Examples with KeyValue org.vcell.util.document.KeyValue used on opensource projects

Example 36 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class HybridSolverTester method main.

public static void main(java.lang.String[] args) {
    VCMongoMessage.enabled = false;
    boolean bAlternate = false;
    if (args.length == 12) {
        bAlternate = true;
    } else if (args.length != 5) {
        System.out.println("usage: HybridSolverTest userid SimID times(delimited by :) dataIndexes(delimited by :) varNames(delimited by :) numRuns outputFileDirectory bCalclOnly dbPassword useridKey rmiServer rmiPort");
        System.out.println("usage: HybridSolverTest userid SimID all postproc varNames(delimited by :) numRuns outputFileDirectory bCalclOnly dbPassword useridKey rmiServer rmiPort");
        System.out.println("usage: HybridSolverTest mathVCMLFileName startingTrialNo numTrials varNames(delimited by :) bPrintTime vcellSite(rel,beta,...)");
        System.exit(1);
    }
    FileWriter fw = null;
    try {
        if (bAlternate) {
            AltArgsHelper altArgsHelper = new AltArgsHelper(args[0], args[1], args[2], args[3], args[4], Integer.parseInt(args[5]), new File(args[6]), Boolean.parseBoolean(args[7]), args[8], args[9], args[10], args[11]);
            // final String user = args[0];
            // final String simID = args[1];
            // final int numRuns = Integer.parseInt(args[5]);
            // 
            // final String simPrefix  = "SimID_"+simID+"_";
            // File userSimDataDir = new File("\\\\cfs02\\raid\\vcell\\users\\"+user);
            // File outputDir = new File(args[6]);
            // boolean bCalcOnly = Boolean.parseBoolean(args[7]);
            // String dbPassword = args[8];
            // String useridKey = args[9];
            // String rmiServer = args[10];
            // String rmiPort = args[11];
            VCSimulationIdentifier vcSimulationIdentifier = new VCSimulationIdentifier(new KeyValue(altArgsHelper.simID), altArgsHelper.user);
            UserLoginInfo userLoginInfo = new UserLoginInfo(altArgsHelper.user.getName(), new DigestedPassword(altArgsHelper.dbPassword));
            File[] trialList = null;
            VCellConnectionHelper vCellConnectionHelper = null;
            File emptyFile = File.createTempFile("hstempty", null);
            try {
                if (!altArgsHelper.bCalcOnly) {
                    // String rmiUrl = "//" + "rmi-alpha.cam.uchc.edu" + ":" + "40106" + "/"+"VCellBootstrapServer";
                    // String rmiUrl = "//" + "rmi-alpha.cam.uchc.edu" + ":" + "40112" + "/"+"VCellBootstrapServer";
                    String rmiUrl = "//" + altArgsHelper.rmiServer + ".cam.uchc.edu" + ":" + altArgsHelper.rmiPort + "/" + "VCellBootstrapServer";
                    vCellConnectionHelper = new VCellConnectionHelper(userLoginInfo, rmiUrl);
                    for (int runIndex = 0; runIndex < altArgsHelper.numRuns; runIndex++) {
                        System.out.println("-----     Starting run " + (runIndex + 1) + " of " + altArgsHelper.numRuns);
                        runSim(userLoginInfo, vcSimulationIdentifier, vCellConnectionHelper);
                        if (trialList == null) {
                            System.out.println("Sim ran, getting trial list for " + altArgsHelper.simPrefix + " please wait...");
                            trialList = altArgsHelper.userSimDataDir.listFiles(new FileFilter() {

                                @Override
                                public boolean accept(File pathname) {
                                    // }
                                    return pathname.getName().startsWith(altArgsHelper.simPrefix) && !pathname.getName().endsWith(".simtask.xml");
                                }
                            });
                        }
                        System.out.println("-----     Copying run " + (runIndex + 1) + " of " + altArgsHelper.numRuns);
                        File outputRunDir = makeOutputRunDir(altArgsHelper.outputDir, runIndex);
                        for (int j = 0; j < trialList.length; j++) {
                            File localCopyFile = new File(outputRunDir, trialList[j].getName());
                            try {
                                // copy remote sim data file to local
                                FileUtils.copyFile(trialList[j], localCopyFile);
                                // delete remote
                                trialList[j].delete();
                            } catch (Exception e) {
                                System.out.println("failed to copy '" + trialList[j].getAbsolutePath() + "', error=" + e.getMessage() + ".  Putting empty file as placeholder");
                                try {
                                    // copy empty file to local in place of problematic remote sim data file, later analysis will skip it
                                    FileUtils.copyFile(emptyFile, localCopyFile);
                                } catch (Exception e2) {
                                    System.out.println("Faild to copy file and failed to copy empty, " + e2.getMessage());
                                }
                            }
                        }
                    }
                }
                // calc stats
                String dateStr = dateFormat.format(new Date());
                String outPrefix = altArgsHelper.simID + "_" + dateStr + "_0";
                File outputFile = new File(altArgsHelper.outputDir, outPrefix + ".csv");
                while (outputFile.exists()) {
                    outPrefix = TokenMangler.getNextEnumeratedToken(outPrefix);
                    outputFile = new File(altArgsHelper.outputDir, outPrefix + ".csv");
                }
                fw = new FileWriter(outputFile);
                fw.write("\"" + altArgsHelper.toString() + "\"\n");
                for (int runIndex = 0; runIndex < altArgsHelper.numRuns; runIndex++) {
                    makeAltCSV(altArgsHelper, fw, runIndex, makeOutputRunDir(altArgsHelper.outputDir, runIndex));
                }
                fw.close();
            } finally {
                if (!altArgsHelper.bCalcOnly) {
                    File[] straglers = altArgsHelper.userSimDataDir.listFiles(new FileFilter() {

