Merge pull request #85 from milancurcic/keras-reader-cnn

Read Conv2D, MaxPooling2D, and Flatten layers from Keras

Author: milancurcic

CMakeLists.txt

@@ -17,6 +17,7 @@ include(FetchContent)
 include(cmake/options.cmake)
 include(cmake/compilers.cmake)
 
+include(cmake/functional.cmake)
 include(cmake/h5fortran.cmake)
 include(cmake/json.cmake)
 
@@ -62,7 +63,13 @@ add_library(neural
   src/nf/io/nf_io_hdf5.f90
   src/nf/io/nf_io_hdf5_submodule.f90
 )
-target_link_libraries(neural PRIVATE h5fortran::h5fortran HDF5::HDF5 jsonfortran::jsonfortran)
+
+target_link_libraries(neural PRIVATE
+  functional::functional
+  h5fortran::h5fortran
+  HDF5::HDF5
+  jsonfortran::jsonfortran
+)
 
 install(TARGETS neural)
 

README.md

@@ -2,7 +2,7 @@
 
 [![GitHub issues](https://img.shields.io/github/issues/modern-fortran/neural-fortran.svg)](https://github.com/modern-fortran/neural-fortran/issues)
 
-A parallel neural net microframework. 
+A parallel framework for deep learning.
 Read the paper [here](https://arxiv.org/abs/1902.06714).
 
 * [Features](https://github.com/modern-fortran/neural-fortran#features)
@@ -18,9 +18,11 @@ Read the paper [here](https://arxiv.org/abs/1902.06714).
 
 * Dense, fully connected neural layers
 * Convolutional and max-pooling layers (experimental, forward propagation only)
+* Flatten layers (forward and backward pass)
+* Loading dense and convolutional models from Keras h5 files
 * Stochastic and mini-batch gradient descent for back-propagation
 * Data-based parallelism
-* Several activation functions
+* Several activation functions and their derivatives
 
 ### Available layer types
 
@@ -48,16 +50,18 @@ Required dependencies are:
 * A Fortran compiler
 * [HDF5](https://www.hdfgroup.org/downloads/hdf5/)
   (must be provided by the OS package manager or your own build from source)
-* [h5fortran](https://github.com/geospace-code/h5fortran),
+* [functional-fortran](https://github.com/wavebitscientific/functional-fortran),
+  [h5fortran](https://github.com/geospace-code/h5fortran),
   [json-fortran](https://github.com/jacobwilliams/json-fortran)
-  (both handled by neural-fortran's build systems, no need for a manual install)
+  (all handled by neural-fortran's build systems, no need for a manual install)
 * [fpm](https://github.com/fortran-lang/fpm) or
   [CMake](https://cmake.org) for building the code
 
 Optional dependencies are:
 
 * OpenCoarrays (for parallel execution with GFortran)
-* BLAS, MKL (optional)
+* BLAS, MKL, or similar (for offloading `matmul` and `dot_product` calls)
+* curl (for downloading testing and example datasets)
 
 Compilers tested include:
 
@@ -200,13 +204,15 @@ examples, in increasing level of complexity:
   dataset
 4. [cnn](example/cnn.f90): Creating and running forward a simple CNN using
   `input`, `conv2d`, `maxpool2d`, `flatten`, and `dense` layers.
-5. [mnist_from_keras](example/mnist_from_keras.f90): Creating a pre-trained
-  model from a Keras HDF5 file.
+5. [dense_from_keras](example/dense_from_keras.f90): Creating a pre-trained
+  dense model from a Keras HDF5 file and running the inference.
+6. [cnn_from_keras](example/cnn_from_keras.f90): Creating a pre-trained
+  convolutional model from a Keras HDF5 file and running the inference.
 
 The examples also show you the extent of the public API that's meant to be
 used in applications, i.e. anything from the `nf` module.
 
-The MNIST example uses [curl](https://curl.se/) to download the dataset,
+Examples 3-6 rely on [curl](https://curl.se/) to download the needed datasets,
 so make sure you have it installed on your system.
 Most Linux OSs have it out of the box.
 The dataset will be downloaded only the first time you run the example in any

cmake/functional.cmake

@@ -0,0 +1,18 @@
+FetchContent_Declare(functional
+  GIT_REPOSITORY https://github.com/wavebitscientific/functional-fortran
+  GIT_TAG 0.6.1
+  GIT_SHALLOW true
+)
+
+FetchContent_Populate(functional)
+
+add_library(functional ${functional_SOURCE_DIR}/src/functional.f90)
+target_include_directories(functional PUBLIC
+$<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/include>
+$<INSTALL_INTERFACE:include>
+)
+
+add_library(functional::functional INTERFACE IMPORTED GLOBAL)
+target_link_libraries(functional::functional INTERFACE functional)
+
+install(TARGETS functional)

