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Example 1 with OptModelKenworthyGaussian

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

the class KenworthyWorkflowTest method analyzeKeyworthy.

/**
 * Fits raw image time series data to uniform disk models (with Guassian or Uniform fluorescence).
 *
 * @param rawTimeSeriesImages
 * @param localWorkspace
 * @throws Exception
 */
private static void analyzeKeyworthy(ImageTimeSeries<UShortImage> rawTimeSeriesImages, LocalWorkspace localWorkspace) throws Exception {
    new DisplayTimeSeriesOp().displayImageTimeSeries(rawTimeSeriesImages, "raw images", (WindowListener) null);
    double cellThreshold = 0.5;
    GeometryRoisAndBleachTiming cellROIresults = new GenerateCellROIsFromRawFrapTimeSeriesOp().generate(rawTimeSeriesImages, cellThreshold);
    ROI backgroundROI = cellROIresults.backgroundROI_2D;
    ROI cellROI = cellROIresults.cellROI_2D;
    int indexOfFirstPostbleach = cellROIresults.indexOfFirstPostbleach;
    new DisplayImageOp().displayImage(backgroundROI.getRoiImages()[0], "background ROI", null);
    new DisplayImageOp().displayImage(cellROI.getRoiImages()[0], "cell ROI", null);
    NormalizedFrapDataResults normResults = new GenerateNormalizedFrapDataOp().generate(rawTimeSeriesImages, backgroundROI, indexOfFirstPostbleach);
    ImageTimeSeries<FloatImage> normalizedTimeSeries = normResults.normalizedFrapData;
    FloatImage prebleachAvg = normResults.prebleachAverage;
    FloatImage normalizedPostbleach = normalizedTimeSeries.getAllImages()[0];
    new DisplayTimeSeriesOp().displayImageTimeSeries(normalizedTimeSeries, "normalized images", (WindowListener) null);
    // 
    // create a single bleach ROI by thresholding
    // 
    double bleachThreshold = 0.80;
    ROI bleachROI = new GenerateBleachRoiOp().generateBleachRoi(normalizedPostbleach, cellROI, bleachThreshold);
    // 
    // only use bleach ROI for fitting etc.
    // 
    // ROI[] dataROIs = new ROI[] { bleachROI };
    // 
    // fit 2D Gaussian to normalized data to determine center, radius and K factor of bleach (assuming exp(-exp
    // 
    FitBleachSpotOpResults fitSpotResults = new FitBleachSpotOp().fit(NormalizedSampleFunction.fromROI(bleachROI), normalizedTimeSeries.getAllImages()[0]);
    double bleachFactorK_GaussianFit = fitSpotResults.bleachFactorK_GaussianFit;
    double bleachRadius_GaussianFit = fitSpotResults.bleachRadius_GaussianFit;
    double bleachRadius_ROI = fitSpotResults.bleachRadius_ROI;
    double centerX_GaussianFit = fitSpotResults.centerX_GaussianFit;
    double centerX_ROI = fitSpotResults.centerX_ROI;
    double centerY_GaussianFit = fitSpotResults.centerY_GaussianFit;
    double centerY_ROI = fitSpotResults.centerY_ROI;
    NormalizedSampleFunction[] sampleFunctions = new NormalizedSampleFunction[] { NormalizedSampleFunction.fromROI(bleachROI) };
    // 
    // get reduced data and errors for each ROI
    // 
    RowColumnResultSet reducedData = new GenerateReducedDataOp().generateReducedData(normalizedTimeSeries, sampleFunctions);
    RowColumnResultSet measurementErrors = new ComputeMeasurementErrorOp().computeNormalizedMeasurementError(sampleFunctions, indexOfFirstPostbleach, rawTimeSeriesImages, prebleachAvg, null);
    ErrorFunction errorFunction = new ErrorFunctionKenworthy(reducedData);
    // 
    // 2 parameter uniform disk model
    // 
    OptModel uniformDisk2OptModel = new OptModelKenworthyUniformDisk2P(bleachRadius_ROI);
    String title_u2 = "Uniform Disk Model - 2 parameters, (Rn=" + bleachRadius_ROI + ")";
    OptContext uniformDisk2Context = new Generate2DOptContextOp().generate2DOptContext(uniformDisk2OptModel, reducedData, measurementErrors, errorFunction);
    new DisplayInteractiveModelOp().displayOptModel(uniformDisk2Context, sampleFunctions, localWorkspace, title_u2, null);
    // 
    // 3 parameter uniform disk model
    // 
    OptModel uniformDisk3OptModel = new OptModelKenworthyUniformDisk3P(bleachRadius_ROI);
    OptContext uniformDisk3Context = new Generate2DOptContextOp().generate2DOptContext(uniformDisk3OptModel, reducedData, measurementErrors, errorFunction);
    String title_u3 = "Uniform Disk Model - 3 parameters, (Rn=" + bleachRadius_ROI + ")";
    new DisplayInteractiveModelOp().displayOptModel(uniformDisk3Context, sampleFunctions, localWorkspace, title_u3, null);
    // 
    // GaussianFit parameter uniform disk model
    // 
    FloatImage prebleachBleachAreaImage = new FloatImage(prebleachAvg);
    // mask-out all but the bleach area
    prebleachBleachAreaImage.and(bleachROI.getRoiImages()[0]);
    double prebleachAvgInROI = prebleachBleachAreaImage.getImageStatistics().meanValue;
    OptModel gaussian2OptModel = new OptModelKenworthyGaussian(prebleachAvgInROI, bleachFactorK_GaussianFit, bleachRadius_GaussianFit, bleachRadius_ROI);
    OptContext gaussianDisk2Context = new Generate2DOptContextOp().generate2DOptContext(gaussian2OptModel, reducedData, measurementErrors, errorFunction);
    String title_g2 = "Gaussian Disk Model - 2 parameters (prebleach=" + prebleachAvgInROI + ",K=" + bleachFactorK_GaussianFit + ",Re=" + bleachRadius_GaussianFit + ",Rnom=" + bleachRadius_ROI + ")";
    new DisplayInteractiveModelOp().displayOptModel(gaussianDisk2Context, sampleFunctions, localWorkspace, title_g2, null);
}
Also used : OptModelKenworthyGaussian(org.vcell.vmicro.workflow.data.OptModelKenworthyGaussian) GenerateCellROIsFromRawFrapTimeSeriesOp(org.vcell.vmicro.op.GenerateCellROIsFromRawFrapTimeSeriesOp) FloatImage(cbit.vcell.VirtualMicroscopy.FloatImage) OptContext(org.vcell.vmicro.workflow.data.OptContext) OptModel(org.vcell.vmicro.workflow.data.OptModel) DisplayImageOp(org.vcell.vmicro.op.display.DisplayImageOp) DisplayTimeSeriesOp(org.vcell.vmicro.op.display.DisplayTimeSeriesOp) NormalizedSampleFunction(org.vcell.vmicro.workflow.data.NormalizedSampleFunction) DisplayInteractiveModelOp(org.vcell.vmicro.op.display.DisplayInteractiveModelOp) GenerateReducedDataOp(org.vcell.vmicro.op.GenerateReducedDataOp) OptModelKenworthyUniformDisk2P(org.vcell.vmicro.workflow.data.OptModelKenworthyUniformDisk2P) FitBleachSpotOp(org.vcell.vmicro.op.FitBleachSpotOp) ErrorFunctionKenworthy(org.vcell.vmicro.workflow.data.ErrorFunctionKenworthy) RowColumnResultSet(cbit.vcell.math.RowColumnResultSet) ErrorFunction(org.vcell.vmicro.workflow.data.ErrorFunction) GeometryRoisAndBleachTiming(org.vcell.vmicro.op.GenerateCellROIsFromRawFrapTimeSeriesOp.GeometryRoisAndBleachTiming) NormalizedFrapDataResults(org.vcell.vmicro.op.GenerateNormalizedFrapDataOp.NormalizedFrapDataResults) GenerateBleachRoiOp(org.vcell.vmicro.op.GenerateBleachRoiOp) Generate2DOptContextOp(org.vcell.vmicro.op.Generate2DOptContextOp) ROI(cbit.vcell.VirtualMicroscopy.ROI) ComputeMeasurementErrorOp(org.vcell.vmicro.op.ComputeMeasurementErrorOp) FitBleachSpotOpResults(org.vcell.vmicro.op.FitBleachSpotOp.FitBleachSpotOpResults) GenerateNormalizedFrapDataOp(org.vcell.vmicro.op.GenerateNormalizedFrapDataOp) OptModelKenworthyUniformDisk3P(org.vcell.vmicro.workflow.data.OptModelKenworthyUniformDisk3P)

