update pynxtools + plugins, use new MPES example

cf43464e · Lukas Pielsticker · 83ac7a03 · cf43464e · cf43464e · cf43464e
Commit cf43464e authored 6 months ago by Lukas Pielsticker
--- a/default_plugins.txt
+++ b/default_plugins.txt
@@ -2,7 +2,7 @@ git+https://github.com/FAIRmat-NFDI/nomad-perovskite-solar-cells-database.git@f3
 git+https://github.com/FAIRmat-NFDI/nomad-porous-materials.git@522f4a3208077f534f1c5e886527ee2104283d0b
 git+https://github.com/FAIRmat-NFDI/nomad-aitoolkit.git@b203f8eb28dc4b6771a39d5c5b7ad3d9d8583ac8
 nomad-simulations==0.0.1
-pynxtools[convert]==0.5.0
+pynxtools[convert]==0.7.0
 nomad-schema-plugin-run>=1.0.1
 nomad-schema-plugin-simulation-workflow>=1.0.1
 nomad-normalizer-plugin-bandstructure>=1.0

--- a/examples/data/mpes/E2 ARPES postprocessing.ipynb
+++ b/examples/data/mpes/E2 ARPES postprocessing.ipynb
--- a/examples/data/mpes/E4 Convert to k-space.ipynb
+++ b/examples/data/mpes/E4 Convert to k-space.ipynb
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Convert measurement angles to k-space\n",
+    "\n",
+    "In this example, we will use the NeXus format to automatically detect and read the angles from an ARPES measurement and do a k-space conversion with pyArpes."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "import warnings\n",
+    "warnings.filterwarnings(\"ignore\")\n",
+    "import numpy as np\n",
+    "\n",
+    "from arpes.io import load_data\n",
+    "from arpes.endstations.plugin.nexus import NeXusEndstation\n",
+    "from arpes.utilities.conversion import convert_to_kspace\n",
+    "\n",
+    "\n",
+    "%matplotlib inline"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Download data\n",
+    "\n",
+    "First we need to automatically download the data from [Nomad](https://nomad-lab.eu/prod/v1/api/v1/entries/xV9yMspIyXMfia6nNw3NIbnlZ91H/raw/Scan1496.nxs)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "! curl -o Scan1496.nxs https://nomad-lab.eu/prod/v1/api/v1/entries/xV9yMspIyXMfia6nNw3NIbnlZ91H/raw/Scan1496.nxs"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Load data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "Scan1496 = load_data(\"Scan1496.nxs\", location=NeXusEndstation)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Apply rotational offset from experimental geometry"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "Scan1496.S.apply_offsets({\n",
+    "    \"chi\": 19/180*np.pi,\n",
+    "})"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Subtract photon energy"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "Scan1496_shifted = Scan1496\n",
+    "Scan1496_shifted['eV'] = Scan1496_shifted['eV'] - Scan1496.attrs[\"hv\"].magnitude"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We read all metadata from the nexus file into xarray attributes for easy programmatic access."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "Scan1496_shifted.attrs"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We can easily readout interesting values including their units, e.g., the incident photon energy of the beam:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "Scan1496_shifted.attrs['instrument/beam_probe/incident_energy']"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Generate Fermi surface"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "fsmap = Scan1496_shifted.S.generic_fermi_surface(0)\n",
+    "fsmap.S.plot()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Convert into k-space"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "fsmap_converted = convert_to_kspace(\n",
+    "    fsmap,\n",
+    "    kx=np.linspace(-.6, .6, 400),\n",
+    "    ky=np.linspace(-1.2, 1.2, 400),\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "fsmap_converted.T.plot()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "Scan1496_converted = convert_to_kspace(\n",
+    "    Scan1496,\n",
+    "    kx=np.linspace(-.6, .6, 400),\n",
+    "    ky=np.linspace(-1.2, 1.2, 400),\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "Scan1496_converted.S.generic_fermi_surface(0).T.plot()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "Scan1496.loc[{\"eV\":slice(1, 1.2)}].sum(dim=\"eV\").S.plot()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "Scan1496_converted.loc[{\"eV\":slice(1, 1.2)}].sum(dim=\"eV\").S.plot()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.12"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "a164666994e9db75450cd7016dd7e51d42ea6e7c1e5e8017af1f8068ca906367"
+   }
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
+%% Cell type:markdown id: tags:
+# Convert measurement angles to k-space
+In this example, we will use the NeXus format to automatically detect and read the angles from an ARPES measurement and do a k-space conversion with pyArpes.
+%% Cell type:code id: tags:
+``` python
+import warnings
+warnings.filterwarnings("ignore")
+import numpy as np
+from arpes.io import load_data
+from arpes.endstations.plugin.nexus import NeXusEndstation
+from arpes.utilities.conversion import convert_to_kspace
+%matplotlib inline
+```
+%% Cell type:markdown id: tags:
+# Download data
+First we need to automatically download the data from [Nomad](https://nomad-lab.eu/prod/v1/api/v1/entries/xV9yMspIyXMfia6nNw3NIbnlZ91H/raw/Scan1496.nxs).
+%% Cell type:code id: tags:
+``` python
+! curl -o Scan1496.nxs https://nomad-lab.eu/prod/v1/api/v1/entries/xV9yMspIyXMfia6nNw3NIbnlZ91H/raw/Scan1496.nxs
+```
+%% Cell type:markdown id: tags:
+## Load data
+%% Cell type:code id: tags:
+``` python
+Scan1496 = load_data("Scan1496.nxs", location=NeXusEndstation)
+```
+%% Cell type:markdown id: tags:
+Apply rotational offset from experimental geometry
+%% Cell type:code id: tags:
+``` python
+Scan1496.S.apply_offsets({
+    "chi": 19/180*np.pi,
+})
+```
+%% Cell type:markdown id: tags:
+Subtract photon energy
+%% Cell type:code id: tags:
+``` python
+Scan1496_shifted = Scan1496
+Scan1496_shifted['eV'] = Scan1496_shifted['eV'] - Scan1496.attrs["hv"].magnitude
+```
+%% Cell type:markdown id: tags:
+We read all metadata from the nexus file into xarray attributes for easy programmatic access.
