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

Example 1 with Parameter

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

the class BatchRunXmlProducer method getXML.

/**
 * This method returns a XML representation
 * for a frap batch run including
 */
private static Element getXML(FRAPBatchRunWorkspace param) throws XmlParseException, cbit.vcell.parser.ExpressionException {
    Element batchRunNode = new Element(MicroscopyXMLTags.FrapBatchRunTag);
    // Get selected model index
    Element selectedModelIdxElem = new Element(MicroscopyXMLTags.BatchRunSelectedModelTypeTag);
    selectedModelIdxElem.setText(mangle(param.getSelectedModel() + ""));
    batchRunNode.addContent(selectedModelIdxElem);
    // Get average model parameters
    Element parametersNode = new Element(MicroscopyXMLTags.ModelParametersTag);
    Parameter[] avgParams = param.getAverageParameters();
    if (avgParams != null) {
        if (param.getSelectedModel() == FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT && avgParams.length == FRAPModel.NUM_MODEL_PARAMETERS_ONE_DIFF) {
            parametersNode.setAttribute(MicroscopyXMLTags.PrimaryRateAttrTag, avgParams[FRAPModel.INDEX_PRIMARY_DIFF_RATE].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.PrimaryFractionAttTag, avgParams[FRAPModel.INDEX_PRIMARY_FRACTION].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.BleachWhileMonitoringTauAttrTag, avgParams[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess() + "");
        } else if (param.getSelectedModel() == FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS && avgParams.length == FRAPModel.NUM_MODEL_PARAMETERS_TWO_DIFF) {
            parametersNode.setAttribute(MicroscopyXMLTags.PrimaryRateAttrTag, avgParams[FRAPModel.INDEX_PRIMARY_DIFF_RATE].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.PrimaryFractionAttTag, avgParams[FRAPModel.INDEX_PRIMARY_FRACTION].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.BleachWhileMonitoringTauAttrTag, avgParams[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.SecondRateAttrTag, avgParams[FRAPModel.INDEX_SECONDARY_DIFF_RATE].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.SecondFractionAttTag, avgParams[FRAPModel.INDEX_SECONDARY_FRACTION].getInitialGuess() + "");
        } else if (param.getSelectedModel() == FRAPModel.IDX_MODEL_REACTION_OFF_RATE && avgParams.length == FRAPModel.NUM_MODEL_PARAMETERS_REACTION_OFF_RATE) {
            parametersNode.setAttribute(MicroscopyXMLTags.BleachWhileMonitoringTauAttrTag, avgParams[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.BindingSiteConcentrationAttTag, avgParams[FRAPModel.INDEX_BINDING_SITE_CONCENTRATION].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.ReactionOffRateAttTag, avgParams[FRAPModel.INDEX_OFF_RATE].getInitialGuess() + "");
        }
    }
    batchRunNode.addContent(parametersNode);
    // Get frap study file lists
    if (param.getFrapStudies() != null && param.getFrapStudies().size() > 0) {
        Element frapStudyListNode = new Element(MicroscopyXMLTags.FrapStudyListTag);
        frapStudyListNode.setAttribute(MicroscopyXMLTags.NumFrapStudyListAttrTag, Integer.toString(param.getFrapStudies().size()));
        ArrayList<FRAPStudy> frapList = param.getFrapStudies();
        for (int i = 0; i < frapList.size(); i++) {
            if (frapList.get(i).getXmlFilename() != null) {
                Element fileNameNode = new Element(MicroscopyXMLTags.FrapFileNameTag);
                fileNameNode.addContent(frapList.get(i).getXmlFilename());
                frapStudyListNode.addContent(fileNameNode);
            }
        }
        batchRunNode.addContent(frapStudyListNode);
    }
    return batchRunNode;
}

Example 2 with Parameter

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

the class BatchRunDetailsPanel method actionPerformed.

