public class H4Vdata extends CompoundDS
A vdata is like a table that consists of a collection of records whose values are stored in fixed-length fields. All records have the same structure and all values in each field have the same data type. Vdatas are uniquely identified by a name, a class, and a series of individual field names.
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
isMemberSelected, memberDims, memberNames, memberOrders, memberTypes, numberOfMembers, separator
chunkSize, compression, convertByteToString, convertedBuf, data, datatype, dimNames, dims, enumConverted, isDataLoaded, maxDims, nPoints, originalBuf, rank, selectedDims, selectedIndex, selectedStride, startDims
fileFormat, linkTargetObjName, oid
Constructor and Description |
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H4Vdata(FileFormat theFile,
java.lang.String name,
java.lang.String path) |
H4Vdata(FileFormat theFile,
java.lang.String name,
java.lang.String path,
long[] oid)
Creates an H4Vdata object with specific name and path.
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Modifier and Type | Method and Description |
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void |
close(int vsid)
Closes access to the object.
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Datatype |
getDatatype()
Returns the datatype object of the dataset.
|
int |
getFieldCount()
Returns the number of fields.
|
int[] |
getFieldOrders()
Returns the orders of fields
|
java.util.List |
getMetadata()
Retrieves the metadata such as attributes from file.
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java.util.List |
getMetadata(int... attrPropList) |
int |
getRecordCount()
Returns the number of records.
|
boolean |
hasAttribute()
Check if the object has any attributes attached.
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void |
init()
Initializes the H4Vdata such as dimension sizes of this dataset.
|
int |
open()
Opens an existing object such as dataset or group for access.
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java.lang.Object |
read()
Reads the data from file.
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byte[] |
readBytes()
Reads the raw data of the dataset from file to a byte array.
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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.
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copy, getMemberCount, getMemberNames, getMemberOrders, getMemberTypes, getMemeberDims, getSelectedMemberCount, getSelectedMemberOrders, getSelectedMemberTypes, isMemberSelected, selectMember, setMemberSelection
byteToString, clear, clearData, 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 H4Vdata(FileFormat theFile, java.lang.String name, java.lang.String path)
public H4Vdata(FileFormat theFile, java.lang.String name, java.lang.String path, long[] oid)
theFile
- the HDF file.name
- the name of this H4Vdata.path
- the full path of this H4Vdata.oid
- the unique identifier of this data object.public boolean hasAttribute()
DataFormat
public Datatype getDatatype()
Dataset
getDatatype
in class 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 vsid)
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 int getRecordCount()
public int getFieldCount()
public int[] getFieldOrders()
public java.util.List getMetadata(int... attrPropList) throws java.lang.Exception
java.lang.Exception