Examples with Parameter cbit.vcell.opt.Parameter used on opensource projects

Example 36 with Parameter

use of cbit.vcell.opt.Parameter in project vcell by virtualcell.

the class FRAPParamTest method runProfileLikelihood.

public void runProfileLikelihood() {
    String errorMsg = checkFrapStudyValidity();
    if (!errorMsg.equals("")) {
        System.out.println("Application terminated due to " + errorMsg);
        System.exit(1);
    } else {
        try {
            ClientTaskStatusSupport ctss = new ClientTaskStatusSupport() {

                public void setProgress(int progress) {
                    System.out.println(progress);
                }

                public void setMessage(String message) {
                    System.out.println(message);
                }

                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");
                }
            };
            // get startign index
            if (frapStudy.getStartingIndexForRecovery() == null) {
                int index = FRAPDataAnalysis.calculateRecoveryIndex(frapStudy.getFrapData());
                frapStudy.setStartingIndexForRecovery(index);
            }
            // get dependent rois
            if (frapStudy.getFrapData().getRois().length < 4) {
                frapStudy.refreshDependentROIs();
            }
            // get selected ROIs
            if (frapStudy.getSelectedROIsForErrorCalculation() == null) {
                boolean[] selectedROIs = new boolean[FRAPData.VFRAP_ROI_ENUM.values().length];
                int counter = 0;
                for (FRAPData.VFRAP_ROI_ENUM roiEnum : FRAPData.VFRAP_ROI_ENUM.values()) {
                    if (roiEnum.name().equals(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()) || roiEnum.name().equals(FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name())) {
                        counter++;
                        continue;
                    }
                    if (frapStudy.getFrapData().getRoi(roiEnum.name()).getNonzeroPixelsCount() > 0) {
                        selectedROIs[counter] = true;
                        counter++;
                    }
                }
                frapStudy.setSelectedROIsForErrorCalculation(selectedROIs);
            }
            // get frap opt data
            if (frapStudy.getFrapOptData() == null) {
                if (!FRAPWorkspace.areExternalDataOK(getLocalWorkspace(), frapStudy.getFrapDataExternalDataInfo(), frapStudy.getRoiExternalDataInfo())) {
                    // if external files are missing/currupt or ROIs are changed, create keys and save them
                    frapStudy.setFrapDataExternalDataInfo(FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.IMAGE_EXTDATA_NAME));
                    frapStudy.setRoiExternalDataInfo(FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.ROI_EXTDATA_NAME));
                    frapStudy.saveROIsAsExternalData(localWorkspace, frapStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), frapStudy.getStartingIndexForRecovery());
                    frapStudy.saveImageDatasetAsExternalData(localWorkspace, frapStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier(), frapStudy.getStartingIndexForRecovery());
                }
                // run ref sim
                frapStudy.setFrapOptData(new FRAPOptData(frapStudy, FRAPModel.NUM_MODEL_PARAMETERS_ONE_DIFF, localWorkspace, ctss));
            }
            FRAPOptData optData = frapStudy.getFrapOptData();
            // create frapModels
            if (frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] == null) {
                frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] = new FRAPModel(FRAPModel.MODEL_TYPE_ARRAY[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT], null, null, null);
                if (frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters() == null) {
                    frapStudy.getFrapOptData().setNumEstimatedParams(FRAPModel.NUM_MODEL_PARAMETERS_ONE_DIFF);
                    Parameter[] initialParams = FRAPModel.getInitialParameters(frapStudy.getFrapData(), FRAPModel.MODEL_TYPE_ARRAY[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT], frapStudy.getStartingIndexForRecovery());
                    Parameter[] bestParameters = frapStudy.getFrapOptData().getBestParamters(initialParams, frapStudy.getSelectedROIsForErrorCalculation());
                    frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].setModelParameters(bestParameters);
                }
            }
            if (frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS] == null) {
                frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS] = new FRAPModel(FRAPModel.MODEL_TYPE_ARRAY[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS], null, null, null);
                if (frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].getModelParameters() == null) {
                    frapStudy.getFrapOptData().setNumEstimatedParams(FRAPModel.NUM_MODEL_PARAMETERS_TWO_DIFF);
                    Parameter[] initialParams = FRAPModel.getInitialParameters(frapStudy.getFrapData(), FRAPModel.MODEL_TYPE_ARRAY[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS], frapStudy.getStartingIndexForRecovery());
                    Parameter[] bestParameters = frapStudy.getFrapOptData().getBestParamters(initialParams, frapStudy.getSelectedROIsForErrorCalculation());
                    frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].setModelParameters(bestParameters);
                }
            }
            // try diffusion with one diffusing component model
            System.out.println("Evaluating parameters in diffusion with one diffusing compoent model...");
            Parameter[] bestParameters = frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters();
            ProfileData[] profileData = optData.evaluateParameters(bestParameters, ctss);
            // output profile likelihood
            File outputDir_oneComponent = new File(getLocalWorkspace().getDefaultWorkspaceDirectory() + SUB_DIRECTORY + "OneComponent_SAVED_AT_" + BeanUtils.generateDateTimeString() + System.getProperty("file.separator"));
            if (!outputDir_oneComponent.exists()) {
                outputDir_oneComponent.mkdirs();
            }
            for (int i = 0; i < profileData.length; i++) {
                ProfileDataElement profileDataElement = profileData[i].getProfileDataElements().get(0);
                outputProfileLikelihood(profileData[i].getProfileDataElements(), profileDataElement.getParamName(), outputDir_oneComponent);
            }
            // try diffusion with two diffusing components model
            System.out.println("Evaluating parameters in diffusion with two diffusing compoents model...");
            bestParameters = frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].getModelParameters();
            profileData = optData.evaluateParameters(bestParameters, ctss);
            // output profile likelihood
            File outputDir_twoComponents = new File(getLocalWorkspace().getDefaultWorkspaceDirectory() + SUB_DIRECTORY + "TwoComponents_SAVED_AT_" + BeanUtils.generateDateTimeString() + System.getProperty("file.separator"));
            if (!outputDir_twoComponents.exists()) {
                outputDir_twoComponents.mkdirs();
            }
            for (int i = 0; i < profileData.length; i++) {
                ProfileDataElement profileDataElement = profileData[i].getProfileDataElements().get(0);
                outputProfileLikelihood(profileData[i].getProfileDataElements(), profileDataElement.getParamName(), outputDir_twoComponents);
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
            System.exit(1);
        }
    }
}

