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

Example 6 with Parameter

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

the class EstParams_ReacBindingDescriptor method aboutToDisplayPanel.

public void aboutToDisplayPanel() {
    FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
    FRAPModel[] frapModels = fStudy.getModels();
    Parameter[] params = null;
    // get parameters to display in reaction binding panel
    if (frapModels[FRAPModel.IDX_MODEL_DIFF_BINDING] != null && frapModels[FRAPModel.IDX_MODEL_DIFF_BINDING].getModelParameters() != null) {
        params = frapModels[FRAPModel.IDX_MODEL_DIFF_BINDING].getModelParameters();
        ((EstParams_ReacBindingPanel) getPanelComponent()).setCurrentSimResults(frapModels[FRAPModel.IDX_MODEL_DIFF_BINDING].getData());
        ((EstParams_ReacBindingPanel) getPanelComponent()).setCurrentRawSimTimePoints(frapModels[FRAPModel.IDX_MODEL_DIFF_BINDING].getTimepoints());
    } else {
        ((EstParams_ReacBindingPanel) getPanelComponent()).setCurrentSimResults(null);
        ((EstParams_ReacBindingPanel) getPanelComponent()).setCurrentRawSimTimePoints(null);
        if (frapModels[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] != null && frapModels[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters() != null) {
            params = FRAPModel.createReacBindingParametersFromDiffusionParameters(frapModels[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters());
        } else // no parameters are available
        {
            try {
                params = FRAPModel.getInitialParameters(fStudy.getFrapData(), FRAPModel.MODEL_TYPE_ARRAY[FRAPModel.IDX_MODEL_DIFF_BINDING], fStudy.getStartingIndexForRecovery());
            } catch (Exception ex) {
                ex.printStackTrace(System.out);
                DialogUtils.showErrorDialog((getPanelComponent()), "Error getting parameters for diffusion plus binding model." + ex.getMessage());
            }
        }
    }
    ((EstParams_ReacBindingPanel) getPanelComponent()).setReacBindingParams(params);
    try {
        ((EstParams_ReacBindingPanel) getPanelComponent()).setData(fStudy.getFrapData(), params, fStudy.getFrapData().getImageDataset().getImageTimeStamps(), fStudy.getStartingIndexForRecovery(), fStudy.getSelectedROIsForErrorCalculation());
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
        DialogUtils.showErrorDialog((getPanelComponent()), "Error plotting data for diffusion plus binding model." + ex.getMessage());
    }
}

Example 7 with Parameter

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

the class EstParams_ReacBindingPanel method activateReacDiffEstPanel.

