holoj
Class HoloJUtils
java.lang.Objectholoj.HoloJUtils
- public final class HoloJUtils
- extends java.lang.Object
Class HoloJUtils contains static methods to perform useful task such as FFT and other mathematics.
| Constructor Summary | |
HoloJUtils()
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| Method Summary | |
static ij.process.FloatProcessor |
add(ij.process.ImageProcessor op1,
ij.process.ImageProcessor op2)
Add each pixel ImageProcessor to pixels of another ImageProcessor one-by-one. |
static HoloJProcessor |
addPhase(HoloJProcessor processor,
double angle)
Add to the source HoloJProcessor the specified phase in radians. |
HoloJProcessor |
addPhasePlate(HoloJProcessor processor,
double[] plateArray)
Add to the specified HoloJProcessor a phase plate stored in a double array. |
static double[] |
arrangeToComplexArray(double[] real,
double[] complex)
Arranges the two double array in a single double array with the sequence: re1,im1,re2,im2,...,reN,imN. |
static double[][][] |
arrangeToComplexMatrix(double[] real,
double[] complex,
int rowWidth)
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static double[] |
butterworthMask(int width,
int height,
int radius,
double c)
Creates a Butterworth filter mask and store it as double array. |
static ij.ImagePlus |
butterworthMaskImage(int width,
int height,
int radius,
double c,
java.lang.String title)
Creates an ImagePlus containing a Butterworth filter mask. |
static void |
c2cfft(double[] data,
int[] nn,
int isign)
Computes the Fast Fourier Transform of data passed as argument. |
static double[] |
circularMask(int width,
int height,
int radius)
Creates a circular mask and store it as double array. |
static HoloJProcessor |
divide(HoloJProcessor operand,
double value)
Divide by scalar value the real and complex pixels of HoloJProcessor operand and returns the result in a new HoloJProcessor. |
static HoloJProcessor |
divide(HoloJProcessor operand1,
HoloJProcessor operand2)
Returns the HoloJProcessor result of the complex division of operand1 by operand2. |
static ij.process.FloatProcessor |
divide(ij.process.ImageProcessor op1,
ij.process.ImageProcessor op2)
Divide pixels of ImageProcessor by pixels of another ImageProcessor one-by-one. |
static double[] |
extractComplexPixels(double[] input)
Extract the complex part of the complex array arranged with arrangeToComplexArray. |
static double[] |
extractRealPixels(double[] input)
Extract the real part of the complex array arranged with arrangeToComplexArray. |
static java.awt.Point |
getMaximumPosition(HoloJProcessor processor)
Finds the maximum of the modulus of pixels of HoloJProcessor. |
static java.awt.Point |
getMaximumPosition(HoloJProcessor processor,
ij.gui.Roi selection)
Finds the maximum of the modulus of HoloJProcessor pixels in the region specified by the selection. |
static ij.process.ImageProcessor |
getPhaseRenormalizedProcessor(ij.process.ImageProcessor source)
Renormalize the dynamic range of the source ImageProcessor to the range 2Pi. |
static java.awt.Point |
getSidebandCenter(HoloJProcessor processor,
int side)
Finds the position of the maximum lateral peak of the spectrum of HoloJProcessor. |
static ij.process.FloatProcessor |
makeCosProcessor(ij.process.ImageProcessor source)
Calculates the cosine of pixels in source. |
static ij.process.ImageProcessor |
makeInverseParabolicMask(int width,
int height)
Creates an inverse parabolic mask (intensity=1/(x^2+x^y)). |
static ij.process.ImageProcessor |
makeParabolicMask(int width,
int height)
Creates a parabolic mask (intensity=x^2+x^y). |
static ij.process.ImageProcessor |
makeSimmetricProcessor(ij.process.ImageProcessor source)
Makes a new ImageProcessor by mirroring the source processor. |
static ij.process.FloatProcessor |
makeSinProcessor(ij.process.ImageProcessor source)
Calculates the sine of pixels in source. |
static double |
modulus(double real,
double imaginary)
Calculates the modulus of complex number with real and imaginary parts passed as arguments. |
static ij.process.FloatProcessor |
multiply(double factor,
ij.process.ImageProcessor op1)
Multiply each pixel of ImageProcessor for the specified scalar factor. |
static HoloJProcessor |
multiply(HoloJProcessor operand,
double value)
Multiplies thbye scalar value the real and complex pixels of HoloJProcessor operand ad return the result in a new HoloJProcessor. |
static HoloJProcessor |
multiply(HoloJProcessor operand1,
HoloJProcessor operand2)
Returns an HoloJProcessor result from the complex multiplication of operand1 pixels for operand2 pixels. |
