diff --git a/pom.xml b/pom.xml
index 07534cb08f3c819c6ce972a35d7a8b3c738d2bcb..061aebae96da6f0c541782c16fff159f0be21308 100644
--- a/pom.xml
+++ b/pom.xml
@@ -11,7 +11,7 @@
</parent>
<artifactId>connected-components</artifactId>
- <version>4.8.9</version>
+ <version>5.0.0</version>
<packaging>jar</packaging>
diff --git a/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponent.java b/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponent.java
index fe242f983ab038d1eb57080429822b3ac956a2ef..dfa7b47030215f8e49c7c3faae7119e5b189cbdd 100644
--- a/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponent.java
+++ b/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponent.java
@@ -1,12 +1,22 @@
-package plugins.adufour.connectedcomponents;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Iterator;
+/*
+ * 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 javax.vecmath.Point3d;
-import javax.vecmath.Point3i;
-import javax.vecmath.Vector3d;
+package plugins.adufour.connectedcomponents;
import icy.image.IcyBufferedImage;
import icy.roi.ROI;
@@ -19,6 +29,13 @@ import plugins.kernel.roi.roi2d.ROI2DArea;
import plugins.kernel.roi.roi3d.ROI3DArea;
import plugins.nchenouard.spot.Detection;
+import javax.vecmath.Point3d;
+import javax.vecmath.Point3i;
+import javax.vecmath.Vector3d;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+
public class ConnectedComponent extends Detection implements Iterable<Point3i> {
private int c = -1;
@@ -45,7 +62,7 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
private final ArrayList<Point3i> points;
/**
- * the array of contour points of this object
+ * the array of this object contour points
*/
private Point3i[] contourPoints;
@@ -62,13 +79,13 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
*
* @param initialCapacity int
*/
- public ConnectedComponent(int initialCapacity) {
+ public ConnectedComponent(final int initialCapacity) {
super(0, 0, 0, 0);
this.points = new ArrayList<>(initialCapacity);
coordsSum = new Point3d();
}
- void addPointInternal(Point3i point) {
+ void addPointInternal(final Point3i point) {
points.add(point);
// accumulate coordinates to compute the mass center
@@ -84,7 +101,7 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
*
* @param point the point to add
*/
- public void addPoint(Point3i point) {
+ public void addPoint(final Point3i point) {
addPointInternal(point);
updateDetectionCoords();
}
@@ -95,7 +112,7 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
*
* @param point the point to add
*/
- void removePointInternal(Point3i point) {
+ void removePointInternal(final Point3i point) {
if (!points.remove(point))
return;
@@ -116,39 +133,26 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
}
/**
- * @return true is the object touches the image edge along X
+ * @return true, if the object touches the image edge along X
*/
public boolean isOnEdgeX() {
return onEdgeX;
}
/**
- * @return true is the object touches the image edge along Y
+ * @return true, if the object touches the image edge along Y
*/
public boolean isOnEdgeY() {
return onEdgeY;
}
/**
- * @return true is the object touches the image edge along Z (always true for 2D images)
+ * @return true, if the object touches the image edge along Z (always true for 2D images)
*/
public boolean isOnEdgeZ() {
return onEdgeZ;
}
- /**
- * Computes the bounding box of this component, and stores the result into the given arguments
- *
- * @param start the first corner of the bounding box in X-Y-Z order (Upper-Left hand-Top)
- * @param end the second corner of the bounding box in X-Y-Z order (Lower-Right hand-Bottom)
- * @deprecated Use {@link ConnectedComponentDescriptor#computeBoundingBox(ConnectedComponent, Point3i, Point3i)}
- * instead
- */
- @Deprecated
- public void computeBoundingBox(Point3i start, Point3i end) {
- shapeDescriptor.computeBoundingBox(this, start, end);
- }
-
/**
* Computes the average intensity of the component on each channel of the given sequence, at the
* time point where this component was found
@@ -156,7 +160,7 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @param sequence Sequence
* @return an array containing the average intensity of the component in each band
*/
- public double[] computeMeanIntensity(Sequence sequence) {
+ public double[] computeMeanIntensity(final Sequence sequence) {
return computeMeanIntensity(sequence, t);
}
@@ -168,13 +172,13 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @param t int
* @return an array containing the average intensity of the component in each band
*/
- public double[] computeMeanIntensity(Sequence sequence, int t) {
- double[] intensitySum = new double[sequence.getSizeC()];
+ public double[] computeMeanIntensity(final Sequence sequence, final int t) {
+ final double[] intensitySum = new double[sequence.getSizeC()];
- for (Point3i point : points) {
- int offsetXY = point.x + point.y * sequence.getSizeX();
+ for (final Point3i point : points) {
+ final int offsetXY = point.x + point.y * sequence.getSizeX();
- Object dataCXY = sequence.getDataXYC(t, point.z);
+ final Object dataCXY = sequence.getDataXYC(t, point.z);
for (int c = 0; c < intensitySum.length; c++)
intensitySum[c] += Array1DUtil.getValue(((Object[]) dataCXY)[c], offsetXY,
@@ -193,7 +197,7 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @param sequence Sequence
* @return an array containing the average intensity of the component in each band
*/
- public double[] computeMinIntensity(Sequence sequence) {
+ public double[] computeMinIntensity(final Sequence sequence) {
return computeMinIntensity(sequence, t);
}
@@ -205,17 +209,17 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @param t int
* @return an array containing the average intensity of the component in each band
*/
- public double[] computeMinIntensity(Sequence sequence, int t) {
- double[] minIntensity = new double[sequence.getSizeC()];
+ public double[] computeMinIntensity(final Sequence sequence, final int t) {
+ final double[] minIntensity = new double[sequence.getSizeC()];
Arrays.fill(minIntensity, Double.MAX_VALUE);
- for (Point3i point : points) {
- int offsetXY = point.x + point.y * sequence.getSizeX();
+ for (final Point3i point : points) {
+ final int offsetXY = point.x + point.y * sequence.getSizeX();
- Object dataCXY = sequence.getImage(t, point.z).getDataXYC();
+ final Object dataCXY = sequence.getImage(t, point.z).getDataXYC();
for (int c = 0; c < minIntensity.length; c++) {
- double val = Array1DUtil.getValue(((Object[]) dataCXY)[c], offsetXY,
+ final double val = Array1DUtil.getValue(((Object[]) dataCXY)[c], offsetXY,
sequence.getDataType_().isSigned());
if (val < minIntensity[c])
minIntensity[c] = val;
@@ -231,7 +235,7 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @param sequence Sequence
* @return an array containing the average intensity of the component in each band
*/
- public double[] computeMaxIntensity(Sequence sequence) {
+ public double[] computeMaxIntensity(final Sequence sequence) {
return computeMaxIntensity(sequence, t);
}
@@ -243,16 +247,16 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @param t int
* @return an array containing the average intensity of the component in each band
*/
- public double[] computeMaxIntensity(Sequence sequence, int t) {
- double[] maxIntensity = new double[sequence.getSizeC()];
+ public double[] computeMaxIntensity(final Sequence sequence, final int t) {
+ final double[] maxIntensity = new double[sequence.getSizeC()];
- for (Point3i point : points) {
- int offsetXY = point.x + point.y * sequence.getSizeX();
+ for (final Point3i point : points) {
+ final int offsetXY = point.x + point.y * sequence.getSizeX();
- Object dataCXY = sequence.getImage(t, point.z).getDataXYC();
+ final Object dataCXY = sequence.getImage(t, point.z).getDataXYC();
for (int c = 0; c < maxIntensity.length; c++) {
- double val = Array1DUtil.getValue(((Object[]) dataCXY)[c], offsetXY,
+ final double val = Array1DUtil.getValue(((Object[]) dataCXY)[c], offsetXY,
sequence.getDataType_().isSigned());
if (val > maxIntensity[c])
maxIntensity[c] = val;
@@ -262,20 +266,20 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
}
/**
