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partial support for h5 format
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@baptiste
baptiste committed Jun 17, 2024
1 parent 9e88394 commit ad2f592
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Showing 3 changed files with 446 additions and 122 deletions.
206 changes: 202 additions & 4 deletions src/HDFfive.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ MODULE HDFfive
implicit none
private
!
public :: h5_crtgrp, h5_wrt2file, h5_wrtvec2file
public :: h5_crtgrp, h5_wrt2file, h5_wrtvec2file, h5_rd_vec, h5_rd_file

contains

Expand Down Expand Up @@ -75,7 +75,7 @@ subroutine h5_crtgrp(filename_, main_grpname, subgrpsname)
! Close FORTRAN interface.
!
CALL h5close_f(error)
if (allocated(group_id)) deallocate (group_id)
if (allocated(group_id)) deallocate(group_id)
end subroutine h5_crtgrp

!--------------------------------------------------------------------
Expand Down Expand Up @@ -208,7 +208,7 @@ SUBROUTINE h5_wrt2file(filename_, groupname, dsetname, dset_data, attribute) !w

!Create the data space for the second dataset.
!
CALL h5screate_simple_f(rank, dims, dataspace_id, error)
CALL h5screate_simple_f(rank, dims, dataspace_id, error)

! Create the second dataset in group "Group_A" with default properties.
!
Expand Down Expand Up @@ -243,7 +243,7 @@ SUBROUTINE h5_wrt2file(filename_, groupname, dsetname, dset_data, attribute) !w
! Close FORTRAN interface.
!
CALL h5close_f(error)

!if (allocated(group_id)) deallocate(group_id)
END SUBROUTINE h5_wrt2file
!-------------------------------------------------------------------

Expand Down Expand Up @@ -290,5 +290,203 @@ SUBROUTINE h5_wrt_attr(attribute, dataset_id)
END SUBROUTINE h5_wrt_attr

!------------------------------------------------------------------
SUBROUTINE h5_rd_vec(filename_, groupname, dsetname, dset_data) !, attribute)
!============================================================
! This subroutine reads data in a dataset in an existing group.
!============================================================

!USE HDF5 ! This module contains all necessary modules

IMPLICIT NONE

!---------------------------------------------------
! Start of variable declarations.
!---------------------------------------------------
! Passed variables

CHARACTER(*), intent(in) :: filename_ ! File name
!CHARACTER(LEN=4), PARAMETER :: dsetname = "FT" ! Dataset name
CHARACTER(*), intent(in) :: groupname != "MyGroup/Group_A" ! Group name
CHARACTER(*), intent(in) :: dsetname ! = "MyGroup/dset1" ! Dataset name
! CHARACTER(LEN=256), OPTIONAL, intent(in) :: attribute !Ati: I think this is not needed
!REAL(8), intent(out) :: dset_data(:,:) ! output data


INTEGER(HID_T) :: file_id ! File identifier
INTEGER(HID_T) :: dataset_id ! Dataset identifier
INTEGER(HID_T) :: space_id ! Dataspace identifier
INTEGER(HID_T) :: dtype_id ! Dataspace identifier
INTEGER(HID_T) :: group_id ! Group identifier
INTEGER :: error ! Error flag
INTEGER :: i, j, cols, rows
INTEGER(HSIZE_T) :: npoints
REAL(KIND = 8), intent(out), DIMENSION(:), ALLOCATABLE :: dset_data
INTEGER(HSIZE_T), DIMENSION(1) :: dims, maxdims
INTEGER :: rank


!print *, 'Starting HDF5 Fortran Read'

! Initialize FORTRAN interface.

CALL h5open_f(error)


! Open an existing file.

CALL h5fopen_f (filename_, H5F_ACC_RDWR_F, file_id, error)

CALL h5gopen_f(file_id, groupname, group_id, error) !groupname should be complete!
! Open an existing dataset.

CALL h5dopen_f(group_id, dsetname, dataset_id, error) ! CALL h5dopen_f(file_id, dsetname, dataset_id, error) original


!Get dataspace ID
CALL h5dget_space_f(dataset_id, space_id,error)


!Get dataspace dims
CALL h5sget_simple_extent_ndims_f (space_id, rank, error)
! print *, 'rank'
! print *, rank

CALL h5sget_simple_extent_dims_f(space_id,dims, maxdims, error)
! print *, dims
! print *, maxdims

if (rank == 0) then
dims(1) = 1
end if
if (ALLOCATED(dset_data)) DEALLOCATE(dset_data)
ALLOCATE(dset_data(dims(1)))
!Get data
CALL h5dread_f(dataset_id, H5T_NATIVE_DOUBLE, dset_data, dims, error) ! CALL h5dread_f(dataset_id, H5T_NATIVE_INTEGER, dset_data, data_dims, error)
CALL h5dclose_f(dataset_id, error)
CALL h5sclose_f(space_id, error)
CALL h5gclose_f(group_id, error)
CALL h5fclose_f(file_id, error)
CALL h5close_f(error)

