A B C D E F G H I J L M N O P R S T U V W X Y

A

AbstractColorProviderPixelSelectorOverlay - Class in adams.flow.transformer.pixelselector

Overlay that uses a color provider for the painting the various elements of the overlay.

AbstractColorProviderPixelSelectorOverlay() - Constructor for class adams.flow.transformer.pixelselector.AbstractColorProviderPixelSelectorOverlay

AbstractFFmpegPlugin - Class in adams.flow.sink.ffmpeg

Ancestor for FFmpeg plugins.

AbstractFFmpegPlugin() - Constructor for class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

AbstractFFmpegPluginWithOptions - Class in adams.flow.sink.ffmpeg

Ancestor for FFmpeg plugins that offers the user to specify additional input/output options.

AbstractFFmpegPluginWithOptions() - Constructor for class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

AbstractImageFlattener<T extends AbstractImage> - Class in adams.data.image

Abstract base class for AbstractImage flattening operations.

AbstractImageFlattener() - Constructor for class adams.data.image.AbstractImageFlattener

AbstractImageJFlattener - Class in adams.data.imagej.flattener

Abstract base class for ImageJ flattening operations.

AbstractImageJFlattener() - Constructor for class adams.data.imagej.flattener.AbstractImageJFlattener

AbstractImageJTransformer - Class in adams.data.imagej.transformer

Abstract base class for ImageJ transformations.

AbstractImageJTransformer() - Constructor for class adams.data.imagej.transformer.AbstractImageJTransformer

AbstractImageTransformer<T extends AbstractImage> - Class in adams.data.image

Abstract base class for AbstractImage transformations.

AbstractImageTransformer() - Constructor for class adams.data.image.AbstractImageTransformer

AbstractJAIFlattener - Class in adams.data.jai.flattener

Abstract base class for JAI flattening operations.

AbstractJAIFlattener() - Constructor for class adams.data.jai.flattener.AbstractJAIFlattener

AbstractJAITransformer - Class in adams.data.jai.transformer

Abstract base class for JAI transformations.

AbstractJAITransformer() - Constructor for class adams.data.jai.transformer.AbstractJAITransformer

AbstractPixelSelectorAction - Class in adams.flow.transformer.pixelselector

Ancestor for actions for the PixelSelector interactive transformer.

AbstractPixelSelectorAction() - Constructor for class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Initializes the object.

AbstractPixelSelectorOverlay - Class in adams.flow.transformer.pixelselector

Ancestor for overlays in the pixel selector GUI, making use of the data stored in the report.

AbstractPixelSelectorOverlay() - Constructor for class adams.flow.transformer.pixelselector.AbstractPixelSelectorOverlay

AbstractSingleColorPixelSelectorOverlay - Class in adams.flow.transformer.pixelselector

Overlay that uses a single, user-defined color.

AbstractSingleColorPixelSelectorOverlay() - Constructor for class adams.flow.transformer.pixelselector.AbstractSingleColorPixelSelectorOverlay

accepts() - Method in class adams.data.conversion.BufferedImageToImageJ

Returns the class that is accepted as input.

accepts() - Method in class adams.data.conversion.ImageJToBufferedImage

Returns the class that is accepted as input.

accepts() - Method in class adams.flow.sink.FFmpeg

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.sink.ImageJWriter

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.sink.ImageMagickWriter

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.sink.JAIWriter

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.transformer.ImageInfo

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.transformer.ImageJFlattener

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.transformer.ImageJReader

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.transformer.ImageJTransformer

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.transformer.ImageMagickReader

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.transformer.ImageMagickTransformer

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.transformer.JAIFlattener

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.transformer.JAIReader

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.transformer.JAITransformer

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.transformer.PixelSelector

Returns the class that the consumer accepts.

accepts() - Method in class adams.flow.transformer.SetImagePixel

Returns the class that the consumer accepts.

actionPerformed(ActionEvent) - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Invoked when an action occurs.

actionsTipText() - Method in class adams.flow.transformer.PixelSelector

Returns the tip text for this property.

adams.core - package adams.core

adams.data.conversion - package adams.data.conversion

adams.data.image - package adams.data.image

adams.data.imagej - package adams.data.imagej

adams.data.imagej.flattener - package adams.data.imagej.flattener

adams.data.imagej.transformer - package adams.data.imagej.transformer

adams.data.jai - package adams.data.jai

adams.data.jai.flattener - package adams.data.jai.flattener

adams.data.jai.transformer - package adams.data.jai.transformer

adams.flow.sink - package adams.flow.sink

adams.flow.sink.ffmpeg - package adams.flow.sink.ffmpeg

adams.flow.source - package adams.flow.source

adams.flow.transformer - package adams.flow.transformer

adams.flow.transformer.pixelselector - package adams.flow.transformer.pixelselector

adams.gui.clipboard - package adams.gui.clipboard

adams.gui.menu - package adams.gui.menu

adams.gui.print - package adams.gui.print

adams.gui.visualization.image.plugins - package adams.gui.visualization.image.plugins

addActionListener(ActionListener) - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Adds a listener for button actions.

AddClassification - Class in adams.flow.transformer.pixelselector

Allows the user to select a pixel location and add a corresponding classification for it.
Stores the location with prefix 'Pixel.X.' and 'Pixel.Y.' and the classification using 'Classification.' as prefix.

AddClassification() - Constructor for class adams.flow.transformer.pixelselector.AddClassification

addImageOverlay(ImageOverlay) - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Adds the image overlay.

additionalInputOptionsTipText() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

Returns the tip text for this property.

additionalOutputOptionsTipText() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

Returns the tip text for this property.

anchorTipText() - Method in class adams.data.jai.flattener.PixelClassifications

Returns the tip text for this property.

anchorTipText() - Method in class adams.data.jai.transformer.Crop

Returns the tip text for this property.

angleTipText() - Method in class adams.data.jai.transformer.Rotate

Returns the tip text for this property.

APPROVE_OPTION - Static variable in class adams.flow.transformer.pixelselector.PixelSelectorPanel

the APPROVE option.

assembleActualInputOptions() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

Assembles the actual input command-line options, not including the additional options or the input file.

assembleActualInputOptions() - Method in class adams.flow.sink.ffmpeg.MovieFromImages

Assembles the command-line, excluding additional options and executable.

assembleActualOutputOptions() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

Assembles the actual output command-line options, not including the additional options.

assembleActualOutputOptions() - Method in class adams.flow.sink.ffmpeg.MovieFromImages

Assembles the command-line, excluding additional options and executable.

assembleInputOptions() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Assembles the input command-line options.

assembleInputOptions() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

Assembles the input command-line options, actual and additional.

assembleInputOptions() - Method in class adams.flow.sink.ffmpeg.GenericPlugin

Assembles the input command-line options.

assembleOutputOptions() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Assembles the ouput command-line options.

assembleOutputOptions() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

Assembles the ouput command-line options.

assembleOutputOptions() - Method in class adams.flow.sink.ffmpeg.GenericPlugin

Assembles the output command-line options.

B

backgroundTipText() - Method in class adams.data.jai.transformer.Rotate

Returns the tip text for this property.

backgroundTipText() - Method in class adams.flow.source.JAICreateImage

Returns the tip text for this property.

BACKUP_CURRENTIMAGES - Static variable in class adams.flow.transformer.ImageJTransformer

the key for storing the current images in the backup.

BACKUP_CURRENTIMAGES - Static variable in class adams.flow.transformer.JAITransformer

the key for storing the current counter in the backup.

BACKUP_QUEUE - Static variable in class adams.flow.transformer.ImageJFlattener

the key for storing the current instances in the backup.

BACKUP_QUEUE - Static variable in class adams.flow.transformer.JAIFlattener

the key for storing the current instances in the backup.

backupState() - Method in class adams.flow.transformer.ImageJFlattener

Backs up the current state of the actor before update the variables.

backupState() - Method in class adams.flow.transformer.ImageJTransformer

Backs up the current state of the actor before update the variables.

backupState() - Method in class adams.flow.transformer.JAIFlattener

Backs up the current state of the actor before update the variables.

backupState() - Method in class adams.flow.transformer.JAITransformer

Backs up the current state of the actor before update the variables.

bitRateTipText() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Returns the tip text for this property.

BottomRightCorner - Class in adams.flow.transformer.pixelselector

Allows the user to select a pixel location of the bottom-right corner.
Stores the location in 'Pixel.Right' and 'Pixel.Bottom'.

BottomRightCorner() - Constructor for class adams.flow.transformer.pixelselector.BottomRightCorner

BufferedImage - Class in adams.gui.clipboard

Copies/pastes buffered images.

BufferedImage() - Constructor for class adams.gui.clipboard.BufferedImage

BufferedImageContainer - Class in adams.data.jai

Image wrapper around a BufferedImage used by JAI.

BufferedImageContainer() - Constructor for class adams.data.jai.BufferedImageContainer

BufferedImageHelper - Class in adams.core

Helper class for BufferedImage objects.

BufferedImageHelper() - Constructor for class adams.core.BufferedImageHelper

BufferedImageToImageJ - Class in adams.data.conversion

Turns a BufferedImage container into an ImageJ one.

BufferedImageToImageJ() - Constructor for class adams.data.conversion.BufferedImageToImageJ

C

CANCEL_OPTION - Static variable in class adams.flow.transformer.pixelselector.PixelSelectorPanel

the CANCEL option.

canExecute(ImagePanel) - Method in class adams.gui.visualization.image.plugins.ImageMagick

Checks whether the plugin can be executed given the specified image panel.

canPaste() - Method in class adams.gui.clipboard.BufferedImage

Checks whether the required data type is available from the clipboard.

check() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Performs a check on the setup.

check() - Method in class adams.flow.transformer.pixelselector.AddClassification

Performs a check on the setup.

checkImage(T) - Method in class adams.data.image.AbstractImageFlattener

Optional checks of the image.

checkImage(T) - Method in class adams.data.image.AbstractImageTransformer

Optional checks of the image.

checkImage(ImagePlusContainer) - Method in class adams.data.imagej.flattener.AbstractImageJFlattener

Optional checks of the image.

checkImage(ImagePlusContainer) - Method in class adams.data.imagej.transformer.AbstractImageJTransformer

Optional checks of the image.

clamp(int) - Method in class adams.data.jai.transformer.GaussianBlur

Clamp a value to the range 0..255

CLASSIFICATION - Static variable in class adams.flow.transformer.pixelselector.AddClassification

the classification prefix.

ClassificationOverlay - Class in adams.flow.transformer.pixelselector

Highlights the chosen classifications.

Some actions that generate data for this overlay:
adams.flow.transformer.pixelselector.AddClassification

Valid options are:

ClassificationOverlay() - Constructor for class adams.flow.transformer.pixelselector.ClassificationOverlay

cleanUp() - Method in class adams.data.image.AbstractImageFlattener

Cleans up data structures, frees up memory.

cleanUp() - Method in class adams.data.image.AbstractImageTransformer

Cleans up data structures, frees up memory.

cleanUp() - Method in class adams.data.imagej.transformer.Command

Cleans up data structures, frees up memory.

cleanUp() - Method in class adams.data.imagej.transformer.PlugInFilter

Cleans up data structures, frees up memory.

cleanUp() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Cleans up data structures, frees up memory.

cleanUpOptions() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Cleans up the options.

clearImageOverlays() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Removes all image overlays.

clearPanel() - Method in class adams.flow.transformer.PixelSelector

Clears the content of the panel.

cloneImage() - Method in class adams.data.imagej.ImagePlusContainer

Returns a clone of the image.

cloneImage() - Method in class adams.data.jai.BufferedImageContainer

Returns a clone of the image.

closeDialog(int) - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Closes the dialog.

colorProviderTipText() - Method in class adams.flow.transformer.pixelselector.AbstractColorProviderPixelSelectorOverlay

Returns the tip text for this property.

colorTipText() - Method in class adams.flow.transformer.pixelselector.AbstractSingleColorPixelSelectorOverlay

Returns the tip text for this property.

colorTipText() - Method in class adams.flow.transformer.SetImagePixel

Returns the tip text for this property.

Command - Class in adams.data.imagej.transformer

A transformer that allows the execution of ImageJ commands.
Note(s):
- the options for the command can be obtained when recording macros
in ImageJ

Valid options are:

Command() - Constructor for class adams.data.imagej.transformer.Command

commandOptionsTipText() - Method in class adams.data.imagej.transformer.Command

Returns the tip text for this property.

commandsTipText() - Method in class adams.data.imagej.transformer.Macro

Returns the tip text for this property.

commandsTipText() - Method in class adams.flow.transformer.ImageMagickTransformer

Returns the tip text for this property.

commandTipText() - Method in class adams.data.imagej.transformer.Command

Returns the tip text for this property.

