Module org.hdfgroup.object

Package hdf.object.h5

Class H5ScalarDS

Object

hdf.object.HObject

hdf.object.Dataset

hdf.object.ScalarDS

hdf.object.h5.H5ScalarDS

All Implemented Interfaces:

DataFormat, MetaDataContainer, Serializable

public class H5ScalarDS
extends ScalarDS
implements MetaDataContainer

H5ScalarDS describes a multi-dimension array of HDF5 scalar or atomic data types, such as byte, int, short, long, float, double and string, and operations performed on the scalar dataset. The library predefines a modest number of datatypes. For details, read HDF5 Datatypes in HDF5 User Guide

Version:

1.1 9/4/2007

Author:

Peter X. Cao

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	isNativeDatatype	flag to indicate if the datatype in file is the same as dataype in memory
protected boolean	refresh	flag to indicate if the dataset buffers should be refreshed.

Fields inherited from class hdf.object.ScalarDS

fillValue, imageDataRange, interlace, INTERLACE_LINE, INTERLACE_PIXEL, INTERLACE_PLANE, isDefaultImageOrder, isFillValueConverted, isImageDisplay, isTrueColor, palette, unsignedConverted

Fields inherited from class hdf.object.Dataset

chunkSize, compression, COMPRESSION_GZIP_TXT, convertByteToString, convertedBuf, data, datatype, dimNames, dims, filters, inited, isDataLoaded, isImage, isNULL, isScalar, isText, maxDims, nPoints, originalBuf, rank, selectedDims, selectedIndex, selectedStride, space_type, startDims, storage, storageLayout

Fields inherited from class hdf.object.HObject

fileFormat, linkTargetObjName, oid, SEPARATOR

Constructor Summary

Constructors

Constructor	Description
H5ScalarDS(FileFormat theFile, String theName, String thePath)	Constructs an instance of a H5 scalar dataset with given file, dataset name and path.
H5ScalarDS(FileFormat theFile, String theName, String thePath, long[] oid)	Deprecated. Not for public use in the future. Using H5ScalarDS(FileFormat, String, String)

Method Summary

Modifier and Type	Method	Description
void	clear()	Removes all of the elements from metadata list.
void	close(long did)	Closes access to the object.
Dataset	copy(Group pgroup, String dstName, long[] dims, Object buff)	Creates a new dataset and writes the data buffer to the new dataset.
static Dataset	create(String name, Group pgroup, Datatype type, long[] dims, long[] maxdims, long[] chunks, int gzip, Object data)	Creates a scalar dataset in a file with/without chunking and compression.
static Dataset	create(String name, Group pgroup, Datatype type, long[] dims, long[] maxdims, long[] chunks, int gzip, Object fillValue, Object data)	Creates a scalar dataset in a file with/without chunking and compression.
void	extend(long[] newDims)	H5Dset_extent verifies that the dataset is at least of size size, extending it if necessary.
Datatype	getDatatype()	Returns the datatype of the data object.
List<Attribute>	getMetadata()	Retrieves the object's metadata, such as attributes, from the file.
List<Attribute>	getMetadata(int... attrPropList)	Retrieves the object's metadata, such as attributes, from the file.
int	getNumberOfPalettes()	Get the number of pallettes for this object.
byte[][]	getPalette()	Returns the palette of this scalar dataset or null if palette does not exist.
String	getPaletteName(int idx)	Get the name of a specific image palette from file.
long[]	getToken()	Get the token for this object.
String	getVirtualFilename(int index)	Gets the source file name at index if dataset is virtual.
int	getVirtualMaps()	Gets the number of source files if dataset is virtual.
boolean	hasAttribute()	Check if the object has any attributes attached.
void	init()	Retrieves datatype and dataspace information from file and sets the dataset in memory.
boolean	isVirtual()	Checks if dataset is virtual.
long	open()	Opens an existing object such as a dataset or group for access.
Object	read()	Reads the data from file.
byte[]	readBytes()	Reads the raw data of the dataset from file to a byte array.
int	readNumberOfPalettes()	reads references of palettes to count the numberOfPalettes.
byte[][]	readPalette(int idx)	Reads a specific image palette from file.
Object	refreshData()	Refreshes the dataset before re-read of data.
void	removeMetadata(Object info)	Deletes an existing piece of metadata from this object.
protected void	resetSelection()	Resets selection of dataspace
void	setName(String newName)	Sets the name of the object.
String	toString(String delimiter, int maxItems)	Returns a string representation of the data value.
void	updateMetadata(Object info)	Updates an existing piece of metadata attached to this object.
void	write(Object buf)	Writes the given data buffer into this dataset in a file.
void	writeMetadata(Object info)	Writes a specific piece of metadata (such as an attribute) into the file.

