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

Example 6 with VCDataIdentifier

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

the class ClientRequestManager method getDataViewerController.

/**
 * Insert the method's description here.
 * Creation date: (6/11/2004 10:53:47 AM)
 * @return cbit.vcell.desktop.controls.DataManager
 * @param vcDataIdentifier cbit.vcell.server.VCDataIdentifier
 */
public DataViewerController getDataViewerController(OutputContext outputContext, Simulation simulation, int jobIndex) throws DataAccessException {
    VCSimulationIdentifier vcSimulationIdentifier = simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier();
    final VCDataIdentifier vcdataIdentifier = new VCSimulationDataIdentifier(vcSimulationIdentifier, jobIndex);
    DataManager dataManager = getDataManager(outputContext, vcdataIdentifier, simulation.isSpatial());
    return new SimResultsViewerController(dataManager, simulation);
}

Example 7 with VCDataIdentifier

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

the class ASCIIExporter method exportParticleData.

/**
 * Insert the method's description here.
 * Creation date: (1/12/00 5:00:28 PM)
 * @return cbit.vcell.export.server.ExportOutput[]
 * @param dsc cbit.vcell.server.DataSetController
 * @param timeSpecs cbit.vcell.export.server.TimeSpecs
 * @throws IOException
 */
private List<ExportOutput> exportParticleData(OutputContext outputContext, long jobID, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, ASCIISpecs asciiSpecs, FileDataContainerManager fileDataContainerManager) throws DataAccessException, IOException {
    VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    TimeSpecs timeSpecs = exportSpecs.getTimeSpecs();
    String simID = vcdID.getID();
    String dataType = ".csv";
    // in switched format, how many rows for each particle
    final int N_PARTICLE_PIECES = 1;
    // get parameters
    boolean switchRowsColumns = asciiSpecs.getSwitchRowsColumns();
    double[] allTimes = timeSpecs.getAllTimes();
    int beginIndex = timeSpecs.getBeginTimeIndex();
    int endIndex = timeSpecs.getEndTimeIndex();
    ParticleDataBlock particleDataBlk = dataServerImpl.getParticleDataBlock(user, vcdID, allTimes[beginIndex]);
    VariableSpecs vs = exportSpecs.getVariableSpecs();
    VCAssert.assertValid(vs);
    String[] vnames = vs.getVariableNames();
    if (vnames.length == 0) {
        throw new IllegalArgumentException("No variables selected");
    }
    // need array for SimulationDescription, later
    final String[] currentVariableName = new String[1];
    ArrayList<ExportOutput> rval = new ArrayList<>(vnames.length);
    Set<String> species = particleDataBlk.getSpecies();
    ParticleProgress particleProgress = null;
    for (String vcellName : vnames) {
        String smoldynSpecies = null;
        for (int i = 0; smoldynSpecies == null && i < SMOLDYN_KEYWORDS_USED.length; i++) {
            SmoldynKeyword kw = SMOLDYN_KEYWORDS_USED[i];
            String smoldynName = SmoldynVCellMapper.vcellToSmoldyn(vcellName, kw);
            if (species.contains(smoldynName)) {
                smoldynSpecies = smoldynName;
            }
        }
        if (smoldynSpecies == null) {
            throw new DataAccessException("Unable to find match for variable name " + vcellName + " in " + StringUtils.join(species, ", "));
        }
        List<Coordinate> particles = particleDataBlk.getCoordinates(smoldynSpecies);
        int numberOfParticles = particles.size();
        int numberOfTimes = endIndex - beginIndex + 1;
        if (particleProgress != null) {
            particleProgress.nextName();
        } else {
            particleProgress = new ParticleProgress(jobID, vcdID, vnames.length, numberOfTimes, numberOfParticles);
        }
        // now make csv formatted data
        StringBuilder header = new StringBuilder();
        StringBuilder[] dataLines = null;
        final int NUMBER_HEADING_LINES = SwitchedRowsHeading.DATA.ordinal();
        if (switchRowsColumns) {
            dataLines = stringBuilderArray(numberOfParticles * N_PARTICLE_PIECES + NUMBER_HEADING_LINES);
            dataLines[SwitchedRowsHeading.TIME.ordinal()].append("Time,");
            final String particleLine = "Particle" + StringUtils.repeat(",x,y,z", numberOfTimes);