- * Computes the closest euclidean distance between any two points of this component and the
+ * Computes the closest Euclidean distance between any two points of this component and the
* given component
*
* @param component the component to compute the distance to
* @return double
*/
- public double distanceTo(ConnectedComponent component) {
+ public double distanceTo(final ConnectedComponent component) {
double distance = Double.MAX_VALUE;
- for (Point3i srcPt : this) {
- Vector3d srcV = new Vector3d(srcPt.x, srcPt.y, srcPt.z);
- for (Point3i dstPt : component) {
- Vector3d dstV = new Vector3d(dstPt.x, dstPt.y, dstPt.z);
+ for (final Point3i srcPt : this) {
+ final Vector3d srcV = new Vector3d(srcPt.x, srcPt.y, srcPt.z);
+ for (final Point3i dstPt : component) {
+ final Vector3d dstV = new Vector3d(dstPt.x, dstPt.y, dstPt.z);
dstV.sub(srcV);
- double length = dstV.length();
+ final double length = dstV.length();
if (length < distance)
distance = length;
}
@@ -297,27 +301,28 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* Computes the major axis of the object, which is the vector between the two most distant
* points of this component. Note that the result vector orientation is meaningless if the
* component is spherical.<br>
- * NOTE: this is an potentially expensive operation: O(N log N)
+ * NOTE: this is a potentially expensive operation: O(N log N)
*
* @return 3D Vector
*/
public Vector3d getMajorAxis() {
double maxDist = 0;
- Vector3d vector = new Vector3d();
- Point3d pid = new Point3d(), pjd = new Point3d();
+ final Vector3d vector = new Vector3d();
+ final Point3d pid = new Point3d();
+ final Point3d pjd = new Point3d();
- int n = points.size();
+ final int n = points.size();
for (int i = 0; i < n - 1; i++) {
- Point3i pi = points.get(i);
+ final Point3i pi = points.get(i);
pid.set(pi.x, pi.y, pi.z);
for (int j = i + 1; j < n; j++) {
- Point3i pj = points.get(j);
+ final Point3i pj = points.get(j);
pjd.set(pj.x, pj.y, pj.z);
// compare the squared distance to save the square root operation
- double dist = pid.distanceSquared(pjd);
+ final double dist = pid.distanceSquared(pjd);
if (dist > maxDist) {
maxDist = dist;
@@ -330,7 +335,7 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
}
void updateDetectionCoords() {
- double factor = 1.0 / getSize();
+ final double factor = 1.0 / getSize();
x = coordsSum.x * factor;
y = coordsSum.y * factor;
z = coordsSum.z * factor;
@@ -382,11 +387,11 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @param point 3D Point
* @return double
*/
- public double getMaxDistanceTo(Point3d point) {
+ public double getMaxDistanceTo(final Point3d point) {
double maxDist = 0;
- for (Point3i p : this) {
- double dist = point.distance(new Point3d(p.x, p.y, p.z));
+ for (final Point3i p : this) {
+ final double dist = point.distance(new Point3d(p.x, p.y, p.z));
if (dist > maxDist)
maxDist = dist;
}
@@ -414,18 +419,19 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @param outputSequence (set to null if not wanted) an output sequence to receive the extracted contour
* @return An array containing all the contour pixels of this component
*/
- public Point3i[] getContourPoints(Sequence outputSequence) {
+ public Point3i[] getContourPoints(final Sequence outputSequence) {
if (contourPoints == null) {
- ArrayList<Point3i> list = new ArrayList<>(getSize() / 2);
+ final ArrayList<Point3i> list = new ArrayList<>(getSize() / 2);
- Point3i min = new Point3i(), max = new Point3i();
+ final Point3i min = new Point3i();
+ final Point3i max = new Point3i();
shapeDescriptor.computeBoundingBox(this, min, max);
- Sequence mask = toSequence();
+ final Sequence mask = toSequence();
final boolean outputVolatile;
- int w = mask.getSizeX();
- int h = mask.getSizeY();
- int d = mask.getSizeZ();
+ final int w = mask.getSizeX();
+ final int h = mask.getSizeY();
+ final int d = mask.getSizeZ();
byte[][] outputMask = null;
@@ -443,16 +449,16 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
else
outputVolatile = false;
- byte[][] mask_z_xy = mask.getDataXYZAsByte(0, 0);
+ final byte[][] mask_z_xy = mask.getDataXYZAsByte(0, 0);
- Point3i localP = new Point3i();
+ final Point3i localP = new Point3i();
if (min.z != max.z) {
mainLoop:
- for (Point3i p : points) {
+ for (final Point3i p : points) {
localP.sub(p, min);
- int xy = localP.y * w + localP.x;
+ final int xy = localP.y * w + localP.x;
if (localP.x == 0 || localP.y == 0 || localP.x == w - 1 || localP.y == h - 1 || localP.z == 0
|| localP.z == d - 1) {
@@ -462,7 +468,7 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
continue;
}
- for (byte[] z : new byte[][]{mask_z_xy[localP.z - 1], mask_z_xy[localP.z],
+ for (final byte[] z : new byte[][]{mask_z_xy[localP.z - 1], mask_z_xy[localP.z],
mask_z_xy[localP.z + 1]})
if (z[xy - w] == 0 || z[xy - 1] == 0 || z[xy + 1] == 0 || z[xy + w] == 0 || z[xy - w - 1] == 0
|| z[xy - w + 1] == 0 || z[xy + w - 1] == 0 || z[xy + w + 1] == 0) {
@@ -479,10 +485,10 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
}
}
else {
- for (Point3i p : points) {
+ for (final Point3i p : points) {
localP.sub(p, min);
- int xy = localP.y * w + localP.x;
+ final int xy = localP.y * w + localP.x;
if (localP.x == 0 || localP.y == 0 || localP.x == w - 1 || localP.y == h - 1) {
list.add(p);
@@ -491,7 +497,7 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
continue;
}
- byte[] z = mask_z_xy[localP.z];
+ final byte[] z = mask_z_xy[localP.z];
if (z[xy - w] == 0 || z[xy - 1] == 0 || z[xy + 1] == 0 || z[xy + w] == 0)
// || z[xy - w - 1] == 0
@@ -510,7 +516,7 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
if ((outputSequence != null) && outputVolatile)
outputSequence.setVolatile(true);
- contourPoints = list.toArray(new Point3i[list.size()]);
+ contourPoints = list.toArray(new Point3i[0]);
}
return contourPoints;
@@ -521,12 +527,12 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @return true if this component intersects (e.g. has at least one voxel overlapping with) the
* specified component
*/
- public boolean intersects(ConnectedComponent component) {
- int thisSize = getSize();
- int componentSize = component.getSize();
+ public boolean intersects(final ConnectedComponent component) {
+ final int thisSize = getSize();
+ final int componentSize = component.getSize();
- Point3i thisPt = new Point3i();
- Point3i componentPt = new Point3i();
+ final Point3i thisPt = new Point3i();
+ final Point3i componentPt = new Point3i();
for (int i = 0; i < thisSize; i++) {
thisPt.set(points.get(i));
@@ -546,12 +552,12 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @param component ConnectedComponent
* @return ConnectedComponent
*/
- public ConnectedComponent intersection(ConnectedComponent component) {
- ConnectedComponent intersection = new ConnectedComponent(0);
+ public ConnectedComponent intersection(final ConnectedComponent component) {
+ final ConnectedComponent intersection = new ConnectedComponent(0);
// construct the intersection
- for (Point3i srcPt : this)
- for (Point3i dstPt : component) {
+ for (final Point3i srcPt : this)
+ for (final Point3i dstPt : component) {
if (srcPt.equals(dstPt)) {
intersection.addPointInternal(srcPt);
break;
@@ -574,23 +580,23 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @param c int
* @param value double
*/
- public void paintOnSequence(Sequence s, int t, int c, double value) throws InterruptedException {
+ public void paintOnSequence(final Sequence s, final int t, final int c, final double value) throws InterruptedException {
DataIteratorUtil.set(new SequenceDataIterator(s, toROI(), true, -1, t, c), value);
}
- public void setC(int c) {
+ public void setC(final int c) {
this.c = c;
}
/**
- * @return a region of interest of type area representing this connected component
+ * @return a ROI of type area representing this connected component
*/
public ROI toROI() {
int z = 0;
- ROI3DArea area3D = new ROI3DArea();
+ final ROI3DArea area3D = new ROI3DArea();
area3D.beginUpdate();
- for (Point3i pt : this) {
+ for (final Point3i pt : this) {
z = pt.z;
area3D.addPoint(pt.x, pt.y, pt.z);
}
@@ -601,7 +607,7 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
return area3D;
