From f6a4b9420f3d2368e104d268903a2e8e45aebcce Mon Sep 17 00:00:00 2001
From: brianreicher <reicher.b@northeastern.edu>
Date: Tue, 7 Nov 2023 09:39:31 -0500
Subject: [PATCH] ACLSD model

---
 src/raygun/torch/models/ACLSDModel.py | 57 +++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 src/raygun/torch/models/ACLSDModel.py

diff --git a/src/raygun/torch/models/ACLSDModel.py b/src/raygun/torch/models/ACLSDModel.py
new file mode 100644
index 00000000..90b251b6
--- /dev/null
+++ b/src/raygun/torch/models/ACLSDModel.py
@@ -0,0 +1,57 @@
+from raygun.torch.networks import UNet
+from raygun.torch.networks.UNet import ConvPass
+import torch
+import logging
+
+torch.backends.cudnn.benchmark = True
+logging.basicConfig(level=logging.INFO)
+
+# long range affs - use 20 output features
+# increase number of downsampling layers for more features in the bottleneck
+class ACLSDModel(torch.nn.Module):
+    def __init__(
+        self,
+        unet_kwargs={
+            "input_nc": 1,
+            "ngf": 12,
+            "fmap_inc_factor": 6,
+            "downsample_factors": [(2, 2, 2), (2, 2, 2), (2, 2, 2)],
+            "constant_upsample": True,
+        },
+        num_affs=3,
+    ):
+        super().__init__()
+
+        self.unet = UNet(**unet_kwargs)
+
+        self.aff_head = ConvPass(
+            unet_kwargs["ngf"], num_affs, [[1, 1, 1]], activation="Sigmoid"
+        )
+
+        self.output_arrays = ["pred_affs"]
+        self.data_dict = {}
+
+    def add_log(self, writer, step):
+        # add loss input image examples
+        for name, data in self.data_dict.items():
+            if len(data.shape) > 3:  # pull out batch dimension if necessary
+                img = data[0].squeeze()
+            else:
+                img = data.squeeze()
+
+            if len(img.shape) == 3:
+                mid = img.shape[0] // 2  # for 3D volume
+                img = img[mid]
+
+            if (
+                (img.min() < 0) and (img.min() >= -1.0) and (img.max() <= 1.0)
+            ):  # scale img to [0,1] if necessary
+                img = (img * 0.5) + 0.5
+            writer.add_image(name, img, global_step=step, dataformats="HW")
+
+    def forward(self, raw):
+        self.data_dict.update({"raw": raw.detach()})
+        z = self.unet(raw)
+        affs = self.aff_head(z)
+
+        return affs