Examples with KeyValue org.vcell.util.document.KeyValue used on opensource projects

Example 1 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class SimulationDataTest method noZero.

/*
	@Test
	public void nameTest( ) {
		KeyValue kv = new KeyValue("8675904");
		for (int j : jIndexes) {
			for (int i = 1; i < 10000; i++) {
				String old = SimulationData.createCanonicalSmoldynOutputFileNameOld(kv, j, i);
				String now = SimulationData.createCanonicalSmoldynOutputFileName(kv, j, i);
				if (!old.equals(now)) {
					System.err.println(old + " and " + now);
				}
				assertTrue(old.equals(now));
			}
		}
	}
	*/
@Test(expected = IllegalArgumentException.class)
public void noZero() {
    KeyValue kv = new KeyValue("8675904");
    String now = SimulationData.createCanonicalSmoldynOutputFileName(kv, 0, 0);
    System.out.println("never see " + now);
}

Example 2 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class VCellDataTest method main.

/**
 * @param args
 */
public static void main(String[] args) {
    try {
        ResourceUtil.setNativeLibraryDirectory();
        KeyValue simKey = new KeyValue("1661241954");
        String pathPrefix = "C:\\Users\\schaff\\.vcell\\simdata\\user\\";
        File meshFile = new File(pathPrefix + "SimID_" + simKey + "_0_.mesh");
        File meshMetricsFile = new File(pathPrefix + "SimID_" + simKey + "_0_.meshmetrics");
        File subdomainFile = new File(pathPrefix + "SimID_" + simKey + "_0_.subdomains");
        File logFile = new File(pathPrefix + "SimID_" + simKey + "_0_.log");
        File zipFile = new File(pathPrefix + "SimID_" + simKey + "_0_00.zip");
        File postprocessingFile = new File(pathPrefix + "SimID_" + simKey + "_0_.hdf5");
        VCellSimFiles vcellFiles = new VCellSimFiles(simKey, 0, meshFile, meshMetricsFile, subdomainFile, logFile, postprocessingFile);
        vcellFiles.addDataFileEntry(zipFile, new File("SimID_" + simKey + "_0_0000.sim"), 0.0);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0001.sim"),0.05);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0002.sim"),0.10);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0003.sim"),0.15);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0004.sim"),0.20);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0005.sim"),0.25);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0006.sim"),0.30);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0007.sim"),0.35);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0008.sim"),0.40);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0009.sim"),0.45);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0010.sim"),0.50);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0011.sim"),0.55);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0012.sim"),0.60);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0013.sim"),0.65);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0014.sim"),0.70);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0015.sim"),0.75);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0016.sim"),0.80);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0017.sim"),0.85);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0018.sim"),0.90);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0019.sim"),0.95);
        // vcellFiles.addDataFileEntry(zipFile,new File("SimID_"+simKey+"_0_0020.sim"),1.0);
        // process each domain separately (only have to process the mesh once for each one)
        CartesianMeshVtkFileWriter cartesianMeshVtkFileWriter = new CartesianMeshVtkFileWriter();
        File destinationDirectory = new File("C:\\Developer\\eclipse\\workspace\\VCell_5.3_visfull\\VtkData\\");
        File[] generatedFiles = cartesianMeshVtkFileWriter.writeVtuExportFiles(vcellFiles, destinationDirectory, null);
        boolean bDisplay = true;
        if (bDisplay) {
            CartesianMeshFileReader reader = new CartesianMeshFileReader();
            CartesianMesh mesh = reader.readFromFiles(vcellFiles);
            ArrayList<String> allDomainNames = new ArrayList<String>();
            allDomainNames.addAll(mesh.getVolumeDomainNames());
            allDomainNames.addAll(mesh.getMembraneDomainNames());
            for (String domain : allDomainNames) {
                for (int timeIndex = 0; timeIndex < vcellFiles.getTimes().size(); timeIndex++) {
                    // String filename = new File(destinationDirectory,vcellFiles.getCannonicalFilePrefix(domain,timeIndex)+".vtu").getAbsolutePath();
                    // vtkUnstructuredGrid vtkgrid = vtkGridUtils.read(filename);
                    // vtkgrid.BuildLinks();
                    // 
                    // String varName0 = vtkgrid.GetCellData().GetArrayName(0);
                    // String varName1 = vtkgrid.GetCellData().GetArrayName(1);
                    // SimpleVTKViewer simpleViewer = new SimpleVTKViewer();
                    // simpleViewer.showGrid(vtkgrid, varName0, varName1);
                    Thread.sleep(1000);
                }
            }
        }
        // CartesianMeshFileReader reader = new CartesianMeshFileReader();
        // CartesianMesh mesh = reader.readFromFiles(vcellFiles);
        // CartesianMeshMapping cartesianMeshMapping = new CartesianMeshMapping();
        // 
        // //String domainName = mesh.meshRegionInfo.getVolumeDomainNames().get(1);
        // String domainName = mesh.meshRegionInfo.getVolumeDomainNames().get(0);
        // 
        // System.out.println("making visMesh for domain "+domainName+" of ["+mesh.meshRegionInfo.getVolumeDomainNames()+"]");
        // VisMesh visMesh = cartesianMeshMapping.fromMeshData(mesh, domainName);
        // final int numElements = visMesh.getPolyhedra().size();
        // final double[] data1 = new double[numElements];
        // final double[] data2 = new double[numElements];
        // 
        // for (int i=0;i<numElements;i++){
        // data1[i] = Math.sin(i/10000.0);
        // data2[i] = Math.cos(i/10000.0);
        // }
        // VisMeshData visData = new VisMeshData() {
        // private String[] names = new String[] { "data1", "data2" };
        // 
        // @Override
        // public String[] getVarNames() {
        // return new String[] { "data1", "data2" };
        // }
        // 
        // @Override
        // public double getTime() {
        // return 0.0;
        // }
        // 
        // @Override
        // public double[] getData(String var) {
        // if (var.equals("data1")){
        // return data1;
        // }else if (var.equals("data2")){
        // return data2;
        // }else{
        // throw new RuntimeException("var "+var+" not found");
        // }
        // }
        // };
        // 
        // VisDomain visDomain = new VisDomain("domain1",visMesh,visData);
        // VtkGridUtils vtkGridUtils = new VtkGridUtils();
        // vtkUnstructuredGrid vtkgrid = vtkGridUtils.getVtkGrid(visDomain);
        // vtkgrid = TestVTK.testWindowedSincPolyDataFilter(vtkgrid);
        // String filenameBinary = "testBinary.vtu";
        // vtkGridUtils.writeXML(vtkgrid, filenameBinary, false);
        // vtkgrid = vtkGridUtils.read(filenameBinary);
        // //vtkgrid.s
        // vtkgrid.BuildLinks();
        // SimpleVTKViewer simpleViewer = new SimpleVTKViewer();
        // String[] varNames = visDomain.getVisMeshData().getVarNames();
        // simpleViewer.showGrid(vtkgrid, varNames[0], varNames[1]);
        System.out.println("ran");
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 3 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class XmlReader method getSimulationVersion.