COMMENT - Static variable in class adams.flow.transformer.ImageMagickTransformer

the start of a line comment.

compareTo(Object) - Method in class adams.data.image.AbstractImageFlattener

Compares this object with the specified object for order.

compareTo(Object) - Method in class adams.data.image.AbstractImageTransformer

Compares this object with the specified object for order.

compressTipText() - Method in class adams.gui.print.TIFFWriter

Returns the tip text for this property.

convolveAndTranspose(Kernel, int[], int[], int, int) - Method in class adams.data.jai.transformer.GaussianBlur

Applies the kernel.

copy(BufferedImage) - Method in class adams.gui.clipboard.BufferedImage

Copies the data to the clipboard.

createHeader(T) - Method in class adams.data.image.AbstractImageFlattener

Creates the header from a template image.

createHeader(ImagePlusContainer) - Method in class adams.data.imagej.flattener.Histogram

Creates the header from a template image.

createHeader(ImagePlusContainer) - Method in class adams.data.imagej.flattener.NamedSetup

Creates the header from a template image.

createHeader(ImagePlusContainer) - Method in class adams.data.imagej.flattener.Pixels

Creates the header from a template image.

createHeader(BufferedImageContainer) - Method in class adams.data.jai.flattener.DFT

Creates the header from a template image.

createHeader(BufferedImageContainer) - Method in class adams.data.jai.flattener.Histogram

Creates the header from a template image.

createHeader(BufferedImageContainer) - Method in class adams.data.jai.flattener.NamedSetup

Creates the header from a template image.

createHeader(BufferedImageContainer) - Method in class adams.data.jai.flattener.PixelClassifications

Creates the header from a template image.

createHeader(BufferedImageContainer) - Method in class adams.data.jai.flattener.Pixels

Creates the header from a template image.

Crop - Class in adams.data.jai.transformer

Crops the image to specified width and height.

Crop() - Constructor for class adams.data.jai.transformer.Crop

Crop.Anchor - Enum in adams.data.jai.transformer

Enumeration for the crop rectangle anchor.\

D

deepCopy(BufferedImage) - Static method in class adams.core.BufferedImageHelper

Returns a copy of a BufferedImage object.

defineOptions() - Method in class adams.data.image.AbstractImageFlattener

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.imagej.flattener.Histogram

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.imagej.flattener.NamedSetup

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.imagej.transformer.Command

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.imagej.transformer.Macro

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.imagej.transformer.NamedSetup

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.imagej.transformer.PlugInFilter

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.imagej.transformer.Resize

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.jai.flattener.Histogram

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.jai.flattener.NamedSetup

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.jai.flattener.PixelClassifications

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.jai.flattener.Pixels

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.jai.transformer.Crop

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.jai.transformer.GaussianBlur

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.jai.transformer.NamedSetup

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.jai.transformer.Resize

Adds options to the internal list of options.

defineOptions() - Method in class adams.data.jai.transformer.Rotate

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.sink.FFmpeg

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.sink.ffmpeg.GenericPlugin

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.sink.ImageJWriter

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.sink.ImageMagickWriter

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.sink.JAIWriter

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.source.JAICreateImage

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.transformer.ImageInfo

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.transformer.ImageJFlattener

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.transformer.ImageJTransformer

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.transformer.ImageMagickTransformer

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.transformer.JAIFlattener

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.transformer.JAITransformer

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.transformer.pixelselector.AbstractColorProviderPixelSelectorOverlay

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.transformer.pixelselector.AbstractSingleColorPixelSelectorOverlay

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.transformer.pixelselector.AddClassification

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.transformer.pixelselector.ClassificationOverlay

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.transformer.PixelSelector

Adds options to the internal list of options.

defineOptions() - Method in class adams.flow.transformer.SetImagePixel

Adds options to the internal list of options.

defineOptions() - Method in class adams.gui.print.TIFFWriter

Adds options to the internal list of options.

destroy() - Method in class adams.data.image.AbstractImageFlattener

Frees up memory in a "destructive" non-reversible way.

destroy() - Method in class adams.data.image.AbstractImageTransformer

Frees up memory in a "destructive" non-reversible way.

destroy() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Frees up memory in a "destructive" non-reversible way.

determineImageType(String) - Method in class adams.flow.sink.ImageJWriter

Determines the image type for the given filename.

determineImageType(String) - Method in class adams.flow.sink.ImageMagickWriter

Determines the image type for the given filename.

determineImageType(String) - Method in class adams.flow.sink.JAIWriter

Determines the image type for the given filename.

DFT - Class in adams.data.jai.flattener

Performs discrete fourier transform (DFT).

DFT() - Constructor for class adams.data.jai.flattener.DFT

disableMediaLib() - Static method in class adams.core.JAIHelper

Disables the "java.lang.NoClassDefFoundError: com/sun/medialib/mlib/Image" exception.

doConvert() - Method in class adams.data.conversion.BufferedImageToImageJ

Performs the actual conversion.

doConvert() - Method in class adams.data.conversion.ImageJToBufferedImage

Performs the actual conversion.

doExecute() - Method in class adams.flow.sink.FFmpeg

Executes the flow item.

doExecute() - Method in class adams.flow.sink.ImageJWriter

Executes the flow item.

doExecute() - Method in class adams.flow.sink.ImageMagickWriter

Executes the flow item.

doExecute() - Method in class adams.flow.sink.JAIWriter

Executes the flow item.

doExecute() - Method in class adams.flow.source.JAICreateImage

Executes the flow item.

doExecute() - Method in class adams.flow.transformer.ImageInfo

Executes the flow item.

doExecute() - Method in class adams.flow.transformer.ImageJFlattener

Executes the flow item.

doExecute() - Method in class adams.flow.transformer.ImageJReader

Executes the flow item.

doExecute() - Method in class adams.flow.transformer.ImageJTransformer

Executes the flow item.

doExecute() - Method in class adams.flow.transformer.ImageMagickReader

Executes the flow item.

doExecute() - Method in class adams.flow.transformer.ImageMagickTransformer

Executes the flow item.

doExecute() - Method in class adams.flow.transformer.JAIFlattener

Executes the flow item.

doExecute() - Method in class adams.flow.transformer.JAIReader

Executes the flow item.

doExecute() - Method in class adams.flow.transformer.JAITransformer

Executes the flow item.

doExecute() - Method in class adams.flow.transformer.PixelSelector

Executes the flow item.

doExecute() - Method in class adams.flow.transformer.SetImagePixel

Executes the flow item.

doFlatten(T) - Method in class adams.data.image.AbstractImageFlattener

Performs the actual flattening of the image.

doFlatten(ImagePlusContainer) - Method in class adams.data.imagej.flattener.Histogram

Performs the actual flattening of the image.

doFlatten(ImagePlusContainer) - Method in class adams.data.imagej.flattener.NamedSetup

Performs the actual flattening of the image.

doFlatten(ImagePlusContainer) - Method in class adams.data.imagej.flattener.Pixels

Performs the actual flattening of the image.

doFlatten(BufferedImageContainer) - Method in class adams.data.jai.flattener.DFT

Performs the actual flattening of the image.

doFlatten(BufferedImageContainer) - Method in class adams.data.jai.flattener.Histogram

Performs the actual flattening of the image.

doFlatten(BufferedImageContainer) - Method in class adams.data.jai.flattener.NamedSetup

Performs the actual flattening of the image.

doFlatten(BufferedImageContainer) - Method in class adams.data.jai.flattener.PixelClassifications

Performs the actual flattening of the image.

doFlatten(BufferedImageContainer) - Method in class adams.data.jai.flattener.Pixels

Performs the actual flattening of the image.

doInteract() - Method in class adams.flow.transformer.PixelSelector

Performs the interaction with the user.

doPaintOverlay(ImagePanel.PaintPanel, Graphics) - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorOverlay

Paints the actual overlay over the image.

doPaintOverlay(ImagePanel.PaintPanel, Graphics) - Method in class adams.flow.transformer.pixelselector.ClassificationOverlay

Paints the actual overlay over the image.

doPaintOverlay(ImagePanel.PaintPanel, Graphics) - Method in class adams.flow.transformer.pixelselector.RectangleOverlay

Paints the actual overlay over the image.

doPaintOverlay(ImagePanel.PaintPanel, Graphics) - Method in class adams.flow.transformer.pixelselector.SimpleOverlay

Paints the actual overlay over the image.

doProcessAction(ActionEvent) - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Reacts to the action event.

doProcessAction(ActionEvent) - Method in class adams.flow.transformer.pixelselector.AddClassification

Reacts to the action event.

doProcessAction(ActionEvent) - Method in class adams.flow.transformer.pixelselector.BottomRightCorner

Reacts to the action event.

doProcessAction(ActionEvent) - Method in class adams.flow.transformer.pixelselector.SimpleSelect

Reacts to the action event.

doProcessAction(ActionEvent) - Method in class adams.flow.transformer.pixelselector.TopLeftCorner

Reacts to the action event.

doTransform(T) - Method in class adams.data.image.AbstractImageTransformer

Performs the actual transforming of the image.

doTransform(ImagePlusContainer) - Method in class adams.data.imagej.transformer.Command

Performs no transformation at all, just returns the input.

doTransform(ImagePlusContainer) - Method in class adams.data.imagej.transformer.Gray8

Performs no transformation at all, just returns the input.

doTransform(ImagePlusContainer) - Method in class adams.data.imagej.transformer.Macro

Performs no transformation at all, just returns the input.

doTransform(ImagePlusContainer) - Method in class adams.data.imagej.transformer.NamedSetup

Performs the transformation.

doTransform(ImagePlusContainer) - Method in class adams.data.imagej.transformer.PassThrough

Performs no transformation at all, just returns the input.

doTransform(ImagePlusContainer) - Method in class adams.data.imagej.transformer.PlugInFilter

Performs no transformation at all, just returns the input.

doTransform(ImagePlusContainer) - Method in class adams.data.imagej.transformer.Resize

Performs no transformation at all, just returns the input.

doTransform(BufferedImageContainer) - Method in class adams.data.jai.transformer.Crop

Performs no transformation at all, just returns the input.

doTransform(BufferedImageContainer) - Method in class adams.data.jai.transformer.GaussianBlur

Performs no transformation at all, just returns the input.

doTransform(BufferedImageContainer) - Method in class adams.data.jai.transformer.Gray8

Performs no transformation at all, just returns the input.

doTransform(BufferedImageContainer) - Method in class adams.data.jai.transformer.NamedSetup

Performs the transformation.

doTransform(BufferedImageContainer) - Method in class adams.data.jai.transformer.PassThrough

Performs no transformation at all, just returns the input.

doTransform(BufferedImageContainer) - Method in class adams.data.jai.transformer.Resize

Performs no transformation at all, just returns the input.

doTransform(BufferedImageContainer) - Method in class adams.data.jai.transformer.Rotate

Performs no transformation at all, just returns the input.

E

editOverlays() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Edits the current overlays.

ENV_IMAGEJ_DIR - Static variable in class adams.core.ImageJHelper

the environment variable to specify an alternative ImageJ directory, just above the "plugins" directory.

ENV_PATH - Static variable in class adams.core.ImageMagickHelper

the environment variable to check.

equals(Object) - Method in class adams.data.image.AbstractImageFlattener

Returns whether the two objects are the same.

equals(Object) - Method in class adams.data.image.AbstractImageTransformer

Returns whether the two objects are the same.

executableTipText() - Method in class adams.flow.sink.FFmpeg

Returns the tip text for this property.

execute() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Performs the ffmpeg execution.

F

FFmpeg - Class in adams.flow.sink

Uses the specified plugin to perform a ffmpeg operation.

FFmpeg() - Constructor for class adams.flow.sink.FFmpeg

fieldsTipText() - Method in class adams.data.image.AbstractImageFlattener

Returns the tip text for this property.

filter(BufferedImage) - Method in class adams.gui.visualization.image.plugins.ImageJTransformer

Filters the image.

filter(BufferedImage) - Method in class adams.gui.visualization.image.plugins.ImageMagick

Filters the image.

filter(BufferedImage) - Method in class adams.gui.visualization.image.plugins.JAITransformer

Filters the image.

finishInit() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Finishes the initialization in the constructor.

flatten(T) - Method in class adams.data.image.AbstractImageFlattener

Process the given image.

flattenAlgorithmTipText() - Method in class adams.flow.transformer.ImageJFlattener

Returns the tip text for this property.

flattenAlgorithmTipText() - Method in class adams.flow.transformer.JAIFlattener

Returns the tip text for this property.

forCommandLine(String) - Static method in class adams.data.imagej.flattener.AbstractImageJFlattener

Instantiates the transformation from the given commandline (i.e., classname and optional options).

forCommandLine(String) - Static method in class adams.data.imagej.transformer.AbstractImageJTransformer

Instantiates the transformation from the given commandline (i.e., classname and optional options).

forCommandLine(String) - Static method in class adams.data.jai.flattener.AbstractJAIFlattener

Instantiates the transformation from the given commandline (i.e., classname and optional options).

forCommandLine(String) - Static method in class adams.data.jai.transformer.AbstractJAITransformer

Instantiates the transformation from the given commandline (i.e., classname and optional options).

forName(String, String[]) - Static method in class adams.data.imagej.flattener.AbstractImageJFlattener

Instantiates the transformation with the given options.

forName(String, String[]) - Static method in class adams.data.imagej.transformer.AbstractImageJTransformer

Instantiates the transformation with the given options.

forName(String, String[]) - Static method in class adams.data.jai.flattener.AbstractJAIFlattener

Instantiates the transformation with the given options.

forName(String, String[]) - Static method in class adams.data.jai.transformer.AbstractJAITransformer

Instantiates the transformation with the given options.

framesPerSecondTipText() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Returns the tip text for this property.

