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Commit 3146a90b authored by Jean-Yves TINEVEZ's avatar Jean-Yves TINEVEZ
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Fix javadoc errors.

parent 752903eb
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Showing with 454 additions and 431 deletions
src/main/java/plugins/adufour/roi/mesh/MeshTopologyException.java
View file @ 3146a90b
......@@ -4,11 +4,12 @@ import plugins.adufour.roi.mesh.polygon.ROI3DTriangularMesh;
/**
* Exception that occurs when the topology of a {@link ROI3DMesh} is inconsistent. A typical example
* is when a {@link ROI3DTriangularMesh} is splitting as a result of a resampling operation, giving
* rise to two new meshes.
* Exception that occurs when the topology of a {@link ROI3DMesh} is
* inconsistent. A typical example is when a {@link ROI3DTriangularMesh} is
* splitting as a result of a resampling operation, giving rise to two new
* meshes.
*
* @see ROI3DTriangularMesh#reSampleToAverageDistance(double, double)
* @see ROI3DTriangularMesh#resample(double, double)
* @author Alexandre Dufour
*/
public class MeshTopologyException extends Exception
......@@ -29,7 +30,7 @@ public class MeshTopologyException extends Exception
* the exception (typically when a mesh vanishes or splits as a result of a
* resampling operation)
*/
public <C extends Cell3D> MeshTopologyException(ROI3DMesh<C> contour, ROI3DMesh<C>[] children)
public <C extends Cell3D> MeshTopologyException(final ROI3DMesh<C> contour, final ROI3DMesh<C>[] children)
{
super("Topology break detected in contour " + contour.hashCode());
this.source = contour;
......
src/main/java/plugins/adufour/roi/mesh/polygon/ROI3DTriangularMesh.java
View file @ 3146a90b
......@@ -17,19 +17,23 @@ import plugins.adufour.roi.mesh.MeshTopologyException;
import plugins.adufour.roi.mesh.Vertex3D;
/**
* Special implementation of {@link ROI3DPolygonalMesh} where the surface is exclusively formed of
* triangular faces, providing additional methods to maintain a constant surface sampling, as
* described in the following publication: <i>Dufour et al., 3D active meshes: fast discrete
* deformable models for cell tracking in 3D time-lapse microscopy. IEEE Transactions on Image
* Processing 20, 2011</i> <br/>
* <br/>
* Example of a polygonal mesh formed exclusively of triangles (quoted from <a
* href="http://en.wikipedia.org/wiki/Polygon_mesh">Wikipedia</a>):<br/>
* <br/>
* <img width="250"
* src="http://upload.wikimedia.org/wikipedia/commons/f/fb/Dolphin_triangle_mesh.png"/> <br/>
* Special implementation of {@link ROI3DPolygonalMesh} where the surface is
* exclusively formed of triangular faces, providing additional methods to
* maintain a constant surface sampling, as described in the following
* publication: <i>Dufour et al., 3D active meshes: fast discrete deformable
* models for cell tracking in 3D time-lapse microscopy. IEEE Transactions on
* Image Processing 20, 2011</i>
* <p>
* Example of a polygonal mesh formed exclusively of triangles (quoted from
* <a href="http://en.wikipedia.org/wiki/Polygon_mesh">Wikipedia</a>):
* <p>
* <img width="250" src=
* "http://upload.wikimedia.org/wikipedia/commons/f/fb/Dolphin_triangle_mesh.png"
* alt="">
* <p>
*
* @see <a href="http://en.wikipedia.org/wiki/Polygon_mesh">Polygon mesh (Wikipedia)</a>
* @see <a href="http://en.wikipedia.org/wiki/Polygon_mesh">Polygon mesh
* (Wikipedia)</a>
* @author Alexandre Dufour
*/
public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
......@@ -52,7 +56,7 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
* @param roi
* the region of interest around which the mesh should be created
*/
public ROI3DTriangularMesh(double sampling, ROI3D roi)
public ROI3DTriangularMesh(final double sampling, final ROI3D roi)
{
if (roi instanceof ROI3DTriangularMesh)
{
......@@ -76,7 +80,7 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
loadFromQuickHull(qh3);
}
catch (Exception e)
catch (final Exception e)
{
vertices.clear();
cells.clear();
......@@ -91,7 +95,7 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
// finish with a proper sampling
resample(sampling, 0.4);
}
catch (MeshTopologyException e)
catch (final MeshTopologyException e)
{
// just ignore here (resampling failed, not a big issue)
System.err.println("Warning: couldn't resample initial contour:");
......@@ -112,28 +116,28 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
roiChanged(true);
}
private void setIcosahedron(Rectangle3D bounds, double sampling)
private void setIcosahedron(final Rectangle3D bounds, final double sampling)
