diff --git a/.gitignore b/.gitignore
index 30c9a54acde67825b40daec3db2670ef0c6a64ea..57f16fb67c1b1589981416b323d7a9debc728665 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,11 +1,41 @@
+/build*
+/workspace
+setting.xml
+release/
target/
-workspace/
-.settings/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
.idea/
-setting.xml
-.project
+*.iws
+*.iml
+*.ipr
+
+### Eclipse ###
+.apt_generated
.classpath
-*.prefs
-*.jardesc
-*.jar
-**/.DS_Store
\ No newline at end of file
+.factorypath
+.project
+.settings
+.springBeans
+.sts4-cache
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/
+
+### Mac OS ###
+**/.DS_Store
+Icon?
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index 8f4dc7ab62fe4ffdbf502b1ceb266184abf0a391..09be7c043bb4b3f893d32057dead94d713d1b0fd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -8,12 +8,12 @@
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>pom-icy</artifactId>
- <version>2.2.0</version>
+ <version>3.0.0-a.1</version>
</parent>
<!-- Project Information -->
<artifactId>intensity-projection</artifactId>
- <version>2.0.0</version>
+ <version>2.0.0-a.1</version>
<name>Intensity Projection plugin</name>
<description>Intensity projection along depth or time with multiple algorithms: mean, max, median, variance, standard deviation, saturated sum. Projection can be restricted to ROI.</description>
@@ -47,15 +47,11 @@
</developer>
</developers>
- <!-- List of project's dependencies -->
<dependencies>
- <!-- The EzPlug library, simplifies writing UI for Icy plugins. -->
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>ezplug</artifactId>
</dependency>
-
- <!-- The EzPlug library, simplifies writing UI for Icy plugins. -->
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>protocols</artifactId>
@@ -66,8 +62,7 @@
<repositories>
<repository>
<id>icy</id>
- <name>Icy's Nexus</name>
- <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
</repository>
</repositories>
</project>
diff --git a/src/main/java/org/bioimageanalysis/icy/image/projection/ProjectionAxis.java b/src/main/java/org/bioimageanalysis/icy/image/projection/ProjectionAxis.java
index bc9d7dede3fbc424fb0c66b2bc54fad1c63f8c7d..a3a3799a0965964df0cd98c7bb759d8032266bee 100644
--- a/src/main/java/org/bioimageanalysis/icy/image/projection/ProjectionAxis.java
+++ b/src/main/java/org/bioimageanalysis/icy/image/projection/ProjectionAxis.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,6 +18,9 @@
package org.bioimageanalysis.icy.image.projection;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
+
/**
* Indicates the direction on which the projection should be performed.
*
@@ -28,12 +31,14 @@ public enum ProjectionAxis {
private final String name;
- ProjectionAxis(final String name) {
+ @Contract(pure = true)
+ ProjectionAxis(final @NotNull String name) {
this.name = name;
}
+ @Contract(pure = true)
@Override
- public String toString() {
+ public @NotNull String toString() {
return name;
}
}
diff --git a/src/main/java/org/bioimageanalysis/icy/image/projection/ProjectionCalculator.java b/src/main/java/org/bioimageanalysis/icy/image/projection/ProjectionCalculator.java
index d96316f941189c7b9f06b82dfe50167a3b817387..e744a89f3c49892846169abd492ca3aceef1845c 100644
--- a/src/main/java/org/bioimageanalysis/icy/image/projection/ProjectionCalculator.java
+++ b/src/main/java/org/bioimageanalysis/icy/image/projection/ProjectionCalculator.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,15 +18,17 @@
package org.bioimageanalysis.icy.image.projection;
-import icy.image.IcyBufferedImage;
-import icy.image.IcyBufferedImageCursor;
-import icy.math.ArrayMath;
-import icy.roi.ROI;
-import icy.sequence.Sequence;
-import icy.sequence.VolumetricImage;
-import icy.type.DataType;
-import icy.util.OMEUtil;
+import org.bioimageanalysis.icy.common.math.ArrayMath;
+import org.bioimageanalysis.icy.common.type.DataType;
import org.bioimageanalysis.icy.image.projection.util.MessageProgressListener;
+import org.bioimageanalysis.icy.model.OMEUtil;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImage;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImageCursor;
+import org.bioimageanalysis.icy.model.roi.ROI;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.model.sequence.VolumetricImage;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
import java.util.*;
import java.util.concurrent.*;
@@ -38,7 +40,6 @@ import java.util.concurrent.*;
* @author Daniel Felipe Gonzalez Obando
*/
public class ProjectionCalculator implements Callable<Sequence> {
-
/**
* Builder class for {@link ProjectionCalculator}s. This allows users to specify the sequence, ROIs, axis and operation before creating the calculator.
*
@@ -57,6 +58,7 @@ public class ProjectionCalculator implements Callable<Sequence> {
*
* @param s Target sequence for the projection.
