import mpicbg.models.AffineModel2D; //导入依赖的package包/类
/**
 * Modifies the specified full scale transform list for the current render context by
 * adding a transform for bounding box offset, scale, and an area offset (for scaled mipmaps).
 *
 * @param  renderTransformList  list of transforms for full scale (and un-clipped) canvas.
 * @param  levelZeroScale       scale factor for transformed components at mipmap level 0.
 * @param  actualMipmapScale    scale factor for transformed components at desired mipmap level.
 * @param  x                    target image left coordinate.
 * @param  y                    target image top coordinate.
 */
public static CoordinateTransformList<CoordinateTransform> addRenderScaleAndOffset(
        final CoordinateTransformList<CoordinateTransform> renderTransformList,
        final double levelZeroScale,
        final double actualMipmapScale,
        final double x,
        final double y) {

    final AffineModel2D scaleAndOffset = new AffineModel2D();

    // always calculate areaOffset for mipmaps
    final double areaOffset = (1 - (actualMipmapScale / levelZeroScale)) * 0.5;

    scaleAndOffset.set(actualMipmapScale,
                       0,
                       0,
                       actualMipmapScale,
                       -(x * actualMipmapScale + areaOffset),
                       -(y * actualMipmapScale + areaOffset));

    renderTransformList.add(scaleAndOffset);

    return renderTransformList;
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
final static protected void addTriangle(
        final ArrayList< Pair< AffineModel2D, double[][] > > av,
        final double[][] pq,
        final int i1,
        final int i2,
        final int i3) {

    final double[][] pqTriangle = new double[][]{
            {pq[0][i1], pq[0][i2], pq[0][i3]},
            {pq[1][i1], pq[1][i2], pq[1][i3]},
            {pq[2][i1], pq[2][i2], pq[2][i3]},
            {pq[3][i1], pq[3][i2], pq[3][i3]}
    };

    av.add(new Pair<AffineModel2D, double[][]>(new AffineModel2D(), pqTriangle));
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
/**
 * Derives center point matches between the two specified tile lists using tileId to correlate the tiles.
 * The {@link #call} method can then be used to derive a moving least squares transform instance
 * from the point matches.
 *
 * @param  montageTiles  collection of tiles from a montage stack.
 * @param  alignTiles    collection of tiles from an align stack.
 * @param  alpha  transform alpha (optional, default is 1.0)
 */
public MovingLeastSquaresBuilder(final Collection<TileSpec> montageTiles,
                                 final Collection<TileSpec> alignTiles,
                                 final Double alpha) {

    readTileSpecs(montageTiles, alignTiles);

    if (w.length == 1) {
        modelClass = TranslationModel2D.class;
    } else if (w.length == 2) {
        modelClass = SimilarityModel2D.class;
    } else {
        modelClass = AffineModel2D.class;
    }

    this.alpha = alpha;
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
/**
 * Sample the average scaling of a given {@link CoordinateTransform} by transferring a set of point samples using
 * the {@link CoordinateTransform} and then least-squares fitting a {@link SimilarityModel2D} to it.
 *
 * @param width  of the samples set
 * @param height of the samples set
 * @param dx     spacing between samples
 *
 * @return average scale factor
 */
public static double sampleAverageScale(final CoordinateTransform ct,
                                        final int width,
                                        final int height,
                                        final double dx) {
    final ArrayList<PointMatch> samples = new ArrayList<>();
    for (double y = 0; y < height; y += dx) {
        for (double x = 0; x < width; x += dx) {
            final Point p = new Point(new double[]{x, y});
            p.apply(ct);
            samples.add(new PointMatch(p, p));
        }
    }
    final AffineModel2D model = new AffineModel2D();
    try {
        model.fit(samples);
    } catch (final NotEnoughDataPointsException | IllDefinedDataPointsException e) {
        LOG.warn("failed to fit samples, returning scale factor of 1", e);
        return 1;
    }
    final double[] data = new double[6];
    model.toArray(data);
    // return 1;
    return Math.sqrt(Math.max(data[0] * data[0] + data[1] * data[1], data[2] * data[2] + data[3] * data[3]));
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
private void testRANSACFilterWithMinValue(final List<PointMatch> candidates,
                                          final int minNumInliers,
                                          final int expectedInliersSizeAfterFilter)
        throws NotEnoughDataPointsException {

    final List<PointMatch> inliers = new ArrayList<>();

    final int iterations = 1000;
    final float maxEpsilon = 20f;
    final float minInlierRatio = 0.0f;
    final float maxTrust = 3.0f;

    final AffineModel2D model = new AffineModel2D();

    model.filterRansac(candidates,
                       inliers,
                       iterations,
                       maxEpsilon,
                       minInlierRatio,
                       minNumInliers,
                       maxTrust);

