HoloJ

holoj
Class HoloJProcessor

java.lang.Object
  holoj.HoloJProcessor

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public class HoloJProcessor

extends java.lang.Object

Class HoloJProcessor contains data and methods to provide high level access and manipulation to complex valued pixel data.

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Constructor Summary

HoloJProcessor(double[] realPixels, double[] complexPixels, int width, int height)           Creates a new object of the HoloJProcessor class.

HoloJProcessor(double[] realPixels, int width, int height)           Creates a new object of the HoloJProcessor class.

HoloJProcessor(ij.process.ImageProcessor ip)           Creates a new object of the class HoloJProcessor.

HoloJProcessor(ij.process.ImageProcessor realIp, ij.process.ImageProcessor complexIp)           Creates a new object of the class HoloJProcessor, starting from data contained in the two ImageProcessors provided.

HoloJProcessor(int width, int height)           Creates a new object of the class HoloJProcessor.

 

Method Summary
void	add(double[] operandArray)           Add to complex pixels the scalar data in operand array.
void	add(HoloJProcessor operand)           Adds the complex pixels of operand HoloJProcessor to real and complex pixels.
void	add(ij.process.ImageProcessor operand)           Add to real pixels the real pixels of operand ImageProcessor.
void	addPhase(double angle)           Add to complex pixels phase the specified radians.
void	addPhasePlate(double[] plateArray)           Add to complex pixels the phase plate specified by the double array.
ij.process.FloatProcessor	createAmplitudeProcessor()           Creates a amplitude ImageProcessor from realPixels and complexPixels.
ij.process.FloatProcessor	createPhaseProcessor()           Creates a phase ImageProcessor from realPixels and complexPixels.
ij.process.FloatProcessor	createPowerSpectrumProcessor()           Creates a power spectrum ImageProcessor from realPixels and complexPixels.
ij.process.FloatProcessor	createSpectrumProcessor()           Creates a spectrum ImageProcessor from realPixels and complexPixels.
void	divide(double[] operandArray)           Divide complex pixels by scalar data in operand array.
void	divide(HoloJProcessor operand)           Divides real and complex pixels by the complex pixels of operand HoloJProcessor.
void	divide(ij.process.ImageProcessor operand)           Divide the real and complex pixels by the real pixels of operand ImageProcessor.
void	doFFT()           Perform Fast Fourier Transform, in the forward direction of data stored in real and complex pixels.
void	doInverseFFT()           Perform Fast Fourier Transform, in the backward direction of data stored in real and complex pixels.
ij.measure.Calibration	getCalibration()           Return the calibration of this HoloJPpocessor.
double[]	getComplexPixelsArray()           Returns a double array containing the complex pixels in row major mode.
int	getHeight()           Returns the height of the image.
java.awt.Point	getMaximumPosition()           Finds the maximum of the modulus of realPixels and complexPixels.
java.awt.Point	getMaximumPosition(ij.gui.Roi selection)           Finds the maximum of the modulus of realPixels and complexPixels in the region specified by the selection.
double[]	getRealPixelsArray()           Returns a double array containing the real pixels in row major mode.
HoloJProcessor	getSideband(java.awt.Point sideCenter, int radius, int scaleFactor, boolean useButterworth)           Returns an HoloJProcessor containing the selected sideband data.
java.awt.Point	getSidebandCenter(int side)           Finds the position of the maximum lateral peak of the spectrum.
int	getSize()           Returns the size of the image.
java.lang.String	getTitle()           Return the title of this HoloJProcessor.
int	getWidth()           Returns the width of the image.
boolean	isSpectrumDomain()           Returns true if the image has being Fourier transformed.
ij.ImagePlus	makeAmplitudeImage(java.lang.String title)           Creates an ImagePlus with the amplitude of data.
ij.ImagePlus	makePhaseImage(java.lang.String title)           Creates an ImagePlus with the phase of data.
ij.ImagePlus	makePowerSpectrumImage(java.lang.String title)           Creates an ImagePlus with the power spectrum of data.
ij.ImagePlus	makeSpectrumImage(java.lang.String title)           Creates an ImagePlus with the spectrum of data.
void	multiply(double[] operandArray)           Multiply complex pixels by scalar data in operand array.
void	multiply(HoloJProcessor operand)           Multiplies real and complex pixels by the complex pixels of operand HoloJProcessor.
void	multiply(ij.process.ImageProcessor operand)           Multiplies real and complex pixels by the scalar pixels of operand ImageProcessor.
void	setCalibration(ij.measure.Calibration newCal)           Set the calibration of this HoloJProcessor to new calibration.
void	setComplexOrigin()           Set origin of this HoloJProcessor to Complex.
void	setComplexPixelsArray(double[] pixels)           Sets complex pixels from a double array of data in row major mode.
void	setRealOrigin()           Set origin of this HoloJProcessor to Real.
void	setRealPixelsArray(double[] pixels)           Sets real pixels from a double array of data in row major mode.
void	setTitle(java.lang.String newTitle)           Set the title of this HoloJProcesor to new title.
void	show(java.lang.String title)           Creates and shows an ImagePlus containing the power spectrum.
void	showAmplitude(java.lang.String title)           Creates and show an ImagePlus displaying the amplitude of data.
void	showPhase(java.lang.String title)           Creates and show an ImagePlus displaying the phase of data.
void	showPowerSpectrum(java.lang.String title)           Creates and show an ImagePlus displaying the power spectrum of data.
void	showSpectrum(java.lang.String title)           Creates and show an ImagePlus displaying the spectrum of data.
void	subtract(double[] operandArray)           Subtract to complex pixels the scalar data in operand array.
void	subtract(HoloJProcessor operand)           Subtracts the complex pixels of operand HoloJProcessor to real and complex pixels.
void	subtract(ij.process.ImageProcessor operand)           Subtract to real pixels, the real pixels of operand ImageProcessor.

