PsdSignature2D (Morphokinetics)

java.lang.Object
- utils.psdAnalysis.PsdSignature2D

```
public class PsdSignature2D
extends java.lang.Object
```
Every surface is associated with a 2D map where each location represents a harmonic frequency and the associated/displayed value represents the squared sum of the real and imaginary amplitudes for that harmonic component (i.e., the power for that frequency). Low frequencies are correlated to large structures, such as hills or valleys, while large frequencies are related to small features, such as meandering steps. PSD maps are statistically equivalent for different images obtained under the same experimental conditions, while the maps change significantly when the conditions are modified. (From Ferrando, Gosalvez, Ayuela, JPC C, 2014, DOI: 10.1021/jp409812x)

Author:

N. Ferrando, J. Alberdi-Rodriguez

Field Summary

Fields
Modifier and Type	Field and Description
`private boolean`	`averaged`
`private float[][]`	`buffer`
`private int`	`dimensions`
`private edu.emory.mathcs.jtransforms.fft.FloatFFT_2D`	`fftCore`
`static int`	`HORIZONTAL_SYMMETRY`
`private int`	`measures`
`private float[][]`	`psd`
`private int`	`psdSizeX`
`private int`	`psdSizeY`
`private float[][]`	`psdTmp`
`private java.util.ArrayList<float[][]>`	`psdVector`
`private Restart`	`restart`
`private java.util.concurrent.Semaphore`	`semaphore`
`private int[]`	`sizes`
`private int`	`surfaceSizeX`
`private int`	`surfaceSizeY`
`static int`	`VERTICAL_SYMMETRY`

Constructor Summary

Constructors
Constructor and Description

PsdSignature2D(int surfaceSizeY, int surfaceSizeX, double extent)

Constructors
Constructor and Description
`PsdSignature2D(int surfaceSizeY, int surfaceSizeX, double extent)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addSurfaceSample(float[][] sampledSurface)`
`void`	`applySymmetryFold(int symmetryType)` It does the average of two points (either vertically or horizontally) and assigns that value to both points.
`static float[][]`	`doOnePsd(float[][] sampledSurface)` Does the PSD of the given surface.
`float`	`getMax()`
`float`	`getMin()`
`float[][]`	`getPsd()`
`void`	`printAvgToFile()`
`void`	`reset()`
`void`	`setRestart(Restart restart)`
`void`	`writePsdBinary(int simulationNumber)` Writes the current PSD to a mko (binary) file.
`void`	`writePsdText(int simulationNumber)` Writes the current PSD to a text file.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - fftCore
```
private edu.emory.mathcs.jtransforms.fft.FloatFFT_2D fftCore
```
  - psd
```
private float[][] psd
```
  - psdVector
```
private java.util.ArrayList<float[][]> psdVector
```
  - psdTmp
```
private float[][] psdTmp
```
  - buffer
```
private float[][] buffer
```
  - measures
```
private int measures
```
  - semaphore
```
private java.util.concurrent.Semaphore semaphore
```
  - averaged
```
private boolean averaged
```
  - psdSizeY
```
private final int psdSizeY
```
  - psdSizeX
```
private final int psdSizeX
```
  - surfaceSizeY
```
private final int surfaceSizeY
```
  - surfaceSizeX
```
private final int surfaceSizeX
```
  - sizes
```
private final int[] sizes
```
  - dimensions
```
private final int dimensions
```
  - restart
```
private Restart restart
```
  - HORIZONTAL_SYMMETRY
```
public static final int HORIZONTAL_SYMMETRY
```
    See Also:
    
    Constant Field Values
  - VERTICAL_SYMMETRY
```
public static final int VERTICAL_SYMMETRY
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - PsdSignature2D
```
public PsdSignature2D(int surfaceSizeY,
                      int surfaceSizeX,
                      double extent)
```
- Method Detail
  - addSurfaceSample
```
public void addSurfaceSample(float[][] sampledSurface)
```
  - doOnePsd
```
public static float[][] doOnePsd(float[][] sampledSurface)
```
    Does the PSD of the given surface.
    
    Parameters:
    
    sampledSurface - given surface
    
    Returns:
    
    PSD
  - getPsd
```
public float[][] getPsd()
```
  - reset
```
public void reset()
```
  - applySymmetryFold
```
public void applySymmetryFold(int symmetryType)
```
    It does the average of two points (either vertically or horizontally) and assigns that value to both points. Those two points are separated from the centre by the same amount and it assumes that the centre is the Cartesian centre.
    
    Parameters:
    
    symmetryType - horizontal or vertical (HORIZONTAL_SYMMETRY or VERTICAL_SYMMETRY)
  - writePsdBinary
```
public void writePsdBinary(int simulationNumber)
```
    Writes the current PSD to a mko (binary) file. The file name will be given by the restart folder and simulationNumber.
    
    Parameters:
    
    simulationNumber - the number of simulation
  - writePsdText
```
public void writePsdText(int simulationNumber)
```
    Writes the current PSD to a text file. The file name will be given by the restart folder and simulationNumber.
    
    Parameters:
    
    simulationNumber - the number of simulation
  - printAvgToFile
```
public void printAvgToFile()
```
  - setRestart
```
public void setRestart(Restart restart)
```
  - getMin
```
public float getMin()
```
  - getMax
```
public float getMax()
```

Class PsdSignature2D

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

fftCore

psd

psdVector

psdTmp

buffer

measures

semaphore

averaged

psdSizeY

psdSizeX

surfaceSizeY

surfaceSizeX

sizes

dimensions

restart

HORIZONTAL_SYMMETRY

VERTICAL_SYMMETRY

Constructor Detail

PsdSignature2D

Method Detail

addSurfaceSample

doOnePsd

getPsd

reset

applySymmetryFold

writePsdBinary

writePsdText

printAvgToFile

setRestart

getMin

getMax