+%% Cell type:code id: tags:
+``` python
+Scan1496_shifted.attrs
+```
+%% Cell type:markdown id: tags:
+We can easily readout interesting values including their units, e.g., the incident photon energy of the beam:
+%% Cell type:code id: tags:
+``` python
+Scan1496_shifted.attrs['instrument/beam_probe/incident_energy']
+```
+%% Cell type:markdown id: tags:
+## Generate Fermi surface
+%% Cell type:code id: tags:
+``` python
+fsmap = Scan1496_shifted.S.generic_fermi_surface(0)
+fsmap.S.plot()
+```
+%% Cell type:markdown id: tags:
+## Convert into k-space
+%% Cell type:code id: tags:
+``` python
+fsmap_converted = convert_to_kspace(
+    fsmap,
+    kx=np.linspace(-.6, .6, 400),
+    ky=np.linspace(-1.2, 1.2, 400),
+)
+```
+%% Cell type:code id: tags:
+``` python
+fsmap_converted.T.plot()
+```
+%% Cell type:code id: tags:
+``` python
+Scan1496_converted = convert_to_kspace(
+    Scan1496,
+    kx=np.linspace(-.6, .6, 400),
+    ky=np.linspace(-1.2, 1.2, 400),
+)
+```
+%% Cell type:code id: tags:
+``` python
+Scan1496_converted.S.generic_fermi_surface(0).T.plot()
+```
+%% Cell type:code id: tags:
+``` python
+Scan1496.loc[{"eV":slice(1, 1.2)}].sum(dim="eV").S.plot()
+```
+%% Cell type:code id: tags:
+``` python
+Scan1496_converted.loc[{"eV":slice(1, 1.2)}].sum(dim="eV").S.plot()
+```
+%% Cell type:code id: tags:
+``` python
+```
--- a/examples/data/mpes/config_file_MoTe2.json
+++ b/examples/data/mpes/config_file_MoTe2.json
+{
+  "/@default": "entry",
+  "/ENTRY[entry]/@default": "data",
+  "/ENTRY[entry]/title": "@attrs:metadata/entry_title",
+  "/ENTRY[entry]/start_time": "@attrs:metadata/timing/acquisition_start",
+  "/ENTRY[entry]/experiment_institution": "Fritz Haber Institute - Max Planck Society",
+  "/ENTRY[entry]/experiment_facility": "Time Resolved ARPES",
+  "/ENTRY[entry]/experiment_laboratory": "Clean Room 4",
+  "/ENTRY/entry_identifier": {
+    "identifier":"@attrs:metadata/entry_identifier"
+  },
+  "/ENTRY[entry]/end_time": "@attrs:metadata/timing/acquisition_stop",
+  "/ENTRY[entry]/duration": "@attrs:metadata/timing/acquisition_duration",
+  "/ENTRY[entry]/duration/@units": "s",
+  "/ENTRY[entry]/collection_time": "@attrs:metadata/timing/collection_time",
+  "/ENTRY[entry]/collection_time/@units": "s",
+  "/ENTRY[entry]/USER[user]": {
+    "name": "@attrs:metadata/user0/name",
+    "role": "@attrs:metadata/user0/role",
+    "affiliation": "@attrs:metadata/user0/affiliation",
+    "address": "@attrs:metadata/user0/address",
+    "email": "@attrs:metadata/user0/email"
+  },
+  "/ENTRY[entry]/INSTRUMENT[instrument]": {
+    "name": "Time-of-flight momentum microscope equipped delay line detector, at the endstation of the high rep-rate HHG source at FHI",
+    "name/@short_name": "TR-ARPES @ FHI",
+    "energy_resolution": {
+      "resolution": 140.0,
+      "resolution/@units": "meV",
+      "physical_quantity": "energy",
+      "type": "estimated"
+    },
+    "RESOLUTION[temporal_resolution]": {
+      "resolution": 35.0,
+      "resolution/@units": "fs",
+      "physical_quantity": "time",
+      "type": "estimated"
+    },
+    "RESOLUTION[momentum_resolution]": {
+      "resolution": "@attrs:metadata/instrument/analyzer/momentum_resolution",
+      "resolution/@units": "1/angstrom",
+      "physical_quantity": "momentum",
+      "type": "estimated"
+    },
+    "pressure_gauge": {
+      "name": "sample_chamber_pressure",
+      "measurement": "pressure",
+      "value": "@attrs:metadata/file/trARPES:XGS600:PressureAC:P_RD",
+      "value/@units": "mbar"
+    },
+    "ELECTRONANALYSER[electronanalyser]": {
+      "description": "SPECS Metis 1000 Momentum Microscope",
+      "device_information": {
+        "vendor": "SPECS GmbH",
+        "model": "Metis 1000 Momentum Microscope"
+      },
+      "fast_axes": [
+        "kx",
+        "ky",
+        "E"
+      ],
+      "slow_axes": "@attrs:metadata/instrument/analyzer/slow_axes",
+      "energy_resolution": {
+        "resolution": 110.0,
+        "resolution/@units": "meV",
+        "physical_quantity": "energy",
+        "type": "estimated"
+      },
+      "momentum_resolution": {
+        "resolution": "@attrs:metadata/instrument/analyzer/momentum_resolution",
+        "resolution/@units": "1/angstrom",
+        "physical_quantity": "momentum",
+        "type": "estimated"
+      },
+      "spatial_resolution": {
+        "resolution": "@attrs:metadata/instrument/analyzer/spatial_resolution",
+        "resolution/@units": "µm",
+        "physical_quantity": "length",
+        "type": "estimated"
+      },
+      "depends_on": "/entry/instrument/electronanalyser/transformations/trans_z",
+      "TRANSFORMATIONS[transformations]": {
+        "AXISNAME[trans_z]": 4.0,
+        "AXISNAME[trans_z]/@depends_on": "rot_y",