public void actionPerformed(ActionEvent e) {
    Object source = e.getSource();
    if (source == addButton) {
        // check file before loading into batch run, if the file has .vfrap extension
        // check if it has the model that is required by the batch run, if no, run the reference simulation and get the parameters
        final Wizard loadWizard = getAddFRAPDataWizard();
        if (loadWizard != null) {
            loadWizard.showModalDialog(new Dimension(550, 640));
            // code return
            if (loadWizard.getReturnCode() == Wizard.FINISH_RETURN_CODE) {
                // get newly added frapstudy
                FRAPStudy fStudy = getBatchRunWorkspace().getWorkingFrapStudy();
                // check if the batch run has results already and the newly loaded data should have same model ready
                int batchRunSelectedModel = getBatchRunWorkspace().getSelectedModel();
                if (getBatchRunWorkspace().isBatchRunResultsAvailable() && fStudy.getModels()[batchRunSelectedModel] != null && fStudy.getFrapModel(batchRunSelectedModel).getModelParameters() != null) {
                    Parameter[] parameters = fStudy.getFrapModel(batchRunSelectedModel).getModelParameters();
                    double[][] fitData = null;
                    if (batchRunSelectedModel == FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT || batchRunSelectedModel == FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS) {
                        FRAPOptData optData = fStudy.getFrapOptData();
                        // newly loaded frapstudy doesn't have estimation data ready, generate the data
                        if (optData == null) {
                            try {
                                optData = new FRAPOptData(fStudy, parameters.length, getLocalWorkspace(), fStudy.getStoredRefData());
                                fStudy.setFrapOptData(optData);
                                fitData = optData.getFitData(parameters);
                            } catch (Exception ex) {
                                ex.printStackTrace(System.out);
                                DialogUtils.showErrorDialog(BatchRunDetailsPanel.this, ex.getMessage());
                            }
                        }
                    } else if (batchRunSelectedModel == FRAPModel.IDX_MODEL_REACTION_OFF_RATE) {
                        FRAPOptFunctions optFunc = fStudy.getFrapOptFunc();
                        if (optFunc == null) {
                            try {
                                optFunc = new FRAPOptFunctions(fStudy);
                                fStudy.setFrapOptFunc(optFunc);
                                fitData = optFunc.getFitData(parameters);
                            } catch (Exception ex2) {
                                ex2.printStackTrace();
                                DialogUtils.showErrorDialog(BatchRunDetailsPanel.this, ex2.getMessage());
                            }
                        }
                    }
                    fStudy.getModels()[batchRunSelectedModel].setData(fitData);
                    // add new data into the frapStudy list in batch run.
                    getBatchRunWorkspace().addFrapStudy(fStudy);
                    // refresh the results
                    getBatchRunWorkspace().refreshBatchRunResults();
                } else // batch run has no results, simply add the frapStudy into
                {
                    getBatchRunWorkspace().addFrapStudy(fStudy);
                }
                // set save flag true when a doc has been added successfully
                getBatchRunWorkspace().setSaveNeeded(true);
                // update tree
                DefaultMutableTreeNode newNode = frapBatchRunViewTree.addBatchRunDocNode(new File(getBatchRunWorkspace().getWorkingFrapStudy().getXmlFilename()));
                // get the new tree node after sorting
                newNode = frapBatchRunViewTree.orderFRAPDocChildren(newNode);
                frapBatchRunViewTree.setSelectionPath(new TreePath(newNode.getPath()));
            } else {
                // load data unsuccessfully, remove the displayed image
                getBatchRunWorkspace().clearWorkingSingleWorkspace();
                // clear tree selection
                frapBatchRunViewTree.clearSelection();
                // clear stored tree selection
                batchRunWorkspace.clearStoredTreeSelection();
            }
        }
    } else if (source == deleteButton) {
        AsynchClientTask deleteFromWorkspaceTask = new AsynchClientTask("deleting file ...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                // remove tree node(doc node removable only)
                DefaultMutableTreeNode parent = frapBatchRunViewTree.removeCurrentNode();
                // handle differently for doc node and results node
                if (// doc node
                parent.equals(BatchRunTree.FRAP_BATCHRUN_DOC_NODE)) {
                    // remove the data & displayed image
                    getBatchRunWorkspace().removeFrapStudy(getBatchRunWorkspace().getWorkingFrapStudy());
                } else if (// results node
                parent.equals(BatchRunTree.FRAP_BATCHRUN_RESULT_NODE)) {
                    getBatchRunWorkspace().clearResultData();
                }
                getBatchRunWorkspace().clearWorkingSingleWorkspace();
            }
        };
        AsynchClientTask deleteFromUITask = new AsynchClientTask("deleting file ...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                // clear tree selection
                frapBatchRunViewTree.clearSelection();
                if (batchRunWorkspace.getFrapStudies() == null || batchRunWorkspace.getFrapStudies().size() < 1) {
                    frapBatchRunViewTree.clearAll();
                } else // if doc has been deleted successfully and frapStudyList still has doc, set save flag true.
                {
                    batchRunWorkspace.setSaveNeeded(true);
                }
                batchRunWorkspace.clearStoredTreeSelection();
                // clear parameter display
                clearParameterDisplay();
            }
        };
        ClientTaskDispatcher.dispatch(BatchRunDetailsPanel.this, new Hashtable<String, Object>(), new AsynchClientTask[] { deleteFromWorkspaceTask, deleteFromUITask }, false, false, false, null, true);
    } else if (source == delAllButton) {
        deleteAllBatchrunDocs();
    }
}

