- gamma(double) - Method in class ij.process.FloatProcessor
-
- gamma(double) - Method in class ij.process.ImageProcessor
-
Performs gamma correction of the image or ROI.
- gamma(double) - Method in class ij.process.ShortProcessor
-
- GenericDialog - Class in ij.gui
-
This class is a customizable modal dialog box.
- GenericDialog() - Constructor for class ij.gui.GenericDialog
-
- GenericDialog(String) - Constructor for class ij.gui.GenericDialog
-
Creates a new GenericDialog with the specified title.
- GenericDialog(String, Frame) - Constructor for class ij.gui.GenericDialog
-
Creates a new GenericDialog using the specified title and parent frame.
- get(int, int) - Method in class ij.process.FloatProcessor
-
- get(int) - Method in class ij.process.FloatProcessor
-
- get(int, int) - Method in class ij.process.ImageProcessor
-
This is a faster version of getPixel() that does not do bounds checking.
- get(int) - Method in class ij.process.ImageProcessor
-
- get(int, int) - Method in class ij.process.ShortProcessor
-
- get(int) - Method in class ij.process.ShortProcessor
-
- get(int) - Method in class ij.wave.Wave
-
- get(int) - Method in class ij.wave.Waves
-
A convenience method for calling getWave.
- get(int) - Method in class org.jah.ephys.Comments
-
- get16BitBufferedImage() - Method in class ij.process.ShortProcessor
-
Returns a copy of this image as a TYPE_USHORT_GRAY BufferedImage.
- getABFVersion() - Method in class org.jah.ephys.abf.ABF
-
- getAbsoluteTime(long) - Method in class org.jah.ephys.abf.ABF
-
- getActiveWindow() - Static method in class ij.WindowManager
-
Returns the front most window or null.
- getAngle(int, int, int, int) - Method in class ij.gui.Roi
-
Returns the angle in degrees between the specified line and a horizontal line.
- getAnnotatedImage(int, int) - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getAnnotations() - Method in class ij.plugin.frame.ChartPlugIn
-
Returns a list of XYAnnotations on the chart.
- getApplet() - Static method in class ij.IJ
-
Returns the Applet that created this ImageJ or null if running as an application.
- getArea() - Method in class ij.gui.Roi
-
Calculates the area of the Roi passed as argument (in pixel values).
- getArea() - Method in class ij.wave.Burst
-
Returns the area under the full burst as y-units*s.
- getAreaCV() - Method in class ij.wave.Bursts
-
- getAreaMean() - Method in class ij.wave.Bursts
-
- getAreas() - Method in class ij.wave.Bursts
-
Returns the area under the full bursts as y-units*s.
- getAreaStderr() - Method in class ij.wave.Bursts
-
- getAreaStdev() - Method in class ij.wave.Bursts
-
- getArray() - Method in class ij.wave.Waves
-
Returns this collection of Waves as an array.
- getAsBufferedImage() - Method in class ij.plugin.frame.ChartPlugIn
-
- getAsColorProcessor() - Method in class ij.plugin.frame.ChartPlugIn
-
- getAutoPulseLaser() - Static method in class org.jah.Configuration_
-
- getAutoThreshold() - Method in class ij.process.ImageProcessor
-
Returns a pixel value (threshold) that can be used to divide the image into objects
and background.
- getAutoThreshold(int[]) - Method in class ij.process.ImageProcessor
-
This is a version of getAutoThreshold() that uses a histogram passed as an argument.
- getAvailableLayoutComponents() - Static method in class ij.WindowManager
-
- getAvailableLayoutComponents(String) - Static method in class ij.WindowManager
-
- getAvailableLayoutComponents(String, boolean) - Static method in class ij.WindowManager
-
- getAvailableLayouts() - Static method in class ij.WindowManager
-
- getAverageDistanceBetweenROIs(Roi[]) - Static method in class org.jah.JAH_Utils
-
Calculates the Euclidean distance between the centroids of two Rois passed as arguments (in pixel values).
- getAvgZProjection(ImagePlus, ImagePlus) - Static method in class org.jah.JAH_Utils
-
- getAxes() - Method in class ij.plugin.frame.ChartPlugIn
-
Returns a list with all the axes.
- getAxis(String) - Method in class ij.plugin.frame.ChartPlugIn
-
Returns the Axis corresponding to the axis label.
- getAxisExtents(String) - Method in class ij.plugin.frame.ChartPlugIn
-
Returns the drawable extents for the axis given by the name.
- getAxisRange(Axis) - Method in class ij.plugin.frame.ChartPlugIn
-
Returns the axis range
- getAxisRange(String) - Method in class ij.plugin.frame.ChartPlugIn
-
Returns the axis range
- getBackgroundValue() - Method in class ij.process.FloatProcessor
-
Always returns 0.
- getBackgroundValue() - Method in class ij.process.ImageProcessor
-
Returns the background fill value.
- getBackgroundValue() - Method in class ij.process.ShortProcessor
-
Always returns 0.
- getBaseDirectory() - Static method in class org.jah.Configuration_
-
- getBestIndex(Color) - Method in class ij.process.ImageProcessor
-
Returns the LUT index that's the best match for this color.
- getBicubicInterpolatedPixel(double, double, ImageProcessor) - Method in class ij.process.FloatProcessor
-
This method is from Chapter 16 of "Digital Image Processing:
An Algorithmic Introduction Using Java" by Burger and Burge
(http://www.imagingbook.com/).
- getBicubicInterpolatedPixel(double, double, ImageProcessor) - Method in class ij.process.ImageProcessor
-
This method is from Chapter 16 of "Digital Image Processing:
An Algorithmic Introduction Using Java" by Burger and Burge
(http://www.imagingbook.com/).
- getBin3ImageHeight() - Static method in class org.jah.Configuration_
-
- getBin3ImageWidth() - Static method in class org.jah.Configuration_
-
- getBitDepth() - Method in class ij.ImagePlus
-
Returns the bit depth, 8, 16, 24 (RGB) or 32.
- getBitDepth() - Method in class ij.ImageStack
-
Returns the bit depth (8=byte, 16=short, 24=RGB, 32=float).
- getBitDepth() - Method in class ij.process.FloatProcessor
-
- getBitDepth() - Method in class ij.process.ImageProcessor
-
Returns the bit depth, 8, 16, 24 (RGB) or 32.
- getBitDepth() - Method in class ij.process.ShortProcessor
-
- getBlankImage(double) - Method in class ij.gui.LayoutComponent
-
- getBoundingRect() - Method in class ij.gui.Roi
-
- getBounds() - Method in class ij.gui.Roi
-
Return this selection's bounding rectangle.
- getBufferedImage() - Method in class ij.ImagePlus
-
Returns a copy of this image as an 8-bit or RGB BufferedImage.
- getBufferedImage() - Method in class ij.process.FloatProcessor
-
Returns this image as an 8-bit BufferedImage.
- getBufferedImage() - Method in class ij.process.ImageProcessor
-
Returns this image as a BufferedImage.
- getBufferedImage() - Method in class ij.process.ShortProcessor
-
Returns this image as an 8-bit BufferedImage .
- getBurst(int) - Method in class ij.wave.Bursts
-
- getBurstEndIndex() - Method in class ij.wave.Burst
-
Gets the burst envelope's start index relative to the original Wave.
- getBurstMarkers() - Method in class ij.wave.Bursts
-
Returns a list of WaveMarkers that can be added to the ChartFramePlugins.
- getBurstMarkers(double) - Method in class ij.wave.Bursts
-
Returns a list of WaveMarkers that can be added to the ChartFramePlugins (markerWidth is in seconds).
- getBurstMarkers(ArrayList) - Static method in class ij.wave.WaveUtils
-
Returns the WaveMarkers of type BURST in the list passed as argument.
- getBurstPeriodAverage(ArrayList) - Static method in class ij.wave.WaveUtils
-
- getBurstPeriodAverage(ArrayList, boolean) - Static method in class ij.wave.WaveUtils
-
- getBurstPeriods(ArrayList) - Static method in class ij.wave.WaveUtils
-
- getBurstPeriods(ArrayList, boolean) - Static method in class ij.wave.WaveUtils
-
- getBurstPeriodStderr(ArrayList) - Static method in class ij.wave.WaveUtils
-
- getBurstPeriodStdev(ArrayList) - Static method in class ij.wave.WaveUtils
-
- getBurstPeriodStdev(ArrayList, boolean) - Static method in class ij.wave.WaveUtils
-
- getBursts(String) - Method in class ij.plugin.frame.WaveManager
-
This gets the Waves and casts them as Bursts if they actually ARE Bursts.
- getBursts(double) - Method in class ij.wave.Wave
-
Identifies bursts based on an absolute threshold crossing algorithm.
- getBursts(double, boolean) - Method in class ij.wave.Wave
-
Identifies bursts based on an absolute threshold crossing algorithm.
- getBursts(String, double, double, double, double, boolean) - Method in class ij.wave.Wave
-
Identifies bursts based on an absolute threshold crossing algorithm.
- getBursts(String, Vector) - Method in class ij.wave.Wave
-
- getBurstsFromLocalMaxima(double, double, Wave) - Method in class ij.wave.Wave
-
Uses the median value of the amplitudeWave as the zero-reference amplitude and assumes 'this' wave is a central finite difference of the amplitude wave to find the relative peak amplitude constrained by the other parameters.
- getBurstsFromLocalMinima(double, double, Wave) - Method in class ij.wave.Wave
-
Uses the median value of the amplitudeWave as the zero-reference amplitude and assumes 'this' wave is a central finite difference of the amplitude wave to find the relative trough amplitude constrained by the other parameters.
- getBurstsFromPeakDetector(double, double, double) - Method in class ij.wave.Wave
-
- getBurstStartIndex() - Method in class ij.wave.Burst
-
Returns the index that this burst's wave starts at relative to a longer wave period.
- getBurstsWithinPeakAmplitudeRange(double, double) - Method in class ij.wave.Bursts
-
Returns the Bursts from this instance that have peaks within the range passed as arguments.
- getBurstTimes() - Method in class ij.wave.Bursts
-
Returns the peak times for all of the bursts in this instance.
- getButtons() - Method in class ij.gui.GenericDialog
-
Returns references to the "OK" ("Yes"), "Cancel",
and if present, "No" buttons as an array.
- getBytesPerPixel() - Method in class ij.ImagePlus
-
Returns the number of bytes per pixel.
- getC() - Method in class ij.ImagePlus
-
Returns the current hyperstack channel position.
- getCalibration() - Method in class ij.ImagePlus
-
Returns this image's calibration.
- getCalibrationTable() - Method in class ij.process.ImageProcessor
-
Returns the calibration table or null.
- getCanvas() - Method in class ij.gui.ImageWindow
-
- getCanvas() - Method in class ij.ImagePlus
-
Returns the ImageCanvas being used to
display this image, or null.
- getCentroid() - Method in class ij.gui.Roi
-
Calculates the centroid point of the Roi passed as argument (in pixel coordinates).
- getChannel() - Method in class ij.ImagePlus
-
- getChannelData(int) - Method in class org.jah.ephys.abf.ABF
-
- getChannelData(int, double, double, int) - Method in class org.jah.ephys.abf.ABF
-
- getChannelData(int, int) - Method in class org.jah.ephys.abf.ABF
-
- getChannelDataByEpoch(Epoch, int, int) - Method in class org.jah.ephys.abf.ABF
-
- getChannelDataByName(String) - Method in class org.jah.ephys.abf.ABF
-
- getChannelIndexByName(String) - Method in class org.jah.ephys.abf.ABF
-
- getChannelIndices() - Method in class org.jah.ephys.abf.ABF
-
- getChannelNameByIndex(int) - Method in class org.jah.ephys.abf.ABF
-
- getChannelNames() - Method in class org.jah.ephys.abf.ABF
-
- getChannelNames(String) - Method in class org.jah.ephys.ElectrophysManager
-
- getChannelNumbers() - Method in class org.jah.ephys.abf.ABF
-
- getChannelProcessor() - Method in class ij.ImagePlus
-
Returns a reference to the current ImageProcessor.
- getChannelUnits() - Method in class org.jah.ephys.abf.ABF
-
- getChart() - Method in class ij.plugin.frame.ChartPlugIn
-
- getCharts() - Static method in class ij.WindowManager
-
- getCheckboxes() - Method in class ij.gui.GenericDialog
-
Returns the Vector containing the Checkboxes.
- getChoices() - Method in class ij.gui.GenericDialog
-
Returns the Vector containing the Choices.
- getClassLoader() - Static method in class ij.IJ
-
Returns the class loader ImageJ uses to run plugins or the
system class loader if Menus.getPlugInsPath() returns null.
- getCleanZscore() - Method in class ij.wave.Wave
-
- getCleanZscore(double) - Method in class ij.wave.Wave
-
This reduces low-frequency oscillations in the truncated zscore -- this can take a while.
- getCleanZscoredWave() - Method in class ij.wave.Wave
-
- getCleanZscoredWave(double) - Method in class ij.wave.Wave
-
This reduces low-frequency oscillations in the truncated zscore -- this can take a while.
- getCleanZscoredWaves() - Method in class ij.wave.Waves
-
Replaces the current instances of Waves with the clean zscored waves.
- getClipboard() - Static method in class ij.ImagePlus
-
Returns the internal clipboard or null if the internal clipboard is empty.
- getCluster1() - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getCluster2() - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getCluster3() - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getCluster4() - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getClusteredWaves(ViewFrame) - Method in class ij.wave.Waves
-
Returns the Waves associated with the front ClusterFramePlugIn's selected cluster.
- getClusters() - Static method in class ij.WindowManager
-
- getClustersLowerBound(Range, Range, Range, Range) - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getClustersUpperBound(Range, Range, Range, Range) - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getColor() - Static method in class ij.gui.Roi
-
Returns the default (global) color used for drawing ROI outlines.
- getColor() - Method in class ij.wave.WaveMarker
-
- getColorModel() - Method in class ij.ImageStack
-
Returns this stack's color model.
- getColorModel() - Method in class ij.process.ImageProcessor
-
Returns this processor's color model.
- getColumn(int, int, int[], int) - Method in class ij.process.ImageProcessor
-
Returns the pixel values down the column starting at (x,y).
- getCombinedDomainXYPlot(Waves, boolean, int, double, double) - Static method in class ij.util.PlotterUtils
-
- getComments() - Method in class ij.wave.Wave
-
- getComments() - Method in class org.jah.ephys.abf.ABF
-
- getComments(Epoch) - Method in class org.jah.ephys.abf.ABF
-
- getComments() - Method in class org.jah.ephys.Comments
-
- getCommentsByEpoch(double, double) - Method in class org.jah.ephys.ElectrophysManager
-
- getCommentsInEpochRange(String, String) - Method in class org.jah.ephys.ElectrophysManager
-
- getCommentsList() - Method in class org.jah.ephys.Comments
-
- getCompositeMode() - Method in class ij.ImagePlus
-
Returns the display mode (IJ.COMPOSITE, IJ.COLOR
or IJ.GRAYSCALE) if this is a CompositeImage, otherwise returns -1.
- getContrast() - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getConvexHull() - Method in class ij.gui.Roi
-
- getCornerDiameter() - Method in class ij.gui.Roi
-
Returns the rounded rectangle corner diameter (pixels).
- getCorrelationTime() - Method in class ij.wave.Wave
-
- getCorrelationValue() - Method in class ij.wave.Wave
-
- getCount() - Method in class ij.plugin.frame.RoiManager
-
Returns the ROI count.
- getCount() - Method in class ij.plugin.frame.WaveManager
-
Returns the Wave count.
- getCPosition() - Method in class ij.gui.Roi
-
Returns the channel position of this ROI, or zero
if this ROI is not associated with a particular channel.
- getCurrentColorModel() - Method in class ij.process.ImageProcessor
-
Returns the current color model, which may have
been modified by setMinAndMax() or setThreshold().
- getCurrentImage() - Static method in class ij.WindowManager
-
Returns a reference to the active image or null if there isn't one.
- getCurrentPasteMode() - Static method in class ij.gui.Roi
-
Returns the current paste transfer mode.
- getCurrentSlice() - Method in class ij.ImagePlus
-
Returns the current stack index (one-based) or 1 if
this is a single image.
- getCurrentWindow() - Static method in class ij.WindowManager
-
Returns the active ImageWindow.
- getData(long, int) - Method in class org.jah.ephys.abf.ABF
-
- getDataByAbsoluteTime(long, int) - Method in class org.jah.ephys.abf.ABF
-
- getDataByRelativeTime(long, int) - Method in class org.jah.ephys.abf.ABF
-
- getDataFormat() - Method in class org.jah.ephys.abf.ABF
-
- getDatasets(ArrayList, XYPlot) - Method in class ij.plugin.frame.ChartPlugIn
-
- getDatasets() - Method in class ij.plugin.frame.ChartPlugIn
-
- getDebugInfo() - Method in class ij.gui.Roi
-
- getDefault16bitRange() - Static method in class ij.ImagePlus
-
Returns the default 16-bit display range, 0 (auto-scaling), 8, 10, 12, 15 or 16.
