feat: ingest motion-corrected micrograph image paths (#309)

src/smartem_backend/api_server.py

@@ -1389,6 +1389,8 @@ async def publish_micrograph_motion_correction_completed(
         micrograph_uuid=micrograph_uuid,
         total_motion=payload.total_motion,
         average_motion=payload.average_motion,
+        motion_corrected_image_path=payload.motion_corrected_image_path,
+        motion_corrected_snapshot_path=payload.motion_corrected_snapshot_path,
     )
     return _publish_or_502(success, "motion_correction_completed", micrograph_uuid)
 

src/smartem_backend/consumer.py

@@ -455,6 +455,10 @@ async def handle_motion_correction_complete(event_data: dict[str, Any]) -> None:
                 .first()
             )
             if micrograph:
+                if event.motion_corrected_image_path is not None:
+                    micrograph.motion_corrected_image_path = event.motion_corrected_image_path
+                if event.motion_corrected_snapshot_path is not None:
+                    micrograph.motion_corrected_snapshot_path = event.motion_corrected_snapshot_path
                 micrograph.updated_at = datetime.now()
                 await session.commit()
         await publish_motion_correction_registered(

src/smartem_backend/migrations/versions/2026_07_08_1200-d5e6f7a8b9c0_add_micrograph_motion_corrected_image_paths.py

@@ -0,0 +1,25 @@
+"""Add micrograph motion-corrected image and snapshot paths
+
+Revision ID: d5e6f7a8b9c0
+Revises: c4d5e6f7a8b9
+Create Date: 2026-07-08 12:00:00.000000
+
+"""
+
+import sqlalchemy as sa
+from alembic import op
+
+revision = "d5e6f7a8b9c0"
+down_revision = "c4d5e6f7a8b9"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    op.add_column("micrograph", sa.Column("motion_corrected_image_path", sa.String(), nullable=True))
+    op.add_column("micrograph", sa.Column("motion_corrected_snapshot_path", sa.String(), nullable=True))
+
+
+def downgrade() -> None:
+    op.drop_column("micrograph", "motion_corrected_snapshot_path")
+    op.drop_column("micrograph", "motion_corrected_image_path")

src/smartem_backend/model/database.py

@@ -223,6 +223,8 @@ class Micrograph(SQLModel, table=True, table_name="micrograph"):
     binning_y: int | None = Field(default=None)
     total_motion: float | None = Field(default=None)
     average_motion: float | None = Field(default=None)
+    motion_corrected_image_path: str | None = Field(default=None)
+    motion_corrected_snapshot_path: str | None = Field(default=None)
     ctf_max_resolution_estimate: float | None = Field(default=None)
     number_of_particles_selected: int | None = Field(default=None)
     number_of_particles_rejected: int | None = Field(default=None)

src/smartem_backend/model/http_request.py

@@ -300,6 +300,8 @@ class MicrographUpdateRequest(MicrographBaseFields):
 class MotionCorrectionCompletedRequest(BaseModel):
     total_motion: float
     average_motion: float
+    motion_corrected_image_path: str | None = None
+    motion_corrected_snapshot_path: str | None = None
 
 
 class MotionCorrectionRegisteredRequest(BaseModel):

src/smartem_backend/model/mq_event.py

@@ -331,6 +331,8 @@ class MotionCorrectionCompleteBody(GenericEventMessageBody):
     micrograph_uuid: str
     total_motion: float
     average_motion: float
+    motion_corrected_image_path: str | None = None
+    motion_corrected_snapshot_path: str | None = None
 
     @model_validator(mode="after")
     def check_model(self):

src/smartem_backend/mq_publisher.py

@@ -367,12 +367,20 @@ async def publish_model_parameter_update(
     return await _publish(MessageQueueEventType.MODEL_PARAMETER_UPDATE, event)
 
 
-async def publish_motion_correction_completed(micrograph_uuid: str, total_motion: float, average_motion: float) -> bool:
+async def publish_motion_correction_completed(
+    micrograph_uuid: str,
+    total_motion: float,
+    average_motion: float,
+    motion_corrected_image_path: str | None = None,
+    motion_corrected_snapshot_path: str | None = None,
+) -> bool:
     event = MotionCorrectionCompleteBody(
         event_type=MessageQueueEventType.MOTION_CORRECTION_COMPLETE,
         micrograph_uuid=micrograph_uuid,
         total_motion=total_motion,
         average_motion=average_motion,
+        motion_corrected_image_path=motion_corrected_image_path,
+        motion_corrected_snapshot_path=motion_corrected_snapshot_path,
     )
     return await _publish(MessageQueueEventType.MOTION_CORRECTION_COMPLETE, event)
 

tests/smartem_backend/test_consumer_async_handlers.py

@@ -179,6 +179,37 @@ async def _stub_publish(*args, **kwargs):
         assert db.add.call_count == 1
         assert db.commit.await_count == 1
 
+    def test_persists_motion_corrected_image_paths(self, db, monkeypatch, stub_publisher):
+        grid_row = MagicMock()
+        grid_row.grid_uuid = "grid-1"
+        micrograph = MagicMock()
+        db.execute.return_value.one.return_value = (grid_row,)
+        db.execute.return_value.scalars.return_value.all.return_value = []
+        db.execute.return_value.scalars.return_value.first.return_value = micrograph
+
+        async def _stub_check(*args, **kwargs):
+            return 0.7
+
+        async def _stub_prior(*args, **kwargs):
+            return None
+
+        async def _stub_publish(*args, **kwargs):
+            return True
+
+        monkeypatch.setattr(consumer, "_check_against_statistics", _stub_check)
+        monkeypatch.setattr(consumer, "prior_update", _stub_prior)
+        monkeypatch.setattr(consumer, "publish_motion_correction_registered", _stub_publish)
+
+        import asyncio
+
+        event = dict(self.base_event)
+        event["motion_corrected_image_path"] = "/dls/mc/mic.mrc"
+        event["motion_corrected_snapshot_path"] = "/dls/mc/mic.mrc.jpeg"
+        asyncio.run(consumer.handle_motion_correction_complete(event))
+
+        assert micrograph.motion_corrected_image_path == "/dls/mc/mic.mrc"
+        assert micrograph.motion_corrected_snapshot_path == "/dls/mc/mic.mrc.jpeg"
+
 
 class TestRefreshPredictions:
     base_event = {

tests/smartem_backend/test_processing_feedback_endpoints.py

@@ -71,8 +71,24 @@ def test_happy_path(self, client, captured):
             "micrograph_uuid": "abc-123",
             "total_motion": 1.5,
             "average_motion": 0.1,
+            "motion_corrected_image_path": None,
+            "motion_corrected_snapshot_path": None,
         }
 
+    def test_image_paths_are_forwarded(self, client, captured):
+        resp = client.post(
+            self.endpoint,
+            json={
+                "total_motion": 1.5,
+                "average_motion": 0.1,
+                "motion_corrected_image_path": "/dls/mc/mic.mrc",
+                "motion_corrected_snapshot_path": "/dls/mc/mic.mrc.jpeg",
+            },
+        )
+        assert resp.status_code == 202
+        assert captured[0].kwargs["motion_corrected_image_path"] == "/dls/mc/mic.mrc"
+        assert captured[0].kwargs["motion_corrected_snapshot_path"] == "/dls/mc/mic.mrc.jpeg"
+
     def test_missing_micrograph_returns_404(self, client, captured):
         client._db.execute.return_value = make_execute_result(None)
         resp = client.post(self.endpoint, json={"total_motion": 1.5, "average_motion": 0.1})