diff --git a/pom.xml b/pom.xml
index d9aaf852d5e665d833c768682bf98b05d19de732..d91741a3d48489814111077e8469a2936f3246be 100644
--- a/pom.xml
+++ b/pom.xml
@@ -11,7 +11,7 @@
</parent>
<artifactId>filter-toolbox</artifactId>
- <version>4.4.4</version>
+ <version>5.0.0</version>
<packaging>jar</packaging>
diff --git a/src/main/java/plugins/adufour/filtering/Convolution.java b/src/main/java/plugins/adufour/filtering/Convolution.java
index dc0f062ac9202152cbb7e78772ecd91bb15f290e..806f3a66bf813f33d61be414df42d5e7d4ca7413 100644
--- a/src/main/java/plugins/adufour/filtering/Convolution.java
+++ b/src/main/java/plugins/adufour/filtering/Convolution.java
@@ -1,8 +1,22 @@
-package plugins.adufour.filtering;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.util.ArrayList;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.Future;
+package plugins.adufour.filtering;
import icy.image.IcyBufferedImage;
import icy.sequence.Sequence;
@@ -12,6 +26,10 @@ import plugins.adufour.vars.lang.Var;
import plugins.adufour.vars.lang.VarBoolean;
import plugins.adufour.vars.util.VarListener;
+import java.util.ArrayList;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.Future;
+
public class Convolution extends Filter {
/**
* Convolve the input sequence with the given kernel with the specified edge condition. The
@@ -26,16 +44,16 @@ public class Convolution extends Filter {
* @param nbIter the number of filter iterations
* @param stopFlag boolean
*/
- public static void convolve(Sequence input, Sequence kernel, boolean zeroEdges, int nbIter, VarBoolean stopFlag) {
+ public static void convolve(final Sequence input, final Sequence kernel, final boolean zeroEdges, final int nbIter, final VarBoolean stopFlag) {
final Convolution c = new Convolution();
- final VarListener<Boolean> l = new VarListener<Boolean>() {
+ final VarListener<Boolean> l = new VarListener<>() {
@Override
- public void valueChanged(Var<Boolean> source, Boolean oldValue, Boolean newValue) {
+ public void valueChanged(final Var<Boolean> source, final Boolean oldValue, final Boolean newValue) {
c.stopFlag.setValue(newValue);
}
@Override
- public void referenceChanged(Var<Boolean> source, Var<? extends Boolean> oldReference, Var<? extends Boolean> newReference) {
+ public void referenceChanged(final Var<Boolean> source, final Var<? extends Boolean> oldReference, final Var<? extends Boolean> newReference) {
}
};
@@ -45,8 +63,8 @@ public class Convolution extends Filter {
Convolution.service.shutdown();
}
- public Sequence convolve(final Sequence sequence, Sequence kernel, final boolean zeroEdges, int nbIter) {
- Sequence out = new Sequence(sequence.getName() + "_" + getDescriptor().getName());
+ public Sequence convolve(final Sequence sequence, final Sequence kernel, final boolean zeroEdges, final int nbIter) {
+ final Sequence out = new Sequence(sequence.getName() + "_" + getDescriptor().getName());
final int width = sequence.getSizeX();
final int height = sequence.getSizeY();
@@ -68,7 +86,7 @@ public class Convolution extends Filter {
// create an array of tasks for multi-thread processing
// => rationale: one task per image line
- ArrayList<Future<?>> tasks = new ArrayList<>(height);
+ final ArrayList<Future<?>> tasks = new ArrayList<>(height);
convolution:
for (int t = 0; t < frames; t++) {
@@ -119,8 +137,8 @@ public class Convolution extends Filter {
inZ = (depth * 2) - inZ - 1;
}
- Object in_XY = in_Z_XY[inZ];
- double[] k_XY = _kernel[kZ];
+ final Object in_XY = in_Z_XY[inZ];
+ final double[] k_XY = _kernel[kZ];
kXY = 0;
@@ -182,7 +200,7 @@ public class Convolution extends Filter {
} // end for(y)
try {
- for (Future<?> f : tasks)
+ for (final Future<?> f : tasks)
f.get();
// at this point all tasks are done so we can store result back
@@ -192,7 +210,7 @@ public class Convolution extends Filter {
// it won't copy data but at least does the data changed
out.setDataXY(t, z, c, out_XY);
}
- catch (InterruptedException | ExecutionException e) {
+ catch (final InterruptedException | ExecutionException e) {
e.printStackTrace();
}
diff --git a/src/main/java/plugins/adufour/filtering/Convolution1D.java b/src/main/java/plugins/adufour/filtering/Convolution1D.java
index 7ce8dcd94876faf2b25e031831d6df57f8408b66..bba600bdd94d73af74b28a64c7bfa6f58c8fea90 100644
--- a/src/main/java/plugins/adufour/filtering/Convolution1D.java
+++ b/src/main/java/plugins/adufour/filtering/Convolution1D.java
@@ -1,9 +1,22 @@
-package plugins.adufour.filtering;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.util.ArrayList;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Future;
+package plugins.adufour.filtering;
import icy.sequence.Sequence;
import icy.system.SystemUtil;
@@ -13,6 +26,11 @@ import icy.type.collection.array.Array1DUtil;
import plugins.adufour.filtering.FilterToolbox.Axis;
import plugins.adufour.vars.lang.VarBoolean;
+import java.util.ArrayList;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Future;
+
/**
* Spatial convolution for separable 1D kernels.
*
@@ -31,7 +49,7 @@ public class Convolution1D {
* @param kernel1D_Z the kernel to use for convolution along Z
* @throws ConvolutionException if a kernel is too large w.r.t. the image size
*/
- public static void convolve(Sequence sequence, Sequence kernel1D_X, Sequence kernel1D_Y, Sequence kernel1D_Z)
+ public static void convolve(final Sequence sequence, final Sequence kernel1D_X, final Sequence kernel1D_Y, final Sequence kernel1D_Z)
throws ConvolutionException {
convolve(sequence, kernel1D_X, kernel1D_Y, kernel1D_Z, 1, new VarBoolean("stop", false));
}
@@ -50,8 +68,8 @@ public class Convolution1D {
* @param stopFlag boolean
* @throws ConvolutionException if a kernel is too large w.r.t. the image size
*/
- public static void convolve(Sequence sequence, Sequence kernel1D_X, Sequence kernel1D_Y, Sequence kernel1D_Z,
- int nbIter, VarBoolean stopFlag) throws ConvolutionException {
+ public static void convolve(final Sequence sequence, final Sequence kernel1D_X, final Sequence kernel1D_Y, final Sequence kernel1D_Z,
+ final int nbIter, final VarBoolean stopFlag) throws ConvolutionException {
if (kernel1D_X == null && kernel1D_Y == null && kernel1D_Z == null)
throw new IllegalArgumentException("Invalid argument: provide at least one non-null kernel");
@@ -84,8 +102,8 @@ public class Convolution1D {
double[] kernelY = null;
double[] kernelZ = null;
- DataType type = sequence.getDataType_();
- double[][] z_xy = new double[sequence.getSizeZ()][sequence.getSizeX() * sequence.getSizeY()];
+ final DataType type = sequence.getDataType_();
+ final double[][] z_xy = new double[sequence.getSizeZ()][sequence.getSizeX() * sequence.getSizeY()];
sequence.beginUpdate();
try {
@@ -140,7 +158,7 @@ public class Convolution1D {
* @throws IllegalArgumentException if all kernels are null or if a kernel has even size
* @throws ConvolutionException if a kernel is too large w.r.t. the image size
*/
- public static void convolve(Sequence sequence, double[] kernelX, double[] kernelY, double[] kernelZ)
+ public static void convolve(final Sequence sequence, final double[] kernelX, final double[] kernelY, final double[] kernelZ)