static ij.process.FloatProcessor |
multiply(ij.process.ImageProcessor op1,
ij.process.ImageProcessor op2)
Multiply each pixel ImageProcessor for pixels of another ImageProcessor one-by-one. |
static HoloJProcessor |
reconstruct(int radius,
int scaleFactor,
java.awt.Point sideCenter,
HoloJProcessor hologram,
boolean useButterworth)
Returns an HoloJProcessor containing reconstructed data. |
static HoloJProcessor |
reconstruct(int radius,
int scaleFactor,
java.awt.Point sideCenter,
HoloJProcessor hologram,
HoloJProcessor reference,
boolean useButterworth)
Returns an HoloJProcessor containing reconstructed data from hologram and reference. |
static void |
resetMin(ij.process.FloatProcessor ip)
Reset the minimum of FloatProcessor to zero. |
static void |
round(ij.process.FloatProcessor ip)
Round each pixel to nearby integer value. |
static HoloJProcessor |
subtract(HoloJProcessor operand,
double realValue,
double complexValue)
Subtract the complex number represented by (realValue, complexValue) from real and complex pixels of HoloJProcessor operand. |
static HoloJProcessor |
subtract(HoloJProcessor operand1,
HoloJProcessor operand2)
Subtracts the complex pixels of operand HoloJProcessor to real and complex pixels. |
static ij.process.FloatProcessor |
subtract(ij.process.ImageProcessor op1,
ij.process.ImageProcessor op2)
Subtract each pixel ImageProcessor to pixels of another ImageProcessor one-by-one. |
static HoloJProcessor |
sum(HoloJProcessor operand,
double realValue,
double complexValue)
Adds the complex number represented by (realValue, complexValue) to real and complex pixels of HoloJProcessor operand. |
static HoloJProcessor |
sum(HoloJProcessor operand1,
HoloJProcessor operand2)
Adds the complex pixels of operand1 HoloJProcessor to real and complex pixels of operand2 and returns the resulting HoloJProcessor. |
static void |
swap(double[] data,
int nx)
Swap the quadrants of data. |
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Constructor Detail |
HoloJUtils
public HoloJUtils()
| Method Detail |
modulus
public static double modulus(double real,
double imaginary)
- Calculates the modulus of complex number with real and imaginary parts passed as arguments.
- Parameters:
real- real part.imaginary- complex part.- Returns:
- the modulus.
arrangeToComplexArray
public static double[] arrangeToComplexArray(double[] real,
double[] complex)
- Arranges the two double array in a single double array with the sequence: re1,im1,re2,im2,...,reN,imN.
- Parameters:
real- real double array.complex- complex double array.- Returns:
- the rearranged double array.
extractRealPixels
public static double[] extractRealPixels(double[] input)
- Extract the real part of the complex array arranged with arrangeToComplexArray.
- Parameters:
input- the input complex array.- Returns:
- the extracted double real parts array.
extractComplexPixels
public static double[] extractComplexPixels(double[] input)
- Extract the complex part of the complex array arranged with arrangeToComplexArray.
- Parameters:
input- the input complex array.- Returns:
- the extracted double complex parts array.
arrangeToComplexMatrix
public static double[][][] arrangeToComplexMatrix(double[] real,
double[] complex,
int rowWidth)
c2cfft
public static void c2cfft(double[] data,
int[] nn,
int isign)
- Computes the Fast Fourier Transform of data passed as argument.
- Parameters:
data- data to be transformed in row-major mode and RE1,CO1,RE2,CO2... sequence.nn- array containing dimensions os data array.isign- forward or reverse direction.
swap
public static void swap(double[] data,
int nx)
- Swap the quadrants of data.
- Parameters:
data- array of data to be swapped.nx- length of a row.
butterworthMask
public static double[] butterworthMask(int width,
int height,
int radius,
double c)
- Creates a Butterworth filter mask and store it as double array.
- Parameters:
width- width of the mask.height- height of the mask.radius- radius of the aperture.c- value of aperture half-width.- Returns:
- a double array with the mask.
butterworthMaskImage
public static ij.ImagePlus butterworthMaskImage(int width,
int height,
int radius,
double c,
java.lang.String title)
- Creates an ImagePlus containing a Butterworth filter mask.
- Parameters:
width- width of the mask.height- height of the mask.radius- radius of the aperture.c- value of aperture half-width.- Returns:
- an ImagePlus containing the mask.
circularMask
public static double[] circularMask(int width,
int height,
int radius)
- Creates a circular mask and store it as double array.
