Thanks Christian, that worked.
···
--
Clay Blankenship * USRA Research Scientist
clay.blankenship@nasa.gov<mailto:clay.b.blankenship@nasa.gov> * 256-961-7638
320 Sparkman Drive * Huntsville, AL 35805 USA
NASA-MSFC Short-Term Prediction Research and Transition (SPoRT) Center
From: Christian Oyarzun <christian.oyarzun@studsvik.com<mailto:christian.oyarzun@studsvik.com>>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Date: Tuesday, July 7, 2015 at 4:01 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Subject: Re: [Hdf-forum] HDF5 string read errors
This is what I use:
subroutine h5ltread_dataset_char_f(file_id,dset_name,data_out,dims,error)
!- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
! High-level HDF5 FORTRAN API for reading a character array.
!- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
use HDF5
!
implicit none
!
integer(HID_T) :: file_id ! File identifier
character(len=*), intent(IN) :: dset_name
integer(HSIZE_T), dimension(*), intent(IN) :: dims ! size of the buffer
character(len=*),dimension(*), intent(INOUT) :: data_out ! data buffer
integer, intent(out) :: error ! Error flag
!
integer(HID_T) :: dset_id ! Dataset identifier
integer(HID_T) :: atype ! Datatype identifier
integer(SIZE_T) :: size ! Datatype size
!
call h5tcopy_f(H5T_NATIVE_CHARACTER,atype,error)
size=len(data_out)
call h5tset_size_f(atype,size,error)
!
call h5dopen_f(file_id,dset_name,dset_id,error)
!
call h5dread_f(dset_id,atype,data_out,dims,error,H5S_ALL_F,H5S_ALL_F,H5P_DEFAULT_F)
!
! End access to the dataset and release resources used by it.
!
call h5dclose_f(dset_id,error)
!
end subroutine h5ltread_dataset_char_f
On Jul 7, 2015, at 4:18 PM, Blankenship, Clay B. (MSFC-ZP12)[USRA] <clay.blankenship@nasa.gov<mailto:clay.blankenship@nasa.gov>> wrote:
When I copy the code from Elena’s example, I get these compile errors:
readsmap.f90(161): error #6404: This name does not have a type, and must have an explicit type. [H5T_FORTRAN_S1]
call h5tcopy_f(H5T_FORTRAN_S1, memtype,istatus)
-----------------^
readsmap.f90(167): error #6285: There is no matching specific subroutine for this generic subroutine call. [H5DREAD_F]
call h5dread_f(dsetid,memtype,f_ptr,istatus,space)
-------^
compilation aborted for readsmap.f90 (code 1)
From: Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Date: Tuesday, July 7, 2015 at 3:05 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Subject: Re: [Hdf-forum] HDF5 string read errors
Hello,
Memory type is not correct when you read array of the fixed size strings. Please take a look at this example
http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/hdf5-examples/1_8/FORTRAN/H5T/h5ex_t_stringC_F03.f90
Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org<http://hdfgroup.org/>
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On Jul 7, 2015, at 10:42 PM, Blankenship, Clay B. (MSFC-ZP12)[USRA] <clay.blankenship@nasa.gov<mailto:clay.blankenship@nasa.gov>> wrote:
Hi,
I am trying to read an HDF5 file using Fortran. I can read all the datasets I need except one which is a string. What am I doing wrong? I can’t find many examples of reading a fixed-length string array.
Thanks!
Here is the relevant output from h5dump:
DATASET "spacecraft_overpass_time_utc" {
DATATYPE H5T_STRING {
STRSIZE 24;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
Here is my Fortran code:
use hdf5
…
integer :: istatus
integer(HID_T) :: fileid,dsetid,datatype
integer, parameter :: n_ease=267264
character*80 :: dsetname(12)
character(len=24), dimension(n_ease) :: tutc_ease
integer(HSIZE_T), dimension(1) :: dims,maxdims,newdims
integer(SIZE_T) :: mysize,sdim
dims(1)=n_ease
!Open fortran interface
call h5open_f(istatus)
call h5fopen_f(fname,H5F_ACC_RDWR_F,fileid,istatus)
dsetname(5)='Soil_Moisture_Retrieval_Data/spacecraft_overpass_time_utc'
call h5dopen_f(fileid,dsetname(5),dsetid,istatus)
call h5dget_type_f(dsetid,datatype,istatus) !datatype is not equal to H5T_STRING!
call h5tget_size_f(datatype,mysize,istatus) !mysize is good
call h5dread_f(dsetid,H5T_STRING,tutc_ease,dims,istatus) !errors here
The errors are:
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: H5Dio.c line 174 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: H5Dio.c line 337 in H5D_read(): unable to set up type info
major: Dataset
minor: Unable to initialize object
#002: H5Dio.c line 836 in H5D_typeinfo_init(): unable to convert between src and dest datatype
major: Dataset
minor: Feature is unsupported
#003: H5T.c line 4459 in H5T_path_find(): no appropriate function for conversion path
major: Datatype
minor: Unable to initialize object
--
Clay Blankenship * USRA Research Scientist
clay.blankenship@nasa.gov<mailto:clay.b.blankenship@nasa.gov> * 256-961-7638
320 Sparkman Drive * Huntsville, AL 35805 USA
NASA-MSFC Short-Term Prediction Research and Transition (SPoRT) Center
_______________________________________________
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_______________________________________________
Hdf-forum is for HDF software users discussion.
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