Examples with CoordinateTransform mpicbg.trakem2.transform.CoordinateTransform used on opensource projects

Example 6 with CoordinateTransform

use of mpicbg.trakem2.transform.CoordinateTransform in project TrakEM2 by trakem2.

the class NonLinearTransformMode method mousePressed.

@Override
public void mousePressed(final MouseEvent me, final int x_p, final int y_p, final double magnification) {
    /* find if clicked on a point */
    p_clicked = null;
    double min = Double.MAX_VALUE;
    final Point mouse = new Point(new double[] { x_p, y_p });
    final double a = 64.0 / magnification / magnification;
    for (final Point p : points) {
        final double sd = Point.squareDistance(p, mouse);
        if (sd < min && sd < a) {
            p_clicked = p;
            min = sd;
        }
    }
    if (me.isShiftDown()) {
        if (null == p_clicked) {
            /* add one */
            try {
                if (points.size() > 0) {
                    /*
						 * Create a pseudo-invertible (TransformMesh) for the screen.
						 */
                    final CoordinateTransform mlst = createCT();
                    final SimilarityModel2D toWorld = new SimilarityModel2D();
                    toWorld.set(1.0 / magnification, 0, srcRect.x, srcRect.y);
                    final SimilarityModel2D toScreen = toWorld.createInverse();
                    final mpicbg.models.CoordinateTransformList<mpicbg.models.CoordinateTransform> ctl = new mpicbg.models.CoordinateTransformList<mpicbg.models.CoordinateTransform>();
                    ctl.add(toWorld);
                    ctl.add(mlst);
                    ctl.add(toScreen);
                    final CoordinateTransformMesh ctm = new CoordinateTransformMesh(ctl, 32, (int) Math.ceil(srcRect.width * magnification), (int) Math.ceil(srcRect.height * magnification));
                    final double[] l = mouse.getL();
                    toScreen.applyInPlace(l);
                    ctm.applyInverseInPlace(l);
                    toWorld.applyInPlace(l);
                }
                points.add(mouse);
                p_clicked = mouse;
            } catch (final Exception e) {
                Utils.log("Could not add point");
                e.printStackTrace();
            }
        } else if (Utils.isControlDown(me)) {
            // remove it
            points.remove(p_clicked);
            p_clicked = null;
        }
    }
}

Example 7 with CoordinateTransform

use of mpicbg.trakem2.transform.CoordinateTransform in project TrakEM2 by trakem2.

the class Patch method appendCoordinateTransform.

/**
 * Append a {@link CoordinateTransform} to the current
 * {@link CoordinateTransformList}.  If there is no transform yet, it just
 * sets it.  If there is only one transform, it replaces it by a list
 * containing both, the existing first.
 */
@SuppressWarnings("unchecked")
public final void appendCoordinateTransform(final CoordinateTransform ct) {
    if (!hasCoordinateTransform())
        setCoordinateTransform(ct);
    else {
        final CoordinateTransformList<CoordinateTransform> ctl;
        final CoordinateTransform this_ct = getCoordinateTransform();
        if (this_ct instanceof CoordinateTransformList<?>)
            ctl = (CoordinateTransformList<CoordinateTransform>) this_ct.copy();
        else {
            ctl = new CoordinateTransformList<CoordinateTransform>();
            ctl.add(this_ct);
        }
        ctl.add(ct);
        setCoordinateTransform(ctl);
    }
}

Example 8 with CoordinateTransform

use of mpicbg.trakem2.transform.CoordinateTransform in project TrakEM2 by trakem2.

the class Patch method makeFlatImage.

