Examples with Dataset ncsa.hdf.object.Dataset used on opensource projects

Example 11 with Dataset

use of ncsa.hdf.object.Dataset in project vcell by virtualcell.

the class DataSetControllerImpl method iterateHDF5.

private static void iterateHDF5(HObject hObject, String indent, DataProcessingHelper dataProcessingHelper) throws Exception {
    if (hObject instanceof Group) {
        Group group = ((Group) hObject);
        printInfo(group, indent);
        if (group.getName().equals("/") || group.getName().equals(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_POSTPROCESSING)) {
            List<HObject> postProcessMembers = ((Group) hObject).getMemberList();
            for (HObject nextHObject : postProcessMembers) {
                iterateHDF5(nextHObject, indent + " ", dataProcessingHelper);
            }
        } else if (group.getName().equals(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_VARIABLESTATISTICS) && dataProcessingHelper.isInfoOnly()) {
            populateStatNamesAndUnits(hObject, dataProcessingHelper);
            List<HObject> statDataAtEachTime = group.getMemberList();
            dataProcessingHelper.statValues = new double[dataProcessingHelper.statVarNames.length][statDataAtEachTime.size()];
            for (HObject nextStatData : statDataAtEachTime) {
                printInfo(nextStatData, indent + " ");
                // always get stats data when ask for info
                processDims(nextStatData, dataProcessingHelper, false);
                double[] stats = (double[]) dataProcessingHelper.tempData;
                int timeIndex = Integer.parseInt(nextStatData.getName().substring("time".length()));
                for (int j = 0; j < stats.length; j++) {
                    dataProcessingHelper.statValues[j][timeIndex] = stats[j];
                }
            }
        } else {
            // must be image data
            if (dataProcessingHelper.isInfoOnly()) {
                dataProcessingHelper.imageNames = new ArrayList<String>();
                dataProcessingHelper.imageISize = new ArrayList<ISize>();
                dataProcessingHelper.imageOrigin = new ArrayList<Origin>();
                dataProcessingHelper.imageExtent = new ArrayList<Extent>();
                Origin imgDataOrigin;
                Extent imgDataExtent;
                HashMap<String, String> attrHashMap = getHDF5Attributes(group);
                if (attrHashMap.size() == 2) {
                    imgDataOrigin = new Origin(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINX)), 0, 0);
                    // this is 1D, however the extentY, Z cannot take 0
                    imgDataExtent = new Extent(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTX)), 1, 1);
                } else if (attrHashMap.size() == 4) {
                    imgDataOrigin = new Origin(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINX)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINY)), 0);
                    // this is 2D, however the extentZ cannot take 0
                    imgDataExtent = new Extent(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTX)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTY)), 1);
                } else if (attrHashMap.size() == 6) {
                    imgDataOrigin = new Origin(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINX)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINY)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINZ)));
                    imgDataExtent = new Extent(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTX)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTY)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTZ)));
                } else {
                    throw new Exception("Unexpected number of origin/extent values");
                }
                dataProcessingHelper.imageNames.add(hObject.getName());
                dataProcessingHelper.imageOrigin.add(imgDataOrigin);
                dataProcessingHelper.imageExtent.add(imgDataExtent);
                // get ISize
                processDims((H5ScalarDS) (((Group) hObject).getMemberList()).get(0), dataProcessingHelper, true);
                long[] dims = dataProcessingHelper.tempDims;
                ISize isize = new ISize((int) dims[0], (int) (dims.length > 1 ? dims[1] : 1), (int) (dims.length > 2 ? dims[2] : 1));
                dataProcessingHelper.imageISize.add(isize);
            } else {
                int currentVarNameIndex = -1;
