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

Example 1 with OptContext

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

the class Generate2DOptContext method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws ExpressionException {
    // get inputs
    RowColumnResultSet normExpDataset = context.getData(normExpData);
    RowColumnResultSet measurementErrorDataset = context.getData(normalizedMeasurementErrors);
    OptModel optmodel = context.getData(optModel);
    // do op
    Generate2DOptContextOp op = new Generate2DOptContextOp();
    ErrorFunction errorFunction = context.getData(this.errorFunction);
    OptContext optcontext = op.generate2DOptContext(optmodel, normExpDataset, measurementErrorDataset, errorFunction);
    // set output
    context.setData(optContext, optcontext);
}

Example 2 with OptContext

use of org.vcell.vmicro.workflow.data.OptContext 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 3 with OptContext

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

the class PhotoactivationExperimentTest method analyzePhotoactivation.

/**
 * Fits raw image time series data to uniform disk models (with Guassian or Uniform fluorescence).
 *
 * @param rawTimeSeriesImages
 * @param localWorkspace
 * @throws Exception
 */
private static void analyzePhotoactivation(ImageTimeSeries<UShortImage> rawTimeSeriesImages, LocalWorkspace localWorkspace) throws Exception {
    // 
    // correct the timestamps (1 per second).
    // 
    double[] timeStamps = rawTimeSeriesImages.getImageTimeStamps();
    for (int i = 0; i < timeStamps.length; i++) {
        timeStamps[i] = i;
    }
    new DisplayTimeSeriesOp().displayImageTimeSeries(rawTimeSeriesImages, "raw images", (WindowListener) null);
    ImageTimeSeries<UShortImage> blurredRaw = blurTimeSeries(rawTimeSeriesImages);
    new DisplayTimeSeriesOp().displayImageTimeSeries(blurredRaw, "blurred raw images", (WindowListener) null);
    double cellThreshold = 0.4;
    GeometryRoisAndActivationTiming cellROIresults = new GenerateCellROIsFromRawPhotoactivationTimeSeriesOp().generate(blurredRaw, cellThreshold);
    ROI backgroundROI = cellROIresults.backgroundROI_2D;
    ROI cellROI = cellROIresults.cellROI_2D;
    int indexOfFirstPostactivation = cellROIresults.indexOfFirstPostactivation;
    boolean backgroundSubtract = false;
    boolean normalizeByPreActivation = false;
    NormalizedPhotoactivationDataResults normResults = new GenerateNormalizedPhotoactivationDataOp().generate(rawTimeSeriesImages, backgroundROI, indexOfFirstPostactivation, backgroundSubtract, normalizeByPreActivation);
    ImageTimeSeries<FloatImage> normalizedTimeSeries = normResults.normalizedPhotoactivationData;
    FloatImage preactivationAvg = normResults.preactivationAverageImage;
    FloatImage normalizedPostactivation = normalizedTimeSeries.getAllImages()[0];
    new DisplayTimeSeriesOp().displayImageTimeSeries(normalizedTimeSeries, "normalized images", (WindowListener) null);
    // 
    // create a single bleach ROI by thresholding
    // 
    double activatedThreshold = 1000;
    ROI activatedROI = new GenerateActivationRoiOp().generateActivatedRoi(blurredRaw.getAllImages()[indexOfFirstPostactivation], cellROI, activatedThreshold);
    new DisplayImageOp().displayImage(activatedROI.getRoiImages()[0], "activated roi", null);
    new DisplayImageOp().displayImage(cellROI.getRoiImages()[0], "cell roi", null);
    new DisplayImageOp().displayImage(backgroundROI.getRoiImages()[0], "background roi", null);
    {
        // 
        // only use bleach ROI for fitting etc.
        // 
        NormalizedSampleFunction[] dataROIs = new NormalizedSampleFunction[] { NormalizedSampleFunction.fromROI(activatedROI) };
        // 
        // get reduced data and errors for each ROI
        // 
        RowColumnResultSet reducedData = new GenerateReducedDataOp().generateReducedData(normalizedTimeSeries, dataROIs);
        RowColumnResultSet measurementErrors = new ComputeMeasurementErrorOp().computeNormalizedMeasurementError(dataROIs, indexOfFirstPostactivation, rawTimeSeriesImages, preactivationAvg, null);
        DisplayPlotOp displayReducedData = new DisplayPlotOp();
        displayReducedData.displayPlot(reducedData, "reduced data", null);
        DisplayPlotOp displayMeasurementError = new DisplayPlotOp();
        displayMeasurementError.displayPlot(measurementErrors, "measurement error", null);
        // 
        // 2 parameter uniform disk model
        // 
        Parameter tau = new Parameter("tau", 0.001, 200.0, 1.0, 0.1);
        Parameter f_init = new Parameter("f_init", 0.5, 4000, 1.0, 1.0);
        Parameter f_final = new Parameter("f_final", 0.01, 4000, 1.0, 0.5);
        Parameter[] parameters = new Parameter[] { tau, f_init, f_final };
        OptModel optModel = new OptModel("photoactivation (activated roi)", parameters) {

