Fix bug causing empty runs to be subtracted twice

This Commit fixes a bug in Polaris.focus that resulted in empty runs to be subtracted twice if the user specifies a sample_empty, the function would subtract first the empty runs specified in the config maps, then the runs specified in sample_empty.

re: #27699

docs/source/release/v4.3.0/diffraction.rst

@@ -39,6 +39,7 @@ Powder Diffraction
 ------------------
 
 - A bug has been fixed that prevented unicode strings being given as a lim file directory in polaris create_total_scattering_pdf merging banks.
+- A bug has been fixed that caused empty runs to be subtracted twice when specifying `sample_empty` in `Polaris.focus`.
 
 Engineering Diffraction
 -----------------------

scripts/Diffraction/isis_powder/routines/focus.py

@@ -32,13 +32,14 @@ def _focus_one_ws(input_workspace, run_number, instrument, perform_vanadium_norm
     if perform_vanadium_norm:
         _test_splined_vanadium_exists(instrument, run_details)
 
-    # Subtract empty instrument runs, as long as this run isn't an empty and user hasn't turned empty subtraction off
-    if not common.runs_overlap(run_number, run_details.empty_runs) and instrument.should_subtract_empty_inst():
+    # Subtract empty instrument runs, as long as this run isn't an empty, user hasn't turned empty subtraction off, or
+    # The user has not supplied a sample empty
+    is_run_empty = common.runs_overlap(run_number, run_details.empty_runs)
+    if not is_run_empty and instrument.should_subtract_empty_inst() and not run_details.sample_empty:
         input_workspace = common.subtract_summed_runs(ws_to_correct=input_workspace, instrument=instrument,
                                                       empty_sample_ws_string=run_details.empty_runs)
-
-    # Subtract a sample empty if specified
-    if run_details.sample_empty:
+    elif run_details.sample_empty:
+        # Subtract a sample empty if specified
         input_workspace = common.subtract_summed_runs(ws_to_correct=input_workspace, instrument=instrument,
                                                       empty_sample_ws_string=run_details.sample_empty,
                                                       scale_factor=instrument._inst_settings.sample_empty_scale)