+        "AXISNAME[trans_z]/@transformation_type": "translation",
+        "AXISNAME[trans_z]/@units": "mm",
+        "AXISNAME[trans_z]/@vector": [
+          0,
+          0,
+          1
+        ],
+        "AXISNAME[rot_y]": -115.0,
+        "AXISNAME[rot_y]/@depends_on": ".",
+        "AXISNAME[rot_y]/@transformation_type": "rotation",
+        "AXISNAME[rot_y]/@units": "degrees",
+        "AXISNAME[rot_y]/@vector": [
+          0,
+          1,
+          0
+        ]
+      }
+    }
+  },
+  "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/COLLECTIONCOLUMN[collectioncolumn]": {
+    "projection": "@attrs:metadata/instrument/analyzer/projection",
+    "scheme": "momentum dispersive",
+    "lens_mode": "@attrs:metadata/instrument/analyzer/lens_mode",
+    "extractor_voltage": "@attrs:metadata/file/KTOF:Lens:Extr:V",
+    "extractor_voltage/@units": "V",
+    "extractor_current": "@attrs:metadata/file/KTOF:Lens:Extr:I",
+    "extractor_current/@units": "µA",
+    "working_distance": 4.0,
+    "working_distance/@units": "mm",
+    "LENS_EM[lens_*{A,B,C,D,E,F,G,H,I,UCA,UFA,Foc}]": {
+      "name": "*",
+      "voltage": "@attrs:metadata/file/KTOF:Lens:*:V",
+      "voltage/@units": "V"
+    },
+    "field_aperture": {
+      "shape": "@attrs:metadata/instrument/analyzer/fa_shape",
+      "size": "@attrs:metadata/instrument/analyzer/fa_size",
+      "size/@units": "µm",
+      "POSITIONER[fa_m1]": {
+        "value": "@attrs:metadata/file/KTOF:Apertures:m1.RBV",
+        "value/@units": "mm"
+      },
+      "POSITIONER[fa_m2]": {
+        "value": "@attrs:metadata/file/KTOF:Apertures:m2.RBV",
+        "value/@units": "mm"
+      }
+    },
+    "contrast_aperture": {
+      "shape": "@attrs:metadata/instrument/analyzer/ca_shape",
+      "size": "@attrs:metadata/instrument/analyzer/ca_size",
+      "size/@units": "µm",
+      "POSITIONER[ca_m3]": {
+        "value": "@attrs:metadata/file/KTOF:Apertures:m3.RBV",
+        "value/@units": "mm"
+      }
+    }
+  },
+  "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]": {
+    "pass_energy": "@attrs:metadata/file/KTOF:Lens:TOF:V",
+    "pass_energy/@units": "eV",
+    "scheme": "tof",
+    "tof_distance": 0.9,
+    "tof_distance/@units": "m"
+  },
+  "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/DETECTOR[detector]": {
+    "amplifier_type": "MCP",
+    "detector_type": "DLD",
+    "sensor_pixels": [
+      1800,
+      1800
+    ],
+    "sensor_pixels/@units": "",
+    "amplifier_bias": "@attrs:metadata/file/KTOF:Lens:MCPfront:V",
+    "amplifier_bias/@units": "V",
+    "amplifier_voltage": "@attrs:metadata/file/KTOF:Lens:MCPback:V",
+    "amplifier_voltage/@units": "V",
+    "detector_voltage": "@attrs:metadata/file/KTOF:Lens:UDLD:V",
+    "detector_voltage/@units": "V"
+  },
+  "/ENTRY[entry]/INSTRUMENT[instrument]/sourceTYPE[source_probe]": {
+    "name": "HHG @ TR-ARPES @ FHI",
+    "probe": "photon",
+    "type": "HHG laser",
+    "mode": "Single Bunch",
+    "frequency": "@attrs:metadata/instrument/beam/probe/frequency",
+    "frequency/@units": "kHz",
+    "associated_beam": "/entry/instrument/beam_probe"
+  },
+  "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_probe]": {
+    "distance": 0.0,
+    "distance/@units": "mm",
+    "incident_energy": "@attrs:metadata/instrument/beam/probe/incident_energy",
+    "incident_energy/@units": "eV",
+    "incident_energy_spread": "@attrs:metadata/instrument/beam/probe/incident_energy_spread",
+    "incident_energy_spread/@units": "eV",
+    "pulse_duration": "@attrs:metadata/instrument/beam/probe/pulse_duration",
+    "pulse_duration/@units": "fs",
+    "incident_polarization": "@attrs:metadata/instrument/beam/probe/incident_polarization",
+    "incident_polarization/@units": "V^2/mm^2",
+    "extent": "@attrs:metadata/instrument/beam/probe/extent",
+    "extent/@units": "µm",
+    "associated_source": "/entry/instrument/source_probe"
+  },
+  "/ENTRY[entry]/INSTRUMENT[instrument]/sourceTYPE[source_pump]": {
+    "name": "OPCPA @ TR-ARPES @ FHI",
+    "probe": "visible light",
+    "type": "Optical Laser",
+    "mode": "Single Bunch",
+    "frequency": "@attrs:metadata/instrument/beam/pump/frequency",
+    "frequency/@units": "kHz",
+    "associated_beam": "/entry/instrument/beam_pump"
+  },
+  "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_pump]": {
+    "distance": 0.0,
+    "distance/@units": "mm",
+    "incident_energy": "@attrs:metadata/instrument/beam/pump/incident_energy",
+    "incident_energy/@units": "eV",
+    "incident_energy_spread": "@attrs:metadata/instrument/beam/pump/incident_energy_spread",
+    "incident_energy_spread/@units": "eV",
+    "incident_wavelength": "@attrs:metadata/instrument/beam/pump/incident_wavelength",
+    "incident_wavelength/@units": "nm",
