Examples with SimulationData cbit.vcell.simdata.SimulationData used on opensource projects

Example 1 with SimulationData

use of cbit.vcell.simdata.SimulationData in project vcell by virtualcell.

the class StochtestRunService method runsolver.

private static void runsolver(Simulation newSimulation, File baseDirectory, int numRuns, TimeSeriesMultitrialData timeSeriesMultitrialData) {
    Simulation versSimulation = null;
    File destDir = null;
    boolean bTimeout = false;
    // int progress = 1;
    for (int trialIndex = 0; trialIndex < numRuns; trialIndex++) {
        System.out.println("\n=====================================\n\nStarting trial " + (trialIndex + 1) + " of " + numRuns + "\n\n==============================\n");
        long startTime = System.currentTimeMillis();
        // }
        try {
            versSimulation = new TempSimulation(newSimulation, false);
            // printout(ruleBasedTestDir.getAbsolutePath());
            destDir = new File(baseDirectory, timeSeriesMultitrialData.datasetName);
            SimulationTask simTask = new SimulationTask(new SimulationJob(versSimulation, 0, null), 0);
            Solver solver = ClientSimManager.createQuickRunSolver(destDir, simTask);
            solver.startSolver();
            while (true) {
                try {
                    Thread.sleep(250);
                } catch (InterruptedException e) {
                    e.printStackTrace();
                }
                if (System.currentTimeMillis() - startTime > 30 * 1000) {
                    // timeout after 30 seconds .. otherwise multiple runs will take forever
                    bTimeout = true;
                    solver.stopSolver();
                    throw new RuntimeException("timed out");
                }
                SolverStatus solverStatus = solver.getSolverStatus();
                if (solverStatus != null) {
                    if (solverStatus.getStatus() == SolverStatus.SOLVER_ABORTED) {
                        throw new RuntimeException(solverStatus.getSimulationMessage().getDisplayMessage());
                    }
                    if (solverStatus.getStatus() != SolverStatus.SOLVER_STARTING && solverStatus.getStatus() != SolverStatus.SOLVER_READY && solverStatus.getStatus() != SolverStatus.SOLVER_RUNNING) {
                        break;
                    }
                }
            }
            SimulationData simData = new SimulationData(simTask.getSimulationJob().getVCDataIdentifier(), destDir, null, null);
            ODEDataBlock odeDataBlock = simData.getODEDataBlock();
            ODESimData odeSimData = odeDataBlock.getODESimData();
            timeSeriesMultitrialData.addDataSet(odeSimData, trialIndex);
        } catch (Exception e) {
            e.printStackTrace();
            File file = new File(baseDirectory, Simulation.createSimulationID(versSimulation.getKey()) + "_solverExc.txt");
            StochtestFileUtils.writeMessageTofile(file, e.getMessage());
            if (bTimeout) {
                throw new RuntimeException("timed out");
            } else {
                throw new RuntimeException("solver failed : " + e.getMessage(), e);
            }
        }
        try {
            Thread.sleep(100);
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
        StochtestFileUtils.clearDir(destDir);
    }
// printout("\n");
}

Example 2 with SimulationData

use of cbit.vcell.simdata.SimulationData in project vcell by virtualcell.

the class TestMissingSimData method checkDataExists.

