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

Example 11 with VCDataIdentifier

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

the class RasterExporter method makeVTKUnstructuredData_VCell.

public ExportOutput[] makeVTKUnstructuredData_VCell(OutputContext outputContext, final JobRequest jobRequest, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, File tmpDir, FileDataContainerManager fileDataContainerManager) throws Exception {
    String simID = exportSpecs.getVCDataIdentifier().getID();
    final VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    VariableSpecs variableSpecs = exportSpecs.getVariableSpecs();
    TimeSpecs timeSpecs = exportSpecs.getTimeSpecs();
    VCellSimFiles vcellFiles = dataServerImpl.getVCellSimFiles(user, vcdID);
    CartesianMeshVtkFileWriter cartesianMeshVtkFileWriter = new CartesianMeshVtkFileWriter();
    File[] vtkFiles = cartesianMeshVtkFileWriter.writeVtuExportFiles(vcellFiles, tmpDir, new CartesianMeshVtkFileWriter.ProgressListener() {

        public void progress(double percentDone) {
            exportServiceImpl.fireExportProgress(jobRequest.getJobID(), vcdID, "VTKUNSTR", percentDone);
        }
    });
    Vector<ExportOutput> exportOutV = new Vector<ExportOutput>();
    for (File file : vtkFiles) {
        String dataID = file.getName().replace(simID.toString(), "");
        ExportOutput exportOut = new ExportOutput(true, ".vtu", simID.toString(), dataID, fileDataContainerManager);
        fileDataContainerManager.manageExistingTempFile(exportOut.getFileDataContainerID(), file);
        exportOutV.add(exportOut);
    }
    ExportOutput[] exportOutputArr = exportOutV.toArray(new ExportOutput[0]);
    return exportOutputArr;
}

Example 12 with VCDataIdentifier

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

the class RasterExporter method makeVTKUnstructuredData.

public ExportOutput[] makeVTKUnstructuredData(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, "VTKUNSTR", (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) {
            int[] regionIDs = new int[mesh.getNumVolumeElements()];
            for (int i = 0; i < regionIDs.length; i++) {
                regionIDs[i] = mesh.getVolumeRegionIndex(i);
            }
            StringWriter stringWriter = new StringWriter();
            writeVTKUnstructuredHeader(ucdInfo, vcdID, stringWriter);
            int CELL_INFO_COUNT = 1 + 4 + (ucdInfo.getNumVolumeNodesZ() > 1 ? 4 : 0);
            stringWriter.write("CELLS " + ucdInfo.getNumVolumeCells() + " " + (ucdInfo.getNumVolumeCells() * CELL_INFO_COUNT) + "\n");
            stringWriter.write(ucdInfo.getVolumeCellsString(true));
            writeVTKCellTypes(ucdInfo, ucdInfo.getNumVolumeCells(), (ucdInfo.getNumVolumeNodesZ() > 1 ? VTK_HEXAHEDRON : VTK_QUAD), stringWriter);
            writeVTKCellData(volumeDataV.toArray(new double[0][]), regionIDs, volumeDataNameV.toArray(new String[0]), stringWriter);
            // AVS_UCD_Exporter.writeUCDVolume(
            // ucdInfo,
            // volumeDataNameV.toArray(new String[0]),
            // volumeDataUnitV.toArray(new String[0]),
            // volumeDataV.toArray(new double[0][]),
            // stringWriter);
            ExportOutput exportOut = new ExportOutput(true, ".vtk", simID.toString(), "vol_" + j, fileDataContainerManager);
            fileDataContainerManager.append(exportOut.getFileDataContainerID(), stringWriter.toString());
            exportOutV.add(exportOut);
        }
        if (membraneDataV.size() > 0) {
            int[] regionIDs = new int[mesh.getNumMembraneElements()];
            for (int i = 0; i < regionIDs.length; i++) {
                regionIDs[i] = mesh.getMembraneRegionIndex(i);
            }
            StringWriter stringWriter = new StringWriter();
            writeVTKUnstructuredHeader(ucdInfoReduced, /*ucdInfo*/
            vcdID, stringWriter);
            int MEMBR_INFO_COUNT = 1 + 2 + (ucdInfo.getNumVolumeNodesZ() > 1 ? 2 : 0);
            stringWriter.write("CELLS " + ucdInfoReduced.getNumMembraneCells() + " " + (ucdInfoReduced.getNumMembraneCells() * MEMBR_INFO_COUNT) + "\n");
            stringWriter.write(ucdInfoReduced.getMembraneCellsString(0, true));
            writeVTKCellTypes(ucdInfoReduced, /*ucdInfo*/
            ucdInfoReduced.getNumMembraneCells(), (ucdInfo.getNumVolumeNodesZ() > 1 ? VTK_QUAD : VTK_LINE), stringWriter);
            writeVTKCellData(membraneDataV.toArray(new double[0][]), regionIDs, membraneDataNameV.toArray(new String[0]), stringWriter);
            // AVS_UCD_Exporter.writeUCDMembrane(
            // ucdInfo,
            // membraneDataNameV.toArray(new String[0]),
            // membraneDataUnitV.toArray(new String[0]),
            // membraneDataV.toArray(new double[0][]),
            // stringWriter);
            ExportOutput exportOut = new ExportOutput(true, ".vtk", 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();
// }
}