{
// start from a regular icosahedron using the golden number PHI
// distance between any vertex pair: 2
// radius of the bounding sphere: PHI
// center of the icosahedron: origin
double PHI = (1.0 + Math.sqrt(5.0)) / 2.0;
final double PHI = (1.0 + Math.sqrt(5.0)) / 2.0;
// Declaration of the vertices
int zA = addVertex(createVertex(new Point3d(PHI, 1, 0)), false, false);
int zB = addVertex(createVertex(new Point3d(-PHI, 1, 0)), false, false);
int zC = addVertex(createVertex(new Point3d(-PHI, -1, 0)), false, false);
int zD = addVertex(createVertex(new Point3d(PHI, -1, 0)), false, false);
int yA = addVertex(createVertex(new Point3d(1, 0, PHI)), false, false);
int yB = addVertex(createVertex(new Point3d(1, 0, -PHI)), false, false);
int yC = addVertex(createVertex(new Point3d(-1, 0, -PHI)), false, false);
int yD = addVertex(createVertex(new Point3d(-1, 0, PHI)), false, false);
int xA = addVertex(createVertex(new Point3d(0, PHI, 1)), false, false);
int xB = addVertex(createVertex(new Point3d(0, -PHI, 1)), false, false);
int xC = addVertex(createVertex(new Point3d(0, -PHI, -1)), false, false);
int xD = addVertex(createVertex(new Point3d(0, PHI, -1)), false, false);
final int zA = addVertex(createVertex(new Point3d(PHI, 1, 0)), false, false);
final int zB = addVertex(createVertex(new Point3d(-PHI, 1, 0)), false, false);
final int zC = addVertex(createVertex(new Point3d(-PHI, -1, 0)), false, false);
final int zD = addVertex(createVertex(new Point3d(PHI, -1, 0)), false, false);
final int yA = addVertex(createVertex(new Point3d(1, 0, PHI)), false, false);
final int yB = addVertex(createVertex(new Point3d(1, 0, -PHI)), false, false);
final int yC = addVertex(createVertex(new Point3d(-1, 0, -PHI)), false, false);
final int yD = addVertex(createVertex(new Point3d(-1, 0, PHI)), false, false);
final int xA = addVertex(createVertex(new Point3d(0, PHI, 1)), false, false);
final int xB = addVertex(createVertex(new Point3d(0, -PHI, 1)), false, false);
final int xC = addVertex(createVertex(new Point3d(0, -PHI, -1)), false, false);
final int xD = addVertex(createVertex(new Point3d(0, PHI, -1)), false, false);
// Declaration of the faces
addCell(yA, xA, yD);
......@@ -169,16 +173,16 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
// double halfSizeX = (bounds.getSizeX() - 1) * pixelSize.x * 0.5;
// double halfSizeY = (bounds.getSizeY() - 1) * pixelSize.y * 0.5;
// double halfSizeZ = (bounds.getSizeZ() - 1) * pixelSize.z * 0.5;
double minX = bounds.getMinX();
double minY = bounds.getMinY();
double minZ = bounds.getMinZ();
double halfSizeX = (bounds.getSizeX() - 1) * 0.5;
double halfSizeY = (bounds.getSizeY() - 1) * 0.5;
double halfSizeZ = (bounds.getSizeZ() - 1) * 0.5;
final double minX = bounds.getMinX();
final double minY = bounds.getMinY();
final double minZ = bounds.getMinZ();
final double halfSizeX = (bounds.getSizeX() - 1) * 0.5;
final double halfSizeY = (bounds.getSizeY() - 1) * 0.5;
final double halfSizeZ = (bounds.getSizeZ() - 1) * 0.5;
Point3d center = new Point3d(minX + halfSizeX, minY + halfSizeY, minZ + halfSizeZ);
final Point3d center = new Point3d(minX + halfSizeX, minY + halfSizeY, minZ + halfSizeZ);
for (Vertex3D v : vertices)
for (final Vertex3D v : vertices)
{
// scale to the final size
v.position.x *= halfSizeX / PHI;
......@@ -206,7 +210,7 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
}
@Override
public Polygon3D createCell(int... vertexIndices)
public Polygon3D createCell(final int... vertexIndices)
{
if (vertexIndices.length != 3)
throw new IllegalArgumentException("A triangle must be defined by exactly 3 vertex indices");
......@@ -224,11 +228,11 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
* @param v2
* another of the vertices at the base of the tetrahedron
*/
private void deleteTetrahedron(int topVertex, int v1, int v2)
private void deleteTetrahedron(final int topVertex, final int v1, final int v2)
{
// find the third vertex at the base of the tetrahedron
int v3 = -1;
for (int n : vertices.get(topVertex).neighbors)
for (final int n : vertices.get(topVertex).neighbors)
{
if ((n != v1) && (n != v2))
v3 = n;
......@@ -250,8 +254,8 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
deleteVertex(topVertex);
}
private static void extractVertices(Integer seed, Set<Vertex3D> visitedVertices, List<Vertex3D> oldPoints,
List<Vertex3D> newPoints)
private static void extractVertices(final Integer seed, final Set<Vertex3D> visitedVertices, final List<Vertex3D> oldPoints,
final List<Vertex3D> newPoints)
{
final Stack<Integer> seeds = new Stack<Integer>();
