Examples with VCSimulationDataIdentifier cbit.vcell.solver.VCSimulationDataIdentifier used on opensource projects

Example 31 with VCSimulationDataIdentifier

use of cbit.vcell.solver.VCSimulationDataIdentifier in project vcell by virtualcell.

the class ChomboSimpleDataViewer method retrieveVariablesAndTimes.

private void retrieveVariablesAndTimes() {
    AsynchClientTask task0 = new AsynchClientTask("clear", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            DefaultComboBoxModel dcm = new DefaultComboBoxModel();
            timeComboBox.setModel(dcm);
            DefaultListModel dlm = new DefaultListModel();
            varList.setModel(dlm);
            solTableModel.clear();
            meshMetricsTableModel.clear();
            meanTextField.setText(null);
            maxErrorTextField.setText(null);
            sumVolFracTextField.setText(null);
            l2ErrorTextField.setText(null);
        }
    };
    AsynchClientTask task1 = new AsynchClientTask("retrieve data", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            String simId = simIdField.getText().trim();
            if (simId == null || simId.length() == 0) {
                throw new RuntimeException("Please provide a simulation id.");
            }
            String username = userNameTextField.getText().trim();
            if (username == null || username.length() == 0) {
                throw new RuntimeException("Please provide a user name.");
            }
            VCSimulationDataIdentifier vcDataId = new VCSimulationDataIdentifier(new VCSimulationIdentifier(new KeyValue(simId), new User(username, null)), 0);
            SimDataInfoHolder simDataInfoHolder = null;
            String datadir = dataDirTextField.getText();
            if (datadir == null || datadir.length() == 0) {
                simDataInfoHolder = createSimulationDataFromRemote(username, vcDataId);
                datadir = simDataInfoHolder.userDir.getParent();
                dataDirTextField.setText(datadir);
            } else {
                simDataInfoHolder = createSimulationDataFromDir(new File(datadir), username, vcDataId);
            }
            simData = simDataInfoHolder.simData;
            simData.readVarAndFunctionDataIdentifiers();
            usernames.add(username);
            userNameTextField.setAutoCompletionWords(usernames);
            datadirs.add(datadir);
            dataDirTextField.setAutoCompletionWords(datadirs);
            simIds.add(simId);
            simIdField.setAutoCompletionWords(simIds);
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("show data", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            double[] times = simData.getDataTimes();
            DefaultComboBoxModel dcm = new DefaultComboBoxModel();
            for (double t : times) {
                dcm.addElement(t);
            }
            timeComboBox.setModel(dcm);
            meshMetricsTableModel.setData(simData.getChomboMesh().getMetricsColumnNames(), simData.getChomboMesh().getMetricsNumbers());
            List<DataSetIdentifier> dsiList = simData.getDataSetIdentifiers();
            DefaultListModel dlm = new DefaultListModel();
            for (DataSetIdentifier dsi : dsiList) {
                dlm.addElement(dsi);
            }
            varList.setModel(dlm);
            if (times.length > 0) {
                timeComboBox.setSelectedIndex(0);
            }
            if (dsiList.size() > 0) {
                varList.setSelectedIndex(0);
            }
            meshMetricsTableModel.refreshTable();
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task0, task1, task2 }, false);
}

Example 32 with VCSimulationDataIdentifier

use of cbit.vcell.solver.VCSimulationDataIdentifier in project vcell by virtualcell.

the class SimResultsViewer method updateScanParamChoices.