 

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

 

Constructor Detail

HoloJProcessor

public HoloJProcessor(int width,
                      int height)

Creates a new object of the class HoloJProcessor. The size of the image are given as parameter. The data pixels are empty and are not initialized.

Parameters:

width - the size of the image along the X-axis

height - the size of the image along the Y-axis

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HoloJProcessor

public HoloJProcessor(ij.process.ImageProcessor ip)

Creates a new object of the class HoloJProcessor. Data is retrieved from ImageProcessor given as argument. ImageProcessor data fill the real pixels data, while complex data is empty and not initialized.

Parameters:

ip - ImageProcessor providing real data value.

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HoloJProcessor

public HoloJProcessor(ij.process.ImageProcessor realIp,
                      ij.process.ImageProcessor complexIp)

Creates a new object of the class HoloJProcessor, starting from data contained in the two ImageProcessors provided.

Parameters:

realIp - ImageProcessor providing real data value.

complexIp - ImageProcessor providing complex data value.

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HoloJProcessor

public HoloJProcessor(double[] realPixels,
                      double[] complexPixels,
                      int width,
                      int height)

Creates a new object of the HoloJProcessor class. Data is provided by two double array containing real and complex pixels.

Parameters:

realPixels - real pixels array.

complexPixels - complex pixels array.

width - image width.

height - image height.

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HoloJProcessor

public HoloJProcessor(double[] realPixels,
                      int width,
                      int height)

Creates a new object of the HoloJProcessor class. Data is provided by double array containing real pixels.

Parameters:

realPixels - real pixels array.

width - image width.

height - image height.

Method Detail

getRealPixelsArray

public double[] getRealPixelsArray()

Returns a double array containing the real pixels in row major mode.

Returns:

the pixels array.

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getComplexPixelsArray

public double[] getComplexPixelsArray()

Returns a double array containing the complex pixels in row major mode.

Returns:

the pixels array.

