Index

A B C D E F G H I K L M N O P R S T U V W X Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

about() - Static method in class loci.plugins.About

About - Class in loci.plugins

Displays a small information dialog about the Bio-Formats Plugins package.

About() - Constructor for class loci.plugins.About

abs() - Method in class loci.plugins.util.RecordedImageProcessor

actionPerformed(ActionEvent) - Method in class loci.plugins.config.ConfigWindow

actionPerformed(ActionEvent) - Method in class loci.plugins.in.SeriesDialog

actionPerformed(ActionEvent) - Method in class loci.plugins.shortcut.ShortcutPanel

Handles button presses.

actionPerformed(ActionEvent) - Method in class loci.plugins.util.DataBrowser

actionPerformed(ActionEvent) - Method in class loci.plugins.util.SearchableWindow

add(double) - Method in class loci.plugins.util.RecordedImageProcessor

add(int) - Method in class loci.plugins.util.RecordedImageProcessor

addCheckbox(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog

Adds a checkbox to the given dialog object corresponding to the boolean option identified by the specified key.

addChoice(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog

Adds a choice to the given dialog object corresponding to the string option identified by the specified key.

addEntry(Comparable<Object>, DefaultListModel) - Static method in class loci.plugins.config.ConfigWindow

addPossible(String) - Method in class loci.plugins.prefs.StringOption

Adds a possible value to the list.

addScrollBars(Container) - Static method in class loci.plugins.util.WindowTools

Adds AWT scroll bars to the given container.

addStatusListener(StatusListener) - Method in class loci.plugins.in.ImagePlusReader

addStatusListener(StatusListener) - Method in class loci.plugins.in.ImportProcess

adjustmentValueChanged(AdjustmentEvent) - Method in class loci.plugins.util.DataBrowser

allowCZIAutostitch() - Static method in class loci.plugins.util.LociPrefs

allowShow - Variable in class loci.plugins.util.DataBrowser

and(int) - Method in class loci.plugins.util.RecordedImageProcessor

anim - Variable in class loci.plugins.util.DataBrowser

animate - Variable in class loci.plugins.util.DataBrowser

append(ILoggingEvent) - Method in class loci.plugins.util.IJStatusEchoer

applyCalibration(ImagePlus) - Method in class loci.plugins.in.Calibrator

Applies spatial calibrations to an image stack.

applyColors(List<ImagePlus>) - Method in class loci.plugins.in.Colorizer

applyMethodStack(List<RecordedImageProcessor.MethodEntry>) - Method in class loci.plugins.util.RecordedImageProcessor

applyTable(int[]) - Method in class loci.plugins.util.RecordedImageProcessor

arg - Variable in class loci.plugins.LociExporter

Argument passed to setup method.

args - Static variable in class loci.plugins.shortcut.ShortcutPanel

Details for installed plugins.

autoscaleBox - Variable in class loci.plugins.in.MainDialog

autoThreshold() - Method in class loci.plugins.util.RecordedImageProcessor

B

BF - Class in loci.plugins

Miscellaneous plugins utility methods.

BFVirtualStack - Class in loci.plugins.util

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

BFVirtualStack(String, IFormatReader, boolean, boolean, boolean) - Constructor for class loci.plugins.util.BFVirtualStack

BIO_FORMATS - Enum constant in enum loci.plugins.util.LibraryChecker.Library

BooleanOption - Class in loci.plugins.prefs

A boolean option for one of the plugins.

BooleanOption(String, boolean, String, String, boolean) - Constructor for class loci.plugins.prefs.BooleanOption

Constructs a boolean option with the given parameters.

BooleanOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.BooleanOption

Constructs a boolean option with the parameters from the given map.

BORDER - Static variable in class loci.plugins.shortcut.ShortcutPanel

Number of pixels for window border.

BrowserOptionsWindow - Class in loci.plugins.util

Extension of JFrame that allows the user to adjust caching settings.

BrowserOptionsWindow(String, Cache, String[]) - Constructor for class loci.plugins.util.BrowserOptionsWindow

buildExtensions() - Method in class loci.plugins.macro.MacroFunctions

Builds the list of extensions, using reflection, from public methods of this class.

C

cache - Variable in class loci.plugins.util.BFVirtualStack

Calibrator - Class in loci.plugins.in

Logic for calibrating images.

Calibrator(ImportProcess) - Constructor for class loci.plugins.in.Calibrator

cancel() - Method in class loci.plugins.in.ImportProcess

Cancels the import process.

canceled - Variable in class loci.plugins.LociImporter

Flag indicating whether last operation was canceled.

canceled - Variable in class loci.plugins.Slicer

Flag indicating whether last operation was canceled.

canceled - Variable in class loci.plugins.Updater

Flag indicating whether last operation was canceled.

canImport(JComponent, DataFlavor[]) - Method in class loci.plugins.shortcut.ShortcutTransferHandler

CellSensWidgets - Class in loci.plugins.config

Custom widgets for configuring Bio-Formats CellSens .vsi support.

CellSensWidgets() - Constructor for class loci.plugins.config.CellSensWidgets

checkClass(String) - Static method in class loci.plugins.util.LibraryChecker

Checks whether the given class is available.

checkImageJ() - Static method in class loci.plugins.util.LibraryChecker

Checks whether ImageJ is new enough for the Bio-Formats plugins.

checkImageJ(String, String) - Static method in class loci.plugins.util.LibraryChecker

Returns true the current ImageJ version is greater than or equal to the specified version.

checkImageJ(String, String, String) - Static method in class loci.plugins.util.LibraryChecker

Returns true the current ImageJ version is greater than or equal to the specified version.

checkJava() - Static method in class loci.plugins.util.LibraryChecker

Checks for a new enough version of the Java Runtime Environment.

checkKey(String, String) - Method in class loci.plugins.in.ImporterOptions

Tests whether the given boolean key is set in the specified options.

checkLatest(String, String) - Static method in class loci.plugins.config.InstallWizard

checkLibrary(String, String, HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker

Checks whether the given class is available; if not, adds the specified JAR file name to the hash set (presumably to report it missing to the user).

checkLibrary(LibraryChecker.Library, HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker

Checks for a required library.

checkMissing(HashSet<String>) - Static method in class loci.plugins.util.LibraryChecker

Reports missing libraries in the given hash set to the user.

checkObsoleteOptions() - Method in class loci.plugins.in.ImporterOptions

Handles obsolete macro keys, for backward compatibility.

cIndex - Variable in class loci.plugins.util.DataBrowser

clearSeries() - Method in class loci.plugins.in.ImporterOptions

cLengths - Variable in class loci.plugins.util.DataBrowser

close() - Method in class loci.plugins.config.TextAreaWriter

Closing a TextAreaWriter does nothing.

close() - Method in class loci.plugins.macro.LociFunctions

close() - Method in class loci.plugins.util.VirtualImagePlus

close() - Method in class loci.plugins.util.VirtualReader

closeFileOnly() - Method in class loci.plugins.macro.LociFunctions

COLOR_MODE_COLORIZED - Static variable in class loci.plugins.in.ImporterOptions

COLOR_MODE_COMPOSITE - Static variable in class loci.plugins.in.ImporterOptions

COLOR_MODE_CUSTOM - Static variable in class loci.plugins.in.ImporterOptions

COLOR_MODE_DEFAULT - Static variable in class loci.plugins.in.ImporterOptions

COLOR_MODE_GRAYSCALE - Static variable in class loci.plugins.in.ImporterOptions

ColorDialog - Class in loci.plugins.in

Bio-Formats Importer custom color chooser dialog box.

ColorDialog(ImportProcess) - Constructor for class loci.plugins.in.ColorDialog

Colorizer - Class in loci.plugins.in

Logic for colorizing images.

Colorizer(ImportProcess) - Constructor for class loci.plugins.in.Colorizer

colorModeChoice - Variable in class loci.plugins.in.MainDialog

COLORS - Enum constant in enum loci.plugins.in.ImportStep

compareTo(Object) - Method in class loci.plugins.config.FormatEntry

compareTo(Object) - Method in class loci.plugins.config.LibraryEntry

compareTo(ThumbLoader.SeriesInfo) - Method in class loci.plugins.in.ThumbLoader.SeriesInfo

COMPLETE - Enum constant in enum loci.plugins.in.ImportStep

concatenate(List<ImagePlus>) - Method in class loci.plugins.in.Concatenator

Concatenates the list of images as appropriate.

concatenateBox - Variable in class loci.plugins.in.MainDialog

Concatenator - Class in loci.plugins.in

Logic for concatenating multiple images together.

Concatenator() - Constructor for class loci.plugins.in.Concatenator

ConfigWindow - Class in loci.plugins.config

A window for managing configuration of the Bio-Formats plugins.

ConfigWindow() - Constructor for class loci.plugins.config.ConfigWindow

constructDialog() - Method in class loci.plugins.in.ColorDialog

constructDialog() - Method in class loci.plugins.in.CropDialog

constructDialog() - Method in class loci.plugins.in.FilePatternDialog

constructDialog() - Method in class loci.plugins.in.IdDialog

constructDialog() - Method in class loci.plugins.in.ImporterDialog

constructDialog() - Method in class loci.plugins.in.LocationDialog

constructDialog() - Method in class loci.plugins.in.MainDialog

constructDialog() - Method in class loci.plugins.in.MemoryDialog

constructDialog() - Method in class loci.plugins.in.RangeDialog

constructDialog() - Method in class loci.plugins.in.SeriesDialog

constructDialog() - Method in class loci.plugins.in.SwapDialog

constructDialog() - Method in class loci.plugins.in.UpgradeDialog

convertToByte(boolean) - Method in class loci.plugins.util.RecordedImageProcessor

convertToFloat() - Method in class loci.plugins.util.RecordedImageProcessor

convertToRGB() - Method in class loci.plugins.util.RecordedImageProcessor

convertToShort(boolean) - Method in class loci.plugins.util.RecordedImageProcessor

convolve(float[], int, int) - Method in class loci.plugins.util.RecordedImageProcessor

convolve3x3(int[]) - Method in class loci.plugins.util.RecordedImageProcessor

copyBits(ImageProcessor, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor

createImage() - Method in class loci.plugins.util.RecordedImageProcessor

createImage(String, ImageStack, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader

Creates an ImagePlus from the given image stack.

createImage(String, List<ImageProcessor>) - Static method in class loci.plugins.in.ImagePlusReader

Creates an ImagePlus from the given image processors.

createProcessor(int, int) - Method in class loci.plugins.util.RecordedImageProcessor

createStack(List<ImageProcessor>, List<String>, List<LUT>) - Static method in class loci.plugins.in.ImagePlusReader

Creates an image stack from the given image processors.

crop() - Method in class loci.plugins.util.RecordedImageProcessor

CROP - Enum constant in enum loci.plugins.in.ImportStep

cropBox - Variable in class loci.plugins.in.MainDialog

CropDialog - Class in loci.plugins.in

Bio-Formats Importer crop options dialog box.

CropDialog(ImportProcess) - Constructor for class loci.plugins.in.CropDialog

Creates a crop options dialog for the Bio-Formats Importer.

cScroll - Variable in class loci.plugins.util.DataBrowser

cSliders - Variable in class loci.plugins.util.DataBrowser

D

DataBrowser - Class in loci.plugins.util

Extension of StackWindow with additional UI trimmings for animation, virtual stack caching options, metadata, and general beautification.