private void updateScanParamChoices(final String message, ListReset listReset) {
    if ((paramScanChoiceTimer = ClientTaskDispatcher.getBlockingTimer(this, null, null, paramScanChoiceTimer, new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e2) {
            updateScanParamChoices(message, listReset);
        }
    }, message)) != null) {
        return;
    }
    int selectedJobIndex = getSelectedParamScanJobIndex();
    // update viewer
    if (selectedJobIndex == -1) {
        if (isODEData) {
            if (listReset != null && odeDataViewer != null && odeDataViewer.getVcDataIdentifier() != null) {
                listReset.reset(odeDataViewer.getVcDataIdentifier());
            } else {
                odeDataViewer.setOdeSolverResultSet(null);
            }
        } else {
            if (listReset != null && pdeDataViewer != null && pdeDataViewer.getPdeDataContext() != null && pdeDataViewer.getPdeDataContext().getVCDataIdentifier() != null) {
                listReset.reset(pdeDataViewer.getPdeDataContext().getVCDataIdentifier());
            } else {
                pdeDataViewer.setPdeDataContext(null);
            }
        }
        return;
    }
    final VCSimulationDataIdentifier vcdid = new VCSimulationDataIdentifier(getSimulation().getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), selectedJobIndex);
    if (isODEData) {
        AsynchClientTask task1 = new AsynchClientTask("get ode results", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                ODEDataManager odeDatamanager = ((ODEDataManager) dataManager).createNewODEDataManager(vcdid);
                hashTable.put("odeDatamanager", odeDatamanager);
            }
        };
        AsynchClientTask task2 = new AsynchClientTask("show results", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                if (hashTable.get(ClientTaskDispatcher.TASK_ABORTED_BY_ERROR) == null) {
                    ODEDataManager odeDatamanager = (ODEDataManager) hashTable.get("odeDatamanager");
                    odeDataViewer.setOdeSolverResultSet(odeDatamanager.getODESolverResultSet());
                    odeDataViewer.setVcDataIdentifier(vcdid);
                } else {
                    odeDataViewer.setOdeSolverResultSet(null);
                }
            }
        };
        ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
    } else {
        AsynchClientTask task1 = new AsynchClientTask("get pde results", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                PDEDataManager pdeDatamanager = ((PDEDataManager) dataManager).createNewPDEDataManager(vcdid, null);
                PDEDataContext newPDEDC = pdeDatamanager.getPDEDataContext();
                PDEDataContext oldPDEDC = pdeDataViewer.getPdeDataContext();
                hashTable.put("newPDEDC", newPDEDC);
                if (oldPDEDC != null && oldPDEDC.getTimePoints().length <= newPDEDC.getTimePoints().length) {
                    DataIdentifier setDid = (newPDEDC.getDataIdentifier() == null ? newPDEDC.getDataIdentifiers()[0] : newPDEDC.getDataIdentifier());
                    if (Arrays.asList(newPDEDC.getDataIdentifiers()).contains(oldPDEDC.getDataIdentifier())) {
                        setDid = oldPDEDC.getDataIdentifier();
                        newPDEDC.setVariableAndTime(setDid, newPDEDC.getTimePoints()[BeanUtils.firstIndexOf(oldPDEDC.getTimePoints(), oldPDEDC.getTimePoint())]);
                    }
                }
            }
        };
        AsynchClientTask task2 = new AsynchClientTask("show results", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                if (hashTable.get(ClientTaskDispatcher.TASK_ABORTED_BY_ERROR) == null) {
                    ClientPDEDataContext newPDEDC = (ClientPDEDataContext) hashTable.get("newPDEDC");
                    pdeDataViewer.setPdeDataContext(newPDEDC);
                    pdeDataViewer.setSimNameSimDataID(new ExportSpecs.SimNameSimDataID(getSimulation().getName(), getSimulation().getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), SimResultsViewer.getParamScanInfo(getSimulation(), vcdid.getJobIndex())));
                } else {
                    if (listReset != null && pdeDataViewer != null && pdeDataViewer.getPdeDataContext() != null && pdeDataViewer.getPdeDataContext().getVCDataIdentifier() != null) {
                        listReset.reset(pdeDataViewer.getPdeDataContext().getVCDataIdentifier());
                    } else {
                        pdeDataViewer.setPdeDataContext(null);
                        pdeDataViewer.setSimNameSimDataID(null);
                    }
                }
            }
        };
        // AsynchClientTask refreshTask = new AsynchClientTask("",AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
        // @Override
        // public void run(Hashtable<String, Object> hashTable) throws Exception {
        // ((ArrayList<AsynchClientTask>)hashTable.get(ClientTaskDispatcher.INTERMEDIATE_TASKS)).addAll(Arrays.asList(pdeDataViewer.getRefreshTasks()));
        // }
        // };
        ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 /*,refreshTask*/
        });
    }
}