Methods inherited from class hdf.object.ScalarDS

addFilteredImageValue, clearData, convertFromUnsignedC, convertToUnsignedC, getFillValue, getFilteredImageValues, getImageDataRange, getInterlace, isDefaultImageOrder, isImage, isImageDisplay, isTrueColor, setImageDataRange, setIsImage, setIsImageDisplay, setPalette

Methods inherited from class hdf.object.Dataset

byteToString, convertFromUnsignedC, convertFromUnsignedC, convertToUnsignedC, convertToUnsignedC, getChunkSize, getCompression, getConvertByteToString, getData, getDepth, getDimNames, getDims, getFilters, getHeight, getMaxDims, getOriginalClass, getRank, getSelectedDims, getSelectedIndex, getSize, getSpaceType, getStartDims, getStorage, getStorageLayout, getStride, getWidth, isInited, isNULL, isScalar, isString, setConvertByteToString, setData, stringToByte, toString, toString, write

Methods inherited from class hdf.object.HObject

createFullname, debug, equals, equals, equalsOID, getFID, getFile, getFileFormat, getFullName, getLinkTargetObjName, getName, getOID, getPath, hashCode, setFullname, setLinkTargetObjName, setPath, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Details

refresh

protected boolean refresh

flag to indicate if the dataset buffers should be refreshed.

isNativeDatatype

protected boolean isNativeDatatype

flag to indicate if the datatype in file is the same as dataype in memory

Constructor Details

H5ScalarDS

public H5ScalarDS(FileFormat theFile,
 String theName,
 String thePath)

Constructs an instance of a H5 scalar dataset with given file, dataset name and path. For example, in H5ScalarDS(h5file, "dset", "/arrays/"), "dset" is the name of the dataset, "/arrays" is the group path of the dataset.

Parameters:

theFile - the file that contains the data object.

theName - the name of the data object, e.g. "dset".

thePath - the full path of the data object, e.g. "/arrays/".

H5ScalarDS

@Deprecated
public H5ScalarDS(FileFormat theFile,
 String theName,
 String thePath,
 long[] oid)

Deprecated.

Not for public use in the future.
Using H5ScalarDS(FileFormat, String, String)

Parameters:

theFile - the file that contains the data object.

theName - the name of the data object, e.g. "dset".

thePath - the full path of the data object, e.g. "/arrays/".

oid - the oid of the data object.

Method Details

open

public long open()

Description copied from class: HObject

Opens an existing object such as a dataset or group for access. The return value is an object identifier obtained by implementing classes such as H5.H5Dopen(). This function is needed to allow other objects to be able to access the object. For instance, H5File class uses the open() function to obtain object identifier for copyAttributes(long src_id, long dst_id) and other purposes. The open() function should be used in pair with close(long) function.

Specified by:

open in class HObject

Returns:

the object identifier if successful; otherwise returns a negative value.

See Also:

• HObject.close(long)

close

public void close(long did)

Description copied from class: HObject

Closes access to the object. Sub-classes must implement this interface because different data objects have their own ways of how the data resources are closed. For example, H5Group.close() calls the hdf.hdf5lib.H5.H5Gclose() method and closes the group resource specified by the group id.

