add test case for vms data analysis

.gitignore

@@ -203,6 +203,7 @@ cython_debug/
 !examples/vms/vms_txt_export.txt
 !tests/data/scienta_txt/Ag_*.txt
 !tests/data/vms_txt_export/vms_txt_export.txt
+!tests/data/vms_analysis/FeO_analyzed_lineshapes_cols.txt
 
 build/
 .python-version

scripts/regenerate_ref_nxs_files.sh

@@ -74,6 +74,13 @@ function update_vms_txt_export_ref {
   cd ..
 }
 
+function update_vms_analysis_ref {
+  cd vms_analysis/
+  echo "Update Vamas data anaylsis export reference"
+  dataconverter dataconverter FeO* eln.yaml --reader $READER --nxdl $NXDL --ignore-undocumented --output vms_analysis.nxs
+  cd ..
+}
+
 project_dir=$(dirname $(dirname $(realpath $0)))
 cd $project_dir/tests/data
 
@@ -86,4 +93,5 @@ update_specs_xml_ref
 update_specs_xy_ref
 update_vms_irregular_ref
 update_vms_regular_ref
-update_vms_txt_export_ref
+update_vms_txt_export_ref
+update_vms_analysis_ref

src/pynxtools_xps/models/backgrounds.py

@@ -26,7 +26,7 @@
 class LinearBackground:
     """Linear background model for XPS spectra that connects the first and last points in the y array."""
 
-    def __init__(self):
+    def __init__(self, *args):
         """
         Initialize the linear background model without predefined parameters.
         The slope and intercept will be calculated based on the input data.
@@ -76,7 +76,7 @@ def formula(self) -> str:
 class StepUp:
     """Step Up background model for XPS spectra, based on the complementary error function."""
 
-    def __init__(self, a0: float, a1: float, a2: float, a3: float):
+    def __init__(self, a0: float, a1: float, a2: float, a3: float, *args):
         """
         Initialize the Step Up background model without predefined parameters.
         """
@@ -122,7 +122,7 @@ def formula(self) -> str:
 class StepDown:
     """Step Down background model for XPS spectra, the reflection of Step Up around the edge position."""
 
-    def __init__(self, a0: float, a1: float, a2: float, a3: float):
+    def __init__(self, a0: float, a1: float, a2: float, a3: float, *args):
         """
         Initialize the Step Up background model without predefined parameters.
         """
@@ -176,7 +176,7 @@ class Shirley:
     tolerance and maximum iterations.
     """
 
-    def __init__(self) -> None:
+    def __init__(self, *args) -> None:
         """Initialize the Shirley background subtraction object."""
         pass
 
@@ -288,7 +288,7 @@ class TougaardU3:
         C (float): Shape parameter that determines the background curvature.
     """
 
-    def __init__(self, E0: float, A: float, C: float):
+    def __init__(self, E0: float, A: float, C: float, *args):
         """
         Initialize the U3 Tougaard model with the required parameters.
 
@@ -343,7 +343,9 @@ def __repr__(self) -> str:
 class TougaardU4:
     """U4 Tougaard background model for XPS spectra."""
 
-    def __init__(self, B: float, C: float, D: float, Eg: float, temp: float = 300.0):
+    def __init__(
+        self, B: float, C: float, D: float, Eg: float, temp: float = 300.0, *args
+    ):
         """
         Initialize the U4 Tougaard model with the required parameters.
 

src/pynxtools_xps/vms/casa_data_model.py

@@ -386,15 +386,17 @@ def calculate_background(self, x: np.ndarray, y: np.ndarray):
             "Shirley": Shirley,
             "Step Up": StepUp,
             "Step Down": StepDown,
+            "U 2 Tougaard": TougaardU3,
             "U 3 Tougaard": TougaardU3,
             "U 4 Tougaard": TougaardU4,
         }
 
-        leading_letters, _ = split_after_letters(self.bg_type)
-        background_params = [float(param) for param in self.cross_section]
+        background_params = [
+            float(param) for param in self.cross_section if float(param)
+        ]
 
         try:
-            background_class = backgrounds[leading_letters]
+            background_class = backgrounds[self.bg_type]
 
             try:
                 background = background_class(*background_params)