Merge remote-tracking branch 'origin/shift_energy_axis' into develop

src/specsscan/config/default.yaml

@@ -2,6 +2,9 @@
 data_path: ""
 # option to enable nested progress bars
 enable_nested_progress_bar: false
+# option to shift by photon energy if available
+shift_by_photon_energy: false
+
 # dictionary containing parameters passed to the SpecsAnalyzer. Will be completed by the SpecsAnalyzer default config parameters
 spa_params:
   apply_fft_filter: false

src/specsscan/config/example_config_FHI.yaml

@@ -2,6 +2,8 @@
 data_path: "path/to/data"
 # option to enable nested progress bars
 enable_nested_progress_bar: false
+# option to shift by photon energy if available
+shift_by_photon_energy: true
 
 # dictionary containing renaming rules for axis names (to change the name in the xarrays)
 coordinate_mapping:
@@ -25,6 +27,17 @@ coordinate_depends:
   Y: "/entry/sample/transformations/trans_y"
   Z: "/entry/sample/transformations/trans_z"
 
+# dictionary of axis labels for the different axes
+coordinate_labels:
+  Ekin: "Kinetic Energy"
+  Angle: "Analyzer Dispersion"
+  polar: "Sample Polar"
+  tilt: "Sample Tilt"
+  azimuth: "Sample Azimuth"
+  X: "X Translation"
+  Y: "Y Translation"
+  Z: "Z Translation"
+
 # dictionary containing units for the respective axes
 units:
   angular0: "degree"

src/specsscan/core.py

@@ -244,6 +244,7 @@ def load_scan(
         # rename coords and store mapping information, if available
         coordinate_mapping = self._config.get("coordinate_mapping", {})
         coordinate_depends = self._config.get("coordinate_depends", {})
+        coordinate_labels = self._config.get("coordinate_labels", {})
         rename_dict = {
             k: coordinate_mapping[k] for k in coordinate_mapping.keys() if k in res_xarray.dims
         }
@@ -252,6 +253,11 @@ def load_scan(
             for k in coordinate_depends.keys()
             if k in res_xarray.dims
         }
+        label_dict = {
+            rename_dict.get(k, k): coordinate_labels[k]
+            for k in coordinate_depends.keys()
+            if k in res_xarray.dims
+        }
 
         # store data for resolved axis coordinates
         for axis in res_xarray.dims:
@@ -266,10 +272,12 @@ def load_scan(
                 slow_axes.remove(k)
                 slow_axes.add(v)
         self._scan_info["coordinate_depends"] = depends_dict
+        self._scan_info["coordinate_label"] = label_dict
 
         for name in res_xarray.dims:
             try:
                 res_xarray[name].attrs["unit"] = self._config["units"][name]
+                res_xarray[name].attrs["long_name"] = label_dict[name]
             except KeyError:
                 pass
 
@@ -293,6 +301,32 @@ def load_scan(
             **{"conversion_parameters": conversion_metadata},
         )
 
+        # shift energy axis
+        photon_energy = 0.0
+        try:
+            photon_energy = self.metadata["elabFTW"]["laser_status"]["probe_photon_energy"]
+        except KeyError:
+            try:
+                photon_energy = self.metadata["elabFTW"]["laser_status"]["probe_photon_energy"]
+            except KeyError:
+                pass
+
+        self.metadata["scan_info"]["reference_energy"] = "vacuum level"
+        if photon_energy and self._config["shift_by_photon_energy"]:
+            logger.info(f"Shifting energy axis by photon energy: -{photon_energy} eV")
+            res_xarray = res_xarray.assign_coords(
+                {
+                    rename_dict["Ekin"]: (
+                        rename_dict["Ekin"],
+                        res_xarray[rename_dict["Ekin"]].data - photon_energy,
+                        res_xarray[rename_dict["Ekin"]].attrs,
+                    ),
+                },
+            )
+            self.metadata["scan_info"]["reference_energy"] = "Fermi edge"
+            self.metadata["scan_info"]["coordinate_label"][rename_dict["Ekin"]] = "E-E_F"
+            res_xarray[rename_dict["Ekin"]].attrs["long_name"] = "E-E_F"
+
         res_xarray.attrs["metadata"] = self.metadata
         self._result = res_xarray
 

src/specsscan/helpers.py

@@ -2,6 +2,7 @@
 from __future__ import annotations
 
 import datetime as dt
+import importlib
 import logging
 from pathlib import Path
 from typing import Any
@@ -410,6 +411,11 @@ def handle_meta(
         complete_dictionary(scan_info, lut_meta),
     )  # merging dictionaries
 
+    # store program version
+    metadata["scan_info"]["program_name"] = "specsanalyzer"
+    metadata["scan_info"]["program_version"] = importlib.metadata.version("specsanalyzer")
+
+    # timing
     logger.info("Collecting time stamps...")
     if "time" in metadata["scan_info"]:
         time_list = [metadata["scan_info"]["time"][0], metadata["scan_info"]["time"][-1]]