Examples with MathDescription cbit.vcell.math.MathDescription used on opensource projects

Example 36 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class OptimizationService method updateMath.

private static void updateMath(SimulationContext simulationContext, final NetworkGenerationRequirements networkGenerationRequirements) throws Exception {
    Geometry geometry = simulationContext.getGeometry();
    if (geometry.getDimension() > 0 && geometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
        geometry.getGeometrySurfaceDescription().updateAll();
    }
    simulationContext.checkValidity();
    MathMapping mathMapping = simulationContext.createNewMathMapping(callback, networkGenerationRequirements);
    MathDescription mathDesc = mathMapping.getMathDescription(callback);
    callback.setProgressFraction(1.0f / 3.0f * 2.0f);
    if (mathDesc != null) {
        simulationContext.setMathDescription(mathDesc);
    }
}

Example 37 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class DocumentValidTask 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);
    if (documentWindowManager.getVCDocument() instanceof BioModel) {
        // try to successfully generate math and geometry region info
        BioModel bioModel = (BioModel) documentWindowManager.getVCDocument();
        SimulationContext[] scArray = bioModel.getSimulationContexts();
        if (scArray != null) {
            MathDescription[] mathDescArray = new MathDescription[scArray.length];
            for (int i = 0; i < scArray.length; i++) {
                // check if all structure sizes are specified
                scArray[i].checkValidity();
                // 
                // compute Geometric Regions if necessary
                // 
                cbit.vcell.geometry.surface.GeometrySurfaceDescription geoSurfaceDescription = scArray[i].getGeometry().getGeometrySurfaceDescription();
                if (geoSurfaceDescription != null && geoSurfaceDescription.getGeometricRegions() == null) {
                    cbit.vcell.geometry.surface.GeometrySurfaceUtils.updateGeometricRegions(geoSurfaceDescription);
                }
                if (scArray[i].getModel() != bioModel.getModel()) {
                    throw new Exception("The BioModel's physiology doesn't match that for Application '" + scArray[i].getName() + "'");
                }
                // 
                // create new MathDescription
                // 
                MathDescription math = scArray[i].createNewMathMapping().getMathDescription();
                // 
                // load MathDescription into SimulationContext
                // (BioModel is responsible for propagating this to all applicable Simulations).
                // 
                mathDescArray[i] = math;
            }
            hashTable.put("mathDescArray", mathDescArray);
        }
        // check issues for errors
        DocumentValidUtil.checkIssuesForErrors(bioModel);
    // Vector<Issue> issueList = new Vector<Issue>();
    // IssueContext issueContext = new IssueContext();
    // bioModel.gatherIssues(issueContext,issueList);
    // for (int i = 0; i < issueList.size(); i++){
    // Issue issue = issueList.elementAt(i);
    // if (issue.getSeverity() == Issue.SEVERITY_ERROR){
    // String errMsg = "Error: ";
    // Object issueSource = issue.getSource();
    // if (issueSource instanceof OutputFunctionIssueSource) {
    // SimulationOwner simulationOwner = ((OutputFunctionIssueSource)issueSource).getOutputFunctionContext().getSimulationOwner();
    // String funcName = ((OutputFunctionIssueSource)issueSource).getAnnotatedFunction().getDisplayName();
    // if (simulationOwner instanceof SimulationContext) {
    // String opErrMsg = "Output Function '" + funcName + "' in application '" + simulationOwner.getName() + "' ";
    // if (issue.getCategory().equals(IssueCategory.OUTPUTFUNCTIONCONTEXT_FUNCTION_EXPBINDING)) {
    // opErrMsg += "refers to an unknown variable. Either the model changed or this version of VCell generates variable names differently.\n\n";
    // }
    // errMsg += opErrMsg;
    // }
    // }
    // throw new Exception(errMsg + issue.getMessage());
    // }
    // }
    }
    if (documentWindowManager.getVCDocument() instanceof cbit.vcell.geometry.Geometry) {
        // try to successfully generate GeometricRegions if spatial and not present.
        cbit.vcell.geometry.Geometry geometry = (cbit.vcell.geometry.Geometry) documentWindowManager.getVCDocument();
        if (geometry.getGeometrySurfaceDescription() != null && geometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
            try {
                cbit.vcell.geometry.surface.GeometrySurfaceUtils.updateGeometricRegions(geometry.getGeometrySurfaceDescription());
            } catch (Exception e) {
                throw new Exception("Error determining regions in spatial geometry '" + geometry.getName() + "': \n" + e.getMessage());
            }
        }
    }
    if (documentWindowManager.getVCDocument() instanceof cbit.vcell.mathmodel.MathModel) {
        // try to successfully generate GeometricRegions if spatial and not present.
        cbit.vcell.mathmodel.MathModel mathModel = (cbit.vcell.mathmodel.MathModel) documentWindowManager.getVCDocument();
        cbit.vcell.geometry.Geometry geometry = mathModel.getMathDescription().getGeometry();
        if (geometry.getGeometrySurfaceDescription() != null && geometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
            try {
                cbit.vcell.geometry.surface.GeometrySurfaceUtils.updateGeometricRegions(geometry.getGeometrySurfaceDescription());
            } catch (Exception e) {
                throw new Exception("Error determining regions in spatial geometry '" + geometry.getName() + "': \n" + e.getMessage());
            }
        }
    }
}