+    "pulse_duration": "@attrs:metadata/instrument/beam/pump/pulse_duration",
+    "pulse_duration/@units": "fs",
+    "incident_polarization": "@attrs:metadata/instrument/beam/pump/incident_polarization",
+    "incident_polarization/@units": "V^2/mm^2",
+    "pulse_energy": "@attrs:metadata/instrument/beam/pump/pulse_energy",
+    "pulse_energy/@units": "µJ",
+    "average_power": "@attrs:metadata/instrument/beam/pump/average_power",
+    "average_power/@units": "mW",
+    "extent": "@attrs:metadata/instrument/beam/pump/extent",
+    "extent/@units": "µm",
+    "fluence": "@attrs:metadata/instrument/beam/pump/fluence",
+    "fluence/@units": "mJ/cm^2",
+    "associated_source": "/entry/instrument/source_pump"
+  },
+  "/ENTRY[entry]/INSTRUMENT[instrument]/MANIPULATOR[manipulator]": {
+    "temperature_sensor": {
+      "name": "sample_temperature",
+      "measurement": "temperature",
+      "value": "@attrs:metadata/file/trARPES:Carving:TEMP_RBV",
+      "value/@units": "K"
+    },
+    "sample_bias_voltmeter": {
+      "name": "sample_bias",
+      "measurement": "voltage",
+      "value": "@attrs:metadata/file/KTOF:Lens:Sample:V",
+      "value/@units": "V"
+    },
+    "depends_on": "/entry/instrument/manipulator/transformations/trans_z",
+    "TRANSFORMATIONS[transformations]": {
+      "AXISNAME[trans_z]": -0.32,
+      "AXISNAME[trans_z]/@depends_on": "rot_z",
+      "AXISNAME[trans_z]/@transformation_type": "translation",
+      "AXISNAME[trans_z]/@units": "m",
+      "AXISNAME[trans_z]/@vector": [
+        0,
+        0,
+        1
+      ],
+      "AXISNAME[rot_z]/@depends_on": "rot_x",
+      "AXISNAME[rot_z]": -25.0,
+      "AXISNAME[rot_z]/@transformation_type": "rotation",
+      "AXISNAME[rot_z]/@units": "degrees",
+      "AXISNAME[rot_z]/@vector": [
+        0,
+        0,
+        1
+      ],
+      "AXISNAME[rot_x]/@depends_on": ".",
+      "AXISNAME[rot_x]": -90.0,
+      "AXISNAME[rot_x]/@transformation_type": "rotation",
+      "AXISNAME[rot_x]/@units": "degrees",
+      "AXISNAME[rot_x]/@vector": [
+        1,
+        0,
+        0
+      ]
+    }
+  },
+  "/ENTRY[entry]/SAMPLE[sample]": {
+    "preparation_date": "@attrs:metadata/sample/preparation_date",
+    "history/notes/type": "text/plain",
+    "history/notes/description": "@attrs:metadata/sample/sample_history",
+    "description": "@attrs:metadata/sample/chemical_formula",
+    "name": "@attrs:metadata/sample/chemical_formula",
+    "situation": "vacuum",
+    "SUBSTANCE[substance]/molecular_formula_hill": "@attrs:metadata/sample/chemical_formula",
+    "temperature_env": {
+      "temperature_sensor": "@link:/entry/instrument/manipulator/temperature_sensor"
+    },
+    "gas_pressure_env": {
+      "pressure_gauge": "@link:/entry/instrument/pressure_gauge"
+    },
+    "bias_env": {
+      "voltmeter": "@link:/entry/instrument/manipulator/sample_bias_voltmeter"
+    },
+    "depends_on": "/entry/sample/transformations/corrected_phi",
+    "TRANSFORMATIONS[transformations]": {
+      "AXISNAME[corrected_phi]/@depends_on": "rot_omg",
+      "AXISNAME[corrected_phi]": 90.0,
+      "AXISNAME[corrected_phi]/@units": "degrees",
+      "AXISNAME[corrected_phi]/@transformation_type": "rotation",
+      "AXISNAME[corrected_phi]/@vector": [
+        0,
+        1,
+        0
+      ],
+      "AXISNAME[rot_omg]/@depends_on": "rot_phi",
+      "AXISNAME[rot_omg]": "@attrs:metadata/file/trARPES:Carving:OMG.RBV",
+      "AXISNAME[rot_omg]/@units": "degrees",
+      "AXISNAME[rot_omg]/@transformation_type": "rotation",
+      "AXISNAME[rot_omg]/@vector": [
+        1,
+        0,
+        0
+      ],
+      "AXISNAME[rot_phi]/@depends_on": "rot_tht",
+      "AXISNAME[rot_phi]": "@attrs:metadata/file/trARPES:Carving:PHI.RBV",
+      "AXISNAME[rot_phi]/@units": "degrees",
+      "AXISNAME[rot_phi]/@transformation_type": "rotation",
+      "AXISNAME[rot_phi]/@vector": [
+        0,
+        1,
+        0
+      ],
+      "AXISNAME[rot_tht]/@depends_on": "trans_z",
+      "AXISNAME[rot_tht]": "@attrs:metadata/file/trARPES:Carving:THT.RBV",
+      "AXISNAME[rot_tht]/@units": "degrees",
+      "AXISNAME[rot_tht]/@transformation_type": "rotation",
+      "AXISNAME[rot_tht]/@vector": [
+        0,
+        0,
+        1
+      ],
+      "AXISNAME[trans_z]/@depends_on": "trans_y",
+      "AXISNAME[trans_z]": "@attrs:metadata/file/trARPES:Carving:TRZ.RBV",
+      "AXISNAME[trans_z]/@units": "mm",
+      "AXISNAME[trans_z]/@transformation_type": "translation",
+      "AXISNAME[trans_z]/@vector": [
+        0,
+        0,
+        1
+      ],
+      "AXISNAME[trans_y]/@depends_on": "trans_x",
+      "AXISNAME[trans_y]": "@attrs:metadata/file/trARPES:Carving:TRY.RBV",
+      "AXISNAME[trans_y]/@units": "mm",
