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Commit f3615f99 authored by Daniel Felipe GONZALEZ OBANDO's avatar Daniel Felipe GONZALEZ OBANDO
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Separated logic from plugin behavior 

- Created FFTCalculator to expose statically FFT calculation from code
instead of creating a new plugin instance
parent 804f8aee
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src/plugins/praveen/fft/FFT.java
+ 6
− 145
View file @ f3615f99
package plugins.praveen.fft;
import cern.colt.function.tdouble.DoubleDoubleFunction;
import edu.emory.mathcs.jtransforms.fft.DoubleFFT_2D;
import edu.emory.mathcs.jtransforms.fft.DoubleFFT_3D;
import icy.image.IcyBufferedImage;
import icy.sequence.Sequence;
import icy.type.DataType;
import icy.type.collection.array.Array1DUtil;
import plugins.adufour.blocks.lang.Block;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.ezplug.EzPlug;
......@@ -14,23 +8,11 @@ import plugins.adufour.ezplug.EzVarBoolean;
import plugins.adufour.ezplug.EzVarEnum;
import plugins.adufour.ezplug.EzVarSequence;
import plugins.adufour.vars.lang.VarSequence;
import plugins.praveen.fft.FFTCalculator.FFTDims;
import plugins.praveen.fft.FFTCalculator.FFTOutputType;
public class FFT extends EzPlug implements Block {
public static enum FFTDims {
FFT_2D("2D (xy)"), FFT_3D("3D (xyz)");
private String stringValue;
FFTDims(String s) { stringValue = s; }
public String toString() { return stringValue; }
}
public static enum FFTOutputType {
MAGNITUDE_PHASE("Magnitude/Phase Pair"), REAL_IMAG("Real/Imaginary Pair");
private String stringValue;
FFTOutputType(String s) { stringValue = s; }
public String toString() { return stringValue; }
}
EzVarSequence input = new EzVarSequence("Input");
EzVarEnum<FFTDims> ndims = new EzVarEnum<FFTDims>("Type", FFTDims.values(), 0);
EzVarEnum<FFTOutputType> outputType = new EzVarEnum<FFTOutputType>("Output as", FFTOutputType.values(), 0);
......@@ -69,18 +51,18 @@ public class FFT extends EzPlug implements Block {
if(ndims.getValue()==FFTDims.FFT_2D)
{
fSequence = FFT_2D(sequence, swap.getValue(), outputType.getValue());
fSequence = FFTCalculator.FFT_2D(sequence, swap.getValue(), outputType.getValue());
}
else
{
if (sequence.getSizeZ() >= 2)
{
fSequence = FFT_3D(sequence, swap.getValue(), outputType.getValue());
fSequence = FFTCalculator.FFT_3D(sequence, swap.getValue(), outputType.getValue());
}
else
{
System.err.println("Sequence depth is 1, so computing 2D FFT instead of 3D.");
fSequence = FFT_2D(sequence, swap.getValue(), outputType.getValue());
fSequence = FFTCalculator.FFT_2D(sequence, swap.getValue(), outputType.getValue());
}
}
......@@ -91,128 +73,7 @@ public class FFT extends EzPlug implements Block {
fSequenceVar.setValue(fSequence);
}
private Sequence FFT_3D(Sequence sequence, boolean swap, FFTOutputType outputType) {
int _w = sequence.getSizeX();
int _h = sequence.getSizeY();
int _z = sequence.getSizeZ();
final DoubleFFT_3D fft = new DoubleFFT_3D(_z, _h, _w);
Sequence fSequence = new Sequence();
fSequence.setName("Fourier Transform 3D");
// allocate the output sequence
for(int k = 0; k < _z; k++)
{
IcyBufferedImage fImage = new IcyBufferedImage(_w, _h, 2, DataType.DOUBLE);
fSequence.setImage(0, k, fImage);
}
double[] fArray = new double[_w*_h*_z*2];
// copy the data in fArray, with proper structure
for(int k = 0; k < _z; k++)
{
Array1DUtil.arrayToDoubleArray(sequence.getDataXY(0, k, 0), 0, fArray, k*_w*_h, _w*_h, sequence.isSignedDataType());
}
fft.realForwardFull(fArray);
// direct reference to 3D byte array data [Z][C][XY] for specified t
double[][][] resultData = fSequence.getDataXYCZAsDouble(0);
DoubleDoubleFunction channel0ApplyFunction = null;
DoubleDoubleFunction channel1ApplyFunction = null;
if(outputType == FFTOutputType.MAGNITUDE_PHASE)
{
channel0ApplyFunction = new ComplexFunctions.Magnitude();
channel1ApplyFunction = new ComplexFunctions.Angle();
fSequence.setChannelName(0, "Magnitude");
fSequence.setChannelName(1, "Phase");
}
else
{
channel0ApplyFunction = new ComplexFunctions.Real();
channel1ApplyFunction = new ComplexFunctions.Imag();
fSequence.setChannelName(0, "Real");
fSequence.setChannelName(1, "Imaginary");
}
AssignFunction3D assignFunction = null;
if(!swap) // No Quadrant swapping. Leave as it is.