DataBrowser(ImagePlus) - Constructor for class loci.plugins.util.DataBrowser

DataBrowser(ImagePlus, ImageCanvas, String[], int[]) - Constructor for class loci.plugins.util.DataBrowser

DataBrowser(ImagePlus, ImageCanvas, String[], int[], XMLWindow) - Constructor for class loci.plugins.util.DataBrowser

debug(String) - Static method in class loci.plugins.BF

defaultValue - Variable in class loci.plugins.prefs.BooleanOption

The option's default value.

defaultValue - Variable in class loci.plugins.prefs.DoubleOption

The option's default value.

defaultValue - Variable in class loci.plugins.prefs.StringOption

The option's default value.

dilate() - Method in class loci.plugins.util.RecordedImageProcessor

DIM_ORDER - Enum constant in enum loci.plugins.in.ImportStep

displayDataBrowser(ImagePlus) - Method in class loci.plugins.in.DisplayHandler

displayDialog(GenericDialog) - Method in class loci.plugins.in.IdDialog

Asks user whether Bio-Formats should automatically check for upgrades, and if so, checks for an upgrade and prompts user to install it.

displayDialog(GenericDialog) - Method in class loci.plugins.in.ImporterDialog

Displays the dialog, or grabs values from macro options.

displayDialog(GenericDialog) - Method in class loci.plugins.in.SeriesDialog

displayDialog(GenericDialog) - Method in class loci.plugins.in.UpgradeDialog

Asks user whether Bio-Formats should automatically check for upgrades, and if so, checks for an upgrade and prompts user to install it.

DisplayHandler - Class in loci.plugins.in

Logic for displaying images and metadata onscreen using ImageJ.

DisplayHandler(ImportProcess) - Constructor for class loci.plugins.in.DisplayHandler

displayImage(ImagePlus) - Method in class loci.plugins.in.DisplayHandler

Displays the given image according to the configured options.

displayImage5D(ImagePlus) - Method in class loci.plugins.in.DisplayHandler

displayImages(ImagePlus[]) - Method in class loci.plugins.in.DisplayHandler

Displays the given images according to the configured options.

displayNormal(ImagePlus) - Method in class loci.plugins.in.DisplayHandler

Displays in a normal ImageJ window.

displayOMEXML() - Method in class loci.plugins.in.DisplayHandler

Displays OME-XML metadata in a tree in its own window.

displayOriginalMetadata() - Method in class loci.plugins.in.DisplayHandler

Displays standard metadata in a table in its own window.

displayROIs(ImagePlus[]) - Method in class loci.plugins.in.DisplayHandler

displayView5D(ImagePlus) - Method in class loci.plugins.in.DisplayHandler

doCrop() - Method in class loci.plugins.in.ImporterOptions

doMustGroup() - Method in class loci.plugins.in.ImporterOptions

doStitchTiles() - Method in class loci.plugins.in.ImporterOptions

DoubleOption - Class in loci.plugins.prefs

A double option for one of the plugins.

DoubleOption(String, boolean, String, String, double) - Constructor for class loci.plugins.prefs.DoubleOption

Constructs a double option with the given parameters.

DoubleOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.DoubleOption

Constructs a double option with the parameters from the given map.

doUpgradeCheck() - Method in class loci.plugins.in.ImporterOptions

download(URLConnection) - Static method in class loci.plugins.config.InstallWizard

download(URLConnection, File) - Static method in class loci.plugins.config.InstallWizard

drawDot(int, int) - Method in class loci.plugins.util.RecordedImageProcessor

drawLine(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor

drawOval(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor

drawPixel(int, int) - Method in class loci.plugins.util.RecordedImageProcessor

drawPolygon(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor

drawRect(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor

drawString(String) - Method in class loci.plugins.util.RecordedImageProcessor

drawString(String, int, int) - Method in class loci.plugins.util.RecordedImageProcessor

duplicate() - Method in class loci.plugins.util.RecordedImageProcessor

E

equals(Object) - Method in class loci.plugins.config.FormatEntry

equals(Object) - Method in class loci.plugins.prefs.OptionsList

erode() - Method in class loci.plugins.util.RecordedImageProcessor

execute() - Method in class loci.plugins.in.ImportProcess

Performs the import preparation process, notifying status listeners at each step.

exp() - Method in class loci.plugins.util.RecordedImageProcessor

Exporter - Class in loci.plugins.out

Core logic for the Bio-Formats Exporter ImageJ plugin.

Exporter(LociExporter, ImagePlus) - Constructor for class loci.plugins.out.Exporter

extensions - Variable in class loci.plugins.macro.MacroFunctions

F

FILE - Enum constant in enum loci.plugins.in.ImportStep

fileGroupOption(String, String[]) - Method in class loci.plugins.macro.LociFunctions

FilePatternDialog - Class in loci.plugins.in

Bio-Formats Importer file pattern dialog box.

FilePatternDialog(ImportProcess) - Constructor for class loci.plugins.in.FilePatternDialog

Creates a file pattern dialog for the Bio-Formats Importer.

fill() - Method in class loci.plugins.util.RecordedImageProcessor

fill(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor

fillOval(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor

fillPolygon(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor

filter(int) - Method in class loci.plugins.util.RecordedImageProcessor

findEdges() - Method in class loci.plugins.util.RecordedImageProcessor

finish(ImportProcess) - Method in class loci.plugins.in.Importer

flipHorizontal() - Method in class loci.plugins.util.RecordedImageProcessor

flipVertical() - Method in class loci.plugins.util.RecordedImageProcessor

flush() - Method in class loci.plugins.config.TextAreaWriter

Flushing a TextAreaWriter does nothing .

focusGained(FocusEvent) - Method in class loci.plugins.in.MainDialog

Handles information pane updates when component focus changes.

focusLost(FocusEvent) - Method in class loci.plugins.in.MainDialog

FormatEntry - Class in loci.plugins.config

A list entry for the configuration window's Formats tab.

FormatEntry(PrintWriter, Object) - Constructor for class loci.plugins.config.FormatEntry

FORMS - Enum constant in enum loci.plugins.util.LibraryChecker.Library

fpsSpin - Variable in class loci.plugins.util.DataBrowser

G

gamma(double) - Method in class loci.plugins.util.RecordedImageProcessor

get(int) - Method in class loci.plugins.util.RecordedImageProcessor

get(int, int) - Method in class loci.plugins.util.RecordedImageProcessor

getAutoscaleInfo() - Method in class loci.plugins.in.ImporterOptions

getAutoThreshold() - Method in class loci.plugins.util.RecordedImageProcessor

getAutoThreshold(int[]) - Method in class loci.plugins.util.RecordedImageProcessor

getBackgroundValue() - Method in class loci.plugins.util.RecordedImageProcessor

getBaseReader() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.READER.

getBestIndex(Color) - Method in class loci.plugins.util.RecordedImageProcessor

getBooleanOption(String) - Method in class loci.plugins.prefs.OptionsList

Gets the boolean option with the given key.

getBufferedImage() - Method in class loci.plugins.util.RecordedImageProcessor

getBuildDate(String[]) - Method in class loci.plugins.macro.LociFunctions

getCache() - Method in class loci.plugins.util.BFVirtualStack

getCalibrationTable() - Method in class loci.plugins.util.RecordedImageProcessor

getCBegin(int) - Method in class loci.plugins.in.ImporterOptions

getCBegin(int) - Method in class loci.plugins.in.ImportProcess

getCCount(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.SERIES.

getCEnd(int) - Method in class loci.plugins.in.ImporterOptions

getCEnd(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getChannelDimCount(Double[]) - Method in class loci.plugins.macro.LociFunctions

getChannelDimLength(Double, Double[]) - Method in class loci.plugins.macro.LociFunctions

getChannelDimType(Double, String[]) - Method in class loci.plugins.macro.LociFunctions

getChannelFiller() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getChannelSeparator() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getCheckboxes(GenericDialog) - Static method in class loci.plugins.util.WindowTools

getChild() - Method in class loci.plugins.util.RecordedImageProcessor

getChoices(GenericDialog) - Static method in class loci.plugins.util.WindowTools

getColorMode() - Method in class loci.plugins.in.ImporterOptions

getColorModeInfo() - Method in class loci.plugins.in.ImporterOptions

getColorModel() - Method in class loci.plugins.util.RecordedImageProcessor

getColorModes() - Method in class loci.plugins.in.ImporterOptions

getColumn(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor

getConcatenateInfo() - Method in class loci.plugins.in.ImporterOptions

getCropInfo() - Method in class loci.plugins.in.ImporterOptions

getCropRegion(int) - Method in class loci.plugins.in.ImporterOptions

getCropRegion(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getCStep(int) - Method in class loci.plugins.in.ImporterOptions

getCStep(int) - Method in class loci.plugins.in.ImportProcess

getCurrentColorModel() - Method in class loci.plugins.util.RecordedImageProcessor

getCurrentFile() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getCurrentFile(String[]) - Method in class loci.plugins.macro.LociFunctions

getCustomColor(int, int) - Method in class loci.plugins.in.ImporterOptions

getCustomColorKey(int, int) - Method in class loci.plugins.in.ImporterOptions

getDefault() - Method in class loci.plugins.prefs.BooleanOption

Gets the default value of the option.

getDefault() - Method in class loci.plugins.prefs.DoubleOption

Gets the default value of the option.

getDefault() - Method in class loci.plugins.prefs.StringOption

Gets the default value of the option.

getDefaultColorModel() - Method in class loci.plugins.util.RecordedImageProcessor

getDefaultCustomColor(int) - Method in class loci.plugins.in.ImporterOptions

getDefaultValue(String) - Method in class loci.plugins.prefs.OptionsList

Gets the default value of the string option with the given key.

getDimensionOrder(String[]) - Method in class loci.plugins.macro.LociFunctions

getDimensionSwapper() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getEffectiveSizeC(Double[]) - Method in class loci.plugins.macro.LociFunctions

getExtensionFunctions() - Method in class loci.plugins.macro.MacroFunctions

getf(int) - Method in class loci.plugins.util.RecordedImageProcessor

getf(int, int) - Method in class loci.plugins.util.RecordedImageProcessor

getFileStitcher() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getFirstTimeInfo() - Method in class loci.plugins.in.ImporterOptions

getFloatArray() - Method in class loci.plugins.util.RecordedImageProcessor

getFontMetrics() - Method in class loci.plugins.util.RecordedImageProcessor

getForceThumbnailsInfo() - Method in class loci.plugins.in.ImporterOptions

getForegroundValue() - Method in class loci.plugins.util.RecordedImageProcessor

getFormat(String, String[]) - Method in class loci.plugins.macro.LociFunctions

getGroupFilesInfo() - Method in class loci.plugins.in.ImporterOptions

getHeight() - Method in class loci.plugins.util.BFVirtualStack

getHeight() - Method in class loci.plugins.util.RecordedImageProcessor

getHeight(IFormatReader, String, int) - Static method in class loci.plugins.util.BFVirtualStack

getHistogram() - Method in class loci.plugins.util.RecordedImageProcessor

getHistogramMax() - Method in class loci.plugins.util.RecordedImageProcessor

getHistogramMin() - Method in class loci.plugins.util.RecordedImageProcessor

getHistogramSize() - Method in class loci.plugins.util.RecordedImageProcessor

getId() - Method in class loci.plugins.in.ImporterOptions

getIdInfo() - Method in class loci.plugins.in.ImporterOptions

getIdLocation() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.READER.

getIdName() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.READER.

getImageCount(Double[]) - Method in class loci.plugins.macro.LociFunctions

getImageCreationDate(String[]) - Method in class loci.plugins.macro.LociFunctions

getImageReader() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.READER.

getIndex(Double, Double, Double, Double[]) - Method in class loci.plugins.macro.LociFunctions

getInfo() - Method in class loci.plugins.prefs.Option

Gets documentation about the option.

