Examples with SpimData mpicbg.spim.data.SpimData used on opensource projects

Example 1 with SpimData

use of mpicbg.spim.data.SpimData in project bigwarp by saalfeldlab.

the class ExportTransformAsXmlTest method showFixedAndWarpedMoving.

private static void showFixedAndWarpedMoving(File warpedXml, File fixedImageXml) throws SpimDataException {
    final SpimData warpedSpimData = new XmlIoSpimData().load(warpedXml.getAbsolutePath());
    final BdvStackSource<?> bdvStackSource = BdvFunctions.show(warpedSpimData).get(0);
    bdvStackSource.setDisplayRange(0, 255);
    final SpimData fixedSpimData = new XmlIoSpimData().load(fixedImageXml.getAbsolutePath());
    final BdvStackSource<?> bdvStackSource2 = BdvFunctions.show(fixedSpimData, BdvOptions.options().addTo(bdvStackSource.getBdvHandle())).get(0);
    bdvStackSource2.setDisplayRange(0, 255);
}

Example 2 with SpimData

use of mpicbg.spim.data.SpimData in project bigwarp by saalfeldlab.

the class BigWarpBdvCommand method run.

@Override
public void run() {
    try {
        final SpimData fixedSpimData = new XmlIoSpimData().load(fixedImageXml.getAbsolutePath());
        final SpimData movingSpimData = new XmlIoSpimData().load(movingImageXml.getAbsolutePath());
        new RepeatingReleasedEventsFixer().install();
        final BigWarp.BigWarpData<?> bigWarpData = BigWarpInit.createBigWarpData(movingSpimData, fixedSpimData);
        bw = new BigWarp(bigWarpData, "Big Warp", new ProgressWriterIJ());
        bw.getViewerFrameP().getViewerPanel().requestRepaint();
        bw.getViewerFrameQ().getViewerPanel().requestRepaint();
        bw.getLandmarkFrame().repaint();
        bw.setMovingSpimData(movingSpimData, movingImageXml);
    } catch (final SpimDataException e) {
        e.printStackTrace();
        return;
    }
}

Example 3 with SpimData

use of mpicbg.spim.data.SpimData in project bigwarp by saalfeldlab.

the class BigWarpImagePlusPlugIn method run.

@Override
public void run(final String arg) {
    if (IJ.versionLessThan("1.40"))
        return;
    // don't need any open windows if we're using N5
    final int[] ids = WindowManager.getIDList();
    // Find any open images
    final int N = ids == null ? 0 : ids.length;
    final String[] titles = new String[N + 1];
    for (int i = 0; i < N; ++i) {
        titles[i] = (WindowManager.getImage(ids[i])).getTitle();
    }
    titles[N] = "<None>";
    // Build a dialog to choose the moving and fixed images
    final GenericDialogPlus gd = new GenericDialogPlus("Big Warp Setup");
    gd.addMessage("Image Selection:");
    ImagePlus currimg = WindowManager.getCurrentImage();
    String current = titles[N];
    if (currimg != null) {
        current = currimg.getTitle();
    }
    gd.addChoice("moving_image", titles, current);
    if (titles.length > 1)
        gd.addChoice("target_image", titles, current.equals(titles[0]) ? titles[1] : titles[0]);
    else
        gd.addChoice("target_image", titles, titles[0]);
    gd.addMessage("\nN5/Zarr/HDF5/BDV-XML");
    gd.addDirectoryOrFileField("Moving", "");
    gd.addStringField("Moving dataset", "");
    gd.addDirectoryOrFileField("Target", "");
    gd.addStringField("Target dataset", "");
    gd.addMessage("");
    gd.addFileField("Landmarks file", "");
    gd.addCheckbox("Apply transform from landmarks", true);
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    final int mvgImgIdx = gd.getNextChoiceIndex();
    final int tgtImgIdx = gd.getNextChoiceIndex();
    movingIp = mvgImgIdx < N ? WindowManager.getImage(ids[mvgImgIdx]) : null;
    targetIp = tgtImgIdx < N ? WindowManager.getImage(ids[tgtImgIdx]) : null;
    final String mvgRoot = gd.getNextString();
    final String mvgDataset = gd.getNextString();
    final String tgtRoot = gd.getNextString();
    final String tgtDataset = gd.getNextString();
    final String landmarkPath = gd.getNextString();
    final boolean applyTransform = gd.getNextBoolean();
    // build bigwarp data
    BigWarpData<?> bigwarpdata = BigWarpInit.initData();
    int id = 0;
    if (movingIp != null) {
        id += BigWarpInit.add(bigwarpdata, movingIp, id, 0, true);
    }
    SpimData movingSpimData = null;
    if (!mvgRoot.isEmpty()) {
        if (openWithImageJ(mvgRoot)) {
            final ImagePlus mvgIpFromFile = IJ.openImage(mvgRoot);
            mvgIpFromFile.show();
            BigWarpInit.add(bigwarpdata, mvgIpFromFile, id, 0, true);
        } else {
            movingSpimData = BigWarpInit.addToData(bigwarpdata, true, id, mvgRoot, mvgDataset);
        }
        id++;
    }
    if (targetIp != null) {
        id += BigWarpInit.add(bigwarpdata, targetIp, id, 0, false);
    }
    if (!tgtRoot.isEmpty()) {
        if (openWithImageJ(tgtRoot)) {
            final ImagePlus tgtIpFromFile = IJ.openImage(tgtRoot);
            tgtIpFromFile.show();
            BigWarpInit.add(bigwarpdata, tgtIpFromFile, id, 0, false);
        } else {
            BigWarpInit.addToData(bigwarpdata, false, id, tgtRoot, tgtDataset);
        }
        id++;
    }
    bigwarpdata.wrapUp();
    // run BigWarp
    try {
        new RepeatingReleasedEventsFixer().install();
        final BigWarp<?> bw = new BigWarp<>(bigwarpdata, "Big Warp", new ProgressWriterIJ());
        if (landmarkPath != null && !landmarkPath.isEmpty()) {
            bw.loadLandmarks(landmarkPath);
            if (applyTransform)
                bw.setIsMovingDisplayTransformed(applyTransform);
        }
        if (movingSpimData != null)
            bw.setMovingSpimData(movingSpimData, new File(mvgRoot));
        bw.getViewerFrameP().getViewerPanel().requestRepaint();
        bw.getViewerFrameQ().getViewerPanel().requestRepaint();
        bw.getLandmarkFrame().repaint();
    } catch (final SpimDataException e) {
        e.printStackTrace();
        return;
    }
}

