Add code to make atlas jpg file

Author: stephen-riggs

src/murfey/server/api/session_control.py

@@ -54,6 +54,7 @@
     SearchMapParameters,
     Visit,
 )
+from murfey.workflows.spa.atlas import atlas_jpg_from_mrc
 from murfey.workflows.spa.flush_spa_preprocess import (
     register_foil_hole as _register_foil_hole,
 )
@@ -319,6 +320,12 @@ def delete_rsyncer(session_id: int, source: Path, db=murfey_db):
 )
 
 
+@spa_router.get("/sessions/{session_id}/make_atlas_jpg")
+def make_atlas_jpg(session_id: MurfeySessionID, atlas_mrc: str, db=murfey_db):
+    session = db.exec(select(Session).where(Session.id == session_id)).one()
+    return atlas_jpg_from_mrc(session.instrument_name, session.visit, Path(atlas_mrc))
+
+
 @spa_router.get("/sessions/{session_id}/grid_squares")
 def get_grid_squares(session_id: MurfeySessionID, db=murfey_db):
     return _get_grid_squares(session_id, db)

src/murfey/workflows/spa/atlas.py

@@ -0,0 +1,35 @@
+from pathlib import Path
+
+import mrcfile
+import PIL.Image
+from werkzeug.utils import secure_filename
+
+from murfey.util.config import get_machine_config
+
+
+def atlas_jpg_from_mrc(instrument_name: str, visit_name: str, atlas_mrc: Path):
+    with mrcfile.read(atlas_mrc) as mrc:
+        data = mrc.data
+
+    machine_config = get_machine_config(instrument_name=instrument_name)[
+        instrument_name
+    ]
+
+    parts = [secure_filename(p) for p in atlas_mrc.parts]
+    visit_idx = parts.index(visit_name)
+    core = Path("/".join(parts[: visit_idx + 1]))
+    sample_id = "Sample"
+    for p in parts:
+        if "Sample" in p:
+            sample_id = p
+            break
+    atlas_jpg_file = (
+        core
+        / machine_config.processed_directory_name
+        / "atlas"
+        / f"{sample_id}_{atlas_mrc.stem}_fullres.jpg"
+    )
+    atlas_jpg_file.parent.mkdir(parents=True, exist_ok=True)
+
+    im = PIL.Image.fromarray(data)
+    im.save(atlas_jpg_file)