Update Multiple Instance Learning Pipeline (#728)

* Update mil pipeline

Signed-off-by: Behrooz <[email protected]>

* Fix a typo

Signed-off-by: Behrooz <[email protected]>

* Tiffile to cucim

Signed-off-by: Behrooz <[email protected]>

* Update to RandGridPatchd

Signed-off-by: Behrooz <[email protected]>

* Fix import

Signed-off-by: Behrooz <[email protected]>

* Add sort_key

Signed-off-by: Behrooz <[email protected]>

* sort key max to min

Signed-off-by: Behrooz <[email protected]>

* Fix patch_size

Signed-off-by: Behrooz <[email protected]>

* Stack patch locations

Signed-off-by: Behrooz <[email protected]>

* Remove location

Signed-off-by: Behrooz <[email protected]>

* Change to fix_num_patches

Signed-off-by: Behrooz <[email protected]>

* Update grid patch

Signed-off-by: Behrooz <[email protected]>

* Add threshold_filter

Signed-off-by: Behrooz <[email protected]>

* Update threshold and add pad_mode=None

Signed-off-by: Behrooz <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update mil pipeline with new grid patch

Signed-off-by: Behrooz <[email protected]>

* Update GridPatch args

Signed-off-by: Behrooz <[email protected]>

* Update LabelEncodeIntegerGraded and sort imports

Signed-off-by: Behrooz <[email protected]>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Nic Ma <[email protected]>

Author: 3 people

pathology/multiple_instance_learning/panda_mil_train_evaluate_pytorch_gpu.py

@@ -1,91 +1,36 @@
-import os
-import time
-import shutil
 import argparse
 import collections.abc
-import gdown
+import os
+import shutil
+import time
 
+import gdown
 import numpy as np
-from sklearn.metrics import cohen_kappa_score
-
 import torch
-import torch.nn as nn
-from torch.cuda.amp import GradScaler, autocast
-
-from torch.utils.tensorboard import SummaryWriter
-from torch.utils.data.distributed import DistributedSampler
-from torch.utils.data.dataloader import default_collate
-
 import torch.distributed as dist
 import torch.multiprocessing as mp
-
+import torch.nn as nn
+from monai.config import KeysCollection
 from monai.data import Dataset, load_decathlon_datalist
-from monai.data.image_reader import WSIReader
+from monai.data.wsi_reader import WSIReader
 from monai.metrics import Cumulative, CumulativeAverage
-from monai.transforms import Transform, Compose, LoadImageD, RandFlipd, RandRotate90d, ScaleIntensityRangeD, ToTensord
-from monai.apps.pathology.transforms import TileOnGridd
 from monai.networks.nets import milmodel
-
-
-def parse_args():
-
-    parser = argparse.ArgumentParser(description="Multiple Instance Learning (MIL) example of classification from WSI.")
-    parser.add_argument(
-        "--data_root", default="/PandaChallenge2020/train_images/", help="path to root folder of images"
-    )
-    parser.add_argument("--dataset_json", default=None, type=str, help="path to dataset json file")
-
-    parser.add_argument("--num_classes", default=5, type=int, help="number of output classes")
-    parser.add_argument("--mil_mode", default="att_trans", help="MIL algorithm")
-    parser.add_argument(
-        "--tile_count", default=44, type=int, help="number of patches (instances) to extract from WSI image"
-    )
-    parser.add_argument("--tile_size", default=256, type=int, help="size of square patch (instance) in pixels")
-
-    parser.add_argument("--checkpoint", default=None, help="load existing checkpoint")
-    parser.add_argument(
-        "--validate",
-        action="store_true",
-        help="run only inference on the validation set, must specify the checkpoint argument",
-    )
-
-    parser.add_argument("--logdir", default=None, help="path to log directory to store Tensorboard logs")
-
-    parser.add_argument("--epochs", default=50, type=int, help="number of training epochs")
-    parser.add_argument("--batch_size", default=4, type=int, help="batch size, the number of WSI images per gpu")
-    parser.add_argument("--optim_lr", default=3e-5, type=float, help="initial learning rate")
-
-    parser.add_argument("--weight_decay", default=0, type=float, help="optimizer weight decay")
-    parser.add_argument("--amp", action="store_true", help="use AMP, recommended")
-    parser.add_argument(
-        "--val_every",
-        default=1,
-        type=int,
-        help="run validation after this number of epochs, default 1 to run every epoch",
-    )
-    parser.add_argument("--workers", default=2, type=int, help="number of workers for data loading")
-
-    ###for multigpu
-    parser.add_argument("--distributed", action="store_true", help="use multigpu training, recommended")
-    parser.add_argument("--world_size", default=1, type=int, help="number of nodes for distributed training")
-    parser.add_argument("--rank", default=0, type=int, help="node rank for distributed training")
-    parser.add_argument(
-        "--dist-url", default="tcp://127.0.0.1:23456", type=str, help="url used to set up distributed training"
-    )
-    parser.add_argument("--dist-backend", default="nccl", type=str, help="distributed backend")
-
-    parser.add_argument(
-        "--quick", action="store_true", help="use a small subset of data for debugging"
-    )  # for debugging
-
-    args = parser.parse_args()
-
-    print("Argument values:")
-    for k, v in vars(args).items():
-        print(k, "=>", v)
-    print("-----------------")
-
-    return args
+from monai.transforms import (
+    Compose,
+    GridPatchd,
+    LoadImaged,
+    MapTransform,
+    RandFlipd,
+    RandGridPatchd,
+    RandRotate90d,
+    ScaleIntensityRanged,
+    ToTensord,
+)
+from sklearn.metrics import cohen_kappa_score
+from torch.cuda.amp import GradScaler, autocast
+from torch.utils.data.dataloader import default_collate
+from torch.utils.data.distributed import DistributedSampler
+from torch.utils.tensorboard import SummaryWriter
 