getInfo(String) - Method in class loci.plugins.prefs.OptionsList

Gets the documentation for the option with the given key.

getInputOrder(int) - Method in class loci.plugins.in.ImporterOptions

getIntArray() - Method in class loci.plugins.util.RecordedImageProcessor

getInterpolate() - Method in class loci.plugins.util.RecordedImageProcessor

getInterpolatedPixel(double, double) - Method in class loci.plugins.util.RecordedImageProcessor

getKey() - Method in class loci.plugins.prefs.Option

Gets the option's key name.

getLabel() - Method in class loci.plugins.prefs.Option

Gets label describing the option.

getLabel(String) - Method in class loci.plugins.prefs.OptionsList

Gets the label for the option with the given key.

getLabels() - Method in class loci.plugins.config.CellSensWidgets

getLabels() - Method in interface loci.plugins.config.IFormatWidgets

getLabels() - Method in class loci.plugins.config.LIFWidgets

getLabels() - Method in class loci.plugins.config.ND2Widgets

getLabels() - Method in class loci.plugins.config.SDTWidgets

getLabels() - Method in class loci.plugins.config.TiffDelegateWidgets

getLabels() - Method in class loci.plugins.config.ZeissCZIWidgets

getLine(double, double, double, double) - Method in class loci.plugins.util.RecordedImageProcessor

getLocation() - Method in class loci.plugins.in.ImporterOptions

getLocationInfo() - Method in class loci.plugins.in.ImporterOptions

getLocations() - Method in class loci.plugins.in.ImporterOptions

getLutUpdateMode() - Method in class loci.plugins.util.RecordedImageProcessor

getMask() - Method in class loci.plugins.util.RecordedImageProcessor

getMaskArray() - Method in class loci.plugins.util.RecordedImageProcessor

getMax() - Method in class loci.plugins.util.RecordedImageProcessor

getMaxThreshold() - Method in class loci.plugins.util.RecordedImageProcessor

getMemoryUsage() - Method in class loci.plugins.in.ImportProcess

Gets a projection of required memory in bytes.

getMessage() - Method in enum loci.plugins.in.ImportStep

getMetadataString(String) - Method in class loci.plugins.in.ImporterMetadata

Returns a string with each key/value pair on its own line.

getMetadataValue(String, String[]) - Method in class loci.plugins.macro.LociFunctions

getMethodStack() - Method in class loci.plugins.util.BFVirtualStack

getMethodStack() - Method in class loci.plugins.util.RecordedImageProcessor

getMin() - Method in class loci.plugins.util.RecordedImageProcessor

getMinMaxCalculator() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getMinThreshold() - Method in class loci.plugins.util.RecordedImageProcessor

getMustGroupInfo() - Method in class loci.plugins.in.ImporterOptions

getNativeDataType() - Method in class loci.plugins.util.ImageProcessorReader

getNChannels() - Method in class loci.plugins.util.RecordedImageProcessor

getNumericFields(GenericDialog) - Static method in class loci.plugins.util.WindowTools

getObject(int) - Method in class loci.plugins.util.ImageProcessorSource

getObjectCount() - Method in class loci.plugins.util.ImageProcessorSource

getOMEMetadata() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.READER.

getOMEXML() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.READER.

getOpenAllSeriesInfo() - Method in class loci.plugins.in.ImporterOptions

getOption(String) - Method in class loci.plugins.prefs.OptionsList

Gets the option with the given key.

getOptions() - Method in class loci.plugins.in.ImportProcess

getOriginalMetadata() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.METADATA.

getPath() - Method in class loci.plugins.util.BFVirtualStack

getPixel(int, int) - Method in class loci.plugins.util.RecordedImageProcessor

getPixel(int, int, int[]) - Method in class loci.plugins.util.RecordedImageProcessor

getPixelCount() - Method in class loci.plugins.util.RecordedImageProcessor

getPixelInterpolated(double, double) - Method in class loci.plugins.util.RecordedImageProcessor

getPixels() - Method in class loci.plugins.util.RecordedImageProcessor

getPixelsCopy() - Method in class loci.plugins.util.RecordedImageProcessor

getPixelsPhysicalSizeX(Double[]) - Method in class loci.plugins.macro.LociFunctions

getPixelsPhysicalSizeY(Double[]) - Method in class loci.plugins.macro.LociFunctions

getPixelsPhysicalSizeZ(Double[]) - Method in class loci.plugins.macro.LociFunctions

getPixelsTimeIncrement(Double[]) - Method in class loci.plugins.macro.LociFunctions

getPixelType(String[]) - Method in class loci.plugins.macro.LociFunctions

getPixelValue(int, int) - Method in class loci.plugins.util.RecordedImageProcessor

getPlanePositionX(Double[], Double) - Method in class loci.plugins.macro.LociFunctions

getPlanePositionY(Double[], Double) - Method in class loci.plugins.macro.LociFunctions

getPlanePositionZ(Double[], Double) - Method in class loci.plugins.macro.LociFunctions

getPlaneTimingDeltaT(Double[], Double) - Method in class loci.plugins.macro.LociFunctions

getPlaneTimingExposureTime(Double[], Double) - Method in class loci.plugins.macro.LociFunctions

getPossible() - Method in class loci.plugins.prefs.StringOption

Gets the list of possible values.

getPossible(String) - Method in class loci.plugins.prefs.OptionsList

Gets the possible values for the string option with the given key.

getProcessor(int) - Method in class loci.plugins.util.BFVirtualStack

getQuietInfo() - Method in class loci.plugins.in.ImporterOptions

getReader() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getReader() - Method in class loci.plugins.util.BFVirtualStack

getRecordedProcessor() - Method in class loci.plugins.util.BFVirtualStack

getRevision(String[]) - Method in class loci.plugins.macro.LociFunctions

getRGBChannelCount(Double[]) - Method in class loci.plugins.macro.LociFunctions

getRoi() - Method in class loci.plugins.util.RecordedImageProcessor

getROIsMode() - Method in class loci.plugins.in.ImporterOptions

getROIsModeInfo() - Method in class loci.plugins.in.ImporterOptions

getROIsModes() - Method in class loci.plugins.in.ImporterOptions

getRow(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor

getSeries(Double[]) - Method in class loci.plugins.macro.LociFunctions

getSeriesCount() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getSeriesCount(Double[]) - Method in class loci.plugins.macro.LociFunctions

getSeriesLabel(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getSeriesMetadataValue(String, String[]) - Method in class loci.plugins.macro.LociFunctions

getSeriesName(String[]) - Method in class loci.plugins.macro.LociFunctions

getShowMetadataInfo() - Method in class loci.plugins.in.ImporterOptions

getShowOMEXMLInfo() - Method in class loci.plugins.in.ImporterOptions

getShowROIsInfo() - Method in class loci.plugins.in.ImporterOptions

getSize() - Method in class loci.plugins.util.BFVirtualStack

getSizeC(Double[]) - Method in class loci.plugins.macro.LociFunctions

getSizeT(Double[]) - Method in class loci.plugins.macro.LociFunctions

getSizeX(Double[]) - Method in class loci.plugins.macro.LociFunctions

getSizeY(Double[]) - Method in class loci.plugins.macro.LociFunctions

getSizeZ(Double[]) - Method in class loci.plugins.macro.LociFunctions

getSliceLabelBaseIndex() - Static method in class loci.plugins.util.LociPrefs

getSliceLabelPattern() - Static method in class loci.plugins.util.LociPrefs

getSnapshotPixels() - Method in class loci.plugins.util.RecordedImageProcessor

getSpecifyRangesInfo() - Method in class loci.plugins.in.ImporterOptions

getSplitChannelsInfo() - Method in class loci.plugins.in.ImporterOptions

getSplitFocalPlanesInfo() - Method in class loci.plugins.in.ImporterOptions

getSplitTimepointsInfo() - Method in class loci.plugins.in.ImporterOptions

getStackFormat() - Method in class loci.plugins.in.ImporterOptions

getStackFormatInfo() - Method in class loci.plugins.in.ImporterOptions

getStackFormats() - Method in class loci.plugins.in.ImporterOptions

getStackOrder() - Method in class loci.plugins.in.ImporterOptions

getStackOrder() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getStackOrderInfo() - Method in class loci.plugins.in.ImporterOptions

getStackOrders() - Method in class loci.plugins.in.ImporterOptions

getStatistics(int, int, double, double) - Method in class loci.plugins.util.VirtualImagePlus

getStep() - Method in enum loci.plugins.in.ImportStep

getStep(int) - Static method in enum loci.plugins.in.ImportStep

getStitchTilesInfo() - Method in class loci.plugins.in.ImporterOptions

getStringOption(String) - Method in class loci.plugins.prefs.OptionsList

Gets the string option with the given key.

getStringWidth(String) - Method in class loci.plugins.util.RecordedImageProcessor

getSubC(Modulo, int) - Static method in class loci.plugins.in.ImagePlusReader

getSubCTypes(Modulo) - Static method in class loci.plugins.in.ImagePlusReader

getSwapDimensionsInfo() - Method in class loci.plugins.in.ImporterOptions

getTBegin(int) - Method in class loci.plugins.in.ImporterOptions

getTBegin(int) - Method in class loci.plugins.in.ImportProcess

getTCount(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.SERIES.

getTEnd(int) - Method in class loci.plugins.in.ImporterOptions

getTEnd(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getTStep(int) - Method in class loci.plugins.in.ImporterOptions

getTStep(int) - Method in class loci.plugins.in.ImportProcess

getUngroupFilesInfo() - Method in class loci.plugins.in.ImporterOptions

getUpgradeCheckInfo() - Method in class loci.plugins.in.ImporterOptions

getUsedFile(Double, String[]) - Method in class loci.plugins.macro.LociFunctions

getUsedFileCount(Double[]) - Method in class loci.plugins.macro.LociFunctions

getValue() - Method in class loci.plugins.prefs.BooleanOption

Gets the current value of the option.

getValue() - Method in class loci.plugins.prefs.DoubleOption

Gets the current value of the option.

getValue() - Method in class loci.plugins.prefs.StringOption

Gets the current value of the option.

getValue(String) - Method in class loci.plugins.prefs.OptionsList

Gets the value of the string option with the given key.

getVersionNumber(String[]) - Method in class loci.plugins.macro.LociFunctions

getVirtualInfo() - Method in class loci.plugins.in.ImporterOptions

getVirtualReader() - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getWidgets() - Method in class loci.plugins.config.CellSensWidgets

getWidgets() - Method in interface loci.plugins.config.IFormatWidgets

getWidgets() - Method in class loci.plugins.config.LIFWidgets

getWidgets() - Method in class loci.plugins.config.ND2Widgets

getWidgets() - Method in class loci.plugins.config.SDTWidgets

getWidgets() - Method in class loci.plugins.config.TiffDelegateWidgets

getWidgets() - Method in class loci.plugins.config.ZeissCZIWidgets

getWidth() - Method in class loci.plugins.util.BFVirtualStack

getWidth() - Method in class loci.plugins.util.RecordedImageProcessor

getWidth(IFormatReader, String, int) - Static method in class loci.plugins.util.BFVirtualStack

getWindowlessInfo() - Method in class loci.plugins.in.ImporterOptions

getZBegin(int) - Method in class loci.plugins.in.ImporterOptions

getZBegin(int) - Method in class loci.plugins.in.ImportProcess

getZCount(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.SERIES.

getZCTCoords(Double, Double[], Double[], Double[]) - Method in class loci.plugins.macro.LociFunctions

getZEnd(int) - Method in class loci.plugins.in.ImporterOptions

getZEnd(int) - Method in class loci.plugins.in.ImportProcess

Valid only after ImportStep.STACK.

getZStep(int) - Method in class loci.plugins.in.ImporterOptions

getZStep(int) - Method in class loci.plugins.in.ImportProcess

groupFilesBox - Variable in class loci.plugins.in.MainDialog

H

handleExtension(String, Object[]) - Method in class loci.plugins.macro.MacroFunctions

harvestResults(GenericDialog) - Method in class loci.plugins.in.ColorDialog

harvestResults(GenericDialog) - Method in class loci.plugins.in.CropDialog

harvestResults(GenericDialog) - Method in class loci.plugins.in.FilePatternDialog

harvestResults(GenericDialog) - Method in class loci.plugins.in.IdDialog

harvestResults(GenericDialog) - Method in class loci.plugins.in.ImporterDialog

harvestResults(GenericDialog) - Method in class loci.plugins.in.LocationDialog

harvestResults(GenericDialog) - Method in class loci.plugins.in.MainDialog

harvestResults(GenericDialog) - Method in class loci.plugins.in.MemoryDialog

harvestResults(GenericDialog) - Method in class loci.plugins.in.RangeDialog

harvestResults(GenericDialog) - Method in class loci.plugins.in.SeriesDialog

harvestResults(GenericDialog) - Method in class loci.plugins.in.SwapDialog

harvestResults(GenericDialog) - Method in class loci.plugins.in.UpgradeDialog

hashCode() - Method in class loci.plugins.config.FormatEntry

hashCode() - Method in class loci.plugins.prefs.OptionsList

HELP_MENU - Static variable in class loci.plugins.shortcut.ShortcutPanel

Name of the 'About Plugins' submenu.

