inra.ijpb.data.image

Class ColorImages

java.lang.Object

inra.ijpb.data.image.ColorImages

public class ColorImages
extends Object

A set of static methods for working with color images.

Author:

David Legland

Method Summary

Modifier and Type	Method and Description
static ij.process.ColorProcessor	binaryOverlay(ij.process.ByteProcessor refImage, ij.process.ImageProcessor binaryMask, Color overlayColor, double overlayOpacity) Applies an overlay of a binary image mask onto a grayscale image, using the specified color and opacity.
static ij.ImagePlus	binaryOverlay(ij.ImagePlus imagePlus, ij.ImagePlus maskPlus, Color color) Applies an overlay of a binary image mask onto a grayscale or color image, using the specified color.
static ij.ImagePlus	binaryOverlay(ij.ImagePlus refImage, ij.ImagePlus binaryMask, Color overlayColor, double overlayOpacity) Applies an overlay of a binary image mask onto a 2D or 3D grayscale image, using the specified color and opacity.
static ij.process.ImageProcessor	binaryOverlay(ij.process.ImageProcessor refImage, ij.process.ImageProcessor mask, Color color) Applies an overlay of a binary image mask onto a grayscale or color image, using the specified color.
static ij.ImageStack	binaryOverlay(ij.ImageStack refImage, ij.ImageStack mask, Color color) Applies an overlay of a binary image mask onto a grayscale or color image, using the specified color.
static ij.ImageStack	binaryOverlay(ij.ImageStack refImage, ij.ImageStack binaryMask, Color overlayColor, double overlayOpacity) Computes the overlay of a binary image over a grayscale image, using an opacity for the binary layer.
static ij.ImagePlus	labelMapOverlay(ij.ImagePlus refImage, ij.ImagePlus labelMap, double overlayOpacity) Applies an overlay of a label map onto a 2D/3D grayscale image, using the specified opacity.
static ij.process.ImageProcessor	labelMapOverlay(ij.process.ImageProcessor refImage, ij.process.ImageProcessor labelMap, double overlayOpacity) Applies an overlay of a label map onto a grayscale image, using the specified opacity.
static ij.ImageStack	labelMapOverlay(ij.ImageStack refImage, ij.ImageStack labelMap, double overlayOpacity) Applies an overlay of a label map onto a 3D grayscale image, using the specified opacity.
static HashMap<String,ij.process.ByteProcessor>	mapChannels(ij.process.ImageProcessor image) Splits the channels of the color image and returns the new ByteImages into a Map, using channel names as key.
static HashMap<String,ij.ImageStack>	mapChannels(ij.ImageStack image) Splits the channels of the 3D color image into three new instances of ImageStack containing ByteProcessors.
static ij.process.ColorProcessor	mergeChannels(Collection<ij.process.ImageProcessor> channels) Creates a new ColorProcessor from a collection of three channels.
static ij.process.ColorProcessor	mergeChannels(ij.process.ImageProcessor red, ij.process.ImageProcessor green, ij.process.ImageProcessor blue) Creates a new ColorProcessor from the red, green and blue channels.
static ij.ImageStack	mergeChannels(ij.ImageStack red, ij.ImageStack green, ij.ImageStack blue) Creates a new color ImageStack from the red, green and blue ImageStack instances.
static void	print(ij.process.ColorProcessor image) Prints the content of the input color image on the console.
static Collection<ij.process.ByteProcessor>	splitChannels(ij.process.ImageProcessor image) Splits the channels of the color image into three new instances of ByteProcessor.
static Collection<ij.ImageStack>	splitChannels(ij.ImageStack image) Splits the channels of the color image into three new instances of ByteProcessor.

Methods inherited from class java.lang.Object

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

Method Detail

print

public static final void print(ij.process.ColorProcessor image)

Prints the content of the input color image on the console. This can be used for debugging (small) images.