throws IllegalArgumentException, ConvolutionException {
if (kernelX == null && kernelY == null && kernelZ == null)
throw new IllegalArgumentException("Invalid argument: provide at least one non-null kernel");
@@ -151,8 +169,8 @@ public class Convolution1D {
if (kernelZ != null && kernelZ.length % 2 == 0)
throw new IllegalArgumentException("Invalid argument: kernel along Z has even size");
- DataType type = sequence.getDataType_();
- double[][] z_xy = new double[sequence.getSizeZ()][sequence.getSizeX() * sequence.getSizeY()];
+ final DataType type = sequence.getDataType_();
+ final double[][] z_xy = new double[sequence.getSizeZ()][sequence.getSizeX() * sequence.getSizeY()];
sequence.beginUpdate();
try {
@@ -199,13 +217,13 @@ public class Convolution1D {
* @param array 2D array
* @throws ConvolutionException if a kernel is too large w.r.t the image size
*/
- public static void convolve(double[][] array, int imageWidth, int imageHeight, double[] kernelX, double[] kernelY,
- double[] kernelZ) throws ConvolutionException {
- Processor service = new Processor(SystemUtil.getNumberOfCPUs() * 2);
+ public static void convolve(final double[][] array, final int imageWidth, final int imageHeight, final double[] kernelX, final double[] kernelY,
+ final double[] kernelZ) throws ConvolutionException {
+ final Processor service = new Processor(SystemUtil.getNumberOfCPUs() * 2);
- int sliceSize = array[0].length;
+ final int sliceSize = array[0].length;
- double[][] temp = new double[array.length][sliceSize];
+ final double[][] temp = new double[array.length][sliceSize];
try {
if (array.length == 1) {
@@ -273,10 +291,10 @@ public class Convolution1D {
}
}
}
- catch (InterruptedException e) {
+ catch (final InterruptedException e) {
Thread.currentThread().interrupt();
}
- catch (ExecutionException e) {
+ catch (final ExecutionException e) {
e.printStackTrace();
}
finally {
@@ -299,17 +317,17 @@ public class Convolution1D {
* @param axis the axis along which to convolve
* @throws ConvolutionException if a kernel is too large w.r.t. the image size
*/
- public static void convolve1D(double[][] input, double[][] output, int width, int height, double[] kernel,
- Axis axis) throws ConvolutionException {
- Processor service = new Processor(SystemUtil.getNumberOfCPUs() * 2);
+ public static void convolve1D(final double[][] input, final double[][] output, final int width, final int height, final double[] kernel,
+ final Axis axis) throws ConvolutionException {
+ final Processor service = new Processor(SystemUtil.getNumberOfCPUs() * 2);
try {
convolve1D(service, input, output, width, height, kernel, axis);
}
- catch (InterruptedException e) {
+ catch (final InterruptedException e) {
Thread.currentThread().interrupt();
}
- catch (ExecutionException e) {
+ catch (final ExecutionException e) {
e.printStackTrace();
}
finally {
@@ -334,8 +352,8 @@ public class Convolution1D {
* @throws ExecutionException Error in execution
* @throws InterruptedException Interruption
*/
- public static void convolve1D(ExecutorService service, final double[][] input, final double[][] output,
- final int width, final int height, final double[] kernel, Axis axis)
+ public static void convolve1D(final ExecutorService service, final double[][] input, final double[][] output,
+ final int width, final int height, final double[] kernel, final Axis axis)
throws ConvolutionException, InterruptedException, ExecutionException {
try {
final int sliceSize = input[0].length;
@@ -344,7 +362,7 @@ public class Convolution1D {
switch (axis) {
case X: {
- ArrayList<Future<?>> tasks = new ArrayList<>(input.length);
+ final ArrayList<Future<?>> tasks = new ArrayList<>(input.length);
for (int z = 0; z < input.length; z++) {
final double[] inSlice = input[z];
@@ -357,8 +375,8 @@ public class Convolution1D {
// store the offset of the first and last elements of the line
// they will be used to compute mirror conditions
- int xStartOffset = xy;
- int xEndOffset = xy + width - 1;
+ final int xStartOffset = xy;
+ final int xEndOffset = xy + width - 1;
// convolve the west border (mirror condition)
@@ -378,7 +396,7 @@ public class Convolution1D {
// convolve the central area until the east border
- int eastBorder = width - kRadius;
+ final int eastBorder = width - kRadius;
for (; x < eastBorder; x++, xy++) {
double value = 0;
@@ -409,7 +427,7 @@ public class Convolution1D {
}));
}
- for (Future<?> task : tasks)
+ for (final Future<?> task : tasks)
task.get();
}
@@ -418,7 +436,7 @@ public class Convolution1D {
case Y: {
final int kRadiusY = kRadius * width;
- ArrayList<Future<?>> tasks = new ArrayList<>(input.length);
+ final ArrayList<Future<?>> tasks = new ArrayList<>(input.length);
for (int z = 0; z < input.length; z++) {
final double[] in = input[z];
@@ -434,7 +452,7 @@ public class Convolution1D {
for (; y < kRadius; y++) {
for (int x = 0; x < width; x++, xy++) {
- int yStartOffset = x;
+ final int yStartOffset = x;
double value = 0;
@@ -452,7 +470,7 @@ public class Convolution1D {
// convolve the central area until the south border
- int southBorder = height - kRadius;
+ final int southBorder = height - kRadius;
for (; y < southBorder; y++) {
for (int x = 0; x < width; x++, xy++) {
@@ -470,7 +488,7 @@ public class Convolution1D {
for (; y < height; y++) {
for (int x = 0; x < width; x++, xy++) {
- int yEndOffset = sliceSize - width + x;
+ final int yEndOffset = sliceSize - width + x;
double value = 0;
@@ -488,14 +506,14 @@ public class Convolution1D {
}));
}
- for (Future<?> task : tasks)
+ for (final Future<?> task : tasks)
task.get();
}
break;
case Z: {
- ArrayList<Future<?>> tasks = new ArrayList<>(input.length);
+ final ArrayList<Future<?>> tasks = new ArrayList<>(input.length);
int z = 0;
for (; z < kRadius; z++) {
@@ -522,7 +540,7 @@ public class Convolution1D {
}));
}
- int bottomBorder = input.length - kRadius;
+ final int bottomBorder = input.length - kRadius;
for (; z < bottomBorder; z++) {
final double[] out = output[z];
@@ -570,14 +588,14 @@ public class Convolution1D {
}));
}
- for (Future<?> task : tasks)
+ for (final Future<?> task : tasks)
task.get();
}
break;
}
}
- catch (ExecutionException e) {
+ catch (final ExecutionException e) {
if (e.getCause() instanceof ArrayIndexOutOfBoundsException) {
throw new ConvolutionException("Filter size is too large along " + axis.name(), e);
}
@@ -585,10 +603,10 @@ public class Convolution1D {
throw e;
}
}
- catch (ArrayIndexOutOfBoundsException e) {
+ catch (final ArrayIndexOutOfBoundsException e) {
throw new ConvolutionException("Filter size is too large along " + axis.name(), e);
}
- catch (RuntimeException e) {
+ catch (final RuntimeException e) {
e.printStackTrace();
}
}
diff --git a/src/main/java/plugins/adufour/filtering/ConvolutionCL.java b/src/main/java/plugins/adufour/filtering/ConvolutionCL.java
index 70d97bbe033056a6db614e7e8d8422f4276c9121..83974ced2e815bdeaf3eb900a98d870ee2ee57e5 100644
--- a/src/main/java/plugins/adufour/filtering/ConvolutionCL.java
+++ b/src/main/java/plugins/adufour/filtering/ConvolutionCL.java