            dataLines[SwitchedRowsHeading.PARTICLE.ordinal()].append(particleLine);
            dataLines[SwitchedRowsHeading.XYZ.ordinal()].append("#,");
            // "first data line"
            final int FDL = SwitchedRowsHeading.DATA.ordinal();
            for (int i = 0; i < numberOfParticles; i++) {
                dataLines[FDL + N_PARTICLE_PIECES * i].append(i);
                dataLines[FDL + N_PARTICLE_PIECES * i].append(',');
            }
        } else {
            dataLines = stringBuilderArray(numberOfTimes);
        }
        currentVariableName[0] = vcellName;
        SimulationDescription simulationDescription = new SimulationDescription(outputContext, user, dataServerImpl, vcdID, false, currentVariableName);
        header.append(simulationDescription.getHeader(dataType));
        if (switchRowsColumns) {
        // implemented using first few data lines
        } else {
            header.append(",Time\n");
            header.append("Particle #,,");
            for (int k = 0; k < numberOfParticles; k++) {
                header.append(k + StringUtils.repeat(',', N_PARTICLE_PIECES));
            }
            header.append("\n,,");
            for (int k = 0; k < numberOfParticles; k++) {
                header.append("x,y,z,");
            }
        }
        final char COMMA = ',';
        int nextTimeIndex = particleProgress.nextTimeIndex(0, false);
        for (int i = beginIndex; i <= endIndex; i++) {
            particleDataBlk = dataServerImpl.getParticleDataBlock(user, vcdID, allTimes[i]);
            particles = particleDataBlk.getCoordinates(smoldynSpecies);
            if (i >= nextTimeIndex) {
                nextTimeIndex = particleProgress.nextTimeIndex(i, true);
            }
            if (switchRowsColumns) {
                // "first data line"
                final int FDL = SwitchedRowsHeading.DATA.ordinal();
                StringBuilder timeSb = dataLines[SwitchedRowsHeading.TIME.ordinal()];
                timeSb.append(allTimes[i]);
                timeSb.append(",,,");
                for (int j = 0; j < numberOfParticles; j++) {
                    StringBuilder sb = dataLines[FDL + N_PARTICLE_PIECES * j];
                    Coordinate coordinate = particles.get(j);
                    sb.append(coordinate.getX());
                    sb.append(COMMA);
                    sb.append(coordinate.getY());
                    sb.append(COMMA);
                    sb.append(coordinate.getZ());
                    sb.append(COMMA);
                }
            } else {
                StringBuilder particleSb = dataLines[i - beginIndex];
                particleSb.append(COMMA);
                particleSb.append(allTimes[i]);
                particleSb.append(COMMA);
                for (int j = 0; j < numberOfParticles; j++) {
                    Coordinate coordinate = particles.get(j);
                    particleSb.append(coordinate.getX());
                    particleSb.append(COMMA);
                    particleSb.append(coordinate.getY());
                    particleSb.append(COMMA);
                    particleSb.append(coordinate.getZ());
                }
            }
        }
        particleProgress.endOfTimes();
        final String dataID = vcellName + "_Particles";
        ExportOutput exportOutputCSV = new ExportOutput(true, dataType, simID, dataID, fileDataContainerManager);
        fileDataContainerManager.append(exportOutputCSV.getFileDataContainerID(), header.toString());
        int nextDataIndex = particleProgress.nextDataIndex(0, false);
        StringBuilder all = new StringBuilder();
        for (int i = 0; i < dataLines.length; i++) {
            final char NEWLINE = '\n';
            all.append(dataLines[i]);
            // kill reference to allow garbage collection
            dataLines[i] = null;
            all.append(NEWLINE);
            if (i >= nextDataIndex) {
                nextDataIndex = particleProgress.nextDataIndex(i, true);
            }
        }
        fileDataContainerManager.append(exportOutputCSV.getFileDataContainerID(), all.toString());
        rval.add(exportOutputCSV);
    }
    return rval;
}

Example 8 with VCDataIdentifier

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

the class IMGExporter method makeMedia.