Specified by:

close in class HObject

Parameters:

did - The object identifier.

init

public void init()

Retrieves datatype and dataspace information from file and sets the dataset in memory. The init() is designed to support lazy operation in a dataset object. When a data object is retrieved from file, the datatype, dataspace and raw data are not loaded into memory. When it is asked to read the raw data from file, init() is first called to get the datatype and dataspace information, then load the raw data from file. init() is also used to reset the selection of a dataset (start, stride and count) to the default, which is the entire dataset for 1D or 2D datasets. In the following example, init() at step 1) retrieves datatype and dataspace information from file. getData() at step 3) reads only one data point. init() at step 4) resets the selection to the whole dataset. getData() at step 4) reads the values of whole dataset into memory.

 dset = (Dataset) file.get(NAME_DATASET);

 // 1) get datatype and dataspace information from file
 dset.init();
 rank = dset.getRank(); // rank = 2, a 2D dataset
 count = dset.getSelectedDims();
 start = dset.getStartDims();
 dims = dset.getDims();

 // 2) select only one data point
 for (int i = 0; i < rank; i++) {
     start[0] = 0;
     count[i] = 1;
 }

 // 3) read one data point
 data = dset.getData();

 // 4) reset selection to the whole dataset
 dset.init();

 // 5) clean the memory data buffer
 dset.clearData();

 // 6) Read the whole dataset
 data = dset.getData();
 

Specified by:

init in interface DataFormat

getToken

public long[] getToken()

Get the token for this object.

Returns:

true if it has any attributes, false otherwise.

hasAttribute

public boolean hasAttribute()

Check if the object has any attributes attached.

Specified by:

hasAttribute in interface MetaDataContainer

Returns:

true if it has any attributes, false otherwise.

getDatatype

public Datatype getDatatype()

Returns the datatype of the data object.

Specified by:

getDatatype in interface DataFormat

Overrides:

getDatatype in class Dataset

Returns:

the datatype of the data object.

refreshData

public Object refreshData()

Refreshes the dataset before re-read of data.

Specified by:

refreshData in interface DataFormat

Overrides:

refreshData in class Dataset

Returns:

the updated data

See Also:

• Dataset.getData()
• DataFormat.read()

clear

public void clear()

Removes all of the elements from metadata list. The list should be empty after this call returns.

Specified by:

clear in interface MetaDataContainer

Overrides:

clear in class Dataset

readBytes

public byte[] readBytes()
                 throws hdf.hdf5lib.exceptions.HDF5Exception

Description copied from class: Dataset

Reads the raw data of the dataset from file to a byte array. readBytes() reads raw data to an array of bytes instead of array of its datatype. For example, for a one-dimension 32-bit integer dataset of size 5, readBytes() returns a byte array of size 20 instead of an int array of 5. readBytes() can be used to copy data from one dataset to another efficiently because the raw data is not converted to its native type, it saves memory space and CPU time.

Specified by:

readBytes in class Dataset

Returns:

the byte array of the raw data.

Throws:

hdf.hdf5lib.exceptions.HDF5Exception

read

public Object read()
            throws Exception

Reads the data from file. read() reads the data from file to a memory buffer and returns the memory buffer. The dataset object does not hold the memory buffer. To store the memory buffer in the dataset object, one must call getData(). By default, the whole dataset is read into memory. Users can also select a subset to read. Subsetting is done in an implicit way. How to Select a Subset A selection is specified by three arrays: start, stride and count.

