Package inra.ijpb.data.image

Class Images3D

java.lang.Object
inra.ijpb.data.image.Images3D
public class Images3D
extends java.lang.Object
A collection of static methods for working on 3D images.
Author:
David Legland

  • Method Summary

    Modifier and Type Method 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

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

  • Method Details

    • 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