From 2df9740b75a686724dcf5c3683743fc86646efb8 Mon Sep 17 00:00:00 2001
From: Thomas <thomas.musset@pasteur.fr>
Date: Sun, 7 Jul 2024 00:38:32 +0200
Subject: [PATCH] updated pom to v2.0.0-a.1, fix classes accordingly to new
architecture, added icon, updated .gitignore
---
.gitignore | 41 ++
SLIC/.gitignore | 10 -
SLIC/pom.xml | 31 -
.../algorithms/danyfel80/islic/CIELab.java | 192 ------
.../algorithms/danyfel80/islic/SLICTask.java | 629 ------------------
.../plugins/danyfel80/islic/LABToRGB.java | 50 --
.../plugins/danyfel80/islic/RGBToLAB.java | 51 --
.../java/plugins/danyfel80/islic/SLIC.java | 135 ----
pom.xml | 35 +
.../algorithms/danyfel80/islic/CIELab.java | 225 +++++++
.../algorithms/danyfel80/islic/SLICTask.java | 601 +++++++++++++++++
.../plugins/danyfel80/islic/LABToRGB.java | 74 +++
.../plugins/danyfel80/islic/RGBToLAB.java | 75 +++
.../java/plugins/danyfel80/islic/SLIC.java | 134 ++++
src/main/resources/slic.png | Bin 0 -> 9879 bytes
15 files changed, 1185 insertions(+), 1098 deletions(-)
create mode 100644 .gitignore
delete mode 100644 SLIC/.gitignore
delete mode 100644 SLIC/pom.xml
delete mode 100644 SLIC/src/main/java/algorithms/danyfel80/islic/CIELab.java
delete mode 100644 SLIC/src/main/java/algorithms/danyfel80/islic/SLICTask.java
delete mode 100644 SLIC/src/main/java/plugins/danyfel80/islic/LABToRGB.java
delete mode 100644 SLIC/src/main/java/plugins/danyfel80/islic/RGBToLAB.java
delete mode 100644 SLIC/src/main/java/plugins/danyfel80/islic/SLIC.java
create mode 100644 pom.xml
create mode 100644 src/main/java/algorithms/danyfel80/islic/CIELab.java
create mode 100644 src/main/java/algorithms/danyfel80/islic/SLICTask.java
create mode 100644 src/main/java/plugins/danyfel80/islic/LABToRGB.java
create mode 100644 src/main/java/plugins/danyfel80/islic/RGBToLAB.java
create mode 100644 src/main/java/plugins/danyfel80/islic/SLIC.java
create mode 100644 src/main/resources/slic.png
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..57f16fb
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,41 @@
+/build*
+/workspace
+setting.xml
+release/
+target/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
+.idea/
+*.iws
+*.iml
+*.ipr
+
+### Eclipse ###
+.apt_generated
+.classpath
+.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/SLIC/.gitignore b/SLIC/.gitignore
deleted file mode 100644
index 95724b8..0000000
--- a/SLIC/.gitignore
+++ /dev/null
@@ -1,10 +0,0 @@
-/.gradle/
-/.settings/
-/bin/
-/build/
-/ecbuild/
-/target/
-/workspace/
-/.classpath
-/.project
-/setting.xml
diff --git a/SLIC/pom.xml b/SLIC/pom.xml
deleted file mode 100644
index 52f1eb1..0000000
--- a/SLIC/pom.xml
+++ /dev/null
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>parent-pom-plugin</artifactId>
- <version>1.0.4</version>
- </parent>
- <artifactId>slic</artifactId>
- <version>1.0.1</version>
- <name>SLIC - Superpixels</name>
- <description/>
- <build>
- </build>
- <dependencies>
- <dependency>
- <groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>ezplug</artifactId>
- </dependency>
- <dependency>
- <groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>protocols</artifactId>
- </dependency>
- </dependencies>
- <repositories>
- <repository>
- <id>icy</id>
- <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
- </repository>
- </repositories>
-</project>
\ No newline at end of file
diff --git a/SLIC/src/main/java/algorithms/danyfel80/islic/CIELab.java b/SLIC/src/main/java/algorithms/danyfel80/islic/CIELab.java
deleted file mode 100644
index 4c6a7e1..0000000
--- a/SLIC/src/main/java/algorithms/danyfel80/islic/CIELab.java
+++ /dev/null
@@ -1,192 +0,0 @@
-package algorithms.danyfel80.islic;
-
-public class CIELab {
-
- public static class XYZ {
-
- private static final double[][] M = { { 0.4124, 0.3576, 0.1805 }, { 0.2126, 0.7152, 0.0722 },
- { 0.0193, 0.1192, 0.9505 } };
- private static final double[][] Mi = { { 3.2406, -1.5372, -0.4986 }, { -0.9689, 1.8758, 0.0415 },
- { 0.0557, -0.2040, 1.0570 } };
-
- public static double[] fromRGB(int[] rgb) {
- return fromRGB(rgb[0], rgb[1], rgb[2]);
- }
-
- public static double[] fromRGB(int R, int G, int B) {
- double[] result = new double[3];
-
- // convert 0..255 into 0..1
- double r = R / 255.0;
- double g = G / 255.0;
- double b = B / 255.0;
-
- // assume sRGB
- if (r <= 0.04045) {
- r = r / 12.92;
- } else {
- r = Math.pow(((r + 0.055) / 1.055), 2.4);
- }
- if (g <= 0.04045) {
- g = g / 12.92;
- } else {
- g = Math.pow(((g + 0.055) / 1.055), 2.4);
- }
- if (b <= 0.04045) {
- b = b / 12.92;
- } else {
- b = Math.pow(((b + 0.055) / 1.055), 2.4);
- }
-
- r *= 100.0;
- g *= 100.0;
- b *= 100.0;
-
- // [X Y Z] = [r g b][M]
- result[0] = (r * M[0][0]) + (g * M[0][1]) + (b * M[0][2]);
- result[1] = (r * M[1][0]) + (g * M[1][1]) + (b * M[1][2]);
- result[2] = (r * M[2][0]) + (g * M[2][1]) + (b * M[2][2]);
-
- return result;
- }
-
- public static int[] toRGB(double[] xyz) {
- return toRGB(xyz[0], xyz[1], xyz[2]);
- }
-
- public static int[] toRGB(double X, double Y, double Z) {
- int[] result = new int[3];
-
- double x = X / 100.0;
- double y = Y / 100.0;
- double z = Z / 100.0;
-
- // [r g b] = [X Y Z][Mi]
- double r = (x * Mi[0][0]) + (y * Mi[0][1]) + (z * Mi[0][2]);
- double g = (x * Mi[1][0]) + (y * Mi[1][1]) + (z * Mi[1][2]);
- double b = (x * Mi[2][0]) + (y * Mi[2][1]) + (z * Mi[2][2]);
-
- // assume sRGB
- if (r > 0.0031308) {
- r = ((1.055 * Math.pow(r, 1.0 / 2.4)) - 0.055);
- } else {
- r = (r * 12.92);
- }
- if (g > 0.0031308) {
- g = ((1.055 * Math.pow(g, 1.0 / 2.4)) - 0.055);
- } else {
- g = (g * 12.92);
- }
- if (b > 0.0031308) {
- b = ((1.055 * Math.pow(b, 1.0 / 2.4)) - 0.055);
- } else {
- b = (b * 12.92);
- }
-
- r = (r < 0) ? 0 : r;
- g = (g < 0) ? 0 : g;
- b = (b < 0) ? 0 : b;
-
- // convert 0..1 into 0..255
- result[0] = (int) Math.round(r * 255);
- result[1] = (int) Math.round(g * 255);
- result[2] = (int) Math.round(b * 255);
-
- return result;
- }
-
- }
-
- private static final double[] whitePoint = { 95.0429, 100.0, 108.8900 }; // D65
-
- public static double[] fromRGB(int[] rgb) {
- return fromXYZ(XYZ.fromRGB(rgb));
- }
-
- public static double[] fromRGB(int r, int g, int b) {
- return fromXYZ(XYZ.fromRGB(r, g, b));
- }
-
- private static double[] fromXYZ(double[] xyz) {
- return fromXYZ(xyz[0], xyz[1], xyz[2]);
- }
-
- public static double[] fromXYZ(double X, double Y, double Z) {
- double x = X / whitePoint[0];
- double y = Y / whitePoint[1];
- double z = Z / whitePoint[2];
-
- if (x > 0.008856) {
- x = Math.pow(x, 1.0 / 3.0);
- }
- else {
- x = (7.787 * x) + (16.0 / 116.0);
- }
- if (y > 0.008856) {
- y = Math.pow(y, 1.0 / 3.0);
- }
- else {
- y = (7.787 * y) + (16.0 / 116.0);
- }
- if (z > 0.008856) {
- z = Math.pow(z, 1.0 / 3.0);
- }
- else {
- z = (7.787 * z) + (16.0 / 116.0);
- }
-
- double[] result = new double[3];
-
- result[0] = (116.0 * y) - 16.0;
- result[1] = 500.0 * (x - y);
- result[2] = 200.0 * (y - z);
-
- return result;
- }
-
- public static int[] toRGB(double[] lab) {
- return XYZ.toRGB(toXYZ(lab));
- }
-
- public static int[] toRGB(double L, double a, double b) {
- return XYZ.toRGB(toXYZ(L, a, b));
- }
-
- public static double[] toXYZ(double[] lab) {
- return toXYZ(lab[0], lab[1], lab[2]);
- }
-
- public static double[] toXYZ(double L, double a, double b) {
- double[] result = new double[3];
-
- double y = (L + 16.0) / 116.0;
- double y3 = Math.pow(y, 3.0);
- double x = (a / 500.0) + y;
- double x3 = Math.pow(x, 3.0);
- double z = y - (b / 200.0);
- double z3 = Math.pow(z, 3.0);
-
- if (y3 > 0.008856) {
- y = y3;
- } else {
- y = (y - (16.0 / 116.0)) / 7.787;
- }
- if (x3 > 0.008856) {
- x = x3;
- } else {
- x = (x - (16.0 / 116.0)) / 7.787;
- }
- if (z3 > 0.008856) {
- z = z3;
- } else {
- z = (z - (16.0 / 116.0)) / 7.787;
- }
-
- // results in 0...100
- result[0] = x * whitePoint[0];
- result[1] = y * whitePoint[1];
- result[2] = z * whitePoint[2];
-
- return result;
- }
-}
diff --git a/SLIC/src/main/java/algorithms/danyfel80/islic/SLICTask.java b/SLIC/src/main/java/algorithms/danyfel80/islic/SLICTask.java
deleted file mode 100644
index cf4420d..0000000
--- a/SLIC/src/main/java/algorithms/danyfel80/islic/SLICTask.java
+++ /dev/null
@@ -1,629 +0,0 @@
-/*
- * Copyright 2010-2016 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 <http://www.gnu.org/licenses/>.