Example 13 with VCDataIdentifier

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

the class RasterExporter method makePLYWithTexData.

public ExportOutput[] makePLYWithTexData(OutputContext outputContext, JobRequest jobRequest, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, FileDataContainerManager fileDataContainerManager) throws Exception {
    String simID = exportSpecs.getVCDataIdentifier().getID();
    VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    cbit.vcell.solvers.CartesianMesh mesh = dataServerImpl.getMesh(user, vcdID);
    TimeSpecs timeSpecs = exportSpecs.getTimeSpecs();
    VariableSpecs variableSpecs = exportSpecs.getVariableSpecs();
    Vector<ExportOutput> exportOutV = new Vector<ExportOutput>();
    RegionImage regionImage = MeshDisplayAdapter.generateRegionImage(mesh, null);
    PLYSpecs plySpecs = (PLYSpecs) exportSpecs.getFormatSpecificSpecs();
    DisplayPreferences[] displayPreferences = plySpecs.getDisplayPreferences();
    // BitSet bInDomain = null;
    // String variableName = variableSpecs.getVariableNames()[0];
    // Domain varDomain = null;
    // DataIdentifier[] dataIdentifiers = dataServerImpl.getDataIdentifiers(outputContext, user, vcdID);
    // for (int i = 0; i < dataIdentifiers.length; i++) {
    // //dataIdentifier.getDomain();
    // if(dataIdentifiers[i].getName().equals(variableName)){
    // varDomain = dataIdentifiers[i].getDomain();
    // break;
    // }
    // }
    // MembraneElement membraneElement = mesh.getMembraneElements()[faceIndex];
    // String memSubdomainName = (varDomain==null?null:mesh.getMembraneSubdomainNamefromMemIndex(faceIndex));
    // boolean bInDomain = (varDomain==null?true:varDomain.getName().equals(memSubdomainName));
    DisplayAdapterService das = new DisplayAdapterService();
    StringWriter stringWriter = new StringWriter();
    PolyTexHelper imgResults = writeStanfordPolygonTex(regionImage, stringWriter, /*,bInDomain*/
    mesh);
    // mesh
    ExportOutput exportOut = new ExportOutput(true, ".ply", simID.toString(), "_memb", fileDataContainerManager);
    fileDataContainerManager.append(exportOut.getFileDataContainerID(), stringWriter.toString());
    exportOutV.add(exportOut);
    // special neighbor annotation image
    ExportOutput textImagetOut0 = new ExportOutput(true, ".png", simID.toString(), "_membAnnot", fileDataContainerManager);
    fileDataContainerManager.append(textImagetOut0.getFileDataContainerID(), imgResults.specialNeighborImage);
    exportOutV.add(textImagetOut0);
    for (int varNameIndex = 0; varNameIndex < variableSpecs.getVariableNames().length; varNameIndex++) {
        if (das.fetchColorModel(displayPreferences[varNameIndex].getColorMode()) == null) {
            if (displayPreferences[varNameIndex].getColorMode().equals(DisplayAdapterService.GRAY)) {
                das.addColorModelForValues(DisplayAdapterService.createGrayColorModel(), DisplayAdapterService.createBlueRedSpecialColors(), displayPreferences[varNameIndex].getColorMode());
            } else {
                das.addColorModelForValues(DisplayAdapterService.createBlueRedColorModel(), DisplayAdapterService.createGraySpecialColors(), displayPreferences[varNameIndex].getColorMode());
            // das.setActiveColorModelID("Contrast");
            }
        }
        // BitSet domainValid = (displayPreferences[varNameIndex]==null?null:(displayPreferences[varNameIndex].getDomainValid()==null?null:displayPreferences[varNameIndex].getDomainValid()));
        ExportSpecs.setupDisplayAdapterService(displayPreferences[varNameIndex], das, displayPreferences[varNameIndex].getScaleSettings());
        for (int j = timeSpecs.getBeginTimeIndex(); j <= timeSpecs.getEndTimeIndex(); j++) {
            BufferedImage image = createTextureImage(imgResults.imageSideSize);
            int[] imgBuffer = ((DataBufferInt) (image.getRaster().getDataBuffer())).getData();
            Arrays.fill(imgBuffer, Integer.MAX_VALUE);
            SimDataBlock simDataBlock = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[varNameIndex], timeSpecs.getAllTimes()[j]);
            for (int k = 0; k < imgResults.dataIndexes.length; k++) {
                if (imgBuffer[k] != Integer.MAX_VALUE) {
                    System.out.println("texture pixel used twice");
                }
                double avgVal = 0;
                for (int l = 0; l < imgResults.dataIndexes[k].length; l++) {
                    avgVal += simDataBlock.getData()[imgResults.dataIndexes[k][l]];
                }
                imgBuffer[k] = das.getColorFromValue(avgVal / imgResults.dataIndexes[k].length);
            }
            byte[] pngImage = flipPNG(image);
            ExportOutput textImagetOut = new ExportOutput(true, ".png", simID.toString(), "_memb_" + variableSpecs.getVariableNames()[varNameIndex] + "_" + j, fileDataContainerManager);
            fileDataContainerManager.append(textImagetOut.getFileDataContainerID(), pngImage);
            exportOutV.add(textImagetOut);
        }
    }
    ExportOutput[] exportOutputArr = exportOutV.toArray(new ExportOutput[0]);
    return exportOutputArr;
}

Example 14 with VCDataIdentifier

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

the class RasterExporter method exportPDEData.