......@@ -272,16 +276,16 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
newPoints.set(currentVertexIndex, currentVertex);
// add the neighbors to the list of seeds
for (int n : currentVertex.neighbors)
for (final int n : currentVertex.neighbors)
seeds.push(Integer.valueOf(n));
}
}
private static void extractFaces(List<Vertex3D> pointsList, List<Polygon3D> oldFaces, List<Polygon3D> newFaces)
private static void extractFaces(final List<Vertex3D> pointsList, final List<Polygon3D> oldFaces, final List<Polygon3D> newFaces)
{
for (Polygon3D face : oldFaces)
for (final Polygon3D face : oldFaces)
{
for (int i : face.vertexIndices)
for (final int i : face.vertexIndices)
{
if (pointsList.get(i) != null)
{
......@@ -308,7 +312,7 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
* @param v3
* @throws MeshTopologyException
*/
private void splitContourAtVertices(int v1, int v2, int v3) throws MeshTopologyException
private void splitContourAtVertices(final int v1, final int v2, final int v3) throws MeshTopologyException
{
List<Polygon3D> resultFaces = null;
List<Vertex3D> resultVertices = null;
......@@ -369,7 +373,7 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
// Fill the hole using the cutting face
// First, add the 3 vertices from the cut
for (int v : new int[] {v1, v2, v3})
for (final int v : new int[] {v1, v2, v3})
{
final Vertex3D newV = vertices.get(v).clone();
......@@ -392,7 +396,7 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
// Add the new face used for the cut
// => find any edge (e.g. v1-v2) to check its ordering
for (Polygon3D f : newFaces)
for (final Polygon3D f : newFaces)
{
if (f.contains(v1) && f.contains(v2))
{
......@@ -474,7 +478,7 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
// }
}
private ROI3DTriangularMesh buildMesh(List<Vertex3D> vertices, List<Polygon3D> faces)
private ROI3DTriangularMesh buildMesh(final List<Vertex3D> vertices, final List<Polygon3D> faces)
{
final ROI3DTriangularMesh result = new ROI3DTriangularMesh();
......@@ -498,19 +502,19 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
{
cells.clear();
for (Vertex3D v : vertices)
for (final Vertex3D v : vertices)
if (v != null)
v.neighbors.clear();
for (Polygon3D f : oldFaces)
for (final Polygon3D f : oldFaces)
{
int v1 = f.vertexIndices[0];
int v2 = f.vertexIndices[1];
int v3 = f.vertexIndices[2];
final int v1 = f.vertexIndices[0];
final int v2 = f.vertexIndices[1];
final int v3 = f.vertexIndices[2];
int centerv1v2 = addVertexBetween(v1, v2);
int centerv2v3 = addVertexBetween(v2, v3);
int centerv3v1 = addVertexBetween(v3, v1);
final int centerv1v2 = addVertexBetween(v1, v2);
final int centerv2v3 = addVertexBetween(v2, v3);
final int centerv3v1 = addVertexBetween(v3, v1);
addCell(v1, centerv1v2, centerv3v1);
addCell(centerv1v2, v2, centerv2v3);
......@@ -526,7 +530,7 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
roiChanged(true);
}
private int addVertexBetween(int v1, int v2)
private int addVertexBetween(final int v1, final int v2)
{
// Create the middle vertex using v1
final Point3d p = new Point3d(vertices.get(v1).position);
......@@ -549,7 +553,7 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
* @throws MeshTopologyException
* if the mesh becomes inconsistent (splitting or vanishing)
*/
public void resample(double distance, double tolerance) throws MeshTopologyException
public void resample(final double distance, final double tolerance) throws MeshTopologyException
{
// safeguard
if (tolerance < 0 || tolerance > 1)
......@@ -693,15 +697,15 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
System.err.println("[MESH RESAMPLING ERROR] Problematic edge: " + e1 + "-" + e2 + ":");
System.err.print(" Vertex " + f1v123[0] + " has neighbors: ");
for (Integer nn : getVertex(f1v123[0]).neighbors)
for (final Integer nn : getVertex(f1v123[0]).neighbors)
System.err.print(nn.intValue() + " ");
System.err.println();
System.err.print(" Vertex " + f1v123[1] + " has neighbors: ");
for (Integer nn : getVertex(f1v123[1]).neighbors)
for (final Integer nn : getVertex(f1v123[1]).neighbors)
System.err.print(nn.intValue() + " ");
System.err.println();
System.err.print(" Vertex " + f1v123[2] + " has neighbors: ");
for (Integer nn : getVertex(f1v123[2]).neighbors)
for (final Integer nn : getVertex(f1v123[2]).neighbors)
System.err.print(nn.intValue() + " ");
System.err.println();
......@@ -741,7 +745,7 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
// if v1 and v2 have a 3rd common neighbor n in addition to f1v3 and f2v3,
// then the mesh has reached a tubular structure.