*/
+ @Contract("null -> fail")
public Builder(final Sequence s) {
if (s == null || s.isEmpty())
throw new IllegalArgumentException("Input sequence is null or empty.");
@@ -138,6 +140,7 @@ public class ProjectionCalculator implements Callable<Sequence> {
private final List<MessageProgressListener> progressListeners;
private boolean computed;
+ @Contract(pure = true)
private ProjectionCalculator() {
progressListeners = new ArrayList<>();
computed = false;
@@ -184,15 +187,17 @@ public class ProjectionCalculator implements Callable<Sequence> {
private Sequence result;
private void createResultSequence() throws InterruptedException {
- result = new Sequence(OMEUtil.createOMEXMLMetadata(seq.getOMEXMLMetadata()),
- op + " " + axis + "-projection of " + seq.getName());
+ result = new Sequence(
+ OMEUtil.createOMEXMLMetadata(seq.getOMEXMLMetadata()),
+ op + " " + axis + "-projection of " + seq.getName()
+ );
final int width = axis == ProjectionAxis.X ? 1 : seq.getSizeX();
final int height = axis == ProjectionAxis.Y ? 1 : seq.getSizeY();
final int depth = axis == ProjectionAxis.Z ? 1 : seq.getSizeZ();
final int frames = axis == ProjectionAxis.T ? 1 : seq.getSizeT();
final int channels = axis == ProjectionAxis.C ? 1 : seq.getSizeC();
- final DataType dataType = seq.getDataType_();
+ final DataType dataType = seq.getDataType();
for (int t = 0; t < frames; t++) {
final VolumetricImage vol = new VolumetricImage();
@@ -209,18 +214,14 @@ public class ProjectionCalculator implements Callable<Sequence> {
for (int c = 0; c < seq.getSizeC(); c++)
result.getColorModel().setColorMap(c, seq.getColorMap(c), true);
}
- notifyProgress(0.01, "Result sequence instatiated");
+ notifyProgress(0.01, "Result sequence instantiated");
}
private void computeProjection() throws InterruptedException, ExecutionException {
switch (axis) {
case X:
- //startProjectionOnPlane();
- //break;
case C:
- //startProjectionOnPlane();
- //break;
case Y:
startProjectionOnPlane();
break;
@@ -252,54 +253,52 @@ public class ProjectionCalculator implements Callable<Sequence> {
}
}
- final ForkJoinPool generalTaskPool = (ForkJoinPool) Executors
- .newWorkStealingPool(Math.max(1, Runtime.getRuntime().availableProcessors() - 1));
-
- final List<Future<IcyBufferedImage>> futures = new ArrayList<>(frames * depth);
- for (t = 0; t < frames; t++) {
- tOff = t * depth;
- for (z = 0; z < depth; z++) {
- final Callable<IcyBufferedImage> task;
- switch (axis) {
- case X:
- task = getImageXProjectionTask(inputPlanes[tOff + z], outputPlanes[tOff + z], t, z, channels,
+ try (final ForkJoinPool generalTaskPool = (ForkJoinPool) Executors.newWorkStealingPool(Math.max(1, Runtime.getRuntime().availableProcessors() - 1))) {
+ final List<Future<IcyBufferedImage>> futures = new ArrayList<>(frames * depth);
+ for (t = 0; t < frames; t++) {
+ tOff = t * depth;
+ for (z = 0; z < depth; z++) {
+ final Callable<IcyBufferedImage> task = switch (axis) {
+ case X -> getImageXProjectionTask(inputPlanes[tOff + z], outputPlanes[tOff + z], t, z, channels,
height, width);
- break;
- case Y:
- task = getImageYProjectionTask(inputPlanes[tOff + z], outputPlanes[tOff + z], t, z, channels,
+ case Y -> getImageYProjectionTask(inputPlanes[tOff + z], outputPlanes[tOff + z], t, z, channels,
height, width);
- break;
- case C:
- task = getImageCProjectionTask(inputPlanes[tOff + z], outputPlanes[tOff + z], t, z, channels,
+ case C -> getImageCProjectionTask(inputPlanes[tOff + z], outputPlanes[tOff + z], t, z, channels,
height, width);
- break;
- default:
- throw new IllegalArgumentException("Wrong axis parameter");
+ default -> throw new IllegalArgumentException("Wrong axis parameter");
+ };
+ futures.add(generalTaskPool.submit(task));
}
- futures.add(generalTaskPool.submit(task));
}
- }
- generalTaskPool.shutdown();
+ generalTaskPool.shutdown();
- int pos;
- for (pos = 0, t = 0; t < frames; t++) {
- for (z = 0; z < depth; z++) {
- try {
- futures.get(pos++).get();
- }
- catch (final InterruptedException | ExecutionException e) {
- generalTaskPool.shutdownNow();
- throw e;
+ int pos;
+ for (pos = 0, t = 0; t < frames; t++) {
+ for (z = 0; z < depth; z++) {
+ try {
+ futures.get(pos++).get();
+ }
+ catch (final InterruptedException | ExecutionException e) {
+ generalTaskPool.shutdownNow();
+ throw e;
+ }
}