// if there is only a single slice, z will tell us
- ROI2DArea area2D = area3D.getSlice(z);
+ final ROI2DArea area2D = area3D.getSlice(z);
area2D.setZ(z);
return area2D;
@@ -614,33 +620,35 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @return Sequence
*/
public Sequence toSequence() {
- Sequence seq = new Sequence();
+ final Sequence seq = new Sequence();
// get the bounding box first
- Point3i start = new Point3i(), end = new Point3i();
+ final Point3i start = new Point3i();
+ final Point3i end = new Point3i();
- computeBoundingBox(start, end);
+ shapeDescriptor.computeBoundingBox(this, start, end);
// initialize the sequence
- int depth = 1 + end.z - start.z;
- int height = 1 + end.y - start.y;
- int width = 1 + end.x - start.x;
+ final int depth = 1 + end.z - start.z;
+ final int height = 1 + end.y - start.y;
+ final int width = 1 + end.x - start.x;
for (int z = 0; z < depth; z++)
seq.setImage(0, z, new IcyBufferedImage(width, height, 1, DataType.UBYTE));
// force non volatile
- boolean v = seq.isVolatile();
+ final boolean v = seq.isVolatile();
seq.setVolatile(false);
try {
// fill up the created sequence
- byte[][] z_xy = seq.getDataXYZAsByte(0, 0);
+ final byte[][] z_xy = seq.getDataXYZAsByte(0, 0);
- for (Point3i point : points)
+ for (final Point3i point : points)
z_xy[point.z - start.z][(point.y - start.y) * width + (point.x - start.x)] = (byte) 1;
- } finally {
+ }
+ finally {
// restore volatile state
seq.setVolatile(v);
}
diff --git a/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponentDescriptor.java b/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponentDescriptor.java
index 21b6d2aaa1f58f944c366b5b3acf02743a432e35..6c7a7fde7cf2bfed3917cbc817302d7245bd9537 100644
--- a/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponentDescriptor.java
+++ b/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponentDescriptor.java
@@ -1,15 +1,22 @@
-package plugins.adufour.connectedcomponents;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
+/*
+ * 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 javax.vecmath.Point2d;
-import javax.vecmath.Point3d;
-import javax.vecmath.Point3i;
-import javax.vecmath.SingularMatrixException;
-import javax.vecmath.Vector3d;
+package plugins.adufour.connectedcomponents;
import Jama.EigenvalueDecomposition;
import Jama.Matrix;
@@ -25,6 +32,12 @@ import plugins.adufour.quickhull.QuickHull3D;
import plugins.adufour.vars.lang.Var;
import plugins.adufour.vars.lang.VarDouble;
+import javax.vecmath.*;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
public class ConnectedComponentDescriptor extends Plugin implements PluginBundled, Block {
Var<ConnectedComponent> varCC = new Var<>("Connected component", ConnectedComponent.class);
@@ -46,12 +59,12 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
}
@Override
- public void declareInput(VarList inputMap) {
+ public void declareInput(final VarList inputMap) {
inputMap.add("component", varCC);
}
@Override
- public void declareOutput(VarList outputMap) {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("perimeter", perimeter);
outputMap.add("long diameter", longAxis);
outputMap.add("short diameter", shortAxis);
@@ -62,14 +75,14 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
@Override
public void run() {
- ConnectedComponent cc = varCC.getValue();
+ final ConnectedComponent cc = varCC.getValue();
if (cc == null)
return;
perimeter.setValue(computePerimeter(cc, null, null));
- double[] ellipseDimensions = computeEllipseDimensions(cc);
+ final double[] ellipseDimensions = computeEllipseDimensions(cc);
longAxis.setValue(ellipseDimensions[0] * 2);
shortAxis.setValue(ellipseDimensions[1] * 2);
@@ -83,12 +96,12 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* @return a triplet representing the radius of the best fitting ellipse (the third value is 0
* for 2D objects)
*/
- public double[] computeEllipseDimensions(ConnectedComponent cc) {
- double[] axes = new double[3];
+ public double[] computeEllipseDimensions(final ConnectedComponent cc) {
+ final double[] axes = new double[3];
try {
if (is2D(cc)) {
- Point2d radii = new Point2d();
+ final Point2d radii = new Point2d();
computeEllipse(cc, null, radii, null, null);
if (radii.x > radii.y) {
axes[0] = radii.x;
@@ -100,14 +113,14 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
}
}
else {
- Point3d radii = new Point3d();
+ final Point3d radii = new Point3d();
computeEllipse(cc, null, radii, null, null);
axes[0] = radii.x;
axes[1] = radii.y;
axes[2] = radii.z;
}
}
- catch (Exception e) {
+ catch (final Exception e) {
// Do nothing
}
@@ -121,7 +134,7 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* @param minBounds the first corner of the bounding box in X-Y-Z order (Upper-Left hand-Top)
* @param maxBounds the second corner of the bounding box in X-Y-Z order (Lower-Right hand-Bottom)
*/
- public void computeBoundingBox(ConnectedComponent cc, Point3i minBounds, Point3i maxBounds) {
+ public void computeBoundingBox(final ConnectedComponent cc, final Point3i minBounds, final Point3i maxBounds) {
if (minBounds != null) {
minBounds.x = Integer.MAX_VALUE;
minBounds.y = Integer.MAX_VALUE;
@@ -134,7 +147,7 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
maxBounds.z = 0;
}
- for (Point3i point : cc) {
+ for (final Point3i point : cc) {
if (minBounds != null) {
minBounds.x = Math.min(minBounds.x, point.x);
minBounds.y = Math.min(minBounds.y, point.y);
@@ -155,7 +168,7 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* @param bsCenter the computed center of the bounding sphere
* @param bsRadius the computed radius of the bounding sphere
*/
- public void computeBoundingSphere(ConnectedComponent cc, Point3d bsCenter, VarDouble bsRadius) {
+ public void computeBoundingSphere(final ConnectedComponent cc, final Point3d bsCenter, final VarDouble bsRadius) {
bsCenter.set(cc.getMassCenter());
bsRadius.setValue(cc.getMaxDistanceTo(bsCenter));
}
@@ -168,20 +181,21 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* extracted contour
* @return The 3D perimeter (or 3D surface) of this component
*/
- public double computePerimeter(ConnectedComponent cc, ArrayList<Point3i> contourPoints, Sequence outputSequence) {
+ public double computePerimeter(final ConnectedComponent cc, final ArrayList<Point3i> contourPoints, final Sequence outputSequence) {
double perimeter = 0;
if (contourPoints != null)
contourPoints.ensureCapacity(cc.getSize() / 2);
- Point3i min = new Point3i(), max = new Point3i();
+ final Point3i min = new Point3i();
+ final Point3i max = new Point3i();
computeBoundingBox(cc, min, max);
- Sequence mask = cc.toSequence();
+ final Sequence mask = cc.toSequence();
final boolean outputVolatile;
- int w = mask.getSizeX();
- int h = mask.getSizeY();
- int d = mask.getSizeZ();
+ final int w = mask.getSizeX();
+ final int h = mask.getSizeY();
+ final int d = mask.getSizeZ();
byte[][] outputMask = null;
@@ -199,19 +213,19 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
else
outputVolatile = false;
- byte[][] mask_z_xy = mask.getDataXYZAsByte(0, 0);
+ final byte[][] mask_z_xy = mask.getDataXYZAsByte(0, 0);
- Point3i localP = new Point3i();
+ final Point3i localP = new Point3i();
// count the edges and corners in 2D/3D
double a = 0, b = 0;
- for (Point3i p : cc) {
+ for (final Point3i p : cc) {
localP.sub(p, min);
- int xy = localP.y * w + localP.x;
+ final int xy = localP.y * w + localP.x;
- byte[] z = mask_z_xy[localP.z];
+ final byte[] z = mask_z_xy[localP.z];
int nbEdges = 0;
@@ -277,11 +291,11 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* @param cc the input component
* @return 1 for a perfect circle (or sphere), and lower than 1 otherwise
*/
- public double computeSphericity(ConnectedComponent cc) {
- double dim = is2D(cc) ? 2.0 : 3.0;
+ public double computeSphericity(final ConnectedComponent cc) {
+ final double dim = is2D(cc) ? 2.0 : 3.0;
- double area = cc.getSize();
- double peri = computePerimeter(cc, null, null);
+ final double area = cc.getSize();
+ final double peri = computePerimeter(cc, null, null);
// some verification code
//
@@ -298,7 +312,7 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
//
// end of the verification code
