Hi Binh-Minh, All,
Thank you for your reply.
Yes, I know how to solve that finally, but I just think there is an
inconsistency in this (any many more) API functions.
First call to this function returns size without extra character for \0
at the end of the string, but second call to this function requires size
parameter to count this extra character for \0 at the end.
I think we should decide if we what to count this extra character for \0
or not and keep consistency in both function calls. So getting "size"
value from the first function call should be directly used in the second
call.
About the h5dump - sure - I know there are different tools which can
help and I actually use HDFView, but this is just for the time of
application development and testing, because the goal is to discover
HDF5 file structure in the application without using any external tools.
Anyway, It seems that was just a minor problem which I had with the HDF5
API, because now the next one looks worse...
Pure C-language API (function-based) seems to work more or less fine,
but when I try to use C++ API I can open the HDF5 file, but when I try
to get the object name (getObjName() method for the top group "." for
example) I get "read access violation" exception...
H5Object::getObjName() function internally uses pure C API where it
calls H5Iget_name() twice: first to get the name size (and build a
buffer for that name) and second to get the name itself. But then this
pure C char* buffer of characters is assigned to std::string which is
returned from that method. The problem is that maybe (but I'm not sure
here) due to some compiler optimizations (made while HDF libraries was
compiled - I just use binaries) this assignment of char* to std::string
is not made by copying the content, but simply reassigning the pointer.
Before this method returns, this char* array is deleted so that's why I
get "read access violation" exception when I try to get this string
content...
Can someone please help me in that problem?
This is the code from that method:
H5std_string H5Object::getObjName() const
{
H5std_string obj_name(""); // object name to return
// Preliminary call to get the size of the object name
ssize_t name_size = H5Iget_name(getId(), NULL, static_cast<size_t>(0));
// If H5Iget_name failed, throw exception
if (name_size < 0)
{
throw Exception(inMemFunc("getObjName"), "H5Iget_name failed");
}
else if (name_size == 0)
{
throw Exception(inMemFunc("getObjName"), "Object must have a
name, but name length is 0");
}
// Object's name exists, retrieve it
else if (name_size > 0)
{
char* name_C = new char[name_size+1]; // temporary C-string
HDmemset(name_C, 0, name_size+1); // clear buffer
// Use overloaded function
name_size = getObjName(name_C, name_size+1);
// Convert the C object name to return
obj_name = name_C;
// Clean up resource
delete []name_C;
}
// Return object's name
return(obj_name);
}
Regards,
Rafal
W dniu 2017-03-28 o 20:14, Binh-Minh Ribler pisze:
Hi Rafal,
You'll need to pass in link_name_size+1 to the final call
of H5Lget_name_by_idx as well.
BTW, you can use h5dump to see the structure of the file, initially.
Thanks,
Binh-Minh
------------------------------------------------------------------------
*From:* Hdf-forum <[email protected]> on behalf of
Rafal Lichwala <[email protected]>
*Sent:* Tuesday, March 28, 2017 4:26 AM
*To:* [email protected]
*Subject:* [Hdf-forum] HDF5 API problems
Hi,
For the purpose of some project I'd like to read HDF5 files in my C++
application using HDF5 API.
First of all I would like to read entire HDF5 file structure to know
where are the groups (their names, attributes etc.) and where I can find
datasets.
The API functions like H5*iterate (non-recursive version) or H5*visit
(recursive version) are rather useless, because their H5*_info_t
structures have very limited information about the object on the given
level in this structure.
Thus I've decided to walk manually through this structure and get as
much information as I can for the given object.
So...
Calling H5Gget_info gives me a number of links at the top ("." group)
which then I can ask for details based on their index. Fine.
Now, having the link index, I can call H5Lget_name_by_idx to get the
link name.
First initial call to that function will return the name size and second
one will return the link name in the properly prepared buffer of char*.
On that stage I found a first problem (a bug I suppose):
Let's assume the link name is "foobar", so it has 6 characters.
Initial call of H5Lget_name_by_idx returns 6, but when I call it again
with "size" parameter set to 6 it fills my buffer with just 5 characters
("fooba") even if the buffer has a proper size of 7 bytes (the 7th for
the final \0).
So it seems I have to increase size by 1 to get the proper link name.
What's the problem here? Maybe it's just my wrong understanding for this
API function?
Code example (returns "fooba" instead of "foobar" in the "link_name"
buffer):
// initial call to get name size
int link_name_size = H5Lget_name_by_idx(file.getId(), ".",
H5_INDEX_NAME, H5_ITER_NATIVE, i, NULL, 0, 0);
// one more byte for \0 at the end
char *link_name = new char[link_name_size + 1];
// final call
H5Lget_name_by_idx(file.getId(), ".", H5_INDEX_NAME, H5_ITER_NATIVE, i,
link_name, link_name_size, 0);
Can someone please explain me what's the problem here?
Regards,
Rafal
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Twitter: https://twitter.com/hdf5
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
--
***
Rafał Lichwała
Poznańskie Centrum Superkomputerowo-Sieciowe
ul. Jana Pawła II nr 10
61-139 Poznań
e-mail: [email protected]
***
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
