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

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getBitDepth() - Method in class acquifer.ij.VirtualImageSeries

getBitDepth() - Method in class acquifer.ij.VirtualPlate

getBoldFont() - Method in class acquifer.ij.BatchDialog

Return the default Font but bold, or null if it is in headless or if the plugin's GUI is not shown.

getChannels() - Method in class acquifer.ij.BatchDialog

Return selected channels, this function should be called after calling BatchDialog.getDefaultInputs().

getChannelsLuts() - Static method in class acquifer.ij.im.plugins.Hyperstack_Maker

Return the list of colours LUT associated to the microscope channels.

getCheckboxesForColumn(int) - Method in class acquifer.ij.BatchDialog

Return the list of checkboxes for wells of a given plate column.

getCheckboxGroup() - Method in class acquifer.ij.BatchDialog

Return a list containing all the checkboxes composing the checkbox group.

getCodeCompletion(CompletionProvider) - Method in enum acquifer.ij.MacroFunction

Return the object necessary to have custom code completion.

getCompletions(CompletionProvider) - Method in class acquifer.ij.MacroCodeCompletion

Provides auto-completion by returning a BasicCompletion for each macro-function.

getCurrentImageDirectory() - Method in class acquifer.ij.BatchDialog

Return path currently in the GUI, if it corresponds to a valid directory, otherwise return null.

getCZT() - Method in class acquifer.ij.im.plugins.HyperstackBrowser

Return an array with the c,z,t values (mind the order) currently entered in the GUI.

getDefaultInputs() - Method in class acquifer.ij.BatchDialog

Read all the default user-inputs (using the getNext*** methods, to be macro-recordable).

getDirectory() - Method in class acquifer.ij.VirtualImageSeries

getDirectory() - Method in class acquifer.ij.VirtualPlate

getDirectoryName() - Method in class acquifer.ij.VirtualPlate

getExtensionDescriptor(MacroExtension) - Method in enum acquifer.ij.MacroFunction

Return ExtensionDescriptor, the object needed to add custom macro-functions.

getExtensionFunctions() - Method in class acquifer.ij.BaseMacroExtensions

Return the list of ExtensionDescriptor to make available custom macro-commands.

getFileName(int) - Method in class acquifer.ij.VirtualImageSeries

getFileName(int) - Method in class acquifer.ij.VirtualPlate

getFont() - Method in class acquifer.ij.BatchDialog

Return the default Font of the GUI when displayed, or null when the plugin call is through the command line.

getHeaderCheckboxes() - Method in class acquifer.ij.BatchDialog

Return a reference to the header checkboxes.

getHeight() - Method in class acquifer.ij.VirtualImageSeries

getHeight() - Method in class acquifer.ij.VirtualPlate

getImageDirectory() - Method in class acquifer.ij.BatchDialog

Return image directory, this function should be called after calling BatchDialog.getDefaultInputs().

getImagePlane(int) - Method in class acquifer.ij.VirtualImageSeries

Return the ImagePlane (or null if missing) at index n (1-based).

getIntegerValue(int) - Method in class acquifer.ij.im.plugins.HyperstackBrowser

Return the integer value of the NumericField input of given index.

getLutNameForChannel(int) - Static method in class acquifer.ij.im.plugins.Hyperstack_Maker

Return the name of the color-LUT associated to a given microscope channel (between 1 and 6).

getLuts() - Static method in class acquifer.ij.im.plugins.Hyperstack_Maker

Returns the list of LUTs advised for the display of hyperstacks channels.

getMatchingDataset(Comparator<ImagePlane>, boolean) - Method in class acquifer.ij.BatchDialog

Return a Dataset representing the data matching the selected dimensions.

getMatchingDataset(boolean) - Method in class acquifer.ij.BatchDialog

Return a Dataset representing the data matching the selected dimensions.

getMatchingDataset() - Method in class acquifer.ij.BatchDialog

Return a Dataset representing the data matching the selected dimensions.

getNextStringAsIntegers() - Method in class acquifer.ij.BatchDialog

Parse a string of comma-separated integers from the next string input field of the dialog in a macro-recordable way.

getNumberOfColumns() - Method in class acquifer.ij.VirtualPlate

Return the number of columns in the montage image.

getNumberOfRows() - Method in class acquifer.ij.VirtualPlate

Return the number of rows in the montage image.

getProcessor(int) - Method in class acquifer.ij.VirtualImageSeries

Return the ImageProcessor for the index n (1-based) or a black ImageProcessor if no ImagePlane is available.

getProcessor(int) - Method in class acquifer.ij.VirtualPlate

Return the ImageProcessor for slice n where 1<=n<=nslices.

getSavedWellCheckboxState(Plate) - Method in class acquifer.ij.BatchDialog

Recover from persistence the state of the checkboxes for the full checkbox group as an array of boolean.

getSize() - Method in class acquifer.ij.VirtualImageSeries

getSize() - Method in class acquifer.ij.VirtualPlate

Return the number of slices in the VirtualPlate/Stack.

getSliceLabel(int) - Method in class acquifer.ij.VirtualImageSeries

Return the slice label for the slice at 1-based index n.

getSliceLabel(int) - Method in class acquifer.ij.VirtualPlate

Return the label of the n-th slice with 1<=n<=nslices.

getSubPosition() - Method in class acquifer.ij.VirtualPlate

Return the well-subposition of the images shown in this montage.

getSubpositions() - Method in class acquifer.ij.BatchDialog

Return selected subpositions, this function should be called after calling BatchDialog.getDefaultInputs().

getTiffInfos(String) - Static method in class acquifer.ij.Utils

Read the tiff metadata from a tif file header using ImageJ built-in functionality (TiffDecoder).

getTimepoints() - Method in class acquifer.ij.BatchDialog

Return selected timepoints, this function should be called after calling BatchDialog.getDefaultInputs().

getWellCheckboxes() - Method in class acquifer.ij.BatchDialog

Return a list containing the checkboxes for the wells selection.

getWells() - Method in class acquifer.ij.BatchDialog

Return the set of wells selected, this function should be called after calling BatchDialog.getDefaultInputs().

getWidth() - Method in class acquifer.ij.VirtualImageSeries

getWidth() - Method in class acquifer.ij.VirtualPlate

getWidthHeightBitDepthFromInfo(FileInfo) - Static method in class acquifer.ij.Utils

Read an image dimensions [width, height, bitDepth] from the header of a tiff image.

getWidthHeightBitDepthFromTiff(String) - Static method in class acquifer.ij.Utils

getZslice() - Method in class acquifer.ij.BatchDialog

Return selected Z-slice, this function should be called after calling BatchDialog.getDefaultInputs().

groupAsHyperStacks(Dataset, MetadataParser) - Static method in class acquifer.ij.im.plugins.Hyperstack_Maker

Make a list of hyperstacks from the ImageSeries contained in a dataset.

groupAsHyperStacks(Dataset) - Static method in class acquifer.ij.im03.plugins.Hyperstack_Maker

Make a list of hyperstack (as ImagePlus) from a dataset.

groupAsHyperStacks(Dataset) - Static method in class acquifer.ij.im04.plugins.Hyperstack_Maker

Make a list of hyperstack (as ImagePlus) from a dataset.

groupedImageInfos - Variable in class acquifer.ij.im.plugins.Hyperstack_Maker

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