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Commit 0c39bd3d authored by Daniel Felipe González Obando's avatar Daniel Felipe González Obando
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using Point and Point3D instead of vecmath

parent cecf0b07
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SLIC/build.gradle
+ 0
− 1
View file @ 0c39bd3d
......@@ -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
......
SLIC/src/algorithms/danyfel80/islic/SLICTask.java
+ 31
− 32
View file @ 0c39bd3d
......@@ -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);
......
SLIC/src/plugins/danyfel80/islic/SLIC.java
+ 0
− 9
View file @ 0c39bd3d
......@@ -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");
......
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