Mind picture segmentation with torch

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When what will not be sufficient

True, generally it’s important to tell apart between totally different sorts of objects. Is {that a} automotive rushing in the direction of me, during which case I’d higher bounce out of the best way? Or is it an enormous Doberman (during which case I’d in all probability do the identical)? Usually in actual life although, as a substitute of coarse-grained classification, what is required is fine-grained segmentation.

Zooming in on pictures, we’re not searching for a single label; as a substitute, we wish to classify each pixel based on some criterion:

In drugs, we could wish to distinguish between totally different cell sorts, or determine tumors.
In varied earth sciences, satellite tv for pc knowledge are used to section terrestrial surfaces.
To allow use of customized backgrounds, video-conferencing software program has to have the ability to inform foreground from background.

Picture segmentation is a type of supervised studying: Some form of floor fact is required. Right here, it is available in type of a masks – a picture, of spatial decision equivalent to that of the enter knowledge, that designates the true class for each pixel. Accordingly, classification loss is calculated pixel-wise; losses are then summed as much as yield an combination for use in optimization.

The “canonical” structure for picture segmentation is U-Web (round since 2015).

U-Web

Right here is the prototypical U-Web, as depicted within the unique Rönneberger et al. paper (Ronneberger, Fischer, and Brox 2015).

Of this structure, quite a few variants exist. You possibly can use totally different layer sizes, activations, methods to realize downsizing and upsizing, and extra. Nevertheless, there may be one defining attribute: the U-shape, stabilized by the “bridges” crossing over horizontally in any respect ranges.

In a nutshell, the left-hand facet of the U resembles the convolutional architectures utilized in picture classification. It successively reduces spatial decision. On the identical time, one other dimension – the channels dimension – is used to construct up a hierarchy of options, starting from very primary to very specialised.

In contrast to in classification, nonetheless, the output ought to have the identical spatial decision because the enter. Thus, we have to upsize once more – that is taken care of by the right-hand facet of the U. However, how are we going to reach at a superb per-pixel classification, now that a lot spatial info has been misplaced?

That is what the “bridges” are for: At every degree, the enter to an upsampling layer is a concatenation of the earlier layer’s output – which went by means of the entire compression/decompression routine – and a few preserved intermediate illustration from the downsizing section. On this method, a U-Web structure combines consideration to element with function extraction.

Mind picture segmentation

With U-Web, area applicability is as broad because the structure is versatile. Right here, we wish to detect abnormalities in mind scans. The dataset, utilized in Buda, Saha, and Mazurowski (2019), accommodates MRI pictures along with manually created FLAIR abnormality segmentation masks. It’s out there on Kaggle.

Properly, the paper is accompanied by a GitHub repository. Under, we intently observe (although not precisely replicate) the authors’ preprocessing and knowledge augmentation code.

As is usually the case in medical imaging, there may be notable class imbalance within the knowledge. For each affected person, sections have been taken at a number of positions. (Variety of sections per affected person varies.) Most sections don’t exhibit any lesions; the corresponding masks are coloured black in every single place.

Listed here are three examples the place the masks do point out abnormalities:

Let’s see if we are able to construct a U-Web that generates such masks for us.

Information

Earlier than you begin typing, here’s a Colaboratory pocket book to conveniently observe alongside.

We use pins to acquire the information. Please see this introduction for those who haven’t used that package deal earlier than.

The dataset will not be that large – it contains scans from 110 totally different sufferers – so we’ll must do with only a coaching and a validation set. (Don’t do that in actual life, as you’ll inevitably find yourself fine-tuning on the latter.)

train_dir <- "knowledge/mri_train"
valid_dir <- "knowledge/mri_valid"

if(dir.exists(train_dir)) unlink(train_dir, recursive = TRUE, power = TRUE)
if(dir.exists(valid_dir)) unlink(valid_dir, recursive = TRUE, power = TRUE)

zip::unzip(information, exdir = "knowledge")

file.rename("knowledge/kaggle_3m", train_dir)

