Java Code Examples for java.nio.FloatBuffer#hasRemaining()

private IplImage getMonitorImage(IplImage floatImage, IplImage maskImage, int pyramidLevel) {
    final int inChannels = floatImage.nChannels();
    final int outChannels = 3;
    final int[] order = inChannels == 3 ? new int[] { 0, 1, 2 } : new int[] { 2, 1, 0 };

    if (monitorImages[pyramidLevel] == null) {
        monitorImages[pyramidLevel] = IplImage.create(floatImage.width(), floatImage.height(), IPL_DEPTH_8U, outChannels);
    }

    FloatBuffer in  = floatImage.getFloatBuffer();
    ByteBuffer mask = maskImage == null ? null : maskImage.getByteBuffer();
    ByteBuffer out  = monitorImages[pyramidLevel].getByteBuffer();
    float[] buffer = new float[4];
    while (in.hasRemaining() && out.hasRemaining() && (mask == null || mask.hasRemaining())) {
        byte m = mask == null ? (byte)0xFF : mask.get();
        for (int z = 0; z < inChannels; z++) {
            buffer[z] = Math.max(0, Math.min(1, Math.abs(in.get())));
        }
        for (int z = 0; z < outChannels; z++) {
            out.put((byte)(m == 0 ? 0 : Math.round(buffer[order[z]]*255)));
        }
    }
    return monitorImages[pyramidLevel];
}
 

public void write(FloatBuffer value, String name, FloatBuffer defVal) throws IOException {
    if (value == null) {
        return;
    }

    Element el = appendElement(name);
    el.setAttribute("size", String.valueOf(value.limit()));
    StringBuilder buf = new StringBuilder();
    int pos = value.position();
    value.rewind();
    int ctr = 0;
    while (value.hasRemaining()) {
        ctr++;
        buf.append(value.get());
        buf.append(" ");
    }
    if (ctr != value.limit())
        throw new IOException("'" + name
            + "' buffer contention resulted in write data consistency.  "
            + ctr + " values written when should have written "
            + value.limit());
    buf.setLength(Math.max(0, buf.length() - 1));
    value.position(pos);
    el.setAttribute(dataAttributeName, buf.toString());
    currentElement = (Element) el.getParentNode();
}
 

public static BoundingBox create(String id, FloatBuffer vertexBuffer, float[] modelMatrix) {
    float xMin = Float.MAX_VALUE, xMax = Float.MIN_VALUE, yMin = Float.MAX_VALUE, yMax = Float.MIN_VALUE, zMin = Float.MAX_VALUE, zMax = Float.MIN_VALUE;
    vertexBuffer = vertexBuffer.asReadOnlyBuffer();
    vertexBuffer.position(0);
    while (vertexBuffer.hasRemaining()) {
        float vertexx = vertexBuffer.get();
        float vertexy = vertexBuffer.get();
        float vertexz = vertexBuffer.get();
        if (vertexx < xMin) {
            xMin = vertexx;
        }
        if (vertexx > xMax) {
            xMax = vertexx;
        }
        if (vertexy < yMin) {
            yMin = vertexy;
        }
        if (vertexy > yMax) {
            yMax = vertexy;
        }
        if (vertexz < zMin) {
            zMin = vertexz;
        }
        if (vertexz > zMax) {
            zMax = vertexz;
        }
    }
    float[] min = new float[]{xMin, yMin, zMin, 1};
    float[] max = new float[]{xMax, yMax, zMax, 1};
    Matrix.multiplyMV(min,0,modelMatrix,0,min,0);
    Matrix.multiplyMV(max,0,modelMatrix,0,max,0);
    return new BoundingBox(id, min[0], max[0], min[1], max[1], min[2], max[2]);
}
 

static public List<Vector3f> getVertexList(Mesh m) {
    List<Vector3f> l = new ArrayList<>();

