Module ij
Package ij.measure

Class Calibration

java.lang.Object
ij.measure.Calibration
All Implemented Interfaces:
java.lang.Cloneable

public class Calibration
extends java.lang.Object
implements java.lang.Cloneable
Calibration objects contain an image's spatial and density calibration data.
  • Field Summary

    Fields 
    Modifier and Type Field Description
    static int CUSTOM  
    static java.lang.String DEFAULT_VALUE_UNIT  
    static int EXP_RECOVERY  
    static int EXP_WITH_OFFSET  
    static int EXPONENTIAL  
    double fps
    Frame rate in frames per second
    double frameInterval
    Frame interval in 'timeUnit's
    static int GAMMA_VARIATE  
    static int GAUSSIAN  
    java.lang.String info
    Plugin writers can use this string to store information about the image.
    static int LOG  
    static int LOG2  
    boolean loop  
    static int NONE  
    double pixelDepth
    Pixel depth in 'unit's
    double pixelHeight
    Pixel height in 'unit's
    double pixelWidth
    Pixel width in 'unit's
    static int POLY2  
    static int POLY3  
    static int POLY4  
    static int POWER  
    static int RODBARD  
    static int RODBARD2  
    static int STRAIGHT_LINE  
    static int UNCALIBRATED_OD  
    double xOrigin
    X origin in pixels.
    double yOrigin
    Y origin in pixels.
    double zOrigin
    Z origin in pixels.
  • Constructor Summary

    Constructors 
    Constructor Description
    Calibration()
    Constructs a new Calibration object using the default values.
    Calibration​(ImagePlus imp)
    Constructs a new Calibration object using the default values.
  • Method Summary

    Modifier and Type Method Description
    boolean calibrated()
    Returns true if this image is density calibrated.
    java.lang.Object clone()  
    Calibration copy()
    Returns a clone of this object.
    void disableDensityCalibration()  
    boolean equals​(Calibration cal)
    Compares two Calibration objects for equality.
    double[] getCoefficients()
    Returns the calibration function coefficients.
    float[] getCTable()
    Returns the calibration table.
    double getCValue​(double value)
    Converts a raw pixel value to a density calibrated value.
    double getCValue​(int value)
    Converts a raw pixel value to a density calibrated value.
    int getFunction()
    Returns the calibration function ID.
    boolean getInvertY()
    Returns the 'invertY' flag.
    double getRawValue​(double value)
    Converts a density calibrated value into a raw pixel value.
    double getRawX​(double x)
    Converts a x-coordinate in physical units to pixels.
    double getRawY​(double y)
    Converts a y-coodinate in physical units to pixels.
    double getRawY​(double y, int imageHeight)
    Converts a y-coodinate in physical units to pixels, taking into account the 'invertY' flag.
    double getRawZ​(double z)
    Converts a z-coodinate in physical units to pixels.
    java.lang.String getTimeUnit()
    Returns the distance unit (e.g.
    java.lang.String getUnit()
    Returns the default length unit (e.g.
    java.lang.String getUnits()
    Returns the plural form of the length unit (e.g.
    java.lang.String getValueUnit()
    Returns the value unit.
    double getX​(double x)
    Converts a x-coodinate in pixels to physical units (e.g.
    java.lang.String getXUnit()
    Returns the X length unit.
    double getY​(double y)
    Converts a y-coordinate in pixels to physical units (e.g.
    double getY​(double y, int imageHeight)
    Converts a y-coordinate in pixels to physical units (e.g.
    java.lang.String getYUnit()
    Returns the Y length unit, or the default unit if 'yunit' is null.
    double getZ​(double z)
    Converts a z-coordinate in pixels to physical units (e.g.
    java.lang.String getZUnit()
    Returns the Z length unit, or the default unit if 'zunit' is null.
    boolean isSigned16Bit()
    Returns true if this is a signed 16-bit image.
    boolean scaled()
    Returns true if this image is spatially calibrated.
    void setCTable​(float[] table, java.lang.String unit)
    Sets the calibration table.
    void setFunction​(int function, double[] coefficients, java.lang.String unit)
    Sets the calibration function, coefficient table and unit (e.g.
    void setFunction​(int function, double[] coefficients, java.lang.String unit, boolean zeroClip)  
    void setImage​(ImagePlus imp)
    Disables the density calibation if the specified image has a differenent bit depth.
    void setInvertY​(boolean invertYCoordinates)
    Sets the 'invertY' flag.
    static void setLoopBackAndForth​(boolean loop)
    Set the default state of the animation "Loop back and forth" flag
    void setSigned16BitCalibration()
    Sets up a calibration function that subtracts 32,768 from pixel values.
    void setTimeUnit​(java.lang.String unit)
    Sets the time unit (e.g.
    void setUnit​(java.lang.String unit)
    Sets the default length unit (e.g.
    void setValueUnit​(java.lang.String unit)
    Sets the value unit.
    void setXUnit​(java.lang.String unit)
    Sets the X length unit.
    void setYUnit​(java.lang.String unit)
    Sets the Y length unit.
    void setZUnit​(java.lang.String unit)
    Sets the Z length unit.
    java.lang.String toString()  
    boolean zeroClip()
    Returns true if zero clipping is enabled.