1. start: offset of a selection
2. stride: determines how many elements to move in each dimension
3. count: number of elements to select in each dimension

getStartDims(), getStride() and getSelectedDims() returns the start, stride and count arrays respectively. Applications can make a selection by changing the values of the arrays. The following example shows how to make a subset. In the example, the dataset is a 4-dimensional array of [200][100][50][10], i.e. dims[0]=200; dims[1]=100; dims[2]=50; dims[3]=10;
We want to select every other data point in dims[1] and dims[2]

 int rank = dataset.getRank(); // number of dimensions of the dataset
 long[] dims = dataset.getDims(); // the dimension sizes of the dataset
 long[] selected = dataset.getSelectedDims(); // the selected size of the
                                              // dataset
 long[] start = dataset.getStartDims(); // the offset of the selection
 long[] stride = dataset.getStride(); // the stride of the dataset
 int[] selectedIndex = dataset.getSelectedIndex(); // the selected
                                                   // dimensions for
                                                   // display

 // select dim1 and dim2 as 2D data for display, and slice through dim0
 selectedIndex[0] = 1;
 selectedIndex[1] = 2;
 selectedIndex[1] = 0;

 // reset the selection arrays
 for (int i = 0; i < rank; i++) {
     start[i] = 0;
     selected[i] = 1;
     stride[i] = 1;
 }

 // set stride to 2 on dim1 and dim2 so that every other data point is
 // selected.
 stride[1] = 2;
 stride[2] = 2;

 // set the selection size of dim1 and dim2
 selected[1] = dims[1] / stride[1];
 selected[2] = dims[1] / stride[2];

 // when dataset.getData() is called, the selection above will be used
 // since
 // the dimension arrays are passed by reference. Changes of these arrays
 // outside the dataset object directly change the values of these array
 // in the dataset object.
 

For ScalarDS, the memory data buffer is a one-dimensional array of byte, short, int, float, double or String type based on the datatype of the dataset.

Specified by:

read in interface DataFormat

Returns:

the data read from file.

Throws:

Exception - if object can not be read

See Also:

• Dataset.getData()
• DataFormat.read()

write

public void write(Object buf)
           throws Exception

Writes the given data buffer into this dataset in a file.

Specified by:

write in interface DataFormat

Parameters:

buf - The buffer that contains the data values.

Throws:

Exception - If there is an error at the HDF5 library level.

getMetadata

public List<Attribute> getMetadata()
                            throws hdf.hdf5lib.exceptions.HDF5Exception

Retrieves the object's metadata, such as attributes, from the file. Metadata, such as attributes, is stored in a List.

Specified by:

getMetadata in interface MetaDataContainer

Returns:

the list of metadata objects.

Throws:

hdf.hdf5lib.exceptions.HDF5Exception - if the metadata can not be retrieved

getMetadata

public List<Attribute> getMetadata(int... attrPropList)
                            throws hdf.hdf5lib.exceptions.HDF5Exception

Retrieves the object's metadata, such as attributes, from the file. Metadata, such as attributes, is stored in a List.

Parameters:

attrPropList - the list of properties to get

Returns:

the list of metadata objects.

Throws:

hdf.hdf5lib.exceptions.HDF5Exception - if the metadata can not be retrieved

writeMetadata

public void writeMetadata(Object info)
                   throws Exception

Writes a specific piece of metadata (such as an attribute) into the file. If an HDF(4&5) attribute exists in the file, this method updates its value. If the attribute does not exist in the file, it creates the attribute in the file and attaches it to the object. It will fail to write a new attribute to the object where an attribute with the same name already exists. To update the value of an existing attribute in the file, one needs to get the instance of the attribute by getMetadata(), change its values, then use writeMetadata() to write the value.

Specified by:

writeMetadata in interface MetaDataContainer

Parameters:

info - the metadata to write.

Throws:

Exception - if the metadata can not be written

removeMetadata

public void removeMetadata(Object info)
                    throws hdf.hdf5lib.exceptions.HDF5Exception

Deletes an existing piece of metadata from this object.

Specified by:

removeMetadata in interface MetaDataContainer

Parameters:

info - the metadata to delete.

Throws:

hdf.hdf5lib.exceptions.HDF5Exception - if the metadata can not be removed

updateMetadata

public void updateMetadata(Object info)
                    throws hdf.hdf5lib.exceptions.HDF5Exception

Updates an existing piece of metadata attached to this object.

Specified by:

updateMetadata in interface MetaDataContainer

Parameters:

info - the metadata to update.

