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

Example 6 with Attribute

use of ncsa.hdf.object.Attribute 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 7 with Attribute

use of ncsa.hdf.object.Attribute 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 8 with Attribute

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

the class DataSetControllerImpl method getHDF5Attributes.

// uncomment it for Debug
// private static String DATASETNAME = "/";
// enum H5O_type {
// H5O_TYPE_UNKNOWN(-1), // Unknown object type
// H5O_TYPE_GROUP(0), // Object is a group
// H5O_TYPE_DATASET(1), // Object is a dataset
// H5O_TYPE_NAMED_DATATYPE(2), // Object is a named data type
// H5O_TYPE_NTYPES(3); // Number of different object types
// private static final Map<Integer, H5O_type> lookup = new HashMap<Integer, H5O_type>();
// 
// static {
// for (H5O_type s : EnumSet.allOf(H5O_type.class))
// lookup.put(s.getCode(), s);
// }
// 
// private int code;
// 
// H5O_type(int layout_type) {
// this.code = layout_type;
// }
// 
// public int getCode() {
// return this.code;
// }
// 
// public static H5O_type get(int code) {
// return lookup.get(code);
// }
// }
// 
// public static void do_iterate(File hdfFile) {
// int file_id = -1;
// 
// // Open a file using default properties.
// try {
// file_id = H5.H5Fopen(hdfFile.getAbsolutePath(), HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
// }
// catch (Exception e) {
// e.printStackTrace();
// }
// 
// // Begin iteration.
// System.out.println("Objects in root group:");
// try {
// if (file_id >= 0) {
// int count = (int)H5.H5Gn_members(file_id, DATASETNAME);
// String[] oname = new String[count];
// int[] otype = new int[count];
// int[] ltype = new int[count];
// long[] orefs = new long[count];
// H5.H5Gget_obj_info_all(file_id, DATASETNAME, oname, otype, ltype, orefs, HDF5Constants.H5_INDEX_NAME);
// 
// // Get type of the object and display its name and type.
// for (int indx = 0; indx < otype.length; indx++) {
// switch (H5O_type.get(otype[indx])) {
// case H5O_TYPE_GROUP:
// System.out.println("  Group: " + oname[indx]);
// break;
// case H5O_TYPE_DATASET:
// System.out.println("  Dataset: " + oname[indx]);
// break;
// case H5O_TYPE_NAMED_DATATYPE:
// System.out.println("  Datatype: " + oname[indx]);
// break;
// default:
// System.out.println("  Unknown: " + oname[indx]);
// }
// }
// }
// }
// catch (Exception e) {
// e.printStackTrace();
// }
// 
// // Close the file.
// try {
// if (file_id >= 0)
// H5.H5Fclose(file_id);
// }
// catch (Exception e) {
// e.printStackTrace();
// }
// }
// public static void populateHDF5(Group g, String indent,DataProcessingOutput0 dataProcessingOutput,boolean bVarStatistics,String imgDataName,Origin imgDataOrigin,Extent imgDataExtent) throws Exception
// {
// if (g == null)
// return;
// 
// List members = g.getMemberList();
// 
// int n = members.size();
// indent += "    ";
// HObject obj = null;
// 
// String nameAtt = "_name";
// String unitAtt = "_unit";
// for (int i=0; i<n; i++){
// 
// obj = (HObject)members.get(i);
// //uncomment for Debug
// /*System.out.print(indent+obj+" ("+obj.getClass().getName()+") isGroup="+(obj instanceof Group));*/
// if(obj.getName().equals(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_VARIABLESTATISTICS)){
// List<Metadata> metaDataL = obj.getMetadata();
// if(metaDataL != null){
// HashMap<String, String> attrHashMap = getHDF5Attributes(obj);//map contains the same number of names and attributes
// String[] variableStatNames = null;
// String[] variableUnits = null;
// Iterator<String> attrIterTemp = attrHashMap.keySet().iterator();
// boolean bHasUnit = false;
// for (int j = 0; j < attrHashMap.size(); j++) {
// String compVal = attrIterTemp.next();
// if(compVal.contains(nameAtt) || compVal.contains(unitAtt)){
// bHasUnit = true;
// break;
// }
// }
// if(bHasUnit){
// variableStatNames = new String[attrHashMap.size()/2];
// variableUnits = new String[attrHashMap.size()/2];
// }else{
// variableStatNames = new String[attrHashMap.size()]; // old way
// }
// Iterator<String> attrIter = attrHashMap.keySet().iterator();
// for (int j = 0; j < attrHashMap.size(); j++) {
// String compVal = attrIter.next();
// int compVarIdx = Integer.parseInt(compVal.substring(5, 6));
// if(compVal.contains(nameAtt)){
// variableStatNames[compVarIdx] = attrHashMap.get(compVal);
// }else if(compVal.contains(unitAtt)){
// variableUnits[compVarIdx] = attrHashMap.get(compVal);
// }else{//old way for var names(e.g. comp_0 = abc) with no "_name" or "_unit"
// variableStatNames[compVarIdx] = attrHashMap.get(compVal);
// }
// }
// dataProcessingOutput.setVariableStatNames(variableStatNames);
// dataProcessingOutput.setVariableUnits(variableUnits);
