Merge branch 'main' into ph-peak-for-sector-alignment

Author: rettigl

.cspell/custom-dictionary.txt

@@ -99,13 +99,17 @@ dtype
 dtypes
 easimon
 ecalibdict
-electronanalyser
+elab
+elabapi
+elabid
+electronanalyzer
 Elektronen
 endstation
 energycal
 energycalfolder
 ENERGYDISPERSION
 ENOSPC
+entityid
 equiscale
 Eref
 errorbar
@@ -266,6 +270,7 @@ ontop
 OPCPA
 openmp
 OPTICALDELAY
+orcid
 otherax
 packetcoders
 Pandoc
@@ -340,6 +345,7 @@ sdir
 segs
 setp
 sfile
+sharelink
 shutil
 Sixten
 sohail
@@ -373,6 +379,7 @@ toctree
 tofseg
 tqdm
 traceseg
+trarpes
 trseg
 Tsec
 txtsize
@@ -385,6 +392,7 @@ ufunc
 unbinned
 uncategorised
 undoc
+userid
 utime
 varnames
 venv

README.md

@@ -1,3 +1,7 @@
+<h1 align="center">
+<img src="docs/_static/logo.png" width="200">
+</h1><br>
+
 [![Documentation Status](https://github.com/OpenCOMPES/sed/actions/workflows/documentation.yml/badge.svg)](https://opencompes.github.io/docs/sed/stable/)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.github.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 ![](https://github.com/OpenCOMPES/sed/actions/workflows/linting.yml/badge.svg?branch=main)

docs/_static/favicon.ico

@@ -13,7 +13,7 @@
 
 import tomlkit
 
-from sed import __version__
+from sed import __version__  # type: ignore[attr-defined]
 
 sys.path.insert(0, os.path.abspath(".."))
 
@@ -105,6 +105,9 @@ def _get_project_meta():
 #
 html_theme = "pydata_sphinx_theme"
 
+html_logo = "_static/logo.png"
+html_favicon = "_static/favicon.ico"
+
 html_theme_options = {
     "github_url": "https://github.com/OpenCOMPES/sed",
     "primary_sidebar_end": ["indices.html"],

docs/_static/logo.png

@@ -29,6 +29,10 @@ MpesLoader
    :members:
    :undoc-members:
 
+.. automodule:: sed.loader.mpes.metadata
+   :members:
+   :undoc-members:
+
 FlashLoader
 ###################################################
 .. automodule:: sed.loader.flash.loader

docs/conf.py

@@ -29,8 +29,9 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 dependencies = [
-    "bokeh>=2.4.2",
+    "bokeh>=2.4.2,<3.7.0",
     "dask>=2021.12.0,<2024.8",
+    "elabapi-python>=5.0",
     "fastdtw>=0.3.4",
     "h5py>=3.6.0",
     "ipympl>=0.9.1",
@@ -43,8 +44,8 @@ dependencies = [
     "pandas>=1.4.1",
     "photutils<2.0",
     "psutil>=5.9.0",
-    "pynxtools-mpes>=0.2.0",
-    "pynxtools>=0.9.0",
+    "pynxtools-mpes>=0.2.2",
+    "pynxtools>=0.10.1",
     "pyyaml>=6.0.0",
     "scipy>=1.8.0",
     "symmetrize>=0.5.5",
@@ -95,8 +96,8 @@ all = [
 
 [tool.coverage.report]
 omit = [
-    "config.py",
-    "config-3.py",
+    "./config.py",
+    "./config-3.py",
 ]
 
 [tool.ruff]

docs/sed/loader.rst

@@ -2004,9 +2004,9 @@ def gather_calibration_metadata(self, calibration: dict = None) -> dict:
         metadata["calibration"] = calibration
         # create empty calibrated axis entries, if they are not present.
         if "kx_axis" not in metadata["calibration"]:
-            metadata["calibration"]["kx_axis"] = 0
+            metadata["calibration"]["kx_axis"] = 0.0
         if "ky_axis" not in metadata["calibration"]:
-            metadata["calibration"]["ky_axis"] = 0
+            metadata["calibration"]["ky_axis"] = 0.0
 
