Restore the lost parameters which may be needed

Author: stephen-riggs

src/murfey/client/contexts/spa.py

@@ -265,6 +265,8 @@ def gather_metadata(
         metadata["image_size_x"] = str(int(metadata["image_size_x"]) * binning_factor)
         metadata["image_size_y"] = str(int(metadata["image_size_y"]) * binning_factor)
         metadata["motion_corr_binning"] = 1 if binning_factor_xml == 2 else 2
+        metadata["gain_ref"] = environment.gain_ref if environment else None
+        metadata["dose_per_frame"] = environment.dose_per_frame if environment else None
         metadata["symmetry"] = (environment.symmetry if environment else None) or "C1"
         metadata["eer_fractionation"] = (
             environment.eer_fractionation if environment else None

src/murfey/client/contexts/tomo.py

@@ -600,6 +600,10 @@ def gather_metadata(
                     float(mdoc_data["PixelSpacing"]) * 1e-10
                 )
             mdoc_metadata["motion_corr_binning"] = binning_factor
+            mdoc_metadata["gain_ref"] = environment.gain_ref if environment else None
+            mdoc_metadata["dose_per_frame"] = (
+                environment.dose_per_frame if environment else None
+            )
             mdoc_metadata["source"] = str(self._basepath)
             mdoc_metadata["tag"] = str(self._basepath)
             mdoc_metadata["tilt_series_tag"] = metadata_file.stem
@@ -610,6 +614,9 @@ def gather_metadata(
             mdoc_metadata["file_extension"] = (
                 f".{mdoc_data_block['SubFramePath'].split('.')[-1]}"
             )
+            mdoc_metadata["eer_fractionation"] = (
+                environment.eer_fractionation if environment else None
+            ) or 20
 
             data_file = mdoc_data_block["SubFramePath"].split("\\")[-1]
             if data_file.split(".")[-1] == "eer":

src/murfey/client/multigrid_control.py

@@ -419,6 +419,10 @@ def _start_dc(self, json, from_form: bool = False):
             json = json.get("form", {})
             # Safely convert all entries into strings, but leave None as-is
             json = {k: str(v) if v is not None else None for k, v in json.items()}
+        self._environment.dose_per_frame = json.get("dose_per_frame")
+        self._environment.gain_ref = json.get("gain_ref")
+        self._environment.symmetry = json.get("symmetry")
+        self._environment.eer_fractionation = json.get("eer_fractionation")
         source = Path(json["source"])
         context = self.analysers[source]._context
         if context: