Merge pull request #3 from tinevez/int-interface

Rename the triangles and vertices interface size() method to return an int.

src/main/java/net/imglib2/mesh/Meshes.java

@@ -69,7 +69,7 @@ public static RealPoint center( final Mesh m )
 			p.move( v );
 
 		for ( int d = 0; d < 3; d++ )
-			p.setPosition( p.getDoublePosition( d ) / m.vertices().size(), d );
+			p.setPosition( p.getDoublePosition( d ) / m.vertices().sizel(), d );
 
 		return p;
 	}
@@ -366,7 +366,7 @@ public static Iterable< BufferMesh > connectedComponents( final Mesh mesh )
 	public static void scale( final Mesh mesh, final double[] scale )
 	{
 		final Vertices vertices = mesh.vertices();
-		final long nVertices = vertices.size();
+		final long nVertices = vertices.sizel();
 		for ( long i = 0; i < nVertices; i++ )
 		{
 			final double x = vertices.x( i );

src/main/java/net/imglib2/mesh/alg/MeshConnectedComponents.java

@@ -18,7 +18,7 @@
 
 /**
  * Connected components algorithm for meshes.
- * 
+ *
  * @author Jean-Yves Tinevez
  *
  */
@@ -27,7 +27,7 @@ public class MeshConnectedComponents
 
 	/**
 	 * Returns the number of connected components in this mesh.
-	 * 
+	 *
 	 * @param mesh
 	 *            the mesh.
 	 * @return the number of connected components.
@@ -36,7 +36,7 @@ public static final int n( final Mesh mesh )
 	{
 		final Triangles triangles = mesh.triangles();
 		final Vertices vertices = mesh.vertices();
-		final int nVertices = ( int ) vertices.size();
+		final int nVertices = vertices.size();
 
 		final TIntObjectHashMap< TIntArrayList > map = triangleMap( mesh );
 		final BitSet visited = new BitSet( nVertices );
@@ -116,15 +116,15 @@ private static final boolean visit( final int v, final BitSet visited, final TIn
 
 	/**
 	 * Returns the map of vertex id to the list of triangles they belong to.
-	 * 
+	 *
 	 * @param mesh
 	 */
 	private static final TIntObjectHashMap< TIntArrayList > triangleMap( final Mesh mesh )
 	{
 		final Triangles triangles = mesh.triangles();
-		final int nTriangles = ( int ) triangles.size();
+		final int nTriangles = triangles.size();
 		final Vertices vertices = mesh.vertices();
-		final int nVertices = ( int ) vertices.size();
+		final int nVertices = vertices.size();
 
 		final TIntObjectHashMap< TIntArrayList > map = new TIntObjectHashMap<>( nVertices );
 		for ( int tid = 0; tid < nTriangles; tid++ )
@@ -166,7 +166,7 @@ public MyCCIterator( final Mesh mesh )
 		{
 			this.mesh = mesh;
 			this.map = triangleMap( mesh );
-			this.nVertices = ( int ) mesh.vertices().size();
+			this.nVertices = mesh.vertices().size();
 			this.visited = new BitSet( nVertices );
 			this.currentStartVertex = 0;
 			this.next = prefetch();

src/main/java/net/imglib2/mesh/alg/MeshCursor.java

@@ -217,7 +217,7 @@ public long getLongPosition( final int d )
 	@Override
 	public Cursor< T > copyCursor()
 	{
-		final BufferMesh dest = new BufferMesh( mesh.vertices().isize(), mesh.triangles().isize() );
+		final BufferMesh dest = new BufferMesh( mesh.vertices().size(), mesh.triangles().size() );
 		Meshes.copy( mesh, dest );
 		return new MeshCursor<>( ra.copyRandomAccess(), dest, cal.clone() );
 	}

src/main/java/net/imglib2/mesh/alg/RemoveDuplicateVertices.java

@@ -7,13 +7,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -47,7 +47,7 @@ public class RemoveDuplicateVertices
 	public static Mesh calculate( final Mesh mesh, final int precision )
 	{
 		final Map< String, IndexedVertex > vertices = new LinkedHashMap<>();
-		final int[][] triangles = new int[ ( int ) mesh.triangles().size() ][ 3 ];
+		final int[][] triangles = new int[ mesh.triangles().size() ][ 3 ];
 
 		int trianglesCount = 0;
 		for ( final net.imglib2.mesh.obj.Triangle triangle : mesh.triangles() )

src/main/java/net/imglib2/mesh/alg/SimplifyMesh.java

@@ -7,13 +7,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -237,7 +237,7 @@ private void readMesh()
 		vertices.clear();
 		refs.clear();
 
