Examples with Workflow org.vcell.workflow.Workflow used on opensource projects

Example 1 with Workflow

use of org.vcell.workflow.Workflow in project vcell by virtualcell.

the class WorkflowTest method getVFrapSimpleExample.

public static Workflow getVFrapSimpleExample(File workingDirectory, File vfrapFile) {
    // 
    // construct the dataflow graph
    // 
    LocalWorkspace localWorkspace = new LocalWorkspace(workingDirectory);
    Workflow workflow = new Workflow("main");
    Repository repository = new MemoryRepository();
    TaskContext context = new TaskContext(workflow, repository, localWorkspace);
    // 
    // workflow parameters
    // 
    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> displayROITitle = workflow.addParameter(String.class, "displayROITitle");
    context.setParameterValue(displayROITitle, "rois");
    WorkflowParameter<String> displayProfileOneTitle = workflow.addParameter(String.class, "displayProfileOneTitle");
    context.setParameterValue(displayProfileOneTitle, "1 Diffusing");
    WorkflowParameter<String> displayProfileTwoWithoutPenaltyTitle = workflow.addParameter(String.class, "displayProfileTwoTitle");
    context.setParameterValue(displayProfileTwoWithoutPenaltyTitle, "2 Diffusing - no penalty");
    WorkflowParameter<String> displayProfileTwoWithPenaltyTitle = workflow.addParameter(String.class, "displayProfileTwoTitle");
    context.setParameterValue(displayProfileTwoWithPenaltyTitle, "2 Diffusing - with penalty");
    WorkflowParameter<String> displayRawImagesTitle = workflow.addParameter(String.class, "displayRawImagesTitle");
    context.setParameterValue(displayRawImagesTitle, "raw Images from " + ImportRawTimeSeriesFromVFrap.class.getName());
    ImportRawTimeSeriesFromVFrap importFromVFrap = new ImportRawTimeSeriesFromVFrap("importFromVFrap");
    workflow.connectParameter(vfrapFileParam, importFromVFrap.vfrapFile);
    workflow.addTask(importFromVFrap);
    DisplayTimeSeries displayRawImages = new DisplayTimeSeries("displayRawImages");
    workflow.connect2(importFromVFrap.rawTimeSeriesImages, displayRawImages.imageTimeSeries);
    workflow.connectParameter(displayRawImagesTitle, displayRawImages.title);
    workflow.addTask(displayRawImages);
    VFrapProcess vfrapProcess = new VFrapProcess("vfrapProcess");
    workflow.connectParameter(bleachThreshold, vfrapProcess.bleachThreshold);
    workflow.connectParameter(cellThreshold, vfrapProcess.cellThreshold);
    workflow.connect2(importFromVFrap.rawTimeSeriesImages, vfrapProcess.rawTimeSeriesImages);
    workflow.addTask(vfrapProcess);
    DisplayDependentROIs displayROIs = new DisplayDependentROIs("displayROis");
    workflow.connect2(vfrapProcess.cellROI_2D, displayROIs.cellROI);
    workflow.connect2(vfrapProcess.imageDataROIs, displayROIs.imageROIs);
    workflow.connectParameter(displayROITitle, displayROIs.title);
    workflow.addTask(displayROIs);
    DisplayProfileLikelihoodPlots displayProfilesOne = new DisplayProfileLikelihoodPlots("displayProfilesOne");
    workflow.connect2(vfrapProcess.profileDataOne, displayProfilesOne.profileData);
    workflow.connectParameter(displayProfileOneTitle, displayProfilesOne.title);
    workflow.addTask(displayProfilesOne);
    DisplayProfileLikelihoodPlots displayProfilesTwoWithPenalty = new DisplayProfileLikelihoodPlots("displayProfilesTwoWithPenalty");
    workflow.connect2(vfrapProcess.profileDataTwoWithPenalty, displayProfilesTwoWithPenalty.profileData);
    workflow.connectParameter(displayProfileTwoWithPenaltyTitle, displayProfilesTwoWithPenalty.title);
    workflow.addTask(displayProfilesTwoWithPenalty);
    return workflow;
}

Example 2 with Workflow

use of org.vcell.workflow.Workflow in project vcell by virtualcell.

the class WorkflowTest 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(repository, 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);
        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 3 with Workflow

use of org.vcell.workflow.Workflow in project vcell by virtualcell.

