Examples with LocalWorkspace org.vcell.vmicro.workflow.data.LocalWorkspace used on opensource projects

Example 11 with LocalWorkspace

use of org.vcell.vmicro.workflow.data.LocalWorkspace in project vcell by virtualcell.

the class KenworthyTest method main.

public static void main(String[] args) {
    if (args.length != 2) {
        System.out.println("expecting 2 arguments");
        System.out.println("usage: java " + Workflow.class.getSimpleName() + " workingdir workflowInputFile");
        System.out.println("workingdir example: " + "D:\\developer\\eclipse\\workspace\\VCell_5.4_vmicro\\datadir");
        System.out.println("workflowInputFile example: " + "D:\\developer\\eclipse\\workspace\\VCell_5.4_vmicro\\workflow1.txt");
        System.exit(1);
    }
    try {
        // PropertyLoader.loadProperties();
        // workflowInputFile "C:\\developer\\eclipse\\workspace\\VCell_5.3_vmicro\\workflow1.txt"
        File workingDirectory = new File(args[0]);
        LocalWorkspace localWorkspace = new LocalWorkspace(workingDirectory);
        Repository repository = new MemoryRepository();
        // String workflowLanguageText = BeanUtils.readBytesFromFile(new File(args[1]), null);
        // Workflow workflow = Workflow.parse(localWorkspace, workflowLanguageText);
        System.err.println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using hard-coded example instead <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<");
        File vfrapFile = new File("D:\\Developer\\eclipse\\workspace_refactor\\VCell_5.4_vmicro\\3D_FRAP_2_ZProjection_Simulation1.vfrap");
        // Workflow workflow = getVFrapSimpleExample(workingDirectory, vfrapFile);
        // Workflow workflow = getFakeDataExample(workingDirectory);
        Workflow workflow = getInteractiveModelWorkflow(repository, workingDirectory);
        TaskContext taskContext = new TaskContext(workflow, repository, localWorkspace);
        ArrayList<Issue> issues = new ArrayList<Issue>();
        IssueContext issueContext = new IssueContext();
        workflow.gatherIssues(issueContext, issues);
        // WorkflowJGraphProxy workflowJGraphProxy = new WorkflowJGraphProxy(workflow);
        // displayWorkflowGraphJGraphX(workflowJGraphProxy);
        WorkflowUtilities.displayWorkflowGraph(workflow);
        WorkflowUtilities.displayWorkflowTable(taskContext);
        workflow.reportIssues(issues, Issue.SEVERITY_INFO, true);
        // 
        // execute the workflow
        // 
        workflow.compute(taskContext, new WorkflowUtilities.Progress());
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 12 with LocalWorkspace

use of org.vcell.vmicro.workflow.data.LocalWorkspace in project vcell by virtualcell.

the class KenworthyTest method getInteractiveModelWorkflow.

