Examples with HDF5Exception ncsa.hdf.hdf5lib.exceptions.HDF5Exception used on opensource projects

Example 1 with HDF5Exception

use of ncsa.hdf.hdf5lib.exceptions.HDF5Exception in project vcell by virtualcell.

the class VH5Path method walk.

/**
 * find next object in sequence
 * @param hobj previous element in sequence
 * @param steps name of each step
 * @param index current step
 * @return next object path, if present
 * @throws HDF5Exception
 */
private static Object walk(Object hobj, String[] steps, int index) throws Exception {
    final boolean isLastIndex = lastIndex(index, steps);
    final String finding = steps[index];
    Group g = BeanUtils.downcast(Group.class, hobj);
    if (g != null) {
        List<HObject> ml = g.getMemberList();
        for (HObject sub : ml) {
            // String full = sub.getFullName();
            if (finding.equals(sub.getName())) {
                if (isLastIndex) {
                    return sub;
                }
                return walk(sub, steps, index + 1);
            }
        }
    }
    H5CompoundDS cds = BeanUtils.downcast(H5CompoundDS.class, hobj);
    if (cds != null) {
        cds.read();
        String[] mn = cds.getMemberNames();
        for (int i = 0; i < mn.length; i++) {
            if (finding.equals(mn[i])) {
                Object c = cds.read();
                Vector<?> vec = BeanUtils.downcast(Vector.class, c);
                if (vec != null) {
                    VCAssert.assertTrue(i < vec.size(), "Disconnect between H5CompoundDS.getMemberNames( )  and returned Vector");
                    Object child = vec.get(i);
                    if (isLastIndex) {
                        return child;
                    }
                } else {
                    throw new UnsupportedOperationException("Unsupported H5CompoundDS subtype " + className(c));
                }
            }
        }
    }
    if (isLastIndex) {
        DataFormat df = BeanUtils.downcast(DataFormat.class, hobj);
        if (df != null && df.hasAttribute()) {
            try {
                @SuppressWarnings("unchecked") List<Object> meta = df.getMetadata();
                for (Object o : meta) {
                    Attribute a = BeanUtils.downcast(Attribute.class, o);
                    if (a != null) {
                        if (finding.equals(a.getName())) {
                            return a.getValue();
                        }
                    } else {
                        lg.warn(concat(steps, finding) + " fetching metadata unexpected type " + className(o));
                    }
                }
            } catch (Exception e) {
                throw new RuntimeException(concat(steps, finding) + " fetching metadata", e);
            }
        }
    }
    return null;
}

Example 2 with HDF5Exception

use of ncsa.hdf.hdf5lib.exceptions.HDF5Exception in project vcell by virtualcell.

the class ASCIIExporter method exportPDEData.

/**
 * This method was created in VisualAge.
 * @throws IOException
 */
private List<ExportOutput> exportPDEData(OutputContext outputContext, long jobID, User user, DataServerImpl dataServerImpl, final VCDataIdentifier orig_vcdID, VariableSpecs variableSpecs, TimeSpecs timeSpecs, GeometrySpecs geometrySpecs, ASCIISpecs asciiSpecs, String contextName, FileDataContainerManager fileDataContainerManager) throws DataAccessException, IOException {
    ExportSpecs.SimNameSimDataID[] simNameSimDataIDs = asciiSpecs.getSimNameSimDataIDs();
    Vector<ExportOutput[]> exportOutputV = new Vector<ExportOutput[]>();
    double progressCounter = 0;
    final int SIM_COUNT = simNameSimDataIDs.length;
    final int PARAMSCAN_COUNT = (asciiSpecs.getExportMultipleParamScans() != null ? asciiSpecs.getExportMultipleParamScans().length : 1);
    final int endTimeIndex = timeSpecs.getEndTimeIndex();
    final int beginTimeIndex = timeSpecs.getBeginTimeIndex();
    final int TIME_COUNT = endTimeIndex - beginTimeIndex + 1;
    double TOTAL_EXPORTS_OPS = 0;
    switch(geometrySpecs.getModeID()) {
        case GEOMETRY_SELECTIONS:
            TOTAL_EXPORTS_OPS = SIM_COUNT * PARAMSCAN_COUNT * variableSpecs.getVariableNames().length * (geometrySpecs.getCurves().length + (geometrySpecs.getPointCount() > 0 ? 1 : 0));
            break;
        case GEOMETRY_SLICE:
            TOTAL_EXPORTS_OPS = SIM_COUNT * PARAMSCAN_COUNT * variableSpecs.getVariableNames().length * TIME_COUNT;
            break;
    }
    File hdf5TempFile = null;
    if (asciiSpecs.getCSVRoiLayout() == ASCIISpecs.csvRoiLayout.time_sim_var) {
        exportOutputV.add(new ExportOutput[] { sofyaFormat(outputContext, jobID, user, dataServerImpl, orig_vcdID, variableSpecs, timeSpecs, geometrySpecs, asciiSpecs, contextName, fileDataContainerManager) });
    } else {
        try {
            // Used if HDF5 format
            int hdf5FileID = -1;
            if (asciiSpecs.isHDF5()) {
                hdf5TempFile = File.createTempFile("pde", ".hdf5");