Example 38 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class ExportDocument 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 {
    VCDocument documentToExport = (VCDocument) hashTable.get("documentToExport");
    File exportFile = fetch(hashTable, EXPORT_FILE, File.class, true);
    ExtensionFilter fileFilter = fetch(hashTable, FILE_FILTER, ExtensionFilter.class, true);
    DocumentManager documentManager = fetch(hashTable, DocumentManager.IDENT, DocumentManager.class, true);
    String resultString = null;
    FileCloseHelper closeThis = null;
    try {
        if (documentToExport instanceof BioModel) {
            if (!(fileFilter instanceof SelectorExtensionFilter)) {
                throw new Exception("Expecting fileFilter type " + SelectorExtensionFilter.class.getName() + " but got " + fileFilter.getClass().getName());
            }
            BioModel bioModel = (BioModel) documentToExport;
            SimulationContext chosenSimContext = fetch(hashTable, SIM_CONTEXT, SimulationContext.class, false);
            ((SelectorExtensionFilter) fileFilter).writeBioModel(documentManager, bioModel, exportFile, chosenSimContext);
        /*		DELETE this after finishing validation testing
			
			// check format requested
			if (fileFilter.getDescription().equals(FileFilters.FILE_FILTER_MATLABV6.getDescription())){
				// matlab from application; get application
		
				SimulationContext chosenSimContext = fetch(hashTable,SIM_CONTEXT,SimulationContext.class, true);
				// regenerate a fresh MathDescription
				MathMapping mathMapping = chosenSimContext.createNewMathMapping();
				MathDescription mathDesc = mathMapping.getMathDescription();
				if(mathDesc != null && !mathDesc.isSpatial() && !mathDesc.isNonSpatialStoch()){
					// do export
					resultString = exportMatlab(exportFile, fileFilter, mathDesc);
				}else{
					throw new Exception("Matlab export failed: NOT an non-spatial deterministic application!");
				}
			} else if (fileFilter.equals(FileFilters.FILE_FILTER_PDF)) {   
				FileOutputStream fos = null;
				try {
					fos = new FileOutputStream(exportFile);
					documentManager.generatePDF(bioModel, fos);				
				} finally {
					if(fos != null) {
						fos.close();					
					}
				}
				return; 									//will take care of writing to the file as well.
			}
			//Export a simulation to Smoldyn input file, if there are parameter scans
			//in simulation, we'll export multiple Smoldyn input files.
			else if (fileFilter.equals(FileFilters.FILE_FILTER_SMOLDYN_INPUT)) 
			{ 
				Simulation selectedSim = (Simulation)hashTable.get("selectedSimulation");
				if (selectedSim != null) {
					int scanCount = selectedSim.getScanCount();
					if(scanCount > 1) // has parameter scan
					{
						String baseExportFileName = exportFile.getPath().substring(0, exportFile.getPath().indexOf("."));
						for(int i=0; i<scanCount; i++)
						{
							SimulationTask simTask = new SimulationTask(new SimulationJob(selectedSim, i, null),0);
							// Need to export each parameter scan into a separate file
							String newExportFileName = baseExportFileName + "_" + i + SMOLDYN_INPUT_FILE_EXTENSION;
							exportFile = new File(newExportFileName);
							