public static Workflow getInteractiveModelWorkflow(Repository repository, File workingDirectory) {
    // 
    // construct the dataflow graph
    // 
    LocalWorkspace localWorkspace = new LocalWorkspace(workingDirectory);
    Workflow workflow = new Workflow("main");
    // 
    // workflow parameters
    // 
    WorkflowParameter<Double> bleachThreshold = workflow.addParameter(Double.class, "bleachThreshold", repository, 0.80);
    WorkflowParameter<Double> cellThreshold = workflow.addParameter(Double.class, "cellThreshold", repository, 0.5);
    WorkflowParameter<Double> cellRadius = workflow.addParameter(Double.class, "cellRadius", repository, 10.0);
    WorkflowParameter<String> cytosolName = workflow.addParameter(String.class, "cytosolName", repository, "cytosol");
    WorkflowParameter<String> extracellularName = workflow.addParameter(String.class, "extracellularName", repository, "ec");
    WorkflowParameter<Double> deltaX = workflow.addParameter(Double.class, "deltaX", repository, 0.3);
    WorkflowParameter<Double> outputTimeStep = workflow.addParameter(Double.class, "outputTimeStep", repository, 0.3);
    // 0.3
    WorkflowParameter<Double> psfSigma = workflow.addParameter(Double.class, "psfSigma", repository, 0.01);
    // circular disk (no K
    WorkflowParameter<Double> bleachRadius = workflow.addParameter(Double.class, "bleachRadius", repository, 4.0);
    // 5.0
    WorkflowParameter<Double> bleachRate = workflow.addParameter(Double.class, "bleachRate", repository, 500.0);
    // 0.3
    WorkflowParameter<Double> bleachDuration = workflow.addParameter(Double.class, "bleachDuraction", repository, 0.003);
    // 1.0
    WorkflowParameter<Double> postbleachDelay = workflow.addParameter(Double.class, "postbleachDelay", repository, 0.001);
    WorkflowParameter<Double> postbleachDuration = workflow.addParameter(Double.class, "postbleachDuraction", repository, 25.0);
    // no bleach while monitoring
    WorkflowParameter<Double> bleachMonitorRate = workflow.addParameter(Double.class, "bleachMonitorRate", repository, 0.0000005);
    WorkflowParameter<Double> primaryDiffusionRate = workflow.addParameter(Double.class, "primaryDiffusionRate", repository, 2.0);
    // primary fraction 100%
    WorkflowParameter<Double> primaryFraction = workflow.addParameter(Double.class, "primaryFraction", repository, 1.0);
    // 20.0
    WorkflowParameter<Double> secondaryDiffusionRate = workflow.addParameter(Double.class, "secondaryDiffusionRate", repository, 0.0);
    // 0.2
    WorkflowParameter<Double> secondaryFraction = workflow.addParameter(Double.class, "secondaryFraction", repository, 0.0);
    // no noise to start
    WorkflowParameter<Boolean> bNoise = workflow.addParameter(Boolean.class, "bNoise", repository, true);
    WorkflowParameter<Double> maxIntensity = workflow.addParameter(Double.class, "maxIntensity", repository, 60000.0);
    Generate2DExpModel_UniformBleach generateExpModel = new Generate2DExpModel_UniformBleach("generateExpModel");
    workflow.connectParameter(bleachDuration, generateExpModel.bleachDuration);
    workflow.connectParameter(bleachMonitorRate, generateExpModel.bleachMonitorRate);
    workflow.connectParameter(bleachRadius, generateExpModel.bleachRadius);
    workflow.connectParameter(bleachRate, generateExpModel.bleachRate);
    workflow.connectParameter(cellRadius, generateExpModel.cellRadius);
    workflow.connectParameter(cytosolName, generateExpModel.cytosolName);
    workflow.connectParameter(deltaX, generateExpModel.deltaX);
    workflow.connectParameter(extracellularName, generateExpModel.extracellularName);
    workflow.connectParameter(outputTimeStep, generateExpModel.outputTimeStep);
    workflow.connectParameter(postbleachDelay, generateExpModel.postbleachDelay);
    workflow.connectParameter(postbleachDuration, generateExpModel.postbleachDuration);
    workflow.connectParameter(primaryDiffusionRate, generateExpModel.primaryDiffusionRate);
    workflow.connectParameter(primaryFraction, generateExpModel.primaryFraction);
    workflow.connectParameter(psfSigma, generateExpModel.psfSigma);
    workflow.connectParameter(secondaryDiffusionRate, generateExpModel.secondaryDiffusionRate);
    workflow.connectParameter(secondaryFraction, generateExpModel.secondaryFraction);
    workflow.addTask(generateExpModel);
    // DisplayBioModel displayBioModel = new DisplayBioModel("displayBioModel");
    // displayBioModel.bioModel.setSource(generateExpModel.bioModel_2D);
    // workflow.addTask(displayBioModel);
    RunFakeSim runFakeSim = new RunFakeSim("runFakeSim");
    workflow.connectParameter(bNoise, runFakeSim.bNoise);
    workflow.connectParameter(maxIntensity, runFakeSim.maxIntensity);
    workflow.connect2(generateExpModel.simulation_2D, runFakeSim.simulation_2D);
    workflow.connect2(generateExpModel.bleachBlackoutBeginTime, runFakeSim.bleachBlackoutBeginTime);
    workflow.connect2(generateExpModel.bleachBlackoutEndTime, runFakeSim.bleachBlackoutEndTime);
    workflow.addTask(runFakeSim);
    // DisplayTimeSeries displayRawImages = new DisplayTimeSeries("displayRawImages");
    // displayRawImages.imageTimeSeries.setSource(runFakeSim.simTimeSeries);
    // displayRawImages.title.setSource(workflow.addParameter(String.class, "displayRawImagesTitle", "raw Images from "+runFakeSim.getClass().getSimpleName()));
    // workflow.addTask(displayRawImages);
    KenworthyProcess kenworthyProcess = new KenworthyProcess("kenworthyProcess");
    workflow.connectParameter(bleachThreshold, kenworthyProcess.bleachThreshold);
    workflow.connectParameter(cellThreshold, kenworthyProcess.cellThreshold);
    workflow.connect2(runFakeSim.simTimeSeries, kenworthyProcess.rawTimeSeriesImages);
    workflow.addTask(kenworthyProcess);
    return workflow;
}

