Examples with ROI cbit.vcell.VirtualMicroscopy.ROI used on opensource projects

Example 51 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class MicroscopyXmlReader method getPrimaryROIs.

/**
 * This method is only called by DataSymbolsPanel to get the primary ROIs
 */
public ROI[] getPrimaryROIs(Element param, /*root, frapstudy element*/
ClientTaskStatusSupport progressListener) throws XmlParseException {
    // get frapData element
    Element frapDataElement = param.getChild(MicroscopyXMLTags.FRAPDataTag);
    Namespace ns = param.getNamespace();
    List<Element> roiList = frapDataElement.getChildren(MicroscopyXMLTags.ROITag);
    ROI[] rois = null;
    int numROIs = 3;
    if (numROIs > 0) {
        rois = new ROI[numROIs];
        Iterator<Element> roiIter = roiList.iterator();
        int index = 0;
        while (roiIter.hasNext()) {
            Element roiElement = roiIter.next();
            if (roiElement.getAttributeValue(MicroscopyXMLTags.ROITypeAttrTag).equals(AnnotatedImageDataset.VFRAP_ROI_ENUM.ROI_BLEACHED.name()) || roiElement.getAttributeValue(MicroscopyXMLTags.ROITypeAttrTag).equals(AnnotatedImageDataset.VFRAP_ROI_ENUM.ROI_BACKGROUND.name()) || roiElement.getAttributeValue(MicroscopyXMLTags.ROITypeAttrTag).equals(AnnotatedImageDataset.VFRAP_ROI_ENUM.ROI_CELL.name())) {
                rois[index++] = getROI(roiElement);
                if (index == 3) {
                    break;
                }
            }
        }
    }
    // reorder ROIs according to the order of FRAPData.VFRAP_ROI_ENUM
    ROI[] reorderedROIs = AnnotatedImageDataset.reorderROIs(rois);
    return reorderedROIs;
}

Example 52 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class FRAPOptData method main.

public static void main(String[] args) {
    String workingDir = "C:\\";
    LocalWorkspace localWorkspace = new LocalWorkspace(new File(workingDir));
    String xmlString;
    try {
        // read original data from file
        System.out.println("start loading original data....");
        String expFileName = "C:/VirtualMicroscopy/testFastD_4_fastFrac_0p5_slowD_1_slowFrac_0p3_ImmobileFrac_0p2_mwb_0p0015_new.vfrap";
        xmlString = XmlUtil.getXMLString(expFileName);
        MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
        FRAPStudy expFrapStudy = xmlReader.getFrapStudy(XmlUtil.stringToXML(xmlString, null).getRootElement(), null);
        expFrapStudy.setXmlFilename(expFileName);
        System.out.println("experimental data time points" + expFrapStudy.getFrapData().getImageDataset().getSizeT());
        System.out.println("finish loading original data....");
        // create reference data
        System.out.println("creating rederence data....");
        FRAPOptData optData = new FRAPOptData(expFrapStudy, 5, localWorkspace, new ClientTaskStatusSupport() {

            public void setProgress(int progress) {
            // TODO Auto-generated method stub
            }

            public void setMessage(String message) {
            // TODO Auto-generated method stub
            }

            public boolean isInterrupted() {
                // TODO Auto-generated method stub
                return false;
            }

            public int getProgress() {
                // TODO Auto-generated method stub
                return 0;
            }