Example 33 with VCSimulationDataIdentifier

use of cbit.vcell.solver.VCSimulationDataIdentifier in project vcell by virtualcell.

the class VCellClientDataServiceImpl method getVCSimulationDataIdentifier.

public VCSimulationDataIdentifier getVCSimulationDataIdentifier(SimulationDataSetRef simulationDataSetRef) throws FileNotFoundException {
    User user = new User(simulationDataSetRef.getUsername(), new KeyValue(simulationDataSetRef.getUserkey()));
    KeyValue simKeyValue = new KeyValue(simulationDataSetRef.getSimId());
    VCSimulationIdentifier vcSimulationIdentifier = new VCSimulationIdentifier(simKeyValue, user);
    if (simulationDataSetRef.isIsLocal()) {
        File primaryDir = ResourceUtil.getLocalRootDir();
        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(null, primaryDir, null);
        ExportServiceImpl localExportServiceImpl = new ExportServiceImpl();
        LocalDataSetControllerProvider localDSCProvider = new LocalDataSetControllerProvider(user, dataSetControllerImpl, localExportServiceImpl);
        VCDataManager vcDataManager = new VCDataManager(localDSCProvider);
        File localSimDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
        VCSimulationDataIdentifier simulationDataIdentifier = new LocalVCSimulationDataIdentifier(vcSimulationIdentifier, 0, localSimDir);
        return simulationDataIdentifier;
    } else {
        VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(vcSimulationIdentifier, simulationDataSetRef.getJobIndex());
        return vcSimulationDataIdentifier;
    }
}

Example 34 with VCSimulationDataIdentifier

use of cbit.vcell.solver.VCSimulationDataIdentifier in project vcell by virtualcell.

the class VCellClientDataServiceImpl method displayPostProcessingDataInVCell.

@Override
public void displayPostProcessingDataInVCell(SimulationDataSetRef simulationDataSetRef) throws NumberFormatException, DataAccessException {
    User vcUser = vcellClient.getRequestManager().getDocumentManager().getUser();
    VCSimulationIdentifier vcSimId = new VCSimulationIdentifier(new KeyValue(simulationDataSetRef.getSimId()), vcUser);
    ClientDocumentManager clientDocumentManager = (ClientDocumentManager) vcellClient.getClientServerManager().getDocumentManager();
    SimulationOwner simulationOwner = null;
    if (simulationDataSetRef.isMathModel) {
        simulationOwner = clientDocumentManager.getMathModel(new KeyValue(simulationDataSetRef.getModelId()));
    } else {
        BioModel bioModel = clientDocumentManager.getBioModel(new KeyValue(simulationDataSetRef.getModelId()));
        simulationOwner = bioModel.getSimulationContext(simulationDataSetRef.getSimulationContextName());
    }
    ArrayList<AnnotatedFunction> outputFunctionsList = simulationOwner.getOutputFunctionContext().getOutputFunctionsList();
    OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
    VCSimulationDataIdentifier vcSimDataId = new VCSimulationDataIdentifier(vcSimId, simulationDataSetRef.getJobIndex());
    PDEDataManager pdeDataManager = (PDEDataManager) vcellClient.getRequestManager().getDataManager(outputContext, vcSimDataId, true);
    final ClientPDEDataContext newClientPDEDataContext = pdeDataManager.getPDEDataContext();
    // this was the code before the windows refactoring; appears to just always get the first window???
    // Enumeration<TopLevelWindowManager> windowManagers = vcellClient.getMdiManager().getWindowManagers();
    // final Window window = FindWindow.getWindow(windowManagers.nextElement().getComponent());
    Optional<TopLevelWindowManager> first = vcellClient.getMdiManager().getWindowManagers().stream().findFirst();
    VCAssert.assertTrue(first.isPresent(), "window manager not present?");
    final Window window = getWindow(first.get().getComponent());
    AsynchClientTask task = new AsynchClientTask("Display Post Processing Statistics", AsynchClientTask.TASKTYPE_SWING_NONBLOCKING, false, false) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            DataProcessingResultsPanel dataProcessingResultsPanel = new DataProcessingResultsPanel();
            dataProcessingResultsPanel.update(newClientPDEDataContext);
            DialogUtils.showComponentOKCancelDialog(window, dataProcessingResultsPanel, "Post Processing Statistics");
        }
    };
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    Vector<AsynchClientTask> tasksV = new Vector<AsynchClientTask>();
    tasksV.add(task);
    AsynchClientTask[] tasks = new AsynchClientTask[tasksV.size()];
    tasksV.copyInto(tasks);
    ClientTaskDispatcher.dispatch(window, hash, tasks, true);
}