- double sph = (Math.pow(Math.PI, 1.0 / dim) / peri) * Math.pow(area * dim * 2, (dim - 1) / dim);
+ final double sph = (Math.pow(Math.PI, 1.0 / dim) / peri) * Math.pow(area * dim * 2, (dim - 1) / dim);
// adjust final rounding off errors (sphericity is always below 1)
return Math.min(1.0, sph);
@@ -313,25 +327,25 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* @return the ratio b/a, where a and b are the two first largest ellipse radii (there are only
* two in 2D)
*/
- public double computeEccentricity(ConnectedComponent cc) {
+ public double computeEccentricity(final ConnectedComponent cc) {
if (is2D(cc)) {
try {
- Point2d radii = new Point2d();
+ final Point2d radii = new Point2d();
computeEllipse(cc, null, radii, null, null);
return radii.x / radii.y;
}
- catch (RuntimeException e) {
+ catch (final RuntimeException e) {
// error during the ellipse computation
return Double.NaN;
}
}
else {
- Point3d radii = new Point3d();
+ final Point3d radii = new Point3d();
try {
computeEllipse(cc, null, radii, null, null);
return radii.x / radii.y;
}
- catch (Exception e) {
+ catch (final Exception e) {
return Double.NaN;
}
}
@@ -342,8 +356,8 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* @return The hull ratio, measured as the ratio between the object volume and its convex hull
* (envelope)
*/
- public double computeHullRatio(ConnectedComponent cc) {
- double hull = computeConvexAreaAndVolume(cc)[1];
+ public double computeHullRatio(final ConnectedComponent cc) {
+ final double hull = computeConvexAreaAndVolume(cc)[1];
return hull == 0.0 ? 0.0 : Math.min(1.0, cc.getSize() / hull);
}
@@ -354,8 +368,9 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* object. The 2 values are returned together because their computation is simultaneous
* (in the 3D case only)
*/
- public double[] computeConvexAreaAndVolume(ConnectedComponent cc) {
- int i = 0, n = cc.getSize();
+ public double[] computeConvexAreaAndVolume(final ConnectedComponent cc) {
+ int i = 0;
+ final int n = cc.getSize();
if (n == 1)
return new double[]{0.0, 1.0};
@@ -365,7 +380,7 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
if (is2D(cc)) {
List<Point2D> points = new ArrayList<>();
- for (Point3i p : cc)
+ for (final Point3i p : cc)
points.add(new Point2D.Double(p.x, p.y));
if (points.size() > 4)
@@ -387,23 +402,23 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
}
else
try {
- Point3d[] points = new Point3d[n];
+ final Point3d[] points = new Point3d[n];
- for (Point3i p : cc)
+ for (final Point3i p : cc)
points[i++] = new Point3d(p.x, p.y, p.z);
- QuickHull3D qhull = new QuickHull3D(points);
- int[][] hullFaces = qhull.getFaces();
- Point3d[] hullPoints = qhull.getVertices();
+ final QuickHull3D qhull = new QuickHull3D(points);
+ final int[][] hullFaces = qhull.getFaces();
+ final Point3d[] hullPoints = qhull.getVertices();
- Vector3d v12 = new Vector3d();
- Vector3d v13 = new Vector3d();
- Vector3d cross = new Vector3d();
+ final Vector3d v12 = new Vector3d();
+ final Vector3d v13 = new Vector3d();
+ final Vector3d cross = new Vector3d();
- for (int[] face : hullFaces) {
- Point3d p1 = hullPoints[face[0]];
- Point3d p2 = hullPoints[face[1]];
- Point3d p3 = hullPoints[face[2]];
+ for (final int[] face : hullFaces) {
+ final Point3d p1 = hullPoints[face[0]];
+ final Point3d p2 = hullPoints[face[1]];
+ final Point3d p3 = hullPoints[face[2]];
v12.sub(p2, p1);
v13.sub(p3, p1);
@@ -415,7 +430,7 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
area += contour * cross.x * (p1.x + p2.x + p3.x);
}
}
- catch (IllegalArgumentException e) {
+ catch (final IllegalArgumentException e) {
// less than 4 points, or coplanarity detected
return new double[]{n, n};
}
@@ -432,17 +447,17 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* @param r the moment order along Z (set to 0 if the object is 2D)
* @return the geometric moment
*/
- public double computeGeometricMoment(ConnectedComponent cc, int p, int q, int r) {
+ public double computeGeometricMoment(final ConnectedComponent cc, final int p, final int q, final int r) {
double moment = 0;
- Point3d center = cc.getMassCenter();
+ final Point3d center = cc.getMassCenter();
if (is2D(cc)) {
- for (Point3i point : cc)
+ for (final Point3i point : cc)
moment += Math.pow(point.x - center.x, p) * Math.pow(point.y - center.y, q);
}
else {
- for (Point3i point : cc)
+ for (final Point3i point : cc)
moment += Math.pow(point.x - center.x, p) * Math.pow(point.y - center.y, q)
* Math.pow(point.z - center.z, r);
}
@@ -461,22 +476,22 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* @param equation (set to null if not wanted) an array of size 9 containing the calculated ellipsoid
* equation
* @throws IllegalArgumentException if the number of points in the component is too low (minimum is 9)
- * @throws SingularMatrixException if the component is flat (i.e. lies in a 2D plane)
+ * @throws SingularMatrixException if the component is flat (i.e., lies in a 2D plane)
*/
- public void computeEllipse(ConnectedComponent cc, Point3d center, Point3d radii, Vector3d[] eigenVectors,
- double[] equation) throws IllegalArgumentException {
- int nPoints = cc.getSize();
+ public void computeEllipse(final ConnectedComponent cc, final Point3d center, final Point3d radii, final Vector3d[] eigenVectors,
+ final double[] equation) throws IllegalArgumentException {
+ final int nPoints = cc.getSize();
if (nPoints < 9) {
throw new IllegalArgumentException("Too few points; need at least 9 to calculate a unique ellipsoid");
}
- Point3i[] points = cc.getPoints();
+ final Point3i[] points = cc.getPoints();
- double[][] d = new double[nPoints][9];
+ final double[][] d = new double[nPoints][9];
for (int i = 0; i < nPoints; i++) {
- double x = points[i].x;
- double y = points[i].y;
- double z = points[i].z;
+ final double x = points[i].x;
+ final double y = points[i].y;
+ final double z = points[i].z;
d[i][0] = (x * x);
d[i][1] = (y * y);
d[i][2] = (z * z);
@@ -488,32 +503,32 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
d[i][8] = (2.0D * z);
}
- Matrix D = new Matrix(d);
- Matrix ones = ones(nPoints, 1);
+ final Matrix D = new Matrix(d);
+ final Matrix ones = ones(nPoints, 1);
- Matrix V;
+ final Matrix V;
try {
V = D.transpose().times(D).inverse().times(D.transpose().times(ones));
}
- catch (RuntimeException e) {
+ catch (final RuntimeException e) {
throw new SingularMatrixException("The component is most probably flat (i.e. lies in a 2D plane)");
}
- double[] v = V.getColumnPackedCopy();
+ final double[] v = V.getColumnPackedCopy();
- double[][] a = {{v[0], v[3], v[4], v[6]}, {v[3], v[1], v[5], v[7]}, {v[4], v[5], v[2], v[8]},
+ final double[][] a = {{v[0], v[3], v[4], v[6]}, {v[3], v[1], v[5], v[7]}, {v[4], v[5], v[2], v[8]},
{v[6], v[7], v[8], -1.0D}};
- Matrix A = new Matrix(a);
- Matrix C = A.getMatrix(0, 2, 0, 2).times(-1.0D).inverse().times(V.getMatrix(6, 8, 0, 0));
- Matrix T = Matrix.identity(4, 4);
+ final Matrix A = new Matrix(a);
+ final Matrix C = A.getMatrix(0, 2, 0, 2).times(-1.0D).inverse().times(V.getMatrix(6, 8, 0, 0));
+ final Matrix T = Matrix.identity(4, 4);
T.setMatrix(3, 3, 0, 2, C.transpose());
- Matrix R = T.times(A.times(T.transpose()));
- double r33 = R.get(3, 3);
- Matrix R02 = R.getMatrix(0, 2, 0, 2);
- EigenvalueDecomposition E = new EigenvalueDecomposition(R02.times(-1.0D / r33));
- Matrix eVal = E.getD();
- Matrix eVec = E.getV();
- Matrix diagonal = diag(eVal);
+ final Matrix R = T.times(A.times(T.transpose()));
+ final double r33 = R.get(3, 3);
+ final Matrix R02 = R.getMatrix(0, 2, 0, 2);
+ final EigenvalueDecomposition E = new EigenvalueDecomposition(R02.times(-1.0D / r33));
+ final Matrix eVal = E.getD();
+ final Matrix eVec = E.getV();
+ final Matrix diagonal = diag(eVal);
if (radii != null)
radii.set(Math.sqrt(1.0D / diagonal.get(0, 0)), Math.sqrt(1.0D / diagonal.get(1, 0)),
@@ -543,15 +558,15 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* calculated algebraic parameters of the fitting ellipse: <i>ax</i><sup>2</sup> + 2
* <i>bxy</i> + <i>cy</i><sup>2</sup> +2<i>dx</i> + 2<i>fy</i> + <i>g</i> = 0. The
* vector <b>A</b> represented in the array is normed, so that ||<b>A</b>||=1.
