- java.lang.Object
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- ij.measure.Calibration
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- 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.
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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 seconddouble
frameInterval
Frame interval in 'timeUnit'sstatic 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'sdouble
pixelHeight
Pixel height in 'unit'sdouble
pixelWidth
Pixel width in 'unit'sstatic 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.
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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.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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.java.lang.String
getXUnits()
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.java.lang.String
getYUnit()
Returns the Y length unit, or the default unit if 'yunit' is null.java.lang.String
getYUnits()
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.java.lang.String
getZUnit()
Returns the Z length unit, or the default unit if 'zunit' is null.java.lang.String
getZUnits()
Returns the plural form of the Z length unit (e.g.boolean
isSigned16Bit()
Returns true if this is a signed 16-bit image.boolean
scaled()
Returns 'true' if this image is spatially calibrated.boolean
scaledOrOffset()
Returns 'true' if this image is spatially calibrated or has offsets.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" flagvoid
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.
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Field Detail
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STRAIGHT_LINE
public static final int STRAIGHT_LINE
- See Also:
- Constant Field Values
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POLY2
public static final int POLY2
- See Also:
- Constant Field Values
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POLY3
public static final int POLY3
- See Also:
- Constant Field Values
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POLY4
public static final int POLY4
- See Also:
- Constant Field Values
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EXPONENTIAL
public static final int EXPONENTIAL
- See Also:
- Constant Field Values
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POWER
public static final int POWER
- See Also:
- Constant Field Values
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LOG
public static final int LOG
- See Also:
- Constant Field Values
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RODBARD
public static final int RODBARD
- See Also:
- Constant Field Values
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GAMMA_VARIATE
public static final int GAMMA_VARIATE
- See Also:
- Constant Field Values
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LOG2
public static final int LOG2
- See Also:
- Constant Field Values
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RODBARD2
public static final int RODBARD2
- See Also:
- Constant Field Values
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EXP_WITH_OFFSET
public static final int EXP_WITH_OFFSET
- See Also:
- Constant Field Values
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GAUSSIAN
public static final int GAUSSIAN
- See Also:
- Constant Field Values
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EXP_RECOVERY
public static final int EXP_RECOVERY
- See Also:
- Constant Field Values
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NONE
public static final int NONE
- See Also:
- Constant Field Values
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UNCALIBRATED_OD
public static final int UNCALIBRATED_OD
- See Also:
- Constant Field Values
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CUSTOM
public static final int CUSTOM
- See Also:
- Constant Field Values
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DEFAULT_VALUE_UNIT
public static final java.lang.String DEFAULT_VALUE_UNIT
- See Also:
- Constant Field Values
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pixelWidth
public double pixelWidth
Pixel width in 'unit's
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pixelHeight
public double pixelHeight
Pixel height in 'unit's
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pixelDepth
public double pixelDepth
Pixel depth in 'unit's
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frameInterval
public double frameInterval
Frame interval in 'timeUnit's
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fps
public double fps
Frame rate in frames per second
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loop
public boolean loop
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xOrigin
public double xOrigin
X origin in pixels.
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yOrigin
public double yOrigin
Y origin in pixels.
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zOrigin
public double zOrigin
Z origin in pixels.
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info
public java.lang.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.
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Constructor Detail
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Calibration
public Calibration(ImagePlus imp)
Constructs a new Calibration object using the default values.
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Calibration
public Calibration()
Constructs a new Calibration object using the default values. For density calibration, the image is assumed to be 8-bits.
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Method Detail
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scaled
public boolean scaled()
Returns 'true' if this image is spatially calibrated.
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scaledOrOffset
public boolean scaledOrOffset()
Returns 'true' if this image is spatially calibrated or has offsets.
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setUnit
public void setUnit(java.lang.String unit)
Sets the default length unit (e.g. "mm", "inch").
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setXUnit
public void setXUnit(java.lang.String unit)
Sets the X length unit.
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setYUnit
public void setYUnit(java.lang.String unit)
Sets the Y length unit.
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setZUnit
public void setZUnit(java.lang.String unit)
Sets the Z length unit.