-		final Point[] meshVerts = new Point[ ( int ) inMesh.vertices().size() ];
+		final Point[] meshVerts = new Point[ inMesh.vertices().size() ];
 		final Iterator< net.imglib2.mesh.obj.Vertex > iterator = inMesh.vertices().iterator();
 		for ( int i = 0; i < inMesh.vertices().size(); i++ )
 		{
@@ -288,7 +288,7 @@ private void readMesh()
 	public Mesh simplify( final float target_percent, final double agressiveness )
 	{
 
-		final int target_count = ( int ) ( inMesh.triangles().size() * target_percent );
+		final int target_count = ( int ) ( inMesh.triangles().sizel() * target_percent );
 		return simplify( target_count, agressiveness );
 	}
 
@@ -315,7 +315,7 @@ private Mesh simplify( final int target_count, final double agressiveness )
 		 * System.out.println(String.format("Simplify Target: %d of %d (%d%%)",
 		 * target_count, triangles.size(), target_count * 100 /
 		 * triangles.size()));
-		 * 
+		 *
 		 * final long timeStart = System.currentTimeMillis();
 		 */
 
@@ -435,7 +435,7 @@ private Mesh simplify( final int target_count, final double agressiveness )
 		// ready
 		/*
 		 * long timeEnd = System.currentTimeMillis();
-		 * 
+		 *
 		 * System.out.println(String.
 		 * format("Simplify: %d/%d %d%% removed in %d ms", triangle_count -
 		 * deleted_triangles, triangle_count, deleted_triangles * 100 /

src/main/java/net/imglib2/mesh/alg/TaubinSmoothing.java

@@ -13,7 +13,7 @@
  * <p>
  * Adapted by the Javascript code of mykolalysenko, MIT license.
  * https://github.com/mikolalysenko/taubin-smooth/blob/master/smooth.js
- * 
+ *
  * @author Jean-Yves Tinevez
  * @see <a href="https://doi.org/10.1109/ICCV.1995.466848">Taubin, G. “Curve and
  *      Surface Smoothing without Shrinkage.” In Proceedings of IEEE
@@ -26,7 +26,7 @@ public class TaubinSmoothing
 	/**
 	 * Smooth the specified mesh using the Taubin smoothing algorithm, with
 	 * default parameters.
-	 * 
+	 *
 	 * @param mesh
 	 *            the mesh to smooth.
 	 * @return a new smoothed mesh.
@@ -39,7 +39,7 @@ public static final BufferMesh smooth( final Mesh mesh )
 	/**
 	 * Smooth the specified mesh using the Taubin smoothing algorithm, using
 	 * cotangent weights.
-	 * 
+	 *
 	 * @param mesh
 	 *            the mesh to smooth.
 	 * @param iters
@@ -66,7 +66,7 @@ public static final BufferMesh smooth( final Mesh mesh, final int iters, final d
 
 	/**
 	 * Smooth the specified mesh using the Taubin smoothing algorithm.
-	 * 
+	 *
 	 * @param mesh
 	 *            the mesh to smooth.
 	 * @param iters
@@ -85,8 +85,8 @@ public static final BufferMesh smooth( final Mesh mesh, final int iters, final d
 	public static final BufferMesh smooth( final Mesh mesh, final int iters, final double lambda, final double mu,
 			final TaubinWeightType weightType )
 	{
-		final int nvs = ( int ) mesh.vertices().size();
-		final int nts = ( int ) mesh.triangles().size();
+		final int nvs = mesh.vertices().size();
+		final int nts = mesh.triangles().size();
 		final BufferMesh meshA = new BufferMesh( nvs, nts );
 		Meshes.copy( mesh, meshA );
 		final BufferMesh meshB = new BufferMesh( nvs, nts );
@@ -114,7 +114,7 @@ public static final BufferMesh smooth( final Mesh mesh, final int iters, final d
 			throw new IllegalArgumentException( "Unhandled weight type: " + weightType );
 		}
 