 
 def train_epoch(model, loader, optimizer, scaler, epoch, args):
@@ -246,22 +191,26 @@ def save_checkpoint(model, epoch, args, filename="model.pt", best_acc=0):
     print("Saving checkpoint", filename)
 
 
-class LabelEncodeIntegerGraded(Transform):
+class LabelEncodeIntegerGraded(MapTransform):
     """
     Convert an integer label to encoded array representation of length num_classes,
     with 1 filled in up to label index, and 0 otherwise. For example for num_classes=5,
     embedding of 2 -> (1,1,0,0,0)
 
     Args:
         num_classes: the number of classes to convert to encoded format.
-        keys: keys of the corresponding items to be transformed
-            Defaults to ``['label']``.
+        keys: keys of the corresponding items to be transformed. Defaults to ``'label'``.
+        allow_missing_keys: don't raise exception if key is missing.
 
     """
 
-    def __init__(self, num_classes, keys=["label"]):
-        super().__init__()
-        self.keys = keys
+    def __init__(
+        self,
+        num_classes: int,
+        keys: KeysCollection = "label",
+        allow_missing_keys: bool = False,
+    ):
+        super().__init__(keys, allow_missing_keys)
         self.num_classes = num_classes
 
     def __call__(self, data):
@@ -278,35 +227,12 @@ def __call__(self, data):
         return d
 
 
-def main():
-
-    args = parse_args()
-
-    if args.dataset_json is None:
-        # download default json datalist
-        resource = "https://drive.google.com/uc?id=1L6PtKBlHHyUgTE4rVhRuOLTQKgD4tBRK"
-        dst = "./datalist_panda_0.json"
-        if not os.path.exists(dst):
-            gdown.download(resource, dst, quiet=False)
-        args.dataset_json = dst
-
-    if args.distributed:
-        ngpus_per_node = torch.cuda.device_count()
-        args.optim_lr = ngpus_per_node * args.optim_lr / 2  # heuristic to scale up learning rate in multigpu setup
-        args.world_size = ngpus_per_node * args.world_size
-
-        print("Multigpu", ngpus_per_node, "rescaled lr", args.optim_lr)
-        mp.spawn(main_worker, nprocs=ngpus_per_node, args=(args,))
-    else:
-        main_worker(0, args)
-
-
 def list_data_collate(batch: collections.abc.Sequence):
-    '''
-        Combine instances from a list of dicts into a single dict, by stacking them along first dim
-        [{'image' : 3xHxW}, {'image' : 3xHxW}, {'image' : 3xHxW}...] - > {'image' : Nx3xHxW}
-        followed by the default collate which will form a batch BxNx3xHxW
-    '''
+    """
+    Combine instances from a list of dicts into a single dict, by stacking them along first dim
+    [{'image' : 3xHxW}, {'image' : 3xHxW}, {'image' : 3xHxW}...] - > {'image' : Nx3xHxW}
+    followed by the default collate which will form a batch BxNx3xHxW
+    """
 
     for i, item in enumerate(batch):
         data = item[0]
@@ -352,37 +278,36 @@ def main_worker(gpu, args):
 
     train_transform = Compose(
         [
-            LoadImageD(keys=["image"], reader=WSIReader, backend="TiffFile", dtype=np.uint8, level=1, image_only=True),
+            LoadImaged(keys=["image"], reader=WSIReader, backend="cucim", dtype=np.uint8, level=1, image_only=True),
             LabelEncodeIntegerGraded(keys=["label"], num_classes=args.num_classes),
-            TileOnGridd(
+            RandGridPatchd(
                 keys=["image"],
-                tile_count=args.tile_count,
-                tile_size=args.tile_size,
-                random_offset=True,
-                background_val=255,
-                return_list_of_dicts=True,
+                patch_size=(args.tile_size, args.tile_size),
+                num_patches=args.tile_count,
+                sort_fn="min",
+                pad_mode=None,
+                constant_values=255,
             ),
             RandFlipd(keys=["image"], spatial_axis=0, prob=0.5),
             RandFlipd(keys=["image"], spatial_axis=1, prob=0.5),
             RandRotate90d(keys=["image"], prob=0.5),
-            ScaleIntensityRangeD(keys=["image"], a_min=np.float32(255), a_max=np.float32(0)),
+            ScaleIntensityRanged(keys=["image"], a_min=np.float32(255), a_max=np.float32(0)),
             ToTensord(keys=["image", "label"]),
         ]
     )
 