+ notifyProgress(0.01 + 0.99 * ((double) t / frames), axis + "-projection: Processed t=" + t);
}
- notifyProgress(0.01 + 0.99 * ((double) t / frames), axis + "-projection: Processed t=" + t);
}
}
- private Callable<IcyBufferedImage> getImageXProjectionTask(final IcyBufferedImage inputPlane,
- final IcyBufferedImage outputPlane, final int t, final int z, final int channels, final int height,
- final int width) {
+ @Contract(pure = true)
+ private @NotNull Callable<IcyBufferedImage> getImageXProjectionTask(
+ final IcyBufferedImage inputPlane,
+ final IcyBufferedImage outputPlane,
+ final int t,
+ final int z,
+ final int channels,
+ final int height,
+ final int width
+ ) {
return () -> {
int channel, line, column, elementsCount;
final double[] elements = new double[width];
@@ -336,9 +335,16 @@ public class ProjectionCalculator implements Callable<Sequence> {
};
}
- private Callable<IcyBufferedImage> getImageYProjectionTask(final IcyBufferedImage inputPlane,
- final IcyBufferedImage outputPlane, final int t, final int z, final int channels, final int height,
- final int width) {
+ @Contract(pure = true)
+ private @NotNull Callable<IcyBufferedImage> getImageYProjectionTask(
+ final IcyBufferedImage inputPlane,
+ final IcyBufferedImage outputPlane,
+ final int t,
+ final int z,
+ final int channels,
+ final int height,
+ final int width
+ ) {
return () -> {
int channel, line, column, elementsCount;
final double[] elements = new double[height];
@@ -376,8 +382,16 @@ public class ProjectionCalculator implements Callable<Sequence> {
};
}
- private Callable<IcyBufferedImage> getImageCProjectionTask(final IcyBufferedImage inputPlane,
- final IcyBufferedImage outputPlane, final int t, final int z, final int channels, final int height, final int width) {
+ @Contract(pure = true)
+ private @NotNull Callable<IcyBufferedImage> getImageCProjectionTask(
+ final IcyBufferedImage inputPlane,
+ final IcyBufferedImage outputPlane,
+ final int t,
+ final int z,
+ final int channels,
+ final int height,
+ final int width
+ ) {
return () -> {
int channel, line, column, elementsCount;
final double[] elements = new double[height];
@@ -430,46 +444,57 @@ public class ProjectionCalculator implements Callable<Sequence> {
final int frames = seq.getSizeT();
final int channels = seq.getSizeC();
- final ForkJoinPool generalTaskPool = (ForkJoinPool) Executors
- .newWorkStealingPool(Math.max(1, Runtime.getRuntime().availableProcessors() / 2));
- final ForkJoinPool volumeTaskPool = (ForkJoinPool) Executors
- .newWorkStealingPool(Math.max(1, Runtime.getRuntime().availableProcessors() - 1));
- int t, c;
- VolumetricImage inputVolume, resultVolume;
- final List<Future<VolumetricImage>> futures = new ArrayList<>(frames * depth);
- for (t = 0; t < frames; t++) {
- inputVolume = seq.getVolumetricImage(t);
- resultVolume = result.getVolumetricImage(t);
- for (c = 0; c < channels; c++) {
- futures.add(generalTaskPool.submit(getImageZProjectionTask(t, c, inputVolume, resultVolume, channels,
- height, width, depth, volumeTaskPool)));
+ try (
+ final ForkJoinPool generalTaskPool = (ForkJoinPool) Executors.newWorkStealingPool(Math.max(1, Runtime.getRuntime().availableProcessors() / 2));
+ final ForkJoinPool volumeTaskPool = (ForkJoinPool) Executors.newWorkStealingPool(Math.max(1, Runtime.getRuntime().availableProcessors() - 1))
+ ) {
+ int t, c;
+ VolumetricImage inputVolume, resultVolume;
+ final List<Future<VolumetricImage>> futures = new ArrayList<>(frames * depth);
+ for (t = 0; t < frames; t++) {
+ inputVolume = seq.getVolumetricImage(t);
+ resultVolume = result.getVolumetricImage(t);
+ for (c = 0; c < channels; c++) {
+ futures.add(generalTaskPool.submit(getImageZProjectionTask(t, c, inputVolume, resultVolume, channels,
+ height, width, depth, volumeTaskPool)));
+ }
}
- }
- generalTaskPool.shutdown();
+ generalTaskPool.shutdown();
- try {
- int pos;
- for (pos = 0, t = 0; t < frames; t++) {
- for (c = 0; c < channels; c++) {
- futures.get(pos++).get();
+ try {
+ int pos;
+ for (pos = 0, t = 0; t < frames; t++) {
+ for (c = 0; c < channels; c++) {
+ futures.get(pos++).get();
+ }
+ notifyProgress(0.01 + 0.99 * ((double) t / frames), axis + "-projection: Processed t=" + t);
}
- notifyProgress(0.01 + 0.99 * ((double) t / frames), axis + "-projection: Processed t=" + t);
+ }
+ catch (final InterruptedException | ExecutionException e) {
