Pynxtools update

.cspell/custom-dictionary.txt

@@ -45,7 +45,7 @@ Ekin
 elab
 elabapi
 elabid
-electronanalyser
+electronanalyzer
 elems
 endstation
 energydispersion
@@ -142,6 +142,7 @@ toctree
 tomlkit
 topfloor
 tqdm
+trarpes
 typehints
 TZCYXS
 undoc

pyproject.toml

@@ -40,8 +40,8 @@ dependencies = [
     "matplotlib>=3.5.1",
     "numpy>=1.21.6",
     "opencv-python>=4.8.1.78",
-    "pynxtools-mpes>=0.2.1",
-    "pynxtools>=0.9.3",
+    "pynxtools-mpes>=0.2.2",
+    "pynxtools>=0.10.1",
     "python-dateutil>=2.8.2",
     "pyyaml>=6.0",
     "xarray>=0.20.2",

src/specsscan/config/example_config_FHI.yaml

@@ -18,8 +18,8 @@ coordinate_mapping:
 
 # dictionary of corresponding NeXus paths for the different axes
 coordinate_depends:
-  Ekin: "/entry/instrument/electronanalyser/energydispersion/kinetic_energy"
-  Angle: "/entry/instrument/electronanalyser/transformations/analyzer_dispersion"
+  Ekin: "/entry/instrument/electronanalyzer/energydispersion/kinetic_energy"
+  Angle: "/entry/instrument/electronanalyzer/transformations/analyzer_dispersion"
   polar: "/entry/sample/transformations/sample_polar"
   tilt: "/entry/sample/transformations/sample_tilt"
   azimuth: "/entry/sample/transformations/sample_azimuth"

src/specsscan/helpers.py

@@ -348,9 +348,6 @@ def parse_info_to_dict(path: Path) -> dict:
     except FileNotFoundError as exc:
         raise FileNotFoundError("info.txt file not found.") from exc
 
-    if "DelayStage" in info_dict and "TimeZero" in info_dict:
-        info_dict["delay"] = mm_to_fs(info_dict["DelayStage"], info_dict["TimeZero"])
-
     return info_dict
 
 
@@ -411,6 +408,13 @@ def handle_meta(
         complete_dictionary(scan_info, lut_meta),
     )  # merging dictionaries
 
+    # Store delay info
+    if "DelayStage" in metadata["scan_info"] and "TimeZero" in metadata["scan_info"]:
+        metadata["scan_info"]["delay"] = mm_to_fs(
+            metadata["scan_info"]["DelayStage"],
+            metadata["scan_info"]["TimeZero"],
+        )
+
     # store program version
     metadata["scan_info"]["program_name"] = "specsanalyzer"
     metadata["scan_info"]["program_version"] = importlib.metadata.version("specsanalyzer")

tests/test_specsscan.py

@@ -318,24 +318,29 @@ def test_conversion_and_save_to_nexus():
     metadata["instrument"] = {}
     # energy resolution
     metadata["instrument"]["energy_resolution"] = 150.0
-    metadata["instrument"]["electronanalyser"] = {}
-    metadata["instrument"]["electronanalyser"]["energy_resolution"] = 120
-    metadata["instrument"]["electronanalyser"]["angular_resolution"] = 0.2
-    metadata["instrument"]["electronanalyser"]["spatial_resolution"] = 0.5
+    metadata["instrument"]["electronanalyzer"] = {}
+    metadata["instrument"]["electronanalyzer"]["energy_resolution"] = 120.0
+    metadata["instrument"]["electronanalyzer"]["angular_resolution"] = 0.2
+    metadata["instrument"]["electronanalyzer"]["spatial_resolution"] = 0.5
 
     # probe beam
     metadata["instrument"]["beam"] = {}
     metadata["instrument"]["beam"]["probe"] = {}
     metadata["instrument"]["beam"]["probe"]["incident_energy"] = 21.7
+    metadata["instrument"]["beam"]["probe"]["frequency"] = 500.0
+    metadata["instrument"]["beam"]["probe"]["incident_energy_spread"] = 0.11
+    metadata["instrument"]["beam"]["probe"]["pulse_duration"] = 20.0
+    metadata["instrument"]["beam"]["probe"]["incident_polarization"] = [1, 1, 0, 0]
+    metadata["instrument"]["beam"]["probe"]["extent"] = [80.0, 80.0]
 
     # sample
     metadata["sample"] = {}
     metadata["sample"]["name"] = "Name"
 
     metadata["scan_info"] = {}
     metadata["scan_info"]["trARPES:XGS600:PressureAC:P_RD"] = 2.5e-11
-    metadata["scan_info"]["trARPES:Carving:TEMP_RBV"] = 70
-    metadata["scan_info"]["trARPES:Sample:Measure"] = 0
+    metadata["scan_info"]["trARPES:Carving:TEMP_RBV"] = 70.0
+    metadata["scan_info"]["trARPES:Sample:Measure"] = 0.0
     res_xarray = sps.load_scan(
         scan=1496,
         path=data_dir,

tutorial/3_specsscan_conversion_to_NeXus.ipynb

@@ -66,11 +66,12 @@
     "metadata['instrument'] = {}\n",
     "# energy resolution\n",
     "metadata['instrument']['energy_resolution'] = 150.\n",
-    "metadata['instrument']['electronanalyser'] = {}\n",
-    "metadata['instrument']['electronanalyser']['energy_resolution'] = 120\n",
-    "metadata['instrument']['electronanalyser']['angular_resolution'] = 0.2\n",
-    "metadata['instrument']['electronanalyser']['spatial_resolution'] = 0.5\n",
-    "\n",
+    "metadata['instrument']['electronanalyzer'] = {}\n",
+    "metadata['instrument']['electronanalyzer']['energy_resolution'] = 120.\n",
+    "metadata['instrument']['electronanalyzer']['angular_resolution'] = 0.2\n",
+    "metadata['instrument']['electronanalyzer']['spatial_resolution'] = 0.5\n",
+    "metadata['instrument']['electronanalyzer']['slit_shape'] = \"curved slit\"\n",
+    "metadata['instrument']['electronanalyzer']['slit_size'] = 1.0\n",
     "#probe beam\n",
     "metadata['instrument']['beam']={}\n",
     "metadata['instrument']['beam']['probe']={}\n",
@@ -105,8 +106,8 @@
     "\n",
     "metadata[\"scan_info\"] = {}\n",
     "metadata[\"scan_info\"][\"trARPES:XGS600:PressureAC:P_RD\"] = 2.5E-11\n",
-    "metadata[\"scan_info\"][\"trARPES:Carving:TEMP_RBV\"] = 70\n",
-    "metadata[\"scan_info\"][\"trARPES:Sample:Measure\"] = 0\n"
+    "metadata[\"scan_info\"][\"trARPES:Carving:TEMP_RBV\"] = 70.\n",
+    "metadata[\"scan_info\"][\"trARPES:Sample:Measure\"] = 0.\n"
    ]
   },
   {
@@ -248,7 +249,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.10.16"
   }
  },
  "nbformat": 4,