Example 3 with Parameter

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

the class FRAPStudyPanel method runSimulationForSelectedModel.

private void runSimulationForSelectedModel() {
    AsynchClientTask prepareRunBindingReactionTask = new AsynchClientTask("Preparing to run simulation ...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
            boolean bExtDataOK = FRAPWorkspace.areExternalDataOK(getLocalWorkspace(), fStudy.getFrapDataExternalDataInfo(), fStudy.getRoiExternalDataInfo());
            if (!bExtDataOK) {
                // refresh rois
                refreshROIs();
                // if external files are missing/currupt or ROIs are changed, create keys and save them
                fStudy.setFrapDataExternalDataInfo(FRAPStudy.createNewExternalDataInfo(getLocalWorkspace(), FRAPStudy.IMAGE_EXTDATA_NAME));
                fStudy.setRoiExternalDataInfo(FRAPStudy.createNewExternalDataInfo(getLocalWorkspace(), FRAPStudy.ROI_EXTDATA_NAME));
                try {
                    fStudy.saveROIsAsExternalData(getLocalWorkspace(), fStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), fStudy.getStartingIndexForRecovery());
                    fStudy.saveImageDatasetAsExternalData(getLocalWorkspace(), fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier(), fStudy.getStartingIndexForRecovery());
                } catch (Exception e) {
                    e.printStackTrace(System.out);
                    (getAnalysisResultsPanel()).setResultsButtonEnabled(false);
                    throw e;
                }
            }
        }
    };
    // -------------------------------------------------------------------------
    AsynchClientTask runReactionBindingTask = new AsynchClientTask("Running simulation ...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
            Parameter[] bestParams = fStudy.getModels()[fStudy.getBestModelIndex().intValue()].getModelParameters();
            if (bestParams.length < 3) {
                return;
            } else {
                if (fStudy != null && fStudy.getBioModel() != null && fStudy.getBioModel().getSimulations() != null && fStudy.getBioModel().getSimulations().length > 0 && fStudy.getBioModel().getSimulations()[0].getVersion() != null && fStudy.getBioModel().getSimulations()[0].getVersion().getVersionKey() != null) {
                    fStudy.getBioModel().getSimulations()[0].getVersion().getVersionKey();
                }
                BioModel bioModel = null;
                try {
                    bioModel = FRAPStudy.createNewSimBioModel(fStudy, bestParams, null, LocalWorkspace.createNewKeyValue(), LocalWorkspace.getDefaultOwner(), fStudy.getStartingIndexForRecovery());
                    // run simulation
                    FRAPStudy.runFVSolverStandalone(new File(getLocalWorkspace().getDefaultSimDataDirectory()), bioModel.getSimulation(0), fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier(), fStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), this.getClientTaskStatusSupport(), false);
                    fStudy.setBioModel(bioModel);
                } catch (Exception e) {
                    if (bioModel != null && bioModel.getSimulations() != null) {
                        FRAPStudy.removeExternalDataAndSimulationFiles(bioModel.getSimulations()[0].getVersion().getVersionKey(), null, null, getLocalWorkspace());
                        (getAnalysisResultsPanel()).setResultsButtonEnabled(false);
                    }
                    throw e;
                }
            }
        }
    };
    AsynchClientTask updateUITask = new AsynchClientTask("Simulation Done.", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VirtualFrapMainFrame.updateStatus("Simulation Done. Click on \'View Spatial Results\' to see simulation results.");
            (getAnalysisResultsPanel()).setResultsButtonEnabled(true);
        }
    };
    // dispatch
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { prepareRunBindingReactionTask, runReactionBindingTask, updateUITask }, true, true, true, null, true);
}