            @Override
            public double[][] getSolution0(double[] newParams, double[] solutionTimePoints) {
                double tau = newParams[0];
                double max = newParams[1];
                double offset = newParams[2];
                double[][] solution = new double[1][solutionTimePoints.length];
                for (int i = 0; i < solution[0].length; i++) {
                    double t = solutionTimePoints[i];
                    solution[0][i] = offset + (max - offset) * Math.exp(-t / tau);
                }
                return solution;
            }

            @Override
            public double getPenalty(double[] parameters2) {
                return 0;
            }
        };
        ErrorFunction errorFunction = new ErrorFunctionNoiseWeightedL2();
        OptContext uniformDisk2Context = new Generate2DOptContextOp().generate2DOptContext(optModel, reducedData, measurementErrors, errorFunction);
        new DisplayInteractiveModelOp().displayOptModel(uniformDisk2Context, dataROIs, localWorkspace, "nonspatial photoactivation - activated ROI only", null);
    }
    {
        // 
        // only activation ROI for chemistry, cellROI for bleaching
        // 
        NormalizedSampleFunction[] dataROIs = new NormalizedSampleFunction[] { NormalizedSampleFunction.fromROI(activatedROI), NormalizedSampleFunction.fromROI(cellROI) };
        // 
        // get reduced data and errors for each ROI
        // 
        RowColumnResultSet reducedData = new GenerateReducedDataOp().generateReducedData(normalizedTimeSeries, dataROIs);
        RowColumnResultSet measurementErrors = new ComputeMeasurementErrorOp().computeNormalizedMeasurementError(dataROIs, indexOfFirstPostactivation, rawTimeSeriesImages, preactivationAvg, null);
        DisplayPlotOp displayReducedData = new DisplayPlotOp();
        displayReducedData.displayPlot(reducedData, "reduced data (2)", null);
        DisplayPlotOp displayMeasurementError = new DisplayPlotOp();
        displayMeasurementError.displayPlot(measurementErrors, "measurement error (2)", null);
        // 
        // 2 parameter uniform disk model
        // 
        Parameter tau_active = new Parameter("tau_active", 0.001, 200.0, 1.0, 0.1);
        Parameter f_active_init = new Parameter("f_active_init", 0.5, 4000, 1.0, 1.0);
        Parameter f_active_amplitude = new Parameter("f_active_amplitude", 0.01, 4000, 1.0, 0.5);
        Parameter f_cell_init = new Parameter("f_cell_init", 0.01, 4000, 1.0, 0.1);
        Parameter f_cell_amplitude = new Parameter("f_cell_amplitude", 0.01, 4000, 1.0, 0.1);
        Parameter tau_cell = new Parameter("tau_cell", 0.00001, 200, 1.0, 1);
        Parameter[] parameters = new Parameter[] { tau_active, f_active_init, f_active_amplitude, tau_cell, f_cell_init, f_cell_amplitude };
        OptModel optModel = new OptModel("photoactivation (activated and cell rois)", parameters) {

