Hi,
I experiencing problems while reading dataset of string with hdf-java. I
can create a new 2 dimension dataset of string with dimension 3 x 2 and
length 100 both in code and HDFview. The h5dump utilities shows as
expected :
$ h5dump test.h5
HDF5 "test.h5" {
GROUP "/" {
DATASET "test" {
DATATYPE H5T_STRING {
STRSIZE 5;
STRPAD H5T_STR_NULLPAD;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SIMPLE { ( 3, 2 ) / ( 3, 2 ) }
DATA {
(0,0): "\000\000\000\000\000", "\000\000\000\000\000",
(1,0): "\000\000\000\000\000", "\000\000\000\000\000",
(2,0): "\000\000\000\000\000", "\000\000\000\000\000"
}
}
}
}
When I read this dataset in hdfview or in my code. The array of data is
not read correctly.
In HDFview, the table shown is represented as a dataset with only one
column. However the metadata indicates 3x2.
In my code using hdf-java, I cannot read completely the dataset. The
read array as only 2 value.
H5ScalarDS dataset = ....
....
long[] dims = dataset.getDims();
The values of dims are [3, 2], which is correct.
Object data = dataset.read();
The Array.getLength(data) is 2, and I expect 6 to read my strings.
There is no problem for dataset with other types, with integer for
example.
I'm using hdf-java-2.7 and HDFView Version 2.7.
Thanks
Guillaume
Guillaume,
Text strings can be only viewed one-dimension a time in HDFView. There is not good
way to show multiple dimensional array of strings. See details at User's Guide at
http://www.hdfgroup.org/hdf-java-html/hdfview/UsersGuide/ug07textview.html.
Bu default, hdf-java only loads strings one dimension a time. However, you can
select whatever subset of your array. For example, the following code will select the
whole dataset.
// set this before dataset.read()
int rank = dataset.getRank();
long[] dims = dataset.getDims();
long[] selected = dataset.getSelectedDims();
System.arraycopy(dims, 0, selected, 0, rank);
Thanks
--pc
···
On 3/29/2011 3:46 AM, Guillaume PRIN wrote:
Hi,
I experiencing problems while reading dataset of string with hdf-java. I
can create a new 2 dimension dataset of string with dimension 3 x 2 and
length 100 both in code and HDFview. The h5dump utilities shows as
expected :
$ h5dump test.h5
HDF5 "test.h5" {
GROUP "/" {
DATASET "test" {
DATATYPE H5T_STRING {
STRSIZE 5;
STRPAD H5T_STR_NULLPAD;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SIMPLE { ( 3, 2 ) / ( 3, 2 ) }
DATA {
(0,0): "\000\000\000\000\000", "\000\000\000\000\000",
(1,0): "\000\000\000\000\000", "\000\000\000\000\000",
(2,0): "\000\000\000\000\000", "\000\000\000\000\000"
}
}
}
When I read this dataset in hdfview or in my code. The array of data is
not read correctly.
In HDFview, the table shown is represented as a dataset with only one
column. However the metadata indicates 3x2.
In my code using hdf-java, I cannot read completely the dataset. The
read array as only 2 value.
H5ScalarDS dataset = ....
....
long[] dims = dataset.getDims();
The values of dims are [3, 2], which is correct.
Object data = dataset.read();
The Array.getLength(data) is 2, and I expect 6 to read my strings.
There is no problem for dataset with other types, with integer for
example.
I'm using hdf-java-2.7 and HDFView Version 2.7.
Thanks
Guillaume
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Here is a method that will get the data as a two dimensional string array.
/**
* Gets a 2d string array from the given hdf5 file and dataset.
···
*
* @param hdfFile the hdf5 file object
* @param path the full path to the dataset
*
* @return the dataset's data
*
* @throws java.lang.Exception
*/
public static String[][] get2dStringArray(FileFormat hdfFile, String path) throws Exception
{
String[][] stringArray = null;
Dataset dataset = (Dataset) hdfFile.get(path);
if (dataset != null)
{
dataset.init();
long[] dims = dataset.getDims();
long[] start = dataset.getStartDims();
stringArray = new String[(int) dims[0]][(int) dims[1]];
for (int i = 0; i< dims[0]; i++)
{
start[0] = i;
byte[] dataRead = dataset.readBytes();
stringArray[i] = Dataset.byteToString(dataRead,
dataset.getDatatype().getDatatypeSize());
}
dataset.clear();
}
return stringArray;
}
--Christian
On 3/29/2011 9:23 AM, Peter Cao wrote:
Guillaume,
Text strings can be only viewed one-dimension a time in HDFView. There is not good
way to show multiple dimensional array of strings. See details at User's Guide at
http://www.hdfgroup.org/hdf-java-html/hdfview/UsersGuide/ug07textview.html.
Bu default, hdf-java only loads strings one dimension a time. However, you can
select whatever subset of your array. For example, the following code will select the
whole dataset.
// set this before dataset.read()
int rank = dataset.getRank();
long[] dims = dataset.getDims();
long[] selected = dataset.getSelectedDims();
System.arraycopy(dims, 0, selected, 0, rank);
Thanks
--pc
On 3/29/2011 3:46 AM, Guillaume PRIN wrote:
Hi,
I experiencing problems while reading dataset of string with hdf-java. I
can create a new 2 dimension dataset of string with dimension 3 x 2 and
length 100 both in code and HDFview. The h5dump utilities shows as
expected :
$ h5dump test.h5
HDF5 "test.h5" {
GROUP "/" {
DATASET "test" {
DATATYPE H5T_STRING {
STRSIZE 5;
STRPAD H5T_STR_NULLPAD;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SIMPLE { ( 3, 2 ) / ( 3, 2 ) }
DATA {
(0,0): "\000\000\000\000\000", "\000\000\000\000\000",
(1,0): "\000\000\000\000\000", "\000\000\000\000\000",
(2,0): "\000\000\000\000\000", "\000\000\000\000\000"
}
}
}
When I read this dataset in hdfview or in my code. The array of data is
not read correctly.
In HDFview, the table shown is represented as a dataset with only one
column. However the metadata indicates 3x2.
In my code using hdf-java, I cannot read completely the dataset. The
read array as only 2 value.
H5ScalarDS dataset = ....
....
long[] dims = dataset.getDims();
The values of dims are [3, 2], which is correct.
Object data = dataset.read();
The Array.getLength(data) is 2, and I expect 6 to read my strings.
There is no problem for dataset with other types, with integer for
example.
I'm using hdf-java-2.7 and HDFView Version 2.7.
Thanks
Guillaume
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