    Assert.assertEquals("invalid number of inliers found with min " + minNumInliers,
                        expectedInliersSizeAfterFilter, inliers.size());
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
@SuppressWarnings( "rawtypes" )
@Override
protected void initModel()
{
	final AffineTransform a = patch.getAffineTransform();
	if ( AffineModel2D.class.isInstance( model ) )
		( ( AffineModel2D )( Object )model ).set( a );
	else if ( SimilarityModel2D.class.isInstance( model ) )
		( ( SimilarityModel2D )( Object )model ).set( a.getScaleX(), a.getShearY(), a.getTranslateX(), a.getTranslateY() );
	else if ( RigidModel2D.class.isInstance( model ) )
		( ( RigidModel2D )( Object )model ).set( a.getScaleX(), a.getShearY(), a.getTranslateX(), a.getTranslateY() );
	else if ( TranslationModel2D.class.isInstance( model ) )
		( ( TranslationModel2D )( Object )model ).set( a.getTranslateX(), a.getTranslateY() );
	else if ( InterpolatedAffineModel2D.class.isInstance( model ) )
		( ( InterpolatedAffineModel2D )( Object )model ).set( a );
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
/**
 * Temporary helper method that creates
 * @param matches
 * @param alpha
 * @return
 * @throws Exception
 */
final static public MovingLeastSquaresTransform2 createMLST( final Collection< PointMatch > matches, final double alpha ) throws Exception
{
	final MovingLeastSquaresTransform2 mlst = new MovingLeastSquaresTransform2();
	mlst.setAlpha( alpha );
	Class< ? extends AbstractAffineModel2D< ? > > c = AffineModel2D.class;
	switch ( matches.size() )
	{
		case 1:
			c = TranslationModel2D.class;
			break;
		case 2:
			c = SimilarityModel2D.class;
			break;
		default:
			break;
	}
	mlst.setModel( c );
	mlst.setMatches( matches );

	return mlst;
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
protected void setupWarpMagBaselineOptions( final CoordinateTransform[] xfm, final int ndim )
{
	if ( ndim == 2 )
	{
		xfm[ 0 ] = new AffineModel2D();
		xfm[ 1 ] = new SimilarityModel2D();
		xfm[ 2 ] = new RigidModel2D();
	}
	else
	{
		xfm[ 0 ] = new AffineModel3D();
		xfm[ 1 ] = new SimilarityModel3D();
		xfm[ 2 ] = new RigidModel3D();
	}
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
/**
 * Uses this stack's scale and the specified aligned stack bounds to convert the specified affine to a
 * full scale version that can be used in an {@link org.janelia.alignment.transform.AffineWarpFieldTransform}.
 *
 * @param  alignedLayerTransformModel  scaled aligned model to convert.
 * @param  alignedStackMinX            minimum X value for the (scaled) aligned stack.
 * @param  alignedStackMinY            minimum Y value for the (scaled) aligned stack.
 *
 * @return full scale relative version of the specified model.
 */
@JsonIgnore
public AffineModel2D getFullScaleRelativeModel(final AffineModel2D alignedLayerTransformModel,
                                               final double alignedStackMinX,
                                               final double alignedStackMinY) {