I

id - Variable in class loci.plugins.util.BFVirtualStack

IdDialog - Class in loci.plugins.in

Bio-Formats Importer id chooser dialog box.

IdDialog(ImportProcess) - Constructor for class loci.plugins.in.IdDialog

Creates an id chooser dialog for the Bio-Formats Importer.

idLoc - Variable in class loci.plugins.in.ImportProcess

idName - Variable in class loci.plugins.in.ImportProcess

IFormatWidgets - Interface in loci.plugins.config

Interface for defining custom widgets for a specific file format reader.

IJStatusEchoer - Class in loci.plugins.util

Echoes status messages to the ImageJ status bar.

IJStatusEchoer() - Constructor for class loci.plugins.util.IJStatusEchoer

IMAGEJ_MSG - Static variable in class loci.plugins.util.LibraryChecker

Message to be displayed if ImageJ is too old for Bio-Formats plugins.

IMAGEJ_VERSION - Static variable in class loci.plugins.util.LibraryChecker

Minimum version of ImageJ necessary for Bio-Formats plugins.

ImagePlusReader - Class in loci.plugins.in

A high-level reader for ImagePlus objects.

ImagePlusReader() - Constructor for class loci.plugins.in.ImagePlusReader

Constructs an ImagePlusReader with the default options.

ImagePlusReader(ImportProcess) - Constructor for class loci.plugins.in.ImagePlusReader

Constructs an ImagePlusReader with the given complete import preparation process.

ImageProcessorReader - Class in loci.plugins.util

A low-level reader for ImageProcessor objects.

ImageProcessorReader() - Constructor for class loci.plugins.util.ImageProcessorReader

Constructs an ImageProcessorReader around a new image reader.

ImageProcessorReader(IFormatReader) - Constructor for class loci.plugins.util.ImageProcessorReader

Constructs an ImageProcessorReader with the given reader.

ImageProcessorSource - Class in loci.plugins.util

Retrieves ImageJ image processors from an image reader.

ImageProcessorSource(IFormatReader) - Constructor for class loci.plugins.util.ImageProcessorSource

importData(JComponent, Transferable) - Method in class loci.plugins.shortcut.ShortcutTransferHandler

Importer - Class in loci.plugins.in

Core logic for the Bio-Formats Importer ImageJ plugin.

Importer(LociImporter) - Constructor for class loci.plugins.in.Importer

ImporterDialog - Class in loci.plugins.in

Abstract superclass of importer dialogs.

ImporterDialog(ImportProcess) - Constructor for class loci.plugins.in.ImporterDialog

ImporterMetadata - Class in loci.plugins.in

Helper class for storing original metadata key/value pairs.

ImporterMetadata(IFormatReader, ImportProcess, boolean) - Constructor for class loci.plugins.in.ImporterMetadata

ImporterOptions - Class in loci.plugins.in

Helper class for managing Bio-Formats Importer options.

ImporterOptions() - Constructor for class loci.plugins.in.ImporterOptions

ImporterPrompter - Class in loci.plugins.in

Helper class for presenting the user with dialog boxes for configuring importer options.

ImporterPrompter(ImportProcess) - Constructor for class loci.plugins.in.ImporterPrompter

ImportProcess - Class in loci.plugins.in

Manages the import preparation process.

ImportProcess() - Constructor for class loci.plugins.in.ImportProcess

ImportProcess(ImporterOptions) - Constructor for class loci.plugins.in.ImportProcess

ImportStep - Enum in loci.plugins.in

An enumeration of the steps in the import preparation process.

includeCZIAttachments() - Static method in class loci.plugins.util.LociPrefs

index - Variable in class loci.plugins.util.SearchableWindow

info - Variable in class loci.plugins.prefs.Option

Documentation about the option, in HTML.

INFO_DEFAULT - Static variable in class loci.plugins.in.MainDialog

Initial message to display in help text box.

infoPane - Variable in class loci.plugins.in.MainDialog

infoTable - Variable in class loci.plugins.in.MainDialog

INI_DEFAULT - Static variable in class loci.plugins.prefs.Option

INI key indicating option's default value.

INI_INFO - Static variable in class loci.plugins.prefs.Option

INI key indicating option's info.

INI_KEY - Static variable in class loci.plugins.prefs.Option

INI key indicating option's key.

INI_LABEL - Static variable in class loci.plugins.prefs.Option

INI key indicating option's label.

INI_POSSIBLE - Static variable in class loci.plugins.prefs.StringOption

INI key indicating option's possible values.

INI_SAVE - Static variable in class loci.plugins.prefs.Option

INI key indicating whether option should be saved to prefs file.

INI_TYPE - Static variable in class loci.plugins.prefs.OptionsList

INI key indicating option's type.

insert(ImageProcessor, int, int) - Method in class loci.plugins.util.RecordedImageProcessor

install(String) - Static method in class loci.plugins.Updater

Install the tools bundle which can be retrieved from the specified path.

InstallWizard - Class in loci.plugins.config

A wizard for walking users through installation of third party libraries and plugins used by the Bio-Formats plugins.

InstallWizard() - Constructor for class loci.plugins.config.InstallWizard

invert() - Method in class loci.plugins.util.RecordedImageProcessor

invertLut() - Method in class loci.plugins.util.RecordedImageProcessor

IS_GLITCHED - Static variable in class loci.plugins.prefs.OptionsDialog

Flag indicating whether to invoke workaround for AWT refresh bug.

isAutoscale() - Method in class loci.plugins.in.ImporterOptions

isCellsensFailOnMissing() - Static method in class loci.plugins.util.LociPrefs

isColorLut() - Method in class loci.plugins.util.RecordedImageProcessor

isColorModeColorized() - Method in class loci.plugins.in.ImporterOptions

isColorModeComposite() - Method in class loci.plugins.in.ImporterOptions

isColorModeCustom() - Method in class loci.plugins.in.ImporterOptions

isColorModeDefault() - Method in class loci.plugins.in.ImporterOptions

isColorModeGrayscale() - Method in class loci.plugins.in.ImporterOptions

isConcatenate() - Method in class loci.plugins.in.ImporterOptions

isFiji() - Static method in class loci.plugins.Updater

Returns true if the current ImageJ instance is actually a Fiji instance.

isFirstTime() - Method in class loci.plugins.in.ImporterOptions

isForceThumbnails() - Method in class loci.plugins.in.ImporterOptions

isGroupFiles() - Method in class loci.plugins.in.ImporterOptions

isGroupFiles(String[]) - Method in class loci.plugins.macro.LociFunctions

isHTTP() - Method in class loci.plugins.in.ImporterOptions

isIndexed(String[]) - Method in class loci.plugins.macro.LociFunctions

isInterleaved(String[]) - Method in class loci.plugins.macro.LociFunctions

isInterleavedSubC(Double, String[]) - Method in class loci.plugins.macro.LociFunctions

isInvertedLut() - Method in class loci.plugins.util.RecordedImageProcessor

isLeicaLIFPhysicalSizeBackwardsCompatible() - Static method in class loci.plugins.util.LociPrefs

isLittleEndian(String[]) - Method in class loci.plugins.macro.LociFunctions

isLocal() - Method in class loci.plugins.in.ImporterOptions

isMetadataComplete(String[]) - Method in class loci.plugins.macro.LociFunctions

isMetadataFiltered(String[]) - Method in class loci.plugins.macro.LociFunctions

isNormalized(Boolean[]) - Method in class loci.plugins.macro.LociFunctions

isOMERO() - Method in class loci.plugins.in.ImporterOptions

isOrderCertain(String[]) - Method in class loci.plugins.macro.LociFunctions

isOriginalMetadataPopulated(Boolean[]) - Method in class loci.plugins.macro.LociFunctions

isPossible(String, String) - Method in class loci.plugins.prefs.OptionsList

Gets whether the specified value is a possible one for the string option with the given key.

isPseudoColorLut() - Method in class loci.plugins.util.RecordedImageProcessor

isQuiet() - Method in class loci.plugins.in.ImporterOptions

isReaderEnabled(Class<? extends IFormatReader>) - Static method in class loci.plugins.util.LociPrefs

isSaved() - Method in class loci.plugins.prefs.Option

Gets whether option should be saved to ImageJ preferences file.

isSaved(String) - Method in class loci.plugins.prefs.OptionsList

Gets whether the option with the given key is saved to the ImageJ preferences file.

isSDTIntensity() - Static method in class loci.plugins.util.LociPrefs

isSeriesOn(int) - Method in class loci.plugins.in.ImporterOptions

isSet(String) - Method in class loci.plugins.prefs.OptionsList

Gets the value of the boolean option with the given key.

isSetByDefault(String) - Method in class loci.plugins.prefs.OptionsList

Gets the default value of the boolean option with the given key.

isShowMetadata() - Method in class loci.plugins.in.ImporterOptions

isShowOMEXML() - Method in class loci.plugins.in.ImporterOptions

isSpecifyRanges() - Method in class loci.plugins.in.ImporterOptions

isSplitChannels() - Method in class loci.plugins.in.ImporterOptions

isSplitFocalPlanes() - Method in class loci.plugins.in.ImporterOptions

isSplitTimepoints() - Method in class loci.plugins.in.ImporterOptions

isSwapDimensions() - Method in class loci.plugins.in.ImporterOptions

isThisType(String, String[]) - Method in class loci.plugins.macro.LociFunctions

isThisTypeFast(String, String[]) - Method in class loci.plugins.macro.LociFunctions

isTiffImageIO() - Static method in class loci.plugins.util.LociPrefs

isUngroupFiles() - Method in class loci.plugins.in.ImporterOptions

isUsingPatternIds() - Method in class loci.plugins.in.ImporterOptions

isViewBrowser() - Method in class loci.plugins.in.ImporterOptions

isViewHyperstack() - Method in class loci.plugins.in.ImporterOptions

isViewImage5D() - Method in class loci.plugins.in.ImporterOptions

isViewNone() - Method in class loci.plugins.in.ImporterOptions

isViewStandard() - Method in class loci.plugins.in.ImporterOptions

isViewView5D() - Method in class loci.plugins.in.ImporterOptions

isVirtual() - Method in class loci.plugins.in.ImporterOptions

isWindowless() - Method in class loci.plugins.in.ImporterOptions

isWindowless() - Method in class loci.plugins.in.ImportProcess

isWindowless(IFormatReader) - Static method in class loci.plugins.util.LociPrefs

Gets whether windowless mode should be used when opening this reader's currently initialized dataset.

itemStateChanged(ItemEvent) - Method in class loci.plugins.config.CellSensWidgets

itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ConfigWindow

itemStateChanged(ItemEvent) - Method in class loci.plugins.config.LIFWidgets

itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ND2Widgets

itemStateChanged(ItemEvent) - Method in class loci.plugins.config.SDTWidgets

itemStateChanged(ItemEvent) - Method in class loci.plugins.config.TiffDelegateWidgets

itemStateChanged(ItemEvent) - Method in class loci.plugins.config.ZeissCZIWidgets

itemStateChanged(ItemEvent) - Method in class loci.plugins.in.MainDialog

Handles toggling of mutually exclusive options.

itemStateChanged(ItemEvent) - Method in class loci.plugins.in.SwapDialog

K

key - Variable in class loci.plugins.prefs.Option

Key name for ImageJ preferences file.