                System.out.println("======== hdf5 file location: " + hdf5TempFile.getAbsolutePath());
                hdf5FileID = H5.H5Fcreate(hdf5TempFile.getAbsolutePath(), HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
            }
            // TreeMap<VCDataIdentifier,TreeMap<String,PointsCurvesSlices>> simsVarnamesDataMap = new TreeMap<VCDataIdentifier,TreeMap<String,PointsCurvesSlices>>();
            PointsCurvesSlices[][] pointsCurvesSlices = new PointsCurvesSlices[SIM_COUNT][variableSpecs.getVariableNames().length];
            for (int i = 0; i < pointsCurvesSlices.length; i++) {
                for (int j = 0; j < pointsCurvesSlices[i].length; j++) {
                    pointsCurvesSlices[i][j] = new PointsCurvesSlices();
                }
            }
            for (int v = 0; v < SIM_COUNT; v++) {
                int simJobIndex = simNameSimDataIDs[v].getDefaultJobIndex();
                VCDataIdentifier vcdID = simNameSimDataIDs[v].getVCDataIdentifier(simJobIndex);
                // 3. simNameSimDataIDs[v].getExportParamScanInfo() != null and asciiSpecs.getExportMultipleParamScans() != null, parameter scan use simNameSimDataIDs[v].getExportParamScanInfo().getParamScanJobIndexes() loop through
                for (int ps = 0; ps < PARAMSCAN_COUNT; ps++) {
                    if (asciiSpecs.getExportMultipleParamScans() != null) {
                        simJobIndex = simNameSimDataIDs[v].getExportParamScanInfo().getParamScanJobIndexes()[asciiSpecs.getExportMultipleParamScans()[ps]];
                        vcdID = simNameSimDataIDs[v].getVCDataIdentifier(simJobIndex);
                    }
                    // Get times for each sim{paramscan} because they may be different
                    final double[] allTimes = dataServerImpl.getDataSetTimes(user, vcdID);
                    if (allTimes.length <= beginTimeIndex || allTimes.length <= endTimeIndex) {
                        throw new DataAccessException("Sim '" + simNameSimDataIDs[v].getSimulationName() + "' id=" + vcdID.getID() + " simJob=" + simJobIndex + ", time array length=" + allTimes.length + " has no endTimeIndex=" + endTimeIndex);
                    }
                    String paramScanInfo = "";
                    if (simNameSimDataIDs[v].getExportParamScanInfo() != null) {
                        for (int i = 0; i < simNameSimDataIDs[v].getExportParamScanInfo().getParamScanConstantNames().length; i++) {
                            String psName = simNameSimDataIDs[v].getExportParamScanInfo().getParamScanConstantNames()[i];
                            paramScanInfo = paramScanInfo + " '" + psName + "'=" + simNameSimDataIDs[v].getExportParamScanInfo().getParamScanConstantValues()[simJobIndex][i];
                        }
                    }
                    // Used if HDF5 format
                    int hdf5GroupID = -1;
                    if (asciiSpecs.isHDF5()) {
                        hdf5GroupID = H5.H5Gcreate(hdf5FileID, vcdID.toString(), HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
                    }
                    String simID = vcdID.getID();
                    String dataType = ".csv";
                    FileDataContainerID fileDataContainerID_header = fileDataContainerManager.getNewFileDataContainerID();
                    SimulationDescription simulationDescription = new SimulationDescription(outputContext, user, dataServerImpl, vcdID, false, null);
                    fileDataContainerManager.append(fileDataContainerID_header, "\"" + "Model: '" + contextName + "'\"\n\"Simulation: '" + simNameSimDataIDs[v].getSimulationName() + "' (" + paramScanInfo + ")\"\n" + simulationDescription.getHeader(dataType));
                    CartesianMesh mesh = dataServerImpl.getMesh(user, vcdID);
                    if (hdf5GroupID != -1) {
                        double[] subTimes = new double[endTimeIndex - beginTimeIndex + 1];
                        for (int st = beginTimeIndex; st <= endTimeIndex; st++) {
                            subTimes[st - beginTimeIndex] = allTimes[st];
                        }
                        // Hdf5Utils.writeHDF5Dataset(hdf5GroupID, PCS.TIMES.name(), new long[] {subTimes.length}, subTimes,false);
                        Hdf5Utils.insertDoubles(hdf5GroupID, PCS.TIMES.name(), new long[] { subTimes.length }, subTimes);
                        // Hdf5Utils.writeHDF5Dataset(hdf5GroupID, PCS.TIMEBOUNDS.name(), new long[] {2}, new int[] {beginTimeIndex,endTimeIndex},false);
                        Hdf5Utils.insertInts(hdf5GroupID, PCS.TIMEBOUNDS.name(), new long[] { 2 }, new int[] { beginTimeIndex, endTimeIndex });
                    }
                    switch(geometrySpecs.getModeID()) {
                        case GEOMETRY_SELECTIONS:
                            {
                                // Set mesh on SpatialSelection because mesh is transient field because it's too big for messaging
