diff --git a/SLIC/build.gradle b/SLIC/build.gradle
index e11883b71d03005019cfc58d4bfbe7001ed83659..6b404701501477297e68b9fa9b558be6fd0db300 100644
--- a/SLIC/build.gradle
+++ b/SLIC/build.gradle
@@ -11,7 +11,6 @@ repositories {
dependencies {
compile 'org.slf4j:slf4j-api:1.7.21'
- compile 'javax.vecmath:vecmath:1.5.2'
compile files("${System.env.ICY_HOME}/icy.jar") // Icy core
compile files("${System.env.ICY_HOME}/lib/bioformats.jar") // bioformats
diff --git a/SLIC/src/algorithms/danyfel80/islic/SLICTask.java b/SLIC/src/algorithms/danyfel80/islic/SLICTask.java
index dc7aac788141476446b5830a42d03c708203e4d6..d63c6bdf833e74d2f8d7a6548fc1552798aa8205 100644
--- a/SLIC/src/algorithms/danyfel80/islic/SLICTask.java
+++ b/SLIC/src/algorithms/danyfel80/islic/SLICTask.java
@@ -19,6 +19,7 @@
package algorithms.danyfel80.islic;
import java.awt.Color;
+import java.awt.Point;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Deque;
@@ -31,17 +32,13 @@ import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors;
import java.util.stream.IntStream;
-import javax.vecmath.Point2i;
-import javax.vecmath.Point3d;
-import javax.vecmath.Point3i;
-import javax.vecmath.Vector3d;
-
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;
/**
@@ -64,8 +61,8 @@ public class SLICTask {
private List<ROI> rois;
private Sequence superPixelsResult;
- private Map<Point3i, double[]> colorLUT;
- private Map<Point2i, Double> distanceLUT;
+ private Map<Point3D.Integer, double[]> colorLUT;
+ private Map<Point, Double> distanceLUT;
public SLICTask(Sequence sequence, int SPSize, double rigidity, boolean computeROIs) {
this.sequence = sequence;
@@ -163,8 +160,8 @@ public class SLICTask {
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()));
+ 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;
}
@@ -179,12 +176,12 @@ public class SLICTask {
}
private double[] getCIELab(double[][] sequenceData, int pos) {
- Point3i rgbPoint = new Point3i();
+
int[] rgbVal = new int[3];
IntStream.range(0, 3).forEach(c -> {
rgbVal[c] = (int) Math.round(255 * (sequenceData[c % sequence.getSizeC()][pos] / sequence.getDataTypeMax()));
});
- rgbPoint.set(rgbVal);
+ Point3D.Integer rgbPoint = new Point3D.Integer(rgbVal);
double[] LAB = colorLUT.get(rgbPoint);
if (LAB == null) {
@@ -244,7 +241,7 @@ public class SLICTask {
diffb = bi - bk;
double dc = Math.sqrt(diffl * diffl + diffa * diffa + diffb * diffb);
- Point2i dPt = new Point2i((int) Math.min(dx, dy), (int) Math.max(dx, dy));
+ 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);
@@ -313,16 +310,16 @@ public class SLICTask {
boolean[] visited = new boolean[clusters.length];
int[] finalClusters = new int[clusters.length];
- List<Point3d> labs = new ArrayList<>(SPnum);
+ List<Point3D.Double> labs = new ArrayList<>(SPnum);
List<Double> areas = new ArrayList<>(SPnum);
- List<Point2i> firstPoints = new ArrayList<>(SPnum);
+ List<Point> firstPoints = new ArrayList<>(SPnum);
// fill known clusters
AtomicInteger usedLabels = new AtomicInteger(0);
IntStream.range(0, SPnum).forEach(i -> {
- Point3d labCenter = new Point3d();
+ Point3D.Double labCenter = new Point3D.Double();
AtomicInteger area = new AtomicInteger(0);
- Point2i p = new Point2i((int) Math.round(cxs[i]), (int) Math.round(cys[i]));
+ 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]) {
@@ -343,9 +340,9 @@ public class SLICTask {
for (int x = 0; x < sequence.getWidth(); x++) {
int pos = x + yOff;
if (!visited[pos]) {
- Point3d labCenter = new Point3d();
+ Point3D.Double labCenter = new Point3D.Double();