@@ -1,77 +1,88 @@
-package plugins.adufour.filtering;
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import java.nio.ByteBuffer;
-import java.nio.FloatBuffer;
+package plugins.adufour.filtering;
-import com.nativelibs4java.opencl.CLContext;
-import com.nativelibs4java.opencl.CLEvent;
-import com.nativelibs4java.opencl.CLException;
-import com.nativelibs4java.opencl.CLFloatBuffer;
-import com.nativelibs4java.opencl.CLKernel;
+import com.nativelibs4java.opencl.*;
import com.nativelibs4java.opencl.CLMem.MapFlags;
import com.nativelibs4java.opencl.CLMem.Usage;
-import com.nativelibs4java.opencl.CLProgram;
-import com.nativelibs4java.opencl.CLQueue;
-
import icy.image.IcyBufferedImage;
import icy.sequence.Sequence;
import icy.type.DataType;
import icy.type.collection.array.Array1DUtil;
import plugins.adufour.vars.lang.VarBoolean;
+import java.nio.ByteBuffer;
+import java.nio.FloatBuffer;
+
public class ConvolutionCL {
public final CLProgram clProgram;
public final CLContext clContext;
public final CLQueue clQueue;
public final CLEvent clEvent = null;
- public ConvolutionCL(CLContext context, CLProgram program, CLQueue queue) {
+ public ConvolutionCL(final CLContext context, final CLProgram program, final CLQueue queue) {
clContext = context;
clQueue = queue;
clProgram = program;
}
- public void convolve(Sequence input, Sequence kernel, boolean zeroEdge, int nbIter, VarBoolean stopFlag) throws CLException {
- String funcName = zeroEdge ? "convolve2D" : "convolve2D_mirror";
+ public void convolve(final Sequence input, final Sequence kernel, final boolean zeroEdge, final int nbIter, final VarBoolean stopFlag) throws CLException {
+ final String funcName = zeroEdge ? "convolve2D" : "convolve2D_mirror";
- CLKernel clKernel;
+ final CLKernel clKernel;
clKernel = clProgram.createKernel(funcName);
- int dataSize = input.getSizeX() * input.getSizeY();
+ final int dataSize = input.getSizeX() * input.getSizeY();
CLEvent event;
- float[] data = new float[dataSize];
+ final float[] data = new float[dataSize];
- CLFloatBuffer cl_inBuffer = clContext.createFloatBuffer(Usage.Input, dataSize);
+ final CLFloatBuffer cl_inBuffer = clContext.createFloatBuffer(Usage.Input, dataSize);
- double[] kernelDouble = kernel.getDataXYAsDouble(0, 0, 0);
+ final double[] kernelDouble = kernel.getDataXYAsDouble(0, 0, 0);
- CLFloatBuffer cl_kBuffer = clContext.createFloatBuffer(Usage.Input, kernelDouble.length);
- FloatBuffer fb_k = cl_kBuffer.map(clQueue, MapFlags.Write);
- for (double d : kernelDouble)
+ final CLFloatBuffer cl_kBuffer = clContext.createFloatBuffer(Usage.Input, kernelDouble.length);
+ final FloatBuffer fb_k = cl_kBuffer.map(clQueue, MapFlags.Write);
+ for (final double d : kernelDouble)
fb_k.put((float) d);
fb_k.rewind();
event = cl_kBuffer.unmap(clQueue, fb_k);
// create a "direct" float buffer
- FloatBuffer outBuffer = ByteBuffer.allocateDirect(dataSize * 4).order(clContext.getByteOrder()).asFloatBuffer();
+ final FloatBuffer outBuffer = ByteBuffer.allocateDirect(dataSize * 4).order(clContext.getByteOrder()).asFloatBuffer();
// share the reference directly with the GPU (no copy)
- CLFloatBuffer cl_outBuffer = clContext.createFloatBuffer(Usage.Output, outBuffer, false);
+ final CLFloatBuffer cl_outBuffer = clContext.createFloatBuffer(Usage.Output, outBuffer, false);
// set the kernel arguments in order
clKernel.setArgs(cl_inBuffer, input.getSizeX(), input.getSizeY(), cl_kBuffer, kernel.getSizeX() >> 1,
kernel.getSizeY() >> 1, cl_outBuffer);
FloatBuffer fb;
- DataType type = input.getDataType_();
+ final DataType type = input.getDataType_();
input.beginUpdate();
try {
for (int t = 0; t < input.getSizeT(); t++) {
for (int z = 0; z < input.getSizeZ(); z++) {
- IcyBufferedImage image = input.getImage(t, z);
+ final IcyBufferedImage image = input.getImage(t, z);
for (int c = 0; c < input.getSizeC(); c++) {
// convert image to float
diff --git a/src/main/java/plugins/adufour/filtering/ConvolutionException.java b/src/main/java/plugins/adufour/filtering/ConvolutionException.java
index 56133e268a9837e9a59a77730fd9e2ebf3dd594d..a5703a9dce1e63aeda3a0e410f761b7baa4ae248 100644
--- a/src/main/java/plugins/adufour/filtering/ConvolutionException.java
+++ b/src/main/java/plugins/adufour/filtering/ConvolutionException.java
@@ -1,7 +1,25 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
public class ConvolutionException extends Exception {
- public ConvolutionException(String message, Throwable cause) {
+ public ConvolutionException(final String message, final Throwable cause) {
super(message, cause);
}
}
diff --git a/src/main/java/plugins/adufour/filtering/Filter.java b/src/main/java/plugins/adufour/filtering/Filter.java
index ea27628ef3620b85ef0c71502371e3622b2f0d9c..7675a2816846e3e8a4315a89cfa362470027970d 100644
--- a/src/main/java/plugins/adufour/filtering/Filter.java
+++ b/src/main/java/plugins/adufour/filtering/Filter.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
import icy.plugin.abstract_.Plugin;
diff --git a/src/main/java/plugins/adufour/filtering/FilterToolbox.java b/src/main/java/plugins/adufour/filtering/FilterToolbox.java
index 16168e70d764f5997c5612a1c1c8ae9d8e455d43..484b8730c086a5502c246e923ff5752bc913561a 100644
--- a/src/main/java/plugins/adufour/filtering/FilterToolbox.java
+++ b/src/main/java/plugins/adufour/filtering/FilterToolbox.java
@@ -1,38 +1,40 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
+import com.nativelibs4java.opencl.*;
+import com.ochafik.io.ReadText;
import icy.gui.frame.progress.FailedAnnounceFrame;
import icy.image.IcyBufferedImage;
import icy.sequence.DimensionId;
import icy.sequence.Sequence;
import icy.sequence.SequenceUtil;
+import icy.system.IcyExceptionHandler;
import icy.system.IcyHandledException;
-
-import java.io.IOException;
-import java.lang.reflect.InvocationTargetException;
-import java.util.ArrayList;
-
-import plugins.adufour.ezplug.EzException;
-import plugins.adufour.ezplug.EzGroup;
-import plugins.adufour.ezplug.EzPlug;
-import plugins.adufour.ezplug.EzStoppable;
-import plugins.adufour.ezplug.EzVarBoolean;
-import plugins.adufour.ezplug.EzVarDimensionPicker;
-import plugins.adufour.ezplug.EzVarDouble;
-import plugins.adufour.ezplug.EzVarDoubleArrayNative;
-import plugins.adufour.ezplug.EzVarEnum;
-import plugins.adufour.ezplug.EzVarInteger;
-import plugins.adufour.ezplug.EzVarPlugin;
-import plugins.adufour.ezplug.EzVarSequence;
+import plugins.adufour.ezplug.*;
import plugins.adufour.vars.lang.Var;
import plugins.adufour.vars.lang.VarBoolean;
import plugins.adufour.vars.util.VarListener;
-import com.nativelibs4java.opencl.CLContext;
-import com.nativelibs4java.opencl.CLException;
-import com.nativelibs4java.opencl.CLProgram;
-import com.nativelibs4java.opencl.CLQueue;
-import com.nativelibs4java.opencl.JavaCL;
-import com.ochafik.io.ReadText;
+import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
+import java.util.ArrayList;
public class FilterToolbox extends EzPlug implements EzStoppable {
private final static int MAX_KERNEL_SIZE = 99;
@@ -101,7 +103,7 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
