From f3615f994eb9deeabf7900ff1d0f850584c678ef Mon Sep 17 00:00:00 2001
From: Daniel Gonzalez <dgonzale@pasteur.fr>
Date: Mon, 23 Mar 2020 17:59:32 +0100
Subject: [PATCH] Separated logic from plugin behavior
- Created FFTCalculator to expose statically FFT calculation from code
instead of creating a new plugin instance
---
src/plugins/praveen/fft/FFT.java | 151 +-----------------
src/plugins/praveen/fft/FFTCalculator.java | 172 +++++++++++++++++++++
2 files changed, 178 insertions(+), 145 deletions(-)
create mode 100644 src/plugins/praveen/fft/FFTCalculator.java
diff --git a/src/plugins/praveen/fft/FFT.java b/src/plugins/praveen/fft/FFT.java
index 68f5b1d..384e94d 100644
--- a/src/plugins/praveen/fft/FFT.java
+++ b/src/plugins/praveen/fft/FFT.java
@@ -1,12 +1,6 @@
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() {
diff --git a/src/plugins/praveen/fft/FFTCalculator.java b/src/plugins/praveen/fft/FFTCalculator.java
new file mode 100644
index 0000000..548d697
--- /dev/null
+++ b/src/plugins/praveen/fft/FFTCalculator.java
@@ -0,0 +1,172 @@
+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;
+ }
+}
--
GitLab