G

GaussianBlur - Class in adams.data.jai.transformer

Performs a gaussian blur.
Original code taken from here:
http://www.jhlabs.com/ip/blurring.html

Valid options are:

GaussianBlur() - Constructor for class adams.data.jai.transformer.GaussianBlur

generateOutput() - Method in class adams.gui.print.TIFFWriter

generates the actual output.

generates() - Method in class adams.data.conversion.BufferedImageToImageJ

Returns the class that is generated as output.

generates() - Method in class adams.data.conversion.ImageJToBufferedImage

Returns the class that is generated as output.

generates() - Method in class adams.flow.source.JAICreateImage

Returns a string describing the object.

generates() - Method in class adams.flow.transformer.ImageInfo

Returns the class of objects that it generates.

generates() - Method in class adams.flow.transformer.ImageJFlattener

Returns the class of objects that it generates.

generates() - Method in class adams.flow.transformer.ImageJReader

Returns the class of objects that it generates.

generates() - Method in class adams.flow.transformer.ImageJTransformer

Returns the class of objects that it generates.

generates() - Method in class adams.flow.transformer.ImageMagickReader

Returns the class of objects that it generates.

generates() - Method in class adams.flow.transformer.ImageMagickTransformer

Returns the class of objects that it generates.

generates() - Method in class adams.flow.transformer.JAIFlattener

Returns the class of objects that it generates.

generates() - Method in class adams.flow.transformer.JAIReader

Returns the class of objects that it generates.

generates() - Method in class adams.flow.transformer.JAITransformer

Returns the class of objects that it generates.

generates() - Method in class adams.flow.transformer.PixelSelector

Returns the class of objects that it generates.

generates() - Method in class adams.flow.transformer.SetImagePixel

Returns the class of objects that it generates.

GenericPlugin - Class in adams.flow.sink.ffmpeg

A generic plugin.

GenericPlugin() - Constructor for class adams.flow.sink.ffmpeg.GenericPlugin

getActions() - Method in class adams.flow.transformer.PixelSelector

Returns the available popup actions.

getActions() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Returns the available popup actions.

getActualScheme() - Method in class adams.data.imagej.flattener.NamedSetup

Returns the named setup.

getActualScheme() - Method in class adams.data.imagej.transformer.NamedSetup

Returns the named setup.

getActualScheme() - Method in class adams.data.jai.flattener.NamedSetup

Returns the named setup.

getActualScheme() - Method in class adams.data.jai.transformer.NamedSetup

Returns the named setup.

getAdditionalInputOptions() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

Returns the additional input options to use.

getAdditionalOutputOptions() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

Returns the additional output options to use.

getAnchor() - Method in class adams.data.jai.flattener.PixelClassifications

Returns where to anchor the position on the rectangle.

getAnchor() - Method in class adams.data.jai.transformer.Crop

Returns where to anchor the position on the rectangle.

getAngle() - Method in class adams.data.jai.transformer.Rotate

Returns the rotation angle.

getBackground() - Method in class adams.data.jai.transformer.Rotate

Returns the color in use for the background.

getBackground() - Method in class adams.flow.source.JAICreateImage

Returns the background color of the image.

getBitRate() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Returns the bit rate in kbits to use.

getBottomRight() - Method in class adams.flow.transformer.pixelselector.RectangleOverlay

Returns the bottom-right corner to paint.

getCaption() - Method in class adams.gui.visualization.image.plugins.ImageJTransformer

Returns the text for the menu item to create.

getCaption() - Method in class adams.gui.visualization.image.plugins.ImageMagick

Returns the text for the menu item to create.

getCaption() - Method in class adams.gui.visualization.image.plugins.JAITransformer

Returns the text for the menu item to create.

getCategory() - Method in class adams.gui.menu.ImageJ

Returns the category of the menu item in which it should appear, i.e., the name of the menu.

getClassificationIndices(BufferedImageContainer) - Method in class adams.data.jai.flattener.PixelClassifications

Returns the classification indices.

getClassificationIndices() - Method in class adams.flow.transformer.pixelselector.ClassificationOverlay

Returns the classification indices.

getColor() - Method in class adams.flow.transformer.pixelselector.AbstractSingleColorPixelSelectorOverlay

Returns the color for the overlay.

getColor() - Method in class adams.flow.transformer.SetImagePixel

Returns the color of the pixel.

getColorProvider() - Method in class adams.flow.transformer.pixelselector.AbstractColorProviderPixelSelectorOverlay

Returns the color provider for the overlay.

getCommand() - Method in class adams.data.imagej.transformer.Command

Returns the command to execute.

getCommandOptions() - Method in class adams.data.imagej.transformer.Command

Returns the options for the command.

getCommands() - Method in class adams.data.imagej.transformer.Macro

Returns the width to resize to.

getCommands() - Method in class adams.flow.transformer.ImageMagickTransformer

Returns the commands in execute.

getCompress() - Method in class adams.gui.print.TIFFWriter

Returns whether to compress the image.

getCustomPopupMenu(MouseEvent) - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Creates a popup menu for the given mouse event.

getDefaultBackground() - Method in class adams.flow.source.JAICreateImage

Returns the default backrgound color of the image.

getDefaultColor() - Method in class adams.flow.transformer.pixelselector.AbstractSingleColorPixelSelectorOverlay

Returns the default color.

getDefaultColorProvider() - Method in class adams.flow.transformer.pixelselector.AbstractColorProviderPixelSelectorOverlay

Returns the default color provider.

getDefaultExecutable() - Method in class adams.flow.sink.FFmpeg

Returns the default executable.

getDefaultHeight() - Method in class adams.flow.source.JAICreateImage

Returns the default height of the image.

getDefaultSplitterPosition() - Method in class adams.flow.transformer.PixelSelector

Returns the default position for the splitter.

getDefaultWidth() - Method in class adams.flow.source.JAICreateImage

Returns the default width of the image.

getDescription() - Method in class adams.gui.print.TIFFWriter

returns the name of the writer, to display in the FileChooser.

getExecutable() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Returns the ffmpeg executable.

getExecutable() - Method in class adams.flow.sink.FFmpeg

Returns the ffmpeg executable.

getExtension() - Method in enum adams.flow.sink.ImageMagickWriter.ImageType

Returns the associated extension.

getExtension() - Method in enum adams.flow.sink.JAIWriter.ImageType

Returns the associated extension.

getExtensions() - Method in class adams.gui.print.TIFFWriter

returns the extensions (incl.

getFields() - Method in class adams.data.image.AbstractImageFlattener

Returns the targets to add.

getFilter(ImagePlusContainer) - Method in class adams.data.imagej.transformer.PlugInFilter

Returns the filter to use.

getFlattenAlgorithm() - Method in class adams.flow.transformer.ImageJFlattener

Returns the flattener in use.

getFlattenAlgorithm() - Method in class adams.flow.transformer.JAIFlattener

Returns the flattener in use.

getFlatteners() - Static method in class adams.data.imagej.flattener.AbstractImageJFlattener

Returns a list with classnames of transformations.

getFlatteners() - Static method in class adams.data.jai.flattener.AbstractJAIFlattener

Returns a list with classnames of transformations.

getFlowClass() - Method in class adams.gui.clipboard.BufferedImage

Returns the supported class.

getFramesPerSecond() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Returns the frames per second to use.

getGlobalInfo() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorOverlay

Returns a string describing the object.

getGlobalInfo() - Method in class adams.flow.transformer.pixelselector.ClassificationOverlay

Returns a string describing the object.

getGlobalInfo() - Method in class adams.flow.transformer.pixelselector.RectangleOverlay

Returns a string describing the object.

getGlobalInfo() - Method in class adams.flow.transformer.pixelselector.SimpleOverlay

Returns a string describing the object.

getHeight() - Method in class adams.data.imagej.ImagePlusContainer

Returns the height of the image.

getHeight() - Method in class adams.data.imagej.transformer.Resize

Returns the height to resize to.

getHeight() - Method in class adams.data.jai.BufferedImageContainer

Returns the height of the image.

getHeight() - Method in class adams.data.jai.flattener.PixelClassifications

Returns the height of the crop rectangle.

getHeight() - Method in class adams.data.jai.transformer.Crop

Returns the height of the crop rectangle.

getHeight() - Method in class adams.data.jai.transformer.Resize

Returns the height to resize to.

getHeight() - Method in class adams.flow.source.JAICreateImage

Returns the height of the image.

getHistogramType() - Method in class adams.data.imagej.flattener.Histogram

Returns the type of histogram to generate.

getHistogramType() - Method in class adams.data.jai.flattener.Histogram

Returns the type of histogram to generate.

getIconName() - Method in class adams.gui.menu.ImageJ

Returns the file name of the icon.

getImage() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorOverlay

Returns the underlying image.

getImage() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Returns the current image.

getImageType() - Method in class adams.flow.sink.ImageJWriter

Returns the type of image to create.

getImageType() - Method in class adams.flow.sink.ImageMagickWriter

Returns the type of image to create.

getImageType() - Method in class adams.flow.sink.JAIWriter

Returns the type of image to create.

getInput() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Returns the input file.

getInputOptions() - Method in class adams.flow.sink.ffmpeg.GenericPlugin

Returns the input options to use.

getInterpolation() - Method in class adams.data.jai.transformer.Rotate

Returns the type of interpolation to perform.

getInterpolationType() - Method in class adams.data.jai.transformer.Resize

Returns the type of interpolation in use.

getLabels() - Method in class adams.flow.transformer.pixelselector.AddClassification

Returns the available classification labels.

getLastActionResult(Class) - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Retrieves the previous result for the specified action if available.

getMenuBar() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Creates a menu bar (singleton per panel object).

getMissingCommandErrorMessage(String) - Static method in class adams.core.ImageMagickHelper

Returns a standard error message if specifiec command is not available.

getMissingConvertErrorMessage() - Static method in class adams.core.ImageMagickHelper

Returns a standard error message if "convert" is not available.

getMousePosition() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Returns the mouse position, if available.

getNextClassificationIndex(Report) - Method in class adams.flow.transformer.pixelselector.AddClassification

Returns the next free classification index.

getNotes() - Method in class adams.data.image.AbstractImageFlattener

Returns the current notes to add as attributes.

getNumSubsampleBits() - Method in class adams.data.jai.transformer.Resize

Returns the precision for subsampling in bits.

getOptionManager() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Returns the option manager.

getOriginX() - Method in class adams.data.jai.transformer.Rotate

Returns the X of the origin.

getOriginY() - Method in class adams.data.jai.transformer.Rotate

Returns the Y of the origin.

getOutputOptions() - Method in class adams.flow.sink.ffmpeg.GenericPlugin

Returns the output options to use.

getOverlays() - Method in class adams.flow.transformer.PixelSelector

Returns the available image overlays.

getOwner() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Sets the owner.

getPanel() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Returns the panel, if available.

getPixelLocation(BufferedImageContainer, int) - Method in class adams.data.jai.flattener.PixelClassifications

Returns the pixel location to paint.

getPixelLocation(int) - Method in class adams.flow.transformer.pixelselector.ClassificationOverlay

Returns the pixel location to paint.

getPixelLocation() - Method in class adams.flow.transformer.pixelselector.SimpleOverlay

Returns the pixel location to paint.

getPixelPosition() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Returns the pixel position, if available.

getPixelRaster(BufferedImage) - Static method in class adams.core.BufferedImageHelper

Returns the pixels of the image as an 2-D int array (row-wise).

getPixels(BufferedImage) - Static method in class adams.core.BufferedImageHelper

Returns all the pixels of the image as an int array (row-wise).

getPlugin() - Method in class adams.flow.sink.FFmpeg

Returns the plugin to use.

getPlugInFilter() - Method in class adams.data.imagej.transformer.PlugInFilter

Returns the classname of the plugin filter in use.