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setRealPixelsArray

public void setRealPixelsArray(double[] pixels)

Sets real pixels from a double array of data in row major mode.

Parameters:

pixels - the pixels array.

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setComplexPixelsArray

public void setComplexPixelsArray(double[] pixels)

Sets complex pixels from a double array of data in row major mode.

Parameters:

pixels - the pixels array.

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getSize

public int getSize()

Returns the size of the image.

Returns:

the image size.

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getWidth

public int getWidth()

Returns the width of the image.

Returns:

the image width.

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getHeight

public int getHeight()

Returns the height of the image.

Returns:

the image height.

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isSpectrumDomain

public boolean isSpectrumDomain()

Returns true if the image has being Fourier transformed.

Returns:

true if image is in spectrum domain.

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add

public void add(HoloJProcessor operand)

Adds the complex pixels of operand HoloJProcessor to real and complex pixels.

Parameters:

operand - theHoloJProcessorr operand.

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subtract

public void subtract(HoloJProcessor operand)

Subtracts the complex pixels of operand HoloJProcessor to real and complex pixels.

Parameters:

operand - theHoloJProcessorr operand.

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multiply

public void multiply(HoloJProcessor operand)

Multiplies real and complex pixels by the complex pixels of operand HoloJProcessor.

Parameters:

operand - theHoloJProcessorr operand.

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multiply

public void multiply(ij.process.ImageProcessor operand)

Multiplies real and complex pixels by the scalar pixels of operand ImageProcessor.

Parameters:

operand - the ImageProcessor operand.

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add

public void add(ij.process.ImageProcessor operand)

Add to real pixels the real pixels of operand ImageProcessor.

Parameters:

operand - the ImageProcessor operand.

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subtract

public void subtract(ij.process.ImageProcessor operand)

Subtract to real pixels, the real pixels of operand ImageProcessor.

Parameters:

operand - the ImageProcessor operand.

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divide

public void divide(ij.process.ImageProcessor operand)

Divide the real and complex pixels by the real pixels of operand ImageProcessor.

Parameters:

operand - the ImageProcessor operand.

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multiply

public void multiply(double[] operandArray)

Multiply complex pixels by scalar data in operand array.

Parameters:

operandArray - the array operand.

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divide

public void divide(double[] operandArray)

Divide complex pixels by scalar data in operand array.

Parameters:

operandArray - the array operand.

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add

public void add(double[] operandArray)

Add to complex pixels the scalar data in operand array.

Parameters:

operandArray - the array operand.

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subtract

public void subtract(double[] operandArray)

Subtract to complex pixels the scalar data in operand array.

Parameters:

operandArray - the array operand.

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divide

public void divide(HoloJProcessor operand)

Divides real and complex pixels by the complex pixels of operand HoloJProcessor.

Parameters:

operand - the HoloJProcessor operand.

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addPhase

public void addPhase(double angle)

Add to complex pixels phase the specified radians.

Parameters:

angle - radians to add.

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addPhasePlate

public void addPhasePlate(double[] plateArray)

Add to complex pixels the phase plate specified by the double array.

Parameters:

plateArray - the array of radians to add.

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setRealOrigin

public void setRealOrigin()

Set origin of this HoloJProcessor to Real.

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setComplexOrigin

public void setComplexOrigin()

Set origin of this HoloJProcessor to Complex.

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setCalibration

public void setCalibration(ij.measure.Calibration newCal)

Set the calibration of this HoloJProcessor to new calibration.

Parameters:

newCal - new calibration to apply.

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getCalibration

public ij.measure.Calibration getCalibration()

Return the calibration of this HoloJPpocessor.

Returns:

the calibration.

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setTitle

public void setTitle(java.lang.String newTitle)

Set the title of this HoloJProcesor to new title.

Parameters:

newTitle - the new title to use.

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getTitle

public java.lang.String getTitle()

Return the title of this HoloJProcessor.

Returns:

the title.

