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 reading, writing and subsetting 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 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 dataet
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.read() is called, the slection above will be used since
// the dimension arrays is passed by reference. Changes of these arrays
// outside the dataset object directly change the values of these array
// in the dataset object.
| 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, unsignedConvertedchunkSize, compression, compression_gzip_txt, convertByteToString, convertedBuf, data, datatype, dimNames, dims, enumConverted, filters, isDataLoaded, maxDims, nPoints, originalBuf, rank, selectedDims, selectedIndex, selectedStride, startDims, storage, storage_layoutfileFormat, linkTargetObjName, oid, separator| Constructor and Description |
|---|
H4SDS(FileFormat theFile,
String name,
String path) |
H4SDS(FileFormat theFile,
String name,
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,
String dname,
long[] dims,
Object buff)
Creates a new dataset and writes the data buffer to the new dataset.
|
static H4SDS |
create(String name,
Group pgroup,
Datatype type,
long[] dims,
long[] maxdims,
long[] chunks,
int gzip,
Object data) |
static H4SDS |
create(String name,
Group pgroup,
Datatype type,
long[] dims,
long[] maxdims,
long[] chunks,
int gzip,
Object fillValue,
Object data)
Creates a new dataset.
|
Datatype |
getDatatype()
Returns the datatype object of the dataset.
|
List |
getMetadata()
Retrieves the metadata such as attributes from file.
|
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 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.
|
byte[][] |
readPalette(int idx)
Reads a specific image palette from file.
|
void |
removeMetadata(Object info)
Deletes an existing metadata from this data object.
|
void |
updateMetadata(Object info)
Updates an existing metadata from this data object.
|
void |
write(Object buf)
Writes a memory buffer to the dataset in file.
|
void |
writeMetadata(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, setPalettebyteToString, clear, convertFromUnsignedC, convertFromUnsignedC, convertToUnsignedC, convertToUnsignedC, getChunkSize, getCompression, getConvertByteToString, getData, getDimNames, getDims, getFilters, getHeight, getMaxDims, getOriginalClass, getRank, getSelectedDims, getSelectedIndex, getSize, getStartDims, getStorage, getStorageLayout, getStride, getWidth, isEnumConverted, isString, setConvertByteToString, setData, setEnumConverted, stringToByte, writedebug, equals, equalsOID, getFID, getFile, getFileFormat, getFullName, getLinkTargetObjName, getName, getOID, getPath, setLinkTargetObjName, setName, setPath, toStringpublic static final int DFTAG_NDG_NETCDF
public H4SDS(FileFormat theFile, String name, String path)
public H4SDS(FileFormat theFile, String name, 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()
DataFormatpublic byte[][] readPalette(int idx)
ScalarDSA scalar dataset may have multiple palettes attached to it. readPalette(int idx) returns a specific palette identified by its index.
readPalette in class ScalarDSidx - the index of the palette to read.public byte[] getPaletteRefs()
ScalarDSA 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 ScalarDSpublic Datatype getDatatype()
DatasetgetDatatype in class Datasetpublic Dataset copy(Group pgroup, String dname, long[] dims, Object buff) throws Exception
DatasetThis 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.
copy in class Datasetpgroup - the group which the dataset is copied to.dname - 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.Exception - if dataset can not be copiedpublic byte[] readBytes() throws hdf.hdflib.HDFException
DatasetreadBytes() 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.
public Object read() throws hdf.hdflib.HDFException
Datasetread() 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.
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.
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 Datasethdf.hdflib.HDFExceptionDataset.getData()public void write(Object buf) throws hdf.hdflib.HDFException
Datasetpublic List getMetadata() throws hdf.hdflib.HDFException
DataFormatMetadata such as attributes are stored in a List.
hdf.hdflib.HDFExceptionpublic void writeMetadata(Object info) throws Exception
DataFormatinfo - the metadata to write.Exception - if the metadata can not be writtenpublic void removeMetadata(Object info) throws hdf.hdflib.HDFException
DataFormatinfo - the metadata to delete.hdf.hdflib.HDFExceptionpublic void updateMetadata(Object info) throws Exception
DataFormatinfo - the metadata to update.Exception - if the metadata can not be updatedpublic int open()
HObjectopen in class HObjectHObject.close(int)public void close(int id)
HObjectSub-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.
public void init()
public byte[][] getPalette()
ScalarDSA 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.
getPalette in class ScalarDSpublic static H4SDS create(String name, Group pgroup, Datatype type, long[] dims, long[] maxdims, long[] chunks, int gzip, Object fillValue, Object data) throws 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.fillValue - the default value.data - the array of data values.Exception - if the dataset can not be createdpublic static H4SDS create(String name, Group pgroup, Datatype type, long[] dims, long[] maxdims, long[] chunks, int gzip, Object data) throws Exception
Exceptionpublic List getMetadata(int... attrPropList) throws Exception
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