Examples with Img net.imglib2.img.Img used on opensource projects

Example 6 with Img

use of net.imglib2.img.Img in project vcell by virtualcell.

the class ProjectService method saveDataset.

private void saveDataset(Dataset dataset, Path path) throws IOException {
    Dataset datasetToSave = dataset.duplicate();
    // SCIFIO cannot save 1-bit images so we must convert to 8-bit
    if (datasetToSave.firstElement() instanceof BitType) {
        @SuppressWarnings("unchecked") Img<BitType> img = (Img<BitType>) dataset.getImgPlus().getImg();
        Img<UnsignedByteType> converted = opService.convert().uint8(img);
        ImgPlus<UnsignedByteType> convertedImgPlus = new ImgPlus<>(converted, dataset.getName());
        datasetToSave.setImgPlus(convertedImgPlus);
    }
    String name = dataset.getName();
    if (FilenameUtils.getExtension(name).isEmpty()) {
        // Default save extension
        name += ".tif";
    }
    Path filePath = Paths.get(path.toString(), name);
    datasetIOService.save(datasetToSave, filePath.toString());
}

Example 7 with Img

use of net.imglib2.img.Img 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();
            model.setFilepath(sbmlSpatialFile.getAbsolutePath());
            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;
}