Example 13 with LocalWorkspace

use of org.vcell.vmicro.workflow.data.LocalWorkspace in project vcell by virtualcell.

the class WorkflowTest method getVFrapExample.

public static Workflow getVFrapExample(Repository repository, File workingDirectory, File vfrapFile) {
    // 
    // construct the dataflow graph
    // 
    LocalWorkspace localWorkspace = new LocalWorkspace(workingDirectory);
    Workflow workflow = new Workflow("main");
    TaskContext context = new TaskContext(workflow, repository, localWorkspace);
    // 
    // workflow parameters
    // 
    WorkflowParameter<Double> maxIntensity = workflow.addParameter(Double.class, "maxIntensity");
    context.setParameterValue(maxIntensity, 10000.0);
    WorkflowParameter<Boolean> bNoise = workflow.addParameter(Boolean.class, "bNoise");
    context.setParameterValue(bNoise, true);
    WorkflowParameter<File> vfrapFileParam = workflow.addParameter(File.class, "vfrapFile");
    context.setParameterValue(vfrapFileParam, vfrapFile);
    WorkflowParameter<Double> bleachThreshold = workflow.addParameter(Double.class, "bleachThreshold");
    context.setParameterValue(bleachThreshold, 0.80);
    WorkflowParameter<Double> cellThreshold = workflow.addParameter(Double.class, "cellThreshold");
    context.setParameterValue(cellThreshold, 0.5);
    WorkflowParameter<String> modelTypeOne = workflow.addParameter(String.class, "modelType");
    context.setParameterValue(modelTypeOne, GenerateRefSimOptModel.ModelType.DiffOne.toString());
    WorkflowParameter<String> modelTypeTwo = workflow.addParameter(String.class, "modelType2");
    context.setParameterValue(modelTypeTwo, GenerateRefSimOptModel.ModelType.DiffTwoWithPenalty.toString());
    WorkflowParameter<String> displayROITitle = workflow.addParameter(String.class, "displayROITitle");
    context.setParameterValue(displayROITitle, "rois");
    // input data from VFrap file
    ImportRawTimeSeriesFromVFrap timeSeriesFromVCell = new ImportRawTimeSeriesFromVFrap("frapImport");
    workflow.connectParameter(vfrapFileParam, timeSeriesFromVCell.vfrapFile);
    workflow.addTask(timeSeriesFromVCell);
    // // input data from HDF5 postprocessing (includes PSF)
    // ImportRawTimeSeriesFromHdf5Fluor timeSeriesFromVCell = new ImportRawTimeSeriesFromHdf5Fluor("t1");
    // timeSeriesFromVCell.bNoise.setSource(bNoise);
    // timeSeriesFromVCell.maxIntensity.setSource(maxIntensity);
    // timeSeriesFromVCell.fluorDataName.setSource(hdf5FluorName);
    // timeSeriesFromVCell.vcellHdf5File.setSource(hdf5File);
    // timeSeriesFromVCell.zSliceIndex.setSource(hdf5ZSliceIndex);
    // workflow.addTask(timeSeriesFromVCell);
    GenerateCellROIsFromRawTimeSeries generateCellROIs = new GenerateCellROIsFromRawTimeSeries("generateCellROIs");
    workflow.connectParameter(cellThreshold, generateCellROIs.cellThreshold);
    workflow.connect2(timeSeriesFromVCell.rawTimeSeriesImages, generateCellROIs.rawTimeSeriesImages);
    workflow.addTask(generateCellROIs);
    GenerateNormalizedFrapData generateNormalizedFrapData = new GenerateNormalizedFrapData("generateNormalizedFrapData");
    workflow.connect2(generateCellROIs.backgroundROI_2D, generateNormalizedFrapData.backgroundROI_2D);
    workflow.connect2(generateCellROIs.indexOfFirstPostbleach, generateNormalizedFrapData.indexOfFirstPostbleach);