- getDefaultChartHeight() - Static method in class org.jah.Configuration_
-
- getDefaultChartWidth() - Static method in class org.jah.Configuration_
-
- getDefaultColorModel() - Method in class ij.process.ImageProcessor
-
Returns the default grayscale IndexColorModel.
- getDefaultFillColor() - Static method in class ij.gui.Roi
-
- getDefaultLeanDisplay() - Static method in class org.jah.Configuration_
-
- getDefaultMarkerWidth() - Static method in class org.jah.Configuration_
-
- getDendroView() - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getDensity() - Method in class ij.wave.Burst
-
Returns the area divided by the duration of the full burst.
- getDifferenceWavesExcludingBursts(Bursts) - Method in class ij.wave.Wave
-
Returns a list of Waves that are not represented by the Bursts passed as argument; this assumes the Bursts are arrayed in the order they appear in this wave.
- getDimensions() - Method in class ij.ImagePlus
-
Returns the dimensions of this image (width, height, nChannels,
nSlices, nFrames) as a 5 element int array.
- getDimensions(boolean) - Method in class ij.ImagePlus
-
- getDirectory(String) - Static method in class ij.IJ
-
Returns the path to the home ("user.home"), startup, ImageJ, plugins, macros,
luts, temp, current or image directory if title is "home", "startup",
"imagej", "plugins", "macros", "luts", "temp", "current", "default", "image", otherwise,
displays a dialog and returns the path to the directory selected by the user.
- getDirectoryURL(String) - Static method in class ij.IJ
-
- getDisplayRangeMax() - Method in class ij.ImagePlus
-
- getDisplayRangeMin() - Method in class ij.ImagePlus
-
- getDomainAxes() - Method in class ij.plugin.frame.ChartPlugIn
-
Returns a list with all the domain axes.
- getDomainAxisRange() - Method in class ij.plugin.frame.ChartPlugIn
-
- getDrawLabels() - Method in class ij.plugin.frame.RoiManager
-
- getDrawOffset() - Method in class ij.gui.Roi
-
Returns true if this is a PolygonRoi that supports sub-pixel
resolution and polygons are drawn on zoomed images offset
down and to the right by 0.5 pixels..
- getDuration() - Method in class ij.wave.Burst
-
Returns the length of the full burst in seconds.
- getDurationCV() - Method in class ij.wave.Bursts
-
- getDurationMean() - Method in class ij.wave.Bursts
-
- getDurations() - Method in class ij.wave.Bursts
-
Returns the length of the full bursts in seconds.
- getDurationStderr() - Method in class ij.wave.Bursts
-
- getDurationStdev() - Method in class ij.wave.Bursts
-
- getElectrophysComments() - Method in class org.jah.ephys.ElectrophysManager
-
- getElectrophysFiles() - Method in class org.jah.ephys.ElectrophysManager
-
- getElectrophysSamplingRateHz() - Static method in class org.jah.Configuration_
-
- getEnd() - Method in class org.jah.ephys.Epoch
-
- getEnd_s() - Method in class org.jah.ephys.Epoch
-
- getEndTime() - Method in class ij.wave.Wave
-
- getEndTime() - Method in class org.jah.ephys.abf.ABF
-
- getEndTime_s(String) - Method in class org.jah.ephys.ElectrophysManager
-
- getEnsembleFiles() - Static method in class ij.wave.WaveUtils
-
- getEnsembleFiles(String) - Static method in class ij.wave.WaveUtils
-
- getEnsembles() - Static method in class ij.wave.WaveUtils
-
- getEnsembles(File[]) - Static method in class ij.wave.WaveUtils
-
- getEphysFile(String) - Method in class org.jah.ephys.ElectrophysManager
-
Returns the EphysFile instance associated with the 'filename' where the filename DOES NOT
contain the path to the file.
- getEphysFile(String, int) - Method in class org.jah.ephys.ElectrophysManager
-
- getEphysFileFilename() - Method in class org.jah.ephys.Epoch
-
- getEphysFilename() - Method in class org.jah.ephys.Epoch
-
- getEpochChannelName() - Static method in class org.jah.Configuration_
-
- getEpochCommentMaxLength() - Static method in class org.jah.Configuration_
-
- getEpochCommentPattern() - Static method in class org.jah.Configuration_
-
- getEpochFactor() - Static method in class org.jah.Configuration_
-
- getEpochsByCommentPattern(String) - Method in class org.jah.ephys.abf.ABF
-
- getEpochsByCommentPattern(String) - Method in class org.jah.ephys.ElectrophysManager
-
- getEpochsByCommentPattern(String, String) - Method in class org.jah.ephys.ElectrophysManager
-
- getEpochsNumber() - Method in class ij.wave.Bursts
-
This returns the number of groups of bursts, that is, if a period time is less than the previous one
we increment a new epoch starting implicitly after a first one.
- getEpochThreshold() - Static method in class org.jah.Configuration_
-
- getErrorMessage() - Method in class ij.gui.GenericDialog
-
Returns an error message if getNextNumber was unable to convert a
string into a number, otherwise, returns null.
- getErrorMessage() - Static method in class ij.IJ
-
Returns the last error message written by IJ.error() or null if there
was no error since the last time this method was called.
- getExperimentDuration() - Method in class org.jah.ephys.abf.ABF
-
- getExperiments() - Method in class org.jah.ephys.ElectrophysManager
-
- getExponentialWave(double[], double, int) - Method in class ij.wave.Wave
-
- getf(int, int) - Method in class ij.process.FloatProcessor
-
- getf(int) - Method in class ij.process.FloatProcessor
-
- getf(int, int) - Method in class ij.process.ImageProcessor
-
Returns the value of the pixel at (x,y) as a float.
- getf(int) - Method in class ij.process.ImageProcessor
-
- getf(int, int) - Method in class ij.process.ShortProcessor
-
- getf(int) - Method in class ij.process.ShortProcessor
-
- getFallTime() - Method in class ij.wave.Burst
-
Returns the time of the maximum amplitude relative to the end of the burst (in seconds).
- getFallTimes() - Method in class ij.wave.Bursts
-
Returns an array of all the fall times of the bursts bursts was computed (in seconds)
- getFallTimeToFwhm() - Method in class ij.wave.Burst
-
Not implemented yet
- getFeretsDiameter() - Method in class ij.gui.Roi
-
Returns Feret's diameter, the greatest distance between
any two points along the ROI boundary.
- getFeretValues() - Method in class ij.gui.Roi
-
Caculates "Feret" (maximum caliper width), "FeretAngle"
and "MinFeret" (minimum caliper width), "FeretX" and "FeretY".
- getFileInfo() - Method in class ij.ImagePlus
-
Returns a FileInfo object containing information, including the
pixel array, needed to save this image.
- getFilename() - Method in class org.jah.ephys.abf.ABF
-
Returns the .abf file associated with this ABF class.
- getFilePath(String) - Static method in class ij.IJ
-
Displays an open file dialog and returns the path to the
choosen file, or returns null if the dialog is canceled.
- getFillColor() - Method in class ij.gui.Roi
-
Returns the fill color used to display this ROI, or null if it is displayed transparently.
- getFloatAngle(double, double, double, double) - Method in class ij.gui.Roi
-
Returns the angle in degrees between the specified line and a horizontal line.
- getFloatArray() - Method in class ij.process.ImageProcessor
-
Returns a copy of the pixel data as a 2D float
array with dimensions [x=0..width-1][y=0..height-1].
- getFloatBounds() - Method in class ij.gui.Roi
-
Return this selection's bounding rectangle.
- getFloatHeight() - Method in class ij.gui.Roi
-
- getFloatPolygon() - Method in class ij.gui.Roi
-
- getFloatWidth() - Method in class ij.gui.Roi
-
- getFont() - Method in class ij.process.ImageProcessor
-
Returns the current font.
- getFont(int) - Static method in class ij.util.PlotterUtils
-
- getFont(int, int) - Static method in class ij.util.PlotterUtils
-
- getFontMetrics() - Method in class ij.process.ImageProcessor
-
Returns the current FontMetrics.
- getFormattedString(String, int, boolean) - Method in class ij.wave.Waves
-
Returns the Waves as a String in a tabular layout where each column is a Wave's data contents.
- getFrame() - Method in class ij.ImagePlus
-
- getFrame(String) - Static method in class ij.WindowManager
-
Obsolete; replaced by getWindow().
- getFrontChart() - Static method in class ij.WindowManager
-
- getFrontCluster() - Static method in class ij.WindowManager
-
- getFrontImage() - Static method in class ij.WindowManager
-
- getFrontLayout() - Static method in class ij.WindowManager
-
- getFrontWindow() - Static method in class ij.WindowManager
-
Obsolete; replaced by getActiveWindow.
- getFullVersion() - Static method in class ij.IJ
-
Returns the ImageJ version and build number as a String, for
example "1.46n05", or 1.46n99 if there is no build number.
- getFwhmDensity() - Method in class ij.wave.Burst
-
Returns the area divided by the FWHM duration.
- getFwhmDuration() - Method in class ij.wave.Burst
-
Gets the full-width at half maximum (FWHM) in seconds.
- getGlobalCalibration() - Method in class ij.ImagePlus
-
Returns the system-wide calibration, or null.
- getHashCode() - Method in class ij.gui.Roi
-
Returns a hashcode for this Roi that typically changes
if it is moved, even though it is still the same object.
- getHeight() - Method in class ij.gui.LayoutComponent
-
- getHeight() - Method in class ij.ImagePlus
-
- getHeight() - Method in class ij.ImageStack
-
- getHeight() - Method in class ij.process.ImageProcessor
-
Returns the height of this image in pixels.
- getHideOverlay() - Method in class ij.ImagePlus
-
- getHistogram() - Method in class ij.process.FloatProcessor
-
Not implemented.
- getHistogram() - Method in class ij.process.ImageProcessor
-
Returns the histogram of the image or ROI.
- getHistogram() - Method in class ij.process.ShortProcessor
-
Returns 65536 bin histogram of the current ROI, which
can be non-rectangular.
- getHistogramMax() - Method in class ij.process.ImageProcessor
-
Returns the maximum histogram value used for histograms of float images.
- getHistogramMin() - Method in class ij.process.ImageProcessor
-
Returns the minimum histogram value used for histograms of float images.
- getHistogramSize() - Method in class ij.process.ImageProcessor
-
Returns the number of float image histogram bins.
- getID() - Method in class ij.ImagePlus
-
Returns this image's unique numeric ID.
- getID() - Method in class org.jah.ephys.Epoch
-
- getIDList() - Static method in class ij.WindowManager
-
Returns a list of the IDs of open images.
- getImage(double) - Method in class ij.gui.LayoutComponent
-
- getImage() - Method in class ij.gui.Roi
-
Returns the ImagePlus associated with this ROI, or null.
- getImage() - Static method in class ij.IJ
-
Returns a reference to the active image, or displays an error
message and aborts the plugin or macro if no images are open.
- getImage() - Method in class ij.ImagePlus
-
Returns this image as a AWT image.
- getImage(boolean) - Method in class ij.plugin.frame.RoiManager
-
- getImage(int) - Static method in class ij.WindowManager
-
For IDs less than zero, returns the ImagePlus with the specified ID.
- getImage(String) - Static method in class ij.WindowManager
-
Returns the first image that has the specified title or null if it is not found.
- getImageArray() - Method in class ij.ImageStack
-
Returns the stack as an array of 1D pixel arrays.
- getImageCount() - Static method in class ij.WindowManager
-
Returns the number of open images.
- getImageID() - Method in class ij.gui.Roi
-
Returns the ID of the image associated with this ROI.
- getImagePlus() - Method in class ij.gui.ImageWindow
-
- getImages() - Static method in class ij.WindowManager
-
- getImageStack() - Method in class ij.ImagePlus
-
Returns the base image stack.
- getImageStackSize() - Method in class ij.ImagePlus
-
If this is a stack, returns the actual number of images in the stack, else returns 1.
- getImageTitles() - Static method in class ij.WindowManager
-
- getImageWindowsVector() - Static method in class ij.WindowManager
-
- getImagingSamplingRateHz() - Static method in class org.jah.Configuration_
-
- getIndex(double) - Method in class ij.wave.Wave
-
Returns the index in the list of values for the time passed as argument.
- getIndexSampleModel() - Method in class ij.process.ImageProcessor
-
- getInfo(StringBuffer, String, XYPlot) - Method in class ij.plugin.frame.ChartPlugIn
-
- getInfo() - Method in class ij.plugin.frame.ChartPlugIn
-
- getInfo() - Method in class ij.wave.Burst
-
Returns general burst statistics as a String.
- getInfo() - Method in class ij.wave.Bursts
-
- getInfo() - Method in class ij.wave.Wave
-
- getInfo() - Method in class org.jah.ephys.abf.ABF
-
- getInfo(String) - Method in class org.jah.ephys.ElectrophysManager
-
- getInfo(String, boolean) - Method in class org.jah.ephys.ElectrophysManager
-
- getInfoProperty() - Method in class ij.ImagePlus
-
Returns the "Info" property string, or null if it is not found.
- getInfos() - Method in class org.jah.ephys.ElectrophysManager
-
- getInitialMagnification() - Method in class ij.gui.ImageWindow
-
- getInsets() - Method in class ij.gui.GenericDialog
-
- getInsets() - Method in class ij.gui.ImageWindow
-
Override Container getInsets() to make room for some text above the image.
- getInstance() - Static method in class ij.IJ
-
Returns a reference to the "ImageJ" frame.
- getInstance() - Static method in class ij.plugin.frame.RoiManager
-
Returns a reference to the ROI Manager
or null if it is not open.
- getInstance() - Static method in class ij.plugin.frame.WaveManager
-
Returns a reference to the Wave Manager
or null if it is not open.
- getInstance() - Static method in class org.jah.ephys.ElectrophysManager
-
- getInstance2() - Static method in class ij.plugin.frame.RoiManager
-
Returns a reference to the ROI Manager window or to the
macro batch mode RoiManager, or null if neither exists.
- getIntArray() - Method in class ij.process.ImageProcessor
-
Returns a copy of the pixel data as a 2D int array with
dimensions [x=0..width-1][y=0..height-1].
- getInterpolate() - Method in class ij.process.ImageProcessor
-
Returns the value of the interpolate field.
- getInterpolatedPixel(double, double) - Method in class ij.process.FloatProcessor
-
Uses the current interpolation method (BILINEAR or BICUBIC)
to calculate the pixel value at real coordinates (x,y).
- getInterpolatedPixel(double, double) - Method in class ij.process.ImageProcessor
-
Uses the current interpolation method (bilinear or bicubic)
to find the pixel value at real coordinates (x,y).
- getInterpolatedPixel(double, double) - Method in class ij.process.ShortProcessor
-
Uses the current interpolation method (BILINEAR or BICUBIC)
to calculate the pixel value at real coordinates (x,y).
- getInterpolatedPolygon() - Method in class ij.gui.Roi
-
Returns, as a FloatPolygon, an interpolated version
of this selection that has points spaced 1.0 pixel apart.
- getInterpolatedPolygon(double, boolean) - Method in class ij.gui.Roi
-
Returns, as a FloatPolygon, an interpolated version of
this selection with points spaced 'interval' pixels apart.
- getInterpolatedPolygon(FloatPolygon, double, boolean) - Method in class ij.gui.Roi
-
- getInterpolatedValue(double, double) - Method in class ij.process.ImageProcessor
-
Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
- getInterpolationMethod() - Method in class ij.process.ImageProcessor
-
Returns the current interpolation method (NONE, BILINEAR or BICUBIC).
- getInterpolationMethods() - Static method in class ij.process.ImageProcessor
-
- getIntStrings(File) - Static method in class org.jah.JAH_Utils
-
- getItemIndex(String) - Method in class ij.plugin.frame.RoiManager
-
- getItemIndex(String) - Method in class ij.plugin.frame.WaveManager
-
- getLastFileIndexBefore(String) - Method in class org.jah.ephys.Comments
-
- getLastStreamLength() - Static method in class org.jah.Configuration_
-
- getLayoutComponent(String) - Method in class ij.plugin.frame.Layout
-
- getLayoutComponent(int, int) - Method in class ij.plugin.frame.Layout
-
- getLayoutComponents() - Method in class ij.plugin.frame.Layout
-
- getLayoutComponents(String) - Method in class ij.plugin.frame.Layout
-
- getLayoutExportDPI() - Static method in class org.jah.Configuration_
-
- getLayoutMode() - Method in class ij.plugin.frame.Layout
-
- getLayoutPanel() - Method in class ij.plugin.frame.Layout
-
- getLayoutSize() - Method in class ij.plugin.frame.Layout
-
- getLeftHorizontalProportions() - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getLeftVerticalProportions() - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getLength() - Method in class ij.gui.Roi
-
Returns the perimeter length.
- getLength() - Method in class ij.wave.Wave
-
Returns the number of elements in this Wave.
- getLength() - Method in class org.jah.ephys.Epoch
-
- getLength_s() - Method in class ij.wave.Wave
-
Returns the length of this Wave in seconds.
