Examples with ViewRegistration mpicbg.spim.data.registration.ViewRegistration used on opensource projects

Example 1 with ViewRegistration

use of mpicbg.spim.data.registration.ViewRegistration in project labkit-ui by juglab.

the class HDF5Saver method oneImageSpimData.

private static <T> SpimDataMinimal oneImageSpimData(List<RandomAccessibleInterval<T>> frames, File basePath) {
    List<TimePoint> timePointList = IntStream.range(0, frames.size()).mapToObj(TimePoint::new).collect(Collectors.toList());
    final TimePoints timePoints = new TimePoints(timePointList);
    final BasicViewSetup setup = new BasicViewSetup(0, "image", (Dimensions) frames.get(0), new FinalVoxelDimensions("pixel", 1, 1, 1));
    final Map<Integer, BasicViewSetup> setups = Collections.singletonMap(0, setup);
    final MissingViews missingViews = null;
    BasicImgLoader imgLoader = new BasicImgLoader() {

        @Override
        public BasicSetupImgLoader<T> getSetupImgLoader(int i) {
            if (i != setup.getId())
                throw new IllegalArgumentException();
            return new BasicSetupImgLoader<T>() {

                @Override
                public RandomAccessibleInterval<T> getImage(int timeId, ImgLoaderHint... imgLoaderHints) {
                    return frames.get(timeId);
                }

                @Override
                public T getImageType() {
                    return Util.getTypeFromInterval(frames.get(0));
                }
            };
        }
    };
    final SequenceDescriptionMinimal sequence = new SequenceDescriptionMinimal(timePoints, setups, imgLoader, missingViews);
    List<ViewRegistration> viewRegistrationList = timePointList.stream().map(x -> new ViewRegistration(x.getId(), setup.getId())).collect(Collectors.toList());
    ViewRegistrations registrations = new ViewRegistrations(viewRegistrationList);
    return new SpimDataMinimal(basePath, sequence, registrations);
}

Example 2 with ViewRegistration

use of mpicbg.spim.data.registration.ViewRegistration in project bigwarp by saalfeldlab.

the class BigWarpBatchTransform method createSpimData.

public static final SpimDataMinimal createSpimData(IFormatReader reader) {
    Hashtable<String, Object> gmeta = reader.getGlobalMetadata();
    // header stuff here TODO
    System.out.println(gmeta);
    // get relevant metadata
    double pw = 1.0;
    double ph = 1.0;
    double pd = 1.0;
    if (gmeta.keySet().contains("XResolution"))
        pw = ((Double) gmeta.get("XResolution")).doubleValue();
    if (gmeta.keySet().contains("YResolution"))
        ph = ((Double) gmeta.get("YResolution")).doubleValue();
    if (gmeta.keySet().contains("Spacing"))
        pd = ((Double) gmeta.get("Spacing")).doubleValue();
    int numSetups = 1;
    int numTimepoints = 1;
    int[] ids = new int[] { 349812342 };
    final File basePath = new File(".");
    String punit = "px";
    if (gmeta.keySet().contains("Unit"))
        punit = (String) gmeta.get("Unit");
    final FinalVoxelDimensions voxelSize = new FinalVoxelDimensions(punit, pw, ph, pd);
    final long w = ((Long) gmeta.get("ImageWidth")).longValue();
    final long h = ((Long) gmeta.get("ImageLength")).longValue();
    // Long.parseLong( (String)gmeta.get("images") );
    final long d = reader.getSizeZ();
    long[] dims = new long[] { w, h, d };
    final FinalDimensions size = new FinalDimensions(new long[] { w, h, d });
    // create setups from channels
    final HashMap<Integer, BasicViewSetup> setups = new HashMap<Integer, BasicViewSetup>(numSetups);
    for (int s = 0; s < numSetups; ++s) {
        final BasicViewSetup setup = new BasicViewSetup(ids[s], String.format("channel %d", ids[s] + 1), size, voxelSize);
        setup.setAttribute(new Channel(ids[s] + 1));
        setups.put(ids[s], setup);
    }
    // create timepoints
    final ArrayList<TimePoint> timepoints = new ArrayList<TimePoint>(numTimepoints);
    for (int t = 0; t < numTimepoints; ++t) timepoints.add(new TimePoint(t));
    // create ViewRegistrations from the images calibration
    final AffineTransform3D sourceTransform = new AffineTransform3D();
    sourceTransform.set(1.0 / pw, 0, 0, 0, 0, 1.0 / ph, 0, 0, 0, 0, pd, 0);
    final ArrayList<ViewRegistration> registrations = new ArrayList<ViewRegistration>();
    for (int t = 0; t < numTimepoints; ++t) for (int s = 0; s < numSetups; ++s) registrations.add(new ViewRegistration(t, ids[s], sourceTransform));
    final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal(new TimePoints(timepoints), setups, new DummyImageLoader<FloatType>(new FloatType(), dims), null);
    SpimDataMinimal spimData = new SpimDataMinimal(basePath, seq, new ViewRegistrations(registrations));
    if (WrapBasicImgLoader.wrapImgLoaderIfNecessary(spimData))
        System.err.println("WARNING:\nOpening <SpimData> dataset that is not suited for interactive browsing.\nConsider resaving as HDF5 for better performance.");
    return spimData;
}

