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org.eclipse.dawnsci.hdf5
Class HDF5Utils



java.lang.Object


org.eclipse.dawnsci.hdf5.HDF5Utils









public class HDF5Utils
extends java.lang.Object











Nested Class Summary

Nested Classes 

Modifier and Type
Class and Description


static class 
HDF5Utils.DatasetType 









Constructor Summary

Constructors 

Constructor and Description


HDF5Utils() 









Method Summary

All Methods Static Methods Concrete Methods Deprecated Methods 

Modifier and Type
Method and Description


static java.lang.String
absolutePathToData(java.lang.String parentPath,
                  java.lang.String name) 


static long
calcLongSize(long[] shape) 


static void
closeDataset(long[] ids) 


static void
createDataset(HDF5File f,
             int compression,
             java.lang.String dataPath,
             int dtype,
             int[] iShape,
             int[] iMaxShape,
             int[] iChunks,
             java.lang.Object fillValue)
Create a dataset in given file



static Dataset
createDataset(java.lang.Object data,
             int[] shape,
             int dtype,
             boolean extend)
Create a dataset from the given data object



static void
createDataset(java.lang.String fileName,
             java.lang.String parentPath,
             java.lang.String name,
             int[] initialShape,
             int[] maxShape,
             int[] chunking,
             int dtype,
             java.lang.Object fill,
             boolean asUnsigned)
Create a dataset in HDF5 file.



static void
createExternalLink(HDF5File f,
                  java.lang.String destination,
                  java.lang.String externalFileName,
                  java.lang.String source)
Create a link to a source node in an external file



static void
createExternalLink(java.lang.String fileName,
                  java.lang.String destination,
                  java.lang.String externalFileName,
                  java.lang.String source)
Create a link to a source node in an external file



static LazyWriteableDataset
createLazyDataset(java.lang.String fileName,
                 java.lang.String parentPath,
                 java.lang.String name,
                 int[] initialShape,
                 int[] maxShape,
                 int[] chunking,
                 int dtype,
                 java.lang.Object fill,
                 boolean asUnsigned)
Create a lazy dataset in HDF5 file



static HDF5Utils.DatasetType
findClassesInComposite(long tid)
Find classes in composite data type



static void
flushDataset(long[] ids) 


static Dataset
getAttrDataset(long locId,
              java.lang.String path,
              long i) 


static int[][]
getDatasetShape(java.lang.String fileName,
               java.lang.String node)
Get dataset shape information from given file



static HDF5Utils.DatasetType
getDatasetType(long typeId,
              long nativeTypeId) 


static int
getDType(int dclass,
        int dsize)
Translate between data type and dataset type



static long
getHDF5type(java.lang.Class<?> clazz)
Get HDF5 data type constants for boxed primitives



static long
getHDF5type(int dtype)
Get HDF5 data type constants for dataset types



static java.lang.String
getLocalHostName()
Gracefully gets the local host name (if there is a mis-configuration or any other issue, "localhost" is returned)



static long
H5Fopen(java.lang.String filePath,
       int flags,
       long fapl)
Deprecated. 
Use H5.H5Fopen(String,int,long) directly




static boolean
hasDataset(java.lang.String fileName,
          java.lang.String node)
Check whether a dataset exists in a file



static boolean
isHDF5(java.lang.String fileName)
Check if file is a HDF5 file



static Dataset
loadDataset(HDF5File fid,
           java.lang.String node)
Load entire dataset from given file



static Dataset
loadDataset(java.lang.String fileName,
           java.lang.String node)
Load entire dataset from given file



static Dataset
loadDataset(java.lang.String fileName,
           java.lang.String node,
           int[] start,
           int[] count,
           int[] step,
           int dtype,
           int isize,
           boolean extend)
Load dataset from given file



static Dataset
loadDatasetWithClose(java.lang.String fileName,
                    java.lang.String node,
                    int[] start,
                    int[] count,
                    int[] step,
                    int dtype,
                    int isize,
                    boolean extend)
Load dataset from given file



static long[]
openDataset(HDF5File f,
           java.lang.String dataPath) 


static Dataset[]
readAttributes(long oid) 


static Dataset[]
readAttributes(long oid,
              java.lang.String path) 


static Dataset[]
readAttributes(java.lang.String fileName,
              java.lang.String path)
Read attributes from group or dataset in given file



static Dataset
readDataset(HDF5File f,
           java.lang.String dataPath,
           int[] start,
           int[] count,
           int[] step,
           int dtype,
           int isize,
           boolean extend)
Read dataset from given file ID



static int[][]
readDatasetShape(HDF5File f,
                java.lang.String dataPath)
Read shape information from a dataset



static void
setDatasetSlice(java.lang.String fileName,
               java.lang.String parentPath,
               java.lang.String name,
               SliceND slice,
               IDataset value)
Set slice of dataset in HDF5 file.



