Added default is_manual_meas in standards acquisition runner

Author: Andrea-gm

autoemx/runners/batch_acquire_experimental_stds.py

@@ -96,6 +96,7 @@ def batch_acquire_experimental_stds(
     development_mode: bool = False,
     verbose: bool = True,
     exp_std_dir: Optional[str] = None,
+    is_manual_meas: bool = False,
 ) -> List[Optional[EMXSp_Composition_Analyzer]]:
     """
     Batch acquisition (and optional quantification) of X-ray spectra for a list of powder samples.
@@ -210,7 +211,9 @@ def batch_acquire_experimental_stds(
     exp_std_dir : str, optional
         Directory where experimental standard results are saved.  
         Default is `None`.
-            
+    is_manual_meas : bool, optional
+        If True, all samples are measured in manual navigation mode unless overridden by 'is_manual_meas' in the sample dict. Default is False.
+
     Returns
     -------
     results : list(EMXSp_Composition_Analyzer)
@@ -264,11 +267,12 @@ def batch_acquire_experimental_stds(
     for std_sample in stds:
         # --- Sample configuration
 
+
         sample_ID = std_sample['ID']
         formula = std_sample['formula']
         center_pos = std_sample['pos']
         sample_type = std_sample['sample_type']
-        is_manual_meas = std_sample['is_manual_meas']
+        is_manual_meas = std_sample.get('is_manual_meas', is_manual_meas)
         els_to_use_for_mean_PB_calc = std_sample.get('els_to_use_for_mean_PB_calc', None)
 
         print_double_separator()

autoemx/scripts/Microscope calibration and standards/Run_Experimental_Standard_Collection.py

@@ -40,9 +40,9 @@
 # =============================================================================
 
 std_list = [
-    {'ID': 'Al','formula': 'Al', 'pos': (26.263,-21.261), 'sample_type': 'bulk', 'is_manual_meas' : False},
+    {'ID': 'Al','formula': 'Al', 'pos': (26.263,-21.261), 'sample_type': 'bulk'},
     # {'ID': 'Al2O3_prec_BM','formula': 'Al2O3', 'pos': (-38.829, 40.011), 'sample_type': 'powder', 'is_manual_meas' : False},
-    {'ID': 'Pt','formula': 'Pt0.99 O0.1', 'pos': (), 'sample_type': 'bulk', 'els_to_use_for_mean_PB_calc' : ['all'],'is_manual_meas' : False},
+    {'ID': 'Pt','formula': 'Pt0.99 O0.1', 'pos': (), 'sample_type': 'bulk', 'els_to_use_for_mean_PB_calc' : ['all'],'is_manual_meas' : True},
 ]
 # els_to_use_for_mean_PB_calc: elements to include as standards; default is ["all"] if sample is "bulk", None otherwise. (all elements/lines). Use ["Fe", "O"] for specific elements, []/["none"] for none.
 
@@ -52,6 +52,8 @@
 working_distance = 8.5 #mm
 is_auto_substrate_detection = False
 
+is_manual_meas = False # If True, all samples are measured in manual navigation mode. Set to False to use automatic navigation for all samples. This can be overridden on a per-sample basis by setting 'is_manual_meas' in the sample dict.
+
 fit_during_collection= True
 update_std_library = True
 # If True, writes fitted corrected PB reference values into EDS_Stds_{voltage}keV.json.
@@ -138,6 +140,7 @@
     spectrum_lims=spectrum_lims,
     use_instrument_background=use_instrument_background,
     min_bckgrnd_cnts=min_bckgrnd_cnts,
+    is_manual_meas=is_manual_meas,
     fit_during_collection= fit_during_collection,
     update_std_library = update_std_library,
     is_auto_substrate_detection=is_auto_substrate_detection,