Parameters:

image - the color image to display on the console

splitChannels

public static final Collection<ij.process.ByteProcessor> splitChannels(ij.process.ImageProcessor image)

Splits the channels of the color image into three new instances of ByteProcessor.

Parameters:

image - the original image, assumed to be a ColorProcessor

Returns:

a collection containing the red, green and blue channels

splitChannels

public static final Collection<ij.ImageStack> splitChannels(ij.ImageStack image)

Splits the channels of the color image into three new instances of ByteProcessor.

Parameters:

image - the original image, assumed to be a ColorProcessor

Returns:

a collection containing the red, green and blue channels

mapChannels

public static final HashMap<String,ij.process.ByteProcessor> mapChannels(ij.process.ImageProcessor image)

Splits the channels of the color image and returns the new ByteImages into a Map, using channel names as key. Example:

 ColorProcessor colorImage = ...
 HashMap<String, ByteProcessor> channels = mapChannels(colorImage);
 ByteProcessor blue = channels.get("blue");
 

Parameters:

image - the original image, assumed to be a ColorProcessor

Returns:

a hashmap indexing the three channels by their names

mapChannels

public static final HashMap<String,ij.ImageStack> mapChannels(ij.ImageStack image)

Splits the channels of the 3D color image into three new instances of ImageStack containing ByteProcessors.

Parameters:

image - the original image, assumed to be a ColorProcessor

Returns:

a collection containing the red, green and blue channels

mergeChannels

public static final ij.process.ColorProcessor mergeChannels(Collection<ij.process.ImageProcessor> channels)

Creates a new ColorProcessor from a collection of three channels.

Parameters:

channels - a collection containing the red, green and blue channels

Returns:

the color image corresponding to the concatenation of the three channels

Throws:

IllegalArgumentException - if the collection contains less than three channels

mergeChannels

public static final ij.process.ColorProcessor mergeChannels(ij.process.ImageProcessor red,
                                                            ij.process.ImageProcessor green,
                                                            ij.process.ImageProcessor blue)

Creates a new ColorProcessor from the red, green and blue channels. Each channel must be an instance of ByteProcessor.

Parameters:

red - the image for the red channel (must be a ByteProcessor)

green - the image for the green channel (must be a ByteProcessor)

blue - the image for the blue channel (must be a ByteProcessor)

Returns:

the color image corresponding to the concatenation of the three channels

Throws:

IllegalArgumentException - if one of the channel is not an instance of ByteProcessor

mergeChannels

public static final ij.ImageStack mergeChannels(ij.ImageStack red,
                                                ij.ImageStack green,
                                                ij.ImageStack blue)

Creates a new color ImageStack from the red, green and blue ImageStack instances. Each channel must contains instances of ByteProcessor.

Parameters:

red - the image for the red channel (must contain ByteProcessor instances)

green - the image for the green channel (must contain ByteProcessor instances)

blue - the image for the blue channel (must contain ByteProcessor instances)

Returns:

the color image corresponding to the concatenation of the three channels

Throws:

IllegalArgumentException - if one of the ImageStack does not contain instances of ByteProcessor

binaryOverlay

public static final ij.ImagePlus binaryOverlay(ij.ImagePlus imagePlus,
                                               ij.ImagePlus maskPlus,
                                               Color color)

Applies an overlay of a binary image mask onto a grayscale or color image, using the specified color. Both images must have the same size.

Parameters:

imagePlus - the original 2D or 3D image used as background

maskPlus - the binary 2D or 3D mask image

color - the color used to display overlay

Returns:

a new ImagePlus instance containing a 2D or 3D color image

binaryOverlay

public static final ij.process.ImageProcessor binaryOverlay(ij.process.ImageProcessor refImage,
                                                            ij.process.ImageProcessor mask,
                                                            Color color)

Applies an overlay of a binary image mask onto a grayscale or color image, using the specified color. Both images must have the same size.

