Hi all,
Can anybody tell me how to go about accessing type information for a H5::FL_PacketTable (C++ API)? I see that H5Dget_type can be used in the C API, but I can't see a way to get the hid of a C++ FL_PacketTable in order to use it.
Thanks,
Chris
--
Dr Chris Jewell
Lecturer in Biostatistics
Institute of Fundamental Sciences
Massey University
Private Bag 11222
Palmerston North 4442
New Zealand
Tel: +64 (0) 6 350 5701 Extn: 3586
Hi,
I have some code to read in an array of vlen strings from an attribute attached to a packet table:
void
getTags(H5::DataSet& dataset, std::vector<std::string>& sTags)
{
std::cout << __FUNCTION__ << " called" << std::endl;
hsize_t aDim; // Num of attributes
H5::Attribute tags = dataset.openAttribute("tags");
tags.getSpace().getSimpleExtentDims(&aDim); // We know this is 1 dimensional
// Prepare data structures
sTags.resize(aDim);
char** readBuff = new char*[aDim];
// Set datatype for the array
H5::PredType paramTag_t = H5::PredType::C_S1;
paramTag_t.setSize(H5T_VARIABLE);
// Read
tags.read(paramTag_t,readBuff);
for(int i=0; i<aDim; ++i)
{
sTags[i].assign(readBuff[i]);
}
// Clean up
H5Dvlen_reclaim(paramTag_t.getId(), tags.getSpace().getId(), H5P_DEFAULT, readBuff);
delete[] readBuff;
std::cout << __FUNCTION__ << " ended" << std::endl;
}
Typically, I call this function from within main() on a H5::DataSet object (the packet table opened as a DataSet to access the attribute). However, if I try to read the attribute twice using the following code:
int main (int argc, const char * argv[])
{
std::vector<std::string> sTags; // Store elements in the attribute
H5::H5File file(argv[1],H5F_ACC_RDONLY,H5P_DEFAULT,H5P_DEFAULT);
H5::DataSet parms = file->openDataSet("thePacketTable"); // Open as dataset to access attrib
// Call getTags twice
getTags(parms, sTags); // Okay
getTags(parms, sTags); // Bombs
return EXIT_SUCCESS;
}
I get the error output at the second call:
getTags called
getTags ended
getTags called
HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
#000: H5A.c line 1085 in H5Aread(): unable to read attribute
major: Attribute
minor: Read failed
#001: H5A.c line 1165 in H5A_read(): datatype conversion failed
major: Attribute
minor: Unable to encode value
#002: H5T.c line 4765 in H5T_convert(): data type conversion failed
major: Attribute
minor: Unable to encode value
#003: H5Tconv.c line 3029 in H5T_conv_vlen(): unable to convert between src and dest datatypes
major: Datatype
minor: Feature is unsupported
#004: H5T.c line 4481 in H5T_path_find(): no appropriate function for conversion path
major: Datatype
minor: Unable to initialize object
Error: H5Aread failed
Is this a bug, or am I doing something silly?
Thanks,
Chris
--
Dr Chris Jewell
Lecturer in Biostatistics
Institute of Fundamental Sciences
Massey University
Private Bag 11222
Palmerston North 4442
New Zealand
Tel: +64 (0) 6 350 5701 Extn: 3586
Hi Chris,
From the error messages, I guess that the datatype passed into "tags.read"
doesn't match the one used when writing. You might want to check the type
paramTag_t. It would be better to get the datatype of the attribute then
pass that in to the "tags.read" call.
Binh-Minh
-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org]
On Behalf Of Jewell, Chris
Sent: Tuesday, July 31, 2012 6:57 PM
To: HDF Users Discussion List
Subject: [Hdf-forum] Error reading array of vlen strings attribute twice
Hi,
I have some code to read in an array of vlen strings from an attribute
attached to a packet table:
void
getTags(H5::DataSet& dataset, std::vector<std::string>& sTags)
{
std::cout << __FUNCTION__ << " called" << std::endl;
hsize_t aDim; // Num of attributes
H5::Attribute tags = dataset.openAttribute("tags");
tags.getSpace().getSimpleExtentDims(&aDim); // We know this is 1
dimensional
// Prepare data structures
sTags.resize(aDim);
char** readBuff = new char*[aDim];
// Set datatype for the array
H5::PredType paramTag_t = H5::PredType::C_S1;
paramTag_t.setSize(H5T_VARIABLE);
// Read
tags.read(paramTag_t,readBuff);
for(int i=0; i<aDim; ++i)
{
sTags[i].assign(readBuff[i]);
}
// Clean up
H5Dvlen_reclaim(paramTag_t.getId(), tags.getSpace().getId(),
H5P_DEFAULT, readBuff);
delete[] readBuff;
std::cout << __FUNCTION__ << " ended" << std::endl;
}
Typically, I call this function from within main() on a H5::DataSet object
(the packet table opened as a DataSet to access the attribute). However, if
I try to read the attribute twice using the following code:
int main (int argc, const char * argv[])
{
std::vector<std::string> sTags; // Store elements in the attribute
H5::H5File file(argv[1],H5F_ACC_RDONLY,H5P_DEFAULT,H5P_DEFAULT);
H5::DataSet parms = file->openDataSet("thePacketTable"); // Open as
dataset to access attrib
// Call getTags twice
getTags(parms, sTags); // Okay
getTags(parms, sTags); // Bombs
return EXIT_SUCCESS;
}
I get the error output at the second call:
getTags called
getTags ended
getTags called
HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
#000: H5A.c line 1085 in H5Aread(): unable to read attribute
major: Attribute
minor: Read failed
#001: H5A.c line 1165 in H5A_read(): datatype conversion failed
major: Attribute
minor: Unable to encode value
#002: H5T.c line 4765 in H5T_convert(): data type conversion failed
major: Attribute
minor: Unable to encode value
#003: H5Tconv.c line 3029 in H5T_conv_vlen(): unable to convert between
src and dest datatypes
major: Datatype
minor: Feature is unsupported
#004: H5T.c line 4481 in H5T_path_find(): no appropriate function for
conversion path
major: Datatype
minor: Unable to initialize object
Error: H5Aread failed
Is this a bug, or am I doing something silly?
Thanks,
Chris
--
Dr Chris Jewell
Lecturer in Biostatistics
Institute of Fundamental Sciences
Massey University
Private Bag 11222
Palmerston North 4442
New Zealand
Tel: +64 (0) 6 350 5701 Extn: 3586
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