{
assignFunction = new AssignFunctions.DirectAssign3D();
}
else
{
assignFunction = new AssignFunctions.SwapAssign3D(); // Swap Quadrants
}
assignFunction.assign(fArray, resultData, _w, _h, _z, 0, channel0ApplyFunction);
assignFunction.assign(fArray, resultData, _w, _h, _z, 1, channel1ApplyFunction);
fSequence.dataChanged();
return fSequence;
}
private Sequence FFT_2D(Sequence sequence, boolean swap, FFTOutputType outputType)
{
Sequence fSequence = new Sequence();
fSequence.setName("Fourier Transform 2D");
int _w = sequence.getSizeX();
int _h = sequence.getSizeY();
int _z = sequence.getSizeZ();
final DoubleFFT_2D fft = new DoubleFFT_2D(_h, _w);
DoubleDoubleFunction channel0Function = null;
DoubleDoubleFunction channel1Function = null;
if(outputType == FFTOutputType.MAGNITUDE_PHASE)
{
channel0Function = new ComplexFunctions.Magnitude();
channel1Function = new ComplexFunctions.Angle();
fSequence.setChannelName(0, "Magnitude");
fSequence.setChannelName(1, "Phase");
}
else // Real/Imaginary Pair
{
channel0Function = new ComplexFunctions.Real();
channel1Function = new ComplexFunctions.Imag();
fSequence.setChannelName(0, "Real");
fSequence.setChannelName(1, "Imaginary");
}
AssignFunction2D assignFunction = null;
if(!swap) //No Quadrant swapping
{
assignFunction = new AssignFunctions.DirectAssign2D();
}
else //Swap quadrants
{
assignFunction = new AssignFunctions.SwapAssign2D();
}
for(int k = 0; k < _z; k++)
{
double[] fArray = new double[_w*_h*2];
Array1DUtil.arrayToDoubleArray(sequence.getDataXY(0, k, 0), 0, fArray, 0, _w*_h, sequence.isSignedDataType());
// Computes 2D forward DFT of real data leaving the result in fArray
// Because the result is stored in fArray, fArray must be of size rows*2*columns,
// with only the first rows*columns elements filled with real data.
fft.realForwardFull(fArray);
IcyBufferedImage resultArray = new IcyBufferedImage(_w, _h, 2, DataType.DOUBLE);
double[][] resultData = resultArray.getDataXYCAsDouble();
assignFunction.assign(fArray, resultData[0], _w, _h, channel0Function);
assignFunction.assign(fArray, resultData[1], _w, _h, channel1Function);
resultArray.dataChanged();
fSequence.setImage(0, k, resultArray);
}
return fSequence;
}
@Override
public void clean() {
......