- * @throws RuntimeException if the ellipse calculation fails (e.g. if a singular matrix is detected)
+ * @throws RuntimeException if the ellipse calculation fails (e.g., if a singular matrix is detected)
*/
- public void computeEllipse(ConnectedComponent cc, Point2d center, Point2d radii, VarDouble angle, double[] equation)
+ public void computeEllipse(final ConnectedComponent cc, final Point2d center, final Point2d radii, final VarDouble angle, final double[] equation)
throws RuntimeException {
- Point3i[] points = cc.getPoints();
- Point3d ccenter = cc.getMassCenter();
+ final Point3i[] points = cc.getPoints();
+ final Point3d ccenter = cc.getMassCenter();
- double[][] d1 = new double[cc.getSize()][3];
- double[][] d2 = new double[cc.getSize()][3];
+ final double[][] d1 = new double[cc.getSize()][3];
+ final double[][] d2 = new double[cc.getSize()][3];
for (int i = 0; i < d1.length; i++) {
final double xixC = points[i].x - ccenter.x;
@@ -566,33 +581,33 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
d2[i][2] = 1;
}
- Matrix D1 = new Matrix(d1);
- Matrix D2 = new Matrix(d2);
+ final Matrix D1 = new Matrix(d1);
+ final Matrix D2 = new Matrix(d2);
- Matrix S1 = D1.transpose().times(D1);
+ final Matrix S1 = D1.transpose().times(D1);
- Matrix S2 = D1.transpose().times(D2);
+ final Matrix S2 = D1.transpose().times(D2);
- Matrix S3 = D2.transpose().times(D2);
+ final Matrix S3 = D2.transpose().times(D2);
- Matrix T = (S3.inverse().times(-1)).times(S2.transpose());
+ final Matrix T = (S3.inverse().times(-1)).times(S2.transpose());
- Matrix M = S1.plus(S2.times(T));
+ final Matrix M = S1.plus(S2.times(T));
- double[][] m = M.getArray();
- double[][] n = {{m[2][0] / 2, m[2][1] / 2, m[2][2] / 2}, {-m[1][0], -m[1][1], -m[1][2]},
+ final double[][] m = M.getArray();
+ final double[][] n = {{m[2][0] / 2, m[2][1] / 2, m[2][2] / 2}, {-m[1][0], -m[1][1], -m[1][2]},
{m[0][0] / 2, m[0][1] / 2, m[0][2] / 2}};
- Matrix N = new Matrix(n);
+ final Matrix N = new Matrix(n);
- EigenvalueDecomposition E = N.eig();
- Matrix eVec = E.getV();
+ final EigenvalueDecomposition E = N.eig();
+ final Matrix eVec = E.getV();
- Matrix R1 = eVec.getMatrix(0, 0, 0, 2);
- Matrix R2 = eVec.getMatrix(1, 1, 0, 2);
- Matrix R3 = eVec.getMatrix(2, 2, 0, 2);
+ final Matrix R1 = eVec.getMatrix(0, 0, 0, 2);
+ final Matrix R2 = eVec.getMatrix(1, 1, 0, 2);
+ final Matrix R3 = eVec.getMatrix(2, 2, 0, 2);
- Matrix cond = (R1.times(4)).arrayTimes(R3).minus(R2.arrayTimes(R2));
+ final Matrix cond = (R1.times(4)).arrayTimes(R3).minus(R2.arrayTimes(R2));
int _f = 0;
for (int i = 0; i < 3; i++) {
@@ -601,16 +616,16 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
break;
}
}
- Matrix A1 = eVec.getMatrix(0, 2, _f, _f);
+ final Matrix A1 = eVec.getMatrix(0, 2, _f, _f);
Matrix A = new Matrix(6, 1);
A.setMatrix(0, 2, 0, 0, A1);
A.setMatrix(3, 5, 0, 0, T.times(A1));
double[] ell = A.getColumnPackedCopy();
- double a4 = ell[3] - 2 * ell[0] * ccenter.x - ell[1] * ccenter.y;
- double a5 = ell[4] - 2 * ell[2] * ccenter.y - ell[1] * ccenter.x;
- double a6 = ell[5] + ell[0] * ccenter.x * ccenter.x + ell[2] * ccenter.y * ccenter.y
+ final double a4 = ell[3] - 2 * ell[0] * ccenter.x - ell[1] * ccenter.y;
+ final double a5 = ell[4] - 2 * ell[2] * ccenter.y - ell[1] * ccenter.x;
+ final double a6 = ell[5] + ell[0] * ccenter.x * ccenter.x + ell[2] * ccenter.y * ccenter.y
+ ell[1] * ccenter.x * ccenter.y - ell[3] * ccenter.x - ell[4] * ccenter.y;
A.set(3, 0, a4);
A.set(4, 0, a5);
@@ -669,26 +684,26 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
angle.setValue(phi);
}
- public boolean is2D(ConnectedComponent cc) {
- Point3i minBB = new Point3i();
- Point3i maxBB = new Point3i();
+ public boolean is2D(final ConnectedComponent cc) {
+ final Point3i minBB = new Point3i();
+ final Point3i maxBB = new Point3i();
computeBoundingBox(cc, minBB, maxBB);
return minBB.z == maxBB.z;
}
- private Matrix diag(Matrix matrix) {
- int min = Math.min(matrix.getRowDimension(), matrix.getColumnDimension());
- double[][] diag = new double[min][1];
+ private Matrix diag(final Matrix matrix) {
+ final int min = Math.min(matrix.getRowDimension(), matrix.getColumnDimension());
+ final double[][] diag = new double[min][1];
for (int i = 0; i < min; i++) {
diag[i][0] = matrix.get(i, i);
}
return new Matrix(diag);
}
- private Matrix ones(int m, int n) {
- double[][] array = new double[m][n];
- for (double[] row : array)
+ private Matrix ones(final int m, final int n) {
+ final double[][] array = new double[m][n];
+ for (final double[] row : array)
Arrays.fill(row, 1.0);
return new Matrix(array, m, n);
}
diff --git a/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponents.java b/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponents.java
index cc010e02f83e48fd49ad57dd26a145412bad063a..baa1be66e19d65f8cec8b8421c9d65bfbd72f340 100644
--- a/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponents.java
+++ b/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponents.java
@@ -1,3 +1,21 @@
+/*
+ * 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/>.
+ */
+
package plugins.adufour.connectedcomponents;
import java.io.File;
@@ -97,7 +115,7 @@ public class ConnectedComponents extends EzPlug implements Block {
*/
public final Comparator<ConnectedComponent> comparator;
- Sorting(Comparator<ConnectedComponent> comparator) {
+ Sorting(final Comparator<ConnectedComponent> comparator) {
this.comparator = comparator;
}
}
@@ -141,7 +159,7 @@ public class ConnectedComponents extends EzPlug implements Block {
addEzComponent(input);
input.addVarChangeListener((source, newValue) -> {
if (newValue != null) {
- boolean doZ = newValue.getSizeZ() > 1;
+ final boolean doZ = newValue.getSizeZ() > 1;
discardEdgesZ.setValue(doZ);
discardEdgesZ.setVisible(doZ);
}
@@ -192,7 +210,7 @@ public class ConnectedComponents extends EzPlug implements Block {
}
@Override
- public void declareInput(VarList inputMap) {
+ public void declareInput(final VarList inputMap) {
inputMap.add("input", input.getVariable());
inputMap.add("method", extractionMethod.getVariable());
inputMap.add("value", background.getVariable());
@@ -207,7 +225,7 @@ public class ConnectedComponents extends EzPlug implements Block {
}
@Override
- public void declareOutput(VarList outputMap) {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("labeled sequence", outputSequence);
outputMap.add("objects", outputCCs);
outputMap.add("list of extracted ROI", outputROIs);
@@ -215,34 +233,34 @@ public class ConnectedComponents extends EzPlug implements Block {
@Override
protected void execute() {
- ArrayList<ConnectedComponent> componentsList = new ArrayList<>();
- Map<Integer, List<ConnectedComponent>> componentsMap;
+ final ArrayList<ConnectedComponent> componentsList = new ArrayList<>();
+ final Map<Integer, List<ConnectedComponent>> componentsMap;
- int min = boundSize.getValue() ? minSize.getValue() : 0;
- int max = boundSize.getValue() ? maxSize.getValue() : Integer.MAX_VALUE;
+ final int min = boundSize.getValue() ? minSize.getValue() : 0;
+ final int max = boundSize.getValue() ? maxSize.getValue() : Integer.MAX_VALUE;
- Sequence output = new Sequence();
+ final Sequence output = new Sequence();
- Sequence inputSequence = input.getValue(true);
+ final Sequence inputSequence = input.getValue(true);
if (inputSequence.getSizeT() == 0)
throw new VarException(input.getVariable(), "Cannot extract connected components from an emtpy sequence !");
// never remove objects touching the Z edge in 2D (that would remove... everything!)