input.addVarChangeListener((source, newValue) -> {
if (newValue == null) return;
- boolean is3D = newValue.getSizeZ() > 1;
+ final boolean is3D = newValue.getSizeZ() > 1;
linearZ.setVisible(is3D);
gaussianZ.setVisible(is3D);
@@ -127,23 +129,24 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
useOpenCL.setVisible(false);
context = JavaCL.createBestContext();
queue = context.createDefaultQueue();
- String programFile = ReadText.readText(ConvolutionCL.class.getResourceAsStream("Convolution.cl"));
+ final String programFile = ReadText.readText(ConvolutionCL.class.getResourceAsStream("Convolution.cl"));
program = context.createProgram(programFile).build();
convolutionCL = new ConvolutionCL(context, program, queue);
useOpenCL.setValue(true);
useOpenCL.setVisible(true);
}
- catch (IOException e) {
+ catch (final IOException e) {
System.out.println("Warning (FilterToolbox): unable to load the OpenCL code. Continuing in pure Java mode.");
- e.printStackTrace();
+ IcyExceptionHandler.showErrorMessage(e, false);
}
- catch (CLException | NoClassDefFoundError e) {
+ catch (final CLException | NoClassDefFoundError e) {
System.out.println("Warning (FilterToolbox): unable to create the OpenCL context. Continuing in pure Java mode.");
- e.printStackTrace();
+ IcyExceptionHandler.showErrorMessage(e, false);
}
- catch (UnsatisfiedLinkError linkError) {
+ catch (final UnsatisfiedLinkError linkError) {
// throw new EzException("Unable to load OpenCL drivers on this system", true);
System.out.println("Warning (FilterToolbox): OpenCL drivers not found. Using basic Java implementation.");
+ IcyExceptionHandler.showErrorMessage(linkError, false);
}
filterType.addVisibilityTriggerTo(useOpenCL, FilterType.CLASSIC, FilterType.SEPARABLE);
@@ -152,13 +155,13 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
addEzComponent(kernel1D);
filterType.addVisibilityTriggerTo(kernel1D, FilterType.SEPARABLE);
- EzGroup groupLinear = new EzGroup("Directions", linearX, linearY, linearZ, linearSeparable);
+ final EzGroup groupLinear = new EzGroup("Directions", linearX, linearY, linearZ, linearSeparable);
addEzComponent(groupLinear);
filterType.addVisibilityTriggerTo(groupLinear, FilterType.SEPARABLE);
kernel1D.addVisibilityTriggerTo(linearSeparable, Kernels1D.CUSTOM);
useOpenCL.addVisibilityTriggerTo(linearZ, false);
- EzGroup groupGaussian = new EzGroup("Gaussian filter", gaussianX, gaussianY, gaussianZ);
+ final EzGroup groupGaussian = new EzGroup("Gaussian filter", gaussianX, gaussianY, gaussianZ);
addEzComponent(groupGaussian);
kernel1D.addVisibilityTriggerTo(groupGaussian, Kernels1D.CUSTOM_GAUSSIAN);
useOpenCL.addVisibilityTriggerTo(gaussianZ, false);
@@ -166,15 +169,15 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
addEzComponent(kernel2D);
filterType.addVisibilityTriggerTo(kernel2D, FilterType.CLASSIC);
- EzGroup gaborGroup = new EzGroup("Gabor 2D", gaborSigma, gaborKx, gaborKy, gaborSymmetric);
+ final EzGroup gaborGroup = new EzGroup("Gabor 2D", gaborSigma, gaborKx, gaborKy, gaborSymmetric);
addEzComponent(gaborGroup);
kernel2D.addVisibilityTriggerTo(gaborGroup, Kernels2D.CUSTOM_GABOR);
- EzGroup customSequenceGroup = new EzGroup("Custom sequence", customKernel, customKernel_T, customKernel_Z, customKernel_C);
+ final EzGroup customSequenceGroup = new EzGroup("Custom sequence", customKernel, customKernel_T, customKernel_Z, customKernel_C);
addEzComponent(customSequenceGroup);
kernel2D.addVisibilityTriggerTo(customSequenceGroup, Kernels2D.CUSTOM_SEQUENCE);
- EzGroup groupSelection = new EzGroup("Selection filter", selectionFilter, selectionRadiusX, selectionRadiusY, selectionRadiusZ);
+ final EzGroup groupSelection = new EzGroup("Selection filter", selectionFilter, selectionRadiusX, selectionRadiusY, selectionRadiusZ);
addEzComponent(groupSelection);
filterType.addVisibilityTriggerTo(groupSelection, FilterType.SELECTION);
@@ -189,7 +192,7 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
kernel2D.addVisibilityTriggerTo(userKernelHeight, Kernels2D.CUSTOM);
// first line of the kernel must always exist
- EzVarDoubleArrayNative firstKernelLine = new EzVarDoubleArrayNative("Line 1", new double[][]{new double[]{1f, 1f, 1f}}, 0, true);
+ final EzVarDoubleArrayNative firstKernelLine = new EzVarDoubleArrayNative("Line 1", new double[][]{new double[]{1f, 1f, 1f}}, 0, true);
kernelLines.add(firstKernelLine);
addEzComponent(firstKernelLine);
kernel1D.addVisibilityTriggerTo(firstKernelLine, Kernels1D.CUSTOM);
@@ -198,11 +201,11 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
// other lines
userKernelHeight.addVarChangeListener((source, newValue) -> {
if (kernelLines.size() < newValue) {
- int nbLines = kernelLines.size();
- int nbNewLines = newValue - nbLines;
+ final int nbLines = kernelLines.size();
+ final int nbNewLines = newValue - nbLines;
for (int i = 1; i <= nbNewLines; i++) {
- int lineNumber = i + nbLines;
- EzVarDoubleArrayNative newLine = new EzVarDoubleArrayNative("Line " + lineNumber, new double[][]{new double[]{1f, 1f, 1f}}, 0, true);
+ final int lineNumber = i + nbLines;
+ final EzVarDoubleArrayNative newLine = new EzVarDoubleArrayNative("Line " + lineNumber, new double[][]{new double[]{1f, 1f, 1f}}, 0, true);
kernelLines.add(newLine);
kernel2D.addVisibilityTriggerTo(newLine, Kernels2D.CUSTOM);
addEzComponent(newLine);
@@ -222,7 +225,7 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
public void execute() {
stopFlag.setValue(false);
- Sequence inSeq = input.getValue(true);
+ final Sequence inSeq = input.getValue(true);
try {
switch (filterType.getValue()) {
case SEPARABLE: {
@@ -237,34 +240,34 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
try {
executeSelectionFilter(inSeq);
}
- catch (Exception e) {
+ catch (final Exception e) {
throw new RuntimeException(e);
}
break;
}
}
}
- catch (InterruptedException e) {
+ catch (final InterruptedException e) {
new FailedAnnounceFrame("Process interrupted !");
}
- catch (CLException.OutOfHostMemory o) {
+ catch (final CLException.OutOfHostMemory o) {
throw new IcyHandledException("Not enough memory to perform the filtering on the GPU. Disable OpenCL and retry.");
}
}
- private void executeSelectionFilter(Sequence inSeq) throws InstantiationException, IllegalAccessException, NoSuchMethodException, InvocationTargetException {
- SelectionFilter filter = (SelectionFilter) selectionFilter.getValue().getPluginClass().getDeclaredConstructor().newInstance();
+ private void executeSelectionFilter(final Sequence inSeq) throws InstantiationException, IllegalAccessException, NoSuchMethodException, InvocationTargetException {
+ final SelectionFilter filter = (SelectionFilter) selectionFilter.getValue().getPluginClass().getDeclaredConstructor().newInstance();
this.filter = filter;
- filter.progress.addListener(new VarListener<Double>() {
+ filter.progress.addListener(new VarListener<>() {
@Override
- public void valueChanged(Var<Double> source, Double oldValue, Double newValue) {
+ public void valueChanged(final Var<Double> source, final Double oldValue, final Double newValue) {