// private static void runSimsNew(String connectURL,String dbSchemaUser, String dbPassword) throws Exception{
// 
// //		VCellBootstrap vCellBootstrap = getVCellBootstrap("rmi-beta.cam.uchc.edu", 40105, "VCellBootstrapServer", 12, false);
// //		VCellBootstrap vCellBootstrap = getVCellBootstrap("rmi-alpha.cam.uchc.edu", 40106, "VCellBootstrapServer", 12, false);
// VCellBootstrap vCellBootstrap = getVCellBootstrap("rmi-alpha.cam.uchc.edu", 40111, "VCellBootstrapServer", 12, false);//Test2
// 
// if(true){
// Hashtable<KeyValue, UserLoginInfo> keyUserLoginInfo = doQuery(connectURL, dbSchemaUser, dbPassword);
// Enumeration<KeyValue> keys = keyUserLoginInfo.keys();
// while(keys.hasMoreElements()){
// KeyValue simKey = keys.nextElement();
// UserLoginInfo userLoginInfo = keyUserLoginInfo.get(simKey);
// VCSimulationIdentifier vcSimulationIdentifier = new VCSimulationIdentifier(simKey, userLoginInfo.getUser());
// acquireThread(vcSimulationIdentifier, vCellBootstrap, userLoginInfo, connectURL, dbSchemaUser, dbPassword);
// }
// return;
// }
// 
// 
// String itemSelectSQL = " select vc_userinfo.userid,vc_userinfo.id userkey,vc_userinfo.digestpw,missingdata.simjobsimref,vc_softwareversion.softwareversion ";
// 
// String sqlPart =
// " from missingdata,vc_simulation,vc_userinfo,vc_softwareversion "+
// " where "+
// " (vc_simulation.id in (select simref from vc_biomodelsim)) and " +
// //				" (vc_simulation.id in (select simref from vc_mathmodelsim)) and " +
// " vc_userinfo.userid='fgao5' and "+
// " vc_userinfo.id = vc_simulation.ownerref and "+
// " missingdata.simjobsimref = vc_simulation.id and "+
// //				" missingdata.dataexists not like 'readable%' and "+
// " (missingdata.dataexists = 'false') "+
// " and missingdata.notes is not null and " +
// " (missingdata.notes like '%Compiled_solvers_no_longer%' or missingdata.notes like '%Connection_refused%')" +
// //				" and missingdata.simjobsimref = 34080002 " +
// //				" or missingdata.dataexists like 'error - %') "+
// //				" and (missingdata.notes is null ) "+
// //				" or missingdata.notes not like 'reran OK%')" +
// " and vc_simulation.parentsimref is null and "+
// " (softwareversion is null or regexp_substr(softwareversion,'^((release)|(rel)|(alpha)|(beta))_version_([[:digit:]]+\\.?)+_build_([[:digit:]]+\\.?)+',1,1,'i') is not null) and "+
// " vc_softwareversion.versionableref (+) = vc_simulation.id " +
// //				" and rownum = 1 ";
// //				" and vc_simulation.id=39116536"
// " order by vc_userinfo.userid";
// 
// //		(mdt.dataexists = 'false' or mdt.dataexists like 'error - %') and
// //		(mdt.notes is null or mdt.notes not like 'reran OK%') and
// 
// //Create hash of sims and userlogininfo
// Hashtable<KeyValue, UserLoginInfo> simToUserLoginInfoHash = new Hashtable<>();
// Statement updateStatement = con.createStatement();
// Statement queryStatement = con.createStatement();
// //Get Count
// ResultSet rset = queryStatement.executeQuery("select count(*) "+sqlPart);
// rset.next();
// int totalCount = rset.getInt(1);
// rset.close();
// //Get sims
// rset = queryStatement.executeQuery(itemSelectSQL+sqlPart);
// UserLoginInfo userLoginInfo = null;
// VCellConnection vcellConnection = null;
// int currentCount = 1;
// while(rset.next()){
// KeyValue simJobSimRef = new KeyValue(rset.getString("simjobsimref"));
// try{
// String softwareVersion = rset.getString("softwareversion");
// String userid = rset.getString("userid");
// System.out.println("-----");
// System.out.println("-----running "+currentCount+" of "+totalCount+"   user="+userid+" simjobsimref="+simJobSimRef);
// currentCount+= 1;
// System.out.println("-----");
// 
// if(!rset.wasNull() && softwareVersion != null){
// StringTokenizer st = new StringTokenizer(softwareVersion, "_");
// st.nextToken();//site name
// st.nextToken();//'Version' literal string
// String majorVersion = st.nextToken();//major version number
// if(majorVersion.equals("5.4")){
// throw new Exception("Alpha-5.4 sims are not being re-run using Beta-5.3 code");
// }
// }
// 
// if(userid.toLowerCase().equals("vcelltestaccount")
// //					 || userid.toLowerCase().equals("anu")