- */
-package algorithms.danyfel80.islic;
-
-import java.awt.Color;
-import java.awt.Point;
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.concurrent.atomic.AtomicInteger;
-import java.util.stream.Collectors;
-import java.util.stream.IntStream;
-
-import icy.image.IcyBufferedImage;
-import icy.roi.BooleanMask2D;
-import icy.roi.ROI;
-import icy.sequence.Sequence;
-import icy.type.DataType;
-import icy.type.collection.array.Array2DUtil;
-import icy.type.point.Point3D;
-import plugins.kernel.roi.roi2d.ROI2DArea;
-
-/**
- * @author Daniel Felipe Gonzalez Obando
- */
-public class SLICTask
-{
-
- private static final double EPSILON = 0.25;
- static int MAX_ITERATIONS = 10;
- static double ERROR_THRESHOLD = 1e-2;
-
- private Sequence sequence;
- private int S;
- private int Sx;
- private int Sy;
- private int SPnum;
- private double rigidity;
-
- private boolean computeROIs;
- private List<ROI> rois;
- private Sequence superPixelsResult;
-
- private Map<Point3D.Integer, double[]> colorLUT;
- private Map<Point, Double> distanceLUT;
-
- public SLICTask(Sequence sequence, int SPSize, double rigidity, boolean computeROIs)
- {
- this.sequence = sequence;
- this.S = SPSize;
- this.Sx = (sequence.getWidth() + S / 2 - 1) / S;
- this.Sy = (sequence.getHeight() + S / 2 - 1) / S;
- this.SPnum = Sx * Sy;
- this.rigidity = rigidity;
-
- this.computeROIs = computeROIs;
-
- colorLUT = new HashMap<>();
- distanceLUT = new HashMap<>();
- }
-
- public void execute()
- {
-
- double[] ls = new double[SPnum];
- double[] as = new double[SPnum];
- double[] bs = new double[SPnum];
-
- double[] cxs = new double[SPnum];
- double[] cys = new double[SPnum];
-
- double[][] sequenceData = Array2DUtil.arrayToDoubleArray(sequence.getDataXYC(0, 0),
- sequence.isSignedDataType());
-
- initialize(ls, as, bs, cxs, cys, sequenceData);
-
- int[] clusters = new int[sequence.getWidth() * sequence.getHeight()];
- double[] distances = Arrays.stream(clusters).mapToDouble(i -> Double.MAX_VALUE).toArray();
-
- int iterations = 0;
- double error = 0;
- do
- {
- assignClusters(sequenceData, clusters, distances, ls, as, bs, cxs, cys);
- error = updateClusters(sequenceData, clusters, ls, as, bs, cxs, cys);
- iterations++;
- System.out.format("Iteration=%d, Error=%f%n", iterations, error);
- }
- while (error > ERROR_THRESHOLD && iterations < MAX_ITERATIONS);
- System.out.format("End of iterations%n");
-
- computeSuperpixels(sequenceData, clusters, ls, as, bs, cxs, cys);
- }
-
- private void initialize(double[] ls, double[] as, double[] bs, double[] cxs, double[] cys, double[][] sequenceData)
- {
-
- IntStream.range(0, SPnum).forEach(sp -> {
- int x, y, yOff, bestx, besty, bestyOff, i, j, yjOff;
- double bestGradient, candidateGradient;
-
- int spx = sp % Sx;
- int spy = sp / Sx;
-
- x = S / 2 + (spx) * S;
- y = S / 2 + (spy) * S;
- yOff = y * sequence.getWidth();
-
- cxs[sp] = bestx = x;
- cys[sp] = besty = y;
- bestyOff = yOff;
- bestGradient = Double.MAX_VALUE;
-
- for (j = -1; j <= 1; j++)
- {
- if (y + j >= 0 && y + j < sequence.getHeight())
- {
- yjOff = (y + j) * sequence.getWidth();
- for (i = -1; i <= 1; i++)
- {
- if (x >= 0 && x < sequence.getWidth() && x + i >= 0 && x + i < sequence.getWidth())
- {
- candidateGradient = getGradient(sequenceData, x + yOff, (x + i) + yjOff);
- if (candidateGradient < bestGradient)
- {
- bestx = x + i;
- besty = y + j;
- bestyOff = yjOff;
- bestGradient = candidateGradient;
- }
- }
- }
- }
- }
-
- cxs[sp] = bestx;
- cys[sp] = besty;
- int bestPos = bestx + bestyOff;
-
- double[] bestLAB = getCIELab(sequenceData, bestPos);
- ls[sp] = bestLAB[0];
- as[sp] = bestLAB[1];
- bs[sp] = bestLAB[2];
-
- });
-
- }
-
- private double getGradient(double[][] data, int pos1, int pos2)
- {
- int[] valRGB1 = new int[3];
- int[] valRGB2 = new int[3];
- IntStream.range(0, 3).forEach(c -> {
- try
- {
- valRGB1[c] = (int) Math.round(255 * (data[c % sequence.getSizeC()][pos1] / sequence.getDataTypeMax()));
- valRGB2[c] = (int) Math.round(255 * (data[c % sequence.getSizeC()][pos2] / sequence.getDataTypeMax()));
- }
- catch (Exception e)
- {
- throw e;
- }
- });
-
- double[] val1 = CIELab.fromRGB(valRGB1);
- double[] val2 = CIELab.fromRGB(valRGB2);
-
- double avgGrad = IntStream.range(0, 3).mapToDouble(c -> val2[c] - val1[c]).average().getAsDouble();
-
- return avgGrad;
- }
-
- private double[] getCIELab(double[][] sequenceData, int pos)
- {
-
- int[] rgbVal = new int[3];
- IntStream.range(0, 3).forEach(c -> {
- rgbVal[c] = (int) Math
- .round(255 * (sequenceData[c % sequence.getSizeC()][pos] / sequence.getDataTypeMax()));
- });
- Point3D.Integer rgbPoint = new Point3D.Integer(rgbVal);
-
- double[] LAB = colorLUT.get(rgbPoint);
- if (LAB == null)
- {
- int[] RGB = new int[3];
- IntStream.range(0, 3).forEach(c -> {
- RGB[c] = (int) Math
- .round(255 * (sequenceData[c % sequence.getSizeC()][pos] / sequence.getDataTypeMax()));
- });
-
- LAB = CIELab.fromRGB(RGB);
- colorLUT.put(rgbPoint, LAB);
- }
- return LAB;
- }
-
- private void assignClusters(double[][] sequenceData, int[] clusters, double[] distances, double[] ls, double[] as,
- double[] bs, double[] cxs, double[] cys)
- {
- // Each cluster
- IntStream.range(0, SPnum).forEach(k -> {
- double ckx = cxs[k], cky = cys[k], lk = ls[k], ak = as[k], bk = bs[k];
- int posk = ((int) ckx) + ((int) cky) * sequence.getWidth();
- distances[posk] = 0;
- clusters[posk] = k;
-
- // 2Sx2S window assignment
- int j, i, yOff;
- for (j = -S; j < S; j++)
- {
- int ciy = (int) (cky + j);
- if (ciy >= 0 && ciy < sequence.getHeight())
- {
- yOff = ciy * sequence.getWidth();
- for (i = -S; i < S; i++)
- {
- int cix = (int) (ckx + i);
- if (cix >= 0 && cix < sequence.getWidth())
- {
- int posi = cix + yOff;
- double[] LABi = getCIELab(sequenceData, posi);
- double li = LABi[0];
- double ai = LABi[1];
- double bi = LABi[2];
-
- double di = getDistance(ckx, cky, lk, ak, bk, i, j, li, ai, bi);
- if (di < distances[posi])
- {
- distances[posi] = di;
- clusters[posi] = clusters[posk];
- }
- }
- }
- }
- }
- });
- }
-
- private double getDistance(double ckx, double cky, double lk, double ak, double bk, int dx, int dy, double li,
- double ai, double bi)
- {
-
- double diffl, diffa, diffb;
- diffl = li - lk;
- diffa = ai - ak;
- diffb = bi - bk;
-
- double dc = Math.sqrt(diffl * diffl + diffa * diffa + diffb * diffb);
- Point dPt = new Point((int) Math.min(dx, dy), (int) Math.max(dx, dy));
- Double ds = distanceLUT.get(dPt);
- if (ds == null)
- {
- ds = Math.sqrt(dx * dx + dy * dy);
- distanceLUT.put(dPt, ds);
- }
- return Math.sqrt(dc * dc + (ds * ds) * (rigidity * rigidity * S));
- }
-
- private double updateClusters(double[][] sequenceData, int[] clusters, double[] ls, double[] as, double[] bs,
- double[] cxs, double[] cys)
- {
-
- double[] newls = new double[SPnum];
- double[] newas = new double[SPnum];
- double[] newbs = new double[SPnum];
- double[] newcxs = new double[SPnum];
- double[] newcys = new double[SPnum];
- int[] cants = new int[SPnum];
-
- // int blockSize = 500;
- // IntStream.iterate(0, sy -> sy+blockSize).limit((int)Math.ceil(sequence.getHeight()/blockSize)).forEach(y0->{
- // int y1 = Math.min(y0+blockSize, sequence.getHeight() - y0);
- // IntStream.iterate(0, sx -> sx+blockSize).limit((int)Math.ceil(sequence.getWidth()/blockSize)).forEach(x0->{
- // int x1 = Math.min(x0+blockSize, sequence.getWidth() - x0);
- // });
- // });
- for (int y = 0, yOff; y < sequence.getHeight(); y++)
- {
- yOff = y * sequence.getWidth();
- for (int x = 0, pos; x < sequence.getWidth(); x++)
- {
- pos = x + yOff;
- int sp = clusters[pos];
- double[] lab = getCIELab(sequenceData, pos);
-
- cants[sp]++;
-
- newls[sp] += (lab[0] - newls[sp]) / cants[sp];
- newas[sp] += (lab[1] - newas[sp]) / cants[sp];
- newbs[sp] += (lab[2] - newbs[sp]) / cants[sp];
- newcxs[sp] += (x - newcxs[sp]) / cants[sp];
- newcys[sp] += (y - newcys[sp]) / cants[sp];
- }
- }
-
- double error = IntStream.range(0, SPnum).mapToDouble(sp -> {
- // double diffl = ls[sp] - newls[sp];