getUI().setProgressBarValue(newValue);
}
@Override
- public void referenceChanged(Var<Double> source, Var<? extends Double> oldReference, Var<? extends Double> newReference) {
+ public void referenceChanged(final Var<Double> source, final Var<? extends Double> oldReference, final Var<? extends Double> newReference) {
}
});
@@ -280,8 +283,8 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
this.filter = null;
}
- private void executeClassic(Sequence inSeq) throws InterruptedException {
- Kernels2D k2d = kernel2D.getValue();
+ private void executeClassic(final Sequence inSeq) throws InterruptedException {
+ final Kernels2D k2d = kernel2D.getValue();
switch (kernel2D.getValue()) {
case CUSTOM_GABOR:
@@ -289,12 +292,12 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
break;
case CUSTOM: {
- ArrayList<Double> kernel1D = new ArrayList<>();
+ final ArrayList<Double> kernel1D = new ArrayList<>();
for (int i = 0; i < userKernelHeight.getValue(); i++)
- for (double d : kernelLines.get(i).getValue())
+ for (final double d : kernelLines.get(i).getValue())
kernel1D.add(d);
- double[] values = new double[kernel1D.size()];
+ final double[] values = new double[kernel1D.size()];
for (int i = 0; i < kernel1D.size(); i++)
values[i] = kernel1D.get(i);
@@ -310,7 +313,7 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
// nothing to do (the filters should already be predefined)
}
- Sequence kernel = k2d.toSequence();
+ final Sequence kernel = k2d.toSequence();
Sequence output = null;
boolean openCL_failed = false;
@@ -321,7 +324,7 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
convolutionCL.convolve(output, kernel, zeroEdge.getValue(), iterations.getValue(), stopFlag);
openCL_failed = false;
}
- catch (Exception e) {
+ catch (final Exception e) {
openCL_failed = true;
e.printStackTrace();
System.err.println("WARNING: Unable to run in OpenCL mode. Switching to CPU mode.");
@@ -331,14 +334,14 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
if (!useOpenCL.getValue() || openCL_failed) {
final Convolution c = new Convolution();
this.filter = c;
- final VarListener<Double> ld = new VarListener<Double>() {
+ final VarListener<Double> ld = new VarListener<>() {
@Override
- public void valueChanged(Var<Double> source, Double oldValue, Double newValue) {
+ public void valueChanged(final Var<Double> source, final Double oldValue, final Double newValue) {
getUI().setProgressBarValue(newValue);
}
@Override
- public void referenceChanged(Var<Double> source, Var<? extends Double> oldReference, Var<? extends Double> newReference) {
+ public void referenceChanged(final Var<Double> source, final Var<? extends Double> oldReference, final Var<? extends Double> newReference) {
}
};
@@ -348,13 +351,14 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
this.filter = null;
}
+ assert output != null;
output.setName(inSeq.getName() + " * " + kernel.getName());
output.updateChannelsBounds(true);
addSequence(output);
}
- private void executeSeparable(Sequence inSeq) throws InterruptedException {
- Kernels1D k1d = kernel1D.getValue();
+ private void executeSeparable(final Sequence inSeq) throws InterruptedException {
+ final Kernels1D k1d = kernel1D.getValue();
Sequence kernelX = null, kernelY = null, kernelZ = null;
@@ -382,7 +386,7 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
case GRADIENT: {
linearSeparable.setValue(false);
- Sequence kernel = k1d.toSequence();
+ final Sequence kernel = k1d.toSequence();
if (linearX.getValue()) {
kernelX = kernel;
@@ -400,7 +404,7 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
break;
case CUSTOM: {
- Sequence kernel = k1d.createCustomKernel1D(kernelLines.get(0).getValue(), false).toSequence();
+ final Sequence kernel = k1d.createCustomKernel1D(kernelLines.get(0).getValue(), false).toSequence();
if (linearX.getValue()) {
kernelX = kernel;
@@ -430,16 +434,18 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
else try {
if (linearSeparable.getValue()) {
// convolve the same data along all required directions sequentially
- Sequence output = SequenceUtil.getCopy(inSeq);
+ final Sequence output = SequenceUtil.getCopy(inSeq);
String newName = output.getName() + " * " + k1d.name() + " (";
if (linearX.getValue()) {
+ assert kernelX != null;
convolutionCL.convolve(output, kernelX, zeroEdge.getValue(), iterations.getValue(), stopFlag);
newName += 'X';
}
if (linearY.getValue()) {
// in OpenCL mode, the kernel along Y has to be vertical
- Sequence kernelY_vertical = new Sequence(new IcyBufferedImage(1, kernelY.getSizeX(), 1, kernelY.getDataType_()));
+ assert kernelY != null;
+ final Sequence kernelY_vertical = new Sequence(new IcyBufferedImage(1, kernelY.getSizeX(), 1, kernelY.getDataType_()));
System.arraycopy(kernelY.getDataXY(0, 0, 0), 0, kernelY_vertical.getDataXY(0, 0, 0), 0, kernelY.getSizeX());
convolutionCL.convolve(output, kernelY_vertical, zeroEdge.getValue(), iterations.getValue(), stopFlag);
newName += 'Y';
@@ -453,16 +459,18 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
else {
// convolve along each direction in separate sequences
if (linearX.getValue()) {
- Sequence output = SequenceUtil.getCopy(inSeq);
+ final Sequence output = SequenceUtil.getCopy(inSeq);
+ assert kernelX != null;
convolutionCL.convolve(output, kernelX, zeroEdge.getValue(), iterations.getValue(), stopFlag);
output.setName(output.getName() + " * " + k1d.name() + " (X)");
output.dataChanged();
addSequence(output);
}
if (linearY.getValue()) {
- Sequence output = SequenceUtil.getCopy(inSeq);
+ final Sequence output = SequenceUtil.getCopy(inSeq);
// in OpenCL mode, the kernel along Y has to be vertical
- Sequence kernelY_vertical = new Sequence(new IcyBufferedImage(1, kernelY.getSizeX(), 1, kernelY.getDataType_()));
+ assert kernelY != null;
+ final Sequence kernelY_vertical = new Sequence(new IcyBufferedImage(1, kernelY.getSizeX(), 1, kernelY.getDataType_()));
System.arraycopy(kernelY.getDataXY(0, 0, 0), 0, kernelY_vertical.getDataXY(0, 0, 0), 0, kernelY.getSizeX());
convolutionCL.convolve(output, kernelY_vertical, zeroEdge.getValue(), iterations.getValue(), stopFlag);
output.setName(output.getName() + " * " + k1d.name() + " (Y)");
@@ -472,7 +480,7 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
// TODO Z
}
}
- catch (Exception e) {
+ catch (final Exception e) {
openCL_failed = true;
e.printStackTrace();
System.err.println("WARNING: Unable to run in OpenCL mode. Continuing in CPU mode.");
@@ -482,7 +490,7 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
if (!useOpenCL.getValue() || openCL_failed) {
if (linearSeparable.getValue()) {
try {
- Sequence output = SequenceUtil.getCopy(inSeq);
+ final Sequence output = SequenceUtil.getCopy(inSeq);
Convolution1D.convolve(output, kernelX, kernelY, kernelZ, iterations.getValue(), stopFlag);
String newName = output.getName() + " * " + k1d.name() + " (";
if (kernelX != null) newName += 'X';
@@ -492,39 +500,39 @@ public class FilterToolbox extends EzPlug implements EzStoppable {
output.dataChanged();
addSequence(output);
}
- catch (ConvolutionException e) {
+ catch (final ConvolutionException e) {
