org.incenp.imagej

Class Helper

java.lang.Object

org.incenp.imagej.Helper

public class Helper
extends Object

A class of static helper methods.

Constructor Summary

Constructors

Constructor and Description
Helper()

Method Summary

Modifier and Type	Method and Description
static void	augmentHyperstack(ij.ImagePlus image, int channels) Augments a hyperstack with empty channel(s).
static int	countBlackPixels(ij.process.ImageProcessor processor) Counts all black pixels in a given image.
static int	countPixels(ij.process.ImageProcessor processor) Counts all non-black pixels in a given image.
static int	countPixels(ij.process.ImageProcessor processor, int threshold) Counts all pixels above the specified threshold.
static int	countWhitePixels(ij.process.ImageProcessor processor) Counts all white pixels in a given image.
static ij.ImagePlus	createAugmentedHyperstack(ij.ImagePlus image, int channels, boolean destroy) Creates a copy of a given hyperstack with added (empty) channel(s).
static double[]	extractVolumes(ij.ImagePlus image) Extracts the volumes occupied by white pixels in a image.
static double[]	extractVolumes(ij.ImagePlus image, boolean allChannels) Extracts the volumes occupied by white pixels in a image.
static double[]	extractVolumes(ij.ImagePlus image, int[] channels) Extracts the volumes occupied by white pixels in a image.
static ij.measure.ResultsTable	getResultsTable(String title) Gets or creates a ResultsTable.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Helper

public Helper()

Method Detail

countBlackPixels

public static int countBlackPixels(ij.process.ImageProcessor processor)

Counts all black pixels in a given image.

Parameters:

processor - the image to count black pixels from

Returns:

the total count of black pixels

countWhitePixels

public static int countWhitePixels(ij.process.ImageProcessor processor)

Counts all white pixels in a given image.

Parameters:

processor - the image to count white pixels from

Returns:

the total count of white pixels

countPixels

public static int countPixels(ij.process.ImageProcessor processor)

Counts all non-black pixels in a given image.

Parameters:

processor - the image to count pixels from

Returns:

the total count of non-black pixels

countPixels

public static int countPixels(ij.process.ImageProcessor processor,
                              int threshold)

Counts all pixels above the specified threshold. This is a convenience method around the ImageStatistics.getStatistics(ImageProcessor, int, Calibration) method.

Parameters:

processor - the image to count pixels from

threshold - only pixels above this value will be counted

Returns:

the total count of pixels above the threshold

extractVolumes

public static double[] extractVolumes(ij.ImagePlus image,
                                      int[] channels)

Extracts the volumes occupied by white pixels in a image. Given a hyperstack, this method counts all the white pixels in the specified channels and multiply the counts by the frame thickness (as found in the hyperstack's metadata).

Parameters:

image - the hyperstack to extract volumes from

channels - a list of channels to extract volumes from. Channel indexes are 1-based.

Returns:

an array containing the extracted volumes. This array is as big as the channels parameter.

extractVolumes

public static double[] extractVolumes(ij.ImagePlus image,
                                      boolean allChannels)

Extracts the volumes occupied by white pixels in a image. This method is similar to extractVolumes(ImagePlus, int[]) but takes a single boolean value instead of a list of channels, indicating whether to process all channels in the image or only the current one.

Parameters:

image - the hyperstack to extract volumes from

allChannels - if true, return volumes for all channels; otherwise return the volume for the current channel only

Returns:

an array containing the extracted volumes

extractVolumes

public static double[] extractVolumes(ij.ImagePlus image)

Extracts the volumes occupied by white pixels in a image. This method is similar to extractVolumes(ImagePlus, int[]) but extracts the volumes from all the channels in the source image.

Parameters:

image - the hyperstack to extract volumes from

Returns:

an array containing the extracted volumes

getResultsTable

public static ij.measure.ResultsTable getResultsTable(String title)

Gets or creates a ResultsTable. If a ResultsTable window with the specified title already exists, this method will return the underlying table; otherwise it will create a new table.

Parameters:

title - the title of the results window to look for

Returns:

the ResultsTable

createAugmentedHyperstack

public static ij.ImagePlus createAugmentedHyperstack(ij.ImagePlus image,
                                                     int channels,
                                                     boolean destroy)

Creates a copy of a given hyperstack with added (empty) channel(s).

Parameters:

image - The source hyperstack to copy.

channels - The number of channels to add.

destroy - If true, the source hyperstack is closed once the copy is over.

Returns:

A copy of the original hyperstack, with the added channel(s).

augmentHyperstack

public static void augmentHyperstack(ij.ImagePlus image,
                                     int channels)

Augments a hyperstack with empty channel(s).

Parameters:

image - the hyperstack to modify

channels - the number of empty channels to add