Calibration (ImageJ 1.52d API)

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 and Description
`static int`	`CUSTOM`
`static 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`
`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 and 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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`calibrated()` Returns true if this image is density calibrated.
`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.
`String`	`getTimeUnit()` Returns the distance unit (e.g.
`String`	`getUnit()` Returns the default length unit (e.g.
`String`	`getUnits()` Returns the plural form of the length unit (e.g.
`String`	`getValueUnit()` Returns the value unit.
`double`	`getX(double x)` Converts a x-coodinate in pixels to physical units (e.g.
`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.
`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.
`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, 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`	`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(String unit)` Sets the time unit (e.g.
`void`	`setUnit(String unit)` Sets the default length unit (e.g.
`void`	`setValueUnit(String unit)` Sets the value unit.
`void`	`setXUnit(String unit)` Sets the X length unit.
`void`	`setYUnit(String unit)` Sets the Y length unit.
`void`	`setZUnit(String unit)` Sets the Z length unit.
`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 Detail
  - STRAIGHT_LINE
```
public static final int STRAIGHT_LINE
```
    See Also:
    
    Constant Field Values
  - POLY2
```
public static final int POLY2
```
    See Also:
    
    Constant Field Values
  - POLY3
```
public static final int POLY3
```
    See Also:
    
    Constant Field Values
  - POLY4
```
public static final int POLY4
```
    See Also:
    
    Constant Field Values
  - EXPONENTIAL
```
public static final int EXPONENTIAL
```
    See Also:
    
    Constant Field Values
  - POWER
```
public static final int POWER
```
    See Also:
    
    Constant Field Values
  - LOG
```
public static final int LOG
```
    See Also:
    
    Constant Field Values
  - RODBARD
```
public static final int RODBARD
```
    See Also:
    
    Constant Field Values
  - GAMMA_VARIATE
```
public static final int GAMMA_VARIATE
```
    See Also:
    
    Constant Field Values
  - LOG2
```
public static final int LOG2
```
    See Also:
    
    Constant Field Values
  - RODBARD2
```
public static final int RODBARD2
```
    See Also:
    
    Constant Field Values
  - EXP_WITH_OFFSET
```
public static final int EXP_WITH_OFFSET
```
    See Also:
    
    Constant Field Values
  - GAUSSIAN
```
public static final int GAUSSIAN
```
    See Also:
    
    Constant Field Values
  - EXP_RECOVERY
```
public static final int EXP_RECOVERY
```
    See Also:
    
    Constant Field Values
  - NONE
```
public static final int NONE
```
    See Also:
    
    Constant Field Values
  - UNCALIBRATED_OD
```
public static final int UNCALIBRATED_OD
```
    See Also:
    
    Constant Field Values
  - CUSTOM
```
public static final int CUSTOM
```
    See Also:
    
    Constant Field Values
  - DEFAULT_VALUE_UNIT
```
public static final String DEFAULT_VALUE_UNIT
```
    See Also:
    
    Constant Field Values
  - 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 Detail
  - 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 Detail
  - scaled
```
public boolean scaled()
```
    Returns true if this image is spatially calibrated.
  - 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").
  - 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

Class Calibration

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

STRAIGHT_LINE

POLY2

POLY3

POLY4

EXPONENTIAL

POWER

LOG

RODBARD

GAMMA_VARIATE

LOG2

RODBARD2

EXP_WITH_OFFSET

GAUSSIAN

EXP_RECOVERY

NONE

UNCALIBRATED_OD

CUSTOM

DEFAULT_VALUE_UNIT

pixelWidth

pixelHeight

pixelDepth

frameInterval

fps

loop

xOrigin

yOrigin

zOrigin

info

Constructor Detail

Calibration

Calibration

Method Detail

scaled

setUnit

setXUnit

setYUnit

setZUnit

getUnit

getXUnit

getYUnit

getZUnit

getUnits

setTimeUnit

getTimeUnit

getX

getY

getY

getZ

getRawX

getRawY

getRawZ

getRawY

setFunction

setFunction

setImage

disableDensityCalibration

getValueUnit

setValueUnit

getCoefficients

calibrated

getFunction

getCTable

setCTable

getCValue

getCValue

getRawValue

copy

clone

equals

isSigned16Bit

setSigned16BitCalibration

zeroClip

setInvertY

getInvertY