inra.ijpb.data.image

Class Images3D

java.lang.Object

inra.ijpb.data.image.Images3D

public class Images3D
extends Object

A collection of static methods for working on 3D images.

Author:

David Legland

Method Summary

Modifier and Type	Method and Description
static ij.ImageStack	adjustDynamic(ij.ImageStack image, double vmin, double vmax) Returns a new instance of ImageStack containing ByteProcessors such that display range is specified by vmin and vmax.
static ij.ImageStack	complement(ij.ImageStack image, double base) Computes the complements of the input image using the specified value as reference, and returns the complemented image.
static Image3D	createWrapper(ij.ImageStack stack) Converts the input ImageStack into an instance of Image3D, depending on the data type stored in the stack.
static void	fill(ij.ImageStack image, double value) Fills the input 3D image with the given value.
static double[]	findMinAndMax(ij.ImagePlus image) Find minimum and maximum value of input image
static double[]	findMinAndMax(ij.ImageStack image) Find minimum and maximum value of input image
static byte[][]	getByteArrays(ij.ImageStack image) Extracts the byte arrays corresponding to the slices of a stack containing instances of ByteProcessor.
static float[][]	getFloatArrays(ij.ImageStack image) Extracts the float arrays corresponding to the slices of a stack containing instances of FloatProcessor.
static short[][]	getShortArrays(ij.ImageStack image) Extracts the short arrays corresponding to the slices of a stack containing instances of ShortProcessor.
static void	invert(ij.ImageStack image) Inverts the values of a 3D image
static boolean	isSameSize(ij.ImageStack image1, ij.ImageStack image2) Deprecated. replaced by ImageUtils.isSameSize(...)
static boolean	isSameType(ij.ImageStack image1, ij.ImageStack image2) Deprecated. replaced by ImageUtils.isSameType(...)
static void	optimizeDisplayRange(ij.ImagePlus image) Optimize display range of 2d/3d image based on its minimum and maximum values
static void	print(ij.ImageStack image) Deprecated. replaced by ImageUtils.print(ImageStack)
static void	replaceValue(ij.ImagePlus image, double initialValue, double finalValue) Deprecated. replaced by ImageUtils.replaceValue(ImagePlus, double, double)

Methods inherited from class java.lang.Object

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

Method Detail

createWrapper

public static final Image3D createWrapper(ij.ImageStack stack)

Converts the input ImageStack into an instance of Image3D, depending on the data type stored in the stack.

Parameters:

stack - the input ImageStack to convert

Returns:

a new instance of Image3D that can be used to access or modify values in original stack

isSameSize

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

Deprecated. replaced by ImageUtils.isSameSize(...)

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

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

Deprecated. replaced by ImageUtils.isSameType(...)

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.

findMinAndMax

public static final double[] findMinAndMax(ij.ImagePlus image)

Find minimum and maximum value of input image

Parameters:

image - input 2d/3d image

Returns:

array of 2 extreme values

findMinAndMax

public static final double[] findMinAndMax(ij.ImageStack image)

Find minimum and maximum value of input image

Parameters:

image - input 2d/3d image

Returns:

array of 2 extreme values

optimizeDisplayRange

public static final void optimizeDisplayRange(ij.ImagePlus image)

Optimize display range of 2d/3d image based on its minimum and maximum values

Parameters:

image - input image

adjustDynamic

public static final ij.ImageStack adjustDynamic(ij.ImageStack image,
                                                double vmin,
                                                double vmax)

Returns a new instance of ImageStack containing ByteProcessors such that display range is specified by vmin and vmax.

Parameters:

image - input image, that can be 8, 16 or 32 bits

vmin - the value that will correspond to 0 in new image

vmax - the value that will correspond to 255 in new image

Returns:

a new ImageStack of byte processors with adjusted dynamic

replaceValue

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

Deprecated. replaced by ImageUtils.replaceValue(ImagePlus, double, double)

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

Parameters:

image - the image to process

initialValue - the value of the elements to replace

finalValue - the new value of the elements

fill

public static final void fill(ij.ImageStack image,
                              double value)

Fills the input 3D image with the given value.

Parameters:

image - the 3D image to process

value - the value used to fill input image

print

public static final void print(ij.ImageStack image)

Deprecated. replaced by ImageUtils.print(ImageStack)

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

complement

public static final ij.ImageStack complement(ij.ImageStack image,
                                             double base)

Computes the complements of the input image using the specified value as reference, and returns the complemented image.

Parameters:

image - the image to complement

base - the reference value for computing complement (ususally 255)

Returns:

the complemented image, with values equal to base value minus values from original image.

invert

public static final void invert(ij.ImageStack image)

Inverts the values of a 3D image

Parameters:

image - input image

getByteArrays

public static final byte[][] getByteArrays(ij.ImageStack image)

Extracts the byte arrays corresponding to the slices of a stack containing instances of ByteProcessor.

Parameters:

image - a 3D image that must contain byte values

Returns:

the array of byte arrays corresponding to each slice

getShortArrays

public static final short[][] getShortArrays(ij.ImageStack image)

Extracts the short arrays corresponding to the slices of a stack containing instances of ShortProcessor.

Parameters:

image - a 3D image that must contain short values

Returns:

the array of short arrays corresponding to each slice

getFloatArrays

public static final float[][] getFloatArrays(ij.ImageStack image)

Extracts the float arrays corresponding to the slices of a stack containing instances of FloatProcessor.

Parameters:

image - a 3D image that must contain float values

Returns:

the array of float arrays corresponding to each slice