Parameters:

refImage - the original image used as background

mask - the binary mask image

color - the color used to display overlay

Returns:

a new ImageProcessor instance containing a 2D color image

binaryOverlay

public static final ij.ImageStack binaryOverlay(ij.ImageStack refImage,
                                                ij.ImageStack mask,
                                                Color color)

Applies an overlay of a binary image mask onto a grayscale or color image, using the specified color. Both images must have the same size.

Parameters:

refImage - the original 3D image used as background

mask - the binary 3D mask image

color - the color used to display overlay

Returns:

a new ImageStack containing a 3D color image

binaryOverlay

public static final ij.ImagePlus binaryOverlay(ij.ImagePlus refImage,
                                               ij.ImagePlus binaryMask,
                                               Color overlayColor,
                                               double overlayOpacity)

Applies an overlay of a binary image mask onto a 2D or 3D grayscale image, using the specified color and opacity. Both images must have the same size.

Parameters:

refImage - the original 2D or 3D image used as background

binaryMask - the binary mask image

overlayColor - the color used to display overlay

overlayOpacity - the overlay opacity, between 0 and 1.

Returns:

a new ImageProcessor instance containing a 2D color image

binaryOverlay

public static final ij.process.ColorProcessor binaryOverlay(ij.process.ByteProcessor refImage,
                                                            ij.process.ImageProcessor binaryMask,
                                                            Color overlayColor,
                                                            double overlayOpacity)

Applies an overlay of a binary image mask onto a grayscale image, using the specified color and opacity. Both images must have the same size.

Parameters:

refImage - the original 2D image used as background

binaryMask - the binary mask image

overlayColor - the color used to display overlay

overlayOpacity - the overlay opacity, between 0 and 1.

Returns:

a new ImageProcessor instance containing a 2D color image

binaryOverlay

public static final ij.ImageStack binaryOverlay(ij.ImageStack refImage,
                                                ij.ImageStack binaryMask,
                                                Color overlayColor,
                                                double overlayOpacity)

Computes the overlay of a binary image over a grayscale image, using an opacity for the binary layer. The result is returned as a Color Stack.

Parameters:

refImage - the grayscale image used as reference.

binaryMask - the binary mask, with non zero values where a overlay must occur

overlayColor - the color used for painting overlay

overlayOpacity - the opacity used for painting overlay, between 0 (totally transparent) and 1 (totally opaque)

Returns:

the result of overlay, as a Color stack

labelMapOverlay

public static final ij.ImagePlus labelMapOverlay(ij.ImagePlus refImage,
                                                 ij.ImagePlus labelMap,
                                                 double overlayOpacity)

Applies an overlay of a label map onto a 2D/3D grayscale image, using the specified opacity. Both images must have the same size.

Parameters:

refImage - the original 2D or 3D image used as background

labelMap - the label map used as overlay

overlayOpacity - the overlay opacity, between 0 and 1.

Returns:

a new ImageProcessor instance containing a 2D color image

labelMapOverlay

public static final ij.process.ImageProcessor labelMapOverlay(ij.process.ImageProcessor refImage,
                                                              ij.process.ImageProcessor labelMap,
                                                              double overlayOpacity)

Applies an overlay of a label map onto a grayscale image, using the specified opacity. Both images must have the same size.

Parameters:

refImage - the original 2D image used as background

labelMap - the label map used as overlay

overlayOpacity - the overlay opacity, between 0 and 1.

Returns:

a new ImageProcessor instance containing a 2D color image

labelMapOverlay

public static final ij.ImageStack labelMapOverlay(ij.ImageStack refImage,
                                                  ij.ImageStack labelMap,
                                                  double overlayOpacity)

Applies an overlay of a label map onto a 3D grayscale image, using the specified opacity. Both images must have the same size.

Parameters:

refImage - the original 3D image used as background

labelMap - the label map used as overlay

overlayOpacity - the overlay opacity, between 0 and 1.

Returns:

a new ImageStack instance containing a 3D color image