// private ParticleInfo checkParticles_unused(final ExportSpecs exportSpecs,User user,DataServerImpl dataServerImpl,final long jobID) 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();
// CartesianMesh cartesianMesh = dataServerImpl.getMesh(user, vcdID);
// int dimension = cartesianMesh.getGeometryDimension();
// 
// String[] variableNames = exportSpecs.getVariableSpecs().getVariableNames();
// 
// File visitExeLocation =
// new File(PropertyLoader.getRequiredProperty(PropertyLoader.visitSmoldynVisitExecutableProperty));
// File visitSmoldynScriptLocation =
// new File(PropertyLoader.getRequiredProperty(PropertyLoader.visitSmoldynScriptPathProperty));
// final File visitSmoldynScriptTempDir = PropertyLoader.getSystemTemporaryDirectory();
// 
// //-----Get all data (from archive if necessary)
// 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());
// }
// simData.getMesh();//gets mesh and meshmetrics files from archive if necessary
// simData.getSubdomainFile();
// simData.getFunctionsFile(false);
// int timeIndex = 1;//smoldyn always begins at timeindex 1
// while(true){
// if(!simData.getSmoldynOutputFile(timeIndex).exists()){//get smoldynOutput files
// break;
// }
// timeIndex++;
// }
// //-----
// 
// File visitDataPathFragment = new File(logFile.getParent(),vcdID.getID()+"_");
// System.out.println(visitExeLocation.getAbsolutePath());
// System.out.println(visitSmoldynScriptLocation.getAbsolutePath());
// System.out.println(visitSmoldynScriptTempDir.getAbsolutePath());
// System.out.println(visitDataPathFragment.getAbsolutePath());
// 
// //if(true){return new ParticleInfo(visitSmoldynScriptTempDir);}
// if(exportSpecs.getTimeSpecs().getAllTimes().length == 1){
// throw new IllegalArgumentException("Time zero not valid for smoldyn particle data");
// }
// int beginIndexTime = exportSpecs.getTimeSpecs().getBeginTimeIndex();
// int endIndexTime = exportSpecs.getTimeSpecs().getEndTimeIndex();
// 
// System.out.println("beginIndexTime="+beginIndexTime+" endIndexTime="+endIndexTime);
// 
// ArrayList<String> args = new ArrayList<String>();
// args.add(visitExeLocation.getAbsolutePath());//location of visit
// args.add("-nowin");
// args.add("-cli");
// args.add("-s");
// 
// args.add(visitSmoldynScriptLocation.getAbsolutePath());//location of the script
// args.add(visitDataPathFragment.getAbsolutePath()); //location of the SimID
// args.add(visitSmoldynScriptTempDir.getAbsolutePath());  // where frames are dumped
// args.add(dimension+""); //dimension
// args.add(beginIndexTime+"");
// args.add(endIndexTime+"");
// args.add(4+"");//particle sphere size
// args.add(FormatSpecificSpecs.SMOLDYN_DEFAULT_FRAME_SIZE.width+"");//frame size X
// args.add(FormatSpecificSpecs.SMOLDYN_DEFAULT_FRAME_SIZE.height+"");//frame size Y
// args.add(variableNames.length+""); // 0 = show all the particles.  >0 == show n different particles, to be listed below
// for (int i = 0; i < variableNames.length; i++) {
// args.add(variableNames[i]);
// }
// 
// final String tempFilePrefix = vcdID.getID()+"_p3d";
// 
// //Monitor progress of smoldyn script
// exportServiceImpl.fireExportProgress(jobID, vcdID, "MEDIA", 0.0);
// final boolean[] finishedFlag = new boolean[] {false};
// final int numTimePoints = exportSpecs.getTimeSpecs().getEndTimeIndex()-exportSpecs.getTimeSpecs().getBeginTimeIndex()+1;
// Thread progressThread = new Thread(new Runnable() {
// public void run() {
// System.out.println("smoldyn progress monitor started");
// while(!finishedFlag[0]){
// int count = 0;
// File[] tempFiles = visitSmoldynScriptTempDir.listFiles();
// for (int i = 0; i < tempFiles.length; i++) {
// if(tempFiles[i].getName().startsWith(tempFilePrefix) ||
// (tempFiles[i].getName().startsWith(vcdID.getID()) &&
// tempFiles[i].getName().endsWith(".jpeg"))){
// count+= 1;
// }
// }
// double progress = .5 * (double)count / (double)(2*numTimePoints);
// exportServiceImpl.fireExportProgress(jobID, vcdID, "MEDIA", progress);
// //System.out.println("All files read="+tempFiles.length+" Files counted="+count+" progress="+progress);
// try {
// Thread.sleep(1000);
// } catch (InterruptedException e) {
// e.printStackTrace();
// return;//This shouldn't happen but if so just quit
// }
// }
// System.out.println("smoldyn progress monitor finished");
// }
// });
// progressThread.start();
// 
// 
// try{
// final long TIME_OUT = 1200000; //20 minutes
// Executable executable = new Executable(args.toArray(new String[0]),TIME_OUT);
// executable.start();//blocking, internal monitoring, return after timeout
// if(!executable.getStatus().equals(ExecutableStatus.COMPLETE)){
// System.out.println(executable.getStderrString());
// System.out.println(executable.getStdoutString());
// throw new Exception("Particle data exporter did not complete normally. "+(executable.getStatus()==null?"":executable.getStatus().toString()));
// }
// }finally{
// finishedFlag[0] = true;