     valid_transform = Compose(
         [
-            LoadImageD(keys=["image"], reader=WSIReader, backend="TiffFile", dtype=np.uint8, level=1, image_only=True),
+            LoadImaged(keys=["image"], reader=WSIReader, backend="cucim", dtype=np.uint8, level=1, image_only=True),
             LabelEncodeIntegerGraded(keys=["label"], num_classes=args.num_classes),
-            TileOnGridd(
+            GridPatchd(
                 keys=["image"],
-                tile_count=None,
-                tile_size=args.tile_size,
-                random_offset=False,
-                background_val=255,
-                return_list_of_dicts=True,
+                patch_size=(args.tile_size, args.tile_size),
+                threshold=0.999 * 3 * 255 * args.tile_size * args.tile_size,
+                pad_mode=None,
+                constant_values=255,
             ),
-            ScaleIntensityRangeD(keys=["image"], a_min=np.float32(255), a_max=np.float32(0)),
+            ScaleIntensityRanged(keys=["image"], a_min=np.float32(255), a_max=np.float32(0)),
             ToTensord(keys=["image", "label"]),
         ]
     )
@@ -540,5 +465,85 @@ def main_worker(gpu, args):
     print("ALL DONE")
 
 
+def parse_args():
+
+    parser = argparse.ArgumentParser(description="Multiple Instance Learning (MIL) example of classification from WSI.")
+    parser.add_argument(
+        "--data_root", default="/PandaChallenge2020/train_images/", help="path to root folder of images"
+    )
+    parser.add_argument("--dataset_json", default=None, type=str, help="path to dataset json file")
+
+    parser.add_argument("--num_classes", default=5, type=int, help="number of output classes")
+    parser.add_argument("--mil_mode", default="att_trans", help="MIL algorithm")
+    parser.add_argument(
+        "--tile_count", default=44, type=int, help="number of patches (instances) to extract from WSI image"
+    )
+    parser.add_argument("--tile_size", default=256, type=int, help="size of square patch (instance) in pixels")
+
+    parser.add_argument("--checkpoint", default=None, help="load existing checkpoint")
+    parser.add_argument(
+        "--validate",
+        action="store_true",
+        help="run only inference on the validation set, must specify the checkpoint argument",
+    )
+
+    parser.add_argument("--logdir", default=None, help="path to log directory to store Tensorboard logs")
+
+    parser.add_argument("--epochs", default=50, type=int, help="number of training epochs")
+    parser.add_argument("--batch_size", default=4, type=int, help="batch size, the number of WSI images per gpu")
+    parser.add_argument("--optim_lr", default=3e-5, type=float, help="initial learning rate")
+
+    parser.add_argument("--weight_decay", default=0, type=float, help="optimizer weight decay")
+    parser.add_argument("--amp", action="store_true", help="use AMP, recommended")
+    parser.add_argument(
+        "--val_every",
+        default=1,
+        type=int,
+        help="run validation after this number of epochs, default 1 to run every epoch",
+    )
+    parser.add_argument("--workers", default=2, type=int, help="number of workers for data loading")
+
+    ###for multigpu
+    parser.add_argument("--distributed", action="store_true", help="use multigpu training, recommended")
+    parser.add_argument("--world_size", default=1, type=int, help="number of nodes for distributed training")
+    parser.add_argument("--rank", default=0, type=int, help="node rank for distributed training")
+    parser.add_argument(
+        "--dist-url", default="tcp://127.0.0.1:23456", type=str, help="url used to set up distributed training"
+    )
+    parser.add_argument("--dist-backend", default="nccl", type=str, help="distributed backend")
+
+    parser.add_argument(
+        "--quick", action="store_true", help="use a small subset of data for debugging"
+    )  # for debugging
+
+    args = parser.parse_args()
+
+    print("Argument values:")
+    for k, v in vars(args).items():
+        print(k, "=>", v)
+    print("-----------------")
+
+    return args
+
+
 if __name__ == "__main__":
-    main()
+
+    args = parse_args()
+
+    if args.dataset_json is None:
+        # download default json datalist
+        resource = "https://drive.google.com/uc?id=1L6PtKBlHHyUgTE4rVhRuOLTQKgD4tBRK"
+        dst = "./datalist_panda_0.json"
+        if not os.path.exists(dst):
+            gdown.download(resource, dst, quiet=False)
+        args.dataset_json = dst
+
+    if args.distributed:
+        ngpus_per_node = torch.cuda.device_count()
+        args.optim_lr = ngpus_per_node * args.optim_lr / 2  # heuristic to scale up learning rate in multigpu setup
+        args.world_size = ngpus_per_node * args.world_size
+
+        print("Multigpu", ngpus_per_node, "rescaled lr", args.optim_lr)
+        mp.spawn(main_worker, nprocs=ngpus_per_node, args=(args,))
+    else:
+        main_worker(0, args)