Example 3 with ViewRegistration

use of mpicbg.spim.data.registration.ViewRegistration in project bigwarp by saalfeldlab.

the class ImagePlusLoader method load.

public SpimDataMinimal load(final int setupIdOffset, ImagePlus imp) {
    // get calibration and image size
    final double pw;
    final double ph;
    final double pd;
    pw = sanitizeCalibration(imp.getCalibration().pixelWidth, "x");
    ph = sanitizeCalibration(imp.getCalibration().pixelHeight, "y");
    pd = sanitizeCalibration(imp.getCalibration().pixelDepth, "z");
    String punit = imp.getCalibration().getUnit();
    if (punit == null || punit.isEmpty())
        punit = "px";
    final FinalVoxelDimensions voxelSize = new FinalVoxelDimensions(punit, pw, ph, pd);
    final int w = imp.getWidth();
    final int h = imp.getHeight();
    final int d = imp.getNSlices();
    final int numTimepoints = imp.getNFrames();
    final int numSetups = imp.getNChannels();
    final FinalDimensions size = new FinalDimensions(new int[] { w, h, d });
    is3d = (d > 1);
    isMultiChannel = (numSetups > 1);
    // create ImgLoader wrapping the image
    final BasicImgLoader imgLoader;
    if (imp.getStack().isVirtual()) {
        switch(imp.getType()) {
            case ImagePlus.GRAY8:
                imgLoader = VirtualStackImageLoader.createUnsignedByteInstance(imp, setupIdOffset);
                break;
            case ImagePlus.GRAY16:
                imgLoader = VirtualStackImageLoader.createUnsignedShortInstance(imp, setupIdOffset);
                break;
            case ImagePlus.GRAY32:
                imgLoader = VirtualStackImageLoader.createFloatInstance(imp, setupIdOffset);
                break;
            case ImagePlus.COLOR_RGB:
            default:
                imgLoader = VirtualStackImageLoader.createARGBInstance(imp, setupIdOffset);
                break;
        }
    } else {
        switch(imp.getType()) {
            case ImagePlus.GRAY8:
                imgLoader = ImageStackImageLoader.createUnsignedByteInstance(imp, setupIdOffset);
                break;
            case ImagePlus.GRAY16:
                imgLoader = ImageStackImageLoader.createUnsignedShortInstance(imp, setupIdOffset);
                break;
            case ImagePlus.GRAY32:
                imgLoader = ImageStackImageLoader.createFloatInstance(imp, setupIdOffset);
                break;
            case ImagePlus.COLOR_RGB:
            default:
                imgLoader = ImageStackImageLoader.createARGBInstance(imp, setupIdOffset);
                break;
        }
    }
    final File basePath = new File(".");
    // create setups from channels
    final HashMap<Integer, BasicViewSetup> setups = new HashMap<Integer, BasicViewSetup>(numSetups);
    for (int s = 0; s < numSetups; ++s) {
        final int id = setupIdOffset + s;
        final BasicViewSetup setup = new BasicViewSetup(setupIdOffset + s, String.format("%s channel %d", imp.getTitle(), id + 1), size, voxelSize);
        setup.setAttribute(new Channel(id + 1));
        setups.put(id, setup);
        settingsMap.put(id, ColorSettings.fromImagePlus(imp, id, s));
    }
    // create timepoints
    final ArrayList<TimePoint> timepoints = new ArrayList<TimePoint>(numTimepoints);
    for (int t = 0; t < numTimepoints; ++t) timepoints.add(new TimePoint(t));
    // create ViewRegistrations from the images calibration
    final AffineTransform3D sourceTransform = new AffineTransform3D();
    sourceTransform.set(pw, 0, 0, 0, 0, ph, 0, 0, 0, 0, pd, 0);
    final ArrayList<ViewRegistration> registrations = new ArrayList<ViewRegistration>();
    for (int t = 0; t < numTimepoints; ++t) for (int s = 0; s < numSetups; ++s) registrations.add(new ViewRegistration(t, setupIdOffset + s, sourceTransform));
    final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal(new TimePoints(timepoints), setups, imgLoader, null);
    SpimDataMinimal spimData = new SpimDataMinimal(basePath, seq, new ViewRegistrations(registrations));
    WrapBasicImgLoader.wrapImgLoaderIfNecessary(spimData);
    return spimData;
}