KEY_AUTOSCALE - Static variable in class loci.plugins.in.ImporterOptions

KEY_COLOR_MODE - Static variable in class loci.plugins.in.ImporterOptions

KEY_CONCATENATE - Static variable in class loci.plugins.in.ImporterOptions

KEY_CROP - Static variable in class loci.plugins.in.ImporterOptions

KEY_FIRST - Static variable in class loci.plugins.in.ImporterOptions

KEY_FORCE_THUMBS - Static variable in class loci.plugins.in.ImporterOptions

KEY_GROUP_FILES - Static variable in class loci.plugins.in.ImporterOptions

KEY_ID - Static variable in class loci.plugins.in.ImporterOptions

KEY_LOCATION - Static variable in class loci.plugins.in.ImporterOptions

KEY_MUST_GROUP - Static variable in class loci.plugins.in.ImporterOptions

KEY_OPEN_ALL_SERIES - Static variable in class loci.plugins.in.ImporterOptions

KEY_PREFIX - Static variable in class loci.plugins.prefs.Option

Prefix to use for all plugins preferences.

KEY_QUIET - Static variable in class loci.plugins.in.ImporterOptions

KEY_ROIS_MODE - Static variable in class loci.plugins.in.ImporterOptions

KEY_SHOW_METADATA - Static variable in class loci.plugins.in.ImporterOptions

KEY_SHOW_OME_XML - Static variable in class loci.plugins.in.ImporterOptions

KEY_SHOW_ROIS - Static variable in class loci.plugins.in.ImporterOptions

KEY_SPECIFY_RANGES - Static variable in class loci.plugins.in.ImporterOptions

KEY_SPLIT_C - Static variable in class loci.plugins.in.ImporterOptions

KEY_SPLIT_T - Static variable in class loci.plugins.in.ImporterOptions

KEY_SPLIT_Z - Static variable in class loci.plugins.in.ImporterOptions

KEY_STACK_FORMAT - Static variable in class loci.plugins.in.ImporterOptions

KEY_STACK_ORDER - Static variable in class loci.plugins.in.ImporterOptions

KEY_STITCH_TILES - Static variable in class loci.plugins.in.ImporterOptions

KEY_SWAP_DIMS - Static variable in class loci.plugins.in.ImporterOptions

KEY_UNGROUP_FILES - Static variable in class loci.plugins.in.ImporterOptions

KEY_UPGRADE_CHECK - Static variable in class loci.plugins.in.ImporterOptions

KEY_VIRTUAL - Static variable in class loci.plugins.in.ImporterOptions

KEY_WINDOWLESS - Static variable in class loci.plugins.in.ImporterOptions

L

label - Variable in class loci.plugins.prefs.Option

Label describing the option, for use with ImageJ dialogs.

labels - Variable in class loci.plugins.config.FormatEntry

libClass - Variable in class loci.plugins.config.LibraryEntry

LibraryChecker - Class in loci.plugins.util

Utility methods for verifying that classes are present and versions are correct.

LibraryChecker.Library - Enum in loci.plugins.util

List of possible libraries for which to check.

LibraryEntry - Class in loci.plugins.config

A list entry for the configuration window's Libraries tab.

LibraryEntry(PrintWriter, String, String, String, String, String, String, String) - Constructor for class loci.plugins.config.LibraryEntry

LibraryEntry(PrintWriter, HashMap<String, String>) - Constructor for class loci.plugins.config.LibraryEntry

license - Variable in class loci.plugins.config.LibraryEntry

LIFWidgets - Class in loci.plugins.config

Custom widgets for configuring Bio-Formats Leica LIF support.

LIFWidgets() - Constructor for class loci.plugins.config.LIFWidgets

lineTo(int, int) - Method in class loci.plugins.util.RecordedImageProcessor

listeners - Variable in class loci.plugins.in.ImagePlusReader

loadOption() - Method in class loci.plugins.prefs.BooleanOption

loadOption() - Method in class loci.plugins.prefs.DoubleOption

loadOption() - Method in class loci.plugins.prefs.Option

Loads the option's value from the ImageJ preferences file.

loadOption() - Method in class loci.plugins.prefs.StringOption

loadOptions() - Method in class loci.plugins.prefs.OptionsList

Loads option values from the ImageJ preferences file.

loadThumb(BufferedImageReader, int, Panel, boolean) - Static method in class loci.plugins.in.ThumbLoader

LOCATION_HTTP - Static variable in class loci.plugins.in.ImporterOptions

LOCATION_LOCAL - Static variable in class loci.plugins.in.ImporterOptions

LOCATION_OMERO - Static variable in class loci.plugins.in.ImporterOptions

LocationDialog - Class in loci.plugins.in

Bio-Formats Importer location chooser dialog box.

LocationDialog(ImportProcess) - Constructor for class loci.plugins.in.LocationDialog

Creates a location chooser dialog for the Bio-Formats Importer.

loci.plugins - package loci.plugins

Bio-Formats Plugins: a collection of plugins for ImageJ, including the Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro Extensions, Data Browser and Stack Slicer.

loci.plugins.config - package loci.plugins.config

Bio-Formats Plugins Configuration plugin for ImageJ.

loci.plugins.in - package loci.plugins.in

Bio-Formats Importer plugin for ImageJ.

loci.plugins.macro - package loci.plugins.macro

Bio-Formats Macro Extensions plugin for ImageJ.

loci.plugins.out - package loci.plugins.out

Bio-Formats Exporter plugin for ImageJ.

loci.plugins.prefs - package loci.plugins.prefs

Classes for managing Bio-Formats plugins preferences.

loci.plugins.shortcut - package loci.plugins.shortcut

Bio-Formats Plugins Shortcut Window plugin for ImageJ.

loci.plugins.util - package loci.plugins.util

Utility classes and methods for the Bio-Formats plugins for ImageJ.

LociConfig - Class in loci.plugins.config

An ImageJ plugin for displaying the Bio-Formats plugins configuration dialog.

LociConfig() - Constructor for class loci.plugins.config.LociConfig

LociExporter - Class in loci.plugins

ImageJ plugin for writing files using the OME Bio-Formats package.

LociExporter() - Constructor for class loci.plugins.LociExporter

LociFunctions - Class in loci.plugins.macro

This class provides macro extensions in ImageJ for Bio-Formats.

LociFunctions() - Constructor for class loci.plugins.macro.LociFunctions

LociImporter - Class in loci.plugins

ImageJ plugin for reading files using the OME Bio-Formats package.

LociImporter() - Constructor for class loci.plugins.LociImporter

LociInstaller - Class in loci.plugins.config

An ImageJ plugin for installing and upgrading libraries related to the Bio-Formats plugins.

LociInstaller() - Constructor for class loci.plugins.config.LociInstaller

LociPrefs - Class in loci.plugins.util

Utility methods for ImageJ preferences for Bio-Formats plugins.

log() - Method in class loci.plugins.util.RecordedImageProcessor

M

MacroFunctions - Class in loci.plugins.macro

Convenience class that simplifies implemention of ImageJ macro extensions.

MacroFunctions() - Constructor for class loci.plugins.macro.MacroFunctions

main(String[]) - Static method in class loci.plugins.About

main(String[]) - Static method in class loci.plugins.config.LociConfig

main(String[]) - Static method in class loci.plugins.in.Importer

Main method, for testing.

MainDialog - Class in loci.plugins.in

Bio-Formats Importer general options dialog box.

MainDialog(ImportProcess) - Constructor for class loci.plugins.in.MainDialog

Creates a general options dialog for the Bio-Formats Importer.

makeCompactGrid(Container, int, int, int, int, int, int) - Static method in class loci.plugins.config.SpringUtilities

Aligns the first rows * cols components of parent in a grid.

makeDummySlider() - Static method in class loci.plugins.util.DataBrowser

makeGrid(Container, int, int, int, int, int, int) - Static method in class loci.plugins.config.SpringUtilities

Aligns the first rows * cols components of parent in a grid.

makeHeavyPanel(Component) - Static method in class loci.plugins.util.DataBrowser

Makes AWT play nicely with Swing components.

makeImageProcessorReader(IFormatReader) - Static method in class loci.plugins.util.ImageProcessorReader

Converts the given reader into a ImageProcessorReader, wrapping if needed.

makeImageReader() - Static method in class loci.plugins.util.LociPrefs

Creates an image reader according to the current configuration settings, including which format readers are currently enabled, as well as format-specific configuration settings.

makeTextField() - Static method in class loci.plugins.config.ConfigWindow

max(double) - Method in class loci.plugins.util.RecordedImageProcessor

MAX_COMPONENTS - Static variable in class loci.plugins.in.SeriesDialog

MAX_SERIES_THUMBS - Static variable in class loci.plugins.in.SeriesDialog

MAX_SERIES_TOGGLES - Static variable in class loci.plugins.in.SeriesDialog

maxValue() - Method in class loci.plugins.util.RecordedImageProcessor

medianFilter() - Method in class loci.plugins.util.RecordedImageProcessor

MemoryDialog - Class in loci.plugins.in

Bio-Formats Importer memory usage confirmation dialog box.

MemoryDialog(ImportProcess) - Constructor for class loci.plugins.in.MemoryDialog

Creates a memory confirmation dialog for the Bio-Formats Importer.

meta - Variable in class loci.plugins.in.ImportProcess

metadata - Variable in class loci.plugins.util.DataBrowser

METADATA - Enum constant in enum loci.plugins.in.ImportStep

metaWindow - Variable in class loci.plugins.util.DataBrowser

min(double) - Method in class loci.plugins.util.RecordedImageProcessor

MIN_BROWSER_WIDTH - Static variable in class loci.plugins.util.DataBrowser

minValue() - Method in class loci.plugins.util.RecordedImageProcessor

MISSING_VERSION_CODE - Static variable in class loci.plugins.config.LibraryEntry

Version code to indicate a missing library.

mouseClicked(MouseEvent) - Method in class loci.plugins.in.MainDialog

mouseEntered(MouseEvent) - Method in class loci.plugins.in.MainDialog

Focuses the component upon mouseover.

mouseExited(MouseEvent) - Method in class loci.plugins.in.MainDialog

mousePressed(MouseEvent) - Method in class loci.plugins.in.MainDialog

mouseReleased(MouseEvent) - Method in class loci.plugins.in.MainDialog

mouseWheelMoved(MouseWheelEvent) - Method in class loci.plugins.util.DataBrowser

moveTo(int, int) - Method in class loci.plugins.util.RecordedImageProcessor

multiply(double) - Method in class loci.plugins.util.RecordedImageProcessor

N

name - Variable in class loci.plugins.config.LibraryEntry

names - Static variable in class loci.plugins.shortcut.ShortcutPanel

Details for installed plugins.

