also xrm files

Author: stephen-riggs

src/murfey/client/analyser.py

@@ -112,7 +112,11 @@ def _find_extension(self, file_path: Path) -> bool:
                 self._extension = Path(subframe_path).suffix
                 return True
         # Check for LIF files and TXRM files separately
-        elif file_path.suffix == ".lif" or file_path.suffix == ".txrm":
+        elif (
+            file_path.suffix == ".lif"
+            or file_path.suffix == ".txrm"
+            or file_path.suffix == ".xrm"
+        ):
             self._extension = file_path.suffix
             return True
         return False
@@ -140,7 +144,7 @@ def _find_context(self, file_path: Path) -> bool:
             return True
 
         # SXT workflow checks
-        if file_path.suffix == ".txrm":
+        if file_path.suffix in (".txrm", ".xrm"):
             self._context = SXTContext("zeiss", self._basepath, self._token)
             return True
 

src/murfey/client/contexts/sxt.py

@@ -57,19 +57,14 @@ def register_sxt_data_collection(
                 "data_collection_tag": tilt_series,
                 "source": str(self._basepath),
                 "tag": tilt_series,
+                "pixel_size_on_image": str(
+                    data_collection_parameters.get("pixel_size_on_image", 100)
+                ),
+                "image_size_x": data_collection_parameters.get("image_size_x", 0),
+                "image_size_y": data_collection_parameters.get("image_size_y", 0),
+                "magnification": data_collection_parameters.get("magnification", 0),
+                "voltage": 0,
             }
-
-            # Once mdoc parameters are known register processing jobs
-            dc_data.update(
-                {
-                    "pixel_size_on_image": data_collection_parameters.get(
-                        "pixel_size_on_image"
-                    ),
-                    "image_size_x": data_collection_parameters.get("image_size_x"),
-                    "image_size_y": data_collection_parameters.get("image_size_y"),
-                    "magnification": data_collection_parameters.get("magnification"),
-                }
-            )
             capture_post(
                 base_url=str(environment.url.geturl()),
                 router_name="workflow.router",