inra.ijpb.data.image

Class ImageUtils

java.lang.Object

inra.ijpb.data.image.ImageUtils

public class ImageUtils
extends Object

A collection of static utility methods for processing 2D or 3D images.

Author:

dlegland

Method Summary

Modifier and Type	Method and Description
static ij.process.ByteProcessor	createByteProcessor(int[][] data) Creates a new ByteProcessor initialized with the content of the input array.
static ij.process.FloatProcessor	createFloatProcessor(float[][] data) Creates a new FloatProcessor initialized with the content of the input array.
static ij.process.ImageProcessor	createImageProcessor(int width, int height, int bitDepth) Creates a new ImageProcessor from image dimensions and bit depth.
static ij.process.ShortProcessor	createShortProcessor(int[][] data) Creates a new ShortProcessor initialized with the content of the input array.
static void	fillRect(ij.process.ImageProcessor image, int x0, int y0, int w, int h, double value) Fills a rectangle within the image with the specified value.
static void	fillRect3d(ij.ImageStack image, int x0, int y0, int z0, int w, int h, int d, double value) Fills a 3D rectangle within the image with the specified value.
static double	findMaxValue(ij.ImagePlus imagePlus) Computes maximum value within the input image.
static double	findMaxValue(ij.process.ImageProcessor image) Computes maximum value within the input 2D image.
static double	findMaxValue(ij.ImageStack image) Computes maximum value in the input 3D image.
static boolean	isColorImage(ij.ImagePlus imagePlus) Checks if the specified image is a color image.
static boolean	isSameSize(ij.ImagePlus image1, ij.ImagePlus image2) Checks if the two input images have the same dimensionality and the same size in each direction.
static boolean	isSameSize(ij.process.ImageProcessor image1, ij.process.ImageProcessor image2) Checks if the two input images have the same size in each direction.
static boolean	isSameSize(ij.ImageStack image1, ij.ImageStack image2) Checks if the two input 3D images have the same size in each direction.
static boolean	isSameType(ij.ImagePlus image1, ij.ImagePlus image2) Checks if the two input images have the same data type.
static boolean	isSameType(ij.process.ImageProcessor image1, ij.process.ImageProcessor image2) Checks if the two input images have the same data type.
static boolean	isSameType(ij.ImageStack image1, ij.ImageStack image2) Checks if the two input 3D images have the same data type.
static void	print(ij.process.ImageProcessor image) Prints the content of the given ImageProcessor on the console.
static void	print(ij.ImageStack image) Prints the content of the given 3D image on the console.
static void	replaceValue(ij.ImagePlus image, double initialValue, double finalValue) Replaces the elements of an image with a given value by a new value.
static void	replaceValue(ij.process.ImageProcessor image, double initialValue, double finalValue) Replaces the elements of a 2D image with a given value by a new value.
static void	replaceValue(ij.ImageStack image, double initialValue, double finalValue) Replaces the elements of a 3D image with a given value by a new value.

Methods inherited from class java.lang.Object

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

Method Detail

createImageProcessor

public static final ij.process.ImageProcessor createImageProcessor(int width,
                                                                   int height,
                                                                   int bitDepth)

Creates a new ImageProcessor from image dimensions and bit depth.

Parameters:

width - the width of the new image

height - the height of the new image

bitDepth - the bit-depth of the new image (must be one of 8, 16, 24, or 32).

Returns:

the new image

createByteProcessor

public static final ij.process.ByteProcessor createByteProcessor(int[][] data)

Creates a new ByteProcessor initialized with the content of the input array.

    ImageProcessor image = ImageUtils.createByteProcessor(new int[][] {
        { 0,  0,  0,  0,  0},  
        { 0, 20, 20, 20,  0},  
        { 0, 20, 50, 20,  0},  
        { 0, 20, 20, 20,  0},  
        { 0,  0,  0,  0,  0},  
    });
 
 

Parameters:

data - the array containing image data, as integer values

Returns:

a new ByteProcessor initialized with data array.

createShortProcessor

public static final ij.process.ShortProcessor createShortProcessor(int[][] data)

Creates a new ShortProcessor initialized with the content of the input array.

    ImageProcessor image = ImageUtils.createShortProcessor(new int[][] {
        { 0,  0,  0,  0,  0},  
        { 0, 20, 20, 20,  0},  
        { 0, 20, 50, 20,  0},  
        { 0, 20, 20, 20,  0},  
        { 0,  0,  0,  0,  0},  
    });
 
 

Parameters:

data - the array containing image data, as integer values

Returns:

a new ShortProcessor initialized with data array.

createFloatProcessor

public static final ij.process.FloatProcessor createFloatProcessor(float[][] data)

Creates a new FloatProcessor initialized with the content of the input array.

    ImageProcessor image = ImageUtils.createFloatProcessor(new float[][] {
        { 0,  0,  0,  0,  0},  
        { 0, 20, 20, 20,  0},  
        { 0, 20, 50, 20,  0},  
        { 0, 20, 20, 20,  0},  
        { 0,  0,  0,  0,  0},  
    });
 
 

Parameters:

data - the array containing image data, as float values

Returns:

a new FloatProcessor initialized with data array.

isColorImage

public static final boolean isColorImage(ij.ImagePlus imagePlus)

Checks if the specified image is a color image.