+ generalTaskPool.shutdownNow();
+ throw e;
+ }
+ finally {
+ volumeTaskPool.shutdown();
}
}
- catch (final InterruptedException | ExecutionException e) {
- generalTaskPool.shutdownNow();
- throw e;
- }
- finally {
- volumeTaskPool.shutdown();
- }
-
}
- private Callable<VolumetricImage> getImageZProjectionTask(final int t, final int c, final VolumetricImage inputVolume,
- final VolumetricImage resultVolume, final int channels, final int height, final int width, final int depth, final ForkJoinPool volumeTaskPool) {
+ @Contract(pure = true)
+ @SuppressWarnings("StatementWithEmptyBody")
+ private @NotNull Callable<VolumetricImage> getImageZProjectionTask(
+ final int t,
+ final int c,
+ final VolumetricImage inputVolume,
+ final VolumetricImage resultVolume,
+ final int channels,
+ final int height,
+ final int width,
+ final int depth,
+ final ForkJoinPool volumeTaskPool
+ ) {
return () -> {
int slice, line, column;
@@ -517,7 +542,10 @@ public class ProjectionCalculator implements Callable<Sequence> {
try {
for (line = 0; line < height; line++) {
- final double[] lineElements = futureLines.get(line).get();
+ notifyProgress(0.01 + 0.99 * ((double) line / height), axis + "-projection: Processed line=" + line);
+ final Future<double[]> future = futureLines.get(line);
+ while (!future.isDone()) ;
+ final double[] lineElements = future.get();
for (column = 0; column < width; column++) {
outputCursor.setSafe(column, line, c, lineElements[column]);
}
@@ -539,46 +567,58 @@ public class ProjectionCalculator implements Callable<Sequence> {
final int frames = seq.getSizeT();
final int channels = seq.getSizeC();
- final ForkJoinPool generalTaskPool = (ForkJoinPool) Executors
- .newWorkStealingPool(Math.max(1, Runtime.getRuntime().availableProcessors() / 2));
- final ForkJoinPool temporalTaskPool = (ForkJoinPool) Executors
- .newWorkStealingPool(Math.max(1, Runtime.getRuntime().availableProcessors() - 1));
- int z, c;
- Sequence inputS, resultS;
- final List<Future<Sequence>> futures = new ArrayList<>(depth);
- for (z = 0; z < depth; z++) {
- for (c = 0; c < channels; c++) {
- inputS = seq;
- resultS = result;
- {
- futures.add(generalTaskPool.submit(getImageTProjectionTask(z, c, inputS, resultS, channels, height,
- width, depth, frames, temporalTaskPool)));
+ try (
+ final ForkJoinPool generalTaskPool = (ForkJoinPool) Executors.newWorkStealingPool(Math.max(1, Runtime.getRuntime().availableProcessors() / 2));
+ final ForkJoinPool temporalTaskPool = (ForkJoinPool) Executors.newWorkStealingPool(Math.max(1, Runtime.getRuntime().availableProcessors() - 1))
+ ) {
+ int z, c;
+ Sequence inputS, resultS;
+ final List<Future<Sequence>> futures = new ArrayList<>(depth);
+ for (z = 0; z < depth; z++) {
+ for (c = 0; c < channels; c++) {
+ inputS = seq;
+ resultS = result;
+ {
+ futures.add(generalTaskPool.submit(getImageTProjectionTask(z, c, inputS, resultS, channels, height, width, depth, frames, temporalTaskPool)));
+ }
}
}
- }
- generalTaskPool.shutdown();
+ generalTaskPool.shutdown();
- try {
- int pos;
- for (pos = 0, z = 0; z < depth; z++) {
- for (c = 0; c < channels; c++) {
- futures.get(pos++).get();
+ try {
+ int pos;
+ for (pos = 0, z = 0; z < depth; z++) {
+ for (c = 0; c < channels; c++) {
+ futures.get(pos++).get();
+ }
+ notifyProgress(0.01 + 0.99 * ((double) z / depth), axis + "-projection: Processed z=" + z);
}
- notifyProgress(0.01 + 0.99 * ((double) z / depth), axis + "-projection: Processed z=" + z);
}
- }
- catch (final InterruptedException | ExecutionException e) {
- generalTaskPool.shutdownNow();
- throw e;
- }
- finally {
- temporalTaskPool.shutdown();
+ catch (final InterruptedException | ExecutionException e) {
+ generalTaskPool.shutdownNow();
+ throw e;
+ }
+ finally {
+ temporalTaskPool.shutdown();
+ }
}
}
- private Callable<Sequence> getImageTProjectionTask(final int z, final int c, final Sequence inputS, final Sequence resultS, final int channels,
- final int height, final int width, final int depth, final int frames, final ForkJoinPool temporalTaskPool) {
+ @Contract(pure = true)
+ @SuppressWarnings("StatementWithEmptyBody")
+ private @NotNull Callable<Sequence> getImageTProjectionTask(
+ final int z,
+ final int c,
+ final Sequence inputS,
+ final Sequence resultS,
+ final int channels,
+ final int height,
+ final int width,