public void activateReacDiffEstPanel() {
    FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
    // check if we can do auto estimation on reaction binding papameters
    Parameter[] params = null;
    if (fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] != null && fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters() != null) {
        params = fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters();
    } else {
        DialogUtils.showErrorDialog(EstParams_ReacBindingPanel.this, "Parameters from 'Diffusion with One Diffusing Component' model " + "is needed for automated estimation of reaction binding parameters.\n" + "Please include the above-mentioned model using 'Choose Model Types' wizard.");
        return;
    }
    if (estGuidePanel == null) {
        estGuidePanel = new FRAPReacDiffEstimationGuidePanel();
    }
    // set initial parameters from diffusion with one diffusing component
    estGuidePanel.setPrimaryParameters(params);
    int choice2 = DialogUtils.showComponentOKCancelDialog(EstParams_ReacBindingPanel.this, estGuidePanel, "FRAP Parameter Estimation Guide");
    if (choice2 == JOptionPane.OK_OPTION) {
        if (estGuidePanel.getParamTable() != null) {
            int rowLen = estGuidePanel.getParamTable().getRowCount();
            for (int i = 0; i < rowLen; i++) {
                String name = ((String) estGuidePanel.getParamTable().getValueAt(i, EstimatedParameterTableModel.COLUMN_NAME));
                double val = ((Double) estGuidePanel.getParamTable().getValueAt(i, EstimatedParameterTableModel.COLUMN_VALUE)).doubleValue();
                if (name.equals(FRAPReacDiffEstimationGuidePanel.paramNames[FRAPReacDiffEstimationGuidePanel.IDX_FreePartDiffRate])) {
                    reactionDiffusionPanel.setFreeDiffRate(val + "");
                } else if (name.equals(FRAPReacDiffEstimationGuidePanel.paramNames[FRAPReacDiffEstimationGuidePanel.IDX_FreePartConc])) {
                    reactionDiffusionPanel.setFreeFraction(val + "");
                } else if (name.equals(FRAPReacDiffEstimationGuidePanel.paramNames[FRAPReacDiffEstimationGuidePanel.IDX_BWMRate])) {
                    reactionDiffusionPanel.setBleachMonitorRate(val + "");
                } else if (name.equals(FRAPReacDiffEstimationGuidePanel.paramNames[FRAPReacDiffEstimationGuidePanel.IDX_ComplexConc])) {
                    reactionDiffusionPanel.setComplexFraction(val + "");
                } else if (name.equals(FRAPReacDiffEstimationGuidePanel.paramNames[FRAPReacDiffEstimationGuidePanel.IDX_ReacPseudoOnRate])) {
                    reactionDiffusionPanel.setOnRate(val + "");
                } else if (name.equals(FRAPReacDiffEstimationGuidePanel.paramNames[FRAPReacDiffEstimationGuidePanel.IDX_ReacOffRate])) {
                    reactionDiffusionPanel.setOffRate(val + "");
                } else if (name.equals(FRAPReacDiffEstimationGuidePanel.paramNames[FRAPReacDiffEstimationGuidePanel.IDX_Immobile])) {
                    reactionDiffusionPanel.setImmobileFraction(val + "");
                }
            }
        // multisourcePlotPane.setDataSources(null);
        }
    }
}

Example 8 with Parameter

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

the class EstParams_ReactionOffRateDescriptor method preNextProcess.

// save model parameters
public ArrayList<AsynchClientTask> preNextProcess() {
    // create AsynchClientTask arraylist
    ArrayList<AsynchClientTask> taskArrayList = new ArrayList<AsynchClientTask>();
    AsynchClientTask saveParametersTask = new AsynchClientTask("", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Parameter[] params = ((EstParams_ReactionOffRatePanel) getPanelComponent()).getCurrentParameters();
            FRAPModel frapModel = getFrapWorkspace().getWorkingFrapStudy().getFrapModel(FRAPModel.IDX_MODEL_REACTION_OFF_RATE);
            frapModel.setModelParameters(params);
            frapModel.setData(((EstParams_ReactionOffRatePanel) getPanelComponent()).getCurrentEstimationResults());
        }
    };
    taskArrayList.add(saveParametersTask);
    return taskArrayList;
}

Example 9 with Parameter

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

the class EstParams_ReactionOffRateDescriptor method aboutToDisplayPanel.

public void aboutToDisplayPanel() {
    FRAPStudy fStudy = frapWorkspace.getWorkingFrapStudy();
    Parameter[] params = fStudy.getModels()[FRAPModel.IDX_MODEL_REACTION_OFF_RATE].getModelParameters();
    try {
        if (params == null) {
            params = fStudy.getFrapOptFunc().getBestParamters(fStudy.getFrapData(), null, true);
        }
        ((EstParams_ReactionOffRatePanel) getPanelComponent()).setData(params, fStudy.getFrapData(), /*fStudy.getFrapOptFunc().getOffRateResults(),*/
        fStudy.getStartingIndexForRecovery());
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
        DialogUtils.showErrorDialog((getPanelComponent()), "Error getting parameters for reaction dominant off rate model.");
    }
}

Example 10 with Parameter

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

the class EstParams_TwoDiffComponentDescriptor method saveModelParameters.

private void saveModelParameters() {
    Parameter[] params = ((EstParams_TwoDiffComponentPanel) getPanelComponent()).getCurrentParameters();
    FRAPModel frapModel = getFrapWorkspace().getWorkingFrapStudy().getFrapModel(FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS);
    frapModel.setModelParameters(params);
    frapModel.setData(((EstParams_TwoDiffComponentPanel) getPanelComponent()).getCurrentEstimationResults());
}