// //Remove temp files created by smoldyn script
// File[] tempFiles = visitSmoldynScriptTempDir.listFiles();
// for (int i = 0; i < tempFiles.length; i++) {
// if(tempFiles[i].getName().startsWith(tempFilePrefix)){
// tempFiles[i].delete();
// }
// }
// }
// return new ParticleInfo(visitSmoldynScriptTempDir);
// }
private static ExportOutput[] makeMedia(ExportServiceImpl exportServiceImpl, OutputContext outputContext, long jobID, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, ClientTaskStatusSupport clientTaskStatusSupport, ParticleInfo particleInfo, FileDataContainerManager fileDataContainerManager) throws RemoteException, IOException, GIFFormatException, DataAccessException, Exception {
    boolean bOverLay = false;
    int sliceIndicator = 0;
    if (particleInfo == null) {
        sliceIndicator = (exportSpecs.getGeometrySpecs().getModeID() == ExportConstants.GEOMETRY_FULL ? FULL_MODE_ALL_SLICES : exportSpecs.getGeometrySpecs().getSliceNumber());
    }
    int imageScale = 0;
    int meshMode = 0;
    int mirroringType = 0;
    int membraneScale = 0;
    double duration = 1.0;
    DisplayPreferences[] displayPreferences = null;
    int volVarMembrOutlineThickness = 1;
    if (exportSpecs.getFormatSpecificSpecs() instanceof ImageSpecs) {
        bOverLay = ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getOverlayMode();
        imageScale = ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getImageScaling();
        volVarMembrOutlineThickness = ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getVolVarMembrOutlineThickness();
        meshMode = ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getMeshMode();
        mirroringType = ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getMirroringType();
        membraneScale = ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getMembraneScaling();
        displayPreferences = ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getDisplayPreferences();
        // convert from milliseconds to seconds
        duration = (double) ((ImageSpecs) exportSpecs.getFormatSpecificSpecs()).getDuration() / 1000.0;
    } else if (exportSpecs.getFormatSpecificSpecs() instanceof MovieSpecs) {
        bOverLay = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getOverlayMode();
        imageScale = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getImageScaling();
        volVarMembrOutlineThickness = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getVolVarMembrOutlineThickness();
        meshMode = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getMeshMode();
        mirroringType = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getMirroringType();
        membraneScale = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getMembraneScaling();
        displayPreferences = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getDisplayPreferences();
        // convert from milliseconds to seconds
        duration = ((MovieSpecs) exportSpecs.getFormatSpecificSpecs()).getDuration() / 1000.0;
    } else {
        throw new DataFormatException("Unknown FormatSpecificSpec " + exportSpecs.getFormatSpecificSpecs().getClass().getName());
    }
    Vector<ExportOutput> exportOutputV = new Vector<ExportOutput>();
    VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    int beginTimeIndex = exportSpecs.getTimeSpecs().getBeginTimeIndex();
    int endTimeIndex = exportSpecs.getTimeSpecs().getEndTimeIndex();
    boolean bSingleTimePoint = beginTimeIndex == endTimeIndex;
    String[] varNames = (particleInfo == null ? exportSpecs.getVariableSpecs().getVariableNames() : new String[] { "smoldynParticleDummy" });
    double[] allTimes = dataServerImpl.getDataSetTimes(user, vcdID);
    int startSlice = (sliceIndicator == FULL_MODE_ALL_SLICES ? 0 : sliceIndicator);
    int sliceCount = FormatSpecificSpecs.getSliceCount(sliceIndicator == FULL_MODE_ALL_SLICES, exportSpecs.getGeometrySpecs().getAxis(), dataServerImpl.getMesh(user, vcdID));
    double progressIncr = 1.0 / (sliceCount * (endTimeIndex - beginTimeIndex + 1) * varNames.length);
    double progress = 0.0;
    MovieHolder movieHolder = new MovieHolder();
    Dimension imageDimension = FormatSpecificSpecs.getImageDimension(meshMode, imageScale, dataServerImpl.getMesh(user, vcdID), exportSpecs.getGeometrySpecs().getAxis());
    int originalWidth = (int) imageDimension.getWidth();
    int originalHeight = (int) imageDimension.getHeight();
    ExportRenderInfo exportRenderInfo = null;
    try {
        for (int sliceNumber = startSlice; sliceNumber < startSlice + sliceCount; sliceNumber++) {
            if (particleInfo == null) {
                PDEOffscreenRenderer offScreenRenderer = new PDEOffscreenRenderer(outputContext, user, dataServerImpl, vcdID);
                offScreenRenderer.setNormalAxis(exportSpecs.getGeometrySpecs().getAxis());
                offScreenRenderer.setSlice(sliceNumber);
