Dear Scot, Thanks for this code! It works fine with Fortran 2003 enabled (gfortran 4.8) Is the addition of vl-string support for attributes in Fortran only for Fortran 2003? I couldn't deduce it from http://www.hdfgroup.org/HDF5/doc/RM/RM_H5A.html#Annot-Write
Regards, Pierre On Wed, Feb 05, 2014 at 05:43:37PM +0000, Scot Breitenfeld wrote: > > I've attached a modified version of h5ex_t_vlstring_F03.f90 to use attributes > instead. This example assumes you have a F2003 compiler and you used > --enable-fortran2003 when you built hdf5. Hope this helps. > > Scot > > > ________________________________________ > From: Hdf-forum <hdf-forum-boun...@lists.hdfgroup.org> on behalf of Pierre de > Buyl <pierre.deb...@chem.kuleuven.be> > Sent: Wednesday, February 05, 2014 8:59 AM > To: hdf-forum@lists.hdfgroup.org > Subject: [Hdf-forum] VL string attribute in Fortran > > Dear hdf community, > > I would like to know whether the absence of a "Read / Write Variable Length > String Datatype (Attribute)" is due to a technical problem. The example page > [1] > does not provide such an example. > > In the context of the H5MD file format [2], we are using (currently) VL string > attributes. If it turns out that we cannot handle those in Fortran, we could > switch to fixed-length strings. > > Regards, > > Pierre de Buyl > > [1] http://www.hdfgroup.org/HDF5/examples/api18-fortran.html > [2] H5MD : HDF5 for molecular data http://nongnu.org/h5md/ > > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > Hdf-forum@lists.hdfgroup.org > http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > !************************************************************ > ! > ! This example shows how to read and write variable-length > ! string attributes to a dataset using h5aread_f and > ! h5awrite_f, and F2003 intrinsics C_LOC and C_F_POINTER. > ! The program first writes variable-length strings attribute > ! Next, it reopens the file, reads back the data, and outputs it to > ! the screen. > ! > ! This file is intended for use with HDF5 Library version 1.8 > ! and --enable-fortran2003 > ! > !************************************************************ > > PROGRAM main > > USE HDF5 > USE ISO_C_BINDING > > IMPLICIT NONE > > CHARACTER(LEN=20), PARAMETER :: filename = "h5ex_vlstring_F03.h5" > CHARACTER(LEN=3) , PARAMETER :: dataset = "DS1" > CHARACTER(LEN=2) , PARAMETER :: attribute = "A1" > > INTEGER(HSIZE_T), PARAMETER :: dim0 = 4 > INTEGER(HID_T) :: file, filetype, space, attr ! Handles > INTEGER :: hdferr > INTEGER(HSIZE_T), DIMENSION(1:1) :: dims = (/dim0/) > > TYPE(C_PTR), DIMENSION(1:dim0), TARGET :: wdata > CHARACTER(len=8, KIND=c_char), DIMENSION(1), TARGET :: A = > "Parting"//C_NULL_CHAR > CHARACTER(len=8, KIND=c_char), DIMENSION(1), TARGET :: B = > "is_such"//C_NULL_CHAR > CHARACTER(len=6, KIND=c_char), DIMENSION(1), TARGET :: C = > "sweet"//C_NULL_CHAR > CHARACTER(len=8, KIND=c_char), DIMENSION(1), TARGET :: D = > "sorrow."//C_NULL_CHAR > TYPE(C_PTR), DIMENSION(:), ALLOCATABLE, TARGET :: rdata ! Read buffer > CHARACTER(len = 8, kind=c_char), POINTER :: data ! A pointer to a Fortran > string > TYPE(C_PTR) :: f_ptr > INTEGER :: i, len > > ! Initialize array of C pointers > wdata(1) = C_LOC(A(1)) > wdata(2) = C_LOC(B(1)) > wdata(3) = C_LOC(C(1)) > wdata(4) = C_LOC(D(1)) > ! > ! Initialize FORTRAN interface. > ! > CALL h5open_f(hdferr) > ! > ! Create a new file using the default properties. > ! > CALL h5fcreate_f(filename, H5F_ACC_TRUNC_F, file, hdferr) > ! > ! Create file and memory datatypes. For this example we will save > ! the strings as C variable length strings, H5T_STRING is defined > ! as a variable length string. > ! > CALL H5Tcopy_f(H5T_STRING, filetype, hdferr) > ! > ! Create dataspace. > ! > CALL h5screate_simple_f(1, dims, space, hdferr) > ! > ! Create the attribute and write the variable-length string data to > ! it. > ! > > CALL h5acreate_f(file, attribute, filetype, space, attr, hdferr) > > f_ptr = C_LOC(wdata(1)) > CALL h5awrite_f(attr, filetype, f_ptr, hdferr ) > ! > ! Close and release resources. > ! > CALL h5aclose_f(attr , hdferr) > CALL h5sclose_f(space, hdferr) > CALL H5Tclose_f(filetype, hdferr) > CALL h5fclose_f(file, hdferr) > ! > ! Now we begin the read section of this example. > ! > ! > ! Open file and attribute. > ! > CALL h5fopen_f(filename, H5F_ACC_RDONLY_F, file, hdferr) > CALL h5aopen_f(file, attribute, attr, hdferr) > > ALLOCATE(rdata(1:dims(1))) > ! > ! Read attribute. > ! > f_ptr = C_LOC(rdata(1)) > CALL h5aread_f(attr, H5T_STRING, f_ptr, hdferr) > ! > ! Output to the screen. > ! > DO i = 1, dims(1) > CALL C_F_POINTER(rdata(i), data) > len = 0 > DO > IF(DATA(len+1:len+1).EQ.C_NULL_CHAR.OR.len.GE.8) EXIT > len = len + 1 > ENDDO > WRITE(*,'(A,"(",I0,"): ",A)') attribute, i, data(1:len) > END DO > > DEALLOCATE(rdata) > > CALL h5aclose_f(attr , hdferr) > CALL h5fclose_f(file , hdferr) > > END PROGRAM main > _______________________________________________ > Hdf-forum is for HDF software users discussion. > Hdf-forum@lists.hdfgroup.org > http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org -- ----------------------------------------------------------- Pierre de Buyl KU Leuven - Polymer Chemistry and Materials T +32 16 327355 W http://homepages.ulb.ac.be/~pdebuyl/ ----------------------------------------------------------- _______________________________________________ Hdf-forum is for HDF software users discussion. Hdf-forum@lists.hdfgroup.org http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