+      "AXISNAME[trans_y]/@transformation_type": "translation",
+      "AXISNAME[trans_y]/@vector": [
+        0,
+        1,
+        0
+      ],
+      "AXISNAME[trans_x]/@depends_on": "/entry/instrument/manipulator/transformations/trans_z",
+      "AXISNAME[trans_x]": "@attrs:metadata/file/trARPES:Carving:TRX.RBV",
+      "AXISNAME[trans_x]/@units": "mm",
+      "AXISNAME[trans_x]/@transformation_type": "translation",
+      "AXISNAME[trans_x]/@vector": [
+        1,
+        0,
+        0
+      ]
+    }
+  },
+  "/ENTRY[entry]/PROCESS_MPES[process]/DISTORTION[distortion]": {
+    "symmetry": "@attrs:metadata/momentum_correction/rotsym",
+    "symmetry/@units": "",
+    "original_centre": "@attrs:metadata/momentum_correction/pcent",
+    "original_centre/@units": "",
+    "original_points": "@attrs:metadata/momentum_correction/pouter",
+    "original_points/@units": "",
+    "cdeform_field": "@attrs:metadata/momentum_correction/cdeform_field",
+    "cdeform_field/@units": "",
+    "rdeform_field": "@attrs:metadata/momentum_correction/rdeform_field",
+    "rdeform_field/@units": ""
+  },
+  "/ENTRY[entry]/PROCESS_MPES[process]/REGISTRATION[registration]": {
+    "depends_on": "/entry/process/registration/transformations/rot_z",
+    "TRANSFORMATIONS[transformations]": {
+      "AXISNAME[trans_x]": "@attrs:metadata/momentum_correction/adjust_params/xtrans",
+      "AXISNAME[trans_x]/@transformation_type": "translation",
+      "AXISNAME[trans_x]/@units": "pixels",
+      "AXISNAME[trans_x]/@vector": "@attrs:metadata/momentum_correction/adjust_params/x_vector",
+      "AXISNAME[trans_x]/@depends_on": ".",
+      "AXISNAME[trans_y]": "@attrs:metadata/momentum_correction/adjust_params/ytrans",
+      "AXISNAME[trans_y]/@units": "pixels",
+      "AXISNAME[trans_y]/@transformation_type": "translation",
+      "AXISNAME[trans_y]/@vector": "@attrs:metadata/momentum_correction/adjust_params/y_vector",
+      "AXISNAME[trans_y]/@depends_on": "trans_x",
+      "AXISNAME[rot_z]": "@attrs:metadata/momentum_correction/adjust_params/angle",
+      "AXISNAME[rot_z]/@units": "degrees",
+      "AXISNAME[rot_z]/@transformation_type": "rotation",
+      "AXISNAME[rot_z]/@offset": "@attrs:metadata/momentum_correction/adjust_params/offset",
+      "AXISNAME[rot_z]/@vector": "@attrs:metadata/momentum_correction/adjust_params/rotation_vector",
+      "AXISNAME[rot_z]/@depends_on": "trans_y"
+    }
+  },
+  "/ENTRY[entry]/PROCESS_MPES[process]/energy_calibration":{
+    "coefficients": "@attrs:metadata/energy_correction/calibration/coefficients",
+    "coefficients/@units": "",
+    "fit_function": "@attrs:metadata/energy_correction/calibration/fit_function",
+    "original_axis": "@attrs:metadata/energy_correction/tof",
+    "original_axis/@units": "ns",
+    "calibrated_axis": "@attrs:metadata/energy_correction/calibration/axis",
+    "calibrated_axis/@units": "eV",
+    "physical_quantity": "energy"
+  },
+  "/ENTRY[entry]/PROCESS_MPES[process]/CALIBRATION[kx_calibration]": {
+    "scaling": "@attrs:metadata/momentum_correction/calibration/scale_kx",
+    "scaling/@units": "",
+    "offset": "@attrs:metadata/momentum_correction/offset_kx",
+    "offset/@units": "",
+    "calibrated_axis": "@attrs:metadata/momentum_correction/calibration/axis_kx",
+    "calibrated_axis/@units": "1/angstrom",
+    "physical_quantity": "momentum"
+  },
+  "/ENTRY[entry]/PROCESS_MPES[process]/CALIBRATION[ky_calibration]": {
+    "scaling": "@attrs:metadata/momentum_correction/calibration/scale_ky",
+    "scaling/@units": "",
+    "offset": "@attrs:metadata/momentum_correction/offset_ky",
+    "offset/@units": "",
+    "calibrated_axis": "@attrs:metadata/momentum_correction/calibration/axis_ky",
+    "calibrated_axis/@units": "1/angstrom",
+    "physical_quantity": "momentum"
+  },
+  "/ENTRY[entry]/data": {
+    "@axes": "@data:dims",
+    "@*_indices": "@data:*.index",
+    "@signal": "data",
+    "data": "@data:data",
+    "data/@units": "counts",
+    "*": "@data:*.data",
+    "*/@units": "@data:*.unit",
+    "energy/@type": "binding"
+  }
+}
\ No newline at end of file
--- a/examples/data/mpes/mpes.scheme.archive.yml
+++ b/examples/data/mpes/mpes.scheme.archive.yml
@@ -8,7 +8,7 @@ definitions:
      m_annotations:
        template:
          reader: mpes
-          nxdl: NXmpes.nxdl
+          nxdl: NXmpes
        eln:
          hide: []
      quantities:

--- a/examples/data/mpes/sed_config/mpes_example_config.yaml
+++ b/examples/data/mpes/sed_config/mpes_example_config.yaml
+core:
+  # Set verbosity of sed
+  verbose: True
+  # The loader to use. The mpes loader allows for loading hdf5 files from the METIS momentum microscope.
+  loader: mpes
+  # Option to use the copy tool to mirror data to a local storage location before processing.