-		final BufferMesh out = new BufferMesh( ( int ) meshA.vertices().size(), ( int ) meshA.triangles().size() );
+		final BufferMesh out = new BufferMesh( meshA.vertices().size(), meshA.triangles().size() );
 		Meshes.calculateNormals( meshA, out );
 		return out;
 	}
@@ -123,8 +123,8 @@ private static void smoothStepCotangent( final Triangles triangles, final Buffer
 			final double[] trace, final double weigth )
 	{
 
-		final int nvs = ( int ) source.vertices().size();
-		final int nts = ( int ) source.triangles().size();
+		final int nvs = source.vertices().size();
+		final int nts = source.triangles().size();
 
 		// Zero target.
 		for ( int i = 0; i < nvs; i++ )
@@ -205,8 +205,8 @@ private static void smoothStepNaive( final Triangles triangles, final BufferMesh
 			final double[] trace, final double weigth )
 	{
 
-		final int nvs = ( int ) source.vertices().size();
-		final int nts = ( int ) source.triangles().size();
+		final int nvs = source.vertices().size();
+		final int nts = source.triangles().size();
 
 		// Zero target.
 		for ( int i = 0; i < nvs; i++ )

src/main/java/net/imglib2/mesh/alg/zslicer/ZSlicer.java

@@ -67,8 +67,8 @@ public static List< Slice > slices( final Mesh mesh, final double[] zs, final do
 		final Triangles triangles = mesh.triangles();
 		final Vertices vertices = mesh.vertices();
 
-		final double[] minZs = new double[ ( int ) triangles.size() ];
-		final double[] maxZs = new double[ ( int ) triangles.size() ];
+		final double[] minZs = new double[ triangles.size() ];
+		final double[] maxZs = new double[ triangles.size() ];
 		for ( int t = 0; t < triangles.size(); t++ )
 		{
 			final long v0 = triangles.vertex0( t );
@@ -256,7 +256,7 @@ public static Slice slice( final Mesh mesh, final double z, final double zScale
 		final Vertices vertices = mesh.vertices();
 
 		final TIntArrayList intersecting = new TIntArrayList();
-		for ( long f = 0; f < triangles.size(); f++ )
+		for ( long f = 0; f < triangles.sizel(); f++ )
 		{
 			final long v0 = triangles.vertex0( f );
 			final long v1 = triangles.vertex1( f );

src/main/java/net/imglib2/mesh/io/ply/PLYMeshIO.java

@@ -224,17 +224,17 @@ public static final byte[] writeBinary( final Mesh mesh )
 				"format binary_little_endian 1.0\n" + //
 				"comment This binary PLY mesh was created with imagej-mesh.\n";
 		final String vertexHeader = "" + //
-				"element vertex " + mesh.vertices().size() + "\n" + //
+				"element vertex " + mesh.vertices().sizel() + "\n" + //
 				"property float x\nproperty float y\nproperty float z\n" + //
 				"property float nx\nproperty float ny\nproperty float nz\n" + //
 				"property float u\nproperty float v\n";
-		final String triangleHeader = "element face " + mesh.triangles().size()
+		final String triangleHeader = "element face " + mesh.triangles().sizel()
 				+ "\nproperty list uchar int vertex_index\n";
 		final String endHeader = "end_header\n";
 		final long bytes = header.getBytes().length + //
 				vertexHeader.getBytes().length + triangleHeader.getBytes().length + endHeader.getBytes().length
-				+ mesh.vertices().size() * vertexBytes + //
-				mesh.triangles().size() * triangleBytes;
+				+ mesh.vertices().sizel() * vertexBytes + //
+				mesh.triangles().sizel() * triangleBytes;
 		if ( bytes > Integer.MAX_VALUE )
 			throw new IllegalArgumentException( "Mesh data too large: " + bytes );
 