getPlugInOptions() - Method in class adams.data.imagej.transformer.PlugInFilter

Returns the options for the plug-in if the dialog gets suppressed.

getQuickInfo() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Returns a quick info about the plugin, which will be displayed in the GUI.

getQuickInfo() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

Returns a quick info about the plugin, which will be displayed in the GUI.

getQuickInfo() - Method in class adams.flow.sink.FFmpeg

Returns a quick info about the actor, which will be displayed in the GUI.

getQuickInfo() - Method in class adams.flow.sink.ImageJWriter

Returns a quick info about the actor, which will be displayed in the GUI.

getQuickInfo() - Method in class adams.flow.sink.ImageMagickWriter

Returns a quick info about the actor, which will be displayed in the GUI.

getQuickInfo() - Method in class adams.flow.sink.JAIWriter

Returns a quick info about the actor, which will be displayed in the GUI.

getQuickInfo() - Method in class adams.flow.source.JAICreateImage

Returns a quick info about the actor, which will be displayed in the GUI.

getQuickInfo() - Method in class adams.flow.transformer.ImageInfo

Returns a quick info about the actor, which will be displayed in the GUI.

getQuickInfo() - Method in class adams.flow.transformer.ImageJFlattener

Returns a quick info about the actor, which will be displayed in the GUI.

getQuickInfo() - Method in class adams.flow.transformer.ImageJTransformer

Returns a quick info about the actor, which will be displayed in the GUI.

getQuickInfo() - Method in class adams.flow.transformer.ImageMagickTransformer

Returns a quick info about the actor, which will be displayed in the GUI.

getQuickInfo() - Method in class adams.flow.transformer.JAIFlattener

Returns a quick info about the actor, which will be displayed in the GUI.

getQuickInfo() - Method in class adams.flow.transformer.JAITransformer

Returns a quick info about the actor, which will be displayed in the GUI.

getQuickInfo() - Method in class adams.flow.transformer.SetImagePixel

Returns a quick info about the actor, which will be displayed in the GUI.

getRadius() - Method in class adams.data.jai.transformer.GaussianBlur

Returns the blur radius.

getRememberLastSelection() - Method in class adams.flow.transformer.pixelselector.AddClassification

Returns whether to remmeber the last selected label.

getResult() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Returns the current result.

getRGBA() - Method in class adams.flow.transformer.SetImagePixel

Returns the RGBA value of the pixel.

getRGBPixels(BufferedImage) - Static method in class adams.core.BufferedImageHelper

Returns all the pixels of the image as an int array (row-wise) with the RGB(A) components as second dimension.

getSeparateRGB() - Method in class adams.data.jai.flattener.PixelClassifications

Returns the setup name.

getSeparateRGB() - Method in class adams.data.jai.flattener.Pixels

Returns the setup name.

getSetup() - Method in class adams.data.imagej.flattener.NamedSetup

Returns the setup name.

getSetup() - Method in class adams.data.imagej.transformer.NamedSetup

Returns the setup name.

getSetup() - Method in class adams.data.jai.flattener.NamedSetup

Returns the setup name.

getSetup() - Method in class adams.data.jai.transformer.NamedSetup

Returns the setup name.

getShowIndex() - Method in class adams.flow.transformer.pixelselector.ClassificationOverlay

Returns whether the index is shown.

getShowLabel() - Method in class adams.flow.transformer.pixelselector.ClassificationOverlay

Returns whether the label is shown.

getSplitterPosition() - Method in class adams.flow.transformer.PixelSelector

Returns the initial position of the splitter in the viewer panel.

getSplitterPosition() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Returns the current location of the splitter/divider.

getSuggestedActions() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorOverlay

Returns some actions that generate data for this overlay.

getSuggestedActions() - Method in class adams.flow.transformer.pixelselector.ClassificationOverlay

Returns some actions that generate data for this overlay.

getSuggestedActions() - Method in class adams.flow.transformer.pixelselector.RectangleOverlay

Returns some actions that generate data for this overlay.

getSuggestedActions() - Method in class adams.flow.transformer.pixelselector.SimpleOverlay

Returns some actions that generate data for this overlay.

getSuppressPlugInDialog() - Method in class adams.data.imagej.transformer.PlugInFilter

Returns whether to suppress the plugin dialog.

getTitle() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Returns the title of the action (used as menu item text).

getTitle() - Method in class adams.flow.transformer.pixelselector.AddClassification

Returns the title of the action (used as menu item text).

getTitle() - Method in class adams.flow.transformer.pixelselector.BottomRightCorner

Returns the title of the action (used as menu item text).

getTitle() - Method in class adams.flow.transformer.pixelselector.SimpleSelect

Returns the title of the action (used as menu item text).

getTitle() - Method in class adams.flow.transformer.pixelselector.TopLeftCorner

Returns the title of the action (used as menu item text).

getTitle() - Method in class adams.gui.menu.ImageJ

Returns the title of the window (and text of menuitem).

getTopLeft() - Method in class adams.flow.transformer.pixelselector.RectangleOverlay

Returns the top-left corner to paint.

getTransformAlgorithm() - Method in class adams.flow.transformer.ImageJTransformer

Returns the transformer in use.

getTransformAlgorithm() - Method in class adams.flow.transformer.JAITransformer

Returns the transformer in use.

getTransformations() - Static method in class adams.data.imagej.transformer.AbstractImageJTransformer

Returns a list with classnames of transformations.

getTransformations() - Static method in class adams.data.jai.transformer.AbstractJAITransformer

Returns a list with classnames of transformations.

getType() - Method in enum adams.flow.sink.ImageMagickWriter.ImageType

Returns the ImageMagick type.

getType() - Method in enum adams.flow.sink.JAIWriter.ImageType

Returns the ImageMagick type.

getType() - Method in class adams.flow.transformer.ImageInfo

Returns the type of information to generate.

getType() - Method in class adams.flow.transformer.SetImagePixel

Returns the type of value to use.

getUserMode() - Method in class adams.gui.menu.ImageJ

Returns the user mode, which determines visibility as well.

getWidth() - Method in class adams.data.imagej.ImagePlusContainer

Returns the width of the image.

getWidth() - Method in class adams.data.imagej.transformer.Resize

Returns the width to resize to.

getWidth() - Method in class adams.data.jai.BufferedImageContainer

Returns the width of the image.

getWidth() - Method in class adams.data.jai.flattener.PixelClassifications

Returns the width of the crop rectangle.

getWidth() - Method in class adams.data.jai.transformer.Crop

Returns the width of the crop rectangle.

getWidth() - Method in class adams.data.jai.transformer.Resize

Returns the width to resize to.

getWidth() - Method in class adams.flow.source.JAICreateImage

Returns the width of the image.

getX() - Method in class adams.data.jai.transformer.Crop

Returns the X position.

getX() - Method in class adams.flow.transformer.SetImagePixel

Returns the X position of the pixel.

getY() - Method in class adams.data.jai.transformer.Crop

Returns the Y position.

getY() - Method in class adams.flow.transformer.SetImagePixel

Returns the X position of the pixel.

globalInfo() - Method in class adams.data.conversion.BufferedImageToImageJ

Returns a string describing the object.

globalInfo() - Method in class adams.data.conversion.ImageJToBufferedImage

Returns a string describing the object.

globalInfo() - Method in class adams.data.imagej.flattener.Histogram

Returns a string describing the object.

globalInfo() - Method in class adams.data.imagej.flattener.NamedSetup

Returns a string describing the object.

globalInfo() - Method in class adams.data.imagej.flattener.Pixels

Returns a string describing the object.

globalInfo() - Method in class adams.data.imagej.transformer.Command

Returns a string describing the object.

globalInfo() - Method in class adams.data.imagej.transformer.Gray8

Returns a string describing the object.

globalInfo() - Method in class adams.data.imagej.transformer.Macro

Returns a string describing the object.

globalInfo() - Method in class adams.data.imagej.transformer.NamedSetup

Returns a string describing the object.

globalInfo() - Method in class adams.data.imagej.transformer.PassThrough

Returns a string describing the object.

globalInfo() - Method in class adams.data.imagej.transformer.PlugInFilter

Returns a string describing the object.

globalInfo() - Method in class adams.data.imagej.transformer.Resize

Returns a string describing the object.

globalInfo() - Method in class adams.data.jai.flattener.DFT

Returns a string describing the object.

globalInfo() - Method in class adams.data.jai.flattener.Histogram

Returns a string describing the object.

globalInfo() - Method in class adams.data.jai.flattener.NamedSetup

Returns a string describing the object.

globalInfo() - Method in class adams.data.jai.flattener.PixelClassifications

Returns a string describing the object.

globalInfo() - Method in class adams.data.jai.flattener.Pixels

Returns a string describing the object.

globalInfo() - Method in class adams.data.jai.transformer.Crop

Returns a string describing the object.

globalInfo() - Method in class adams.data.jai.transformer.GaussianBlur

Returns a string describing the object.

globalInfo() - Method in class adams.data.jai.transformer.Gray8

Returns a string describing the object.

globalInfo() - Method in class adams.data.jai.transformer.NamedSetup

Returns a string describing the object.

globalInfo() - Method in class adams.data.jai.transformer.PassThrough

Returns a string describing the object.

globalInfo() - Method in class adams.data.jai.transformer.Resize

Returns a string describing the object.

globalInfo() - Method in class adams.data.jai.transformer.Rotate

Returns a string describing the object.

globalInfo() - Method in class adams.flow.sink.ffmpeg.GenericPlugin

Returns a string describing the object.

globalInfo() - Method in class adams.flow.sink.FFmpeg

Returns a string describing the object.

globalInfo() - Method in class adams.flow.sink.ffmpeg.MovieFromImages

Returns a string describing the object.

globalInfo() - Method in class adams.flow.sink.ImageJWriter

Returns a string describing the object.

globalInfo() - Method in class adams.flow.sink.ImageMagickWriter

Returns a string describing the object.

globalInfo() - Method in class adams.flow.sink.JAIWriter

Returns a string describing the object.

globalInfo() - Method in class adams.flow.source.JAICreateImage

globalInfo() - Method in class adams.flow.transformer.ImageInfo

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.ImageJFlattener

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.ImageJReader

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.ImageJTransformer

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.ImageMagickReader

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.ImageMagickTransformer

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.JAIFlattener

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.JAIReader

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.JAITransformer

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorOverlay

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.pixelselector.AddClassification

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.pixelselector.BottomRightCorner

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.PixelSelector

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.pixelselector.SimpleSelect

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.pixelselector.TopLeftCorner

Returns a string describing the object.

globalInfo() - Method in class adams.flow.transformer.SetImagePixel

Returns a string describing the object.

globalInfo() - Method in class adams.gui.clipboard.BufferedImage

Returns a string describing the object.

globalInfo() - Method in class adams.gui.print.TIFFWriter

Returns a string describing the object.

Gray8 - Class in adams.data.imagej.transformer

Transforms the image into an 8-bit gray image.

Gray8() - Constructor for class adams.data.imagej.transformer.Gray8

Gray8 - Class in adams.data.jai.transformer

Transforms the image into an 8-bit gray image.

Gray8() - Constructor for class adams.data.jai.transformer.Gray8

H

handleException(String, Throwable) - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Outputs the stacktrace along with the message on stderr and returns a combination of both of them as string.

hasImage() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Checks whether an image is currently displayed.

hasLastActionResult(Class) - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Checks for the specified action whether a previous result is available.

hasMousePosition() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Checks whether a mouse position is available.

hasPanel() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Checks whether a panel is available.

hasPendingOutput() - Method in class adams.flow.source.JAICreateImage

Checks whether there is pending output to be collected after executing the flow item.

hasPendingOutput() - Method in class adams.flow.transformer.ImageJFlattener

Checks whether there is pending output to be collected after executing the flow item.

hasPendingOutput() - Method in class adams.flow.transformer.ImageJTransformer

Checks whether there is pending output to be collected after executing the flow item.

hasPendingOutput() - Method in class adams.flow.transformer.JAIFlattener

Checks whether there is pending output to be collected after executing the flow item.

hasPendingOutput() - Method in class adams.flow.transformer.JAITransformer

Checks whether there is pending output to be collected after executing the flow item.

hasPixelPosition() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Checks whether a pixel position is available.

heightTipText() - Method in class adams.data.imagej.transformer.Resize

Returns the tip text for this property.

heightTipText() - Method in class adams.data.jai.flattener.PixelClassifications

Returns the tip text for this property.

heightTipText() - Method in class adams.data.jai.transformer.Crop

Returns the tip text for this property.

heightTipText() - Method in class adams.data.jai.transformer.Resize

Returns the tip text for this property.

heightTipText() - Method in class adams.flow.source.JAICreateImage

Returns the tip text for this property.

Histogram - Class in adams.data.imagej.flattener

Turns an image into a histogram.
In case of an 8-bit histogram, the image must already be converted to a gray image.