// => split the mesh using the virtual face [v1,v2,n]
for (int n : v1.neighbors)
for (final int n : v1.neighbors)
{
if (v2.neighbors.contains(n) && (n != f1v3) && (n != f2v3))
{
......@@ -767,7 +771,7 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
v1.position.interpolate(v2.position, 0.5);
// 3) Remove v2 from its neighborhood...
for (int n : v2.neighbors)
for (final int n : v2.neighbors)
{
final Vertex3D vn = vertices.get(n);
......@@ -785,7 +789,7 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
// 4) All faces pointing to v2 should point to v1
// System.out.println("replaced vertex " + e2 + ":" + vertices.get(e2) + " by " + e1 + ":"
// + vertices.get(e1));
for (Polygon3D f : cells)
for (final Polygon3D f : cells)
f.replace(e2, e1);
// 5) delete the old vertex and notify its neighbors
......@@ -818,7 +822,7 @@ public class ROI3DTriangularMesh extends ROI3DPolygonalMesh
// SPLIT
// 3) create a vertex in the middle of the edge (it may be merged from an existing one)
int newV = addVertexBetween(e1, e2);
final int newV = addVertexBetween(e1, e2);
// System.out.println("added vertex " + newV);
......
src/main/java/plugins/adufour/roi/mesh/polyhedron/Polyhedron3D.java
View file @ 3146a90b
package plugins.adufour.roi.mesh.polyhedron;
import java.util.List;
import javax.vecmath.Point3d;
import plugins.adufour.roi.mesh.Cell3D;
import plugins.adufour.roi.mesh.ROI3DMesh;
import plugins.adufour.roi.mesh.Vertex3D;
import vtk.vtkCell3D;
/**
* Generic structural element of a {@link ROI3DPolyhedralMesh 3D polyhedral mesh}
* Generic structural element of a {@link ROI3DPolyhedralMesh}
*
* @see Tetrahedron3D
* @author Alexandre Dufour
......@@ -19,14 +12,16 @@ import vtk.vtkCell3D;
public abstract class Polyhedron3D extends Cell3D
{
/**
* Creates a new polygon from the specified vertex indices. This constructor is protected as it
* should not be used directly by client code. Client code should use
* {@link ROI3DPolyhedralMesh#createCell(int[])} instead
*
* @param vertexIndices
* the vertex indices, in an order allowed by the local convention
*/
protected Polyhedron3D(int... vertexIndices)
* Creates a new polygon from the specified vertex indices. This constructor
* is protected as it should not be used directly by client code. Client
* code should use
* {@link ROI3DPolyhedralMesh#createCell(vtk.CellType, int...)} instead
*
* @param vertexIndices
* the vertex indices, in an order allowed by the local
* convention
*/
protected Polyhedron3D(final int... vertexIndices)
{
super(vertexIndices);
}
......
src/main/java/plugins/adufour/roi/mesh/polyhedron/ROI3DPolyhedralMesh.java
View file @ 3146a90b
......@@ -25,13 +25,15 @@ import vtk.vtkUnstructuredGridReader;
import vtk.vtkXMLUnstructuredGridReader;
/**
* <h2>WARNING: Polyhedral meshes are still under development, do *not* use for production work!</h2>
* <br/>
* 3D <u>r</u>egion <u>o</u>f <u>i</u>nterest (ROI) defined as a polyhedral mesh (i.e. a connected
* set of 3D polyhedrons defining the interior of the ROI).<br/>
* <br/>
* This data structure is the dual of {@link ROI3DPolygonalMesh polygon meshes} which only defines
* the contour of the 3D ROI.