!if (allocated(group_id)) deallocate(group_id)
END SUBROUTINE h5_rd_vec

!--------------------------------------------------------
SUBROUTINE h5_rd_file(filename_, groupname, dsetname, dset_data) !, attribute)
!============================================================
! This subroutine reads data in a dataset in an existing group.
!============================================================

!USE HDF5 ! This module contains all necessary modules
USE ISO_C_BINDING
IMPLICIT NONE

!---------------------------------------------------
! Start of variable declarations.
!---------------------------------------------------
! Passed variables

CHARACTER(*), intent(in) :: filename_ ! File name
!CHARACTER(LEN=4), PARAMETER :: dsetname = "FT" ! Dataset name
CHARACTER(*), intent(in) :: groupname != "MyGroup/Group_A" ! Group name
CHARACTER(*), intent(in) :: dsetname ! = "MyGroup/dset1" ! Dataset name
! CHARACTER(LEN=256), OPTIONAL, intent(in) :: attribute !I think this is not needed

INTEGER, PARAMETER :: r_k8 = KIND(0.0d0)
COMPLEX(KIND = r_k8), intent(out), DIMENSION(:,:,:), ALLOCATABLE, TARGET :: dset_data ! output data

INTEGER(HID_T) :: file_id ! File identifier
INTEGER(HID_T) :: dataset_id ! Dataset identifier
INTEGER(HID_T) :: space_id ! Dataspace identifier
INTEGER(HID_T) :: dtype_id ! Dataspace identifier
INTEGER(HID_T) :: group_id ! Group identifier
INTEGER(HID_T) :: memtype ! Group identifier
INTEGER(HID_T) :: sample_type_id
INTEGER :: error ! Error flag
INTEGER :: i, j, cols, rows, shell, rank

INTEGER(HSIZE_T), DIMENSION(3) :: dims
INTEGER(HSIZE_T), DIMENSION(3) :: maxdims
TYPE(C_PTR) :: f_ptr
INTEGER(8) :: real_size, real_complex_size
real_size = storage_size(1_r_k8, r_k8) / 8
real_complex_size = real_size * 2_8 ! a complex is (real,real)



if (ALLOCATED(dset_data)) DEALLOCATE(dset_data)
!print *, 'Starting HDF5 Fortran Read'

! Initialize FORTRAN interface.

CALL h5open_f(error)


! Open an existing file.

CALL h5fopen_f (filename_, H5F_ACC_RDWR_F, file_id, error)

CALL h5gopen_f(file_id, groupname, group_id, error) !groupname should be complete!
! Open an existing dataset.

CALL h5dopen_f(group_id, dsetname, dataset_id, error) ! CALL h5dopen_f(file_id, dsetname, dataset_id, error) original


!Get dataspace ID
CALL h5dget_space_f(dataset_id, space_id,error)


!Get dataspace dims
CALL h5sget_simple_extent_ndims_f (space_id, rank, error)
! print *, 'rank'
! print *, rank

CALL h5sget_simple_extent_dims_f(space_id,dims, maxdims, error)

cols = dims(1)
rows = dims(2)
shell= dims(3)
if (rank == 0)then
cols = 1
rows = 1
shell = 1
end if

ALLOCATE(dset_data(cols, rows, shell))
CALL H5Tcreate_f(H5T_COMPOUND_F, 16_8, sample_type_id,error) !Creates a new datatype, 16_8: for double complex

CALL H5Tinsert_f( sample_type_id, "r", &
0_8, h5kind_to_type(r_k8,H5_REAL_KIND), error)
CALL H5Tinsert_f( sample_type_id, "i", &
real_size, h5kind_to_type(r_k8,H5_REAL_KIND), error)
!Get data
f_ptr = C_LOC(dset_data(1,1,1))
! CALL h5dread_f(dataset_id, H5T_NATIVE_DOUBLE, dset_data, coord_dims, error) ! CALL h5dread_f(dataset_id, H5T_NATIVE_INTEGER, dset_data, data_dims, error)
CALL h5dread_f(dataset_id, sample_type_id, f_ptr, error)

!print *, dset_data


!CALL h5sclose_f(space_id, error)

! Close the second dataset.
!
CALL h5dclose_f(dataset_id, error)
CALL H5Tclose_f(sample_type_id, error)
! Close the group.
!
CALL h5gclose_f(group_id, error)

! Close the file.
!
CALL h5fclose_f(file_id, error)

!
! Close FORTRAN interface.
!
CALL h5close_f(error)
!if (allocated(group_id)) deallocate(group_id)
END SUBROUTINE h5_rd_file


END MODULE
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