nanes.slideset.pi.SilentSlicer
 
getBoundaryPositions(byte[], byte[]) - Method in class org.nanes.slideset.ui.NanoHTTPd.HTTPSession
Find the byte positions where multipart boundaries start.
getBoundaryPositions(byte[], byte[]) - Method in class org.nanes.slideset.ui.NanoHTTPd.HTTPSession
Find the byte positions where multipart boundaries start.
getBrightness() - Method in class org.nanes.slideset.ui.BrightnessContrastRoi
 
getBrightness() - Method in class org.nanes.slideset.ui.BrightnessContrastRoi
 
getChildren() - Method in class org.nanes.slideset.SlideSet
Get a list of this SlideSet's children
getChildren() - Method in class org.nanes.slideset.SlideSet
Get a list of this SlideSet's children
getColumnClass(int) - Method in class org.nanes.slideset.ui.SlideSetTableModel
 
getColumnClass(int) - Method in class org.nanes.slideset.ui.SlideSetTableModel
 
getColumnCount() - Method in class org.nanes.slideset.ui.SlideSetTableModel
 
getColumnCount() - Method in class org.nanes.slideset.ui.SlideSetTableModel
 
getColumnDefaultPath(int) - Method in class org.nanes.slideset.SlideSet
Get the default relative path associated with the column.
getColumnDefaultPath(int) - Method in class org.nanes.slideset.SlideSet
Get the default relative path associated with the column.
getColumnElementClass(int) - Method in class org.nanes.slideset.SlideSet
 
getColumnElementClass(int) - Method in class org.nanes.slideset.SlideSet
 
getColumnElementType(int) - Method in class org.nanes.slideset.SlideSet
Get the DataElement type used in a column.
getColumnElementType(int) - Method in class org.nanes.slideset.SlideSet
Get the DataElement type used in a column.
getColumnFromHeaderEvent(ActionEvent) - Method in class org.nanes.slideset.ui.SlideSetViewer
Find out which column header triggered a popup menu
getColumnFromHeaderEvent(ActionEvent) - Method in class org.nanes.slideset.ui.SlideSetViewer
Find out which column header triggered a popup menu
getColumnIndex(String) - Method in class org.nanes.slideset.SlideSet
Get the index of the first column with a matching name, or -1 if no such column
getColumnIndex(String) - Method in class org.nanes.slideset.SlideSet
Get the index of the first column with a matching name, or -1 if no such column
getColumnMimeType(int) - Method in class org.nanes.slideset.SlideSet
Get the column MIME type
getColumnMimeType(int) - Method in class org.nanes.slideset.SlideSet
Get the column MIME type
getColumnName() - Method in class org.nanes.slideset.dm.ColumnBoundReader
Get the human-readable label for the column
getColumnName() - Method in class org.nanes.slideset.dm.ColumnBoundReader
Get the human-readable label for the column
getColumnName(int) - Method in class org.nanes.slideset.SlideSet
Get the name of a column
getColumnName(int) - Method in class org.nanes.slideset.SlideSet
Get the name of a column
getColumnName(int) - Method in class org.nanes.slideset.ui.SlideSetTableModel
 
getColumnName(int) - Method in class org.nanes.slideset.ui.SlideSetTableModel
 
getColumnNum() - Method in class org.nanes.slideset.dm.ColumnBoundReader
Get the column index
getColumnNum() - Method in class org.nanes.slideset.dm.ColumnBoundReader
Get the column index
getColumnNum() - Method in class org.nanes.slideset.dm.ColumnBoundWriter
Get the column index
getColumnNum() - Method in class org.nanes.slideset.dm.ColumnBoundWriter
Get the column index
getColumnProperties(int) - Method in class org.nanes.slideset.SlideSet
Get the properties of a column
getColumnProperties(int) - Method in class org.nanes.slideset.SlideSet
Get the properties of a column
getColumnReadWritePairs(Class<?>, SlideSet, ArrayList<ColumnBoundReader>, ArrayList<ColumnBoundWriter>) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get ColumnBoundReaderColumnBoundWriter pairs that can be used to read and write the specified type to a column in the provided SlideSet table.
getColumnReadWritePairs(Class<?>, SlideSet, ArrayList<ColumnBoundReader>, ArrayList<ColumnBoundWriter>) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get ColumnBoundReaderColumnBoundWriter pairs that can be used to read and write the specified type to a column in the provided SlideSet table.
getColumnText(SlideSet, int) - Method in class org.nanes.slideset.script.SlideSetScript
Get the contents of a Slide Set table column
getColumnText(SlideSet, String) - Method in class org.nanes.slideset.script.SlideSetScript
Get the contents of a Slide Set table column
getColumnText(SlideSet, int) - Method in class org.nanes.slideset.script.SlideSetScript
Get the contents of a Slide Set table column
getColumnText(SlideSet, String) - Method in class org.nanes.slideset.script.SlideSetScript
Get the contents of a Slide Set table column
getColumnTypeName() - Method in class org.nanes.slideset.dm.ColumnBoundReader
Get a human-readable label for the column type
getColumnTypeName() - Method in class org.nanes.slideset.dm.ColumnBoundReader
Get a human-readable label for the column type
getColumnTypeName(int) - Method in class org.nanes.slideset.SlideSet
Get a human-readable name for the data type of a column.
getColumnTypeName(int) - Method in class org.nanes.slideset.SlideSet
Get a human-readable name for the data type of a column.
getColumnUnderlyingType(int) - Method in class org.nanes.slideset.SlideSet
Get the underlying type used to store data in a column.
getColumnUnderlyingType(int) - Method in class org.nanes.slideset.SlideSet
Get the underlying type used to store data in a column.
getCommandClass() - Method in class org.nanes.slideset.dm.CommandTemplate
Get the command class name
getCommandClass() - Method in class org.nanes.slideset.dm.CommandTemplate
Get the command class name
getCommandTemplate() - Method in class org.nanes.slideset.SlideSet
Get the command template data for this SlideSet
getCommandTemplate() - Method in class org.nanes.slideset.SlideSet
Get the command template data for this SlideSet
getCompatableColumnReaders(Class<?>, SlideSet) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get a list of ColumnBoundReaders that will read data from the given table that are assignment-compatible with the specified class.
getCompatableColumnReaders(Class<?>, SlideSet) - Method in class org.nanes.slideset.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 org.nanes.slideset.dm.DataTypeIDService
Get the list of ElementReaders that will read to the specified type.
getCompatableReaders(Class<?>, ArrayList<Class<? extends ElementReader>>, ArrayList<String>, boolean) - Method in class org.nanes.slideset.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 org.nanes.slideset.dm.DataTypeIDService
Get a list of ElementWriters compatible with a class.
getCompatableWriters(Class<?>, ArrayList<Class<? extends ElementWriter>>, ArrayList<String>, ArrayList<String>) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get a list of ElementWriters compatible with a class.
getContext() - Method in class org.nanes.slideset.SlideSet
Get the SciJava application Context
getContext() - Method in class org.nanes.slideset.SlideSet
Get the SciJava application Context
getContrast() - Method in class org.nanes.slideset.ui.BrightnessContrastRoi
 