            public void addProgressDialogListener(ProgressDialogListener progressDialogListener) {
                throw new RuntimeException("not yet implemented");
            }
        });
        // trying 3 parameters
        // Parameter diff = new cbit.vcell.opt.Parameter(FRAPOptData.PARAMETER_NAMES[FRAPOptData.DIFFUSION_RATE_INDEX], 0, 100, 1.0, Double.parseDouble(expFrapStudy.getFrapModelParameters().diffusionRate));
        // Parameter mobileFrac = new cbit.vcell.opt.Parameter(FRAPOptData.PARAMETER_NAMES[FRAPOptData.MOBILE_FRACTION_INDEX], 0, 1, 1.0, 1/*Double.parseDouble(expFrapStudy.getFrapModelParameters().mobileFraction)*/);
        // Parameter bleachWhileMonitoringRate = new cbit.vcell.opt.Parameter(FRAPOptData.PARAMETER_NAMES[FRAPOptData.BLEACH_WHILE_MONITOR_INDEX], 0, 10, 1.0,  0/*Double.parseDouble(expFrapStudy.getFrapModelParameters().monitorBleachRate)*/);
        // trying 5 parameters
        Parameter diffFastOffset = new cbit.vcell.opt.Parameter("fastDiffOffset", 0, 50, 1.0, 10);
        Parameter mFracFast = new cbit.vcell.opt.Parameter("fastMobileFrac", 0, 1, 1.0, 0.5);
        Parameter diffSlow = new cbit.vcell.opt.Parameter("slowDiffRate", 0, 10, 1.0, 0.1);
        Parameter mFracSlow = new cbit.vcell.opt.Parameter("slowMobileFrac", 0, 1, 1.0, 0.5);
        Parameter bleachWhileMonitoringRate = new cbit.vcell.opt.Parameter("bleachWhileMonitoringRate", 0, 20, 1.0, 0.1);
        Parameter[] inParams = new Parameter[] { diffFastOffset, mFracFast, diffSlow, mFracSlow, bleachWhileMonitoringRate };
        // Parameter diffFast = new cbit.vcell.opt.Parameter("fast_diff_rate", 0, 100, 1.0, 5);
        // Parameter mFracFast = new cbit.vcell.opt.Parameter("fast_mobile_fraction", 0, 1, 1.0, 0.5);
        // Parameter diffSlowFactor = new cbit.vcell.opt.Parameter("slow_diff_factor", 0, 1, 1.0, 0.2);
        // Parameter mFracSlow = new cbit.vcell.opt.Parameter("slow_mobile_fraction", 0, 1, 1.0, 0.5);
        // Parameter bleachWhileMonitoringRate = new cbit.vcell.opt.Parameter("bleach_while_monitoring_rate", 0, 1, 1.0,  0.1);
        // Parameter[] inParams = new Parameter[]{diffFast, mFracFast, diffSlowFactor, mFracSlow, bleachWhileMonitoringRate};
        // add some constraints, like fast mobile fraction + slow mobile fraction should smaller than 1.
        // slower rate should be 5 times smaller than fast rate.....??? 5*slowDiffRate < fastDiffRate
        // Expression exp1 = new Expression("("+mFracFast.getName()+" + "+mFracSlow.getName()+" - 1)");
        // Constraint con1 = new Constraint(ConstraintType.LinearInequality, exp1);
        // Expression exp2 = new Expression("( 4 * "+diffSlow.getName()+" - "+ diffFastOffset.getName() +")");
        // Constraint con2 = new Constraint(ConstraintType.LinearInequality, exp2);
        // Constraint[] cons = new Constraint[2];
        // cons[0] = con1;
        // cons[1] = con2;
        ROI[] rois = expFrapStudy.getFrapData().getRois();
        boolean[] errorOfInterest = new boolean[rois.length];
        for (int i = 0; i < rois.length; i++) {
            if (/*!rois[i].getROIType().equals(RoiType.ROI_BLEACHED)*/
            rois[i].getROIName().equals(FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name()) || rois[i].getROIName().equals(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name())) {
                errorOfInterest[i] = false;
            } else {
                errorOfInterest[i] = true;
            }
        }
        optData.getBestParamters(inParams, errorOfInterest);
    // double[][] result = optData.getFitData(inParams, errorOfInterest); // double[roiLen][timePoints]
    // int indexROI = -1;
    // for(int j = 0; j < expFrapStudy.getFrapData().getRois().length; j++)
    // {
    // if(expFrapStudy.getFrapData().getRois()[j].getROIType().equals(RoiType.ROI_BLEACHED))
    // {
    // indexROI = j;
    // break;
    // }
    // }
    // int index = Integer.parseInt(expFrapStudy.getFrapModelParameters().startIndexForRecovery);
    // for(int i = 0; i < (expFrapStudy.getFrapData().getImageDataset().getImageTimeStamps().length - index); i++)
    // {
    // System.out.println(expFrapStudy.getFrapData().getImageDataset().getImageTimeStamps()[i+index]+"\t"+result[indexROI][i]);
    // }
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 53 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class FRAPOptimizationUtils method refreshNormalizedMeasurementError.