                        @Override
                        public boolean accept(File pathname) {
                            return pathname.getName().startsWith(altArgsHelper.simPrefix);
                        }
                    });
                    if (straglers != null) {
                        for (int i = 0; i < straglers.length; i++) {
                            straglers[i].delete();
                        }
                    }
                }
            }
        } else {
            String site = args[5];
            HybridSolverTester hst = new HybridSolverTester(args[0], Integer.parseInt(args[1]), Integer.parseInt(args[2]), args[3], Boolean.parseBoolean(args[4]));
            hst.runHybridTest(site);
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        System.exit(1);
    } finally {
        if (fw != null) {
            try {
                fw.close();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
}

Example 37 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class ExportMonitorPanelTest method main.

/**
 * main entrypoint - starts the part when it is run as an application
 * @param args java.lang.String[]
 */
public static void main(java.lang.String[] args) {
    try {
        JFrame frame = new javax.swing.JFrame();
        ExportMonitorPanel aExportMonitorPanel;
        aExportMonitorPanel = new ExportMonitorPanel();
        frame.setContentPane(aExportMonitorPanel);
        frame.setSize(aExportMonitorPanel.getSize());
        frame.addWindowListener(new java.awt.event.WindowAdapter() {

            public void windowClosing(java.awt.event.WindowEvent e) {
                System.exit(0);
            }
        });
        frame.show();
        java.awt.Insets insets = frame.getInsets();
        frame.setSize(frame.getWidth() + insets.left + insets.right, frame.getHeight() + insets.top + insets.bottom);
        VCSimulationDataIdentifier vcSimDataId = new VCSimulationDataIdentifier(new VCSimulationIdentifier(new KeyValue("234"), null), 1);
        aExportMonitorPanel.addExportEvent(new ExportEvent(aExportMonitorPanel, 123456789L, null, vcSimDataId.getID(), vcSimDataId.getSimulationKey(), ExportEvent.EXPORT_PROGRESS, "CSV", "", new Double(0.47), null, null), "bogus [application: model]");
        aExportMonitorPanel.addExportEvent(new ExportEvent(aExportMonitorPanel, 987654321L, null, vcSimDataId.getID(), vcSimDataId.getSimulationKey(), ExportEvent.EXPORT_COMPLETE, "GIF", "http://nrcam.uchc.edu/export/987654321.zip", new Double(1), null, null), "simulation [application: model]");
        frame.pack();
        frame.setVisible(true);
    } catch (Throwable exception) {
        System.err.println("Exception occurred in main() of javax.swing.JPanel");
        exception.printStackTrace(System.out);
    }
}

Example 38 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class TestCaseAddPanel method applyTestCaseInfo.

/**
 * Comment
 */
private void applyTestCaseInfo() throws Exception {
    fieldNewTestCaseArr = null;
    if (getMathModelInfo() == null && getbioModelInfo() == null) {
        throw new Exception("Nothing selected, choose either a MathModel or a BioModel/App combination before setting TestCaseInfo");
    // return;
    }
    if (getMathModelInfo() != null && getbioModelInfo() != null) {
        throw new Exception("must choose either a MathModel or a BioModel/App combination (BUT NOT BOTH)");
    // return;
    }
    // testcaseinfo TYPE
    String type = null;
    if (getExactRadioButton().isSelected()) {
        type = TestCaseNew.EXACT;
    } else if (getIvjExactRadioButtonSteady().isSelected()) {
        type = TestCaseNew.EXACT_STEADY;
    } else if (getConstructedRadioButton().isSelected()) {
        type = TestCaseNew.CONSTRUCTED;
    } else if (getRegressionRadioButton().isSelected()) {
        type = TestCaseNew.REGRESSION;
    } else {
        throw new Exception("Solution Type Not Chosen");
    }
    String annotation = null;
    annotation = getAnnotationTextArea().getText();
    if (getMathModelInfo() != null) {
        // 
        // math model selected
        // 
        TestCaseNewMathModel mathTestCase = new TestCaseNewMathModel(null, getMathModelInfo(), type, annotation, null);
        setNewTestCaseArr(new TestCaseNewMathModel[] { mathTestCase });
    } else {
        // 
        if (getappNameArr() == null) {
            throw new Exception("no application(s) selected");
        }
        if (!type.equals(TestCaseNew.REGRESSION)) {
            throw new Exception("BioModel/App test case must be of type 'REGRESSION'");
        }
        org.vcell.util.document.KeyValue[] appKeyArr = null;
        try {
            for (int i = 0; i < getappNameArr().length; i++) {
                if (appKeyArr == null) {
                    appKeyArr = new KeyValue[getappNameArr().length];
                }
                appKeyArr[i] = getTestingFrameworkWindowManager().getSimContextKey(getbioModelInfo(), getappNameArr()[i]);
            }
        } catch (org.vcell.util.DataAccessException e) {
            e.printStackTrace(System.out);
            throw new Exception("Exception while retrieving BioModel SimContextKey");
        }
        if (appKeyArr == null) {
            throw new Exception("BioModel/App test case cannot be created, selected application(s), not found in BioModel");
        }
        TestCaseNewBioModel[] bioTestCaseArr = new TestCaseNewBioModel[appKeyArr.length];
        for (int i = 0; i < bioTestCaseArr.length; i++) {
            bioTestCaseArr[i] = new TestCaseNewBioModel(null, getbioModelInfo(), getappNameArr()[i], appKeyArr[i], type, annotation, null);
        }
        setNewTestCaseArr(bioTestCaseArr);
    }
}

Example 39 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class RunRefSimulationFastOp method runRefSimulation.