Example 37 with Parameter

use of cbit.vcell.opt.Parameter in project vcell by virtualcell.

the class FRAPParamTest method outputProfileLikelihood.

private void outputProfileLikelihood(ArrayList<ProfileDataElement> arg_profileData, String fixedParamName, File outputDir) {
    try {
        System.out.println("Writing profile likelihood...");
        // output results
        String outFileName = outputDir.getAbsolutePath() + "\\" + fixedParamName + "_profileLikelihood" + ".txt";
        File outFile = new File(outFileName);
        FileWriter fstream = new FileWriter(outFile);
        BufferedWriter out = new BufferedWriter(fstream);
        // output profile
        for (int i = 0; i < arg_profileData.size(); i++) {
            out.newLine();
            String rowStr = arg_profileData.get(i).getParameterValue() + "\t" + arg_profileData.get(i).getLikelihood();
            Parameter[] params = arg_profileData.get(i).getBestParameters();
            rowStr = rowStr + "\t";
            for (int j = 0; j < params.length; j++) {
                rowStr = rowStr + "\t" + params[j].getInitialGuess();
            }
            out.write(rowStr);
        }
        out.close();
        System.out.println("Output is done. Restults saved to " + outFileName);
    } catch (IOException e) {
        e.printStackTrace(System.out);
    }
}

