Implement subroutines to read 1-d and 2-d real32 datasets from HDF5

Author: milancurcic

src/nf/io/nf_io_hdf5.f90

@@ -2,24 +2,49 @@ module nf_io_hdf5
 
   !! This module provides convenience functions to read HDF5 files.
 
+  use iso_fortran_env, only: real32
+
   implicit none
 
   private
-  public :: get_hdf5_attribute_string
+  public :: get_hdf5_dataset, hdf5_attribute_string
 
   interface
-
-    module function get_hdf5_attribute_string( &
+    module function hdf5_attribute_string( &
       filename, object_name, attribute_name) result(res)
+      !! Read and return an HDF5 variable-length UTF-8 string attribute.
       character(*), intent(in) :: filename
         !! HDF5 file name
       character(*), intent(in) :: object_name
         !! Object (group, dataset) name
       character(*), intent(in) :: attribute_name
         !! Name of the attribute to read
       character(:), allocatable :: res
-    end function get_hdf5_attribute_string
-
+    end function hdf5_attribute_string
   end interface
 
+  interface get_hdf5_dataset
+
+    module subroutine get_hdf5_dataset_real32_1d(filename, object_name, values)
+      !! Read a 1-d real32 array from an HDF5 dataset.
+      character(*), intent(in) :: filename
+        !! HDF5 file name
+      character(*), intent(in) :: object_name
+        !! Object (dataset) name
+      real(real32), allocatable, intent(in out) :: values(:)
+        !! Array to store the dataset values into
+    end subroutine get_hdf5_dataset_real32_1d
+
+    module subroutine get_hdf5_dataset_real32_2d(filename, object_name, values)
+      !! Read a 2-d real32 array from an HDF5 dataset.
+      character(*), intent(in) :: filename
+        !! HDF5 file name
+      character(*), intent(in) :: object_name
+        !! Object (dataset) name
+      real(real32), allocatable, intent(in out) :: values(:,:)
+        !! Array to store the dataset values into
+    end subroutine get_hdf5_dataset_real32_2d
+  
+  end interface get_hdf5_dataset
+
 end module nf_io_hdf5

src/nf/io/nf_io_hdf5_submodule.f90

@@ -1,5 +1,7 @@
 submodule(nf_io_hdf5) nf_io_hdf5_submodule
 
+  use iso_fortran_env, only: int64, real32, stderr => error_unit
+  use h5fortran, only: hdf5_file
   use hdf5, only: H5F_ACC_RDONLY_F, HID_T, &
                   h5aget_type_f, h5aopen_by_name_f, h5aread_f, &
                   h5fclose_f, h5fopen_f
@@ -9,7 +11,7 @@
 
 contains
 
-  module function get_hdf5_attribute_string( &
+  module function hdf5_attribute_string( &
     filename, object_name, attribute_name) result(res)
 
     character(*), intent(in) :: filename
@@ -41,6 +43,62 @@ module function get_hdf5_attribute_string( &
 
     res = string(:index(string, c_null_char) - 1)
 
-  end function get_hdf5_attribute_string
+  end function hdf5_attribute_string
+
+
+  module subroutine get_hdf5_dataset_real32_1d(filename, object_name, values)
+
+    character(*), intent(in) :: filename
+    character(*), intent(in) :: object_name
+    real(real32), allocatable, intent(in out) :: values(:)
+
+    type(hdf5_file) :: f
+    integer(int64), allocatable :: dims(:)
+
+    call f % open(filename, 'r')
+    call f % shape(object_name, dims)
+
+    ! If values is already allocated, re-allocate only if incorrect shape
+    if (allocated(values)) then
+      if (.not. all(shape(values) == dims)) then
+        deallocate(values)
+        allocate(values(dims(1)))
+      end if
+    else
+      allocate(values(dims(1)))
+    end if
+
+    call f % read(object_name, values)
+    call f % close()
+
+  end subroutine get_hdf5_dataset_real32_1d
+
+
+  module subroutine get_hdf5_dataset_real32_2d(filename, object_name, values)
+
+    character(*), intent(in) :: filename
+    character(*), intent(in) :: object_name
+    real(real32), allocatable, intent(in out) :: values(:,:)
+
+    type(hdf5_file) :: f
+    integer(int64), allocatable :: dims(:)
+
+    call f % open(filename, 'r')
+    call f % shape(object_name, dims)
+
+    ! If values is already allocated, re-allocate only if incorrect shape
+    if (allocated(values)) then
+      if (.not. all(shape(values) == dims)) then
+        deallocate(values)
+        allocate(values(dims(1), dims(2)))
+      end if
+    else
+      allocate(values(dims(1), dims(2)))
+    end if
+
+    call f % read(object_name, values)
+    call f % close()
+
+  end subroutine get_hdf5_dataset_real32_2d
 