                exportRenderInfo = new ExportRenderInfo(offScreenRenderer);
            } else {
                exportRenderInfo = new ExportRenderInfo(particleInfo, allTimes, vcdID, beginTimeIndex);
                Dimension particleImageSize = particleInfo.getImageFrameSize(vcdID);
                originalWidth = particleImageSize.width;
                originalHeight = particleImageSize.height;
            }
            int varNameIndex0 = 0;
            int timeIndex0 = beginTimeIndex;
            int[] overLayPixels = null;
            // set default time if only 1 timepoint
            movieHolder.setSampleDurationSeconds(duration);
            boolean bEndslice = sliceNumber == (startSlice + sliceCount - 1);
            while (true) {
                if (clientTaskStatusSupport != null) {
                    clientTaskStatusSupport.setProgress((int) (progress * 100));
                    if (clientTaskStatusSupport.isInterrupted()) {
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                }
                exportServiceImpl.fireExportProgress(jobID, vcdID, "MEDIA", (particleInfo == null ? progress : .5 + (progress / 2.0)));
                progress += progressIncr;
                MirrorInfo currentSliceTimeMirrorInfo = renderAndMirrorSliceTimePixels(exportRenderInfo, varNames[varNameIndex0], allTimes[timeIndex0], displayPreferences[varNameIndex0], imageScale, membraneScale, meshMode, volVarMembrOutlineThickness, originalWidth, originalHeight, mirroringType);
                if (bOverLay) {
                    if (varNames.length == 1) {
                        overLayPixels = currentSliceTimeMirrorInfo.getPixels();
                    } else {
                        // Overlay append in Y-direction
                        if (overLayPixels == null) {
                            overLayPixels = new int[currentSliceTimeMirrorInfo.getPixels().length * varNames.length];
                        }
                        int appendIndex = currentSliceTimeMirrorInfo.getPixels().length * varNameIndex0;
                        System.arraycopy(currentSliceTimeMirrorInfo.getPixels(), 0, overLayPixels, appendIndex, currentSliceTimeMirrorInfo.getPixels().length);
                    }
                }
                if (timeIndex0 != endTimeIndex) {
                    // calculate duration for each timepoint
                    movieHolder.setSampleDurationSeconds((allTimes[timeIndex0 + 1] - allTimes[timeIndex0]) / (allTimes[endTimeIndex + (endTimeIndex == allTimes.length - 1 ? 0 : 1)] - allTimes[beginTimeIndex]) * duration);
                } else {
                    // when last or only 1 timepoint, use last duration set
                    movieHolder.setSampleDurationSeconds(movieHolder.getSampleDurationSeconds());
                }
                // Index var and time properly
                boolean bBegintime = timeIndex0 == beginTimeIndex;
                boolean bEndTime = timeIndex0 == endTimeIndex;
                if (bOverLay) {
                    varNameIndex0++;
                    if (varNameIndex0 == varNames.length) {
                        String dataID = createDataID(exportSpecs, sliceNumber, "overlay", timeIndex0);
                        createMedia(exportOutputV, vcdID, dataID, exportSpecs, true, bEndslice, bBegintime, bEndTime, bSingleTimePoint, varNames, displayPreferences, movieHolder, overLayPixels, currentSliceTimeMirrorInfo.getMirrorWidth(), currentSliceTimeMirrorInfo.getMirrorHeight() * varNames.length, fileDataContainerManager);
                        varNameIndex0 = 0;
                        timeIndex0++;
                        if (timeIndex0 > endTimeIndex) {
                            break;
                        }
                    }
                } else {
                    String dataID = createDataID(exportSpecs, sliceNumber, varNames[varNameIndex0], timeIndex0);
                    boolean bEndVars = varNameIndex0 == varNames.length - 1;
                    createMedia(exportOutputV, vcdID, dataID, exportSpecs, bEndVars, bEndslice, bBegintime, bEndTime, bSingleTimePoint, new String[] { varNames[varNameIndex0] }, new DisplayPreferences[] { displayPreferences[varNameIndex0] }, movieHolder, currentSliceTimeMirrorInfo.getPixels(), currentSliceTimeMirrorInfo.getMirrorWidth(), currentSliceTimeMirrorInfo.getMirrorHeight(), fileDataContainerManager);
                    timeIndex0++;
                    if (timeIndex0 > endTimeIndex) {
                        timeIndex0 = beginTimeIndex;
                        varNameIndex0++;
                        if (varNameIndex0 == varNames.length) {
                            break;
                        }
                    }
                }
            }
        }
    } finally {
        if (exportRenderInfo != null) {
            exportRenderInfo.cleanup();
        }
    }
    return exportOutputV.toArray(new ExportOutput[0]);
}

