Examples¶
In this section you can see various examples using MedicalTorch API.
U-Net with GM Segmentation Challenge¶
from collections import defaultdict
import time
import os
import numpy as np
from tqdm import tqdm
from tensorboardX import SummaryWriter
from medicaltorch import datasets as mt_datasets
from medicaltorch import models as mt_models
from medicaltorch import transforms as mt_transforms
from medicaltorch import losses as mt_losses
from medicaltorch import metrics as mt_metrics
from medicaltorch import filters as mt_filters
import torch
from torchvision import transforms
from torch.utils.data import DataLoader
from torch import autograd, optim
import torch.backends.cudnn as cudnn
import torch.nn as nn
import torchvision.utils as vutils
cudnn.benchmark = True
def threshold_predictions(predictions, thr=0.999):
thresholded_preds = predictions[:]
low_values_indices = thresholded_preds < thr
thresholded_preds[low_values_indices] = 0
low_values_indices = thresholded_preds >= thr
thresholded_preds[low_values_indices] = 1
return thresholded_preds
def run_main():
train_transform = transforms.Compose([
mt_transforms.CenterCrop2D((200, 200)),
mt_transforms.ElasticTransform(alpha_range=(28.0, 30.0),
sigma_range=(3.5, 4.0),
p=0.3),
mt_transforms.RandomAffine(degrees=4.6,
scale=(0.98, 1.02),
translate=(0.03, 0.03)),
mt_transforms.RandomTensorChannelShift((-0.10, 0.10)),
mt_transforms.ToTensor(),
mt_transforms.NormalizeInstance(),
])
val_transform = transforms.Compose([
mt_transforms.CenterCrop2D((200, 200)),
mt_transforms.ToTensor(),
mt_transforms.NormalizeInstance(),
])
# Here we assume that the SC GM Challenge data is inside the folder
# "../data" and it was previously resampled.
gmdataset_train = mt_datasets.SCGMChallenge2DTrain(root_dir="../data",
subj_ids=range(1, 9),
transform=train_transform,
slice_filter_fn=mt_filters.SliceFilter())
# Here we assume that the SC GM Challenge data is inside the folder
# "../data" and it was previously resampled.
gmdataset_val = mt_datasets.SCGMChallenge2DTrain(root_dir="../data",
subj_ids=range(9, 11),
transform=val_transform)
train_loader = DataLoader(gmdataset_train, batch_size=16,
shuffle=True, pin_memory=True,
collate_fn=mt_datasets.mt_collate,
num_workers=1)
val_loader = DataLoader(gmdataset_val, batch_size=16,
shuffle=True, pin_memory=True,
collate_fn=mt_datasets.mt_collate,
num_workers=1)
model = mt_models.Unet(drop_rate=0.4, bn_momentum=0.1)
model.cuda()
num_epochs = 200
initial_lr = 0.001
optimizer = optim.Adam(model.parameters(), lr=initial_lr)
scheduler = optim.lr_scheduler.CosineAnnealingLR(optimizer, num_epochs)
writer = SummaryWriter(log_dir="log_exp")
for epoch in tqdm(range(1, num_epochs+1)):
start_time = time.time()
scheduler.step()
lr = scheduler.get_lr()[0]
writer.add_scalar('learning_rate', lr, epoch)
model.train()
train_loss_total = 0.0
num_steps = 0
for i, batch in enumerate(train_loader):
input_samples, gt_samples = batch["input"], batch["gt"]
var_input = input_samples.cuda()
var_gt = gt_samples.cuda(async=True)
preds = model(var_input)
loss = mt_losses.dice_loss(preds, var_gt)
train_loss_total += loss.item()
optimizer.zero_grad()
loss.backward()
optimizer.step()
num_steps += 1
if epoch % 5 == 0:
grid_img = vutils.make_grid(input_samples,
normalize=True,
scale_each=True)
writer.add_image('Input', grid_img, epoch)
grid_img = vutils.make_grid(preds.data.cpu(),
normalize=True,
scale_each=True)
writer.add_image('Predictions', grid_img, epoch)
grid_img = vutils.make_grid(gt_samples,
normalize=True,
scale_each=True)
writer.add_image('Ground Truth', grid_img, epoch)
train_loss_total_avg = train_loss_total / num_steps
model.eval()
val_loss_total = 0.0
num_steps = 0
metric_fns = [mt_metrics.dice_score,
mt_metrics.hausdorff_score,
mt_metrics.precision_score,
mt_metrics.recall_score,
mt_metrics.specificity_score,
mt_metrics.intersection_over_union,
mt_metrics.accuracy_score]
metric_mgr = mt_metrics.MetricManager(metric_fns)
for i, batch in enumerate(val_loader):
input_samples, gt_samples = batch["input"], batch["gt"]
with torch.no_grad():
var_input = input_samples.cuda()
var_gt = gt_samples.cuda(async=True)
preds = model(var_input)
loss = mt_losses.dice_loss(preds, var_gt)
val_loss_total += loss.item()
# Metrics computation
gt_npy = gt_samples.numpy().astype(np.uint8)
gt_npy = gt_npy.squeeze(axis=1)
preds = preds.data.cpu().numpy()
preds = threshold_predictions(preds)
preds = preds.astype(np.uint8)
preds = preds.squeeze(axis=1)
metric_mgr(preds, gt_npy)
num_steps += 1
metrics_dict = metric_mgr.get_results()
metric_mgr.reset()
writer.add_scalars('metrics', metrics_dict, epoch)
val_loss_total_avg = val_loss_total / num_steps
writer.add_scalars('losses', {
'val_loss': val_loss_total_avg,
'train_loss': train_loss_total_avg
}, epoch)
end_time = time.time()
total_time = end_time - start_time
tqdm.write("Epoch {} took {:.2f} seconds.".format(epoch, total_time))
writer.add_scalars('losses', {
'train_loss': train_loss_total_avg
}, epoch)
if __name__ == '__main__':
run_main()