+ final int depth,
+ final int frames,
+ final ForkJoinPool temporalTaskPool
+ ) {
return () -> {
int frame, line, column;
final IcyBufferedImageCursor[] inputCursors = new IcyBufferedImageCursor[frames];
@@ -624,7 +664,10 @@ public class ProjectionCalculator implements Callable<Sequence> {
try {
for (line = 0; line < height; line++) {
- final double[] lineElements = futureLines.get(line).get();
+ notifyProgress(0.01 + 0.99 * ((double) line / height), axis + "-projection: Processed line=" + line);
+ final Future<double[]> future = futureLines.get(line);
+ while (!future.isDone()) ;
+ final double[] lineElements = future.get();
for (column = 0; column < width; column++) {
outputCursor.setSafe(column, line, c, lineElements[column]);
}
@@ -663,6 +706,7 @@ public class ProjectionCalculator implements Callable<Sequence> {
progressListeners.forEach(l -> l.onProgress(progress, message));
}
+ @Contract(pure = true)
private Sequence getResultSequence() {
return result;
}
diff --git a/src/main/java/org/bioimageanalysis/icy/image/projection/ProjectionOperationType.java b/src/main/java/org/bioimageanalysis/icy/image/projection/ProjectionOperationType.java
index 49f4cfdf65951b6ff764e2e431ae36823ac7f2b7..12ba559034dd0580da8c37b3b1640525319b8f84 100644
--- a/src/main/java/org/bioimageanalysis/icy/image/projection/ProjectionOperationType.java
+++ b/src/main/java/org/bioimageanalysis/icy/image/projection/ProjectionOperationType.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,22 +18,32 @@
package org.bioimageanalysis.icy.image.projection;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
+
/**
* Represents the operation to be applied when performing an intensity projection on a sequence.
*
* @author Daniel Felipe Gonzalez Obando
*/
public enum ProjectionOperationType {
- MAX("Maximum"), MEAN("Average"), MED("Median"), MIN("Minimum"), STD("Standard Deviation"), SATSUM("Saturated Sum");
+ MAX("Maximum"),
+ MEAN("Average"),
+ MED("Median"),
+ MIN("Minimum"),
+ STD("Standard Deviation"),
+ SATSUM("Saturated Sum");
private final String description;
- ProjectionOperationType(final String description) {
+ @Contract(pure = true)
+ ProjectionOperationType(final @NotNull String description) {
this.description = description;
}
+ @Contract(pure = true)
@Override
- public String toString() {
+ public @NotNull String toString() {
return description;
}
}
diff --git a/src/main/java/org/bioimageanalysis/icy/image/projection/util/MessageProgressListener.java b/src/main/java/org/bioimageanalysis/icy/image/projection/util/MessageProgressListener.java
index a1e70cd553497e12a946cf6de94c39fb767ea36f..ef2088abb3f70826c2703ce42cf5ee7895199990 100644
--- a/src/main/java/org/bioimageanalysis/icy/image/projection/util/MessageProgressListener.java
+++ b/src/main/java/org/bioimageanalysis/icy/image/projection/util/MessageProgressListener.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,6 +18,8 @@
package org.bioimageanalysis.icy.image.projection.util;
+import org.jetbrains.annotations.Nullable;
+
/**
* A Progress event listener that handles events associating a value and a message to them.
*
@@ -30,5 +32,5 @@ public interface MessageProgressListener {
* @param progress The progress value from 0.0 to 1.0. {@link Double#NaN} value should be taken as no change and -1.0 as indeterminate progress.
* @param message The event message. A null value should be taken as no change on the message.
*/
- void onProgress(double progress, String message);
+ void onProgress(double progress, @Nullable String message);
}
diff --git a/src/main/java/org/bioimageanalysis/icy/image/projection/util/SequenceCursor.java b/src/main/java/org/bioimageanalysis/icy/image/projection/util/SequenceCursor.java
index 166ae994caf8c91eef57b3d0c1b91a93929589b1..a0255efa05d70f7ab50e446f75dc133eb20805e6 100644
--- a/src/main/java/org/bioimageanalysis/icy/image/projection/util/SequenceCursor.java
+++ b/src/main/java/org/bioimageanalysis/icy/image/projection/util/SequenceCursor.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,7 +18,8 @@
package org.bioimageanalysis.icy.image.projection.util;
-import icy.sequence.Sequence;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.jetbrains.annotations.NotNull;
import java.util.concurrent.atomic.AtomicBoolean;
@@ -40,7 +41,7 @@ public class SequenceCursor {
*
* @param seq Sequence.