Example 4 with Parameter

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

the class FRAPStudyPanel method showEstimateParamWizard.

private void showEstimateParamWizard() {
    // check if frapOpt data is null? if yes, run ref simulation.
    // check if parameters of each selected models are there, if not, run analytic solution, get best parameters and store parameters
    AsynchClientTask saveTask = new AsynchClientTask("Preparing for parameter estimation ...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
            if (fStudy.hasDiffusionOnlyModel()) {
                // create optdata
                if (fStudy.getFrapOptData() == null) {
                    if (fStudy.getStoredRefData() != null) {
                        getFrapWorkspace().getWorkingFrapStudy().setFrapOptData(new FRAPOptData(fStudy, FRAPModel.NUM_MODEL_PARAMETERS_ONE_DIFF, getLocalWorkspace(), fStudy.getStoredRefData()));
                    } else {
                        // check external data info
                        if (!FRAPWorkspace.areExternalDataOK(getLocalWorkspace(), fStudy.getFrapDataExternalDataInfo(), fStudy.getRoiExternalDataInfo())) {
                            // if external files are missing/currupt or ROIs are changed, create keys and save them
                            fStudy.setFrapDataExternalDataInfo(FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.IMAGE_EXTDATA_NAME));
                            fStudy.setRoiExternalDataInfo(FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.ROI_EXTDATA_NAME));
                            fStudy.saveROIsAsExternalData(localWorkspace, fStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), fStudy.getStartingIndexForRecovery());
                            fStudy.saveImageDatasetAsExternalData(localWorkspace, fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier(), fStudy.getStartingIndexForRecovery());
                        }
                        // run ref sim
                        fStudy.setFrapOptData(new FRAPOptData(fStudy, FRAPModel.NUM_MODEL_PARAMETERS_ONE_DIFF, localWorkspace, this.getClientTaskStatusSupport()));
                        fStudy.setSaveNeeded(true);
                    }
                }
            }
            if (fStudy.hasReactionOnlyOffRateModel()) {
                if (fStudy.getFrapOptFunc() == null) {
                    fStudy.setFrapOptFunc(new FRAPOptFunctions(fStudy));
                }
            }
        }
    };
    AsynchClientTask runOptTask = new AsynchClientTask("Running optimization ...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
            if (fStudy.getSelectedModels() != null && fStudy.getSelectedModels().size() > 0) {
                ArrayList<Integer> models = fStudy.getSelectedModels();
                for (int i = 0; i < models.size(); i++) {
                    if ((models.get(i)).intValue() == FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT) {
                        if (fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters() == null) {
                            fStudy.getFrapOptData().setNumEstimatedParams(FRAPModel.NUM_MODEL_PARAMETERS_ONE_DIFF);
                            Parameter[] initialParams = FRAPModel.getInitialParameters(fStudy.getFrapData(), FRAPModel.MODEL_TYPE_ARRAY[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT], fStudy.getStartingIndexForRecovery());
                            Parameter[] bestParameters = fStudy.getFrapOptData().getBestParamters(initialParams, fStudy.getSelectedROIsForErrorCalculation());
                            fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].setModelParameters(bestParameters);
                            fStudy.setSaveNeeded(true);
                        }
                    } else if ((models.get(i)).intValue() == FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS) {
                        if (fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].getModelParameters() == null) {
                            fStudy.getFrapOptData().setNumEstimatedParams(FRAPModel.NUM_MODEL_PARAMETERS_TWO_DIFF);
                            Parameter[] initialParams = FRAPModel.getInitialParameters(fStudy.getFrapData(), FRAPModel.MODEL_TYPE_ARRAY[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS], fStudy.getStartingIndexForRecovery());
                            Parameter[] bestParameters = fStudy.getFrapOptData().getBestParamters(initialParams, fStudy.getSelectedROIsForErrorCalculation());
                            fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].setModelParameters(bestParameters);
                            fStudy.setSaveNeeded(true);
                        }
                    } else if ((models.get(i)).intValue() == FRAPModel.IDX_MODEL_REACTION_OFF_RATE) {
                        if (fStudy.getModels()[FRAPModel.IDX_MODEL_REACTION_OFF_RATE].getModelParameters() == null) {
                            Parameter[] bestParameters = fStudy.getFrapOptFunc().getBestParamters(fStudy.getFrapData(), null, true);
                            fStudy.getModels()[FRAPModel.IDX_MODEL_REACTION_OFF_RATE].setModelParameters(bestParameters);
                            fStudy.setSaveNeeded(true);
                        }
                    }
