public class H4GRImage extends ScalarDS
Every GR data set must contain the following components: image array, name, pixel type, and dimensions. The name, dimensions, and pixel type must be supplied by the user at the time the GR data set is defined.
An image array is a two-dimensional array of pixels. Each element in an image array corresponds to one pixel and each pixel can consist of a number of color component values or pixel components, e.g., Red-Green-Blue or RGB, Cyan-Magenta-Yellow-Black or CMYK, etc. Pixel components can be represented by different methods (8-bit lookup table or 24-bit direct representation) and may have different data types. The data type of pixel components and the number of components in each pixel are collectively known as the pixel type.
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 are passed by reference. Changes of these arrays
// outside the dataset object directly change the values of these array
// in the dataset object.
fillValue, imageDataRange, interlace, INTERLACE_LINE, INTERLACE_PIXEL, INTERLACE_PLANE, isDefaultImageOrder, isFillValueConverted, isImage, isImageDisplay, isText, isTrueColor, palette, unsignedConvertedchunkSize, compression, compression_gzip_txt, convertByteToString, convertedBuf, data, datatype, dimNames, dims, filters, inited, isDataLoaded, maxDims, nPoints, originalBuf, rank, selectedDims, selectedIndex, selectedStride, startDims, storage, storage_layoutfileFormat, linkTargetObjName, oid, separator| Constructor and Description |
|---|
H4GRImage(FileFormat theFile,
String name,
String path) |
H4GRImage(FileFormat theFile,
String name,
String path,
long[] oid)
Creates a H4GRImage object with specific name, path, and object ID.
|
| Modifier and Type | Method and Description |
|---|---|
void |
close(long grid)
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 H4GRImage |
create(String name,
Group pgroup,
Datatype type,
long[] dims,
long[] maxdims,
long[] chunks,
int gzip,
int ncomp,
int interlace,
Object data)
Creates a new image.
|
int |
getComponentCount()
Returns the number of components of this image data.
|
Datatype |
getDatatype()
Returns the datatype of the data object.
|
List |
getMetadata()
Retrieves the object's metadata, such as attributes, from the 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() |
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.
|
byte[][] |
readPalette(int idx)
Reads a specific image palette from file.
|
void |
removeMetadata(Object info)
Deletes an existing piece of metadata from this object.
|
void |
updateMetadata(Object info)
Updates an existing piece of metadata attached to this object.
|
void |
write(Object buf)
Writes a memory buffer to the object in the file.
|
void |
writeMetadata(Object info)
Writes a specific piece of metadata (such as an attribute) into the file.
|
addFilteredImageValue, clearData, convertFromUnsignedC, convertToUnsignedC, getFillValue, getFilteredImageValues, getImageDataRange, getInterlace, getPaletteName, isDefaultImageOrder, isImage, isImageDisplay, isTrueColor, 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, getVirtualFilename, getVirtualMaps, getWidth, isInited, isString, isVirtual, setConvertByteToString, setData, stringToByte, writedebug, equals, equalsOID, getFID, getFile, getFileFormat, getFullName, getLinkTargetObjName, getName, getOID, getPath, setLinkTargetObjName, setName, setPath, toStringpublic H4GRImage(FileFormat theFile, String name, String path)
public H4GRImage(FileFormat theFile, String name, String path, long[] oid)
theFile - the HDF file.name - the name of this H4GRImage.path - the full path of this H4GRImage.oid - the unique identifier of this data object.public boolean hasAttribute()
MetaDataContainerpublic 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[][] 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()
DataFormatgetDatatype in interface DataFormatgetDatatype in class Datasetpublic 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
DataFormatread() 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.
hdf.hdflib.HDFExceptionDataFormat.getData()public void write(Object buf) throws hdf.hdflib.HDFException
DataFormatbuf - the data to writehdf.hdflib.HDFExceptionpublic List getMetadata() throws hdf.hdflib.HDFException
MetaDataContainerMetadata, such as attributes, is stored in a List.
hdf.hdflib.HDFExceptionpublic void writeMetadata(Object info) throws Exception
MetaDataContainerinfo - the metadata to write.Exception - if the metadata can not be writtenpublic void removeMetadata(Object info) throws hdf.hdflib.HDFException
MetaDataContainerinfo - the metadata to delete.hdf.hdflib.HDFExceptionpublic void updateMetadata(Object info) throws Exception
MetaDataContainerinfo - the metadata to update.Exception - if the metadata can not be updatedpublic long open()
HObjectopen in class HObjectHObject.close(long)public void close(long grid)
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 int getComponentCount()
public static H4GRImage create(String name, Group pgroup, Datatype type, long[] dims, long[] maxdims, long[] chunks, int gzip, int ncomp, int interlace, 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.ncomp - number of components of the image data.interlace - the interlace mode.data - the array of data values.Exception - if the image can not be createdpublic List getMetadata(int... attrPropList) throws Exception
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