Examples with Dataset net.imagej.Dataset used on opensource projects

Example 6 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class CompareView method getDatasetOverlayMap.

public HashMap<Dataset, List<Overlay>> getDatasetOverlayMap(OverlayService overlayService) {
    HashMap<Dataset, List<Overlay>> result = new HashMap<>();
    for (Dataset dataset : datasetImagePanelMap.keySet()) {
        ImageDisplay display = datasetImagePanelMap.get(dataset);
        // Bug in ImageJ that returns two of each overlay, so must refrain from adding duplicates
        List<Overlay> overlays = new ArrayList<>();
        for (Overlay overlay : overlayService.getOverlays(display)) {
            if (!overlays.contains(overlay)) {
                overlays.add(overlay);
            }
        }
        result.put(dataset, overlays);
    }
    return result;
}

Example 7 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class PlotImageStats method run.

@Override
public void run() {
    Plot plot = new ColorPlot("Frame mean intensity", "Time", "Mean intensity");
    StringBuilder legendLabels = new StringBuilder();
    for (int i = 0; i < datasets.size(); i++) {
        RandomAccessibleInterval<T> data = datasets.get(i);
        if (data instanceof Dataset) {
            legendLabels.append(((Dataset) data).getName());
            legendLabels.append(": ");
        }
        Pair<double[], double[]> xyPair = (Pair<double[], double[]>) ops.run("imageStatsForPlotting", ImageStatsForPlotting.MEAN, data, mask);
        plot.addPoints(xyPair.getA(), xyPair.getB(), Plot.LINE);
        legendLabels.append("ROI ");
        legendLabels.append(i + 1);
        legendLabels.append("\n");
    }
    plot.addLegend(legendLabels.toString());
    plot.show();
}

Example 8 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class PlotCellRegionStats method run.

@Override
public void run() {
    Plot plot = new ColorPlot("Cell region mean intensity", "Time", "Mean intensity");
    StringBuilder legendLabels = new StringBuilder();
    for (int i = 0; i < datasets.size(); i++) {
        RandomAccessibleInterval<T> data = datasets.get(i);
        if (data instanceof Dataset) {
            legendLabels.append(((Dataset) data).getName());
            legendLabels.append(": ");
        }
        RandomAccessibleInterval<T> cropped = ops.transform().crop(data, mask);
        displayService.createDisplay(cropped);
    }
}

Example 9 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class ProjectService method saveAs.

public Task<Void, String> saveAs(Project project, File root) {
    final Task<Void, String> task = new Task<Void, String>() {

        @Override
        protected Void doInBackground() throws Exception {
            int numToSave = project.getData().size() + project.getGeometry().size() + project.getModels().size() + project.getResults().size();
            int numSaved = 0;
            String rootPath = root.getAbsolutePath();
            Path dataPath = Paths.get(rootPath, "data");
            Path geometryPath = Paths.get(rootPath, "geometry");
            Path modelsPath = Paths.get(rootPath, "models");
            Path resultsPath = Paths.get(rootPath, "results");
            try {
                // Save data
                Files.createDirectories(dataPath);
                FileUtils.cleanDirectory(dataPath.toFile());
                for (Dataset dataset : project.getData()) {
                    setSubtask(dataset.getName());
                    saveDataset(dataset, dataPath);
                    numSaved++;
                    setProgress(numSaved * 100 / numToSave);
                }
                // Save geometry
                Files.createDirectories(geometryPath);
                FileUtils.cleanDirectory(geometryPath.toFile());
                for (Dataset dataset : project.getGeometry()) {
                    setSubtask(dataset.getName());
                    saveDataset(dataset, geometryPath);
                    numSaved++;
                    setProgress(numSaved * 100 / numToSave);
                }
                // Save models
                Files.createDirectories(modelsPath);
                FileUtils.cleanDirectory(modelsPath.toFile());
                for (VCellModel model : project.getModels()) {
                    setSubtask(model.getName());
                    saveModel(model, modelsPath);
                    numSaved++;
                    setProgress(numSaved * 100 / numToSave);
                }
                // Save results
                Files.createDirectories(resultsPath);
                FileUtils.cleanDirectory(resultsPath.toFile());
                for (Dataset dataset : project.getResults()) {
                    setSubtask(dataset.getName());
                    saveDataset(dataset, resultsPath);
                    numSaved++;
                    setProgress(numSaved * 100 / numToSave);
                }
            } catch (IOException e) {
                e.printStackTrace();
            }
            currentProjectRoot = root;
            return null;
        }