- boolean discardEdgesAlongZ = (inputSequence.getSizeZ() > 1 && discardEdgesZ.getValue());
+ final boolean discardEdgesAlongZ = (inputSequence.getSizeZ() > 1 && discardEdgesZ.getValue());
try {
if (extractionMethod.getValue() == ExtractionType.ROI) {
- int width = inputSequence.getWidth();
- int height = inputSequence.getHeight();
+ final int width = inputSequence.getWidth();
+ final int height = inputSequence.getHeight();
//Sequence labeledSequence = new Sequence(inputSequence.getMetadata());
- Sequence labeledSequence = new Sequence(inputSequence.getOMEXMLMetadata());
+ final Sequence labeledSequence = new Sequence(inputSequence.getOMEXMLMetadata());
for (int t = 0; t < inputSequence.getSizeT(); t++)
for (int z = 0; z < inputSequence.getSizeZ(); z++)
labeledSequence.setImage(t, z, new IcyBufferedImage(width, height, 1, DataType.USHORT));
short cpt = 1;
- for (ROI roi : inputSequence.getROIs())
+ for (final ROI roi : inputSequence.getROIs())
DataIteratorUtil.set(new SequenceDataIterator(labeledSequence, roi, true), cpt++ & 0xffff);
componentsMap = extractConnectedComponents(labeledSequence, 0, ExtractionType.BACKGROUND_LABELED,
@@ -254,7 +272,7 @@ public class ConnectedComponents extends EzPlug implements Block {
discardEdgesAlongZ, min, max, output);
}
}
- catch (InterruptedException e) {
+ catch (final InterruptedException e) {
new FailedAnnounceFrame(e.getMessage());
return;
}
@@ -262,7 +280,7 @@ public class ConnectedComponents extends EzPlug implements Block {
outputSequence.setValue(output);
int nbObjects = 0;
- for (List<ConnectedComponent> ccs : componentsMap.values()) {
+ for (final List<ConnectedComponent> ccs : componentsMap.values()) {
nbObjects += ccs.size();
componentsList.addAll(ccs);
}
@@ -280,58 +298,58 @@ public class ConnectedComponents extends EzPlug implements Block {
}
if (exportSwPool.getValue()) {
- DetectionResult result = convertToDetectionResult(componentsMap, input.getValue());
- SwimmingObject object = new SwimmingObject(result, "Set of " + nbObjects + " connected components");
+ final DetectionResult result = convertToDetectionResult(componentsMap, input.getValue());
+ final SwimmingObject object = new SwimmingObject(result, "Set of " + nbObjects + " connected components");
Icy.getMainInterface().getSwimmingPool().add(object);
}
if (exportROI.getValue() || outputROIs.isReferenced()) {
if (output.getSizeZ() > 1) {
- ArrayList<ROI3DArea> rois = new ArrayList<>(componentsMap.size());
+ final ArrayList<ROI3DArea> rois = new ArrayList<>(componentsMap.size());
int ccID = 1;
- for (List<ConnectedComponent> ccs : componentsMap.values())
- for (ConnectedComponent cc : ccs) {
- ROI3DArea area = new ROI3DArea();
+ for (final List<ConnectedComponent> ccs : componentsMap.values())
+ for (final ConnectedComponent cc : ccs) {
+ final ROI3DArea area = new ROI3DArea();
area.setName("Object #" + ccID++);
area.beginUpdate();
- for (Point3i pt : cc)
+ for (final Point3i pt : cc)
area.addPoint(pt.x, pt.y, pt.z);
area.setT(cc.getT());
area.endUpdate();
rois.add(area);
}
- outputROIs.setValue(rois.toArray(new ROI3DArea[rois.size()]));
+ outputROIs.setValue(rois.toArray(new ROI3DArea[0]));
}
else {
- ArrayList<ROI2DArea> rois = new ArrayList<>(componentsMap.size());
+ final ArrayList<ROI2DArea> rois = new ArrayList<>(componentsMap.size());
- for (List<ConnectedComponent> ccs : componentsMap.values())
- for (ConnectedComponent cc : ccs) {
- ROI2DArea area = new ROI2DArea();
+ for (final List<ConnectedComponent> ccs : componentsMap.values())
+ for (final ConnectedComponent cc : ccs) {
+ final ROI2DArea area = new ROI2DArea();
area.beginUpdate();
- for (Point3i pt : cc)
+ for (final Point3i pt : cc)
area.addPoint(pt.x, pt.y);
area.setT(cc.getT());
area.endUpdate();
rois.add(area);
}
- outputROIs.setValue(rois.toArray(new ROI2DArea[rois.size()]));
+ outputROIs.setValue(rois.toArray(new ROI2DArea[0]));
}
if (exportROI.getValue()) {
// replace all ROI on the input by the new ones
- Sequence in = input.getValue();
+ final Sequence in = input.getValue();
in.beginUpdate();
- for (ROI roi : input.getValue().getROIs())
+ for (final ROI roi : input.getValue().getROIs())
in.removeROI(roi);
- for (ROI roi : outputROIs.getValue())
+ for (final ROI roi : outputROIs.getValue())
in.addROI(roi);
in.endUpdate();
@@ -342,7 +360,7 @@ public class ConnectedComponents extends EzPlug implements Block {
int page = 1;
WritableSheet sheet;
- WritableWorkbook workbook;
+ final WritableWorkbook workbook;
try {
File f = exportExcelFile.getValue(true);
@@ -351,14 +369,14 @@ public class ConnectedComponents extends EzPlug implements Block {
workbook = XLSUtil.createWorkbook(f);
sheet = XLSUtil.createNewPage(workbook, "Page " + page);
}
- catch (Exception e) {
+ catch (final Exception e) {
throw new IcyHandledException(e.getMessage());
}
- Sequence s = input.getValue();
- Point4d resolution = new Point4d(s.getPixelSizeX(), s.getPixelSizeY(), s.getPixelSizeZ(),
+ final Sequence s = input.getValue();
+ final Point4d resolution = new Point4d(s.getPixelSizeX(), s.getPixelSizeY(), s.getPixelSizeZ(),
s.getTimeInterval());
- double voxelSize = resolution.x * resolution.y * resolution.z;
+ final double voxelSize = resolution.x * resolution.y * resolution.z;
String res = "Sequence resolution:";
res += " X=" + StringUtil.toStringEx(resolution.x, 5);
res += ", Y=" + StringUtil.toStringEx(resolution.y, 5);
@@ -397,12 +415,12 @@ public class ConnectedComponents extends EzPlug implements Block {
XLSUtil.setCellString(sheet, 27, 1, "convex perimeter");
XLSUtil.setCellString(sheet, 28, 1, "convex volume");
- ConnectedComponentDescriptor shapeDescriptor = new ConnectedComponentDescriptor();
+ final ConnectedComponentDescriptor shapeDescriptor = new ConnectedComponentDescriptor();
int cpt = 2;
- for (Integer time : componentsMap.keySet())
- for (ConnectedComponent cc : componentsMap.get(time)) {
- boolean is2D = shapeDescriptor.is2D(cc);
- Point3d center = cc.getMassCenter();
+ for (final Integer time : componentsMap.keySet())
+ for (final ConnectedComponent cc : componentsMap.get(time)) {
+ final boolean is2D = shapeDescriptor.is2D(cc);
+ final Point3d center = cc.getMassCenter();
center.x *= resolution.x;
center.y *= resolution.y;
center.z *= resolution.z;
@@ -414,13 +432,13 @@ public class ConnectedComponents extends EzPlug implements Block {
XLSUtil.setCellNumber(sheet, 5, cpt, shapeDescriptor.computePerimeter(cc, null, null));
XLSUtil.setCellNumber(sheet, 6, cpt, cc.getSize() * voxelSize);
XLSUtil.setCellNumber(sheet, 7, cpt, shapeDescriptor.computeSphericity(cc));
- double[] radiuses = shapeDescriptor.computeEllipseDimensions(cc);
+ final double[] radiuses = shapeDescriptor.computeEllipseDimensions(cc);
XLSUtil.setCellNumber(sheet, 8, cpt, radiuses[0]);
XLSUtil.setCellNumber(sheet, 9, cpt, radiuses[1]);
XLSUtil.setCellNumber(sheet, 10, cpt, radiuses[2]);
XLSUtil.setCellNumber(sheet, 11, cpt, shapeDescriptor.computeEccentricity(cc));
- double[] contour_area = shapeDescriptor.computeConvexAreaAndVolume(cc);
+ final double[] contour_area = shapeDescriptor.computeConvexAreaAndVolume(cc);
XLSUtil.setCellNumber(sheet, 12, cpt, contour_area[1] == 0.0 ? 0.0 : Math.min(1.0, cc.getSize() / contour_area[1]));
XLSUtil.setCellNumber(sheet, 13, cpt, shapeDescriptor.computeGeometricMoment(cc, 1, 0, 0));
XLSUtil.setCellNumber(sheet, 14, cpt, shapeDescriptor.computeGeometricMoment(cc, 0, 1, 0));
@@ -469,7 +487,7 @@ public class ConnectedComponents extends EzPlug implements Block {
try {
XLSUtil.saveAndClose(workbook);
}
- catch (Exception e) {
+ catch (final Exception e) {
throw new IcyHandledException(e.getMessage());
}
}
@@ -504,10 +522,10 @@ public class ConnectedComponents extends EzPlug implements Block {
* Creates a new label with the given value. If no parent is set to this label, the given
* value will be the final one
*
- * @param value the pixel value
- * @param label the label value
+ * @param value the pixel value
+ * @param label the label value
*/
- Label(double value, int label) {
+ Label(final double value, final int label) {
this.imageValue = value;
this.targetLabelValue = label;
}
@@ -532,7 +550,7 @@ public class ConnectedComponents extends EzPlug implements Block {
* @see ExtractionType
* @see ConnectedComponent
*/
- public static Map<Integer, List<ConnectedComponent>> extractConnectedComponents(Sequence inputSequence, Sequence labeledSequence) {
+ public static Map<Integer, List<ConnectedComponent>> extractConnectedComponents(final Sequence inputSequence, final Sequence labeledSequence) {
return extractConnectedComponents(inputSequence, false, 0, Integer.MAX_VALUE, labeledSequence);
}
@@ -550,7 +568,7 @@ public class ConnectedComponents extends EzPlug implements Block {
* @see ExtractionType
* @see ConnectedComponent
*/
- public static Map<Integer, List<ConnectedComponent>> extractConnectedComponents(Sequence inputSequence, int minSize, int maxSize, Sequence labeledSequence) {
