From 03b5fcbccee86d183865dab72d7ea8be98f1018b Mon Sep 17 00:00:00 2001
From: Thomas <thomas.musset@pasteur.fr>
Date: Tue, 4 Jul 2023 16:55:20 +0200
Subject: [PATCH] updated pom, optimized code for java 11
---
pom.xml | 2 +-
.../plugins/adufour/roi/LabelExtractor.java | 124 ++++++++++--------
2 files changed, 70 insertions(+), 56 deletions(-)
diff --git a/pom.xml b/pom.xml
index f39c844..158ce2e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -11,7 +11,7 @@
</parent>
<artifactId>label-extractor</artifactId>
- <version>1.5.2</version>
+ <version>2.0.0</version>
<packaging>jar</packaging>
diff --git a/src/main/java/plugins/adufour/roi/LabelExtractor.java b/src/main/java/plugins/adufour/roi/LabelExtractor.java
index e9edd05..4b8ad5c 100644
--- a/src/main/java/plugins/adufour/roi/LabelExtractor.java
+++ b/src/main/java/plugins/adufour/roi/LabelExtractor.java
@@ -1,9 +1,22 @@
-package plugins.adufour.roi;
+/*
+ * 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.HashMap;
-import java.util.List;
-import java.util.Map;
+package plugins.adufour.roi;
import icy.image.IcyBufferedImage;
import icy.roi.ROI;
@@ -12,15 +25,16 @@ import icy.type.DataType;
import icy.type.collection.array.Array1DUtil;
import plugins.adufour.blocks.lang.Block;
import plugins.adufour.blocks.util.VarList;
-import plugins.adufour.ezplug.EzPlug;
-import plugins.adufour.ezplug.EzStoppable;
-import plugins.adufour.ezplug.EzVarDouble;
-import plugins.adufour.ezplug.EzVarEnum;
-import plugins.adufour.ezplug.EzVarSequence;
+import plugins.adufour.ezplug.*;
import plugins.adufour.vars.lang.VarROIArray;
import plugins.kernel.roi.roi2d.ROI2DArea;
import plugins.kernel.roi.roi3d.ROI3DArea;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
/**
* Toolbox to extract regions of interest (ROI) from a labeled image or sequence based on its
* connected components.<br>
@@ -62,20 +76,20 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
@Override
public String toString() {
- String name = super.toString();
+ final String name = super.toString();
return name.charAt(0) + name.substring(1).toLowerCase().replace('_', ' ');
}
}
@Override
- public void declareInput(VarList inputMap) {
+ public void declareInput(final VarList inputMap) {
inputMap.add("input sequence", inSeq.getVariable());
inputMap.add("extract mode", type.getVariable());
inputMap.add("value", value.getVariable());
}
@Override
- public void declareOutput(VarList outputMap) {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("ROI", outROI);
}
@@ -86,18 +100,18 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
@Override
protected void execute() {
- List<ROI> rois = extractLabels(inSeq.getValue(true), type.getValue(), value.getValue());
+ final List<ROI> rois = extractLabels(inSeq.getValue(true), type.getValue(), value.getValue());
if (getUI() != null) {
- Sequence outputSequence = outSeq.getValue(true);
+ final Sequence outputSequence = outSeq.getValue(true);
outputSequence.beginUpdate();
- for (ROI roi : rois)
+ for (final ROI roi : rois)
outputSequence.addROI(roi);
outputSequence.endUpdate();
}
else {
- outROI.setValue(rois.toArray(new ROI[rois.size()]));
+ outROI.setValue(rois.toArray(new ROI[0]));
}
}
@@ -135,7 +149,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
* @param value the pixel value
* @param label the label value
*/
- ConnectedComponent(double value, int label) {
+ ConnectedComponent(final double value, final int label) {
this.imageValue = value;
this.targetLabel = label;
}
@@ -169,16 +183,16 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
* </ul>
* @return List of ROI
*/
- public static List<ROI> extractLabels(Sequence sequence, ExtractionType whatToExtract, double value) {
- ArrayList<ROI> roi = new ArrayList<>();
+ public static List<ROI> extractLabels(final Sequence sequence, final ExtractionType whatToExtract, final double value) {
+ final ArrayList<ROI> roi = new ArrayList<>();
int objID = 1;
for (int t = 0; t < sequence.getSizeT(); t++)
for (int c = 0; c < sequence.getSizeC(); c++) {
- for (ROI label : extractLabels(sequence, t, c, whatToExtract, value)) {
+ for (final ROI label : extractLabels(sequence, t, c, whatToExtract, value)) {
// rename each ROI, but replace the ID
- String shortName = label.getName().substring(label.getName().indexOf(" ("));
+ final String shortName = label.getName().substring(label.getName().indexOf(" ("));
label.setName("Object #" + objID++ + shortName);
roi.add(label);
}
@@ -211,21 +225,21 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
* </ul>
* @return List of ROI
*/
- public static List<ROI> extractLabels(Sequence sequence, int t, int c, ExtractionType whatToExtract, double value) {
- int width = sequence.getSizeX();
- int height = sequence.getSizeY();
- int slice = width * height;
- int depth = sequence.getSizeZ();
- boolean is3D = depth > 1;
- DataType dataType = sequence.getDataType_();
+ public static List<ROI> extractLabels(final Sequence sequence, final int t, final int c, final ExtractionType whatToExtract, final double value) {
+ final int width = sequence.getSizeX();
+ final int height = sequence.getSizeY();
+ final int slice = width * height;
+ final int depth = sequence.getSizeZ();
+ final boolean is3D = depth > 1;
+ final DataType dataType = sequence.getDataType_();