*/
- public SequenceCursor(final Sequence seq) {
+ public SequenceCursor(final @NotNull Sequence seq) {
this.seq = seq;
this.volumeCursors = new VolumetricImageCursor[seq.getSizeT()];
this.sequenceChanged = new AtomicBoolean();
@@ -75,8 +76,7 @@ public class SequenceCursor {
* @throws IndexOutOfBoundsException If the position is not in the image.
* @throws RuntimeException If the data type is not a valid format.
*/
- public synchronized void set(final int x, final int y, final int z, final int t, final int c, final double val)
- throws IndexOutOfBoundsException, RuntimeException {
+ public synchronized void set(final int x, final int y, final int z, final int t, final int c, final double val) throws IndexOutOfBoundsException, RuntimeException {
getVolumeCursor(t).set(x, y, z, c, val);
sequenceChanged.set(true);
}
@@ -94,8 +94,7 @@ public class SequenceCursor {
* @throws IndexOutOfBoundsException If the position is not in the image.
* @throws RuntimeException If the data type is not a valid format.
*/
- public synchronized void setSafe(final int x, final int y, final int z, final int t, final int c, final double val)
- throws IndexOutOfBoundsException, RuntimeException {
+ public synchronized void setSafe(final int x, final int y, final int z, final int t, final int c, final double val) throws IndexOutOfBoundsException, RuntimeException {
getVolumeCursor(t).setSafe(x, y, z, c, val);
sequenceChanged.set(true);
}
@@ -103,7 +102,7 @@ public class SequenceCursor {
private int currentT;
private VolumetricImageCursor currentCursor;
- private synchronized VolumetricImageCursor getVolumeCursor(final int t) throws IndexOutOfBoundsException {
+ private synchronized @NotNull VolumetricImageCursor getVolumeCursor(final int t) throws IndexOutOfBoundsException {
if (currentT != t) {
if (volumeCursors[t] == null) {
volumeCursors[t] = new VolumetricImageCursor(seq, t);
@@ -129,7 +128,7 @@ public class SequenceCursor {
}
@Override
- public String toString() {
+ public @NotNull String toString() {
return "last T=" + currentT + " " + ((currentCursor != null) ? currentCursor.toString() : "");
}
}
diff --git a/src/main/java/org/bioimageanalysis/icy/image/projection/util/VolumetricImageCursor.java b/src/main/java/org/bioimageanalysis/icy/image/projection/util/VolumetricImageCursor.java
index 7d3f1083a251bfec37d79023b96be84ddf3f8ed0..c12d681b8b7ed00c5b40ac9f17a0f096ebfc19ab 100644
--- a/src/main/java/org/bioimageanalysis/icy/image/projection/util/VolumetricImageCursor.java
+++ b/src/main/java/org/bioimageanalysis/icy/image/projection/util/VolumetricImageCursor.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,9 +18,10 @@
package org.bioimageanalysis.icy.image.projection.util;
-import icy.image.IcyBufferedImageCursor;
-import icy.sequence.Sequence;
-import icy.sequence.VolumetricImage;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImageCursor;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.model.sequence.VolumetricImage;
+import org.jetbrains.annotations.NotNull;
import java.util.concurrent.atomic.AtomicBoolean;
@@ -44,7 +45,7 @@ public class VolumetricImageCursor {
*
* @param vol Target volume.
*/
- public VolumetricImageCursor(final VolumetricImage vol) {
+ public VolumetricImageCursor(final @NotNull VolumetricImage vol) {
this.vol = vol;
planeCursors = new IcyBufferedImageCursor[vol.getSize()];
volumeChanged = new AtomicBoolean(false);
@@ -57,7 +58,7 @@ public class VolumetricImageCursor {
* @param seq Target sequence.
* @param t Time position where the volume is located in {@code seq}.
*/
- public VolumetricImageCursor(final Sequence seq, final int t) {
+ public VolumetricImageCursor(final @NotNull Sequence seq, final int t) {
this(seq.getVolumetricImage(t));
}
@@ -88,8 +89,7 @@ public class VolumetricImageCursor {
* @throws IndexOutOfBoundsException If the position is not in the image.
* @throws RuntimeException If the data type is not a valid format.
*/
- public synchronized void set(final int x, final int y, final int z, final int c, final double val)
- throws IndexOutOfBoundsException, RuntimeException {
+ public synchronized void set(final int x, final int y, final int z, final int c, final double val) throws IndexOutOfBoundsException, RuntimeException {
getPlaneCursor(z).set(x, y, c, val);
volumeChanged.set(true);
}
@@ -106,8 +106,7 @@ public class VolumetricImageCursor {
* @throws IndexOutOfBoundsException If the position is not in the image.
* @throws RuntimeException If the data type is not a valid format.
