Package qupath.lib.display

Class DirectServerChannelInfo

java.lang.Object
qupath.lib.display.DirectServerChannelInfo
All Implemented Interfaces:
ChannelDisplayInfo, ChannelDisplayInfo.ModifiableChannelDisplayInfo, SingleChannelDisplayInfo
public class DirectServerChannelInfo extends Object
ChannelInfo intended for use with a single or multichannel image (possibly fluorescence) where the pixel's value is used to scale a single color according to a specified display range according to the following rules:
  • If the pixel's value is >= maxDisplay, the pure color is used.
  • If the pixel's value is <= minDisplay, the black is used.
  • Otherwise, a scaled version of the color is used
The end result is like having a lookup table (LUT) that stretches from black to the 'pure' color specified, but without actually generating the LUT.

  • Field Details

    • df

      protected static final DecimalFormat df

    • CM_GRAYSCALE

      protected static final IndexColorModel CM_GRAYSCALE

    • CM_GRAYSCALE_INVERTED

      protected static final IndexColorModel CM_GRAYSCALE_INVERTED

    • minAllowed

      protected float minAllowed

    • maxAllowed

      protected float maxAllowed

    • minDisplay

      protected float minDisplay

    • maxDisplay

      protected float maxDisplay

    • clipToAllowed

      protected boolean clipToAllowed

  • Constructor Details

    • DirectServerChannelInfo

      public DirectServerChannelInfo(ImageData<BufferedImage> imageData, int channel)
      Constructor.
      Parameters:
      imageData - the image
      channel - the channel number (0-based index)

  • Method Details

    • getChannel

      public int getChannel()
      Get the channel number.
      Returns:

    • getName

      public String getName()
      Description copied from interface: ChannelDisplayInfo
      Get the channel name. This may also be returned by the toString() method.
      Returns:

    • getOriginalChannelName

      public String getOriginalChannelName()
      Get the original channel name, extracted for the current ImageData if available. This differs from getName() in that it does not append the channel number, or return a default name if no ImageData is present.
      Returns:
      the channel name, or null if no image is available

    • getColorModel

      protected ColorModel getColorModel(ChannelDisplayMode mode)
      Get a ColorModel to use with a specified ChannelDisplayMode when converting a value to RGB.
      Parameters:
      mode -
      Returns:

    • setLUTColor

      public void setLUTColor(int r, int g, int b)
      Set the 'maximum' color, which defines the lookup table to use.
      Parameters:
      r - red component (0-255)
      g - green component (0-255)
      b - blue component (0-255)

    • getValue

      public float getValue(BufferedImage img, int x, int y)
      Description copied from interface: SingleChannelDisplayInfo
      Extract the value for a single pixel of an image.
      Parameters:
      img - the image
      x - x-coordinate of the pixel
      y - y-coordinate of the pixel
      Returns:
      the value of the pixel

    • getValues

      public float[] getValues(BufferedImage img, int x, int y, int w, int h, float[] array)
      Description copied from interface: SingleChannelDisplayInfo
      Extract values for a square of pixels from an image.
      Parameters:
      img - the image
      x - x-coordinate of the top left corner of the region to extract
      y - y-coordinate of the top left corner of the region to extract
      w - width of the region to extract
      h - height of the region to extract
      array - optional array that may be used to store the output values
      Returns:
      array of values

    • doesSomething

      public boolean doesSomething()
      Description copied from interface: ChannelDisplayInfo
      Returns true if this does something - anything - and false otherwise. For example, this will return false if we have an RGB image with no transformations of any kind applied (e.g. brightness/contrast)
      Returns:

    • isAdditive

      public boolean isAdditive()
      Description copied from interface: ChannelDisplayInfo
      Returns true if this channel can be used additively to create a composite image display; returns false if this channel wants all the color information to itself, so can't be displayed with others.
      Returns:

    • getColor

      public Integer getColor()
      Description copied from interface: ChannelDisplayInfo
      Predominate color used when this ChannelDisplayInfo uses a Color LUT (e.g. Color.RED for a red channel). Returns null if there is no appropriate color choice, or the image is RGB.
      Returns:

    • isMutable

      public boolean isMutable()
      Description copied from interface: SingleChannelDisplayInfo
      Check if SingleChannelDisplayInfo.getValue(BufferedImage, int, int) returns fixed values, or if they are dependent on other properties of the ImageData.

      For example, a transform based on color deconvolution should be flagged as mutable because stain vectors change, while a simple channel separation is not considered mutable (since the pixel values for the underlying image remain constant in QuPath).

