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

Example 11 with HObject

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

the class DataSetControllerImpl method printInfo.

private static void printInfo(HObject hObject, String indent) throws Exception {
    if (true) {
        return;
    }
    System.out.println(indent + hObject.getName() + ":" + hObject.getClass().getName());
    List metaDatas = hObject.getMetadata();
    for (Object metaData : metaDatas) {
        if (metaData instanceof Attribute) {
            Attribute attribute = (Attribute) metaData;
            System.out.println(indent + "metadata=" + attribute.getName() + " " + attribute.getType().getDatatypeDescription());
        } else {
            System.out.println(indent + "metadata=" + metaData.getClass().getName());
        }
    }
}

Example 12 with HObject

use of ncsa.hdf.object.HObject 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 13 with HObject

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

the class DataSet method readHdf5SolutionMetaData.

private void readHdf5SolutionMetaData(InputStream is) throws Exception {
    File tempFile = null;
    FileFormat solFile = null;
    try {
        tempFile = createTempHdf5File(is);
        FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
        solFile = fileFormat.createInstance(tempFile.getAbsolutePath(), FileFormat.READ);
        solFile.open();
        DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) solFile.getRootNode();
        Group rootGroup = (Group) rootNode.getUserObject();
        List<HObject> solGroups = rootGroup.getMemberList();
        for (HObject memberGroup : solGroups) {
            if (memberGroup instanceof Group && memberGroup.getName().equals("solution")) {
                Group solGroup = (Group) memberGroup;
                List<HObject> memberList = solGroup.getMemberList();
                for (HObject member : memberList) {
                    if (!(member instanceof Dataset)) {
                        continue;
                    }
                    Dataset dataset = (Dataset) member;
                    String dsname = dataset.getName();
                    int vt = -1;
                    String domain = null;
                    List<Attribute> solAttrList = dataset.getMetadata();
                    for (Attribute attr : solAttrList) {
                        String attrName = attr.getName();
                        if (attrName.equals("variable type")) {
                            Object obj = attr.getValue();
                            vt = ((int[]) obj)[0];
                        } else if (attrName.equals("domain")) {
                            Object obj = attr.getValue();
                            domain = ((String[]) obj)[0];
                        }
                    }
                    long[] dims = dataset.getDims();
                    String varName = domain == null ? dsname : domain + Variable.COMBINED_IDENTIFIER_SEPARATOR + dsname;
                    dataBlockList.addElement(DataBlock.createDataBlock(varName, vt, (int) dims[0], 0));
                }
                break;
            }
        }
    } finally {
        try {
            if (solFile != null) {
                solFile.close();
            }
            if (tempFile != null) {
                if (!tempFile.delete()) {
                    System.err.println("couldn't delete temp file " + tempFile);
                }
            }
        } catch (Exception e) {
        // ignore
        }
    }
}

Example 14 with HObject

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

the class DataSet method readMBSDataMetadata.

private void readMBSDataMetadata() throws Exception {
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    FileFormat solFile = null;
    try {
        solFile = fileFormat.createInstance(fileName, FileFormat.READ);
        solFile.open();
        DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) solFile.getRootNode();
        Group rootGroup = (Group) rootNode.getUserObject();
        Group solutionGroup = null;
        for (Object member : rootGroup.getMemberList()) {
            String memberName = ((HObject) member).getName();
            if (member instanceof Group) {
                MBSDataGroup group = MBSDataGroup.valueOf(memberName);
                if (group == MBSDataGroup.Solution) {
                    solutionGroup = (Group) member;
                    break;
                }
            }
        }
        if (solutionGroup == null) {
            throw new Exception("Group " + MBSDataGroup.Solution + " not found");
        }
        // find any timeGroup
        Group timeGroup = null;
        for (Object member : solutionGroup.getMemberList()) {
            String memberName = ((HObject) member).getName();
            if (member instanceof Group && memberName.startsWith("time")) {
                timeGroup = (Group) member;
                break;
            }
        }
        if (timeGroup == null) {
            throw new Exception("No time group found");
        }
        // find all the datasets in that time group
        for (Object member : timeGroup.getMemberList()) {
            if (member instanceof Dataset) {
                List<Attribute> solAttrList = ((Dataset) member).getMetadata();
                int size = 0;
                String varName = null;
                VariableType varType = null;
                for (Attribute attr : solAttrList) {
                    String attrName = attr.getName();
                    Object attrValue = attr.getValue();
                    if (attrName.equals(MSBDataAttribute.name.name())) {
                        varName = ((String[]) attrValue)[0];
                    } else if (attrName.equals(MSBDataAttribute.size.name())) {
                        size = ((int[]) attrValue)[0];
                    } else if (attrName.equals(MSBDataAttribute.type.name())) {
                        String vt = ((String[]) attrValue)[0];
                        if (vt.equals(MSBDataAttributeValue.Point.name())) {
                            varType = VariableType.POINT_VARIABLE;
                        } else if (vt.equals(MSBDataAttributeValue.Volume.name())) {
                            varType = VariableType.VOLUME;
                        } else if (vt.equals(MSBDataAttributeValue.PointSubDomain.name())) {
                        // Position for PointSubdomain
                        }
                    }
                }
                if (varType == VariableType.VOLUME) {
                    // only display volume
                    dataBlockList.addElement(DataBlock.createDataBlock(varName, varType.getType(), size, 0));
                }
                if (varType == VariableType.POINT_VARIABLE) {
                    // only display volume
                    dataBlockList.addElement(DataBlock.createDataBlock(varName, varType.getType(), size, 0));
                }
            }
        }
    } finally {
        if (solFile != null) {
            try {
                solFile.close();
            } catch (Exception e) {
            // ignore
            }
        }
    }
}

Example 15 with HObject

use of ncsa.hdf.object.HObject 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();
        }
    }
}