*/
- public synchronized void setSafe(final int x, final int y, final int z, final int c, final double val)
- throws IndexOutOfBoundsException, RuntimeException {
+ public synchronized void setSafe(final int x, final int y, final int z, final int c, final double val) throws IndexOutOfBoundsException, RuntimeException {
getPlaneCursor(z).setSafe(x, y, c, val);
volumeChanged.set(true);
}
@@ -115,7 +114,7 @@ public class VolumetricImageCursor {
private IcyBufferedImageCursor currentCursor;
private int currentZ;
- private synchronized IcyBufferedImageCursor getPlaneCursor(final int z) throws IndexOutOfBoundsException {
+ private synchronized @NotNull IcyBufferedImageCursor getPlaneCursor(final int z) throws IndexOutOfBoundsException {
if (currentZ != z) {
if (planeCursors[z] == null) {
planeCursors[z] = new IcyBufferedImageCursor(vol.getImage(z));
diff --git a/src/main/java/plugins/adufour/projection/Projection.java b/src/main/java/plugins/adufour/projection/Projection.java
index 6a5e9a0001048b3668e9bcf51e087ee7b7911b74..b8640ee496820abda39be2e759e2511ea813f769 100644
--- a/src/main/java/plugins/adufour/projection/Projection.java
+++ b/src/main/java/plugins/adufour/projection/Projection.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,16 +18,17 @@
package plugins.adufour.projection;
-import icy.main.Icy;
-import icy.plugin.PluginLauncher;
-import icy.plugin.PluginLoader;
-import icy.roi.ROI;
-import icy.sequence.Sequence;
-import icy.system.IcyExceptionHandler;
-import icy.system.IcyHandledException;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
import org.bioimageanalysis.icy.image.projection.ProjectionAxis;
import org.bioimageanalysis.icy.image.projection.ProjectionCalculator;
import org.bioimageanalysis.icy.image.projection.ProjectionOperationType;
+import org.bioimageanalysis.icy.model.roi.ROI;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
import plugins.adufour.blocks.lang.Block;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.ezplug.*;
@@ -36,21 +37,29 @@ import plugins.adufour.vars.lang.VarSequence;
import java.util.Collections;
import java.util.List;
+@IcyPluginName("Intensity Projection")
+@IcyPluginIcon(path = "/plugins/adufour/projection/icon/icon_32.png")
public class Projection extends EzPlug implements Block, EzStoppable {
public enum ProjectionDirection {
Z, T, C, Y, X
}
public enum ProjectionType {
- MAX("Maximum"), MEAN("Average"), MED("Median"), MIN("Minimum"), STD("Standard Deviation"),
+ MAX("Maximum"),
+ MEAN("Average"),
+ MED("Median"),
+ MIN("Minimum"),
+ STD("Standard Deviation"),
SATSUM("Saturated Sum");
private final String description;
+ @Contract(pure = true)
ProjectionType(final String description) {
this.description = description;
}
+ @Contract(pure = true)
@Override
public String toString() {
return description;
@@ -79,7 +88,7 @@ public class Projection extends EzPlug implements Block, EzStoppable {
}
@Override
- public void declareInput(final VarList inputMap) {
+ public void declareInput(final @NotNull VarList inputMap) {
initCommonVars();
inputMap.add("input", input.getVariable());
inputMap.add("projection direction", projectionDir.getVariable());
@@ -96,7 +105,7 @@ public class Projection extends EzPlug implements Block, EzStoppable {
}
@Override
- public void declareOutput(final VarList outputMap) {
+ public void declareOutput(final @NotNull VarList outputMap) {
output = new VarSequence("projected sequence", null);
outputMap.add("projection output", output);
}
@@ -113,8 +122,8 @@ public class Projection extends EzPlug implements Block, EzStoppable {
computeCalculator();
}
catch (final Exception e) {
- IcyExceptionHandler.showErrorMessage(e, true);
- throw new IcyHandledException("Error while projecting: " + e.getMessage(), e);
+ IcyLogger.error(this.getClass(), e, "Error while projecting.");
+ return;
}
setOutput();
internalClean();
@@ -132,42 +141,27 @@ public class Projection extends EzPlug implements Block, EzStoppable {
rois = restrictToROI.getValue(true) ? inputSequence.getROIs() : Collections.emptyList();
}
- private static ProjectionAxis getAxis(final ProjectionDirection direction) {
- switch (direction) {
- case X:
- return ProjectionAxis.X;
- case Y:
- return ProjectionAxis.Y;
- case C:
- return ProjectionAxis.C;
- case Z:
- return ProjectionAxis.Z;
- case T:
- return ProjectionAxis.T;
-
- default:
- throw new IllegalArgumentException("" + direction);
- }
+ @Contract(pure = true)
+ private static @NotNull ProjectionAxis getAxis(final @NotNull ProjectionDirection direction) {
+ return switch (direction) {
+ case X -> ProjectionAxis.X;
+ case Y -> ProjectionAxis.Y;
+ case C -> ProjectionAxis.C;
+ case Z -> ProjectionAxis.Z;
+ case T -> ProjectionAxis.T;
+ };
}
- private static ProjectionOperationType getOperation(final ProjectionType type) {
- switch (type) {
- case MAX:
- return ProjectionOperationType.MAX;
- case MEAN:
- return ProjectionOperationType.MEAN;
- case MED:
- return ProjectionOperationType.MED;
- case MIN:
- return ProjectionOperationType.MIN;
- case SATSUM:
- return ProjectionOperationType.SATSUM;
- case STD:
- return ProjectionOperationType.STD;
-
- default:
- throw new IllegalArgumentException("" + type);
- }
+ @Contract(pure = true)
+ private static @NotNull ProjectionOperationType getOperation(final @NotNull ProjectionType type) {
+ return switch (type) {
+ case MAX -> ProjectionOperationType.MAX;
+ case MEAN -> ProjectionOperationType.MEAN;
+ case MED -> ProjectionOperationType.MED;
+ case MIN -> ProjectionOperationType.MIN;
+ case SATSUM -> ProjectionOperationType.SATSUM;
+ case STD -> ProjectionOperationType.STD;
+ };
}
private Sequence resultSequence;
@@ -188,7 +182,7 @@ public class Projection extends EzPlug implements Block, EzStoppable {
}
}
- private void onProgress(final double progress, final String message) {
+ private void onProgress(final double progress, final @Nullable String message) {
if (!isHeadLess()) {
getUI().setProgressBarValue(progress);
getUI().setProgressBarMessage(message);
@@ -242,7 +236,11 @@ public class Projection extends EzPlug implements Block, EzStoppable {
* @throws Exception If the projection cannot be correctly done.