                for (int i = 0; i < dataProcessingHelper.specificVarNames.length; i++) {
                    if (group.getName().equals(dataProcessingHelper.specificVarNames[i])) {
                        currentVarNameIndex = i;
                        break;
                    }
                }
                if (currentVarNameIndex == -1) {
                    // skip this group
                    return;
                }
                dataProcessingHelper.specificDataValues[currentVarNameIndex] = new double[(dataProcessingHelper.specificTimePointHelper.isAllTimePoints() ? dataProcessingHelper.times.length : dataProcessingHelper.specificTimePointHelper.getTimePoints().length)][];
                List<HObject> imageDataAtEachTime = ((Group) hObject).getMemberList();
                int foundTimePointIndex = 0;
                for (HObject nextImageData : imageDataAtEachTime) {
                    // if(dataProcessingHelper.isInfoOnly()){
                    // printInfo(nextImageData,indent+" ");
                    // processDims(nextImageData, dataProcessingHelper,true);
                    // long[] dims = dataProcessingHelper.tempDims;
                    // ISize isize = new ISize((int)dims[0], (int)(dims.length>1?dims[1]:1), (int)(dims.length>2?dims[2]:1));
                    // dataProcessingHelper.imageISize.add(isize);
                    // break;//only need 1st one for info
                    // }else{
                    int hdf5GroupTimeIndex = Integer.parseInt(nextImageData.getName().substring(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_TIMEPREFIX.length()));
                    if (dataProcessingHelper.specificTimePointHelper.isAllTimePoints() || dataProcessingHelper.specificTimePointHelper.getTimePoints()[foundTimePointIndex] == dataProcessingHelper.times[hdf5GroupTimeIndex]) {
                        int timeIndex = (dataProcessingHelper.specificTimePointHelper.isAllTimePoints() ? hdf5GroupTimeIndex : foundTimePointIndex);
                        processDims(nextImageData, dataProcessingHelper, false);
                        long[] dims = dataProcessingHelper.tempDims;
                        ISize isize = new ISize((int) dims[0], (int) (dims.length > 1 ? dims[1] : 1), (int) (dims.length > 2 ? dims[2] : 1));
                        if (dataProcessingHelper.specificDataIndexHelper.isAllDataIndexes()) {
                            dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex] = (double[]) dataProcessingHelper.tempData;
                        } else if (dataProcessingHelper.specificDataIndexHelper.isSingleSlice()) {
                            dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex] = new double[isize.getX() * isize.getY()];
                            System.arraycopy((double[]) dataProcessingHelper.tempData, dataProcessingHelper.specificDataIndexHelper.getSliceIndex() * (isize.getX() * isize.getY()), dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex], 0, isize.getX() * isize.getY());
                        } else {
                            dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex] = new double[dataProcessingHelper.specificDataIndexHelper.getDataIndexes().length];
                            for (int i = 0; i < dataProcessingHelper.specificDataIndexHelper.getDataIndexes().length; i++) {
                                dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex][i] = ((double[]) dataProcessingHelper.tempData)[dataProcessingHelper.specificDataIndexHelper.getDataIndexes()[i]];
                            }
                        }
                        foundTimePointIndex++;
                        if (!dataProcessingHelper.specificTimePointHelper.isAllTimePoints() && foundTimePointIndex == dataProcessingHelper.specificTimePointHelper.getTimePoints().length) {
                            // break out after we get our data
                            break;
                        }
                    }
                // }
                }
            }
        }
    } else if (hObject instanceof Dataset) {
        Dataset dataset = (Dataset) hObject;
        printInfo(dataset, indent);
        if (dataset.getName().equals(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_TIMES)) {
            processDims(hObject, dataProcessingHelper, false);
            dataProcessingHelper.times = (double[]) dataProcessingHelper.tempData;
        }
    } else if (hObject instanceof Datatype) {
        printInfo(hObject, indent);
    } else {
        printInfo(hObject, indent);
    }
}