 end submodule nf_io_hdf5_submodule

src/nf/nf_keras_submodule.f90

@@ -1,7 +1,7 @@
 submodule(nf_keras) nf_keras_submodule
 
   use json_module, only: json_core, json_value
-  use nf_io_hdf5, only: get_hdf5_attribute_string
+  use nf_io_hdf5, only: hdf5_attribute_string
 
   implicit none
 
@@ -21,9 +21,7 @@ module function get_keras_h5_layers(filename) result(res)
     integer :: n, num_layers, num_elements
     logical :: found
 
-    model_config_string = get_hdf5_attribute_string( &
-      filename, '.', 'model_config' &
-    )
+    model_config_string = hdf5_attribute_string(filename, '.', 'model_config')
 
     call json % parse(model_config_json, model_config_string)
     call json % get(model_config_json, 'config.layers', layers_json)

test/test_io_hdf5.f90

@@ -1,57 +1,52 @@
 program test_io_hdf5
 
-  use iso_fortran_env, only: int64, stderr => error_unit
+  use iso_fortran_env, only: stderr => error_unit
   use nf_datasets, only: download_and_unpack, keras_model_dense_mnist_url
-  use nf_io_hdf5, only: get_hdf5_attribute_string
-  use h5fortran, only: hdf5_file
+  use nf_io_hdf5, only: hdf5_attribute_string, get_hdf5_dataset
 
   implicit none
 
   character(:), allocatable :: attr
   character(*), parameter :: test_data_path = 'keras_dense_mnist.h5'
-  type(hdf5_file) :: f
   real, allocatable :: bias(:), weights(:,:)
-  integer(int64), allocatable :: dims(:)
 
   logical :: file_exists
   logical :: ok = .true.
 
   inquire(file=test_data_path, exist=file_exists)
   if (.not. file_exists) call download_and_unpack(keras_model_dense_mnist_url)
 
-  attr = get_hdf5_attribute_string(test_data_path, '.', 'backend')
+  attr = hdf5_attribute_string(test_data_path, '.', 'backend')
 
   if (.not. attr == 'tensorflow') then
     ok = .false.
     write(stderr, '(a)') &
       'HDF5 variable length string attribute was read correctly.. failed'
   end if
 
-  call f % open(test_data_path, 'r')
+  ! Read 1-d real32 dataset
+  call get_hdf5_dataset( &
+    test_data_path, &
+    '/model_weights/dense/dense/bias:0', &
+    bias &
+  )
 
-  call f % shape('/model_weights/dense/dense/bias:0', dims)
-  allocate(bias(dims(1)))
-  bias = 0
-  call f % read('/model_weights/dense/dense/bias:0', bias)
+  ! Read 2-d real32 dataset
+  call get_hdf5_dataset(test_data_path, &
+    '/model_weights/dense/dense/kernel:0', &
+    weights &
+  )
 
-  if (.not. all(dims == [30])) then
+  if (.not. all(shape(bias) == [30])) then
     ok = .false.
     write(stderr, '(a)') 'HDF5 1-d dataset dims inquiry is correct.. failed'
   end if
 
-  call f % shape('/model_weights/dense/dense/kernel:0', dims)
-  allocate(weights(dims(1), dims(2)))
-  weights = 0
-  call f % read('/model_weights/dense/dense/kernel:0', weights)
-
-  if (.not. all(dims == [30, 784])) then
+  if (.not. all(shape(weights) == [30, 784])) then
     ok = .false.
-    print *, dims
     write(stderr, '(a)') 'HDF5 2-d dataset dims inquiry is correct.. failed'
   end if
 
-  call f % close()
-
   if (ok) then
     print '(a)', 'test_io_hdf5: All tests passed.'
   else