Utils for loading, augmenting and writing 3D medical images on PyTorch.
Project description
torchio
Installation
I recommend cloning and doing an editable installation, as this is still very experimental and changes very often.
git clone https://github.com/fepegar/torchio.git
pip install --editable torchio
Examples
Training
import time
import multiprocessing as mp
from torch.utils.data import DataLoader
from torchvision.transforms import Compose
from torchio.sampler import ImageSampler
from torchio.utils import create_dummy_dataset
from torchio import ImagesDataset, Queue
from torchio.transforms import (
ZNormalization,
RandomNoise,
RandomFlip,
RandomAffine,
)
# Define training and patches sampling parameters
num_epochs = 4
patch_size = 128
queue_length = 100
samples_per_volume = 10
batch_size = 4
def model(batch, sleep_time=0.1):
"""Dummy function to simulate a forward pass through the network"""
time.sleep(sleep_time)
return batch
# Create a dummy dataset in the temporary directory, for this example
subjects_paths = create_dummy_dataset(
num_images=100,
size_range=(193, 229),
force=False,
)
# Each element of subjects_paths is a dictionary:
# subject = {
# 'one_image': dict(path=path_to_one_image, type=torchio.INTENSITY),
# 'another_image': dict(path=path_to_another_image, type=torchio.INTENSITY),
# 'a_label': dict(path=path_to_a_label, type=torchio.LABEL),
# )
# Define transforms for data normalization and augmentation
transforms = (
ZNormalization(),
RandomNoise(std_range=(0, 0.25)),
RandomAffine(scales=(0.9, 1.1), angles=(-10, 10)),
RandomFlip(axes=(0,)),
)
transform = Compose(transforms)
subjects_dataset = ImagesDataset(subjects_paths, transform)
sample = subjects_dataset[0]
# Run a benchmark for different numbers of workers
workers = range(mp.cpu_count() + 1)
for num_workers in workers:
print('Number of workers:', num_workers)
# Define the dataset as a queue of patches
queue_dataset = Queue(
subjects_dataset,
queue_length,
samples_per_volume,
patch_size,
ImageSampler,
num_workers=num_workers,
)
batch_loader = DataLoader(queue_dataset, batch_size=batch_size)
start = time.time()
for epoch_index in range(num_epochs):
for batch in batch_loader:
logits = model(batch)
print('Time:', int(time.time() - start), 'seconds')
print()
Output:
Number of workers: 0
Time: 394 seconds
Number of workers: 1
Time: 372 seconds
Number of workers: 2
Time: 278 seconds
Number of workers: 3
Time: 259 seconds
Number of workers: 4
Time: 242 seconds
Inference
import torch
from torch.utils.data import DataLoader
from tqdm import tqdm
from torchio.inference import GridSampler, GridAggregator
def model(arg):
"""Mock PyTorch model"""
return arg
patch_size = 128, 128, 128
patch_overlap = 4, 4, 4
batch_size = 6
CHANNELS_DIMENSION = 1
# Let's create a dummy volume
input_array = torch.rand((193, 229, 193)).numpy()
# More info about patch-based inference in NiftyNet docs:
# https://niftynet.readthedocs.io/en/dev/window_sizes.html
grid_sampler = GridSampler(input_array, patch_size, patch_overlap)
aggregator = GridAggregator(input_array, patch_overlap)
patch_loader = DataLoader(grid_sampler, batch_size=batch_size)
with torch.no_grad():
for patches_batch in tqdm(patch_loader):
input_tensor = patches_batch['image']
locations = patches_batch['location']
logits = model(input_tensor) # some model
labels = logits.argmax(dim=CHANNELS_DIMENSION, keepdim=True)
outputs = labels
aggregator.add_batch(outputs, locations)
output_array = aggregator.output_array
======= History
0.2.0 (2019-12-06)
- First release on PyPI.
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