                }
            }
        }
    };
    AsynchClientTask evaulateCITask = new AsynchClientTask("Evaluating confidence intervals for model parameters ...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
            if (fStudy.getSelectedModels() != null && fStudy.getSelectedModels().size() > 0) {
                ArrayList<Integer> models = fStudy.getSelectedModels();
                for (int i = 0; i < models.size(); i++) {
                    if ((models.get(i)).intValue() == FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT) {
                        if (fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters() != null && fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters().length > 0) {
                            Parameter[] currentParams = fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters();
                            fStudy.getFrapOptData().setNumEstimatedParams(currentParams.length);
                            ProfileData[] profileData = null;
                            if (fStudy.getProfileData_oneDiffComponent() != null) {
                                profileData = fStudy.getProfileData_oneDiffComponent();
                            } else {
                                profileData = fStudy.getFrapOptData().evaluateParameters(currentParams, this.getClientTaskStatusSupport());
                                fStudy.setProfileData_oneDiffComponent(profileData);
                                fStudy.setSaveNeeded(true);
                            }
                        }
                    } else if ((models.get(i)).intValue() == FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS) {
                        if (fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].getModelParameters() != null && fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].getModelParameters().length > 0) {
                            Parameter[] currentParams = fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].getModelParameters();
                            fStudy.getFrapOptData().setNumEstimatedParams(currentParams.length);
                            ProfileData[] profileData = null;
                            if (fStudy.getProfileData_twoDiffComponents() != null) {
                                profileData = fStudy.getProfileData_twoDiffComponents();
                            } else {
                                profileData = fStudy.getFrapOptData().evaluateParameters(currentParams, this.getClientTaskStatusSupport());
                                fStudy.setProfileData_twoDiffComponents(profileData);
                                fStudy.setSaveNeeded(true);
                            }
                        }
                    } else if ((models.get(i)).intValue() == FRAPModel.IDX_MODEL_REACTION_OFF_RATE) {
                        if (fStudy.getModels()[FRAPModel.IDX_MODEL_REACTION_OFF_RATE].getModelParameters() != null && fStudy.getModels()[FRAPModel.IDX_MODEL_REACTION_OFF_RATE].getModelParameters().length > 0) {
                            Parameter[] currentParams = fStudy.getModels()[FRAPModel.IDX_MODEL_REACTION_OFF_RATE].getModelParameters();
                            ProfileData[] profileData = null;
                            if (fStudy.getProfileData_reactionOffRate() != null) {
                                profileData = fStudy.getProfileData_reactionOffRate();
                            } else {
                                profileData = fStudy.getFrapOptFunc().evaluateParameters(currentParams, this.getClientTaskStatusSupport());
                                fStudy.setProfileData_reactionOffRate(profileData);
                                fStudy.setSaveNeeded(true);
                            }
                        }
                    }
                }
            }
            hashTable.put(FRAPSTUDY_KEY, fStudy);
        }
    };
    AsynchClientTask showDialogTask = new AsynchClientTask("Showing estimation results ...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // get frap models  before the wizard
            FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
            FRAPModel[] oldFrapModels = new FRAPModel[FRAPModel.NUM_MODEL_TYPES];
            for (int i = 0; i < fStudy.getModels().length; i++) {
                if (fStudy.getModels()[i] != null) {
                    FRAPModel model = fStudy.getModels()[i];
                    oldFrapModels[i] = new FRAPModel(new String(model.getModelIdentifer()), model.duplicateParameters(), null, model.duplicateTimePoints());
                }
            }
            // get best model index before the wizard
            Integer oldBestModelIndex = null;
            if (fStudy.getBestModelIndex() != null) {
                oldBestModelIndex = new Integer(fStudy.getBestModelIndex().intValue());
                // put old best model index into hashtable
                hashTable.put(BEST_MODEL_KEY, oldBestModelIndex);
            }
            // put old frapmodels in hashtable
            hashTable.put(FRAPMODELS_KEY, oldFrapModels);
            // show wizard
            final Wizard estParamWizard = getEstimateParametersWizard();
            SwingUtilities.invokeLater(new Runnable() {