- getLine(double, double, double, double) - Method in class ij.process.ImageProcessor
-
Returns an array containing the pixel values along the
line starting at (x1,y1) and ending at (x2,y2).
- getLineWidth() - Method in class ij.process.ImageProcessor
-
Returns the current line width.
- getList() - Method in class ij.plugin.frame.RoiManager
-
Returns the selection list.
- getList() - Method in class ij.plugin.frame.WaveManager
-
Returns the selection list.
- getLJDAC0ScalingFactor() - Static method in class org.jah.Configuration_
-
- getLJDAC0YOffset() - Static method in class org.jah.Configuration_
-
- getLocalCalibration() - Method in class ij.ImagePlus
-
Returns this image's local calibration, ignoring
the "Global" calibration flag.
- getLocationAsString(int, int) - Method in class ij.ImagePlus
-
Converts the current cursor location to a string.
- getLog() - Static method in class ij.IJ
-
Returns the contents of the Log window or null if the Log window is not open.
- getLut() - Method in class ij.process.ImageProcessor
-
- getLuts() - Static method in class ij.IJ
-
Returns, as an array of strings, a list of the LUTs in the Image/Lookup Tables menu.
- getLuts() - Method in class ij.ImagePlus
-
- getLutUpdateMode() - Method in class ij.process.ImageProcessor
-
Returns the LUT update mode, which can be RED_LUT, BLACK_AND_WHITE_LUT,
OVER_UNDER_LUT or NO_LUT_UPDATE.
- getMagnification() - Method in class ij.gui.Roi
-
- getMarkers() - Method in class ij.plugin.frame.ChartPlugIn
-
Returns a reference to the list of WaveMarkers on the chart.
- getMarkers(String) - Method in class ij.plugin.frame.ChartPlugIn
-
Returns the list of a type of markers, but should only be used for read-only.
- getMarkersByType(ArrayList, String) - Static method in class ij.wave.WaveUtils
-
Filters the WaveMarkers in the argument by type.
- getMarkerTypes() - Method in class ij.plugin.frame.ChartPlugIn
-
- getMask() - Method in class ij.gui.Roi
-
Always returns null for rectangular Roi's
- getMask() - Method in class ij.ImagePlus
-
For images with irregular ROIs, returns a byte mask, otherwise, returns
null.
- getMask() - Method in class ij.process.ImageProcessor
-
For images with irregular ROIs, returns a mask, otherwise,
returns null.
- getMaskArray() - Method in class ij.process.ImageProcessor
-
Returns a reference to the mask pixel array, or null if there is no mask.
- getMax() - Method in class ij.process.FloatProcessor
-
Returns the largest displayed pixel value.
- getMax() - Method in class ij.process.ImageProcessor
-
Returns the largest displayed pixel value.
- getMax() - Method in class ij.process.ShortProcessor
-
Returns the largest displayed pixel value.
- getMaximumAmplitude() - Method in class ij.wave.Burst
-
Should be the same as getPeakAmplitude()
- getMaximumAmplitudeIndex() - Method in class ij.wave.Burst
-
The index within the burst period that the maximum amplitude is at.
- getMaximumBounds() - Method in class ij.gui.ImageWindow
-
- getMaxPositionNumber() - Method in class ij.gui.Rois
-
- getMaxPositionNumber() - Method in class ij.plugin.frame.RoiManager
-
- getMaxThreshold() - Method in class ij.process.ImageProcessor
-
Returns the upper threshold level.
- getMaxValue() - Method in class ij.wave.Wave
-
- getMaxValue(double, double) - Method in class ij.wave.Wave
-
- getMaxValue(int, int) - Method in class ij.wave.Wave
-
- getMaxValue() - Method in class ij.wave.Waves
-
Gets the maximum value across all the Waves in this instance.
- getMaxValue(ImageProcessor) - Static method in class org.jah.JAH_Utils
-
- getMaxValueTime() - Method in class ij.wave.Wave
-
- getMaxValueTime(double, double) - Method in class ij.wave.Wave
-
Returns the time that the max value of the Wave is achieved (in seconds).
- getMaxValueTime(int, int) - Method in class ij.wave.Wave
-
- getMaxVisiblePlotPoints() - Static method in class org.jah.Configuration_
-
- getMeanValue(double, double) - Method in class ij.wave.Wave
-
- getMeanValue() - Method in class ij.wave.Wave
-
- getMedianValue(double, double) - Method in class ij.wave.Wave
-
- getMedianValue() - Method in class ij.wave.Wave
-
- getMessage() - Method in class ij.gui.GenericDialog
-
Returns a reference to the Label or MultiLineLabel created by the
last addMessage() call, or null if addMessage() was not called.
- getMiddleDividerLocation() - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getMin() - Method in class ij.process.FloatProcessor
-
Returns the smallest displayed pixel value.
- getMin() - Method in class ij.process.ImageProcessor
-
Returns the smallest displayed pixel value.
- getMin() - Method in class ij.process.ShortProcessor
-
Returns the smallest displayed pixel value.
- getMinimumAmplitude() - Method in class ij.wave.Burst
-
The minimum amplitude in the burst envelope.
- getMinimumPulseStepValue() - Static method in class org.jah.Configuration_
-
- getMinPositionNumber() - Method in class ij.gui.Rois
-
- getMinPositionNumber() - Method in class ij.plugin.frame.RoiManager
-
- getMinThreshold() - Method in class ij.process.ImageProcessor
-
Returns the lower threshold level.
- getMinValue() - Method in class ij.wave.Wave
-
- getMinValue(double, double) - Method in class ij.wave.Wave
-
- getMinValue(int, int) - Method in class ij.wave.Wave
-
- getMinValue() - Method in class ij.wave.Waves
-
Gets the minimum value across all the Waves in this instance.
- getMinValueTime() - Method in class ij.wave.Wave
-
- getMinValueTime(double, double) - Method in class ij.wave.Wave
-
Returns the time that the min value of the Wave is achieved (in seconds).
- getMinValueTime(int, int) - Method in class ij.wave.Wave
-
- getName() - Method in class ij.gui.Roi
-
Returns the name of this ROI, or null.
- getName(int) - Method in class ij.plugin.frame.RoiManager
-
Returns the name of the ROI with the specified index,
or null if the index is out of range.
- getName(String) - Static method in class ij.plugin.frame.RoiManager
-
Returns the name of the ROI with the specified index.
- getName(String) - Static method in class ij.plugin.frame.WaveManager
-
Returns the name of the Wave with the specified index.
- getName(int) - Static method in class ij.plugin.frame.WaveManager
-
- getName() - Method in class ij.wave.Bursts
-
- getName() - Method in class ij.wave.Wave
-
Sets the name of this wave
- getName() - Method in class org.jah.ephys.abf.ABF
-
- getName() - Method in class org.jah.ephys.Epoch
-
- getNames() - Method in class ij.wave.Waves
-
- getNamesByCluster(TreeDrawerNode) - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getNamesByCluster(TreeDrawerNode, ArrayList) - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getNChannels() - Method in class ij.ImagePlus
-
Returns the number of channels.
- getNChannels() - Method in class ij.process.ImageProcessor
-
Returns the number of color channels in the image.
- getNDimensions() - Method in class ij.ImagePlus
-
Returns the number of dimensions (2, 3, 4 or 5).
- getNeighborhood(int, int, double[][]) - Method in class ij.process.ImageProcessor
-
Experimental
- getNextBoolean() - Method in class ij.gui.GenericDialog
-
Returns the state of the next checkbox.
- getNextChoice() - Method in class ij.gui.GenericDialog
-
Returns the selected item in the next popup menu.
- getNextChoiceIndex() - Method in class ij.gui.GenericDialog
-
Returns the index of the selected item in the next popup menu.
- getNextEpoch(int) - Method in class org.jah.ephys.abf.ABF
-
- getNextEpoch(String) - Method in class org.jah.ephys.ElectrophysManager
-
- getNextNumber() - Method in class ij.gui.GenericDialog
-
Returns the contents of the next numeric field,
or NaN if the field does not contain a number.
- getNextRadioButton() - Method in class ij.gui.GenericDialog
-
Returns the selected item in the next radio button group.
- getNextRoi() - Method in class ij.gui.Roi
-
JAH: I added this!
- getNextString() - Method in class ij.gui.GenericDialog
-
Returns the contents of the next text field.
- getNextText() - Method in class ij.gui.GenericDialog
-
Returns the contents of the next textarea.
- getNFrames() - Method in class ij.ImagePlus
-
Returns the number of frames (time-points).
- getNonImageTitles() - Static method in class ij.WindowManager
-
Returns an array containing the titles of non-image Frames and Dialogs.
- getNonImageWindows() - Static method in class ij.WindowManager
-
Returns an array containing a list of the non-image Frames.
- getNonImageWindowsVector() - Static method in class ij.WindowManager
-
- getNormalizedZAxisProfile(Analyzer, Calibration, ImageStack, Roi) - Static method in class org.jah.JAH_Utils
-
- getNSlices() - Method in class ij.ImagePlus
-
Returns the image depth (number of z-slices).
- getNthImageID(int) - Static method in class ij.WindowManager
-
Returns the ID of the Nth open image.
- getNumber(String, double) - Static method in class ij.IJ
-
Allows the user to enter a number in a dialog box.
- getNumberOfADC() - Method in class org.jah.ephys.abf.ABF
-
- getNumberOfEpisodes() - Method in class org.jah.ephys.abf.ABF
-
- getNumberOfPulseAmplitudeSteps() - Static method in class org.jah.Configuration_
-
- getNumberOfPulsesInTrain() - Static method in class org.jah.Configuration_
-
- getNumberOfRows() - Method in class org.jah.ephys.abf.ABF
-
- getNumberOfSamplesPerChannel() - Method in class org.jah.ephys.abf.ABF
-
- getNumberOfSamplesPerEpisode() - Method in class org.jah.ephys.abf.ABF
-
- getNumElements() - Method in class ij.wave.Bursts
-
The number of bursts in this instance.
- getNumericFields() - Method in class ij.gui.GenericDialog
-
Returns the Vector containing the numeric TextFields.
- getOpenAsHyperStack() - Method in class ij.ImagePlus
-
- getOperationMode() - Method in class org.jah.ephys.abf.ABF
-
- getOriginalFileInfo() - Method in class ij.ImagePlus
-
Returns the FileInfo object that was used to open this image.
- getOverlay() - Method in class ij.ImagePlus
-
Returns the current overly, or null if this image does not have an overlay.
- getOverlay() - Method in class ij.process.ImageProcessor
-
- getPaintScale(String, int) - Method in class ij.plugin.frame.ChartPlugIn
-
Gets the PaintScale for a Wave rendered using the XYBlockRenderer (e.g., 3D plots)
- getPaintScale(XYPlot, int) - Method in class ij.plugin.frame.ChartPlugIn
-
- getParent() - Method in class ij.gui.LayoutComponent
-
- getPasteMode() - Method in class ij.gui.Roi
-
Returns the current paste transfer mode, or NOT_PASTING (-1)
if no paste operation is in progress.
- getPeakAmp() - Method in class ij.wave.Burst
-
Gets the maximum amplitude for this burst period.
- getPeakAmpCV() - Method in class ij.wave.Bursts
-
- getPeakAmpMean() - Method in class ij.wave.Bursts
-
- getPeakAmps() - Method in class ij.wave.Bursts
-
- getPeakAmpStderr() - Method in class ij.wave.Bursts
-
- getPeakAmpStdev() - Method in class ij.wave.Bursts
-
- getPeakDetectionHighThreshold() - Static method in class org.jah.Configuration_
-
- getPeakDetectionLowThreshold() - Static method in class org.jah.Configuration_
-
- getPeakTime() - Method in class ij.wave.Burst
-
Gets the peak time in seconds relative to the longer wave period.
- getPeriodBursts() - Method in class ij.wave.Bursts
-
Returns just the bursts that were used to compute periods that could traverse multiple epochs.
- getPeriodCV() - Method in class ij.wave.Bursts
-
The coefficient of variation of the periods in this instance
- getPeriodMean() - Method in class ij.wave.Bursts
-
The mean of the periods in this instance
- getPeriodNumber() - Method in class ij.wave.Bursts
-
The number of periods in this instance (should be n-1) unless there are epoch gaps (where burst time restarts from 0).
- getPeriods() - Method in class ij.wave.Bursts
-
Returns an array of all the periods between bursts (in seconds)
- getPeriodStderr() - Method in class ij.wave.Bursts
-
The standard error of the periods in this instance
- getPeriodStdev() - Method in class ij.wave.Bursts
-
The standard deviation of the periods in this instance
- getPeriodsTimes() - Method in class ij.wave.Bursts
-
Returns an array of all the times the periods between bursts was computed (in seconds)
- getPixel(int, int) - Method in class ij.ImagePlus
-
Returns the pixel value at (x,y) as a 4 element array.
- getPixel(int, int) - Method in class ij.process.FloatProcessor
-
Returns a pixel value that must be converted using
Float.intBitsToFloat().
- getPixel(int, int, int[]) - Method in class ij.process.FloatProcessor
-
Returns the value of the pixel at (x,y) in a
one element int array.
- getPixel(int, int) - Method in class ij.process.ImageProcessor
-
Returns the value of the pixel at (x,y).
- getPixel(int, int, int[]) - Method in class ij.process.ImageProcessor
-
Returns the samples for the pixel at (x,y) in an int array.
- getPixel(int, int) - Method in class ij.process.ShortProcessor
-
- getPixelCount() - Method in class ij.process.ImageProcessor
-
- getPixelInterpolated(double, double) - Method in class ij.process.FloatProcessor
-
- getPixelInterpolated(double, double) - Method in class ij.process.ImageProcessor
-
Uses the current interpolation method to find the pixel value at real coordinates (x,y).
- getPixelInterpolated(double, double) - Method in class ij.process.ShortProcessor
-
- getPixels(int) - Method in class ij.ImageStack
-
Returns the pixel array for the specified slice, were 1<=n<=nslices.
- getPixels() - Method in class ij.process.FloatProcessor
-
Returns a reference to the float array containing
this image's pixel data.
- getPixels() - Method in class ij.process.ImageProcessor
-
Returns a reference to this image's pixel array.
- getPixels() - Method in class ij.process.ShortProcessor
-
Returns a reference to the short array containing this image's
pixel data.
- getPixelsCopy() - Method in class ij.process.FloatProcessor
-
Returns a copy of the pixel data.
- getPixelsCopy() - Method in class ij.process.ImageProcessor
-
Returns a copy of the pixel data.
- getPixelsCopy() - Method in class ij.process.ShortProcessor
-
Returns a copy of the pixel data.
- getPixelValue(int, int) - Method in class ij.process.FloatProcessor
-
Returns the value of the pixel at (x,y) as a float.
- getPixelValue(int, int) - Method in class ij.process.ImageProcessor
-
Returns the value of the pixel at (x,y).
- getPixelValue(int, int) - Method in class ij.process.ShortProcessor
-
Returns the value of the pixel at (x,y) as a float.
- getPolygon() - Method in class ij.gui.Roi
-
Returns the outline of this selection as a Polygon, or
null if this is a straight line selection.
- getPosition() - Method in class ij.gui.Roi
-
Returns the stack position (image number) of this ROI, or
zero if the ROI is not associated with a particular stack image.
- getPostPulseDetectionDelay() - Static method in class org.jah.Configuration_
-
- getPreviewCheckbox() - Method in class ij.gui.GenericDialog
-
Returns a reference to the Preview Checkbox.
- getPreviousEpoch(int) - Method in class org.jah.ephys.abf.ABF
-
- getPreviousEpoch(String) - Method in class org.jah.ephys.ElectrophysManager
-
- getPreviousRoi() - Method in class ij.gui.Roi
-
JAH: I added this!
- getProcessingDirectory() - Static method in class org.jah.Configuration_
-
- getProcessor() - Static method in class ij.IJ
-
Returns the active image or stack slice as an ImageProcessor, or displays
an error message and aborts the plugin or macro if no images are open.
- getProcessor() - Method in class ij.ImagePlus
-
Returns a reference to the current ImageProcessor.
- getProcessor(int) - Method in class ij.ImageStack
-
Returns an ImageProcessor for the specified slice,
were 1<=n<=nslices.
- getProp(String) - Method in class ij.ImagePlus
-
Returns the value from the "Info" property string associated
with 'key', or null if the key is not found.
- getProperties() - Method in class ij.gui.Roi
-
- getProperties() - Method in class ij.ImagePlus
-
Returns this image's Properties.
- getProperty(String) - Method in class ij.gui.Roi
-
- getProperty(String) - Method in class ij.ImagePlus
-
Returns the property associated with 'key'.