+  use_copy_tool: False
+  # path to the root of the source data directory
+  copy_tool_source: "/path/to/data/"
+  # path to the root or the local data storage
+  copy_tool_dest: "/path/to/localDataStore/"
+  # optional keyworkds for the copy tool:
+  copy_tool_kwds:
+    # number of parallel copy jobs
+    ntasks: 20
+    # group id to set for copied files and folders
+    gid: 1001
+dataframe:
+  # hdf5 group names to read from the h5 files (for mpes reader)
+  hdf5_groupnames: ["Stream_0", "Stream_1", "Stream_2", "Stream_4"]
+  # aliases to assign to the dataframe columns for the corresponding hdf5 streams
+  hdf5_aliases:
+    Stream_0: "X"
+    Stream_1: "Y"
+    Stream_2: "t"
+    Stream_4: "ADC"
+  # dataframe column name for the time stamp column
+  time_stamp_alias: "timeStamps"
+  # hdf5 group name containing eventIDs occuring at every millisecond (used to calculate timestamps)
+  ms_markers_group: "msMarkers"
+  # hdf5 attribute containing the timestamp of the first event in a file
+  first_event_time_stamp_key: "FirstEventTimeStamp"
+  # Time stepping in seconds of the succesive events in the timed dataframe
+  timed_dataframe_unit_time: 0.001
+  # list of columns to apply jitter to
+  jitter_cols: ["X", "Y", "t", "ADC"]
+  # dataframe column containing x coordinates
+  x_column: "X"
+  # dataframe column containing y coordinates
+  y_column: "Y"
+  # dataframe column containing time-of-flight data
+  tof_column: "t"
+  # dataframe column containing analog-to-digital data
+  adc_column: "ADC"
+  # dataframe column containing corrected x coordinates
+  corrected_x_column: "Xm"
+  # dataframe column containing corrected y coordinates
+  corrected_y_column: "Ym"
+  # dataframe column containing corrected time-of-flight data
+  corrected_tof_column: "tm"
+  # dataframe column containing kx coordinates
+  kx_column: "kx"
+  # dataframe column containing ky coordinates
+  ky_column: "ky"
+  # dataframe column containing energy data
+  energy_column: "energy"
+  # dataframe column containing delay data
+  delay_column: "delay"
+  # time length of a base time-of-flight bin in ns
+  tof_binwidth: 4.125e-12
+  # Binning factor of the tof_column-data compared to tof_binwidth (2^(tof_binning-1))
+  tof_binning: 2
+  # binning factor used for the adc coordinate (2^(adc_binning-1))
+  adc_binning: 3
+  # Default units for dataframe entries
+  units:
+    X: 'step'
+    Y: 'step'
+    t: 'step'
+    tof_voltage: 'V'
+    extractor_voltage: 'V'
+    extractor_current: 'A'
+    cryo_temperature: 'K'
+    sample_temperature: 'K'
+    dld_time: 'ns'
+    delay: 'ps'
+    timeStamp: 's'
+    energy: 'eV'
+    E: 'eV'
+    kx: '1/A'
+    ky: '1/A'
+energy:
+  # Number of bins to use for energy calibration traces
+  bins: 1000
+  # Bin ranges to use for energy calibration curves (for tof_binning=0)
+  ranges: [128000, 138000]
+  # hdf5 path to attribute storing bias information for a given file
+  bias_key: "@KTOF:Lens:Sample:V"
+  # Option to normalize energy calibration traces
+  normalize: True
+  # Pixel range for smoothing
+  normalize_span: 7
+  # Spline order for smoothing
+  normalize_order: 1
+  # Radius parameter for fastdtw algorithm to find path correspondence
+  fastdtw_radius: 2
+  # Window around a peak to make sure that no other peaks are present
+  peak_window: 7
+  # Mehtod to use for energy calibration
+  calibration_method: "lmfit"
+  # Energy scale to use for energy calibration
+  energy_scale: "kinetic"
+  # Approximate position of the high-energy-cutoff in tof_column bins,
+  # used for displaying a graph to choose the energy correction function parameters.
+  tof_fermi: 132250
+  # TOF range to visualize for the correction tool around tof_fermi
+  tof_width: [-600, 1000]
+  # x-intergration range for the correction tool around the center pixel
+  x_width: [-20, 20]
+  # y-intergration range for the correction tool around the center pixel
+  y_width: [-20, 20]
+  # High intensity cutoff for the visulaization tool
+  color_clip: 300
+  correction:
+    # Correction type
+    correction_type: "Lorentzian"
+    # Correction amplitude
+    amplitude: 2.5
+    # center coordinates for the correction (in detector coordinates)
+    center: [730.0, 730.0]
+    # gamma value for the Lorentzian correction (same for x and y)
+    gamma: 920.0
+    # sigma value for the gaussian correction (same for x and y)
+    sigma: 700.0
+    # diameter value for the radial correction (same for x and y)
+    diameter: 3000.0
+  # Default energy calibration
+  calibration:
+    # time-of-flight distance (in m)
+    d: 1.058206295066418
+    # time offset (in ns)
+    t0: 7.684410678887588e-07
+    # energy offset (in eV)
+    E0: -30.440035779171833
+    # energy scale of calibration
+    energy_scale: "kinetic"
+momentum:
+  # binning axes to use for momentum correction/calibration.
+  # Axes names starting with "@" refer to keys in the "dataframe" section
+  axes: ["@x_column", "@y_column", "@tof_column"]
+  # Bin numbers used for the respective axes
+  bins: [512, 512, 300]
+  # bin ranges to use (in unbinned detector coordinates)
+  ranges: [[-256, 1792], [-256, 1792], [132000, 136000]]
+  # The x/y pixel ranges of the detector
+  detector_ranges: [[0, 2048], [0, 2048]]
+  # The center pixel of the detector in the binned x/y coordinates
+  center_pixel: [256, 256]
+  # Sigma parameter for feature selection (intensity above background)
+  sigma: 5
+  # FWHM parameter for feature selection (width of features to extract)
+  fwhm: 8
+  # Sigma_radius parameter for feature selection (variation of radius size)
+  sigma_radius: 1
+  # default momentum calibration
+  calibration:
+    # x momentum scaleing factor
+    kx_scale: 0.010729535670610963
+    # y momentum scaleing factor
+    ky_scale: 0.010729535670610963
+    # x BZ center pixel
+    x_center: 256.0
+    # y BZ center pixel
+    y_center: 256.0
+    # x start value of the calibration dataset
+    rstart: -256.
+    # y start value of the calibration dataset
+    cstart: -256.
+    # x direction pixel stepping of the calibration dataset
+    rstep: 4.0
+    # y direction pixel stepping of the calibration dataset
+    cstep: 4.0
+  correction:
+    # default feature points used for calculating the distortion correction.
+    feature_points: [[203.2, 341.96], [299.16, 345.32], [350.25, 243.70], [304.38, 149.88], [199.52, 152.48], [154.28, 242.27], [248.29, 248.62]]
+    # rotational symmetry of the structure used for correction. Should be an even number
+    rotation_symmetry: 6
+    # Option whether the center of the structure is included in the feature points.
+    include_center: True
+    # Option whether the center should be included in the correction algorithm
+    use_center: True
+delay:
+  # value ranges of the analog-to-digital converter axes used for encoding the delay stage position
+  # (in unbinned coordinates)
+  adc_range: [1900, 25600]
+  # hdf5 attribute containing the starting point of the delay stage
+  p1_key: "@trARPES:DelayStage:p1"
+  # hdf5 attribute containing the end point of the delay stage
+  p2_key: "@trARPES:DelayStage:p2"
+  # hdf5 attribute containing the t0 value of the delay stage
+  t0_key: "@trARPES:DelayStage:t0"
+binning:
+  # Histogram computation mode to use.