Example 9 with VCDataIdentifier

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

the class RasterExporter method makeVTKUnstructuredData0.

public ExportOutput[] makeVTKUnstructuredData0(OutputContext outputContext, JobRequest jobRequest, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, FileDataContainerManager fileDataContainerManager) throws Exception {
    VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    boolean bChombo = dataServerImpl.isChombo(user, vcdID);
    final File tmpDir = PropertyLoader.getSystemTemporaryDirectory();
    if (bChombo) {
        return makeVTKUnstructuredData_Chombo(outputContext, jobRequest, user, dataServerImpl, exportSpecs, tmpDir, fileDataContainerManager);
    } else {
        return makeVTKUnstructuredData_VCell(outputContext, jobRequest, user, dataServerImpl, exportSpecs, tmpDir, fileDataContainerManager);
    }
}

Example 10 with VCDataIdentifier

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

the class RasterExporter method makeUCDData.

public ExportOutput[] makeUCDData(OutputContext outputContext, JobRequest jobRequest, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, FileDataContainerManager fileDataContainerManager) throws Exception {
    String simID = exportSpecs.getVCDataIdentifier().getID();
    VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    VariableSpecs variableSpecs = exportSpecs.getVariableSpecs();
    TimeSpecs timeSpecs = exportSpecs.getTimeSpecs();
    cbit.vcell.solvers.CartesianMesh mesh = dataServerImpl.getMesh(user, vcdID);
    CartesianMesh.UCDInfo ucdInfo = mesh.getUCDInfo();
    CartesianMesh.UCDInfo ucdInfoReduced = ucdInfo.removeNonMembraneGridNodes();
    Vector<ExportOutput> exportOutV = new Vector<ExportOutput>();
    // for (int i = 0; i < variableSpecs.getVariableNames().length; i++){
    for (int j = timeSpecs.getBeginTimeIndex(); j <= timeSpecs.getEndTimeIndex(); j++) {
        exportServiceImpl.fireExportProgress(jobRequest.getJobID(), vcdID, "UCD", (double) (j - timeSpecs.getBeginTimeIndex()) / (double) (timeSpecs.getEndTimeIndex() - timeSpecs.getBeginTimeIndex() + 1));
        // String fileID = simID + "_Full_" + formatTime(timeSpecs.getAllTimes()[j]) + "time_" + variableSpecs.getVariableNames().length + "vars";
        // File datafile = new File(tempDir, fileID + "_data.ucd");
        // FileWriter fileWriter = new FileWriter(datafile);
        Vector<double[]> volumeDataV = new Vector<double[]>();
        Vector<String> volumeDataNameV = new Vector<String>();
        Vector<String> volumeDataUnitV = new Vector<String>();
        Vector<double[]> membraneDataV = new Vector<double[]>();
        Vector<String> membraneDataNameV = new Vector<String>();
        Vector<String> membraneDataUnitV = new Vector<String>();
        for (int k = 0; k < variableSpecs.getVariableNames().length; k++) {
            SimDataBlock simDataBlock = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[k], timeSpecs.getAllTimes()[j]);
            if (simDataBlock.getVariableType().equals(VariableType.VOLUME)) {
                volumeDataNameV.add(variableSpecs.getVariableNames()[k]);