- // double diffa = as[sp] - newas[sp];
- // double diffb = bs[sp] - newbs[sp];
- double diffx = cxs[sp] - newcxs[sp];
- double diffy = cys[sp] - newcys[sp];
-
- ls[sp] = newls[sp];
- as[sp] = newas[sp];
- bs[sp] = newbs[sp];
- cxs[sp] = newcxs[sp];
- cys[sp] = newcys[sp];
-
- return Math.sqrt(diffx * diffx + diffy * diffy/* + diffl * diffl + diffa * diffa + diffb * diffb */);
- }).sum() / SPnum;
-
- return error;
- }
-
- private void computeSuperpixels(double[][] sequenceData, int[] clusters, double[] ls, double[] as, double[] bs,
- double[] cxs, double[] cys)
- {
-
- boolean[] visited = new boolean[clusters.length];
- int[] finalClusters = new int[clusters.length];
-
- List<Point3D.Double> labs = new ArrayList<>(SPnum);
- List<Double> areas = new ArrayList<>(SPnum);
- List<Point> firstPoints = new ArrayList<>(SPnum);
-
- // fill known clusters
- AtomicInteger usedLabels = new AtomicInteger(0);
- IntStream.range(0, SPnum).forEach(i -> {
- Point3D.Double labCenter = new Point3D.Double();
- AtomicInteger area = new AtomicInteger(0);
- Point p = new Point((int) Math.round(cxs[i]), (int) Math.round(cys[i]));
- int pPos = p.x + p.y * sequence.getWidth();
-
- if (clusters[pPos] == i && !visited[pPos])
- {
- findAreaAndColor(sequenceData, clusters, finalClusters, visited, p, labCenter, area,
- usedLabels.getAndIncrement());
- labs.add(labCenter);
- areas.add(area.get() / (double) (S * S));
- firstPoints.add(p);
- }
-
- });
-
- int firstUnknownCluster = usedLabels.get();
-
- // fill independent clusters
- for (int y = 0; y < sequence.getHeight(); y++)
- {
- int yOff = y * sequence.getWidth();
- for (int x = 0; x < sequence.getWidth(); x++)
- {
- int pos = x + yOff;
- if (!visited[pos])
- {
- Point3D.Double labCenter = new Point3D.Double();
- AtomicInteger area = new AtomicInteger(0);
- Point p = new Point(x, y);
-
- findAreaAndColor(sequenceData, clusters, finalClusters, visited, p, labCenter, area,
- usedLabels.getAndIncrement());
-
- labs.add(labCenter);
- areas.add(area.get() / (double) (S * S));
- firstPoints.add(p);
- }
- }
- }
-
- // System.out.println("unvisited = " + IntStream.range(0, visited.length).filter(i -> visited[i] == false).sum());
-
- // find neighbors and merge independent clusters
- boolean[] mergedClusters = new boolean[usedLabels.get()];
- int[] mergedRefs = IntStream.range(0, usedLabels.get()).toArray();
- IntStream.range(firstUnknownCluster, usedLabels.get()).forEach(i -> {
- List<Integer> neighbors = findNeighbors(finalClusters, visited, firstPoints.get(i));
- if (neighbors.size() > 0)
- {
- int bestNeighbour = neighbors.get(0);
- double bestL = Double.MAX_VALUE;
-
- // boolean found = false;
- for (Integer j : neighbors)
- {
- if (j < i)
- {
- // found = true;
- double l = computeL(labs, areas, i, j);
- if (l < bestL)
- {
- bestNeighbour = j;
- bestL = l;
- }
- }
- }
- /*
- * if (!found) { for (Integer j: neighbors) { double l = computeL(labs,
- * areas, i, j); if (l < bestL) { bestNeighbour = j; bestL = l; } } }
- *
- * if (found) {
- */
- double rArea = areas.get(i);
- double relSPSize = rArea / 4;
- relSPSize *= relSPSize;
-
- double coeff = relSPSize * (1.0 + bestL);
- if (coeff < EPSILON)
- {
- mergedClusters[i] = true;
- mergedRefs[i] = bestNeighbour;
- }
- // } else {
- // mergedClusters[i] = true;
- // mergedRefs[i] = bestNeighbour;
- // }
- }
- else
- {
- System.err.format("Cluster at (%d, %d) has no neighbors", firstPoints.get(i).x, firstPoints.get(i).y);
- }
- });
- IntStream.range(firstUnknownCluster, usedLabels.get()).forEach(i -> {
- if (mergedClusters[i])
- {
- int appliedLabel = i;
- while (appliedLabel != mergedRefs[appliedLabel])
- {
- appliedLabel = mergedRefs[appliedLabel];
- }
- findAreaAndColor(sequenceData, clusters, finalClusters, visited, firstPoints.get(i),
- new Point3D.Double(), new AtomicInteger(0), appliedLabel);
- }
-
- });
-
- if (this.computeROIs)
- {
- // Create and add ROIs to sequence
- this.rois = new ArrayList<>();
- IntStream.range(0, usedLabels.get()).forEach(i -> {
- if (!mergedClusters[i])
- {
- ROI2DArea roi = defineROI(finalClusters, firstPoints.get(i), labs.get(i));
- rois.add(roi);
- }
- });
- sequence.addROIs(rois, false);
- }
- else
- {
- List<int[]> rgbs = labs.stream().map(lab -> CIELab.toRGB(lab.x, lab.y, lab.z)).collect(Collectors.toList());
- superPixelsResult = new Sequence(
- new IcyBufferedImage(sequence.getWidth(), sequence.getHeight(), 3, DataType.UBYTE));
-
- superPixelsResult.setPixelSizeX(sequence.getPixelSizeX());
- superPixelsResult.setPixelSizeY(sequence.getPixelSizeY());
- superPixelsResult.setPixelSizeZ(sequence.getPixelSizeZ());
- superPixelsResult.setPositionX(sequence.getPositionX());
- superPixelsResult.setPositionY(sequence.getPositionY());
- superPixelsResult.setPositionZ(sequence.getPositionZ());
-
- superPixelsResult.beginUpdate();
- double[][] spData = Array2DUtil.arrayToDoubleArray(superPixelsResult.getDataXYC(0, 0),
- superPixelsResult.isSignedDataType());
- for (int y = 0, yOff; y < sequence.getHeight(); y++)
- {
- yOff = y * sequence.getWidth();
- for (int x = 0; x < sequence.getWidth(); x++)
- {
- final int pos = x + yOff;
- int[] rgbVal = rgbs.get(finalClusters[pos]);
-
- IntStream.range(0, 3).forEach(c -> {
- spData[c][pos] = rgbVal[c];
- });
-
- }
- }
- Array2DUtil.doubleArrayToArray(spData, superPixelsResult.getDataXYC(0, 0));
- superPixelsResult.dataChanged();
- superPixelsResult.endUpdate();
- }
- }
-
- private void findAreaAndColor(double[][] sequenceData, int[] clusters, int[] newClusters, boolean[] visited,
- Point p, Point3D.Double labCenter, AtomicInteger area, int label)
- {
- int posp = p.x + p.y * sequence.getWidth();
- area.set(0);
- labCenter.x = 0d;
- labCenter.y = 0d;
- labCenter.z = 0d;
-
- Deque<Point> q = new LinkedList<>();
- int val = clusters[posp];
-
- visited[posp] = true;
- q.add(p);
-
- while (!q.isEmpty())
- {
- Point pti = q.pop();
- int posi = pti.x + pti.y * sequence.getWidth();
-
- newClusters[posi] = label;
- area.getAndIncrement();
- double[] labi = getCIELab(sequenceData, posi);
- labCenter.x += (labi[0] - labCenter.x) / area.get();
- labCenter.y += (labi[1] - labCenter.y) / area.get();
- labCenter.z += (labi[2] - labCenter.z) / area.get();
-
- int[] ds = new int[] {0, -1, 0, 1, 0};
- for (int is = 1; is < ds.length; is++)
- {
- Point ptn = new Point(pti.x + ds[is - 1], pti.y + ds[is]);
- int posn = ptn.x + ptn.y * sequence.getWidth();
- if (sequence.getBounds2D().contains(ptn.x, ptn.y) && !visited[posn] && clusters[posn] == val)
- {
- visited[posn] = true;
- q.add(ptn);
- }
- }
-
- }
- }
-
- private List<Integer> findNeighbors(int[] newClusters, boolean[] visited, Point p)
- {
- int posp = p.x + p.y * sequence.getWidth();
-
- HashSet<Integer> neighs = new HashSet<>();
-
- Deque<Point> q = new LinkedList<>();
- int val = newClusters[posp];
-
- visited[posp] = false;
- q.add(p);
-
- while (!q.isEmpty())
- {
- Point pti = q.pop();
-
- int[] ds = new int[] {0, -1, 0, 1, 0};
- for (int is = 1; is < ds.length; is++)
- {
- Point ptn = new Point(pti.x + ds[is - 1], pti.y + ds[is]);
- int posn = ptn.x + ptn.y * sequence.getWidth();
- if (sequence.getBounds2D().contains(ptn.x, ptn.y))
- {
- if (newClusters[posn] == val)
- {
- if (visited[posn])
- {
- visited[posn] = false;
- q.add(ptn);
- }
- }
- else
- {
- neighs.add(newClusters[posn]);
- }
- }
- }
-
- }
- return new ArrayList<Integer>(neighs);
- }
-
- private double computeL(List<Point3D.Double> labs, List<Double> areas, int i, Integer j)
- {
- Point3D.Double diffLab = new Point3D.Double();
- diffLab.x = labs.get(j).x - labs.get(i).x;
- diffLab.y = labs.get(j).y - labs.get(i).y;
- diffLab.z = labs.get(j).z - labs.get(i).z;
-
- try
- {
- return diffLab.length() / areas.get(j);
- }
- catch (Exception e)
- {
- throw e;
- }
- }
-
- private ROI2DArea defineROI(int[] newClusters, Point p, Point3D.Double labP)
- {
- int posp = p.x + p.y * sequence.getWidth();
- double[] lab = new double[] {labP.x, labP.y, labP.z};
- int[] rgb = CIELab.toRGB(lab);
