Examples with Task org.vcell.imagej.common.gui.Task used on opensource projects

Example 1 with Task

use of org.vcell.imagej.common.gui.Task in project vcell by virtualcell.

the class VCellModelService method getVCellImageForModel.

public Task<BufferedImage, Void> getVCellImageForModel(VCellModel vCellModel) {
    Task<BufferedImage, Void> task = new Task<BufferedImage, Void>() {

        @Override
        protected BufferedImage doInBackground() throws Exception {
            try {
                BufferedImage img = ImageIO.read(new URL("https://" + HOST + ":" + PORT + "/biomodel/" + vCellModel.getBiomodelKey() + "/diagram"));
                System.out.println("read " + img.toString());
                return img;
            } catch (IOException e) {
                System.out.println("Could not load image for: " + vCellModel.getName());
            }
            return null;
        }
    };
    return task;
}

Example 2 with Task

use of org.vcell.imagej.common.gui.Task in project vcell by virtualcell.

the class VCellModelService method getModels.

public Task<List<VCellModel>, String> getModels(VCellService vCellService) {
    final Task<List<VCellModel>, String> task = new Task<List<VCellModel>, String>() {

        @Override
        protected List<VCellModel> doInBackground() throws Exception {
            boolean bIgnoreCertProblems = true;
            boolean bIgnoreHostMismatch = true;
            VCellApiClient vCellApiClient = null;
            List<VCellModel> vCellModels = new ArrayList<VCellModel>();
            try {
                vCellApiClient = new VCellApiClient(HOST, PORT, bIgnoreCertProblems, bIgnoreHostMismatch);
                vCellApiClient.authenticate("ImageJ", "richarddberlin", false);
                BioModelsQuerySpec querySpec = new BioModelsQuerySpec();
                querySpec.owner = "tutorial";
                final BiomodelRepresentation[] biomodelReps = vCellApiClient.getBioModels(querySpec);
                final int modelsToLoad = biomodelReps.length;
                int modelsLoaded = 0;
                for (BiomodelRepresentation biomodelRep : biomodelReps) {
                    setSubtask(biomodelRep.getName());
                    ApplicationRepresentation[] applicationReps = biomodelRep.getApplications();
                    if (applicationReps.length > 0) {
                        String vcml = getVCML(biomodelRep);
                        if (vcml != null) {
                            SBMLDocument sbml = vCellService.getSBML(vcml, applicationReps[0].getName());
                            VCellModel vCellModel = new VCellModel(biomodelRep.getName(), biomodelRep.getBmKey(), sbml);
                            vCellModels.add(vCellModel);
                            modelsLoaded++;
                            setProgress(modelsLoaded * 100 / modelsToLoad);
                        } else {
                            System.err.println("failed to return VCML for " + biomodelRep.bmKey);
                        }
                    }
                }
            } catch (Exception e) {
                e.printStackTrace(System.out);
            }
            return vCellModels;
        }
    };
    return task;
}

Example 3 with Task

use of org.vcell.imagej.common.gui.Task in project vcell by virtualcell.

the class VCellService method runSimulation.

private static Task<List<Dataset>, SimulationState> runSimulation(final SimulationServiceImpl client, final VCellModel vCellModel, final SimulationSpec simSpec, final List<Species> outputSpecies, final boolean shouldCreateIndividualDatasets, final OpService opService, final DatasetService datasetService) throws IOException, XMLStreamException {
    final Task<List<Dataset>, SimulationState> task = new Task<List<Dataset>, SimulationState>() {

        @Override
        protected List<Dataset> doInBackground() throws Exception {
            setSubtask(SimulationState.notRun);
            final File sbmlSpatialFile = new File(vCellModel.getName() + ".xml");
            new SBMLWriter().write(vCellModel.getSbmlDocument(), sbmlSpatialFile);
            final SBMLModel model = new SBMLModel(sbmlSpatialFile);
            final SimulationInfo simulationInfo = client.computeModel(model, simSpec);
            try {
                Thread.sleep(500);
            } catch (final InterruptedException e) {
                e.printStackTrace();
            }
            setSubtask(SimulationState.running);
            while (client.getStatus(simulationInfo).getSimState() == SimulationState.running) {
                System.out.println("waiting for simulation results");
                try {
                    Thread.sleep(500);
                } catch (final InterruptedException e) {
                    e.printStackTrace();
                }
            }
            if (client.getStatus(simulationInfo).getSimState() == SimulationState.failed) {
                setSubtask(SimulationState.failed);
                return null;
            }
            final List<Dataset> results = new ArrayList<>();
            final List<VariableInfo> vars = client.getVariableList(simulationInfo);
            final List<Double> times = client.getTimePoints(simulationInfo);
            for (final VariableInfo var : vars) {
                if (outputSpecies.stream().anyMatch(species -> species.getId().equals(var.getVariableVtuName()))) {
                    // Get data for first time point and determine dimensions
                    List<Double> data = client.getData(simulationInfo, var, 0);
                    final int[] dimensions = getDimensions(data, times);
                    final Img<DoubleType> img = opService.create().img(dimensions);
                    final RandomAccess<DoubleType> imgRA = img.randomAccess();
                    // Copy data to the ImgLib2 Img
                    for (int t = 0; t < times.size(); t++) {
                        data = client.getData(simulationInfo, var, t);
                        for (int d = 0; d < data.size(); d++) {
                            imgRA.setPosition(new int[] { d, t });
                            imgRA.get().set(data.get(d));
                        }
                    }
                    // Create ImageJ Dataset and add to results
                    final Dataset dataset = datasetService.create(img);
                    dataset.setName(var.getVariableVtuName());
                    results.add(dataset);
                }
            }
            // If desired, add all datasets with the same dimensions
            if (!shouldCreateIndividualDatasets && !results.isEmpty()) {
                // First, group datasets according to dimensions
                final List<List<Dataset>> datasetGroups = new ArrayList<>();
                final List<Dataset> initialGroup = new ArrayList<>();
                initialGroup.add(results.get(0));
                datasetGroups.add(initialGroup);
                for (int i = 1; i < results.size(); i++) {
                    final Dataset result = results.get(i);
                    for (final List<Dataset> datasetGroup : datasetGroups) {
                        final Dataset[] datasets = new Dataset[] { datasetGroup.get(0), result };
                        if (Datasets.areSameSize(datasets, 0, 1)) {
                            datasetGroup.add(result);
                        } else {
                            final List<Dataset> newGroup = new ArrayList<>();
                            newGroup.add(result);
                            datasetGroups.add(newGroup);
                        }
                    }
                }
                final List<Dataset> summedResults = new ArrayList<>();
                for (final List<Dataset> datasetGroup : datasetGroups) {
                    final Img<DoubleType> sum = opService.create().img(datasetGroup.get(0));
                    for (final Dataset dataset : datasetGroup) {
                        @SuppressWarnings("unchecked") final RandomAccessibleInterval<DoubleType> current = (Img<DoubleType>) dataset.getImgPlus().getImg();
                        opService.math().add(sum, sum, current);
                    }
                    final Dataset result = datasetService.create(sum);
                    result.setName(datasetGroup.stream().map(d -> d.getName()).collect(Collectors.joining("+")));
                    summedResults.add(result);
                }
                return summedResults;
            }
            setSubtask(SimulationState.done);
            return results;
        }
    };
    return task;
}

Example 4 with Task

use of org.vcell.imagej.common.gui.Task 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;
}

Example 5 with Task

use of org.vcell.imagej.common.gui.Task 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;
}