throw new EzException(this, e.getMessage(), true);
}
}
else {
if (linearX.getValue()) try {
- Sequence output = SequenceUtil.getCopy(inSeq);
+ final Sequence output = SequenceUtil.getCopy(inSeq);
Convolution1D.convolve(output, kernelX, null, null, iterations.getValue(), stopFlag);
output.setName(output.getName() + " * " + k1d.name() + " (X)");
output.dataChanged();
addSequence(output);
}
- catch (ConvolutionException e) {
+ catch (final ConvolutionException e) {
throw new EzException(this, e.getMessage(), true);
}
if (linearY.getValue()) try {
- Sequence output = SequenceUtil.getCopy(inSeq);
+ final Sequence output = SequenceUtil.getCopy(inSeq);
Convolution1D.convolve(output, null, kernelY, null, iterations.getValue(), stopFlag);
output.setName(output.getName() + " * " + k1d.name() + " (Y)");
output.dataChanged();
addSequence(output);
}
- catch (ConvolutionException e) {
+ catch (final ConvolutionException e) {
throw new EzException(this, e.getMessage(), true);
}
if (linearZ.getValue()) try {
- Sequence output = SequenceUtil.getCopy(inSeq);
+ final Sequence output = SequenceUtil.getCopy(inSeq);
Convolution1D.convolve(output, null, null, kernelZ, iterations.getValue(), stopFlag);
output.setName(output.getName() + " * " + k1d.name() + " (Z)");
output.dataChanged();
addSequence(output);
}
- catch (ConvolutionException e) {
+ catch (final ConvolutionException e) {
throw new EzException(this, e.getMessage(), true);
}
}
diff --git a/src/main/java/plugins/adufour/filtering/GaussianFilter.java b/src/main/java/plugins/adufour/filtering/GaussianFilter.java
index c36edfc3d4453fad27c6befd457ad8f9f7fffdee..7b341d7cec9c8e7681f3f8e9137a92cc0924ad87 100644
--- a/src/main/java/plugins/adufour/filtering/GaussianFilter.java
+++ b/src/main/java/plugins/adufour/filtering/GaussianFilter.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
import icy.gui.frame.progress.FailedAnnounceFrame;
@@ -31,14 +49,14 @@ public class GaussianFilter extends Plugin implements Block, PluginBundled {
try {
output.setValue(filter(input.getValue(true), gX.getValue(), gY.getValue(), gZ.getValue()));
}
- catch (InterruptedException e) {
+ catch (final InterruptedException e) {
new FailedAnnounceFrame("Process interrupted !");
}
}
@Override
- public void declareInput(VarList inputMap) {
- RangeModel<Double> constraint = new DoubleRangeModel(0.0, 0.0, 1000.0, 0.1);
+ public void declareInput(final VarList inputMap) {
+ final RangeModel<Double> constraint = new DoubleRangeModel(0.0, 0.0, 1000.0, 0.1);
gX.setDefaultEditorModel(constraint);
gY.setDefaultEditorModel(constraint);
gZ.setDefaultEditorModel(constraint);
@@ -49,7 +67,7 @@ public class GaussianFilter extends Plugin implements Block, PluginBundled {
}
@Override
- public void declareOutput(VarList outputMap) {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("output", output);
}
@@ -66,20 +84,19 @@ public class GaussianFilter extends Plugin implements Block, PluginBundled {
* @param sigmaY the standard deviation of the gaussian along the Y axis (set to 0 if not needed)
* @param sigmaZ the standard deviation of the gaussian along the Z axis (set to 0 if not needed)
* @return a filtered version of the input sequence
- * @throws InterruptedException
*/
- public static Sequence filter(Sequence in, double sigmaX, double sigmaY, double sigmaZ) throws InterruptedException {
- double[] gaussianX = Kernels1D.CUSTOM_GAUSSIAN.createGaussianKernel1D(sigmaX).getData();
- double[] gaussianY = Kernels1D.CUSTOM_GAUSSIAN.createGaussianKernel1D(sigmaY).getData();
- double[] gaussianZ = Kernels1D.CUSTOM_GAUSSIAN.createGaussianKernel1D(sigmaZ).getData();
+ public static Sequence filter(final Sequence in, final double sigmaX, final double sigmaY, final double sigmaZ) throws InterruptedException {
+ final double[] gaussianX = Kernels1D.CUSTOM_GAUSSIAN.createGaussianKernel1D(sigmaX).getData();
+ final double[] gaussianY = Kernels1D.CUSTOM_GAUSSIAN.createGaussianKernel1D(sigmaY).getData();
+ final double[] gaussianZ = Kernels1D.CUSTOM_GAUSSIAN.createGaussianKernel1D(sigmaZ).getData();
- Sequence filtered = SequenceUtil.getCopy(in);
+ final Sequence filtered = SequenceUtil.getCopy(in);
filtered.setName(in.getName() + "_filtered");
try {
Convolution1D.convolve(filtered, gaussianX, gaussianY, gaussianZ == null ? null : filtered.getSizeZ() > 1 ? gaussianZ : null);
}
- catch (Exception e) {
+ catch (final Exception e) {
throw new RuntimeException("GaussianFilter: " + e.getMessage());
}
diff --git a/src/main/java/plugins/adufour/filtering/IKernel.java b/src/main/java/plugins/adufour/filtering/IKernel.java
index d426108b3de1ae67e25cf7ccada35f990d882de1..04b6b2893bcb6db481d6674bc178c63921ebe016 100644
--- a/src/main/java/plugins/adufour/filtering/IKernel.java
+++ b/src/main/java/plugins/adufour/filtering/IKernel.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
import icy.sequence.Sequence;
diff --git a/src/main/java/plugins/adufour/filtering/Kernels1D.java b/src/main/java/plugins/adufour/filtering/Kernels1D.java
index e7351a15f01969bd0fb56554d85533ec51e89462..83f2caad75bfe4e18f77f014db6d93968652fff3 100644
--- a/src/main/java/plugins/adufour/filtering/Kernels1D.java
+++ b/src/main/java/plugins/adufour/filtering/Kernels1D.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
import icy.image.IcyBufferedImage;
@@ -26,7 +44,7 @@ public enum Kernels1D implements IKernel {
private final boolean isSeparable;
- Kernels1D(double[] data, boolean isSeparable) {
+ Kernels1D(final double[] data, final boolean isSeparable) {
this.data = data;
this.isSeparable = isSeparable;
}
@@ -35,14 +53,16 @@ public enum Kernels1D implements IKernel {
return isSeparable;
}
+ @Override
public Sequence toSequence() {
- IcyBufferedImage kernelImage = new IcyBufferedImage(data.length, 1, 1, DataType.DOUBLE);
+ final IcyBufferedImage kernelImage = new IcyBufferedImage(data.length, 1, 1, DataType.DOUBLE);
kernelImage.setDataXYAsDouble(0, data);
- Sequence kernel = new Sequence(kernelImage);
+ final Sequence kernel = new Sequence(kernelImage);
kernel.setName(this.toString());
return kernel;
}
+ @Override
public double[] getData() {
return data;
}
@@ -54,16 +74,16 @@ public enum Kernels1D implements IKernel {
* @param sigma the standard deviation of the gaussian
* @return the kernel as a sequence, or null if sigma is 0
*/
- public Kernels1D createGaussianKernel1D(double sigma) {
+ public Kernels1D createGaussianKernel1D(final double sigma) {
if (sigma < 1.0e-10) {
this.data = new double[]{1};
return this;
}
- double sigma2 = sigma * sigma;
- int k = (int) Math.ceil(sigma * 3.0f);
+ final double sigma2 = sigma * sigma;
+ final int k = (int) Math.ceil(sigma * 3.0f);
- int width = 2 * k + 1;
+ final int width = 2 * k + 1;
this.data = new double[width];
@@ -79,7 +99,7 @@ public enum Kernels1D implements IKernel {
* @param isNormalized true if the given values are already normalized to [0-1]
* @return Sets the kernel values
*/
- public Kernels1D createCustomKernel1D(double[] data, boolean isNormalized) {
+ public Kernels1D createCustomKernel1D(final double[] data, final boolean isNormalized) {
