Package mgui.image.util

Class WindowedColourModel

java.lang.Object
java.awt.image.ColorModel
mgui.image.util.WindowedColourModel
All Implemented Interfaces:
java.awt.Transparency, java.lang.Cloneable, XMLObject
public class WindowedColourModel
extends java.awt.image.ColorModel
implements java.lang.Cloneable, XMLObject
Colour model useful for representing medical images. Values are scaled and translated to fit scale and intercept parameters, and windowed to a specified window width (contrast) and window middle (brightness). Colours are indexed to a specified colour map.

NB: This colour model is mutable, meaning that it can be changed and its changes will be reflected in all objects that reference it. Use the clone() method to make a copy of a particular model state.

NB: an alpha of zero will always map to zero; this is necessary for the current implementation of Volume3DTexture, which requires a power-of-two volume, part of which will be outside the bounds of any non-power-of-two volume, and thus should be always invisible.

Since:
1.0
Version:
1.0
Author:
Andrew Reid

  • Nested Class Summary

    Nested classes/interfaces inherited from interface mgui.interfaces.xml.XMLObject

    XMLObject.XMLEncoding, XMLObject.XMLType

  • Field Summary

    Fields
    Modifier and Type Field Description
    protected double alpha  
    protected double alphaMax  
    protected double alphaMin  
    protected int channels  
    protected ColourMap colourMap  
    int data_size  
    protected int discrete_min  
    protected java.util.HashMap<java.lang.Integer,​java.lang.Integer> index_map  
    protected double intercept  
    boolean is_discrete  
    boolean is_solid  
    protected boolean low_is_transparent  
    protected int map_size  
    protected byte[] rgba  
    protected double scale  
    protected int[] solid_colour  
    protected double window_mid  
    protected double window_width  

    Fields inherited from class java.awt.image.ColorModel

    pixel_bits, transferType

    Fields inherited from interface java.awt.Transparency

    BITMASK, OPAQUE, TRANSLUCENT

  • Constructor Summary

    Constructors
    Constructor Description
    WindowedColourModel()
    Constructor produces a greyscale model of type DataBuffer.TYPE_DOUBLE.
    WindowedColourModel​(int transferType)
    Constructor produces a greyscale model of type transferType.
    WindowedColourModel​(ColourMap cm, double min, double max, boolean has_alpha, int transfer_type)
    Constructor specifying min and max values only.
    WindowedColourModel​(ColourMap cm, double scale, double intercept, double window_mid, double window_width, boolean has_alpha, int transferType)
    Constructors specifying the full set of model parameters.

  • Method Summary

    Modifier and Type Method Description
    java.lang.Object clone()  
    java.awt.image.SampleModel createCompatibleSampleModel​(int w, int h)  
    java.awt.image.WritableRaster createCompatibleWritableRaster​(int w, int h)  
    double getAlpha()  
    int getAlpha​(int pixel)  
    int getAlpha​(java.lang.Object inData)  
    int getAlphaIndex()  
    double getAlphaMax()  
    double getAlphaMin()  
    int getBlue​(int pixel)  
    int getBlue​(java.lang.Object inData)  
    int getBlueIndex()  
    ColourMap getColourMap()  
    java.lang.String getDTD()
    Returns the Data Type Declaration (DTD) for this object's XML representation
    int getGreen​(int pixel)  
    int getGreen​(java.lang.Object inData)  
    int getGreenIndex()  
    boolean getHasAlpha()  
    double getIntercept()  
    double getInverseMappedValue​(double value)
    Maps a value according to the inverse of the linear window model:
    double[] getLimits()
    Returns the limits of this windowed model
    java.lang.String getLocalName()
    Returns the local name associated with this XML object.
    boolean getLowIsTransparent()  
    double getMappedValue​(double value)
    Maps a value according to the linear window model:
    int getRed​(int pixel)  
    int getRed​(java.lang.Object inData)  
    int getRedIndex()  
    int getRGB​(int pixel)  
    int getRGB​(java.lang.Object inData)  
    double getScale()  
    java.lang.String getShortXML​(int tab)
    Returns a short XML representation of this object.
    java.awt.Color getSolidColour()  
    double getWindowMid()  
    double getWindowWidth()  
    java.lang.String getXML()
    Returns this object's XML representation as a single string.
    java.lang.String getXML​(int tab)
    Returns this object's XML representation as a single string.
    java.lang.String getXMLSchema()
    Returns the XML schema for this object's XML representation
    static double getZeroValue​(int transferType)
    Returns the "zero" value for the given transfer type.
    void handleXMLElementEnd​(java.lang.String localName)
    Handles the end of an XML element.
    void handleXMLElementStart​(java.lang.String localName, org.xml.sax.Attributes attributes, XMLObject.XMLType type)
    Handles the start of an XML element.
    void handleXMLString​(java.lang.String s)
    Handles a string within an XML element.
    boolean isCompatibleRaster​(java.awt.image.Raster raster)  
    void setAlpha​(double alpha)  
    void setAlphaMax​(double alphaMax)  
    void setAlphaMin​(double alphaMin)  
    boolean setColourMap​(ColourMap cm)  
    void setFromColourModel​(WindowedColourModel model)  
    void setHasAlpha​(boolean b)  
    void setIntercept​(double i)  
    void setIsSolidColour​(boolean b)  
    void setLimits​(double[] limits)
    Set the window from limits.
    void setLimits​(double min, double max)
    Set the window from limits.
    void setLowIsTransparent​(boolean b)  
    void setScale​(double s)  
    void setSolidColour​(java.awt.Color clr)  
    void setWindowMid​(double mid)  
    void setWindowWidth​(double width)  
    void writeXML​(int tab, java.io.Writer writer)
    Writes the XML representation of this object to file.
    void writeXML​(int tab, java.io.Writer writer, ProgressUpdater progress_bar)
    Writes the XML representation of this object to file, as XMLType.Normal.
    void writeXML​(int tab, java.io.Writer writer, XMLOutputOptions options, ProgressUpdater progress_bar)
    Writes the XML representation of this object to file.