Example 38 with Parameter

use of cbit.vcell.opt.Parameter in project vcell by virtualcell.

the class EstParams_ReactionOffRatePanel method displayResults.

private void displayResults(FRAPData frapData, int startIndexRecovery) throws ExpressionException, DivideByZeroException {
    Parameter[] currentParams = offRateParamPanel.getCurrentParameters();
    if (frapData == null || currentParams == null) {
        multisourcePlotPane.setDataSources(null);
    } else {
        double[] frapDataTimeStamps = frapData.getImageDataset().getImageTimeStamps();
        // Experiment - Cell ROI Average
        double[] temp_background = frapData.getAvgBackGroundIntensity();
        double[] preBleachAvgXYZ = FrapDataUtils.calculatePreBleachAverageXYZ(frapData, startIndexRecovery);
        /*double[] cellRegionData = FRAPDataAnalysis.getAverageROIIntensity(frapData, frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()),preBleachAvgXYZ,temp_background);
			ReferenceData expCellAvgData = new SimpleReferenceData(new String[] { ReservedSymbol.TIME.getName(), "CellROIAvg" }, new double[] { 1.0, 1.0 }, new double[][] {frapDataTimeStamps, cellRegionData });
			DataSource expCellAvgDataSource = new DataSource.DataSourceReferenceData("exp", expCellAvgData);
			//Analytic - Cell ROI Average with Bleach while monitor
			ODESolverResultSet bleachWhileMonitorOdeSolverResultSet = new ODESolverResultSet();
			bleachWhileMonitorOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(ReservedSymbol.TIME.getName()));
			Expression cellAvgExp = new Expression(FRAPOptFunctions.FUNC_CELL_INTENSITY);
			// substitute parameter values 
			cellAvgExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_I_inicell), new Expression(cellRegionData[startIndexRecovery]));
			cellAvgExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_BWM_RATE), new Expression(currentParams[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess()));
			// time shift
			cellAvgExp.substituteInPlace(new Expression(ReservedSymbol.TIME.getName()), new Expression(ReservedSymbol.TIME.getName()+"-"+frapDataTimeStamps[startIndexRecovery]));
			try {
				bleachWhileMonitorOdeSolverResultSet.addFunctionColumn(
					new FunctionColumnDescription(
						cellAvgExp,
						"CellROIAvg",
						null,"bleachWhileMonitorFit",true));
			} catch (ExpressionException e) {
				e.printStackTrace();
			}
			for (int i = startIndexRecovery; i < frapDataTimeStamps.length; i++) 
			{
				bleachWhileMonitorOdeSolverResultSet.addRow(new double[] { frapDataTimeStamps[i] });
			}
			DataSource bleachWhileMonitorDataSource = new DataSource.DataSourceOdeSolverResultSet("fit", bleachWhileMonitorOdeSolverResultSet);*/
        // experimental bleach region average intensity curve
        double[] bleachRegionData = FRAPDataAnalysis.getAverageROIIntensity(frapData, frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()), preBleachAvgXYZ, temp_background);
        ;
        ReferenceData expRefData = new SimpleReferenceData(new String[] { ReservedVariable.TIME.getName(), "BleachROIAvg" }, new double[] { 1.0, 1.0 }, new double[][] { frapDataTimeStamps, bleachRegionData });
        DataSource expBleachDataSource = new DataSource.DataSourceReferenceData("exp", expRefData);
        // Analytic - bleach region average intensity with bleach while monitoring rate
        ODESolverResultSet koffFitOdeSolverResultSet = new ODESolverResultSet();
        koffFitOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(ReservedVariable.TIME.getName()));
        Expression bleachedAvgExp = frapWorkspace.getWorkingFrapStudy().getFrapOptFunc().getRecoveryExpressionWithCurrentParameters(currentParams);
        try {
            koffFitOdeSolverResultSet.addFunctionColumn(new FunctionColumnDescription(bleachedAvgExp, "BleachROIAvg", null, "recoveryFit", true));
        } catch (ExpressionException e) {
            e.printStackTrace();
        }
        double[] truncatedTimes = new double[frapDataTimeStamps.length - startIndexRecovery];
        for (int i = startIndexRecovery; i < frapDataTimeStamps.length; i++) {
            koffFitOdeSolverResultSet.addRow(new double[] { frapDataTimeStamps[i] });
            truncatedTimes[i - startIndexRecovery] = frapDataTimeStamps[i];
        }
        setCurrentEstimationResults(frapWorkspace.getWorkingFrapStudy().getFrapOptFunc().createData(bleachedAvgExp.flatten(), truncatedTimes));
        DataSource koffFitDataSource = new DataSource.DataSourceRowColumnResultSet("fit", koffFitOdeSolverResultSet);
        multisourcePlotPane.setDataSources(new DataSource[] { expBleachDataSource, koffFitDataSource /*, expCellAvgDataSource , bleachWhileMonitorDataSource*/
        });
        multisourcePlotPane.selectAll();
    }
}