                                SpatialSelection[] spatialSelections = geometrySpecs.getSelections();
                                for (int i = 0; i < spatialSelections.length; i++) {
                                    if (spatialSelections[i].getMesh() == null) {
                                        spatialSelections[i].setMesh(mesh);
                                    } else if (!spatialSelections[i].getMesh().getISize().compareEqual(mesh.getISize()) || spatialSelections[i].getMesh().getNumMembraneElements() != mesh.getNumMembraneElements()) {
                                        // check just sizes not areas,normals,etc...
                                        // This will throw fail message
                                        spatialSelections[i].setMesh(mesh);
                                    }
                                // int hdf5DatasetID = -1;
                                // int hdf5DataspaceID = -1;
                                // if(hdf5GroupID != -1) {
                                // long[] dims = new long[spatialSelections[i].getMesh().getGeometryDimension()];
                                // String s = "";
                                // for(int j=0; j<dims.length;j++) {
                                // if(j!=0) {
                                // s+="x";
                                // }
                                // dims[j] = (j==0?spatialSelections[j].getMesh().getISize().getX():(j==1?spatialSelections[j].getMesh().getISize().getY():spatialSelections[j].getMesh().getISize().getZ()));
                                // s+=dims[j];
                                // }
                                // hdf5DataspaceID = H5.H5Screate_simple(dims.length, dims, null);
                                // hdf5DataspaceIDs.add(H5.H5Dcreate(hdf5GroupID, dims.length+"D java double "+s,HDF5Constants.H5T_NATIVE_DOUBLE, hdf5DataspaceID,HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT));
                                // }
                                }
                                Vector<ExportOutput> outputV = new Vector<ExportOutput>();
                                if (geometrySpecs.getPointCount() > 0) {
                                    // assemble single point data together (uses more compact formatting)
                                    String dataID = "_Points_vars(" + geometrySpecs.getPointCount() + ")_times(" + (endTimeIndex - beginTimeIndex + 1) + ")";
                                    // StringBuilder data1 = new StringBuilder(data.toString());
                                    ExportOutput exportOutput1 = new ExportOutput(true, dataType, simID, dataID, /* + variableSpecs.getVariableNames()[i]*/
                                    fileDataContainerManager);
                                    fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), fileDataContainerID_header);
                                    // Used if HDF5 format
                                    int hdf5GroupPointID = -1;
                                    if (asciiSpecs.isHDF5()) {
                                        hdf5GroupPointID = H5.H5Gcreate(hdf5GroupID, "Points", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
                                    }
                                    for (int varNameIndx = 0; varNameIndx < variableSpecs.getVariableNames().length; varNameIndx++) {
                                        // Used if HDF5 format
                                        int hdf5GroupVarID = -1;
                                        if (asciiSpecs.isHDF5()) {
                                            hdf5GroupVarID = H5.H5Gcreate(hdf5GroupPointID, variableSpecs.getVariableNames()[varNameIndx], HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
                                        }
                                        fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), getPointsTimeSeries(pointsCurvesSlices[v][varNameIndx], hdf5GroupVarID, outputContext, user, dataServerImpl, vcdID, variableSpecs.getVariableNames()[varNameIndx], geometrySpecs, allTimes, beginTimeIndex, endTimeIndex, asciiSpecs.getSwitchRowsColumns(), fileDataContainerManager));
                                        fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), "\n");
                                        progressCounter++;
                                        exportServiceImpl.fireExportProgress(jobID, orig_vcdID, "CSV", progressCounter / TOTAL_EXPORTS_OPS);
                                        if (hdf5GroupVarID != -1) {
                                            H5.H5Gclose(hdf5GroupVarID);
                                        }
                                    }
                                    outputV.add(exportOutput1);
                                    if (hdf5GroupPointID != -1) {
                                        H5.H5Gclose(hdf5GroupPointID);