+  hist_mode: "numba"
+  # Mode for hostogram recombination to use
+  mode: "fast"
+  # Whether to display a progress bar
+  pbar: True
+  # Number of parallel binning threads to use
+  num_cores: 20
+  # Number of multithreading threads per worker thread
+  threads_per_worker: 4
+  # API for numpy multithreading
+  threadpool_API: "blas"
+histogram:
+  # number of bins used for histogram visualization
+  bins: [80, 80, 80, 80]
+  # default axes to use for histgram visualization.
+  # Axes names starting with "@" refer to keys in the "dataframe" section
+  axes: ["@x_column", "@y_column", "@tof_column", "@adc_column"]
+  # default ranges to use for histogram visualization (in unbinned detector coordinates)
+  ranges: [[0, 1800], [0, 1800], [128000, 138000], [0, 32000]]
+metadata:
+  # URL of the epics archiver request engine
+  archiver_url: "http://aa0.fhi-berlin.mpg.de:17668/retrieval/data/getData.json?pv="
+  # EPICS channels to collect from EPICS archiver
+  epics_pvs: ["KTOF:Lens:Extr:I", "trARPES:Carving:TEMP_RBV", "trARPES:XGS600:PressureAC:P_RD", "KTOF:Lens:UDLD:V", "KTOF:Lens:Sample:V", "KTOF:Apertures:m1.RBV", "KTOF:Apertures:m2.RBV", "KTOF:Apertures:m3.RBV", "trARPES:Carving:TRX.RBV", "trARPES:Carving:TRY.RBV", "trARPES:Carving:TRZ.RBV", "trARPES:Carving:THT.RBV", "trARPES:Carving:PHI.RBV", "trARPES:Carving:OMG.RBV"]
+  # hdf5 attribute containing the field aperture "in" motor position
+  fa_in_channel: 'KTOF:Apertures:m1.RBV'
+  # hdf5 attribute containing the field aperture "hor" motor position
+  fa_hor_channel: 'KTOF:Apertures:m2.RBV'
+  # hdf5 attribute containing the contrast aperture "in" motor position
+  ca_in_channel: 'KTOF:Apertures:m3.RBV'
+  # dictionary containing contrast and field aperture motor positions and sizes
+  aperture_config:
+    "2018-01-23T19:35:15":
+      fa_size:
+        '750': [[-3.0, -1.4], [-5.4, -4.6]]
+        grid: [[-3.0, -1.4], [0.15, 1.75]]
+        '1500': [[-3.0, -1.4], [6.25, 7.75]]
+        '200': [[3.3, 4.4], [-5.4, -4.6]]
+        '500': [[3.3, 4.4], [0.15, 1.75]]
+        '1000': [[3.3, 4.4], [6.25, 7.75]]
+        '20': [[9.6, 10.1], [-5.4, -4.6]]
+        '50': [[9.6, 10.1], [0.15, 1.75]]
+        '100': [[9.6, 10.1], [6.25, 7.75]]
+        open: [[-15, -9.0], [-15, -8.9]]
+      ca_size:
+        '50': [8.0, 8.4]
+        '200': [-0.5, -0.9]
+        '100': [3.4, 3.8]
+        grid: [-5.3, -5.9]
+        open: [-12.0, -8]
+    "2020-01-23T19:35:15":
+      fa_size:
+        '750': [[-6.2, -4.8], [5.0, 6.0]]
+        grid: [[-6.2, -4.8], [-0.7, -0.3]]
+        '500': [[-6.2, -4.8], [-7.0, -6.0]]
+        '200': [[0.5, 0.9], [-0.7, -0.3]]
+        '100': [[0.5, 0.9], [-7.0, -6.0]]
+        '300': [[0.5, 0.9], [5.0, 6.0]]
+        '10': [[6.5, 6.9], [-7.0, -6.0]]
+        '20': [[6.5, 6.9], [-0.7, -0.3]]
+        '50': [[6.5, 6.9], [5.0, 6.0]]
+        open: [[-15, -8.5], [-15, -8.9]]
+      ca_size:
+        '50': [9.0, 11.0]
+        '300': [-0.1, 0.1]
+        '200': [0.7, 1.5]
+        '100': [5.1, 5.9]
+        grid: [-5.5, -5.2]
+        open: [-15, -8.5]
+  # dictionary containing lens mode configurations
+  lens_mode_config:
+    "6kV_kmodem4.0_20VTOF_v3.sav":
+      Extr: 6000.0
+      UCA: 1200
+      UFA: 600.0
+      Z1: 2452.9
+      Z2: 1489.9
+      A: 420.07
+      B: 2494.8
+      C: 489.2
+      D: 228.05
+      E: 113.82
+      F: 54.232
+      G: 20.0
+      H: 25.5
+      I: 36.0
+      TOF: 20.0
+      MCPfront: 20.0
+    "6kV_kmodem4.0_30VTOF_453ns_focus.sav":
+      Extr: 6000.0
+      UCA: 1200
+      UFA: 600.0
+      Z1: 2452.9
+      Z2: 1489.9
+      A: 403.07
+      B: 2500
+      C: 422.25
+      D: 208.88
+      E: 199.49
+      F: 68.735
+      G: 30.0
+      H: 30.0
+      I: 44.5
+      TOF: 30.0
+      MCPfront: 30.0
+nexus:
+  # pynxtools reader to use for saving NXmpes files
+  reader: "mpes"
+  # NeXus application definition to use for saving
+  definition: "NXmpes"
+  # List conatining additional input files to be handed to the pynxtools converter tool,
+  # e.g. containing a configuration file, and additional metadata.