Histogram() - Constructor for class adams.data.imagej.flattener.Histogram

Histogram - Class in adams.data.jai.flattener

Turns an image into a histogram.
In case of an 8-bit histogram, the image must already be converted to a gray image.

Histogram() - Constructor for class adams.data.jai.flattener.Histogram

Histogram.HistogramType - Enum in adams.data.imagej.flattener

The type of histogram to generate.

Histogram.HistogramType - Enum in adams.data.jai.flattener

The type of histogram to generate.

histogramTypeTipText() - Method in class adams.data.imagej.flattener.Histogram

Returns the tip text for this property.

histogramTypeTipText() - Method in class adams.data.jai.flattener.Histogram

Returns the tip text for this property.

I

ImageInfo - Class in adams.flow.transformer

Obtains information from the picture passing through.

ImageInfo() - Constructor for class adams.flow.transformer.ImageInfo

ImageInfo.InfoType - Enum in adams.flow.transformer

The type of information to retrieve.

ImageJ - Class in adams.gui.menu

Starts the ImageJ GUI.

ImageJ() - Constructor for class adams.gui.menu.ImageJ

Initializes the menu item with no owner.

ImageJ(AbstractApplicationFrame) - Constructor for class adams.gui.menu.ImageJ

Initializes the menu item.

ImageJFlattener - Class in adams.flow.transformer

Applies an ImageJ flattener to the incoming image and outputs the generated WEKA Instance(s).

ImageJFlattener() - Constructor for class adams.flow.transformer.ImageJFlattener

ImageJHelper - Class in adams.core

Helper class for ImageJ.

ImageJHelper() - Constructor for class adams.core.ImageJHelper

ImageJReader - Class in adams.flow.transformer

Reads any file format that ImageJ can read.

ImageJReader() - Constructor for class adams.flow.transformer.ImageJReader

ImageJToBufferedImage - Class in adams.data.conversion

Turns an ImageJ container into a BufferedImage one.

ImageJToBufferedImage() - Constructor for class adams.data.conversion.ImageJToBufferedImage

ImageJTransformer - Class in adams.flow.transformer

Applies an ImageJ transformation to the incoming image and outputs the generated image(s).

ImageJTransformer() - Constructor for class adams.flow.transformer.ImageJTransformer

ImageJTransformer - Class in adams.gui.visualization.image.plugins

Allows the user to apply an ImageJ transformer to an image in the ImageViewer.

ImageJTransformer() - Constructor for class adams.gui.visualization.image.plugins.ImageJTransformer

ImageJWriter - Class in adams.flow.sink

Actor for saving an ImagePlus object as image file.

ImageJWriter() - Constructor for class adams.flow.sink.ImageJWriter

ImageJWriter.ImageType - Enum in adams.flow.sink

The type of the image to create.

ImageMagick - Class in adams.gui.visualization.image.plugins

Allows the user to apply ImageMagick commands.

ImageMagick() - Constructor for class adams.gui.visualization.image.plugins.ImageMagick

ImageMagickHelper - Class in adams.core

Helper class for ImageMagick (http://www.imagemagick.org/).

ImageMagickHelper() - Constructor for class adams.core.ImageMagickHelper

ImageMagickReader - Class in adams.flow.transformer

Reads any file format that ImageMagick can read.
NB: Uses im4java, i.e., ImageMagick (http://www.imagemagick.org/) executables must be available on the PATH.

ImageMagickReader() - Constructor for class adams.flow.transformer.ImageMagickReader

ImageMagickTransformer - Class in adams.flow.transformer

Converts an image using ImageMagick.
In order to make entering of commands easier, they can be spread over multiple lines and line comments can be inserted as well (a line comment starts with '#').

NB: Uses im4java, i.e., ImageMagick (http://www.imagemagick.org/) executables must be available on the PATH.

ImageMagickTransformer() - Constructor for class adams.flow.transformer.ImageMagickTransformer

ImageMagickWriter - Class in adams.flow.sink

Writes an image to disk using ImageMagick (http://www.imagemagick.org/).

ImageMagickWriter() - Constructor for class adams.flow.sink.ImageMagickWriter

ImageMagickWriter.ImageType - Enum in adams.flow.sink

The type of the image to create.

imageOverlays() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Returns an iterator over all the image overlays.

ImagePlusContainer - Class in adams.data.imagej

Image wrapper around an ImagePlus used by ImageJ.

ImagePlusContainer() - Constructor for class adams.data.imagej.ImagePlusContainer

imageTypeTipText() - Method in class adams.flow.sink.ImageJWriter

Returns the tip text for this property.

imageTypeTipText() - Method in class adams.flow.sink.ImageMagickWriter

Returns the tip text for this property.

imageTypeTipText() - Method in class adams.flow.sink.JAIWriter

Returns the tip text for this property.

initGUI() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Initializes the widgets.

initialize() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Initializes the members.

initialize() - Method in class adams.flow.transformer.ImageJFlattener

Initializes the members.

initialize() - Method in class adams.flow.transformer.ImageJTransformer

Initializes the members.

initialize() - Method in class adams.flow.transformer.JAIFlattener

Initializes the members.

initialize() - Method in class adams.flow.transformer.JAITransformer

Initializes the members.

initialize() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Initializes the members.

initialize() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Initializes the members.

inputOptionsTipText() - Method in class adams.flow.sink.ffmpeg.GenericPlugin

Returns the tip text for this property.

interpolationTipText() - Method in class adams.data.jai.transformer.Rotate

Returns the tip text for this property.

interpolationTypeTipText() - Method in class adams.data.jai.transformer.Resize

Returns the tip text for this property.

isConvertAvailable() - Static method in class adams.core.ImageMagickHelper

Checks whether the "convert" utility is available.

isSingleton() - Method in class adams.gui.menu.ImageJ

Whether the panel can only be displayed once.

J

JAICreateImage - Class in adams.flow.source

Generates an empty image with the specified dimensions.

JAICreateImage() - Constructor for class adams.flow.source.JAICreateImage

JAIFlattener - Class in adams.flow.transformer

Applies an JAI flattener to the incoming image and outputs the generated WEKA Instance(s).

JAIFlattener() - Constructor for class adams.flow.transformer.JAIFlattener

JAIHelper - Class in adams.core

Helper class for JAI operations.

JAIHelper() - Constructor for class adams.core.JAIHelper

JAIReader - Class in adams.flow.transformer

Reads any file format that Java Advanced Imaging (JAI) can read.

JAIReader() - Constructor for class adams.flow.transformer.JAIReader

JAITransformer - Class in adams.flow.transformer

Applies an JAI transformation to the incoming image and outputs the generated image(s).

JAITransformer() - Constructor for class adams.flow.transformer.JAITransformer

JAITransformer - Class in adams.gui.visualization.image.plugins

Allows the user to apply a JAI transformer to an image in the ImageViewer.

JAITransformer() - Constructor for class adams.gui.visualization.image.plugins.JAITransformer

JAIWriter - Class in adams.flow.sink

Writes an image to disk using Java Advanced Imaging (JAI).

JAIWriter() - Constructor for class adams.flow.sink.JAIWriter

JAIWriter.ImageType - Enum in adams.flow.sink

The type of the image to create.

L

labelsTipText() - Method in class adams.flow.transformer.pixelselector.AddClassification

Returns the tip text for this property.

launch() - Method in class adams.gui.menu.ImageJ

Launches the functionality of the menu item.

M

m_ActionListeners - Variable in class adams.flow.transformer.pixelselector.PixelSelectorPanel

the action listeners.

m_Actions - Variable in class adams.flow.transformer.PixelSelector

the actions that are available from the popup menu.

m_Actions - Variable in class adams.flow.transformer.pixelselector.PixelSelectorPanel

the actions that are available from the popup menu.

m_ActualFilter - Variable in class adams.data.imagej.transformer.PlugInFilter

the actual filter.

m_ActualScheme - Variable in class adams.data.imagej.flattener.NamedSetup

the actual scheme.

m_ActualScheme - Variable in class adams.data.imagej.transformer.NamedSetup

the actual scheme.

m_ActualScheme - Variable in class adams.data.jai.flattener.NamedSetup

the actual scheme.

m_ActualScheme - Variable in class adams.data.jai.transformer.NamedSetup

the actual scheme.

m_AdditionalInputOptions - Variable in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

additional input options to use for ffmpeg.

m_AdditionalInputOptions - Variable in class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

additional input options to use for ffmpeg.

m_AdditionalOutputOptions - Variable in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

additional output options to use for ffmpeg.

m_AdditionalOutputOptions - Variable in class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

additional output options to use for ffmpeg.

m_Anchor - Variable in class adams.data.jai.flattener.PixelClassifications

where to anchor the position on the rectangle.

m_Anchor - Variable in class adams.data.jai.transformer.Crop

where to anchor the position on the rectangle.

m_Angle - Variable in class adams.data.jai.transformer.Rotate

the angle to rotate the image by.

m_Approved - Variable in class adams.flow.transformer.PixelSelector

whether the user approved (or canceled) the dialog.

m_Background - Variable in class adams.data.jai.transformer.Rotate

the background color.

m_Background - Variable in class adams.flow.source.JAICreateImage

the background color.

m_BitRate - Variable in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

the bitrate in kbits to use.

m_ButtonCancel - Variable in class adams.flow.transformer.pixelselector.PixelSelectorPanel

the Cancel button.

m_ButtonOK - Variable in class adams.flow.transformer.pixelselector.PixelSelectorPanel

the OK button.

m_Color - Variable in class adams.flow.transformer.pixelselector.AbstractSingleColorPixelSelectorOverlay

the color of the overlay.

m_Color - Variable in class adams.flow.transformer.SetImagePixel

the color of the pixel.

m_ColorProvider - Variable in class adams.flow.transformer.pixelselector.AbstractColorProviderPixelSelectorOverlay

the color of the overlay.

m_Command - Variable in class adams.data.imagej.transformer.Command

the command to run.

m_CommandOptions - Variable in class adams.data.imagej.transformer.Command

the options for the command.

m_Commands - Variable in class adams.data.imagej.transformer.Macro

the macro commands.

m_Commands - Variable in class adams.flow.transformer.ImageMagickTransformer

the commands to execute.

m_Compress - Variable in class adams.gui.print.TIFFWriter

whether to compress the image.

m_ConvertPresent - Static variable in class adams.core.ImageMagickHelper

whether "convert" is present.

m_CurrentImages - Variable in class adams.flow.transformer.ImageJTransformer

the generated images.

m_CurrentImages - Variable in class adams.flow.transformer.JAITransformer

the generated images.

m_Executable - Variable in class adams.flow.sink.FFmpeg

the ffmpeg executable.

m_Fields - Variable in class adams.data.image.AbstractImageFlattener

fields to add to the output data.

m_FlattenAlgorithm - Variable in class adams.flow.transformer.ImageJFlattener

the transformer to apply to the image.

m_FlattenAlgorithm - Variable in class adams.flow.transformer.JAIFlattener

the transformer to apply to the image.

m_FramesPerSecond - Variable in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

the frames per second to use.

m_Header - Variable in class adams.data.image.AbstractImageFlattener

the current header.

m_Height - Variable in class adams.data.imagej.transformer.Resize

the new height.

m_Height - Variable in class adams.data.jai.flattener.PixelClassifications

the height of the crop rectangle.

m_Height - Variable in class adams.data.jai.transformer.Crop

the height of the crop rectangle.

m_Height - Variable in class adams.data.jai.transformer.Resize

the new height.

m_Height - Variable in class adams.flow.source.JAICreateImage

the height of the image.

m_HistogramType - Variable in class adams.data.imagej.flattener.Histogram

the type of histogram to generate.

m_HistogramType - Variable in class adams.data.jai.flattener.Histogram

the type of histogram to generate.

m_Image - Variable in class adams.flow.transformer.pixelselector.AbstractPixelSelectorOverlay

the underlying image.

m_Image - Variable in class adams.flow.transformer.pixelselector.PixelSelectorPanel

the current image container.

m_ImagePanel - Variable in class adams.flow.transformer.pixelselector.PixelSelectorPanel

the image panel.

m_ImageType - Variable in class adams.flow.sink.ImageJWriter

the image type to create.

m_ImageType - Variable in class adams.flow.sink.ImageMagickWriter

the image type to create.

m_ImageType - Variable in class adams.flow.sink.JAIWriter

the image type to create.

m_Input - Variable in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

the input file.

m_InputOptions - Variable in class adams.flow.sink.ffmpeg.GenericPlugin

input options to use for ffmpeg.

m_Interpolation - Variable in class adams.data.jai.transformer.Rotate

the interpolation type.

m_InterpolationType - Variable in class adams.data.jai.transformer.Resize

the type of interpolation to perform.