                                    }
                                }
                                if (geometrySpecs.getCurves().length != 0) {
                                    // assemble curve (non-single point) data together
                                    String dataID = "_Curves_vars(" + (geometrySpecs.getCurves().length) + ")_times(" + (endTimeIndex - beginTimeIndex + 1) + ")";
                                    // StringBuilder data1 = new StringBuilder(data.toString());
                                    ExportOutput exportOutput1 = new ExportOutput(true, dataType, simID, dataID, /* + variableSpecs.getVariableNames()[i]*/
                                    fileDataContainerManager);
                                    fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), fileDataContainerID_header);
                                    // Used if HDF5 format
                                    int hdf5GroupPointID = -1;
                                    if (asciiSpecs.isHDF5()) {
                                        hdf5GroupPointID = H5.H5Gcreate(hdf5GroupID, "Curves", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
                                    }
                                    for (int varNameIndx = 0; varNameIndx < variableSpecs.getVariableNames().length; varNameIndx++) {
                                        // Used if HDF5 format
                                        int hdf5GroupVarID = -1;
                                        if (asciiSpecs.isHDF5()) {
                                            hdf5GroupVarID = H5.H5Gcreate(hdf5GroupPointID, variableSpecs.getVariableNames()[varNameIndx], HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
                                        }
                                        pointsCurvesSlices[v][varNameIndx].data.put(PCS.CURVES, new TreeMap<String, TreeMap<PCS, Object>>());
                                        for (int s = 0; s < geometrySpecs.getCurves().length; s++) {
                                            if (!GeometrySpecs.isSinglePoint(geometrySpecs.getCurves()[s])) {
                                                fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), getCurveTimeSeries(hdf5GroupVarID, pointsCurvesSlices[v][varNameIndx], outputContext, user, dataServerImpl, vcdID, variableSpecs.getVariableNames()[varNameIndx], geometrySpecs.getCurves()[s], allTimes, beginTimeIndex, endTimeIndex, asciiSpecs.getSwitchRowsColumns(), fileDataContainerManager));
                                                fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), "\n");
                                                progressCounter++;
                                                exportServiceImpl.fireExportProgress(jobID, orig_vcdID, "CSV", progressCounter / TOTAL_EXPORTS_OPS);
                                            }
                                        }
                                        if (hdf5GroupVarID != -1) {
                                            H5.H5Gclose(hdf5GroupVarID);
                                        }
                                    }
                                    outputV.add(exportOutput1);
                                    if (hdf5GroupPointID != -1) {
                                        H5.H5Gclose(hdf5GroupPointID);
                                    }
                                }
                                exportOutputV.add(outputV.toArray(new ExportOutput[0]));
                                break;
                            }
                        case GEOMETRY_SLICE:
                        case GEOMETRY_FULL:
                            {
                                int sliceNumber = geometrySpecs.getSliceNumber();
                                if (geometrySpecs.getModeID() == GEOMETRY_FULL) {
                                    sliceNumber = -1;
                                }
                                String dataID = "_Slice_" + Coordinate.getNormalAxisPlaneName(geometrySpecs.getAxis()) + "_" + sliceNumber + "_";
                                ExportOutput[] output = new ExportOutput[variableSpecs.getVariableNames().length * TIME_COUNT];
                                SliceHelper sliceHelper = new SliceHelper(TIME_COUNT, (hdf5GroupID != -1), Coordinate.getNormalAxisPlaneName(geometrySpecs.getAxis()), sliceNumber, asciiSpecs.getSwitchRowsColumns(), mesh);
                                for (int j = 0; j < variableSpecs.getVariableNames().length; j++) {
                                    sliceHelper.setHDF5GroupVarID(hdf5GroupID, variableSpecs.getVariableNames()[j]);
                                    for (int i = 0; i < TIME_COUNT; i++) {
                                        StringBuilder inset = new StringBuilder(Integer.toString(i + beginTimeIndex));
                                        inset.reverse();
                                        inset.append("000");