getContrast() - Method in class org.nanes.slideset.ui.BrightnessContrastRoi
 
getCreationParams() - Method in class org.nanes.slideset.SlideSet
Get the creation parameters of this SlideSet
getCreationParams() - Method in class org.nanes.slideset.SlideSet
Get the creation parameters of this SlideSet
getDataElement(int, int) - Method in class org.nanes.slideset.SlideSet
getDataElement(int, int) - Method in class org.nanes.slideset.SlideSet
getDataTypeIDService() - Method in class org.nanes.slideset.script.SlideSetScript
Get the DataTypeIDService for managing and matching data types.
getDataTypeIDService() - Method in class org.nanes.slideset.script.SlideSetScript
Get the DataTypeIDService for managing and matching data types.
getDefaultLinkCount(int) - Method in class org.nanes.slideset.SlideSet
Get the counter for default links for a column.
getDefaultLinkCount(int) - Method in class org.nanes.slideset.SlideSet
Get the counter for default links for a column.
getDefaultLinkExtension(int) - Method in class org.nanes.slideset.SlideSet
Get the default link extension for a column.
getDefaultLinkExtension(int) - Method in class org.nanes.slideset.SlideSet
Get the default link extension for a column.
getDefaultLinkPrefix(int) - Method in class org.nanes.slideset.SlideSet
Get the prefix for default links for a column.
getDefaultLinkPrefix(int) - Method in class org.nanes.slideset.SlideSet
Get the prefix for default links for a column.
getElementTypes(boolean) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get a list of DataElement types in the index.
getElementTypes(boolean) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get a list of DataElement types in the index.
getFirstPathInstructionEnd(String) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Get the end index of the first path data instruction in pathData.
getFirstPathInstructionEnd(String) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Get the end index of the first path data instruction in pathData.
getFirstPathInstructionEnd(String) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Get the end index of the first path data instruction in pathData.
getFirstPathInstructionEnd(String) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Get the end index of the first path data instruction in pathData.
getFirstTransformEnd(String) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Get the index of the end of the first transform string in a transform attribute list.
getFirstTransformEnd(String) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Get the index of the end of the first transform string in a transform attribute list.
getFirstTransformEnd(String) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Get the index of the end of the first transform string in a transform attribute list.
getFirstTransformEnd(String) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Get the index of the end of the first transform string in a transform attribute list.
getHelp(String) - Method in interface org.nanes.slideset.ui.HelpLoader
 
getHelp() - Method in interface org.nanes.slideset.ui.HelpLoader
 
getHelp(String) - Method in interface org.nanes.slideset.ui.HelpLoader
 
getHelp() - Method in interface org.nanes.slideset.ui.HelpLoader
 
getHelp(String) - Method in class org.nanes.slideset.ui.HttpHelpLoader
Open a documentation page.
getHelp() - Method in class org.nanes.slideset.ui.HttpHelpLoader
 
getHelp(String) - Method in class org.nanes.slideset.ui.HttpHelpLoader
Open a documentation page.
getHelp() - Method in class org.nanes.slideset.ui.HttpHelpLoader
 
getHelp - Variable in class org.nanes.slideset.ui.PluginInputMatcherFrame
Button to view the relevant documentation, if applicable
getHelp - Variable in class org.nanes.slideset.ui.PluginInputMatcherFrame
Button to view the relevant documentation, if applicable
getHelp(String) - Method in class org.nanes.slideset.ui.SlideSetLauncher
Load documentation in a web browser.
getHelp(String) - Method in class org.nanes.slideset.ui.SlideSetLauncher
Load documentation in a web browser.
getImaegJ() - Method in class org.nanes.slideset.script.SlideSetScript
Get the ImageJ instance bound to this class
getImaegJ() - Method in class org.nanes.slideset.script.SlideSetScript
Get the ImageJ instance bound to this class
getImageNames() - Method in class org.nanes.slideset.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 org.nanes.slideset.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 org.nanes.slideset.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.
getImageNames() - Method in class org.nanes.slideset.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 org.nanes.slideset.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.
getImageSetNames() - Method in class org.nanes.slideset.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 org.nanes.slideset.dm.CommandTemplate
Get the command input choice parameters.
getInputChoices(ArrayList<Integer>, ArrayList<Object>) - Method in class org.nanes.slideset.dm.CommandTemplate
Get the command input choice parameters.
getInputChoices(ArrayList<Integer>, ArrayList<Object>) - Method in class org.nanes.slideset.io.CommandSkeletonService.CommandTemplateInputPicker
 
getInputChoices(ArrayList<Integer>, ArrayList<Object>) - Method in class org.nanes.slideset.io.CommandSkeletonService.CommandTemplateInputPicker
 
getInputChoices(ArrayList<Integer>, ArrayList<Object>) - Method in interface org.nanes.slideset.pi.PluginInputPicker
Get chosen options for assignment of each plugin input value.
getInputChoices(ArrayList<Integer>, ArrayList<Object>) - Method in interface org.nanes.slideset.pi.PluginInputPicker
Get chosen options for assignment of each plugin input value.
getInputChoices(ArrayList<Integer>, ArrayList<Object>) - Method in class org.nanes.slideset.script.PluginInputMatcher
 
getInputChoices(ArrayList<Integer>, ArrayList<Object>) - Method in class org.nanes.slideset.script.PluginInputMatcher
 
getInputChoices(ArrayList<Integer>, ArrayList<Object>) - Method in class org.nanes.slideset.ui.PluginInputMatcherFrame
 
getInputChoices(ArrayList<Integer>, ArrayList<Object>) - Method in class org.nanes.slideset.ui.PluginInputMatcherFrame
 
getIrregularProfile(Roi, ImageProcessor) - Method in class org.nanes.slideset.pi.SilentSlicer
 
getIrregularProfile(Roi, ImageProcessor) - Method in class org.nanes.slideset.pi.SilentSlicer
 
getItemText(int, int) - Method in class org.nanes.slideset.SlideSet
Get a text representation of an item, i.e.
getItemText(int, int) - Method in class org.nanes.slideset.SlideSet
Get a text representation of an item, i.e.
getLine(ImageProcessor, double, double, double, double, float[]) - Method in class org.nanes.slideset.pi.SilentSlicer
 
getLine(ImageProcessor, double, double, double, double, float[]) - Method in class org.nanes.slideset.pi.SilentSlicer
 
getMaximum() - Method in class org.nanes.slideset.ui.BrightnessContrastRoi
 
getMaximum() - Method in class org.nanes.slideset.ui.BrightnessContrastRoi
 
getMimeReadableName(String) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get the human-readable name of an MIME type, if it is registered in the index.
getMimeReadableName(String) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get the human-readable name of an MIME type, if it is registered in the index.
getMimeType() - Method in class org.nanes.slideset.dm.DataElement
Get the MIME type of this element
getMimeType() - Method in class org.nanes.slideset.dm.DataElement
Get the MIME type of this element
getMimeTypes() - Method in class org.nanes.slideset.dm.DataTypeIDService
Get a list of MIME types from the index
getMimeTypes() - Method in class org.nanes.slideset.dm.DataTypeIDService
Get a list of MIME types from the index
getMinimum() - Method in class org.nanes.slideset.ui.BrightnessContrastRoi
 
