Add Joint Training

finetuning/livecell/joint_training/joint_finetuning.py

@@ -0,0 +1,159 @@
+import os
+import argparse
+
+import torch
+
+import torch_em
+from torch_em.model import UNETR
+from torch_em.loss import DiceBasedDistanceLoss
+from torch_em.data.datasets import get_livecell_loader
+from torch_em.transform.label import PerObjectDistanceTransform
+
+import micro_sam.training as sam_training
+from micro_sam.util import export_custom_sam_model
+
+
+def get_dataloaders(patch_shape, data_path, cell_type=None):
+    """This returns the livecell data loaders implemented in torch_em:
+    https://github.com/constantinpape/torch-em/blob/main/torch_em/data/datasets/livecell.py
+    It will automatically download the livecell data.
+
+    Note: to replace this with another data loader you need to return a torch data loader
+    that retuns `x, y` tensors, where `x` is the image data and `y` are the labels.
+    The labels have to be in a label mask instance segmentation format.
+    I.e. a tensor of the same spatial shape as `x`, with each object mask having its own ID.
+    Important: the ID 0 is reseved for background, and the IDs must be consecutive
+    """
+    label_transform = PerObjectDistanceTransform(
+        distances=True, boundary_distances=True, directed_distances=False, foreground=True, instances=True, min_size=25
+    )
+    raw_transform = sam_training.identity  # the current workflow avoids rescaling the inputs to [-1, 1]
+    train_loader = get_livecell_loader(
+        path=data_path, patch_shape=patch_shape, split="train", batch_size=2, num_workers=16,
+        cell_types=cell_type, download=True, shuffle=True, label_transform=label_transform,
+        raw_transform=raw_transform, label_dtype=torch.float32
+    )
+    val_loader = get_livecell_loader(
+        path=data_path, patch_shape=patch_shape, split="val", batch_size=1, num_workers=16,
+        cell_types=cell_type, download=True, shuffle=True, label_transform=label_transform,
+        raw_transform=raw_transform, label_dtype=torch.float32
+    )
+
+    return train_loader, val_loader
+
+
+def finetune_livecell(args):
+    """Example code for finetuning SAM on LiveCELL"""
+    # override this (below) if you have some more complex set-up and need to specify the exact gpu
+    device = "cuda" if torch.cuda.is_available() else "cpu"
+
+    # training settings:
+    model_type = args.model_type
+    checkpoint_path = None  # override this to start training from a custom checkpoint
+    patch_shape = (520, 704)  # the patch shape for training
+    n_objects_per_batch = 25  # this is the number of objects per batch that will be sampled
+    freeze_parts = args.freeze  # override this to freeze different parts of the model
+
+    # get the trainable segment anything model
+    model = sam_training.get_trainable_sam_model(
+        model_type=model_type,
+        device=device,
+        checkpoint_path=checkpoint_path,
+        freeze=freeze_parts
+    )
+    model.to(device)
+
+    # let's get the UNETR model for automatic instance segmentation pipeline
+    unetr = UNETR(
+        backbone="sam",
+        encoder=model.sam.image_encoder,
+        out_channels=3,
+        use_sam_stats=True,
+        final_activation="Sigmoid",
+        use_skip_connection=False
+    )
+    unetr.to(device)
+
+    # let's get the parameters for SAM and the decoder from UNETR
