public class H4SDS extends ScalarDS
The data contained in an SDS array has a data type associated with it. The standard data types supported by the SD interface include 32- and 64-bit floating-point numbers, 8-, 16- and 32-bit signed integers, 8-, 16- and 32-bit unsigned integers, and 8-bit characters.
How to Select a Subset
Dataset defines APIs for read, write and subet a dataset. No function is defined to select a subset of a data array. The selection is done in an implicit way. Function calls to dimension information such as getSelectedDims() return an array of dimension values, which is a reference to the array in the dataset object. Changes of the array outside the dataset object directly change the values of the array in the dataset object. It is like pointers in C.
The following is an example of how to make a subset. In the example, the dataset
is a 4-dimension with size 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 points in dims[1] and dims[2]
int rank = dataset.getRank(); // number of dimension of the dataset long[] dims = dataset.getDims(); // the dimension sizes of the dataset long[] selected = dataset.getSelectedDims(); // the selected size of the dataet long[] start = dataset.getStartDims(); // the off set 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
Modifier and Type | Field and Description |
---|---|
static int |
DFTAG_NDG_NETCDF
tag for netCDF datasets.
|
fillValue, imageDataRange, interlace, INTERLACE_LINE, INTERLACE_PIXEL, INTERLACE_PLANE, isDefaultImageOrder, isFillValueConverted, isImage, isImageDisplay, isText, isTrueColor, isUnsigned, palette, unsignedConverted
chunkSize, compression, convertByteToString, convertedBuf, data, datatype, dimNames, dims, enumConverted, isDataLoaded, maxDims, nPoints, originalBuf, rank, selectedDims, selectedIndex, selectedStride, startDims
fileFormat, linkTargetObjName, oid, separator
Constructor and Description |
---|
H4SDS(FileFormat theFile,
java.lang.String name,
java.lang.String path) |
H4SDS(FileFormat theFile,
java.lang.String name,
java.lang.String path,
long[] oid)
Creates an H4SDS object with specific name and path.
|
Modifier and Type | Method and Description |
---|---|
void |
close(int id)
Closes access to the object.
|
Dataset |
copy(Group pgroup,
java.lang.String dname,
long[] dims,
java.lang.Object buff)
Creates a new dataset and writes the data buffer to the new dataset.
|
static H4SDS |
create(java.lang.String name,
Group pgroup,
Datatype type,
long[] dims,
long[] maxdims,
long[] chunks,
int gzip,
java.lang.Object data) |
static H4SDS |
create(java.lang.String name,
Group pgroup,
Datatype type,
long[] dims,
long[] maxdims,
long[] chunks,
int gzip,
java.lang.Object fillValue,
java.lang.Object data)
Creates a new dataset.
|
Datatype |
getDatatype()
Returns the datatype object of the dataset.
|
java.util.List |
getMetadata()
Retrieves the metadata such as attributes from file.
|
java.util.List |
getMetadata(int... attrPropList) |
byte[][] |
getPalette()
Returns the palette of this scalar dataset or null if palette does not exist.
|
byte[] |
getPaletteRefs()
Returns the byte array of palette refs.
|
boolean |
hasAttribute()
Check if the object has any attributes attached.
|
void |
init()
Initializes the H4SDS such as dimension size of this dataset.
|
int |
open()
Opens an existing object such as dataset or group for access.
|
java.lang.Object |
read()
Reads the data from file.
|
byte[] |
readBytes()
Reads the raw data of the dataset from file to a byte array.
|
byte[][] |
readPalette(int idx)
Reads a specific image palette from file.
|
void |
removeMetadata(java.lang.Object info)
Deletes an existing metadata from this data object.
|
void |
write(java.lang.Object buf)
Writes a memory buffer to the dataset in file.
|
void |
writeMetadata(java.lang.Object info)
Writes a specific metadata (such as attribute) into file.