m_Labels - Variable in class adams.flow.transformer.pixelselector.AddClassification

the classification labels to use.

m_LastActionResult - Variable in class adams.flow.transformer.pixelselector.PixelSelectorPanel

the last action result for a selector action.

m_MenuBar - Variable in class adams.flow.transformer.pixelselector.PixelSelectorPanel

the menu bar.

m_Notes - Variable in class adams.data.image.AbstractImageFlattener

the notes to add as attributes.

m_NumSubsampleBits - Variable in class adams.data.jai.transformer.Resize

the number of subsample bits.

m_OptionManager - Variable in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

for managing the available options.

m_OriginX - Variable in class adams.data.jai.transformer.Rotate

the X origin.

m_OriginY - Variable in class adams.data.jai.transformer.Rotate

the Y origin.

m_OutputFile - Variable in class adams.flow.sink.FFmpeg

the output file.

m_OutputOptions - Variable in class adams.flow.sink.ffmpeg.GenericPlugin

output options to use for ffmpeg.

m_OutputToken - Variable in class adams.flow.source.JAICreateImage

the generated image token.

m_Overlays - Variable in class adams.flow.transformer.PixelSelector

the overlays to use.

m_Owner - Variable in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

the owning actor.

m_Plugin - Variable in class adams.flow.sink.FFmpeg

the plugin to execute.

m_PlugInFilter - Variable in class adams.data.imagej.transformer.PlugInFilter

the classname of the plugin-filter.

m_PlugInOptions - Variable in class adams.data.imagej.transformer.PlugInFilter

the options for the plugin (if dialog suppressed).

m_PluginsDirectorySet - Static variable in class adams.core.ImageJHelper

whether the plugins directory has been set already.

m_Queue - Variable in class adams.flow.transformer.ImageJFlattener

the generated Instance objects.

m_Queue - Variable in class adams.flow.transformer.JAIFlattener

the generated Instance objects.

m_Radius - Variable in class adams.data.jai.transformer.GaussianBlur

the radius to use.

m_RememberLastSelection - Variable in class adams.flow.transformer.pixelselector.AddClassification

whether to remember the last selection.

m_ReportTable - Variable in class adams.flow.transformer.pixelselector.PixelSelectorPanel

the report table.

m_Result - Variable in class adams.flow.transformer.pixelselector.PixelSelectorPanel

the result (ok or cancel).

m_RGBA - Variable in class adams.flow.transformer.SetImagePixel

the RGBA value of the pixel.

m_SeparateRGB - Variable in class adams.data.jai.flattener.PixelClassifications

whether to output the RGB values in separate attributes.

m_SeparateRGB - Variable in class adams.data.jai.flattener.Pixels

whether to output the RGB values in separate attributes.

m_Setup - Variable in class adams.data.imagej.flattener.NamedSetup

the name of the setup to load.

m_Setup - Variable in class adams.data.imagej.transformer.NamedSetup

the name of the setup to load.

m_Setup - Variable in class adams.data.jai.flattener.NamedSetup

the name of the setup to load.

m_Setup - Variable in class adams.data.jai.transformer.NamedSetup

the name of the setup to load.

m_ShowIndex - Variable in class adams.flow.transformer.pixelselector.ClassificationOverlay

whether to display the index.

m_ShowLabel - Variable in class adams.flow.transformer.pixelselector.ClassificationOverlay

whether to display the label.

m_SplitPane - Variable in class adams.flow.transformer.pixelselector.PixelSelectorPanel

the split pane.

m_SplitterPosition - Variable in class adams.flow.transformer.PixelSelector

the position of the splitter.

m_SuppressPlugInDialog - Variable in class adams.data.imagej.transformer.PlugInFilter

whether to suppress the plugin dialog.

m_TransformAlgorithm - Variable in class adams.flow.transformer.ImageJTransformer

the transformer to apply to the image.

m_TransformAlgorithm - Variable in class adams.flow.transformer.JAITransformer

the transformer to apply to the image.

m_Type - Variable in class adams.flow.transformer.ImageInfo

the type of information to generate.

m_Type - Variable in class adams.flow.transformer.SetImagePixel

what type of value to use for the pixel.

m_Width - Variable in class adams.data.imagej.transformer.Resize

the new width.

m_Width - Variable in class adams.data.jai.flattener.PixelClassifications

the width of the crop rectangle.

m_Width - Variable in class adams.data.jai.transformer.Crop

the width of the crop rectangle.

m_Width - Variable in class adams.data.jai.transformer.Resize

the new width.

m_Width - Variable in class adams.flow.source.JAICreateImage

the width of the image.

m_X - Variable in class adams.data.jai.transformer.Crop

the X position of the crop rectangle.

m_X - Variable in class adams.flow.transformer.SetImagePixel

the X position of the pixel (1-based).

m_Y - Variable in class adams.data.jai.transformer.Crop

the Y position of the crop rectangle.

m_Y - Variable in class adams.flow.transformer.SetImagePixel

the Y position of the pixel (1-based).

Macro - Class in adams.data.imagej.transformer

Executes the macro commands to transform the image.
Due to ImageJ's architecture, only a single ImageJ instance is available in a process at any given time.

Macro() - Constructor for class adams.data.imagej.transformer.Macro

makeKernel(float) - Method in class adams.data.jai.transformer.GaussianBlur

Make a Gaussian blur kernel.

matches(File) - Method in enum adams.flow.sink.ImageMagickWriter.ImageType

Checks whether the file matches the extension of this item.

matches(String) - Method in enum adams.flow.sink.ImageMagickWriter.ImageType

Checks whether the file matches the extension of this item.

matches(File) - Method in enum adams.flow.sink.JAIWriter.ImageType

Checks whether the file matches the extension of this item.

matches(String) - Method in enum adams.flow.sink.JAIWriter.ImageType

Checks whether the file matches the extension of this item.

MOUSE_POSITION - Static variable in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

the mouse position key.

MovieFromImages - Class in adams.flow.sink.ffmpeg

Creates a movie out of a range of images.

MovieFromImages() - Constructor for class adams.flow.sink.ffmpeg.MovieFromImages

N

NamedSetup - Class in adams.data.imagej.flattener

Applies an ImageJ flattener that is referenced via its global setup name (see 'NamedSetups').

NamedSetup() - Constructor for class adams.data.imagej.flattener.NamedSetup

NamedSetup - Class in adams.data.imagej.transformer

Applies an ImageJ flattener that is referenced via its global setup name (see 'NamedSetups').

NamedSetup() - Constructor for class adams.data.imagej.transformer.NamedSetup

NamedSetup - Class in adams.data.jai.flattener

Applies a JAI flattener that is referenced via its global setup name (see 'NamedSetups').

NamedSetup() - Constructor for class adams.data.jai.flattener.NamedSetup

NamedSetup - Class in adams.data.jai.transformer

Applies an JAI flattener that is referenced via its global setup name (see 'NamedSetups').

NamedSetup() - Constructor for class adams.data.jai.transformer.NamedSetup

newArray(int) - Method in class adams.data.image.AbstractImageFlattener

Returns a double array filled with missing values.

newOptionManager() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Returns a new instance of the option manager.

newPanel() - Method in class adams.flow.transformer.PixelSelector

Creates the panel to display in the dialog.

notesTipText() - Method in class adams.data.image.AbstractImageFlattener

Returns the tip text for this property.

notifyActionListeners(int) - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Notifies all the action listeners.

numSubsampleBitsTipText() - Method in class adams.data.jai.transformer.Resize

Returns the tip text for this property.

O

originXTipText() - Method in class adams.data.jai.transformer.Rotate

Returns the tip text for this property.

originYTipText() - Method in class adams.data.jai.transformer.Rotate

Returns the tip text for this property.

output() - Method in class adams.flow.source.JAICreateImage

Returns the generated token.

output() - Method in class adams.flow.transformer.ImageJFlattener

Returns the generated token.

output() - Method in class adams.flow.transformer.ImageJTransformer

Returns the generated token.

output() - Method in class adams.flow.transformer.JAIFlattener

Returns the generated token.

output() - Method in class adams.flow.transformer.JAITransformer

Returns the generated token.

outputFileTipText() - Method in class adams.flow.sink.FFmpeg

Returns the tip text for this property.

outputFileTipText() - Method in class adams.flow.sink.ImageJWriter

Returns the tip text for this property.

outputFileTipText() - Method in class adams.flow.sink.ImageMagickWriter

Returns the tip text for this property.

outputFileTipText() - Method in class adams.flow.sink.JAIWriter

Returns the tip text for this property.

outputOptionsTipText() - Method in class adams.flow.sink.ffmpeg.GenericPlugin

Returns the tip text for this property.

overlaysTipText() - Method in class adams.flow.transformer.PixelSelector

Returns the tip text for this property.

P

paintOverlay(ImagePanel.PaintPanel, Graphics) - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorOverlay

Paints the overlay over the image.

PANEL - Static variable in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

the panel this action is for.

parse(String) - Method in enum adams.data.imagej.flattener.Histogram.HistogramType

Parses the given string and returns the associated enum.

parse(String) - Method in enum adams.data.jai.flattener.Histogram.HistogramType

Parses the given string and returns the associated enum.

parse(String) - Method in enum adams.flow.sink.ImageMagickWriter.ImageType

Parses the given string and returns the associated enum.

parse(String) - Method in enum adams.flow.sink.JAIWriter.ImageType

Parses the given string and returns the associated enum.

PassThrough - Class in adams.data.imagej.transformer

A dummy transform that just passes the image through.

PassThrough() - Constructor for class adams.data.imagej.transformer.PassThrough

PassThrough - Class in adams.data.jai.transformer

A dummy transform that just passes the image through.

PassThrough() - Constructor for class adams.data.jai.transformer.PassThrough

paste() - Method in class adams.gui.clipboard.BufferedImage

Pastes the data from the clipboard.

performDFT(BufferedImageContainer) - Method in class adams.data.jai.flattener.DFT

Performs DFT on the image.

PIXEL_BOTTOM - Static variable in class adams.flow.transformer.pixelselector.BottomRightCorner

the pixel location bottom.

PIXEL_LEFT - Static variable in class adams.flow.transformer.pixelselector.TopLeftCorner

the pixel location left.

PIXEL_POSITION - Static variable in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

the pixel position key.

PIXEL_RIGHT - Static variable in class adams.flow.transformer.pixelselector.BottomRightCorner

the pixel location right.

PIXEL_TOP - Static variable in class adams.flow.transformer.pixelselector.TopLeftCorner

the pixel location top.

PIXEL_X - Static variable in class adams.flow.transformer.pixelselector.AddClassification

the pixel location X prefix.

PIXEL_X - Static variable in class adams.flow.transformer.pixelselector.SimpleSelect

the pixel location X.

PIXEL_Y - Static variable in class adams.flow.transformer.pixelselector.AddClassification

the pixel location Y prefix.

PIXEL_Y - Static variable in class adams.flow.transformer.pixelselector.SimpleSelect

the pixel location Y.

PixelClassifications - Class in adams.data.jai.flattener

Generates an instance for each pixel classification that is stored in the image's report.
Pixel classifications are generated with the adams.flow.transformer.PixelSelector transformer, using the adams.flow.transformer.pixelselector.AddClassification action.

PixelClassifications() - Constructor for class adams.data.jai.flattener.PixelClassifications

Pixels - Class in adams.data.imagej.flattener

Gets all the pixels of the image.

Pixels() - Constructor for class adams.data.imagej.flattener.Pixels

Pixels - Class in adams.data.jai.flattener

Gets all the pixels of the image.

Pixels() - Constructor for class adams.data.jai.flattener.Pixels

PixelSelector - Class in adams.flow.transformer

Allows the user to select pixels.

PixelSelector() - Constructor for class adams.flow.transformer.PixelSelector

PixelSelectorPanel - Class in adams.flow.transformer.pixelselector

Combines an ImagePanel and a Report table.

PixelSelectorPanel() - Constructor for class adams.flow.transformer.pixelselector.PixelSelectorPanel

PlugInFilter - Class in adams.data.imagej.transformer

A transformer that allows the use of ImageJ's plug-in filters.
Notes:
- the filter must implement 'ij.plugin.filter.PlugInFilter'
- the filter can pop-up a window to enter additional parameters,
the first time it is executed, depending on the filter implementation
(you can suppress this with supplying the options manually)
- the manual options string can be obtained when recording macros
in ImageJ
- the filter must be in the classpath of the application

Valid options are:

PlugInFilter() - Constructor for class adams.data.imagej.transformer.PlugInFilter

plugInFilterTipText() - Method in class adams.data.imagej.transformer.PlugInFilter

Returns the tip text for this property.

plugInOptionsTipText() - Method in class adams.data.imagej.transformer.PlugInFilter

Returns the tip text for this property.

pluginTipText() - Method in class adams.flow.sink.FFmpeg

Returns the tip text for this property.

postProcessHeader(Instances) - Method in class adams.data.image.AbstractImageFlattener

Post-processes the header, adding fields and notes.

postProcessInstance(T, Instance) - Method in class adams.data.image.AbstractImageFlattener

Post-processes the generated instance, adding notes and fields.