this.data = new double[data.length];
System.arraycopy(data, 0, this.data, 0, data.length);
if (!isNormalized)
@@ -91,12 +111,11 @@ public enum Kernels1D implements IKernel {
* Normalizes the given kernel such that the values sum up to 1
*
* @param data the kernel data in Z-XY order
- * @return
*/
- private static double[] normalize(double[] data) {
+ private static double[] normalize(final double[] data) {
double accu = 0;
- for (double d : data)
+ for (final double d : data)
accu += d;
if (accu != 1 && accu != 0) {
diff --git a/src/main/java/plugins/adufour/filtering/Kernels2D.java b/src/main/java/plugins/adufour/filtering/Kernels2D.java
index 29d52ef55e2249fd65e5e3173958515120d7e40c..66a977af272068744463c11b9c4aa73492c6b75f 100644
--- a/src/main/java/plugins/adufour/filtering/Kernels2D.java
+++ b/src/main/java/plugins/adufour/filtering/Kernels2D.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
import icy.image.IcyBufferedImage;
@@ -94,7 +112,7 @@ public enum Kernels2D implements IKernel {
private double[] data;
- Kernels2D(int width, int height, double[] data) {
+ Kernels2D(final int width, final int height, final double[] data) {
this.width = width;
this.height = height;
if (data != null) this.data = Kernels2D.normalize(data);
@@ -107,8 +125,8 @@ public enum Kernels2D implements IKernel {
* @param isSymmetric true if the values are symmetric (cosine), anti-symmetric (sine) otherwise
* @return Creates an isotropic 2D Gabor kernel
*/
- public Kernels2D createGaborKernel2D(double sigma, double k_x, double k_y, boolean isSymmetric) {
- int k = (int) Math.floor(sigma * 3.0);
+ public Kernels2D createGaborKernel2D(final double sigma, final double k_x, final double k_y, final boolean isSymmetric) {
+ final int k = (int) Math.floor(sigma * 3.0);
this.width = 2 * k + 1;
this.height = 2 * k + 1;
@@ -135,12 +153,12 @@ public enum Kernels2D implements IKernel {
* @param isNormalized true if the given values are already normalized to [0-1]
* @return Sets the kernel values manually
*/
- public Kernels2D createCustomKernel2D(double[][] kernel, boolean isNormalized) {
+ public Kernels2D createCustomKernel2D(final double[][] kernel, final boolean isNormalized) {
this.width = kernel.length;
this.height = kernel[0].length;
this.data = new double[width * height];
int offset = 0;
- for (double[] line : kernel) {
+ for (final double[] line : kernel) {
System.arraycopy(line, 0, this.data, offset, line.length);
offset += line.length;
}
@@ -156,7 +174,7 @@ public enum Kernels2D implements IKernel {
* @param width int
* @param isNormalized true if the given values are already normalized to [0-1]
*/
- public Kernels2D createCustomKernel2D(double[] kernel, int width, int height, boolean isNormalized) {
+ public Kernels2D createCustomKernel2D(final double[] kernel, final int width, final int height, final boolean isNormalized) {
this.width = width;
this.height = height;
this.data = new double[width * height];
@@ -171,9 +189,8 @@ public enum Kernels2D implements IKernel {
* @param z the slice to take values from
* @param c the channel to take values from
* @return Sets the kernel values using the given sequence
- * @throws InterruptedException
*/
- public Kernels2D createCustomKernel2D(Sequence kernel2D, int t, int z, int c) throws InterruptedException {
+ public Kernels2D createCustomKernel2D(final Sequence kernel2D, final int t, final int z, final int c) throws InterruptedException {
this.width = kernel2D.getSizeX();
this.height = kernel2D.getSizeY();
if (width % 2 == 0 || height % 2 == 0) throw new IllegalArgumentException("Kernel sequence must have odd dimensions");
@@ -186,12 +203,11 @@ public enum Kernels2D implements IKernel {
* Normalizes the given kernel such that the values sum up to 1
*
* @param data the kernel data in Z-XY order
- * @return
*/
- private static double[] normalize(double[] data) {
+ private static double[] normalize(final double[] data) {
double sum = 0;
- for (double d : data)
+ for (final double d : data)
sum += d;
if (sum != 1 && sum != 0) {
@@ -204,13 +220,14 @@ public enum Kernels2D implements IKernel {
@Override
public Sequence toSequence() {
- IcyBufferedImage kernelImage = new IcyBufferedImage(width, height, 1, DataType.DOUBLE);
+ final IcyBufferedImage kernelImage = new IcyBufferedImage(width, height, 1, DataType.DOUBLE);
kernelImage.setDataXYAsDouble(0, data);
- Sequence kernel = new Sequence(kernelImage);
+ final Sequence kernel = new Sequence(kernelImage);
kernel.setName(this.toString());
return kernel;
}
+ @Override
public double[] getData() {
return data;
}
diff --git a/src/main/java/plugins/adufour/filtering/LocalMax.java b/src/main/java/plugins/adufour/filtering/LocalMax.java
index 31d80dc8e2605ef0cb0f1ccd525fb90d33a76c86..77f53f8eabad887d53553249ec14293720aae4e8 100644
--- a/src/main/java/plugins/adufour/filtering/LocalMax.java
+++ b/src/main/java/plugins/adufour/filtering/LocalMax.java
@@ -1,12 +1,30 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
public class LocalMax extends SelectionFilter {
@Override
- double process(double currentValue, double[] neighborhood, int neighborhoodSize) {
+ double process(final double currentValue, final double[] neighborhood, final int neighborhoodSize) {
double defaultValue = 0.0;
for (int i = 0; i < neighborhoodSize; i++) {
- double d = neighborhood[i];
+ final double d = neighborhood[i];
if (d > currentValue) return 0.0;
if (defaultValue == 0.0 && d < currentValue) defaultValue = 1.0;
}
diff --git a/src/main/java/plugins/adufour/filtering/Max.java b/src/main/java/plugins/adufour/filtering/Max.java
index 03bb73789580eea4a0c98bcb49e7cdf15ceb7114..931efe317b8f3636eacf4bcc13d31475df8b0e08 100644
--- a/src/main/java/plugins/adufour/filtering/Max.java
+++ b/src/main/java/plugins/adufour/filtering/Max.java
@@ -1,11 +1,29 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
public class Max extends SelectionFilter {
@Override
- double process(double currentValue, double[] neighborhood, int neighborhoodSize) {
+ double process(final double currentValue, final double[] neighborhood, final int neighborhoodSize) {
double max = neighborhood[0];
for (int i = 1; i < neighborhoodSize; i++) {
- double d = neighborhood[i];
+ final double d = neighborhood[i];
if (d > max) max = d;
}
return max;
diff --git a/src/main/java/plugins/adufour/filtering/Mean.java b/src/main/java/plugins/adufour/filtering/Mean.java
index aa5b1745da8c9f7e6b7c72632bfaf5ad0f8157a4..8b7f1dd4d7a6d1c98397d0c4e5ca8815fc230207 100644
--- a/src/main/java/plugins/adufour/filtering/Mean.java
+++ b/src/main/java/plugins/adufour/filtering/Mean.java
@@ -1,8 +1,26 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
public class Mean extends SelectionFilter {
@Override
- double process(double currentValue, double[] neighborhood, int neighborhoodSize) {
+ double process(final double currentValue, final double[] neighborhood, final int neighborhoodSize) {
double sum = neighborhood[0];
for (int i = 1; i < neighborhoodSize; i++)
sum += neighborhood[i];
diff --git a/src/main/java/plugins/adufour/filtering/Median.java b/src/main/java/plugins/adufour/filtering/Median.java