    Methods inherited from class java.awt.image.ColorModel

    coerceData, equals, finalize, getAlphaRaster, getColorSpace, getComponents, getComponents, getComponentSize, getComponentSize, getDataElement, getDataElement, getDataElements, getDataElements, getDataElements, getNormalizedComponents, getNormalizedComponents, getNumColorComponents, getNumComponents, getPixelSize, getRGBdefault, getTransferType, getTransparency, getUnnormalizedComponents, hasAlpha, hashCode, isAlphaPremultiplied, isCompatibleSampleModel, toString

    Methods inherited from class java.lang.Object

    getClass, notify, notifyAll, wait, wait, wait

  • Field Details

    • rgba

      protected byte[] rgba

    • colourMap

      protected ColourMap colourMap

    • channels

      protected int channels

    • data_size

      public int data_size

    • map_size

      protected int map_size

    • scale

      protected double scale

    • intercept

      protected double intercept

    • window_mid

      protected double window_mid

    • window_width

      protected double window_width

    • alphaMin

      protected double alphaMin

    • alphaMax

      protected double alphaMax

    • is_discrete

      public boolean is_discrete

    • is_solid

      public boolean is_solid

    • discrete_min

      protected int discrete_min

    • alpha

      protected double alpha

    • low_is_transparent

      protected boolean low_is_transparent

    • index_map

      protected java.util.HashMap<java.lang.Integer,​java.lang.Integer> index_map

    • solid_colour

      protected int[] solid_colour

  • Constructor Details

    • WindowedColourModel

      public WindowedColourModel()
      Constructor produces a greyscale model of type DataBuffer.TYPE_DOUBLE.
      Parameters:
      transfer_type -

    • WindowedColourModel

      public WindowedColourModel​(int transferType)
      Constructor produces a greyscale model of type transferType.
      Parameters:
      transferType -

    • WindowedColourModel

      public WindowedColourModel​(ColourMap cm, double min, double max, boolean has_alpha, int transfer_type)
      Constructor specifying min and max values only.
      Parameters:
      cm -
      min -
      max -
      has_alpha -
      transfer_type -

    • WindowedColourModel

      public WindowedColourModel​(ColourMap cm, double scale, double intercept, double window_mid, double window_width, boolean has_alpha, int transferType)
      Constructors specifying the full set of model parameters.
      Parameters:
      cm -
      scale -
      intercept -
      window_mid -
      window_width -
      has_alpha -
      transferType -

  • Method Details

    • setIsSolidColour

      public void setIsSolidColour​(boolean b)

    • setSolidColour

      public void setSolidColour​(java.awt.Color clr)

    • getSolidColour

      public java.awt.Color getSolidColour()

    • setHasAlpha

      public void setHasAlpha​(boolean b)

    • getHasAlpha

      public boolean getHasAlpha()

    • getScale

      public double getScale()

    • getIntercept

      public double getIntercept()

    • setScale

      public void setScale​(double s)

    • setIntercept

      public void setIntercept​(double i)

    • setWindowMid

      public void setWindowMid​(double mid)