- getProperty(String) - Static method in class org.jah.Configuration_
-
- getProperty(String, String) - Static method in class org.jah.Configuration_
-
- getPropertyCount() - Method in class ij.gui.Roi
-
- getPropertyDouble(String, String) - Static method in class org.jah.Configuration_
-
- getPrototypeOverlay() - Method in class ij.gui.Roi
-
- getPulseAmplitude() - Static method in class org.jah.Configuration_
-
- getPulseContinuousMax() - Static method in class org.jah.Configuration_
-
- getPulseContinuousMin() - Static method in class org.jah.Configuration_
-
- getPulseFrequency() - Static method in class org.jah.Configuration_
-
- getPulseGaussianMean() - Static method in class org.jah.Configuration_
-
- getPulseGaussianStdD() - Static method in class org.jah.Configuration_
-
- getPulseLength() - Static method in class org.jah.Configuration_
-
- getPulseStartDelay() - Static method in class org.jah.Configuration_
-
- getPulseTrainStartDelay() - Static method in class org.jah.Configuration_
-
- getRadioButtonGroups() - Method in class ij.gui.GenericDialog
-
Returns the Vector that contains the RadioButtonGroups.
- getRangeAxes() - Method in class ij.plugin.frame.ChartPlugIn
-
Returns a list with all the range axes.
- getRelativeEpochs(String, double) - Method in class org.jah.ephys.abf.ABF
-
- getRelativeEpochs(int, double) - Method in class org.jah.ephys.abf.ABF
-
- getRelativeTime(long) - Method in class org.jah.ephys.abf.ABF
-
- getRenderer() - Method in class ij.plugin.frame.ChartPlugIn
-
- getRight() - Method in class org.jah.ephys.Comment
-
- getRiseTime() - Method in class ij.wave.Burst
-
Returns the time of the maximum amplitude relative to the start of the burst (in seconds).
- getRiseTimeFromFwhm() - Method in class ij.wave.Burst
-
Not implemented yet
- getRiseTimes() - Method in class ij.wave.Bursts
-
Returns an array of all the rise times of the bursts bursts was computed (in seconds)
- getRoi(int) - Method in class ij.gui.Rois
-
- getRoi() - Method in class ij.ImagePlus
-
Returns the current selection, or null if there is no selection.
- getRoi() - Method in class ij.ImageStack
-
- getRoi(String) - Method in class ij.plugin.frame.RoiManager
-
- getRoi() - Method in class ij.process.ImageProcessor
-
Returns a Rectangle that represents the current
region of interest.
- getRoi() - Method in class ij.wave.Wave
-
Returns an Roi associated with this Wave.
- getRoiArea(Roi) - Static method in class org.jah.JAH_Utils
-
Calculates the area of the Roi passed as argument (in pixel values).
- getRoiCentroid(Roi) - Static method in class org.jah.JAH_Utils
-
Calculates the centroid point of the Roi passed as argument (in pixel coordinates).
- getRoiIndex(Roi) - Method in class ij.plugin.frame.RoiManager
-
- getROIs() - Method in class ij.plugin.frame.RoiManager
-
Returns the ROI Hashtable.
- getRois() - Method in class ij.wave.Waves
-
Returns an array of Rois associated with each of the Waves in this instance.
- getRoisAsArray() - Method in class ij.gui.Rois
-
Returns the ROIs as an array.
- getRoisAsArray() - Method in class ij.plugin.frame.RoiManager
-
Returns the ROIs as an array.
- getRoisAsArray() - Static method in class org.jah.JAH_Utils
-
A utility function for returning all the Rois in the RoiManager.
- getRoisAtPosition(int) - Method in class ij.gui.Rois
-
- getRoisAtPosition(int) - Method in class ij.plugin.frame.RoiManager
-
- getRoisByNames(ArrayList) - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getRoisForWaves(Waves) - Static method in class ij.plugin.frame.RoiManager
-
- getRoiWave(ImagePlus, Roi[]) - Static method in class ij.wave.Wave
-
- getRoiWave(ImagePlus, Roi) - Static method in class ij.wave.Wave
-
Creates a new Wave from Roi passed as argument the ImagePlus passed as argument.
- getRoiWaves(ImagePlus) - Static method in class ij.wave.Waves
-
Creates a new set of Waves from the selected ROIs in the RoiManager and the ImagePlus passed as argument.
- getRoiWaves(ImagePlus, Rois, boolean) - Static method in class ij.wave.Waves
-
- getRoiWaves(ImagePlus, Roi[], boolean) - Static method in class ij.wave.Waves
-
Creates a new set of Waves from Roi passed as argument the ImagePlus passed as argument by forwardly traversing through the next related Rois.
- getRoundRectArcSize() - Method in class ij.gui.Roi
-
Obsolete; replaced by getCornerDiameter().
- getRow(int, int, int[], int) - Method in class ij.process.ImageProcessor
-
Returns the pixel values along the horizontal line starting at (x,y).
- getRow(int, int, float[], int) - Method in class ij.process.ImageProcessor
-
Returns the pixel values along the horizontal line starting at (x,y).
- getRow(long) - Method in class org.jah.ephys.abf.ABF
-
- getRowByAbsoluteTime(long) - Method in class org.jah.ephys.abf.ABF
-
- getRowByRelativeTime(long) - Method in class org.jah.ephys.abf.ABF
-
- getRowNumberByAbsoluteTime(long) - Method in class org.jah.ephys.abf.ABF
-
- getRowNumberByRelativeTime(long) - Method in class org.jah.ephys.abf.ABF
-
- getSamplingRate() - Method in class org.jah.ephys.abf.ABF
-
- getSamplingRateHz() - Method in class ij.wave.Wave
-
Returns the sampling rate of this wave in Hz
- getScaledStroke() - Method in class ij.gui.Roi
-
- getScaleFactor() - Method in class ij.gui.LayoutComponent
-
- getScrambledWave() - Method in class ij.wave.Wave
-
Returns the same Wave but with an new start location within the waveform depending on the value of a uniformly random number -- the new Wave wraps to maintain the same length as the original instance.
- getScrambledWaves() - Method in class ij.wave.Waves
-
- getScreenSize() - Static method in class ij.IJ
-
Returns the size, in pixels, of the primary display.
- getSelectedEpoch() - Method in class org.jah.ephys.ElectrophysManager
-
- getSelectedEpochName() - Method in class org.jah.ephys.ElectrophysManager
-
- getSelectedIndex() - Method in class ij.plugin.frame.RoiManager
-
- getSelectedIndexes() - Method in class ij.plugin.frame.RoiManager
-
- getSelectedIndexes() - Method in class ij.plugin.frame.WaveManager
-
- getSelectedRoi() - Method in class ij.plugin.frame.RoiManager
-
- getSelectedRoisAsArray() - Method in class ij.plugin.frame.RoiManager
-
Returns the selected ROIs as an array, or
all the ROIs if none are selected.
- getSelectedRoisAsArray() - Static method in class org.jah.JAH_Utils
-
A utility function for returning the selected Rois in the RoiManager.
- getSelectedRoisAsVector() - Static method in class org.jah.JAH_Utils
-
- getSelectedWave() - Method in class ij.plugin.frame.WaveManager
-
- getSelectedWaves() - Method in class ij.plugin.frame.WaveManager
-
- getSelectedWavesAsArray() - Method in class ij.plugin.frame.WaveManager
-
Returns the selected Waves as an array, or
all the Waves if none are selected.
- getSelectedWavesAsArray() - Static method in class org.jah.JAH_Utils
-
A utility function for returning the selected Waves in the WaveManager.
- getSelectedWavesAsVector() - Static method in class org.jah.JAH_Utils
-
- getSeriesIndex(String, XYPlot) - Method in class ij.plugin.frame.ChartPlugIn
-
This function will loop until up to MAX_SERIES_INDEX_WAIT_ms to try to
get a non-zero series index.
- getServerAddress() - Static method in class org.jah.Configuration_
-
- getShortSliceLabel(int) - Method in class ij.ImageStack
-
Returns a shortened version (up to the first 60 characters or first newline and
suffix removed) of the label of the specified slice.
- getShortTitle() - Method in class ij.ImagePlus
-
Returns a shortened version of image name that does not
include spaces or a file name extension.
- getSize() - Method in class ij.ImageStack
-
Returns the number of slices in this stack.
- getSizeOfNumberInBytes() - Method in class org.jah.ephys.abf.ABF
-
- getSlice() - Method in class ij.ImagePlus
-
- getSliceLabel(int) - Method in class ij.ImageStack
-
Returns the label of the specified slice, were 1<=n<=nslices.
- getSliceLabels() - Method in class ij.ImageStack
-
Returns the slice labels as an array of Strings.
- getSliceNumber(String) - Method in class ij.plugin.frame.RoiManager
-
Returns the slice number associated with the specified name,
or -1 if the name does not include a slice number.
- getSliceNumber() - Method in class ij.process.ImageProcessor
-
- getSliders() - Method in class ij.gui.GenericDialog
-
Returns the Vector containing the sliders (Scrollbars).
- getSmoothingPercent() - Static method in class org.jah.Configuration_
-
- getSnapshotPixels() - Method in class ij.process.FloatProcessor
-
- getSnapshotPixels() - Method in class ij.process.ImageProcessor
-
Returns a reference to the snapshot (undo) buffer, or null.
- getSnapshotPixels() - Method in class ij.process.ShortProcessor
-
- getSource() - Method in class ij.gui.LayoutComponent
-
- getSpikeUnits() - Method in class ij.wave.Wave
-
Returns the spike units as a new wave -- this is defined as an absolute (value-median) > thresholdFactor*stdev where the
stdevFactorAsThreshold defaults to 3.0.
- getSpikeUnits(double) - Method in class ij.wave.Wave
-
Returns the spike units as a new wave -- this is defined as an absolute (value-median) > thresholdFactor*stdev.
- getSplitPane() - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- getStack() - Method in class ij.ImagePlus
-
Returns the image stack.
- getStackIndex(int, int, int) - Method in class ij.ImagePlus
-
Returns that stack index (one-based) corresponding to the specified position.
- getStackSize() - Method in class ij.ImagePlus
-
If this is a stack, returns the number of slices, else returns 1.
- getStackTrace(Exception) - Static method in class org.jah.JAH_Utils
-
Returns a String representing the stack trace of the Exception passed as argument.
- getStart() - Method in class org.jah.ephys.Epoch
-
- getStart_s() - Method in class org.jah.ephys.Epoch
-
- getStartTime() - Method in class ij.ImagePlus
-
Returns the time in milliseconds when
startTiming() was last called.
- getStartTime() - Method in class ij.wave.Wave
-
- getStartTime() - Method in class org.jah.ephys.abf.ABF
-
- getStartTime_s(String) - Method in class org.jah.ephys.ElectrophysManager
-
- getState() - Method in class ij.gui.Roi
-
- getStatistics() - Method in class ij.ImagePlus
-
Returns an ImageStatistics object generated using the standard
measurement options (area, mean, mode, min and max).
- getStatistics(int) - Method in class ij.ImagePlus
-
Returns an ImageStatistics object generated using the
specified measurement options.
- getStatistics(int, int) - Method in class ij.ImagePlus
-
Returns an ImageStatistics object generated using the
specified measurement options and histogram bin count.
- getStatistics(int, int, double, double) - Method in class ij.ImagePlus
-
Returns an ImageStatistics object generated using the
specified measurement options, histogram bin count and histogram range.
- getStatistics() - Method in class ij.process.ImageProcessor
-
- getStdevValue(double, double) - Method in class ij.wave.Wave
-
- getStdevValue() - Method in class ij.wave.Wave
-
- getStimulusMarkers() - Method in class ij.wave.Bursts
-
Returns a list of WaveMarkers (as stimulus markers) that can be added to the ChartFramePlugins.
- getStimulusMarkers(double) - Method in class ij.wave.Bursts
-
Returns a list of WaveMarkers (as stimulus markers) that can be added to the ChartFramePlugins (markerWidth is in seconds).
- getStimulusMarkers(ArrayList) - Static method in class ij.wave.WaveUtils
-
Returns the WaveMarkers of type STIMULUS in the list passed as argument.
- getStoredValue() - Method in class ij.wave.WaveMarker
-
- getString(String, String) - Static method in class ij.IJ
-
Allows the user to enter a string in a dialog box.
- getStringFields() - Method in class ij.gui.GenericDialog
-
Returns the Vector containing the string TextFields.
- getStringWidth(String) - Method in class ij.process.ImageProcessor
-
Returns the width in pixels of the specified string.
- getStroke() - Method in class ij.gui.Roi
-
Returns the Stroke used to draw this ROI, or null if no Stroke is used.
- getStrokeColor() - Method in class ij.gui.Roi
-
Returns the the color used to draw the ROI outline or null if the default color is being used.
- getStrokeWidth() - Method in class ij.gui.Roi
-
Returns the lineWidth.
- getT() - Method in class ij.ImagePlus
-
Returns the current hyperstack frame position.
- getTag() - Method in class org.jah.ephys.Comment
-
- getTags() - Method in class org.jah.ephys.abf.ABF
-
- getTempCurrentImage() - Static method in class ij.WindowManager
-
Returns the temporary current image for this thread, or null.
- getTemporalHistogram(double) - Method in class ij.wave.Wave
-
- getText() - Method in class org.jah.ephys.Comment
-
- getTextArea1() - Method in class ij.gui.GenericDialog
-
Returns a reference to textArea1.
- getTextArea2() - Method in class ij.gui.GenericDialog
-
Returns a reference to textArea2.
- getTextPanel() - Static method in class ij.IJ
-
Returns a reference to the "Results" window TextPanel.
- getThresholdCrossingingIndex(double, int) - Method in class ij.wave.Burst
-
Returns the index of the burst data array corresponding to the first time the burst crosses the threshold relative to the burst array.
- getThresholdCrossingTime(double, int) - Method in class ij.wave.Burst
-
Returns the first time the burst crosses the threshold (in seconds) relative to the reference wave.
- getTime() - Method in class org.jah.ephys.Comment
-
- getTimestamp() - Static method in class org.jah.JAH_Utils
-
- getTitle() - Method in class ij.gui.LayoutComponent
-
- getTitle() - Static method in class ij.IJ
-
- getTitle() - Method in class ij.ImagePlus
-
Returns the image name.
- getToolName() - Static method in class ij.IJ
-
Returns the name of the current tool.
- getTPosition() - Method in class ij.gui.Roi
-
Returns the frame position of this ROI, or zero
if this ROI is not associated with a particular frame.
- getTrace(String, int) - Static method in class org.jah.JAH_Utils
-
- getTriggerMarkers() - Method in class ij.plugin.frame.ChartPlugIn
-
Returns the list of trigger markers, but should only be used for read-only.
- getTruncatedZscoredWave(boolean) - Method in class ij.wave.Wave
-
This returns the wave from "getZscoredWave" truncated below 0.0 and clones the wave if specified by the argument, otherwise replaces the current Wave.
- getTruncatedZscoredWave() - Method in class ij.wave.Wave
-
- getTruncatedZscoredWaves() - Method in class ij.wave.Waves
-
Replaces the current instances of Waves with the truncated zscored waves.
- getType() - Method in class ij.gui.LayoutComponent
-
- getType() - Method in class ij.gui.Roi
-
- getType() - Method in class ij.ImagePlus
-
Returns the current image type (ImagePlus.GRAY8, ImagePlus.GRAY16,
ImagePlus.GRAY32, ImagePlus.COLOR_256 or ImagePlus.COLOR_RGB).
- getType() - Method in class ij.wave.Wave
-
- getType() - Method in class ij.wave.WaveMarker
-
- getType() - Method in class org.jah.ephys.Epoch
-
- getTypeAsString() - Method in class ij.gui.Roi
-
Convenience method that converts Roi type to a human-readable form.
- getTypeAsString() - Method in class ij.wave.Wave
-
- getTypeAsString() - Method in class org.jah.ephys.Epoch
-
- getTypes() - Static method in class ij.wave.WaveMarker
-
- getUniqueName() - Method in class ij.plugin.frame.Layout
-
- getUniqueName(String) - Static method in class ij.WindowManager
-
Returns a unique name by adding, before the extension, -1, -2, etc.
- getUniqueTitle(String) - Static method in class ij.util.PlotterUtils
-
- getUnits() - Method in class ij.wave.Wave
-
- getValue(String) - Method in class ij.gui.GenericDialog
-
- getValueAt(double) - Method in class ij.wave.Wave
-
Returns the value of the wave at the specified time (in seconds).
- getValues() - Method in class ij.wave.Wave
-
Returns the values of this Wave.
- getValues(int) - Method in class ij.wave.Wave
-
Returns a decimated array corresponding to the waveform and picks out the max/min values for the decimation.
- getValues(int, int) - Method in class ij.wave.Wave
-
- getValues(double, double) - Method in class ij.wave.Wave
-
Returns just the values of the current Wave between the times passed as argument.
- getVersion() - Static method in class ij.IJ
-
Returns the ImageJ version number as a string.
- getVoxel(int, int, int) - Method in class ij.ImageStack
-
Returns, as a double, the specified voxel.
- getVoxels(int, int, int, int, int, int, float[]) - Method in class ij.ImageStack
-
Experimental
- getVoxels(int, int, int, int, int, int, float[], int) - Method in class ij.ImageStack
-
Experimental
- getWave(String) - Method in class ij.plugin.frame.ChartPlugIn
-
Returns the Wave from the chart with the given name.
