Examples with Geometry cbit.vcell.geometry.Geometry used on opensource projects

Example 91 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class GeometryViewer method setGeometry.

/**
 * Sets the geometry property (cbit.vcell.geometry.Geometry) value.
 * @param geometry The new value for the property.
 * @see #getGeometry
 */
public void setGeometry(Geometry newValue) {
    if (ivjGeometry != newValue) {
        try {
            Geometry oldValue = getGeometry();
            if (oldValue != null) {
                oldValue.getGeometrySpec().removePropertyChangeListener(this);
            }
            if (newValue != null) {
                newValue.getGeometrySpec().addPropertyChangeListener(this);
            }
            ivjGeometry = newValue;
            if (ivjGeometry != null) {
                refreshSize();
                getImagePlaneManagerPanel1().setSourceDataInfo(null);
                refreshSourceDataInfo();
                getGeometrySubVolumePanel().setGeometry(ivjGeometry);
                getCurveRendererGeometry1().setGeometry(ivjGeometry);
                surfaceViewer.setGeometry(ivjGeometry);
                resolvedLocationTablePanel.setGeometrySurfaceDescription(ivjGeometry.getGeometrySurfaceDescription());
                if (ivjGeometry.getDimension() == 0) {
                    getJButtonChangeDomain().setEnabled(false);
                    tabbedPane.setVisible(false);
                    getJButtonReplace().setText(REPLACE_GEOMETRY_NONSPATIAL_LABEL);
                    getJButtonExport().setEnabled(false);
                    // compartmental
                    getIvjButtonEditImage().setEnabled(false);
                } else {
                    getJButtonReplace().setText(REPLACE_GEOMETRY_SPATIAL_LABEL);
                    getJButtonChangeDomain().setEnabled(true);
                    getJButtonExport().setEnabled(documentWindowManager != null);
                    getIvjButtonEditImage().setEnabled(true);
                    tabbedPane.setVisible(true);
                }
                if (getGeometryOwner() instanceof SimulationContext) {
                    SimulationContext sc = (SimulationContext) getGeometryOwner();
                    boolean replaceEnabled = false;
                    switch(sc.getApplicationType()) {
                        case RULE_BASED_STOCHASTIC:
                            replaceEnabled = false;
                            break;
                        case NETWORK_DETERMINISTIC:
                        case NETWORK_STOCHASTIC:
                            replaceEnabled = true;
                            break;
                    }
                    getJButtonReplace().setEnabled(replaceEnabled);
                }
                updateSurfaceView();
            }
            firePropertyChange("geometry", oldValue, newValue);
        } catch (java.lang.Throwable ivjExc) {
            handleException(ivjExc);
        }
    }
    ;
}

Example 92 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class GeometryViewer method resample.

private void resample() {
    AsynchClientTask precomputeCurrentGeometryTask = new AsynchClientTask("computing surfaces for existing geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (getGeometry().getGeometrySurfaceDescription().getRegionImage() == null) {
                getGeometry().precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, true);
            }
        }
    };
    AsynchClientTask sampleSizeTask = new AsynchClientTask("specify sample size", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCImage currSampledImage = getGeometry().getGeometrySpec().getSampledImage().getCurrentValue();
            int currNumSamples = currSampledImage.getNumXYZ();
            ISize currSize = new ISize(currSampledImage.getNumX(), currSampledImage.getNumY(), currSampledImage.getNumZ());
            ISize sampleSize_times_ten = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), currNumSamples * 10);
            ISize sampleSize_div_ten = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), currNumSamples / 10);
            ISize sampleSize_1e2 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e2);
            ISize sampleSize_1e3 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e3);
            ISize sampleSize_1e4 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e4);
            ISize sampleSize_1e5 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e5);
            ISize sampleSize_1e6 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e6);
            ISize sampleSize_1e7 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e7);
            ISize sampleSize_1e8 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e8);
            String[] columnNames = new String[] { "description", "num samples", "(X,Y,Z)" };
            Object[][] rowData = new Object[][] { new Object[] { "same size", new Integer(currSize.getXYZ()), currSize }, new Object[] { "10 times smaller", new Integer(sampleSize_div_ten.getXYZ()), sampleSize_div_ten }, new Object[] { "10 times bigger", new Integer(sampleSize_times_ten.getXYZ()), sampleSize_times_ten }, new Object[] { "        100 samples", new Integer(sampleSize_1e2.getXYZ()), sampleSize_1e2 }, new Object[] { "      1,000 samples", new Integer(sampleSize_1e3.getXYZ()), sampleSize_1e3 }, new Object[] { "     10,000 samples", new Integer(sampleSize_1e4.getXYZ()), sampleSize_1e4 }, new Object[] { "    100,000 samples", new Integer(sampleSize_1e5.getXYZ()), sampleSize_1e5 }, new Object[] { "  1,000,000 samples", new Integer(sampleSize_1e6.getXYZ()), sampleSize_1e6 }, new Object[] { " 10,000,000 samples", new Integer(sampleSize_1e7.getXYZ()), sampleSize_1e7 }, new Object[] { "100,000,000 samples", new Integer(sampleSize_1e8.getXYZ()), sampleSize_1e8 } };
            int[] selectedRows = DialogUtils.showComponentOKCancelTableList(GeometryViewer.this, "sample size", columnNames, rowData, ListSelectionModel.SINGLE_SELECTION);
            ISize sampleSize = (ISize) rowData[selectedRows[0]][2];
            hashTable.put("sampleSize", sampleSize);
        }
    };
    AsynchClientTask resampleTask = new AsynchClientTask("resample geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ISize sampleSize = (ISize) hashTable.get("sampleSize");
            Geometry newGeometry = RayCaster.resampleGeometry(new GeometryThumbnailImageFactoryAWT(), getGeometry(), sampleSize);
            hashTable.put("newGeometry", newGeometry);
        }
    };
    AsynchClientTask setGeometryTask = new AsynchClientTask("loading geometry", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Geometry newGeometry = (Geometry) hashTable.get("newGeometry");
            if (getGeometryOwner() instanceof SimulationContext) {
                ((SimulationContext) getGeometryOwner()).setGeometry(newGeometry);
            } else if (getGeometryOwner() instanceof MathModel) {
                ((MathModel) getGeometryOwner()).getMathDescription().setGeometry(newGeometry);
            } else {
                throw new RuntimeException("unexpected geometry owner, could not set resampled geometry");
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { precomputeCurrentGeometryTask, sampleSizeTask, resampleTask, setGeometryTask }, false);
}

Example 93 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class ChooseFile method showGeometryModelXMLFileChooser.

// // Check structure sized and select a simulation to export to SBML
// if (isSbml) {
// // get user choice of structure and its size and computes absolute sizes of compartments using the StructureSizeSolver.
// Structure[] structures = bioModel.getModel().getStructures();
// // get the nonspatial simulationContexts corresponding to names in applicableAppNameList
// // This is needed in ApplnSelectionAndStructureSizeInputPanel
// 
// SimulationContext[] applicableSimContexts = applicableSimContext.toArray(new SimulationContext[applicableSimContext.size()]);
// 
// String strucName = null;
// double structSize = 1.0;
// int structSelection = -1;
// int option = JOptionPane.CANCEL_OPTION;
// Simulation chosenSimulation = null;
// 
// ApplnSelectionAndStructureSizeInputPanel applnStructInputPanel = null;
// while (structSelection < 0) {
// applnStructInputPanel = new ApplnSelectionAndStructureSizeInputPanel();
// applnStructInputPanel.setSimContexts(applicableSimContexts);
// applnStructInputPanel.setStructures(structures);
// applnStructInputPanel.setPreferredSize(new java.awt.Dimension(350, 400));
// applnStructInputPanel.setMaximumSize(new java.awt.Dimension(350, 400));
// option = DialogUtils.showComponentOKCancelDialog(currentWindow, applnStructInputPanel, "Select Application and Specify Structure Size to Export:");
// structSelection = applnStructInputPanel.getStructSelectionIndex();
// if (option == JOptionPane.CANCEL_OPTION || option == JOptionPane.CLOSED_OPTION) {
// break;
// } else if (option == JOptionPane.OK_OPTION && structSelection < 0) {
// DialogUtils.showErrorDialog(currentWindow, "Please select a structure and set its size");
// }
// }
// 
// if (option == JOptionPane.OK_OPTION) {
// applnStructInputPanel.applyStructureNameAndSizeValues();
// strucName = applnStructInputPanel.getSelectedStructureName();
// chosenSimContext = applnStructInputPanel.getSelectedSimContext();
// hashTable.put("selectedSimContext", chosenSimContext);
// 
// GeometryContext geoContext = chosenSimContext.getGeometryContext();
// if (!fileFilter.getDescription().equals(FileFilters.FILE_FILTER_SBML_31_SPATIAL.getDescription())) {
// // calculate structure Sizes only if appln is not spatial
// structSize = applnStructInputPanel.getStructureSize();
// // Invoke StructureSizeEvaluator to compute absolute sizes of compartments if all sizes are not set
// if ( (geoContext.isAllSizeSpecifiedNull() && geoContext.isAllVolFracAndSurfVolSpecifiedNull()) ||
// ((strucName == null || structSize <= 0.0) && (geoContext.isAllSizeSpecifiedNull() && geoContext.isAllVolFracAndSurfVolSpecified())) ||
// (!geoContext.isAllSizeSpecifiedPositive() && geoContext.isAllVolFracAndSurfVolSpecifiedNull()) ||
// (!geoContext.isAllSizeSpecifiedPositive() && !geoContext.isAllVolFracAndSurfVolSpecified()) ||
// (geoContext.isAllSizeSpecifiedNull() && !geoContext.isAllVolFracAndSurfVolSpecified()) ) {
// DialogUtils.showErrorDialog(currentWindow, "Cannot export to SBML without compartment sizes being set. This can be automatically " +
// " computed if the absolute size of at least one compartment and the relative sizes (Surface-to-volume-ratio/Volume-fraction) " +
// " of all compartments are known. Sufficient information is not available to perform this computation." +
// "\n\nThis can be fixed by going back to the application '" + chosenSimContext.getName() + "' and setting structure sizes in the 'StructureMapping' tab.");
// throw UserCancelException.CANCEL_XML_TRANSLATION;
// }
// if (!geoContext.isAllSizeSpecifiedPositive() && geoContext.isAllVolFracAndSurfVolSpecified()) {
// Structure chosenStructure = chosenSimContext.getModel().getStructure(strucName);
// StructureMapping chosenStructMapping = chosenSimContext.getGeometryContext().getStructureMapping(chosenStructure);
// StructureSizeSolver.updateAbsoluteStructureSizes(chosenSimContext, chosenStructure, structSize, chosenStructMapping.getSizeParameter().getUnitDefinition());
// }
// } else {
// if (!geoContext.isAllUnitSizeParameterSetForSpatial()) {
// DialogUtils.showErrorDialog(currentWindow, "Cannot export to SBML without compartment size ratios being set."  +
// "\n\nThis can be fixed by going back to the application '" + chosenSimContext.getName() + "' and setting structure" +
// " size ratios in the 'StructureMapping' tab.");
// throw UserCancelException.CANCEL_XML_TRANSLATION;
// }
// }
// 
// // Select simulation whose overrides need to be exported
// // If simContext doesn't have simulations, don't pop up simulationSelectionPanel
// Simulation[] sims = bioModel.getSimulations(chosenSimContext);
// // display only those simulations that have overrides in the simulationSelectionPanel.
// Vector<Simulation> orSims = new Vector<Simulation>();
// for (int s = 0; (sims != null) && (s < sims.length); s++) {
// if (sims[s].getMathOverrides().hasOverrides()) {
// orSims.addElement(sims[s]);
// }
// }
// Simulation[] overriddenSims = (Simulation[])BeanUtils.getArray(orSims, Simulation.class);
// if (overriddenSims.length > 0) {
// SimulationSelectionPanel simSelectionPanel = new SimulationSelectionPanel();
// simSelectionPanel.setPreferredSize(new java.awt.Dimension(600, 400));
// simSelectionPanel.setMaximumSize(new java.awt.Dimension(600, 400));
// simSelectionPanel.setSimulations(overriddenSims);
// int simOption = DialogUtils.showComponentOKCancelDialog(currentWindow, simSelectionPanel, "Select Simulation whose overrides should be exported:");
// if (simOption == JOptionPane.OK_OPTION) {
// chosenSimulation = simSelectionPanel.getSelectedSimulation();
// if (chosenSimulation != null) {
// hashTable.put("selectedSimulation", chosenSimulation);
// }
// } else if (simOption == JOptionPane.CANCEL_OPTION || simOption == JOptionPane.CLOSED_OPTION) {
// // User did not choose a simulation whose overrides are required to be exported.
// // Without that information, cannot export successfully into SBML,
// // Hence canceling the entire export to SBML operation.
// throw UserCancelException.CANCEL_XML_TRANSLATION;
// }
// }
// } else if (option == JOptionPane.CANCEL_OPTION || option == JOptionPane.CLOSED_OPTION) {
// // User did not choose to set size for any structure.
// // Without that information, cannot export successfully into SBML,
// // Hence canceling the entire export to SBML operation.
// throw UserCancelException.CANCEL_XML_TRANSLATION;
// }
// 
// if (chosenSimulation != null) {
// // rename file to contain exported simulation.
// String ext = FilenameUtils.getExtension(selectedFileName);
// String base = FilenameUtils.getBaseName(selectedFileName);
// String path = FilenameUtils.getPath(selectedFileName);
// base += "_"  + TokenMangler.mangleToSName(chosenSimulation.getName());
// selectedFileName = path + base + ext;
// selectedFile.renameTo(new File(selectedFileName));
// }
// resetPreferredFilePath(selectedFile, userPreferences);
// return selectedFile;
// }
/**
 * Export to Geometry
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
private File showGeometryModelXMLFileChooser(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    Geometry geom = (Geometry) hashTable.get("documentToExport");
    JFrame currentWindow = (JFrame) hashTable.get("currentWindow");
    UserPreferences userPreferences = (UserPreferences) hashTable.get("userPreferences");
    TopLevelWindowManager topLevelWindowManager = (TopLevelWindowManager) hashTable.get("topLevelWindowManager");
    Component comp = (Component) hashTable.get("component");
    comp = (comp == null ? (currentWindow == null ? (topLevelWindowManager == null ? null : topLevelWindowManager.getComponent()) : currentWindow) : comp);
    File defaultPath = userPreferences.getCurrentDialogPath();
    VCFileChooser fileChooser = new VCFileChooser(defaultPath);
    fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
    fileChooser.setMultiSelectionEnabled(false);
    // fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_VCML);
    fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_PDF);
    if (geom.getDimension() > 0) {
        fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_AVS);
        fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_STL);
        fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_PLY);
    }
    // remove all selector
    fileChooser.removeChoosableFileFilter(fileChooser.getAcceptAllFileFilter());
    // set the default file filter...
    fileChooser.setFileFilter(FileFilters.FILE_FILTER_VCML);
    fileChooser.setSelectedFile(new java.io.File(TokenMangler.fixTokenStrict(geom.getName())));
    fileChooser.setDialogTitle("Export Virtual Cell Geometry As...");
    if (fileChooser.showSaveDialog(comp) != JFileChooser.APPROVE_OPTION) {
        // user didn't choose save
        throw UserCancelException.CANCEL_FILE_SELECTION;
    } else {
        File selectedFile = fileChooser.getSelectedFile();
        javax.swing.filechooser.FileFilter fileFilter = fileChooser.getFileFilter();
        if (selectedFile == null) {
            // no file selected (no name given)
            throw UserCancelException.CANCEL_FILE_SELECTION;
        } else {
            // /
            String selectedFileName = recordAndRemoveExtension(selectedFile.getPath());
            String n = selectedFile.getPath().toLowerCase();
            if (fileFilter == FileFilters.FILE_FILTER_VCML && !n.endsWith(".vcml")) {
                selectedFile = new File(selectedFileName + ".vcml");
            } else if (fileFilter == FileFilters.FILE_FILTER_PDF && !n.endsWith(".pdf")) {
                selectedFile = new File(selectedFileName + ".pdf");
            }
            if (fileFilter == null) {
                throw new Exception("No file save type was selected.");
            }
            checkForOverwrites(selectedFile, comp, userPreferences);
            // put the filter in the hash so the export task knows what to do...
            hashTable.put("fileFilter", fileFilter);
            resetPreferredFilePath(selectedFile, userPreferences);
            return selectedFile;
        }
    }
}

Example 94 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class DeleteOldDocument method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    DocumentWindowManager dwm = (DocumentWindowManager) fetch(hashTable, DOCUMENT_WINDOW_MANAGER);
    VCDocument currentDocument = dwm.getVCDocument();
    DocumentManager documentManager = (DocumentManager) fetch(hashTable, DOCUMENT_MANAGER);
    switch(currentDocument.getDocumentType()) {
        case BIOMODEL_DOC:
            {
                // make the info
                BioModel oldBioModel = (BioModel) currentDocument;
                BioModelInfo oldBioModelInfo = documentManager.getBioModelInfo(oldBioModel.getVersion().getVersionKey());
                // delete document
                documentManager.delete(oldBioModelInfo);
                break;
            }
        case MATHMODEL_DOC:
            {
                // make the info
                MathModel oldMathModel = (MathModel) currentDocument;
                MathModelInfo oldMathModelInfo = documentManager.getMathModelInfo(oldMathModel.getVersion().getVersionKey());
                // delete document
                documentManager.delete(oldMathModelInfo);
                break;
            }
        case GEOMETRY_DOC:
            {
                // make the info
                Geometry oldGeometry = (Geometry) currentDocument;
                GeometryInfo oldGeometryInfo = documentManager.getGeometryInfo(oldGeometry.getVersion().getVersionKey());
                // delete document
                documentManager.delete(oldGeometryInfo);
                break;
            }
        default:
            break;
    }
}

Example 95 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class RunSims method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    DocumentWindowManager documentWindowManager = (DocumentWindowManager) hashTable.get(CommonTask.DOCUMENT_WINDOW_MANAGER.name);
    ClientSimManager clientSimManager = (ClientSimManager) hashTable.get("clientSimManager");
    // DocumentManager documentManager = (DocumentManager)hashTable.get(CommonTask.DOCUMENT_MANAGER.name);
    JobManager jobManager = (JobManager) hashTable.get("jobManager");
    Simulation[] simulations = (Simulation[]) hashTable.get("simulations");
    Hashtable<Simulation, Throwable> failures = new Hashtable<Simulation, Throwable>();
    if (simulations != null && simulations.length > 0) {
        // we need to get the new ones if a save occurred...
        if (hashTable.containsKey(SaveDocument.DOC_KEY)) {
            VCDocument savedDocument = (VCDocument) hashTable.get(SaveDocument.DOC_KEY);
            Simulation[] allSims = null;
            if (savedDocument instanceof BioModel) {
                allSims = ((BioModel) savedDocument).getSimulations();
            } else if (savedDocument instanceof MathModel) {
                allSims = ((MathModel) savedDocument).getSimulations();
            }
            Vector<Simulation> v = new Vector<Simulation>();
            for (int i = 0; i < simulations.length; i++) {
                for (int j = 0; j < allSims.length; j++) {
                    if (simulations[i].getName().equals(allSims[j].getName())) {
                        v.add(allSims[j]);
                        break;
                    }
                }
            }
            simulations = (Simulation[]) BeanUtils.getArray(v, Simulation.class);
        }
        for (Simulation sim : simulations) {
            try {
                int dimension = sim.getMathDescription().getGeometry().getDimension();
                if (clientSimManager.getSimulationStatus(sim).isCompleted()) {
                    // completed
                    String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_1, sim.getName());
                    String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                    if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                        continue;
                    }
                }
                DataProcessingInstructions dataProcessingInstructions = sim.getDataProcessingInstructions();
                try {
                    if (dataProcessingInstructions != null) {
                        dataProcessingInstructions.getSampleImageFieldData(sim.getVersion().getOwner());
                    }
                } catch (Exception ex) {
                    DialogUtils.showErrorDialog(documentWindowManager.getComponent(), "Problem found in simulation '" + sim.getName() + "':\n" + ex.getMessage());
                    continue;
                }
                if (dimension > 0) {
                    MeshSpecification meshSpecification = sim.getMeshSpecification();
                    boolean bCellCentered = sim.hasCellCenteredMesh();
                    if (meshSpecification != null && !meshSpecification.isAspectRatioOK(bCellCentered)) {
                        String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_2, sim.getName(), "\u0394x=" + meshSpecification.getDx(bCellCentered) + "\n" + "\u0394y=" + meshSpecification.getDy(bCellCentered) + (dimension < 3 ? "" : "\n\u0394z=" + meshSpecification.getDz(bCellCentered)));
                        String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                        if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                            continue;
                        }
                    }
                    if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.Smoldyn)) {
                        if (!isSmoldynTimeStepOK(sim)) {
                            double s = smoldynTimestepVars.getSpatialResolution();
                            double dMax = smoldynTimestepVars.getMaxDiffusion();
                            double condn = (s * s) / (2.0 * dMax);
                            String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_3, Double.toString(s), Double.toString(dMax), Double.toString(condn));
                            DialogUtils.showErrorDialog(documentWindowManager.getComponent(), warningMessage);
                            continue;
                        }
                    }
                    // check the number of regions if the simulation mesh is coarser.