private NrrdInfo[] exportPDEData(OutputContext outputContext, long jobID, User user, DataServerImpl dataServerImpl, VCDataIdentifier vcdID, VariableSpecs variableSpecs, TimeSpecs timeSpecs2, GeometrySpecs geometrySpecs, RasterSpecs rasterSpecs, FileDataContainerManager fileDataContainerManager) throws RemoteException, DataAccessException, IOException {
    CartesianMesh mesh = dataServerImpl.getMesh(user, vcdID);
    DataProcessingOutputInfo dataProcessingOutputInfo = null;
    // check if any of export variables are PostProcess and if so try to get PostProcessOutputInfo
    exportServiceImpl.fireExportProgress(jobID, vcdID, "Check PostProcess", 0.0);
    DataIdentifier[] dataIdentifiers = dataServerImpl.getDataIdentifiers(outputContext, user, vcdID);
    for (int i = 0; i < dataIdentifiers.length; i++) {
        for (int j = 0; j < variableSpecs.getVariableNames().length; j++) {
            if (variableSpecs.getVariableNames()[j].equals(dataIdentifiers[i].getName()) && VariableType.POSTPROCESSING.equals(dataIdentifiers[i].getVariableType())) {
                try {
                    // we need PostProcessOutputInfo
                    exportServiceImpl.fireExportProgress(jobID, vcdID, "Read PostProcess", 0.0);
                    dataProcessingOutputInfo = (DataProcessingOutputInfo) dataServerImpl.doDataOperation(user, new DataOperation.DataProcessingOutputInfoOP(vcdID, false, outputContext));
                    break;
                } catch (Exception e) {
                    throw new DataAccessException("Export variable '" + variableSpecs.getVariableNames()[j] + "' is PostProcessing type.  Error reading PostProcessing data: " + e.getClass().getName() + " " + e.getMessage());
                }
            }
        }
    }
    long lastUpdateTime = 0;
    switch(rasterSpecs.getFormat()) {
        case NRRD_SINGLE:
            {
                switch(geometrySpecs.getModeID()) {
                    case GEOMETRY_FULL:
                        {
                            NrrdInfo nrrdInfo = NRRDHelper.getSizeCheckedNrrdHelper(variableSpecs, mesh.getISize(), mesh.getExtent(), dataProcessingOutputInfo).createSingleFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs, rasterSpecs, timeSpecs2);
                            int progressIndex = 1;
                            int progressEnd = variableSpecs.getVariableNames().length * (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                    lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-snglfull", jobID, vcdID, progressIndex, progressEnd);
                                    progressIndex++;
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    NRRDHelper.appendDoubleData(nrrdInfo, fileDataContainerManager, data, variableSpecs.getVariableNames()[i]);
                                }
                            }
                            nrrdInfo = NrrdWriter.writeNRRD(nrrdInfo, fileDataContainerManager);
                            return new NrrdInfo[] { nrrdInfo };
                        }
                    case GEOMETRY_SLICE:
                        {
                            NrrdInfo sliceNrrdInfo = createSliceNrrdHelper(mesh, dataProcessingOutputInfo, vcdID, variableSpecs, timeSpecs2, geometrySpecs, rasterSpecs, fileDataContainerManager).createSingleFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs, rasterSpecs, timeSpecs2);
                            int progressIndex = 1;
                            int progressEnd = variableSpecs.getVariableNames().length * (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                    lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-snglslice", jobID, vcdID, progressIndex, progressEnd);
                                    progressIndex++;