    workflow.connect2(timeSeriesFromVCell.rawTimeSeriesImages, generateNormalizedFrapData.rawImageTimeSeries);
    workflow.addTask(generateNormalizedFrapData);
    GenerateBleachROI generateROIs = new GenerateBleachROI("generateROIs");
    workflow.connectParameter(bleachThreshold, generateROIs.bleachThreshold);
    workflow.connect2(generateCellROIs.cellROI_2D, generateROIs.cellROI_2D);
    workflow.connect2(generateNormalizedFrapData.normalizedFrapData, generateROIs.normalizedTimeSeries);
    workflow.addTask(generateROIs);
    GenerateDependentImageROIs generateDependentROIs = new GenerateDependentImageROIs("generateDependentROIs");
    workflow.connect2(generateCellROIs.cellROI_2D, generateDependentROIs.cellROI_2D);
    workflow.connect2(generateROIs.bleachedROI_2D, generateDependentROIs.bleachedROI_2D);
    workflow.addTask(generateDependentROIs);
    DisplayDependentROIs displayDependentROIs = new DisplayDependentROIs("displayDependentROIs");
    workflow.connect2(generateDependentROIs.imageDataROIs, displayDependentROIs.imageROIs);
    workflow.connect2(generateCellROIs.cellROI_2D, displayDependentROIs.cellROI);
    workflow.connectParameter(displayROITitle, displayDependentROIs.title);
    workflow.addTask(displayDependentROIs);
    GenerateReducedData generateReducedNormalizedData = new GenerateReducedData("generateReducedNormalizedData");
    workflow.connect2(generateNormalizedFrapData.normalizedFrapData, generateReducedNormalizedData.imageTimeSeries);
    workflow.connect2(generateDependentROIs.imageDataROIs, generateReducedNormalizedData.imageDataROIs);
    workflow.addTask(generateReducedNormalizedData);
    ComputeMeasurementError computeMeasurementError = new ComputeMeasurementError("computeMeasurementError");
    workflow.connect2(generateDependentROIs.imageDataROIs, computeMeasurementError.imageDataROIs);
    workflow.connect2(generateCellROIs.indexOfFirstPostbleach, computeMeasurementError.indexFirstPostbleach);
    workflow.connect2(generateNormalizedFrapData.prebleachAverage, computeMeasurementError.prebleachAverage);
    workflow.connect2(timeSeriesFromVCell.rawTimeSeriesImages, computeMeasurementError.rawImageTimeSeries);
    workflow.addTask(computeMeasurementError);
    // 
    // SLOW WAY
    // 
    // RunRefSimulation runRefSimulationFull = new RunRefSimulation("runRefSimulationFull");
    // runRefSimulationFull.cellROI_2D.setSource(generateCellROIs.cellROI_2D);
    // runRefSimulationFull.normalizedTimeSeries.setSource(generateNormalizedFrapData.normalizedFrapData);
    // workflow.addTask(runRefSimulationFull);
    // GenerateReducedRefData generateReducedRefSimData = new GenerateReducedRefData("generateReducedRefSimData");
    // generateReducedRefSimData.imageTimeSeries.setSource(runRefSimulationFull.refSimTimeSeries);
    // generateReducedRefSimData.imageDataROIs.setSource(generateDependentROIs.imageDataROIs);
    // workflow.addTask(generateReducedRefSimData);
    // Generate2DOptContext generate2DOptContextFull = new Generate2DOptContext("generate2DOptContextFull");
    // generate2DOptContextFull.normalizedMeasurementErrors.setSource(computeMeasurementError.normalizedMeasurementError);
    // generate2DOptContextFull.modelType.setSource(modelType);
    // generate2DOptContextFull.normExpData.setSource(generateReducedNormalizedData.reducedROIData);
    // generate2DOptContextFull.refSimData.setSource(generateReducedRefSimData.reducedROIData);