Throws:

hdf.hdf5lib.exceptions.HDF5Exception - if the metadata can not be updated

setName

public void setName(String newName)
             throws Exception

Description copied from class: HObject

Sets the name of the object. setName (String newName) changes the name of the object in the file.

Overrides:

setName in class HObject

Parameters:

newName - The new name of the object.

Throws:

Exception - if name is root or contains separator

resetSelection

protected void resetSelection()

Resets selection of dataspace

Overrides:

resetSelection in class Dataset

create

public static Dataset create(String name,
 Group pgroup,
 Datatype type,
 long[] dims,
 long[] maxdims,
 long[] chunks,
 int gzip,
 Object data)
                      throws Exception

Creates a scalar dataset in a file with/without chunking and compression.

Parameters:

name - the name of the dataset to create.

pgroup - parent group where the new dataset is created.

type - the datatype of the dataset.

dims - the dimension size of the dataset.

maxdims - the max dimension size of the dataset. maxdims is set to dims if maxdims = null.

chunks - the chunk size of the dataset. No chunking if chunk = null.

gzip - GZIP compression level (1 to 9). No compression if gzip<=0.

data - the array of data values.

Returns:

the new scalar dataset if successful; otherwise returns null.

Throws:

Exception - if there is a failure.

create

public static Dataset create(String name,
 Group pgroup,
 Datatype type,
 long[] dims,
 long[] maxdims,
 long[] chunks,
 int gzip,
 Object fillValue,
 Object data)
                      throws Exception

Creates a scalar dataset in a file with/without chunking and compression. The following example shows how to create a string dataset using this function.

 H5File file = new H5File("test.h5", H5File.CREATE);
 int max_str_len = 120;
 Datatype strType = new H5Datatype(Datatype.CLASS_STRING, max_str_len, Datatype.NATIVE,
 Datatype.NATIVE); int size = 10000; long dims[] = { size }; long chunks[] = { 1000 }; int gzip = 9;
 String strs[] = new String[size];

 for (int i = 0; i < size; i++)
     strs[i] = String.valueOf(i);

 file.open();
 file.createScalarDS("/1D scalar strings", null, strType, dims, null, chunks, gzip, strs);

 try {
     file.close();
 }
 catch (Exception ex) {
 }
 

Parameters:

name - the name of the dataset to create.

pgroup - parent group where the new dataset is created.

type - the datatype of the dataset.

dims - the dimension size of the dataset.

maxdims - the max dimension size of the dataset. maxdims is set to dims if maxdims = null.

chunks - the chunk size of the dataset. No chunking if chunk = null.

gzip - GZIP compression level (1 to 9). No compression if gzip<=0.

fillValue - the default data value.

data - the array of data values.

Returns:

the new scalar dataset if successful; otherwise returns null.

Throws:

Exception - if there is a failure.

copy

public Dataset copy(Group pgroup,
 String dstName,
 long[] dims,
 Object buff)
             throws Exception

Description copied from class: Dataset

Creates a new dataset and writes the data buffer to the new dataset. This function allows applications to create a new dataset for a given data buffer. For example, users can select a specific interesting part from a large image and create a new image with the selection. The new dataset retains the datatype and dataset creation properties of this dataset.

Specified by:

copy in class Dataset

Parameters:

pgroup - the group which the dataset is copied to.

dstName - the name of the new dataset.

dims - the dimension sizes of the the new dataset.

buff - the data values of the subset to be copied.

Returns:

the new dataset.

Throws:

Exception - if dataset can not be copied

getNumberOfPalettes

public int getNumberOfPalettes()

Get the number of pallettes for this object.

