diff --git a/src/main/java/net/imglib2/mesh/Meshes.java b/src/main/java/net/imglib2/mesh/Meshes.java index 6eb45e3..005c7e1 100644 --- a/src/main/java/net/imglib2/mesh/Meshes.java +++ b/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 ); diff --git a/src/main/java/net/imglib2/mesh/alg/MeshConnectedComponents.java b/src/main/java/net/imglib2/mesh/alg/MeshConnectedComponents.java index b5830a4..bb70cec 100644 --- a/src/main/java/net/imglib2/mesh/alg/MeshConnectedComponents.java +++ b/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(); diff --git a/src/main/java/net/imglib2/mesh/alg/MeshCursor.java b/src/main/java/net/imglib2/mesh/alg/MeshCursor.java index 840b50b..6f9adc8 100644 --- a/src/main/java/net/imglib2/mesh/alg/MeshCursor.java +++ b/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() ); } diff --git a/src/main/java/net/imglib2/mesh/alg/RemoveDuplicateVertices.java b/src/main/java/net/imglib2/mesh/alg/RemoveDuplicateVertices.java index 19012f2..990a3d9 100644 --- a/src/main/java/net/imglib2/mesh/alg/RemoveDuplicateVertices.java +++ b/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() ) diff --git a/src/main/java/net/imglib2/mesh/alg/SimplifyMesh.java b/src/main/java/net/imglib2/mesh/alg/SimplifyMesh.java index 7ac41aa..bd3a72f 100644 --- a/src/main/java/net/imglib2/mesh/alg/SimplifyMesh.java +++ b/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 / diff --git a/src/main/java/net/imglib2/mesh/alg/TaubinSmoothing.java b/src/main/java/net/imglib2/mesh/alg/TaubinSmoothing.java index 601b066..a31ee66 100644 --- a/src/main/java/net/imglib2/mesh/alg/TaubinSmoothing.java +++ b/src/main/java/net/imglib2/mesh/alg/TaubinSmoothing.java @@ -13,7 +13,7 @@ *

* Adapted by the Javascript code of mykolalysenko, MIT license. * https://github.com/mikolalysenko/taubin-smooth/blob/master/smooth.js - * + * * @author Jean-Yves Tinevez * @see 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++ ) diff --git a/src/main/java/net/imglib2/mesh/alg/zslicer/ZSlicer.java b/src/main/java/net/imglib2/mesh/alg/zslicer/ZSlicer.java index 13d1c8a..a4b95f5 100644 --- a/src/main/java/net/imglib2/mesh/alg/zslicer/ZSlicer.java +++ b/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 ); diff --git a/src/main/java/net/imglib2/mesh/io/ply/PLYMeshIO.java b/src/main/java/net/imglib2/mesh/io/ply/PLYMeshIO.java index b990ab8..e882c22 100644 --- a/src/main/java/net/imglib2/mesh/io/ply/PLYMeshIO.java +++ b/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() ) { diff --git a/src/main/java/net/imglib2/mesh/io/stl/STLMeshIO.java b/src/main/java/net/imglib2/mesh/io/stl/STLMeshIO.java index d7d8692..22b6e2d 100644 --- a/src/main/java/net/imglib2/mesh/io/stl/STLMeshIO.java +++ b/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 ); } diff --git a/src/main/java/net/imglib2/mesh/obj/Triangles.java b/src/main/java/net/imglib2/mesh/obj/Triangles.java index 3217222..c0486d9 100644 --- a/src/main/java/net/imglib2/mesh/obj/Triangles.java +++ b/src/main/java/net/imglib2/mesh/obj/Triangles.java @@ -46,9 +46,9 @@ public interface Triangles extends Iterable< Triangle > Mesh mesh(); /** - * Number of triangles in the collection. + * Number of triangles in the collection as a long value. */ - long size(); + long sizel(); /** * Number of triangles in the collection as an int value. @@ -56,9 +56,9 @@ public interface Triangles extends Iterable< Triangle > * @throws RuntimeException * if the number of triangles exceeds {@link