-
- int val = newClusters[posp];
- Rectangle seqBounds = sequence.getBounds2D();
- ROI2DArea roi1 = new ROI2DArea(new BooleanMask2D());
- IntStream.range(0, newClusters.length).filter(pi -> newClusters[pi] == val)
- .forEach(pi -> roi1.addPoint(pi % seqBounds.width, pi / seqBounds.width));// .forEach(pi -> bMask[pi] = true);
-
- roi1.setColor(new Color(rgb[0], rgb[1], rgb[2]));
- return roi1;
- }
-
- public Sequence getResultSequence()
- {
- return this.superPixelsResult;
- }
-}
diff --git a/SLIC/src/main/java/plugins/danyfel80/islic/LABToRGB.java b/SLIC/src/main/java/plugins/danyfel80/islic/LABToRGB.java
deleted file mode 100644
index 769ac46..0000000
--- a/SLIC/src/main/java/plugins/danyfel80/islic/LABToRGB.java
+++ /dev/null
@@ -1,50 +0,0 @@
-package plugins.danyfel80.islic;
-
-import java.util.stream.IntStream;
-
-import algorithms.danyfel80.islic.CIELab;
-import icy.image.IcyBufferedImage;
-import icy.sequence.Sequence;
-import icy.type.DataType;
-import icy.type.collection.array.Array2DUtil;
-import plugins.adufour.ezplug.EzPlug;
-import plugins.adufour.ezplug.EzVarSequence;
-
-public class LABToRGB extends EzPlug {
-
- EzVarSequence inLabSequence;
-
- @Override
- protected void initialize() {
- inLabSequence = new EzVarSequence("LAB sequence");
- addEzComponent(inLabSequence);
- }
-
- @Override
- protected void execute() {
- Sequence labSequence = inLabSequence.getValue();
- Sequence rgbSequence = new Sequence(new IcyBufferedImage(labSequence.getWidth(), labSequence.getHeight(),3, DataType.UBYTE));
-
- double[][] labIm = Array2DUtil.arrayToDoubleArray(labSequence.getDataXYC(0, 0), labSequence.isSignedDataType());
-
- rgbSequence.beginUpdate();
- double[][] rgbIm = Array2DUtil.arrayToDoubleArray(rgbSequence.getDataXYC(0, 0), rgbSequence.isSignedDataType());
- IntStream.range(0, rgbIm[0].length).forEach(pos->{
- double[] lab = IntStream.range(0, 3).mapToDouble(c->labIm[c][pos]).toArray();
- int[] rgb = CIELab.toRGB(lab);
- IntStream.range(0, 3).forEach(c->rgbIm[c][pos] = rgb[c]);
- });
- Array2DUtil.doubleArrayToArray(rgbIm, rgbSequence.getDataXYC(0, 0));
- rgbSequence.dataChanged();
- rgbSequence.endUpdate();
-
-
- addSequence(rgbSequence);
- }
-
- @Override
- public void clean() {
- // TODO Auto-generated method stub
- }
-
-}
diff --git a/SLIC/src/main/java/plugins/danyfel80/islic/RGBToLAB.java b/SLIC/src/main/java/plugins/danyfel80/islic/RGBToLAB.java
deleted file mode 100644
index ac6139a..0000000
--- a/SLIC/src/main/java/plugins/danyfel80/islic/RGBToLAB.java
+++ /dev/null
@@ -1,51 +0,0 @@
-package plugins.danyfel80.islic;
-
-import java.util.stream.IntStream;
-
-import algorithms.danyfel80.islic.CIELab;
-import icy.image.IcyBufferedImage;
-import icy.sequence.Sequence;
-import icy.type.DataType;
-import icy.type.collection.array.Array2DUtil;
-import plugins.adufour.ezplug.EzPlug;
-import plugins.adufour.ezplug.EzVarSequence;
-
-public class RGBToLAB extends EzPlug {
-
- EzVarSequence inRgbSequence;
-
- @Override
- protected void initialize() {
- inRgbSequence = new EzVarSequence("RGB sequence");
- addEzComponent(inRgbSequence);
- }
-
- @Override
- protected void execute() {
-
- Sequence rgbSequence = inRgbSequence.getValue();
- Sequence labSequence = new Sequence(
- new IcyBufferedImage(rgbSequence.getWidth(), rgbSequence.getHeight(), 3, DataType.DOUBLE));
-
- double[][] rgbIm = Array2DUtil.arrayToDoubleArray(rgbSequence.getDataXYC(0, 0), rgbSequence.isSignedDataType());
-
- labSequence.beginUpdate();
- double[][] labIm = Array2DUtil.arrayToDoubleArray(labSequence.getDataXYC(0, 0), labSequence.isSignedDataType());
- IntStream.range(0, labIm[0].length).forEach(pos -> {
- int[] rgb = IntStream.range(0, 3).map(c -> (int) Math.round(255 * (rgbIm[c][pos] / rgbSequence.getDataTypeMax())))
- .toArray();
- double[] lab = CIELab.fromRGB(rgb);
- IntStream.range(0, 3).forEach(c -> labIm[c][pos] = lab[c]);
- });
- Array2DUtil.doubleArrayToArray(labIm, labSequence.getDataXYC(0, 0));
- labSequence.dataChanged();
- labSequence.endUpdate();
-
- labSequence.setName(rgbSequence.getName() + "_LAB");
- addSequence(labSequence);
- }
-
- @Override
- public void clean() {}
-
-}
diff --git a/SLIC/src/main/java/plugins/danyfel80/islic/SLIC.java b/SLIC/src/main/java/plugins/danyfel80/islic/SLIC.java
deleted file mode 100644
index ea1dc51..0000000
--- a/SLIC/src/main/java/plugins/danyfel80/islic/SLIC.java
+++ /dev/null
@@ -1,135 +0,0 @@
-package plugins.danyfel80.islic;
-
-import algorithms.danyfel80.islic.SLICTask;
-import icy.gui.dialog.MessageDialog;
-import icy.main.Icy;
-import icy.plugin.PluginLauncher;
-import icy.plugin.PluginLoader;
-import plugins.adufour.blocks.lang.Block;
-import plugins.adufour.blocks.util.VarList;
-import plugins.adufour.ezplug.EzPlug;
-import plugins.adufour.ezplug.EzVarBoolean;
-import plugins.adufour.ezplug.EzVarDouble;
-import plugins.adufour.ezplug.EzVarInteger;
-import plugins.adufour.ezplug.EzVarSequence;
-
-public class SLIC extends EzPlug implements Block
-{
-
- private EzVarSequence inSequence;
- private EzVarInteger inSPSize;
- private EzVarDouble inSPReg;
- private EzVarBoolean inIsROIOutput;
-
- private EzVarSequence outSequence;
-
- @Override
- protected void initialize()
- {
- inSequence = new EzVarSequence("Sequence");
- inSPSize = new EzVarInteger("Superpixel size");
- inSPReg = new EzVarDouble("Superpixels regularity");
- inIsROIOutput = new EzVarBoolean("Output as ROIs", false);
-
- inSPSize.setValue(30);
- inSPReg.setValue(0.2);
-
- addEzComponent(inSequence);
- addEzComponent(inSPSize);
- addEzComponent(inSPReg);
- addEzComponent(inIsROIOutput);
- }
-
- @Override
- public void declareInput(VarList inputMap)
- {
- inSequence = new EzVarSequence("Sequence");
- inSPSize = new EzVarInteger("Superpixel size");
- inSPReg = new EzVarDouble("Superpixels regularity");
- inIsROIOutput = new EzVarBoolean("Output as ROIs", false);
-
- inSPSize.setValue(30);
- inSPReg.setValue(0.2);
-
- inputMap.add(inSequence.name, inSequence.getVariable());
- inputMap.add(inSPSize.name, inSPSize.getVariable());
- inputMap.add(inSPReg.name, inSPReg.getVariable());
- inputMap.add(inIsROIOutput.name, inIsROIOutput.getVariable());
- }
-
- @Override
- public void declareOutput(VarList outputMap)
- {
- outSequence = new EzVarSequence("Result");
-
- outputMap.add(outSequence.name, outSequence.getVariable());
- }
-
- @Override
- protected void execute()
- {
- long procTime, startTime, endTime;
- SLICTask task;
- try
- {
- task = new SLICTask(inSequence.getValue(), inSPSize.getValue(), inSPReg.getValue(),
- inIsROIOutput.getValue());
- }
- catch (Exception e)
- {
- e.printStackTrace();
- if (!this.isHeadLess())
- {
- MessageDialog.showDialog("Initialization Error",
- String.format("SLIC could not start properly: " + e.getMessage()), MessageDialog.ERROR_MESSAGE);
- }
- return;
- }
- startTime = System.currentTimeMillis();
- try
- {
- task.execute();
- }
- catch (Exception e)
- {
- e.printStackTrace();
- if (!this.isHeadLess())
- {
- MessageDialog.showDialog("Runtime Error",
- String.format("SLIC could not run properly: " + e.getMessage()), MessageDialog.ERROR_MESSAGE);
- }
- return;
- }
-
- endTime = System.currentTimeMillis();
- procTime = endTime - startTime;
- System.out.println(String.format("SLIC finished in %d milliseconds", procTime));
- if (!this.inIsROIOutput.getValue())
- {
- task.getResultSequence().setName(inSequence.getValue().getName() + String.format("_SLIC(size=%s,reg=%.2f)",
- inSPSize.getValue().intValue(), inSPReg.getValue().doubleValue()));
- }
- if (!this.isHeadLess())
- {
- MessageDialog.showDialog(String.format("SLIC finished in %d milliseconds", procTime));
- addSequence(task.getResultSequence());
- }
- else
- {
- outSequence.setValue(task.getResultSequence());
- }
-
- }
-
- @Override
- public void clean()
- {
- // TODO Auto-generated method stub
- }
-
- public static void main(String[] args)
- {
- Icy.main(args);
- PluginLauncher.start(PluginLoader.getPlugin(SLIC.class.getName()));
- }
-}
