Merge pull request #112 from constantinpape/self-training

Implement MeanTeacher Trainer

.github/workflows/test.yaml

@@ -11,7 +11,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8, 3.9]
+        python-version: ["3.9", "3.10"]
 
     steps:
       - name: Checkout

environment_cpu.yaml

@@ -8,7 +8,7 @@ dependencies:
     - bioimageio.core >=0.5.0
     - cpuonly
     - python-elf
-    - pytorch
+    - pytorch >=2.0
     - tensorboard
     - tifffile
     - torchvision

environment_gpu.yaml

@@ -8,7 +8,8 @@ dependencies:
     - affogato
     - bioimageio.core >=0.5.0
     - python-elf
-    - pytorch-cuda=11.6  # you may need to update the pytorch version to match your system
+    - pytorch >=2.0
+    - pytorch-cuda>=11.7  # you may need to update the pytorch version to match your system
     - tensorboard
     - tifffile
     - torchvision

experiments/livecell/train_boundaries.py

@@ -62,7 +62,7 @@ def check_loader(args, train=True, val=True, n_images=5):
         check_loader(loader, n_images)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     parser = torch_em.util.parser_helper(default_batch_size=8)
     parser.add_argument("--cell_type", default=None)
     args = parser.parse_args()

experiments/probabilistic_domain_adaptation/livecell/README.md

@@ -0,0 +1,4 @@
+# Prelim. results
+
+-> UNet results are a bit worse than from Anwai, double check how the training differs.
+-> Mean Teacher improves results.

experiments/probabilistic_domain_adaptation/livecell/check_result.py

@@ -0,0 +1,19 @@
+import argparse
+import pandas as pd
+
+
+def check_result(path):
+    table = pd.read_csv(path)
+    print(table)
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("paths", nargs="+")
+    args = parser.parse_args()
+    for path in args.paths:
+        check_result(path)
+
+
+if __name__ == "__main__":
+    main()

