Make full-resolution jpg files of atlases

src/murfey/client/analyser.py

@@ -15,6 +15,7 @@
 from typing import Type
 
 from murfey.client.context import Context
+from murfey.client.contexts.atlas import AtlasContext
 from murfey.client.contexts.clem import CLEMContext
 from murfey.client.contexts.spa import SPAModularContext
 from murfey.client.contexts.spa_metadata import SPAMetadataContext
@@ -135,7 +136,7 @@ def _find_context(self, file_path: Path) -> bool:
 
         # Tomography and SPA workflow checks
         if "atlas" in file_path.parts:
-            self._context = SPAMetadataContext("epu", self._basepath)
+            self._context = AtlasContext("epu", self._basepath)
             return True
 
         if "Metadata" in file_path.parts or file_path.name == "EpuSession.dm":
@@ -266,7 +267,7 @@ def _analyse(self):
                             )
                         except Exception as e:
                             logger.error(f"Exception encountered: {e}")
-                        if "atlas" not in transferred_file.parts:
+                        if not isinstance(self._context, AtlasContext):
                             if not dc_metadata:
                                 try:
                                     dc_metadata = self._context.gather_metadata(
@@ -308,6 +309,10 @@ def _analyse(self):
                     )
                     self.post_transfer(transferred_file)
 
+                elif isinstance(self._context, AtlasContext):
+                    logger.debug(f"File {transferred_file.name!r} is part of the atlas")
+                    self.post_transfer(transferred_file)
+
                 # Handle files with tomography and SPA context differently
                 elif not self._extension or self._unseen_xml:
                     valid_extension = self._find_extension(transferred_file)
@@ -325,36 +330,35 @@ def _analyse(self):
                             )
                         except Exception as e:
                             logger.error(f"Exception encountered: {e}")
-                        if "atlas" not in transferred_file.parts:
-                            if not dc_metadata:
-                                try:
-                                    dc_metadata = self._context.gather_metadata(
-                                        mdoc_for_reading
-                                        or self._xml_file(transferred_file),
-                                        environment=self._environment,
-                                    )
-                                except KeyError as e:
-                                    logger.error(
-                                        f"Metadata gathering failed with a key error for key: {e.args[0]}"
-                                    )
-                                    raise e
-                            if not dc_metadata or not self._force_mdoc_metadata:
-                                mdoc_for_reading = None
-                                self._unseen_xml.append(transferred_file)
-                            if dc_metadata:
-                                self._unseen_xml = []
-                                if dc_metadata.get("file_extension"):
-                                    self._extension = dc_metadata["file_extension"]
-                                else:
-                                    dc_metadata["file_extension"] = self._extension
-                                dc_metadata["acquisition_software"] = (
-                                    self._context._acquisition_software
+                        if not dc_metadata:
+                            try:
+                                dc_metadata = self._context.gather_metadata(
+                                    mdoc_for_reading
+                                    or self._xml_file(transferred_file),
+                                    environment=self._environment,
                                 )
-                                self.notify(
-                                    {
-                                        "form": dc_metadata,
-                                    }
+                            except KeyError as e:
+                                logger.error(
+                                    f"Metadata gathering failed with a key error for key: {e.args[0]}"
                                 )
+                                raise e
+                        if not dc_metadata or not self._force_mdoc_metadata:
+                            mdoc_for_reading = None
+                            self._unseen_xml.append(transferred_file)
+                        if dc_metadata:
+                            self._unseen_xml = []
+                            if dc_metadata.get("file_extension"):
+                                self._extension = dc_metadata["file_extension"]
+                            else:
+                                dc_metadata["file_extension"] = self._extension
+                            dc_metadata["acquisition_software"] = (
+                                self._context._acquisition_software
+                            )
+                            self.notify(
+                                {
+                                    "form": dc_metadata,
+                                }
+                            )
                 elif isinstance(
                     self._context,
                     (

src/murfey/client/contexts/atlas.py

@@ -0,0 +1,51 @@
+import logging
+from pathlib import Path
+from typing import Optional
+
+import requests
+
+from murfey.client.context import Context
+from murfey.client.contexts.spa import _get_source
+from murfey.client.contexts.spa_metadata import _atlas_destination
+from murfey.client.instance_environment import MurfeyInstanceEnvironment
+from murfey.util.api import url_path_for
+from murfey.util.client import authorised_requests, capture_post
+
+logger = logging.getLogger("murfey.client.contexts.spa_metadata")
+
+requests.get, requests.post, requests.put, requests.delete = authorised_requests()
+
+
+class AtlasContext(Context):
+    def __init__(self, acquisition_software: str, basepath: Path):
+        super().__init__("Atlas", acquisition_software)
+        self._basepath = basepath
+
+    def post_transfer(
+        self,
+        transferred_file: Path,
+        environment: Optional[MurfeyInstanceEnvironment] = None,
+        **kwargs,
+    ):
+        super().post_transfer(
+            transferred_file=transferred_file,
+            environment=environment,
+            **kwargs,
+        )
+
+        if (
+            environment
+            and "Atlas_" in transferred_file.stem
+            and transferred_file.suffix == ".mrc"
+        ):
+            source = _get_source(transferred_file, environment)
+            if source:
+                transferred_atlas_name = (
+                    _atlas_destination(environment, source, transferred_file)
+                    / environment.samples[source].atlas.parent
+                    / transferred_file.name
+                )
+                capture_post(
+                    f"{str(environment.url.geturl())}{url_path_for('session_control.spa_router', 'make_atlas_jpg', session_id=environment.murfey_session)}",
+                    json={"atlas_mrc": transferred_atlas_name},
+                )

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)

tests/client/test_analyser.py

@@ -3,6 +3,7 @@
 import pytest
 
 from murfey.client.analyser import Analyser
+from murfey.client.contexts.atlas import AtlasContext
 from murfey.client.contexts.clem import CLEMContext
 from murfey.client.contexts.spa import SPAModularContext
 from murfey.client.contexts.spa_metadata import SPAMetadataContext
@@ -28,7 +29,7 @@
     ["visit/FoilHole_01234_fractions.tiff", SPAModularContext],
     ["visit/FoilHole_01234_EER.eer", SPAModularContext],
     # SPA metadata
-    ["atlas/atlas.mrc", SPAMetadataContext],
+    ["atlas/atlas.mrc", AtlasContext],
     ["visit/EpuSession.dm", SPAMetadataContext],
     ["visit/Metadata/GridSquare.dm", SPAMetadataContext],
     # CLEM LIF file