Examples with Point net.imglib2.Point used on opensource projects

Example 11 with Point

use of net.imglib2.Point 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;
}

Example 12 with Point

use of net.imglib2.Point in project java-docs-samples by GoogleCloudPlatform.

the class Snippets method writeTimeSeries.

/**
 * Demonstrates writing a time series value for the metric type
 * 'custom.google.apis.com/my_metric'.
 * <p>
 * This method assumes `my_metric` descriptor has already been created as a
 * DOUBLE value_type and GAUGE metric kind. If the metric descriptor
 * doesn't exist, it will be auto-created.
 */
// CHECKSTYLE OFF: VariableDeclarationUsageDistance
void writeTimeSeries() throws IOException {
    // [START monitoring_write_timeseries]
    String projectId = System.getProperty("projectId");
    // Instantiates a client
    MetricServiceClient metricServiceClient = MetricServiceClient.create();
    // Prepares an individual data point
    TimeInterval interval = TimeInterval.newBuilder().setEndTime(Timestamps.fromMillis(System.currentTimeMillis())).build();
    TypedValue value = TypedValue.newBuilder().setDoubleValue(123.45).build();
    Point point = Point.newBuilder().setInterval(interval).setValue(value).build();
    List<Point> pointList = new ArrayList<>();
    pointList.add(point);
    ProjectName name = ProjectName.of(projectId);
    // Prepares the metric descriptor
    Map<String, String> metricLabels = new HashMap<>();
    Metric metric = Metric.newBuilder().setType("custom.googleapis.com/my_metric").putAllLabels(metricLabels).build();
    // Prepares the monitored resource descriptor
    Map<String, String> resourceLabels = new HashMap<>();
    resourceLabels.put("instance_id", "1234567890123456789");
    resourceLabels.put("zone", "us-central1-f");
    MonitoredResource resource = MonitoredResource.newBuilder().setType("gce_instance").putAllLabels(resourceLabels).build();
    // Prepares the time series request
    TimeSeries timeSeries = TimeSeries.newBuilder().setMetric(metric).setResource(resource).addAllPoints(pointList).build();
    List<TimeSeries> timeSeriesList = new ArrayList<>();
    timeSeriesList.add(timeSeries);
    CreateTimeSeriesRequest request = CreateTimeSeriesRequest.newBuilder().setName(name.toString()).addAllTimeSeries(timeSeriesList).build();
    // Writes time series data
    metricServiceClient.createTimeSeries(request);
    System.out.println("Done writing time series value.");
// [END monitoring_write_timeseries]
}

Example 13 with Point

use of net.imglib2.Point in project java-docs-samples by GoogleCloudPlatform.

the class QuickstartSample method main.

public static void main(String... args) throws Exception {
    // Your Google Cloud Platform project ID
    String projectId = System.getProperty("projectId");
    if (projectId == null) {
        System.err.println("Usage: QuickstartSample -DprojectId=YOUR_PROJECT_ID");
        return;
    }
    // Instantiates a client
    MetricServiceClient metricServiceClient = MetricServiceClient.create();
    // Prepares an individual data point
    TimeInterval interval = TimeInterval.newBuilder().setEndTime(Timestamps.fromMillis(System.currentTimeMillis())).build();
    TypedValue value = TypedValue.newBuilder().setDoubleValue(123.45).build();
    Point point = Point.newBuilder().setInterval(interval).setValue(value).build();
    List<Point> pointList = new ArrayList<>();
    pointList.add(point);
    ProjectName name = ProjectName.of(projectId);
    // Prepares the metric descriptor
    Map<String, String> metricLabels = new HashMap<String, String>();
    metricLabels.put("store_id", "Pittsburg");
    Metric metric = Metric.newBuilder().setType("custom.googleapis.com/stores/daily_sales").putAllLabels(metricLabels).build();
    // Prepares the monitored resource descriptor
    Map<String, String> resourceLabels = new HashMap<String, String>();
    resourceLabels.put("project_id", projectId);
    MonitoredResource resource = MonitoredResource.newBuilder().setType("global").putAllLabels(resourceLabels).build();
    // Prepares the time series request
    TimeSeries timeSeries = TimeSeries.newBuilder().setMetric(metric).setResource(resource).addAllPoints(pointList).build();
    List<TimeSeries> timeSeriesList = new ArrayList<>();
    timeSeriesList.add(timeSeries);
    CreateTimeSeriesRequest request = CreateTimeSeriesRequest.newBuilder().setName(name.toString()).addAllTimeSeries(timeSeriesList).build();
    // Writes time series data
    metricServiceClient.createTimeSeries(request);
    System.out.printf("Done writing time series data.%n");
    metricServiceClient.close();
}

Example 14 with Point

use of net.imglib2.Point in project java-docs-samples by GoogleCloudPlatform.

the class BigQueryRunner method prepareMetric.

// Returns a metric time series with a single int64 data point.
private TimeSeries prepareMetric(MetricDescriptor requiredMetric, long metricValue) {
    TimeInterval interval = TimeInterval.newBuilder().setEndTime(Timestamps.fromMillis(System.currentTimeMillis())).build();
    TypedValue value = TypedValue.newBuilder().setInt64Value(metricValue).build();
    Point point = Point.newBuilder().setInterval(interval).setValue(value).build();
    List<Point> pointList = Lists.newArrayList();
    pointList.add(point);
    Metric metric = Metric.newBuilder().setType(requiredMetric.getName()).build();
    return TimeSeries.newBuilder().setMetric(metric).addAllPoints(pointList).build();
}

Example 15 with Point

use of net.imglib2.Point in project java-mapollage by trixon.

the class Operation method addPolygons.

private void addPolygons(Folder polygonParent, List<Feature> features) {
    for (Feature feature : features) {
        if (feature instanceof Folder) {
            Folder folder = (Folder) feature;
            if (folder != mPathFolder && folder != mPathGapFolder && folder != mPolygonFolder) {
                System.out.println("ENTER FOLDER=" + folder.getName());
                System.out.println("PARENT FOLDER=" + polygonParent.getName());
                Folder polygonFolder = polygonParent.createAndAddFolder().withName(folder.getName()).withOpen(true);
                mFolderPolygonInputs.put(polygonFolder, new ArrayList<>());
                addPolygons(polygonFolder, folder.getFeature());
                System.out.println("POLYGON FOLDER=" + polygonFolder.getName() + " CONTAINS");
                if (mFolderPolygonInputs.get(polygonFolder) != null) {
                    addPolygon(folder.getName(), mFolderPolygonInputs.get(polygonFolder), polygonParent);
                }
                System.out.println("EXIT FOLDER=" + folder.getName());
                System.out.println("");
            }
        }
        if (feature instanceof Placemark) {
            Placemark placemark = (Placemark) feature;
            System.out.println("PLACEMARK=" + placemark.getName() + "(PARENT=)" + polygonParent.getName());
            Point point = (Point) placemark.getGeometry();
            point.getCoordinates().forEach((coordinate) -> {
                mFolderPolygonInputs.get(polygonParent).add(coordinate);
            });
        }
    }
}