+    joint_model_params = [params for params in model.parameters()]  # sam parameters
+    for name, params in unetr.named_parameters():  # unetr's decoder parameters
+        if not name.startswith("encoder"):
+            joint_model_params.append(params)
+
+    # all the stuff we need for training
+    optimizer = torch.optim.Adam(joint_model_params, lr=1e-5)
+    scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer, mode="min", factor=0.9, patience=10, verbose=True)
+    train_loader, val_loader = get_dataloaders(patch_shape=patch_shape, data_path=args.input_path)
+
+    # this class creates all the training data for a batch (inputs, prompts and labels)
+    convert_inputs = sam_training.ConvertToSamInputs()
+
+    checkpoint_name = "livecell_sam"
+    trainer = sam_training.JointSamTrainer(
+        name=checkpoint_name,
+        save_root=args.save_root,
+        train_loader=train_loader,
+        val_loader=val_loader,
+        model=model,
+        optimizer=optimizer,
+        # currently we compute loss batch-wise, else we pass channelwise True
+        loss=torch_em.loss.DiceLoss(channelwise=False),
+        metric=torch_em.loss.DiceLoss(),
+        device=device,
+        lr_scheduler=scheduler,
+        logger=sam_training.JointSamLogger,
+        log_image_interval=100,
+        mixed_precision=True,
+        convert_inputs=convert_inputs,
+        n_objects_per_batch=n_objects_per_batch,
+        n_sub_iteration=8,
+        compile_model=False,
+        mask_prob=0.5,  # (optional) overwrite to provide the probability of using mask inputs while training
+        unetr=unetr,
+        instance_loss=DiceBasedDistanceLoss(mask_distances_in_bg=True),
+        instance_metric=DiceBasedDistanceLoss(mask_distances_in_bg=True)
+    )
+    trainer.fit(args.iterations)
+    if args.export_path is not None:
+        checkpoint_path = os.path.join(
+            "" if args.save_root is None else args.save_root, "checkpoints", checkpoint_name, "best.pt"
+        )
+        export_custom_sam_model(
+            checkpoint_path=checkpoint_path,
+            model_type=model_type,
+            save_path=args.export_path,
+        )
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Finetune Segment Anything for the LiveCELL dataset.")
+    parser.add_argument(
+        "--input_path", "-i", default="/scratch/usr/nimanwai/data/livecell/",
+        help="The filepath to the LiveCELL data. If the data does not exist yet it will be downloaded."
+    )
+    parser.add_argument(
+        "--model_type", "-m", default="vit_b",
+        help="The model type to use for fine-tuning. Either vit_h, vit_b or vit_l."
+    )
+    parser.add_argument(
+        "--save_root", "-s",
+        help="Where to save the checkpoint and logs. By default they will be saved where this script is run."
+    )
+    parser.add_argument(
+        "--iterations", type=int, default=int(1e5),
+        help="For how many iterations should the model be trained? By default 100k."
+    )
+    parser.add_argument(
+        "--export_path", "-e",
+        help="Where to export the finetuned model to. The exported model can be used in the annotation tools."
+    )
+    parser.add_argument(
+        "--freeze", type=str, nargs="+", default=None,
+        help="Which parts of the model to freeze for finetuning."
+    )
+    args = parser.parse_args()
+    finetune_livecell(args)
+
+
+if __name__ == "__main__":
+    main()

