use of org.vcell.workflow.Repository 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;
}
use of org.vcell.workflow.Repository 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);
}
}
use of org.vcell.workflow.Repository 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);
}
}
use of org.vcell.workflow.Repository in project vcell by virtualcell.
the class WorkflowObjectsPanel method runButtonPressed.
private void runButtonPressed() throws Exception {
if (taskContext != null) {
LocalWorkspace localWorkspace = new LocalWorkspace(new File("C:\\temp\\"));
Repository repository = new MemoryRepository();
taskContext.getWorkflow().compute(taskContext, new ClientTaskStatusSupport() {
@Override
public void setMessage(String message) {
System.out.println("message = " + message);
}
@Override
public void setProgress(int progress) {
System.out.println("progress = " + progress);
}
@Override
public int getProgress() {
return 0;
}
@Override
public boolean isInterrupted() {
return false;
}
@Override
public void addProgressDialogListener(ProgressDialogListener progressDialogListener) {
}
});
}
}
use of org.vcell.workflow.Repository 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);
}
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