							PrintWriter pw = new PrintWriter(exportFile);
							SmoldynFileWriter smf = new SmoldynFileWriter(pw, true, null, simTask, false);
							smf.write();
							pw.close();	
						}
					}
					else if(scanCount == 1)// regular simulation, no parameter scan
					{
						SimulationTask simTask = new SimulationTask(new SimulationJob(selectedSim, 0, null),0);
						// export the simulation to the selected file
						PrintWriter pw = new PrintWriter(exportFile);
						SmoldynFileWriter smf = new SmoldynFileWriter(pw, true, null, simTask, false);
						smf.write();
						pw.close();
					}
					else
					{
						throw new Exception("Simulation scan count is smaller than 1.");
					}
				}
				return;
													
			} else {
				// convert it if other format
				if (!fileFilter.equals(FileFilters.FILE_FILTER_VCML)) {
					// SBML or CellML; get application name
					if ((fileFilter.equals(FileFilters.FILE_FILTER_SBML_12)) || (fileFilter.equals(FileFilters.FILE_FILTER_SBML_21)) || 
						(fileFilter.equals(FileFilters.FILE_FILTER_SBML_22)) || (fileFilter.equals(FileFilters.FILE_FILTER_SBML_23)) || 
						(fileFilter.equals(FileFilters.FILE_FILTER_SBML_24)) || (fileFilter.equals(FileFilters.FILE_FILTER_SBML_31_CORE)) || 
						(fileFilter.equals(FileFilters.FILE_FILTER_SBML_31_SPATIAL)) ) {
						SimulationContext selectedSimContext = (SimulationContext)hashTable.get("selectedSimContext");
						Simulation selectedSim = (Simulation)hashTable.get("selectedSimulation");
						int sbmlLevel = 0;
						int sbmlVersion = 0;
						int sbmlPkgVersion = 0;
						boolean bIsSpatial = false;
						if ((fileFilter.equals(FileFilters.FILE_FILTER_SBML_12))) {
							sbmlLevel = 1;
							sbmlVersion = 2;
						} else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_21)) {
							sbmlLevel = 2;
							sbmlVersion = 1;
						} else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_22)) {
							sbmlLevel = 2;
							sbmlVersion = 2;
						} else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_23)) {
							sbmlLevel = 2;
							sbmlVersion = 3;
						} else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_24)) {
							sbmlLevel = 2;
							sbmlVersion = 4;
						} else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_31_CORE)) {
							sbmlLevel = 3;
							sbmlVersion = 1;
						} else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_31_SPATIAL)) {
							sbmlLevel = 3;
							sbmlVersion = 1;
							sbmlPkgVersion = 1;
							bIsSpatial = true;
						}
						if (selectedSim == null) {
							resultString = XmlHelper.exportSBML(bioModel, sbmlLevel, sbmlVersion, sbmlPkgVersion, bIsSpatial, selectedSimContext, null);
							XmlUtil.writeXMLStringToFile(resultString, exportFile.getAbsolutePath(), true);
							return;
						} else {
							for (int sc = 0; sc < selectedSim.getScanCount(); sc++) {
								SimulationJob simJob = new SimulationJob(selectedSim, sc, null);
								resultString = XmlHelper.exportSBML(bioModel, sbmlLevel, sbmlVersion, sbmlPkgVersion, bIsSpatial, selectedSimContext, simJob);
								// Need to export each parameter scan into a separate file 
								String newExportFileName = exportFile.getPath().substring(0, exportFile.getPath().indexOf(".xml")) + "_" + sc + ".xml";
								exportFile.renameTo(new File(newExportFileName));
								XmlUtil.writeXMLStringToFile(resultString, exportFile.getAbsolutePath(), true);
							}
							return;
						}
					} else if (fileFilter.equals(FileFilters.FILE_FILTER_BNGL)) {
						RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
						StringWriter bnglStringWriter = new StringWriter();
						PrintWriter pw = new PrintWriter(bnglStringWriter);
						RbmNetworkGenerator.writeBngl(bioModel, pw);
						resultString = bnglStringWriter.toString();
						pw.close();
						