        @Override
        protected void process(List<String> chunks) {
            super.process(chunks);
        }
    };
    return task;
}

Example 10 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class ProjectService method load.

public Task<Project, String> load(File root) {
    final Task<Project, String> task = new Task<Project, String>() {

        @Override
        protected Project doInBackground() throws Exception {
            Project project = new Project(root.getName());
            String rootPath = root.getAbsolutePath();
            File[] dataFiles = Paths.get(rootPath, "data").toFile().listFiles();
            File[] geometryFiles = Paths.get(rootPath, "geometry").toFile().listFiles();
            File[] modelDirectories = Paths.get(rootPath, "models").toFile().listFiles();
            File[] resultsFiles = Paths.get(rootPath, "results").toFile().listFiles();
            int numFiles = dataFiles.length + geometryFiles.length + modelDirectories.length + resultsFiles.length;
            int numLoaded = 0;
            if (dataFiles != null) {
                for (File dataFile : dataFiles) {
                    try {
                        setSubtask(dataFile.getName());
                        Dataset data = datasetIOService.open(dataFile.getAbsolutePath());
                        project.getData().add(data);
                        numLoaded++;
                        setProgress(numLoaded * 100 / numFiles);
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }
            if (geometryFiles != null) {
                for (File geometryFile : geometryFiles) {
                    try {
                        setSubtask(geometryFile.getName());
                        Dataset geometry = datasetIOService.open(geometryFile.getAbsolutePath());
                        // Geometry datasets are saved as 8-bit images so we must convert back to 1-bit
                        if (geometry.firstElement() instanceof UnsignedByteType) {
                            @SuppressWarnings("unchecked") Img<UnsignedByteType> img = (Img<UnsignedByteType>) geometry.getImgPlus().getImg();
                            Img<BitType> converted = opService.convert().bit(img);
                            ImgPlus<BitType> convertedImgPlus = new ImgPlus<>(converted, geometry.getName());
                            geometry.setImgPlus(convertedImgPlus);
                        }
                        project.getGeometry().add(geometry);
                        numLoaded++;
                        setProgress(numLoaded * 100 / numFiles);
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }
            if (modelDirectories != null) {
                for (File modelDirectory : modelDirectories) {
                    setSubtask(modelDirectory.getName());
                    SBMLDocument sbmlDocument = null;
                    BufferedImage image = null;
                    File[] modelFiles = modelDirectory.listFiles();
                    System.out.println(modelFiles.length);
                    // Invalid model directory
                    if (modelFiles.length > 2)
                        continue;
                    for (File modelFile : modelFiles) {
                        System.out.println(modelFile.getName());
                        if (FilenameUtils.getExtension(modelFile.getName()).equals("xml")) {
                            sbmlDocument = new SBMLReader().readSBML(modelFile);
                            System.out.println("Loaded sbml");
                        } else if (FilenameUtils.getExtension(modelFile.getName()).equals("png")) {
                            image = ImageIO.read(modelFile);
                            System.out.println("Loaded image");
                        }
                    }
                    if (sbmlDocument != null) {
                        VCellModel vCellModel = new VCellModel(modelDirectory.getName(), null, sbmlDocument);
                        vCellModel.setImage(image);
                        project.getModels().add(vCellModel);
                        System.out.println("Added model");
                    }
                    numLoaded++;
                    setProgress(numLoaded * 100 / numFiles);
                }
            }
            if (resultsFiles != null) {
                for (File resultsFile : resultsFiles) {
                    try {
                        setSubtask(resultsFile.getName());
                        Dataset results = datasetIOService.open(resultsFile.getAbsolutePath());
                        // Loading 1-dimensional tif images adds a dimension
                        // so must crop out empty dimensions
                        @SuppressWarnings("unchecked") ImgPlus<T> imgPlus = (ImgPlus<T>) results.getImgPlus();
                        int numDimensions = imgPlus.numDimensions();
                        long[] dimensions = new long[2 * imgPlus.numDimensions()];
                        for (int i = 0; i < numDimensions; i++) {
                            dimensions[i] = 0;
                            dimensions[i + numDimensions] = imgPlus.dimension(i) - 1;
                        }
                        FinalInterval interval = Intervals.createMinMax(dimensions);
                        ImgPlus<T> cropped = opService.transform().crop(imgPlus, interval, true);
                        results.setImgPlus(cropped);
                        project.getResults().add(results);
                        numLoaded++;
                        setProgress(numLoaded * 100 / numFiles);
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }
            currentProjectRoot = root;
            return project;
        }
    };
    return task;
}