* @see ProjectionCalculator
*/
- public static Sequence zProjection(final Sequence in, final ProjectionType projection, final boolean multiThread) throws Exception {
+ public static Sequence zProjection(
+ final Sequence in,
+ final ProjectionType projection,
+ final boolean multiThread
+ ) throws Exception {
return zProjection(in, projection, multiThread, false);
}
@@ -259,10 +257,19 @@ public class Projection extends EzPlug implements Block, EzStoppable {
* @throws Exception If the projection cannot be correctly done.
* @see ProjectionCalculator
*/
- public static Sequence zProjection(final Sequence in, final ProjectionType projection, final boolean multiThread, final boolean restrictToROI) throws Exception {
+ public static Sequence zProjection(
+ final Sequence in,
+ final ProjectionType projection,
+ final boolean multiThread,
+ final boolean restrictToROI
+ ) throws Exception {
final List<ROI> rois = restrictToROI ? in.getROIs() : Collections.emptyList();
- final ProjectionCalculator calculator = new ProjectionCalculator.Builder(in).axis(ProjectionAxis.Z)
- .operation(getOperation(projection)).addRois(rois).build();
+ final ProjectionCalculator calculator = new ProjectionCalculator
+ .Builder(in)
+ .axis(ProjectionAxis.Z)
+ .operation(getOperation(projection))
+ .addRois(rois)
+ .build();
return calculator.call();
}
@@ -277,7 +284,11 @@ public class Projection extends EzPlug implements Block, EzStoppable {
* @throws Exception If the projection cannot be correctly done.
* @see ProjectionCalculator
*/
- public static Sequence tProjection(final Sequence in, final ProjectionType projection, final boolean multiThread) throws Exception {
+ public static Sequence tProjection(
+ final Sequence in,
+ final ProjectionType projection,
+ final boolean multiThread
+ ) throws Exception {
return tProjection(in, projection, multiThread, false);
}
@@ -294,23 +305,19 @@ public class Projection extends EzPlug implements Block, EzStoppable {
* @throws Exception If the projection cannot be correctly done.
* @see ProjectionCalculator
*/
- public static Sequence tProjection(final Sequence in, final ProjectionType projection, final boolean multiThread, final boolean restrictToROI) throws Exception {
+ public static Sequence tProjection(
+ final Sequence in,
+ final ProjectionType projection,
+ final boolean multiThread,
+ final boolean restrictToROI
+ ) throws Exception {
final List<ROI> rois = restrictToROI ? in.getROIs() : Collections.emptyList();
- final ProjectionCalculator calculator = new ProjectionCalculator.Builder(in).axis(ProjectionAxis.T)
- .operation(getOperation(projection)).addRois(rois).build();
+ final ProjectionCalculator calculator = new ProjectionCalculator
+ .Builder(in)
+ .axis(ProjectionAxis.T)
+ .operation(getOperation(projection))
+ .addRois(rois)
+ .build();
return calculator.call();
}
-
- /**
- * Main method used for testing.
- *
- * @param args Input arguments.
- */
- public static void main(final String[] args) {
- // start icy
- Icy.main(args);
-
- // then start plugin
- PluginLauncher.start(PluginLoader.getPlugin(Projection.class.getName()));
- }
}
diff --git a/src/main/resources/plugins/adufour/projection/icon/icon_32.png b/src/main/resources/plugins/adufour/projection/icon/icon_32.png
new file mode 100644
index 0000000000000000000000000000000000000000..5dc83272bac2de94fcc0cd3feba5bdb227752022
Binary files /dev/null and b/src/main/resources/plugins/adufour/projection/icon/icon_32.png differ