Add Unet KITS19 in PyTorch

.github/workflows/test.yml

@@ -227,6 +227,8 @@ jobs:
       S3_URL_IMAGENET_DATASET_LABELS: ${{ secrets.S3_URL_IMAGENET_DATASET_LABELS }}
       S3_URL_COCO_DATASET: ${{ secrets.S3_URL_COCO_DATASET }}
       S3_URL_COCO_DATASET_ANNOTATIONS: ${{ secrets.S3_URL_COCO_DATASET_ANNOTATIONS }}
+      S3_URL_KITS19_REDUCED_DATASET: ${{ secrets.S3_URL_KITS19_REDUCED_DATASET }}
+      S3_URL_UNET_KITS_PYTORCH_FP32: ${{ secrets.S3_URL_UNET_KITS_PYTORCH_FP32 }}
       S3_URL_COVOST2_DATASET: ${{ secrets.S3_URL_COVOST2_DATASET }}
       HF_HUB_TOKEN: ${{ secrets.HF_HUB_TOKEN }}
     steps:

computer_vision/semantic_segmentation/unet_3d/kits_19/run.py

@@ -1,5 +1,7 @@
 # SPDX-License-Identifier: Apache-2.0
 # Copyright (c) 2024, Ampere Computing LLC
+
+
 try:
     from utils import misc  # noqa
 except ModuleNotFoundError:
@@ -18,31 +20,6 @@
     sys.exit(1)
 
 
-def parse_args():
-    import argparse
-    parser = argparse.ArgumentParser(description="Run 3D Unet KiTS 2019 model.")
-    parser.add_argument("-m", "--model_path",
-                        type=str,
-                        help="path to the model")
-    parser.add_argument("-p", "--precision",
-                        type=str, choices=["fp32"], required=True,
-                        help="precision of the model provided")
-    parser.add_argument("-f", "--framework",
-                        type=str, default="tf",
-                        choices=["tf"],
-                        help="specify the framework in which a model should be run")
-    parser.add_argument("--timeout",
-                        type=float, default=60.0,
-                        help="timeout in seconds")
-    parser.add_argument("--num_runs",
-                        type=int,
-                        help="number of passes through network to execute")
-    parser.add_argument("--kits_path",
-                        type=str,
-                        help="path to directory with KiTS19 dataset")
-    return parser.parse_args()
-
-
 def run_tf_fp(model_path, num_runs, timeout, kits_path):
     import numpy as np
     import tensorflow as tf
@@ -64,27 +41,47 @@ def run_single_pass(tf_runner, kits):
     return run_model(run_single_pass, runner, dataset, 1, num_runs, timeout)
 
 
+def run_pytorch_fp(model_path, num_runs, timeout, kits_path):
+    import torch
+    import numpy as np
+    import tensorflow as tf
+    from utils.pytorch import PyTorchRunnerV2
+    from utils.cv.kits import KiTS19
+    from utils.benchmark import run_model
+
+    def run_single_pass(pytorch_runner, kits):
+        output = pytorch_runner.run(1, torch.from_numpy(np.expand_dims(kits.get_input_array(), axis=0)))
+        kits.submit_predictions(tf.convert_to_tensor(output.numpy()))
+
+    dataset = KiTS19(dataset_dir_path=kits_path)
+    model = torch.jit.load(model_path, map_location=torch.device('cpu')).eval()
+    model = torch.jit.freeze(model)
+    runner = PyTorchRunnerV2(model)
+
+    return run_model(run_single_pass, runner, dataset, 1, num_runs, timeout)
+
+
 def run_tf_fp32(model_path, num_runs, timeout, kits_path, **kwargs):
     return run_tf_fp(model_path, num_runs, timeout, kits_path)
 
 
+def run_pytorch_fp32(model_path, num_runs, timeout, kits_path, **kwargs):
+    return run_pytorch_fp(model_path, num_runs, timeout, kits_path)
+
+
 def main():
-    from utils.misc import print_goodbye_message_and_die
-    args = parse_args()
-    if args.framework == "tf":
-        if args.model_path is None:
-            print_goodbye_message_and_die(
-                "a path to model is unspecified!")
-
-        if args.precision == "fp32":
-            run_tf_fp32(**vars(args))
-        else:
-            print_goodbye_message_and_die(
-                "this model seems to be unsupported in a specified precision: " + args.precision)
+    from utils.helpers import DefaultArgParser
+    parser = DefaultArgParser(["tf", "pytorch"])
+    parser.require_model_path()
+    parser.add_argument("--kits_path",
+                        type=str,
+                        help="path to directory with KiTS19 dataset")
 