Example 39 with Parameter

use of cbit.vcell.opt.Parameter in project vcell by virtualcell.

the class EstParams_TwoDiffComponentDescriptor method aboutToDisplayPanel.

public void aboutToDisplayPanel() {
    FRAPStudy fStudy = frapWorkspace.getWorkingFrapStudy();
    Parameter[] params = fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].getModelParameters();
    try {
        if (params == null) {
            params = FRAPModel.getInitialParameters(fStudy.getFrapData(), FRAPModel.MODEL_TYPE_ARRAY[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS], fStudy.getStartingIndexForRecovery());
        }
        ((EstParams_TwoDiffComponentPanel) getPanelComponent()).setData(fStudy.getFrapOptData(), fStudy.getFrapData(), params, fStudy.getFrapData().getImageDataset().getImageTimeStamps(), fStudy.getStartingIndexForRecovery(), fStudy.getSelectedROIsForErrorCalculation());
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
        DialogUtils.showErrorDialog((getPanelComponent()), "Error getting parameters for diffusion with one diffusing component model.");
    }
}

Example 40 with Parameter

use of cbit.vcell.opt.Parameter in project vcell by virtualcell.

the class FRAPDiffOneParamPanel method createParameterArray.

private static Parameter[] createParameterArray(double diffusionRate, double mobileFraction, double monitorBleachRate) {
    Parameter[] params = null;
    Parameter diff = new Parameter(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_PRIMARY_DIFF_RATE], FRAPModel.REF_DIFFUSION_RATE_PARAM.getLowerBound(), FRAPModel.REF_DIFFUSION_RATE_PARAM.getUpperBound(), FRAPModel.REF_DIFFUSION_RATE_PARAM.getScale(), diffusionRate);
    Parameter mobileFrac = new Parameter(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_PRIMARY_FRACTION], FRAPModel.REF_MOBILE_FRACTION_PARAM.getLowerBound(), FRAPModel.REF_MOBILE_FRACTION_PARAM.getUpperBound(), FRAPModel.REF_MOBILE_FRACTION_PARAM.getScale(), mobileFraction);
    Parameter bleachWhileMonitoringRate = new Parameter(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_BLEACH_MONITOR_RATE], FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getLowerBound(), FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getUpperBound(), FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getScale(), monitorBleachRate);
    params = new Parameter[FRAPModel.NUM_MODEL_PARAMETERS_ONE_DIFF];
    params[FRAPModel.INDEX_PRIMARY_DIFF_RATE] = diff;
    params[FRAPModel.INDEX_PRIMARY_FRACTION] = mobileFrac;
    params[FRAPModel.INDEX_BLEACH_MONITOR_RATE] = bleachWhileMonitoringRate;
    return params;
}