Example 12 with Dataset

use of ncsa.hdf.object.Dataset in project vcell by virtualcell.

the class SimDataReader method getNextDataAtCurrentTimeChombo.

private void getNextDataAtCurrentTimeChombo(double[][] returnValues) throws Exception {
    if (zipFilenNames == null || zipFilenNames[masterTimeIndex] == null) {
        return;
    }
    if (currentZipFile == null || !currentZipFileName.equals(zipFilenNames[masterTimeIndex])) {
        close();
        currentZipFile = new ZipFile(zipFilenNames[masterTimeIndex]);
        currentZipFileName = zipFilenNames[masterTimeIndex];
    }
    File tempFile = null;
    FileFormat solFile = null;
    try {
        tempFile = DataSet.createTempHdf5File(currentZipFile, simDataFileNames[masterTimeIndex]);
        FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
        solFile = fileFormat.createInstance(tempFile.getAbsolutePath(), FileFormat.READ);
        solFile.open();
        for (int k = 0; k < varNames.length; ++k) {
            try {
                boolean bExtrapolatedValue = false;
                String varName = varNames[k];
                if (varName.endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
                    bExtrapolatedValue = true;
                    varName = varName.substring(0, varName.lastIndexOf(InsideVariable.INSIDE_VARIABLE_SUFFIX));
                } else if (varName.endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
                    bExtrapolatedValue = true;
                    varName = varName.substring(0, varName.lastIndexOf(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX));
                }
                double[] sol = null;
                if (bExtrapolatedValue) {
                    sol = DataSet.readChomboExtrapolatedValues(varName, solFile);
                } else {
                    String varPath = Hdf5Utils.getVarSolutionPath(varNames[k]);
                    HObject solObj = FileFormat.findObject(solFile, varPath);
                    if (solObj instanceof Dataset) {
                        Dataset dataset = (Dataset) solObj;
                        sol = (double[]) dataset.read();
                    }
                }
                if (sol != null) {
                    for (int l = 0; l < varIndexes[k].length; ++l) {
                        int idx = varIndexes[k][l];
                        double val = sol[idx];
                        returnValues[k][l] = val;
                    }
                }
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new DataAccessException(e.getMessage(), e);
            }
        }
    } finally {
        try {
            if (solFile != null) {
                solFile.close();
            }
            if (tempFile != null) {
                if (!tempFile.delete()) {
                    System.err.println("couldn't delete temp file " + tempFile.getAbsolutePath());
                }
            }
        } catch (Exception e) {
        // ignore
        }
    }
    ++masterTimeIndex;
    if (masterTimeIndex >= times.length) {
        close();
    }
}

Example 13 with Dataset

use of ncsa.hdf.object.Dataset in project vcell by virtualcell.

the class SimulationDataSpatialHdf5 method retrieveSimDataSet.

public SimDataSet retrieveSimDataSet(double time, String varName) throws Exception {
    File tempFile = getTempSimHdf5File(time);
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    FileFormat solFile = fileFormat.createInstance(tempFile.getAbsolutePath(), FileFormat.READ);
    solFile.open();
    DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) solFile.getRootNode();
    Group rootGroup = (Group) rootNode.getUserObject();
    Group solGroup = (Group) rootGroup.getMemberList().get(0);
    SimDataSet simDataSet = new SimDataSet();
    List<HObject> memberList = solGroup.getMemberList();
    for (HObject member : memberList) {
        if (!(member instanceof Dataset)) {
            continue;
        }
        Dataset dataset = (Dataset) member;
        String dsname = dataset.getName();
        if (!dsname.equals(varName)) {
            continue;
        }
        simDataSet.solValues = (double[]) dataset.read();
        List<Attribute> attrList = dataset.getMetadata();
        for (Attribute attr : attrList) {
            String attrName = attr.getName();
            Object val = attr.getValue();
            double dval = 0;
            if (val instanceof double[]) {
                dval = ((double[]) val)[0];
            }
            if (attrName.equals(SOLUTION_DATASET_ATTR_MAX_ERROR)) {
                simDataSet.maxError = dval;
            } else if (attrName.equals(SOLUTION_DATASET_ATTR_MEAN)) {
                simDataSet.mean = dval;
            } else if (attrName.equals(SOLUTION_DATASET_ATTR_RELATIVE_L2ERROR)) {
                simDataSet.l2Error = dval;
            } else if (attrName.equals(SOLUTION_DATASET_ATTR_SUM_VOLFRAC)) {
                simDataSet.sumVolFrac = dval;
            }
        }
        break;
    }
    return simDataSet;
}

Example 14 with Dataset

use of ncsa.hdf.object.Dataset in project vcell by virtualcell.

the class SimulationDataSpatialHdf5 method readMeshFile.

