createResNetWithSpatialTransformerNetworkModel3D: 3-D implementation of the ResNet deep learning architecture...

In ANTsX/ANTsRNet: Neural Networks for Medical Image Processing

3-D implementation of the ResNet deep learning architecture with a preceding spatial transformer network layer.

Description

Creates a keras model of the ResNet deep learning architecture for image classification with a spatial transformer network (STN) layer. The paper is available here:

Usage

createResNetWithSpatialTransformerNetworkModel3D(
  inputImageSize,
  numberOfOutputs = 1000,
  layers = 1:4,
  residualBlockSchedule = c(3, 4, 6, 3),
  lowestResolution = 64,
  cardinality = 1,
  resampledSize = c(64, 64, 64),
  numberOfSpatialTransformerUnits = 50,
  mode = c("classification", "regression")
)

Arguments

inputImageSize	Used for specifying the input tensor shape. The shape (or dimension) of that tensor is the image dimensions followed by the number of channels (e.g., red, green, and blue). The batch size (i.e., number of training images) is not specified a priori.
numberOfOutputs	Number of segmentation labels.
layers	a vector determining the number of 'filters' defined at for each layer.
residualBlockSchedule	vector defining the how many residual blocks repeats.
lowestResolution	number of filters at the initial layer.
cardinality	perform ResNet (cardinality = 1) or ResNeXt (cardinality != 1 but powers of 2—try '32' )
resampledSize	output image size of the spatial transformer network.
numberOfSpatialTransformerUnits	number of units in the dense layer.
mode	'classification' or 'regression'. Default = 'classification'.

Details

    https://arxiv.org/abs/1512.03385

Value

an ResNet keras model

Author(s)

Tustison NJ

Examples

## Not run: 

library( ANTsRNet )
library( keras )

mnistData <- dataset_mnist()
numberOfLabels <- 10

# Extract a small subset for something that can run quickly

X_trainSmall <- mnistData$train$x[1:10,,]
X_trainSmall <- array( data = X_trainSmall, dim = c( dim( X_trainSmall ), 1 ) )
Y_trainSmall <- to_categorical( mnistData$train$y[1:10], numberOfLabels )

X_testSmall <- mnistData$test$x[1:10,,]
X_testSmall <- array( data = X_testSmall, dim = c( dim( X_testSmall ), 1 ) )
Y_testSmall <- to_categorical( mnistData$test$y[1:10], numberOfLabels )

# We add a dimension of 1 to specify the channel size

inputImageSize <- c( dim( X_trainSmall )[2:3], 1 )

model <- createResNetWithSpatialTransformerNetworkModel2D(
  inputImageSize = inputImageSize,
  numberOfOutputs = numberOfLabels )

model %>% compile( loss = 'categorical_crossentropy',
  optimizer = optimizer_adam( lr = 0.0001 ),
  metrics = c( 'categorical_crossentropy', 'accuracy' ) )

track <- model %>% fit( X_trainSmall, Y_trainSmall, verbose = 1,
  epochs = 1, batch_size = 2, shuffle = TRUE, validation_split = 0.5 )

# Now test the model

testingMetrics <- model %>% evaluate( X_testSmall, Y_testSmall )
predictedData <- model %>% predict( X_testSmall, verbose = 1 )


## End(Not run)

ANTsX/ANTsRNet documentation built on April 23, 2024, 1:24 p.m.