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doFFT

public void doFFT()

Perform Fast Fourier Transform, in the forward direction of data stored in real and complex pixels. If source image is real, performes a RealToComplex transform using IJ FHT class.

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doInverseFFT

public void doInverseFFT()

Perform Fast Fourier Transform, in the backward direction of data stored in real and complex pixels.

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show

public void show(java.lang.String title)

Creates and shows an ImagePlus containing the power spectrum. The method uses showPowerSpectrum.

Parameters:

title - title for the image displayied.

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showPowerSpectrum

public void showPowerSpectrum(java.lang.String title)

Creates and show an ImagePlus displaying the power spectrum of data.

Parameters:

title - the title of the displayied image.

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showSpectrum

public void showSpectrum(java.lang.String title)

Creates and show an ImagePlus displaying the spectrum of data.

Parameters:

title - the title of the displayied image.

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showAmplitude

public void showAmplitude(java.lang.String title)

Creates and show an ImagePlus displaying the amplitude of data.

Parameters:

title - the title of the displayied image.

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showPhase

public void showPhase(java.lang.String title)

Creates and show an ImagePlus displaying the phase of data.

Parameters:

title - the title of the displayied image.

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makePowerSpectrumImage

public ij.ImagePlus makePowerSpectrumImage(java.lang.String title)

Creates an ImagePlus with the power spectrum of data.

Parameters:

title - the title of the image.

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makeSpectrumImage

public ij.ImagePlus makeSpectrumImage(java.lang.String title)

Creates an ImagePlus with the spectrum of data.

Parameters:

title - the title of the image.

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makeAmplitudeImage

public ij.ImagePlus makeAmplitudeImage(java.lang.String title)

Creates an ImagePlus with the amplitude of data.

Parameters:

title - the title of the image.

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makePhaseImage

public ij.ImagePlus makePhaseImage(java.lang.String title)

Creates an ImagePlus with the phase of data.

Parameters:

title - the title of the image.

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createPowerSpectrumProcessor

public ij.process.FloatProcessor createPowerSpectrumProcessor()

Creates a power spectrum ImageProcessor from realPixels and complexPixels.

Returns:

the FloatProcessor

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createSpectrumProcessor

public ij.process.FloatProcessor createSpectrumProcessor()

Creates a spectrum ImageProcessor from realPixels and complexPixels.

Returns:

the FloatProcessor

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createAmplitudeProcessor

public ij.process.FloatProcessor createAmplitudeProcessor()

Creates a amplitude ImageProcessor from realPixels and complexPixels.

Returns:

the FloatProcessor

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createPhaseProcessor

public ij.process.FloatProcessor createPhaseProcessor()

Creates a phase ImageProcessor from realPixels and complexPixels.

Returns:

the FloatProcessor

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getMaximumPosition

public java.awt.Point getMaximumPosition()

Finds the maximum of the modulus of realPixels and complexPixels.

Returns:

the maximum position.

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getMaximumPosition

public java.awt.Point getMaximumPosition(ij.gui.Roi selection)

Finds the maximum of the modulus of realPixels and complexPixels in the region specified by the selection.

Parameters:

selection - selected area of the pixels.

Returns:

the maximum position.

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getSidebandCenter

public java.awt.Point getSidebandCenter(int side)

Finds the position of the maximum lateral peak of the spectrum. The method search for the maximum of the spectrum excluding a circular region of radius 20 pixels centered around the origin of the spectrum.

Parameters:

side - side of the spectrum where to look for the maximum.

Returns:

the sideband position.

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getSideband

public HoloJProcessor getSideband(java.awt.Point sideCenter,
                                  int radius,
                                  int scaleFactor,
                                  boolean useButterworth)

Returns an HoloJProcessor containing the selected sideband data.

Parameters:

sideCenter - Point of sideband center.

radius - radius of the selected region.

scaleFactor - scale factor of final reconstructed image.

useButterworth - flag for using soft aperture.

Returns:

the selected sideband.