Integer#MAX_VALUE}. */ - default int isize() + default int size() { - final long size = size(); + final long size = sizel(); if ( size >= Integer.MAX_VALUE ) throw new RuntimeException( "Too many triangles: " + size ); return ( int ) size; @@ -200,7 +200,7 @@ default int addf( final int v0, final int v1, final int v2, final float nx, fina * Index of triangle's third vertex. * @return Index of newly added triangle. */ - default long addf( long v0, long v1, long v2 ) + default long addf( final long v0, final long v1, final long v2 ) { // (v1 - v0) x (v2 - v0) @@ -455,32 +455,6 @@ default long add( final long v0, final long v1, final long v2 ) return add( v0, v1, v2, nx / nmag, ny / nmag, nz / nmag ); } - /** - * Adds a triangle to the mesh's triangles list, using int - * indices. - *

- * Normal is computed with counterclockwise (i.e., right-hand) orientation. - *

- * - * @param v0 - * Index of triangle's first vertex. - * @param v1 - * Index of triangle's second vertex. - * @param v2 - * Index of triangle's third vertex. - * @return Index of newly added triangle. - * @throws RuntimeException - * if the return triangle index exceeds - * {@link Integer#MAX_VALUE}. - */ - default int add( final int v0, final int v1, final int v2 ) - { - final long t = add( ( long ) v0, ( long ) v1, ( long ) v2 ); - if ( t >= Integer.MAX_VALUE ) - throw new RuntimeException( "Index too large: " + t ); - return ( int ) t; - } - /** * Adds a triangle to the mesh's triangles list. *

@@ -574,7 +548,7 @@ default Iterator< Triangle > iterator() private long index = -1; - private Triangle triangle = new Triangle() + private final Triangle triangle = new Triangle() { @Override @@ -593,7 +567,7 @@ public long index() @Override public boolean hasNext() { - return index + 1 < size(); + return index + 1 < sizel(); } @Override diff --git a/src/main/java/net/imglib2/mesh/obj/Vertices.java b/src/main/java/net/imglib2/mesh/obj/Vertices.java index 8ab48c1..7068456 100644 --- a/src/main/java/net/imglib2/mesh/obj/Vertices.java +++ b/src/main/java/net/imglib2/mesh/obj/Vertices.java @@ -43,8 +43,8 @@ public interface Vertices extends Iterable< Vertex > /** The mesh to which the collection of vertices belongs. */ Mesh mesh(); - /** Number of vertices in the collection. */ - long size(); + /** Number of vertices in the collection as a long value. */ + long sizel(); /** * Number of vertices in the collection as an int value. @@ -52,9 +52,9 @@ public interface Vertices extends Iterable< Vertex > * @throws RuntimeException * if the number of vertices exceed {@link Integer#MAX_VALUE}. */ - default int isize() + default int size() { - final long size = size(); + final long size = sizel(); if ( size >= Integer.MAX_VALUE ) throw new RuntimeException( "Too many vertices: " + size ); return ( int ) size; @@ -133,11 +133,11 @@ long addf( float x, float y, float z, // * @throws RuntimeException * if the number of vertices exceed {@link Integer#MAX_VALUE}. */ - default int addfi( float x, float y, float z, // - float nx, float ny, float nz, // - float u, float v ) + default int addfi( final float x, final float y, final float z, // + final float nx, final float ny, final float nz, // + final float u, final float v ) { - long vi = addf( x, y, z, nx, ny, nz, u, v ); + final long vi = addf( x, y, z, nx, ny, nz, u, v ); if ( vi >= Integer.MAX_VALUE ) throw new RuntimeException( "Too many vertices: " + vi ); return ( int ) vi; @@ -300,13 +300,13 @@ default