Package qupath.lib.color

Class ColorDeconvolutionHelper

java.lang.Object
qupath.lib.color.ColorDeconvolutionHelper
public class ColorDeconvolutionHelper extends Object
Static methods to assist with color deconvolution.
Author:
Pete Bankhead

  • Constructor Summary

    Constructors
    Constructor
    Description
    ColorDeconvolutionHelper()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    convertPixelsToOpticalDensities(float[] px, double maxValue, boolean use8BitLUT)
    For originally-8-bit images, optical densities can usually be computed faster by preallocating a LUT with the 0-255 required values.
    static double[]
    estimateWhiteValues(int[] rgb)
    Estimate white (background) values for a brightfield image.
    static StainVector
    generateMedianStainVectorFromPixels(String name, int[] rgb, double redMax, double greenMax, double blueMax)
    Determine median RGB optical densities for an array of pixels (packed RGB), and combine these into a StainVector with the specified name.
    static float[]
    getBlueOpticalDensities(int[] rgb, double maxValue, float[] px)
    Convert red channel of packed rgb pixel to optical density values, using a specified maximum value.
    static float[]
    getGreenOpticalDensities(int[] rgb, double maxValue, float[] px)
    Convert red channel of packed rgb pixel to optical density values, using a specified maximum value.
    static int
    getMedianRGB(int[] rgb)
    Determine median of RGB values.
    static float[]
    getRedOpticalDensities(int[] rgb, double maxValue, float[] px)
    Convert red channel of packed rgb pixel to optical density values, using a specified maximum value.
    static final double
    makeOD(double val, double max)
    Convert a single pixel value to an optical density as max(0, -log10(val/max).
    static final double
    makeODByLUT(float val, double[] OD_LUT)
    Convert a float pixel to an optical density value using a pre-computed lookup table.
    static final double
    makeODByLUT(int val, double[] OD_LUT)
    Convert an int pixel to an optical density value using a pre-computed lookup table.
    static double[]
    makeODLUT(double maxValue)
    Create an optical density lookup table with 256 entries, normalizing to the specified background value.
    static double[]
    makeODLUT(double maxValue, int nValues)
    Create an optical density lookup table, normalizing to the specified background value.
    static ColorDeconvolutionStains
    refineColorDeconvolutionStains(int[] rgb, ColorDeconvolutionStains stains, double minStain, double percentageClipped)
    Attempt to automatically refine color deconvolution stains based upon pixel values.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • ColorDeconvolutionHelper

      public ColorDeconvolutionHelper()

  • Method Details

    • makeOD

      public static final double makeOD(double val, double max)
      Convert a single pixel value to an optical density as max(0, -log10(val/max). where val is clipped to be >= 1.
      Parameters:
      val -
      max -
      Returns:

    • makeODByLUT

      public static final double makeODByLUT(int val, double[] OD_LUT)
      Convert an int pixel to an optical density value using a pre-computed lookup table. This is likely to be much faster than calling makeOD(double, double).
      Parameters:
      val -
      OD_LUT -
      Returns:
      See Also:

    • makeODByLUT

      public static final double makeODByLUT(float val, double[] OD_LUT)
      Convert a float pixel to an optical density value using a pre-computed lookup table. This is likely to be much faster than calling makeOD(double, double), but involves rounding the float first.
      Parameters:
      val -
      OD_LUT -
      Returns:
      See Also:

    • makeODLUT

      public static double[] makeODLUT(double maxValue)
      Create an optical density lookup table with 256 entries, normalizing to the specified background value.
      Parameters:
      maxValue -
      Returns:
      See Also:

    • makeODLUT

      public static double[] makeODLUT(double maxValue, int nValues)
      Create an optical density lookup table, normalizing to the specified background value.
      Parameters:
      maxValue - background (white value)
      nValues - number of values to include in the lookup table
      Returns:

    • convertPixelsToOpticalDensities

      public static void convertPixelsToOpticalDensities(float[] px, double maxValue, boolean use8BitLUT)
      For originally-8-bit images, optical densities can usually be computed faster by preallocating a LUT with the 0-255 required values. Otherwise, log values need to be calculated for every pixel (which can be relatively slow).
      Parameters:
      px -
      maxValue -
      use8BitLUT -

    • getRedOpticalDensities

      public static float[] getRedOpticalDensities(int[] rgb, double maxValue, float[] px)
      Convert red channel of packed rgb pixel to optical density values, using a specified maximum value.
      Parameters:
      rgb -
      maxValue -
      px - optional array used for output
      Returns:

    • getGreenOpticalDensities

      public static float[] getGreenOpticalDensities(int[] rgb, double maxValue, float[] px)
      Convert red channel of packed rgb pixel to optical density values, using a specified maximum value.
      Parameters:
      rgb -
      maxValue -
      px - optional array used for output
      Returns:

    • getBlueOpticalDensities

      public static float[] getBlueOpticalDensities(int[] rgb, double maxValue, float[] px)
      Convert red channel of packed rgb pixel to optical density values, using a specified maximum value.
      Parameters:
      rgb -
      maxValue -
      px - optional array used for output
      Returns:

    • generateMedianStainVectorFromPixels

      public static StainVector generateMedianStainVectorFromPixels(String name, int[] rgb, double redMax, double greenMax, double blueMax)
      Determine median RGB optical densities for an array of pixels (packed RGB), and combine these into a StainVector with the specified name.
      Parameters:
      name -
      rgb -
      redMax -
      greenMax -
      blueMax -
      Returns:

    • getMedianRGB

      public static int getMedianRGB(int[] rgb)
      Determine median of RGB values. The median of each channel is computed separately.
      Parameters:
      rgb - array of packed RGB values
      Returns:

    • refineColorDeconvolutionStains

      public static ColorDeconvolutionStains refineColorDeconvolutionStains(int[] rgb, ColorDeconvolutionStains stains, double minStain, double percentageClipped)
      Attempt to automatically refine color deconvolution stains based upon pixel values.

      Warning! This is really only for testing - it has not be very extensively validated.

      The method used is based very loosely on that of Macenko et al. (2009), but avoids eigenvalue computations in favor of determining an initial stain inputs. TODO: Improve automatic stain vector refinement.

      Parameters:
      rgb -
      stains -
      minStain - minimum optical density for each RGB channel (default 0.15)
      percentageClipped -
      Returns:

    • estimateWhiteValues

      public static double[] estimateWhiteValues(int[] rgb)
      Estimate white (background) values for a brightfield image.

      The algorithm computes histograms for each RGB channel, and takes the mode of the histogram in the region of the histogram > the mean value for that channel.

      Parameters:
      rgb - an array of packed RGB values
      Returns:
      an array containing estimated [red, green and blue] background values