// //					 || userid.toLowerCase().equals("fgao")
// //					 || userid.toLowerCase().equals("liye")
// //					 || userid.toLowerCase().equals("schaff")
// //					 || userid.toLowerCase().equals("ignovak")
// //					 || userid.toLowerCase().equals("jditlev")
// //					 || userid.toLowerCase().equals("sensation")
// ){
// continue;
// }
// String userkey = rset.getString("userkey");
// if(userLoginInfo == null || !userLoginInfo.getUserName().equals(userid)){
// userLoginInfo = new UserLoginInfo(userid,DigestedPassword.createAlreadyDigested(rset.getString("digestpw")));
// userLoginInfo.setUser(new User(userid, new KeyValue(userkey)));
// vcellConnection = null;
// }
// VCSimulationIdentifier vcSimulationIdentifier = new VCSimulationIdentifier(simJobSimRef, userLoginInfo.getUser());
// 
// 
// //
// //
// //
// if(true){
// acquireThread(vcSimulationIdentifier, vCellBootstrap, userLoginInfo, connectURL, dbSchemaUser, dbPassword);
// continue;
// }
// 
// try{
// if(vcellConnection != null){
// vcellConnection.getMessageEvents();
// }
// }catch(Exception e){
// e.printStackTrace();
// //assume disconnected
// vcellConnection = null;
// }
// if(vcellConnection == null){
// vcellConnection = vCellBootstrap.getVCellConnection(userLoginInfo);
// vcellConnection.getMessageEvents();
// }
// 
// SimulationStatusPersistent initSimulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(vcSimulationIdentifier.getSimulationKey());
// 
// System.out.println("initial status="+initSimulationStatus);
// //				if(!initSimulationStatus.isCompleted() || !initSimulationStatus.getHasData()){
// //					continue;
// //				}
// 
// 
// BigString simXML = vcellConnection.getUserMetaDbServer().getSimulationXML(simJobSimRef);
// Simulation sim = XmlHelper.XMLToSim(simXML.toString());
// //				SolverDescription solverDescription = sim.getSolverTaskDescription().getSolverDescription();
// //				if(solverDescription.equals(SolverDescription.StochGibson)  || solverDescription.equals(SolverDescription.FiniteVolume)){
// //					//These 2 solvers give too much trouble so skip
// //					System.out.println("--skipping solver");
// ////					notCompletedSimIDs.add(simIDAndJobID.simID.toString());
// //					return;
// //				}
// 
// 
// //				if(!sim.isSpatial()){
// //					continue;
// //				}
// //				if(sim.getSolverTaskDescription().isSerialParameterScan()/* || sim.getSolverTaskDescription().getExpectedNumTimePoints() > 20*/){
// //					continue;
// //				}
// 
// int scanCount = sim.getScanCount();
// //				if(true){return;}
// SimulationStatusPersistent simulationStatus = null;
// SimulationInfo simulationInfo = sim.getSimulationInfo();
// if(!simulationInfo.getAuthoritativeVCSimulationIdentifier().getSimulationKey().equals(vcSimulationIdentifier.getSimulationKey())){
// throw new Exception("Unexpected authoritative and sim id are not the same");
// }
// vcellConnection.getSimulationController().startSimulation(vcSimulationIdentifier, scanCount);
// long startTime = System.currentTimeMillis();
// while(simulationStatus == null || simulationStatus.isStopped() || simulationStatus.isCompleted() || simulationStatus.isFailed()){
// Thread.sleep(2000);
// simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(vcSimulationIdentifier.getSimulationKey());
// if(simulationStatus.isFailed() && !initSimulationStatus.isFailed()){
// break;
// }
// MessageEvent[] messageEvents = vcellConnection.getMessageEvents();
// if((System.currentTimeMillis()-startTime) > 30000){
// throw new Exception("-----Sim finished too fast or took too long to start, status= "+simulationStatus);
// }
// System.out.println(simulationStatus);
// }
// SimulationStatusPersistent lastSimStatus = simulationStatus;
// while(!simulationStatus.isStopped() && !simulationStatus.isCompleted() && !simulationStatus.isFailed()){
// for(int i = 0;i<3;i++){
// MessageEvent[] messageEvents = vcellConnection.getMessageEvents();
// Thread.sleep(1000);
// }
// simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(vcSimulationIdentifier.getSimulationKey());
// if(!simulationStatus.toString().equals(lastSimStatus.toString())){
// lastSimStatus = simulationStatus;
// System.out.println("running status="+simulationStatus);