         return metadata
 

pyproject.toml

@@ -6,9 +6,7 @@
   "/ENTRY[entry]/experiment_institution": "Deutsches Elektronen-Synchrotron DESY",
   "/ENTRY[entry]/experiment_facility": "Free-Electron Laser FLASH",
   "/ENTRY[entry]/experiment_laboratory": "@attrs:metadata/creationLocation",
-  "/ENTRY/entry_identifier": {
-    "identifier":"@attrs:metadata/pid"
-  },
+  "/ENTRY/identifierNAME[entry_identifier]": "@attrs:metadata/pid",
   "/ENTRY[entry]/USER[user0]": {
     "name": "!@attrs:metadata/principalInvestigator",
     "role": "Principal investigator",
@@ -48,7 +46,7 @@
       "value/@units": "@attrs:metadata/scientificMetadata/sample/sample_pressure/unit"
     }
   },
-  "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]": {
+  "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYZER[electronanalyzer]": {
     "description": "HEXTOF Momentum Microscope",
     "device_information": {
       "vendor": "None",
@@ -78,7 +76,7 @@
       "type": "estimated"
     }
   },
-  "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/COLLECTIONCOLUMN[collectioncolumn]": {
+  "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYZER[electronanalyzer]/COLLECTIONCOLUMN[collectioncolumn]": {
     "projection": "@attrs:metadata/scientificMetadata/Collection/projection",
     "scheme": "momentum dispersive",
     "lens_mode": "@attrs:metadata/scientificMetadata/Collection/lens_mode",
@@ -107,19 +105,18 @@
       }
     }
   },
-  "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]": {
+  "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYZER[electronanalyzer]/ENERGYDISPERSION[energydispersion]": {
     "pass_energy": "@attrs:metadata/scientificMetadata/Collection/tof_voltage",
     "pass_energy/@units": "V",
     "scheme": "tof",
     "tof_distance": 0.8,
     "tof_distance/@units": "m"
   },
-  "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/DETECTOR[detector]": {
+  "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYZER[electronanalyzer]/ELECTRON_DETECTOR[detector]": {
     "amplifier_type": "MCP",
-    "detector_type": "DLD",
-    "sensor_pixels": [2024, 2048]
+    "detector_type": "DLD"
   },
-  "/ENTRY[entry]/INSTRUMENT[instrument]/sourceTYPE[source_probe]": {
+  "/ENTRY[entry]/INSTRUMENT[instrument]/source_probe": {
     "name": "@attrs:metadata/scientificMetadata/Source/name",
     "probe": "@attrs:metadata/scientificMetadata/Source/probe",
     "type": "@attrs:metadata/scientificMetadata/Source/type",
@@ -128,7 +125,7 @@
     "frequency/@units": "@attrs:metadata/scientificMetadata/Source/repetition_rate/unit",
     "associated_beam": "/entry/instrument/beam_probe"
   },
-  "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_probe]": {
+  "/ENTRY[entry]/INSTRUMENT[instrument]/beam_probe": {
     "distance": 0.0,
     "distance/@units": "mm",
     "incident_energy": "@attrs:metadata/scientificMetadata/Source/photon_energy/value",
@@ -146,16 +143,16 @@
     "energy_dispersion": "@attrs:metadata/scientificMetadata/Source/dispersion/value",
     "energy_dispersion/@units": "@attrs:metadata/scientificMetadata/Source/dispersion/unit"
   },
-  "/ENTRY[entry]/INSTRUMENT[instrument]/sourceTYPE[source_pump]": {
+  "/ENTRY[entry]/INSTRUMENT[instrument]/source_pump": {
     "name": "PIGLET @ FLASH @ DESY",
     "probe": "visible light",
     "type": "Optical Laser",
     "mode": "Single Bunch",
-    "frequency": 1000,
+    "frequency": 1000.0,
     "frequency/@units": "kHz",
     "associated_beam": "/entry/instrument/beam_pump"
   },
-  "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_pump]": {
+  "/ENTRY[entry]/INSTRUMENT[instrument]/beam_pump": {
     "distance": 0.0,
     "distance/@units": "mm",
     "incident_wavelength": "@attrs:metadata/scientificMetadata/Laser/wavelength/value",
@@ -195,7 +192,7 @@
     "gas_pressure_env": {
       "pressure_gauge": "@link:/entry/instrument/pressure_gauge"
     },
-    "bias": {
+    "bias_env": {
       "voltmeter": "@link:/entry/instrument/manipulator/sample_bias_voltmeter"
     }
   },
@@ -207,6 +204,6 @@
     "data/@units": "counts",
     "AXISNAME[*]": "@data:*.data",
     "AXISNAME[*]/@units": "@data:*.unit",
-    "energy/@type": "@attrs:metadata/energy_calibration/calibration/energy_scale"
+    "AXISNAME[energy]/@type": "@attrs:metadata/energy_calibration/calibration/energy_scale"
   }
 }