static void
setExistingDatasetSlice(java.lang.String fileName,
                       java.lang.String parentPath,
                       java.lang.String name,
                       SliceND slice,
                       IDataset value)
Set slice of dataset in HDF5 file.



static int[]
toIntArray(long[] in)
Convert long array to integer array



static long[]
toLongArray(int[] in)
Convert integer array to long array



static void
writeAttributes(HDF5File f,
               java.lang.String path,
               IDataset... attributes)
Write attributes to a group or dataset in given file



static void
writeAttributes(java.lang.String fileName,
               java.lang.String path,
               boolean isGroup,
               IDataset... attributes)
Write attributes to a group or dataset in given file.



static void
writeDataset(HDF5File f,
            java.lang.String dataPath,
            IDataset data)
Write a dataset in given file



static void
writeDataset(java.lang.String fileName,
            java.lang.String parentPath,
            IDataset data)
Write a dataset in HDF5 file.



static void
writeDatasetSlice(HDF5File f,
                 java.lang.String dataPath,
                 SliceND slice,
                 IDataset value)
Write to a slice in a dataset







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





getLocalHostName
public static java.lang.String getLocalHostName()
Gracefully gets the local host name (if there is a mis-configuration or any other issue, "localhost" is returned)

Returns:
local host name








isHDF5
public static boolean isHDF5(java.lang.String fileName)
Check if file is a HDF5 file

Parameters:
fileName - 
Returns:
true if it can be read as an HDF5 file








createDataset
public static Dataset createDataset(java.lang.Object data,
                                    int[] shape,
                                    int dtype,
                                    boolean extend)
Create a dataset from the given data object

Parameters:
data - 
shape - 
dtype - 
extend - true dataset for unsigned types
Returns:
dataset








getDType
public static int getDType(int dclass,
                           int dsize)
Translate between data type and dataset type

Parameters:
dclass - data type class
dsize - data type element size in bytes
Returns:
dataset type








getHDF5type
public static long getHDF5type(java.lang.Class<?> clazz)
Get HDF5 data type constants for boxed primitives

Parameters:
clazz - 
Returns:








getHDF5type
public static long getHDF5type(int dtype)
Get HDF5 data type constants for dataset types

Parameters:
dtype - 
Returns:








loadDatasetWithClose
public static Dataset loadDatasetWithClose(java.lang.String fileName,
                                           java.lang.String node,
                                           int[] start,
                                           int[] count,
                                           int[] step,
                                           int dtype,
                                           int isize,
                                           boolean extend)
                                    throws ScanFileHolderException
Load dataset from given file

Parameters:
fileName - 
node - 
start - 
count - 
step - 
dtype - 
isize - 
extend - 
Returns:
dataset
Throws:
java.lang.Exception
ScanFileHolderException








loadDataset
public static Dataset loadDataset(java.lang.String fileName,
                                  java.lang.String node)
                           throws ScanFileHolderException
Load entire dataset from given file

Parameters:
fileName - 
node - 
Returns:
dataset
Throws:
java.lang.Exception
ScanFileHolderException








loadDataset
public static Dataset loadDataset(HDF5File fid,
                                  java.lang.String node)
                           throws ScanFileHolderException
Load entire dataset from given file

Parameters:
fileName - 
node - 
Returns:
dataset
Throws:
java.lang.Exception
ScanFileHolderException








hasDataset
public static boolean hasDataset(java.lang.String fileName,
                                 java.lang.String node)
                          throws ScanFileHolderException
Check whether a dataset exists in a file

Parameters:
fileName - 
node - 
Returns:
dataset
Throws:
java.lang.Exception
ScanFileHolderException








loadDataset
public static Dataset loadDataset(java.lang.String fileName,
                                  java.lang.String node,
                                  int[] start,
                                  int[] count,
                                  int[] step,
                                  int dtype,
                                  int isize,
                                  boolean extend)
                           throws ScanFileHolderException
Load dataset from given file

Parameters:
fileName - 
node - 
start - 
count - 
step - 
dtype - 
isize - 
extend - 
Returns:
dataset
Throws:
java.lang.Exception
ScanFileHolderException








getDatasetShape
public static int[][] getDatasetShape(java.lang.String fileName,
                                      java.lang.String node)
                               throws ScanFileHolderException
Get dataset shape information from given file