ND2Widgets - Class in loci.plugins.config

Custom widgets for configuring Bio-Formats ND2 support.

ND2Widgets() - Constructor for class loci.plugins.config.ND2Widgets

needPrompt() - Method in class loci.plugins.in.ColorDialog

needPrompt() - Method in class loci.plugins.in.CropDialog

needPrompt() - Method in class loci.plugins.in.FilePatternDialog

needPrompt() - Method in class loci.plugins.in.IdDialog

needPrompt() - Method in class loci.plugins.in.ImporterDialog

needPrompt() - Method in class loci.plugins.in.LocationDialog

needPrompt() - Method in class loci.plugins.in.MainDialog

needPrompt() - Method in class loci.plugins.in.MemoryDialog

needPrompt() - Method in class loci.plugins.in.RangeDialog

needPrompt() - Method in class loci.plugins.in.SeriesDialog

needPrompt() - Method in class loci.plugins.in.SwapDialog

needPrompt() - Method in class loci.plugins.in.UpgradeDialog

noise(double) - Method in class loci.plugins.util.RecordedImageProcessor

NORMAL_MENU - Static variable in class loci.plugins.shortcut.ShortcutPanel

Name of the 'Bio-Formats' submenu.

notes - Variable in class loci.plugins.config.LibraryEntry

notifyListeners(StatusEvent) - Method in class loci.plugins.in.ImagePlusReader

notifyListeners(StatusEvent) - Method in class loci.plugins.in.ImportProcess

O

OME_JAVA_XML - Enum constant in enum loci.plugins.util.LibraryChecker.Library

open(String) - Method in class loci.plugins.shortcut.ShortcutPanel

Opens the given location (e.g., file) with the Bio-Formats Importer plugin.

openAllSeries() - Method in class loci.plugins.in.ImporterOptions

openAllSeriesBox - Variable in class loci.plugins.in.MainDialog

OPENER_PLUGIN - Static variable in class loci.plugins.shortcut.ShortcutPanel

Name of plugin to use for opening dropped files.

openerIndex - Static variable in class loci.plugins.shortcut.ShortcutPanel

Index of plugin to use to open dropped files.

openImage(String, Double) - Method in class loci.plugins.macro.LociFunctions

openImagePlus() - Method in class loci.plugins.in.ImagePlusReader

Opens one or more ImagePlus objects corresponding to the reader's associated options.

openImagePlus(String) - Static method in class loci.plugins.BF

openImagePlus(String) - Method in class loci.plugins.macro.LociFunctions

openImagePlus(ImporterOptions) - Static method in class loci.plugins.BF

openPlane(int, int, int, int, int) - Method in class loci.plugins.util.ImageProcessorReader

openProcessors(int) - Method in class loci.plugins.util.ImageProcessorReader

Creates an ImageJ image processor object for the image plane at the given position.

openProcessors(int, int, int, int, int) - Method in class loci.plugins.util.ImageProcessorReader

Returns an array of ImageProcessors that represent the given slice.

openROIs(IMetadata, ImagePlus[]) - Static method in class loci.plugins.util.ROIHandler

Look for ROIs in the given OMEXMLMetadata; if any are present, apply them to the given images and display them in the ROI manager.

openROIs(IMetadata, ImagePlus[], boolean) - Static method in class loci.plugins.util.ROIHandler

Opens the rois and converts them into ImageJ Rois.

openROIs(IMetadata, ImagePlus[], boolean, String) - Static method in class loci.plugins.util.ROIHandler

Opens the rois and converts them into ImageJ Rois.

openSubImage(String, Double, Double, Double, Double, Double) - Method in class loci.plugins.macro.LociFunctions

openThumbImage(String, Double) - Method in class loci.plugins.macro.LociFunctions

openThumbImagePlus() - Method in class loci.plugins.in.ImagePlusReader

openThumbImagePlus(String) - Static method in class loci.plugins.BF

openThumbImagePlus(String) - Method in class loci.plugins.macro.LociFunctions

openThumbImagePlus(ImporterOptions) - Static method in class loci.plugins.BF

openThumbProcessors(int) - Method in class loci.plugins.util.ImageProcessorReader

Option - Class in loci.plugins.prefs

Base class for an option for one of the plugins.

Option(String, boolean, String, String) - Constructor for class loci.plugins.prefs.Option

Constructs an option with the given parameters.

options - Variable in class loci.plugins.in.DisplayHandler

options - Variable in class loci.plugins.in.ImporterDialog

options - Variable in class loci.plugins.prefs.OptionsList

Table of options defining this set of preferences.

options - Variable in class loci.plugins.util.DataBrowser

OptionsDialog - Class in loci.plugins.prefs

Base class for options dialogs.

OptionsDialog(OptionsList) - Constructor for class loci.plugins.prefs.OptionsDialog

Creates a new options dialog with the given associated options.

optionsList - Variable in class loci.plugins.prefs.OptionsDialog

Options list associated with the dialog.

OptionsList - Class in loci.plugins.prefs

Base class for ImageJ preferences for plugins.

OptionsList(String, Class<?>) - Constructor for class loci.plugins.prefs.OptionsList

OptionsList(IniList) - Constructor for class loci.plugins.prefs.OptionsList

optionsWindow - Variable in class loci.plugins.util.DataBrowser

or(int) - Method in class loci.plugins.util.RecordedImageProcessor

ORDER_DEFAULT - Static variable in class loci.plugins.in.ImporterOptions

ORDER_XYCTZ - Static variable in class loci.plugins.in.ImporterOptions

ORDER_XYCZT - Static variable in class loci.plugins.in.ImporterOptions

ORDER_XYTCZ - Static variable in class loci.plugins.in.ImporterOptions

ORDER_XYTZC - Static variable in class loci.plugins.in.ImporterOptions

ORDER_XYZCT - Static variable in class loci.plugins.in.ImporterOptions

ORDER_XYZTC - Static variable in class loci.plugins.in.ImporterOptions

P

pack() - Method in class loci.plugins.util.DataBrowser

Overridden pack method to allow us to delay initial window sizing.

panel - Variable in class loci.plugins.util.SearchableWindow

parseArg(String) - Method in class loci.plugins.in.ImporterOptions

Parses the plugin argument for parameter values.

parseList(String) - Static method in class loci.plugins.prefs.StringOption

Parses a string of comma-separated values into a list of tokens.

parseOption(String) - Method in class loci.plugins.prefs.BooleanOption

parseOption(String) - Method in class loci.plugins.prefs.DoubleOption

parseOption(String) - Method in class loci.plugins.prefs.Option

Parses the option's value from the given argument string.

parseOption(String) - Method in class loci.plugins.prefs.StringOption

parseOptions(String) - Method in class loci.plugins.in.Importer

Parses core options.

parseOptions(String) - Method in class loci.plugins.prefs.OptionsList

Parses option values from the given argument string.

path - Variable in class loci.plugins.config.LibraryEntry

placeWindow(Window) - Static method in class loci.plugins.util.WindowTools

Places the given window at a nice location on screen, either centered below the ImageJ window if there is one, or else centered on screen.

plugins - Static variable in class loci.plugins.shortcut.ShortcutPanel

Details for installed plugins.

possibleValues - Variable in class loci.plugins.prefs.StringOption

List of possible values.

PREF_CELLSENS_FAIL - Static variable in class loci.plugins.util.LociPrefs

PREF_CZI_ATTACHMENT - Static variable in class loci.plugins.util.LociPrefs

PREF_CZI_AUTOSTITCH - Static variable in class loci.plugins.util.LociPrefs

PREF_LEICA_LIF_PHYSICAL_SIZE - Static variable in class loci.plugins.util.LociPrefs

PREF_ND2_CHUNKMAP - Static variable in class loci.plugins.util.LociPrefs

PREF_READER_ENABLED - Static variable in class loci.plugins.util.LociPrefs

PREF_READER_WINDOWLESS - Static variable in class loci.plugins.util.LociPrefs

PREF_SDT_INTENSITY - Static variable in class loci.plugins.util.LociPrefs

PREF_SLICE_LABEL_BASE_INDEX - Static variable in class loci.plugins.util.LociPrefs

PREF_SLICE_LABEL_PATTERN - Static variable in class loci.plugins.util.LociPrefs

PREF_TIFF_IMAGEIO - Static variable in class loci.plugins.util.LociPrefs

printSizes(Component) - Static method in class loci.plugins.config.SpringUtilities

A debugging utility that prints to stdout the component's minimum, preferred, and maximum sizes.

process - Variable in class loci.plugins.in.DisplayHandler

process - Variable in class loci.plugins.in.ImagePlusReader

Import preparation process managing Bio-Formats readers and other state.

process - Variable in class loci.plugins.in.ImporterDialog

progress(boolean, int, int) - Static method in class loci.plugins.BF

PROP_LUT - Static variable in class loci.plugins.in.ImagePlusReader

Special property prefix for storing planar LUTs.

PROP_SERIES - Static variable in class loci.plugins.in.ImagePlusReader

Special property for storing series number associated with the image.

putColumn(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor

putPixel(int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor

putPixel(int, int, int[]) - Method in class loci.plugins.util.RecordedImageProcessor

putPixelValue(int, int, double) - Method in class loci.plugins.util.RecordedImageProcessor

putRow(int, int, int[], int) - Method in class loci.plugins.util.RecordedImageProcessor

R

RANGE - Enum constant in enum loci.plugins.in.ImportStep

RangeDialog - Class in loci.plugins.in

Bio-Formats Importer range chooser dialog box.

RangeDialog(ImportProcess) - Constructor for class loci.plugins.in.RangeDialog

Creates a range chooser dialog for the Bio-Formats Importer.

reader - Variable in class loci.plugins.util.BFVirtualStack

reader - Variable in class loci.plugins.util.ImageProcessorSource

Image reader from which to draw ImageProcessors.

READER - Enum constant in enum loci.plugins.in.ImportStep

readerName - Variable in class loci.plugins.config.FormatEntry

readFromOverlays() - Static method in class loci.plugins.util.ROIHandler

Returns rois if any from the overlay.

readFromRoiManager() - Static method in class loci.plugins.util.ROIHandler

Returns the rois if any stored in the ROI manager.

readPixels(ImagePlusReader, ImporterOptions, DisplayHandler) - Method in class loci.plugins.in.Importer

RecordedImageProcessor - Class in loci.plugins.util

Image processor extension that records commands executed upon it.