+ public static Map<Integer, List<ConnectedComponent>> extractConnectedComponents(final Sequence inputSequence, final int minSize, final int maxSize, final Sequence labeledSequence) {
return extractConnectedComponents(inputSequence, false, minSize, maxSize, labeledSequence);
}
@@ -569,7 +587,7 @@ public class ConnectedComponents extends EzPlug implements Block {
* @see ExtractionType
* @see ConnectedComponent
*/
- public static Map<Integer, List<ConnectedComponent>> extractConnectedComponents(Sequence inputSequence, boolean isInputLabeled, int minSize, int maxSize, Sequence labeledSequence) {
+ public static Map<Integer, List<ConnectedComponent>> extractConnectedComponents(final Sequence inputSequence, final boolean isInputLabeled, final int minSize, final int maxSize, final Sequence labeledSequence) {
return extractConnectedComponents(inputSequence, 0,
isInputLabeled ? ExtractionType.BACKGROUND_LABELED : ExtractionType.BACKGROUND, minSize, maxSize,
labeledSequence);
@@ -591,7 +609,7 @@ public class ConnectedComponents extends EzPlug implements Block {
* @see ExtractionType
* @see ConnectedComponent
*/
- public static Map<Integer, List<ConnectedComponent>> extractConnectedComponents(Sequence inputSequence, double value, ExtractionType type, int minSize, int maxSize, Sequence labeledSequence) {
+ public static Map<Integer, List<ConnectedComponent>> extractConnectedComponents(final Sequence inputSequence, final double value, final ExtractionType type, final int minSize, final int maxSize, final Sequence labeledSequence) {
return extractConnectedComponents(inputSequence, value, type, false, false, false, minSize, maxSize, labeledSequence);
}
@@ -618,31 +636,31 @@ public class ConnectedComponents extends EzPlug implements Block {
* @see ConnectedComponent
*/
public static Map<Integer, List<ConnectedComponent>> extractConnectedComponents(
- Sequence inputSequence, double value, ExtractionType type, boolean noEdgeX, boolean noEdgeY, boolean noEdgeZ, int minSize, int maxSize, Sequence labeledSequence
+ final Sequence inputSequence, final double value, final ExtractionType type, final boolean noEdgeX, final boolean noEdgeY, final boolean noEdgeZ, final int minSize, final int maxSize, Sequence labeledSequence
) {
if (inputSequence == null || inputSequence.getSizeT() == 0)
throw new IllegalArgumentException("Cannot extract connected components from an empty sequence !");
- int width = inputSequence.getSizeX();
- int height = inputSequence.getSizeY();
+ final int width = inputSequence.getSizeX();
+ final int height = inputSequence.getSizeY();
if (labeledSequence == null)
labeledSequence = new Sequence();
- Map<Integer, List<ConnectedComponent>> componentsMap = new TreeMap<>();
+ final Map<Integer, List<ConnectedComponent>> componentsMap = new TreeMap<>();
for (int t = 0; t < inputSequence.getSizeT(); t++) {
for (int z = 0; z < inputSequence.getSizeZ(); z++)
labeledSequence.setImage(t, z, new IcyBufferedImage(width, height, 1, DataType.UINT));
- VolumetricImage volIN = inputSequence.getVolumetricImage(t);
- VolumetricImage volOUT = labeledSequence.getVolumetricImage(t);
+ final VolumetricImage volIN = inputSequence.getVolumetricImage(t);
+ final VolumetricImage volOUT = labeledSequence.getVolumetricImage(t);
- List<ConnectedComponent> components = extractConnectedComponents(volIN, value, type, noEdgeX, noEdgeY,
+ final List<ConnectedComponent> components = extractConnectedComponents(volIN, value, type, noEdgeX, noEdgeY,
noEdgeZ, minSize, maxSize, volOUT);
// int cpt=1;
- for (ConnectedComponent cc : components) {
+ for (final ConnectedComponent cc : components) {
cc.setT(t);
// System.out.println(t + "\t" + cpt++ + "\t" + (int)cc.getMassCenter().x + "\t" +
// (int)cc.getMassCenter().y);
@@ -679,7 +697,7 @@ public class ConnectedComponents extends EzPlug implements Block {
* @see ConnectedComponent
*/
public static List<ConnectedComponent> extractConnectedComponents(
- VolumetricImage stack, double value, ExtractionType type, boolean noEdgeX, boolean noEdgeY, boolean noEdgeZ, int minSize, int maxSize
+ final VolumetricImage stack, final double value, final ExtractionType type, final boolean noEdgeX, final boolean noEdgeY, final boolean noEdgeZ, final int minSize, final int maxSize
) {
return extractConnectedComponents(stack, value, type, noEdgeX, noEdgeY, noEdgeZ, minSize, maxSize, new VolumetricImage());
}
@@ -710,18 +728,18 @@ public class ConnectedComponents extends EzPlug implements Block {
* @see ConnectedComponent
*/
public static List<ConnectedComponent> extractConnectedComponents(
- VolumetricImage stack, double value, ExtractionType type, boolean noEdgeX, boolean noEdgeY, boolean noEdgeZ, int minSize, int maxSize, final VolumetricImage labeledStack
+ final VolumetricImage stack, final double value, final ExtractionType type, final boolean noEdgeX, final boolean noEdgeY, final boolean noEdgeZ, final int minSize, final int maxSize, final VolumetricImage labeledStack
) throws NullPointerException {
- int width = stack.getFirstImage().getSizeX();
- int height = stack.getFirstImage().getSizeY();
- int depth = stack.getSize();
+ final int width = stack.getFirstImage().getSizeX();
+ final int height = stack.getFirstImage().getSizeY();
+ final int depth = stack.getSize();
- int[] neighborLabelValues = new int[13];
+ final int[] neighborLabelValues = new int[13];
int neighborhoodSize = 0;
- boolean extractUserValue = (type == ExtractionType.VALUE);
+ final boolean extractUserValue = (type == ExtractionType.VALUE);
- Label[] labels = new Label[width * height * depth];
+ final Label[] labels = new Label[width * height * depth];
// first image pass: naive labeling with simple backward neighborhood
@@ -736,14 +754,14 @@ public class ConnectedComponents extends EzPlug implements Block {
final IcyBufferedImage currentSliceImage = labeledStack.getImage(z);
// retrieve the direct pointer to the current slice
- int[] _labelsInCurrentSlice = currentSliceImage.getDataXYAsInt(0);
+ final int[] _labelsInCurrentSlice = currentSliceImage.getDataXYAsInt(0);
// retrieve a direct pointer to the previous slice
- int[] _labelsInUpperSlice = (z == 0) ? null : labeledStack.getImage(z - 1).getDataXYAsInt(0);
+ final int[] _labelsInUpperSlice = (z == 0) ? null : labeledStack.getImage(z - 1).getDataXYAsInt(0);
int voxelOffset = 0;
- Object inputData = stack.getImage(z).getDataXY(0);
- DataType dataType = stack.getImage(z).getDataType_();
+ final Object inputData = stack.getImage(z).getDataXY(0);
+ final DataType dataType = stack.getImage(z).getDataType_();
for (int y = 0; y < height; y++) {
onEdgeY = (y == 0 || y == height - 1);
@@ -751,9 +769,9 @@ public class ConnectedComponents extends EzPlug implements Block {
for (int x = 0; x < width; x++, voxelOffset++) {
onEdgeX = (x == 0 || x == width - 1);
- double pixelValue = Array1DUtil.getValue(inputData, voxelOffset, dataType);
+ final double pixelValue = Array1DUtil.getValue(inputData, voxelOffset, dataType);
- boolean pixelEqualsUserValue = (pixelValue == value);
+ final boolean pixelEqualsUserValue = (pixelValue == value);
// do not process the current pixel if:
// - extractUserValue is true and pixelEqualsUserValue is false
@@ -794,7 +812,7 @@ public class ConnectedComponents extends EzPlug implements Block {
}
}
else {
- int north = voxelOffset - width;
+ final int north = voxelOffset - width;
if (x == 0) {
// e n n
@@ -830,7 +848,7 @@ public class ConnectedComponents extends EzPlug implements Block {
}
else {
if (y == 0) {
- int south = voxelOffset + width;
+ final int south = voxelOffset + width;
if (x == 0) {
// e e e | e e e
@@ -871,7 +889,7 @@ public class ConnectedComponents extends EzPlug implements Block {
}
}
else if (y == height - 1) {
- int north = voxelOffset - width;
+ final int north = voxelOffset - width;
if (x == 0) {
// e n n | e n n
@@ -919,8 +937,8 @@ public class ConnectedComponents extends EzPlug implements Block {
}
}
else {
- int north = voxelOffset - width;
- int south = voxelOffset + width;
+ final int north = voxelOffset - width;
+ final int south = voxelOffset + width;
if (x == 0) {
// e n n | e n n
@@ -938,8 +956,8 @@ public class ConnectedComponents extends EzPlug implements Block {
neighborhoodSize = 8;
}
else if (x == width - 1) {
- int northwest = north - 1;
- int west = voxelOffset - 1;
+ final int northwest = north - 1;
+ final int west = voxelOffset - 1;
// n n e | n n e
// n n e | n x e
@@ -957,11 +975,11 @@ public class ConnectedComponents extends EzPlug implements Block {
neighborhoodSize = 9;
}
else {
- int northwest = north - 1;
- int west = voxelOffset - 1;
- int northeast = north + 1;
- int southwest = south - 1;
- int southeast = south + 1;
+ final int northwest = north - 1;
+ final int west = voxelOffset - 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 .