PROPERTY_PLUGINS_DIR - Static variable in class adams.core.ImageJHelper

the system property that ImageJ queries for the plugins directory.

pruneBackup() - Method in class adams.flow.transformer.ImageJFlattener

Removes entries from the backup.

pruneBackup() - Method in class adams.flow.transformer.ImageJTransformer

Removes entries from the backup.

pruneBackup() - Method in class adams.flow.transformer.JAIFlattener

Removes entries from the backup.

pruneBackup() - Method in class adams.flow.transformer.JAITransformer

Removes entries from the backup.

R

radiusTipText() - Method in class adams.data.jai.transformer.GaussianBlur

Returns the tip text for this property.

read(File) - Static method in class adams.core.ImageMagickHelper

Reads a BufferedImage from the file.

read(URL) - Static method in class adams.core.ImageMagickHelper

Reads a BufferedImage from a URL.

read(InputStream) - Static method in class adams.core.ImageMagickHelper

Reads a BufferedImage from the stream.

read(File) - Static method in class adams.core.JAIHelper

Loads the specified file.

read(String) - Static method in class adams.core.JAIHelper

Loads the specified file.

RectangleOverlay - Class in adams.flow.transformer.pixelselector

Simply highlights the selected pixel

Some actions that generate data for this overlay:
adams.flow.transformer.pixelselector.TopLeftCorner
adams.flow.transformer.pixelselector.BottomRightCorner

Valid options are:

RectangleOverlay() - Constructor for class adams.flow.transformer.pixelselector.RectangleOverlay

rememberLastSelectionTipText() - Method in class adams.flow.transformer.pixelselector.AddClassification

Returns the tip text for this property.

removeActionListener(ActionListener) - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Removes a listener for button actions.

removeImageOverlay(ImageOverlay) - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Removes the image overlay.

reset() - Method in class adams.data.image.AbstractImageFlattener

Resets the scheme, i.e., the header information.

reset() - Method in class adams.data.imagej.flattener.NamedSetup

Resets the filter.

reset() - Method in class adams.data.imagej.transformer.NamedSetup

Resets the filter.

reset() - Method in class adams.data.imagej.transformer.PlugInFilter

Resets the scheme.

reset() - Method in class adams.data.jai.flattener.NamedSetup

Resets the filter.

reset() - Method in class adams.data.jai.transformer.NamedSetup

Resets the filter.

reset() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Resets the scheme.

reset() - Method in class adams.flow.transformer.ImageJFlattener

Resets the scheme.

reset() - Method in class adams.flow.transformer.JAIFlattener

Resets the scheme.

reset() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Resets the scheme.

Resize - Class in adams.data.imagej.transformer

Resizes the image to predefined width and height.

Resize() - Constructor for class adams.data.imagej.transformer.Resize

Resize - Class in adams.data.jai.transformer

Resizes the image to predefined width and height.

Resize() - Constructor for class adams.data.jai.transformer.Resize

Resize.InterpolationType - Enum in adams.data.jai.transformer

Type of interpolaction.

restoreState(Hashtable<String, Object>) - Method in class adams.flow.transformer.ImageJFlattener

Restores the state of the actor before the variables got updated.

restoreState(Hashtable<String, Object>) - Method in class adams.flow.transformer.ImageJTransformer

Restores the state of the actor before the variables got updated.

restoreState(Hashtable<String, Object>) - Method in class adams.flow.transformer.JAIFlattener

Restores the state of the actor before the variables got updated.

restoreState(Hashtable<String, Object>) - Method in class adams.flow.transformer.JAITransformer

Restores the state of the actor before the variables got updated.

RGBATipText() - Method in class adams.flow.transformer.SetImagePixel

Returns the tip text for this property.

Rotate - Class in adams.data.jai.transformer

Rotates an image by a defined number of degrees.

Rotate() - Constructor for class adams.data.jai.transformer.Rotate

Rotate.InterpolationType - Enum in adams.data.jai.transformer

The types of interpolations.

S

separateRGBTipText() - Method in class adams.data.jai.flattener.PixelClassifications

Returns the tip text for this property.

separateRGBTipText() - Method in class adams.data.jai.flattener.Pixels

Returns the tip text for this property.

setActions(AbstractPixelSelectorAction[]) - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Sets the available popup actions.

setActions(AbstractPixelSelectorAction[]) - Method in class adams.flow.transformer.PixelSelector

Sets the available popup actions.

setAdditionalInputOptions(String) - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

Sets the additional input options to use.

setAdditionalOutputOptions(String) - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPluginWithOptions

Sets the additional output options to use.

setAnchor(Crop.Anchor) - Method in class adams.data.jai.flattener.PixelClassifications

Sets where to anchor the position on the rectangle.

setAnchor(Crop.Anchor) - Method in class adams.data.jai.transformer.Crop

Sets where to anchor the position on the rectangle.

setAngle(double) - Method in class adams.data.jai.transformer.Rotate

Sets the rotation angle.

setBackground(Color) - Method in class adams.data.jai.transformer.Rotate

Sets the color to use for the background.

setBackground(Color) - Method in class adams.flow.source.JAICreateImage

Sets the background color of the image.

setBitRate(int) - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Sets the bit rate in kbits to use.

setColor(Color) - Method in class adams.flow.transformer.pixelselector.AbstractSingleColorPixelSelectorOverlay

Sets the color for the overlay.

setColor(Color) - Method in class adams.flow.transformer.SetImagePixel

Sets the color of the pixel.

setColorProvider(AbstractColorProvider) - Method in class adams.flow.transformer.pixelselector.AbstractColorProviderPixelSelectorOverlay

Sets the color provider for the overlay.

setCommand(String) - Method in class adams.data.imagej.transformer.Command

Sets the command to execute.

setCommandOptions(String) - Method in class adams.data.imagej.transformer.Command

Sets the options for the command.

setCommands(BaseText) - Method in class adams.data.imagej.transformer.Macro

Sets the width to resize to.

setCommands(BaseText) - Method in class adams.flow.transformer.ImageMagickTransformer

Sets the commands to execute.

setCompress(boolean) - Method in class adams.gui.print.TIFFWriter

Sets whether to compress the image.

setExecutable(PlaceholderFile) - Method in class adams.flow.sink.FFmpeg

Sets the ffmpeg executable.

setFields(Field[]) - Method in class adams.data.image.AbstractImageFlattener

Sets the targets to add.

setFlattenAlgorithm(AbstractImageJFlattener) - Method in class adams.flow.transformer.ImageJFlattener

Sets the flattener to use.

setFlattenAlgorithm(AbstractJAIFlattener) - Method in class adams.flow.transformer.JAIFlattener

Sets the flattener to use.

setFramesPerSecond(int) - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Sets the frames per second to use.

setHeight(int) - Method in class adams.data.imagej.transformer.Resize

Sets the height to resize to.

setHeight(int) - Method in class adams.data.jai.flattener.PixelClassifications

Sets the height of the crop rectangle.

setHeight(int) - Method in class adams.data.jai.transformer.Crop

Sets the height of the crop rectangle.

setHeight(int) - Method in class adams.data.jai.transformer.Resize

Sets the height to resize to.

setHeight(int) - Method in class adams.flow.source.JAICreateImage

Sets the height of the image.

setHistogramType(Histogram.HistogramType) - Method in class adams.data.imagej.flattener.Histogram

Sets the type of histogram to generate.

setHistogramType(Histogram.HistogramType) - Method in class adams.data.jai.flattener.Histogram

Sets the type of histogram to generate.

setImage(AbstractImage) - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorOverlay

Sets the underlying image.

setImage(AbstractImage) - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Sets the image.

SetImagePixel - Class in adams.flow.transformer

Obtains information from the picture passing through.

SetImagePixel() - Constructor for class adams.flow.transformer.SetImagePixel

SetImagePixel.PixelValueType - Enum in adams.flow.transformer

Enumeration that determines what value to use for the pixel.

setImageType(ImageJWriter.ImageType) - Method in class adams.flow.sink.ImageJWriter

Sets the type of image to create.

setImageType(ImageMagickWriter.ImageType) - Method in class adams.flow.sink.ImageMagickWriter

Sets the type of image to create.

setImageType(JAIWriter.ImageType) - Method in class adams.flow.sink.JAIWriter

Sets the type of image to create.

setInput(PlaceholderFile) - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Sets the input file.

setInputOptions(String) - Method in class adams.flow.sink.ffmpeg.GenericPlugin

Sets the input options to use.

setInterpolation(Rotate.InterpolationType) - Method in class adams.data.jai.transformer.Rotate

Sets the type of interpolation to perform.

setInterpolationType(Resize.InterpolationType) - Method in class adams.data.jai.transformer.Resize

Sets the type of interpolation to use.

setLabels(BaseString[]) - Method in class adams.flow.transformer.pixelselector.AddClassification

Sets the available classification labels.

setLastActionResult(Class, Object) - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Stores the result for the specified action.

setMousePosition(Point) - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Stores the mouse position in the action.

setNotes(BaseString[]) - Method in class adams.data.image.AbstractImageFlattener

Sets the notes to add as attributes.

setNumSubsampleBits(int) - Method in class adams.data.jai.transformer.Resize

Sets the precision for subsampling in bits.

setOriginX(int) - Method in class adams.data.jai.transformer.Rotate

Sets the X of the origin.

setOriginY(int) - Method in class adams.data.jai.transformer.Rotate

Sets the Y of the origin.

setOutputOptions(String) - Method in class adams.flow.sink.ffmpeg.GenericPlugin

Sets the output options to use.

setOverlays(AbstractPixelSelectorOverlay[]) - Method in class adams.flow.transformer.PixelSelector

Sets the available image overlays.

setOwner(FFmpeg) - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Sets the owner.

setPanel(PixelSelectorPanel) - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Stores the panel in the action.

setPixelPosition(Point) - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Stores the pixel position in the action.

setPlugin(AbstractFFmpegPlugin) - Method in class adams.flow.sink.FFmpeg

Sets the plugin to use.

setPlugInFilter(String) - Method in class adams.data.imagej.transformer.PlugInFilter

Sets the classname of the plugin filter to use.

setPlugInOptions(String) - Method in class adams.data.imagej.transformer.PlugInFilter

Sets the options for the plug-in if the dialog gets suppressed.

setPluginsDirectory() - Static method in class adams.core.ImageJHelper

Sets the ImageJ directory as ".$PROJECTHOME/imagej" and the plugins directory therefore as ".$PROJECTHOME/imagej/plugins"

setRadius(double) - Method in class adams.data.jai.transformer.GaussianBlur

Sets the blur radius.

setRememberLastSelection(boolean) - Method in class adams.flow.transformer.pixelselector.AddClassification

Sets whether to remember the last selected label.

setRGBA(int) - Method in class adams.flow.transformer.SetImagePixel

Sets the RGBA value of the pixel.

setSeparateRGB(boolean) - Method in class adams.data.jai.flattener.PixelClassifications

Sets whether to separate the RGB values or not.

setSeparateRGB(boolean) - Method in class adams.data.jai.flattener.Pixels

Sets whether to separate the RGB values or not.

setSetup(NamedSetup) - Method in class adams.data.imagej.flattener.NamedSetup

Sets the setup name.

setSetup(NamedSetup) - Method in class adams.data.imagej.transformer.NamedSetup

Sets the setup name.

setSetup(NamedSetup) - Method in class adams.data.jai.flattener.NamedSetup

Sets the setup name.

setSetup(NamedSetup) - Method in class adams.data.jai.transformer.NamedSetup

Sets the setup name.

setShowIndex(boolean) - Method in class adams.flow.transformer.pixelselector.ClassificationOverlay

Sets whether to show the index.

setShowLabel(boolean) - Method in class adams.flow.transformer.pixelselector.ClassificationOverlay

Sets whether to show the label.

setSplitterPosition(int) - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Sets the location of the splitter/divider.

setSplitterPosition(int) - Method in class adams.flow.transformer.PixelSelector

Sets the initial position of the splitter in the viewer panel.

setSuppressPlugInDialog(boolean) - Method in class adams.data.imagej.transformer.PlugInFilter

Sets whether to suppress the plugin dialog.

setTransformAlgorithm(AbstractImageJTransformer) - Method in class adams.flow.transformer.ImageJTransformer

Sets the transformer to use.

setTransformAlgorithm(AbstractJAITransformer) - Method in class adams.flow.transformer.JAITransformer

Sets the transformer to use.