final Map<Integer, ConnectedComponent> ccs = new HashMap<>();
final Map<Integer, ROI> roiMap = new HashMap<>();
- int[] neighborLabels = new int[13];
+ final int[] neighborLabels = new int[13];
int nbNeighbors = 0;
- boolean extractUserValue = (whatToExtract == ExtractionType.SPECIFIC_LABEL);
+ final boolean extractUserValue = (whatToExtract == ExtractionType.SPECIFIC_LABEL);
// temporary label buffer
final Sequence labelSequence = new Sequence();
@@ -242,7 +256,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
try {
_labelsHere = new int[slice];
}
- catch (OutOfMemoryError error) {
+ catch (final OutOfMemoryError error) {
// not enough memory --> pass in virtual mode
if (!virtual) {
labelSequence.setVolatile(true);
@@ -257,7 +271,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
// if (is3D) System.out.println("[Label Extractor] First pass (Z" + z + ")");
- Object inputData = sequence.getDataXY(t, z, c);
+ final Object inputData = sequence.getDataXY(t, z, c);
for (int y = 0, inOffset = 0; y < height; y++) {
if (Thread.currentThread().isInterrupted())
@@ -306,7 +320,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
}
}
else {
- int north = inOffset - width;
+ final int north = inOffset - width;
if (x == 0) {
// e n n
@@ -342,7 +356,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
}
else {
if (y == 0) {
- int south = inOffset + width;
+ final int south = inOffset + width;
if (x == 0) {
// e e e | e e e
@@ -383,7 +397,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
}
}
else if (y == height - 1) {
- int north = inOffset - width;
+ final int north = inOffset - width;
if (x == 0) {
// e n n | e n n
@@ -431,8 +445,8 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
}
}
else {
- int north = inOffset - width;
- int south = inOffset + width;
+ final int north = inOffset - width;
+ final int south = inOffset + width;
if (x == 0) {
// e n n | e n n
@@ -450,8 +464,8 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
nbNeighbors = 8;
}
else if (x == width - 1) {
- int northwest = north - 1;
- int west = inOffset - 1;
+ final int northwest = north - 1;
+ final int west = inOffset - 1;
// n n e | n n e
// n n e | n x e
@@ -469,11 +483,11 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
nbNeighbors = 9;
}
else {
- int northwest = north - 1;
- int west = inOffset - 1;
- int northeast = north + 1;
- int southwest = south - 1;
- int southeast = south + 1;
+ final int northwest = north - 1;
+ final int west = inOffset - 1;
+ final int northeast = north + 1;
+ final int southwest = south - 1;
+ final int southeast = south + 1;
// n n n | n n n
// n n n | n x .
@@ -506,7 +520,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
int currentLabel = Integer.MAX_VALUE;
for (int i = 0; i < nbNeighbors; i++) {
- int neighborLabel = neighborLabels[i];
+ final int neighborLabel = neighborLabels[i];
// "zero" neighbors belong to the background...
if (neighborLabel == 0)
@@ -536,17 +550,17 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
// -> browse the neighborhood again
// --> fuse high labels with low labels
- ConnectedComponent currentCC = ccs.get(currentLabel);
- int currentTargetLabel = currentCC.getTargetLabel();
+ final ConnectedComponent currentCC = ccs.get(currentLabel);
+ final int currentTargetLabel = currentCC.getTargetLabel();
for (int i = 0; i < nbNeighbors; i++) {
- int neighborLabel = neighborLabels[i];
+ final int neighborLabel = neighborLabels[i];
if (neighborLabel == 0)
continue; // no object in this pixel
- ConnectedComponent neighborCC = ccs.get(neighborLabel);
- int neighborTargetLabel = neighborCC.getTargetLabel();
+ final ConnectedComponent neighborCC = ccs.get(neighborLabel);
+ final int neighborTargetLabel = neighborCC.getTargetLabel();
if (neighborTargetLabel == currentTargetLabel)
continue;
@@ -601,7 +615,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
int finalLabel = 0;
for (int currentLabel = highestKnownLabel; currentLabel > 0; currentLabel--) {
- ConnectedComponent currentCC = ccs.get(currentLabel);
+ final ConnectedComponent currentCC = ccs.get(currentLabel);
// if the target label is higher than or equal to the current label
if (currentCC.targetLabel >= currentLabel) {
@@ -637,7 +651,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
continue;
// retrieve the image value (for naming purposes)
- double imageValue = ccs.get(targetLabel).imageValue;
+ final double imageValue = ccs.get(targetLabel).imageValue;
// if a fusion was indicated, retrieve the final label value
targetLabel = ccs.get(targetLabel).getTargetLabel();
@@ -645,7 +659,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
// store the current pixel in the component
if (is3D) {
if (!roiMap.containsKey(targetLabel)) {
- ROI3DArea roi3D = new ROI3DArea();
+ final ROI3DArea roi3D = new ROI3DArea();
roi3D.setName("Object #" + targetLabel + " (value: " + imageValue + ")");
roi3D.setT(t);
roi3D.setC(c);
@@ -656,7 +670,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
}
else {
if (!roiMap.containsKey(targetLabel)) {
- ROI2DArea roi2D = new ROI2DArea();
+ final ROI2DArea roi2D = new ROI2DArea();
roi2D.setName("Object #" + targetLabel + " (value: " + imageValue + ")");
roi2D.setZ(0);
roi2D.setT(t);
--
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