the class WorkflowFileTest 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 {
        File workingDirectory = new File(args[0]);
        LocalWorkspace localWorkspace = new LocalWorkspace(workingDirectory);
        String workflowLanguageText = BeanUtils.readBytesFromFile(new File(args[1]), null);
        Repository repository = new MemoryRepository();
        Workflow workflow = Workflow.parse(repository, localWorkspace, workflowLanguageText);
        TaskContext taskContext = new TaskContext(workflow, repository, localWorkspace);
        WorkflowUtilities.displayWorkflowGraph(taskContext.getWorkflow());
        WorkflowUtilities.displayWorkflowTable(taskContext);
        WorkflowUtilities.displayWorkflowGraphJGraphX(new WorkflowJGraphProxy(taskContext));
        ArrayList<Issue> issues = new ArrayList<Issue>();
        taskContext.getWorkflow().reportIssues(issues, Issue.SEVERITY_INFO, true);
        // 
        // execute the workflow
        // 
        taskContext.getWorkflow().compute(taskContext, new WorkflowUtilities.Progress());
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 4 with Workflow

use of org.vcell.workflow.Workflow in project vcell by virtualcell.

the class OptModelParamPanel method computeProfileLikelihood.

public void computeProfileLikelihood() {
    final Repository repository = new MemoryRepository();
    Workflow workflow = new Workflow("profileLikelihoodWorkflow");
    final TaskContext context = new TaskContext(workflow, repository, localWorkspace);
    System.err.println("OptModelParamPanel.showParameterEvaluation(): how do we pass in the initial guess to ProfileLikelihood code??? should be an independent input to ProfileLikelihood so that it is explicit ... and OptContext is immutable.????");
    final RunProfileLikelihoodGeneral runProfileLikelihoodGeneral = new RunProfileLikelihoodGeneral("internal");
    WorkflowParameter<OptContext> optContextParam = workflow.addParameter(OptContext.class, "optContext", repository, optContext);
    workflow.connectParameter(optContextParam, runProfileLikelihoodGeneral.optContext);
    workflow.addTask(runProfileLikelihoodGeneral);
    final DisplayProfileLikelihoodPlots displayProfileLikelihoodPlots = new DisplayProfileLikelihoodPlots("displayProfileLikihood");
    workflow.connect2(runProfileLikelihoodGeneral.profileData, displayProfileLikelihoodPlots.profileData);
    WorkflowParameter<String> titleParam = workflow.addParameter(String.class, "title", repository, "profile likelihood");
    workflow.connectParameter(titleParam, displayProfileLikelihoodPlots.title);
    workflow.addTask(displayProfileLikelihoodPlots);
    AsynchClientTask evaluateTask = new AsynchClientTask("Prepare to evaluate parameters ...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            runProfileLikelihoodGeneral.compute(context, getClientTaskStatusSupport());
        }
    };
    AsynchClientTask showResultTask = new AsynchClientTask("Showing profile likelihood and confidence intervals ...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            displayProfileLikelihoodPlots.compute(context, getClientTaskStatusSupport());
        }
    };
    // dispatch
    ClientTaskDispatcher.dispatch(OptModelParamPanel.this, new Hashtable<String, Object>(), new AsynchClientTask[] { evaluateTask, showResultTask }, false, true, null, true);
}

Example 5 with Workflow

use of org.vcell.workflow.Workflow in project vcell by virtualcell.

the class WorkflowObjectsTableModel method computeData.

/**
 * Insert the method's description here.
 * Creation date: (9/23/2003 1:24:52 PM)
 * @return cbit.vcell.model.Parameter
 * @param row int
 */
protected List<WorkflowObject> computeData() {
    ArrayList<WorkflowObject> allWorkflowObjectList = new ArrayList<WorkflowObject>();
    if (taskContext == null) {
        return null;
    }
    Workflow workflow = taskContext.getWorkflow();
    if (bTasks) {
        allWorkflowObjectList.addAll(workflow.getTasks());
    }
    if (bParameters) {
        allWorkflowObjectList.addAll(workflow.getParameters());
    }
    if (bTaskInputs) {
        for (Task task : workflow.getTasks()) {
            allWorkflowObjectList.addAll(task.getInputs());
        }
    }
    if (bTaskOutputs) {
        for (Task task : workflow.getTasks()) {
            allWorkflowObjectList.addAll(task.getOutputs());
        }
    }
    boolean bSearchInactive = searchText == null || searchText.length() == 0;
    String lowerCaseSearchText = bSearchInactive ? null : searchText.toLowerCase();
    ArrayList<WorkflowObject> workflowObjectList = new ArrayList<WorkflowObject>();
    for (WorkflowObject workflowObject : allWorkflowObjectList) {
        if (bSearchInactive || getValue(workflowObject).toLowerCase().contains(lowerCaseSearchText) || getName(workflowObject).toLowerCase().contains(lowerCaseSearchText) || getType(workflowObject).toLowerCase().contains(lowerCaseSearchText) || getStatus(taskContext, workflowObject).toLowerCase().contains(lowerCaseSearchText)) {
            workflowObjectList.add(workflowObject);
        }
    }
    return workflowObjectList;
}