    final AffineTransform affine = new AffineTransform();
    affine.scale(1 / scale, 1 / scale);
    affine.translate(-alignedStackMinX, -alignedStackMinY);
    affine.concatenate(alignedLayerTransformModel.createAffine());
    affine.scale(scale, scale);
    final AffineModel2D model = new AffineModel2D();
    model.set(affine);
    return model;
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
/**
 * Scale all vertex coordinates in target space
 *
 * @param scale
 */
public void scaleTarget(final double scale) {
    for (final Pair<AffineModel2D, double[][]> apq : av)
        for (int j = 0; j < apq.b[2].length; ++j) {
            apq.b[2][j] *= scale;
            apq.b[3][j] *= scale;
        }
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
/**
 * Translate all vertex coordinates
 *
 * @param scale
 */
public void translate(final double x, final double y) {
    for (final Pair<AffineModel2D, double[][]> apq : av)
        for (int j = 0; j < apq.b[2].length; ++j) {
            apq.b[0][j] += x;
            apq.b[1][j] += y;
            apq.b[2][j] += x;
            apq.b[3][j] += y;
        }
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
/**
 * Scale all vertex coordinates
 *
 * @param scale
 */
public void translateTarget(final double x, final double y) {
    for (final Pair<AffineModel2D, double[][]> apq : av)
        for (int j = 0; j < apq.b[2].length; ++j) {
            apq.b[2][j] += x;
            apq.b[3][j] += y;
        }
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
MapTriangleThread(final AtomicInteger i,
                  final List<Pair<AffineModel2D, double[][]>> triangles,
                  final PixelMapper pixelMapper) {
    this.i = i;
    this.triangles = triangles;
    this.pixelMapper = pixelMapper;
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
/**
 * Create an affine transformation that compensates for both scale and pixel shift of a mipmap level that was
 * generated by top-left pixel averaging.
 */
public static AffineModel2D createScaleLevelTransform(final int scaleLevel) {
    final AffineModel2D a = new AffineModel2D();
    final int scale = 1 << scaleLevel;
    final double t = (scale - 1) * 0.5;
    a.set(scale, 0, 0, scale, t, t);
    return a;
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
@Test
public void testGetFullScaleRelativeModel() throws Exception {

    final int tier = 1;
    final Integer tierRow = 0;
    final Integer tierColumn = 1;
    final Integer totalTierRowCount = 3;
    final Integer totalTierColumnCount = 3;
    final Double scale = 0.33133797120207087;
    final Bounds fullScaleBounds = new Bounds(59816.0, 64495.0, 1.0, 64678.0, 70676.0, 3.0);

    final StackId roughTilesStackId = new StackId("testOwner", "tilesProject", "roughTiles");

    final HierarchicalStack tier1Stack =
            new HierarchicalStack(roughTilesStackId,
                                  tier,
                                  tierRow,
                                  tierColumn,
                                  totalTierRowCount,
                                  totalTierColumnCount,
                                  scale,
                                  fullScaleBounds);

    final AffineModel2D model = getModel(1.000018855057, -0.000005117870,
                                         -0.000003681924, 1.000001492098,
                                         26.995723857002,  6.610488526292);

    final double[] expectedArray = new double[6];
    model.toArray(expectedArray);
    expectedArray[4] = expectedArray[4] / scale;
    expectedArray[5] = expectedArray[5] / scale;

    final AffineModel2D relativeModel = tier1Stack.getFullScaleRelativeModel(model, 0, 0);
    final double[] array = new double[6];
    relativeModel.toArray(array);

    for (int i = 0; i < expectedArray.length; i++) {
        Assert.assertEquals("invalid value for index " + i, expectedArray[i], array[i], 0.0001);
    }
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
private AffineModel2D getModel(final double m00,
                               final double m10,
                               final double m01,
                               final double m11,
                               final double m02,
                               final double m12) {
    final AffineModel2D model = new AffineModel2D();
    model.set(m00, m10, m01, m11, m02, m12);
    return model;
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
MapTriangleThread(
		final AtomicInteger i,
		final List< AffineModel2D > triangles,
		final CrackTransformMesh transform,
		final ImageProcessor source,
		final ImageProcessor target )
{
	this.i = i;
	this.triangles = triangles;
	this.transform = transform;
	this.source = source;
	this.target = target;
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
MapTriangleInverseThread(
		final AtomicInteger i,
		final List< AffineModel2D > triangles,
		final CrackTransformMesh transform,
		final ImageProcessor source,
		final ImageProcessor target )
{
	this.i = i;
	this.triangles = triangles;
	this.transform = transform;
	this.source = source;
	this.target = target;
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
MapTriangleInverseInterpolatedThread(
		final AtomicInteger i,
		final List< AffineModel2D > triangles,
		final CrackTransformMesh transform,
		final ImageProcessor source,
		final ImageProcessor target )
{
	this.i = i;
	this.triangles = triangles;
	this.transform = transform;
	this.source = source;
	this.target = target;
}
 

import mpicbg.models.AffineModel2D; //导入依赖的package包/类
final static protected <T extends NumericType<T>> void mapTriangleInterpolated(
		final CrackTransformMesh m, 
		final Collection<AffineModel2D> aiList,
		final RandomAccessibleInterval<T> source,
		final IterableInterval<T> target )
{
	NLinearInterpolatorFactory<T> interp = new NLinearInterpolatorFactory<T>(); 
	mapTriangleInterpolated(
			m, aiList, source,target, interp );
}