Package hdf.object

Class ScalarDS

Object

hdf.object.HObject

hdf.object.Dataset

hdf.object.ScalarDS

All Implemented Interfaces:

DataFormat, MetaDataContainer, Serializable

public abstract class ScalarDS
extends Dataset

A scalar dataset is a multiple dimension array of scalar points. The Datatype of a scalar dataset must be an atomic datatype. Common datatypes of scalar datasets include char, byte, short, int, long, float, double and string.

A ScalarDS can be an image or spreadsheet data. ScalarDS defines methods to deal with both images and spreadsheets.

ScalarDS is an abstract class. Current implementing classes are the H4SDS, H5GRImage and H5ScalarDS.

Version:

1.1 9/4/2007

Author:

Peter X. Cao

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected Object	fillValue	The fill value of the dataset.
protected double[]	imageDataRange	The min-max range of image data values.
protected int	interlace	The interlace mode of the stored raster image data.
static int	INTERLACE_LINE	Indicates that each pixel component of RGB is stored as a scan line.
static int	INTERLACE_PIXEL	Indicates that the pixel RGB values are contiguous.
static int	INTERLACE_PLANE	Indicates that each pixel component of RGB is stored as a plane.
protected boolean	isDefaultImageOrder	Flag to indicate if the dataset is displayed as an image with default order of dimensions.
boolean	isFillValueConverted	Flag to indicate if the FillValue is converted from unsigned C.
protected boolean	isImage	True if this dataset is an image.
protected boolean	isImageDisplay	Flag to indicate if the dataset is displayed as an image.
protected boolean	isText	True if this dataset is ASCII text.
protected boolean	isTrueColor	True if this dataset is a true color image.
protected byte[][]	palette	The indexed RGB color model with 256 colors.
protected boolean	unsignedConverted	Flag to indicate is the original unsigned C data is converted.

Fields inherited from class hdf.object.Dataset

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

Fields inherited from class hdf.object.HObject

fileFormat, linkTargetObjName, oid, SEPARATOR

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	addFilteredImageValue(Number x)	Add a value that will be filtered out in an image.
void	clearData()	Clears the current data buffer in memory and forces the next read() to load the data from file.
Object	convertFromUnsignedC()	Converts the data values of this dataset to appropriate Java integer if they are unsigned integers.
Object	convertToUnsignedC()	Converts Java integer data of this dataset back to unsigned C-type integer data if they are unsigned integers.
Object	getFillValue()	Returns the fill values for the dataset.
List<Number>	getFilteredImageValues()	Get a list of values that will be filtered out in an image.
double[]	getImageDataRange()	Returns the (min, max) pair of image data range.
int	getInterlace()	Returns the interlace mode of a true color image (RGB).
abstract 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.
abstract byte[]	getPaletteRefs()	Returns the byte array of palette refs.
boolean	isDefaultImageOrder()	Returns true if this dataset is displayed as an image with default image order.
boolean	isImage()	Returns true if this dataset is an image.
boolean	isImageDisplay()	Returns true if this dataset is displayed as an image.
boolean	isTrueColor()
abstract byte[][]	readPalette(int idx)	Reads a specific image palette from file.
void	setImageDataRange(double min, double max)	Sets data range for an image.
void	setIsImage(boolean b)	Sets the flag to indicate this dataset is an image.
void	setIsImageDisplay(boolean b)	Sets the flag to display the dataset as an image.
void	setPalette(byte[][] pal)	Sets the palette for this dataset.

Methods inherited from class hdf.object.Dataset

byteToString, clear, convertFromUnsignedC, convertFromUnsignedC, convertToUnsignedC, convertToUnsignedC, copy, getChunkSize, getCompression, getConvertByteToString, getData, getDatatype, getDimNames, getDims, getFilters, getHeight, getMaxDims, getOriginalClass, getRank, getSelectedDims, getSelectedIndex, getSize, getStartDims, getStorage, getStorageLayout, getStride, getVirtualFilename, getVirtualMaps, getWidth, isInited, isString, isVirtual, readBytes, setConvertByteToString, setData, stringToByte, write

Methods inherited from class hdf.object.HObject

close, debug, equals, equals, equalsOID, getFID, getFile, getFileFormat, getFullName, getLinkTargetObjName, getName, getOID, getPath, hashCode, open, setLinkTargetObjName, setName, setPath, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface hdf.object.DataFormat

init, read, write

Methods inherited from interface hdf.object.MetaDataContainer

getMetadata, hasAttribute, removeMetadata, updateMetadata, writeMetadata

Field Detail

INTERLACE_PIXEL

public static final int INTERLACE_PIXEL

Indicates that the pixel RGB values are contiguous.

See Also:

Constant Field Values

INTERLACE_LINE

public static final int INTERLACE_LINE

Indicates that each pixel component of RGB is stored as a scan line.

See Also:

Constant Field Values

INTERLACE_PLANE

public static final int INTERLACE_PLANE

Indicates that each pixel component of RGB is stored as a plane.

See Also:

Constant Field Values

interlace

protected int interlace

The interlace mode of the stored raster image data. Valid values are INTERLACE_PIXEL, INTERLACE_LINE and INTERLACE_PLANE.

imageDataRange

protected double[] imageDataRange

The min-max range of image data values. For example, [0, 255] indicates the min is 0, and the max is 255.

palette

protected byte[][] palette

The indexed RGB color model with 256 colors.