// }
// //					MessageEvent[] messageEvents = vcellConnection.getMessageEvents();
// //					for (int i = 0; messageEvents != null && i < messageEvents.length; i++) {
// //						System.out.println(messageEvents[i]);
// //					}
// }
// 
// if(!lastSimStatus.isCompleted()){
// throw new Exception("Unexpected run status: "+lastSimStatus.toString());
// }
// 
// 
// String updatestr = "update missingdata set notes='"+DB_NOTES_SIM_RUNOK_CODE+"' where simjobsimref="+simJobSimRef;
// System.out.println(updatestr);
// updateStatement.executeUpdate(updatestr);
// con.commit();
// }catch(Exception e){
// e.printStackTrace();
// String errString = TokenMangler.fixTokenStrict(DB_NOTES_SIM_ERROR_CODE+e.getClass().getSimpleName()+" "+e.getMessage());
// if(errString.length() > 256){
// errString = errString.substring(0, 256);
// }
// String updatestr = "update missingdata set notes='"+errString+"' where simjobsimref="+simJobSimRef;
// System.out.println(updatestr);
// updateStatement.executeUpdate(updatestr);
// con.commit();
// }
// }
// 
// }
private static void checkDataExists(Connection con, boolean bExistOnly) throws SQLException {
    AmplistorCredential amplistorCredential = AmplistorUtilsTest.getAmplistorCredential();
    Statement queryStatement = con.createStatement();
    Statement updateStatement = con.createStatement();
    // Hashtable<KeyValue, Exception> errorHash = new Hashtable<>();
    String sql = "select missingdata.*,parentsimref " + " from missingdata,vc_simulation,vc_userinfo" + " where vc_simulation.id = missingdata.simjobsimref and" + " vc_simulation.parentsimref is null and " + " vc_simulation.ownerref=vc_userinfo.id and " + " missingdata.notes is not null and " + " (missingdata.notes like '%exceeded_maximum%' " + " or missingdata.notes ='recheck dataexists' )" + // " vc_userinfo.userid='schaff' "+
    " order by missingdata.userid";
    ResultSet rset = queryStatement.executeQuery(sql);
    while (rset.next()) {
        // if(!rset.getString("dataexists").equals("tbd")){
        // continue;
        // }
        KeyValue simJobSimRef = null;
        KeyValue parentsimref = null;
        User user = null;
        try {
            simJobSimRef = new KeyValue(rset.getString("simjobsimref"));
            parentsimref = (rset.getString("parentsimref") == null ? null : new KeyValue(rset.getString("parentsimref")));
            user = new User(rset.getString("userid"), new KeyValue(rset.getString("userinfoid")));
            int jobIndex = rset.getInt("jobindex");
            File primaryDataDir = new File("\\\\cfs02\\ifs\\raid\\vcell\\users\\" + user.getName());
            String updatestr = null;
            File filePathNamePrime = new File(primaryDataDir, SimulationData.createCanonicalSimLogFileName(simJobSimRef, 0, false));
            if (filePathNamePrime.exists()) {
                updatestr = "fileNewPrime";
            } else if (new File(primaryDataDir, SimulationData.createCanonicalSimLogFileName(simJobSimRef, 0, true)).exists()) {
                updatestr = "fileOldPrime";
            } else if (parentsimref != null && new File(primaryDataDir, SimulationData.createCanonicalSimLogFileName(parentsimref, 0, false)).exists()) {
                updatestr = "fileNewParent";
            } else if (parentsimref != null && new File(primaryDataDir, SimulationData.createCanonicalSimLogFileName(parentsimref, 0, true)).exists()) {
                updatestr = "fileOldParent";
            } else if (AmplistorUtils.bFileExists(new URL(AmplistorUtils.DEFAULT_AMPLI_SERVICE_VCELL_URL + user.getName() + "/" + filePathNamePrime.getName()), amplistorCredential)) {
                updatestr = "ampliNewPrime";
            } else if (AmplistorUtils.bFileExists(new URL(AmplistorUtils.DEFAULT_AMPLI_SERVICE_VCELL_URL + user.getName() + "/" + SimulationData.createCanonicalSimLogFileName(simJobSimRef, 0, true)), amplistorCredential)) {
                updatestr = "ampliOldPrime";
            } else if (parentsimref != null && AmplistorUtils.bFileExists(new URL(AmplistorUtils.DEFAULT_AMPLI_SERVICE_VCELL_URL + user.getName() + "/" + SimulationData.createCanonicalSimLogFileName(parentsimref, 0, false)), amplistorCredential)) {