					} else if (fileFilter.equals(FileFilters.FILE_FILTER_NFSIM)) {
						// TODO: get the first thing we find for now, in the future we'll need to modify ChooseFile 
						//       to only offer the applications / simulations with bngl content
						SimulationContext simContexts[] = bioModel.getSimulationContexts();
						SimulationContext aSimulationContext = simContexts[0];
						Simulation selectedSim = aSimulationContext.getSimulations(0);
						//Simulation selectedSim = (Simulation)hashTable.get("selectedSimulation");
						SimulationTask simTask = new SimulationTask(new SimulationJob(selectedSim, 0, null),0);
						long randomSeed = 0;	// a fixed seed will allow us to run reproducible simulations
						//long randomSeed = System.currentTimeMillis();
						NFsimSimulationOptions nfsimSimulationOptions = new NFsimSimulationOptions();
						// we get the data we need from the math description
						Element root = NFsimXMLWriter.writeNFsimXML(simTask, randomSeed, nfsimSimulationOptions);
						Document doc = new Document();
						doc.setRootElement(root);
						XMLOutputter xmlOut = new XMLOutputter();
						resultString = xmlOut.outputString(doc);
	
					} else if (fileFilter.equals(FileFilters.FILE_FILTER_CELLML)) {
						Integer chosenSimContextIndex = (Integer)hashTable.get("chosenSimContextIndex");
						String applicationName = bioModel.getSimulationContext(chosenSimContextIndex.intValue()).getName();
						resultString = XmlHelper.exportCellML(bioModel, applicationName);
						// cellml still uses default character encoding for now ... maybe UTF-8 in the future
					} else if (fileFilter.equals(FileFilters.FILE_FILTER_SEDML)) {
						// export the entire biomodel to a SEDML file (for now, only non-spatial,non-stochastic applns)
						int sedmlLevel = 1;
						int sedmlVersion = 1;
						String sPath = FileUtils.getFullPathNoEndSeparator(exportFile.getAbsolutePath());
						String sFile = FileUtils.getBaseName(exportFile.getAbsolutePath());
						String sExt = FileUtils.getExtension(exportFile.getAbsolutePath());
						