// dataProcessingOutput.setVariableStatValues(new double[variableStatNames.length][dataProcessingOutput.getTimes().length]);
// bVarStatistics = true;
// }
// }else if(obj instanceof H5ScalarDS){
// H5ScalarDS h5ScalarDS = (H5ScalarDS)obj;
// h5ScalarDS.init();
// long[] dims = h5ScalarDS.getDims();
// 
// //make sure all dimensions are selected for loading if 3D
// //note: for 3D, only 1st slice selected by default
// long[] selectedDims = h5ScalarDS.getSelectedDims();
// if(selectedDims != null && selectedDims.length > 2){
// //changes internal class variable used during read
// selectedDims[2] = dims[2];
// }
// 
// //load all data
// Object data = h5ScalarDS.read();
// 
// if(dims != null){
// if(dims.length > 1){
// //For HDF5View (x stored in index 1) and (y stored in index 0) so must switch back to normal assumption
// long dimsY = dims[0];
// dims[0] = dims[1];
// dims[1] = dimsY;
// }
// //uncomment for Debug
// /*System.out.print(" dims=(");
// for (int j = 0; j < dims.length; j++) {
// System.out.print((j>0?"x":"")+dims[j]);
// }
// System.out.print(")");*/
// }
// 
// //        	System.out.print(" len="+times.length);
// if(obj.getName().equals(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_TIMES)){
// double[] times = (double[])data;
// dataProcessingOutput.setTimes(times);
// }else if(bVarStatistics){
// double[] stats = (double[])data;
// int timeIndex = Integer.parseInt(obj.getName().substring("time".length()));
// for (int j = 0; j < stats.length; j++) {
// dataProcessingOutput.getVariableStatValues()[j][timeIndex] = stats[j];
// }
// }else{
// double min = ((double[])data)[0];
// double max = min;
// for (int j = 0; j < ((double[])data).length; j++) {
// min = Math.min(min, ((double[])data)[j]);
// max = Math.max(max, ((double[])data)[j]);
// }
// int xSize = (int)dims[0];
// int ySize = (int)(dims.length>1?dims[1]:1);
// int zSize = (int)(dims.length>2?dims[2]:1);
// SourceDataInfo sourceDataInfo =
// new SourceDataInfo(SourceDataInfo.RAW_VALUE_TYPE, (double[])data, (imgDataExtent==null?new Extent(1,1,1):imgDataExtent), (imgDataOrigin==null?null:imgDataOrigin), new Range(min, max), 0, xSize, 1, ySize, xSize, zSize, xSize*ySize);
// Vector<SourceDataInfo> otherData = dataProcessingOutput.getDataGenerators().get(imgDataName);
// int timeIndex = Integer.parseInt(obj.getName().substring(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_TIMEPREFIX.length()));
// otherData.add(sourceDataInfo);
// if(otherData.size()-1 != timeIndex){
// throw new Exception("Error HDF5 parse: added data index does not match timeIndex");
// }
// }
// }else if (obj instanceof H5Group && !obj.getName().equals(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_POSTPROCESSING)){
// bVarStatistics = false;
// imgDataName = obj.getName();
// dataProcessingOutput.getDataGenerators().put(imgDataName, new Vector<SourceDataInfo>());
// 
// List<Metadata> metaDataL = obj.getMetadata();
// if(metaDataL != null){//assume 6 attributes defining origin and extent
// HashMap<String, String> attrHashMap = getHDF5Attributes(obj);
// if(attrHashMap.size() == 2){
// imgDataOrigin = new Origin(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINX)), 0, 0);
// imgDataExtent = new Extent(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTX)), 1, 1);//this is 1D, however the extentY, Z cannot take 0
// }
// 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);
// imgDataExtent = new Extent(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTX)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTY)), 1);//this is 2D, however the extentZ cannot take 0
// }
// 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)));
// }
// }
// 
// }
// System.out.println();
// 
// if (obj instanceof Group)
// {
// populateHDF5((Group)obj, indent,dataProcessingOutput,bVarStatistics,imgDataName,imgDataOrigin,imgDataExtent);
// }
// }
// }
private static HashMap<String, String> getHDF5Attributes(HObject hObject) throws Exception {
    HashMap<String, String> attrHashMap = new HashMap<String, String>();
    List<Metadata> metaDataL = hObject.getMetadata();
    if (metaDataL != null) {
        for (int j = 0; j < metaDataL.size(); j++) {
            Attribute attr = (Attribute) metaDataL.get(j);
            String attrValue = attr.toString(",");
            // System.out.print(" "+attr.getName()+"='"+attrValue+"'");
            attrHashMap.put(attr.getName(), attr.toString(","));
        }
    }
    return attrHashMap;
}

Example 9 with Attribute

use of ncsa.hdf.object.Attribute 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 10 with Attribute

use of ncsa.hdf.object.Attribute 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;
}