                updatestr = "ampliNewParent";
            } else if (parentsimref != null && AmplistorUtils.bFileExists(new URL(AmplistorUtils.DEFAULT_AMPLI_SERVICE_VCELL_URL + user.getName() + "/" + SimulationData.createCanonicalSimLogFileName(parentsimref, 0, true)), amplistorCredential)) {
                updatestr = "ampliOldParent";
            } else {
                updatestr = "false";
            }
            if (bExistOnly || updatestr.equals("false")) {
                updateStatement.executeUpdate("update missingdata set dataexists='" + updatestr + "' where simjobsimref=" + simJobSimRef.toString());
                con.commit();
                continue;
            }
            // Log file exists, now check if the data can really be read
            VCSimulationIdentifier vcSimulationIdentifier = new VCSimulationIdentifier(simJobSimRef, user);
            VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(vcSimulationIdentifier, jobIndex);
            // Try to read log,times and simdata to see if this data is well formed
            SimDataAmplistorInfo simDataAmplistorInfo = AmplistorUtils.getSimDataAmplistorInfoFromPropertyLoader();
            SimulationData simData = new SimulationData(vcSimulationDataIdentifier, primaryDataDir, null, simDataAmplistorInfo);
            double[] dataTimes = simData.getDataTimes();
            DataIdentifier[] dataIdentifiers = simData.getVarAndFunctionDataIdentifiers(null);
            DataIdentifier readDataIdentifier = null;
            for (DataIdentifier dataIdentifier : dataIdentifiers) {
                if (!dataIdentifier.isFunction()) {
                    if (simData.getIsODEData()) {
                        ODEDataBlock odeDataBlock = simData.getODEDataBlock();
                        odeDataBlock.getODESimData().getRow(dataTimes.length - 1);
                    } else {
                        simData.getSimDataBlock(null, dataIdentifier.getName(), dataTimes[dataTimes.length - 1]);
                    }
                    readDataIdentifier = dataIdentifier;
                    break;
                }
            }
            System.out.println(BeanUtils.forceStringSize("user= " + user.getName(), 20, " ", false) + " simref= " + BeanUtils.forceStringSize(simJobSimRef.toString(), 14, " ", false) + " numTimes= " + BeanUtils.forceStringSize(dataTimes.length + "", 8, " ", true) + " readDataID= " + BeanUtils.forceStringSize(readDataIdentifier.getName() + "", 20, " ", true));
            updatestr = "update missingdata set dataexists='readable' where simjobsimref=" + simJobSimRef.toString();
        // String updatestr = "update missingdata set dataexists='true' where"+
        // " userinfoid="+user.getID().toString()+
        // " and simjobsimref="+simJobSimRef.toString()+
        // " and maxtaskid="+rset.getString("maxtaskid")+
        // " and jobindex="+jobIndex;
        // updateStatement.executeUpdate(updatestr);
        // con.commit();
        } catch (Exception e) {
            if (simJobSimRef == null) {
                e.printStackTrace();
            // throw new SQLException("Error querying",e);
            } else {
                String errString = e.getClass().getSimpleName() + " " + e.getMessage();
                if (errString.length() > 512) {
                    errString = errString.substring(0, 512);
                }
                String updatestr = "update missingdata set dataexists='error - " + TokenMangler.fixTokenStrict(errString) + "' where simjobsimref=" + simJobSimRef.toString();
                // updateStatement.executeUpdate(updatestr);
                // con.commit();
                System.out.println(BeanUtils.forceStringSize("user= " + (user == null ? "unavailable" : user.getName()), 20, " ", false) + " simref= " + BeanUtils.forceStringSize(simJobSimRef.toString(), 14, " ", false) + " parentsimref= " + BeanUtils.forceStringSize((parentsimref == null ? "NULL" : parentsimref.toString()), 14, " ", false) + " failed= " + e.getMessage());
            // errorHash.put(simJobSimRef,e);
            }
        }
    }
    rset.close();
// return errorHash;
}

