Moved CLEM context determination logic to the start of the '_find_context' function, as it conflicts with some of the metadata determindation logic for SPA and Tomo

Author: tieneupin

src/murfey/client/analyser.py

@@ -118,21 +118,6 @@ def _find_context(self, file_path: Path) -> bool:
         in the Context classes themselves.
         """
         logger.debug(f"Finding context using file {str(file_path)!r}")
-        if "atlas" in file_path.parts:
-            self._context = SPAMetadataContext("epu", self._basepath)
-            return True
-
-        if "Metadata" in file_path.parts or file_path.name == "EpuSession.dm":
-            self._context = SPAMetadataContext("epu", self._basepath)
-            return True
-        elif (
-            "Batch" in file_path.parts
-            or "SearchMaps" in file_path.parts
-            or "Thumbnails" in file_path.parts
-            or file_path.name == "Session.dm"
-        ):
-            self._context = TomographyMetadataContext("tomo", self._basepath)
-            return True
 
         # CLEM workflow checks
         # Look for LIF and XLIF files
@@ -141,9 +126,9 @@ def _find_context(self, file_path: Path) -> bool:
             return True
         # Look for TIFF files associated with CLEM workflow
         # Leica's autosave mode seems to name the TIFFs in the format
-        # PostionXX--ZXX-CXX.tif
+        # PostionXX--ZXX--CXX.tif
         if (
-            "--" in file_path.name
+            all(pattern in file_path.name for pattern in ("--Z", "--C"))
             and file_path.suffix in (".tiff", ".tif")
             and self._environment
         ):
@@ -159,6 +144,22 @@ def _find_context(self, file_path: Path) -> bool:
                 return True
 
         # Tomography and SPA workflow checks
+        if "atlas" in file_path.parts:
+            self._context = SPAMetadataContext("epu", self._basepath)
+            return True
+
+        if "Metadata" in file_path.parts or file_path.name == "EpuSession.dm":
+            self._context = SPAMetadataContext("epu", self._basepath)
+            return True
+        elif (
+            "Batch" in file_path.parts
+            or "SearchMaps" in file_path.parts
+            or "Thumbnails" in file_path.parts
+            or file_path.name == "Session.dm"
+        ):
+            self._context = TomographyMetadataContext("tomo", self._basepath)
+            return True
+
         split_file_stem = file_path.stem.split("_")
         if split_file_stem:
             if split_file_stem[-1] == "gain":