getMinimum() - Method in class org.nanes.slideset.ui.BrightnessContrastRoi
 
getMyJarPath() - Method in class org.nanes.slideset.ui.HttpHelpLoader.AboutPage
 
getMyJarPath() - Method in class org.nanes.slideset.ui.HttpHelpLoader.AboutPage
 
getName() - Method in class org.nanes.slideset.SlideSet
Get the name of this SlideSet
getName() - Method in class org.nanes.slideset.SlideSet
Get the name of this SlideSet
getNeighbors(long[], int, int) - Method in class org.nanes.slideset.pi.ThresholdSegmentation
Get the 4-connected neighborhood in the x-y plane
getNeighbors(long[], int, int) - Method in class org.nanes.slideset.pi.ThresholdSegmentation
Get the 4-connected neighborhood in the x-y plane
getNewColumnElement(int) - Method in class org.nanes.slideset.SlideSet
Generate a new DataElement appropriate for the selected column.
getNewColumnElement(int) - Method in class org.nanes.slideset.SlideSet
Generate a new DataElement appropriate for the selected column.
getNextPoint(long[], ArrayList<long[][]>) - Method in class org.nanes.slideset.pi.ThresholdSegmentation
Find the edge in set with one point matching p.
getNextPoint(long[], ArrayList<long[][]>) - Method in class org.nanes.slideset.pi.ThresholdSegmentation
Find the edge in set with one point matching p.
getNumCols() - Method in class org.nanes.slideset.SlideSet
Get the number of columns
getNumCols() - Method in class org.nanes.slideset.SlideSet
Get the number of columns
getNumResults(Map<String, Object>) - Method in class org.nanes.slideset.pi.SlideSetPluginLoader
Checks to make sure that all results are either length 1 (i.e.
getNumResults(Map<String, Object>) - Method in class org.nanes.slideset.pi.SlideSetPluginLoader
Checks to make sure that all results are either length 1 (i.e.
getNumRows() - Method in class org.nanes.slideset.SlideSet
Get the number of rows
getNumRows() - Method in class org.nanes.slideset.SlideSet
Get the number of rows
getOrthoLine(ImageProcessor, int, int, int, int, float[]) - Method in class org.nanes.slideset.pi.SilentSlicer
 
getOrthoLine(ImageProcessor, int, int, int, int, float[]) - Method in class org.nanes.slideset.pi.SilentSlicer
 
getOutputChoices(ArrayList<Integer>, ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Method in class org.nanes.slideset.dm.CommandTemplate
Set the command output choices.
getOutputChoices(ArrayList<Integer>, ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Method in class org.nanes.slideset.dm.CommandTemplate
Set the command output choices.
getOutputChoices(ArrayList<Integer>, ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Method in class org.nanes.slideset.io.CommandSkeletonService.CommandTemplateOutputPicker
 
getOutputChoices(ArrayList<Integer>, ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Method in class org.nanes.slideset.io.CommandSkeletonService.CommandTemplateOutputPicker
 
getOutputChoices(ArrayList<Integer>, ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Method in interface org.nanes.slideset.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 interface org.nanes.slideset.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 org.nanes.slideset.script.PluginOutputMatcher
 
getOutputChoices(ArrayList<Integer>, ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Method in class org.nanes.slideset.script.PluginOutputMatcher
 
getOutputChoices(ArrayList<Integer>, ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Method in class org.nanes.slideset.ui.PluginOutputMatcherFrame
 
getOutputChoices(ArrayList<Integer>, ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Method in class org.nanes.slideset.ui.PluginOutputMatcherFrame
 
getOutputStackSize(double, double, int) - Method in class org.nanes.slideset.pi.SilentSlicer
 
getOutputStackSize(double, double, int) - Method in class org.nanes.slideset.pi.SilentSlicer
 
getOwner() - Method in class org.nanes.slideset.dm.DataElement
Get the SlideSet table which owns this element
getOwner() - Method in class org.nanes.slideset.dm.DataElement
Get the SlideSet table which owns this element
getParent() - Method in class org.nanes.slideset.SlideSet
Get the parent of this SlideSet
getParent() - Method in class org.nanes.slideset.SlideSet
Get the parent of this SlideSet
getPath() - Method in class org.nanes.slideset.pi.WekaClassifierFile
 
getPath() - Method in class org.nanes.slideset.pi.WekaClassifierFile
 
getPlanarAxes(AbstractOverlay, int[]) - Method in class org.nanes.slideset.dm.write.AbstractOverlaysToSVGFileWriter
Get the X and Y axis indeces for an overlay
getPlanarAxes(AbstractOverlay, int[]) - Method in class org.nanes.slideset.dm.write.AbstractOverlaysToSVGFileWriter
Get the X and Y axis indeces for an overlay
getPluginInfo() - Method in class org.nanes.slideset.pi.SlideSetPluginLoader
Get a list of available SlideSetPlugins
getPluginInfo() - Method in class org.nanes.slideset.pi.SlideSetPluginLoader
Get a list of available SlideSetPlugins
getPluginMenuPaths() - Method in class org.nanes.slideset.pi.SlideSetPluginLoader
Get a list of the plugin paths, i.e.
getPluginMenuPaths() - Method in class org.nanes.slideset.pi.SlideSetPluginLoader
Get a list of the plugin paths, i.e.
getPort() - Method in class org.nanes.slideset.ui.JarHTTPd
Get the port on which the server is listening.
getPort() - Method in class org.nanes.slideset.ui.JarHTTPd
Get the port on which the server is listening.
getPrimitiveWrapper(Class<?>) - Method in class org.nanes.slideset.dm.DataTypeIDService
Returns the wrapper class for a primitive type.
getPrimitiveWrapper(Class<?>) - Method in class org.nanes.slideset.dm.DataTypeIDService
Returns the wrapper class for a primitive type.
getReadableElementType(Class<? extends DataElement>, String) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get a human-readable name for a DataElement type— MIME type pair
getReadableElementType(Class<? extends DataElement>, String) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get a human-readable name for a DataElement type— MIME type pair
getReaderElementType(Class<? extends ElementReader>) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get the DataElement type read by an ElementReader type.
getReaderElementType(Class<? extends ElementReader>) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get the DataElement type read by an ElementReader type.
getReaderMimeTypes(Class<? extends ElementReader>) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get the list of MIME types that can be read by an ElementReader type.
getReaderMimeTypes(Class<? extends ElementReader>) - Method in class org.nanes.slideset.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 org.nanes.slideset.pi.SlideSetPluginLoader
Create a list of ColumnBoundReaders for each input
getReaders(Iterable<ModuleItem<?>>, SlideSet, PluginInputPicker, String, CommandTemplate) - Method in class org.nanes.slideset.pi.SlideSetPluginLoader
Create a list of ColumnBoundReaders for each input
getReaderUnderlyingType(Class<? extends ElementReader>) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get the underlying type read by an ElementReader type.
getReaderUnderlyingType(Class<? extends ElementReader>) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get the underlying type read by an ElementReader type.
getRealType() - Method in class org.nanes.slideset.dm.AbstractOverlaysAlias
 
getRealType() - Method in class org.nanes.slideset.dm.AbstractOverlaysAlias
 
getRealType() - Method in class org.nanes.slideset.dm.RoisAlias
 
getRealType() - Method in class org.nanes.slideset.dm.RoisAlias
 
getRealType() - Method in interface org.nanes.slideset.dm.TypeAlias
The real type referenced by this alias type
getRealType() - Method in interface org.nanes.slideset.dm.TypeAlias
The real type referenced by this alias type
getRoiLenth(AbstractOverlay) - Static method in class org.nanes.slideset.pi.ROILengths
Calculate the length, in pixels, of an AbstractOverlay border.
getRoiLenth(AbstractOverlay) - Static method in class org.nanes.slideset.pi.ROILengths
Calculate the length, in pixels, of an AbstractOverlay border.
getRoiSetNames() - Method in class org.nanes.slideset.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 org.nanes.slideset.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 org.nanes.slideset.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.
getRoiSetNames() - Method in class org.nanes.slideset.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 org.nanes.slideset.ui.SlideSetTableModel
 