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..324627d
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <parent>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>pom-icy</artifactId>
+ <version>3.0.0-a.1</version>
+ </parent>
+
+ <artifactId>slic</artifactId>
+ <version>2.0.0-a.1</version>
+
+ <name>SLIC - Superpixels</name>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>ezplug</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>protocols</artifactId>
+ </dependency>
+ </dependencies>
+
+ <repositories>
+ <repository>
+ <id>icy</id>
+ <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
+ </repository>
+ </repositories>
+</project>
\ No newline at end of file
diff --git a/src/main/java/algorithms/danyfel80/islic/CIELab.java b/src/main/java/algorithms/danyfel80/islic/CIELab.java
new file mode 100644
index 0000000..020c402
--- /dev/null
+++ b/src/main/java/algorithms/danyfel80/islic/CIELab.java
@@ -0,0 +1,225 @@
+/*
+ * Copyright (c) 2010-2024. 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 algorithms.danyfel80.islic;
+
+import org.jetbrains.annotations.NotNull;
+
+public class CIELab {
+ public static class XYZ {
+ private static final double[][] M = {
+ {0.4124, 0.3576, 0.1805},
+ {0.2126, 0.7152, 0.0722},
+ {0.0193, 0.1192, 0.9505}
+ };
+ private static final double[][] Mi = {
+ {3.2406, -1.5372, -0.4986},
+ {-0.9689, 1.8758, 0.0415},
+ {0.0557, -0.2040, 1.0570}
+ };
+
+ public static double @NotNull [] fromRGB(final int @NotNull [] rgb) {
+ return fromRGB(rgb[0], rgb[1], rgb[2]);
+ }
+
+ public static double @NotNull [] fromRGB(final int R, final int G, final int B) {
+ final double[] result = new double[3];
+
+ // convert 0..255 into 0..1
+ double r = R / 255.0;
+ double g = G / 255.0;
+ double b = B / 255.0;
+
+ // assume sRGB
+ if (r <= 0.04045) {
+ r = r / 12.92;
+ }
+ else {
+ r = Math.pow(((r + 0.055) / 1.055), 2.4);
+ }
+ if (g <= 0.04045) {
+ g = g / 12.92;
+ }
+ else {
+ g = Math.pow(((g + 0.055) / 1.055), 2.4);
+ }
+ if (b <= 0.04045) {
+ b = b / 12.92;
+ }
+ else {
+ b = Math.pow(((b + 0.055) / 1.055), 2.4);
+ }
+
+ r *= 100.0;
+ g *= 100.0;
+ b *= 100.0;
+
+ // [X Y Z] = [r g b][M]
+ result[0] = (r * M[0][0]) + (g * M[0][1]) + (b * M[0][2]);
+ result[1] = (r * M[1][0]) + (g * M[1][1]) + (b * M[1][2]);
+ result[2] = (r * M[2][0]) + (g * M[2][1]) + (b * M[2][2]);
+
+ return result;
+ }
+
+ public static int @NotNull [] toRGB(final double @NotNull [] xyz) {
+ return toRGB(xyz[0], xyz[1], xyz[2]);
+ }
+
+ public static int @NotNull [] toRGB(final double X, final double Y, final double Z) {
+ final int[] result = new int[3];
+
+ final double x = X / 100.0;
+ final double y = Y / 100.0;
+ final double z = Z / 100.0;
+
+ // [r g b] = [X Y Z][Mi]
+ double r = (x * Mi[0][0]) + (y * Mi[0][1]) + (z * Mi[0][2]);
+ double g = (x * Mi[1][0]) + (y * Mi[1][1]) + (z * Mi[1][2]);
+ double b = (x * Mi[2][0]) + (y * Mi[2][1]) + (z * Mi[2][2]);
+
+ // assume sRGB
+ if (r > 0.0031308) {
+ r = ((1.055 * Math.pow(r, 1.0 / 2.4)) - 0.055);
+ }
+ else {
+ r = (r * 12.92);
+ }
+ if (g > 0.0031308) {
+ g = ((1.055 * Math.pow(g, 1.0 / 2.4)) - 0.055);
+ }
+ else {
+ g = (g * 12.92);
+ }
+ if (b > 0.0031308) {
+ b = ((1.055 * Math.pow(b, 1.0 / 2.4)) - 0.055);
+ }
+ else {
+ b = (b * 12.92);
+ }
+
+ r = (r < 0) ? 0 : r;
+ g = (g < 0) ? 0 : g;
+ b = (b < 0) ? 0 : b;
+
+ // convert 0..1 into 0..255
+ result[0] = (int) Math.round(r * 255);
+ result[1] = (int) Math.round(g * 255);
+ result[2] = (int) Math.round(b * 255);
+
+ return result;
+ }
+
+ }
+
+ private static final double[] whitePoint = {95.0429, 100.0, 108.8900}; // D65
+
+ public static double @NotNull [] fromRGB(final int[] rgb) {
+ return fromXYZ(XYZ.fromRGB(rgb));
+ }
+
+ public static double @NotNull [] fromRGB(final int r, final int g, final int b) {
+ return fromXYZ(XYZ.fromRGB(r, g, b));
+ }
+
+ private static double @NotNull [] fromXYZ(final double @NotNull [] xyz) {
+ return fromXYZ(xyz[0], xyz[1], xyz[2]);
+ }
+
+ public static double @NotNull [] fromXYZ(final double X, final double Y, final double Z) {
+ double x = X / whitePoint[0];
+ double y = Y / whitePoint[1];
+ double z = Z / whitePoint[2];
+
+ if (x > 0.008856) {
+ x = Math.pow(x, 1.0 / 3.0);
+ }
+ else {
+ x = (7.787 * x) + (16.0 / 116.0);
+ }
+ if (y > 0.008856) {
+ y = Math.pow(y, 1.0 / 3.0);
+ }
+ else {
+ y = (7.787 * y) + (16.0 / 116.0);
+ }
+ if (z > 0.008856) {
+ z = Math.pow(z, 1.0 / 3.0);
+ }
+ else {
+ z = (7.787 * z) + (16.0 / 116.0);
+ }
+
+ final double[] result = new double[3];
+
+ result[0] = (116.0 * y) - 16.0;
+ result[1] = 500.0 * (x - y);
+ result[2] = 200.0 * (y - z);
+
+ return result;
+ }
+
+ public static int @NotNull [] toRGB(final double[] lab) {
+ return XYZ.toRGB(toXYZ(lab));
+ }
+
+ public static int @NotNull [] toRGB(final double L, final double a, final double b) {
+ return XYZ.toRGB(toXYZ(L, a, b));
+ }
+
+ public static double @NotNull [] toXYZ(final double @NotNull [] lab) {
+ return toXYZ(lab[0], lab[1], lab[2]);
+ }
+
+ public static double @NotNull [] toXYZ(final double L, final double a, final double b) {
+ final double[] result = new double[3];
+
+ double y = (L + 16.0) / 116.0;
+ final double y3 = Math.pow(y, 3.0);
+ double x = (a / 500.0) + y;
+ final double x3 = Math.pow(x, 3.0);
+ double z = y - (b / 200.0);
+ final double z3 = Math.pow(z, 3.0);
+
+ if (y3 > 0.008856) {
+ y = y3;
+ }
+ else {
+ y = (y - (16.0 / 116.0)) / 7.787;
+ }
+ if (x3 > 0.008856) {
+ x = x3;
+ }
+ else {
+ x = (x - (16.0 / 116.0)) / 7.787;
+ }
+ if (z3 > 0.008856) {
+ z = z3;
+ }
+ else {
+ z = (z - (16.0 / 116.0)) / 7.787;
+ }
+
+ // results in 0...100
+ result[0] = x * whitePoint[0];
+ result[1] = y * whitePoint[1];
+ result[2] = z * whitePoint[2];
+
+ return result;
+ }
+}
diff --git a/src/main/java/algorithms/danyfel80/islic/SLICTask.java b/src/main/java/algorithms/danyfel80/islic/SLICTask.java
new file mode 100644
index 0000000..254b508
--- /dev/null
+++ b/src/main/java/algorithms/danyfel80/islic/SLICTask.java
@@ -0,0 +1,601 @@
+/*
+ * Copyright (c) 2010-2024. 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 algorithms.danyfel80.islic;
+
+import org.bioimageanalysis.extension.kernel.roi.roi2d.ROI2DArea;
+import org.bioimageanalysis.icy.common.collection.array.Array2DUtil;
+import org.bioimageanalysis.icy.common.geom.point.Point3D;
+import org.bioimageanalysis.icy.common.type.DataType;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImage;
+import org.bioimageanalysis.icy.model.roi.ROI;
+import org.bioimageanalysis.icy.model.roi.mask.BooleanMask2D;
+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 java.awt.*;
+import java.util.List;
+import java.util.*;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.stream.IntStream;
+
+/**
+ * @author Daniel Felipe Gonzalez Obando
+ */
+public class SLICTask {
+ private static final double EPSILON = 0.25;
+ static int MAX_ITERATIONS = 10;
+ static double ERROR_THRESHOLD = 1e-2;
+
+ private final Sequence sequence;
+ private final int S;
+ private final int Sx;
+ private final int Sy;
+ private final int SPnum;
+ private final double rigidity;
+
+ private final boolean computeROIs;
+ private List<ROI> rois;
+ private Sequence superPixelsResult;
+
+ private final Map<Point3D.Integer, double[]> colorLUT;
+ private final Map<Point, Double> distanceLUT;
+
+ public SLICTask(@NotNull final Sequence sequence, final int SPSize, final double rigidity, final boolean computeROIs) {
+ this.sequence = sequence;
+ this.S = SPSize;
+ this.Sx = (sequence.getWidth() + S / 2 - 1) / S;
+ this.Sy = (sequence.getHeight() + S / 2 - 1) / S;
+ this.SPnum = Sx * Sy;
+ this.rigidity = rigidity;
+
+ this.computeROIs = computeROIs;
+
+ colorLUT = new HashMap<>();
+ distanceLUT = new HashMap<>();
+ }
+
+ public void execute() {
+ final double[] ls = new double[SPnum];
+ final double[] as = new double[SPnum];
+ final double[] bs = new double[SPnum];
+
+ final double[] cxs = new double[SPnum];
+ final double[] cys = new double[SPnum];
+