+  input_files: ["config_file.json"]
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -9,7 +9,7 @@ anyio==4.6.0              # via httpx, starlette, watchfiles, -r requirements.tx
 arrow==1.3.0              # via isoduration, -r requirements.txt
 ase==3.22.1               # via matid, -r requirements.txt, nomad-lab (pyproject.toml)
 asgiref==3.8.1            # via -r requirements.txt, nomad-lab (pyproject.toml)
-astroid==3.3.4            # via nomad-lab (pyproject.toml)
+astroid==3.3.5            # via nomad-lab (pyproject.toml)
 asttokens==2.4.1          # via devtools
 async-generator==1.10     # via jupyterhub, -r requirements.txt
 async-property==0.2.2     # via python-keycloak, -r requirements.txt
@@ -41,7 +41,7 @@ cycler==0.12.1            # via matplotlib, -r requirements.txt
 decorator==5.1.1          # via validators, -r requirements.txt
 deprecation==2.1.0        # via python-keycloak, -r requirements.txt
 devtools==0.12.2          # via nomad-lab (pyproject.toml)
-dnspython==2.6.1          # via email-validator, pymongo, -r requirements.txt
+dnspython==2.7.0          # via email-validator, pymongo, -r requirements.txt
 docker==7.1.0             # via dockerspawner, -r requirements.txt
 dockerspawner==13.0.0     # via -r requirements.txt, nomad-lab (pyproject.toml)
 docstring-parser==0.16    # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -169,13 +169,13 @@ python-dateutil==2.9.0.post0  # via arrow, celery, elasticsearch-dsl, ghp-import
 python-dotenv==1.0.1      # via uvicorn, -r requirements.txt
 python-gitlab==2.10.1     # via nomad-lab (pyproject.toml)
 python-json-logger==2.0.2  # via jupyter-telemetry, -r requirements.txt, nomad-lab (pyproject.toml)
-python-keycloak==4.6.0    # via -r requirements.txt, nomad-lab (pyproject.toml)
+python-keycloak==4.6.2    # via -r requirements.txt, nomad-lab (pyproject.toml)
 python-logstash==0.4.6    # via -r requirements.txt, nomad-lab (pyproject.toml)
 python-magic==0.4.24      # via -r requirements.txt, nomad-lab (pyproject.toml)
 python-magic-bin==0.4.14 ; sys_platform == 'win32'  # via -r requirements.txt, nomad-lab (pyproject.toml)
 python-multipart==0.0.12  # via -r requirements.txt, nomad-lab (pyproject.toml)
 pytz==2024.2              # via mkdocs-git-revision-date-localized-plugin, mongomock, pandas, -r requirements.txt, nomad-lab (pyproject.toml)
-pywin32==306 ; sys_platform == 'win32'  # via docker, -r requirements.txt
+pywin32==307 ; sys_platform == 'win32'  # via docker, -r requirements.txt
 pyyaml==6.0.2             # via mkdocs, mkdocs-get-deps, mkdocs-macros-plugin, pybtex, pymdown-extensions, pyyaml-env-tag, uvicorn, -r requirements.txt, nomad-lab (pyproject.toml)
 pyyaml-env-tag==0.1       # via mkdocs
 rdflib==5.0.0             # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -190,7 +190,7 @@ rfc3987==1.3.8            # via jsonschema, -r requirements.txt
 rope==0.21.0              # via nomad-lab (pyproject.toml)
 ruamel-yaml==0.18.6       # via jupyter-telemetry, oauthenticator, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
 ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'  # via ruamel-yaml, -r requirements.txt
-ruff==0.6.8               # via nomad-lab (pyproject.toml)
+ruff==0.6.9               # via nomad-lab (pyproject.toml)
 runstats==2.0.0           # via -r requirements.txt, nomad-lab (pyproject.toml)
 scikit-learn==1.5.2       # via matid, -r requirements.txt, nomad-lab (pyproject.toml)
 scipy==1.14.1             # via ase, pymatgen, scikit-learn, -r requirements.txt, nomad-lab (pyproject.toml)
@@ -214,11 +214,11 @@ structlog==24.4.0         # via -r requirements.txt, nomad-lab (pyproject.toml)
 sympy==1.13.3             # via pymatgen, -r requirements.txt
 tabulate==0.8.9           # via nomad-openbis, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
 tenacity==9.0.0           # via plotly, -r requirements.txt
-termcolor==2.4.0          # via mkdocs-macros-plugin
+termcolor==2.5.0          # via mkdocs-macros-plugin
 texttable==1.7.0          # via nomad-openbis, -r requirements.txt
 threadpoolctl==3.5.0      # via scikit-learn, -r requirements.txt
 tifffile==2024.9.20       # via h5grove, -r requirements.txt
-tomli==2.0.2 ; python_full_version <= '3.11'  # via coverage
+tomli==2.0.2 ; python_full_version == '3.11'  # via coverage
 toposort==1.10            # via -r requirements.txt, nomad-lab (pyproject.toml)
 tornado==6.4.1            # via jupyterhub, -r requirements.txt
 tqdm==4.66.5              # via pyedr, pymatgen, -r requirements.txt

--- a/requirements-plugins.txt
+++ b/requirements-plugins.txt
--- a/requirements.txt
+++ b/requirements.txt
@@ -35,7 +35,7 @@ cryptography==43.0.1      # via certipy, jwcrypto, pyjwt, rfc3161ng
 cycler==0.12.1            # via matplotlib
 decorator==5.1.1          # via validators
 deprecation==2.1.0        # via python-keycloak
-dnspython==2.6.1          # via email-validator, pymongo
+dnspython==2.7.0          # via email-validator, pymongo
 docker==7.1.0             # via dockerspawner
 dockerspawner==13.0.0     # via nomad-lab (pyproject.toml)
 docstring-parser==0.16    # via nomad-lab (pyproject.toml)
@@ -132,13 +132,13 @@ pyrsistent==0.20.0        # via jsonschema
 python-dateutil==2.9.0.post0  # via arrow, celery, elasticsearch-dsl, jupyterhub, matplotlib, nomad-openbis, pandas, rfc3161ng
 python-dotenv==1.0.1      # via uvicorn
 python-json-logger==2.0.2  # via jupyter-telemetry, nomad-lab (pyproject.toml)
-python-keycloak==4.6.0    # via nomad-lab (pyproject.toml)
+python-keycloak==4.6.2    # via nomad-lab (pyproject.toml)
 python-logstash==0.4.6    # via nomad-lab (pyproject.toml)
 python-magic==0.4.24      # via nomad-lab (pyproject.toml)
 python-magic-bin==0.4.14 ; sys_platform == 'win32'  # via nomad-lab (pyproject.toml)
 python-multipart==0.0.12  # via nomad-lab (pyproject.toml)
 pytz==2024.2              # via mongomock, pandas, nomad-lab (pyproject.toml)
-pywin32==306 ; sys_platform == 'win32'  # via docker
+pywin32==307 ; sys_platform == 'win32'  # via docker
 pyyaml==6.0.2             # via pybtex, uvicorn, nomad-lab (pyproject.toml)
 rdflib==5.0.0             # via nomad-lab (pyproject.toml)
 rdkit==2023.9.5           # via nomad-lab (pyproject.toml)