getRowCount() - Method in class org.nanes.slideset.ui.SlideSetTableModel
 
getSelectedCommand() - Method in class org.nanes.slideset.ui.CommandPicker
 
getSelectedCommand() - Method in class org.nanes.slideset.ui.CommandPicker
 
getSelectedSlideSets() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Get a list of the SlideSets selected in the tree
getSelectedSlideSets() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Get a list of the SlideSets selected in the tree
getSize(double, double, int) - Method in class org.nanes.slideset.pi.SilentSlicer
 
getSize(double, double, int) - Method in class org.nanes.slideset.pi.SilentSlicer
 
getSlice(ImagePlus, double, double, double, double, String) - Method in class org.nanes.slideset.pi.SilentSlicer
 
getSlice(ImagePlus, double, double, double, double, String) - Method in class org.nanes.slideset.pi.SilentSlicer
 
getSlideSetPluginLoader() - Method in class org.nanes.slideset.script.SlideSetScript
Get the SlideSetPluginLoader for preparing and running Slide Set commands.
getSlideSetPluginLoader() - Method in class org.nanes.slideset.script.SlideSetScript
Get the SlideSetPluginLoader for preparing and running Slide Set commands.
getTableForWriters(ArrayList<String>, ArrayList<Class<? extends ElementWriter>>, SlideSet, ArrayList<ColumnBoundWriter>) - Method in class org.nanes.slideset.dm.DataTypeIDService
Create a table with column types matching the specified list of ElementWriter classes.
getTableForWriters(ArrayList<String>, ArrayList<Class<? extends ElementWriter>>, SlideSet, ArrayList<ColumnBoundWriter>) - Method in class org.nanes.slideset.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 org.nanes.slideset.ui.SlideSetTreeRenderer
 
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.nanes.slideset.ui.SlideSetTreeRenderer
 
getTreeRoot() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Get the SlideSet at the root of the tree
getTreeRoot() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Get the SlideSet at the root of the tree
getTypeAlias(Class<?>) - Method in class org.nanes.slideset.dm.DataTypeIDService
Replace a TypeAlias type with it's 'real' type.
getTypeAlias(Class<?>) - Method in class org.nanes.slideset.dm.DataTypeIDService
Replace a TypeAlias type with it's 'real' type.
getUnderlying() - Method in class org.nanes.slideset.dm.DataElement
Get this element's "underlying" value
getUnderlying() - Method in class org.nanes.slideset.dm.DataElement
Get this element's "underlying" value
getUnderlying(int, int) - Method in class org.nanes.slideset.SlideSet
Get an item as the underlying data object, i.e.
getUnderlying(int, int) - Method in class org.nanes.slideset.SlideSet
Get an item as the underlying data object, i.e.
getUnderlyingText() - Method in class org.nanes.slideset.dm.BooleanElement
 
getUnderlyingText() - Method in class org.nanes.slideset.dm.BooleanElement
 
getUnderlyingText() - Method in class org.nanes.slideset.dm.DataElement
Get a String representation of this element's "underlying" value
getUnderlyingText() - Method in class org.nanes.slideset.dm.DataElement
Get a String representation of this element's "underlying" value
getUnderlyingText() - Method in class org.nanes.slideset.dm.DoubleElement
 
getUnderlyingText() - Method in class org.nanes.slideset.dm.DoubleElement
 
getUnderlyingText() - Method in class org.nanes.slideset.dm.FileLinkElement
 
getUnderlyingText() - Method in class org.nanes.slideset.dm.FileLinkElement
 
getUnderlyingText() - Method in class org.nanes.slideset.dm.IntegerElement
 
getUnderlyingText() - Method in class org.nanes.slideset.dm.IntegerElement
 
getUnderlyingText() - Method in class org.nanes.slideset.dm.StringElement
 
getUnderlyingText() - Method in class org.nanes.slideset.dm.StringElement
 
getUnfilledInputs(Module, Iterable<ModuleItem<?>>) - Method in class org.nanes.slideset.pi.SlideSetPluginLoader
Get a list of inputs that have not been filled
getUnfilledInputs(Module, Iterable<ModuleItem<?>>) - Method in class org.nanes.slideset.pi.SlideSetPluginLoader
Get a list of inputs that have not been filled
getValueAt(int, int) - Method in class org.nanes.slideset.ui.SlideSetTableModel
 
getValueAt(int, int) - Method in class org.nanes.slideset.ui.SlideSetTableModel
 
getValuesOnLine(double, double, double, double, double) - Method in class org.nanes.slideset.pi.CountIntersections
 
getValuesOnLine(double, double, double, double, double) - Method in class org.nanes.slideset.pi.CountIntersections
 
getView() - Method in class org.nanes.slideset.ui.BrightnessContrastRoi
 
getView() - Method in class org.nanes.slideset.ui.BrightnessContrastRoi
 
getWorkingDirectory() - Method in class org.nanes.slideset.SlideSet
Get the working directory of this SlideSet
getWorkingDirectory() - Method in class org.nanes.slideset.SlideSet
Get the working directory of this SlideSet
getWriter() - Method in class org.nanes.slideset.dm.ColumnBoundWriter
Get the bound writer
getWriter() - Method in class org.nanes.slideset.dm.ColumnBoundWriter
Get the bound writer
getWriterElementType(Class<? extends ElementWriter>) - Method in class org.nanes.slideset.dm.DataTypeIDService
Get the DataElement type written by an ElementWriter type.
getWriterElementType(Class<? extends ElementWriter>) - Method in class org.nanes.slideset.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 org.nanes.slideset.pi.SlideSetPluginLoader
Prepare for plugin results be creating a results table and appropriate ColumnBoundWriters to write the results to it
getWriters(ArrayList<ModuleItem<?>>, boolean, PluginOutputPicker, ArrayList<ColumnBoundWriter>, SlideSet, String[], ArrayList<Integer>, ArrayList<String>, ArrayList<String>, ArrayList<String>, CommandTemplate) - Method in class org.nanes.slideset.pi.SlideSetPluginLoader
Prepare for plugin results be creating a results table and appropriate ColumnBoundWriters to write the results to it
getXMLService() - Method in class org.nanes.slideset.script.SlideSetScript
Get the XMLService for reading and writing Slide Set data files.
getXMLService() - Method in class org.nanes.slideset.script.SlideSetScript
Get the XMLService for reading and writing Slide Set data files.
GIF - Static variable in class org.nanes.slideset.dm.MIME
 
