Smartem workflow fixes and single-gs tiles

src/murfey/client/contexts/atlas.py

@@ -116,12 +116,12 @@ def post_transfer_epu(
         ):
             source = _get_source(transferred_file, environment)
             if source:
-                atlas_mrc = transferred_file.with_suffix(".mrc")
+                atlas_jpg = transferred_file.with_suffix(".jpg")
                 transferred_atlas_jpg = _atlas_destination(
                     environment,
                     source,
                     Path(self._machine_config.get("rsync_basepath", "")),
-                ) / atlas_mrc.relative_to(source.parent).with_suffix(".jpg")
+                ) / atlas_jpg.relative_to(source.parent)
 
                 with open(transferred_file, "rb") as atlas_xml:
                     atlas_xml_data = xmltodict.parse(atlas_xml)
@@ -183,16 +183,16 @@ def post_transfer_epu(
 
             # Make sure a dcg is requested before doing grid squares
             source = _get_source(transferred_file, environment)
-            atlas_mrc_glob = list(transferred_file.parent.glob("Atlas_*.mrc"))
+            atlas_jpg_glob = list(transferred_file.parent.glob("Atlas_*.jpg"))
 
             if source:
-                if atlas_mrc_glob:
-                    atlas_mrc = atlas_mrc_glob[0]
+                if atlas_jpg_glob:
+                    atlas_jpg = atlas_jpg_glob[0]
                     transferred_atlas: str | Path = _atlas_destination(
                         environment,
                         source,
                         Path(self._machine_config.get("rsync_basepath", "")),
-                    ) / atlas_mrc.relative_to(source.parent)
+                    ) / atlas_jpg.relative_to(source.parent)
                 else:
                     transferred_atlas = ""
                 capture_post(

src/murfey/server/api/session_control.py

@@ -375,6 +375,7 @@ def register_atlas(
         murfey.server._transport_object.send(
             murfey.server._transport_object.feedback_queue,
             {
+                "register": "spa.smartem_atlas",
                 "session_id": session_id,
                 "atlas_registration_data": atlas_registration_data.model_dump(),
             },

src/murfey/util/spa_metadata.py

@@ -95,7 +95,8 @@ def get_grid_square_atlas_positions(
                 break
         if not required_key:
             continue
-        for gs in nodes[required_key]:
+        if isinstance(nodes[required_key], dict):
+            gs = nodes[required_key]
             if not isinstance(gs, dict):
                 continue
             if not grid_square or gs["key"] == grid_square:
@@ -115,7 +116,43 @@ def get_grid_square_atlas_positions(
                     float(gs["value"]["b:PositionOnTheAtlas"]["c:Rotation"]),
                 )
                 if grid_square:
-                    break
+                    return gs_pix_positions
+        else:
+            for gs in nodes[required_key]:
+                if not isinstance(gs, dict):
+                    continue
+                if not grid_square or gs["key"] == grid_square:
+                    gs_pix_positions[gs["key"]] = (
+                        int(
+                            float(
+                                gs["value"]["b:PositionOnTheAtlas"]["c:Center"]["d:x"]
+                            )
+                        ),
+                        int(
+                            float(
+                                gs["value"]["b:PositionOnTheAtlas"]["c:Center"]["d:y"]
+                            )
+                        ),
+                        float(gs["value"]["b:PositionOnTheAtlas"]["c:Physical"]["d:x"])
+                        * 1e9,
+                        float(gs["value"]["b:PositionOnTheAtlas"]["c:Physical"]["d:y"])
+                        * 1e9,
+                        int(
+                            float(
+                                gs["value"]["b:PositionOnTheAtlas"]["c:Size"]["d:width"]
+                            )
+                        ),
+                        int(
+                            float(
+                                gs["value"]["b:PositionOnTheAtlas"]["c:Size"][
+                                    "d:height"
+                                ]
+                            )
+                        ),
+                        float(gs["value"]["b:PositionOnTheAtlas"]["c:Rotation"]),
+                    )
+                    if grid_square:
+                        return gs_pix_positions
     return gs_pix_positions
 
 

src/murfey/workflows/spa/smartem_atlas.py

@@ -31,7 +31,7 @@
 
 def smartem_atlas(message: dict, murfey_db: SQLModelSession):
     session_id = message.get("session_id")
-    atlas_registration_data = AtlasRegistration(message["atlas_registration_data"])
+    atlas_registration_data = AtlasRegistration(**message["atlas_registration_data"])
     if SMARTEM_ACTIVE and atlas_registration_data.acquisition_uuid is not None:
         session = murfey_db.exec(
             select(MurfeySession).where(MurfeySession.id == session_id)

tests/client/contexts/test_atlas.py

@@ -102,7 +102,7 @@ def test_atlas_context_dm(mock_capture_post, tmp_path):
     # Write sample dm file
     atlas_dm = tmp_path / "cm12345-6/Supervisor_atlas/Sample2/Atlas/Atlas.dm"
     atlas_dm.parent.mkdir(parents=True)
-    (tmp_path / "cm12345-6/Supervisor_atlas/Sample2/Atlas/Atlas_01.mrc").touch()
+    (tmp_path / "cm12345-6/Supervisor_atlas/Sample2/Atlas/Atlas_01.jpg").touch()
     grid_square_values = (
         "<value><b:PositionOnTheAtlas>"
         "<c:Center><d:x>1200</d:x><d:y>1500</d:y></c:Center>"
@@ -147,7 +147,7 @@ def test_atlas_context_dm(mock_capture_post, tmp_path):
             "experiment_type_id": 44,  # Atlas
             "tag": str(atlas_dm.parent),
             "sample": 2,
-            "atlas": "/base/destination/cm12345-6/Supervisor_atlas/Sample2/Atlas/Atlas_01.mrc",
+            "atlas": "/base/destination/cm12345-6/Supervisor_atlas/Sample2/Atlas/Atlas_01.jpg",
             "create_smartem_grid": True,
             "acquisition_uuid": "uuid1",
         },