Examples with DoubleType net.imglib2.type.numeric.real.DoubleType used on opensource projects

Example 66 with DoubleType

use of net.imglib2.type.numeric.real.DoubleType in project imagej-ops by imagej.

the class OpServiceTest method testOpByType.

/**
 * Tests {@link OpService#op(Class, Object...)}.
 */
@Test
public void testOpByType() {
    final DoubleType value = new DoubleType(123.456);
    final Op op = ops.op(InfinityOp.class, value);
    assertSame(InfinityOp.class, op.getClass());
    assertFalse(Double.isInfinite(value.get()));
    op.run();
    assertTrue(Double.isInfinite(value.get()));
}

Example 67 with DoubleType

use of net.imglib2.type.numeric.real.DoubleType in project imagej-ops by imagej.

the class OpServiceTest method testAliases.

/**
 * Tests {@link OpService#run(String, Object...)} with op aliases.
 */
@Test
public void testAliases() {
    final DoubleType value = new DoubleType(123.456);
    assertFalse(Double.isInfinite(value.get()));
    final Object result = ops.run("infin", value);
    assertSame(value, result);
    assertTrue(Double.isInfinite(value.get()));
    value.set(0.0);
    assertFalse(Double.isInfinite(value.get()));
    final Object result2 = ops.run("inf", value);
    assertSame(value, result2);
    assertTrue(Double.isInfinite(value.get()));
    value.set(0.0);
    boolean noSuchAlias = false;
    try {
        ops.run("infini", value);
    } catch (final IllegalArgumentException exc) {
        noSuchAlias = true;
    }
    assertTrue(noSuchAlias);
}

Example 68 with DoubleType

use of net.imglib2.type.numeric.real.DoubleType in project imagej-ops by imagej.

the class OpServiceTest method testRunByType.

/**
 * Tests {@link OpService#run(Class, Object...)}.
 */
@Test
public void testRunByType() {
    final DoubleType value = new DoubleType(123.456);
    assertFalse(Double.isInfinite(value.get()));
    final Object result = ops.run(InfinityOp.class, value);
    assertSame(value, result);
    assertTrue(Double.isInfinite(value.get()));
}

Example 69 with DoubleType

use of net.imglib2.type.numeric.real.DoubleType in project imagej-ops by imagej.

the class BoxCount method calculate.

/**
 * Counts the number of foreground sections in the interval repeatedly with
 * different size sections
 *
 * @param input an n-dimensional binary interval
 * @return A list of (log(foreground count), -log(section size))
 *         {@link ValuePair} objects for curve fitting
 */
@Override
public List<ValuePair<DoubleType, DoubleType>> calculate(final RandomAccessibleInterval<B> input) {
    final List<ValuePair<DoubleType, DoubleType>> points = new ArrayList<>();
    final int dimensions = input.numDimensions();
    final long[] sizes = new long[dimensions];
    final long numTranslations = 1 + gridMoves;
    input.dimensions(sizes);
    for (long sectionSize = maxSize; sectionSize >= minSize; sectionSize /= scaling) {
        final long translationAmount = Math.max(1, sectionSize / numTranslations);
        final Stream<long[]> translations = translationStream(numTranslations, translationAmount, dimensions - 1, new long[dimensions]);
        final LongStream foregroundCounts = countTranslatedGrids(input, translations, sizes, sectionSize);
        final long foreground = foregroundCounts.min().orElse(0);
        final double logSize = -Math.log(sectionSize);
        final double logCount = Math.log(foreground);
        final ValuePair<DoubleType, DoubleType> point = new ValuePair<>(new DoubleType(logSize), new DoubleType(logCount));
        points.add(point);
    }
    return points;
}

Example 70 with DoubleType

use of net.imglib2.type.numeric.real.DoubleType 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;
}