Add skip frion (#87)

* Add skip frion

* Add useful check

* Update arrakis/rmsynth_oncuts.py

Co-authored-by: Copilot <[email protected]>

* Update arrakis/rmsynth_oncuts.py

Co-authored-by: Copilot <[email protected]>

---------

Co-authored-by: Copilot <[email protected]>

Author: AlecThomson

arrakis/process_region.py

@@ -83,7 +83,7 @@ def process_merge(args, host: str, inter_dir: str, task_runner) -> None:
             fit_function=args.fit_function,
             tt0=args.tt0,
             tt1=args.tt1,
-            ion=False,
+            ion=False,  # Always False as we don't do Frion twice
             do_own_fit=args.do_own_fit,
         )
         if not args.skip_rmsynth

arrakis/process_spice.py

@@ -133,7 +133,7 @@ def process_spice(args, host: str, task_runner: BaseTaskRunner) -> None:
             fit_function=args.fit_function,
             tt0=args.tt0,
             tt1=args.tt1,
-            ion=True,
+            ion=True if not args.skip_frion else False,
             do_own_fit=args.do_own_fit,
         )
         if not args.skip_rmsynth

arrakis/rmsynth_oncuts.py

@@ -283,7 +283,14 @@ def extract_single_spectrum(
         key = f"{stokes}_file_ion"
     else:
         key = f"{stokes}_file"
-    filename = outdir / field_dict[key]
+
+    file_stem = field_dict.get(key)
+    if file_stem is None:
+        msg = f"Key {key} not found in database entry. Check if previous step was run."
+        raise ValueError(msg)
+    else:
+        file_stem = str(file_stem)
+    filename = outdir / file_stem
     try:
         with fits.open(filename, mode="denywrite", memmap=True) as hdulist:
             hdu = hdulist[0]