                    Geometry mathGeometry = sim.getMathDescription().getGeometry();
                    ISize newSize = meshSpecification.getSamplingSize();
                    ISize defaultSize = mathGeometry.getGeometrySpec().getDefaultSampledImageSize();
                    if (!sim.getSolverTaskDescription().getSolverDescription().isChomboSolver()) {
                        int defaultTotalVolumeElements = mathGeometry.getGeometrySurfaceDescription().getVolumeSampleSize().getXYZ();
                        int newTotalVolumeElements = meshSpecification.getSamplingSize().getXYZ();
                        if (defaultTotalVolumeElements > newTotalVolumeElements) {
                            // coarser
                            Geometry resampledGeometry = (Geometry) BeanUtils.cloneSerializable(mathGeometry);
                            GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
                            geoSurfaceDesc.setVolumeSampleSize(newSize);
                            geoSurfaceDesc.updateAll();
                            if (mathGeometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
                                mathGeometry.getGeometrySurfaceDescription().updateAll();
                            }
                            int defaultNumGeometricRegions = mathGeometry.getGeometrySurfaceDescription().getGeometricRegions().length;
                            int numGeometricRegions = geoSurfaceDesc.getGeometricRegions().length;
                            if (numGeometricRegions != defaultNumGeometricRegions) {
                                String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_4, newSize.getX() + (dimension > 1 ? " x " + newSize.getY() : "") + (dimension > 2 ? " x " + newSize.getZ() : ""), sim.getName(), numGeometricRegions, defaultNumGeometricRegions);
                                String result = PopupGenerator.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                                if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                                    continue;
                                }
                            }
                        }
                        if (mathGeometry.getGeometrySpec().hasImage()) {
                            // if it's an image.
                            if (defaultSize.getX() + 1 < newSize.getX() || defaultSize.getY() + 1 < newSize.getY() || defaultSize.getZ() + 1 < newSize.getZ()) {
                                // finer
                                String defaultSizeString = (defaultSize.getX() + 1) + (dimension > 1 ? " x " + (defaultSize.getY() + 1) : "") + (dimension > 2 ? " x " + (defaultSize.getZ() + 1) : "");
                                String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_5, newSize.getX() + (dimension > 1 ? " x " + newSize.getY() : "") + (dimension > 2 ? " x " + newSize.getZ() : ""), sim.getName(), defaultSizeString, defaultSizeString);
                                String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                                if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                                    continue;
                                }
                            }
                        }
                    }
                    boolean bGiveWarning = false;
                    for (int i = 0; i < sim.getScanCount(); i++) {
                        if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.SundialsPDE)) {
                            SimulationJob simJob = new SimulationJob(sim, i, null);
                            if (simJob.getSimulationSymbolTable().hasTimeVaryingDiffusionOrAdvection()) {
                                bGiveWarning = true;
                                break;
                            }
                        }
                    }
                    if (bGiveWarning) {
                        String warningMessage = VCellErrorMessages.RunSims_6;
                        String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                        if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                            continue;
                        }
                    }
                }
                SimulationInfo simInfo = sim.getSimulationInfo();
                if (simInfo != null) {
                    // 
                    // translate to common ancestral simulation (oldest mathematically equivalent simulation)
                    // 
                    SimulationStatus simulationStatus = jobManager.startSimulation(simInfo.getAuthoritativeVCSimulationIdentifier(), sim.getScanCount());
                    // updateStatus
                    clientSimManager.updateStatusFromStartRequest(sim, simulationStatus);
                } else {
                    // this should really not happen...
                    throw new RuntimeException(">>>>>>>>>> trying to run an unsaved simulation...");
                }
            } catch (Throwable exc) {
                exc.printStackTrace(System.out);
                failures.put(sim, exc);
            }
        }
    }
    // we deal with individual request failures here, passing down only other things (that break the whole thing down) to dispatcher
    if (!failures.isEmpty()) {
        Enumeration<Simulation> en = failures.keys();
        while (en.hasMoreElements()) {
            Simulation sim = en.nextElement();
            Throwable exc = (Throwable) failures.get(sim);
            // // updateStatus
            // SimulationStatus simulationStatus = clientSimManager.updateStatusFromStartRequest(sim, true, exc.getMessage());
            // notify user
            PopupGenerator.showErrorDialog(documentWindowManager, "Failed to start simulation'" + sim.getName() + "'\n" + exc.getMessage());
        }
    }
}