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

Example 1 with Datatype

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

the class VH5Dataset method info.

public static void info(H5ScalarDS ds) throws Exception {
    Datatype dt = ds.getDatatype();
    System.out.println(dt.getFullName());
    System.out.println(dt.getDatatypeDescription());
    int n = dt.toNative();
    Datatype nt = new H5Datatype(n);
    // dt = dt.getBasetype();
    System.out.println(nt.getFullName());
    System.out.println(nt.getDatatypeDescription());
    System.out.println(H5Client.parseMeta(dt));
// ds.init();
// int did = ds.open();
// ds.read();
// 
// int cdt = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND,128);
// int vtype = H5.H5Tvlen_create(cdt);
// int ndims = ds.getRank();
// long dims[] = new long[ndims];
// long maxdims[] = new long[ndims];
// int space = H5.H5Dget_space(did);
// H5.H5Sget_simple_extent_dims(space, dims,maxdims);
// System.out.println(StringUtils.join(dims));
// long bsize = H5.H5Dvlen_get_buf_size_long(did,vtype,space);
// 
// double bdata[][] = new double[2][(int)dims[0]];
// int status = H5.H5Dread(did,vtype,HDF5Constants.H5S_ALL,HDF5Constants.H5S_ALL,HDF5Constants.H5P_DEFAULT,bdata);
// System.out.println(status);
}

Example 2 with Datatype

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

the class H5FileStructure method createFile.

/**
 * create the file and add groups and dataset into the file, which is the
 * same as javaExample.H5DatasetCreate
 *
 * @see javaExample.HDF5DatasetCreate
 * @throws Exception
 */
private static void createFile() throws Exception {
    // retrieve an instance of H5File
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    if (fileFormat == null) {
        System.err.println("Cannot find HDF5 FileFormat.");
        return;
    }
    // create a new file with a given file name.
    H5File testFile = (H5File) fileFormat.createFile(fname, FileFormat.FILE_CREATE_DELETE);
    if (testFile == null) {
        System.err.println("Failed to create file:" + fname);
        return;
    }
    // open the file and retrieve the root group
    testFile.open();
    Group root = (Group) ((javax.swing.tree.DefaultMutableTreeNode) testFile.getRootNode()).getUserObject();
    // create groups at the root
    Group g1 = testFile.createGroup("integer arrays", root);
    Group g2 = testFile.createGroup("float arrays", root);
    // create 2D 32-bit (4 bytes) integer dataset of 20 by 10
    Datatype dtype = testFile.createDatatype(Datatype.CLASS_INTEGER, 4, Datatype.NATIVE, Datatype.NATIVE);
    Dataset dataset = testFile.createScalarDS("2D 32-bit integer 20x10", g1, dtype, dims2D, null, null, 0, null);
    // create 3D 8-bit (1 byte) unsigned integer dataset of 20 by 10 by 5
    dtype = testFile.createDatatype(Datatype.CLASS_INTEGER, 1, Datatype.NATIVE, Datatype.SIGN_NONE);
    dataset = testFile.createScalarDS("3D 8-bit unsigned integer 20x10x5", g1, dtype, dims3D, null, null, 0, null);
    // create 2D 64-bit (8 bytes) double dataset of 20 by 10
    dtype = testFile.createDatatype(Datatype.CLASS_FLOAT, 8, Datatype.NATIVE, -1);
    dataset = testFile.createScalarDS("2D 64-bit double 20x10", g2, dtype, dims2D, null, null, 0, null);
    // create 3D 32-bit (4 bytes) float dataset of 20 by 10 by 5
    dtype = testFile.createDatatype(Datatype.CLASS_FLOAT, 4, Datatype.NATIVE, -1);
    dataset = testFile.createScalarDS("3D 32-bit float  20x10x5", g2, dtype, dims3D, null, null, 0, null);
    // close file resource
    testFile.close();
}

Example 3 with Datatype

use of ncsa.hdf.object.Datatype 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 4 with Datatype

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

the class VH5Dataset method info.

public void info(H5CompoundDS ds) throws Exception {
    Datatype dt = ds.getDatatype();
    String[] mn = ds.getMemberNames();
    System.out.println(ArrayUtils.toString(mn));
    System.out.println(dt.getFullName());
    System.out.println(dt.getDatatypeDescription());
    Object obj = ds.read();
    Collection<?> coll = BeanUtils.downcast(Collection.class, obj);
    VCAssert.assertTrue(coll.size() == mn.length, "collection matches names");
    int i = 0;
    for (Object o : coll) {
        System.out.println(mn[i++] + " ");
        analyze(o);
    }
}