Example 3 with SimulationData

use of cbit.vcell.simdata.SimulationData in project vcell by virtualcell.

the class VFrapXmlHelper method LoadVFrapSpecialImages.

// // load and compute prebleach average and first postbleach images
// public void LoadVFrapSpecialImages(AnnotatedImageDataset annotatedImages, int startingIndexRecovery)
// {
// // unnormalized prebleach average
// prebleachAvg = new double[annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getNumXYZ()];
// for(int j = 0; j < prebleachAvg.length; j++)
// {
// double pixelTotal = 0;
// for(int i = 0 ; i < startingIndexRecovery; i++)
// {
// pixelTotal = pixelTotal + (annotatedImages.getImageDataset().getImage(0, 0, i).getPixels()[j] & 0x0000FFFF);
// }
// prebleachAvg[j] = pixelTotal/startingIndexRecovery;
// }
// 
// // unnormalized first post bleach
// firstPostBleach = new double[annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getNumXYZ()];
// short[] pixels = annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getPixels();
// for(int i = 0; i< pixels.length; i++)
// {
// firstPostBleach[i] = pixels[i] & 0x0000FFFF;
// }
// }
// 
// Locate the special images within the vFrap files and load them in memory
// 
public static boolean LoadVFrapSpecialImages(Hashtable<String, Object> hashTable, Element vFrapRoot) throws IOException, DataAccessException, MathException, ImageException {
    // ------ parse the vfrap file and the log/zip files referred within -----
    // many channels of 1 timepoint each
    int NumTimePoints = 1;
    // the channels: prebleach, postbleach, roi1, roi2 ... roiN
    int NumChannels = tokenNames.length;
    String[] channelNames = new String[NumChannels];
    VariableType[] channelTypes = new VariableType[NumChannels];
    DataSymbolType[] channelVFrapImageType = new DataSymbolType[NumChannels];
    double[][][] pixData = new double[NumTimePoints][NumChannels][];
    // get the path of the file tagged with "ROIExternalDataInfoTag" and open it
    Element roiExternalDataInfoElement = vFrapRoot.getChild(MicroscopyXMLTags.ROIExternalDataInfoTag);
    if (roiExternalDataInfoElement == null) {
        // can't load FieldData for some reason, fall back to importing the biomodel only
        return false;
    }
    // <ROIExternalDataInfo Filename="c:\vFrap\VirtualMicroscopy\SimulationData\SimID_1282941232246_0_.log">
    // <ExternalDataIdentifier Name="timeData" KeyValue="1282941232246" OwnerName="SimulationData" OwnerKey="0" />
    // </ImageDatasetExternalDataInfo>
    // c:\VirtualMicroscopy\SimulationData\SimID_1284149203811_0_.log
    String filename = (roiExternalDataInfoElement).getAttributeValue("Filename");
    Element childElement = (roiExternalDataInfoElement).getChild("ExternalDataIdentifier");
    if (childElement == null) {
        // can't load FieldData for some reason, fall back to importing the biomodel only
        return false;
    }
    StringTokenizer tokens = new StringTokenizer(filename, "/\\.");
    final ArrayList<String> tokenArray = new ArrayList<String>();
    while (tokens.hasMoreElements()) {
        tokenArray.add(tokens.nextToken());
    }
    final String dataID = tokenArray.get(tokenArray.size() - 2);
    final String userName = tokenArray.get(tokenArray.size() - 3);
    VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {

        public String getID() {
            return dataID;
        }

        public KeyValue getDataKey() {
            return null;
        }

        public User getOwner() {
            return new User(userName, new KeyValue("123345432334"));
        }
    };
    // ------- recover simulation data for this user name, load the images in memory ------------
    // ex  c:\\VirtualMicroscopy\\SimulationData
    String userDirName = filename.substring(0, filename.indexOf(dataID) - 1);
    File userDir = new File(userDirName);
    SimulationData.SimDataAmplistorInfo simDataAmplistorInfo = AmplistorUtils.getSimDataAmplistorInfoFromPropertyLoader();
    SimulationData simData = new SimulationData(vcDataIdentifier, userDir, null, simDataAmplistorInfo);
    // build a valid mesh in 2 steps, what we have in simData is incomplete
    CartesianMesh incompleteMesh = simData.getMesh();
    Extent extent = incompleteMesh.getExtent();
    ISize isize = new ISize(incompleteMesh.getSizeX(), incompleteMesh.getSizeY(), incompleteMesh.getSizeZ());
    Origin origin = new Origin(0, 0, 0);
    CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
    DataIdentifier[] dataIdentifiers = simData.getVarAndFunctionDataIdentifiers(null);
    double[] times = simData.getDataTimes();
    for (int i = 0; i < dataIdentifiers.length; i++) {
        // ex: prebleach_avg, postbleach_first, postbleach_last, bleached_mask, cell_mask, ring1_mask,... ring8_mask
        System.out.println(dataIdentifiers[i].getName());
        for (double time : times) {
            // this loops only once, we have just 1 timepoint for each "special" image
            SimDataBlock simDataBlock = simData.getSimDataBlock(null, dataIdentifiers[i].getName(), time);
            channelNames[i] = dataIdentifiers[i].getName();
            channelTypes[i] = VariableType.VOLUME;
            channelVFrapImageType[i] = SymbolEquivalence.typeFromToken(dataIdentifiers[i].getName());
            pixData[0][i] = simDataBlock.getData();
            // var = prebleach_avg, time = 0.0, data = { 1.0832530361887216 1.0832530361887216 1.0832530361887216 1.0 .... }
            System.out.print("var = " + dataIdentifiers[i].getName() + ", time = " + time + ", data = { ");
            // show a few
            for (int j = 0; j < 5; j++) {
                System.out.print(pixData[0][i][j] + " ");
            }
            // show a few
            ;
            // show a few
            System.out.println(" ... ");
        }
    }
    hashTable.put("mesh", mesh);
    hashTable.put("pixData", pixData);
    hashTable.put("channelNames", channelNames);
    hashTable.put("channelTypes", channelTypes);
    hashTable.put("channelVFrapImageType", channelVFrapImageType);
    return true;
}

Example 4 with SimulationData

use of cbit.vcell.simdata.SimulationData in project vcell by virtualcell.

the class IMGExporter method getParticleFiles.

private File[] getParticleFiles(ExportSpecs exportSpecs, User user, DataServerImpl dataServerImpl) throws Exception {
    // int particleMode = FormatSpecificSpecs.PARTICLE_NONE;
    // if(exportSpecs.getFormatSpecificSpecs() instanceof ImageSpecs){
    // particleMode = ((ImageSpecs)exportSpecs.getFormatSpecificSpecs()).getParticleMode();
    // }else if (exportSpecs.getFormatSpecificSpecs() instanceof MovieSpecs){
    // particleMode = ((MovieSpecs)exportSpecs.getFormatSpecificSpecs()).getParticleMode();
    // }
    // if(particleMode == FormatSpecificSpecs.PARTICLE_NONE){
    // return null;
    // }
    final VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    SimulationData.SimDataAmplistorInfo simDataAmplistorInfo = AmplistorUtils.getSimDataAmplistorInfoFromPropertyLoader();
    SimulationData simData = new SimulationData(vcdID, new File(PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty), vcdID.getOwner().getName()), new File(PropertyLoader.getProperty(PropertyLoader.primarySimDataDirInternalProperty, null), vcdID.getOwner().getName()), simDataAmplistorInfo);
    File logFile = simData.getLogFile();
    if (!logFile.exists()) {
        throw new Exception("ImgExport particle, Couldn't find Log file " + logFile.getAbsolutePath());
    }
    ArrayList<File> smoldynPointFiles = new ArrayList<>();
    // smoldyn always begins at timeindex 1
    int timeIndex = 1;
    while (true) {
        File smoldynOutFile = simData.getSmoldynOutputFile(timeIndex);
        if (!smoldynOutFile.exists()) {
            // get smoldynOutput files
            break;
        } else {
            smoldynPointFiles.add(smoldynOutFile);
        }
        timeIndex++;
    }
    if (smoldynPointFiles.size() == 0) {
        return null;
    }
    return smoldynPointFiles.toArray(new File[0]);
}

Example 5 with SimulationData

use of cbit.vcell.simdata.SimulationData 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();
}