            @Override
            public double[][] getSolution0(double[] newParams, double[] solutionTimePoints) {
                double tau_active = newParams[0];
                double max_active = newParams[1];
                double amplitude_active = newParams[2];
                double tau_cell = newParams[3];
                double max_cell = newParams[4];
                double amplitude_cell = newParams[5];
                final int ACTIVE_ROI = 0;
                final int CELL_ROI = 1;
                final int NUM_ROIS = 2;
                double[][] solution = new double[NUM_ROIS][solutionTimePoints.length];
                for (int i = 0; i < solution[0].length; i++) {
                    double t = solutionTimePoints[i];
                    solution[ACTIVE_ROI][i] = (max_active - amplitude_active) + (amplitude_active) * Math.exp(-t / tau_active) * Math.exp(-t / tau_cell);
                    solution[CELL_ROI][i] = (max_cell - amplitude_cell) + (amplitude_cell) * Math.exp(-t / tau_cell);
                }
                return solution;
            }

            @Override
            public double getPenalty(double[] parameters2) {
                return 0;
            }
        };
        ErrorFunctionNoiseWeightedL2 errorFunction = new ErrorFunctionNoiseWeightedL2();
        OptContext uniformDisk2Context = new Generate2DOptContextOp().generate2DOptContext(optModel, reducedData, measurementErrors, errorFunction);
        new DisplayInteractiveModelOp().displayOptModel(uniformDisk2Context, dataROIs, localWorkspace, "nonspatial photoactivation - activated and cell ROIs", null);
    }
}

Example 4 with OptContext

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

the class VFrapProcess method compute.