                public void run() {
                    estParamWizard.showModalDialog(new Dimension(1000, 750));
                }
            });
            // put wizard in hashtable in order to check return code in next task
            hashTable.put(EST_PARAM_WIZARD_KEY, estParamWizard);
        }
    };
    AsynchClientTask updateSaveStatusTask = new AsynchClientTask("...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Wizard estParamWizard = (Wizard) hashTable.get(EST_PARAM_WIZARD_KEY);
            // get old values from hashtable
            FRAPModel[] oldFrapModels = (FRAPModel[]) hashTable.get(FRAPMODELS_KEY);
            Integer oldBestModelIndex = (Integer) hashTable.get(BEST_MODEL_KEY);
            // get new values
            Integer newBestModelIndex = getFrapWorkspace().getWorkingFrapStudy().getBestModelIndex();
            if (estParamWizard.getReturnCode() == Wizard.FINISH_RETURN_CODE) {
                if (!getFrapWorkspace().getWorkingFrapStudy().areFRAPModelsEqual(oldFrapModels) || (oldBestModelIndex == null && newBestModelIndex != null) || (oldBestModelIndex != null && newBestModelIndex == null) || (oldBestModelIndex != null && newBestModelIndex != null && oldBestModelIndex.intValue() != newBestModelIndex.intValue())) {
                    getFrapWorkspace().getWorkingFrapStudy().setSaveNeeded(true);
                }
            }
        }
    };
    // dispatch
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { saveTask, runOptTask, evaulateCITask, showDialogTask, updateSaveStatusTask }, true, true, true, null, true);
}

Example 5 with Parameter

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

the class EstParams_OneDiffComponentPanel method loadBatchRunParameters.

public void loadBatchRunParameters(File inFile) {
    String xmlString;
    try {
        xmlString = XmlUtil.getXMLString(inFile.getAbsolutePath());
        BatchRunXmlReader batchRunXmlReader = new BatchRunXmlReader();
        FRAPBatchRunWorkspace tempBatchRunWorkspace = batchRunXmlReader.getBatchRunWorkspace(XmlUtil.stringToXML(xmlString, null).getRootElement());
        Parameter[] parameters = tempBatchRunWorkspace.getAverageParameters();
        if (parameters != null && parameters.length > 0 && parameters.length == FRAPModel.NUM_MODEL_PARAMETERS_ONE_DIFF) {
            String paramMsg = "Replace the current parameters with the following parameter values: \n\n";
            for (int i = 0; i < parameters.length; i++) {
                paramMsg = paramMsg + parameters[i].getName() + ": " + parameters[i].getInitialGuess() + "\n";
            }
            String choice = DialogUtils.showWarningDialog(this, paramMsg, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
            if (choice == UserMessage.OPTION_OK) {
                getPureDiffusionPanel().setParameterValues(parameters[FRAPModel.INDEX_PRIMARY_DIFF_RATE].getInitialGuess(), parameters[FRAPModel.INDEX_PRIMARY_FRACTION].getInitialGuess(), parameters[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess());
            }
        } else {
            throw new Exception("Parameters are null or number of applied parameters don't match the number (3) of parameters for diffusion with one diffusing component.");
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        DialogUtils.showErrorDialog(this, e.getMessage());
    }
}