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getUnit
public java.lang.String getUnit()
Returns the default length unit (e.g. "micron", "inch").
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getXUnit
public java.lang.String getXUnit()
Returns the X length unit.
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getYUnit
public java.lang.String getYUnit()
Returns the Y length unit, or the default unit if 'yunit' is null.
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getZUnit
public java.lang.String getZUnit()
Returns the Z length unit, or the default unit if 'zunit' is null.
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getUnits
public java.lang.String getUnits()
Returns the plural form of the length unit (e.g. "microns", "inches").
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getXUnits
public java.lang.String getXUnits()
Returns the plural form of the X length unit (e.g. "microns", "inches"), or of the default unit if 'xunit' is null.
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getYUnits
public java.lang.String getYUnits()
Returns the plural form of the Y length unit (e.g. "microns", "inches"), or of the default unit if 'yunit' is null.
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getZUnits
public java.lang.String getZUnits()
Returns the plural form of the Z length unit (e.g. "microns", "inches"), or of the default unit if 'zunit' is null.
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setTimeUnit
public void setTimeUnit(java.lang.String unit)
Sets the time unit (e.g. "sec", "msec").
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getTimeUnit
public java.lang.String getTimeUnit()
Returns the distance unit (e.g. "sec", "msec").
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getX
public double getX(double x)
Converts a x-coodinate in pixels to physical units (e.g. mm).
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getY
public double getY(double y)
Converts a y-coordinate in pixels to physical units (e.g. mm).
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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.
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getZ
public double getZ(double z)
Converts a z-coordinate in pixels to physical units (e.g. mm).
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getRawX
public double getRawX(double x)
Converts a x-coordinate in physical units to pixels.
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getRawY
public double getRawY(double y)
Converts a y-coodinate in physical units to pixels.
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getRawZ
public double getRawZ(double z)
Converts a z-coodinate in physical units to pixels.
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getRawY
public double getRawY(double y, int imageHeight)
Converts a y-coodinate in physical units to pixels, taking into account the 'invertY' flag.
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setFunction
public void setFunction(int function, double[] coefficients, java.lang.String unit)
Sets the calibration function, coefficient table and unit (e.g. "OD").
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setFunction
public void setFunction(int function, double[] coefficients, java.lang.String unit, boolean zeroClip)
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setImage
public void setImage(ImagePlus imp)
Disables the density calibation if the specified image has a differenent bit depth.
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disableDensityCalibration
public void disableDensityCalibration()
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getValueUnit
public java.lang.String getValueUnit()
Returns the value unit.
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setValueUnit
public void setValueUnit(java.lang.String unit)
Sets the value unit.
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getCoefficients
public double[] getCoefficients()
Returns the calibration function coefficients.
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calibrated
public boolean calibrated()
Returns true if this image is density calibrated.
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getFunction
public int getFunction()
Returns the calibration function ID.
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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.
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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.
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getCValue
public double getCValue(int value)
Converts a raw pixel value to a density calibrated value.
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getCValue
public double getCValue(double value)
Converts a raw pixel value to a density calibrated value.
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getRawValue
public double getRawValue(double value)
Converts a density calibrated value into a raw pixel value.
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copy
public Calibration copy()
Returns a clone of this object.
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clone
public java.lang.Object clone()
- Overrides:
clone
in classjava.lang.Object
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equals
public boolean equals(Calibration cal)
Compares two Calibration objects for equality.
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isSigned16Bit
public boolean isSigned16Bit()
Returns true if this is a signed 16-bit image.
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setSigned16BitCalibration
public void setSigned16BitCalibration()
Sets up a calibration function that subtracts 32,768 from pixel values.
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zeroClip
public boolean zeroClip()
Returns true if zero clipping is enabled.
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setInvertY
public void setInvertY(boolean invertYCoordinates)
Sets the 'invertY' flag.
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getInvertY
public boolean getInvertY()
Returns the 'invertY' flag.
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setLoopBackAndForth
public static void setLoopBackAndForth(boolean loop)
Set the default state of the animation "Loop back and forth" flag
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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