From 0b49aa761e3c508f5490d5060be9950f77f798f0 Mon Sep 17 00:00:00 2001
From: brianreicher <reicher.b@northeastern.edu>
Date: Tue, 7 Nov 2023 11:25:55 -0500
Subject: [PATCH] ACLSD system

---
 src/raygun/torch/systems/ACLSD.py | 107 ++++++++++++++++++++++++++++++
 1 file changed, 107 insertions(+)
 create mode 100644 src/raygun/torch/systems/ACLSD.py

diff --git a/src/raygun/torch/systems/ACLSD.py b/src/raygun/torch/systems/ACLSD.py
new file mode 100644
index 0000000..612dde5
--- /dev/null
+++ b/src/raygun/torch/systems/ACLSD.py
@@ -0,0 +1,107 @@
+import itertools
+import logging
+from matplotlib import pyplot as plt
+import torch
+import daisy
+
+import gunpowder as gp
+import numpy as np
+
+torch.backends.cudnn.benchmark = True
+
+from raygun.io import ACLSDDataPipe
+from raygun.torch.models import ACLSDModel
+from raygun.torch.losses import WeightedMSELoss_ACLSD
+from raygun.torch.optimizers import get_base_optimizer
+from raygun.torch.systems import BaseSystem
+
+
+class ACLSD(BaseSystem):
+    def __init__(self, config=None):
+        super().__init__(
+            default_config="../default_configs/default_ACLSD_conf.json",
+            config=config,
+        )
+        self.logger = logging.Logger(__name__, "INFO")
+
+        if self.ndims is None:
+            self.ndims = sum(np.array(self.voxel_size) == np.min(self.voxel_size))
+
+        self.neighborhood = np.array(self.neighborhood)
+        if self.n_diagonals > 0:
+            pos_diag = np.round(
+                self.n_diagonals
+                * np.sin(np.linspace(0, np.pi, num=self.n_diagonals, endpoint=False))
+            )
+            neg_diag = np.round(
+                self.n_diagonals
+                * np.cos(np.linspace(0, np.pi, num=self.n_diagonals, endpoint=False))
+            )
+            stacked_diag = np.stack([0 * pos_diag, pos_diag, neg_diag], axis=-1)
+            self.neighborhood = np.concatenate(
+                [self.neighborhood, stacked_diag]
+            ).astype(np.int8)
+
+        self.voxel_size = gp.Coordinate(self.voxel_size)
+        self.output_size = gp.Coordinate(self.output_shape) * gp.Coordinate(
+            self.voxel_size
+        )
+        self.input_size = gp.Coordinate(self.input_shape) * gp.Coordinate(
+            self.voxel_size
+        )
+
+    def setup_networks(self):
+        pass
+
+    def setup_model(self):
+        self.model = ACLSDModel(**self.model_kwargs)
+
+    def setup_optimization(self):
+        self.optimizer = get_base_optimizer(self.optim_type)(
+            params=self.model.parameters(), **self.optim_kwargs
+        )
+
+        self.loss = WeightedMSELoss_ACLSD(**self.loss_kwargs)
+
+    def setup_datapipes(self):
+        kws = [
+            "ndims",
+            "output_size",
+            "voxel_size",
+            "neighborhood",
+            "lsd_kwargs",
+            "batch_size",
+            "pad",
+            "random_location_kwargs",
+            "reject_kwargs",
+            "grow_boundary",
+        ]
+
+        dp_kwargs = {"srcs": self.sources}
+        for kw in kws:
+            if hasattr(self, kw) and getattr(self, kw) is not None:
+                dp_kwargs[kw] = getattr(self, kw)
+
+        self.datapipes = {"main": ACLSDDataPipe(**dp_kwargs)}
+
+        self.arrays = self.datapipes["main"].arrays
+
+    def make_request(self, mode: str = "train"):
+        # create request
+        request = gp.BatchRequest()
+        for array_name, array in self.arrays.items():
+            if array_name == "raw":
+                extents = self.input_size
+            else:
+                extents = self.output_size
+
+            request.add(array, extents, self.voxel_size)
+
+        return request
+
+
+if __name__ == "__main__":
+    system = ACLSD(config="./train_conf.json")
+    system.logger.info("MTLSD system loaded. Training...")
+    _ = system.train()
+    system.logger.info("Done training!")