Merge pull request #220 from FAIRmat-NFDI/xps-fixes

Hotfixes for XPS reader

examples/xps/eln_data_sle.yaml

@@ -15,7 +15,7 @@ user:
   address: Lukas Pielsticker
   orcid: 0000-0001-9361-8333
   email: [email protected]
-Instrument:
+instrument:
   device_information:
     vendor: SPECS GmbH
     model: Custom NAP-XPS instrument
@@ -36,19 +36,19 @@ Instrument:
     distance:
       value: 0.0
       unit: mm
-  Electronanalyser:
+  analyser:
     description: hemispherical
     device_information:
       vendor: SPECS GmbH
       model: PHOIBOS 150 NAP
       identifier: null
-    Collectioncolumn:
+    collectioncolumn:
       scheme: angular dispersive
       device_information:
         vendor: SPECS GmbH
         model: PHOIBOS 150 NAP
         identifier: null
-    Energydispersion:
+    energydispersion:
       scheme: hemispherical
       diameter:
         unit: mm
@@ -57,14 +57,14 @@ Instrument:
         vendor: SPECS GmbH
         model: PHOIBOS 150
         identifier: null
-    Detector:
+    detector:
       amplifier_type: channeltron
-      detector_type: Multi-anode   
+      detector_type: Multi-anode
       device_information:
         vendor: Surface Concept GmbH
         model: 1D-DLD detector
         identifier: null
-  Manipulator:
+  manipulator:
     device_information:
       vendor: SPECS GmbH
       model: 5-axis manipulator
@@ -84,15 +84,15 @@ Instrument:
       heater_power:
         value: 0.0
         unit: W
-      Pid:
+      pid:
         setpoint:
           value: 298.0
           unit: K
     cryostat:
       name: null
       physical_quantity: null
       type: null
-      Pid:
+      pid:
         setpoint: null
     drain_current_amperemeter:
       name: Amperemeter 1.0
@@ -113,7 +113,7 @@ Instrument:
       name: XPS sample potentiostat
       physical_quantity: voltage
       type: potentiostat
-      Pid:
+      pid:
         setpoint:
           value: 0.0
           unit: V
@@ -139,13 +139,13 @@ Instrument:
       value:
         value: null
         unit: null
-Sample:
+sample:
   name: Polycristalline Au foil
   sample_id: S718
   atom_types: Au
   physical_form: foil
   situation: vacuum
-  Substance:
+  substance:
     name: Au
     molecular_mass:
       value: 196.96657

pynxtools/dataconverter/readers/xps/reader.py

@@ -112,7 +112,7 @@ def get_entries_and_detectors(config_dict, xps_data_dict):
                         # Iteration over scan
                         for data_var in data.data_vars:
                             if chan_count in data_var:
-                                detector_num = data_var.split("_chan_")[-1]
+                                detector_num = data_var.split(chan_count)[-1]
                                 detector_nm = f"detector{detector_num}"
                                 DETECTOR_SET.add(detector_nm)
             except AttributeError:
@@ -144,9 +144,10 @@ def fill_data_group(key, key_part, entries_values, config_dict, template):
         data_group_key = data_field_key.rsplit("/data", 1)[0]
 
         if key_part == "energy":
-            energy_field_key = f"{data_group_key}/energy"
+            # Here, we need to take here if the data/entry is
+            # written directly in the future.
+            energy_field_key = data_group_key
             energy = np.array(xr_data.coords["energy"].values)
-            print(energy)
             template[energy_field_key] = energy
 
         else:
@@ -208,7 +209,7 @@ def fill_detector_group(key, entries_values, config_dict, xps_data_dict, templat
 
         for data_var in data_vars:
             if chan_count in data_var:
-                detector_num = data_var.split("_chan_")[-1]
+                detector_num = data_var.split(chan_count)[-1]
                 detector_nm = f"detector{detector_num}"
                 detector_scans[detector_nm] += [xr_data[data_var].data]
                 cycle_scan_num = data_var.split(chan_count)[0]
@@ -244,19 +245,21 @@ def fill_template_with_value(key, value, template):
     if value is None or str(value) == "None":
         return
 
-    # Do for all entry names
-    for entry in ENTRY_SET:
-        atom_types: List = []
-        if "chemical_formula" in key:
-            atom_types = list(extract_atom_types(value))
+    atom_types: List = []
+    if "chemical_formula" in key:
+        atom_types = list(extract_atom_types(value))
 
-        if isinstance(value, datetime.datetime):
-            value = value.isoformat()
+    if isinstance(value, datetime.datetime):
+        value = value.isoformat()
 
-        elif isinstance(value, dict) and LINK_TOKEN in value:
-            link_text = value[LINK_TOKEN]
-            link_text = link_text.replace("entry", f"{entry}")
-            value = {LINK_TOKEN: link_text}
+    elif isinstance(value, dict) and LINK_TOKEN in value:
+        initial_link_text = value[LINK_TOKEN]
+
+    # Do for all entry names
+    for entry in ENTRY_SET:
+        if isinstance(value, dict) and LINK_TOKEN in value:
+            # Reset link to original
+            value[LINK_TOKEN] = initial_link_text.replace("entry", f"{entry}")
 
         modified_key = key.replace("[entry]", f"[{entry}]")
 
@@ -273,8 +276,8 @@ def fill_template_with_value(key, value, template):
                         # link.
                         link_text = link_text.replace("detector", f"{detector}")
                         value = {LINK_TOKEN: link_text}
-
                 template[detr_key] = value
+
         else:
             template[modified_key] = value
 

pynxtools/dataconverter/readers/xps/sle/sle_specs.py

@@ -278,7 +278,7 @@ def _update_xps_dict_with_spectrum(self, spectrum, key_map):
         channels = [key for key in spectrum["data"] if "cps_ch_" in key]
         for channel in channels:
             ch_no = channel.rsplit("_")[-1]
-            channel_key = f"{scan_key}_chan_{ch_no}"
+            channel_key = f"{scan_key}_chan{ch_no}"
             detector_data_key = (
                 f"{path_map['detector']}/{detector_data_key_child}"
                 f"_channels_Channel_{ch_no}/counts"

pynxtools/dataconverter/readers/xps/txt/txt_scienta.py

@@ -206,7 +206,7 @@ def _update_xps_dict_with_spectrum(self, spectrum, key_map):
         )
 
         # Write channel data to 'data'.
-        channel_key = f"{scan_key}_chan_0"
+        channel_key = f"{scan_key}_chan0"
         self._xps_dict["data"][entry][channel_key] = xr.DataArray(
             data=intensity, coords={"energy": energy}
         )