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#' @title Train ResNet classification models
#' @name sits_resnet
#'
#' @author Gilberto Camara, \email{gilberto.camara@@inpe.br}
#' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
#' @author Felipe Souza, \email{lipecaso@@gmail.com}
#' @author Alber Sanchez, \email{alber.ipia@@inpe.br}
#' @author Charlotte Pelletier, \email{charlotte.pelletier@@univ-ubs.fr}
#' @author Daniel Falbel, \email{dfalbel@@gmail.com}
#'
#' @description Use a ResNet architecture for classifying image time series.
#' The ResNet (or deep residual network) was proposed by a team
#' in Microsoft Research for 2D image classification.
#' ResNet tries to address the degradation of accuracy
#' in a deep network. The idea is to replace a deep network
#' with a combination of shallow ones.
#' In the paper by Fawaz et al. (2019), ResNet was considered the best method
#' for time series classification, using the UCR dataset.
#' Please refer to the paper for more details.
#'
#' The R-torch version is based on the code made available by Zhiguang Wang,
#' author of the original paper. The code was developed in python using keras.
#'
#' https://github.com/cauchyturing
#' (repo: UCR_Time_Series_Classification_Deep_Learning_Baseline)
#'
#' The R-torch version also considered the code by Ignacio Oguiza,
#' whose implementation is available at
#' https://github.com/timeseriesAI/tsai/blob/main/tsai/models/ResNet.py.
#'
#' There are differences between Wang's Keras code and Oguiza torch code.
#' In this case, we have used Wang's keras code as the main reference.
#'
#' @references Hassan Fawaz, Germain Forestier, Jonathan Weber,
#' Lhassane Idoumghar, and Pierre-Alain Muller,
#' "Deep learning for time series classification: a review",
#' Data Mining and Knowledge Discovery, 33(4): 917--963, 2019.
#'
#' Zhiguang Wang, Weizhong Yan, and Tim Oates,
#' "Time series classification from scratch with deep neural networks:
#' A strong baseline",
#' 2017 international joint conference on neural networks (IJCNN).
#'
#' @param samples Time series with the training samples.
#' @param samples_validation Time series with the validation samples. if the
#' \code{samples_validation} parameter is provided,
#' the \code{validation_split} parameter is ignored.
#' @param blocks Number of 1D convolutional filters for
#' each block of three layers.
#' @param kernels Size of the 1D convolutional kernels
#' @param epochs Number of iterations to train the model.
#' for each layer of each block.
#' @param batch_size Number of samples per gradient update.
#' @param validation_split Fraction of training data
#' to be used as validation data.
#' @param optimizer Optimizer function to be used.
#' @param opt_hparams Hyperparameters for optimizer:
#' lr : Learning rate of the optimizer
#' eps: Term added to the denominator
#' to improve numerical stability.
#' weight_decay: L2 regularization
#' @param lr_decay_epochs Number of epochs to reduce learning rate.
#' @param lr_decay_rate Decay factor for reducing learning rate.
#' @param patience Number of epochs without improvements until
#' training stops.
#' @param min_delta Minimum improvement in loss function
#' to reset the patience counter.
#' @param verbose Verbosity mode (TRUE/FALSE). Default is FALSE.
#'
#' @return A fitted model to be used for classification.
#'
#' @note
#' Please refer to the sits documentation available in
#' <https://e-sensing.github.io/sitsbook/> for detailed examples.