@@ -994,7 +1012,7 @@ public class ConnectedComponents extends EzPlug implements Block {
// and assign that minimum label right now
for (int i = 0; i < neighborhoodSize; i++) {
- int neighborLabelValue = neighborLabelValues[i];
+ final int neighborLabelValue = neighborLabelValues[i];
// zero labels are not interesting...
if (neighborLabelValue == 0)
@@ -1027,19 +1045,19 @@ public class ConnectedComponents extends EzPlug implements Block {
// -> change their value to currentVoxelLabelValue
// -> change their target to currentVoxelLabel
- Label currentVoxelLabel = labels[currentVoxelLabelValue];
+ final Label currentVoxelLabel = labels[currentVoxelLabelValue];
for (int i = 0; i < neighborhoodSize; i++) {
- int neighborLabelValue = neighborLabelValues[i];
+ final int neighborLabelValue = neighborLabelValues[i];
if (neighborLabelValue > currentVoxelLabelValue) {
- Label label = labels[neighborLabelValue];
+ final Label label = labels[neighborLabelValue];
if (type == ExtractionType.BACKGROUND_LABELED && label.imageValue != pixelValue)
continue;
- int finalLabelValue = label.getFinalLabelValue();
- Label finalLabel = labels[finalLabelValue];
+ final int finalLabelValue = label.getFinalLabelValue();
+ final Label finalLabel = labels[finalLabelValue];
if (currentVoxelLabel.targetLabelValue == finalLabelValue)
continue;
@@ -1072,7 +1090,7 @@ public class ConnectedComponents extends EzPlug implements Block {
// end of the first pass, all pixels have a label
// (though might not be unique within a given component)
- HashMap<Integer, ConnectedComponent> componentsMap = new HashMap<>();
+ final HashMap<Integer, ConnectedComponent> componentsMap = new HashMap<>();
// fusion strategy: fuse higher labels with lower ones
// "highestKnownLabel" holds the highest known label
@@ -1081,14 +1099,14 @@ public class ConnectedComponents extends EzPlug implements Block {
int finalLabel = 0;
for (int labelValue = highestKnownLabel; labelValue > 0; labelValue--) {
- Label label = labels[labelValue];
+ final Label label = labels[labelValue];
- int targetLabelValue = label.targetLabelValue;
+ final int targetLabelValue = label.targetLabelValue;
if (targetLabelValue < labelValue) {
// label should be fused to targetLabel
- Label targetLabel = labels[targetLabelValue];
+ final Label targetLabel = labels[targetLabelValue];
// -> add label's size to targetLabel
targetLabel.size += label.size;
@@ -1126,7 +1144,7 @@ public class ConnectedComponents extends EzPlug implements Block {
// -> add this label to the list of valid labels
- ConnectedComponent component = new ConnectedComponent(label.size);
+ final ConnectedComponent component = new ConnectedComponent(label.size);
component.onEdgeX = label.onEdgeX;
component.onEdgeY = label.onEdgeY;
component.onEdgeZ = label.onEdgeZ;
@@ -1139,7 +1157,7 @@ public class ConnectedComponents extends EzPlug implements Block {
for (int z = 0; z < depth; z++) {
final IcyBufferedImage sliceImage = labeledStack.getImage(z);
- int[] _outputSlice = sliceImage.getDataXYAsInt(0);
+ final int[] _outputSlice = sliceImage.getDataXYAsInt(0);
int pixelOffset = 0;
@@ -1171,13 +1189,13 @@ public class ConnectedComponents extends EzPlug implements Block {
return new ArrayList<>(componentsMap.values());
}
- public static DetectionResult convertToDetectionResult(Map<Integer, List<ConnectedComponent>> detections, Sequence sequence) {
+ public static DetectionResult convertToDetectionResult(final Map<Integer, List<ConnectedComponent>> detections, final Sequence sequence) {
- DetectionResult detectionResult = new DetectionResult();
- for (Integer t : detections.keySet())
- for (ConnectedComponent cc : detections.get(t)) {
+ final DetectionResult detectionResult = new DetectionResult();
+ for (final Integer t : detections.keySet())
+ for (final ConnectedComponent cc : detections.get(t)) {
// TODO: add points information
- Spot spot = new Spot(cc.getMassCenter().x, cc.getMassCenter().y, cc.getMassCenter().z);
+ final Spot spot = new Spot(cc.getMassCenter().x, cc.getMassCenter().y, cc.getMassCenter().z);
detectionResult.addDetection(t, spot);
}
@@ -1194,37 +1212,38 @@ public class ConnectedComponents extends EzPlug implements Block {
* @param components Map of List of ConnectedComponent
* @param comparator Comparator of ConnectedComponents
*/
- public static void createLabeledSequence(Sequence output, Map<Integer, List<ConnectedComponent>> components, Comparator<ConnectedComponent> comparator) {
+ public static void createLabeledSequence(final Sequence output, final Map<Integer, List<ConnectedComponent>> components, final Comparator<ConnectedComponent> comparator) {
if (comparator == null)
return;
- int width = output.getSizeX();
- int[] ids = new int[output.getSizeC()];
+ final int width = output.getSizeX();
+ final int[] ids = new int[output.getSizeC()];
Arrays.fill(ids, 1);
- for (Integer t : components.keySet()) {
+ for (final Integer t : components.keySet()) {
for (int c = 0; c < output.getSizeC(); c++) {
// retrieve all objects in that channel
- ArrayList<ConnectedComponent> cComponents = new ArrayList<>();
- for (ConnectedComponent cc : components.get(t)) {
+ final ArrayList<ConnectedComponent> cComponents = new ArrayList<>();
+ for (final ConnectedComponent cc : components.get(t)) {
if (cc.getC() == -1 || cc.getC() == c)
cComponents.add(cc);
}
- ConnectedComponent[] ccs = cComponents.toArray(new ConnectedComponent[cComponents.size()]);
+ final ConnectedComponent[] ccs = cComponents.toArray(new ConnectedComponent[0]);
Arrays.sort(ccs, comparator);
final boolean outputVolatile = output.isVolatile();
try {
- int[][] data = output.getDataXYZAsInt(t, c);
+ final int[][] data = output.getDataXYZAsInt(t, c);
- for (ConnectedComponent cc : ccs) {
- for (Point3i pt : cc) {
+ for (final ConnectedComponent cc : ccs) {
+ for (final Point3i pt : cc) {
data[pt.z][pt.y * width + pt.x] = ids[c];
}
ids[c]++;
}
- } finally {
+ }
+ finally {
// restore back volatile state
output.setVolatile(outputVolatile);
}