GIF - Static variable in class org.nanes.slideset.dm.MIME
 
gLength - Variable in class org.nanes.slideset.pi.SilentSlicer
 
gLength - Variable in class org.nanes.slideset.pi.SilentSlicer
 
GLOBAL - Static variable in class org.nanes.slideset.ui.BrightnessContrastRoi
 
GLOBAL - Static variable in class org.nanes.slideset.ui.BrightnessContrastRoi
 
gmtFrmt - Static variable in class org.nanes.slideset.ui.NanoHTTPd
GMT date formatter
gmtFrmt - Static variable in class org.nanes.slideset.ui.NanoHTTPd
GMT date formatter
goImageBack - Variable in class org.nanes.slideset.ui.RoiEditor
 
goImageBack - Variable in class org.nanes.slideset.ui.RoiEditor
 
goImageBack - Variable in class org.nanes.slideset.ui.RoiEditorIJ1
 
goImageBack - Variable in class org.nanes.slideset.ui.RoiEditorIJ1
 
goImageNext - Variable in class org.nanes.slideset.ui.RoiEditor
 
goImageNext - Variable in class org.nanes.slideset.ui.RoiEditor
 
goImageNext - Variable in class org.nanes.slideset.ui.RoiEditorIJ1
 
goImageNext - Variable in class org.nanes.slideset.ui.RoiEditorIJ1
 
green - Variable in class org.nanes.slideset.pi.BorderStats
 
green - Variable in class org.nanes.slideset.pi.BorderStats
 
green - Variable in class org.nanes.slideset.pi.RegionStats
 
green - Variable in class org.nanes.slideset.pi.RegionStats
 
gT - Variable in class org.nanes.slideset.pi.BorderStats
 
gT - Variable in class org.nanes.slideset.pi.BorderStats
 
gT - Variable in class org.nanes.slideset.pi.RegionStats
 
gT - Variable in class org.nanes.slideset.pi.RegionStats
 
gx1 - Variable in class org.nanes.slideset.pi.SilentSlicer
 
gx1 - Variable in class org.nanes.slideset.pi.SilentSlicer
 
gx2 - Variable in class org.nanes.slideset.pi.SilentSlicer
 
gx2 - Variable in class org.nanes.slideset.pi.SilentSlicer
 
gy1 - Variable in class org.nanes.slideset.pi.SilentSlicer
 
gy1 - Variable in class org.nanes.slideset.pi.SilentSlicer
 
gy2 - Variable in class org.nanes.slideset.pi.SilentSlicer
 
gy2 - Variable in class org.nanes.slideset.pi.SilentSlicer
 

H

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

I

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

J

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

K

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

L

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

M

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

N

n - Variable in class org.nanes.slideset.pi.SilentSlicer
 
n - Variable in class org.nanes.slideset.pi.SilentSlicer
 
name - Variable in class org.nanes.slideset.dm.DataTypeIDService.DataElementRecord
Element human-readable name
name - Variable in class org.nanes.slideset.dm.DataTypeIDService.DataElementRecord
Element human-readable name
name - Variable in class org.nanes.slideset.dm.DataTypeIDService.ReaderRecord
Human-readable name for the reader
name - Variable in class org.nanes.slideset.dm.DataTypeIDService.ReaderRecord
Human-readable name for the reader
name - Variable in class org.nanes.slideset.dm.DataTypeIDService.WriterRecord
Human-readable name for the writer
name - Variable in class org.nanes.slideset.dm.DataTypeIDService.WriterRecord
Human-readable name for the writer
name - Variable in class org.nanes.slideset.SlideSet
Name of this SlideSet
name - Variable in class org.nanes.slideset.SlideSet
Name of this SlideSet
NanoHTTPd - Class in org.nanes.slideset.ui
A simple, tiny, nicely embeddable HTTP 1.0 server in Java
NanoHTTPd - Class in org.nanes.slideset.ui
A simple, tiny, nicely embeddable HTTP 1.0 server in Java
NanoHTTPd(int) - Constructor for class org.nanes.slideset.ui.NanoHTTPd
Starts a HTTP server to given port.
NanoHTTPd(int) - Constructor for class org.nanes.slideset.ui.NanoHTTPd
Starts a HTTP server to given port.
NanoHTTPd.HTTPSession - Class in org.nanes.slideset.ui
Handles one session, i.e.
NanoHTTPd.HTTPSession - Class in org.nanes.slideset.ui
Handles one session, i.e.
NanoHTTPd.Response - Class in org.nanes.slideset.ui
HTTP response.
NanoHTTPd.Response - Class in org.nanes.slideset.ui
HTTP response.
newFile() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Start a new file
newFile() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Start a new file
nil - Static variable in class org.nanes.slideset.pi.CreateMask
 
nil - Static variable in class org.nanes.slideset.pi.CreateMask
 
nil - Static variable in class org.nanes.slideset.pi.CreateMaskMulti
 
nil - Static variable in class org.nanes.slideset.pi.CreateMaskMulti
 
nointerpolate - Variable in class org.nanes.slideset.pi.SilentSlicer
 
nointerpolate - Variable in class org.nanes.slideset.pi.SilentSlicer
 
NoPluginInputSourceException - Exception in org.nanes.slideset.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 - Exception in org.nanes.slideset.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 org.nanes.slideset.ex.NoPluginInputSourceException
Creates a new instance of NoPluginInputSourceException without detail message.
NoPluginInputSourceException(String) - Constructor for exception org.nanes.slideset.ex.NoPluginInputSourceException
Constructs an instance of NoPluginInputSourceException with the specified detail message.
NoPluginInputSourceException(Throwable) - Constructor for exception org.nanes.slideset.ex.NoPluginInputSourceException
 
NoPluginInputSourceException(String, Throwable) - Constructor for exception org.nanes.slideset.ex.NoPluginInputSourceException
 
NoPluginInputSourceException() - Constructor for exception org.nanes.slideset.ex.NoPluginInputSourceException
Creates a new instance of NoPluginInputSourceException without detail message.
NoPluginInputSourceException(String) - Constructor for exception org.nanes.slideset.ex.NoPluginInputSourceException
Constructs an instance of NoPluginInputSourceException with the specified detail message.
NoPluginInputSourceException(Throwable) - Constructor for exception org.nanes.slideset.ex.NoPluginInputSourceException
 
NoPluginInputSourceException(String, Throwable) - Constructor for exception org.nanes.slideset.ex.NoPluginInputSourceException
 
noRoi - Variable in class org.nanes.slideset.pi.SilentSlicer
 
noRoi - Variable in class org.nanes.slideset.pi.SilentSlicer
 
notFloat - Variable in class org.nanes.slideset.pi.SilentSlicer
 
notFloat - Variable in class org.nanes.slideset.pi.SilentSlicer
 
numRows - Variable in class org.nanes.slideset.SlideSet
Number of rows in the SlideSet
numRows - Variable in class org.nanes.slideset.SlideSet
Number of rows in the SlideSet

O

offsetBottomRightEdges(PolygonRegionOfInterest, int, int) - Method in class org.nanes.slideset.pi.ThresholdSegmentation
Offset the bottom and right edges of an ROI outlining pixels as a workaround for issues with the contains() method.
offsetBottomRightEdges(PolygonRegionOfInterest, int, int) - Method in class org.nanes.slideset.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 org.nanes.slideset.ui.PluginInputMatcherFrame
 
okPressed - Variable in class org.nanes.slideset.ui.PluginInputMatcherFrame
 
okPressed - Variable in class org.nanes.slideset.ui.PluginOutputMatcherFrame
 
okPressed - Variable in class org.nanes.slideset.ui.PluginOutputMatcherFrame
 
onEvent(OverlayUpdatedEvent) - Method in class org.nanes.slideset.ui.RoiEditor
Check to see if one of the ROIs has been changed
onEvent(OverlayRestructuredEvent) - Method in class org.nanes.slideset.ui.RoiEditor
Check to see if one of the ROIs has been restructured
onEvent(OverlayCreatedEvent) - Method in class org.nanes.slideset.ui.RoiEditor
Handle an ROI creation
onEvent(OverlayDeletedEvent) - Method in class org.nanes.slideset.ui.RoiEditor
Handle an ROI deletion
onEvent(OverlayUpdatedEvent) - Method in class org.nanes.slideset.ui.RoiEditor
Check to see if one of the ROIs has been changed
onEvent(OverlayRestructuredEvent) - Method in class org.nanes.slideset.ui.RoiEditor
Check to see if one of the ROIs has been restructured
onEvent(OverlayCreatedEvent) - Method in class org.nanes.slideset.ui.RoiEditor
Handle an ROI creation
onEvent(OverlayDeletedEvent) - Method in class org.nanes.slideset.ui.RoiEditor
Handle an ROI deletion
openPath - Variable in class org.nanes.slideset.ui.SlideSetLauncher
Path to the currently open file
openPath - Variable in class org.nanes.slideset.ui.SlideSetLauncher
Path to the currently open file
openROIManager - Variable in class org.nanes.slideset.ui.RoiEditor
 