                volumeDataUnitV.add("unknown");
                volumeDataV.add(simDataBlock.getData());
            } else {
                membraneDataNameV.add(variableSpecs.getVariableNames()[k]);
                membraneDataUnitV.add("unknown");
                membraneDataV.add(simDataBlock.getData());
            }
        }
        if (volumeDataV.size() > 0) {
            StringWriter stringWriter = new StringWriter();
            AVS_UCD_Exporter.writeUCDVolGeomAndData(ucdInfo, volumeDataNameV.toArray(new String[0]), volumeDataUnitV.toArray(new String[0]), volumeDataV.toArray(new double[0][]), stringWriter);
            ExportOutput exportOut = new ExportOutput(true, ".ucd", simID.toString(), "_vol_" + j, fileDataContainerManager);
            fileDataContainerManager.append(exportOut.getFileDataContainerID(), stringWriter.toString());
            exportOutV.add(exportOut);
        }
        if (membraneDataV.size() > 0) {
            StringWriter stringWriter = new StringWriter();
            AVS_UCD_Exporter.writeUCDMembGeomAndData(ucdInfoReduced, /*ucdInfo*/
            membraneDataNameV.toArray(new String[0]), membraneDataUnitV.toArray(new String[0]), membraneDataV.toArray(new double[0][]), stringWriter);
            ExportOutput exportOut = new ExportOutput(true, ".ucd", simID.toString(), "_memb_" + j, fileDataContainerManager);
            fileDataContainerManager.append(exportOut.getFileDataContainerID(), stringWriter.toString());
            exportOutV.add(exportOut);
        }
    // AVS_UCD_Exporter.writeUCD(mesh,
    // (volumeDataNameV.size() == 0?null:volumeDataNameV.toArray(new String[0])),
    // (volumeDataUnitV.size() == 0?null:volumeDataUnitV.toArray(new String[0])),
    // (volumeDataV.size() == 0?null:volumeDataV.toArray(new double[0][])),
    // 
    // (membraneDataNameV.size() == 0?null:membraneDataNameV.toArray(new String[0])),
    // (membraneDataUnitV.size() == 0?null:membraneDataUnitV.toArray(new String[0])),
    // (membraneDataV.size() == 0?null:membraneDataV.toArray(new double[0][])),
    // stringWriter);
    // ExportOutput exportOut = new ExportOutput(true,".ucd",simID.toString(),fileID,stringWriter.toString().getBytes());
    // exportOutV.add(exportOut);
    }
    // }
    ExportOutput[] exportOutputArr = exportOutV.toArray(new ExportOutput[0]);
    return exportOutputArr;
// String fileID = simID + "_Full_" + NUM_TIMES + "times_" + variableSpecs.getVariableNames().length + "vars";
// File datafile = new File(tempDir, fileID + "_data.nrrd");
// nrrdInfo.setDatafile(datafile.getName());
// DataOutputStream out = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(datafile)));
// try {
// for (int i = 0; i < variableSpecs.getVariableNames().length; i++){
// for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++){
// double[] data = dataServerImpl.getSimDataBlock(user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
// for (int k = 0; k < data.length; k++){
// out.writeDouble(data[k]);
// }
// }
// }
// } catch (IOException exc) {
// throw new DataAccessException(exc.toString());
// } finally {
// out.close();
// }
}