/*
	 * Calculate Measurement error for data that is normalized 
	 * and averaged at each ROI ring.
	 * The first dimension is ROI rings(according to the Enum in FRAPData)
	 * The second dimension is time points (from starting index to the end) 
	 */
public static double[][] refreshNormalizedMeasurementError(FRAPStudy frapStudy) throws Exception {
    FRAPData fData = frapStudy.getFrapData();
    ImageDataset imgDataset = fData.getImageDataset();
    double[] timeStamp = imgDataset.getImageTimeStamps();
    int startIndexRecovery = frapStudy.getStartingIndexForRecovery();
    int roiLen = FRAPData.VFRAP_ROI_ENUM.values().length;
    double[][] sigma = new double[roiLen][timeStamp.length - startIndexRecovery];
    double[] prebleachAvg = FrapDataUtils.calculatePreBleachAverageXYZ(fData, startIndexRecovery);
    for (int roiIdx = 0; roiIdx < roiLen; roiIdx++) {
        ROI roi = fData.getRoi((FRAPData.VFRAP_ROI_ENUM.values()[roiIdx]).name());
        if (roi != null) {
            short[] roiData = roi.getPixelsXYZ();
            for (int timeIdx = startIndexRecovery; timeIdx < timeStamp.length; timeIdx++) {
                short[] rawTimeData = AnnotatedImageDataset.collectAllZAtOneTimepointIntoOneArray(imgDataset, timeIdx);
                if (roiData.length != rawTimeData.length || roiData.length != prebleachAvg.length || rawTimeData.length != prebleachAvg.length) {
                    throw new Exception("ROI data and image data are not in the same length.");
                } else {
                    // loop through ROI
                    int roiPixelCounter = 0;
                    double sigmaVal = 0;
                    for (int i = 0; i < roiData.length; i++) {
                        if (roiData[i] != 0) {
                            sigmaVal = sigmaVal + ((rawTimeData[i] & 0x0000FFFF)) / (prebleachAvg[i] * prebleachAvg[i]);
                            roiPixelCounter++;
                        }
                    }
                    if (roiPixelCounter == 0) {
                        sigmaVal = 0;
                    } else {
                        sigmaVal = Math.sqrt(sigmaVal) / roiPixelCounter;
                    }
                    sigma[roiIdx][timeIdx - startIndexRecovery] = sigmaVal;
                }
            }
        }
    }
    // }
    return sigma;
}

Example 54 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class FRAPStudy method spatialAnalysis.