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    appendSlice(variableSpecs.getVariableNames()[i], data, sliceNrrdInfo, mesh, geometrySpecs, fileDataContainerManager);
                                }
                            }
                            sliceNrrdInfo = NrrdWriter.writeNRRD(sliceNrrdInfo, fileDataContainerManager);
                            return new NrrdInfo[] { sliceNrrdInfo };
                        }
                    default:
                        {
                            throw new DataAccessException("NRRD export from slice not yet supported");
                        }
                }
            }
        case NRRD_BY_TIME:
            {
                switch(geometrySpecs.getModeID()) {
                    case GEOMETRY_FULL:
                        {
                            NRRDHelper nrrdHelper = NRRDHelper.getSizeCheckedNrrdHelper(variableSpecs, mesh.getISize(), mesh.getExtent(), dataProcessingOutputInfo);
                            Vector<NrrdInfo> nrrdinfoV = new Vector<NrrdInfo>();
                            int progressIndex = 1;
                            int progressEnd = (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-timefull", jobID, vcdID, progressIndex, progressEnd);
                                progressIndex++;
                                NrrdInfo nrrdInfo = nrrdHelper.createTimeFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs, timeSpecs2.getAllTimes()[j], rasterSpecs);
                                nrrdinfoV.add(nrrdInfo);
                                for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    NRRDHelper.appendDoubleData(nrrdInfo, fileDataContainerManager, data, variableSpecs.getVariableNames()[i]);
                                }
                                NrrdWriter.writeNRRD(nrrdInfo, fileDataContainerManager);
                            }
                            if (nrrdinfoV.size() > 0) {
                                NrrdInfo[] nrrdinfoArr = new NrrdInfo[nrrdinfoV.size()];
                                nrrdinfoV.copyInto(nrrdinfoArr);
                                return nrrdinfoArr;
                            }
                            return null;
                        }
                    case GEOMETRY_SLICE:
                        {
                            Vector<NrrdInfo> nrrdinfoV = new Vector<NrrdInfo>();
                            int progressIndex = 1;
                            int progressEnd = (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-timeslice", jobID, vcdID, progressIndex, progressEnd);
                                progressIndex++;
                                NrrdInfo sliceNrrdInfo = createSliceNrrdHelper(mesh, dataProcessingOutputInfo, vcdID, variableSpecs, timeSpecs2, geometrySpecs, rasterSpecs, fileDataContainerManager).createTimeFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs, timeSpecs2.getAllTimes()[j], rasterSpecs);
                                nrrdinfoV.add(sliceNrrdInfo);
                                for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    appendSlice(variableSpecs.getVariableNames()[i], data, sliceNrrdInfo, mesh, geometrySpecs, fileDataContainerManager);
                                }
                                NrrdWriter.writeNRRD(sliceNrrdInfo, fileDataContainerManager);
                            }
                            if (nrrdinfoV.size() > 0) {
                                NrrdInfo[] nrrdinfoArr = new NrrdInfo[nrrdinfoV.size()];
                                nrrdinfoV.copyInto(nrrdinfoArr);
                                return nrrdinfoArr;
                            }
                            return null;
                        }
                    default:
                        {
                            throw new DataAccessException("NRRD export from slice not yet supported");