example/CMakeLists.txt

@@ -1,4 +1,16 @@
-foreach(execid cnn mnist mnist_from_keras simple sine)
+foreach(execid
+  cnn
+  cnn_from_keras
+  dense_from_keras
+  mnist
+  simple
+  sine
+)
   add_executable(${execid} ${execid}.f90)
-  target_link_libraries(${execid} PRIVATE neural h5fortran::h5fortran jsonfortran::jsonfortran ${LIBS})
+  target_link_libraries(${execid} PRIVATE
+    neural
+    h5fortran::h5fortran
+    jsonfortran::jsonfortran
+    ${LIBS}
+  )
 endforeach()

example/cnn_from_keras.f90

@@ -0,0 +1,58 @@
+program cnn_from_keras
+
+  ! This example demonstrates loading a convolutional model
+  ! pre-trained on the MNIST dataset from a Keras HDF5
+  ! file and running an inferrence on the testing dataset.
+
+  use nf, only: network, label_digits, load_mnist
+  use nf_datasets, only: download_and_unpack, keras_cnn_mnist_url
+
+  implicit none
+
+  type(network) :: net
+  real, allocatable :: training_images(:,:), training_labels(:)
+  real, allocatable :: validation_images(:,:), validation_labels(:)
+  real, allocatable :: testing_images(:,:), testing_labels(:)
+  character(*), parameter :: keras_cnn_path = 'keras_cnn_mnist.h5'
+  logical :: file_exists
+  real :: acc
+
+  inquire(file=keras_cnn_path, exist=file_exists)
+  if (.not. file_exists) call download_and_unpack(keras_cnn_mnist_url)
+
+  call load_mnist(training_images, training_labels, &
+                  validation_images, validation_labels, &
+                  testing_images, testing_labels)
+
+  print '("Loading a pre-trained CNN model from Keras")'
+  print '(60("="))'
+
+  net = network(keras_cnn_path)
+
+  call net % print_info()
+
+  if (this_image() == 1) then
+    acc = accuracy( &
+      net, &
+      reshape(testing_images(:,:), shape=[1,28,28,size(testing_images,2)]), &
+      label_digits(testing_labels) &
+    )
+    print '(a,f5.2,a)', 'Accuracy: ', acc * 100, ' %'
+  end if
+
+contains
+
+  real function accuracy(net, x, y)
+    type(network), intent(in out) :: net
+    real, intent(in) :: x(:,:,:,:), y(:,:)
+    integer :: i, good
+    good = 0
+    do i = 1, size(x, dim=4)
+      if (all(maxloc(net % output(x(:,:,:,i))) == maxloc(y(:,i)))) then
+        good = good + 1
+      end if
+    end do
+    accuracy = real(good) / size(x, dim=4)
+  end function accuracy
+
+end program cnn_from_keras

example/mnist_from_keras.f90 renamed to example/dense_from_keras.f90

@@ -1,31 +1,32 @@
-program mnist_from_keras
+program dense_from_keras
 
-  ! This example demonstrates loading a pre-trained MNIST model from Keras
-  ! from an HDF5 file and running an inferrence on the testing dataset.
+  ! This example demonstrates loading a dense model
+  ! pre-trained on the MNIST dataset from a Keras HDF5
+  ! file and running an inferrence on the testing dataset.
 
   use nf, only: network, label_digits, load_mnist
-  use nf_datasets, only: download_and_unpack, keras_model_dense_mnist_url
+  use nf_datasets, only: download_and_unpack, keras_dense_mnist_url
 
   implicit none
 
   type(network) :: net
   real, allocatable :: training_images(:,:), training_labels(:)
   real, allocatable :: validation_images(:,:), validation_labels(:)
   real, allocatable :: testing_images(:,:), testing_labels(:)
-  character(*), parameter :: test_data_path = 'keras_dense_mnist.h5'
+  character(*), parameter :: keras_dense_path = 'keras_dense_mnist.h5'
   logical :: file_exists
 
-  inquire(file=test_data_path, exist=file_exists)
-  if (.not. file_exists) call download_and_unpack(keras_model_dense_mnist_url)
+  inquire(file=keras_dense_path, exist=file_exists)
+  if (.not. file_exists) call download_and_unpack(keras_dense_mnist_url)
 
   call load_mnist(training_images, training_labels, &
                   validation_images, validation_labels, &
                   testing_images, testing_labels)
 
-  print '("Loading a pre-trained MNIST model from Keras")'
+  print '("Loading a pre-trained dense model from Keras")'
   print '(60("="))'
 