/**
 * Creates an ImageProcessor of the specified type.
 *  @param type Any of ImagePlus.GRAY_8, GRAY_16, GRAY_32 or COLOR_RGB.
 *  @param srcRect the box in world coordinates to make an image out of.
 *  @param scale may be up to 1.0.
 *  @param patches The list of patches to paint. The first gets painted first (at the bottom).
 *  @param background The color with which to paint the outsides where no image paints into.
 *  @param setMinAndMax defines whether the min and max of each Patch is set before pasting the Patch.
 *
 * For exporting while blending the display ranges (min,max) and respecting alpha masks, see {@link ExportUnsignedShort}.
 */
public static ImageProcessor makeFlatImage(final int type, final Layer layer, final Rectangle srcRect, final double scale, final Collection<Patch> patches, final Color background, final boolean setMinAndMax) {
    final ImageProcessor ip;
    final int W, H;
    if (scale < 1) {
        W = (int) (srcRect.width * scale);
        H = (int) (srcRect.height * scale);
    } else {
        W = srcRect.width;
        H = srcRect.height;
    }
    switch(type) {
        case ImagePlus.GRAY8:
            ip = new ByteProcessor(W, H);
            break;
        case ImagePlus.GRAY16:
            ip = new ShortProcessor(W, H);
            break;
        case ImagePlus.GRAY32:
            ip = new FloatProcessor(W, H);
            break;
        case ImagePlus.COLOR_RGB:
            ip = new ColorProcessor(W, H);
            break;
        default:
            Utils.logAll("Cannot create an image of type " + type + ".\nSupported types: 8-bit, 16-bit, 32-bit and RGB.");
            return null;
    }
    // Fill with background
    if (null != background && Color.black != background) {
        ip.setColor(background);
        ip.fill();
    }
    AffineModel2D sc = null;
    if (scale < 1.0) {
        sc = new AffineModel2D();
        sc.set(scale, 0, 0, scale, 0, 0);
    }
    for (final Patch p : patches) {
        // TODO patches seem to come in in inverse order---find out why
        // A list to represent all the transformations that the Patch image has to go through to reach the scaled srcRect image
        final CoordinateTransformList<CoordinateTransform> list = new CoordinateTransformList<CoordinateTransform>();
        final AffineTransform at = new AffineTransform();
        at.translate(-srcRect.x, -srcRect.y);
        at.concatenate(p.getAffineTransform());
        // 1. The coordinate tranform of the Patch, if any
        if (p.hasCoordinateTransform()) {
            final CoordinateTransform ct = p.getCoordinateTransform();
            list.add(ct);
            // Remove the translation in the patch_affine that the ct added to it
            final Rectangle box = Patch.getCoordinateTransformBoundingBox(p, ct);
            at.translate(-box.x, -box.y);
        }
        // 2. The affine transform of the Patch
        final AffineModel2D patch_affine = new AffineModel2D();
        patch_affine.set(at);
        list.add(patch_affine);
        // 3. The desired scaling
        if (null != sc)
            patch_affine.preConcatenate(sc);
        final CoordinateTransformMesh mesh = new CoordinateTransformMesh(list, p.meshResolution, p.getOWidth(), p.getOHeight());
        final mpicbg.ij.TransformMeshMapping<CoordinateTransformMesh> mapping = new mpicbg.ij.TransformMeshMapping<CoordinateTransformMesh>(mesh);
        // 4. Convert the patch to the required type
        ImageProcessor pi = p.getImageProcessor();
        if (setMinAndMax) {
            pi = pi.duplicate();
            pi.setMinAndMax(p.min, p.max);
        }
        switch(type) {
            case ImagePlus.GRAY8:
                pi = pi.convertToByte(true);
                break;
            case ImagePlus.GRAY16:
                pi = pi.convertToShort(true);
                break;
            case ImagePlus.GRAY32:
                pi = pi.convertToFloat();
                break;
            default:
                // ImagePlus.COLOR_RGB and COLOR_256
                pi = pi.convertToRGB();
                break;
        }
        /* TODO for taking into account independent min/max setting for each patch,
			 * we will need a mapping with an `intensity transfer function' to be implemented.
			 * --> EXISTS already as mpicbg/trakem2/transform/ExportUnsignedShort.java
			 */
        mapping.mapInterpolated(pi, ip);
    }
    return ip;
}

Example 9 with CoordinateTransform

use of mpicbg.trakem2.transform.CoordinateTransform in project TrakEM2 by trakem2.

the class Patch method keyPressed.