src/plugins/praveen/fft/FFTCalculator.java 0 → 100644
+ 172
− 0
View file @ f3615f99
package plugins.praveen.fft;
import cern.colt.function.tdouble.DoubleDoubleFunction;
import edu.emory.mathcs.jtransforms.fft.DoubleFFT_2D;
import edu.emory.mathcs.jtransforms.fft.DoubleFFT_3D;
import icy.image.IcyBufferedImage;
import icy.sequence.Sequence;
import icy.type.DataType;
import icy.type.collection.array.Array1DUtil;
public class FFTCalculator
{
public static enum FFTDims
{
FFT_2D("2D (xy)"), FFT_3D("3D (xyz)");
private String stringValue;
FFTDims(String s)
{
stringValue = s;
}
public String toString()
{
return stringValue;
}
}
public static enum FFTOutputType
{
MAGNITUDE_PHASE("Magnitude/Phase Pair"), REAL_IMAG("Real/Imaginary Pair");
private String stringValue;
FFTOutputType(String s)
{
stringValue = s;
}
public String toString()
{
return stringValue;
}
}
public static Sequence FFT_3D(Sequence sequence, boolean swap, FFTOutputType outputType)
{
int _w = sequence.getSizeX();
int _h = sequence.getSizeY();
int _z = sequence.getSizeZ();
final DoubleFFT_3D fft = new DoubleFFT_3D(_z, _h, _w);
Sequence fSequence = new Sequence();
fSequence.setName("Fourier Transform 3D");
// allocate the output sequence
for (int k = 0; k < _z; k++)
{
IcyBufferedImage fImage = new IcyBufferedImage(_w, _h, 2, DataType.DOUBLE);
fSequence.setImage(0, k, fImage);
}
double[] fArray = new double[_w * _h * _z * 2];
// copy the data in fArray, with proper structure
for (int k = 0; k < _z; k++)
{
Array1DUtil.arrayToDoubleArray(sequence.getDataXY(0, k, 0), 0, fArray, k * _w * _h, _w * _h,
sequence.isSignedDataType());
}
fft.realForwardFull(fArray);
// direct reference to 3D byte array data [Z][C][XY] for specified t
double[][][] resultData = fSequence.getDataXYCZAsDouble(0);
DoubleDoubleFunction channel0ApplyFunction = null;
DoubleDoubleFunction channel1ApplyFunction = null;
if (outputType == FFTOutputType.MAGNITUDE_PHASE)
{
channel0ApplyFunction = new ComplexFunctions.Magnitude();
channel1ApplyFunction = new ComplexFunctions.Angle();
fSequence.setChannelName(0, "Magnitude");
fSequence.setChannelName(1, "Phase");
}
else
{
channel0ApplyFunction = new ComplexFunctions.Real();
channel1ApplyFunction = new ComplexFunctions.Imag();
fSequence.setChannelName(0, "Real");
fSequence.setChannelName(1, "Imaginary");
}
AssignFunction3D assignFunction = null;
if (!swap) // No Quadrant swapping. Leave as it is.
{
assignFunction = new AssignFunctions.DirectAssign3D();
}
else
{
assignFunction = new AssignFunctions.SwapAssign3D(); // Swap Quadrants
}
assignFunction.assign(fArray, resultData, _w, _h, _z, 0, channel0ApplyFunction);
assignFunction.assign(fArray, resultData, _w, _h, _z, 1, channel1ApplyFunction);
fSequence.dataChanged();
return fSequence;
}
public static Sequence FFT_2D(Sequence sequence, boolean swap, FFTOutputType outputType)
{
Sequence fSequence = new Sequence();
fSequence.setName("Fourier Transform 2D");
int _w = sequence.getSizeX();
int _h = sequence.getSizeY();
int _z = sequence.getSizeZ();
final DoubleFFT_2D fft = new DoubleFFT_2D(_h, _w);
DoubleDoubleFunction channel0Function = null;
DoubleDoubleFunction channel1Function = null;
if (outputType == FFTOutputType.MAGNITUDE_PHASE)
{
channel0Function = new ComplexFunctions.Magnitude();
channel1Function = new ComplexFunctions.Angle();
fSequence.setChannelName(0, "Magnitude");
fSequence.setChannelName(1, "Phase");
}
else // Real/Imaginary Pair
{
channel0Function = new ComplexFunctions.Real();
channel1Function = new ComplexFunctions.Imag();
fSequence.setChannelName(0, "Real");
fSequence.setChannelName(1, "Imaginary");
}
AssignFunction2D assignFunction = null;
if (!swap) // No Quadrant swapping
{
assignFunction = new AssignFunctions.DirectAssign2D();
}
else // Swap quadrants
{
assignFunction = new AssignFunctions.SwapAssign2D();
}
for (int k = 0; k < _z; k++)
{
double[] fArray = new double[_w * _h * 2];
Array1DUtil.arrayToDoubleArray(sequence.getDataXY(0, k, 0), 0, fArray, 0, _w * _h,
sequence.isSignedDataType());
// Computes 2D forward DFT of real data leaving the result in fArray
// Because the result is stored in fArray, fArray must be of size rows*2*columns,
// with only the first rows*columns elements filled with real data.
fft.realForwardFull(fArray);
IcyBufferedImage resultArray = new IcyBufferedImage(_w, _h, 2, DataType.DOUBLE);
double[][] resultData = resultArray.getDataXYCAsDouble();
assignFunction.assign(fArray, resultData[0], _w, _h, channel0Function);
assignFunction.assign(fArray, resultData[1], _w, _h, channel1Function);
resultArray.dataChanged();
fSequence.setImage(0, k, resultArray);
}
return fSequence;
}
}
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