feat: gnn-based inference

AllenInstitute · Apr 16, 2024 · e064313 · e064313
1 parent 1c34588
commit e064313
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Showing 3 changed files with 27 additions and 4 deletions.
diff --git a/src/deep_neurographs/machine_learning/feature_generation.py b/src/deep_neurographs/machine_learning/feature_generation.py
@@ -335,7 +335,6 @@ def generate_skel_features(neurograph, proposals):
                 n_nearby_leafs(neurograph, proposal),
                 get_radii(neurograph, proposal),
                 get_avg_radii(neurograph, proposal),
-                get_avg_branch_lens(neurograph, proposal),
                 get_directionals(neurograph, proposal, 8),
                 get_directionals(neurograph, proposal, 16),
                 get_directionals(neurograph, proposal, 32),

diff --git a/src/deep_neurographs/machine_learning/inference.py b/src/deep_neurographs/machine_learning/inference.py
@@ -156,7 +156,7 @@ def predict(
     confidence_threshold=0.7,
 ):
     # Generate features
-    features = feature_generation.run_on_proposals(
+    features = feature_generation.run(
         neurograph,
         model_type,
         search_radius,
@@ -167,18 +167,26 @@ def predict(
     dataset = ml_utils.init_dataset(neurograph, features, model_type)
 
     # Run model
+    idx_to_edge = get_idxs(dataset, model_type)
     proposal_probs = run_model(dataset, model, model_type)
     accepts, graph = build.get_accepted_proposals(
         neurograph,
         graph,
         proposal_probs,
-        dataset["idx_to_edge"],
+        idx_to_edge,
         high_threshold=0.95,
         low_threshold=confidence_threshold,
     )
     return accepts, graph
 
 
+def get_idxs(dataset, model_type):
+    if "Graph" in model_type:
+        return dataset.idxs_proposals["idx_to_edge"]
+    else:
+        return dataset["idx_to_edge"]
+
+
 # -- Whole Brain Seed-Based Inference --
 def build_from_soma(
     neurograph, labels_path, chunk_origin, chunk_shape=CHUNK_SHAPE, n_hops=1

diff --git a/src/deep_neurographs/machine_learning/ml_utils.py b/src/deep_neurographs/machine_learning/ml_utils.py
@@ -15,7 +15,7 @@
 import torch
 from sklearn.ensemble import AdaBoostClassifier, RandomForestClassifier
 
-from deep_neurographs.machine_learning import feature_generation
+from deep_neurographs.machine_learning import feature_generation, graph_datasets
 from deep_neurographs.machine_learning.datasets import (
     ImgProposalDataset,
     MultiModalDataset,
@@ -152,6 +152,22 @@ def get_dataset(inputs, targets, model_type, transform, lengths):
 
 def init_dataset(
     neurographs, features, model_type, block_ids=None, transform=False
+):
+    if "Graph" in model_type:
+        dataset = graph_datasets.init(neurographs, features)
+    else:
+        dataset =  init_proposal_dataset(
+            neurographs,
+            features,
+            model_type,
+            block_ids=block_ids,
+            transform=transform
+        )
+    return dataset
+
+
+def init_proposal_dataset(
+    neurographs, features, model_type, block_ids=None, transform=False
 ):
     # Extract features
     inputs, targets, idx_transforms = feature_generation.get_matrix(