- Parameters:
width- width of the mask.height- height of the mask.radius- radius of the aperture.- Returns:
- a double array with the mask.
getMaximumPosition
public static java.awt.Point getMaximumPosition(HoloJProcessor processor)
- Finds the maximum of the modulus of pixels of HoloJProcessor.
- Parameters:
processor- the HoloJProcessor.- Returns:
- the maximum position as a Point.
getMaximumPosition
public static java.awt.Point getMaximumPosition(HoloJProcessor processor, ij.gui.Roi selection)
- Finds the maximum of the modulus of HoloJProcessor pixels in the region specified by the selection.
- Parameters:
processor- HoloJProcessor to use.selection- selected area of the pixels.- Returns:
- the maximum position.
getSidebandCenter
public static java.awt.Point getSidebandCenter(HoloJProcessor processor, int side)
- Finds the position of the maximum lateral peak of the spectrum of HoloJProcessor.
The method search for the maximum of the spectrum excluding a circular region of radius 20 pixels centered around the origin of the spectrum and assuming the processor is in spectrum domain.
- Parameters:
processor- the HoloJProcessor.side- the selected side of spectrum.- Returns:
- the sideband center position.
sum
public static HoloJProcessor sum(HoloJProcessor operand, double realValue, double complexValue)
- Adds the complex number represented by (realValue, complexValue) to real and complex pixels of HoloJProcessor operand.
- Parameters:
operand- HoloJProcessor.realValue- real part of operand.complexValue- complex part of operand.- Returns:
- the resulting HoloJProcessor.
subtract
public static HoloJProcessor subtract(HoloJProcessor operand, double realValue, double complexValue)
- Subtract the complex number represented by (realValue, complexValue) from real and complex pixels of HoloJProcessor operand.
- Parameters:
operand- HoloJProcessor.realValue- real part of operand.complexValue- complex part of operand.- Returns:
- the resulting HoloJProcessor.
multiply
public static HoloJProcessor multiply(HoloJProcessor operand, double value)
- Multiplies thbye scalar value the real and complex pixels of HoloJProcessor operand ad return the result in a new HoloJProcessor.
- Parameters:
operand- HoloJProcessor.value- scalar value multiplier.- Returns:
- the resulting HoloJProcessor.
divide
public static HoloJProcessor divide(HoloJProcessor operand, double value)
- Divide by scalar value the real and complex pixels of HoloJProcessor operand and returns the result in a new HoloJProcessor.
- Parameters:
operand- HoloJProcessor.value- scalar value multiplier.- Returns:
- the resulting HoloJProcessor.
sum
public static HoloJProcessor sum(HoloJProcessor operand1, HoloJProcessor operand2)
- Adds the complex pixels of operand1 HoloJProcessor to real and complex pixels of operand2 and returns the resulting HoloJProcessor.
- Parameters:
operand1- the first HoloJProcessor operand.operand2- the second HoloJProcessor operand.- Returns:
- the resulting HoloJProcessor.
subtract
public static HoloJProcessor subtract(HoloJProcessor operand1, HoloJProcessor operand2)
- Subtracts the complex pixels of operand HoloJProcessor to real and complex pixels.
- Parameters:
operand1- the HoloJProcessor first operand.operand2- the HoloJProcessor second operand.- Returns:
- the resulting HoloJProcessor.
multiply
public static HoloJProcessor multiply(HoloJProcessor operand1, HoloJProcessor operand2)
- Returns an HoloJProcessor result from the complex multiplication of operand1 pixels for operand2 pixels.
- Parameters:
operand1- the HoloJProcessor first operand.operand2- the HoloJProcessor second operand.- Returns:
- the resulting HoloJProcessor.
divide
public static HoloJProcessor divide(HoloJProcessor operand1, HoloJProcessor operand2)
- Returns the HoloJProcessor result of the complex division of operand1 by operand2.
- Parameters:
operand1- the HoloJProcessor first operand.operand2- the HoloJProcessor second operand.- Returns:
- the resulting HoloJProcessor.
reconstruct
public static HoloJProcessor reconstruct(int radius, int scaleFactor, java.awt.Point sideCenter, HoloJProcessor hologram, boolean useButterworth)
- Returns an HoloJProcessor containing reconstructed data.
- Parameters:
radius- radius of reconstructed frequency region.scaleFactor- scale factor of final reconstructed image.hologram- hologram to be reconstructed.useButterworth- flag for using soft aperture.- Returns:
- the reconstructed image.
reconstruct
public static HoloJProcessor reconstruct(int radius, int scaleFactor, java.awt.Point sideCenter, HoloJProcessor hologram, HoloJProcessor reference, boolean useButterworth)
- Returns an HoloJProcessor containing reconstructed data from hologram and reference.