Example 4 with ViewRegistration

use of mpicbg.spim.data.registration.ViewRegistration in project multiview-simulation by PreibischLab.

the class SimulatedBeadsImgLoader2 method createViewRegistrationsFromImgLoader.

public static ViewRegistrations createViewRegistrationsFromImgLoader(SimulatedBeadsImgLoader2 imgLoader, double relativeTileError, boolean centerAngles) {
    SimulateBeads2 sb = imgLoader.getSimulateBeads();
    final HashMap<ViewId, ViewRegistration> viewRegistrationList = new HashMap<ViewId, ViewRegistration>();
    final RealInterval tilesExtent = sb.getTilesExtent();
    double[] center = new double[tilesExtent.numDimensions()];
    tilesExtent.realMax(center);
    for (int d = 0; d < center.length; d++) center[d] /= -2.0;
    for (int tp : new ArrayList<>(sb.tpTransforms.keySet()).stream().sorted().collect(Collectors.toList())) {
        int vid = 0;
        for (int a : new ArrayList<>(sb.angleTransforms.keySet()).stream().sorted().collect(Collectors.toList())) for (int channel : new ArrayList<>(sb.channelTransforms.keySet()).stream().sorted().collect(Collectors.toList())) for (int illum : new ArrayList<>(sb.illumTransforms.keySet()).stream().sorted().collect(Collectors.toList())) for (int tile : new ArrayList<>(sb.tileTransforms.keySet()).stream().sorted().collect(Collectors.toList())) {
            final VoxelDimensions voxelSize = new FinalVoxelDimensions("pixels", 1, 1, 1);
            final Dimensions dim = imgLoader.getSimulateBeads().getImg(0, a, channel, tile, illum);
            final ViewRegistration viewRegistration = new ViewRegistration(tp, vid++);
            final double calX = voxelSize.dimension(0);
            final double calY = voxelSize.dimension(1);
            final double calZ = voxelSize.dimension(2);
            final AffineTransform3D m = new AffineTransform3D();
            m.set(calX, 0.0f, 0.0f, 0.0f, 0.0f, calY, 0.0f, 0.0f, 0.0f, 0.0f, calZ, 0.0f);
            final ViewTransform vt = new ViewTransformAffine("calibration", m);
            viewRegistration.preconcatenateTransform(vt);
            double[] translation = sb.tileTransforms.get(tile).inverse().getTranslation();
            for (int i = 0; i < translation.length; i++) translation[i] *= relativeTileError;
            AffineTransform3D atr = new AffineTransform3D();
            atr.translate(translation);
            final ViewTransform vtT = new ViewTransformAffine("translation", atr.copy());
            viewRegistration.preconcatenateTransform(vtT);
            if (centerAngles) {
                AffineTransform3D centerTr = new AffineTransform3D();
                centerTr.translate(center);
                final ViewTransform centerVt = new ViewTransformAffine("center angle", centerTr.copy());
                viewRegistration.preconcatenateTransform(centerVt);
            }
            final ViewTransform vtA = new ViewTransformAffine("rotation", sb.angleTransforms.get(a));
            viewRegistration.preconcatenateTransform(vtA);
            viewRegistrationList.put(viewRegistration, viewRegistration);
        }
    }
    return new ViewRegistrations(viewRegistrationList);
}