/**
 * This method returns a Version object from an XML representation.
 * Creation date: (3/16/2001 3:41:24 PM)
 * @return cbit.sql.Version
 * @param param org.jdom.Element
 */
private SimulationVersion getSimulationVersion(Element xmlVersion) throws XmlParseException {
    if (xmlVersion == null) {
        return null;
    }
    // determine if it should be processed using the 'fromVersionable'
    if (xmlVersion.getAttributeValue(XMLTags.FromVersionableTag) == null || Boolean.valueOf(xmlVersion.getAttributeValue(XMLTags.FromVersionableTag)).booleanValue() || this.readKeysFlag == false) {
        // this came from a versionable object, so skip! Or it should not explicitly import the information inside the Version
        return null;
    }
    // Read all the attributes
    // *name
    String name = unMangle(xmlVersion.getAttributeValue(XMLTags.NameAttrTag));
    // *key
    String temp = xmlVersion.getAttributeValue(XMLTags.KeyValueAttrTag);
    KeyValue key = new KeyValue(temp);
    // *owner
    Element tempElement = xmlVersion.getChild(XMLTags.OwnerTag, vcNamespace);
    User owner = new User(unMangle(tempElement.getAttributeValue(XMLTags.NameAttrTag)), new KeyValue(tempElement.getAttributeValue(XMLTags.IdentifierAttrTag)));
    // *access
    GroupAccess groupAccess = getGroupAccess(xmlVersion.getChild(XMLTags.GroupAccessTag, vcNamespace));
    // *Branchpointref
    temp = xmlVersion.getAttributeValue(XMLTags.BranchPointRefTag);
    KeyValue branchpointref = null;
    if (temp != null) {
        branchpointref = new KeyValue(temp);
    }
    // *BranchID
    java.math.BigDecimal branchId = new java.math.BigDecimal(xmlVersion.getAttributeValue(XMLTags.BranchIdAttrTag));
    // *Flag
    temp = xmlVersion.getAttributeValue(XMLTags.FlagAttrTag);
    VersionFlag flag = VersionFlag.fromInt(Integer.parseInt(temp));
    // *Date
    java.util.Date date = null;
    temp = xmlVersion.getAttributeValue(XMLTags.DateAttrTag);
    if (temp != null) {
        try {
            SimpleDateFormat simpleDateFormat = new SimpleDateFormat(BeanUtils.vcDateFormat, Locale.US);
            date = simpleDateFormat.parse(temp);
        } catch (java.text.ParseException e) {
            e.printStackTrace();
            throw new XmlParseException("Invalid date:" + temp, e);
        }
    }
    // *DataSimulationRef
    KeyValue parentSimRefKey = null;
    tempElement = xmlVersion.getChild(XMLTags.ParentSimRefTag, vcNamespace);
    if (tempElement != null) {
        parentSimRefKey = new KeyValue(tempElement.getAttributeValue(XMLTags.KeyValueAttrTag));
    }
    // *Annotation
    String annotation = null;
    String annotationText = xmlVersion.getChildText(XMLTags.AnnotationTag, vcNamespace);
    if (annotationText != null && annotationText.length() > 0) {
        annotation = unMangle(annotationText);
    }
    // Create and return the version object
    return new SimulationVersion(key, name, owner, groupAccess, branchpointref, branchId, date, flag, annotation, parentSimRefKey);
}

