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createConvolutionalAutoencoderModel.R
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createConvolutionalAutoencoderModel.R
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#' Function for creating a 2-D symmetric convolutional autoencoder model.
#'
#' Builds a convolutional autoencoder based on the specified array
#' definining the number of units in the encoding branch. Ported to
#' Keras R from the Keras python implementation here:
#'
#' \url{https://github.com/XifengGuo/DCEC}
#'
#' @param inputImageSize vector definining spatial dimensions + channels
#' @param numberOfFiltersPerLayer vector defining the number of convolutional
#' filters in the encoding branch per layer
#' @param convolutionKernelSize kernel size fo the convolutional filters
#' @param deconvolutionKernelSize kernel size fo the convolutional transpose
#' filters
#'
#' @return two models: the convolutional encoder and convolutional auto-encoder
#'
#' @author Tustison NJ
#' @examples
#'
#' library( ANTsRNet )
#' library( keras )
#'
#' ae <- createConvolutionalAutoencoderModel2D( c( 32, 32, 1 ) )
#'
#' @export
createConvolutionalAutoencoderModel2D <- function( inputImageSize,
numberOfFiltersPerLayer = c( 32, 64, 128, 10 ),
convolutionKernelSize = c( 5, 5 ),
deconvolutionKernelSize = c( 5, 5 ) )
{
activation <- 'relu'
strides <- c( 2, 2 )
numberOfEncodingLayers <- length( numberOfFiltersPerLayer ) - 1
factor <- 2^numberOfEncodingLayers
padding <- 'valid'
if( inputImageSize[1] %% factor == 0 )
{
padding <- 'same'
}
inputs <- layer_input( shape = inputImageSize )
encoder <- inputs
for( i in seq_len( numberOfEncodingLayers ) )
{
localPadding <- 'same'
kernelSize <- convolutionKernelSize
if( i == numberOfEncodingLayers )
{
localPadding <- padding
kernelSize <- convolutionKernelSize - 2
}
encoder <- encoder %>%
layer_conv_2d( filters = numberOfFiltersPerLayer[i],
kernel_size = kernelSize, strides = strides,
activation = activation, padding = localPadding )
}
encoder <- encoder %>%
layer_flatten() %>%
layer_dense( units = tail( numberOfFiltersPerLayer, 1 ) )
autoencoder <- encoder
penultimateNumberOfFilters <-
numberOfFiltersPerLayer[numberOfEncodingLayers]
numberOfUnitsForEncoderOutput <- penultimateNumberOfFilters *
prod( floor( inputImageSize[1:2] / factor ) )
autoencoder <- autoencoder %>%
layer_dense( units = numberOfUnitsForEncoderOutput, activation = activation )
autoencoder <- autoencoder %>%
layer_reshape( target_shape = c( floor( inputImageSize[1:2] / factor ),
penultimateNumberOfFilters ) )
for( i in seq( from = numberOfEncodingLayers, to = 2, by = -1 ) )
{
localPadding <- 'same'
kernelSize <- deconvolutionKernelSize
if( i == numberOfEncodingLayers )
{
localPadding <- padding
kernelSize <- deconvolutionKernelSize - 2
}
autoencoder <- autoencoder %>%
layer_conv_2d_transpose( filters = numberOfFiltersPerLayer[i-1],
kernel_size = kernelSize, strides = strides,
padding = localPadding )
}
autoencoder <- autoencoder %>%
layer_conv_2d_transpose( filters = tail( inputImageSize, 1 ),
kernel_size = deconvolutionKernelSize, strides = strides,
padding = 'same' )
autoencoderModel <- keras_model( inputs = inputs, outputs = autoencoder )
encoderModel <- keras_model( inputs = inputs, outputs = encoder )
return( list(
convolutionalAutoencoderModel = autoencoderModel,
convolutionalEncoderModel = encoderModel ) )
}
#' Function for creating a 3-D symmetric convolutional autoencoder model.
#'
#' Builds a convolutional autoencoder based on the specified array
#' definining the number of units in the encoding branch. Ported to
#' Keras R from the Keras python implementation here:
#'
#' \url{https://github.com/XifengGuo/DCEC}
#'
#' @param inputImageSize vector definining spatial dimensions + channels
#' @param numberOfFiltersPerLayer vector defining the number of convolutional
#' filters in the encoding branch per layer
#' @param convolutionKernelSize kernel size fo the convolutional filters
#' @param deconvolutionKernelSize kernel size fo the convolutional transpose
#' filters
#'
#' @return two models: the convolutional encoder and convolutional auto-encoder
#'
#' @author Tustison NJ
#' @examples
#'
#' library( ANTsRNet )
#' library( keras )
#'
#' ae <- createConvolutionalAutoencoderModel2D( c( 32, 32, 1 ) )
#'
#' @export
createConvolutionalAutoencoderModel3D <- function( inputImageSize,
numberOfFiltersPerLayer = c( 32, 64, 128, 10 ),
convolutionKernelSize = c( 5, 5, 5 ),
deconvolutionKernelSize = c( 5, 5, 5 ) )
{
activation <- 'relu'
strides <- c( 2, 2, 2 )
numberOfEncodingLayers <- length( numberOfFiltersPerLayer ) - 1
factor <- numberOfEncodingLayers^2
padding <- 'valid'
if( inputImageSize[1] %% factor == 0 )
{
padding <- 'same'
}
inputs <- layer_input( shape = inputImageSize )
encoder <- inputs
for( i in seq_len( numberOfEncodingLayers ) )
{
localPadding <- 'same'
kernelSize <- convolutionKernelSize
if( i == numberOfEncodingLayers )
{
localPadding <- padding
kernelSize <- convolutionKernelSize - 2
}
encoder <- encoder %>%
layer_conv_3d( filters = numberOfFiltersPerLayer[i],
kernel_size = convolutionKernelSize, strides = strides,
activation = activation, padding = localPadding )
}
encoder <- encoder %>%
layer_flatten() %>%
layer_dense( units = tail( numberOfFiltersPerLayer, 1 ) )
autoencoder <- encoder
penultimateNumberOfFilters <-
numberOfFiltersPerLayer[numberOfEncodingLayers]
numberOfUnitsForEncoderOutput <- penultimateNumberOfFilters *
prod( floor( inputImageSize[1:3] / factor ) )
autoencoder <- autoencoder %>%
layer_dense( units = numberOfUnitsForEncoderOutput, activation = activation )
autoencoder <- autoencoder %>%
layer_reshape( target_shape = c( floor( inputImageSize[1:3] / factor ),
penultimateNumberOfFilters ) )
for( i in seq( from = numberOfEncodingLayers, to = 2, by = -1 ) )
{
localPadding <- 'same'
kernelSize <- deconvolutionKernelSize
if( i == numberOfEncodingLayers )
{
localPadding <- padding
kernelSize <- deconvolutionKernelSize - 2
}
autoencoder <- autoencoder %>%
layer_conv_3d_transpose( filters = numberOfFiltersPerLayer[i-1],
kernel_size = kernelSize, strides = strides,
padding = localPadding )
}
autoencoder <- autoencoder %>%
layer_conv_3d_transpose( filters = tail( inputImageSize, 1 ),
kernel_size = deconvolutionKernelSize, strides = strides,
padding = 'same' )
autoencoderModel <- keras_model( inputs = inputs, outputs = autoencoder )
encoderModel <- keras_model( inputs = inputs, outputs = encoder )
return( list(
convolutionalAutoencoderModel = autoencoderModel,
convolutionalEncoderModel = encoderModel ) )
}