+ final double[][] sequenceData = Array2DUtil.arrayToDoubleArray(
+ sequence.getDataXYC(0, 0),
+ sequence.isSignedDataType()
+ );
+
+ initialize(ls, as, bs, cxs, cys, sequenceData);
+
+ final int[] clusters = new int[sequence.getWidth() * sequence.getHeight()];
+ final double[] distances = Arrays.stream(clusters).mapToDouble(i -> Double.MAX_VALUE).toArray();
+
+ int iterations = 0;
+ double error; // = 0;
+ do {
+ assignClusters(sequenceData, clusters, distances, ls, as, bs, cxs, cys);
+ error = updateClusters(sequenceData, clusters, ls, as, bs, cxs, cys);
+ iterations++;
+ IcyLogger.trace(this.getClass(), String.format("Iteration=%d, Error=%f", iterations, error));
+ }
+ while (error > ERROR_THRESHOLD && iterations < MAX_ITERATIONS);
+ IcyLogger.trace(this.getClass(), "End of iterations%n");
+
+ computeSuperpixels(sequenceData, clusters, ls, as, bs, cxs, cys);
+ }
+
+ private void initialize(final double[] ls, final double[] as, final double[] bs, final double[] cxs, final double[] cys, final double[][] sequenceData) {
+ IntStream.range(0, SPnum).forEach(sp -> {
+ final int x;
+ final int y;
+ final int yOff;
+ int bestx;
+ int besty;
+ int bestyOff;
+ int i;
+ int j;
+ int yjOff;
+ double bestGradient, candidateGradient;
+
+ final int spx = sp % Sx;
+ final int spy = sp / Sx;
+
+ x = S / 2 + (spx) * S;
+ y = S / 2 + (spy) * S;
+ yOff = y * sequence.getWidth();
+
+ cxs[sp] = bestx = x;
+ cys[sp] = besty = y;
+ bestyOff = yOff;
+ bestGradient = Double.MAX_VALUE;
+
+ for (j = -1; j <= 1; j++) {
+ if (y + j >= 0 && y + j < sequence.getHeight()) {
+ yjOff = (y + j) * sequence.getWidth();
+ for (i = -1; i <= 1; i++) {
+ if (x >= 0 && x < sequence.getWidth() && x + i >= 0 && x + i < sequence.getWidth()) {
+ candidateGradient = getGradient(sequenceData, x + yOff, (x + i) + yjOff);
+ if (candidateGradient < bestGradient) {
+ bestx = x + i;
+ besty = y + j;
+ bestyOff = yjOff;
+ bestGradient = candidateGradient;
+ }
+ }
+ }
+ }
+ }
+
+ cxs[sp] = bestx;
+ cys[sp] = besty;
+ final int bestPos = bestx + bestyOff;
+
+ final double[] bestLAB = getCIELab(sequenceData, bestPos);
+ ls[sp] = bestLAB[0];
+ as[sp] = bestLAB[1];
+ bs[sp] = bestLAB[2];
+ });
+ }
+
+ private double getGradient(final double[][] data, final int pos1, final int pos2) {
+ final int[] valRGB1 = new int[3];
+ final int[] valRGB2 = new int[3];
+ IntStream.range(0, 3).forEach(c -> {
+ try {
+ valRGB1[c] = (int) Math.round(255 * (data[c % sequence.getSizeC()][pos1] / sequence.getDataTypeMax()));
+ valRGB2[c] = (int) Math.round(255 * (data[c % sequence.getSizeC()][pos2] / sequence.getDataTypeMax()));
+ }
+ catch (final Exception e) {
+ IcyLogger.error(this.getClass(), e, "Error while getting gradient.");
+ throw e;
+ }
+ });
+
+ final double[] val1 = CIELab.fromRGB(valRGB1);
+ final double[] val2 = CIELab.fromRGB(valRGB2);
+
+ return IntStream.range(0, 3).mapToDouble(c -> val2[c] - val1[c]).average().orElseThrow();
+ }
+
+ private double @NotNull [] getCIELab(final double[][] sequenceData, final int pos) {
+ final int[] rgbVal = new int[3];
+ IntStream.range(0, 3).forEach(c -> rgbVal[c] = (int) Math
+ .round(255 * (sequenceData[c % sequence.getSizeC()][pos] / sequence.getDataTypeMax())));
+ final Point3D.Integer rgbPoint = new Point3D.Integer(rgbVal);
+
+ double[] LAB = colorLUT.get(rgbPoint);
+ if (LAB == null) {
+ final int[] RGB = new int[3];
+ IntStream.range(0, 3).forEach(c -> RGB[c] = (int) Math
+ .round(255 * (sequenceData[c % sequence.getSizeC()][pos] / sequence.getDataTypeMax())));
+
+ LAB = CIELab.fromRGB(RGB);
+ colorLUT.put(rgbPoint, LAB);
+ }
+ return LAB;
+ }
+
+ private void assignClusters(
+ final double[][] sequenceData,
+ final int[] clusters,
+ final double[] distances,
+ final double[] ls,
+ final double[] as,
+ final double[] bs,
+ final double[] cxs,
+ final double[] cys
+ ) {
+ // Each cluster
+ IntStream.range(0, SPnum).forEach(k -> {
+ final double ckx = cxs[k];
+ final double cky = cys[k];
+ final double lk = ls[k];
+ final double ak = as[k];
+ final double bk = bs[k];
+ final int posk = ((int) ckx) + ((int) cky) * sequence.getWidth();
+ distances[posk] = 0;
+ clusters[posk] = k;
+
+ // 2Sx2S window assignment
+ int j, i, yOff;
+ for (j = -S; j < S; j++) {
+ final int ciy = (int) (cky + j);
+ if (ciy >= 0 && ciy < sequence.getHeight()) {
+ yOff = ciy * sequence.getWidth();
+ for (i = -S; i < S; i++) {
+ final int cix = (int) (ckx + i);
+ if (cix >= 0 && cix < sequence.getWidth()) {
+ final int posi = cix + yOff;
+ final double[] LABi = getCIELab(sequenceData, posi);
+ final double li = LABi[0];
+ final double ai = LABi[1];
+ final double bi = LABi[2];
+
+ final double di = getDistance(ckx, cky, lk, ak, bk, i, j, li, ai, bi);
+ if (di < distances[posi]) {
+ distances[posi] = di;
+ clusters[posi] = clusters[posk];
+ }
+ }
+ }
+ }
+ }
+ });
+ }
+
+ private double getDistance(
+ final double ckx,
+ final double cky,
+ final double lk,
+ final double ak,
+ final double bk,
+ final int dx,
+ final int dy,
+ final double li,
+ final double ai,
+ final double bi
+ ) {
+ final double diffl;
+ final double diffa;
+ final double diffb;
+ diffl = li - lk;
+ diffa = ai - ak;
+ diffb = bi - bk;
+
+ final double dc = Math.sqrt(diffl * diffl + diffa * diffa + diffb * diffb);
+ final Point dPt = new Point(Math.min(dx, dy), Math.max(dx, dy));
+ final Double ds = distanceLUT.computeIfAbsent(dPt, k -> Math.sqrt(dx * dx + dy * dy));
+ return Math.sqrt(dc * dc + (ds * ds) * (rigidity * rigidity * S));
+ }
+
+ private double updateClusters(
+ final double[][] sequenceData,
+ final int[] clusters,
+ final double[] ls,
+ final double[] as,
+ final double[] bs,
+ final double[] cxs,
+ final double[] cys
+ ) {
+ final double[] newls = new double[SPnum];
+ final double[] newas = new double[SPnum];
+ final double[] newbs = new double[SPnum];
+ final double[] newcxs = new double[SPnum];
+ final double[] newcys = new double[SPnum];
+ final int[] cants = new int[SPnum];
+
+ // int blockSize = 500;
+ // IntStream.iterate(0, sy -> sy+blockSize).limit((int)Math.ceil(sequence.getHeight()/blockSize)).forEach(y0->{
+ // int y1 = Math.min(y0+blockSize, sequence.getHeight() - y0);
+ // IntStream.iterate(0, sx -> sx+blockSize).limit((int)Math.ceil(sequence.getWidth()/blockSize)).forEach(x0->{
+ // int x1 = Math.min(x0+blockSize, sequence.getWidth() - x0);
+ // });
+ // });
+ for (int y = 0, yOff; y < sequence.getHeight(); y++) {
+ yOff = y * sequence.getWidth();
+ for (int x = 0, pos; x < sequence.getWidth(); x++) {
+ pos = x + yOff;
+ final int sp = clusters[pos];
+ final double[] lab = getCIELab(sequenceData, pos);
+
+ cants[sp]++;
+
+ newls[sp] += (lab[0] - newls[sp]) / cants[sp];
+ newas[sp] += (lab[1] - newas[sp]) / cants[sp];
+ newbs[sp] += (lab[2] - newbs[sp]) / cants[sp];
+ newcxs[sp] += (x - newcxs[sp]) / cants[sp];
+ newcys[sp] += (y - newcys[sp]) / cants[sp];
+ }
+ }
+
+ return IntStream.range(0, SPnum).mapToDouble(sp -> {
+ // double diffl = ls[sp] - newls[sp];
+ // double diffa = as[sp] - newas[sp];
+ // double diffb = bs[sp] - newbs[sp];
+ final double diffx = cxs[sp] - newcxs[sp];
+ final double diffy = cys[sp] - newcys[sp];
+
+ ls[sp] = newls[sp];
+ as[sp] = newas[sp];
+ bs[sp] = newbs[sp];
+ cxs[sp] = newcxs[sp];
+ cys[sp] = newcys[sp];
+
+ return Math.sqrt(diffx * diffx + diffy * diffy/* + diffl * diffl + diffa * diffa + diffb * diffb */);
+ }).sum() / SPnum;
+ }
+
+ private void computeSuperpixels(
+ final double[][] sequenceData,
+ final int @NotNull [] clusters,
+ final double[] ls,
+ final double[] as,
+ final double[] bs,
+ final double[] cxs,
+ final double[] cys
+ ) {
+ final boolean[] visited = new boolean[clusters.length];
+ final int[] finalClusters = new int[clusters.length];
+
+ final List<Point3D.Double> labs = new ArrayList<>(SPnum);
+ final List<Double> areas = new ArrayList<>(SPnum);
+ final List<Point> firstPoints = new ArrayList<>(SPnum);
+
+ // fill known clusters
+ final AtomicInteger usedLabels = new AtomicInteger(0);
+ IntStream.range(0, SPnum).forEach(i -> {