+    args = parser.parse()
+    if args.framework == 'tf':
+        run_tf_fp32(**vars(parser.parse()))
     else:
-        print_goodbye_message_and_die(
-            "this model seems to be unsupported in a specified framework: " + args.framework)
+        run_pytorch_fp32(**vars(parser.parse()))
 
 
 if __name__ == "__main__":

licensing/approved_urls.json

@@ -38,6 +38,8 @@
     "https://ampereaidevelopus.s3.amazonaws.com/releases/1.10.0/binaries/install_ampere_pytorch_u22_1_10_0.sh)",
     "https://ampereaimodelzoo.s3.eu-central-1.amazonaws.com/lookups_aml/banshee%40ampere_pytorch_1.10.0%40yolo_v8_s.json",
     "https://ampereaimodelzoo.s3.eu-central-1.amazonaws.com/sklearn2onnx/linear_regression_optimized.joblib",
-    "https://www.dropbox.com/s/ft54q1gi060vm2x/Task004_Hippocampus.zip?dl=1"
+    "https://www.dropbox.com/s/ft54q1gi060vm2x/Task004_Hippocampus.zip?dl=1",
+    "https://ampereaimodelzoo.s3.eu-central-1.amazonaws.com/3d_unet_kits_pytorch_fp32.ptc",
+    "https://ampereaimodelzoo.s3.eu-central-1.amazonaws.com/kits19_reduced.tar.gz"
   ]
 }

tests/test_pytorch_models.py

@@ -227,6 +227,41 @@ def wrapper(**kwargs):
         self.assertTrue(acc["f1"] / f1_ref > 0.95)
 
 
+class UNET_KITS(unittest.TestCase):
+    def setUp(self):
+        self.dataset_path = pathlib.Path(get_downloads_path(), "kits19")
+        if not self.dataset_path.exists():
+            # url = os.environ.get("S3_URL_KITS19_REDUCED_DATASET")
+            url = "https://ampereaimodelzoo.s3.eu-central-1.amazonaws.com/kits19_reduced.tar.gz"
+            assert url is not None
+            subprocess.run(f"wget -P /tmp {url}".split(),
+                           check=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+            subprocess.run(f"tar -xf /tmp/kits19_reduced.tar.gz -C {get_downloads_path()}".split(),
+                           check=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+            subprocess.run("rm /tmp/kits19_reduced.tar.gz".split(),
+                           check=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+
+        self.model_path = pathlib.Path(get_downloads_path(), "3d_unet_kits_pytorch_fp32.ptc")
+        if not self.model_path.exists():
+            # url = os.environ.get("S3_URL_UNET_KITS_PYTORCH_FP32")
+            url = "https://ampereaimodelzoo.s3.eu-central-1.amazonaws.com/3d_unet_kits_pytorch_fp32.ptc"
+            subprocess.run(f"wget -P {get_downloads_path()} {url}".split(),
+                           check=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+
+    def test_unet_kits(self):
+        from computer_vision.semantic_segmentation.unet_3d.kits_19.run import run_pytorch_fp32
+
+        def wrapper(**kwargs):
+            kwargs["q"].put(run_pytorch_fp32(**kwargs)[0])
+
+        mean_kidney_acc, mean_tumor_acc = 0.927, 0.837
+        acc = run_process(wrapper, {"model_path": self.model_path, "kits_path": self.dataset_path,
+                                    "batch_size": 1, "num_runs": 500, "timeout": 200, "debug": True})
+
+        self.assertTrue(acc["mean_kidney_acc"] / mean_kidney_acc > 0.90)
+        self.assertTrue(acc["mean_tumor_acc"] / mean_tumor_acc > 0.80)
+
+
 def download_imagenet_maybe():
     dataset_path = pathlib.Path(get_downloads_path(), "ILSVRC2012_onspecta")
     if not dataset_path.exists():