private RowColumnResultSet runRefSimulation(ROI cellROI, ROI[] imageDataROIs, UShortImage psf, FloatImage initRefConc, double experimentalRecoveryTime, LocalWorkspace localWorkspace, ClientTaskStatusSupport progressListener) throws Exception {
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    // 
    // save first image from normalized time series as the initial concentration field data
    // 
    ExternalDataInfo initialConcentrationExtData = createNewExternalDataInfo(localWorkspace, INITCONC_EXTDATA_NAME);
    Extent extent = initRefConc.getExtent();
    Origin origin = initRefConc.getOrigin();
    ISize isize = new ISize(initRefConc.getNumX(), initRefConc.getNumY(), initRefConc.getNumZ());
    saveExternalData(initRefConc, INITCONC_EXTDATA_VARNAME, initialConcentrationExtData.getExternalDataIdentifier(), localWorkspace);
    FieldFunctionArguments initConditionFFA = new FieldFunctionArguments(INITCONC_EXTDATA_NAME, INITCONC_EXTDATA_VARNAME, new Expression(0.0), VariableType.VOLUME);
    // 
    // save ROIs as a multivariate field data
    // 
    ExternalDataInfo roiExtData = createNewExternalDataInfo(localWorkspace, ROI_EXTDATA_NAME);
    saveROIsAsExternalData(imageDataROIs, localWorkspace, roiExtData.getExternalDataIdentifier());
    ArrayList<FieldFunctionArguments> roiFFAs = new ArrayList<FieldFunctionArguments>();
    for (ROI roi : imageDataROIs) {
        roiFFAs.add(new FieldFunctionArguments(ROI_EXTDATA_NAME, ROI_MASK_NAME_PREFIX + roi.getROIName(), new Expression(0.0), VariableType.VOLUME));
    }
    // 
    // save PSF as a field data
    // 
    ExternalDataInfo psfExtData = createNewExternalDataInfo(localWorkspace, PSF_EXTDATA_NAME);
    savePsfAsExternalData(psf, PSF_EXTDATA_VARNAME, psfExtData.getExternalDataIdentifier(), localWorkspace);
    FieldFunctionArguments psfFFA = new FieldFunctionArguments(PSF_EXTDATA_NAME, PSF_EXTDATA_VARNAME, new Expression(0.0), VariableType.VOLUME);
    TimeBounds timeBounds = getEstimatedRefTimeBound(experimentalRecoveryTime);
    double timeStepVal = REFERENCE_DIFF_DELTAT;
    Expression chirpedDiffusionRate = new Expression(REFERENCE_DIFF_RATE_COEFFICIENT + "*(t+" + REFERENCE_DIFF_DELTAT + ")");
    BioModel bioModel = createRefSimBioModel(simKey, owner, origin, extent, cellROI, timeStepVal, timeBounds, VAR_NAME, new Expression(initConditionFFA.infix()), psfFFA, chirpedDiffusionRate);
    if (progressListener != null) {
        progressListener.setMessage("Running Reference Simulation...");
    }
    // run simulation
    Simulation simulation = bioModel.getSimulation(0);
    ROIDataGenerator roiDataGenerator = getROIDataGenerator(localWorkspace, imageDataROIs);
    simulation.getMathDescription().getPostProcessingBlock().addDataGenerator(roiDataGenerator);
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), simulation, initialConcentrationExtData.getExternalDataIdentifier(), roiExtData.getExternalDataIdentifier(), psfExtData.getExternalDataIdentifier(), progressListener, true);
    KeyValue referenceSimKeyValue = simulation.getVersion().getVersionKey();
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(referenceSimKeyValue, LocalWorkspace.getDefaultOwner());
    VCSimulationDataIdentifier vcSimDataID = new VCSimulationDataIdentifier(vcSimID, 0);
    File hdf5File = new File(localWorkspace.getDefaultSimDataDirectory(), vcSimDataID.getID() + SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_HDF5);
    // get post processing info (time points, variable sizes)
    DataOperation.DataProcessingOutputInfoOP dataOperationInfo = new DataOperation.DataProcessingOutputInfoOP(null, /*no vcDataIdentifier OK*/
    false, null);
    DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) DataSetControllerImpl.getDataProcessingOutput(dataOperationInfo, hdf5File);
    // get post processing data
    DataOperation.DataProcessingOutputDataValuesOP dataOperationDataValues = new DataOperation.DataProcessingOutputDataValuesOP(null, /*no vcDataIdentifier OK*/
    ROI_EXTDATA_NAME, TimePointHelper.createAllTimeTimePointHelper(), DataIndexHelper.createSliceDataIndexHelper(0), null, null);
    DataOperationResults.DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataOperationResults.DataProcessingOutputDataValues) DataSetControllerImpl.getDataProcessingOutput(dataOperationDataValues, hdf5File);
    // 
    // delete the simulation files
    // 
    // 
    // remove reference simulation files and field data files
    // 
    File userDir = new File(localWorkspace.getDefaultSimDataDirectory());
    File[] oldSimFilesToDelete = getSimulationFileNames(userDir, referenceSimKeyValue);
    for (int i = 0; oldSimFilesToDelete != null && i < oldSimFilesToDelete.length; i++) {
        oldSimFilesToDelete[i].delete();
    }
    deleteCanonicalExternalData(localWorkspace, initialConcentrationExtData.getExternalDataIdentifier());
    deleteCanonicalExternalData(localWorkspace, roiExtData.getExternalDataIdentifier());
    deleteCanonicalExternalData(localWorkspace, roiExtData.getExternalDataIdentifier());
    // get ref sim time points (distorted by time dilation acceleration)
    double[] rawRefDataTimePoints = dataProcessingOutputInfo.getVariableTimePoints();
    // get shifted time points
    double[] correctedRefDataTimePoints = shiftTimeForBaseDiffRate(rawRefDataTimePoints);
    double[][] refData = dataProcessingOutputDataValues.getDataValues();
    // 
    // for rowColumnResultSet with { "t", "roi1", .... , "roiN" } for reference data
    // 
    int numROIs = imageDataROIs.length;
    String[] columnNames = new String[numROIs + 1];
    columnNames[0] = "t";
    for (int i = 0; i < numROIs; i++) {
        columnNames[i + 1] = imageDataROIs[i].getROIName();
    }
    RowColumnResultSet reducedData = new RowColumnResultSet(columnNames);
    for (int i = 0; i < correctedRefDataTimePoints.length; i++) {
        double[] row = new double[numROIs + 1];
        row[0] = correctedRefDataTimePoints[i];
        double[] roiData = refData[i];
        for (int j = 0; j < numROIs; j++) {
            // roiData[0] is the average over the cell .. postbleach this shouldn't change for pure diffusion
            row[j + 1] = roiData[j + 1];
        }
        reducedData.addRow(row);
    }
    return reducedData;
}

Example 40 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class RunRefSimulationFastOp method createNewExternalDataInfo.

private ExternalDataInfo createNewExternalDataInfo(LocalContext localWorkspace, String extDataIDName) {
    File targetDir = new File(localWorkspace.getDefaultSimDataDirectory());
    KeyValue key = LocalWorkspace.createNewKeyValue();
    User owner = LocalWorkspace.getDefaultOwner();
    ExternalDataIdentifier newImageDataExtDataID = new ExternalDataIdentifier(key, owner, extDataIDName);
    String filename = new File(targetDir, newImageDataExtDataID.getID() + SimDataConstants.LOGFILE_EXTENSION).getAbsolutePath();
    ExternalDataInfo newImageDataExtDataInfo = new ExternalDataInfo(newImageDataExtDataID, filename);
    return newImageDataExtDataInfo;
}