index a0b0ab036aa2696e7e0d1a4ae6290ad53c5a72f3..faeda645be6cb47b0d8b621a43a079567707863c 100644
--- a/src/main/java/plugins/adufour/filtering/Median.java
+++ b/src/main/java/plugins/adufour/filtering/Median.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
public class Median extends SelectionFilter {
@@ -10,8 +28,8 @@ public class Median extends SelectionFilter {
* @return the k-th smallest value in the array
*/
@Override
- double process(double currentValue, double[] data, int length) {
- int k = length >> 1;
+ double process(final double currentValue, final double[] data, int length) {
+ final int k = length >> 1;
int i, j, mid, l = 1;
double a, temp;
diff --git a/src/main/java/plugins/adufour/filtering/RemoveOutliers.java b/src/main/java/plugins/adufour/filtering/RemoveOutliers.java
index a8868e0f182c88470e1032fa611612c420398e0f..42d3745d3c9d9816bbaf144b42f7c2945d8d5522 100644
--- a/src/main/java/plugins/adufour/filtering/RemoveOutliers.java
+++ b/src/main/java/plugins/adufour/filtering/RemoveOutliers.java
@@ -1,8 +1,26 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
public class RemoveOutliers extends SelectionFilter {
@Override
- double process(double currentValue, double[] neighborhood, int neighborHoodSize) {
+ double process(final double currentValue, final double[] neighborhood, final int neighborHoodSize) {
double mean = 0, stdev2 = 0;
// mean
diff --git a/src/main/java/plugins/adufour/filtering/SelectionFilter.java b/src/main/java/plugins/adufour/filtering/SelectionFilter.java
index 58d68086dd6b7f74af63a53a862c42ade9b1b883..32f5779f3c9ad13af4d7298831c4aae43b64d000 100644
--- a/src/main/java/plugins/adufour/filtering/SelectionFilter.java
+++ b/src/main/java/plugins/adufour/filtering/SelectionFilter.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
import icy.image.IcyBufferedImage;
@@ -32,8 +50,8 @@ public abstract class SelectionFilter extends Filter {
* the input sequence will be internally converted to double precision. However the result will
* be converted back to the same type as the given input sequence <i>with re-scaling</i>.
*/
- public Sequence filterSquare(Sequence sequence, int... radius) {
- Sequence out = new Sequence(sequence.getOMEXMLMetadata());
+ public Sequence filterSquare(final Sequence sequence, final int... radius) {
+ final Sequence out = new Sequence(sequence.getOMEXMLMetadata());
out.setName(sequence.getName() + "_" + getDescriptor().getName());
stopFlag.setValue(false);
@@ -60,7 +78,7 @@ public abstract class SelectionFilter extends Filter {
// create an array of tasks for multi-thread processing
// => rationale: one task per image line
- ArrayList<Future<?>> tasks = new ArrayList<>(height);
+ final ArrayList<Future<?>> tasks = new ArrayList<>(height);
convolution:
for (int t = 0; t < sequence.getSizeT(); t++) {
@@ -90,7 +108,7 @@ public abstract class SelectionFilter extends Filter {
// submit a new filtering task for the current line
tasks.add(service.submit(() -> {
- double[] neighborhood = new double[maxNeighbors];
+ final double[] neighborhood = new double[maxNeighbors];
int inX, inY, inZ;
int inXY, outXY = lineOffset;
@@ -102,12 +120,12 @@ public abstract class SelectionFilter extends Filter {
currentPixel = Array1DUtil.getValue(_inXY, outXY, type);
int localNeighborHoodSize = 0;
- int minXinclusive = Math.max(x - kWidth, 0);
- int maxXexclusive = Math.min(x + kWidth + 1, width);
+ final int minXinclusive = Math.max(x - kWidth, 0);
+ final int maxXexclusive = Math.min(x + kWidth + 1, width);
// browse the neighborhood along Z
for (inZ = minZinclusive; inZ < maxZexclusive; inZ++) {
- Object neighborSlice = in_Z_XY[inZ];
+ final Object neighborSlice = in_Z_XY[inZ];
// browse the neighborhood along Y
for (inY = minYinclusive; inY < maxYexclusive; inY++) {
@@ -137,10 +155,10 @@ public abstract class SelectionFilter extends Filter {
} // end for(y)
try {
- for (Future<?> f : tasks)
+ for (final Future<?> f : tasks)
f.get();
}
- catch (InterruptedException | ExecutionException e) {
+ catch (final InterruptedException | ExecutionException e) {
Thread.currentThread().interrupt();
return out;
}
diff --git a/src/main/java/plugins/adufour/filtering/SelectionFilterBlock.java b/src/main/java/plugins/adufour/filtering/SelectionFilterBlock.java
index 99f6b73b022e9cc3dfcbd4f609134a636e552938..780d134aec3b41295f0bc6c134a149ee2257e88d 100644
--- a/src/main/java/plugins/adufour/filtering/SelectionFilterBlock.java
+++ b/src/main/java/plugins/adufour/filtering/SelectionFilterBlock.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
import icy.plugin.abstract_.Plugin;
@@ -22,11 +40,11 @@ public class SelectionFilterBlock extends Plugin implements Block {
@Override
public void run() {
- SelectionFilter selectionFilter;
+ final SelectionFilter selectionFilter;
try {
selectionFilter = filter.newInstance();
}
- catch (Exception e) {
+ catch (final Exception e) {
throw new RuntimeException("Unable to create the " + filter.getValueAsString() + " filter");
}
@@ -34,7 +52,7 @@ public class SelectionFilterBlock extends Plugin implements Block {
}
@Override
- public void declareInput(VarList inputMap) {
+ public void declareInput(final VarList inputMap) {
inputMap.add("input sequence", input);
inputMap.add("filter", filter);
inputMap.add("filter radius (X)", radiusX.getVariable());
@@ -43,7 +61,7 @@ public class SelectionFilterBlock extends Plugin implements Block {
}
@Override
- public void declareOutput(VarList outputMap) {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("filtered sequence", output);
}
diff --git a/src/main/java/plugins/adufour/filtering/StandardDeviation.java b/src/main/java/plugins/adufour/filtering/StandardDeviation.java
index 06e254002107283af228f706da280797a331fced..7843e28df42c99b356453e41a3b27c76e9b62cad 100644
--- a/src/main/java/plugins/adufour/filtering/StandardDeviation.java
+++ b/src/main/java/plugins/adufour/filtering/StandardDeviation.java
@@ -1,8 +1,26 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
public class StandardDeviation extends SelectionFilter {
@Override
- double process(double currentValue, double[] neighborhood, int neighborHoodSize) {
+ double process(final double currentValue, final double[] neighborhood, final int neighborHoodSize) {
double mean = 0, var = 0;
for (int i = 0; i < neighborHoodSize; i++)
diff --git a/src/main/java/plugins/adufour/filtering/Variance.java b/src/main/java/plugins/adufour/filtering/Variance.java
index 85f74dbfd4e8adfbdae66b0e88085177614d1b66..f00f5591e1c001a49c9f89c405b4fc6db056ada5 100644
--- a/src/main/java/plugins/adufour/filtering/Variance.java
+++ b/src/main/java/plugins/adufour/filtering/Variance.java
@@ -1,8 +1,26 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.filtering;
public class Variance extends SelectionFilter {
@Override
- double process(double currentValue, double[] neighborhood, int neighborHoodSize) {
+ double process(final double currentValue, final double[] neighborhood, final int neighborHoodSize) {
double mean = 0, var = 0;
for (int i = 0; i < neighborHoodSize; i++)