Examples with Geometry cbit.vcell.geometry.Geometry used on opensource projects

Example 81 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class ClientRequestManager method createFDOSFromSurfaceFile.

public static FieldDataFileOperationSpec createFDOSFromSurfaceFile(File surfaceFile) throws Exception {
    SurfaceCollection surfaceCollection = createSurfaceCollectionFromSurfaceFile(surfaceFile);
    if (surfaceCollection != null) {
        Geometry geometry = RayCaster.createGeometryFromSTL(new GeometryThumbnailImageFactoryAWT(), surfaceCollection, 1000000);
        FieldDataFileOperationSpec fdfos = new FieldDataFileOperationSpec();
        fdfos.origin = geometry.getOrigin();
        fdfos.extent = geometry.getExtent();
        VCImage image = geometry.getGeometrySpec().getImage();
        if (image.getNumPixelClasses() == 1) {
            throw new Exception("STL import failed during processing, pixelclass count=1");
        }
        fdfos.isize = new ISize(image.getNumX(), image.getNumY(), image.getNumZ());
        byte[] pixels = image.getPixels();
        short[] dataToSegment = new short[image.getNumXYZ()];
        for (int i = 0; i < pixels.length; i++) {
            dataToSegment[i] = pixels[i];
        }
        fdfos.shortSpecData = new short[][][] { { dataToSegment } };
        return fdfos;
    }
    return null;
}

Example 82 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class OptXmlWriter method getModelXML.

public static Element getModelXML(PdeObjectiveFunction pdeObjectiveFunction, String[] parameterNames) {
    Element modelElement = new Element(OptXmlTags.Model_Tag);
    try {
        SpatialReferenceData refData = pdeObjectiveFunction.getReferenceData();
        double refDataEndTime = refData.getDataByRow(refData.getNumDataRows() - 1)[0];
        // 
        // post the problem either as an IDA or CVODE model
        // 
        org.vcell.util.document.SimulationVersion simVersion = new org.vcell.util.document.SimulationVersion(new KeyValue("12345"), "name", new org.vcell.util.document.User("user", new KeyValue("123")), new org.vcell.util.document.GroupAccessNone(), // versionBranchPointRef
        null, // branchID
        new java.math.BigDecimal(1.0), new java.util.Date(), org.vcell.util.document.VersionFlag.Archived, "", null);
        Simulation simulation = new Simulation(simVersion, pdeObjectiveFunction.getMathDescription());
        simulation.getMeshSpecification().setSamplingSize(refData.getDataISize());
        double[] times = refData.getDataByColumn(0);
        double minDt = Double.POSITIVE_INFINITY;
        for (int i = 1; i < times.length; i++) {
            minDt = Math.min(minDt, times[i] - times[i - 1]);
        }
        simulation.getSolverTaskDescription().setTimeBounds(new cbit.vcell.solver.TimeBounds(0.0, refDataEndTime));
        simulation.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolume);
        simulation.getSolverTaskDescription().setTimeStep(new TimeStep(minDt / 5, minDt / 5, minDt / 5));
        // clone and resample geometry
        Geometry resampledGeometry = null;
        try {
            resampledGeometry = (Geometry) BeanUtils.cloneSerializable(simulation.getMathDescription().getGeometry());
            GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
            ISize newSize = simulation.getMeshSpecification().getSamplingSize();
            geoSurfaceDesc.setVolumeSampleSize(newSize);
            geoSurfaceDesc.updateAll();
        } catch (Exception e) {
            e.printStackTrace();
            throw new SolverException(e.getMessage());
        }
        SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, 0, pdeObjectiveFunction.getFieldDataIDSs()), 0);
        StringWriter simulationInputStringWriter = new StringWriter();
        FiniteVolumeFileWriter fvFileWriter = new FiniteVolumeFileWriter(new PrintWriter(simulationInputStringWriter, true), simTask, resampledGeometry, pdeObjectiveFunction.getWorkingDirectory());
        fvFileWriter.write(parameterNames);
        simulationInputStringWriter.close();
        modelElement.setAttribute(OptXmlTags.ModelType_Attr, OptXmlTags.ModelType_Attr_FVSOLVER);
        CDATA simulationInputText = new CDATA(simulationInputStringWriter.getBuffer().toString());
        modelElement.addContent(simulationInputText);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new OptimizationException("failed to create fv input file: " + e.getMessage());
    }
    return modelElement;
}

Example 83 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class XmlHelper method simToXML.