openROIManager() - Method in class org.nanes.slideset.ui.RoiEditor
Open the ImageJ overlay manager window
openROIManager - Variable in class org.nanes.slideset.ui.RoiEditor
 
openROIManager() - Method in class org.nanes.slideset.ui.RoiEditor
Open the ImageJ overlay manager window
openROIManager() - Method in class org.nanes.slideset.ui.RoiEditorIJ1
Open the IJ1 ROI Manager and line it up below the ROI Editor pane.
openROIManager() - Method in class org.nanes.slideset.ui.RoiEditorIJ1
Open the IJ1 ROI Manager and line it up below the ROI Editor pane.
openXML() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Open a new file selected using a dialog - do not run on event thread
openXML(File) - Method in class org.nanes.slideset.ui.SlideSetLauncher
Open a specified file
openXML() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Open a new file selected using a dialog - do not run on event thread
openXML(File) - Method in class org.nanes.slideset.ui.SlideSetLauncher
Open a specified file
OperationCanceledException - Exception in org.nanes.slideset.ex
Thrown when a SlideSet operation has been canceled.
OperationCanceledException - Exception in org.nanes.slideset.ex
Thrown when a SlideSet operation has been canceled.
OperationCanceledException() - Constructor for exception org.nanes.slideset.ex.OperationCanceledException
Creates a new instance of OperationCanceledException without detail message.
OperationCanceledException(String) - Constructor for exception org.nanes.slideset.ex.OperationCanceledException
Constructs an instance of OperationCanceledException with the specified detail message.
OperationCanceledException(Throwable) - Constructor for exception org.nanes.slideset.ex.OperationCanceledException
 
OperationCanceledException(String, Throwable) - Constructor for exception org.nanes.slideset.ex.OperationCanceledException
 
OperationCanceledException() - Constructor for exception org.nanes.slideset.ex.OperationCanceledException
Creates a new instance of OperationCanceledException without detail message.
OperationCanceledException(String) - Constructor for exception org.nanes.slideset.ex.OperationCanceledException
Constructs an instance of OperationCanceledException with the specified detail message.
OperationCanceledException(Throwable) - Constructor for exception org.nanes.slideset.ex.OperationCanceledException
 
OperationCanceledException(String, Throwable) - Constructor for exception org.nanes.slideset.ex.OperationCanceledException
 
optionIndex - Variable in class org.nanes.slideset.ui.PluginInputMatcherFrame
An index to match choices in each combo box to the appropriate SlideSet column index
optionIndex - Variable in class org.nanes.slideset.ui.PluginInputMatcherFrame
An index to match choices in each combo box to the appropriate SlideSet column index
optionIndex - Variable in class org.nanes.slideset.ui.PluginOutputMatcherFrame
Index of TypeCode options
optionIndex - Variable in class org.nanes.slideset.ui.PluginOutputMatcherFrame
Index of TypeCode options
org.nanes.slideset - package org.nanes.slideset
Slide Set tables and the ImageJ plugin
org.nanes.slideset.dm - package org.nanes.slideset.dm
Classes implementing the data model
org.nanes.slideset.dm.read - package org.nanes.slideset.dm.read
Readers for converting "underlying" data to "processed" data
org.nanes.slideset.dm.write - package org.nanes.slideset.dm.write
Writers for converting "processed" data to "underlying" data
org.nanes.slideset.ex - package org.nanes.slideset.ex
Error handling
org.nanes.slideset.io - package org.nanes.slideset.io
Read and write data files
org.nanes.slideset.pi - package org.nanes.slideset.pi
Slide Set commands and plugin management
org.nanes.slideset.script - package org.nanes.slideset.script
 
org.nanes.slideset.ui - package org.nanes.slideset.ui
The Slide Set user interface
os - Variable in class org.nanes.slideset.ui.RoiEditor
 
os - Variable in class org.nanes.slideset.ui.RoiEditor
 
OtsuSegmentation - Class in org.nanes.slideset.pi
Segment an image using Otsu's method.
OtsuSegmentation - Class in org.nanes.slideset.pi
Segment an image using Otsu's method.
OtsuSegmentation() - Constructor for class org.nanes.slideset.pi.OtsuSegmentation
 
OtsuSegmentation() - Constructor for class org.nanes.slideset.pi.OtsuSegmentation
 
out - Variable in class org.nanes.slideset.pi.WekaSegmentationWrapper
 
out - Variable in class org.nanes.slideset.pi.WekaSegmentationWrapper
 
outputChoices - Variable in class org.nanes.slideset.dm.CommandTemplate
Output choices
outputChoices - Variable in class org.nanes.slideset.dm.CommandTemplate
Output choices
outputChoices - Variable in class org.nanes.slideset.script.PluginOutputMatcher
 
outputChoices - Variable in class org.nanes.slideset.script.PluginOutputMatcher
 
outputDirs - Variable in class org.nanes.slideset.dm.CommandTemplate
Output directories
outputDirs - Variable in class org.nanes.slideset.dm.CommandTemplate
Output directories
outputExts - Variable in class org.nanes.slideset.dm.CommandTemplate
Output file extensions
outputExts - Variable in class org.nanes.slideset.dm.CommandTemplate
Output file extensions
outputPres - Variable in class org.nanes.slideset.dm.CommandTemplate
Output file prefixes
outputPres - Variable in class org.nanes.slideset.dm.CommandTemplate
Output file prefixes
outputSanityChecks() - Method in class org.nanes.slideset.ui.PluginOutputMatcherFrame
 
outputSanityChecks() - Method in class org.nanes.slideset.ui.PluginOutputMatcherFrame
 