RecordedImageProcessor(ImageProcessor) - Constructor for class loci.plugins.util.RecordedImageProcessor

RecordedImageProcessor(ImageProcessor, int, ImageProcessor[]) - Constructor for class loci.plugins.util.RecordedImageProcessor

removePossible(String) - Method in class loci.plugins.prefs.StringOption

Removes a possible value from the list.

removeStatusListener(StatusListener) - Method in class loci.plugins.in.ImagePlusReader

removeStatusListener(StatusListener) - Method in class loci.plugins.in.ImportProcess

reorder(ImagePlus, String, String) - Static method in class loci.plugins.Slicer

Reorder the given ImagePlus's stack.

reportException(Throwable) - Static method in class loci.plugins.util.WindowTools

Reports the given exception with stack trace in an ImageJ error dialog.

reportException(Throwable, boolean) - Static method in class loci.plugins.util.WindowTools

Reports the given exception with stack trace in an ImageJ error dialog.

reportException(Throwable, boolean, String) - Static method in class loci.plugins.util.WindowTools

Reports the given exception with stack trace in an ImageJ error dialog.

reset() - Method in class loci.plugins.util.RecordedImageProcessor

reset(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor

resetBinaryThreshold() - Method in class loci.plugins.util.RecordedImageProcessor

resetMinAndMax() - Method in class loci.plugins.util.RecordedImageProcessor

resetRoi() - Method in class loci.plugins.util.RecordedImageProcessor

resetThreshold() - Method in class loci.plugins.util.RecordedImageProcessor

resize(int) - Method in class loci.plugins.util.RecordedImageProcessor

resize(int, int) - Method in class loci.plugins.util.RecordedImageProcessor

reslice(ImagePlus, boolean, boolean, boolean, String) - Method in class loci.plugins.Slicer

ROIHandler - Class in loci.plugins.util

Utility class for managing regions of interest within ImageJ.

ROIHandler() - Constructor for class loci.plugins.util.ROIHandler

ROIS_MODE_MANAGER - Static variable in class loci.plugins.in.ImporterOptions

ROIS_MODE_OVERLAY - Static variable in class loci.plugins.in.ImporterOptions

roisModeChoice - Variable in class loci.plugins.in.MainDialog

rotate(double) - Method in class loci.plugins.util.RecordedImageProcessor

rotateLeft() - Method in class loci.plugins.util.RecordedImageProcessor

rotateRight() - Method in class loci.plugins.util.RecordedImageProcessor

run() - Method in class loci.plugins.config.ConfigWindow

Populate configuration information in a separate thread.

run() - Method in class loci.plugins.in.ThumbLoader

Does the work of loading the thumbnails.

run() - Method in class loci.plugins.out.Exporter

Executes the plugin.

run(ImageProcessor) - Method in class loci.plugins.LociExporter

Executes the plugin.

run(ImageProcessor) - Method in class loci.plugins.Slicer

run(String) - Method in class loci.plugins.About

run(String) - Method in class loci.plugins.config.LociConfig

Executes the plugin.

run(String) - Method in class loci.plugins.config.LociInstaller

Executes the plugin.

run(String) - Method in class loci.plugins.in.Importer

Executes the plugin.

run(String) - Method in class loci.plugins.LociImporter

Executes the plugin.

run(String) - Method in class loci.plugins.macro.LociFunctions

run(String) - Method in class loci.plugins.macro.MacroFunctions

run(String) - Method in class loci.plugins.shortcut.ShortcutPanel

Executes the plugin.

run(String) - Method in class loci.plugins.Updater

runPlugIn(String, String) - Static method in class loci.plugins.shortcut.ShortcutPanel

Executes the given plugin, in a separate thread.

S

save - Variable in class loci.plugins.prefs.Option

Whether option state should be saved to ImageJ preferences file.

saveOption() - Method in class loci.plugins.prefs.BooleanOption

saveOption() - Method in class loci.plugins.prefs.DoubleOption

saveOption() - Method in class loci.plugins.prefs.Option

Saves the option's value to the ImageJ preferences file.

saveOption() - Method in class loci.plugins.prefs.StringOption

saveOptions() - Method in class loci.plugins.prefs.OptionsList

Saves option values to the ImageJ preferences file.

saveROIs(MetadataStore) - Static method in class loci.plugins.util.ROIHandler

Save ROIs in the ROI manager to the given MetadataStore.

scale(double, double) - Method in class loci.plugins.util.RecordedImageProcessor

SDTWidgets - Class in loci.plugins.config

Custom widgets for configuring Bio-Formats SDT support.

SDTWidgets() - Constructor for class loci.plugins.config.SDTWidgets

SearchableWindow - Class in loci.plugins.util

Text panel with search capabilities.

SearchableWindow(String, String, String, int, int) - Constructor for class loci.plugins.util.SearchableWindow

selectLine(int) - Method in class loci.plugins.util.SearchableWindow

SERIES - Enum constant in enum loci.plugins.in.ImportStep

SeriesDialog - Class in loci.plugins.in

Bio-Formats Importer series chooser dialog box.

SeriesDialog(ImportProcess) - Constructor for class loci.plugins.in.SeriesDialog

Creates a series chooser dialog for the Bio-Formats Importer.

SeriesInfo(int, int) - Constructor for class loci.plugins.in.ThumbLoader.SeriesInfo

set(int, int) - Method in class loci.plugins.util.RecordedImageProcessor

set(int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor

setAntialiasedText(boolean) - Method in class loci.plugins.util.RecordedImageProcessor

setAutoscale(boolean) - Method in class loci.plugins.in.ImporterOptions

setAutoThreshold(int, int) - Method in class loci.plugins.util.RecordedImageProcessor

setBackgroundValue(double) - Method in class loci.plugins.util.RecordedImageProcessor

setCalibrationTable(float[]) - Method in class loci.plugins.util.RecordedImageProcessor

setCBegin(int, int) - Method in class loci.plugins.in.ImporterOptions

setCEnd(int, int) - Method in class loci.plugins.in.ImporterOptions

setClipRect(Rectangle) - Method in class loci.plugins.util.RecordedImageProcessor

setColor(int) - Method in class loci.plugins.util.RecordedImageProcessor

setColor(Color) - Method in class loci.plugins.util.RecordedImageProcessor

setColorMode(String) - Method in class loci.plugins.in.ImporterOptions

setColorModel(ColorModel) - Method in class loci.plugins.util.RecordedImageProcessor

setConcatenate(boolean) - Method in class loci.plugins.in.ImporterOptions

setCrop(boolean) - Method in class loci.plugins.in.ImporterOptions

setCropRegion(int, Region) - Method in class loci.plugins.in.ImporterOptions

setCStep(int, int) - Method in class loci.plugins.in.ImporterOptions

setCustomColor(int, int, Color) - Method in class loci.plugins.in.ImporterOptions

setDoRecording(boolean) - Method in class loci.plugins.util.RecordedImageProcessor

setf(int, float) - Method in class loci.plugins.util.RecordedImageProcessor

setf(int, int, float) - Method in class loci.plugins.util.RecordedImageProcessor

setFirstTime(boolean) - Method in class loci.plugins.in.ImporterOptions

setFloatArray(float[][]) - Method in class loci.plugins.util.RecordedImageProcessor

setFont(Font) - Method in class loci.plugins.util.RecordedImageProcessor

setForceThumbnails(boolean) - Method in class loci.plugins.in.ImporterOptions

setGroupFiles(boolean) - Method in class loci.plugins.in.ImporterOptions

setGroupFiles(String) - Method in class loci.plugins.macro.LociFunctions

setHistogramRange(double, double) - Method in class loci.plugins.util.RecordedImageProcessor

setHistogramSize(int) - Method in class loci.plugins.util.RecordedImageProcessor

setId(String) - Method in class loci.plugins.in.ImporterOptions

setId(String) - Method in class loci.plugins.macro.LociFunctions

setInputOrder(int, String) - Method in class loci.plugins.in.ImporterOptions

setIntArray(int[][]) - Method in class loci.plugins.util.RecordedImageProcessor

setInterpolate(boolean) - Method in class loci.plugins.util.RecordedImageProcessor

setJustification(int) - Method in class loci.plugins.util.RecordedImageProcessor

setLineWidth(int) - Method in class loci.plugins.util.RecordedImageProcessor

setLocation(String) - Method in class loci.plugins.in.ImporterOptions

setLutAnimation(boolean) - Method in class loci.plugins.util.RecordedImageProcessor

setLUTs(LUT[]) - Method in class loci.plugins.util.VirtualImagePlus

setMask(ImageProcessor) - Method in class loci.plugins.util.RecordedImageProcessor

setMetadataFiltered(String) - Method in class loci.plugins.macro.LociFunctions

setMinAndMax(double, double) - Method in class loci.plugins.util.RecordedImageProcessor

setMustGroup(boolean) - Method in class loci.plugins.in.ImporterOptions

setNormalized(Boolean) - Method in class loci.plugins.macro.LociFunctions

setOpenAllSeries(boolean) - Method in class loci.plugins.in.ImporterOptions

setOriginalMetadataPopulated(Boolean) - Method in class loci.plugins.macro.LociFunctions

setPixels(int, FloatProcessor) - Method in class loci.plugins.util.RecordedImageProcessor

setPixels(Object) - Method in class loci.plugins.util.RecordedImageProcessor

setPlaneIndexes(int[]) - Method in class loci.plugins.util.BFVirtualStack

setProgressBar(ProgressBar) - Method in class loci.plugins.util.RecordedImageProcessor

setQuiet(boolean) - Method in class loci.plugins.in.ImporterOptions

setReader(IFormatReader) - Method in class loci.plugins.util.VirtualImagePlus

setRefCount(int) - Method in class loci.plugins.util.VirtualReader

setRoi(int, int, int, int) - Method in class loci.plugins.util.RecordedImageProcessor

setRoi(Roi) - Method in class loci.plugins.util.RecordedImageProcessor

setRoi(Polygon) - Method in class loci.plugins.util.RecordedImageProcessor

setRoi(Rectangle) - Method in class loci.plugins.util.RecordedImageProcessor

setROIsMode(String) - Method in class loci.plugins.in.ImporterOptions

setSeries(Double) - Method in class loci.plugins.macro.LociFunctions

setSeriesList(String) - Method in class loci.plugins.in.ImportProcess

setSeriesOn(int, boolean) - Method in class loci.plugins.in.ImporterOptions

setShowMetadata(boolean) - Method in class loci.plugins.in.ImporterOptions

setShowOMEXML(boolean) - Method in class loci.plugins.in.ImporterOptions

setShowROIs(boolean) - Method in class loci.plugins.in.ImporterOptions

setSlice(int) - Method in class loci.plugins.util.VirtualImagePlus

setSnapshotCopyMode(boolean) - Method in class loci.plugins.util.RecordedImageProcessor

setSnapshotPixels(Object) - Method in class loci.plugins.util.RecordedImageProcessor

setSpecifyRanges(boolean) - Method in class loci.plugins.in.ImporterOptions

setSplitChannels(boolean) - Method in class loci.plugins.in.ImporterOptions

setSplitFocalPlanes(boolean) - Method in class loci.plugins.in.ImporterOptions

setSplitTimepoints(boolean) - Method in class loci.plugins.in.ImporterOptions

setStackFormat(String) - Method in class loci.plugins.in.ImporterOptions

setStackOrder(String) - Method in class loci.plugins.in.ImporterOptions

setStitchTiles(boolean) - Method in class loci.plugins.in.ImporterOptions

setSwapDimensions(boolean) - Method in class loci.plugins.in.ImporterOptions

setTBegin(int, int) - Method in class loci.plugins.in.ImporterOptions

setTEnd(int, int) - Method in class loci.plugins.in.ImporterOptions

setThreshold(double, double, int) - Method in class loci.plugins.util.RecordedImageProcessor

setTStep(int, int) - Method in class loci.plugins.in.ImporterOptions

setUngroupFiles(boolean) - Method in class loci.plugins.in.ImporterOptions

setup(String, ImagePlus) - Method in class loci.plugins.LociExporter

Sets up the writer.

setup(String, ImagePlus) - Method in class loci.plugins.Slicer

setUpgradeCheck(boolean) - Method in class loci.plugins.in.ImporterOptions

setUsingPatternIds(boolean) - Method in class loci.plugins.in.ImporterOptions

setValue(boolean) - Method in class loci.plugins.prefs.BooleanOption

Sets the current value of the option.

setValue(double) - Method in class loci.plugins.prefs.DoubleOption

Sets the current value of the option.

setValue(double) - Method in class loci.plugins.util.RecordedImageProcessor

setValue(String) - Method in class loci.plugins.prefs.StringOption

Sets the current value of the option.

setValue(String, boolean) - Method in class loci.plugins.prefs.OptionsList

Sets the value of the boolean option with the given key.

setValue(String, String) - Method in class loci.plugins.prefs.OptionsList

Sets the value of the string option with the given key.

setVirtual(boolean) - Method in class loci.plugins.in.ImporterOptions

setVisible(boolean) - Method in class loci.plugins.util.DataBrowser

Overridden show method to allow us to delay initial window display.

setWindowless(boolean) - Method in class loci.plugins.in.ImporterOptions

setXML(String) - Method in class loci.plugins.util.DataBrowser

Sets XML block associated with this window.

setZBegin(int, int) - Method in class loci.plugins.in.ImporterOptions

setZEnd(int, int) - Method in class loci.plugins.in.ImporterOptions

setZStep(int, int) - Method in class loci.plugins.in.ImporterOptions

sharpen() - Method in class loci.plugins.util.RecordedImageProcessor

SHORTCUT_PLUGIN - Static variable in class loci.plugins.shortcut.ShortcutPanel

Name of this plugin, ignored when parsing the plugins list.

shortcutPanel - Variable in class loci.plugins.shortcut.ShortcutTransferHandler

Associated shortcut panel.