finetuning/livecell/joint_training/unetr_inference.py

@@ -0,0 +1,133 @@
+import os
+import h5py
+import argparse
+import numpy as np
+import pandas as pd
+from glob import glob
+from tqdm import tqdm
+from pathlib import Path
+import imageio.v3 as imageio
+from collections import OrderedDict
+
+import torch
+
+from torch_em.model import UNETR
+from torch_em.util import segmentation
+from torch_em.util.prediction import predict_with_padding
+
+from elf.evaluation import mean_segmentation_accuracy
+
+from micro_sam.util import get_sam_model
+
+
+def get_unetr_model(model_type, checkpoint, device):
+    # let's get the sam finetuned model
+    predictor = get_sam_model(
+        model_type=model_type
+    )
+
+    # load the model with the respective unetr model state
+    model = UNETR(
+        encoder=predictor.model.image_encoder,
+        out_channels=3,
+        use_sam_stats=True,
+        final_activation="Sigmoid",
+        use_skip_connection=False
+    )
+
+    sam_state = torch.load(checkpoint, map_location="cpu")["model_state"]
+    # let's get the vit parameters from sam
+    encoder_state = []
+    prune_prefix = "sam.image_"
+    for k, v in sam_state.items():
+        if k.startswith(prune_prefix):
+            encoder_state.append((k[len(prune_prefix):], v))
+    encoder_state = OrderedDict(encoder_state)
+
+    decoder_state = torch.load(checkpoint, map_location="cpu")["decoder_state"]
+
+    unetr_state = OrderedDict(list(encoder_state.items()) + list(decoder_state.items()))
+    model.load_state_dict(unetr_state)
+    model.to(device)
+    model.eval()
+
+    return model
+
+
+def predict_for_unetr(inputs, save_dir, model, device):
+    save_dir = os.path.join(save_dir, "results")
+    os.makedirs(save_dir, exist_ok=True)
+
+    with torch.no_grad():
+        for img_path in tqdm(glob(os.path.join(inputs, "images", "livecell_test_images", "*")),
+                             desc="Run unetr inference"):
+            fname = Path(img_path).stem
+            save_path = os.path.join(save_dir, f"{fname}.h5")
+            if os.path.exists(save_path):
+                continue
+
+            input_ = imageio.imread(img_path)
+
+            outputs = predict_with_padding(model, input_, device=device, min_divisible=(16, 16))
+            fg, cdist, bdist = outputs.squeeze()
+            dm_seg = segmentation.watershed_from_center_and_boundary_distances(
+                cdist, bdist, fg, min_size=50,
+                center_distance_threshold=0.5,
+                boundary_distance_threshold=0.6,
+                distance_smoothing=1.0
+            )
+
+            with h5py.File(save_path, "a") as f:
+                ds = f.require_dataset("segmentation", shape=dm_seg.shape, compression="gzip", dtype=dm_seg.dtype)
+                ds[:] = dm_seg
+
+
+def evaluation_for_unetr(inputs, save_dir, csv_path):
+    if os.path.exists(csv_path):
+        return
+
+    msa_list, sa50_list = [], []
+    for gt_path in tqdm(glob(os.path.join(inputs, "annotations", "livecell_test_images", "*", "*")),
+                        desc="Run unetr evaluation"):
+        gt = imageio.imread(gt_path)
+        fname = Path(gt_path).stem
+
+        output_file = os.path.join(save_dir, "results", f"{fname}.h5")
+        with h5py.File(output_file, "r") as f:
+            instances = f["segmentation"][:]
+
+        msa, sa_acc = mean_segmentation_accuracy(instances, gt, return_accuracies=True)
+        msa_list.append(msa)
+        sa50_list.append(sa_acc[0])
+
+    res_dict = {
+        "LiveCELL": "Metrics",
+        "mSA": np.mean(msa_list),
+        "SA50": np.mean(sa50_list)
+    }
+    df = pd.DataFrame.from_dict([res_dict])
+    df.to_csv(csv_path)
+
+
+def main(args):
+    device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+
+    # let's get the unetr model (initialized with the joint training setup)
+    model = get_unetr_model(model_type=args.model_type, checkpoint=args.checkpoint, device=device)
+
+    # let's get the predictions
+    predict_for_unetr(inputs=args.inputs, save_dir=args.save_dir, model=model, device=device)
+
+    # let's evaluate the predictions
+    evaluation_for_unetr(inputs=args.inputs, save_dir=args.save_dir, csv_path=args.csv_path)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-i", "--inputs", default="/scratch/usr/nimanwai/data/livecell/")
+    parser.add_argument("-c", "--checkpoint", type=str, required=True)
+    parser.add_argument("-m", "--model_type", type=str, default="vit_b")
+    parser.add_argument("--save_dir", type=str, required=True)
+    parser.add_argument("--csv_path", type=str, default="livecell_joint_training.csv")
+    args = parser.parse_args()
+    main(args)

micro_sam/training/__init__.py

@@ -3,3 +3,4 @@
 
 from .sam_trainer import SamTrainer, SamLogger
 from .util import ConvertToSamInputs, get_trainable_sam_model, identity
+from .joint_sam_trainer import JointSamTrainer, JointSamLogger