Add buildRegionGraphOnly fast path, fix merge scoring, update SNEMI config

lib/waterz:
- Add buildRegionGraphOnly() to frontend_agglomerate: builds scored
  region graph without RegionMerging or priority queue overhead
- Fix get_region_graph default scoring: use raw MeanAffinity (not
  OneMinus) so merge_segments gets correct descending sort order
- Expose via _agglomerate.build_region_graph_only() Python API

connectomics:
- Update prediction naming utilities
- Update SNEMI config paths

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: Donglai Wei

connectomics/training/lightning/utils.py

@@ -454,10 +454,39 @@ def _sanitize_decode_component(text: str) -> str:
         safe_text = re.sub(r"-{2,}", "-", safe_text)
         return safe_text.strip("-")
 
+    gated_value_groups = {
+        "branch_merge": [
+            "branch_iou_threshold",
+            "branch_best_buddy",
+            "branch_one_sided_threshold",
+            "branch_one_sided_min_size",
+            "branch_affinity_threshold",
+        ],
+        "dust_merge": [
+            "dust_merge_size",
+            "dust_merge_affinity",
+            "dust_remove_size",
+        ],
+    }
+
     def _flatten_decode_values(value) -> list[str]:
         if hasattr(value, "items"):
+            value_dict = dict(value)
+            gated_keys = set()
+            for gate_key, value_keys in gated_value_groups.items():
+                gate_value = value_dict.get(gate_key)
+                if isinstance(gate_value, bool):
+                    gated_keys.add(gate_key)
+                    gated_keys.update(k for k in value_keys if k in value_dict)
+
             result: list[str] = []
-            for _key, nested_value in sorted(dict(value).items()):
+            for key, nested_value in sorted(value_dict.items()):
+                if key in gated_keys:
+                    if key in gated_value_groups and nested_value is True:
+                        for grouped_key in gated_value_groups[key]:
+                            if grouped_key in value_dict:
+                                result.extend(_flatten_decode_values(value_dict[grouped_key]))
+                    continue
                 result.extend(_flatten_decode_values(nested_value))
             return result
         if isinstance(value, (list, tuple)):

tests/unit/test_lit_utils.py

@@ -272,3 +272,53 @@ def test_format_decode_tag_includes_all_decoding_parameters():
     ]
 
     assert format_decode_tag(cfg) == "_waterz_256-watershed-aff50_his256-true-0.1-0.2-0.4"
+
+
+def test_format_decode_tag_gates_dust_and_branch_parameter_groups():
+    cfg = Config()
+    cfg.inference.decoding = [
+        {
+            "name": "decode_waterz",
+            "kwargs": {
+                "branch_merge": True,
+                "branch_iou_threshold": 0.5,
+                "branch_best_buddy": True,
+                "branch_one_sided_threshold": 0.8,
+                "branch_one_sided_min_size": 100,
+                "branch_affinity_threshold": 0.0,
+                "dust_merge": True,
+                "dust_merge_size": 800,
+                "dust_merge_affinity": 0.3,
+                "dust_remove_size": 600,
+                "merge_function": "aff85_his256",
+                "thresholds": 0.5,
+            },
+        }
+    ]
+
+    assert format_decode_tag(cfg) == "_waterz_0.5-true-0.8-100-0-800-0.3-600-aff85_his256-0.5"
+
+
+def test_format_decode_tag_skips_disabled_dust_and_branch_parameter_groups():
+    cfg = Config()
+    cfg.inference.decoding = [
+        {
+            "name": "decode_waterz",
+            "kwargs": {
+                "branch_merge": False,
+                "branch_iou_threshold": 0.5,
+                "branch_best_buddy": True,
+                "branch_one_sided_threshold": 0.8,
+                "branch_one_sided_min_size": 100,
+                "branch_affinity_threshold": 0.0,
+                "dust_merge": False,
+                "dust_merge_size": 800,
+                "dust_merge_affinity": 0.3,
+                "dust_remove_size": 600,
+                "merge_function": "aff85_his256",
+                "thresholds": 0.5,
+            },
+        }
+    ]
+
+    assert format_decode_tag(cfg) == "_waterz_aff85_his256-0.5"

tutorials/neuron_snemi.yaml

@@ -88,7 +88,7 @@ test:
         thresholds: 0.5
         merge_function: aff85_his256
         aff_threshold: [0.1, 0.999]
-        dust_merge: false              # enable dust merge postprocessing
+        dust_merge: true              # enable dust merge postprocessing
         dust_merge_size: 800
         dust_merge_affinity: 0.3
         dust_remove_size: 600