@Override
public void keyPressed(final KeyEvent ke) {
    final Object source = ke.getSource();
    if (!(source instanceof DisplayCanvas))
        return;
    final DisplayCanvas dc = (DisplayCanvas) source;
    final Roi roi = dc.getFakeImagePlus().getRoi();
    final int mod = ke.getModifiers();
    switch(ke.getKeyCode()) {
        case KeyEvent.VK_C:
            // Ignoring masks: outside is already black, and ImageJ cannot handle alpha masks.
            if (0 == (mod ^ (Event.SHIFT_MASK | Event.ALT_MASK))) {
                // Place the source image, untransformed, into clipboard:
                final ImagePlus imp = getImagePlus();
                if (null != imp)
                    imp.copy(false);
            } else if (0 == mod || (0 == (mod ^ Event.SHIFT_MASK))) {
                CoordinateTransformList<CoordinateTransform> list = null;
                if (hasCoordinateTransform()) {
                    list = new CoordinateTransformList<CoordinateTransform>();
                    list.add(getCoordinateTransform());
                }
                if (0 == mod) {
                    // SHIFT is not down
                    final AffineModel2D am = new AffineModel2D();
                    am.set(this.at);
                    if (null == list)
                        list = new CoordinateTransformList<CoordinateTransform>();
                    list.add(am);
                }
                ImageProcessor ip;
                if (null != list) {
                    final TransformMesh mesh = new TransformMesh(list, meshResolution, o_width, o_height);
                    final TransformMeshMapping mapping = new TransformMeshMapping(mesh);
                    ip = mapping.createMappedImageInterpolated(getImageProcessor());
                } else {
                    ip = getImageProcessor();
                }
                new ImagePlus(this.title, ip).copy(false);
            }
            ke.consume();
            break;
        case KeyEvent.VK_F:
            // fill mask with current ROI using
            if (null != roi && M.isAreaROI(roi)) {
                Bureaucrat.createAndStart(new Worker.Task("Filling image mask") {

                    @Override
                    public void exec() {
                        getLayerSet().addDataEditStep(Patch.this);
                        if (0 == mod) {
                            addAlphaMask(roi, ProjectToolbar.getForegroundColorValue());
                        } else if (0 == (mod ^ Event.SHIFT_MASK)) {
                            // shift is down: fill outside
                            try {
                                final Area localRoi = M.areaInInts(M.getArea(roi)).createTransformedArea(at.createInverse());
                                final Area invLocalRoi = new Area(new Rectangle(0, 0, getOWidth(), getOHeight()));
                                invLocalRoi.subtract(localRoi);
                                addAlphaMaskLocal(invLocalRoi, ProjectToolbar.getForegroundColorValue());
                            } catch (final NoninvertibleTransformException e) {
                                IJError.print(e);
                                return;
                            }
                        }
                        getLayerSet().addDataEditStep(Patch.this);
                        // wait
                        try {
                            updateMipMaps().get();
                        } catch (final Throwable t) {
                            IJError.print(t);
                        }
                        Display.repaint();
                    }
                }, project);
            }
            // capturing:
            ke.consume();
            break;
        default:
            super.keyPressed(ke);
            break;
    }
}

Example 10 with CoordinateTransform

use of mpicbg.trakem2.transform.CoordinateTransform in project TrakEM2 by trakem2.

the class NonLinearTransformMode method doPainterUpdate.

@Override
protected void doPainterUpdate(final Rectangle r, final double m) {
    try {
        final CoordinateTransform mlst = createCT();
        final SimilarityModel2D toWorld = new SimilarityModel2D();
        toWorld.set(1.0 / m, 0, r.x - ScreenPatchRange.pad / m, r.y - ScreenPatchRange.pad / m);
        final mpicbg.models.CoordinateTransformList<mpicbg.models.CoordinateTransform> ctl = new mpicbg.models.CoordinateTransformList<mpicbg.models.CoordinateTransform>();
        ctl.add(toWorld);
        ctl.add(mlst);
        ctl.add(toWorld.createInverse());
        final CoordinateTransformMesh ctm = new CoordinateTransformMesh(ctl, 32, r.width * m + 2 * ScreenPatchRange.pad, r.height * m + 2 * ScreenPatchRange.pad);
        final TransformMeshMappingWithMasks<CoordinateTransformMesh> mapping = new TransformMeshMappingWithMasks<CoordinateTransformMesh>(ctm);
        // keep a pointer to the current list
        final HashMap<Paintable, GroupingMode.ScreenPatchRange<?>> screenPatchRanges = this.screenPatchRanges;
        for (final GroupingMode.ScreenPatchRange spr : screenPatchRanges.values()) {
            if (screenPatchRanges != this.screenPatchRanges) {
                // TODO should it call itself:  doPainterUpdate( r, m );
                break;
            }
            spr.update(mapping);
        }
    } catch (final NotEnoughDataPointsException e) {
    } catch (final NoninvertibleModelException e) {
    } catch (final IllDefinedDataPointsException e) {
    } catch (final Exception e) {
        e.printStackTrace();
    }
}