Example 35 with VCSimulationDataIdentifier

use of cbit.vcell.solver.VCSimulationDataIdentifier in project vcell by virtualcell.

the class HybridSolverTester method makeAltCSV.

private static void makeAltCSV(AltArgsHelper altArgsHelper, FileWriter fw, int runIndex, File userSimDataDir) throws Exception {
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(new KeyValue(altArgsHelper.simID), altArgsHelper.user);
    boolean bInit = runIndex == 0;
    ArrayList<Double> simTimes = new ArrayList<Double>();
    StringTokenizer st = null;
    if (altArgsHelper.times.equals("all")) {
    } else {
        st = new StringTokenizer(altArgsHelper.times, ":");
        while (st.hasMoreTokens()) {
            double timePoint = Double.parseDouble(st.nextToken());
            simTimes.add(timePoint);
        }
    }
    SimLocHelper simLocHelper0 = null;
    ArrayList<String> simVars = new ArrayList<String>();
    st = new StringTokenizer(altArgsHelper.varnames, ":");
    while (st.hasMoreTokens()) {
        String var = st.nextToken();
        simVars.add(var);
    }
    int jobCounter = 0;
    final int TIME_SPACE_EXTRA = 0;
    double[][][] trialData = null;
    while (true) {
        VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(vcSimID, jobCounter);
        SimulationData simData = null;
        DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = null;
        try {
            simData = new SimulationData(vcSimulationDataIdentifier, userSimDataDir, null, null);
            dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) DataSetControllerImpl.getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(vcSimulationDataIdentifier, true, null), new File(userSimDataDir, SimulationData.createCanonicalPostProcessFileName(vcSimulationDataIdentifier)));
        } catch (FileNotFoundException e) {
            if (jobCounter == 0) {
                System.out.println("found no trials matching SimID=" + altArgsHelper.simID + " in user dir " + userSimDataDir.getAbsolutePath());
            } else {
                System.out.println("found " + jobCounter + " trials in dir " + userSimDataDir.getAbsolutePath() + " matching SimID=" + altArgsHelper.simID);
            }
            break;
        } catch (Exception e) {
            e.printStackTrace();
        }
        if (dataProcessingOutputInfo == null) {
            System.out.println("No postprocessing found for " + jobCounter + " trials in dir " + userSimDataDir.getAbsolutePath() + " matching SimID=" + altArgsHelper.simID);
            jobCounter++;
            continue;
        }
        if (simLocHelper0 == null && !altArgsHelper.dataIndexes.equals(POSTPROC)) {
            simLocHelper0 = calcSimLocs(altArgsHelper.dataIndexes, simData.getMesh());
        }
        if (jobCounter == 0) {
            double[] allDatasetTimes = simData.getDataTimes();
            if (altArgsHelper.times.equals("all")) {
                for (double thisTime : allDatasetTimes) {
                    simTimes.add(thisTime);
                }
            } else {
                // Convert user input times to actual data times
                for (int times = 0; times < simTimes.size(); times++) {
                    double masterDelta = Double.POSITIVE_INFINITY;
                    double timePoint = -1;
                    for (int j = 0; j < allDatasetTimes.length; j++) {
                        double tempDelta = Math.abs(simTimes.get(times) - allDatasetTimes[j]);
                        if (tempDelta < masterDelta) {
                            masterDelta = tempDelta;
                            timePoint = allDatasetTimes[j];
                            if (tempDelta == 0) {