-  net = network(test_data_path)
+  net = network(keras_dense_path)
 
   call net % print_info()
 
@@ -48,4 +49,4 @@ real function accuracy(net, x, y)
     accuracy = real(good) / size(x, dim=2)
   end function accuracy
 
-end program mnist_from_keras
+end program dense_from_keras

fpm.toml

@@ -1,5 +1,5 @@
 name = "neural-fortran"
-version = "0.5.0"
+version = "0.6.0"
 license = "MIT"
 author = "Milan Curcic"
 maintainer = "[email protected]"
@@ -10,5 +10,6 @@ external-modules = "hdf5"
 link = ["hdf5", "hdf5_fortran"]
 
 [dependencies]
+functional = { git = "https://github.com/wavebitscientific/functional-fortran" }
 h5fortran = { git = "https://github.com/geospace-code/h5fortran" }
 json-fortran = { git = "https://github.com/jacobwilliams/json-fortran" }

src/nf/io/nf_io_hdf5.f90

@@ -31,7 +31,7 @@ module subroutine get_hdf5_dataset_real32_1d(filename, object_name, values)
         !! HDF5 file name
       character(*), intent(in) :: object_name
         !! Object (dataset) name
-      real(real32), allocatable, intent(in out) :: values(:)
+      real(real32), allocatable, intent(out) :: values(:)
         !! Array to store the dataset values into
     end subroutine get_hdf5_dataset_real32_1d
 
@@ -41,10 +41,20 @@ module subroutine get_hdf5_dataset_real32_2d(filename, object_name, values)
         !! HDF5 file name
       character(*), intent(in) :: object_name
         !! Object (dataset) name
-      real(real32), allocatable, intent(in out) :: values(:,:)
+      real(real32), allocatable, intent(out) :: values(:,:)
         !! Array to store the dataset values into
     end subroutine get_hdf5_dataset_real32_2d
 
+    module subroutine get_hdf5_dataset_real32_4d(filename, object_name, values)
+      !! Read a 4-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(out) :: values(:,:,:,:)
+        !! Array to store the dataset values into
+    end subroutine get_hdf5_dataset_real32_4d
+
   end interface get_hdf5_dataset
 
 end module nf_io_hdf5

src/nf/io/nf_io_hdf5_submodule.f90

@@ -50,23 +50,15 @@ 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(:)
+    real(real32), allocatable, intent(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
+    allocate(values(dims(1)))
 
     call f % read(object_name, values)
     call f % close()
@@ -78,27 +70,42 @@ 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(:,:)
+    real(real32), allocatable, intent(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
+    allocate(values(dims(1), dims(2)))
 
     call f % read(object_name, values)
     call f % close()
 
+    ! Transpose the array to respect Keras's storage order
+    values = transpose(values)
+
   end subroutine get_hdf5_dataset_real32_2d
 
+
+  module subroutine get_hdf5_dataset_real32_4d(filename, object_name, values)
+
+    character(*), intent(in) :: filename
+    character(*), intent(in) :: object_name
+    real(real32), allocatable, intent(out) :: values(:,:,:,:)
+
+    type(hdf5_file) :: f
+    integer(int64), allocatable :: dims(:)
+
+    call f % open(filename, 'r')
+    call f % shape(object_name, dims)
+
+    allocate(values(dims(1), dims(2), dims(3), dims(4)))
+
+    call f % read(object_name, values)
+    call f % close()
+
+  end subroutine get_hdf5_dataset_real32_4d
+
 end submodule nf_io_hdf5_submodule

src/nf/nf_datasets.f90

@@ -8,13 +8,19 @@ module nf_datasets
 
   private
 
-  public :: download_and_unpack, keras_model_dense_mnist_url, mnist_url
+  public :: &
+    download_and_unpack, &
+    keras_cnn_mnist_url, &
+    keras_dense_mnist_url, &
+    mnist_url
 
   character(*), parameter :: keras_snippets_baseurl = &
     'https://github.com/neural-fortran/keras-snippets/files'
   character(*), parameter :: neural_fortran_baseurl = &
     'https://github.com/modern-fortran/neural-fortran/files'
-  character(*), parameter :: keras_model_dense_mnist_url = &
+  character(*), parameter :: keras_cnn_mnist_url = &
+    keras_snippets_baseurl // '/8892585/keras_cnn_mnist.tar.gz'
+  character(*), parameter :: keras_dense_mnist_url = &
     keras_snippets_baseurl // '/8788739/keras_dense_mnist.tar.gz'
   character(*), parameter :: mnist_url = &
     neural_fortran_baseurl // '/8498876/mnist.tar.gz'