Overrides:

getNumberOfPalettes in class ScalarDS

Returns:

the number of palettes if it has any, 0 otherwise.

getPalette

public byte[][] getPalette()

Description copied from class: ScalarDS

Returns the palette of this scalar dataset or null if palette does not exist. A Scalar dataset can be displayed as spreadsheet data or an image. When a scalar dataset is displayed as an image, the palette or color table may be needed to translate a pixel value to color components (for example, red, green, and blue). Some scalar datasets have no palette and some datasets have one or more than one palettes. If an associated palette exists but is not loaded, this interface retrieves the palette from the file and returns the palette. If the palette is loaded, it returns the palette. It returns null if there is no palette associated with the dataset. Current implementation only supports palette model of indexed RGB with 256 colors. Other models such as YUV", "CMY", "CMYK", "YCbCr", "HSV will be supported in the future. The palette values are stored in a two-dimensional byte array and are arranges by color components of red, green and blue. palette[][] = byte[3][256], where, palette[0][], palette[1][] and palette[2][] are the red, green and blue components respectively. Sub-classes have to implement this interface. HDF4 and HDF5 images use different libraries to retrieve the associated palette.

Overrides:

getPalette in class ScalarDS

Returns:

the 2D palette byte array.

getPaletteName

public String getPaletteName(int idx)

Description copied from class: ScalarDS

Get the name of a specific image palette from file. A scalar dataset may have multiple palettes attached to it. getPaletteName(int idx) returns the name of a specific palette identified by its index.

Overrides:

getPaletteName in class ScalarDS

Parameters:

idx - the index of the palette to retrieve the name.

Returns:

The name of the palette

readPalette

public byte[][] readPalette(int idx)

Description copied from class: ScalarDS

Reads a specific image palette from file. A scalar dataset may have multiple palettes attached to it. readPalette(int idx) returns a specific palette identified by its index.

Overrides:

readPalette in class ScalarDS

Parameters:

idx - the index of the palette to read.

Returns:

the image palette

readNumberOfPalettes

public int readNumberOfPalettes()

reads references of palettes to count the numberOfPalettes.

Returns:

the number of palettes referenced.

extend

public void extend(long[] newDims)
            throws hdf.hdf5lib.exceptions.HDF5Exception

H5Dset_extent verifies that the dataset is at least of size size, extending it if necessary. The dimensionality of size is the same as that of the dataspace of the dataset being changed. This function can be applied to the following datasets: 1) Any dataset with unlimited dimensions 2) A dataset with fixed dimensions if the current dimension sizes are less than the maximum sizes set with maxdims (see H5Screate_simple)

Parameters:

newDims - the dimension target size

Throws:

hdf.hdf5lib.exceptions.HDF5Exception - If there is an error at the HDF5 library level.

isVirtual

public boolean isVirtual()

Description copied from class: Dataset

Checks if dataset is virtual. Sub-classes must replace this default implementation.

Overrides:

isVirtual in class Dataset

Returns:

true if the dataset is virtual; otherwise returns false.

getVirtualFilename

public String getVirtualFilename(int index)

Description copied from class: Dataset

Gets the source file name at index if dataset is virtual. Sub-classes must replace this default implementation.

Overrides:

getVirtualFilename in class Dataset

Parameters:

index - index of the source file name if dataset is virtual.

Returns:

filename if the dataset is virtual; otherwise returns null.

getVirtualMaps

public int getVirtualMaps()

Description copied from class: Dataset

Gets the number of source files if dataset is virtual. Sub-classes must replace this default implementation.

Overrides:

getVirtualMaps in class Dataset

Returns:

the list size if the dataset is virtual; otherwise returns negative.

toString

public String toString(String delimiter,
 int maxItems)

Description copied from class: Dataset

Returns a string representation of the data value. For example, "0, 255". For a compound datatype, it will be a 1D array of strings with field members separated by the delimiter. For example, "{0, 10.5}, {255, 20.0}, {512, 30.0}" is a compound attribute of {int, float} of three data points.

Overrides:

toString in class Dataset

Parameters:

delimiter - The delimiter used to separate individual data points. It can be a comma, semicolon, tab or space. For example, toString(",") will separate data by commas.

maxItems - The maximum number of Array values to return

Returns:

the string representation of the data values.