                                        inset.setLength(4);
                                        inset.reverse();
                                        String dataID1 = dataID + variableSpecs.getVariableNames()[j] + "_" + inset.toString();
                                        ExportOutput exportOutput1 = new ExportOutput(true, dataType, simID, dataID1, /* + variableSpecs.getVariableNames()[i]*/
                                        fileDataContainerManager);
                                        fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), fileDataContainerID_header);
                                        fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), getSlice(sliceHelper, mesh, allTimes, outputContext, user, dataServerImpl, vcdID, variableSpecs.getVariableNames()[j], i + beginTimeIndex, Coordinate.getNormalAxisPlaneName(geometrySpecs.getAxis()), sliceNumber, asciiSpecs.getSwitchRowsColumns(), fileDataContainerManager));
                                        output[j * TIME_COUNT + i] = exportOutput1;
                                        // if(sliceHelper.hdf5GroupVarID != -1) {
                                        // if(sliceHelper.isMembrane) {
                                        // 
                                        // }else {
                                        // //Select next section of destination to copy-to
                                        // H5.H5Sselect_hyperslab(sliceHelper.hdf5DataspaceIDValues, HDF5Constants.H5S_SELECT_SET, new long[] {0,0,i}, null, new long[] {sliceHelper.sizeXYZ[sliceHelper.outerSizeIndex],sliceHelper.sizeXYZ[sliceHelper.innerSizeIndex],1},null);
                                        // //Copy from extracted sliceData to hdf5 file dataset
                                        // H5.H5Dwrite_double(sliceHelper.hdf5DatasetIDValues, HDF5Constants.H5T_NATIVE_DOUBLE, sliceHelper.hdf5DataspaceIDSlice, sliceHelper.hdf5DataspaceIDValues, HDF5Constants.H5P_DEFAULT, sliceHelper.sliceData);
                                        // H5.H5Sselect_none(sliceHelper.hdf5DataspaceIDValues);
                                        // }
                                        // }
                                        progressCounter++;
                                        exportServiceImpl.fireExportProgress(jobID, orig_vcdID, "CSV", progressCounter / TOTAL_EXPORTS_OPS);
                                    }
                                    sliceHelper.closeHDF5GroupAndValues();
                                }
                                if (hdf5GroupID != -1) {
                                    H5.H5Sclose(sliceHelper.hdf5DataspaceIDSlice);
                                }
                                exportOutputV.add(output);
                                break;
                            }
                        default:
                            {
                                throw new DataAccessException("Unexpected geometry modeID");
                            }
                    }
                    if (hdf5GroupID != -1) {
                        H5.H5Gclose(hdf5GroupID);
                    }
                }
            }
            if (hdf5FileID != -1) {
                H5.H5Fclose(hdf5FileID);
            }
        } catch (HDF5Exception e) {
            e.printStackTrace();
            throw new DataAccessException("HDF5 error:" + e.getMessage(), e);
        }
    }
    if (asciiSpecs.isHDF5()) {
        VCDataIdentifier vcdID = simNameSimDataIDs[0].getVCDataIdentifier(0);
        final ExportOutput exportOutput = new ExportOutput(true, ".hdf5", vcdID.getID(), "" + jobID, fileDataContainerManager);
        fileDataContainerManager.append(exportOutput.getFileDataContainerID(), hdf5TempFile.getAbsolutePath());
        return Arrays.asList(new ExportOutput[] { exportOutput });
    }
    if (exportOutputV.size() == 1) {
        // geometry_slice
        return Arrays.asList(exportOutputV.elementAt(0));
    }
    // geometry_selections (all are same length as first element)
    ArrayList<ExportOutput> combinedExportOutput = new ArrayList<>();
    for (int i = 0; i < exportOutputV.elementAt(0).length; i++) {
        String DATATYPE = exportOutputV.elementAt(0)[i].getDataType();
        String DATAID = exportOutputV.elementAt(0)[i].getDataID();
        ExportOutput eo = new ExportOutput(true, DATATYPE, "MultiSimulation", DATAID, fileDataContainerManager);
        // FileDataContainer container = fileDataContainerManager.getFileDataContainer(combinedExportOutput[i].getFileDataContainerID());
        for (int j = 0; j < exportOutputV.size(); j++) {
            fileDataContainerManager.append(eo.getFileDataContainerID(), exportOutputV.elementAt(j)[i].getFileDataContainerID());
            fileDataContainerManager.append(eo.getFileDataContainerID(), "\n");
        }
        combinedExportOutput.add(eo);
    }
    return combinedExportOutput;
}