- getWave(String) - Method in class ij.plugin.frame.WaveManager
-
- getWave(int) - Method in class ij.wave.Waves
-
Returns the Wave at the given index in the collection.
- getWave(String) - Method in class ij.wave.Waves
-
- getWave(EphysFile, String, int) - Method in class org.jah.ephys.Epoch
-
- getWaveForBurstAnalysisFromLocalMaxima(double) - Method in class ij.wave.Wave
-
Returns a new Wave that has a moving average filter applied to it and then a central finite difference applied.
- getWaveRange(int, int) - Method in class ij.wave.Wave
-
Returns a duplicate Wave from the startIndex to the startIndex+length index.
- getWaveRange(double, double) - Method in class ij.wave.Wave
-
Returns a duplicate Wave from the startTime_s up to endTime_s.
- getWaveRanges(double, double) - Method in class ij.wave.Waves
-
Returns a new Waves object where each Wave encompasses the range of startTime_s up to endTime_s of the original Wave.
- getWaves(String) - Method in class ij.plugin.frame.ChartPlugIn
-
Returns the Waves from the chart with the given filter mask.
- getWaves() - Method in class ij.plugin.frame.ChartPlugIn
-
Returns all the Waves from the chart.
- getWaves() - Method in class ij.plugin.frame.WaveManager
-
- getWaves(String) - Method in class ij.plugin.frame.WaveManager
-
- getWaves(String, String) - Method in class ij.plugin.frame.WaveManager
-
- getWaves() - Method in class org.jah.ephys.Epoch
-
- getWavesAsArray() - Method in class ij.plugin.frame.WaveManager
-
Returns the Waves as an array.
- getWavesAsArray() - Static method in class org.jah.JAH_Utils
-
A utility function for returning all the Waves in the WaveManager.
- getWavesByName(File) - Method in class ij.wave.Waves
-
- getWavesFromMatFile(String) - Static method in class ij.wave.WaveUtils
-
- getWavesHashtable() - Method in class ij.plugin.frame.WaveManager
-
Returns the Wave Hashtable.
- getWavesWithLengthAtLeast(int) - Method in class ij.wave.Waves
-
- getWfdSrcInputDirectory() - Static method in class org.jah.Configuration_
-
- getWidth() - Method in class ij.gui.LayoutComponent
-
- getWidth() - Method in class ij.ImagePlus
-
- getWidth() - Method in class ij.ImageStack
-
- getWidth() - Method in class ij.process.ImageProcessor
-
Returns the width of this image in pixels.
- getWidth() - Method in class ij.wave.WaveMarker
-
Returns the width of the marker in units of seconds.
- getWindow() - Method in class ij.ImagePlus
-
Returns the ImageWindow that is being used to display
this image.
- getWindow(String) - Static method in class ij.WindowManager
-
Returns the window (a Frame or a Dialog) with the specified
title, or null if a window with that title is not found.
- getWindowCount() - Static method in class ij.WindowManager
-
Returns the number of open image windows.
- getX() - Method in class ij.gui.LayoutComponent
-
- getXBase() - Method in class ij.gui.Roi
-
- getXStartOffset() - Method in class ij.wave.Wave
-
An offset for the first element in the wave.
- getXVal() - Method in class ij.wave.WaveMarker
-
- getXValues() - Method in class ij.wave.Wave
-
Returns the time (i.e., 'x') values associated with this Wave.
- getXWave() - Method in class ij.wave.Wave
-
- getXYDatasetForWave(String) - Method in class ij.plugin.frame.ChartPlugIn
-
- getXYPlot() - Method in class ij.plugin.frame.ChartPlugIn
-
- getXYPlot(Wave, boolean, int, double, double) - Static method in class ij.util.PlotterUtils
-
- getXYPlot(Waves, boolean, int, double, double) - Static method in class ij.util.PlotterUtils
-
- getXYPlotForWave(String) - Method in class ij.plugin.frame.ChartPlugIn
-
- getXYZAnnotations(Waves) - Static method in class ij.util.PlotterUtils
-
- getXYZAnnotations(Waves, int) - Static method in class ij.util.PlotterUtils
-
- getXYZAnnotations(Waves, int, Font) - Static method in class ij.util.PlotterUtils
-
- getXYZDataset(Waves) - Static method in class ij.util.PlotterUtils
-
- getY() - Method in class ij.gui.LayoutComponent
-
- getYBase() - Method in class ij.gui.Roi
-
- getYValues() - Method in class ij.wave.Wave
-
Returns the same values as the getValues function.
- getZ() - Method in class ij.ImagePlus
-
Returns the current hyperstack slice position.
- getZAxisProfile(Analyzer, Calibration, ImageStack, Roi) - Static method in class org.jah.JAH_Utils
-
- getZPosition() - Method in class ij.gui.Roi
-
Returns the slice position of this ROI, or zero
if this ROI is not associated with a particular slice.
- getZProjection(ImagePlus, int) - Static method in class org.jah.JAH_Utils
-
A convenience function for projecting a time-series to one plane using the method specified in the argument.
- getZscoredWave(boolean) - Method in class ij.wave.Wave
-
Returns a clone copy of this wave
but where each value in the series has the z-scored value (i.e., the mean of the Wave will be 0 and the stdev=1).
- getZscoredWave() - Method in class ij.wave.Wave
-
- gLUT1 - Variable in class ij.process.ImageProcessor
-
- gLUT2 - Variable in class ij.process.ImageProcessor
-
- GRAY16 - Static variable in class ij.ImagePlus
-
16-bit grayscale (unsigned)
- GRAY32 - Static variable in class ij.ImagePlus
-
32-bit floating-point grayscale
- GRAY8 - Static variable in class ij.ImagePlus
-
8-bit grayscale (unsigned)
- GRAYSCALE - Static variable in class ij.IJ
-
Image display modes
- grow(int, int) - Method in class ij.gui.Roi
-
- radioButtonGroups - Variable in class ij.gui.GenericDialog
-
- raster - Variable in class ij.process.ImageProcessor
-
- readObject(ObjectInputStream) - Method in class ij.wave.Wave
-
- recalcExponentialWave(Wave, double[]) - Static method in class ij.wave.Wave
-
- RECTANGLE - Static variable in class ij.gui.Roi
-
- RED_LUT - Static variable in class ij.process.ImageProcessor
-
- redirectErrorMessages() - Static method in class ij.IJ
-
Causes IJ.error() output to be temporarily redirected to the "Log" window.
- redirectErrorMessages(boolean) - Static method in class ij.IJ
-
Set 'true' and IJ.error() output will be temporarily redirected to the "Log" window.
- redirectingErrorMessages() - Static method in class ij.IJ
-
Returns the state of the 'redirectErrorMessages' flag, which is set by File/Import/Image Sequence.
- refreshDomainAxes() - Method in class ij.plugin.frame.ChartPlugIn
-
- register(Class) - Static method in class ij.IJ
-
Adds the specified class to a Vector to keep it from being garbage
collected, which would cause the classes static fields to be reset.
- remove(int) - Method in class org.jah.ephys.Comments
-
- remove(Comment) - Method in class org.jah.ephys.Comments
-
- removeAllMarkers() - Method in class ij.plugin.frame.ChartPlugIn
-
Removes all WaveMarkers from the chart.
- removeEventListener(IJEventListener) - Static method in class ij.IJ
-
- removeImageListener(ImageListener) - Static method in class ij.ImagePlus
-
- removeJScrollBars() - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- removeJScrollBars(Container) - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- removeMarker(WaveMarker) - Method in class ij.plugin.frame.ChartPlugIn
-
Removes the marker passed as argument from the chart.
- removeMarkerAt(int, int) - Method in class ij.plugin.frame.ChartPlugIn
-
Remove the WaveMarker at the specified coordinates.
- removeMarkers(String) - Method in class ij.plugin.frame.ChartPlugIn
-
- removeRedundantBursts() - Method in class ij.wave.Bursts
-
Removes duplicate bursts from this instance
- removeWaveListener(WaveListener) - Method in class ij.wave.Wave
-
- removeWindow(Window) - Static method in class ij.WindowManager
-
Removes the specified window from the Window menu.
- removeWindow(Frame) - Static method in class ij.WindowManager
-
Removes the specified Frame from the Window menu.
- rename(String) - Static method in class ij.IJ
-
Renames the currently front image with the String passed as an argument.
- rename(String, String) - Method in class ij.plugin.frame.RoiManager
-
- rename(String) - Method in class ij.plugin.frame.RoiManager
-
- rename(String, boolean) - Method in class ij.plugin.frame.RoiManager
-
- rename(String, String) - Method in class ij.plugin.frame.WaveManager
-
- rename(String) - Method in class ij.plugin.frame.WaveManager
-
- renameResults(String) - Static method in class ij.IJ
-
Renames a results window.
- renameResults(String, String) - Static method in class ij.IJ
-
Changes the name of a results window from 'oldTitle' to 'newTitle'.
- repaintImageWindows() - Static method in class ij.WindowManager
-
Repaints all open image windows.
- repaintWindow() - Method in class ij.ImagePlus
-
Calls draw to draw the image and also repaints the
image window to force the information displayed above
the image (dimension, type, size) to be updated.
- replaceWave(String, Wave) - Method in class ij.plugin.frame.ChartPlugIn
-
- rescale(double, double) - Method in class ij.gui.Roi
-
- rescale() - Method in class ij.plugin.frame.RoiManager
-
- rescale(int, int) - Method in class ij.plugin.frame.RoiManager
-
- reset() - Method in class ij.process.FloatProcessor
-
- reset(ImageProcessor) - Method in class ij.process.FloatProcessor
-
- reset() - Method in class ij.process.ImageProcessor
-
Restores the pixel data from the snapshot (undo) buffer.
- reset(ImageProcessor) - Method in class ij.process.ImageProcessor
-
Restores pixels from the snapshot buffer that are
within the rectangular roi but not part of the mask.
- reset() - Method in class ij.process.ShortProcessor
-
- reset(ImageProcessor) - Method in class ij.process.ShortProcessor
-
- resetBinaryThreshold() - Method in class ij.process.ImageProcessor
-
Resets the threshold if minThreshold=maxThreshold and lutUpdateMode=NO_LUT_UPDATE.
- resetClassLoader() - Static method in class ij.IJ
-
- resetClipboard() - Static method in class ij.ImagePlus
-
Clears the internal clipboard.
- resetCursor() - Method in class org.jah.ephys.abf.ABF
-
- resetCursor(String) - Method in class org.jah.ephys.ElectrophysManager
-
- resetDisplayRange() - Method in class ij.ImagePlus
-
- resetEscape() - Static method in class ij.IJ
-
This method sets the Esc key to the "up" position.
- resetMinAndMax() - Static method in class ij.IJ
-
Resets the minimum and maximum displayed pixel values of the
current image to be the same as the min and max pixel values.
- resetMinAndMax(ImagePlus) - Static method in class ij.IJ
-
Resets the minimum and maximum displayed pixel values of the
specified image to be the same as the min and max pixel values.
- resetMinAndMax() - Method in class ij.process.FloatProcessor
-
Recalculates the min and max values used to scale pixel
values to 0-255 for display.
- resetMinAndMax() - Method in class ij.process.ImageProcessor
-
For short and float images, recalculates the min and max
image values needed to correctly display the image.
- resetMinAndMax() - Method in class ij.process.ShortProcessor
-
Recalculates the min and max values used to scale pixel
values to 0-255 for display.
- resetRoi() - Method in class ij.process.ImageProcessor
-
Sets the ROI (Region of Interest) and clipping rectangle to the entire image.
- resetStack() - Method in class ij.ImagePlus
-
- resetThreshold() - Static method in class ij.IJ
-
Disables thresholding on the current image.
- resetThreshold(ImagePlus) - Static method in class ij.IJ
-
Disables thresholding on the specified image.
- resetThreshold() - Method in class ij.process.ImageProcessor
-
Disables thresholding.
- resize(int, int) - Method in class ij.process.FloatProcessor
-
Creates a new FloatProcessor containing a scaled copy of this image or selection.
- resize(int, int) - Method in class ij.process.ImageProcessor
-
Creates a new ImageProcessor containing a scaled copy of this image or ROI.
- resize(int) - Method in class ij.process.ImageProcessor
-
Creates a new ImageProcessor containing a scaled copy
of this image or ROI, with the aspect ratio maintained.
- resize(int, int, boolean) - Method in class ij.process.ImageProcessor
-
Creates a new ImageProcessor containing a scaled copy of this image or ROI.
- resize(int, int) - Method in class ij.process.ShortProcessor
-
Creates a new ShortProcessor containing a scaled copy of this image or selection.
- resizeLinearly(int, int) - Method in class ij.process.ImageProcessor
-
Use linear interpolation to resize images that have a width or height of one.
- RESIZING - Static variable in class ij.gui.Roi
-
- restoreAutoBounds() - Method in class ij.plugin.frame.ChartPlugIn
-
- restoreRoi() - Method in class ij.ImagePlus
-
- reverse() - Method in class ij.wave.Waves
-
- revert() - Method in class ij.ImagePlus
-
Implements the File/Revert command.
- RIGHT_JUSTIFY - Static variable in class ij.process.ImageProcessor
-
Right justify text.
- rLUT1 - Variable in class ij.process.ImageProcessor
-
- rLUT2 - Variable in class ij.process.ImageProcessor
-
- Roi - Class in ij.gui
-
A rectangular region of interest and superclass for the other ROI classes.
- Roi(int, int, int, int) - Constructor for class ij.gui.Roi
-
Creates a rectangular ROI.
- Roi(double, double, double, double) - Constructor for class ij.gui.Roi
-
Creates a rectangular ROI using double arguments.
- Roi(int, int, int, int, int) - Constructor for class ij.gui.Roi
-
Creates a new rounded rectangular ROI.
- Roi(double, double, double, double, int) - Constructor for class ij.gui.Roi
-
Creates a rounded rectangular ROI using double arguments.
- Roi(Rectangle) - Constructor for class ij.gui.Roi
-
Creates a new rectangular Roi.
- Roi(int, int, ImagePlus) - Constructor for class ij.gui.Roi
-
Starts the process of creating a user-defined rectangular Roi,
where sx and sy are the starting screen coordinates.
- Roi(int, int, ImagePlus, int) - Constructor for class ij.gui.Roi
-
Starts the process of creating a user-defined rectangular Roi,
where sx and sy are the starting screen coordinates.
- Roi(int, int, int, int, ImagePlus) - Constructor for class ij.gui.Roi
-
Deprecated.
- roi - Variable in class ij.ImagePlus
-
- roi - Variable in class ij.wave.Wave
-
- ROIColor - Static variable in class ij.gui.Roi
-
- roiHeight - Variable in class ij.process.ImageProcessor
-
- RoiManager - Class in ij.plugin.frame
-
This plugin implements the Analyze/Tools/ROI Manager command.
- RoiManager() - Constructor for class ij.plugin.frame.RoiManager
-
- RoiManager(boolean) - Constructor for class ij.plugin.frame.RoiManager
-
- Rois - Class in ij.gui
-
- Rois() - Constructor for class ij.gui.Rois
-
The default constructor
- roiWidth - Variable in class ij.process.ImageProcessor
-
- roiX - Variable in class ij.process.ImageProcessor
-
- roiY - Variable in class ij.process.ImageProcessor
-
- rotate(double) - Method in class ij.process.FloatProcessor
-
Rotates the image or ROI 'angle' degrees clockwise.
- rotate(double) - Method in class ij.process.ImageProcessor
-
Rotates the image or selection 'angle' degrees clockwise.
- rotate(double) - Method in class ij.process.ShortProcessor
-
Rotates the image or ROI 'angle' degrees clockwise.
- rotateLeft() - Method in class ij.process.ImageProcessor
-
Rotates the entire image 90 degrees counter-clockwise.
- rotateRight() - Method in class ij.process.ImageProcessor
-
Rotates the entire image 90 degrees clockwise.
- rtrim(String) - Static method in class org.jah.JAH_Utils
-
From http://stackoverflow.com/questions/15567010/what-is-a-good-alternative-of-ltrim-and-rtrim-in-java
- run(String) - Static method in class ij.IJ
-
Runs an ImageJ command.
- run(String, String) - Static method in class ij.IJ
-
Runs an ImageJ command, with options that are passed to the
GenericDialog and OpenDialog classes.
- run(ImagePlus, String, String) - Static method in class ij.IJ
-
Runs an ImageJ command using the specified image and options.
- run(String) - Method in class ij.plugin.frame.ChartPlugIn
-
- run(String) - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- run() - Method in class org.jah.ephys.ElectrophysManager
-
- runCommand(String) - Method in class ij.plugin.frame.RoiManager
-
Executes the ROI Manager "Add", "Add & Draw", "Update", "Delete", "Measure", "Draw",
"Show All", Show None", "Fill", "Deselect", "Select All", "Combine", "AND", "XOR", "Split",
"Sort" or "Multi Measure" command.
- runCommand(String, String) - Method in class ij.plugin.frame.RoiManager
-
Executes the ROI Manager "Open", "Save" or "Rename" command.