#' @examples
#' if (sits_run_examples()) {
#' # create a ResNet model
#' torch_model <- sits_train(samples_modis_ndvi, sits_resnet())
#' # plot the model
#' plot(torch_model)
#' # create a data cube from local files
#' data_dir <- system.file("extdata/raster/mod13q1", package = "sits")
#' cube <- sits_cube(
#' source = "BDC",
#' collection = "MOD13Q1-6",
#' data_dir = data_dir
#' )
#' # classify a data cube
#' probs_cube <- sits_classify(
#' data = cube, ml_model = torch_model, output_dir = tempdir()
#' )
#' # plot the probability cube
#' plot(probs_cube)
#' # smooth the probability cube using Bayesian statistics
#' bayes_cube <- sits_smooth(probs_cube, output_dir = tempdir())
#' # plot the smoothed cube
#' plot(bayes_cube)
#' # label the probability cube
#' label_cube <- sits_label_classification(
#' bayes_cube,
#' output_dir = tempdir()
#' )
#' # plot the labelled cube
#' plot(label_cube)
#' }
#' @export
sits_resnet <- function(samples = NULL,
samples_validation = NULL,
blocks = c(64, 128, 128),
kernels = c(7, 5, 3),
epochs = 100,
batch_size = 64,
validation_split = 0.2,
optimizer = torch::optim_adamw,
opt_hparams = list(
lr = 0.001,
eps = 1e-08,
weight_decay = 1e-06
),
lr_decay_epochs = 1,
lr_decay_rate = 0.95,
patience = 20,
min_delta = 0.01,
verbose = FALSE) {
# set caller for error msg
.check_set_caller("sits_resnet")
# Function that trains a torch model based on samples
train_fun <- function(samples) {
# Avoid add a global variable for 'self'
self <- NULL
# Verifies if 'torch' and 'luz' packages is installed
.check_require_packages(c("torch", "luz"))
# Pre-conditions:
.check_samples_train(samples)
.check_int_parameter(blocks)
.check_int_parameter(kernels,
min = 1,
len_min = length(blocks),
len_max = length(blocks)
)
.check_int_parameter(epochs)
.check_int_parameter(batch_size)
.check_null_parameter(optimizer)
# Check validation_split parameter if samples_validation is not passed
if (!.has(samples_validation))
.check_num_parameter(validation_split, exclusive_min = 0, max = 0.5)
# Check opt_hparams
# Get parameters list and remove the 'param' parameter
optim_params_function <- formals(optimizer)[-1]
if (!is.null(opt_hparams)) {
.check_lst_parameter(opt_hparams,
msg = .conf("messages", ".check_opt_hparams")
)
.check_chr_within(
x = names(opt_hparams),
within = names(optim_params_function),
msg = .conf("messages", ".check_opt_hparams")
)
optim_params_function <- utils::modifyList(
x = optim_params_function, val = opt_hparams
)
}
# Other pre-conditions:
.check_int_parameter(lr_decay_epochs)
.check_num_parameter(lr_decay_rate, exclusive_min = 0, max = 1)
.check_int_parameter(patience)
.check_num_parameter(min_delta, min = 0)
.check_lgl_parameter(verbose)
# Samples labels
labels <- sits_labels(samples)
# Samples bands
bands <- sits_bands(samples)
# Samples timeline
timeline <- sits_timeline(samples)
# Create numeric labels vector
code_labels <- seq_along(labels)
names(code_labels) <- labels
# Number of labels, bands, and number of samples (used below)
n_labels <- length(labels)
n_bands <- length(bands)
n_times <- .samples_ntimes(samples)
# Data normalization
ml_stats <- .samples_stats(samples)
train_samples <- .predictors(samples)
train_samples <- .pred_normalize(pred = train_samples, stats = ml_stats)
# Post condition: is predictor data valid?
.check_predictors(pred = train_samples, samples = samples)
if (!is.null(samples_validation)) {
.check_samples_validation(
samples_validation = samples_validation, labels = labels,
timeline = timeline, bands = bands
)
# Test samples are extracted from validation data
test_samples <- .predictors(samples_validation)
test_samples <- .pred_normalize(
pred = test_samples, stats = ml_stats
)
} else {
# Split the data into training and validation data sets
# Create partitions different splits of the input data
test_samples <- .pred_sample(
pred = train_samples, frac = validation_split
)
# Remove the lines used for validation
sel <- !train_samples[["sample_id"]] %in%
test_samples[["sample_id"]]
train_samples <- train_samples[sel, ]
}
n_samples_train <- nrow(train_samples)
n_samples_test <- nrow(test_samples)
# Shuffle the data
train_samples <- train_samples[sample(
nrow(train_samples), nrow(train_samples)
), ]
test_samples <- test_samples[sample(
nrow(test_samples), nrow(test_samples)
), ]
# Organize data for model training
train_x <- array(
data = as.matrix(.pred_features(train_samples)),
dim = c(n_samples_train, n_times, n_bands)
)
train_y <- unname(code_labels[.pred_references(train_samples)])
# Create the test data
test_x <- array(
data = as.matrix(.pred_features(test_samples)),
dim = c(n_samples_test, n_times, n_bands)
)
test_y <- unname(code_labels[.pred_references(test_samples)])