experiments/probabilistic_domain_adaptation/livecell/common.py

@@ -0,0 +1,234 @@
+import argparse
+import os
+from glob import glob
+
+try:
+    import imageio.v2 as imageio
+except ImportError:
+    import imageio
+import numpy as np
+import pandas as pd
+import torch
+import torch_em
+
+from elf.evaluation import dice_score
+from torch_em.data.datasets.livecell import (get_livecell_loader,
+                                             _download_livecell_images,
+                                             _download_livecell_annotations)
+from torch_em.model import UNet2d
+from torch_em.util.prediction import predict_with_padding
+from torchvision import transforms
+from tqdm import tqdm
+
+CELL_TYPES = ["A172", "BT474", "BV2", "Huh7", "MCF7", "SHSY5Y", "SkBr3", "SKOV3"]
+
+
+#
+# The augmentations we use for the LiveCELL experiments:
+# - weak augmenations: blurring and additive gaussian noise
+# - strong augmentations: TODO
+#
+
+
+def weak_augmentations(p=0.25):
+    norm = torch_em.transform.raw.standardize
+    aug = transforms.Compose([
+        norm,
+        transforms.RandomApply([torch_em.transform.raw.GaussianBlur()], p=p),
+        transforms.RandomApply([torch_em.transform.raw.AdditiveGaussianNoise(
+            scale=(0, 0.15), clip_kwargs=False)], p=p
+        ),
+    ])
+    return torch_em.transform.raw.get_raw_transform(normalizer=norm, augmentation1=aug)
+
+
+# TODO
+def strong_augmentations():
+    pass
+
+
+#
+# Model and prediction functionality: the models we use in all experiments
+#
+
+def get_unet():
+    return UNet2d(in_channels=1, out_channels=1, initial_features=64, final_activation="Sigmoid", depth=4)
+
+
+def load_model(model, ckpt, state="model_state", device=None):
+    state = torch.load(os.path.join(ckpt, "best.pt"))[state]
+    model.load_state_dict(state)
+    if device is not None:
+        model.to(device)
+    return model
+
+
+# use get_model and prediction_function to customize this, e.g. for using it with the PUNet
+# set model_state to "teacher_state" when using this with a mean-teacher method
+def evaluate_transfered_model(
+    args, ct_src, method, get_model=get_unet, prediction_function=None, model_state="model_state"
+):
+    image_folder = os.path.join(args.input, "images", "livecell_test_images")
+    label_root = os.path.join(args.input, "annotations", "livecell_test_images")
+
+    results = {"src": [ct_src]}
+    device = torch.device("cuda")
+
+    thresh = args.confidence_threshold
+    with torch.no_grad():
+        for ct_trg in CELL_TYPES:
+
+            if ct_trg == ct_src:
+                results[ct_trg] = None
+                continue
+
+            out_folder = None if args.output is None else os.path.join(
+                args.output, f"thresh-{thresh}", ct_src, ct_trg
+            )
+            if out_folder is not None:
+                os.makedirs(out_folder, exist_ok=True)
+
+            ckpt = f"checkpoints/{method}/thresh-{thresh}/{ct_src}/{ct_trg}"
+            model = get_model()
+            model = load_model(model, ckpt, device=device, state=model_state)
+
+            label_paths = glob(os.path.join(label_root, ct_trg, "*.tif"))
+            scores = []
+            for label_path in tqdm(label_paths, desc=f"Predict for src={ct_src}, trgt={ct_trg}"):
+
+                labels = imageio.imread(label_path)
+                if out_folder is None:
+                    out_path = None
+                else:
+                    out_path = os.path.join(out_folder, os.path.basename(label_path))
+                    if os.path.exists(out_path):
+                        pred = imageio.imread(out_path)
+                        score = dice_score(pred, labels, threshold_seg=None, threshold_gt=0)
+                        scores.append(score)
+                        continue
+
+                image_path = os.path.join(image_folder, os.path.basename(label_path))
+                assert os.path.exists(image_path)
+                image = imageio.imread(image_path)
+                image = torch_em.transform.raw.standardize(image)
+                pred = predict_with_padding(
+                    model, image, min_divisible=(16, 16), device=device, prediction_function=prediction_function,
+                ).squeeze()
+                assert image.shape == labels.shape
+                score = dice_score(pred, labels, threshold_seg=None, threshold_gt=0)
+                if out_path is not None:
+                    imageio.imwrite(out_path, pred)
+                scores.append(score)
+
+            results[ct_trg] = np.mean(scores)
+    return pd.DataFrame(results)
+
+
+# use get_model and prediction_function to customize this, e.g. for using it with the PUNet
+def evaluate_source_model(args, ct_src, method, get_model=get_unet, prediction_function=None):
+    ckpt = f"checkpoints/{method}/{ct_src}"
+    model = get_model()
+    model = torch_em.util.get_trainer(ckpt).model
+
+    image_folder = os.path.join(args.input, "images", "livecell_test_images")
+    label_root = os.path.join(args.input, "annotations", "livecell_test_images")
+
+    results = {"src": [ct_src]}
+    device = torch.device("cuda")
+
+    with torch.no_grad():
+        for ct_trg in CELL_TYPES:
+
+            out_folder = None if args.output is None else os.path.join(args.output, ct_src, ct_trg)
+            if out_folder is not None:
+                os.makedirs(out_folder, exist_ok=True)
+
+            label_paths = glob(os.path.join(label_root, ct_trg, "*.tif"))
+            scores = []
+            for label_path in tqdm(label_paths, desc=f"Predict for src={ct_src}, trgt={ct_trg}"):
+
+                labels = imageio.imread(label_path)
+                if out_folder is None:
+                    out_path = None
+                else:
+                    out_path = os.path.join(out_folder, os.path.basename(label_path))
+                    if os.path.exists(out_path):
+                        pred = imageio.imread(out_path)
+                        score = dice_score(pred, labels, threshold_seg=None, threshold_gt=0)
+                        scores.append(score)
+                        continue
+
+                image_path = os.path.join(image_folder, os.path.basename(label_path))
+                assert os.path.exists(image_path)
+                image = imageio.imread(image_path)
+                image = torch_em.transform.raw.standardize(image)
+                pred = predict_with_padding(
+                    model, image, min_divisible=(16, 16), device=device, prediction_function=prediction_function
+                ).squeeze()
+                assert image.shape == labels.shape
+                score = dice_score(pred, labels, threshold_seg=None, threshold_gt=0)
+                if out_path is not None:
+                    imageio.imwrite(out_path, pred)
+                scores.append(score)
+
+            results[ct_trg] = np.mean(scores)
+    return pd.DataFrame(results)
+
+
+#
+# Other utility functions: loaders, parser
+#
+
+
+def _get_image_paths(args, split, cell_type):
+    _download_livecell_images(args.input, download=True)
+    image_paths, _ = _download_livecell_annotations(args.input, split, download=True,
+                                                    cell_types=[cell_type], label_path=None)
+    return image_paths
+
+
+def get_unsupervised_loader(args, split, cell_type, teacher_augmentation, student_augmentation):
+    patch_shape = (512, 512)
+
+    def _parse_aug(aug):
+        if aug == "weak":
+            return weak_augmentations()
+        elif aug == "strong":
+            return strong_augmentations()
+        assert callable(aug)
+        return aug
+
+    raw_transform = torch_em.transform.get_raw_transform()
+    transform = torch_em.transform.get_augmentations(ndim=2)
+
+    image_paths = _get_image_paths(args, split, cell_type)
+
+    augmentations = (_parse_aug(teacher_augmentation), _parse_aug(student_augmentation))
+    ds = torch_em.data.RawImageCollectionDataset(
+        image_paths, patch_shape, raw_transform, transform,
+        augmentations=augmentations
+    )
+    loader = torch_em.segmentation.get_data_loader(ds, batch_size=args.batch_size, num_workers=8, shuffle=True)
+    return loader
+
+
+def get_supervised_loader(args, split, cell_type):
+    patch_shape = (512, 512)
+    loader = get_livecell_loader(
+        args.input, patch_shape, split,
+        download=True, binary=True, batch_size=args.batch_size,
+        cell_types=[cell_type], num_workers=8, shuffle=True,
+    )
+    return loader
+
+
+def get_parser(default_batch_size=8, default_iterations=int(1e5)):
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-i", "--input", required=True)
+    parser.add_argument("-p", "--phase", required=True)
+    parser.add_argument("-b", "--batch_size", default=default_batch_size, type=int)
+    parser.add_argument("-n", "--n_iterations", default=default_iterations, type=int)
+    parser.add_argument("-s", "--save_root")
+    parser.add_argument("-c", "--cell_types", nargs="+", default=CELL_TYPES)
+    parser.add_argument("-o", "--output")
+    return parser