Parameters:
fileName - 
dataPath - 
Returns:
null for when there's no data; two empty arrays for a zero-rank dataset;
  shape, max shape otherwise
Throws:
ScanFileHolderException








readDatasetShape
public static int[][] readDatasetShape(HDF5File f,
                                       java.lang.String dataPath)
                                throws NexusException
Read shape information from a dataset

Parameters:
f - 
dataPath - 
Returns:
null for when there's no data; two empty arrays for a zero-rank dataset;
  shape, max shape otherwise
Throws:
NexusException








readDataset
public static Dataset readDataset(HDF5File f,
                                  java.lang.String dataPath,
                                  int[] start,
                                  int[] count,
                                  int[] step,
                                  int dtype,
                                  int isize,
                                  boolean extend)
                           throws NexusException
Read dataset from given file ID

Parameters:
f - 
dataPath - 
start - 
count - 
step - 
dtype - (can be -1 for dataset type from file)
isize - (can be -1 for item size from file)
extend - 
Returns:
dataset
Throws:
NexusException








absolutePathToData
public static java.lang.String absolutePathToData(java.lang.String parentPath,
                                                  java.lang.String name)

Returns:
the absolute path to data








createDataset
public static void createDataset(java.lang.String fileName,
                                 java.lang.String parentPath,
                                 java.lang.String name,
                                 int[] initialShape,
                                 int[] maxShape,
                                 int[] chunking,
                                 int dtype,
                                 java.lang.Object fill,
                                 boolean asUnsigned)
                          throws ScanFileHolderException
Create a dataset in HDF5 file. Create the file if necessary

Parameters:
fileName - 
parentPath - path to group containing dataset
name - name of dataset
initialShape - 
maxShape - 
chunking - 
dtype - dataset type
fill - 
asUnsigned - 
Throws:
ScanFileHolderException








createLazyDataset
public static LazyWriteableDataset createLazyDataset(java.lang.String fileName,
                                                     java.lang.String parentPath,
                                                     java.lang.String name,
                                                     int[] initialShape,
                                                     int[] maxShape,
                                                     int[] chunking,
                                                     int dtype,
                                                     java.lang.Object fill,
                                                     boolean asUnsigned)
Create a lazy dataset in HDF5 file

Parameters:
fileName - 
parentPath - 
name - 
initialShape - 
maxShape - 
chunking - 
dtype - 
fill - 
asUnsigned - 
Returns:








createDataset
public static void createDataset(HDF5File f,
                                 int compression,
                                 java.lang.String dataPath,
                                 int dtype,
                                 int[] iShape,
                                 int[] iMaxShape,
                                 int[] iChunks,
                                 java.lang.Object fillValue)
                          throws NexusException
Create a dataset in given file

Parameters:
f - 
compression - 
dataPath - 
dtype - 
iShape - 
iMaxShape - 
iChunks - 
fillValue - 
Throws:
NexusException








writeDataset
public static void writeDataset(java.lang.String fileName,
                                java.lang.String parentPath,
                                IDataset data)
                         throws ScanFileHolderException
Write a dataset in HDF5 file. Create the file if necessary

Parameters:
fileName - 
parentPath - path to group containing dataset
data - 
Throws:
ScanFileHolderException
java.lang.IllegalArgumentException - when data has null or empty name








writeDataset
public static void writeDataset(HDF5File f,
                                java.lang.String dataPath,
                                IDataset data)
                         throws NexusException
Write a dataset in given file

Parameters:
f - 
dataPath - 
data - 
Throws:
NexusException








writeAttributes
public static void writeAttributes(java.lang.String fileName,
                                   java.lang.String path,
                                   boolean isGroup,
                                   IDataset... attributes)
                            throws ScanFileHolderException
Write attributes to a group or dataset in given file. When writing to group,
 this checks if group exists in file and creates group if not

Parameters:
fileName - 
path - 
isGroup - 
attributes - 
Throws:
ScanFileHolderException








writeAttributes
public static void writeAttributes(HDF5File f,
                                   java.lang.String path,
                                   IDataset... attributes)
                            throws NexusException
Write attributes to a group or dataset in given file

Parameters:
f - 
path - 
attributes - 
Throws:
NexusException
java.lang.IllegalArgumentException - when any attribute has null or empty name








setDatasetSlice
public static void setDatasetSlice(java.lang.String fileName,
                                   java.lang.String parentPath,
                                   java.lang.String name,
                                   SliceND slice,
                                   IDataset value)
                            throws ScanFileHolderException
Set slice of dataset in HDF5 file. Create file if necessary

