ucl.physiol.neuroconstruct.neuroml.hdf5
Class Hdf5Utils

java.lang.Object
  ucl.physiol.neuroconstruct.neuroml.hdf5.Hdf5Utils

public class Hdf5Utils
extends Object

Utilities file for generating HDF5 files. Note this helper API is limited to the structures and conventions used in HDF5 files generated by neuroConstruct, and should only be used for reading/writing those!!

Author:

Padraig Gleeson

Constructor Summary

Hdf5Utils()

Method Summary

static void	close(ncsa.hdf.object.h5.H5File h5File)
static ncsa.hdf.object.h5.H5File	createH5file(File file)
static String	getFirstStringValAttr(ArrayList<ncsa.hdf.object.Attribute> attrs, String attrName)
static ncsa.hdf.object.Group	getRootGroup(ncsa.hdf.object.h5.H5File h5File)
static ncsa.hdf.object.Attribute	getSimpleAttr(String name, String value, ncsa.hdf.object.h5.H5File h5File)
static void	main(String[] args)
static void	open(ncsa.hdf.object.h5.H5File h5File)
static ncsa.hdf.object.h5.H5File	openForRead(File f)
static ncsa.hdf.object.h5.H5File	openH5file(File file)
static DataSet	parse1DDataset(ncsa.hdf.object.Dataset d, boolean includePoints, Properties p)
static float[][]	parse2Ddataset(ncsa.hdf.object.Dataset d)
static ArrayList<DataSet>	parse2DDataset(ncsa.hdf.object.Dataset d, boolean includePoints, Properties p)
static String	parseAttribute(ncsa.hdf.object.Attribute a, String indent, Properties p, boolean returnOnlyValueString)
static ArrayList<ncsa.hdf.object.Attribute>	parseDatasetForAttributes(ncsa.hdf.object.Dataset d)
static ArrayList<ncsa.hdf.object.Attribute>	parseGroupForAttributes(ncsa.hdf.object.Group g)
static ArrayList<DataSet>	parseGroupForDatasets(ncsa.hdf.object.Group g, boolean includePoints)
static ArrayList<DataStore>	parseGroupForDataStores(ncsa.hdf.object.Group g, boolean includePoints)
static void	printGroup(ncsa.hdf.object.Group g, String indent)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Hdf5Utils

public Hdf5Utils()

Method Detail

getSimpleAttr

public static ncsa.hdf.object.Attribute getSimpleAttr(String name,
                                                      String value,
                                                      ncsa.hdf.object.h5.H5File h5File)
                                               throws Exception

Throws:

Exception

createH5file

public static ncsa.hdf.object.h5.H5File createH5file(File file)
                                              throws Hdf5Exception

Throws:

Hdf5Exception

openH5file

public static ncsa.hdf.object.h5.H5File openH5file(File file)
                                            throws Hdf5Exception

Throws:

Hdf5Exception

open

public static void open(ncsa.hdf.object.h5.H5File h5File)
                 throws Hdf5Exception

Throws:

Hdf5Exception

openForRead

public static ncsa.hdf.object.h5.H5File openForRead(File f)
                                             throws Hdf5Exception

Throws:

Hdf5Exception

close

public static void close(ncsa.hdf.object.h5.H5File h5File)
                  throws Hdf5Exception

Throws:

Hdf5Exception

getFirstStringValAttr

public static String getFirstStringValAttr(ArrayList<ncsa.hdf.object.Attribute> attrs,
                                           String attrName)

parseGroupForAttributes

public static ArrayList<ncsa.hdf.object.Attribute> parseGroupForAttributes(ncsa.hdf.object.Group g)
                                                                    throws Hdf5Exception

Throws:

Hdf5Exception

parseDatasetForAttributes

public static ArrayList<ncsa.hdf.object.Attribute> parseDatasetForAttributes(ncsa.hdf.object.Dataset d)
                                                                      throws Hdf5Exception

Throws:

Hdf5Exception

getRootGroup

public static ncsa.hdf.object.Group getRootGroup(ncsa.hdf.object.h5.H5File h5File)
                                          throws Hdf5Exception

Throws:

Hdf5Exception

parseAttribute

public static String parseAttribute(ncsa.hdf.object.Attribute a,
                                    String indent,
                                    Properties p,
                                    boolean returnOnlyValueString)

parseGroupForDataStores

public static ArrayList<DataStore> parseGroupForDataStores(ncsa.hdf.object.Group g,
                                                           boolean includePoints)
                                                    throws Hdf5Exception

Throws:

Hdf5Exception

parseGroupForDatasets

public static ArrayList<DataSet> parseGroupForDatasets(ncsa.hdf.object.Group g,
                                                       boolean includePoints)
                                                throws Exception

Throws:

Exception

parse2Ddataset

public static float[][] parse2Ddataset(ncsa.hdf.object.Dataset d)
                                throws Hdf5Exception

Throws:

Hdf5Exception

parse2DDataset

public static ArrayList<DataSet> parse2DDataset(ncsa.hdf.object.Dataset d,
                                                boolean includePoints,
                                                Properties p)

parse1DDataset

public static DataSet parse1DDataset(ncsa.hdf.object.Dataset d,
                                     boolean includePoints,
                                     Properties p)

printGroup

public static void printGroup(ncsa.hdf.object.Group g,
                              String indent)
                       throws Exception

Throws:

Exception

main

public static void main(String[] args)
                 throws IOException,
                        Hdf5Exception

Throws:

IOException

Hdf5Exception