      Returns:

    • getRGB

      public int getRGB(float value, ChannelDisplayMode mode)
      Get a suitable RGB value for displaying a pixel with the specified value
      Parameters:
      value -
      mode -
      Returns:

    • getRGB

      public int getRGB(BufferedImage img, int x, int y, ChannelDisplayMode mode)
      Description copied from interface: ChannelDisplayInfo
      Get the RGB value that would be used to display a particular pixel
      Specified by:
      getRGB in interface ChannelDisplayInfo
      Parameters:
      img -
      x -
      y -
      mode -
      Returns:

    • getValueAsString

      public String getValueAsString(BufferedImage img, int x, int y)
      Description copied from interface: ChannelDisplayInfo
      Get a string representation of a pixel's value. This might be a single number, or 3 numbers for an RGB image where the channel includes all values.
      Specified by:
      getValueAsString in interface ChannelDisplayInfo
      Parameters:
      img -
      x -
      y -
      Returns:

    • getRGB

      public int[] getRGB(BufferedImage img, int[] rgb, ChannelDisplayMode mode)
      Description copied from interface: ChannelDisplayInfo
      Get the RGB values that would be used to display all the pixels of an image
      Specified by:
      getRGB in interface ChannelDisplayInfo
      Parameters:
      img -
      rgb -
      mode -
      Returns:

    • updateRGBAdditive

      public void updateRGBAdditive(BufferedImage img, int[] rgb, ChannelDisplayMode mode)
      Description copied from interface: ChannelDisplayInfo
      Update an array of existing pixels (packed RGB) additively using the colors to display a specified image. May throw an UnsupportedOperationException if isAdditive() returns false;
      Specified by:
      updateRGBAdditive in interface ChannelDisplayInfo
      Parameters:
      img -
      rgb -
      mode -

    • getImageData

      protected ImageData<BufferedImage> getImageData()

    • getImageServer

      protected ImageServer<BufferedImage> getImageServer()

    • setMinMaxAllowed

      public void setMinMaxAllowed(float minAllowed, float maxAllowed)
      Description copied from interface: ChannelDisplayInfo.ModifiableChannelDisplayInfo
      Set the maximum permissible range for the image display.

      For an 8-bit image, that should be 0 and 255.

      For a 16-bit image, fewer bits might actually be used... therefore the full range of 0-2^16-1 may be too much.

      Also, for a 32-bit floating point image the limits are rather harder to define in a general way. This method makes it possible to restrict the permissible range to something sensible. Brightness/contrast/min/max sliders may make use of this.

      Specified by:
      setMinMaxAllowed in interface ChannelDisplayInfo.ModifiableChannelDisplayInfo
      Parameters:
      minAllowed -
      maxAllowed -

    • isBrightnessContrastRescaled

      public boolean isBrightnessContrastRescaled()
      Description copied from interface: ChannelDisplayInfo
      Returns true if rescaling according to min & max display levels is applied, false if the full display range is used.
      Specified by:
      isBrightnessContrastRescaled in interface ChannelDisplayInfo
      Returns:

    • setMinDisplay

      public void setMinDisplay(float minDisplay)
      Description copied from interface: ChannelDisplayInfo.ModifiableChannelDisplayInfo
      Set the min display value for this channel. Note that it is *strongly* advised to use ImageDisplay.setMinMaxDisplay instead since this helps ensure that the ImageDisplay fires appropriate events etc.
      Specified by:
      setMinDisplay in interface ChannelDisplayInfo.ModifiableChannelDisplayInfo
      Parameters:
      minDisplay -
      See Also:

    • setMaxDisplay

      public void setMaxDisplay(float maxDisplay)
      Description copied from interface: ChannelDisplayInfo.ModifiableChannelDisplayInfo
      Set the max display value for this channel. Note that it is *strongly* advised to use ImageDisplay.setMinMaxDisplay instead since this helps ensure that the ImageDisplay fires appropriate events etc.
      Specified by:
      setMaxDisplay in interface ChannelDisplayInfo.ModifiableChannelDisplayInfo
      Parameters:
      maxDisplay -
      See Also:

    • getMinAllowed

      public float getMinAllowed()
      Description copied from interface: ChannelDisplayInfo
      Get the min allowed display value. This is only a hint.
      Specified by:
      getMinAllowed in interface ChannelDisplayInfo
      Returns:

    • getMaxAllowed

      public float getMaxAllowed()
      Description copied from interface: ChannelDisplayInfo
      Get the max allowed display value. This is only a hint.
      Specified by:
      getMaxAllowed in interface ChannelDisplayInfo
      Returns:

    • getMinDisplay

      public float getMinDisplay()
      Description copied from interface: ChannelDisplayInfo
      Get the min display value. This is used to control the brightness/contrast when painting.
      Specified by:
      getMinDisplay in interface ChannelDisplayInfo
      Returns:

    • getMaxDisplay

      public float getMaxDisplay()
      Description copied from interface: ChannelDisplayInfo
      Get the max display value. This is used to control the brightness/contrast when painting.
      Specified by:
      getMaxDisplay in interface ChannelDisplayInfo
      Returns:

    • updateRGBAdditive

      public int updateRGBAdditive(BufferedImage img, int x, int y, int rgb, ChannelDisplayMode mode)
      Description copied from interface: ChannelDisplayInfo
      Update an existing pixel (packed RGB) additively using the color used to display a specified one
      Specified by:
      updateRGBAdditive in interface ChannelDisplayInfo
      Parameters:
      img -
      x -
      y -
      rgb -
      mode -
      Returns:

    • toString

      public String toString()
      Overrides:
      toString in class Object