Keep only a misc set of parameters and leave indexing and peakfinding to be sent in misc.

src/calng/CrystfelRunner.py

@@ -244,13 +244,7 @@ class CrystfelRunner(PythonDevice):
             .commit(),
 
             VECTOR_STRING_ELEMENT(expected)
-            .key("crystfelArgs.peakfinding")
-            .assignmentOptional()
-            .defaultValue([])
-            .commit(),
-
-            VECTOR_STRING_ELEMENT(expected)
-            .key("crystfelArgs.indexing")
+            .key("crystfelArgs.misc")
             .assignmentOptional()
             .defaultValue(
                 [
@@ -258,15 +252,6 @@ class CrystfelRunner(PythonDevice):
                     "--int-radius=3,5,7",
                     "--local-bg-radius=3",
                     "--max-res=1600",
-                ]
-            )
-            .commit(),
-
-            VECTOR_STRING_ELEMENT(expected)
-            .key("crystfelArgs.misc")
-            .assignmentOptional()
-            .defaultValue(
-                [
                     "--highres=0.4",
                 ]
             )
@@ -462,9 +447,7 @@ class CrystfelRunner(PythonDevice):
             self.get("crystfelArgs.unitcellPath"),
             "--no-mask-data",
         ]
-        if self.get("crystfelArgs.doPeakfinding"):
-            args.extend(reparse_fix_comma_mess(self.get("crystfelArgs.peakfinding")))
-        else:
+        if not self.get("crystfelArgs.doPeakfinding"):
             args.extend(
                 [
                     "--no-revalidate",  # otherwise, throws away peaks?
@@ -472,7 +455,6 @@ class CrystfelRunner(PythonDevice):
                 ]
             )
 
-        args.extend(reparse_fix_comma_mess(self.get("crystfelArgs.indexing")))
         args.extend(reparse_fix_comma_mess(self.get("crystfelArgs.misc")))
         self.set("crystfelArgs.commandline", " ".join(args))
         # TODO: cd somewhere for the indexamajig folder?