# it is a duplicate, once more containing kaggle_3m (evidently a packaging error on Kaggle)
# we simply take away it
unlink("knowledge/lgg-mri-segmentation", recursive = TRUE)

dir.create(valid_dir)

Of these 110 sufferers, we maintain 30 for validation. Some extra file manipulations, and we’re arrange with a pleasant hierarchical construction, with train_dir and valid_dir holding their per-patient sub-directories, respectively.

valid_indices <- pattern(1:size(sufferers), 30)

sufferers <- record.dirs(train_dir, recursive = FALSE)

for (i in valid_indices) {
  dir.create(file.path(valid_dir, basename(sufferers[i])))
  for (f in record.information(sufferers[i])) {    
    file.rename(file.path(train_dir, basename(sufferers[i]), f), file.path(valid_dir, basename(sufferers[i]), f))    
  }
  unlink(file.path(train_dir, basename(sufferers[i])), recursive = TRUE)
}

We now want a dataset that is aware of what to do with these information.

Dataset

Like each torch dataset, this one has initialize() and .getitem() strategies. initialize() creates a listing of scan and masks file names, for use by .getitem() when it really reads these information. In distinction to what we’ve seen in earlier posts, although , .getitem() doesn’t merely return input-target pairs so as. As a substitute, every time the parameter random_sampling is true, it would carry out weighted sampling, preferring gadgets with sizable lesions. This feature will likely be used for the coaching set, to counter the category imbalance talked about above.

The opposite method coaching and validation units will differ is use of knowledge augmentation. Coaching pictures/masks could also be flipped, re-sized, and rotated; possibilities and quantities are configurable.

An occasion of brainseg_dataset encapsulates all this performance:

brainseg_dataset <- dataset(
  identify = "brainseg_dataset",
  
  initialize = operate(img_dir,
                        augmentation_params = NULL,
                        random_sampling = FALSE) {
    self$pictures <- tibble(
      img = grep(
        record.information(
          img_dir,
          full.names = TRUE,
          sample = "tif",
          recursive = TRUE
        ),
        sample = 'masks',
        invert = TRUE,
        worth = TRUE
      ),
      masks = grep(
        record.information(
          img_dir,
          full.names = TRUE,
          sample = "tif",
          recursive = TRUE
        ),
        sample = 'masks',
        worth = TRUE
      )
    )
    self$slice_weights <- self$calc_slice_weights(self$pictures$masks)
    self$augmentation_params <- augmentation_params
    self$random_sampling <- random_sampling
  },
  
  .getitem = operate(i) {
    index <-
      if (self$random_sampling == TRUE)
        pattern(1:self$.size(), 1, prob = self$slice_weights)
    else
      i
    
    img <- self$pictures$img[index] %>%
      image_read() %>%
      transform_to_tensor() 
    masks <- self$pictures$masks[index] %>%
      image_read() %>%
      transform_to_tensor() %>%
      transform_rgb_to_grayscale() %>%
      torch_unsqueeze(1)
    
    img <- self$min_max_scale(img)
    
    if (!is.null(self$augmentation_params)) {
      scale_param <- self$augmentation_params[1]
      c(img, masks) %<-% self$resize(img, masks, scale_param)
      
      rot_param <- self$augmentation_params[2]
      c(img, masks) %<-% self$rotate(img, masks, rot_param)
      
      flip_param <- self$augmentation_params[3]
      c(img, masks) %<-% self$flip(img, masks, flip_param)
      
    }
    record(img = img, masks = masks)
  },
  
  .size = operate() {
    nrow(self$pictures)
  },
  
  calc_slice_weights = operate(masks) {
    weights <- map_dbl(masks, operate(m) {
      img <-
        as.integer(magick::image_data(image_read(m), channels = "grey"))
      sum(img / 255)
    })
    
    sum_weights <- sum(weights)
    num_weights <- size(weights)
    
    weights <- weights %>% map_dbl(operate(w) {
      w <- (w + sum_weights * 0.1 / num_weights) / (sum_weights * 1.1)
    })
    weights
  },
  
