Register all grid squares from atlases

src/murfey/client/contexts/atlas.py

@@ -7,6 +7,7 @@
 from murfey.client.context import Context, _atlas_destination, _get_source
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 from murfey.util.client import capture_post
+from murfey.util.spa_metadata import get_grid_square_atlas_positions
 
 logger = logging.getLogger("murfey.client.contexts.atlas")
 
@@ -158,3 +159,52 @@ def post_transfer_epu(
                 logger.info(
                     f"Registered data collection group for atlas {str(transferred_atlas_jpg)!r}"
                 )
+
+        elif environment and transferred_file.name == "Atlas.dm":
+            # Register all grid squares on this atlas
+            gs_pix_positions = get_grid_square_atlas_positions(transferred_file)
+            for gs, pos_data in gs_pix_positions.items():
+                if pos_data:
+                    capture_post(
+                        base_url=str(environment.url.geturl()),
+                        router_name="session_control.spa_router",
+                        function_name="register_grid_square",
+                        token=self._token,
+                        instrument_name=environment.instrument_name,
+                        session_id=environment.murfey_session,
+                        gsid=int(gs),
+                        data={
+                            "tag": str(transferred_file.parent),
+                            "x_location": pos_data[0],
+                            "y_location": pos_data[1],
+                            "x_stage_position": pos_data[2],
+                            "y_stage_position": pos_data[3],
+                            "width": pos_data[4],
+                            "height": pos_data[5],
+                            "angle": pos_data[6],
+                        },
+                    )
+            if gs_pix_positions:
+                for p in transferred_file.parts:
+                    if p.startswith("Sample"):
+                        sample = int(p.replace("Sample", ""))
+                        break
+                else:
+                    logger.warning(
+                        f"Sample could not be identified for {transferred_file}"
+                    )
+                    return
+                capture_post(
+                    base_url=str(environment.url.geturl()),
+                    router_name="session_control.spa_router",
+                    function_name="register_atlas",
+                    token=self._token,
+                    instrument_name=environment.instrument_name,
+                    session_id=environment.murfey_session,
+                    data={
+                        "name": f"{environment.visit}-sample-{sample}",
+                        "acquisition_uuid": environment.acquisition_uuid,
+                        "register_grid": True,
+                        "tag": str(transferred_file.parent),
+                    },
+                )

src/murfey/client/contexts/spa_metadata.py

@@ -152,7 +152,7 @@ def post_transfer(
                                     "angle": pos_data[6],
                                 },
                             )
-                    if pos_data:
+                    if gs_pix_positions:
                         capture_post(
                             base_url=str(environment.url.geturl()),
                             router_name="session_control.spa_router",

src/murfey/server/api/workflow.py

@@ -232,6 +232,7 @@ def register_dc_group(
         )
     ).all():
         # Case where we switch from atlas to processing
+        original_tag = dcg_murfey[0].tag
         dcg_murfey[0].tag = dcg_params.tag or dcg_murfey[0].tag
         if _transport_object:
             _transport_object.send(
@@ -243,6 +244,13 @@ def register_dc_group(
                 },
             )
         db.add(dcg_murfey[0])
+        for grid_square in db.exec(
+            select(GridSquare)
+            .where(GridSquare.tag == original_tag)
+            .where(GridSquare.session_id == session_id)
+        ).all():
+            grid_square.tag = dcg_params.tag or original_tag
+            db.add(grid_square)
         db.commit()
     else:
         dcg_parameters = {

tests/client/contexts/test_atlas.py

@@ -33,10 +33,7 @@ def test_atlas_context_mrc(mock_capture_post, tmp_path):
     atlas_mrc.parent.mkdir(parents=True)
     atlas_mrc.touch()
 
-    context.post_transfer(
-        atlas_mrc,
-        environment=env,
-    )
+    context.post_transfer(atlas_mrc, environment=env)
     mock_capture_post.assert_called_once_with(
         base_url="http://localhost:8000",
         router_name="session_control.spa_router",
@@ -72,10 +69,7 @@ def test_atlas_context_xml(mock_capture_post, tmp_path):
             "</numericValue></x></pixelSize></SpatialScale></MicroscopeImage>"
         )
 