* <h2>WARNING: Polyhedral meshes are still under development, do *not* use for
* production work!</h2>
* <p>
* 3D <u>r</u>egion <u>o</u>f <u>i</u>nterest (ROI) defined as a polyhedral mesh
* (i.e. a connected set of 3D polyhedrons defining the interior of the ROI).
* <p>
* <p>
* This data structure is the dual of {@link ROI3DPolygonalMesh polygon meshes}
* which only defines the contour of the 3D ROI.
*
* @author Alexandre Dufour
*/
......@@ -81,7 +83,7 @@ public class ROI3DPolyhedralMesh extends ROI3DMesh<Polyhedron3D>
* </ul>
*/
@Override
public Polyhedron3D createCell(CellType type, int... vertexIndices)
public Polyhedron3D createCell(final CellType type, final int... vertexIndices)
{
if (type == CellType.POLYGON)
throw new IllegalArgumentException("Cannot create a polygon for a polyhedral mesh");
......@@ -101,7 +103,7 @@ public class ROI3DPolyhedralMesh extends ROI3DMesh<Polyhedron3D>
}
@Override
protected void updateVTKMesh(vtkPointSet vtkPointSet, Tuple3d pixelSize)
protected void updateVTKMesh(final vtkPointSet vtkPointSet, final Tuple3d pixelSize)
{
// we have vtkUnstructuredGrid here
final vtkUnstructuredGrid vtkGrid = (vtkUnstructuredGrid) vtkPointSet;
......@@ -173,13 +175,13 @@ public class ROI3DPolyhedralMesh extends ROI3DMesh<Polyhedron3D>
// }
@Override
public void loadFromVTK(File vtkFile, boolean useLegacyReader)
public void loadFromVTK(final File vtkFile, final boolean useLegacyReader)
{
final vtkUnstructuredGrid gridData;
if (useLegacyReader)
{
vtkUnstructuredGridReader legacyReader = new vtkUnstructuredGridReader();
final vtkUnstructuredGridReader legacyReader = new vtkUnstructuredGridReader();
legacyReader.SetFileName(vtkFile.getPath());
legacyReader.Update();
legacyReader.GetOutput();
......@@ -188,7 +190,7 @@ public class ROI3DPolyhedralMesh extends ROI3DMesh<Polyhedron3D>
}
else
{
vtkXMLUnstructuredGridReader reader = new vtkXMLUnstructuredGridReader();
final vtkXMLUnstructuredGridReader reader = new vtkXMLUnstructuredGridReader();
reader.SetFileName(vtkFile.getPath());
reader.Update();
gridData = reader.GetOutput();
......@@ -199,7 +201,7 @@ public class ROI3DPolyhedralMesh extends ROI3DMesh<Polyhedron3D>
}
@Override
protected void addVtkCell(vtkCell cell)
protected void addVtkCell(final vtkCell cell)
{
final CellType cellType = CellType.GetCellType(cell.GetCellType());
final vtkIdList ids = cell.GetPointIds();
......@@ -260,7 +262,7 @@ public class ROI3DPolyhedralMesh extends ROI3DMesh<Polyhedron3D>
// get mask from polydata (may fail if the polyData is too large)
binaryImage = VtkUtil.getBinaryImageData(polyData, null);
}
catch (Exception e)
catch (final Exception e)
{
// cleanup
polyData.Delete();
......
src/main/java/plugins/adufour/roi/mesh/polyhedron/Wedge3D.java
View file @ 3146a90b
......@@ -4,9 +4,9 @@ import vtk.vtkCell3D;
import vtk.vtkWedge;
/**
* Specialized implementation of a polyhedron in the form of a wedge (2 parallel polygons with equal
* number of points). <br/>
* <br/>
* Specialized implementation of a polyhedron in the form of a wedge (2 parallel
* polygons with equal number of points).
* <p>
* Vertex ordering convention: (A1, ..., An, B1, ..., Bn)
* <ul>
* <li>Each half of the index buffer describes one face of the wedge</li>
......@@ -18,7 +18,7 @@ import vtk.vtkWedge;
*/
public class Wedge3D extends Polyhedron3D
{
public Wedge3D(int... vertexIndices)
public Wedge3D(final int... vertexIndices)
{
super(vertexIndices);
......
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