  min_max_scale = operate(x) {
    min = x$min()$merchandise()
    max = x$max()$merchandise()
    x$clamp_(min = min, max = max)
    x$add_(-min)$div_(max - min + 1e-5)
    x
  },
  
  resize = operate(img, masks, scale_param) {
    img_size <- dim(img)[2]
    rnd_scale <- runif(1, 1 - scale_param, 1 + scale_param)
    img <- transform_resize(img, dimension = rnd_scale * img_size)
    masks <- transform_resize(masks, dimension = rnd_scale * img_size)
    diff <- dim(img)[2] - img_size
    if (diff > 0) {
      prime <- ceiling(diff / 2)
      left <- ceiling(diff / 2)
      img <- transform_crop(img, prime, left, img_size, img_size)
      masks <- transform_crop(masks, prime, left, img_size, img_size)
    } else {
      img <- transform_pad(img,
                           padding = -c(
                             ceiling(diff / 2),
                             flooring(diff / 2),
                             ceiling(diff / 2),
                             flooring(diff / 2)
                           ))
      masks <- transform_pad(masks, padding = -c(
        ceiling(diff / 2),
        flooring(diff /
                2),
        ceiling(diff /
                  2),
        flooring(diff /
                2)
      ))
    }
    record(img, masks)
  },
  
  rotate = operate(img, masks, rot_param) {
    rnd_rot <- runif(1, 1 - rot_param, 1 + rot_param)
    img <- transform_rotate(img, angle = rnd_rot)
    masks <- transform_rotate(masks, angle = rnd_rot)
    
    record(img, masks)
  },
  
  flip = operate(img, masks, flip_param) {
    rnd_flip <- runif(1)
    if (rnd_flip > flip_param) {
      img <- transform_hflip(img)
      masks <- transform_hflip(masks)
    }
    
    record(img, masks)
  }
)

After instantiation, we see now we have 2977 coaching pairs and 952 validation pairs, respectively:

train_ds <- brainseg_dataset(
  train_dir,
  augmentation_params = c(0.05, 15, 0.5),
  random_sampling = TRUE
)

size(train_ds)
# 2977

valid_ds <- brainseg_dataset(
  valid_dir,
  augmentation_params = NULL,
  random_sampling = FALSE
)

size(valid_ds)
# 952

As a correctness examine, let’s plot a picture and related masks:

par(mfrow = c(1, 2), mar = c(0, 1, 0, 1))

img_and_mask <- valid_ds[27]
img <- img_and_mask[[1]]
masks <- img_and_mask[[2]]

img$permute(c(2, 3, 1)) %>% as.array() %>% as.raster() %>% plot()
masks$squeeze() %>% as.array() %>% as.raster() %>% plot()

With torch, it’s easy to examine what occurs whenever you change augmentation-related parameters. We simply choose a pair from the validation set, which has not had any augmentation utilized as but, and name valid_ds$<augmentation_func()> straight. Only for enjoyable, let’s use extra “excessive” parameters right here than we do in precise coaching. (Precise coaching makes use of the settings from Mateusz’ GitHub repository, which we assume have been rigorously chosen for optimum efficiency.)

img_and_mask <- valid_ds[77]
img <- img_and_mask[[1]]
masks <- img_and_mask[[2]]

imgs <- map (1:24, operate(i) {
  
  # scale issue; train_ds actually makes use of 0.05
  c(img, masks) %<-% valid_ds$resize(img, masks, 0.2) 
  c(img, masks) %<-% valid_ds$flip(img, masks, 0.5)
  # rotation angle; train_ds actually makes use of 15
  c(img, masks) %<-% valid_ds$rotate(img, masks, 90) 
  img %>%
    transform_rgb_to_grayscale() %>%
    as.array() %>%
    as_tibble() %>%
    rowid_to_column(var = "Y") %>%
    collect(key = "X", worth = "worth", -Y) %>%
    mutate(X = as.numeric(gsub("V", "", X))) %>%
    ggplot(aes(X, Y, fill = worth)) +
    geom_raster() +
    theme_void() +
    theme(legend.place = "none") +
    theme(facet.ratio = 1)
  