Example 4 with SpimData

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

the class SimulatedBeadsImgLoader method spimdataExample.

public static SpimData spimdataExample(final int[] angles, final int axis, final int numPoints, final double[] sigma, final Interval range) {
    final TimePoints timepoints = LegacySimulatedBeadsImgLoader.createTimepoints();
    final ArrayList<ViewSetup> setups = LegacySimulatedBeadsImgLoader.createViewSetups(angles, axis, range);
    final MissingViews missingViews = null;
    final SimulateBeads sb = new SimulateBeads(angles, axis, numPoints, range, range, sigma);
    final SequenceDescription sequenceDescription = new SequenceDescription(timepoints, setups, null, missingViews);
    final ImgLoader imgLoader = new SimulatedBeadsImgLoader(sb);
    sequenceDescription.setImgLoader(imgLoader);
    // get the minimal resolution of all calibrations
    final double minResolution = 1.0;
    final ViewRegistrations viewRegistrations = LegacySimulatedBeadsImgLoader.createViewRegistrations(sequenceDescription.getViewDescriptions(), minResolution);
    // finally create the SpimData itself based on the sequence description and the view registration
    final SpimData spimData = new SpimData(new File(""), sequenceDescription, viewRegistrations);
    return spimData;
}

Example 5 with SpimData

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

the class SimulatedBeadsImgLoader2 method createSpimData.

public static SpimData createSpimData(int numPoints, double[] sigma, Interval rangeSimulation, Interval intervalRender, int rotAxis, double[] ratations, List<double[]> channelShifts, List<double[]> illumShifts, List<double[]> timeShifts, List<double[]> tileShifts, double relativeTileError, boolean centerAngles) {
    SimulateBeads2 sb = new SimulateBeads2(numPoints, sigma, rangeSimulation, intervalRender);
    SimulatedBeadsImgLoader2 loader = new SimulatedBeadsImgLoader2(sb, rotAxis, ratations, channelShifts, illumShifts, timeShifts, tileShifts);
    SequenceDescription sd = new SequenceDescription(createTimePointsFromImgLoader(loader), createViewSetupsFromImgLoader(loader), null, new MissingViews(new ArrayList<>()));
    sd.setImgLoader(loader);
    SpimData res = new SpimData(new File(""), sd, createViewRegistrationsFromImgLoader(loader, relativeTileError, centerAngles));
    return res;
}