						SEDMLExporter sedmlExporter = null;
						if (bioModel instanceof BioModel) {
							sedmlExporter = new SEDMLExporter(bioModel, sedmlLevel, sedmlVersion);
							resultString = sedmlExporter.getSEDMLFile(sPath);
						} else {
							throw new RuntimeException("unsupported Document Type " + bioModel.getClass().getName() + " for SedML export");
						}
						if(sExt.equals("sedx")) {
							sedmlExporter.createManifest(sPath, sFile);
							String sedmlFileName = sPath + FileUtils.WINDOWS_SEPARATOR + sFile + ".sedml";
							XmlUtil.writeXMLStringToFile(resultString, sedmlFileName, true);
							sedmlExporter.addSedmlFileToList(sFile + ".sedml");
							sedmlExporter.addSedmlFileToList("manifest.xml");
							sedmlExporter.createZipArchive(sPath, sFile);
							return;
						} else {
							XmlUtil.writeXMLStringToFile(resultString, exportFile.getAbsolutePath(), true);
						}
					}
				} else {
					// if format is VCML, get it from biomodel.
					bioModel.getVCMetaData().cleanupMetadata();
					resultString = XmlHelper.bioModelToXML(bioModel);
					XmlUtil.writeXMLStringToFile(resultString, exportFile.getAbsolutePath(), true);
					return;
				}
			}*/
        } else if (documentToExport instanceof MathModel) {
            MathModel mathModel = (MathModel) documentToExport;
            // check format requested
            if (fileFilter.equals(FileFilters.FILE_FILTER_MATLABV6)) {
                // check if it's ODE
                if (mathModel.getMathDescription() != null && (!mathModel.getMathDescription().isSpatial() && !mathModel.getMathDescription().isNonSpatialStoch())) {
                    MathDescription mathDesc = mathModel.getMathDescription();
                    resultString = exportMatlab(exportFile, fileFilter, mathDesc);
                } else {
                    throw new Exception("Matlab export failed: NOT an non-spatial deterministic model.");
                }
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_PDF)) {
                FileOutputStream fos = new FileOutputStream(exportFile);
                documentManager.generatePDF(mathModel, fos);
                fos.close();
                // will take care of writing to the file as well.
                return;
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_VCML)) {
                resultString = XmlHelper.mathModelToXML(mathModel);
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_CELLML)) {
                resultString = XmlHelper.exportCellML(mathModel, null);
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_23)) {
                resultString = XmlHelper.exportSBML(mathModel, 2, 3, 0, false, null, null);
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_24)) {
                resultString = XmlHelper.exportSBML(mathModel, 2, 4, 0, false, null, null);
            } else // in simulation, we'll export multiple Smoldyn input files.
            if (fileFilter.equals(FileFilters.FILE_FILTER_SMOLDYN_INPUT)) {
                Simulation selectedSim = (Simulation) hashTable.get("selectedSimulation");
                if (selectedSim != null) {
                    int scanCount = selectedSim.getScanCount();
                    // -----
                    String baseExportFileName = (scanCount == 1 ? null : exportFile.getPath().substring(0, exportFile.getPath().indexOf(".")));
                    for (int i = 0; i < scanCount; i++) {
                        SimulationTask simTask = new SimulationTask(new SimulationJob(selectedSim, i, null), 0);
                        // Need to export each parameter scan into a separate file
                        File localExportFile = (scanCount == 1 ? exportFile : new File(baseExportFileName + "_" + i + SMOLDYN_INPUT_FILE_EXTENSION));
                        FileCloseHelper localCloseThis = new FileCloseHelper(localExportFile);
                        try {
                            SmoldynFileWriter smf = new SmoldynFileWriter(localCloseThis.getPrintWriter(), true, null, simTask, false);
                            smf.write();
                        } finally {
                            if (localCloseThis != null) {
                                localCloseThis.close();
                            }
                        }
                    }
                }
                return;
            }
        } else if (documentToExport instanceof Geometry) {
            Geometry geom = (Geometry) documentToExport;
            if (fileFilter.equals(FileFilters.FILE_FILTER_PDF)) {
                documentManager.generatePDF(geom, (closeThis = new FileCloseHelper(exportFile)).getFileOutputStream());
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_VCML)) {
                resultString = XmlHelper.geometryToXML(geom);
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_AVS)) {
                cbit.vcell.export.AVS_UCD_Exporter.writeUCDGeometryOnly(geom.getGeometrySurfaceDescription(), (closeThis = new FileCloseHelper(exportFile)).getFileWriter());
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_STL)) {
                // make sure filename end with .stl
                File stlFile = exportFile;
                if (!exportFile.getName().toLowerCase().endsWith(".stl")) {
                    stlFile = new File(exportFile.getParentFile(), exportFile.getName() + ".stl");
                }
                cbit.vcell.geometry.surface.StlExporter.writeBinaryStl(geom.getGeometrySurfaceDescription(), (closeThis = new FileCloseHelper(stlFile)).getRandomAccessFile("rw"));
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_PLY)) {
                writeStanfordPolygon(geom.getGeometrySurfaceDescription(), (closeThis = new FileCloseHelper(exportFile)).getFileWriter());
            }
        }
        if (resultString != null) {
            (closeThis = new FileCloseHelper(exportFile)).getFileWriter().write(resultString);
        }
    } finally {
        if (closeThis != null) {
            closeThis.close();
        }
    }
}

Example 39 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class BioModelTreePanel method actionsOnClick.