- runCommand(String, String, double) - Method in class ij.plugin.frame.RoiManager
-
Adds the current selection to the ROI Manager, using the
specified color (a 6 digit hex string) and line width.
- runCommand(String) - Method in class ij.plugin.frame.WaveManager
-
Executes the Wave Manager "Import", "Add & Draw", "Update", "Delete", "Plot", "Info", "Draw",
"Show All", Show None", "Fill", "Deselect", "Select All", "Combine", "AND", "XOR", "Split",
"Sort" or "Multi Measure" command.
- runCommand(String, String) - Method in class ij.plugin.frame.WaveManager
-
Executes the Wave Manager "Open", "Save" or "Rename" command.
- runCommand(String, String, double) - Method in class ij.plugin.frame.WaveManager
-
Adds the current selection to the Wave Manager, using the
specified color (a 6 digit hex string) and line width.
- runMacro(String) - Static method in class ij.IJ
-
Runs the macro contained in the string macro.
- runMacro(String, String) - Static method in class ij.IJ
-
Runs the macro contained in the string macro.
- runMacroFile(String, String) - Static method in class ij.IJ
-
Runs the specified macro or script file in the current thread.
- runMacroFile(String) - Static method in class ij.IJ
-
Runs the specified macro file.
- running - Variable in class ij.gui.ImageWindow
-
This variable is set false if the user presses the escape key or closes the window.
- running2 - Variable in class ij.gui.ImageWindow
-
This variable is set false if the user clicks in this
window, presses the escape key, or closes the window.
- runPlugIn(ImagePlus, String, String) - Static method in class ij.IJ
-
Runs the specified plugin using the specified image.
- runPlugIn(String, String) - Static method in class ij.IJ
-
Runs the specified plugin and returns a reference to it.
- runPlugIn(String, String, String) - Static method in class ij.IJ
-
Runs the specified plugin and returns a reference to it.
- sampleModel - Variable in class ij.process.ImageProcessor
-
- samplingRate_Hz - Variable in class ij.wave.Wave
-
- save(String) - Static method in class ij.IJ
-
Saves the current image, lookup table, selection or text window to the specified file path.
- save(ImagePlus, String) - Static method in class ij.IJ
-
Saves the specified image, lookup table or selection to the specified file path.
- save(String) - Method in class ij.plugin.frame.RoiManager
-
- save(String) - Method in class ij.plugin.frame.WaveManager
-
- save() - Method in class ij.plugin.frame.WaveManager
-
- save(String) - Method in class ij.wave.Wave
-
- save(String) - Method in class ij.wave.Waves
-
- save(String) - Method in class org.jah.ephys.Comments
-
- save(String) - Method in class org.jah.ephys.Epoch
-
- save(File) - Method in class org.jah.ephys.Epoch
-
- saveAs(String, String) - Static method in class ij.IJ
-
- saveAs(ImagePlus, String, String) - Static method in class ij.IJ
-
- saveAsText(String) - Method in class ij.wave.Wave
-
Saves the waveform to the text file with a default of 3 decimal places.
- saveAsText(String, int) - Method in class ij.wave.Wave
-
Saves the waveform to the text file with the number of decimal places passed as argument.
- saveAsTiff(ImagePlus, String) - Static method in class ij.IJ
-
Saves the specified image in TIFF format.
- saveChannels(String[], int, String, boolean, boolean, boolean, boolean, double, double) - Method in class org.jah.ephys.abf.ABF
-
- saveChart(String) - Method in class ij.plugin.frame.ChartPlugIn
-
- saveChart() - Method in class ij.plugin.frame.ChartPlugIn
-
- saveChartAsEPS(String) - Method in class ij.plugin.frame.ChartPlugIn
-
- saveComments() - Method in class org.jah.ephys.Comments
-
- saveEpochTables(Hashtable) - Method in class org.jah.ephys.ElectrophysManager
-
- saveEPS(String) - Method in class ij.plugin.frame.ChartPlugIn
-
- saveLayout() - Method in class ij.plugin.frame.Layout
-
- saveLayout(String) - Method in class ij.plugin.frame.Layout
-
- saveLayout(File) - Method in class ij.plugin.frame.Layout
-
- saveLayoutTemplate() - Method in class ij.plugin.frame.Layout
-
- saveLayoutTemplate(String) - Method in class ij.plugin.frame.Layout
-
- saveLayoutTemplate(File) - Method in class ij.plugin.frame.Layout
-
- saveMarkers(String) - Method in class ij.plugin.frame.ChartPlugIn
-
Saves the WaveMarkers to the file specified by the argument.
- saveMarkers(List, String) - Static method in class ij.wave.WaveUtils
-
- saveMarkers(List, String, boolean) - Static method in class ij.wave.WaveUtils
-
- saveNextEpoch(String, String) - Method in class org.jah.ephys.ElectrophysManager
-
- saveRoi(String) - Method in class ij.gui.Roi
-
Saves the ROI at the explicit path provided and does not add .roi to the end.
- saveRoi() - Method in class ij.ImagePlus
-
- saveSelectedAsText() - Method in class ij.plugin.frame.WaveManager
-
- saveSelectedAsText(String, int) - Method in class ij.plugin.frame.WaveManager
-
- saveString(String, String) - Static method in class ij.IJ
-
Saves a string as a file.
- scale(double, double) - Method in class ij.process.FloatProcessor
-
Scales the image or selection using the specified scale factors.
- scale(double, double) - Method in class ij.process.ImageProcessor
-
Scales the image by the specified factors.
- scale(double, double) - Method in class ij.process.ShortProcessor
-
Scales the image or selection using the specified scale factors.
- scaleBufferedImage(BufferedImage, double) - Method in class ij.gui.LayoutComponent
-
- screenX(int) - Method in class ij.gui.Roi
-
- screenXD(double) - Method in class ij.gui.Roi
-
- screenY(int) - Method in class ij.gui.Roi
-
- screenYD(double) - Method in class ij.gui.Roi
-
- scrollbar - Variable in class ij.plugin.frame.ChartPlugIn
-
- select(String) - Method in class ij.plugin.frame.RoiManager
-
- select(int) - Method in class ij.plugin.frame.RoiManager
-
Assigns the ROI at the specified index to the current image.
- select(ImagePlus, int) - Method in class ij.plugin.frame.RoiManager
-
- select(ImagePlus, int, boolean) - Method in class ij.plugin.frame.RoiManager
-
Assigns the ROI at the specified index to 'imp'.
- select(int, boolean, boolean) - Method in class ij.plugin.frame.RoiManager
-
- select(String) - Method in class ij.plugin.frame.WaveManager
-
- select(int) - Method in class ij.plugin.frame.WaveManager
-
Assigns the Wave at the specified index to the current image.
- select(ImagePlus, int) - Method in class ij.plugin.frame.WaveManager
-
Assigns the Wave at the specified index to 'imp'.
- select(int, boolean, boolean) - Method in class ij.plugin.frame.WaveManager
-
- select(Waves) - Method in class ij.plugin.frame.WaveManager
-
- selectLayoutComponent(LayoutComponent) - Method in class ij.plugin.frame.Layout
-
- selectLayoutComponents(Rectangle) - Method in class ij.plugin.frame.Layout
-
- selectWindow(int) - Static method in class ij.IJ
-
For IDs less than zero, activates the image with the specified ID.
- selectWindow(String) - Static method in class ij.IJ
-
Activates the window with the specified title.
- sendChannelDataToWaveManager(String, String) - Method in class org.jah.ephys.ElectrophysManager
-
- sendDataToWaveManager(String) - Method in class org.jah.ephys.ElectrophysManager
-
- sendDataToWaveManager(String, double, double) - Method in class org.jah.ephys.ElectrophysManager
-
- sendEpisodicDataToWaveManager(String) - Method in class org.jah.ephys.ElectrophysManager
-
- sendEpochByNameToWaveManager(String) - Static method in class org.jah.ephys.ElectrophysManager
-
- sendEpochByNameToWaveManager(String, String) - Static method in class org.jah.ephys.ElectrophysManager
-
- sendEpochToWaveManager(Epoch) - Static method in class org.jah.ephys.ElectrophysManager
-
- sendNextEpochToWaveManager(String) - Method in class org.jah.ephys.ElectrophysManager
-
- sendNextEpochToWaveManager(String, String) - Method in class org.jah.ephys.ElectrophysManager
-
- sendNextEpochToWaveManager(String, boolean) - Method in class org.jah.ephys.ElectrophysManager
-
- sendNextEpochToWaveManager(String, String, boolean) - Method in class org.jah.ephys.ElectrophysManager
-
- sendPreviousEpochToWaveManager(String) - Method in class org.jah.ephys.ElectrophysManager
-
- sendTemplateToWfdIV(String) - Static method in class org.jah.JAH_Utils
-
A convenience function to send a holographic mask to WfdIV, note: only actually sends
the file if Configuration_.isAutoSendingTemplatesToWfdIV() is true.
- set(int, int, int) - Method in class ij.process.FloatProcessor
-
- set(int, int) - Method in class ij.process.FloatProcessor
-
- set(double) - Method in class ij.process.FloatProcessor
-
- set(int, int, int) - Method in class ij.process.ImageProcessor
-
This is a faster version of putPixel() that does not clip
out of range values and does not do bounds checking.
- set(int, int) - Method in class ij.process.ImageProcessor
-
- set(double) - Method in class ij.process.ImageProcessor
-
Assigns 'value' to each pixel in the image or ROI.
- set(int, int, int) - Method in class ij.process.ShortProcessor
-
- set(int, int) - Method in class ij.process.ShortProcessor
-
- set(double) - Method in class ij.process.ShortProcessor
-
- set(int, double) - Method in class ij.wave.Wave
-
- setActivated() - Method in class ij.ImagePlus
-
Called by ImageWindow.windowActivated().
- setAntialiasedText(boolean) - Method in class ij.process.ImageProcessor
-
Specifies whether or not text is drawn using antialiasing.
- setAntialiasRendering(boolean) - Method in class ij.ImagePlus
-
Enable/disable use of antialiasing by the flatten() method.
- setAutoloadingLayoutTemplates(boolean) - Static method in class org.jah.Configuration_
-
- setAutonamingStreams(boolean) - Static method in class org.jah.Configuration_
-
- setAutoPulseLaser(boolean) - Static method in class org.jah.Configuration_
-
- setAutosaving(boolean) - Static method in class org.jah.Configuration_
-
- setAutosavingHistory(boolean) - Static method in class org.jah.Configuration_
-
- setAutoSendingTemplatesToWfdIV(boolean) - Static method in class org.jah.Configuration_
-
- setAutoThreshold(ImagePlus, String) - Static method in class ij.IJ
-
- setAutoThreshold(String) - Method in class ij.process.ImageProcessor
-
- setAutoThreshold(String, boolean, int) - Method in class ij.process.ImageProcessor
-
- setAutoThreshold(Method, boolean) - Method in class ij.process.ImageProcessor
-
- setAutoThreshold(Method, boolean, int) - Method in class ij.process.ImageProcessor
-
- setAutoThreshold(int, int) - Method in class ij.process.ImageProcessor
-
Automatically sets the lower and upper threshold levels, where 'method'
must be ISODATA or ISODATA2 and 'lutUpdate' must be RED_LUT,
BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
- setAxesListening(boolean) - Method in class ij.plugin.frame.ChartPlugIn
-
- setAxisExtents(Axis, double, double) - Method in class ij.plugin.frame.ChartPlugIn
-
- setAxisRange(Axis, double, double) - Method in class ij.plugin.frame.ChartPlugIn
-
- setAxisRange(String, Range) - Method in class ij.plugin.frame.ChartPlugIn
-
Sets the axis range for the wave or axis name.
- setAxisTicks(String, double, int) - Method in class ij.plugin.frame.ChartPlugIn
-
Sets the tick increment and number of ticks for the axis with the name passed as argument.
- setAxisVisible(String, boolean) - Method in class ij.plugin.frame.ChartPlugIn
-
Sets if the axis is visible by the wave or axis name.
- setBackgroundColor(int, int, int) - Static method in class ij.IJ
-
Sets the background color.
- setBackgroundValue(double) - Method in class ij.process.FloatProcessor
-
Does nothing.
- setBackgroundValue(double) - Method in class ij.process.ImageProcessor
-
Sets the background fill value used by the rotate() and scale() methods.
- setBackgroundValue(double) - Method in class ij.process.ShortProcessor
-
Does nothing.
- setBaseDirectory(String) - Static method in class org.jah.Configuration_
-
- setBin3ImageHeight(int) - Static method in class org.jah.Configuration_
-
- setBin3ImageWidth(int) - Static method in class org.jah.Configuration_
-
- setBinaryThreshold() - Method in class ij.process.ImageProcessor
-
- setBlankValues(double, String, double) - Method in class ij.wave.Wave
-
- setC(int) - Method in class ij.ImagePlus
-
Sets the hyperstack channel position (one based).
- setCalibration(Calibration) - Method in class ij.ImagePlus
-
Sets this image's calibration.
- setCalibrationTable(float[]) - Method in class ij.process.ImageProcessor
-
Set a lookup table used by getPixelValue(), getLine() and
convertToFloat() to calibrate pixel values.
- setCancelLabel(String) - Method in class ij.gui.GenericDialog
-
Sets a replacement label for the "Cancel" button.
- setClipRect(Rectangle) - Method in class ij.process.ImageProcessor
-
Updates the clipping rectangle used by lineTo(), drawLine(), drawDot() and drawPixel().
- setColor(Color) - Static method in class ij.gui.Roi
-
Sets the default (global) color used for ROI outlines.
- setColor(Color) - Method in class ij.ImagePlus
-
Sets current foreground color.
- setColor(Color) - Method in class ij.process.FloatProcessor
-
Sets the foreground fill/draw color.
- setColor(Color) - Method in class ij.process.ImageProcessor
-
Sets the default fill/draw value to the pixel
value closest to the specified color.
- setColor(int) - Method in class ij.process.ImageProcessor
-
Sets the default fill/draw value.
- setColor(double) - Method in class ij.process.ImageProcessor
-
Sets the default fill/draw value.
- setColor(Color) - Method in class ij.process.ShortProcessor
-
Sets the foreground fill/draw color.
- setColorModel(ColorModel) - Method in class ij.ImageStack
-
Assigns a new color model to this stack.
- setColorModel(ColorModel) - Method in class ij.process.ImageProcessor
-
Sets the color model.
- setColumnHeadings(String) - Static method in class ij.IJ
-
Clears the "Results" window and sets the column headings to
those in the tab-delimited 'headings' String.
- setComments(Comments) - Method in class ij.wave.Wave
-
- setContrast(double) - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- setCornerDiameter(int) - Method in class ij.gui.Roi
-
Sets the rounded rectangle corner diameter (pixels).
- setCorrelationTime(double) - Method in class ij.wave.Wave
-
- setCorrelationValue(double) - Method in class ij.wave.Wave
-
- setCurrentRow(int) - Method in class org.jah.ephys.abf.ABF
-
- setCurrentWindow(ImageWindow) - Static method in class ij.WindowManager
-
Makes the image contained in the specified window the active image.
- setDebugMode(boolean) - Static method in class ij.IJ
-
Enable/disable debug mode.
- setDefault16bitRange(int) - Static method in class ij.ImagePlus
-
Set the default 16-bit display range, where 'bitDepth' must be 0 (auto-scaling),
8 (0-255), 10 (0-1023), 12 (0-4095, 15 (0-32767) or 16 (0-65535).
- setDefaultChartHeight(int) - Static method in class org.jah.Configuration_
-
- setDefaultChartWidth(int) - Static method in class org.jah.Configuration_
-
- setDefaultColors() - Static method in class ij.wave.WaveMarker
-
- setDefaultFillColor(Color) - Static method in class ij.gui.Roi
-
- setDefaultLeanDisplay(boolean) - Static method in class org.jah.Configuration_
-
- setDefaultMarkerWidth(double) - Static method in class org.jah.Configuration_
-
- setDimensions(int, int, int) - Method in class ij.ImagePlus
-
Sets the 3rd, 4th and 5th dimensions, where
nChannels*nSlices*nFrames
must be equal to the stack size.
- setDisplayRange(double, double) - Method in class ij.ImagePlus
-
Sets the display range of the current channel.
- setDisplayRange(double, double, int) - Method in class ij.ImagePlus
-
Sets the display range of specified channels in an RGB image, where 4=red,
2=green, 1=blue, 6=red+green, etc.
- setDomainAxisExtents(XYPlot, double, double) - Method in class ij.plugin.frame.ChartPlugIn
-
- setDomainAxisRange(double, double) - Method in class ij.plugin.frame.ChartPlugIn
-
- setDomainAxisRange(XYPlot, double, double) - Method in class ij.plugin.frame.ChartPlugIn
-
- setDrawOffset(boolean) - Method in class ij.gui.Roi
-
- setDuration(double) - Method in class ij.wave.Burst
-
- setEchoChar(char) - Method in class ij.gui.GenericDialog
-
Sets the echo character for the next string field.