# Set torch seed
torch::torch_manual_seed(sample.int(10^5, 1))
# Block associated to ResNet
resnet_block <- torch::nn_module(
classname = "block_resnet",
initialize = function(in_channels,
out_channels,
kernels) {
# create first convolution block
self$conv_block1 <- .torch_batch_conv1D_batch_norm_relu(
input_dim = in_channels,
output_dim = out_channels,
kernel_size = kernels[[1]],
padding = "same"
)
# create second convolution block
self$conv_block2 <- .torch_conv1D_batch_norm_relu(
input_dim = out_channels,
output_dim = out_channels,
kernel_size = kernels[[2]],
padding = "same"
)
# create third convolution block
self$conv_block3 <- .torch_conv1D_batch_norm(
input_dim = out_channels,
output_dim = out_channels,
kernel_size = kernels[[3]],
padding = "same"
)
# create shortcut
self$shortcut <- .torch_conv1D_batch_norm(
input_dim = in_channels,
output_dim = out_channels,
kernel_size = 1,
padding = "same"
)
# activation
self$act <- torch::nn_relu()
},
forward = function(x) {
res <- self$shortcut(x)
x <- self$conv_block1(x)
x <- self$conv_block2(x)
x <- self$conv_block3(x)
x <- torch::torch_add(x, res)
x <- self$act(x)
return(x)
}
)
# Define the ResNet architecture
resnet_model <- torch::nn_module(
classname = "model_resnet",
initialize = function(n_bands, n_times, n_labels, blocks, kernels) {
self$res_block1 <- resnet_block(n_bands,
blocks[[1]],
kernels
)
self$res_block2 <- resnet_block(blocks[[1]],
blocks[[2]],
kernels
)
self$res_block3 <- resnet_block(blocks[[2]],
blocks[[3]],
kernels
)
self$gap <- torch::nn_adaptive_avg_pool1d(output_size = n_bands)
# flatten 3D tensor to 2D tensor
self$flatten <- torch::nn_flatten()
# classification using softmax
self$softmax <- torch::nn_sequential(
torch::nn_linear(blocks[[3]] * n_bands, n_labels),
torch::nn_softmax(dim = -1)
)
},
forward = function(x) {
x <- torch::torch_transpose(x, 2, 3)
x <- x |>
self$res_block1() |>
self$res_block2() |>
self$res_block3() |>
self$gap() |>
self$flatten() |>
self$softmax()
}
)
# train the model using luz
torch_model <-
luz::setup(
module = resnet_model,
loss = torch::nn_cross_entropy_loss(),
metrics = list(luz::luz_metric_accuracy()),
optimizer = optimizer
) |>
luz::set_hparams(
n_bands = n_bands,
n_times = n_times,
n_labels = n_labels,
blocks = blocks,
kernels = kernels
) |>
luz::set_opt_hparams(
!!!optim_params_function
) |>
luz::fit(
data = list(train_x, train_y),
epochs = epochs,
valid_data = list(test_x, test_y),
callbacks = list(
luz::luz_callback_early_stopping(
monitor = "valid_loss",
mode = "min",
patience = patience,
min_delta = min_delta
),
luz::luz_callback_lr_scheduler(
torch::lr_step,
step_size = lr_decay_epochs,
gamma = lr_decay_rate
)
),
dataloader_options = list(batch_size = batch_size),
verbose = verbose
)
# Serialize model
serialized_model <- .torch_serialize_model(torch_model[["model"]])
# Function that predicts labels of input values
predict_fun <- function(values) {
# Verifies if torch package is installed
.check_require_packages("torch")
# Set torch threads to 1
# Note: function does not work on MacOS
suppressWarnings(torch::torch_set_num_threads(1))
# Unserialize model
torch_model[["model"]] <- .torch_unserialize_model(serialized_model)
# Used to check values (below)
n_input_pixels <- nrow(values)
# Transform input into a 3D tensor
# Reshape the 2D matrix into a 3D array
n_samples <- nrow(values)
n_times <- .samples_ntimes(samples)
n_bands <- length(bands)
# Performs data normalization
values <- .pred_normalize(pred = values, stats = ml_stats)
values <- array(
data = as.matrix(values), dim = c(n_samples, n_times, n_bands)
)
# if CUDA is available, transform to torch data set
# Load into GPU
if (torch::cuda_is_available()) {
values <- .as_dataset(values)
# We need to transform in a dataloader to use the batch size
values <- torch::dataloader(
values, batch_size = 2^15
)
# Do GPU classification
values <- .try(
stats::predict(object = torch_model, values),
.msg_error = .conf("messages", ".check_gpu_memory_size")
)
} else {
# Do CPU classification
values <- stats::predict(object = torch_model, values)
}
# Convert to tensor CPU
values <- torch::as_array(
x = torch::torch_tensor(values, device = "cpu")
)
.check_processed_values(
values = values, n_input_pixels = n_input_pixels
)
# Update the columns names to labels
colnames(values) <- labels
return(values)
}
# Set model class
predict_fun <- .set_class(
predict_fun, "torch_model", "sits_model", class(predict_fun)
)
return(predict_fun)
}
# If samples is informed, train a model and return a predict function
# Otherwise give back a train function to train the model later
result <- .factory_function(samples, train_fun)
return(result)
}
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