public static VFrapProcessResults compute(ImageTimeSeries rawTimeSeriesImages, double bleachThreshold, double cellThreshold, LocalWorkspace localWorkspace, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    GenerateCellROIsFromRawFrapTimeSeriesOp generateCellROIs = new GenerateCellROIsFromRawFrapTimeSeriesOp();
    GeometryRoisAndBleachTiming geometryAndTiming = generateCellROIs.generate(rawTimeSeriesImages, cellThreshold);
    GenerateNormalizedFrapDataOp generateNormalizedFrapData = new GenerateNormalizedFrapDataOp();
    NormalizedFrapDataResults normalizedFrapResults = generateNormalizedFrapData.generate(rawTimeSeriesImages, geometryAndTiming.backgroundROI_2D, geometryAndTiming.indexOfFirstPostbleach);
    GenerateBleachRoiOp generateROIs = new GenerateBleachRoiOp();
    ROI bleachROI = generateROIs.generateBleachRoi(normalizedFrapResults.normalizedFrapData.getAllImages()[0], geometryAndTiming.cellROI_2D, bleachThreshold);
    GenerateDependentImageROIsOp generateDependentROIs = new GenerateDependentImageROIsOp();
    ROI[] dataROIs = generateDependentROIs.generate(geometryAndTiming.cellROI_2D, bleachROI);
    NormalizedSampleFunction[] roiSampleFunctions = new NormalizedSampleFunction[dataROIs.length];
    for (int i = 0; i < dataROIs.length; i++) {
        roiSampleFunctions[i] = NormalizedSampleFunction.fromROI(dataROIs[i]);
    }
    GenerateReducedDataOp generateReducedNormalizedData = new GenerateReducedDataOp();
    RowColumnResultSet reducedData = generateReducedNormalizedData.generateReducedData(normalizedFrapResults.normalizedFrapData, roiSampleFunctions);
    ComputeMeasurementErrorOp computeMeasurementError = new ComputeMeasurementErrorOp();
    RowColumnResultSet measurementError = computeMeasurementError.computeNormalizedMeasurementError(roiSampleFunctions, geometryAndTiming.indexOfFirstPostbleach, rawTimeSeriesImages, normalizedFrapResults.prebleachAverage, clientTaskStatusSupport);
    GenerateTrivial2DPsfOp psf_2D = new GenerateTrivial2DPsfOp();
    UShortImage psf = psf_2D.generateTrivial2D_Psf();
    // RunRefSimulationOp runRefSimulationFull = new RunRefSimulationOp();
    // GenerateReducedROIDataOp generateReducedRefSimData = new GenerateReducedROIDataOp();
    RunRefSimulationFastOp runRefSimulationFast = new RunRefSimulationFastOp();
    RowColumnResultSet refData = runRefSimulationFast.runRefSimFast(geometryAndTiming.cellROI_2D, normalizedFrapResults.normalizedFrapData, dataROIs, psf, localWorkspace, clientTaskStatusSupport);
    final double refDiffusionRate = 1.0;
    double[] refSimTimePoints = refData.extractColumn(0);
    int numRois = refData.getDataColumnCount() - 1;
    int numRefSimTimes = refData.getRowCount();
    double[][] refSimData = new double[numRois][numRefSimTimes];
    for (int roi = 0; roi < numRois; roi++) {
        double[] roiData = refData.extractColumn(roi + 1);
        for (int t = 0; t < numRefSimTimes; t++) {
            refSimData[roi][t] = roiData[t];
        }
    }
    ErrorFunction errorFunction = new ErrorFunctionNoiseWeightedL2();
    OptModelOneDiff optModelOneDiff = new OptModelOneDiff(refSimData, refSimTimePoints, refDiffusionRate);
    Generate2DOptContextOp generate2DOptContextOne = new Generate2DOptContextOp();
    OptContext optContextOneDiff = generate2DOptContextOne.generate2DOptContext(optModelOneDiff, reducedData, measurementError, errorFunction);
    RunProfileLikelihoodGeneralOp runProfileLikelihoodOne = new RunProfileLikelihoodGeneralOp();
    ProfileData[] profileDataOne = runProfileLikelihoodOne.runProfileLikihood(optContextOneDiff, clientTaskStatusSupport);
    // OptModelTwoDiffWithoutPenalty optModelTwoDiffWithoutPenalty = new OptModelTwoDiffWithoutPenalty(refSimData, refSimTimePoints, refDiffusionRate);
    // Generate2DOptContextOp generate2DOptContextTwoWithoutPenalty = new Generate2DOptContextOp();
    // OptContext optContextTwoDiffWithoutPenalty = generate2DOptContextTwoWithoutPenalty.generate2DOptContext(optModelTwoDiffWithoutPenalty, reducedData, measurementError);
    // RunProfileLikelihoodGeneralOp runProfileLikelihoodTwoWithoutPenalty = new RunProfileLikelihoodGeneralOp();
    // ProfileData[] profileDataTwoWithoutPenalty = runProfileLikelihoodTwoWithoutPenalty.runProfileLikihood(optContextTwoDiffWithoutPenalty, clientTaskStatusSupport);
    OptModelTwoDiffWithPenalty optModelTwoDiffWithPenalty = new OptModelTwoDiffWithPenalty(refSimData, refSimTimePoints, refDiffusionRate);
    Generate2DOptContextOp generate2DOptContextTwoWithPenalty = new Generate2DOptContextOp();
    OptContext optContextTwoDiffWithPenalty = generate2DOptContextTwoWithPenalty.generate2DOptContext(optModelTwoDiffWithPenalty, reducedData, measurementError, errorFunction);
    RunProfileLikelihoodGeneralOp runProfileLikelihoodTwoWithPenalty = new RunProfileLikelihoodGeneralOp();
    ProfileData[] profileDataTwoWithPenalty = runProfileLikelihoodTwoWithPenalty.runProfileLikihood(optContextTwoDiffWithPenalty, clientTaskStatusSupport);
    // 
    // SLOW WAY
    // 
    // runRefSimulationFull.cellROI_2D,generateCellROIs.cellROI_2D);
    // runRefSimulationFull.normalizedTimeSeries,generateNormalizedFrapData.normalizedFrapData);
    // workflow.addTask(runRefSimulationFull);
    // generateReducedRefSimData.imageTimeSeries,runRefSimulationFull.refSimTimeSeries);
    // generateReducedRefSimData.imageDataROIs,generateDependentROIs.imageDataROIs);
    // workflow.addTask(generateReducedRefSimData);
    // DataHolder<RowColumnResultSet> reducedROIData = generateReducedRefSimData.reducedROIData;
    // DataHolder<Double> refSimDiffusionRate = runRefSimulationFull.refSimDiffusionRate;
    VFrapProcessResults results = new VFrapProcessResults(dataROIs, geometryAndTiming.cellROI_2D, bleachROI, normalizedFrapResults.normalizedFrapData, reducedData, profileDataOne, profileDataTwoWithPenalty);
    return results;
}

Example 5 with OptContext

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

the class RunProfileLikelihoodGeneral method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get input
    OptContext optContext = context.getData(this.optContext);
    // do op
    RunProfileLikelihoodGeneralOp op = new RunProfileLikelihoodGeneralOp();
    ProfileData[] profileData = op.runProfileLikihood(optContext, clientTaskStatusSupport);
    // set output
    context.setData(this.profileData, profileData);
}