Aggregations

FloatImage (cbit.vcell.VirtualMicroscopy.FloatImage)1 ROI (cbit.vcell.VirtualMicroscopy.ROI)1 RowColumnResultSet (cbit.vcell.math.RowColumnResultSet)1 ComputeMeasurementErrorOp (org.vcell.vmicro.op.ComputeMeasurementErrorOp)1 FitBleachSpotOp (org.vcell.vmicro.op.FitBleachSpotOp)1 FitBleachSpotOpResults (org.vcell.vmicro.op.FitBleachSpotOp.FitBleachSpotOpResults)1 Generate2DOptContextOp (org.vcell.vmicro.op.Generate2DOptContextOp)1 GenerateBleachRoiOp (org.vcell.vmicro.op.GenerateBleachRoiOp)1 GenerateCellROIsFromRawFrapTimeSeriesOp (org.vcell.vmicro.op.GenerateCellROIsFromRawFrapTimeSeriesOp)1 GeometryRoisAndBleachTiming (org.vcell.vmicro.op.GenerateCellROIsFromRawFrapTimeSeriesOp.GeometryRoisAndBleachTiming)1 GenerateNormalizedFrapDataOp (org.vcell.vmicro.op.GenerateNormalizedFrapDataOp)1 NormalizedFrapDataResults (org.vcell.vmicro.op.GenerateNormalizedFrapDataOp.NormalizedFrapDataResults)1 GenerateReducedDataOp (org.vcell.vmicro.op.GenerateReducedDataOp)1 DisplayImageOp (org.vcell.vmicro.op.display.DisplayImageOp)1 DisplayInteractiveModelOp (org.vcell.vmicro.op.display.DisplayInteractiveModelOp)1 DisplayTimeSeriesOp (org.vcell.vmicro.op.display.DisplayTimeSeriesOp)1 ErrorFunction (org.vcell.vmicro.workflow.data.ErrorFunction)1 ErrorFunctionKenworthy (org.vcell.vmicro.workflow.data.ErrorFunctionKenworthy)1 NormalizedSampleFunction (org.vcell.vmicro.workflow.data.NormalizedSampleFunction)1 OptContext (org.vcell.vmicro.workflow.data.OptContext)1