Examples with NrrdInfo cbit.vcell.export.nrrd.NrrdInfo used on opensource projects

Example 1 with NrrdInfo

use of cbit.vcell.export.nrrd.NrrdInfo 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 2 with NrrdInfo

use of cbit.vcell.export.nrrd.NrrdInfo in project vcell by virtualcell.

the class ImageJHelper method vcellWantImage0.

private static File vcellWantImage0(ClientTaskStatusSupport clientTaskStatusSupport, String description, ImageJConnection imageJConnection) throws Exception {
    if (clientTaskStatusSupport != null) {
        clientTaskStatusSupport.setMessage("Waiting for ImageJ to send image...");
    }
    // Create nrrd file from socket input
    // integer (dimensions)
    imageJConnection.dis.readInt();
    // get size of the standard 5 dimensions in this order (width, height, nChannels, nSlices, nFrames)
    int xsize = imageJConnection.dis.readInt();
    int ysize = imageJConnection.dis.readInt();
    imageJConnection.dis.readInt();
    imageJConnection.dis.readInt();
    imageJConnection.dis.readInt();
    // read data
    int slices = imageJConnection.dis.readInt();
    byte[] data = new byte[slices * xsize * ysize * Double.BYTES];
    ByteBuffer byteBuffer = ByteBuffer.wrap(data);
    for (int i = 0; i < slices; i++) {
        if (clientTaskStatusSupport != null) {
            clientTaskStatusSupport.setMessage("Reading Fiji/ImageJ slice " + (i + 1) + " of " + slices + "...");
            if (clientTaskStatusSupport.isInterrupted()) {
                throw UserCancelException.CANCEL_GENERIC;
            }
        }
        String arraytype = imageJConnection.dis.readUTF();
        int arrLength = imageJConnection.dis.readInt();
        if (arraytype.equals(byte[].class.getName())) {
            // byte array
            byte[] bytes = new byte[arrLength];
            int numread = 0;
            while (numread != bytes.length) {
                numread += imageJConnection.dis.read(bytes, numread, bytes.length - numread);
            }
            for (int j = 0; j < bytes.length; j++) {
                byteBuffer.putDouble((double) Byte.toUnsignedInt(bytes[j]));
            }
            System.out.println("bytesRead=" + numread);
        } else if (arraytype.equals(short[].class.getName())) {
            // short array
            short[] shorts = new short[arrLength];
            for (int j = 0; j < shorts.length; j++) {
                shorts[j] = imageJConnection.dis.readShort();
                byteBuffer.putDouble((double) Short.toUnsignedInt(shorts[j]));
            }
            System.out.println("shortsRead=" + shorts.length);
        }
    }
    if (clientTaskStatusSupport != null) {
        clientTaskStatusSupport.setMessage("Converting slices to file...");
        if (clientTaskStatusSupport.isInterrupted()) {
            throw UserCancelException.CANCEL_GENERIC;
        }
    }
    NrrdInfo nrrdInfo = NrrdInfo.createBasicNrrdInfo(5, new int[] { xsize, ysize, slices, 1, 1 }, "double", "raw", NrrdInfo.createXYZTVMap());
    FileDataContainerManager fileDataContainerManager = new FileDataContainerManager();
    nrrdInfo.setDataFileID(fileDataContainerManager.getNewFileDataContainerID());
    fileDataContainerManager.append(nrrdInfo.getDataFileID(), byteBuffer.array());
    NrrdWriter.writeNRRD(nrrdInfo, fileDataContainerManager);
    File tempFile = File.createTempFile("fijinrrd", ".nrrd");
    fileDataContainerManager.writeAndFlush(nrrdInfo.getHeaderFileID(), new FileOutputStream(tempFile));
    if (clientTaskStatusSupport != null) {
        clientTaskStatusSupport.setMessage("Finished ImageJ data conversion...");
        if (clientTaskStatusSupport.isInterrupted()) {
            throw UserCancelException.CANCEL_GENERIC;
        }
    }
    return tempFile;
}

Example 3 with NrrdInfo

use of cbit.vcell.export.nrrd.NrrdInfo in project vcell by virtualcell.

the class ExportServiceImpl method makeRemoteFile.