})

plot_grid(plotlist = imgs, nrow = 4)

Now we nonetheless want the information loaders, after which, nothing retains us from continuing to the subsequent large activity: constructing the mannequin.

batch_size <- 4
train_dl <- dataloader(train_ds, batch_size)
valid_dl <- dataloader(valid_ds, batch_size)

Mannequin

Our mannequin properly illustrates the form of modular code that comes “naturally” with torch. We method issues top-down, beginning with the U-Web container itself.

unet takes care of the worldwide composition – how far “down” will we go, shrinking the picture whereas incrementing the variety of filters, after which how will we go “up” once more?

Importantly, it is usually within the system’s reminiscence. In ahead(), it retains observe of layer outputs seen going “down,” to be added again in going “up.”

unet <- nn_module(
  "unet",
  
  initialize = operate(channels_in = 3,
                        n_classes = 1,
                        depth = 5,
                        n_filters = 6) {
    
    self$down_path <- nn_module_list()
    
    prev_channels <- channels_in
    for (i in 1:depth) {
      self$down_path$append(down_block(prev_channels, 2 ^ (n_filters + i - 1)))
      prev_channels <- 2 ^ (n_filters + i -1)
    }
    
    self$up_path <- nn_module_list()
    
    for (i in ((depth - 1):1)) {
      self$up_path$append(up_block(prev_channels, 2 ^ (n_filters + i - 1)))
      prev_channels <- 2 ^ (n_filters + i - 1)
    }
    
    self$final = nn_conv2d(prev_channels, n_classes, kernel_size = 1)
  },
  
  ahead = operate(x) {
    
    blocks <- record()
    
    for (i in 1:size(self$down_path)) {
      x <- self$down_path[[i]](x)
      if (i != size(self$down_path)) {
        blocks <- c(blocks, x)
        x <- nnf_max_pool2d(x, 2)
      }
    }
    
    for (i in 1:size(self$up_path)) {  
      x <- self$up_path[[i]](x, blocks[[length(blocks) - i + 1]]$to(gadget = gadget))
    }
    
    torch_sigmoid(self$final(x))
  }
)

unet delegates to 2 containers slightly below it within the hierarchy: down_block and up_block. Whereas down_block is “simply” there for aesthetic causes (it instantly delegates to its personal workhorse, conv_block), in up_block we see the U-Web “bridges” in motion.

down_block <- nn_module(
  "down_block",
  
  initialize = operate(in_size, out_size) {
    self$conv_block <- conv_block(in_size, out_size)
  },
  
  ahead = operate(x) {
    self$conv_block(x)
  }
)

up_block <- nn_module(
  "up_block",
  
  initialize = operate(in_size, out_size) {
    
    self$up = nn_conv_transpose2d(in_size,
                                  out_size,
                                  kernel_size = 2,
                                  stride = 2)
    self$conv_block = conv_block(in_size, out_size)
  },
  
  ahead = operate(x, bridge) {
    
    up <- self$up(x)
    torch_cat(record(up, bridge), 2) %>%
      self$conv_block()
  }
)

Lastly, a conv_block is a sequential construction containing convolutional, ReLU, and dropout layers.

conv_block <- nn_module( 
  "conv_block",
  
  initialize = operate(in_size, out_size) {
    
    self$conv_block <- nn_sequential(
      nn_conv2d(in_size, out_size, kernel_size = 3, padding = 1),
      nn_relu(),
      nn_dropout(0.6),
      nn_conv2d(out_size, out_size, kernel_size = 3, padding = 1),
      nn_relu()
    )
  },
  
  ahead = operate(x){
    self$conv_block(x)
  }
)

Now instantiate the mannequin, and presumably, transfer it to the GPU:

gadget <- torch_device(if(cuda_is_available()) "cuda" else "cpu")
mannequin <- unet(depth = 5)$to(gadget = gadget)

Optimization

We prepare our mannequin with a mixture of cross entropy and cube loss.

The latter, although not shipped with torch, could also be applied manually:

calc_dice_loss <- operate(y_pred, y_true) {
  
  clean <- 1
  y_pred <- y_pred$view(-1)
  y_true <- y_true$view(-1)
  intersection <- (y_pred * y_true)$sum()
  
  1 - ((2 * intersection + clean) / (y_pred$sum() + y_true$sum() + clean))
}

dice_weight <- 0.3

Optimization makes use of stochastic gradient descent (SGD), along with the one-cycle studying charge scheduler launched within the context of picture classification with torch.

optimizer <- optim_sgd(mannequin$parameters, lr = 0.1, momentum = 0.9)

num_epochs <- 20

scheduler <- lr_one_cycle(
  optimizer,
  max_lr = 0.1,
  steps_per_epoch = size(train_dl),
  epochs = num_epochs
)

Coaching

The coaching loop then follows the standard scheme. One factor to notice: Each epoch, we save the mannequin (utilizing torch_save()), so we are able to later choose one of the best one, ought to efficiency have degraded thereafter.

train_batch <- operate(b) {
  
  optimizer$zero_grad()
  output <- mannequin(b[[1]]$to(gadget = gadget))
  goal <- b[[2]]$to(gadget = gadget)
  
  bce_loss <- nnf_binary_cross_entropy(output, goal)
  dice_loss <- calc_dice_loss(output, goal)
  loss <-  dice_weight * dice_loss + (1 - dice_weight) * bce_loss
  
  loss$backward()
  optimizer$step()
  scheduler$step()

  record(bce_loss$merchandise(), dice_loss$merchandise(), loss$merchandise())
  
}

valid_batch <- operate(b) {
  
  output <- mannequin(b[[1]]$to(gadget = gadget))
  goal <- b[[2]]$to(gadget = gadget)

  bce_loss <- nnf_binary_cross_entropy(output, goal)
  dice_loss <- calc_dice_loss(output, goal)
  loss <-  dice_weight * dice_loss + (1 - dice_weight) * bce_loss
  
  record(bce_loss$merchandise(), dice_loss$merchandise(), loss$merchandise())
  
}

for (epoch in 1:num_epochs) {
  
  mannequin$prepare()
  train_bce <- c()
  train_dice <- c()
  train_loss <- c()
  
  coro::loop(for (b in train_dl) {
    c(bce_loss, dice_loss, loss) %<-% train_batch(b)
    train_bce <- c(train_bce, bce_loss)
    train_dice <- c(train_dice, dice_loss)
    train_loss <- c(train_loss, loss)
  })
  
  torch_save(mannequin, paste0("model_", epoch, ".pt"))
  
  cat(sprintf("nEpoch %d, coaching: loss:%3f, bce: %3f, cube: %3fn",
              epoch, imply(train_loss), imply(train_bce), imply(train_dice)))
  
  mannequin$eval()
  valid_bce <- c()
  valid_dice <- c()
  valid_loss <- c()
  
  i <- 0
  coro::loop(for (b in tvalid_dl) {
    
    i <<- i + 1
    c(bce_loss, dice_loss, loss) %<-% valid_batch(b)
    valid_bce <- c(valid_bce, bce_loss)
    valid_dice <- c(valid_dice, dice_loss)
    valid_loss <- c(valid_loss, loss)
    
  })
  
  cat(sprintf("nEpoch %d, validation: loss:%3f, bce: %3f, cube: %3fn",
              epoch, imply(valid_loss), imply(valid_bce), imply(valid_dice)))
}

Epoch 1, coaching: loss:0.304232, bce: 0.148578, cube: 0.667423
Epoch 1, validation: loss:0.333961, bce: 0.127171, cube: 0.816471

Epoch 2, coaching: loss:0.194665, bce: 0.101973, cube: 0.410945
Epoch 2, validation: loss:0.341121, bce: 0.117465, cube: 0.862983

[...]

Epoch 19, coaching: loss:0.073863, bce: 0.038559, cube: 0.156236
Epoch 19, validation: loss:0.302878, bce: 0.109721, cube: 0.753577

Epoch 20, coaching: loss:0.070621, bce: 0.036578, cube: 0.150055
Epoch 20, validation: loss:0.295852, bce: 0.101750, cube: 0.748757

Analysis

On this run, it’s the ultimate mannequin that performs greatest on the validation set. Nonetheless, we’d like to point out methods to load a saved mannequin, utilizing torch_load() .

As soon as loaded, put the mannequin into eval mode:

saved_model <- torch_load("model_20.pt") 

mannequin <- saved_model
mannequin$eval()

Now, since we don’t have a separate take a look at set, we already know the common out-of-sample metrics; however ultimately, what we care about are the generated masks. Let’s view some, displaying floor fact and MRI scans for comparability.

# with out random sampling, we would primarily see lesion-free patches
eval_ds <- brainseg_dataset(valid_dir, augmentation_params = NULL, random_sampling = TRUE)
eval_dl <- dataloader(eval_ds, batch_size = 8)

batch <- eval_dl %>% dataloader_make_iter() %>% dataloader_next()

par(mfcol = c(3, 8), mar = c(0, 1, 0, 1))

for (i in 1:8) {
  
  img <- batch[[1]][i, .., drop = FALSE]
  inferred_mask <- mannequin(img$to(gadget = gadget))
  true_mask <- batch[[2]][i, .., drop = FALSE]$to(gadget = gadget)
  
  bce <- nnf_binary_cross_entropy(inferred_mask, true_mask)$to(gadget = "cpu") %>%
    as.numeric()
  dc <- calc_dice_loss(inferred_mask, true_mask)$to(gadget = "cpu") %>% as.numeric()
  cat(sprintf("nSample %d, bce: %3f, cube: %3fn", i, bce, dc))
  

  inferred_mask <- inferred_mask$to(gadget = "cpu") %>% as.array() %>% .[1, 1, , ]
  
  inferred_mask <- ifelse(inferred_mask > 0.5, 1, 0)
  
  img[1, 1, ,] %>% as.array() %>% as.raster() %>% plot()
  true_mask$to(gadget = "cpu")[1, 1, ,] %>% as.array() %>% as.raster() %>% plot()
  inferred_mask %>% as.raster() %>% plot()
}

We additionally print the person cross entropy and cube losses; relating these to the generated masks would possibly yield helpful info for mannequin tuning.

Pattern 1, bce: 0.088406, cube: 0.387786}

Pattern 2, bce: 0.026839, cube: 0.205724

Pattern 3, bce: 0.042575, cube: 0.187884

Pattern 4, bce: 0.094989, cube: 0.273895

Pattern 5, bce: 0.026839, cube: 0.205724

Pattern 6, bce: 0.020917, cube: 0.139484

Pattern 7, bce: 0.094989, cube: 0.273895

Pattern 8, bce: 2.310956, cube: 0.999824

Whereas removed from good, most of those masks aren’t that dangerous – a pleasant consequence given the small dataset!

Wrapup

This has been our most advanced torch put up to this point; nonetheless, we hope you’ve discovered the time effectively spent. For one, amongst purposes of deep studying, medical picture segmentation stands out as extremely societally helpful. Secondly, U-Web-like architectures are employed in lots of different areas. And at last, we as soon as extra noticed torch’s flexibility and intuitive conduct in motion.

Thanks for studying!

Buda, Mateusz, Ashirbani Saha, and Maciej A. Mazurowski. 2019. “Affiliation of Genomic Subtypes of Decrease-Grade Gliomas with Form Options Mechanically Extracted by a Deep Studying Algorithm.” Computer systems in Biology and Medication 109: 218–25. https://doi.org/https://doi.org/10.1016/j.compbiomed.2019.05.002.

Ronneberger, Olaf, Philipp Fischer, and Thomas Brox. 2015. “U-Web: Convolutional Networks for Biomedical Picture Segmentation.” CoRR abs/1505.04597. http://arxiv.org/abs/1505.04597.

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