double nz( final long vIndex ) } /** U value of vertex texture coordinate, as a double. */ - default double u( long vIndex ) + default double u( final long vIndex ) { return uf( vIndex ); } /** V value of vertex texture coordinate, as a double. */ - default double v( long vIndex ) + default double v( final long vIndex ) { return vf( vIndex ); } @@ -367,9 +367,9 @@ default int addi( final double x, final double y, final double z ) * V value of vertex texture coordinate. * @return Index of newly added vertex. */ - default long add( double x, double y, double z, // - double nx, double ny, double nz, // - double u, double v ) + default long add( final double x, final double y, final double z, // + final double nx, final double ny, final double nz, // + final double u, final double v ) { return addf( ( float ) x, ( float ) y, ( float ) z, // ( float ) nx, ( float ) ny, ( float ) nz, // @@ -400,9 +400,9 @@ default long add( double x, double y, double z, // * @throws RuntimeException * if the number of vertices exceed {@link Integer#MAX_VALUE}. */ - default int addi( double x, double y, double z, // - double nx, double ny, double nz, // - double u, double v ) + default int addi( final double x, final double y, final double z, // + final double nx, final double ny, final double nz, // + final double u, final double v ) { return addfi( ( float ) x, ( float ) y, ( float ) z, // ( float ) nx, ( float ) ny, ( float ) nz, // @@ -521,7 +521,7 @@ default Iterator< Vertex > iterator() private long index = -1; - private Vertex vertex = new Vertex() + private final Vertex vertex = new Vertex() { @Override @@ -540,7 +540,7 @@ public long index() @Override public boolean hasNext() { - return index + 1 < size(); + return index + 1 < sizel(); } @Override diff --git a/src/main/java/net/imglib2/mesh/obj/naive/NaiveDoubleMesh.java b/src/main/java/net/imglib2/mesh/obj/naive/NaiveDoubleMesh.java index 6223820..2f08043 100644 --- a/src/main/java/net/imglib2/mesh/obj/naive/NaiveDoubleMesh.java +++ b/src/main/java/net/imglib2/mesh/obj/naive/NaiveDoubleMesh.java @@ -90,7 +90,7 @@ public Mesh mesh() } @Override - public long size() + public long sizel() { return xs.size(); } @@ -317,7 +317,7 @@ public Mesh mesh() } @Override - public long size() + public long sizel() { return v1s.size(); } diff --git a/src/main/java/net/imglib2/mesh/obj/naive/NaiveFloatMesh.java b/src/main/java/net/imglib2/mesh/obj/naive/NaiveFloatMesh.java index c49d92d..7ef9cee 100644 --- a/src/main/java/net/imglib2/mesh/obj/naive/NaiveFloatMesh.java +++ b/src/main/java/net/imglib2/mesh/obj/naive/NaiveFloatMesh.java @@ -90,7 +90,7 @@ public Mesh mesh() } @Override - public long size() + public long sizel() { return xs.size(); } @@ -235,7 +235,7 @@ public Mesh mesh() } @Override - public long size() + public long sizel() { return v1s.size(); } diff --git a/src/main/java/net/imglib2/mesh/obj/nio/BufferMesh.java b/src/main/java/net/imglib2/mesh/obj/nio/BufferMesh.java index a670696..ff01ff5 100644 --- a/src/main/java/net/imglib2/mesh/obj/nio/BufferMesh.java +++ b/src/main/java/net/imglib2/mesh/obj/nio/BufferMesh.java @@ -140,7 +140,7 @@ public Mesh mesh() } @Override - public long size() + public long sizel() { return verts.limit() / V_STRIDE; } @@ -197,7 +197,7 @@ public float vf( long vIndex ) public long addf( float x, float y, float z, float nx, float ny, float nz, float u, float v ) { - final long index = size(); + final long index = sizel(); grow( verts, V_STRIDE ); verts.put( x ); verts.put( y ); @@ -287,7 +287,7 @@ public Mesh mesh() } @Override - public long size() + public long sizel() { return indices.limit() / I_STRIDE; } @@ -331,7 +331,7 @@ public float nzf( long tIndex ) @Override public long addf( long v0, long v1, long v2, float nx, float ny, float nz ) { - final long index = size(); + final long index = sizel(); grow( indices, I_STRIDE ); indices.put( safeInt( v0 ) ); indices.put( safeInt( v1 ) ); diff --git a/src/main/java/net/imglib2/mesh/obj/transform/TranslateMesh.java b/src/main/java/net/imglib2/mesh/obj/transform/TranslateMesh.java index 15aa3b6..5b91c6b 100644 --- a/src/main/java/net/imglib2/mesh/obj/transform/TranslateMesh.java +++ b/src/main/java/net/imglib2/mesh/obj/transform/TranslateMesh.java @@ -121,7 +121,7 @@ public float zf() @Override public boolean hasNext() { - return index + 1 < size(); + return index + 1 < sizel(); } @Override @@ -140,9 +140,9 @@ public Mesh mesh() } @Override - public long size() + public long sizel() { - return invs.size(); + return invs.sizel(); } @Override diff --git a/src/test/java/net/imglib2/mesh/AbstractMeshTest.java b/src/test/java/net/imglib2/mesh/AbstractMeshTest.java index baad995..b514745 100644 --- a/src/test/java/net/imglib2/mesh/AbstractMeshTest.java +++ b/src/test/java/net/imglib2/mesh/AbstractMeshTest.java @@ -77,7 +77,7 @@ public void testMesh() throws Exception t0v2x, t0v2y, t0v2z, // t0nx, t0ny, t0nz ); // - assertEquals( 3, mesh.vertices().size() ); + assertEquals( 3, mesh.vertices().sizel() ); final double t1v0x = 13, t1v0y = 14, t1v0z = 15; final double t1v1x = 16, t1v1y = 17, t1v1z = 18; @@ -89,7 +89,7 @@ public void testMesh() throws Exception t1v2x, t1v2y, t1v2z, // t1nx, t1ny, t1nz ); // - assertEquals( 6, mesh.vertices().size() ); + assertEquals( 6, mesh.vertices().sizel() ); final double t2v0x = 25, t2v0y = 26, t2v0z = 27; final double t2v1x = 28, t2v1y = 29, t2v1z = 30; @@ -100,7 +100,7 @@ public void testMesh() throws Exception final long t2v2 = mesh.vertices().add( t2v2x, t2v2y, t2v2z ); final long t2 = mesh.triangles().add( t2v0, t2v1, t2v2, t2nx, t2ny, t2nz ); - assertEquals( 9, mesh.vertices().size() ); + assertEquals( 9, mesh.vertices().sizel() ); assertVertex( mesh, 0, t0v0x, t0v0y, t0v0z ); assertVertex( mesh, 1, t0v1x, t0v1y, t0v1z ); assertVertex( mesh, 2, t0v2x, t0v2y, t0v2z ); @@ -111,7 +111,7 @@ public void testMesh() throws Exception assertVertex( mesh, 7, t2v1x, t2v1y, t2v1z ); assertVertex( mesh, 8, t2v2x, t2v2y, t2v2z ); - assertEquals( 3, mesh.triangles().size() ); + assertEquals( 3, mesh.triangles().sizel() ); final Set< Long > vertexIndices = new HashSet<>(); assertTriangle( mesh, vertexIndices, 0, // t0v0x, t0v0y, t0v0z, // @@ -167,10 +167,10 @@ public void testTriangleNormal() throws URISyntaxException, IOException lazyInputMesh.vertices().add( 1, 0, -1 ); lazyInputMesh.triangles().add( 0, 1, 2 ); - Mesh outMesh = new BufferMesh( ( int ) inputMesh.vertices().size(), ( int ) inputMesh.triangles().size() ); + Mesh outMesh = new BufferMesh( ( int ) inputMesh.vertices().sizel(), ( int ) inputMesh.triangles().sizel() ); Meshes.calculateNormals( inputMesh, outMesh ); - for ( int idx = 0; idx < inputMesh.triangles().size(); idx++ ) + for ( int idx = 0; idx < inputMesh.triangles().sizel(); idx++ ) { // calculateNormals test assertTriangleNormal( inputMesh, 0, outMesh.triangles().nx( idx ), outMesh.triangles().ny( idx ), outMesh.triangles().nz( idx ) ); diff --git a/src/test/java/net/imglib2/mesh/MeshesTest.java b/src/test/java/net/imglib2/mesh/MeshesTest.java index a559e09..ef0ab0f 100644 --- a/src/test/java/net/imglib2/mesh/MeshesTest.java +++ b/src/test/java/net/imglib2/mesh/MeshesTest.java @@ -83,7 +83,7 @@ public void testRemoveDuplicateVertices() Mesh mesh = createMeshWithNoise(); Mesh res = Meshes.removeDuplicateVertices( mesh, 2 ); - assertEquals( 4, res.vertices().size() ); + assertEquals( 4, res.vertices().sizel() ); assertEquals( p1.getDoublePosition( 0 ), res.vertices().x( 0 ), EPSILON ); assertEquals( p1.getDoublePosition( 1 ), res.vertices().y( 0 ), EPSILON ); @@ -102,7 +102,7 @@ public void testRemoveDuplicateVertices() assertEquals( p4.getDoublePosition( 2 ), res.vertices().z( 3 ), EPSILON ); res = Meshes.removeDuplicateVertices( mesh, 3 ); - assertEquals( 6, res.vertices().size() ); + assertEquals( 6, res.vertices().sizel() ); } @Test @@ -111,7 +111,7 @@ public void testMarchingCubesBooleanType() LabelRegion< String > ROI = createLabelRegion( getTestImage3D(), 1, 255 ); Mesh mesh = getMesh(); final Mesh result = Meshes.marchingCubes( ROI ); - assertEquals( mesh.triangles().size(), result.triangles().size() ); + assertEquals( mesh.triangles().sizel(), result.triangles().sizel() ); final Iterator< Triangle > expectedFacets = mesh.triangles().iterator(); final Iterator< Triangle > actualFacets = result.triangles().iterator(); while ( expectedFacets.hasNext() && actualFacets.hasNext() ) @@ -137,7 +137,7 @@ public void testMarchingCubesRealType() LabelRegion< String > ROI = createLabelRegion( getTestImage3D(), 1, 255 ); Mesh mesh = getMesh(); final Mesh result = Meshes.marchingCubes( ROI, 1.0 ); - assertEquals( mesh.triangles().size(), result.triangles().size() ); + assertEquals( mesh.triangles().sizel(), result.triangles().sizel() ); final Iterator< Triangle > expectedFacets = mesh.triangles().iterator(); final Iterator< Triangle > actualFacets = result.triangles().iterator(); while ( expectedFacets.hasNext() && actualFacets.hasNext() ) diff --git a/src/test/java/net/imglib2/mesh/alg/MeshCursorTest.java b/src/test/java/net/imglib2/mesh/alg/MeshCursorTest.java index 685fe65..9885bb9 100644 --- a/src/test/java/net/imglib2/mesh/alg/MeshCursorTest.java +++ b/src/test/java/net/imglib2/mesh/alg/MeshCursorTest.java @@ -109,7 +109,7 @@ private static final void test( final Img< UnsignedByteType > img, final int exp // Build a mesh from the source image.. final Mesh m = Meshes.marchingCubes( img, expected / 2. ); final Mesh m2 = Meshes.removeDuplicateVertices( m, 2 ); - final BufferMesh mesh = new BufferMesh( m2.vertices().isize(), m2.triangles().isize() ); + final BufferMesh mesh = new BufferMesh( m2.vertices().size(), m2.triangles().size() ); Meshes.calculateNormals( m2, mesh ); // Test we are iterating strictly inside the cube. diff --git a/src/test/java/net/imglib2/mesh/alg/TaubinSmoothingDemo.java b/src/test/java/net/imglib2/mesh/alg/TaubinSmoothingDemo.java index 74bf7a8..b315e0b 100644 --- a/src/test/java/net/imglib2/mesh/alg/TaubinSmoothingDemo.java +++ b/src/test/java/net/imglib2/mesh/alg/TaubinSmoothingDemo.java @@ -30,7 +30,7 @@ public static void main( final String[] args ) throws IOException // Add noise. final Random ran = new Random( 45l ); - for ( int i = 0; i < mesh.vertices().size(); i++ ) + for ( int i = 0; i < mesh.vertices().sizel(); i++ ) { final double x = mesh.vertices().x( i ); final double y = mesh.vertices().y( i );