/**
 * Comment
 */
private void actionsOnClick(MouseEvent mouseEvent) {
    DefaultMutableTreeNode currentTreeSelection = (DefaultMutableTreeNode) getJTree2().getLastSelectedPathComponent();
    Object selectedObject = null;
    if (currentTreeSelection == null) {
        return;
    }
    selectedObject = currentTreeSelection.getUserObject();
    // double click
    if (mouseEvent.getClickCount() == 2) {
        if (selectedObject instanceof SimulationContext) {
            fireActionPerformed(new ActionEvent(this, mouseEvent.getID(), GuiConstants.ACTIONCMD_OPEN_APPLICATION, mouseEvent.getModifiers()));
        } else if (selectedObject instanceof Annotation) {
            editAnnotation();
        } else if (selectedObject instanceof MathDescription) {
            fireActionPerformed(new ActionEvent(this, mouseEvent.getID(), GuiConstants.ACTIONCMD_OPEN_APPLICATION_MATH, mouseEvent.getModifiers()));
        } else if (selectedObject instanceof Geometry) {
            fireActionPerformed(new ActionEvent(this, mouseEvent.getID(), GuiConstants.ACTIONCMD_OPEN_APPLICATION_GEOMETRY, mouseEvent.getModifiers()));
        } else if (selectedObject instanceof Simulation) {
            fireActionPerformed(new ActionEvent(this, mouseEvent.getID(), GuiConstants.ACTIONCMD_OPEN_APPLICATION_SIMULATION, mouseEvent.getModifiers()));
        } else if (selectedObject instanceof MathType) {
            // deterministic or stochastic or rule-bsaed
            fireActionPerformed(new ActionEvent(this, mouseEvent.getID(), GuiConstants.ACTIONCMD_OPEN_APPLICATION_DETSTOCH, mouseEvent.getModifiers()));
        }
        return;
    }
    // right click
    if (mouseEvent.isPopupTrigger()) {
        Point mousePoint = mouseEvent.getPoint();
        if (selectedObject instanceof BioModel) {
            getBioModelPopupMenu().show(getJTree2(), mousePoint.x, mousePoint.y);
        } else if (selectedObject instanceof SimulationContext) {
            getAppPopupMenu().show(getJTree2(), mousePoint.x, mousePoint.y);
        } else if (selectedObject instanceof Simulation) {
            getSimPopupMenu().show(getJTree2(), mousePoint.x, mousePoint.y);
        }
        if (selectedObject instanceof Annotation) {
            getEditAnnotationPopupMenu().show(getJTree2(), mousePoint.x, mousePoint.y);
        }
    }
}

Example 40 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class MembraneParticleDiffusionVisitor method visitBioModel.

public void visitBioModel(BioModel bioModel, PrintStream logFilePrintStream) {
    try {
        logFilePrintStream.println(bioModel.getVersion().getName() + "  " + bioModel.getVersion().getDate() + "  " + bioModel.getVersion().getVersionKey());
        SimulationContext[] simContexts = bioModel.getSimulationContexts();
        for (int i = 0; i < simContexts.length; i++) {
            SimulationContext simContext = simContexts[i];
            MathDescription mathDescription = simContext.getMathDescription();
            if (simContext.isStoch() && simContext.getGeometry().getDimension() > 0) {
                if (hasMembraneDiffusion(mathDescription)) {
                    logFilePrintStream.println("membraneDiffusion: " + mathDescription.getKey());
                    mathKeyStream.println(bioModel.getVersion().getOwner().getName() + ",\"" + bioModel.getName() + "\"," + bioModel.getVersion().getVersionKey() + ",BioModel," + mathDescription.getKey());
                    mathKeyStream.flush();
                }
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
        logFilePrintStream.println(" failed " + e.getMessage());
    }
}