@@ -246,12 +246,12 @@ public static final byte[] writeBinary( final Mesh mesh )
 		buffer.put( endHeader.getBytes() );
 
 		// Do not populate file if there are no vertices
-		if ( mesh.vertices().size() == 0 )
+		if ( mesh.vertices().sizel() == 0 )
 			return buffer.array();
 
 		// Write vertices
 		final TLongIntHashMap refToVertId = //
-				new TLongIntHashMap( ( int ) mesh.vertices().size() );
+				new TLongIntHashMap( mesh.vertices().size() );
 		int vertId = 0;
 		for ( final Vertex v : mesh.vertices() )
 		{
@@ -282,21 +282,21 @@ public static final byte[] writeBinary( final Mesh mesh )
 	public static final byte[] writeAscii( final Mesh mesh ) throws IOException
 	{
 		final String header = "ply\nformat ascii 1.0\ncomment This binary PLY mesh was created with imagej-mesh.\n";
-		final String vertexHeader = "element vertex " + mesh.vertices().size()
+		final String vertexHeader = "element vertex " + mesh.vertices().sizel()
 				+ "\nproperty float x\nproperty float y\nproperty float z\nproperty float nx\nproperty float ny\nproperty float nz\nproperty float u\n property float v\n";
-		final String triangleHeader = "element face " + mesh.triangles().size()
+		final String triangleHeader = "element face " + mesh.triangles().sizel()
 				+ "\nproperty list uchar int vertex_index\n";
 		final String endHeader = "end_header\n";
 
 		// TODO: Fail fast more robustly if mesh is too large.
 		// But need to modify the API to not return a byte[].
-		if ( mesh.vertices().size() > Integer.MAX_VALUE )
+		if ( mesh.vertices().sizel() > Integer.MAX_VALUE )
 			throw new IllegalArgumentException( "Too many vertices: " + //
-					mesh.vertices().size() );
+					mesh.vertices().sizel() );
 
-		if ( mesh.triangles().size() > Integer.MAX_VALUE )
+		if ( mesh.triangles().sizel() > Integer.MAX_VALUE )
 			throw new IllegalArgumentException( "Too many triangles: " + //
-					mesh.triangles().size() );
+					mesh.triangles().sizel() );
 
 		final ByteArrayOutputStream os = new ByteArrayOutputStream();
 
@@ -308,14 +308,14 @@ public static final byte[] writeAscii( final Mesh mesh ) throws IOException
 		writer.write( endHeader );
 
 		// Do not populate file if there are no vertices
-		if ( mesh.vertices().size() == 0 )
+		if ( mesh.vertices().sizel() == 0 )
 		{
 			writer.flush();
 			return os.toByteArray();
 		}
 
 		// Write vertices
-		final TLongIntHashMap refToVertId = new TLongIntHashMap( ( int ) mesh.vertices().size() );
+		final TLongIntHashMap refToVertId = new TLongIntHashMap( mesh.vertices().size() );
 		int vertId = 0;
 		for ( final Vertex v : mesh.vertices() )
 		{

src/main/java/net/imglib2/mesh/io/stl/STLMeshIO.java

@@ -88,7 +88,7 @@ public static final void read( final Mesh mesh, final byte[] data )
 	/** Writes the facets into a byte[] that can then be saved into a file */
 	public static final byte[] write( final Mesh mesh )
 	{
-		final long facetCount = mesh == null ? 0 : mesh.triangles().size();
+		final long facetCount = mesh == null ? 0 : mesh.triangles().sizel();
 		final long longBytes = HEADER_BYTES + COUNT_BYTES + facetCount * FACET_BYTES;
 		if ( longBytes > Integer.MAX_VALUE )
 		{ throw new IllegalArgumentException( "Too many triangles: " + facetCount ); }