These functions should no longer be _ functions

Author: stephen-riggs

src/murfey/client/contexts/spa.py

@@ -22,11 +22,11 @@
     get_machine_config_client,
 )
 from murfey.util.spa_metadata import (
-    _foil_hole_data,
-    _foil_hole_from_file,
-    _get_grid_square_atlas_positions,
-    _grid_square_data,
-    _grid_square_from_file,
+    foil_hole_data,
+    foil_hole_from_file,
+    get_grid_square_atlas_positions,
+    grid_square_data,
+    grid_square_from_file,
 )
 
 logger = logging.getLogger("murfey.client.contexts.spa")
@@ -371,7 +371,7 @@ def _position_analysis(
         source: Path,
         machine_config: dict,
     ) -> Optional[int]:
-        grid_square = _grid_square_from_file(transferred_file)
+        grid_square = grid_square_from_file(transferred_file)
         grid_square_metadata_file = _grid_square_metadata_file(
             transferred_file,
             [Path(p) for p in machine_config["data_directories"]],
@@ -413,12 +413,12 @@ def _position_analysis(
                     local_atlas_path = (
                         Path(visit_path) / environment.samples[source].atlas
                     )
-                    gs_pix_position = _get_grid_square_atlas_positions(
+                    gs_pix_position = get_grid_square_atlas_positions(
                         local_atlas_path,
                         grid_square=str(grid_square),
                     )[str(grid_square)]
             gs_url = f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/grid_square/{grid_square}"
-            gs = _grid_square_data(
+            gs = grid_square_data(
                 grid_square_metadata_file,
                 grid_square,
             )
@@ -453,14 +453,14 @@ def _position_analysis(
                     "angle": gs_pix_position[6],
                 },
             )
-        foil_hole = _foil_hole_from_file(transferred_file)
+        foil_hole = foil_hole_from_file(transferred_file)
         if foil_hole not in self._foil_holes[grid_square]:
             fh_url = f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/grid_square/{grid_square}/foil_hole"
             if (
                 grid_square_metadata_file.is_file()
                 and environment.murfey_session is not None
             ):
-                fh = _foil_hole_data(
+                fh = foil_hole_data(
                     grid_square_metadata_file,
                     foil_hole,
                     grid_square,

src/murfey/client/contexts/spa_metadata.py

@@ -6,9 +6,10 @@
 import xmltodict
 
 from murfey.client.context import Context
-from murfey.client.contexts.spa import _get_grid_square_atlas_positions, _get_source
+from murfey.client.contexts.spa import _get_source
 from murfey.client.instance_environment import MurfeyInstanceEnvironment, SampleInfo
 from murfey.util import authorised_requests, capture_post, get_machine_config_client
+from murfey.util.spa_metadata import get_grid_square_atlas_positions
 
 logger = logging.getLogger("murfey.client.contexts.spa_metadata")
 
@@ -116,7 +117,7 @@ def post_transfer(
                     .get(str(source), [])
                 )
                 if registered_grid_squares:
-                    gs_pix_positions = _get_grid_square_atlas_positions(
+                    gs_pix_positions = get_grid_square_atlas_positions(
                         source_visit_dir / partial_path
                     )
                     for gs in registered_grid_squares:

src/murfey/util/spa_metadata.py

@@ -38,18 +38,18 @@ class GridSquareInfo(NamedTuple):
     tag: str = ""
 
 
-def _grid_square_from_file(f: Path) -> int:
+def grid_square_from_file(f: Path) -> int:
     for p in f.parts:
         if p.startswith("GridSquare"):
             return int(p.split("_")[1])
     raise ValueError(f"Grid square ID could not be determined from path {f}")
 
 
-def _foil_hole_from_file(f: Path) -> int:
+def foil_hole_from_file(f: Path) -> int:
     return int(f.name.split("_")[1])
 
 
-def _get_grid_square_atlas_positions(xml_path: Path, grid_square: str = "") -> Dict[
+def get_grid_square_atlas_positions(xml_path: Path, grid_square: str = "") -> Dict[
     str,
     Tuple[
         Optional[int],
@@ -117,7 +117,7 @@ def _get_grid_square_atlas_positions(xml_path: Path, grid_square: str = "") -> D
     return gs_pix_positions
 
 
-def _grid_square_data(xml_path: Path, grid_square: int) -> GridSquareInfo:
+def grid_square_data(xml_path: Path, grid_square: int) -> GridSquareInfo:
     image_paths = list(
         (xml_path.parent.parent).glob(
             f"Images-Disc*/GridSquare_{grid_square}/GridSquare_*.jpg"
@@ -147,7 +147,7 @@ def _grid_square_data(xml_path: Path, grid_square: int) -> GridSquareInfo:
     return GridSquareInfo(id=grid_square)
 
 
-def _foil_hole_data(xml_path: Path, foil_hole: int, grid_square: int) -> FoilHoleInfo:
+def foil_hole_data(xml_path: Path, foil_hole: int, grid_square: int) -> FoilHoleInfo:
     with open(xml_path, "r") as xml:
         for_parsing = xml.read()
         data = xmltodict.parse(for_parsing)

src/murfey/workflows/spa/flush_spa_preprocess.py

@@ -16,11 +16,11 @@
 from murfey.util.processing_params import default_spa_parameters
 from murfey.util.spa_metadata import (
     GridSquareInfo,
-    _foil_hole_data,
-    _foil_hole_from_file,
-    _get_grid_square_atlas_positions,
-    _grid_square_data,
-    _grid_square_from_file,
+    foil_hole_data,
+    foil_hole_from_file,
+    get_grid_square_atlas_positions,
+    grid_square_data,
+    grid_square_from_file,
 )
 
 logger = logging.getLogger("murfey.workflows.spa.flush_spa_preprocess")
@@ -188,15 +188,15 @@ def _flush_position_analysis(
     ).one()
 
     # Work out the grid square and associated metadata file
-    grid_square = _grid_square_from_file(movie_path)
+    grid_square = grid_square_from_file(movie_path)
     grid_square_metadata_file = _grid_square_metadata_file(movie_path, grid_square)
     if grid_square_metadata_file:
-        gs = _grid_square_data(grid_square_metadata_file, grid_square)
+        gs = grid_square_data(grid_square_metadata_file, grid_square)
     else:
         gs = GridSquareInfo(id=grid_square)
     if data_collection_group.atlas:
         # If an atlas if present, work out where this grid square is on it
-        gs_pix_position = _get_grid_square_atlas_positions(
+        gs_pix_position = get_grid_square_atlas_positions(
             data_collection_group.atlas,
             grid_square=str(grid_square),
         )[str(grid_square)]
@@ -231,9 +231,9 @@ def _flush_position_analysis(
     register_grid_square(session_id, gs.id, grid_square_parameters, murfey_db)
 
     # Find the foil hole info and register it
-    foil_hole = _foil_hole_from_file(movie_path)
+    foil_hole = foil_hole_from_file(movie_path)
     if grid_square_metadata_file:
-        fh = _foil_hole_data(
+        fh = foil_hole_data(
             grid_square_metadata_file,
             foil_hole,
             grid_square,