Parameters:

imagePlus - the instance of ImagePlus to check

Returns:

true if the type is COLOR_256 or COLOR_RGB.

isSameSize

public static final boolean isSameSize(ij.ImagePlus image1,
                                       ij.ImagePlus image2)

Checks if the two input images have the same dimensionality and the same size in each direction.

Parameters:

image1 - the first image

image2 - the second image

Returns:

true if both images have same dimensionality and same size.

isSameSize

public static final boolean isSameSize(ij.process.ImageProcessor image1,
                                       ij.process.ImageProcessor image2)

Checks if the two input images have the same size in each direction.

Parameters:

image1 - the first image

image2 - the second image

Returns:

true if both images have same width and height, and false otherwise.

isSameSize

public static final boolean isSameSize(ij.ImageStack image1,
                                       ij.ImageStack image2)

Checks if the two input 3D images have the same size in each direction.

Parameters:

image1 - the first image

image2 - the second image

Returns:

true if both images have same width, height and number of slices, and false otherwise.

isSameType

public static final boolean isSameType(ij.ImagePlus image1,
                                       ij.ImagePlus image2)

Checks if the two input images have the same data type.

Parameters:

image1 - the first image

image2 - the second image

Returns:

true if both images have the same data type, given by the bit depth.

isSameType

public static final boolean isSameType(ij.process.ImageProcessor image1,
                                       ij.process.ImageProcessor image2)

Checks if the two input images have the same data type.

Parameters:

image1 - the first image

image2 - the second image

Returns:

true if both images have the same data type, given by the bit depth.

isSameType

public static final boolean isSameType(ij.ImageStack image1,
                                       ij.ImageStack image2)

Checks if the two input 3D images have the same data type.

Parameters:

image1 - the first image

image2 - the second image

Returns:

true if both images have the same data type, given by the bit depth.

fillRect

public static final void fillRect(ij.process.ImageProcessor image,
                                  int x0,
                                  int y0,
                                  int w,
                                  int h,
                                  double value)

Fills a rectangle within the image with the specified value. This will replace by the specified value all the pixels within image that are located:

• between x0 (inclusive) and x0+width-1 (inclusive)
• between y0 (inclusive) and y0+height-1 (inclusive)

Parameters:

image - the image to process.

x0 - the x-coordinate of the left corner of the rectangle to fill

y0 - the y-coordinate of the top corner of the rectangle to fill

w - the width of the rectangle to fill, in pixels

h - the height of the rectangle to fill, in pixels

value - the value to fill the rectangle with

fillRect3d

public static final void fillRect3d(ij.ImageStack image,
                                    int x0,
                                    int y0,
                                    int z0,
                                    int w,
                                    int h,
                                    int d,
                                    double value)

Fills a 3D rectangle within the image with the specified value. This will replace by the specified value all the pixels within image that are located:

• between x0 (inclusive) and x0+width-1 (inclusive)
• between y0 (inclusive) and y0+height-1 (inclusive)
• between z0 (inclusive) and z0+depth-1 (inclusive)

Parameters:

image - the image to process.

x0 - the x-coordinate of the left corner of the rectangle to fill

y0 - the y-coordinate of the top corner of the rectangle to fill

z0 - the z-coordinate of the front corner of the rectangle to fill

w - the width of the rectangle to fill, in voxels

h - the height of the rectangle to fill, in voxels

d - the depth of the rectangle to fill, in voxels

value - the value to fill the 3D rectangle with

findMaxValue

public static final double findMaxValue(ij.ImagePlus imagePlus)

Computes maximum value within the input image.

Parameters:

imagePlus - the image the analyze

Returns:

the maximum value within the image, as a double.

findMaxValue

public static final double findMaxValue(ij.process.ImageProcessor image)

Computes maximum value within the input 2D image. This method may be used to compute display range of result ImagePlus.

Parameters:

image - the image the analyze

Returns:

the maximum value within the image, as a double.

findMaxValue

public static final double findMaxValue(ij.ImageStack image)

Computes maximum value in the input 3D image. This method may be used to compute display range of result ImagePlus.

Parameters:

image - the 3D image the analyze

Returns:

the maximum value within the image, as a double.

replaceValue

public static final void replaceValue(ij.ImagePlus image,
                                      double initialValue,
                                      double finalValue)

Replaces the elements of an image with a given value by a new value.

Parameters:

image - the image to process

initialValue - the value of the elements to replace

finalValue - the new value of the elements

replaceValue

public static final void replaceValue(ij.process.ImageProcessor image,
                                      double initialValue,
                                      double finalValue)

Replaces the elements of a 2D image with a given value by a new value.

Parameters:

image - the 3D image to process

initialValue - the value of the elements to replace

finalValue - the new value of the elements

replaceValue

public static final void replaceValue(ij.ImageStack image,
                                      double initialValue,
                                      double finalValue)

Replaces the elements of a 3D image with a given value by a new value.

Parameters:

image - the 3D image to process

initialValue - the value of the elements to replace

finalValue - the new value of the elements

print

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

Prints the content of the given ImageProcessor on the console. This can be used for debugging (small) images.

Parameters:

image - the image to display on the console

print

public static final void print(ij.ImageStack image)

Prints the content of the given 3D image on the console. This can be used for debugging (small) images.

Parameters:

image - the 3D image to display on the console