The palette values are stored in a two-dimensional byte array and arrange 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.

isImage

protected boolean isImage

True if this dataset is an image.

isTrueColor

protected boolean isTrueColor

True if this dataset is a true color image.

isText

protected boolean isText

True if this dataset is ASCII text.

unsignedConverted

protected boolean unsignedConverted

Flag to indicate is the original unsigned C data is converted.

fillValue

protected Object fillValue

The fill value of the dataset.

isImageDisplay

protected boolean isImageDisplay

Flag to indicate if the dataset is displayed as an image.

isDefaultImageOrder

protected boolean isDefaultImageOrder

Flag to indicate if the dataset is displayed as an image with default order of dimensions.

isFillValueConverted

public boolean isFillValueConverted

Flag to indicate if the FillValue is converted from unsigned C.

Constructor Detail

ScalarDS

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

Constructs an instance of a ScalarDS with specific name and path. An HDF data object must have a name. The path is the group path starting from the root.

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/".

ScalarDS

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

Deprecated.

Not for public use in the future.
Using ScalarDS(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 v of the data object.

Method Detail

clearData

public void clearData()

Description copied from class: Dataset

Clears the current data buffer in memory and forces the next read() to load the data from file.

The function read() loads data from file into memory only if the data is not read. If data is already in memory, read() just returns the memory buffer. Sometimes we want to force read() to re-read data from file. For example, when the selection is changed, we need to re-read the data.

Specified by:

clearData in interface DataFormat

Overrides:

clearData in class Dataset

See Also:

Dataset.getData(), DataFormat.read()

convertFromUnsignedC

public Object convertFromUnsignedC()

Converts the data values of this dataset to appropriate Java integer if they are unsigned integers.

Returns:

the converted data buffer.

See Also:

Dataset.convertToUnsignedC(Object), Dataset.convertFromUnsignedC(Object, Object)

convertToUnsignedC

public Object convertToUnsignedC()

Converts Java integer data of this dataset back to unsigned C-type integer data if they are unsigned integers.

Returns:

the converted data buffer.

See Also:

Dataset.convertToUnsignedC(Object), Dataset.convertToUnsignedC(Object, Object), Dataset.convertFromUnsignedC(Object data_in)

getPalette

public abstract byte[][] getPalette()

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.

Returns:

the 2D palette byte array.

setPalette

public final void setPalette(byte[][] pal)

Sets the palette for this dataset.

Parameters:

pal - the 2D palette byte array.

readPalette

public abstract byte[][] readPalette(int idx)

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.

Parameters:

idx - the index of the palette to read.

Returns:

the image palette

getPaletteName

public String getPaletteName(int idx)

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.

Parameters:

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

Returns:

The name of the palette

getPaletteRefs

public abstract byte[] getPaletteRefs()

Returns the byte array of palette refs.

A palette reference is an object reference that points to the palette dataset.

For example, Dataset "Iceberg" has an attribute of object reference "Palette". The arrtibute "Palette" has value "2538" that is the object reference of the palette data set "Iceberg Palette".

Returns:

null if there is no palette attribute attached to this dataset.

isImage

public final boolean isImage()

Returns true if this dataset is an image.

For all Images, they must have an attribute called "CLASS". The value of this attribute is "IMAGE". For more details, read HDF5 Image and Palette Specification

Returns:

true if the dataset is an image; otherwise, returns false.

isImageDisplay

public final boolean isImageDisplay()

Returns true if this dataset is displayed as an image.

A ScalarDS can be displayed as an image or a spreadsheet in a table.

Returns:

true if this dataset is displayed as an image; otherwise, returns false.

isDefaultImageOrder

public final boolean isDefaultImageOrder()

Returns true if this dataset is displayed as an image with default image order.

A ScalarDS can be displayed as an image with different orders of dimensions.

Returns:

true if this dataset is displayed as an image with default image order; otherwise, returns false.

setIsImageDisplay

public final void setIsImageDisplay(boolean b)

Sets the flag to display the dataset as an image.

Parameters:

b - if b is true, display the dataset as an image

setIsImage

public final void setIsImage(boolean b)

Sets the flag to indicate this dataset is an image.

Parameters:

b - if b is true, the dataset is an image.

setImageDataRange

public final void setImageDataRange(double min,
                                    double max)

Sets data range for an image.

Parameters:

min - the data range start.

max - the data range end.

addFilteredImageValue

public void addFilteredImageValue(Number x)

Add a value that will be filtered out in an image.

Parameters:

x - value to be filtered

getFilteredImageValues

public List<Number> getFilteredImageValues()

Get a list of values that will be filtered out in an image.

Returns:

the list of Image values

isTrueColor

public final boolean isTrueColor()

Returns:

true if this dataset is a true color image.

getInterlace

public final int getInterlace()

Returns the interlace mode of a true color image (RGB). Valid values:

     INTERLACE_PIXEL -- RGB components are contiguous, i.e. rgb, rgb, rgb, ...
     INTERLACE_LINE -- each RGB component is stored as a scan line
     INTERLACE_PLANE -- each RGB component is stored as a plane
 

Returns:

the interlace mode of a true color image (RGB).

getImageDataRange

public double[] getImageDataRange()

Returns the (min, max) pair of image data range.

Returns:

the (min, max) pair of image data range.

getFillValue

public final Object getFillValue()

Returns the fill values for the dataset.

Returns:

the fill values for the dataset.