AtomicInteger area = new AtomicInteger(0);
- Point2i p = new Point2i(x, y);
+ Point p = new Point(x, y);
findAreaAndColor(sequenceData, clusters, finalClusters, visited, p, labCenter, area,
usedLabels.getAndIncrement());
@@ -408,7 +405,7 @@ public class SLICTask {
while (appliedLabel != mergedRefs[appliedLabel]) {
appliedLabel = mergedRefs[appliedLabel];
}
- findAreaAndColor(sequenceData, clusters, finalClusters, visited, firstPoints.get(i), new Point3d(),
+ findAreaAndColor(sequenceData, clusters, finalClusters, visited, firstPoints.get(i), new Point3D.Double(),
new AtomicInteger(0), appliedLabel);
}
@@ -450,20 +447,22 @@ public class SLICTask {
}
}
- private void findAreaAndColor(double[][] sequenceData, int[] clusters, int[] newClusters, boolean[] visited,
- Point2i p, Point3d labCenter, AtomicInteger area, int label) {
+ 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.set(0, 0, 0);
+ labCenter.x = 0d;
+ labCenter.y = 0d;
+ labCenter.z = 0d;
- Deque<Point2i> q = new LinkedList<>();
+ Deque<Point> q = new LinkedList<>();
int val = clusters[posp];
visited[posp] = true;
q.add(p);
while (!q.isEmpty()) {
- Point2i pti = q.pop();
+ Point pti = q.pop();
int posi = pti.x + pti.y * sequence.getWidth();
newClusters[posi] = label;
@@ -475,7 +474,7 @@ public class SLICTask {
int[] ds = new int[] {0, -1, 0, 1, 0};
for (int is = 1; is < ds.length; is++) {
- Point2i ptn = new Point2i(pti.x + ds[is - 1], pti.y + ds[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;
@@ -486,23 +485,23 @@ public class SLICTask {
}
}
- private List<Integer> findNeighbors(int[] newClusters, boolean[] visited, Point2i p) {
+ private List<Integer> findNeighbors(int[] newClusters, boolean[] visited, Point p) {
int posp = p.x + p.y * sequence.getWidth();
HashSet<Integer> neighs = new HashSet<>();
- Deque<Point2i> q = new LinkedList<>();
+ Deque<Point> q = new LinkedList<>();
int val = newClusters[posp];
visited[posp] = false;
q.add(p);
while (!q.isEmpty()) {
- Point2i pti = q.pop();
+ Point pti = q.pop();
int[] ds = new int[] {0, -1, 0, 1, 0};
for (int is = 1; is < ds.length; is++) {
- Point2i ptn = new Point2i(pti.x + ds[is - 1], pti.y + ds[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) {
@@ -520,8 +519,8 @@ public class SLICTask {
return new ArrayList<Integer>(neighs);
}
- private double computeL(List<Point3d> labs, List<Double> areas, int i, Integer j) {
- Vector3d diffLab = new Vector3d();
+ 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;
@@ -533,7 +532,7 @@ public class SLICTask {
}
}
- private ROI2DArea defineROI(int[] newClusters, Point2i p, Point3d labP) {
+ 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);
diff --git a/SLIC/src/plugins/danyfel80/islic/SLIC.java b/SLIC/src/plugins/danyfel80/islic/SLIC.java
index 9cdb8402021d5240d66c850bc2ec6871b493b9f3..48aef85ec211a36f4d935aafc7dde871fafd6de9 100644
--- a/SLIC/src/plugins/danyfel80/islic/SLIC.java
+++ b/SLIC/src/plugins/danyfel80/islic/SLIC.java
@@ -17,15 +17,6 @@ public class SLIC extends EzPlug {
@Override
protected void initialize() {
- try {
- Class.forName("javax.vecmath.Point2i");
- Class.forName("javax.vecmath.Point3d");
- Class.forName("javax.vecmath.Point3i");
- Class.forName("javax.vecmath.Vector3d");
- } catch (ClassNotFoundException e) {
- System.err.println("Could not load proper vecmath version: " + e);
- e.printStackTrace();
- }
inSequence = new EzVarSequence("Sequence");
inSPSize = new EzVarInteger("Superpixel size");
inSPReg = new EzVarDouble("Superpixels regularity");