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How to use it
The HDF Object Package is used by Java applications to access HDF4 and HDF5 files without directly calling the HDF4 and HDF5 library APIs. Library calls are encapsulated into respective classes. The HDF Object Package requires the The Java HDF Interface (JHI) and The Java HDF5 Interface (JHI5). Figure 2 shows the relationship of the packages.
Figure 2. The Software packages
Set CLASSPATH
Before you use the HDF object package, you must set the Java CLASSPATH.At Solaris, OS X or Linux
Suppose you install the HDF object package at /home/usr/hdfobj.setenv CLASSPATH $CLASSPATH:/home/usr/hdfobj/*:
export CLASSPATH
At Windows
Suppose you install the HDF object package at c:\apps\hdfobj.setenv CLASSPATH=%CLASSPATH%;c:\apps\hdfobj\*;
Set Library Path
The object package should include the HDF4 and HDF5 library. To use the object package, you must set the path to the library. Otherwise, you will get "java.lang.UnsatisfiedLinkError".At unix
Suppose you install the HDF object package at /home/usr/hdfobj.For Solaris, OS X or Linux
setenv PATH $PATH:/home/usr/hdfobj/lib
At Windows
Suppose you install the HDF object package at c:\apps\hdfobj.
setenv PATH=%PATH%;c:\apps\hdfobj\lib
How to select a subset
Dataset defines APIs for reading and writing to a dataset, but 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 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[2] = 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.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.
Examples
The following examples show you how to use the object package. The examples demonstrate how to access HDF4 and HDF files without any direct function calls to the HDF4 or HDF5 library.Create File
H4FileCreate.javaH5FileCreate.java
These two examples show you how to create an empty HDF4/5 file using the "HDF Object Package (Java)".
Create Group
H4GroupCreate.javaH5GroupCreate.java
These two examples show you how to create HDF4/5 groups using the "HDF Object Package (Java)". The examples create the group structure:
"/" (root)
g1
g11
g12
g2
g21
g22
Create Datatype/Dataset
H4DatasetCreate.javaH5DatasetCreate.java
These two examples show you how to create HDF4/5 datasets using the "HDF Object Package (Java)". The examples create the group structure and datasets:
"/" (root)
integer arrays
2D 32-bit integer 20x10
3D unsigned 8-bit integer 20x10x5
float arrays
2D 64-bit double 20x10
3D 32-bit float 20x10x5
Retrieve File Structure
H4FileStructure.javaH5FileStructure.java
These two examples show you how to retrieve HDF file structure using the "HDF Object Package (Java)". The examples create the group structure and datasets, and print out the file structure:
"/" (root)
integer arrays
2D 32-bit integer 20x10
3D unsigned 8-bit integer 20x10x5
float arrays
2D 64-bit double 20x10
3D 32-bit float 20x10x5
Read/Write Dataset
H4DatasetRead.javaH5DatasetRead.java
These two examples show you how to read/write HDF datasets using the "HDF Object Package (Java)". The examples create an integer dataset, and read and write data values:
"/" (root)
2D 32-bit integer 20x10
Create Attribute/Read/Write Attribute
H4AttributeCreate.javaH5AttributeCreate.java
These two examples show you how to create/read/write HDF attributes using the "HDF Object Package (Java)". The example creates an attribute and reads and writes the attribute value:
"/" (root)
2D 32-bit integer 20x10
(attribute: name="data range", value=[0, 10000])
Select Subset
H4SubsetSelect.javaH5SubsetSelect.java
These two examples show you how to select a subset using the "HDF Object Package (Java)". The example creates an integer dataset and reads a subset of the dataset:
"/" (root)
2D 32-bit integer 20x10
The whole 20x10 data set is
1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007, 1008, 1009 1100, 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1109 1200, 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209 1300, 1301, 1302, 1303, 1304, 1305, 1306, 1307, 1308, 1309 1400, 1401, 1402, 1403, 1404, 1405, 1406, 1407, 1408, 1409 1500, 1501, 1502, 1503, 1504, 1505, 1506, 1507, 1508, 1509 1600, 1601, 1602, 1603, 1604, 1605, 1606, 1607, 1608, 1609 1700, 1701, 1702, 1703, 1704, 1705, 1706, 1707, 1708, 1709 1800, 1801, 1802, 1803, 1804, 1805, 1806, 1807, 1808, 1809 1900, 1901, 1902, 1903, 1904, 1905, 1906, 1907, 1908, 1909 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 2100, 2101, 2102, 2103, 2104, 2105, 2106, 2107, 2108, 2109 2200, 2201, 2202, 2203, 2204, 2205, 2206, 2207, 2208, 2209 2300, 2301, 2302, 2303, 2304, 2305, 2306, 2307, 2308, 2309 2400, 2401, 2402, 2403, 2404, 2405, 2406, 2407, 2408, 2409 2500, 2501, 2502, 2503, 2504, 2505, 2506, 2507, 2508, 2509 2600, 2601, 2602, 2603, 2604, 2605, 2606, 2607, 2608, 2609 2700, 2701, 2702, 2703, 2704, 2705, 2706, 2707, 2708, 2709 2800, 2801, 2802, 2803, 2804, 2805, 2806, 2807, 2808, 2809 2900, 2901, 2902, 2903, 2904, 2905, 2906, 2907, 2908, 2909
Subset: start=(4, 2), size=(5, 3) and stride=(3, 2). The subset values are:
1402,1404,1406 1702,1704,1706 2002,2004,2006 2302,2304,2306 2602,2604,2606
- - Last modified: 12 October 2016