+ final Point3D.Double labCenter = new Point3D.Double();
+ final AtomicInteger area = new AtomicInteger(0);
+ final Point p = new Point((int) Math.round(cxs[i]), (int) Math.round(cys[i]));
+ final int pPos = p.x + p.y * sequence.getWidth();
+
+ if (clusters[pPos] == i && !visited[pPos]) {
+ findAreaAndColor(sequenceData, clusters, finalClusters, visited, p, labCenter, area,
+ usedLabels.getAndIncrement());
+ labs.add(labCenter);
+ areas.add(area.get() / (double) (S * S));
+ firstPoints.add(p);
+ }
+ });
+
+ final int firstUnknownCluster = usedLabels.get();
+
+ // fill independent clusters
+ for (int y = 0; y < sequence.getHeight(); y++) {
+ final int yOff = y * sequence.getWidth();
+ for (int x = 0; x < sequence.getWidth(); x++) {
+ final int pos = x + yOff;
+ if (!visited[pos]) {
+ final Point3D.Double labCenter = new Point3D.Double();
+ final AtomicInteger area = new AtomicInteger(0);
+ final Point p = new Point(x, y);
+
+ findAreaAndColor(sequenceData, clusters, finalClusters, visited, p, labCenter, area,
+ usedLabels.getAndIncrement());
+
+ labs.add(labCenter);
+ areas.add(area.get() / (double) (S * S));
+ firstPoints.add(p);
+ }
+ }
+ }
+
+ // System.out.println("unvisited = " + IntStream.range(0, visited.length).filter(i -> visited[i] == false).sum());
+
+ // find neighbors and merge independent clusters
+ final boolean[] mergedClusters = new boolean[usedLabels.get()];
+ final int[] mergedRefs = IntStream.range(0, usedLabels.get()).toArray();
+ IntStream.range(firstUnknownCluster, usedLabels.get()).forEach(i -> {
+ final List<Integer> neighbors = findNeighbors(finalClusters, visited, firstPoints.get(i));
+ if (!neighbors.isEmpty()) {
+ int bestNeighbour = neighbors.getFirst();
+ double bestL = Double.MAX_VALUE;
+
+ // boolean found = false;
+ for (final Integer j : neighbors) {
+ if (j < i) {
+ // found = true;
+ final double l = computeL(labs, areas, i, j);
+ if (l < bestL) {
+ bestNeighbour = j;
+ bestL = l;
+ }
+ }
+ }
+ /*
+ * if (!found) { for (Integer j: neighbors) { double l = computeL(labs,
+ * areas, i, j); if (l < bestL) { bestNeighbour = j; bestL = l; } } }
+ *
+ * if (found) {
+ */
+ final double rArea = areas.get(i);
+ double relSPSize = rArea / 4;
+ relSPSize *= relSPSize;
+
+ final double coeff = relSPSize * (1.0 + bestL);
+ if (coeff < EPSILON) {
+ mergedClusters[i] = true;
+ mergedRefs[i] = bestNeighbour;
+ }
+ // } else {
+ // mergedClusters[i] = true;
+ // mergedRefs[i] = bestNeighbour;
+ // }
+ }
+ else {
+ IcyLogger.error(
+ this.getClass(),
+ String.format("Cluster at (%d, %d) has no neighbors.", firstPoints.get(i).x, firstPoints.get(i).y)
+ );
+ }
+ });
+ IntStream.range(firstUnknownCluster, usedLabels.get()).forEach(i -> {
+ if (mergedClusters[i]) {
+ int appliedLabel = i;
+ while (appliedLabel != mergedRefs[appliedLabel]) {
+ appliedLabel = mergedRefs[appliedLabel];
+ }
+ findAreaAndColor(sequenceData, clusters, finalClusters, visited, firstPoints.get(i),
+ new Point3D.Double(), new AtomicInteger(0), appliedLabel);
+ }
+
+ });
+
+ if (this.computeROIs) {
+ // Create and add ROIs to sequence
+ this.rois = new ArrayList<>();
+ IntStream.range(0, usedLabels.get()).forEach(i -> {
+ if (!mergedClusters[i]) {
+ final ROI2DArea roi = defineROI(finalClusters, firstPoints.get(i), labs.get(i));
+ rois.add(roi);
+ }
+ });
+ sequence.addROIs(rois, false);
+ }
+ else {
+ final List<int[]> rgbs = labs.stream().map(lab -> CIELab.toRGB(lab.x, lab.y, lab.z)).toList();
+ superPixelsResult = new Sequence(new IcyBufferedImage(sequence.getWidth(), sequence.getHeight(), 3, DataType.UBYTE));
+
+ superPixelsResult.setPixelSizeX(sequence.getPixelSizeX());
+ superPixelsResult.setPixelSizeY(sequence.getPixelSizeY());
+ superPixelsResult.setPixelSizeZ(sequence.getPixelSizeZ());
+ superPixelsResult.setPositionX(sequence.getPositionX());
+ superPixelsResult.setPositionY(sequence.getPositionY());
+ superPixelsResult.setPositionZ(sequence.getPositionZ());
+
+ superPixelsResult.beginUpdate();
+ final double[][] spData = Array2DUtil.arrayToDoubleArray(superPixelsResult.getDataXYC(0, 0),
+ superPixelsResult.isSignedDataType());
+ for (int y = 0, yOff; y < sequence.getHeight(); y++) {
+ yOff = y * sequence.getWidth();
+ for (int x = 0; x < sequence.getWidth(); x++) {
+ final int pos = x + yOff;
+ final int[] rgbVal = rgbs.get(finalClusters[pos]);
+
+ IntStream.range(0, 3).forEach(c -> spData[c][pos] = rgbVal[c]);
+
+ }
+ }
+ Array2DUtil.doubleArrayToArray(spData, superPixelsResult.getDataXYC(0, 0));
+ superPixelsResult.dataChanged();
+ superPixelsResult.endUpdate();
+ }
+ }
+
+ private void findAreaAndColor(
+ final double[][] sequenceData,
+ final int @NotNull [] clusters,
+ final int[] newClusters,
+ final boolean @NotNull [] visited,
+ @NotNull final Point p,
+ final Point3D.@NotNull Double labCenter,
+ @NotNull final AtomicInteger area,
+ final int label
+ ) {
+ final int posp = p.x + p.y * sequence.getWidth();
+ area.set(0);
+ labCenter.x = 0d;
+ labCenter.y = 0d;
+ labCenter.z = 0d;
+
+ final Deque<Point> q = new LinkedList<>();
+ final int val = clusters[posp];
+
+ visited[posp] = true;
+ q.add(p);
+
+ while (!q.isEmpty()) {
+ final Point pti = q.pop();
+ final int posi = pti.x + pti.y * sequence.getWidth();
+
+ newClusters[posi] = label;
+ area.getAndIncrement();
+ final double[] labi = getCIELab(sequenceData, posi);
+ labCenter.x += (labi[0] - labCenter.x) / area.get();
+ labCenter.y += (labi[1] - labCenter.y) / area.get();
+ labCenter.z += (labi[2] - labCenter.z) / area.get();
+
+ final int[] ds = new int[]{0, -1, 0, 1, 0};
+ for (int is = 1; is < ds.length; is++) {
+ final Point ptn = new Point(pti.x + ds[is - 1], pti.y + ds[is]);
+ final int posn = ptn.x + ptn.y * sequence.getWidth();
+ if (sequence.getBounds2D().contains(ptn.x, ptn.y) && !visited[posn] && clusters[posn] == val) {
+ visited[posn] = true;
+ q.add(ptn);
+ }
+ }
+
+ }
+ }
+
+ @Contract("_, _, _ -> new")
+ private @NotNull List<Integer> findNeighbors(final int @NotNull [] newClusters, final boolean @NotNull [] visited, @NotNull final Point p) {
+ final int posp = p.x + p.y * sequence.getWidth();
+
+ final HashSet<Integer> neighs = new HashSet<>();
+
+ final Deque<Point> q = new LinkedList<>();
+ final int val = newClusters[posp];
+
+ visited[posp] = false;
+ q.add(p);
+
+ while (!q.isEmpty()) {
+ final Point pti = q.pop();
+
+ final int[] ds = new int[]{0, -1, 0, 1, 0};
+ for (int is = 1; is < ds.length; is++) {
+ final Point ptn = new Point(pti.x + ds[is - 1], pti.y + ds[is]);
+ final int posn = ptn.x + ptn.y * sequence.getWidth();
+ if (sequence.getBounds2D().contains(ptn.x, ptn.y)) {
+ if (newClusters[posn] == val) {
+ if (visited[posn]) {
+ visited[posn] = false;
+ q.add(ptn);
+ }
+ }
+ else {
+ neighs.add(newClusters[posn]);
+ }
+ }
+ }
+
+ }
+ return new ArrayList<>(neighs);
+ }
+
+ private double computeL(@NotNull final List<Point3D.Double> labs, final List<Double> areas, final int i, final Integer j) {
+ final Point3D.Double diffLab = new Point3D.Double();
+ diffLab.x = labs.get(j).x - labs.get(i).x;
+ diffLab.y = labs.get(j).y - labs.get(i).y;
+ diffLab.z = labs.get(j).z - labs.get(i).z;
+
+ try {
+ return diffLab.length() / areas.get(j);
+ }
+ catch (final Exception e) {
+ IcyLogger.error(this.getClass(), e);
+ throw e;
+ }
+ }
+
+ private @NotNull ROI2DArea defineROI(final int @NotNull [] newClusters, @NotNull final Point p, final Point3D.@NotNull Double labP) {
+ final int posp = p.x + p.y * sequence.getWidth();
+ final double[] lab = new double[]{labP.x, labP.y, labP.z};
+ final int[] rgb = CIELab.toRGB(lab);
+
+ final int val = newClusters[posp];
+ final Rectangle seqBounds = sequence.getBounds2D();
+ final ROI2DArea roi1 = new ROI2DArea(new BooleanMask2D());
+ IntStream.range(0, newClusters.length)
+ .filter(pi -> newClusters[pi] == val)
+ .forEach(pi -> roi1.addPoint(pi % seqBounds.width, pi / seqBounds.width));// .forEach(pi -> bMask[pi] = true);
+
+ roi1.setColor(new Color(rgb[0], rgb[1], rgb[2]));
+ return roi1;
+ }
+