                                break;
                            }
                        }
                    }
                    System.out.println("User time=" + simTimes.get(times) + " converted to dataset time=" + timePoint);
                    simTimes.set(times, timePoint);
                }
            }
            trialData = new double[simTimes.size()][(simLocHelper0 == null ? 1 : simLocHelper0.boxToLocs.size())][simVars.size()];
        }
        if (bInit && jobCounter == 0) {
            // print state vars
            DataIdentifier[] dataIdentifiers = simData.getVarAndFunctionDataIdentifiers(null);
            for (int j = 0; j < dataIdentifiers.length; j++) {
                System.out.println(dataIdentifiers[j]);
            }
            printheader(altArgsHelper, simTimes, simLocHelper0, simVars, fw, TIME_SPACE_EXTRA);
        }
        for (int times = 0; times < simTimes.size(); times++) {
            double timePoint = simTimes.get(times);
            for (int vars = 0; vars < simVars.size(); vars++) {
                double[] data = null;
                if (altArgsHelper.dataIndexes.equals(POSTPROC)) {
                    data = dataProcessingOutputInfo.getVariableStatValues().get(simVars.get(vars) + "_average");
                } else {
                    SimDataBlock simDataBlock = simData.getSimDataBlock(null, simVars.get(vars), timePoint);
                    data = simDataBlock.getData();
                }
                for (int locs = 0; locs < trialData[times].length; locs++) {
                    double val;
                    if (simLocHelper0 != null && simLocHelper0.boxToLocs.get(locs).size() == 1) {
                        // point
                        // System.out.println("pointIndex="+simLocHelper.boxToLocs.get(locs).get(0));
                        val = data[simLocHelper0.boxToLocs.get(locs).get(0)];
                    } else if (simLocHelper0 != null) {
                        // box, calculate the average, could be concentration or counts
                        double accum = 0;
                        for (Integer locIndex : simLocHelper0.boxToLocs.get(locs)) {
                            // System.out.println("boxIndex="+locIndex);
                            accum += data[locIndex];
                        }
                        val = accum / simLocHelper0.boxToLocs.get(locs).size();
                    } else {
                        // PostProcess
                        if (times < data.length) {
                            val = data[times];
                        } else {
                            val = Double.NaN;
                        }
                    }
                    trialData[times][locs][vars] = val;
                }
            }
        }
        fw.write("r=" + runIndex + " s=" + jobCounter + ",");
        for (int times = 0; times < simTimes.size(); times++) {
            for (int locs = 0; locs < trialData[times].length; locs++) {
                for (int vars = 0; vars < simVars.size(); vars++) {
                    // System.out.println("job="+jobCounter+" time="+simTimes.get(times)+" loc="+simLocHelper.boxToID.get(locs)+" var="+simVars.get(vars)+" data="+trialData[times][locs][vars]);
                    boolean isNan = Double.isNaN(trialData[times][locs][vars]);
                    fw.write((isNan ? "" : trialData[times][locs][vars]) + ",");
                }
                fw.write(",");
            }
            for (int timeSpace = 0; timeSpace < TIME_SPACE_EXTRA; timeSpace++) {
                fw.write(",");
            }
        }
        fw.write("\n");
        jobCounter++;
    }
    fw.flush();
}