    FloatBuffer vb = m.getVertices();
    while( vb.hasRemaining() ) {
        float x = vb.get();
        float y = vb.get();
        float z = vb.get();
        l.add( new Vector3f(x, y, z) );
    }

    vb.flip();

    return l;
}
 

@Deprecated
private void generateBoundingBox() {
	// get vertices of geometry
	FloatBuffer vertices = null; // geometry.getVerticesBuffer();
	vertices.rewind(); // set position to zero

	float[] min = { Float.MAX_VALUE, Float.MAX_VALUE, Float.MAX_VALUE };
	float[] max = { Float.MIN_VALUE, Float.MIN_VALUE, Float.MIN_VALUE };

	float[] vertex = new float[3];

	while (vertices.hasRemaining()) {
		vertex[0] = vertices.get(); // x
		vertex[1] = vertices.get(); // y
		vertex[2] = vertices.get(); // z

		min[0] = Math.min(min[0], vertex[0]);
		max[0] = Math.max(max[0], vertex[0]);
		min[1] = Math.min(min[1], vertex[1]);
		max[1] = Math.max(max[1], vertex[1]);
		min[2] = Math.min(min[2], vertex[2]);
		max[2] = Math.max(max[2], vertex[2]);
	}

	boundingPoints[0] = new float[] { min[0], min[1], min[2] }; // -x,-y,-z
	boundingPoints[1] = new float[] { min[0], min[1], max[2] }; // -x,-y,z
	boundingPoints[2] = new float[] { max[0], min[1], max[2] }; // x,-y,z
	boundingPoints[3] = new float[] { max[0], min[1], min[2] }; // x,-y,-z

	boundingPoints[4] = new float[] { min[0], max[1], min[2] }; // -x, y, -z
	boundingPoints[5] = new float[] { min[0], max[1], max[2] }; // -x, y, z
	boundingPoints[6] = new float[] { max[0], max[1], max[2] }; // ...
	boundingPoints[7] = new float[] { max[0], max[1], min[2] };
}
 

@Override
public void write(FloatBuffer value, String name, FloatBuffer defVal) throws IOException {
    if (value == null) {
        return;
    }

    Element el = appendElement(name);
    el.setAttribute("size", String.valueOf(value.limit()));
    StringBuilder buf = new StringBuilder();
    int pos = value.position();
    value.rewind();
    int ctr = 0;
    while (value.hasRemaining()) {
        ctr++;
        buf.append(value.get());
        buf.append(" ");
    }
    if (ctr != value.limit()) {
        throw new IOException("'" + name
            + "' buffer contention resulted in write data consistency.  "
            + ctr + " values written when should have written "
            + value.limit());
    }
    
    if (buf.length() > 0) {
        //remove last space
        buf.setLength(buf.length() - 1);
    }
    
    value.position(pos);
    el.setAttribute(dataAttributeName, buf.toString());
    currentElement = (Element) el.getParentNode();
}
 

public static BoundingBox create(String id, FloatBuffer vertexBuffer, float[] modelMatrix) {
    float xMin = Float.MAX_VALUE, xMax = -Float.MAX_VALUE, yMin = Float.MAX_VALUE, yMax = -Float.MAX_VALUE, zMin =
            Float.MAX_VALUE, zMax = -Float.MAX_VALUE;
    vertexBuffer = vertexBuffer.asReadOnlyBuffer();
    vertexBuffer.position(0);
    while (vertexBuffer.hasRemaining()) {
        float vertexx = vertexBuffer.get();
        float vertexy = vertexBuffer.get();
        float vertexz = vertexBuffer.get();
        if (vertexx < xMin) {
            xMin = vertexx;
        }
        if (vertexx > xMax) {
            xMax = vertexx;
        }
        if (vertexy < yMin) {
            yMin = vertexy;
        }
        if (vertexy > yMax) {
            yMax = vertexy;
        }
        if (vertexz < zMin) {
            zMin = vertexz;
        }
        if (vertexz > zMax) {
            zMax = vertexz;
        }
    }
    float[] min = new float[]{xMin, yMin, zMin, 1};
    float[] max = new float[]{xMax, yMax, zMax, 1};
    Matrix.multiplyMV(min,0,modelMatrix,0,min,0);
    Matrix.multiplyMV(max,0,modelMatrix,0,max,0);
    return new BoundingBox(id, min[0], max[0], min[1], max[1], min[2], max[2]);
}
 

public static void mult(FloatBuffer a, FloatBuffer b, FloatBuffer store) {
	a.clear(); b.clear(); store.clear();
	while(a.hasRemaining()) {
		store.put(a.get()*b.get());
	}
}
 

public static graphics.scenery.Mesh toScenery( final net.imagej.mesh.Mesh mesh, final boolean center ) {
        final int vCount = //
                ( int ) Math.min( Integer.MAX_VALUE, mesh.vertices().size() );
        final int tCount = //
                ( int ) Math.min( Integer.MAX_VALUE, mesh.triangles().size() );

