Add atlas information registration routes for display purposes

Author: d-j-hatton

src/murfey/client/contexts/spa_metadata.py

@@ -4,6 +4,7 @@
 
 import requests
 import xmltodict
+from PIL import Image
 
 from murfey.client.context import Context
 from murfey.client.contexts.spa import _get_grid_square_atlas_positions, _get_source
@@ -64,6 +65,38 @@ def post_transfer(
             visitless_path = Path(
                 str(transferred_file).replace(f"/{environment.visit}", "")
             )
+            visit_index_of_transferred_file = transferred_file.parts.index(
+                environment.visit
+            )
+            atlas_xml_path = list(
+                (
+                    Path(
+                        "/".join(
+                            transferred_file.parts[
+                                : visit_index_of_transferred_file + 1
+                            ]
+                        )
+                    )
+                    / partial_path
+                ).parent.glob("Atlas_*.xml")
+            )[0]
+            with open(atlas_xml_path, "rb") as atlas_xml:
+                atlas_xml_data = xmltodict.parse(atlas_xml)
+                atlas_original_pixel_size = atlas_xml_data["MicroscopeImage"][
+                    "SpatialScale"
+                ]["pixelSize"]["x"]["numericValue"]
+                readout_width = float(
+                    atlas_xml_data["MicroscopeImage"]["SpatialScale"]["pixelSize"]["x"][
+                        "numericValue"
+                    ]
+                )
+
+            # need to calculate the pixel size of the downscaled image
+            atlas_im = Image.open(atlas_xml_path.with_suffix(".jpg"))
+            atlas_pixel_size = atlas_original_pixel_size * (
+                readout_width / atlas_im.width
+            )
+
             source = _get_source(
                 visitless_path.parent / "Images-Disc1" / visitless_path.name,
                 environment,
@@ -90,6 +123,7 @@ def post_transfer(
                         / environment.samples[source].atlas
                     ),
                     "sample": environment.samples[source].sample,
+                    "atlas_pixel_size": atlas_pixel_size,
                 }
                 capture_post(url, json=dcg_data)
                 registered_grid_squares = (

src/murfey/server/__init__.py

@@ -23,6 +23,7 @@
 from fastapi.templating import Jinja2Templates
 from importlib_metadata import EntryPoint  # For type hinting only
 from ispyb.sqlalchemy._auto_db_schema import (
+    Atlas,
     AutoProcProgram,
     Base,
     DataCollection,
@@ -43,6 +44,7 @@
 from werkzeug.utils import secure_filename
 
 import murfey
+import murfey.server.ispyb
 import murfey.server.prometheus as prom
 import murfey.server.websocket
 import murfey.util.db as db
@@ -2628,8 +2630,17 @@ def feedback_callback(header: dict, message: dict) -> None:
                         experimentTypeId=message["experiment_type_id"],
                     )
                     dcgid = _register(record, header)
+                    atlas_record = Atlas(
+                        dataCollectionGroupId=dcgid,
+                        atlasImage=message.get("atlas", ""),
+                        pixelSize=message.get("atlas_pixel_size", 0),
+                        cassetteSlot=message.get("sample"),
+                    )
+                    if _transport_object:
+                        atlas_id = _transport_object.do_insert_atlas(atlas_record)
                     murfey_dcg = db.DataCollectionGroup(
                         id=dcgid,
+                        atlas_id=atlas_id,
                         session_id=message["session_id"],
                         tag=message.get("tag"),
                     )
@@ -2654,6 +2665,14 @@ def feedback_callback(header: dict, message: dict) -> None:
                     }
                 _transport_object.transport.ack(header)
             return None
+        elif message["register"] == "atlas_update":
+            if _transport_object:
+                _transport_object.do_update_atlas(
+                    message["atlas_id"],
+                    message["atlas"],
+                    message["atlas_pixel_size"],
+                    message["sample"],
+                )
         elif message["register"] == "data_collection":
             murfey_session_id = message["session_id"]
             ispyb_session_id = murfey.server.ispyb.get_session_id(

src/murfey/server/api/__init__.py

@@ -1335,15 +1335,30 @@ def register_dc_group(
     ).all():
         dcg_murfey[0].atlas = dcg_params.atlas
         dcg_murfey[0].sample = dcg_params.sample
+        dcg_murfey[0].atlas_pixel_size = dcg_params.atlas_pixel_size
         db.add(dcg_murfey[0])
         db.commit()
+        if _transport_object:
+            _transport_object.send(
+                _transport_object.feedback_queue,
+                {
+                    "register": "atlas_update",
+                    "atlas_id": dcg_murfey.atlas_id,
+                    "atlas": dcg_params.atlas,
+                    "sample": dcg_params.sample,
+                    "atlas_pixel_size": dcg_params.atlas_pixel_size,
+                },
+            )
     else:
         dcg_parameters = {
             "start_time": str(datetime.datetime.now()),
             "experiment_type": dcg_params.experiment_type,
             "experiment_type_id": dcg_params.experiment_type_id,
             "tag": dcg_params.tag,
             "session_id": session_id,
+            "atlas": dcg_params.atlas,
+            "sample": dcg_params.sample,
+            "atlas_pixel_size": dcg_params.atlas_pixel_size,
         }
 
         if _transport_object:

src/murfey/server/ispyb.py

@@ -12,6 +12,7 @@
 import workflows.transport
 from fastapi import Depends
 from ispyb.sqlalchemy import (
+    Atlas,
     AutoProcProgram,
     BLSample,
     BLSampleGroup,
@@ -91,6 +92,41 @@ def do_insert_data_collection_group(
             )
         return {"success": False, "return_value": None}
 
+    def do_insert_atlas(self, record: Atlas):
+        try:
+            with Session() as db:
+                db.add(record)
+                db.commit()
+                log.info(f"Created Atlas {record.atlasId}")
+                return {"success": True, "return_value": record.atlasId}
+        except ispyb.ISPyBException as e:
+            log.error(
+                "Inserting Atlas entry caused exception '%s'.",
+                e,
+                exc_info=True,
+            )
+        return {"success": False, "return_value": None}
+
+    def do_update_atlas(
+        self, atlas_id: int, atlas_image: str, pixel_size: float, slot: int
+    ):
+        try:
+            with Session() as db:
+                atlas = db.query(Atlas).filter(Atlas.atlasId == atlas_id).one()
+                atlas.atlasImage = atlas_image
+                atlas.pixelSize = pixel_size
+                atlas.cassetteSlot = slot
+                db.add(atlas)
+                db.commit()
+                return {"success": True, "return_value": atlas.atlasId}
+        except ispyb.ISPyBException as e:
+            log.error(
+                "Updating Atlas entry caused exception '%s'.",
+                e,
+                exc_info=True,
+            )
+        return {"success": False, "return_value": None}
+
     def send(self, queue: str, message: dict, new_connection: bool = False):
         if self.transport:
             if not self.transport.is_connected():

src/murfey/util/models.py

@@ -47,6 +47,7 @@ class DCGroupParameters(BaseModel):
     tag: str
     atlas: str = ""
     sample: Optional[int] = None
+    atlas_pixel_size: int = 0
 
 
 class DCParameters(BaseModel):