+ public Sequence getResultSequence() {
+ return this.superPixelsResult;
+ }
+}
diff --git a/src/main/java/plugins/danyfel80/islic/LABToRGB.java b/src/main/java/plugins/danyfel80/islic/LABToRGB.java
new file mode 100644
index 0000000..48ebd3d
--- /dev/null
+++ b/src/main/java/plugins/danyfel80/islic/LABToRGB.java
@@ -0,0 +1,74 @@
+/*
+ * Copyright (c) 2010-2024. 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.danyfel80.islic;
+
+import algorithms.danyfel80.islic.CIELab;
+import org.bioimageanalysis.icy.common.collection.array.Array2DUtil;
+import org.bioimageanalysis.icy.common.type.DataType;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImage;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import plugins.adufour.ezplug.EzPlug;
+import plugins.adufour.ezplug.EzVarSequence;
+
+import java.util.stream.IntStream;
+
+@IcyPluginName("LAB to RGB")
+@IcyPluginIcon(path = "/slic.png")
+public class LABToRGB extends EzPlug {
+ EzVarSequence inLabSequence;
+
+ @Override
+ protected void initialize() {
+ inLabSequence = new EzVarSequence("LAB sequence");
+ addEzComponent(inLabSequence);
+ }
+
+ @Override
+ protected void execute() {
+ final Sequence labSequence = inLabSequence.getValue();
+ final Sequence rgbSequence = new Sequence(new IcyBufferedImage(labSequence.getWidth(),
+ labSequence.getHeight(),
+ 3,
+ DataType.UBYTE
+ ));
+
+ final double[][] labIm = Array2DUtil.arrayToDoubleArray(labSequence.getDataXYC(0, 0), labSequence.isSignedDataType());
+
+ rgbSequence.beginUpdate();
+ final double[][] rgbIm = Array2DUtil.arrayToDoubleArray(rgbSequence.getDataXYC(0, 0), rgbSequence.isSignedDataType());
+ IntStream.range(0, rgbIm[0].length).forEach(pos -> {
+ final double[] lab = IntStream.range(0, 3).mapToDouble(c -> labIm[c][pos]).toArray();
+ final int[] rgb = CIELab.toRGB(lab);
+ IntStream.range(0, 3).forEach(c -> rgbIm[c][pos] = rgb[c]);
+ });
+ Array2DUtil.doubleArrayToArray(rgbIm, rgbSequence.getDataXYC(0, 0));
+ rgbSequence.dataChanged();
+ rgbSequence.endUpdate();
+
+
+ addSequence(rgbSequence);
+ }
+
+ @Override
+ public void clean() {
+ //
+ }
+}
diff --git a/src/main/java/plugins/danyfel80/islic/RGBToLAB.java b/src/main/java/plugins/danyfel80/islic/RGBToLAB.java
new file mode 100644
index 0000000..f9ceee5
--- /dev/null
+++ b/src/main/java/plugins/danyfel80/islic/RGBToLAB.java
@@ -0,0 +1,75 @@
+/*
+ * Copyright (c) 2010-2024. 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.danyfel80.islic;
+
+import algorithms.danyfel80.islic.CIELab;
+import org.bioimageanalysis.icy.common.collection.array.Array2DUtil;
+import org.bioimageanalysis.icy.common.type.DataType;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImage;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import plugins.adufour.ezplug.EzPlug;
+import plugins.adufour.ezplug.EzVarSequence;
+
+import java.util.stream.IntStream;
+
+@IcyPluginName("RGB to LAB")
+@IcyPluginIcon(path = "/slic.png")
+public class RGBToLAB extends EzPlug {
+ EzVarSequence inRgbSequence;
+
+ @Override
+ protected void initialize() {
+ inRgbSequence = new EzVarSequence("RGB sequence");
+ addEzComponent(inRgbSequence);
+ }
+
+ @Override
+ protected void execute() {
+ final Sequence rgbSequence = inRgbSequence.getValue();
+ final Sequence labSequence = new Sequence(new IcyBufferedImage(
+ rgbSequence.getWidth(),
+ rgbSequence.getHeight(),
+ 3,
+ DataType.DOUBLE
+ ));
+
+ final double[][] rgbIm = Array2DUtil.arrayToDoubleArray(rgbSequence.getDataXYC(0, 0), rgbSequence.isSignedDataType());
+
+ labSequence.beginUpdate();
+ final double[][] labIm = Array2DUtil.arrayToDoubleArray(labSequence.getDataXYC(0, 0), labSequence.isSignedDataType());
+ IntStream.range(0, labIm[0].length).forEach(pos -> {
+ final int[] rgb = IntStream.range(0, 3).map(c -> (int) Math.round(255 * (rgbIm[c][pos] / rgbSequence.getDataTypeMax()))).toArray();
+ final double[] lab = CIELab.fromRGB(rgb);
+ IntStream.range(0, 3).forEach(c -> labIm[c][pos] = lab[c]);
+ });
+ Array2DUtil.doubleArrayToArray(labIm, labSequence.getDataXYC(0, 0));
+ labSequence.dataChanged();
+ labSequence.endUpdate();
+
+ labSequence.setName(rgbSequence.getName() + "_LAB");
+ addSequence(labSequence);
+ }
+
+ @Override
+ public void clean() {
+
+ }
+}
diff --git a/src/main/java/plugins/danyfel80/islic/SLIC.java b/src/main/java/plugins/danyfel80/islic/SLIC.java
new file mode 100644
index 0000000..9bc58bd
--- /dev/null
+++ b/src/main/java/plugins/danyfel80/islic/SLIC.java
@@ -0,0 +1,134 @@
+/*
+ * Copyright (c) 2010-2024. 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.danyfel80.islic;
+
+import algorithms.danyfel80.islic.SLICTask;
+import org.bioimageanalysis.icy.Icy;
+import org.bioimageanalysis.icy.extension.plugin.PluginLauncher;
+import org.bioimageanalysis.icy.extension.plugin.PluginLoader;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.jetbrains.annotations.NotNull;
+import plugins.adufour.blocks.lang.Block;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.ezplug.*;
+
+@IcyPluginName("SLIC")
+@IcyPluginIcon(path = "/slic.png")
+public class SLIC extends EzPlug implements Block {
+ private EzVarSequence inSequence;
+ private EzVarInteger inSPSize;
+ private EzVarDouble inSPReg;
+ private EzVarBoolean inIsROIOutput;
+
+ private EzVarSequence outSequence;
+
+ @Override
+ protected void initialize() {
+ inSequence = new EzVarSequence("Sequence");
+ inSPSize = new EzVarInteger("Superpixel size");
+ inSPReg = new EzVarDouble("Superpixels regularity");
+ inIsROIOutput = new EzVarBoolean("Output as ROIs", false);
+
+ inSPSize.setValue(30);
+ inSPReg.setValue(0.2);
+
+ addEzComponent(inSequence);
+ addEzComponent(inSPSize);
+ addEzComponent(inSPReg);
+ addEzComponent(inIsROIOutput);
+ }
+
+ @Override
+ public void declareInput(final @NotNull VarList inputMap) {
+ inSequence = new EzVarSequence("Sequence");
+ inSPSize = new EzVarInteger("Superpixel size");
+ inSPReg = new EzVarDouble("Superpixels regularity");
+ inIsROIOutput = new EzVarBoolean("Output as ROIs", false);
+
+ inSPSize.setValue(30);
+ inSPReg.setValue(0.2);
+
+ inputMap.add(inSequence.name, inSequence.getVariable());
+ inputMap.add(inSPSize.name, inSPSize.getVariable());
+ inputMap.add(inSPReg.name, inSPReg.getVariable());
+ inputMap.add(inIsROIOutput.name, inIsROIOutput.getVariable());
+ }
+
+ @Override
+ public void declareOutput(final @NotNull VarList outputMap) {
+ outSequence = new EzVarSequence("Result");
+
+ outputMap.add(outSequence.name, outSequence.getVariable());
+ }
+
+ @Override
+ protected void execute() {
+ final long procTime;
+ final long startTime;
+ final long endTime;
+ final SLICTask task;
+ try {
+ task = new SLICTask(inSequence.getValue(), inSPSize.getValue(), inSPReg.getValue(),
+ inIsROIOutput.getValue());
+ }
+ catch (final Exception e) {
+ IcyLogger.error(this.getClass(), e, "SLIC could not start properly.");
+ return;
+ }
+ startTime = System.currentTimeMillis();
+ try {
+ task.execute();
+ }
+ catch (final Exception e) {
+ IcyLogger.error(this.getClass(), e, "SLIC could not run properly.");
+ return;
+ }
+
+ endTime = System.currentTimeMillis();
+ procTime = endTime - startTime;
+ IcyLogger.info(this.getClass(), String.format("SLIC finished in %d milliseconds", procTime));
+ if (!this.inIsROIOutput.getValue()) {
+ task.getResultSequence().setName(inSequence.getValue().getName() + String.format(
+ "_SLIC(size=%s,reg=%.2f)",
+ inSPSize.getValue(),
+ inSPReg.getValue())
+ );
+ }
+ if (!this.isHeadLess()) {
+ addSequence(task.getResultSequence());
+ }
+ else {
+ outSequence.setValue(task.getResultSequence());
+ }
+
+ }
+
+ @Override
+ public void clean() {
+ //
+ }
+
+ @SuppressWarnings("resource")
+ public static void main(final String[] args) {
+ Icy.main(args);
+ PluginLauncher.start(PluginLoader.getPlugin(SLIC.class.getName()));
+ }
+}
diff --git a/src/main/resources/slic.png b/src/main/resources/slic.png
new file mode 100644
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--
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