        // Convert the mesh to an NIO-backed one.
        BufferMesh bufferMesh = new BufferMesh( vCount, tCount );

        Meshes.calculateNormals( mesh, bufferMesh );// Force recalculation of normals because not all meshes are safe

//        if( mesh instanceof BufferMesh ) {
//            // TODO: Check that BufferMesh capacities & positions are compatible.
//            // Need to double check what Scenery assumes about the given buffers.
//            bufferMesh = ( BufferMesh ) mesh;
//        } else {
//            // Copy the mesh into a BufferMesh.
//            bufferMesh = new BufferMesh( vCount, tCount );
//            Meshes.copy( mesh, bufferMesh );
//        }

        // Extract buffers from the BufferMesh.
        final FloatBuffer verts = bufferMesh.vertices().verts();
        final FloatBuffer vNormals = bufferMesh.vertices().normals();
        final FloatBuffer texCoords = bufferMesh.vertices().texCoords();
        final IntBuffer indices = bufferMesh.triangles().indices();

        // Prepare the buffers for Scenery to ingest them.
        // Sets capacity to equal position, then resets position to 0.
        verts.flip();
        if( center ) {// Do 2 passes, 1 to find center, and the other to shift
            double[] v = new double[] {0.0,0.0,0.0};// used for tally of coords and mean
            int coord = 0;// coordinate index
            int n = 0;// num verts
            while( verts.hasRemaining() ) {
                v[coord] += verts.get();
                if( coord == 0 ) n++;
                coord = ( coord + 1 ) % 3;
            }
            verts.flip();
            // Take average
            for( int k = 0; k < 3; k++ ) v[k] /= n;
            // Center shift
            coord = 0;
            float val;
            while( verts.hasRemaining() ) {
                val = verts.get();
                // Write
                verts.put(verts.position()-1,val-(float)v[coord]);
                coord = ( coord + 1 ) % 3;
            }
            verts.flip();
        }

        vNormals.flip();
        texCoords.flip();
        indices.flip();

        // Create and populate the Scenery mesh.
        graphics.scenery.Mesh scMesh = new graphics.scenery.Mesh();
        scMesh.setVertices( verts );
        scMesh.setNormals( vNormals );
        scMesh.setTexcoords( texCoords );
        scMesh.setIndices( indices );


        scMesh.setBoundingBox( scMesh.generateBoundingBox() );
        scMesh.setDirty( true );

        return scMesh;
    }
 

public static void main(String[] args) {
    ByteBuffer bb = ByteBuffer.wrap(new byte[]{0,0,0,0,0,0,0,'a'});
    bb.rewind();
    System.out.print("Byte Buffer ");
    while (bb.hasRemaining())
        System.out.print(bb.position() + " -> " + bb.get() + ", ");
    System.out.println();

    CharBuffer cb = ((ByteBuffer)bb.rewind()).asCharBuffer();
    System.out.print("Char Buffer ");
    while (cb.hasRemaining())
        System.out.print(cb.position() + " -> " + cb.get() + ", ");
    System.out.println();

    ShortBuffer sb = ((ByteBuffer)bb.rewind()).asShortBuffer();
    System.out.print("Short Buffer ");
    while (sb.hasRemaining())
        System.out.print(sb.position() + " -> " + sb.get() + ", ");
    System.out.println();

    IntBuffer ib = ((ByteBuffer)bb.rewind()).asIntBuffer();
    System.out.print("Int Buffer ");
    while (ib.hasRemaining())
        System.out.print(ib.position() + " -> " + ib.get());
    System.out.println();