public ExportEvent makeRemoteFile(OutputContext outputContext, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, boolean bSaveAsZip, ClientTaskStatusSupport clientTaskStatusSupport) throws DataAccessException {
    // if export completes successfully, we return the generated event for logging
    if (user == null) {
        throw new DataAccessException("ERROR: user is null");
    }
    JobRequest newExportJob = JobRequest.createExportJobRequest(user);
    jobRequestIDs.put(new Long(newExportJob.getJobID()), user);
    if (lg.isTraceEnabled())
        lg.trace("ExportServiceImpl.makeRemoteFile(): " + newExportJob + ", " + exportSpecs);
    String fileFormat = null;
    switch(exportSpecs.getFormat()) {
        case CSV:
            fileFormat = "CSV";
            break;
        case QUICKTIME:
            fileFormat = "MOV";
            break;
        case GIF:
        case ANIMATED_GIF:
            fileFormat = "GIF";
            break;
        case FORMAT_JPEG:
            fileFormat = "JPEG";
            break;
        case NRRD:
            fileFormat = "NRRD";
            break;
        case IMAGEJ:
            fileFormat = "IMAGEJ";
            break;
    }
    fireExportStarted(newExportJob.getJobID(), exportSpecs.getVCDataIdentifier(), fileFormat);
    try {
        String exportBaseURL = PropertyLoader.getRequiredProperty(PropertyLoader.exportBaseURLProperty);
        String exportBaseDir = PropertyLoader.getRequiredProperty(PropertyLoader.exportBaseDirInternalProperty);
        // we need to make new output
        if (lg.isTraceEnabled())
            lg.trace("ExportServiceImpl.makeRemoteFile(): Starting new export job: " + newExportJob);
        FileDataContainerManager fileDataContainerManager = new FileDataContainerManager();
        try {
            ExportOutput[] exportOutputs = null;
            switch(exportSpecs.getFormat()) {
                case CSV:
                    Collection<ExportOutput> asciiOut = asciiExporter.makeASCIIData(outputContext, newExportJob, user, dataServerImpl, exportSpecs, fileDataContainerManager);
                    exportOutputs = asciiOut.toArray(new ExportOutput[asciiOut.size()]);
                    return makeRemoteFile(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob, fileDataContainerManager);
                case QUICKTIME:
                case GIF:
                case FORMAT_JPEG:
                case ANIMATED_GIF:
                    exportOutputs = imgExporter.makeMediaData(outputContext, newExportJob, user, dataServerImpl, exportSpecs, clientTaskStatusSupport, fileDataContainerManager);
                    boolean bOverrideZip = exportOutputs.length == 1;
                    if (bSaveAsZip && !bOverrideZip) {
                        return makeRemoteFile(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob, fileDataContainerManager);
                    } else {
                        return makeRemoteFile_Unzipped(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob, fileDataContainerManager);
                    }
                case NRRD:
                case IMAGEJ:
                    NrrdInfo[] nrrdInfos = rrExporter.makeRasterData(outputContext, newExportJob, user, dataServerImpl, exportSpecs, fileDataContainerManager);
                    return makeRemoteFile(fileFormat, exportBaseDir, exportBaseURL, nrrdInfos, exportSpecs, newExportJob, fileDataContainerManager);
                case UCD:
                    exportOutputs = rrExporter.makeUCDData(outputContext, newExportJob, user, dataServerImpl, exportSpecs, fileDataContainerManager);
                    return makeRemoteFile(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob, fileDataContainerManager);
                case PLY:
                    exportOutputs = rrExporter.makePLYWithTexData(outputContext, newExportJob, user, dataServerImpl, exportSpecs, fileDataContainerManager);
                    return makeRemoteFile(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob, fileDataContainerManager);
                case VTK_IMAGE:
                    exportOutputs = rrExporter.makeVTKImageData(outputContext, newExportJob, user, dataServerImpl, exportSpecs, fileDataContainerManager);
                    return makeRemoteFile(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob, fileDataContainerManager);
                case VTK_UNSTRUCT:
                    exportOutputs = rrExporter.makeVTKUnstructuredData0(outputContext, newExportJob, user, dataServerImpl, exportSpecs, fileDataContainerManager);
                    return makeRemoteFile(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob, fileDataContainerManager);
                default:
                    throw new DataAccessException("Unknown export format requested");
            }
        } finally {
            fileDataContainerManager.closeAllAndDelete();
        }
    } catch (UserCancelException ex) {
        throw ex;
    } catch (Throwable exc) {
        lg.error(exc.getMessage(), exc);
        fireExportFailed(newExportJob.getJobID(), exportSpecs.getVCDataIdentifier(), fileFormat, exc.getMessage());
        throw new DataAccessException(exc.getMessage());
    }
}