Module ij
Package ij.measure

Class Calibration

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

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

    Fields
    Modifier and Type
    Field
    Description
    static final int
     
    static final String
     
    static final int
     
    static final int
     
    static final int
     
    double
    Frame rate in frames per second
    double
    Frame interval in 'timeUnit's
    static final int
     
    static final int
     
    Plugin writers can use this string to store information about the image.
    static final int
     
    static final int
     
    boolean
     
    static final int
     
    double
    Pixel depth in 'unit's
    double
    Pixel height in 'unit's
    double
    Pixel width in 'unit's
    static final int
     
    static final int
     
    static final int
     
    static final int
     
    static final int
     
    static final int
     
    static final int
     
    static final int
     
    double
    X origin in pixels.
    double
    Y origin in pixels.
    double
    Z origin in pixels.
  • Constructor Summary

    Constructors
    Constructor
    Description
    Constructs a new Calibration object using the default values.
    Constructs a new Calibration object using the default values.
  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    Returns true if this image is density calibrated.
     
    Returns a clone of this object.
    void
     
    boolean
    Compares two Calibration objects for equality.
    double[]
    Returns the calibration function coefficients.
    float[]
    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
    Returns the calibration function ID.
    boolean
    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.
    Returns the distance unit (e.g.
    Returns the default length unit (e.g.
    Returns the plural form of the length unit (e.g.
    Returns the value unit.
    double
    getX(double x)
    Converts a x-coodinate in pixels to physical units (e.g.
    Returns the X length unit.
    Returns the plural form of the X length unit (e.g.
    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.
    Returns the Y length unit, or the default unit if 'yunit' is null.
    Returns the plural form of the Y length unit (e.g.
    double
    getZ(double z)
    Converts a z-coordinate in pixels to physical units (e.g.
    Returns the Z length unit, or the default unit if 'zunit' is null.
    Returns the plural form of the Z length unit (e.g.
    boolean
    Returns true if this is a signed 16-bit image.
    boolean
    Returns 'true' if this image is spatially calibrated.
    boolean
    Returns 'true' if this image is spatially calibrated or has offsets.
    void
    setCTable(float[] table, String unit)
    Sets the calibration table.
    void
    setFunction(int function, double[] coefficients, String unit)
    Sets the calibration function, coefficient table and unit (e.g.
    void
    setFunction(int function, double[] coefficients, String unit, boolean zeroClip)
     
    void
    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
    Sets up a calibration function that subtracts 32,768 from pixel values.
    void
    Sets the time unit (e.g.
    void
    Sets the default length unit (e.g.
    void
    Sets the value unit.
    void
    Sets the X length unit.
    void
    Sets the Y length unit.
    void
    Sets the Z length unit.
     
    boolean
    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

    • STRAIGHT_LINE

      public static final int STRAIGHT_LINE
      See Also:
    • POLY2

      public static final int POLY2
      See Also:
    • POLY3

      public static final int POLY3
      See Also:
    • POLY4

      public static final int POLY4
      See Also:
    • EXPONENTIAL

      public static final int EXPONENTIAL
      See Also:
    • POWER

      public static final int POWER
      See Also:
    • LOG

      public static final int LOG
      See Also:
    • RODBARD

      public static final int RODBARD
      See Also:
    • GAMMA_VARIATE

      public static final int GAMMA_VARIATE
      See Also:
    • LOG2

      public static final int LOG2
      See Also:
    • RODBARD2

      public static final int RODBARD2
      See Also:
    • EXP_WITH_OFFSET

      public static final int EXP_WITH_OFFSET
      See Also:
    • GAUSSIAN

      public static final int GAUSSIAN
      See Also:
    • EXP_RECOVERY

      public static final int EXP_RECOVERY
      See Also:
    • NONE

      public static final int NONE
      See Also:
    • UNCALIBRATED_OD

      public static final int UNCALIBRATED_OD
      See Also:
    • CUSTOM

      public static final int CUSTOM
      See Also:
    • DEFAULT_VALUE_UNIT

      public static final String DEFAULT_VALUE_UNIT
      See Also:
    • pixelWidth

      public double pixelWidth
      Pixel width in 'unit's
    • pixelHeight

      public double pixelHeight
      Pixel height in 'unit's
    • pixelDepth

      public double pixelDepth
      Pixel depth in 'unit's
    • frameInterval

      public double frameInterval
      Frame interval in 'timeUnit's
    • fps

      public double fps
      Frame rate in frames per second
    • loop

      public boolean loop
    • xOrigin

      public double xOrigin
      X origin in pixels.
    • yOrigin

      public double yOrigin
      Y origin in pixels.
    • zOrigin

      public double zOrigin
      Z origin in pixels.
    • info

      public String info
      Plugin writers can use this string to store information about the image. This string is saved in the TIFF header if it is not longer than 64 characters and it contains no '=' or '\n' characters.
  • 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.
    • scaledOrOffset

      public boolean scaledOrOffset()
      Returns 'true' if this image is spatially calibrated or has offsets.
    • setUnit

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

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

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

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

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

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

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

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

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

      public String getXUnits()
      Returns the plural form of the X length unit (e.g. "microns", "inches"), or of the default unit if 'xunit' is null.
    • getYUnits

      public String getYUnits()
      Returns the plural form of the Y length unit (e.g. "microns", "inches"), or of the default unit if 'yunit' is null.
    • getZUnits

      public String getZUnits()
      Returns the plural form of the Z length unit (e.g. "microns", "inches"), or of the default unit if 'zunit' is null.
    • setTimeUnit

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

      public 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, String unit)
      Sets the calibration function, coefficient table and unit (e.g. "OD").
    • setFunction

      public void setFunction(int function, double[] coefficients, 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 String getValueUnit()
      Returns the value unit.
    • setValueUnit

      public void setValueUnit(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, 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 Object clone()
      Overrides:
      clone in class 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 String toString()
      Overrides:
      toString in class Object