|
addFilteredImageValue, clearData, convertFromUnsignedC, convertToUnsignedC, getFillValue, getFilteredImageValues, getImageDataRange, getInterlace, getPaletteName, isDefaultImageOrder, isImage, isImageDisplay, isText, isTrueColor, isUnsigned, setImageDataRange, setIsImage, setIsImageDisplay, setPalette
byteToString, clear, convertFromUnsignedC, convertFromUnsignedC, convertToUnsignedC, convertToUnsignedC, getChunkSize, getCompression, getConvertByteToString, getData, getDimNames, getDims, getHeight, getMaxDims, getOriginalClass, getRank, getSelectedDims, getSelectedIndex, getSize, getStartDims, getStride, getWidth, isEnumConverted, isString, setConvertByteToString, setData, setEnumConverted, stringToByte, write
debug, equalsOID, getFID, getFile, getFileFormat, getFullName, getLinkTargetObjName, getName, getOID, getPath, setLinkTargetObjName, setName, setPath, toString
public static final int DFTAG_NDG_NETCDF
public H4SDS(FileFormat theFile, java.lang.String name, java.lang.String path)
public H4SDS(FileFormat theFile, java.lang.String name, java.lang.String path, long[] oid)
theFile
- the HDF file.name
- the name of this H4SDS.path
- the full path of this H4SDS.oid
- the unique identifier of this data object.public boolean hasAttribute()
DataFormat
public byte[][] readPalette(int idx)
ScalarDS
A scalar dataset may have multiple palettes attached to it. readPalette(int idx) returns a specific palette identified by its index.
readPalette
in class ScalarDS
idx
- the index of the palette to read.public byte[] getPaletteRefs()
ScalarDS
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".
getPaletteRefs
in class ScalarDS
public Datatype getDatatype()
Dataset
getDatatype
in class Dataset
public Dataset copy(Group pgroup, java.lang.String dname, long[] dims, java.lang.Object buff) throws java.lang.Exception
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.
public byte[] readBytes() throws HDFException
Dataset
readBytes() reads raw data to an array of bytes instead of array of its datatype. For example, for an one-dimension 32-bit integer dataset of size 5, the readBytes() returns of 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.
readBytes
in class Dataset
HDFException
public java.lang.Object read() throws HDFException
Dataset
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 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.
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 dimension 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 off set 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 points are // 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 an one-dimensional array of byte, short, int, float, double or String type based on the datatype of the dataset.
For CompoundDS, the memory data object is an java.util.List object. Each element of the list is a data array that corresponds to a compound field.
For example, if compound dataset "comp" has the following nested structure, and member datatypes
comp --> m01 (int) comp --> m02 (float) comp --> nest1 --> m11 (char) comp --> nest1 --> m12 (String) comp --> nest1 --> nest2 --> m21 (long) comp --> nest1 --> nest2 --> m22 (double)getData() returns a list of six arrays: {int[], float[], char[], String[], long[] and double[]}.
read
in class Dataset
HDFException
Dataset.getData()
public void write(java.lang.Object buf) throws HDFException
Dataset
write
in class Dataset
buf
- the data to writeHDFException
public java.util.List getMetadata() throws HDFException
DataFormat
Metadata such as attributes are stored in a List.
HDFException
public void writeMetadata(java.lang.Object info) throws java.lang.Exception
DataFormat
If an HDF(4&5) attribute exists in file, the method updates its value. If the attribute does not exists in file, it creates the attribute in 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 file, one needs to get the instance of the attribute by getMetadata(), change its values, and use writeMetadata() to write the value.
info
- the metadata to write.java.lang.Exception
public void removeMetadata(java.lang.Object info) throws HDFException
DataFormat
info
- the metadata to delete.HDFException
public int open()
HObject
open
in class HObject
HObject.close(int)
public void close(int id)
HObject
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 ncsa.hdf.hdf5lib.H5.H5Gclose() method and closes the group resource specified by the group id.
public void init()
public byte[][] getPalette()
ScalarDS
Scalar dataset can be displayed as spreadsheet data or image. When a scalar dataset is chosen to display 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 not loaded, this interface retrieves the palette from the file and returns the palette. If the palette is loaded, it returnd the palette. It returns null if there is no palette assciated 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 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.
Sub-classes have to implement this interface. HDF4 and HDF5 images use different libraries to retrieve the associated palette.
getPalette
in class ScalarDS
public static H4SDS create(java.lang.String name, Group pgroup, Datatype type, long[] dims, long[] maxdims, long[] chunks, int gzip, java.lang.Object fillValue, java.lang.Object data) throws java.lang.Exception
name
- the name of the dataset to create.pgroup
- the parent group of the new dataset.type
- the datatype of the dataset.dims
- the dimension size of the dataset.maxdims
- the max dimension size of the dataset.chunks
- the chunk size of the dataset.gzip
- the level of the gzip compression.data
- the array of data values.java.lang.Exception
public static H4SDS create(java.lang.String name, Group pgroup, Datatype type, long[] dims, long[] maxdims, long[] chunks, int gzip, java.lang.Object data) throws java.lang.Exception
java.lang.Exception
public java.util.List getMetadata(int... attrPropList) throws java.lang.Exception
java.lang.Exception