- setEditMode(ImagePlus, boolean) - Method in class ij.plugin.frame.RoiManager
-
- setEditMode(ImagePlus, boolean) - Method in class ij.plugin.frame.WaveManager
-
- setElectrophysSamplingRateHz(double) - Static method in class org.jah.Configuration_
-
- setEnd(long) - Method in class org.jah.ephys.Epoch
-
- setEnd_s(double) - Method in class org.jah.ephys.Epoch
-
- setEphysFileFilename(String) - Method in class org.jah.ephys.Epoch
-
- setEphysFilename(String) - Method in class org.jah.ephys.Epoch
-
- setEpochChannelName(String) - Static method in class org.jah.Configuration_
-
- setEpochCommentMaxLength(int) - Static method in class org.jah.Configuration_
-
- setEpochCommentPattern(String) - Static method in class org.jah.Configuration_
-
- setEpochFactor(double) - Static method in class org.jah.Configuration_
-
- setEpochThreshold(double) - Static method in class org.jah.Configuration_
-
- setExceptionHandler(IJ.ExceptionHandler) - Static method in class ij.IJ
-
Installs a custom exception handler that
overrides the handleException() method.
- setExportWithTimes(boolean) - Static method in class org.jah.Configuration_
-
- setf(int, int, float) - Method in class ij.process.FloatProcessor
-
- setf(int, float) - Method in class ij.process.FloatProcessor
-
- setf(int, int, float) - Method in class ij.process.ImageProcessor
-
Sets the value of the pixel at (x,y) to 'value'.
- setf(int, float) - Method in class ij.process.ImageProcessor
-
- setf(int, int, float) - Method in class ij.process.ShortProcessor
-
- setf(int, float) - Method in class ij.process.ShortProcessor
-
- setFileInfo(FileInfo) - Method in class ij.ImagePlus
-
Saves this image's FileInfo so it can be later
retieved using getOriginalFileInfo().
- setFillColor(Color) - Method in class ij.gui.Roi
-
Sets the fill color used to display this ROI, or set to null to display it transparently.
- setFloatArray(float[][]) - Method in class ij.process.ImageProcessor
-
Replaces the pixel data with contents of the specified 2D float array.
- setFont(Font) - Method in class ij.process.ImageProcessor
-
Sets the font used by drawString().
- setFontMetrics(FontMetrics) - Method in class ij.gui.LayoutComponent
-
- setForegroundColor(int, int, int) - Static method in class ij.IJ
-
Sets the foreground color.
- setGlobalCalibration(Calibration) - Method in class ij.ImagePlus
-
Sets the system-wide calibration.
- setHelpLabel(String) - Method in class ij.gui.GenericDialog
-
Sets a replacement label for the "Help" button.
- setHideOverlay(boolean) - Method in class ij.ImagePlus
-
- setHistogramRange(double, double) - Method in class ij.process.ImageProcessor
-
Set the range used for histograms of float images.
- setHistogramSize(int) - Method in class ij.process.ImageProcessor
-
Set the number of bins to be used for histograms of float images.
- setID(String) - Method in class org.jah.ephys.Epoch
-
- setIgnoreClipRect(boolean) - Method in class ij.gui.Roi
-
- setIgnoreFlush(boolean) - Method in class ij.ImagePlus
-
- setImage(ImagePlus) - Method in class ij.gui.ImageWindow
-
- setImage(ImagePlus) - Method in class ij.gui.Roi
-
- setImage(Image) - Method in class ij.ImagePlus
-
Replaces the image, if any, with the one specified.
- setImage(ImagePlus) - Method in class ij.ImagePlus
-
Replaces this image with the specified ImagePlus.
- setImagingSamplingRateHz(double) - Static method in class org.jah.Configuration_
-
- setInputEvent(InputEvent) - Static method in class ij.IJ
-
- setInsets(int, int, int) - Method in class ij.gui.GenericDialog
-
Set the insets (margins), in pixels, that will be
used for the next component added to the dialog.
- setInstanceColor(Color) - Method in class ij.gui.Roi
-
- setIntArray(int[][]) - Method in class ij.process.ImageProcessor
-
Replaces the pixel data with contents of the specified 2D int array.
- setInterpolate(boolean) - Method in class ij.process.ImageProcessor
-
This method has been replaced by setInterpolationMethod().
- setInterpolationMethod(int) - Method in class ij.process.ImageProcessor
-
Use this method to set the interpolation method (NONE,
BILINEAR or BICUBIC) used by scale(), resize() and rotate().
- setIsTemplate(boolean) - Method in class ij.gui.LayoutComponent
-
- setJustification(int) - Method in class ij.process.ImageProcessor
-
Sets the justification used by drawString(), where justification
is CENTER_JUSTIFY, RIGHT_JUSTIFY or LEFT_JUSTIFY.
- setKeyDown(int) - Static method in class ij.IJ
-
- setKeyUp(int) - Static method in class ij.IJ
-
- setLastStreamLength(int) - Static method in class org.jah.Configuration_
-
- setLayoutComponent(int, ImagePlus) - Method in class ij.plugin.frame.Layout
-
- setLayoutComponent(int, Frame) - Method in class ij.plugin.frame.Layout
-
- setLayoutComponentPosition(String, int, int) - Method in class ij.plugin.frame.Layout
-
- setLayoutExportDPI(int) - Static method in class org.jah.Configuration_
-
- setLayoutSize(int, int) - Method in class ij.plugin.frame.Layout
-
- setLayoutSize(Dimension) - Method in class ij.plugin.frame.Layout
-
- setLeanDisplay(boolean) - Method in class ij.plugin.frame.ChartPlugIn
-
If the argument is true, the axis lines and ticks are removed.
- setLeftHorizontalProportions(float[]) - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- setLeftVerticalProportions(float[]) - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- setLineWidth(int) - Method in class ij.gui.Roi
-
- setLineWidth(int) - Method in class ij.process.ImageProcessor
-
Sets the line width used by lineTo() and drawDot().
- setListener(ElectrophysManager_Frame) - Method in class org.jah.ephys.ElectrophysManager
-
- setLJDAC0ScalingFactor(double) - Static method in class org.jah.Configuration_
-
- setLJDAC0YOffset(double) - Static method in class org.jah.Configuration_
-
- setLocation(int, int) - Method in class ij.gui.LayoutComponent
-
- setLocation(int, int) - Method in class ij.gui.Roi
-
Set the location of the ROI in image coordinates.
- setLocation(double, double) - Method in class ij.gui.Roi
-
Set the location of the ROI in image coordinates.
- setLocationAndSize(int, int, int, int) - Method in class ij.gui.ImageWindow
-
Moves and resizes this window.
- setLocked(boolean) - Method in class ij.plugin.frame.Layout
-
- setLogging(boolean) - Static method in class org.jah.Configuration_
-
- setLut(LUT) - Method in class ij.process.ImageProcessor
-
- setLutAnimation(boolean) - Method in class ij.process.ImageProcessor
-
For 16 and 32 bit processors, set 'lutAnimation' true
to have createImage() use the cached 8-bit version
of the image.
- setMask(ImageProcessor) - Method in class ij.process.ImageProcessor
-
Defines a byte mask that limits processing to an
irregular ROI.
- setMaxVisiblePlotPoints(double) - Static method in class org.jah.Configuration_
-
- setMiddleDividerLocation(int) - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- setMinAndMax(double, double) - Static method in class ij.IJ
-
Sets the display range (minimum and maximum displayed pixel values) of the current image.
- setMinAndMax(ImagePlus, double, double) - Static method in class ij.IJ
-
Sets the display range (minimum and maximum displayed pixel values) of the specified image.
- setMinAndMax(double, double, int) - Static method in class ij.IJ
-
Sets the minimum and maximum displayed pixel values on the specified RGB
channels, where 4=red, 2=green and 1=blue.
- setMinAndMax(double, double) - Method in class ij.process.FloatProcessor
-
Sets the min and max variables that control how real
pixel values are mapped to 0-255 screen values.
- setMinAndMax(double, double) - Method in class ij.process.ImageProcessor
-
This image will be displayed by mapping pixel values in the
range min-max to screen values in the range 0-255.
- setMinAndMax(double, double) - Method in class ij.process.ShortProcessor
-
Sets the min and max variables that control how real
pixel values are mapped to 0-255 screen values.
- setMinimumPulseStepValue(double) - Static method in class org.jah.Configuration_
-
- setMultipleMode(boolean) - Method in class ij.plugin.frame.RoiManager
-
- setName(String) - Method in class ij.gui.Roi
-
Sets the name of this ROI.
- setName(String) - Method in class ij.wave.Bursts
-
- setName(String) - Method in class ij.wave.Wave
-
Returns the name of this wave
- setName(String) - Method in class org.jah.ephys.abf.ABF
-
- setName(String) - Method in class org.jah.ephys.Epoch
-
- setNextLocation(Point) - Static method in class ij.gui.ImageWindow
-
Causes the next image to be displayed at the specified location.
- setNextLocation(int, int) - Static method in class ij.gui.ImageWindow
-
Causes the next image to be displayed at the specified location.
- setNextRoi(Roi) - Method in class ij.gui.Roi
-
JAH: I added this!
- setNonScalable(boolean) - Method in class ij.gui.Roi
-
Set 'nonScalable' true to have TextRois in a display
list drawn at a fixed location and size.
- setNumberOfPulseAmplitudeSteps(int) - Static method in class org.jah.Configuration_
-
- setNumberOfPulsesInTrain(int) - Static method in class org.jah.Configuration_
-
- setOKLabel(String) - Method in class ij.gui.GenericDialog
-
Sets a replacement label for the "OK" button.
- setOpenAsHyperStack(boolean) - Method in class ij.ImagePlus
-
- setOverColor(int, int, int) - Static method in class ij.process.ImageProcessor
-
Sets the upper Over/Under threshold color.
- setOverlay(Overlay) - Method in class ij.ImagePlus
-
Installs a list of ROIs that will be drawn on this image as a non-destructive overlay.
- setOverlay(Shape, Color, BasicStroke) - Method in class ij.ImagePlus
-
Creates an Overlay from the specified Shape, Color
and BasicStroke, and assigns it to this image.
- setOverlay(Roi, Color, int, Color) - Method in class ij.ImagePlus
-
Creates an Overlay from the specified ROI, and assigns it to this image.
- setOverlay(Overlay) - Method in class ij.process.ImageProcessor
-
This method is used to display virtual stack overlays.
- setPaintScale(String, Color, int) - Method in class ij.plugin.frame.ChartPlugIn
-
- setPaintScale(XYPlot, Color, int) - Method in class ij.plugin.frame.ChartPlugIn
-
- setPaintScale(XYPlot, PaintScale, int) - Method in class ij.plugin.frame.ChartPlugIn
-
- setPaintScale(String, PaintScale, int) - Method in class ij.plugin.frame.ChartPlugIn
-
Sets the PaintScale for a Wave rendered using the XYBlockRenderer (e.g., 3D plots)
- setParent(ImageObserver) - Method in class ij.gui.LayoutComponent
-
- setPasteMode(int) - Static method in class ij.gui.Roi
-
Sets the Paste transfer mode.
- setPasteMode(String) - Static method in class ij.IJ
-
Sets the transfer mode used by the Edit/Paste command, where mode is "Copy", "Blend", "Average", "Difference",
"Transparent", "Transparent2", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", or "Divide".
- setPeakAmp(double) - Method in class ij.wave.Burst
-
- setPeakDetectionHighThreshold(double) - Static method in class org.jah.Configuration_
-
- setPeakDetectionLowThreshold(double) - Static method in class org.jah.Configuration_
-
- setPeakTime(double) - Method in class ij.wave.Burst
-
- setPixels(Object, int) - Method in class ij.ImageStack
-
Assigns a pixel array to the specified slice,
were 1<=n<=nslices.
- setPixels(Object) - Method in class ij.process.FloatProcessor
-
- setPixels(int, FloatProcessor) - Method in class ij.process.FloatProcessor
-
Sets the pixels, and min&max values from a FloatProcessor.
- setPixels(Object) - Method in class ij.process.ImageProcessor
-
Sets a new pixel array for the image.
- setPixels(int, FloatProcessor) - Method in class ij.process.ImageProcessor
-
Sets the pixels (of one color channel for RGB images) from a FloatProcessor.
- setPixels(Object) - Method in class ij.process.ShortProcessor
-
- setPixels(int, FloatProcessor) - Method in class ij.process.ShortProcessor
-
Sets the pixels from a FloatProcessor, no scaling.
- setPosition(int) - Method in class ij.gui.Roi
-
Sets the stack position (image number) of this ROI.
- setPosition(int, int, int) - Method in class ij.gui.Roi
-
Sets the hyperstack position of this ROI.
- setPosition(int, int, int) - Method in class ij.ImagePlus
-
Sets the current hyperstack position and updates the display,
where 'channel', 'slice' and 'frame' are one-based indexes.
- setPosition(int) - Method in class ij.ImagePlus
-
Set the current hyperstack position based on the stack index 'n' (one-based).
- setPositionWithoutUpdate(int, int, int) - Method in class ij.ImagePlus
-
Sets the current hyperstack position without updating the display,
where 'channel', 'slice' and 'frame' are one-based indexes.
- setPostPulseDetectionDelay(double) - Static method in class org.jah.Configuration_
-
- setPreviousRoi(Roi) - Method in class ij.gui.Roi
-
JAH: I added this!
- setProcessingDirectory(String) - Static method in class org.jah.Configuration_
-
- setProcessor(ImageProcessor) - Method in class ij.ImagePlus
-
Replaces the ImageProcessor with the one specified and updates the
display.
- setProcessor(String, ImageProcessor) - Method in class ij.ImagePlus
-
Replaces the ImageProcessor with the one specified and updates the display.
- setProcessor(ImageProcessor, int) - Method in class ij.ImageStack
-
Assigns the pixel array of an ImageProcessor to the
specified slice, were 1<=n<=nslices.
- setProgressBar(ProgressBar) - Method in class ij.process.ImageProcessor
-
Assigns a progress bar to this processor.
- setProperties(String) - Method in class ij.gui.Roi
-
- setProperty(String, String) - Method in class ij.gui.Roi
-
- setProperty(String, Object) - Method in class ij.ImagePlus
-
Adds a key-value pair to this image's properties.
- setProperty(String, String) - Static method in class org.jah.Configuration_
-
- setPrototypeOverlay(Overlay) - Method in class ij.gui.Roi
-
- setPulseAmplitude(double) - Static method in class org.jah.Configuration_
-
- setPulseContinuousMax(double) - Static method in class org.jah.Configuration_
-
- setPulseContinuousMin(double) - Static method in class org.jah.Configuration_
-
- setPulseFrequency(double) - Static method in class org.jah.Configuration_
-
- setPulseGaussianMean(double) - Static method in class org.jah.Configuration_
-
- setPulseGaussianStdD(double) - Static method in class org.jah.Configuration_
-
- setPulseLength(int) - Static method in class org.jah.Configuration_
-
- setPulseStartDelay(double) - Static method in class org.jah.Configuration_
-
- setPulseTrainStartDelay(double) - Static method in class org.jah.Configuration_
-
- setRangeAxisExtents(XYPlot, double, double) - Method in class ij.plugin.frame.ChartPlugIn
-
- setRangeAxisRange(double, double) - Method in class ij.plugin.frame.ChartPlugIn
-
- setRangeAxisRange(XYPlot, double, double) - Method in class ij.plugin.frame.ChartPlugIn
-
- setRoi(Roi) - Method in class ij.ImagePlus
-
Assigns the specified ROI to this image and displays it.
- setRoi(Roi, boolean) - Method in class ij.ImagePlus
-
Assigns 'newRoi' to this image and displays it if 'updateDisplay' is true.
- setRoi(int, int, int, int) - Method in class ij.ImagePlus
-
Creates a rectangular selection.
- setRoi(Rectangle) - Method in class ij.ImagePlus
-
Creates a rectangular selection.
- setRoi(Rectangle) - Method in class ij.ImageStack
-
- setRoi(Rectangle) - Method in class ij.process.ImageProcessor
-
Defines a rectangular region of interest and sets the mask
to null if this ROI is not the same size as the previous one.
- setRoi(int, int, int, int) - Method in class ij.process.ImageProcessor
-
Defines a rectangular region of interest and sets the mask to
null if this ROI is not the same size as the previous one.
- setRoi(Roi) - Method in class ij.process.ImageProcessor
-
Defines a non-rectangular region of interest that will consist of a
rectangular ROI and a mask.
- setRoi(Polygon) - Method in class ij.process.ImageProcessor
-
Defines a polygonal region of interest that will consist of a
rectangular ROI and a mask.
- setRoi(Roi) - Method in class ij.wave.Wave
-
Sets an Roi associated with this Wave.
- setRoundRectArcSize(int) - Method in class ij.gui.Roi
-
Obsolete; replaced by setCornerDiameter().