setType(ImageInfo.InfoType) - Method in class adams.flow.transformer.ImageInfo

Sets the type of information to generate.

setType(SetImagePixel.PixelValueType) - Method in class adams.flow.transformer.SetImagePixel

Sets the type of value to use.

setUp() - Method in class adams.flow.sink.ffmpeg.AbstractFFmpegPlugin

Checks the configuration.

setUp() - Method in class adams.flow.sink.FFmpeg

Initializes the item for flow execution.

setUp() - Method in class adams.flow.sink.ImageJWriter

Initializes the item for flow execution.

setUp() - Method in class adams.flow.sink.ImageMagickWriter

Initializes the item for flow execution.

setUp() - Method in class adams.flow.transformer.ImageJFlattener

Initializes the item for flow execution.

setUp() - Method in class adams.flow.transformer.ImageJReader

Initializes the item for flow execution.

setUp() - Method in class adams.flow.transformer.ImageJTransformer

Initializes the item for flow execution.

setUp() - Method in class adams.flow.transformer.ImageMagickReader

Initializes the item for flow execution.

setUp() - Method in class adams.flow.transformer.ImageMagickTransformer

Initializes the item for flow execution.

setUp() - Method in class adams.flow.transformer.PixelSelector

Initializes the item for flow execution.

setupTipText() - Method in class adams.data.imagej.flattener.NamedSetup

Returns the tip text for this property.

setupTipText() - Method in class adams.data.imagej.transformer.NamedSetup

Returns the tip text for this property.

setupTipText() - Method in class adams.data.jai.flattener.NamedSetup

Returns the tip text for this property.

setupTipText() - Method in class adams.data.jai.transformer.NamedSetup

Returns the tip text for this property.

setWidth(int) - Method in class adams.data.imagej.transformer.Resize

Sets the width to resize to.

setWidth(int) - Method in class adams.data.jai.flattener.PixelClassifications

Sets the width of the crop rectangle.

setWidth(int) - Method in class adams.data.jai.transformer.Crop

Sets the width of the crop rectangle.

setWidth(int) - Method in class adams.data.jai.transformer.Resize

Sets the width to resize to.

setWidth(int) - Method in class adams.flow.source.JAICreateImage

Sets the width of the image.

setX(int) - Method in class adams.data.jai.transformer.Crop

Sets the X position.

setX(int) - Method in class adams.flow.transformer.SetImagePixel

Sets the X position of the pixel.

setY(int) - Method in class adams.data.jai.transformer.Crop

Sets the Y position.

setY(int) - Method in class adams.flow.transformer.SetImagePixel

Sets the Y position of the pixel.

shallowCopy() - Method in class adams.data.image.AbstractImageFlattener

Returns a shallow copy of itself, i.e., based on the commandline options.

shallowCopy(boolean) - Method in class adams.data.image.AbstractImageFlattener

Returns a shallow copy of itself, i.e., based on the commandline options.

shallowCopy() - Method in class adams.data.image.AbstractImageTransformer

Returns a shallow copy of itself, i.e., based on the commandline options.

shallowCopy(boolean) - Method in class adams.data.image.AbstractImageTransformer

Returns a shallow copy of itself, i.e., based on the commandline options.

shallowCopy() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorOverlay

Returns a shallow copy of itself.

shallowCopy(boolean) - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorOverlay

Returns a shallow copy of itself.

showIndexTipText() - Method in class adams.flow.transformer.pixelselector.ClassificationOverlay

Returns the tip text for this property.

showLabelTipText() - Method in class adams.flow.transformer.pixelselector.ClassificationOverlay

Returns the tip text for this property.

SimpleOverlay - Class in adams.flow.transformer.pixelselector

Simply highlights the selected pixel

Some actions that generate data for this overlay:
adams.flow.transformer.pixelselector.SimpleSelect

Valid options are:

SimpleOverlay() - Constructor for class adams.flow.transformer.pixelselector.SimpleOverlay

SimpleSelect - Class in adams.flow.transformer.pixelselector

Allows the user to select a pixel location.
Stores the location in 'Pixel.X' and 'Pixel.Y'.

SimpleSelect() - Constructor for class adams.flow.transformer.pixelselector.SimpleSelect

splitterPositionTipText() - Method in class adams.flow.transformer.PixelSelector

Returns the tip text for this property.

suppressPlugInDialogTipText() - Method in class adams.data.imagej.transformer.PlugInFilter

Returns the tip text for this property.

T

tableChanged(TableModelEvent) - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Whenever the data in the report changes.

TIFFWriter - Class in adams.gui.print

Outputs TIFF images.

TIFFWriter() - Constructor for class adams.gui.print.TIFFWriter

toBufferedImage() - Method in class adams.data.imagej.ImagePlusContainer

Turns the image into a buffered image.

toBufferedImage() - Method in class adams.data.jai.BufferedImageContainer

Turns the image into a buffered image.

toCommandLine() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Returns the commandline string.

toDisplay() - Method in enum adams.data.imagej.flattener.Histogram.HistogramType

Returns the display string.

toDisplay() - Method in enum adams.data.jai.flattener.Histogram.HistogramType

Returns the display string.

toDisplay() - Method in enum adams.flow.sink.ImageMagickWriter.ImageType

Returns the display string.

toDisplay() - Method in enum adams.flow.sink.JAIWriter.ImageType

Returns the display string.

TopLeftCorner - Class in adams.flow.transformer.pixelselector

Allows the user to select a pixel location of the top-left corner.
Stores the location in 'Pixel.Left' and 'Pixel.Top'.

TopLeftCorner() - Constructor for class adams.flow.transformer.pixelselector.TopLeftCorner

toRaw() - Method in enum adams.data.imagej.flattener.Histogram.HistogramType

Returns the raw enum string.

toRaw() - Method in enum adams.data.jai.flattener.Histogram.HistogramType

Returns the raw enum string.

toRaw() - Method in enum adams.flow.sink.ImageMagickWriter.ImageType

Returns the raw enum string.

toRaw() - Method in enum adams.flow.sink.JAIWriter.ImageType

Returns the raw enum string.

toString() - Method in enum adams.data.imagej.flattener.Histogram.HistogramType

Returns the display string.

toString(AbstractOption, Object) - Static method in enum adams.data.imagej.flattener.Histogram.HistogramType

Returns the enum as string.

toString() - Method in enum adams.data.jai.flattener.Histogram.HistogramType

Returns the display string.

toString(AbstractOption, Object) - Static method in enum adams.data.jai.flattener.Histogram.HistogramType

Returns the enum as string.

toString() - Method in enum adams.flow.sink.ImageMagickWriter.ImageType

Returns the display string.

toString(AbstractOption, Object) - Static method in enum adams.flow.sink.ImageMagickWriter.ImageType

Returns the enum as string.

toString() - Method in enum adams.flow.sink.JAIWriter.ImageType

Returns the display string.

toString(AbstractOption, Object) - Static method in enum adams.flow.sink.JAIWriter.ImageType

Returns the enum as string.

toString() - Method in class adams.flow.transformer.pixelselector.AbstractPixelSelectorAction

Returns a string representation of the options.

transform(T) - Method in class adams.data.image.AbstractImageTransformer

Transforms the given image.

transformAlgorithmTipText() - Method in class adams.flow.transformer.ImageJTransformer

Returns the tip text for this property.

transformAlgorithmTipText() - Method in class adams.flow.transformer.JAITransformer

Returns the tip text for this property.

typeTipText() - Method in class adams.flow.transformer.ImageInfo

Returns the tip text for this property.

typeTipText() - Method in class adams.flow.transformer.SetImagePixel

Returns the tip text for this property.

U

unwrap(Token) - Method in class adams.gui.clipboard.BufferedImage

Unwraps the actual data from the token.

update() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Updates the report/image.

updateImage() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Updates the image.

updateProvenance(ProvenanceContainer) - Method in class adams.flow.transformer.ImageJFlattener

Updates the provenance information in the provided container.

updateProvenance(ProvenanceContainer) - Method in class adams.flow.transformer.ImageJReader

Updates the provenance information in the provided container.

updateProvenance(ProvenanceContainer) - Method in class adams.flow.transformer.ImageJTransformer

Updates the provenance information in the provided container.

updateProvenance(ProvenanceContainer) - Method in class adams.flow.transformer.ImageMagickReader

Updates the provenance information in the provided container.

updateProvenance(ProvenanceContainer) - Method in class adams.flow.transformer.ImageMagickTransformer

Updates the provenance information in the provided container.

updateProvenance(ProvenanceContainer) - Method in class adams.flow.transformer.JAIFlattener

Updates the provenance information in the provided container.

updateProvenance(ProvenanceContainer) - Method in class adams.flow.transformer.JAIReader

Updates the provenance information in the provided container.

updateProvenance(ProvenanceContainer) - Method in class adams.flow.transformer.JAITransformer

Updates the provenance information in the provided container.

updateProvenance(ProvenanceContainer) - Method in class adams.flow.transformer.PixelSelector

Updates the provenance information in the provided container.

updateReport() - Method in class adams.flow.transformer.pixelselector.PixelSelectorPanel

Updates the report.

V

valueOf(String) - Static method in enum adams.data.imagej.flattener.Histogram.HistogramType

Returns the enum constant of this type with the specified name.

valueOf(AbstractOption, String) - Static method in enum adams.data.imagej.flattener.Histogram.HistogramType

Returns an enum generated from the string.

valueOf(String) - Static method in enum adams.data.jai.flattener.Histogram.HistogramType

Returns the enum constant of this type with the specified name.

valueOf(AbstractOption, String) - Static method in enum adams.data.jai.flattener.Histogram.HistogramType

Returns an enum generated from the string.

valueOf(String) - Static method in enum adams.data.jai.transformer.Crop.Anchor

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum adams.data.jai.transformer.Resize.InterpolationType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum adams.data.jai.transformer.Rotate.InterpolationType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum adams.flow.sink.ImageJWriter.ImageType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum adams.flow.sink.ImageMagickWriter.ImageType

Returns the enum constant of this type with the specified name.

valueOf(AbstractOption, String) - Static method in enum adams.flow.sink.ImageMagickWriter.ImageType

Returns an enum generated from the string.

valueOf(String) - Static method in enum adams.flow.sink.JAIWriter.ImageType

Returns the enum constant of this type with the specified name.

valueOf(AbstractOption, String) - Static method in enum adams.flow.sink.JAIWriter.ImageType

Returns an enum generated from the string.

valueOf(String) - Static method in enum adams.flow.transformer.ImageInfo.InfoType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum adams.flow.transformer.SetImagePixel.PixelValueType

Returns the enum constant of this type with the specified name.

values() - Static method in enum adams.data.imagej.flattener.Histogram.HistogramType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum adams.data.jai.flattener.Histogram.HistogramType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum adams.data.jai.transformer.Crop.Anchor

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum adams.data.jai.transformer.Resize.InterpolationType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum adams.data.jai.transformer.Rotate.InterpolationType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum adams.flow.sink.ImageJWriter.ImageType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum adams.flow.sink.ImageMagickWriter.ImageType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum adams.flow.sink.JAIWriter.ImageType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum adams.flow.transformer.ImageInfo.InfoType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum adams.flow.transformer.SetImagePixel.PixelValueType

Returns an array containing the constants of this enum type, in the order they are declared.

W

widthTipText() - Method in class adams.data.imagej.transformer.Resize

Returns the tip text for this property.

widthTipText() - Method in class adams.data.jai.flattener.PixelClassifications

Returns the tip text for this property.

widthTipText() - Method in class adams.data.jai.transformer.Crop

Returns the tip text for this property.

widthTipText() - Method in class adams.data.jai.transformer.Resize

Returns the tip text for this property.

widthTipText() - Method in class adams.flow.source.JAICreateImage

Returns the tip text for this property.

wrap(BufferedImage) - Method in class adams.gui.clipboard.BufferedImage

Wraps the data from the clipboard in a flow token.

wrapUp() - Method in class adams.flow.transformer.ImageJFlattener

Cleans up after the execution has finished.

wrapUp() - Method in class adams.flow.transformer.ImageJTransformer

Cleans up after the execution has finished.

wrapUp() - Method in class adams.flow.transformer.JAIFlattener

Cleans up after the execution has finished.

wrapUp() - Method in class adams.flow.transformer.JAITransformer

Cleans up after the execution has finished.

X

XTipText() - Method in class adams.data.jai.transformer.Crop

Returns the tip text for this property.

XTipText() - Method in class adams.flow.transformer.SetImagePixel

Returns the tip text for this property.

Y

YTipText() - Method in class adams.data.jai.transformer.Crop

Returns the tip text for this property.

YTipText() - Method in class adams.flow.transformer.SetImagePixel

Returns the tip text for this property.

A B C D E F G H I J L M N O P R S T U V W X Y