-    context.post_transfer(
-        atlas_xml,
-        environment=env,
-    )
+    context.post_transfer(atlas_xml, environment=env)
     dcg_data = {
         "experiment_type_id": 44,  # Atlas
         "tag": str(atlas_xml.parent),
@@ -95,3 +89,87 @@ def test_atlas_context_xml(mock_capture_post, tmp_path):
         session_id=1,
         data=dcg_data,
     )
+
+
+@patch("murfey.client.contexts.atlas.capture_post")
+def test_atlas_context_dm(mock_capture_post, tmp_path):
+    env = MurfeyInstanceEnvironment(
+        url=urlparse("http://localhost:8000"),
+        client_id=0,
+        sources=[tmp_path / "cm12345-6"],
+        default_destinations={
+            tmp_path / "cm12345-6": f"{tmp_path}/destination/cm12345-6"
+        },
+        instrument_name="m01",
+        visit="cm12345-6",
+        murfey_session=1,
+        acquisition_uuid="uuid1",
+    )
+
+    # Write sample dm file
+    atlas_dm = tmp_path / "cm12345-6/Supervisor_atlas/Sample2/Atlas/Atlas.dm"
+    atlas_dm.parent.mkdir(parents=True)
+    grid_square_values = (
+        "<value><b:PositionOnTheAtlas>"
+        "<c:Center><d:x>1200</d:x><d:y>1500</d:y></c:Center>"
+        "<c:Physical><d:x>2</d:x><d:y>3</d:y></c:Physical>"
+        "<c:Size><d:width>130</d:width><d:height>560</d:height></c:Size>"
+        "<c:Rotation>0.14</c:Rotation>"
+        "</b:PositionOnTheAtlas></value>"
+    )
+    with open(atlas_dm, "w") as new_xml:
+        new_xml.write(
+            "<AtlasSessionXml><Atlas><TilesEfficient><_items>"
+            # First tile with two grid squares
+            "<TileXml><Nodes><KeyValuePairs><KeyValuePairOfintNodeXml1>"
+            f"<key>101</key>{grid_square_values}"
+            "</KeyValuePairOfintNodeXml1><KeyValuePairOfintNodeXml1>"
+            f"<key>102</key>{grid_square_values}"
+            "</KeyValuePairOfintNodeXml1></KeyValuePairs></Nodes></TileXml>"
+            # Second tile with two grid squares
+            "<TileXml><Nodes><KeyValuePairs><KeyValuePairOfintNodeXml1>"
+            f"<key>103</key>{grid_square_values}"
+            "</KeyValuePairOfintNodeXml1><KeyValuePairOfintNodeXml1>"
+            f"<key>104</key>{grid_square_values}"
+            "</KeyValuePairOfintNodeXml1></KeyValuePairs></Nodes></TileXml>"
+            # Close all
+            "</_items></TilesEfficient></Atlas></AtlasSessionXml>"
+        )
+
+    context = AtlasContext("tomo", tmp_path, {}, "token")
+    context.post_transfer(atlas_dm, environment=env)
+
+    assert mock_capture_post.call_count == 5
+    mock_capture_post.assert_any_call(
+        base_url="http://localhost:8000",
+        router_name="session_control.spa_router",
+        function_name="register_grid_square",
+        token="token",
+        instrument_name="m01",
+        session_id=1,
+        gsid=101,
+        data={
+            "tag": str(atlas_dm.parent),
+            "x_location": 1200,
+            "y_location": 1500,
+            "x_stage_position": 2e9,
+            "y_stage_position": 3e9,
+            "width": 130,
+            "height": 560,
+            "angle": 0.14,
+        },
+    )
+    mock_capture_post.assert_any_call(
+        base_url="http://localhost:8000",
+        router_name="session_control.spa_router",
+        function_name="register_atlas",
+        token="token",
+        instrument_name="m01",
+        session_id=1,
+        data={
+            "name": "cm12345-6-sample-2",
+            "acquisition_uuid": "uuid1",
+            "register_grid": True,
+            "tag": str(atlas_dm.parent),
+        },
+    )