                        }
                }
            }
        case NRRD_BY_VARIABLE:
            {
                switch(geometrySpecs.getModeID()) {
                    case GEOMETRY_FULL:
                        {
                            Vector<NrrdInfo> nrrdinfoV = new Vector<NrrdInfo>();
                            int progressIndex = 1;
                            int progressEnd = variableSpecs.getVariableNames().length * (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                NRRDHelper nrrdhelHelper = new NRRDHelper(variableSpecs.getVariableNames()[i], mesh.getISize(), mesh.getExtent(), dataProcessingOutputInfo);
                                NrrdInfo nrrdInfo = nrrdhelHelper.createVariableFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2, rasterSpecs);
                                nrrdinfoV.add(nrrdInfo);
                                for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                    lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-varsfull", jobID, vcdID, progressIndex, progressEnd);
                                    progressIndex++;
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    NRRDHelper.appendDoubleData(nrrdInfo, fileDataContainerManager, data, variableSpecs.getVariableNames()[i]);
                                }
                                nrrdInfo = NrrdWriter.writeNRRD(nrrdInfo, fileDataContainerManager);
                            }
                            if (nrrdinfoV.size() > 0) {
                                NrrdInfo[] nrrdinfoArr = new NrrdInfo[nrrdinfoV.size()];
                                nrrdinfoV.copyInto(nrrdinfoArr);
                                return nrrdinfoArr;
                            }
                            return null;
                        }
                    case GEOMETRY_SLICE:
                        {
                            Vector<NrrdInfo> nrrdinfoV = new Vector<NrrdInfo>();
                            int progressIndex = 1;
                            int progressEnd = variableSpecs.getVariableNames().length * (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                NrrdInfo sliceNrrdInfo = createSliceNrrdHelper(mesh, dataProcessingOutputInfo, vcdID, variableSpecs, timeSpecs2, geometrySpecs, rasterSpecs, fileDataContainerManager).createVariableFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2, rasterSpecs);
                                nrrdinfoV.add(sliceNrrdInfo);
                                for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                    lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-varsfull", jobID, vcdID, progressIndex, progressEnd);
                                    progressIndex++;
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    appendSlice(variableSpecs.getVariableNames()[i], data, sliceNrrdInfo, mesh, geometrySpecs, fileDataContainerManager);
                                }
                                NrrdWriter.writeNRRD(sliceNrrdInfo, fileDataContainerManager);
                            }
                            if (nrrdinfoV.size() > 0) {
                                NrrdInfo[] nrrdinfoArr = new NrrdInfo[nrrdinfoV.size()];
                                nrrdinfoV.copyInto(nrrdinfoArr);
                                return nrrdinfoArr;
                            }
                            return null;
                        }
                    default:
                        {
                            throw new DataAccessException("NRRD export from slice not yet supported");
                        }
                }
            }
        default:
            {
                throw new DataAccessException("Multiple NRRD file export not yet supported");
            }
    }
}