Example 4 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class XmlReader method getAnalyticSubVolume.

/**
 * This method returns an AnalyticSubVolume object from a XML representation.
 * Creation date: (5/1/2001 5:26:17 PM)
 * @return cbit.vcell.geometry.AnalyticSubVolume
 * @param param org.jdom.Element
 */
private AnalyticSubVolume getAnalyticSubVolume(Element param) throws XmlParseException {
    // retrieve the attributes
    String name = param.getAttributeValue(XMLTags.NameAttrTag);
    int handle = Integer.parseInt(param.getAttributeValue(XMLTags.HandleAttrTag));
    // process the key
    KeyValue key = null;
    String temp = param.getAttributeValue(XMLTags.KeyValueAttrTag);
    if (temp != null && temp.length() > 0 && this.readKeysFlag) {
        key = new KeyValue(temp);
    }
    // Retrieve the expression
    temp = param.getChildText(XMLTags.AnalyticExpressionTag, vcNamespace);
    if (temp == null) {
        throw new XmlParseException("A Problem occured while retrieving the analytic expression of the AnalyticSubvolume " + name);
    }
    Expression newexpression = unMangleExpression(temp);
    // Create the AnalyticCompartment
    AnalyticSubVolume newsubvolume = null;
    try {
        newsubvolume = new AnalyticSubVolume(key, name, newexpression, handle);
    } catch (ExpressionException e) {
        e.printStackTrace();
        throw new XmlParseException("An ExpressionException occured when creating the new AnalyticSubvolume " + name, e);
    }
    return newsubvolume;
}

Example 5 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class ParameterEstimationTaskSimulatorIDA method getRowColumnRestultSetByBestEstimations.

public RowColumnResultSet getRowColumnRestultSetByBestEstimations(ParameterEstimationTask parameterEstimationTask, String[] paramNames, double[] paramValues) throws Exception {
    // create a temp simulation based on math description
    KeyValue key = new KeyValue("" + Math.abs(new Random().nextLong()));
    SimulationVersion dummyVersion = new SimulationVersion(key, "name", new User("temp", new KeyValue("1")), null, null, null, null, null, null, null);
    Simulation simulation = new Simulation(dummyVersion, parameterEstimationTask.getSimulationContext().getMathDescription());
    ReferenceData refData = parameterEstimationTask.getModelOptimizationSpec().getReferenceData();
    double[] times = refData.getDataByColumn(0);
    double endTime = times[times.length - 1];
    ExplicitOutputTimeSpec exTimeSpec = new ExplicitOutputTimeSpec(times);
    // set simulation ending time and output interval
    simulation.getSolverTaskDescription().setTimeBounds(new TimeBounds(0, endTime));
    simulation.getSolverTaskDescription().setOutputTimeSpec(exTimeSpec);
    // set parameters as math overrides
    MathOverrides mathOverrides = simulation.getMathOverrides();
    for (int i = 0; i < paramNames.length; i++) {
        mathOverrides.putConstant(new Constant(paramNames[i], new Expression(paramValues[i])));
    }
    SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, 0, null), 0);
    IDASolverStandalone idaSolver = new IDASolverStandalone(simTask, ResourceUtil.getLocalSimDir("temp"), false);
    // startSolver();
    idaSolver.runSolver();
    Thread.sleep(1000);
    long startTimeMS = System.currentTimeMillis();
    while (idaSolver.getSolverStatus().isRunning() && System.currentTimeMillis() < (startTimeMS + 10000L)) {
        Thread.sleep(500);
    }
    ODESolverResultSet resultset = idaSolver.getODESolverResultSet();
    return resultset;
}