outputSlices - Variable in class org.nanes.slideset.pi.SilentSlicer
 
outputSlices - Variable in class org.nanes.slideset.pi.SilentSlicer
 
outputZSpacing - Variable in class org.nanes.slideset.pi.SilentSlicer
 
outputZSpacing - Variable in class org.nanes.slideset.pi.SilentSlicer
 
overlap - Variable in class org.nanes.slideset.pi.ROIOverlap
 
overlap - Variable in class org.nanes.slideset.pi.ROIOverlap
 
overlay - Variable in class org.nanes.slideset.pi.ROILengths
 
overlay - Variable in class org.nanes.slideset.pi.ROILengths
 
owner - Variable in class org.nanes.slideset.dm.DataElement
 
owner - Variable in class org.nanes.slideset.dm.DataElement
 

P

p1ds - Variable in class org.nanes.slideset.pi.UnmixAbsorbance
 
p1ds - Variable in class org.nanes.slideset.pi.UnmixAbsorbance
 
p2ds - Variable in class org.nanes.slideset.pi.UnmixAbsorbance
 
p2ds - Variable in class org.nanes.slideset.pi.UnmixAbsorbance
 
pageIndex - Variable in class org.nanes.slideset.ui.HttpHelpLoader
 
pageIndex - Variable in class org.nanes.slideset.ui.HttpHelpLoader
 
pane - Variable in class org.nanes.slideset.ui.SlideSetViewer
 
pane - Variable in class org.nanes.slideset.ui.SlideSetViewer
 
parent - Variable in class org.nanes.slideset.SlideSet
Parent of this SlideSet
parent - Variable in class org.nanes.slideset.SlideSet
Parent of this SlideSet
parentFields - Variable in class org.nanes.slideset.dm.CommandTemplate
Parent fields to copy
parentFields - Variable in class org.nanes.slideset.dm.CommandTemplate
Parent fields to copy
parseCircle(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a circle element
parseCircle(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a circle element
parseCircle(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a circle element
parseCircle(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a circle element
parseDocument(Document) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Get the list of overlays that can be created from the DOM
parseDocument(Document) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Get the list of overlays that can be created from the DOM
parseDocument(Document) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Get the list of ROIs that can be created from the DOM
parseDocument(Document) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Get the list of ROIs that can be created from the DOM
parseEllipse(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from an ellipse element
parseEllipse(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from an ellipse element
parseEllipse(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from an ellipse element
parseEllipse(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from an ellipse element
parseLength(String) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Parse an SVG length String (possibly with units), and convert to pixels
parseLength(String) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Parse an SVG length String (possibly with units), and convert to pixels
parseLength(String) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Parse an SVG length String (possibly with units), and convert to pixels
parseLength(String) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Parse an SVG length String (possibly with units), and convert to pixels
parseLine(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a line element.
parseLine(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a line element.
parseLine(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a line element.
parseLine(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a line element.
parseListOfNumbers(String) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Parse a list of numbers, possibly with units
parseListOfNumbers(String) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Parse a list of numbers, possibly with units
parseListOfNumbers(String) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Parse a list of numbers, possibly with units
parseListOfNumbers(String) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Parse a list of numbers, possibly with units
parseListOfPoints(String) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Parse a list of points, as used in polygon and polyline elements
parseListOfPoints(String) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Parse a list of points, as used in polygon and polyline elements
parseListOfPoints(String) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Parse a list of points, as used in polygon and polyline elements
parseListOfPoints(String) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Parse a list of points, as used in polygon and polyline elements
parseNode(Node) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from an SVG node
parseNode(Node) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from an SVG node
parseNode(Node) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an overlay from an SVG node
parseNode(Node) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an overlay from an SVG node
parsePath(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a path element
parsePath(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a path element
parsePath(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a path element May return a different type of ROI, depending on the data:
parsePath(Element) - Method in class org.nanes.slideset.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 org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a polygon element
parsePolygon(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a polygon element
parsePolygon(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a polygon element
parsePolygon(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a polygon element
parsePolyline(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a polyline element
parsePolyline(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a polyline element
parsePolyline(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a polyline element
parsePolyline(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a polyline element
parseRect(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a rect element
parseRect(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Generate an overlay from a rect element
parseRect(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a rect element
parseRect(Element) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Generate an ROI from a rect element
parseRecursiveMenuAdd(String[], String, JMenu) - Method in class org.nanes.slideset.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) - Method in class org.nanes.slideset.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 org.nanes.slideset.ui.UIUtil
Add a menu item to a menu tree, along with sub-menu nodes if needed
parseRecursiveMenuAdd(String[], String, JMenu, ActionListener) - Static method in class org.nanes.slideset.ui.UIUtil
Add a menu item to a menu tree, along with sub-menu nodes if needed
parseRGBtoPigment(String, int) - Method in class org.nanes.slideset.pi.UnmixAbsorbance
Parse a whitespace-separated RGB string to an array of absorbance values
parseRGBtoPigment(String, int) - Method in class org.nanes.slideset.pi.UnmixAbsorbance
Parse a whitespace-separated RGB string to an array of absorbance values
parseTransform(double[], String) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Transform a coordinate pair
parseTransform(double[], String) - Method in class org.nanes.slideset.dm.read.SVGFileToAbstractOverlayReader
Transform a coordinate pair
parseTransform(double[], String) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Transform a coordinate pair
parseTransform(double[], String) - Method in class org.nanes.slideset.dm.read.SVGFileToIJ1ROIReader
Transform a coordinate pair
path - Variable in class org.nanes.slideset.pi.WekaClassifierFile
 
path - Variable in class org.nanes.slideset.pi.WekaClassifierFile
 
pickAndRunCommand() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Launch a CommandPicker dialog, and run the selected ImageJ Command.
pickAndRunCommand() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Launch a CommandPicker dialog, and run the selected ImageJ Command.
pigmentOne - Variable in class org.nanes.slideset.pi.UnmixAbsorbance
 
pigmentOne - Variable in class org.nanes.slideset.pi.UnmixAbsorbance
 
pigmentTwo - Variable in class org.nanes.slideset.pi.UnmixAbsorbance
 
pigmentTwo - Variable in class org.nanes.slideset.pi.UnmixAbsorbance
 
PLANE - Static variable in class org.nanes.slideset.ui.BrightnessContrastRoi
 
PLANE - Static variable in class org.nanes.slideset.ui.BrightnessContrastRoi
 
PluginInputMatcher - Class in org.nanes.slideset.script
A scriptable (i.e.
PluginInputMatcher - Class in org.nanes.slideset.script
A scriptable (i.e.
PluginInputMatcher() - Constructor for class org.nanes.slideset.script.PluginInputMatcher
 
PluginInputMatcher() - Constructor for class org.nanes.slideset.script.PluginInputMatcher
 
PluginInputMatcherFrame - Class in org.nanes.slideset.ui
GUI for assigning SlideSet columns to plugin inputs
PluginInputMatcherFrame - Class in org.nanes.slideset.ui
GUI for assigning SlideSet columns to plugin inputs
PluginInputMatcherFrame(SlideSet, ImageJ, DataTypeIDService) - Constructor for class org.nanes.slideset.ui.PluginInputMatcherFrame
 
PluginInputMatcherFrame(SlideSet, ImageJ, DataTypeIDService) - Constructor for class org.nanes.slideset.ui.PluginInputMatcherFrame
 
PluginInputPicker - Interface in org.nanes.slideset.pi
Scheme for selecting among available options for assigning plugin input parameter values.
PluginInputPicker - Interface in org.nanes.slideset.pi
Scheme for selecting among available options for assigning plugin input parameter values.
PluginOutputMatcher - Class in org.nanes.slideset.script
A scriptable (i.e.
PluginOutputMatcher - Class in org.nanes.slideset.script
A scriptable (i.e.
PluginOutputMatcher() - Constructor for class org.nanes.slideset.script.PluginOutputMatcher
 
PluginOutputMatcher() - Constructor for class org.nanes.slideset.script.PluginOutputMatcher
 
PluginOutputMatcherFrame - Class in org.nanes.slideset.ui
GUI for selecting options for handling plugin outputs.
PluginOutputMatcherFrame - Class in org.nanes.slideset.ui
GUI for selecting options for handling plugin outputs.
PluginOutputMatcherFrame(ImageJ, DataTypeIDService) - Constructor for class org.nanes.slideset.ui.PluginOutputMatcherFrame
 
PluginOutputMatcherFrame(ImageJ, DataTypeIDService) - Constructor for class org.nanes.slideset.ui.PluginOutputMatcherFrame
 