ShortcutPanel - Class in loci.plugins.shortcut

A plugin that displays a small window containing shortcuts to the plugins, including the Bio-Formats Importer, Bio-Formats Exporter, Stack Colorizer and Stack Slicer.

ShortcutPanel() - Constructor for class loci.plugins.shortcut.ShortcutPanel

Constructs a shortcut panel.

ShortcutTransferHandler - Class in loci.plugins.shortcut

Drag and drop transfer handler for Bio-Formats Plugins Shortcut Window.

ShortcutTransferHandler(ShortcutPanel) - Constructor for class loci.plugins.shortcut.ShortcutTransferHandler

Constructs a new shortcut panel drag and drop transfer handler.

showDialog() - Method in class loci.plugins.in.ImporterDialog

showDialog() - Method in class loci.plugins.prefs.OptionsDialog

Displays the options dialog, returning the status of the operation.

showDialogs(ImportProcess) - Method in class loci.plugins.in.Importer

showMetadataBox - Variable in class loci.plugins.in.MainDialog

showMetadataWindow() - Method in class loci.plugins.util.DataBrowser

Displays the OME-XML metadata window onscreen.

showOMEXMLBox - Variable in class loci.plugins.in.MainDialog

showOptionsWindow() - Method in class loci.plugins.util.DataBrowser

Displays the caching options window onscreen.

showROIs() - Method in class loci.plugins.in.ImporterOptions

showROIsBox - Variable in class loci.plugins.in.MainDialog

sleep(long) - Method in class loci.plugins.prefs.OptionsDialog

Blocks the current thread for the specified number of milliseconds.

Slicer - Class in loci.plugins

A plugin for splitting an image stack into separate channels, focal planes and/or time points.

Slicer() - Constructor for class loci.plugins.Slicer

smooth() - Method in class loci.plugins.util.RecordedImageProcessor

snapshot() - Method in class loci.plugins.util.RecordedImageProcessor

specifyRangesBox - Variable in class loci.plugins.in.MainDialog

splitCBox - Variable in class loci.plugins.in.MainDialog

splitTBox - Variable in class loci.plugins.in.MainDialog

splitZBox - Variable in class loci.plugins.in.MainDialog

SpringUtilities - Class in loci.plugins.config

A 1.4 file that provides utility methods for creating form- or grid-style layouts with SpringLayout.

SpringUtilities() - Constructor for class loci.plugins.config.SpringUtilities

sqr() - Method in class loci.plugins.util.RecordedImageProcessor

sqrt() - Method in class loci.plugins.util.RecordedImageProcessor

STACK - Enum constant in enum loci.plugins.in.ImportStep

stackFormatChoice - Variable in class loci.plugins.in.MainDialog

stackOrderChoice - Variable in class loci.plugins.in.MainDialog

status - Variable in class loci.plugins.config.LibraryEntry

status(boolean, String) - Static method in class loci.plugins.BF

STATUS_CANCELED - Static variable in class loci.plugins.prefs.OptionsDialog

STATUS_FINISHED - Static variable in class loci.plugins.prefs.OptionsDialog

STATUS_OK - Static variable in class loci.plugins.prefs.OptionsDialog

statusUpdated(StatusEvent) - Method in class loci.plugins.in.DisplayHandler

Reports status updates via ImageJ's status bar mechanism.

statusUpdated(StatusEvent) - Method in class loci.plugins.in.ImporterPrompter

stitchTilesBox - Variable in class loci.plugins.in.MainDialog

stop() - Method in class loci.plugins.in.ThumbLoader

Instructs the thumbnail loader to stop loading thumbnails.

StringOption - Class in loci.plugins.prefs

A string option for one of the plugins.

StringOption(String, boolean, String, String, String, Vector<String>) - Constructor for class loci.plugins.prefs.StringOption

Constructs a string option with the given parameters.

StringOption(HashMap<String, String>) - Constructor for class loci.plugins.prefs.StringOption

Constructs a string option with the parameters from the given map.

success - Variable in class loci.plugins.LociImporter

Flag indicating whether last operation was successful.

suffixes - Variable in class loci.plugins.config.FormatEntry

SwapDialog - Class in loci.plugins.in

Bio-Formats Importer dimension swapper dialog box.

SwapDialog(ImportProcess) - Constructor for class loci.plugins.in.SwapDialog

Creates a dimension swapper dialog for the Bio-Formats Importer.

swapDimsBox - Variable in class loci.plugins.in.MainDialog

swapPixelArrays() - Method in class loci.plugins.util.RecordedImageProcessor

T

TextAreaWriter - Class in loci.plugins.config

Writer implementation that writes to a JTextArea document.

TextAreaWriter(JTextArea) - Constructor for class loci.plugins.config.TextAreaWriter

Constructs a new TextAreaWriter around the given text area component.

threshold(int) - Method in class loci.plugins.util.RecordedImageProcessor

ThumbLoader - Class in loci.plugins.in

Loads thumbnails for Bio-Formats Importer series chooser in a separate thread.

ThumbLoader(IFormatReader, Panel[], Dialog) - Constructor for class loci.plugins.in.ThumbLoader

Constructs a new thumbnail loader.

ThumbLoader.SeriesInfo - Class in loci.plugins.in

Helper class for sorting series by image plane size.

TiffDelegateWidgets - Class in loci.plugins.config

Custom widgets for configuring Bio-Formats TIFF support.

TiffDelegateWidgets() - Constructor for class loci.plugins.config.TiffDelegateWidgets

toFloat(int, FloatProcessor) - Method in class loci.plugins.util.RecordedImageProcessor

toggleAnimation() - Method in class loci.plugins.util.DataBrowser

Toggles whether the data browser is animating.

toString() - Method in class loci.plugins.config.FormatEntry

toString() - Method in class loci.plugins.config.LibraryEntry

toString() - Method in class loci.plugins.in.ImporterMetadata

toString() - Method in class loci.plugins.util.RecordedImageProcessor

translate(int, int) - Method in class loci.plugins.util.RecordedImageProcessor

tScroll - Variable in class loci.plugins.util.DataBrowser

type - Variable in class loci.plugins.config.LibraryEntry

TYPE_BOOLEAN - Static variable in class loci.plugins.prefs.OptionsList

String indicating option is of type boolean.

TYPE_STRING - Static variable in class loci.plugins.prefs.OptionsList

String indicating option is of type string.

U

ungroupFilesBox - Variable in class loci.plugins.in.MainDialog

updateComposite(int[], int) - Method in class loci.plugins.util.RecordedImageProcessor

Updater - Class in loci.plugins

A plugin for updating the Bio-Formats plugins.

Updater() - Constructor for class loci.plugins.Updater

UpgradeDialog - Class in loci.plugins.in

Bio-Formats Importer upgrade checker dialog box.

UpgradeDialog(ImportProcess) - Constructor for class loci.plugins.in.UpgradeDialog

Creates an upgrade checker dialog for the Bio-Formats Importer.

url - Variable in class loci.plugins.config.LibraryEntry

URL_BF_SOFTWARE - Static variable in class loci.plugins.util.LibraryChecker

URL for Bio-Formats web page.

URL_BIO_FORMATS_IMAGEJ - Static variable in class loci.plugins.About

URL of Bio-Formats ImageJ web page.

URL_DATA_BROWSER - Static variable in class loci.plugins.About

URL of Data Browser web page.

URL_JAVADOCS - Static variable in class loci.plugins.macro.LociFunctions

URL for Javadocs.

URL_SOFTWARE - Static variable in class loci.plugins.About

URL of the Bio-Formats web page.

useND2Chunkmap() - Static method in class loci.plugins.util.LociPrefs

V

value - Variable in class loci.plugins.prefs.BooleanOption

The option's current value.

value - Variable in class loci.plugins.prefs.DoubleOption

The option's current value.

value - Variable in class loci.plugins.prefs.StringOption

The option's current value.

valueChanged(ListSelectionEvent) - Method in class loci.plugins.config.ConfigWindow

valueOf(String) - Static method in enum loci.plugins.in.ImportStep

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum loci.plugins.util.LibraryChecker.Library

Returns the enum constant of this type with the specified name.

values() - Static method in enum loci.plugins.in.ImportStep

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum loci.plugins.util.LibraryChecker.Library

Returns an array containing the constants of this enum type, in the order they are declared.

version - Variable in class loci.plugins.config.LibraryEntry

VIEW_BROWSER - Static variable in class loci.plugins.in.ImporterOptions

VIEW_HYPERSTACK - Static variable in class loci.plugins.in.ImporterOptions

VIEW_IMAGE_5D - Static variable in class loci.plugins.in.ImporterOptions

VIEW_NONE - Static variable in class loci.plugins.in.ImporterOptions

VIEW_STANDARD - Static variable in class loci.plugins.in.ImporterOptions

VIEW_VIEW_5D - Static variable in class loci.plugins.in.ImporterOptions

virtualBox - Variable in class loci.plugins.in.MainDialog

VirtualImagePlus - Class in loci.plugins.util

Extension of ImagePlus that supports Bio-Formats-driven virtual stacks.

VirtualImagePlus(String, ImageStack) - Constructor for class loci.plugins.util.VirtualImagePlus

VirtualReader - Class in loci.plugins.util

TODO

VirtualReader(IFormatReader) - Constructor for class loci.plugins.util.VirtualReader

W

warn(boolean, String) - Static method in class loci.plugins.BF

wasCanceled() - Method in class loci.plugins.in.ImportProcess

Gets whether the import process was canceled.

widgets - Variable in class loci.plugins.config.FormatEntry

WindowTools - Class in loci.plugins.util

Utility methods for managing ImageJ dialogs and windows.

write(char[], int, int) - Method in class loci.plugins.config.TextAreaWriter

Writes the given characters to the associated text area component.

X

xml - Variable in class loci.plugins.util.DataBrowser

xmlWindow - Variable in class loci.plugins.in.DisplayHandler

xor(int) - Method in class loci.plugins.util.RecordedImageProcessor

Z

ZeissCZIWidgets - Class in loci.plugins.config

Custom widgets for configuring Bio-Formats Zeiss CZI support.

ZeissCZIWidgets() - Constructor for class loci.plugins.config.ZeissCZIWidgets

zScroll - Variable in class loci.plugins.util.DataBrowser

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