    • getWindowMid

      public double getWindowMid()

    • setWindowWidth

      public void setWindowWidth​(double width)

    • getWindowWidth

      public double getWindowWidth()

    • setLowIsTransparent

      public void setLowIsTransparent​(boolean b)

    • getLowIsTransparent

      public boolean getLowIsTransparent()

    • setLimits

      public void setLimits​(double[] limits)
      Set the window from limits.
      Parameters:
      limits -

    • setLimits

      public void setLimits​(double min, double max)
      Set the window from limits.
      Parameters:
      min -
      max -

    • getLimits

      public double[] getLimits()
      Returns the limits of this windowed model
      Returns:

    • getRedIndex

      public int getRedIndex()

    • getGreenIndex

      public int getGreenIndex()

    • getBlueIndex

      public int getBlueIndex()

    • getAlphaIndex

      public int getAlphaIndex()

    • createCompatibleWritableRaster

      public java.awt.image.WritableRaster createCompatibleWritableRaster​(int w, int h)
      Overrides:
      createCompatibleWritableRaster in class java.awt.image.ColorModel

    • createCompatibleSampleModel

      public java.awt.image.SampleModel createCompatibleSampleModel​(int w, int h)
      Overrides:
      createCompatibleSampleModel in class java.awt.image.ColorModel

    • isCompatibleRaster

      public boolean isCompatibleRaster​(java.awt.image.Raster raster)
      Overrides:
      isCompatibleRaster in class java.awt.image.ColorModel

    • getRGB

      public int getRGB​(int pixel)
      Overrides:
      getRGB in class java.awt.image.ColorModel

    • getRGB

      public int getRGB​(java.lang.Object inData)
      Overrides:
      getRGB in class java.awt.image.ColorModel

    • getRed

      public int getRed​(java.lang.Object inData)
      Overrides:
      getRed in class java.awt.image.ColorModel

    • getRed

      public int getRed​(int pixel)
      Specified by:
      getRed in class java.awt.image.ColorModel

    • getGreen

      public int getGreen​(java.lang.Object inData)
      Overrides:
      getGreen in class java.awt.image.ColorModel

    • getGreen

      public int getGreen​(int pixel)
      Specified by:
      getGreen in class java.awt.image.ColorModel

    • getBlue

      public int getBlue​(java.lang.Object inData)
      Overrides:
      getBlue in class java.awt.image.ColorModel

    • getBlue

      public int getBlue​(int pixel)
      Specified by:
      getBlue in class java.awt.image.ColorModel

    • getAlpha

      public int getAlpha​(java.lang.Object inData)
      Overrides:
      getAlpha in class java.awt.image.ColorModel

    • getAlpha

      public int getAlpha​(int pixel)
      Specified by:
      getAlpha in class java.awt.image.ColorModel

    • getMappedValue

      public double getMappedValue​(double value)
      Maps a value according to the linear window model:

      Y = (value - intercept) * scale * m + b

      where m = data_size * window_width

      and b = data_size * (window_mid - 0.5)

      Parameters:
      value -
      Returns:

    • getInverseMappedValue

      public double getInverseMappedValue​(double value)
      Maps a value according to the inverse of the linear window model:

      Y = (value - b) / (scale * m) + intercept

      where m = data_size * window_width

      and b = data_size * (window_mid - 0.5)

      Parameters:
      value -
      Returns:

    • getZeroValue

      public static double getZeroValue​(int transferType)
      Returns the "zero" value for the given transfer type. This value is used to set transparency for masked pixels.
      Parameters:
      transferType -
      Returns:

    • setColourMap

      public boolean setColourMap​(ColourMap cm)

    • getColourMap

      public ColourMap getColourMap()

    • setFromColourModel

      public void setFromColourModel​(WindowedColourModel model)

    • clone

      public java.lang.Object clone()
      Overrides:
      clone in class java.lang.Object

    • getAlphaMin

      public double getAlphaMin()

    • setAlphaMin

      public void setAlphaMin​(double alphaMin)

    • getAlphaMax

      public double getAlphaMax()

    • setAlphaMax

      public void setAlphaMax​(double alphaMax)

    • getAlpha

      public double getAlpha()

    • setAlpha

      public void setAlpha​(double alpha)

    • getDTD

      public java.lang.String getDTD()
      Description copied from interface: XMLObject
      Returns the Data Type Declaration (DTD) for this object's XML representation

      See http://en.wikipedia.org/wiki/Document_Type_Definition for a description.