Parameters:
fileName - 
parentPath - 
name - 
slice - 
value - 
Throws:
ScanFileHolderException








setExistingDatasetSlice
public static void setExistingDatasetSlice(java.lang.String fileName,
                                           java.lang.String parentPath,
                                           java.lang.String name,
                                           SliceND slice,
                                           IDataset value)
                                    throws ScanFileHolderException
Set slice of dataset in HDF5 file. Create file if necessary

Parameters:
fileName - 
parentPath - 
name - 
slice - 
value - 
Throws:
ScanFileHolderException








openDataset
public static long[] openDataset(HDF5File f,
                                 java.lang.String dataPath)
                          throws NexusException

Parameters:
f - 
dataPath - 
Returns:
Throws:
NexusException








flushDataset
public static void flushDataset(long[] ids)
                         throws NexusException

Parameters:
ids - 
Throws:
NexusException








closeDataset
public static void closeDataset(long[] ids)
                         throws NexusException

Parameters:
ids - 
Throws:
NexusException








writeDatasetSlice
public static void writeDatasetSlice(HDF5File f,
                                     java.lang.String dataPath,
                                     SliceND slice,
                                     IDataset value)
                              throws NexusException
Write to a slice in a dataset

Parameters:
f - 
dataPath - 
slice - 
value - 
Throws:
NexusException








H5Fopen
public static long H5Fopen(java.lang.String filePath,
                           int flags,
                           long fapl)
                    throws HDF5LibraryException,
                           java.lang.NullPointerException
Deprecated. Use H5.H5Fopen(String,int,long) directly
Wrapper to fix super block status flag issue

Parameters:
filePath - 
flags - 
fapl - 
Returns:
file ID
Throws:
HDF5LibraryException
java.lang.NullPointerException








readAttributes
public static Dataset[] readAttributes(long oid)
                                throws NexusException

Throws:
NexusException








readAttributes
public static Dataset[] readAttributes(java.lang.String fileName,
                                       java.lang.String path)
                                throws NexusException,
                                       ScanFileHolderException
Read attributes from group or dataset in given file

Parameters:
fileName - 
groupPath - 
Throws:
ScanFileHolderException
NexusException








readAttributes
public static Dataset[] readAttributes(long oid,
                                       java.lang.String path)
                                throws NexusException

Throws:
NexusException








createExternalLink
public static void createExternalLink(java.lang.String fileName,
                                      java.lang.String destination,
                                      java.lang.String externalFileName,
                                      java.lang.String source)
                               throws ScanFileHolderException
Create a link to a source node in an external file

Parameters:
fileName - file name where link will be created
destination - path of created link
externalFileName - external file
source - path of source node
Throws:
ScanFileHolderException








createExternalLink
public static void createExternalLink(HDF5File f,
                                      java.lang.String destination,
                                      java.lang.String externalFileName,
                                      java.lang.String source)
                               throws NexusException
Create a link to a source node in an external file

Parameters:
f - 
destination - path of created link (if ends with  then use name from source)
externalFileName - external file
source - path of source node
Throws:
ScanFileHolderException
NexusException








findClassesInComposite
public static HDF5Utils.DatasetType findClassesInComposite(long tid)
                                                    throws HDF5LibraryException,
                                                           NexusException
Find classes in composite data type

Parameters:
tid - 
Returns:
Throws:
HDF5LibraryException
NexusException








getDatasetType
public static HDF5Utils.DatasetType getDatasetType(long typeId,
                                                   long nativeTypeId)
                                            throws NexusException,
                                                   HDF5LibraryException

Throws:
NexusException
HDF5LibraryException








getAttrDataset
public static Dataset getAttrDataset(long locId,
                                     java.lang.String path,
                                     long i)
                              throws NexusException

Throws:
NexusException








calcLongSize
public static long calcLongSize(long[] shape)







toLongArray
public static final long[] toLongArray(int[] in)
Convert integer array to long array

Parameters:
in - 
Returns:
long array








toIntArray
public static int[] toIntArray(long[] in)
Convert long array to integer array

Parameters:
in - 
Returns:
integer array














Skip navigation links




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Package
Class
Tree
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Index
Help




Prev Class
Next Class


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Summary: 
Nested | 
Field | 
Constr | 
Method


Detail: 
Field | 
Constr | 
Method