Example 15 with VCDataIdentifier

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

the class RasterExporter method makeVTKImageData.

public ExportOutput[] makeVTKImageData(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);
    Vector<ExportOutput> exportOutV = new Vector<ExportOutput>();
    for (int j = timeSpecs.getBeginTimeIndex(); j <= timeSpecs.getEndTimeIndex(); j++) {
        exportServiceImpl.fireExportProgress(jobRequest.getJobID(), vcdID, "VTKIMG", (double) (j - timeSpecs.getBeginTimeIndex()) / (double) (timeSpecs.getEndTimeIndex() - timeSpecs.getBeginTimeIndex() + 1));
        StringBuffer sb = new StringBuffer();
        sb.append("# vtk DataFile Version 2.0" + "\n");
        sb.append("Simulation " + vcdID.toString() + "\n");
        sb.append("ASCII" + "\n");
        sb.append("DATASET STRUCTURED_POINTS" + "\n");
        sb.append("DIMENSIONS " + mesh.getSizeX() + " " + mesh.getSizeY() + " " + mesh.getSizeZ() + "\n");
        sb.append("SPACING " + mesh.getExtent().getX() + " " + mesh.getExtent().getY() + " " + mesh.getExtent().getZ() + "\n");
        sb.append("ORIGIN " + mesh.getOrigin().getX() + " " + mesh.getOrigin().getY() + " " + mesh.getOrigin().getZ() + "\n");
        sb.append("POINT_DATA " + mesh.getNumVolumeElements() + "\n");
        // write volume region ids
        sb.append("SCALARS " + "regionID" + " double 1" + "\n");
        sb.append("LOOKUP_TABLE default" + "\n");
        int yzSize = mesh.getSizeY() * mesh.getSizeZ();
        int index = 0;
        for (int yz = 0; yz < yzSize; yz++) {
            for (int x = 0; x < mesh.getSizeX(); x++) {
                sb.append((x != 0 ? " " : "") + mesh.getVolumeRegionIndex(index));
                index++;
            }
            sb.append("\n");
        }
        sb.append("\n");
        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)) {
                sb.append("SCALARS " + variableSpecs.getVariableNames()[k] + " double 1" + "\n");
                sb.append("LOOKUP_TABLE default" + "\n");
                double[] volumeData = simDataBlock.getData();
                index = 0;
                for (int yz = 0; yz < yzSize; yz++) {
                    for (int x = 0; x < mesh.getSizeX(); x++) {
                        sb.append((x != 0 ? " " : "") + volumeData[index]);
                        index++;
                    }
                    sb.append("\n");
                }
                ExportOutput exportOut = new ExportOutput(true, ".vtk", simID.toString(), "_vol_" + j, fileDataContainerManager);
                fileDataContainerManager.append(exportOut.getFileDataContainerID(), sb.toString());
                exportOutV.add(exportOut);
            } else {
                throw new RuntimeException("VTK Image format only for volume data");
            }
        }
    }
    ExportOutput[] exportOutputArr = exportOutV.toArray(new ExportOutput[0]);
    return exportOutputArr;
}