Example 5 with ViewRegistration

use of mpicbg.spim.data.registration.ViewRegistration in project bigdataviewer-biop-tools by BIOP.

the class LifReOrdered method constructSpimData.

public AbstractSpimData constructSpimData() {
    Map<Integer, ViewSetup> idToNewViewSetups = new HashMap<>();
    // No Illumination
    List<ViewSetup> newViewSetups = new ArrayList<>();
    int maxTimePoint = spimdataOrigin.getViewRegistrations().getViewRegistrations().keySet().stream().map(this::originToReorderedLocation).mapToInt(viewId -> viewId.getTimePointId()).max().getAsInt() + 1;
    logger.debug("Reordered spimdata max timepoint = " + maxTimePoint);
    List<TimePoint> timePoints = new ArrayList<>();
    IntStream.range(0, maxTimePoint).forEach(tp -> timePoints.add(new TimePoint(tp)));
    final ArrayList<ViewRegistration> registrations = new ArrayList<>();
    List<ViewId> missingViews = new ArrayList<>();
    spimdataOrigin.getViewRegistrations().getViewRegistrations().keySet().stream().forEach(originViewId -> {
        ViewId newViewId = originToReorderedLocation(originViewId);
        // Create ViewSetup if it doesn't exist
        if (!idToNewViewSetups.containsKey(newViewId.getViewSetupId())) {
            BasicViewSetup bvs = (BasicViewSetup) spimdataOrigin.getSequenceDescription().getViewSetups().get(originViewId.getViewSetupId());
            ViewSetup newViewSetup = new ViewSetup(newViewId.getViewSetupId(), bvs.getName(), bvs.getSize(), bvs.getVoxelSize(), bvs.getAttribute(Channel.class), bvs.getAttribute(Angle.class), bvs.getAttribute(Illumination.class));
            bvs.getAttributes().forEach((name, entity) -> {
                logger.debug("ViewSetupId : " + bvs.getId() + " " + name + ":" + entity);
                newViewSetup.setAttribute(entity);
            });
            newViewSetups.add(newViewSetup);
            idToNewViewSetups.put(newViewId.getViewSetupId(), newViewSetup);
        }
        // Create View Registration
        registrations.add(new ViewRegistration(newViewId.getTimePointId(), newViewId.getViewSetupId(), spimdataOrigin.getViewRegistrations().getViewRegistration(originViewId).getModel()));
    });
    newViewSetups.forEach(vs -> logger.debug(vs.getName()));
    logger.debug("Reordered spimdata number of setups = " + newViewSetups.size());
    SequenceDescription sd = new SequenceDescription(new TimePoints(timePoints), newViewSetups, null, new MissingViews(missingViews));
    sd.setImgLoader(new ReorderedImageLoader(this, sd, 4, 2));
    final SpimData spimData = new SpimData(null, sd, new ViewRegistrations(registrations));
    return spimData;
}