public static String simToXML(Simulation sim) throws XmlParseException {
    String simString = null;
    if (sim == null) {
        throw new XmlParseException("Invalid input for Simulation: " + sim);
    }
    Xmlproducer xmlProducer = new Xmlproducer(true);
    // cannot be null
    MathDescription md = sim.getMathDescription();
    Geometry geom = md.getGeometry();
    Element container = new Element(SIM_CONTAINER);
    Element mathElement = xmlProducer.getXML(md);
    Element simElement = xmlProducer.getXML(sim);
    if (geom != null) {
        Element geomElement = xmlProducer.getXML(geom);
        container.addContent(geomElement);
    } else {
        System.err.println("No corresponding geometry for the simulation: " + sim.getName());
    }
    container.addContent(mathElement);
    container.addContent(simElement);
    container = XmlUtil.setDefaultNamespace(container, Namespace.getNamespace(XMLTags.VCML_NS));
    simString = XmlUtil.xmlToString(container);
    return simString;
}

Example 84 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class XmlHelper method simTaskToXML.

public static String simTaskToXML(SimulationTask simTask) throws XmlParseException {
    String simTaskString = null;
    if (simTask == null) {
        throw new XmlParseException("Invalid input for SimulationTask: " + simTask);
    }
    Xmlproducer xmlProducer = new Xmlproducer(true);
    SimulationJob simJob = simTask.getSimulationJob();
    Simulation sim = simJob.getSimulation();
    Element container = new Element(SimulationTask_tag);
    int taskId = simTask.getTaskID();
    container.setAttribute(TaskId_attr, "" + taskId);
    int jobIndex = simJob.getJobIndex();
    container.setAttribute(JobIndex_attr, "" + jobIndex);
    String computeResource = simTask.getComputeResource();
    if (computeResource != null) {
        Element computeResourceElement = new Element(ComputeResource_tag);
        Text text = new Text(computeResource);
        computeResourceElement.addContent(text);
        container.addContent(computeResourceElement);
    }
    FieldDataIdentifierSpec[] fdisSpecs = simJob.getFieldDataIdentifierSpecs();
    if (fdisSpecs != null) {
        for (FieldDataIdentifierSpec fdisSpec : fdisSpecs) {
            Element fdisElement = new Element(FieldFunctionIdentifierSpec_tag);
            fdisElement.setText(fdisSpec.toCSVString());
            container.addContent(fdisElement);
        }
    }
    MathDescription md = sim.getMathDescription();
    Element mathElement = xmlProducer.getXML(md);
    container.addContent(mathElement);
    Element simElement = xmlProducer.getXML(sim);
    container.addContent(simElement);
    Geometry geom = md.getGeometry();
    if (geom != null) {
        Element geomElement = xmlProducer.getXML(geom);
        container.addContent(geomElement);
    } else {
        System.err.println("No corresponding geometry for the simulation: " + sim.getName());
    }
    container = XmlUtil.setDefaultNamespace(container, Namespace.getNamespace(XMLTags.VCML_NS));
    simTaskString = XmlUtil.xmlToString(container);
    return simTaskString;
}

Example 85 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class XmlHelper method XMLToGeometry.

static Geometry XMLToGeometry(XMLSource xmlSource, boolean printkeys) throws XmlParseException {
    Geometry geometry = null;
    if (xmlSource == null) {
        throw new XmlParseException("Invalid xml for Geometry.");
    }
    Document xmlDoc = xmlSource.getXmlDoc();
    // NOTES:
    // * The root element can be <Biomodel> (old-style vcml) OR <vcml> (new-style vcml)
    // * With the old-style vcml, the namespace was " "
    // * With the new-style vcml, there is an intermediate stage where the namespace for <vcml> root
    // was set to "http://sourceforge.net/projects/VCell/version0.4" for some models and
    // "http://sourceforge.net/projects/vcell/vcml" for some models; and the namespace for child element
    // <biomdel>, etc. was " "
    // * The final new-style vcml has (should have) the namespace "http://sourceforge.net/projects/vcell/vcml"
    // for <vcml> and all children elements.
    // The code below attempts to take care of this situation.
    Element root = xmlDoc.getRootElement();
    Namespace ns = null;
    if (root.getName().equals(XMLTags.VcmlRootNodeTag)) {
        // NEW WAY - with xml string containing xml declaration, vcml element, namespace, etc ...
        ns = root.getNamespace();
        Element geoRoot = root.getChild(XMLTags.GeometryTag, ns);
        if (geoRoot == null) {
            geoRoot = root.getChild(XMLTags.GeometryTag);
            // geoRoot was null, so obtained the <Geometry> element with namespace " ";
            // Re-set the namespace so that the correct XMLReader constructor is invoked.
            ns = null;
        }
        root = geoRoot;
    }
    // else - root is assumed to be old-style vcml with <Geometry> as root.
    // common for both new-style (with xml declaration, vcml element, etc) and old-style (geometry is root)
    // If namespace is null, xml is the old-style xml with geometry as root, so invoke XMLReader without namespace argument.
    XmlReader reader = null;
    if (ns == null) {
        reader = new XmlReader(printkeys);
    } else {
        reader = new XmlReader(printkeys, ns);
    }
    geometry = reader.getGeometry(root);
    geometry.refreshDependencies();
    return geometry;
}