- setSamplingRateHz(double) - Method in class ij.wave.Wave
-
Sets the sampling rate of this wave in Hz
- setScaleFactor(double) - Method in class ij.gui.LayoutComponent
-
- setSelected(Waves) - Method in class ij.plugin.frame.WaveManager
-
- setSelectedFromNames(String[]) - Method in class ij.plugin.frame.RoiManager
-
- setSelectedFromRoiManager() - Method in class ij.plugin.frame.WaveManager
-
- setSelectedFromWaveManager() - Method in class ij.plugin.frame.RoiManager
-
- setSelectedFromWaves(Waves) - Method in class ij.plugin.frame.RoiManager
-
JAH: Fix this implementation to work correctly
- setSelectedIndexes(int[]) - Method in class ij.plugin.frame.RoiManager
-
Temporarily selects multiple ROIs, where 'indexes' is an array of integers,
each greater than or equal to 0 and less than the value returned by getCount().
- setSelectedIndexes(int[]) - Method in class ij.plugin.frame.WaveManager
-
- setServerAddress(String) - Static method in class org.jah.Configuration_
-
- setSize(int) - Method in class ij.ImagePlus
-
- setSize(int, int) - Method in class ij.ImagePlus
-
- setSlice(int) - Static method in class ij.IJ
-
Switches to the specified stack slice, where 1<='slice'<=stack-size.
- setSlice(int) - Method in class ij.ImagePlus
-
Displays the specified stack image, where 1<=n<=stackSize.
- setSliceLabel(String, int) - Method in class ij.ImageStack
-
Sets the label of the specified slice, were 1<=n<=nslices.
- setSliceNumber(int) - Method in class ij.process.ImageProcessor
-
PlugInFilterRunner uses this method to set the slice number.
- setSliceWithoutUpdate(int) - Method in class ij.ImagePlus
-
Displays the specified stack image (1<=n<=stackSize)
without updating the display.
- setSmoothingPercent(double) - Static method in class org.jah.Configuration_
-
- setSnapshotCopyMode(boolean) - Method in class ij.process.ImageProcessor
-
The getPixelsCopy() method returns a reference to the
snapshot buffer if it is not null and 'snapshotCopyMode' is true.
- setSnapshotPixels(Object) - Method in class ij.process.FloatProcessor
-
- setSnapshotPixels(Object) - Method in class ij.process.ImageProcessor
-
Sets a new pixel array for the snapshot (undo) buffer.
- setSnapshotPixels(Object) - Method in class ij.process.ShortProcessor
-
- setSource(Object) - Method in class ij.gui.LayoutComponent
-
- setStack(ImageStack) - Method in class ij.ImagePlus
-
Replaces the image with the specified stack and updates the display.
- setStack(String, ImageStack) - Method in class ij.ImagePlus
-
Replaces the image with the specified stack and updates
the display.
- setStack(ImageStack, int, int, int) - Method in class ij.ImagePlus
-
- setStart(long) - Method in class org.jah.ephys.Epoch
-
- setStart_s(double) - Method in class org.jah.ephys.Epoch
-
- setStoredValue(double) - Method in class ij.wave.WaveMarker
-
- setStroke(BasicStroke) - Method in class ij.gui.Roi
-
Sets the Stroke used to draw this ROI.
- setStrokeColor(Color) - Method in class ij.gui.Roi
-
Sets the color used by this ROI to draw its outline.
- setStrokeWidth(float) - Method in class ij.gui.Roi
-
Sets the width of the line used to draw this ROI.
- setStrokeWidth(double) - Method in class ij.gui.Roi
-
This is a version of setStrokeWidth() that accepts a double argument.
- setT(int) - Method in class ij.ImagePlus
-
Sets the hyperstack frame position (one based).
- setTempCurrentImage(ImagePlus) - Static method in class ij.WindowManager
-
Makes the specified image temporarily the active
image for this thread.
- setTempCurrentImage(Thread, ImagePlus) - Static method in class ij.WindowManager
-
Sets a temporary image for the specified thread.
- setTextPanel(TextPanel) - Static method in class ij.IJ
-
TextWindow calls this method with a null argument when the "Results" window is closed.
- setThreshold(double, double) - Static method in class ij.IJ
-
Sets the lower and upper threshold levels and displays the image
using red to highlight thresholded pixels.
- setThreshold(double, double, String) - Static method in class ij.IJ
-
Sets the lower and upper threshold levels and displays the image using
the specified displayMode ("Red", "Black & White", "Over/Under" or "No Update").
- setThreshold(ImagePlus, double, double) - Static method in class ij.IJ
-
Sets the lower and upper threshold levels of the specified image.
- setThreshold(ImagePlus, double, double, String) - Static method in class ij.IJ
-
Sets the lower and upper threshold levels of the specified image and updates the display using
the specified displayMode ("Red", "Black & White", "Over/Under" or "No Update").
- setThreshold(double, double, int) - Method in class ij.process.FloatProcessor
-
- setThreshold(double, double, int) - Method in class ij.process.ImageProcessor
-
Sets the lower and upper threshold levels.
- setThreshold(double, double, int) - Method in class ij.process.ShortProcessor
-
- setTitle(String) - Method in class ij.gui.LayoutComponent
-
- setTitle(String) - Method in class ij.ImagePlus
-
Sets the image name.
- setTool(int) - Static method in class ij.IJ
-
Switches to the specified tool, where id = Toolbar.RECTANGLE (0),
Toolbar.OVAL (1), etc.
- setTool(String) - Static method in class ij.IJ
-
Switches to the specified tool, where 'name' is "rect", "elliptical",
"brush", etc.
- setToolTipText(String) - Method in class ij.wave.WaveMarker
-
- setTreeColor(TreeDrawerNode, Color) - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- setTreeColors() - Method in class ij.plugin.frame.ClusterFramePlugIn
-
- setType(int) - Method in class ij.ImagePlus
-
- setType(int) - Method in class ij.wave.Wave
-
- setType(String) - Method in class ij.wave.WaveMarker
-
- setType(int) - Method in class org.jah.ephys.Epoch
-
- setTypeByString(String) - Method in class org.jah.ephys.Epoch
-
- setUnderColor(int, int, int) - Static method in class ij.process.ImageProcessor
-
Set the lower Over/Under thresholding color.
- setUnits(String) - Method in class ij.wave.Wave
-
- setup() - Method in class ij.gui.GenericDialog
-
- setupDialog(ImagePlus, int) - Static method in class ij.IJ
-
Displays a "Process all images?" dialog.
- setUseBicubic(boolean) - Static method in class ij.process.ImageProcessor
-
- setValue(double) - Method in class ij.process.FloatProcessor
-
Sets the default fill/draw value.
- setValue(double) - Method in class ij.process.ImageProcessor
-
Sets the default fill/draw value.
- setValue(double) - Method in class ij.process.ShortProcessor
-
Sets the default fill/draw value, where 0<=value<=65535).
- setValues(double[]) - Method in class ij.wave.Wave
-
Sets the contents of this Wave to the values passed as argument.
- setVoxel(int, int, int, double) - Method in class ij.ImageStack
-
- setVoxels(int, int, int, int, int, int, float[]) - Method in class ij.ImageStack
-
Experimental
- setVoxels(int, int, int, int, int, int, float[], int) - Method in class ij.ImageStack
-
Experimental
- setWaveColor(String, Color) - Method in class ij.plugin.frame.ChartPlugIn
-
- setWaveColor(Wave, Color) - Method in class ij.plugin.frame.ChartPlugIn
-
- setWaveStyle(String, String) - Method in class ij.plugin.frame.ChartPlugIn
-
- setWaveStyle(String, String, Object) - Method in class ij.plugin.frame.ChartPlugIn
-
Changes the renderer for the Wave to that of 'style'.
- setWaveStyle(String, Object) - Method in class ij.plugin.frame.ChartPlugIn
-
Changes the renderer for the Wave to that of 'style'.
- setWfdSrcInputDirectory(String) - Static method in class org.jah.Configuration_
-
- setWidth(double) - Method in class ij.wave.WaveMarker
-
Sets the width of the marker in units of seconds.
- setWindow(ImageWindow) - Method in class ij.ImagePlus
-
This method should only be called from an ImageWindow.
- setWindow(Window) - Static method in class ij.WindowManager
-
The specified Window becomes the front window.
- setWindow(Frame) - Static method in class ij.WindowManager
-
The specified frame becomes the front window, the one returnd by getFrontWindow().
- setX(int) - Method in class ij.gui.LayoutComponent
-
- setXStartOffset(int) - Method in class ij.wave.Wave
-
An offset for the first element in the wave.
- setXStartOffsetTime(double) - Method in class ij.wave.Wave
-
An offset for the first element in the wave.
- setXVal(double) - Method in class ij.wave.WaveMarker
-
- setXWave(Wave) - Method in class ij.wave.Wave
-
- setXYPlotStyle(XYPlot, String, int, Object) - Method in class ij.plugin.frame.ChartPlugIn
-
This should be protected.
- setXYPlotStyleOptions(XYPlot, int, Object) - Method in class ij.plugin.frame.ChartPlugIn
-
- setY(int) - Method in class ij.gui.LayoutComponent
-
- setZ(int) - Method in class ij.ImagePlus
-
Sets the hyperstack slice position (one based).
- sharpen() - Method in class ij.process.ImageProcessor
-
Sharpens the image or ROI using a 3x3 convolution kernel.
- shiftKeyDown() - Static method in class ij.IJ
-
Returns true if the shift key is down.
- ShortProcessor - Class in ij.process
-
ShortProcessors contain a 16-bit unsigned image
and methods that operate on that image.
- ShortProcessor(int, int, short[], ColorModel) - Constructor for class ij.process.ShortProcessor
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Creates a new ShortProcessor using the specified pixel array and ColorModel.
- ShortProcessor(int, int) - Constructor for class ij.process.ShortProcessor
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Creates a blank ShortProcessor using the default grayscale LUT that
displays zero as black.
- ShortProcessor(BufferedImage) - Constructor for class ij.process.ShortProcessor
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Creates a ShortProcessor from a TYPE_USHORT_GRAY BufferedImage.
- ShortProcessor(int, int, short[], ColorModel, boolean) - Constructor for class ij.process.ShortProcessor
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- ShortProcessor(int, int, boolean) - Constructor for class ij.process.ShortProcessor
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Obsolete.
- show() - Method in class ij.ImagePlus
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Opens a window to display this image and clears the status bar.
- show(String) - Method in class ij.ImagePlus
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Opens a window to display this image and displays
'statusMessage' in the status bar.
- SHOW_ALL - Static variable in class ij.plugin.frame.RoiManager
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- SHOW_NONE - Static variable in class ij.plugin.frame.RoiManager
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- showAll(int) - Method in class ij.plugin.frame.RoiManager
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- showBottomProgress(double) - Static method in class ij.IJ
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- showDetails() - Method in class ij.plugin.frame.ChartPlugIn
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- showDialog() - Method in class ij.gui.GenericDialog
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Displays this dialog box.
- showDynamicChart(Roi) - Static method in class ij.util.PlotterUtils
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- showHistogram(String, String, String, HistogramDataset) - Static method in class ij.util.PlotterUtils
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- showMarker() - Method in class ij.wave.WaveMarker
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- showMarkers(String) - Method in class ij.plugin.frame.ChartPlugIn
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Shows all WaveMarkers with the given type in the chart.
- showMessage(String) - Static method in class ij.IJ
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Displays a message in a dialog box titled "Message".
- showMessage(String, String) - Static method in class ij.IJ
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Displays a message in a dialog box with the specified title.
- showMessageWithCancel(String, String) - Static method in class ij.IJ
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Displays a message in a dialog box with the specified title.
- showPolarPlot(String, XYDataset) - Static method in class ij.util.PlotterUtils
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- showProgress(double) - Static method in class ij.IJ
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Updates the progress bar, where 0<=progress<=1.0.
- showProgress(int, int) - Static method in class ij.IJ
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Updates the progress bar, where the length of the bar is set to
(currentValue+1)/finalValue of the maximum bar length.
- showProgress(double) - Method in class ij.process.ImageProcessor
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- showStackTrace(Exception) - Static method in class org.jah.JAH_Utils
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Prints the stack trace of the Exception passed as argument to stdout.
- showStackTrace() - Static method in class org.jah.JAH_Utils
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Prints a stack trace to stdout from the current location in the code.
- showStatus() - Method in class ij.gui.Roi
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- showStatus(String) - Static method in class ij.IJ
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Displays a message in the ImageJ status bar.
- showTime(ImagePlus, long, String) - Static method in class ij.IJ
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- showTime(ImagePlus, long, String, int) - Static method in class ij.IJ
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- showTopProgress(double) - Static method in class ij.IJ
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- showWaves(Waves, String) - Static method in class ij.util.PlotterUtils
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- showWaves(Waves, String, boolean) - Static method in class ij.util.PlotterUtils
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- showWaves(Waves, String, boolean, boolean) - Static method in class ij.util.PlotterUtils
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- showWaves(Waves) - Static method in class ij.util.PlotterUtils
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- showWaves(Waves, String, boolean, boolean, Vector) - Static method in class ij.util.PlotterUtils
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- showWaves(Waves, String, boolean, boolean, Vector, double, double) - Static method in class ij.util.PlotterUtils
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- shuffle() - Method in class ij.wave.Waves
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- size() - Method in class org.jah.ephys.Comments
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- slider - Variable in class ij.gui.GenericDialog
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- smooth() - Method in class ij.process.ImageProcessor
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Replaces each pixel with the 3x3 neighborhood mean.
- snapshot() - Method in class ij.process.FloatProcessor
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- snapshot() - Method in class ij.process.ImageProcessor
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Makes a copy of this image's pixel data that can be
later restored using reset() or reset(mask).
- snapshot() - Method in class ij.process.ShortProcessor
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- snapshotHeight - Variable in class ij.process.ImageProcessor
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- snapshotWidth - Variable in class ij.process.ImageProcessor
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- sort() - Method in class ij.wave.Waves
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- sort(boolean) - Method in class ij.wave.Waves
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Crosscorrelates each Wave with the average of all the Waves and returns them sorted by
the highest correlation value at the earliest lag time or at the zero lag if indicated by the argument.
- source - Variable in class ij.process.ImageProcessor
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- spaceBarDown() - Static method in class ij.IJ
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Returns true if the space bar is down.
- split(double) - Method in class ij.wave.Wave
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Splits the Wave instance into two Waves at the time passed as argument (in seconds).
- splitABF(long, String, String, String) - Method in class org.jah.ephys.abf.ABF
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- splitSelectedWaves() - Method in class ij.plugin.frame.WaveManager
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- splitSelectedWaves(double) - Method in class ij.plugin.frame.WaveManager
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- sqr() - Method in class ij.process.FloatProcessor
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- sqr() - Method in class ij.process.ImageProcessor
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Performs a square transform on the image or ROI.
- sqr() - Method in class ij.process.ShortProcessor
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- sqrt() - Method in class ij.process.FloatProcessor
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- sqrt() - Method in class ij.process.ImageProcessor
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Performs a square root transform on the image or ROI.
- sqrt() - Method in class ij.process.ShortProcessor
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- startPaste(ImagePlus) - Method in class ij.gui.Roi
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- startTiming() - Method in class ij.ImagePlus
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Calls System.currentTimeMillis() to save the current
time so it can be retrieved later using getStartTime()
to calculate the elapsed time of an operation.
- statusbar - Variable in class ij.plugin.frame.ChartPlugIn
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- statusLine - Variable in class ij.plugin.frame.ChartPlugIn
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- stdev - Static variable in class ij.wave.Bursts
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- stdev - Static variable in class ij.wave.Wave
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- STIMULUS - Static variable in class ij.wave.WaveMarker
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- stop - Variable in class org.jah.ephys.ElectrophysManager
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- stopRunning() - Method in class org.jah.ephys.ElectrophysManager
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- stringField - Variable in class ij.gui.GenericDialog
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- stripFilename(String) - Static method in class org.jah.JAH_Utils
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This utility function strips a file path all the way to the actual filename in a platform-independent manner.
- stripName(String) - Method in class ij.plugin.frame.ClusterFramePlugIn
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- stroke - Variable in class ij.gui.Roi
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- strokeColor - Variable in class ij.gui.Roi
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- subPixelResolution() - Method in class ij.gui.Roi
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Returns true if this is a slection that supports sub-pixel resolution.
- subtract(double) - Method in class ij.process.ImageProcessor
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Subtracts 'value' from each pixel in the image or ROI.
- subtract(double) - Method in class ij.wave.Wave
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Subtracts each element within this Wave by the value passed as argument and fires a waveChanged event.
- subtractWave(Wave) - Method in class ij.wave.Wave
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Subtracts the contents of the Wave passed as argument, to this Wave instance index-by-index.
- sum - Static variable in class ij.wave.Burst
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- sum(double, double) - Method in class ij.wave.Wave
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Sums all the values within the Wave inclusively between the times passed as argument.
- suppressPluginNotFoundError() - Static method in class ij.IJ
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Temporarily suppress "plugin not found" errors.
- swapPixelArrays() - Method in class ij.process.FloatProcessor
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Swaps the pixel and snapshot (undo) arrays.
- swapPixelArrays() - Method in class ij.process.ImageProcessor
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Swaps the pixel and snapshot (undo) buffers.
- swapPixelArrays() - Method in class ij.process.ShortProcessor
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Swaps the pixel and snapshot (undo) arrays.