Uploading contents of MONAI-extra-test-data

create_data.py

@@ -0,0 +1,100 @@
+import json
+import os
+import torch
+from typing import Any, Dict, Sequence
+
+import monai.networks.nets as nets
+
+
+def create_model_test_data(
+    model_name: str,
+    model_params: Dict[str, Any],
+    input_shape: Sequence[int],
+) -> None:
+    """
+    Create test data to check model consistency
+
+    Args:
+        model_class: Name of model to be tested.
+        model_params: Dictionary of parameters to construct object.
+        input_shape: Tuple of dimensions (B, C, H, W, [D]).
+
+    .. code-block:: python
+
+        # network params
+        unet_params = {
+            "dimensions" : 3,
+            "in_channels" : 4,
+            "out_channels" : 2,
+            "channels": (4, 8, 16, 32),
+            "strides": (2, 4, 1),
+            "kernel_size" : 5,
+            "up_kernel_size" : 3,
+            "num_res_units": 2,
+            "act": "relu",
+            "dropout": 0.1,
+        }
+        # in shape
+        input_shape = (1, unet_params["in_channels"], 64, 64, 64)
+        # create data
+        create_model_test_data("UNet", unet_params, input_shape)
+    """
+    model_name = model_name.lower()
+    base_folder = os.path.dirname(os.path.abspath(__file__))
+
+    # get next unused folder
+    i=0
+    while True:
+        out_folder = os.path.join(base_folder, f"{model_name}_{i}")
+        if not os.path.isdir(out_folder):
+            print("\n\nCreating output folder: " + out_folder)
+            os.mkdir(out_folder)
+            break
+        i += 1
+    out_path_no_ext = os.path.join(out_folder, f"{model_name}_{i}")
+
+    # Create model
+    model = nets.__dict__[model_name](**model_params)
+    model.eval()
+
+    # Create input data
+    num_elements = int(torch.Tensor(input_shape).prod())
+    in_data = torch.arange(num_elements).reshape(input_shape).float()
+
+    # Forward pass data
+    out_data = model(in_data)
+
+    # Save in data, out data and model
+    data_path = out_path_no_ext + ".pt"
+    to_save = {"in_data": in_data, "out_data": out_data, "model": model.state_dict()}
+    print("Writing data output to .pt: " + data_path)
+    torch.save(to_save, data_path)
+
+    # Save parameters
+    json_params = out_path_no_ext + ".json"
+    with open(json_params, "w+") as f:
+        print("Writing network parameters to .json: " + json_params)
+        json.dump(model_params, f)
+
+
+
+# default
+if __name__ == "__main__":
+
+    # network params
+    unet_params = {
+        "dimensions" : 3,
+        "in_channels" : 4,
+        "out_channels" : 2,
+        "channels": (4, 8, 16, 32),
+        "strides": (2, 4, 1),
+        "kernel_size" : 5,
+        "up_kernel_size" : 3,
+        "num_res_units": 2,
+        "act": "relu",
+        "dropout": 0.1,
+    }
+    # in shape
+    input_shape = (1, unet_params["in_channels"], 64, 64, 64)
+    # create data
+    create_model_test_data("UNet", unet_params, input_shape)

dynunet_0/Dynunet_1.json

@@ -0,0 +1 @@
+{"spatial_dims": 3, "in_channels": 4, "out_channels": 2, "kernel_size": [3, 3, 3, 1], "strides": [2, 2, 2, 2], "upsample_kernel_size": [2, 2, 2]}

dynunet_0/Dynunet_1.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:662e895f07075f3ab6ca8b5bf7473ba26b57a3525ef6c7b3d4ff85ff4907d63c
+size 11569537

dynunet_0/dynunet_0.py

@@ -0,0 +1,16 @@
+from create_data import create_model_test_data
+strides = (2, 2, 2, 2)
+
+# network params
+params = {
+    "spatial_dims": 3,
+    "in_channels": 4,
+    "out_channels": 2,
+    "kernel_size": (3, 3, 3, 1),
+    "strides": strides,
+    "upsample_kernel_size": strides[1:],
+}
+# in shape
+input_shape = (1, params["in_channels"], 64, 64, 64)
+# create data
+create_model_test_data("DynUNet", params, input_shape)

unet_0/Unet_0.json

@@ -0,0 +1 @@
+{"spatial_dims": 3, "in_channels": 4, "out_channels": 2, "channels": [4, 8, 16, 32], "strides": [2, 4, 1], "kernel_size": 5, "up_kernel_size": 3, "num_res_units": 2, "act": "relu", "dropout": 0.1}

unet_0/Unet_0.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:09573859799471a60debc13635cb79a5cf6c7351c443399a65491a89294545d3
+size 7453957