    Methods inherited from class java.lang.Object

    equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
  • Field Details

  • Constructor Details

    • Calibration

      public Calibration​(ImagePlus imp)
      Constructs a new Calibration object using the default values.
    • Calibration

      public Calibration()
      Constructs a new Calibration object using the default values. For density calibration, the image is assumed to be 8-bits.
  • Method Details

    • scaled

      public boolean scaled()
      Returns true if this image is spatially calibrated.
    • setUnit

      public void setUnit​(java.lang.String unit)
      Sets the default length unit (e.g. "mm", "inch").
    • setXUnit

      public void setXUnit​(java.lang.String unit)
      Sets the X length unit.
    • setYUnit

      public void setYUnit​(java.lang.String unit)
      Sets the Y length unit.
    • setZUnit

      public void setZUnit​(java.lang.String unit)
      Sets the Z length unit.
    • getUnit

      public java.lang.String getUnit()
      Returns the default length unit (e.g. "micron", "inch").
    • getXUnit

      public java.lang.String getXUnit()
      Returns the X length unit.
    • getYUnit

      public java.lang.String getYUnit()
      Returns the Y length unit, or the default unit if 'yunit' is null.
    • getZUnit

      public java.lang.String getZUnit()
      Returns the Z length unit, or the default unit if 'zunit' is null.
    • getUnits

      public java.lang.String getUnits()
      Returns the plural form of the length unit (e.g. "microns", "inches").
    • setTimeUnit

      public void setTimeUnit​(java.lang.String unit)
      Sets the time unit (e.g. "sec", "msec").
    • getTimeUnit

      public java.lang.String getTimeUnit()
      Returns the distance unit (e.g. "sec", "msec").
    • getX

      public double getX​(double x)
      Converts a x-coodinate in pixels to physical units (e.g. mm).
    • getY

      public double getY​(double y)
      Converts a y-coordinate in pixels to physical units (e.g. mm).
    • getY

      public double getY​(double y, int imageHeight)
      Converts a y-coordinate in pixels to physical units (e.g. mm), taking into account the invertY and global "Invert Y Coordinates" flags.
    • getZ

      public double getZ​(double z)
      Converts a z-coordinate in pixels to physical units (e.g. mm).
    • getRawX

      public double getRawX​(double x)
      Converts a x-coordinate in physical units to pixels.
    • getRawY

      public double getRawY​(double y)
      Converts a y-coodinate in physical units to pixels.
    • getRawZ

      public double getRawZ​(double z)
      Converts a z-coodinate in physical units to pixels.
    • getRawY

      public double getRawY​(double y, int imageHeight)
      Converts a y-coodinate in physical units to pixels, taking into account the 'invertY' flag.
    • setFunction

      public void setFunction​(int function, double[] coefficients, java.lang.String unit)
      Sets the calibration function, coefficient table and unit (e.g. "OD").
    • setFunction

      public void setFunction​(int function, double[] coefficients, java.lang.String unit, boolean zeroClip)
    • setImage

      public void setImage​(ImagePlus imp)
      Disables the density calibation if the specified image has a differenent bit depth.
    • disableDensityCalibration

      public void disableDensityCalibration()
    • getValueUnit

      public java.lang.String getValueUnit()
      Returns the value unit.
    • setValueUnit

      public void setValueUnit​(java.lang.String unit)
      Sets the value unit.
    • getCoefficients

      public double[] getCoefficients()
      Returns the calibration function coefficients.
    • calibrated

      public boolean calibrated()
      Returns true if this image is density calibrated.
    • getFunction

      public int getFunction()
      Returns the calibration function ID.
    • getCTable

      public float[] getCTable()
      Returns the calibration table. With 8-bit images, the table has a length of 256. With 16-bit images, the length is 65536.
    • setCTable

      public void setCTable​(float[] table, java.lang.String unit)
      Sets the calibration table. With 8-bit images, the table must have a length of 256. With 16-bit images, it must be 65536.
    • getCValue

      public double getCValue​(int value)
      Converts a raw pixel value to a density calibrated value.
    • getCValue

      public double getCValue​(double value)
      Converts a raw pixel value to a density calibrated value.
    • getRawValue

      public double getRawValue​(double value)
      Converts a density calibrated value into a raw pixel value.
    • copy

      public Calibration copy()
      Returns a clone of this object.
    • clone

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

      public boolean equals​(Calibration cal)
      Compares two Calibration objects for equality.
    • isSigned16Bit

      public boolean isSigned16Bit()
      Returns true if this is a signed 16-bit image.
    • setSigned16BitCalibration

      public void setSigned16BitCalibration()
      Sets up a calibration function that subtracts 32,768 from pixel values.
    • zeroClip

      public boolean zeroClip()
      Returns true if zero clipping is enabled.
    • setInvertY

      public void setInvertY​(boolean invertYCoordinates)
      Sets the 'invertY' flag.
    • getInvertY

      public boolean getInvertY()
      Returns the 'invertY' flag.
    • setLoopBackAndForth

      public static void setLoopBackAndForth​(boolean loop)
      Set the default state of the animation "Loop back and forth" flag
    • toString

      public java.lang.String toString()
      Overrides:
      toString in class java.lang.Object