PluginOutputPicker - Interface in org.nanes.slideset.pi
Scheme for selecting among available options for handling plugin output values.
PluginOutputPicker - Interface in org.nanes.slideset.pi
Scheme for selecting among available options for handling plugin output values.
plugins - Variable in class org.nanes.slideset.pi.SlideSetPluginLoader
 
plugins - Variable in class org.nanes.slideset.pi.SlideSetPluginLoader
 
PNG - Static variable in class org.nanes.slideset.dm.MIME
 
PNG - Static variable in class org.nanes.slideset.dm.MIME
 
PointsTable - Class in org.nanes.slideset.pi
Extract coordinates from PointRois into a table
PointsTable - Class in org.nanes.slideset.pi
Extract coordinates from PointRois into a table
PointsTable() - Constructor for class org.nanes.slideset.pi.PointsTable
 
PointsTable() - Constructor for class org.nanes.slideset.pi.PointsTable
 
populateText() - Method in class org.nanes.slideset.ui.SlideSetPropertiesViewer
 
populateText() - Method in class org.nanes.slideset.ui.SlideSetPropertiesViewer
 
populateTree(DefaultMutableTreeNode, SlideSet) - Method in class org.nanes.slideset.ui.SlideSetLauncher
Iteratively populate the tree pane
populateTree(DefaultMutableTreeNode, SlideSet) - Method in class org.nanes.slideset.ui.SlideSetLauncher
Iteratively populate the tree pane
popupMenuHash - Variable in class org.nanes.slideset.ui.SlideSetViewer
Index specifying popup menus associated with various components
popupMenuHash - Variable in class org.nanes.slideset.ui.SlideSetViewer
Index specifying popup menus associated with various components
popupMenus - Variable in class org.nanes.slideset.ui.SlideSetLauncher
 
popupMenus - Variable in class org.nanes.slideset.ui.SlideSetLauncher
 
port - Variable in class org.nanes.slideset.ui.HttpHelpLoader
 
port - Variable in class org.nanes.slideset.ui.HttpHelpLoader
 
pre - Static variable in class org.nanes.slideset.ui.HttpHelpLoader
 
pre - Static variable in class org.nanes.slideset.ui.HttpHelpLoader
 
print(String) - Method in class org.nanes.slideset.ui.SlideSetLog
Relay a message to the log listeners.
print(String) - Method in class org.nanes.slideset.ui.SlideSetLog
Relay a message to the log listeners.
println(String) - Method in class org.nanes.slideset.ui.SlideSetLog
Relay a message (with newline character appended) to the log listeners.
println(String) - Method in class org.nanes.slideset.ui.SlideSetLog
Relay a message (with newline character appended) to the log listeners.
printLogHead() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Print a header message to the info window
printLogHead() - Method in class org.nanes.slideset.ui.SlideSetLauncher
Print a header message to the info window
prob - Variable in class org.nanes.slideset.pi.WekaSegmentationWrapper
 
prob - Variable in class org.nanes.slideset.pi.WekaSegmentationWrapper
 
processedType - Variable in class org.nanes.slideset.dm.DataTypeIDService.ReaderRecord
Type returned by this reader's read() method
processedType - Variable in class org.nanes.slideset.dm.DataTypeIDService.ReaderRecord
Type returned by this reader's read() method
processedType - Variable in class org.nanes.slideset.dm.DataTypeIDService.WriterRecord
Type accepted by this writer's write() method
processedType - Variable in class org.nanes.slideset.dm.DataTypeIDService.WriterRecord
Type accepted by this writer's write() method
prominence - Variable in class org.nanes.slideset.pi.FindMaxima
 
prominence - Variable in class org.nanes.slideset.pi.FindMaxima
 
ps - Variable in class org.nanes.slideset.dm.DataTypeIDService
 
ps - Variable in class org.nanes.slideset.dm.DataTypeIDService
 
ps - Variable in class org.nanes.slideset.io.XMLService
 
ps - Variable in class org.nanes.slideset.io.XMLService
 
putColumn(ImageProcessor, int, int, float[], int) - Method in class org.nanes.slideset.pi.SilentSlicer
 
putColumn(ImageProcessor, int, int, float[], int) - Method in class org.nanes.slideset.pi.SilentSlicer
 
putRow(ImageProcessor, int, int, float[], int) - Method in class org.nanes.slideset.pi.SilentSlicer
 
putRow(ImageProcessor, int, int, float[], int) - Method in class org.nanes.slideset.pi.SilentSlicer
 
pw - Variable in class org.nanes.slideset.io.CSVService
 
pw - Variable in class org.nanes.slideset.io.CSVService
 

R

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

S

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

T

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

U

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

V

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

W

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

X

x - Variable in class org.nanes.slideset.pi.PointsTable
 
x - Variable in class org.nanes.slideset.pi.PointsTable
 
x - Variable in class org.nanes.slideset.pi.SilentSlicer
 
x - Variable in class org.nanes.slideset.pi.SilentSlicer
 
xbase - Variable in class org.nanes.slideset.pi.SilentSlicer
 
xbase - Variable in class org.nanes.slideset.pi.SilentSlicer
 
XML - Static variable in class org.nanes.slideset.dm.MIME
 
XML - Static variable in class org.nanes.slideset.dm.MIME
 
xmls - Variable in class org.nanes.slideset.script.SlideSetScript
 
xmls - Variable in class org.nanes.slideset.script.SlideSetScript
 
xmls - Variable in class org.nanes.slideset.ui.SlideSetLauncher
 
xmls - Variable in class org.nanes.slideset.ui.SlideSetLauncher
 
XMLService - Class in org.nanes.slideset.io
Writes SlideSet data as an XML file and generates a SlideSet from saved XML data.
XMLService - Class in org.nanes.slideset.io
Writes SlideSet data as an XML file and generates a SlideSet from saved XML data.
XMLService(ImageJ, DataTypeIDService) - Constructor for class org.nanes.slideset.io.XMLService
 
XMLService(ImageJ, DataTypeIDService) - Constructor for class org.nanes.slideset.io.XMLService
 
xsr - Variable in class org.nanes.slideset.io.CommandSkeletonService
 
xsr - Variable in class org.nanes.slideset.io.CommandSkeletonService
 
xsr - Variable in class org.nanes.slideset.io.XMLService
 
xsr - Variable in class org.nanes.slideset.io.XMLService
 
xsw - Variable in class org.nanes.slideset.io.CommandSkeletonService
 
xsw - Variable in class org.nanes.slideset.io.CommandSkeletonService
 
xsw - Variable in class org.nanes.slideset.io.XMLService
 
xsw - Variable in class org.nanes.slideset.io.XMLService
 

Y

y - Variable in class org.nanes.slideset.pi.PointsTable
 
y - Variable in class org.nanes.slideset.pi.PointsTable
 
y - Variable in class org.nanes.slideset.pi.SilentSlicer
 
y - Variable in class org.nanes.slideset.pi.SilentSlicer
 
ybase - Variable in class org.nanes.slideset.pi.SilentSlicer
 
ybase - Variable in class org.nanes.slideset.pi.SilentSlicer
 

Z

ZIP - Static variable in class org.nanes.slideset.dm.MIME
 
ZIP - Static variable in class org.nanes.slideset.dm.MIME
 
zProj - Variable in class org.nanes.slideset.pi.ZProject
 
zProj - Variable in class org.nanes.slideset.pi.ZProject
 
ZProject - Class in org.nanes.slideset.pi
Maximum-intensity Z-projection
ZProject - Class in org.nanes.slideset.pi
Maximum-intensity Z-projection
ZProject() - Constructor for class org.nanes.slideset.pi.ZProject
 
ZProject() - Constructor for class org.nanes.slideset.pi.ZProject
 
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