public static ChomboMesh readMeshFile(File chomboMeshFile) throws Exception {
    // if (chomboMesh != null)
    // {
    // return;
    // }
    ChomboMesh chomboMesh = new ChomboMesh();
    // File mfile = new File(userDirectory, getMeshFileName());
    if (H5.H5open() < 0) {
        throw new Exception("H5.H5open() failed");
    }
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    if (fileFormat == null) {
        throw new Exception("FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5) failed, returned null.");
    }
    FileFormat meshFile = fileFormat.createInstance(chomboMeshFile.getAbsolutePath(), FileFormat.READ);
    meshFile.open();
    DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) meshFile.getRootNode();
    Group rootGroup = (Group) rootNode.getUserObject();
    Group meshGroup = (Group) rootGroup.getMemberList().get(0);
    List<Attribute> meshAttrList = meshGroup.getMetadata();
    for (Attribute attr : meshAttrList) {
        String attrName = attr.getName();
        Object value = attr.getValue();
        if (attrName.equals(MESH_ATTR_DIMENSION)) {
            chomboMesh.dimension = ((int[]) value)[0];
        } else {
            String[] valueStrArray = (String[]) value;
            String value0 = valueStrArray[0];
            StringTokenizer st = new StringTokenizer(value0, "{,} ");
            List<Double> valueList = new ArrayList<Double>();
            while (st.hasMoreTokens()) {
                String token = st.nextToken();
                valueList.add(Double.parseDouble(token));
            }
            if (attrName.equals(MESH_ATTR_DX)) {
                for (int i = 0; i < valueList.size(); ++i) {
                    chomboMesh.dx[i] = valueList.get(i);
                }
            } else if (attrName.equals(MESH_ATTR_EXTENT)) {
                for (int i = 0; i < valueList.size(); ++i) {
                    chomboMesh.extent[i] = valueList.get(i);
                }
            } else if (attrName.equals(MESH_ATTR_NX)) {
                for (int i = 0; i < valueList.size(); ++i) {
                    chomboMesh.nx[i] = valueList.get(i).intValue();
                }
            } else if (attrName.equals(MESH_ATTR_ORIGIN)) {
                for (int i = 0; i < valueList.size(); ++i) {
                    chomboMesh.origin[i] = valueList.get(i);
                }
            }
        }
    }
    List<HObject> memberList = meshGroup.getMemberList();
    for (HObject member : memberList) {
        if (member instanceof Dataset) {
            Dataset dataset = (Dataset) member;
            Vector vectValues = (Vector) dataset.read();
            String name = dataset.getName();
            if (name.equals(BOXES_DATASET)) {
            // not needed right now
            } else if (name.equals(METRICS_DATASET)) {
                H5CompoundDS compoundDataSet = (H5CompoundDS) dataset;
                chomboMesh.metricsColumnNames = compoundDataSet.getMemberNames();
                int c = -1;
                int[] index = (int[]) vectValues.get(++c);
                int[] i = (int[]) vectValues.get(++c);
                int[] j = (int[]) vectValues.get(++c);
                int[] k = null;
                if (chomboMesh.dimension == 3) {
                    k = (int[]) vectValues.get(++c);
                }
                double[] x = (double[]) vectValues.get(++c);
                double[] y = (double[]) vectValues.get(++c);
                double[] z = null;
                if (chomboMesh.dimension == 3) {
                    z = (double[]) vectValues.get(++c);
                }
                double[] normalx = (double[]) vectValues.get(++c);
                double[] normaly = (double[]) vectValues.get(++c);
                double[] normalz = null;
                if (chomboMesh.dimension == 3) {
                    normalz = (double[]) vectValues.get(++c);
                }
                double[] volFrac = (double[]) vectValues.get(++c);
                double[] areaFrac = (double[]) vectValues.get(++c);
                for (int n = 0; n < index.length; ++n) {
                    ChomboMeshMetricsEntry entry = new ChomboMeshMetricsEntry(index[n], i[n], j[n], k == null ? 0 : k[n], x[n], y[n], z == null ? 0 : z[n], normalx[n], normaly[n], normalz == null ? 0 : normalz[n], volFrac[n], areaFrac[n]);
                    chomboMesh.metrics.add(entry);
                }
            } else if (name.equals(SURFACE_DATASET)) {
            // not needed right now
            } else if (name.equals(SLICE_VIEW_DATASET)) {
            // not needed right now
            }
        }
    }
    return chomboMesh;
}

Example 15 with Dataset

use of ncsa.hdf.object.Dataset in project vcell by virtualcell.

the class H5FileStructure method printGroup.

/**
 * Recursively print a group and its members.
 *
 * @throws Exception
 */
private static void printGroup(Group g, String indent) throws Exception {
    if (g == null)
        return;
    java.util.List members = g.getMemberList();
    int n = members.size();
    indent += "    ";
    HObject obj = null;
    for (int i = 0; i < n; i++) {
        obj = (HObject) members.get(i);
        System.out.println(indent + obj);
        if (obj instanceof Group) {
            printGroup((Group) obj, indent);
        }
        Dataset ds = BeanUtils.downcast(Dataset.class, obj);
        if (ds != null && ds.getName().equals("elements")) {
            // if (ds != null && ds.getName().equals("boundaries")) {
            VH5Dataset vds = new VH5Dataset(ds);
            vds.info();
            vds.meta();
        }
    }
}