Remove serialem logic

Author: stephen-riggs

src/murfey/client/analyser.py

@@ -181,30 +181,6 @@ def _find_context(self, file_path: Path) -> bool:
                     self._context = TomographyContext("tomo", self._basepath)
                     self.parameters_model = ProcessingParametersTomo
                 return True
-
-            # Files with these suffixes belong to the serial EM tomography workflow
-            if file_path.suffix in (".mrc", ".tiff", ".tif", ".eer"):
-                # Ignore batch files and search maps
-                if any(p in file_path.parts for p in ("Batch", "SearchMaps")):
-                    return False
-                # Ignore JPG files
-                if file_path.with_suffix(".jpg").is_file():
-                    return False
-                # Ignore the averaged movies written out by the Falcon
-                if (
-                    len(
-                        list(
-                            file_path.parent.glob(
-                                f"{file_path.name}*{file_path.suffix}"
-                            )
-                        )
-                    )
-                    > 1
-                ):
-                    return False
-                self._context = TomographyContext("serialem", self._basepath)
-                self.parameters_model = ProcessingParametersTomo
-                return True
         return False
 
     def post_transfer(self, transferred_file: Path):
@@ -295,12 +271,7 @@ def _analyse(self):
                             if not dc_metadata:
                                 try:
                                     dc_metadata = self._context.gather_metadata(
-                                        (
-                                            transferred_file.with_suffix(".mdoc")
-                                            if self._context._acquisition_software
-                                            == "serialem"
-                                            else self._xml_file(transferred_file)
-                                        ),
+                                        self._xml_file(transferred_file),
                                         environment=self._environment,
                                     )
                                 except NotImplementedError:

src/murfey/client/contexts/tomo.py

@@ -400,33 +400,6 @@ def _add_tomo_tilt(
             required_strings=required_strings,
         )
 
-    def _add_serialem_tilt(
-        self, file_path: Path, environment: MurfeyInstanceEnvironment | None = None
-    ) -> List[str]:
-        delimiters = ("_", "-")
-        for d in delimiters:
-            if file_path.name.count(d) > 1:
-                delimiter = d
-                break
-        else:
-            delimiter = delimiters[0]
-
-        def _extract_tilt_series(p: Path) -> str:
-            split = p.name.split(delimiter)
-            for s in split:
-                if s.isdigit():
-                    return s
-            raise ValueError(
-                f"No digits found in {p.name} after splitting on {delimiter}"
-            )
-
-        return self._add_tilt(
-            file_path,
-            lambda x: ".".join(x.name.split(delimiter)[-1].split(".")[:-1]),
-            environment=environment,
-            required_strings=[],
-        )
-
     def post_transfer(
         self,
         transferred_file: Path,
@@ -464,10 +437,8 @@ def post_transfer(
                         required_strings=kwargs.get("required_strings")
                         or required_strings,
                     )
-                elif self._acquisition_software == "serialem":
-                    completed_tilts = self._add_serialem_tilt(
-                        transferred_file, environment=environment
-                    )
+                else:
+                    logger.warning(f"Unknown data file {transferred_file}")
             if transferred_file.suffix == ".mdoc":
                 with open(transferred_file, "r") as md:
                     tilt_series = transferred_file.stem

src/murfey/client/multigrid_control.py

@@ -23,7 +23,7 @@
 from murfey.util.api import url_path_for
 from murfey.util.client import capture_delete, capture_post, get_machine_config_client
 
-log = logging.getLogger("murfey.client.mutligrid_control")
+log = logging.getLogger("murfey.client.multigrid_control")
 
 
 @dataclass

src/murfey/util/dummy_setup.py

@@ -24,7 +24,7 @@ def initialise(dummy_location: Path) -> Path:
         yaml.dump(
             {
                 "m12": {
-                    "acquisition_software": ["epu", "tomo", "serialem"],
+                    "acquisition_software": ["epu", "tomo"],
                     "data_directories": [str(detector_dir)],
                     "rsync_basepath": str(dummy_location),
                     "calibrations": {"dummy": 0},