    FloatBuffer fb = ((ByteBuffer)bb.rewind()).asFloatBuffer();
    System.out.print("Float Buffer ");
    while (fb.hasRemaining())
        System.out.print(fb.position() + " -> " + fb.get() + ", ");
    System.out.println();

    LongBuffer lb = ((ByteBuffer)bb.rewind()).asLongBuffer();
    System.out.print("Long Buffer ");
    while (lb.hasRemaining())
        System.out.print(lb.position() + " -> " + lb.get() + ", ");
    System.out.println();

    DoubleBuffer db = ((ByteBuffer)bb.rewind()).asDoubleBuffer();
    System.out.print("Double Buffer ");
    while (db.hasRemaining())
        System.out.print(db.position() + " -> " + db.get() + ", ");
    System.out.println();
}
 

/**
 * Loads latitude or longitude shifts data. This method should be invoked twice:
 *
 * <ol>
 *   <li>On an instance created for the latitude shifts file with a {@code latitude} argument set to null.</li>
 *   <li>On an instance created for the longitude shifts file with a {@code latitude} argument set to the
 *       instance created in the previous step.</li>
 * </ol>
 *
 * The result is stored in the {@link #grid} field.
 *
 * @param fb               a {@code FloatBuffer} view over the full {@link #buffer} range.
 * @param latitudeShifts   the previously loaded latitude shifts, or {@code null} if not yet loaded.
 * @param longitudeShifts  the file for the longitude grid.
 */
final void readGrid(final FloatBuffer fb, final Loader latitudeShifts, final Path longitudeShifts)
        throws IOException, FactoryException, NoninvertibleTransformException
{
    final int dim;
    final double scale;
    if (latitudeShifts == null) {
        dim   = 1;                                              // Dimension of latitudes.
        scale = DEGREES_TO_SECONDS * Δy;                        // NADCON shifts are positive north.
        grid  = new DatumShiftGridFile.Float<>(2, Units.DEGREE, Units.DEGREE,
                true, x0, y0, Δx, Δy, nx, ny, PARAMETERS, file, longitudeShifts);
        grid.accuracy = SECOND_PRECISION / DEGREES_TO_SECONDS;
    } else {
        if (x0 != latitudeShifts.x0 || Δx != latitudeShifts.Δx || nx != latitudeShifts.nx ||
            y0 != latitudeShifts.y0 || Δy != latitudeShifts.Δy || ny != latitudeShifts.ny || nz != latitudeShifts.nz)
        {
            throw new FactoryException(Errors.format(Errors.Keys.MismatchedGridGeometry_2,
                    latitudeShifts.file.getFileName(), file.getFileName()));
        }
        dim   = 0;                                              // Dimension of longitudes
        scale = -DEGREES_TO_SECONDS * Δx;                       // NADCON shifts are positive west.
        grid  = latitudeShifts.grid;                            // Continue writing in existing grid.
    }
    final float[] array = grid.offsets[dim];
    if (ascii != null) {
        for (int i=0; i<array.length; i++) {
            array[i] = (float) (Double.parseDouble(nextWord()) / scale);
        }
    } else {
        /*
         * Transfer all data from the FloatBuffer to the float[] array, except one float at the beginning
         * of every row which must be skipped. That skipped float value is not a translation value and is
         * expected to be always zero.
         */
        syncView(fb);
        int forCurrentRow = 0;
        for (int i=0; i<array.length;) {
            if (forCurrentRow == 0) {
                if (!fb.hasRemaining()) {
                    fillBuffer(fb);
                }
                if (fb.get() != 0) {
                    throw unexpectedFormat();
                }
                forCurrentRow = nx;
            }
            int remaining = fb.remaining();
            if (remaining == 0) {
                fillBuffer(fb);
                remaining = fb.remaining();
            }
            final int n = Math.min(forCurrentRow, remaining);
            fb.get(array, i, n);
            forCurrentRow -= n;
            i += n;
        }
        /*
         * Convert seconds to degrees for consistency with the unit declared at the beginning of this method,
         * then divide by cell size for consistency with the 'isCellRatio = true' configuration.
         */
        for (int i=0; i<array.length; i++) {
            array[i] /= scale;
        }
    }
}