public static SpatialAnalysisResults spatialAnalysis(PDEDataManager simulationDataManager, int startingIndexForRecovery, double startingForRecoveryExperimentalTime, Parameter[] modelParameters, FRAPData frapData, double[] preBleachAverageXYZ) throws Exception {
    String[] varNames = new String[] { SPECIES_NAME_PREFIX_COMBINED };
    AnalysisParameters analysisParameters = new AnalysisParameters(modelParameters);
    // 
    // for each simulation time step, get the data under each ROI <indexed by ROI, then diffusion
    // 
    // preallocate arrays for all data first
    Hashtable<CurveInfo, double[]> curveHash = new Hashtable<CurveInfo, double[]>();
    ArrayList<int[]> nonZeroIndicesForROI = new ArrayList<int[]>();
    for (int i = 0; i < SpatialAnalysisResults.ORDERED_ROINAMES.length; i++) {
        // for (int j = 0; j < diffusionRates.length; j++) {
        curveHash.put(new CurveInfo(analysisParameters, SpatialAnalysisResults.ORDERED_ROINAMES[i]), new double[frapData.getImageDataset().getImageTimeStamps().length - startingIndexForRecovery]);
        // }
        ROI roi_2D = frapData.getRoi(SpatialAnalysisResults.ORDERED_ROINAMES[i]);
        nonZeroIndicesForROI.add(roi_2D.getRoiImages()[0].getNonzeroIndices());
    }
    // 
    // collect data for experiment (over all ROIs), normalized with pre-bleach average
    // 
    double[] avgBkIntensity = frapData.getAvgBackGroundIntensity();
    for (int i = 0; i < SpatialAnalysisResults.ORDERED_ROINAMES.length; i++) {
        double[] normalizedAverageFluorAtEachTimeUnderROI = new double[frapData.getImageDataset().getImageTimeStamps().length];
        for (int j = 0; j < normalizedAverageFluorAtEachTimeUnderROI.length; j++) {
            normalizedAverageFluorAtEachTimeUnderROI[j] = frapData.getAverageUnderROI(j, frapData.getRoi(SpatialAnalysisResults.ORDERED_ROINAMES[i]), preBleachAverageXYZ, avgBkIntensity[j]);
        }
        curveHash.put(new CurveInfo(null, SpatialAnalysisResults.ORDERED_ROINAMES[i]), normalizedAverageFluorAtEachTimeUnderROI);
    }
    // 
    // get times to compare experimental data with simulated results.
    // 
    double[] shiftedSimTimes = null;
    if (simulationDataManager != null) {
        double[] simTimes = simulationDataManager.getDataSetTimes();
        shiftedSimTimes = simTimes.clone();
        for (int j = 0; j < simTimes.length; j++) {
            // timeStamps[startingIndexOfRecovery];
            shiftedSimTimes[j] = simTimes[j] + startingForRecoveryExperimentalTime;
        }
        // curveHash was intialized with exp time data length. so, we have to replace it with the real sim data length.
        if (simTimes.length != (frapData.getImageDataset().getImageTimeStamps().length - startingIndexForRecovery)) {
            for (int k = 0; k < SpatialAnalysisResults.ORDERED_ROINAMES.length; k++) {
                CurveInfo ci = new CurveInfo(analysisParameters, SpatialAnalysisResults.ORDERED_ROINAMES[k]);
                curveHash.remove(ci);
                curveHash.put(ci, new double[simTimes.length]);
            }
        }
        for (int i = 0; i < simTimes.length; i++) {
            for (int j = 0; j < varNames.length; j++) {
                SimDataBlock simDataBlock = simulationDataManager.getSimDataBlock(varNames[j], simTimes[i]);
                double[] data = simDataBlock.getData();
                for (int k = 0; k < SpatialAnalysisResults.ORDERED_ROINAMES.length; k++) {
                    CurveInfo ci = new CurveInfo(analysisParameters, SpatialAnalysisResults.ORDERED_ROINAMES[k]);
                    int[] roiIndices = nonZeroIndicesForROI.get(k);
                    if (roiIndices != null && roiIndices.length > 0) {
                        double accum = 0.0;
                        for (int index = 0; index < roiIndices.length; index++) {
                            accum += data[roiIndices[index]];
                        }
                        double[] values = curveHash.get(ci);
                        values[i] = accum / roiIndices.length;
                    }
                }
            }
        }
    }
    SpatialAnalysisResults spatialAnalysisResults = new SpatialAnalysisResults(new AnalysisParameters[] { analysisParameters }, shiftedSimTimes, curveHash);
    return spatialAnalysisResults;
}

Example 55 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class FRAPStudy method calculatePrebleachAvg_oneValue.

public static double calculatePrebleachAvg_oneValue(FRAPData arg_frapData, int arg_startingIndexForRecovery) {
    double accum = 0;
    int counter = 0;
    double[] prebleachAvgXYZ = FrapDataUtils.calculatePreBleachAverageXYZ(arg_frapData, arg_startingIndexForRecovery);
    ROI cellROI = arg_frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
    for (int i = 0; i < prebleachAvgXYZ.length; i++) {
        if (cellROI.getPixelsXYZ()[i] != 0) {
            accum = accum + prebleachAvgXYZ[i];
            counter++;
        }
    }
    return (accum / counter);
}