    // generate2DOptContextFull.refSimDiffusionRate.setSource(runRefSimulationFull.refSimDiffusionRate);
    // workflow.addTask(generate2DOptContextFull);
    // 
    // FAST WAY
    // 
    GenerateTrivial2DPsf psf_2D = new GenerateTrivial2DPsf("psf_2D");
    workflow.addTask(psf_2D);
    RunRefSimulationFast runRefSimulationFast = new RunRefSimulationFast("runRefSimulationFast");
    workflow.connect2(generateCellROIs.cellROI_2D, runRefSimulationFast.cellROI_2D);
    workflow.connect2(generateNormalizedFrapData.normalizedFrapData, runRefSimulationFast.normalizedTimeSeries);
    workflow.connect2(generateDependentROIs.imageDataROIs, runRefSimulationFast.imageDataROIs);
    workflow.connect2(psf_2D.psf_2D, runRefSimulationFast.psf);
    workflow.addTask(runRefSimulationFast);
    // 
    // model with One mobile fraction
    // 
    {
        GenerateRefSimOptModel generateRefSimOptModelOne = new GenerateRefSimOptModel("generateRefSimOptModel");
        workflow.connectParameter(modelTypeOne, generateRefSimOptModelOne.modelType);
        workflow.connect2(runRefSimulationFast.reducedROIData, generateRefSimOptModelOne.refSimData);
        workflow.connect2(runRefSimulationFast.refSimDiffusionRate, generateRefSimOptModelOne.refSimDiffusionRate);
        workflow.addTask(generateRefSimOptModelOne);
        Generate2DOptContext generate2DOptContextOne = new Generate2DOptContext("generate2DOptContextOne");
        workflow.connect2(computeMeasurementError.normalizedMeasurementError, generate2DOptContextOne.normalizedMeasurementErrors);
        workflow.connect2(generateReducedNormalizedData.reducedROIData, generate2DOptContextOne.normExpData);
        workflow.connect2(generateRefSimOptModelOne.optModel, generate2DOptContextOne.optModel);
        workflow.addTask(generate2DOptContextOne);
        RunProfileLikelihoodGeneral runProfileLikelihoodOne = new RunProfileLikelihoodGeneral("runProfileLikelihoodOne");
        workflow.connect2(generate2DOptContextOne.optContext, runProfileLikelihoodOne.optContext);
        workflow.addTask(runProfileLikelihoodOne);
    }
    // 
    // model with One mobile fraction
    // 
    GenerateRefSimOptModel generateRefSimOptModelTwo = new GenerateRefSimOptModel("generateRefSimOptModelTwo");
    workflow.connectParameter(modelTypeTwo, generateRefSimOptModelTwo.modelType);
    workflow.connect2(runRefSimulationFast.reducedROIData, generateRefSimOptModelTwo.refSimData);
    workflow.connect2(runRefSimulationFast.refSimDiffusionRate, generateRefSimOptModelTwo.refSimDiffusionRate);
    workflow.addTask(generateRefSimOptModelTwo);
    Generate2DOptContext generate2DOptContextTwo = new Generate2DOptContext("generate2DOptContextTwo");
    workflow.connect2(computeMeasurementError.normalizedMeasurementError, generate2DOptContextTwo.normalizedMeasurementErrors);
    workflow.connect2(generateRefSimOptModelTwo.optModel, generate2DOptContextTwo.optModel);
    workflow.connect2(generateReducedNormalizedData.reducedROIData, generate2DOptContextTwo.normExpData);
    workflow.addTask(generate2DOptContextTwo);
    RunProfileLikelihoodGeneral runProfileLikelihoodTwo = new RunProfileLikelihoodGeneral("runProfileLikelihoodTwo");
    workflow.connect2(generate2DOptContextTwo.optContext, runProfileLikelihoodTwo.optContext);
    workflow.addTask(runProfileLikelihoodTwo);
    return workflow;
}