- Parameters:
radius- radius of reconstructed frequency region.scaleFactor- scale factor of final reconstructed image.hologram- hologram to be reconstructed.reference- hologram used as reference in void.useButterworth- flag for using soft aperture.- Returns:
- the reconstructed image.
makeCosProcessor
public static ij.process.FloatProcessor makeCosProcessor(ij.process.ImageProcessor source)
- Calculates the cosine of pixels in source.
- Parameters:
source- the source ImaeProcessor.- Returns:
- a FloatProcessor containing the cosine.
makeSinProcessor
public static ij.process.FloatProcessor makeSinProcessor(ij.process.ImageProcessor source)
- Calculates the sine of pixels in source.
- Parameters:
source- the source ImaeProcessor.- Returns:
- a FloatProcessor containing the sine.
makeSimmetricProcessor
public static ij.process.ImageProcessor makeSimmetricProcessor(ij.process.ImageProcessor source)
- Makes a new ImageProcessor by mirroring the source processor.
- Parameters:
source- source ImageProcessor.- Returns:
- the symmetric ImageProcessor.
getPhaseRenormalizedProcessor
public static ij.process.ImageProcessor getPhaseRenormalizedProcessor(ij.process.ImageProcessor source)
- Renormalize the dynamic range of the source ImageProcessor to the range 2Pi.
- Parameters:
source- source ImageProcessor.- Returns:
- a renormalized ImageProcessor.
makeParabolicMask
public static ij.process.ImageProcessor makeParabolicMask(int width,
int height)
- Creates a parabolic mask (intensity=x^2+x^y).
- Parameters:
width- width of the mask.height- height of the mask.- Returns:
- the ImageProcessor mask.
makeInverseParabolicMask
public static ij.process.ImageProcessor makeInverseParabolicMask(int width,
int height)
- Creates an inverse parabolic mask (intensity=1/(x^2+x^y)).
- Parameters:
width- width of the mask.height- height of the mask.- Returns:
- the ImageProcessor mask.
multiply
public static ij.process.FloatProcessor multiply(ij.process.ImageProcessor op1,
ij.process.ImageProcessor op2)
- Multiply each pixel ImageProcessor for pixels of another ImageProcessor one-by-one.
- Parameters:
op1- ImageProcessor 1.op2- ImageProcessor 2.- Returns:
- the resulting ImageProcessor.
multiply
public static ij.process.FloatProcessor multiply(double factor,
ij.process.ImageProcessor op1)
- Multiply each pixel of ImageProcessor for the specified scalar factor.
- Parameters:
factor- scalar factor.op1- ImageProcessor.- Returns:
- the resulting FloatProcessor.
divide
public static ij.process.FloatProcessor divide(ij.process.ImageProcessor op1,
ij.process.ImageProcessor op2)
- Divide pixels of ImageProcessor by pixels of another ImageProcessor one-by-one.
- Parameters:
op1- ImageProcessor 1.op2- ImageProcessor 2.- Returns:
- the resulting ImageProcessor.
add
public static ij.process.FloatProcessor add(ij.process.ImageProcessor op1,
ij.process.ImageProcessor op2)
- Add each pixel ImageProcessor to pixels of another ImageProcessor one-by-one.
- Parameters:
op1- ImageProcessor 1.op2- ImageProcessor 2.- Returns:
- the resulting ImageProcessor.
subtract
public static ij.process.FloatProcessor subtract(ij.process.ImageProcessor op1,
ij.process.ImageProcessor op2)
- Subtract each pixel ImageProcessor to pixels of another ImageProcessor one-by-one.
- Parameters:
op1- ImageProcessor 1.op2- ImageProcessor 2.- Returns:
- the resulting ImageProcessor.
resetMin
public static void resetMin(ij.process.FloatProcessor ip)
- Reset the minimum of FloatProcessor to zero.
- Parameters:
ip- source FloatProcessor.
round
public static void round(ij.process.FloatProcessor ip)
- Round each pixel to nearby integer value.
- Parameters:
ip- source FloatProcessor.
addPhase
public static HoloJProcessor addPhase(HoloJProcessor processor, double angle)
- Add to the source HoloJProcessor the specified phase in radians.
- Parameters:
processor- an HoloJProcessor.angle- radians to add.- Returns:
- the resulting HoloJProcessor.
addPhasePlate
public HoloJProcessor addPhasePlate(HoloJProcessor processor, double[] plateArray)
- Add to the specified HoloJProcessor a phase plate stored in a double array.
- Parameters:
processor- the HoloJProcessor.plateArray- a phase plate.- Returns:
- the resulting HoloJProcessor.