      Specified by:
      getDTD in interface XMLObject
      Returns:

    • getXMLSchema

      public java.lang.String getXMLSchema()
      Description copied from interface: XMLObject
      Returns the XML schema for this object's XML representation

      See http://en.wikipedia.org/wiki/XML_schema.

      Specified by:
      getXMLSchema in interface XMLObject
      Returns:

    • getXML

      public java.lang.String getXML()
      Description copied from interface: XMLObject
      Returns this object's XML representation as a single string. NOTE: this is not feasible for larger objects and containers, thus may not be implemented for these objects. Use the XMLObject.writeXML(int,java.io.Writer,mgui.io.standard.xml.XMLOutputOptions,mgui.interfaces.ProgressUpdater) functions to write larger objects to file.
      Specified by:
      getXML in interface XMLObject
      Returns:

    • getXML

      public java.lang.String getXML​(int tab)
      Description copied from interface: XMLObject
      Returns this object's XML representation as a single string. NOTE: this is not feasible for larger objects and containers, thus may not be implemented for these objects. Use the XMLObject.writeXML(int,java.io.Writer,mgui.io.standard.xml.XMLOutputOptions,mgui.interfaces.ProgressUpdater) functions to write larger objects to file.
      Specified by:
      getXML in interface XMLObject
      Parameters:
      tab - The number of tabs to place before the opening XML wrapper
      Returns:

    • handleXMLElementStart

      public void handleXMLElementStart​(java.lang.String localName, org.xml.sax.Attributes attributes, XMLObject.XMLType type) throws org.xml.sax.SAXException
      Description copied from interface: XMLObject
      Handles the start of an XML element.
      Specified by:
      handleXMLElementStart in interface XMLObject
      Parameters:
      localName - Local name of the element
      attributes - Set of element attributes
      type - The XMLType of this element
      Throws:
      org.xml.sax.SAXException

    • handleXMLElementEnd

      public void handleXMLElementEnd​(java.lang.String localName) throws org.xml.sax.SAXException
      Description copied from interface: XMLObject
      Handles the end of an XML element.
      Specified by:
      handleXMLElementEnd in interface XMLObject
      Parameters:
      localName - Local name of the element
      Throws:
      org.xml.sax.SAXException

    • handleXMLString

      public void handleXMLString​(java.lang.String s) throws org.xml.sax.SAXException
      Description copied from interface: XMLObject
      Handles a string within an XML element.
      Specified by:
      handleXMLString in interface XMLObject
      Parameters:
      s - String to handle
      Throws:
      org.xml.sax.SAXException

    • getLocalName

      public java.lang.String getLocalName()
      Description copied from interface: XMLObject
      Returns the local name associated with this XML object.
      Specified by:
      getLocalName in interface XMLObject
      Returns:

    • writeXML

      public void writeXML​(int tab, java.io.Writer writer, XMLOutputOptions options, ProgressUpdater progress_bar) throws java.io.IOException
      Description copied from interface: XMLObject
      Writes the XML representation of this object to file. The basic contract for this method is that it should not write a newline character at its start or end. The default format of XMLFormat.Ascii will be used.
      Specified by:
      writeXML in interface XMLObject
      Parameters:
      tab - The number of tabs to place before the XML text
      writer - The writer
      options - XMLOutputOptions defining the write parameters
      progress_bar - Optional progress updater (may be null)
      Throws:
      java.io.IOException

    • writeXML

      public void writeXML​(int tab, java.io.Writer writer, ProgressUpdater progress_bar) throws java.io.IOException
      Description copied from interface: XMLObject
      Writes the XML representation of this object to file, as XMLType.Normal. The default format of XMLFormat.Ascii will be used. The basic contract for this method is that it should not write a newline character at its start or end.
      Specified by:
      writeXML in interface XMLObject
      Parameters:
      tab - The number of tabs to place before the XML text
      writer - The writer
      progress_bar - Optional progress updater (may be null)
      Throws:
      java.io.IOException

    • writeXML

      public void writeXML​(int tab, java.io.Writer writer) throws java.io.IOException
      Description copied from interface: XMLObject
      Writes the XML representation of this object to file. The basic contract for this method is that it should not write a newline character at its start or end. The default format of XMLFormat.Ascii will be used.
      Specified by:
      writeXML in interface XMLObject
      Parameters:
      tab - The number of tabs to place before the XML text
      writer - The writer
      Throws:
      java.io.IOException

    • getShortXML

      public java.lang.String getShortXML​(int tab)
      Description copied from interface: XMLObject
      Returns a short XML representation of this object.
      Specified by:
      getShortXML in interface XMLObject
      Returns: