FAIRmat-NFDI · rettigl · Mar 20, 2025 · Mar 14, 2025 · Mar 19, 2025 · Mar 20, 2025
diff --git a/.cspell/custom-dictionary.txt b/.cspell/custom-dictionary.txt
@@ -7,13 +7,15 @@ Bessy
 binarywave
 bnote
 caplog
+codemirror
 configfile
 dataconverter
 Dobener
 dsml
 Dyna
 Ecut
 FEMTOSPEX
+FIELDNAME
 fluence
 fluences
 fontawesome

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -30,7 +30,7 @@ jobs:
         run: |
           curl -LsSf https://astral.sh/uv/install.sh | sh
       - name: Install nomad
-        if: "${{ matrix.python_version != '3.8'}}"
+        if: "${{ matrix.python_version != '3.8' && matrix.python_version != '3.9'}}"
         run: |
           uv pip install nomad-lab[infrastructure]@git+https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git
       - name: Install package

diff --git a/CITATION.cff b/CITATION.cff
@@ -1,41 +1,41 @@
-cff-version: 1.2.0
-title: 'pynxtools-igor: A pynxtools reader plugin for Wavemetrics Igor Pro data'
-version: 0.1.0
-message:
-  If you use this software, please cite it using the
-  metadata from this file.
-type: software
-authors:
-  - given-names: Florian
-    family-names: Dobener
-    orcid: 'https://orcid.org/0000-0003-1987-6224'
-  - given-names: Laurenz
-    family-names: Rettig
-    orcid: 'https://orcid.org/0000-0002-0725-6696'
-  - given-names: Lukas
-    family-names: Pielsticker
-    orcid: 'https://orcid.org/0000-0001-9361-8333'
-
-doi: TODO
-repository-code: 'https://github.com/FAIRmat-NFDI/pynxtools-igor'
-url: TODO
-keywords:
-  - Wavemetrics
-  - Igor Pro
-  - NOMAD
-  - pynxtools
-  - NeXus
-abstract:
-  pynxtools-igor is a free, and open-source data software for converting data stored 
-  with Wavemetrics [Igor Pro](https://www.wavemetrics.com/) into the [NeXus](https://www.nexusformat.org/) 
-  format. It is implemented as a plugin for [pynxtools](https://github.com/FAIRmat-NFDI/pynxtools) and 
-  allows to read, translate, and standardize data from Igor Pro binary waves and packed experiment files. 
-  Depending on the domain of data, pynxtools allows to ensure compliance with various NeXus application 
-  definitions.
-
-  pynxtools-igor is developed both as a standalone reader and as a tool within NOMAD, an open-source data
-  management platform for materials science ((https://nomad-lab.eu/nomad-lab/).
-
-  The work is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 460197019 (FAIRmat)
-  (https://gepris.dfg.de/gepris/projekt/460197019?language=en).
+cff-version: 1.2.0
+title: 'pynxtools-igor: A pynxtools reader plugin for Wavemetrics Igor Pro data'
+version: 0.1.1
+message:
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Florian
+    family-names: Dobener
+    orcid: 'https://orcid.org/0000-0003-1987-6224'
+  - given-names: Laurenz
+    family-names: Rettig
+    orcid: 'https://orcid.org/0000-0002-0725-6696'
+  - given-names: Lukas
+    family-names: Pielsticker
+    orcid: 'https://orcid.org/0000-0001-9361-8333'
+
+doi: TODO
+repository-code: 'https://github.com/FAIRmat-NFDI/pynxtools-igor'
+url: TODO
+keywords:
+  - Wavemetrics
+  - Igor Pro
+  - NOMAD
+  - pynxtools
+  - NeXus
+abstract:
+  pynxtools-igor is a free, and open-source data software for converting data stored 
+  with Wavemetrics [Igor Pro](https://www.wavemetrics.com/) into the [NeXus](https://www.nexusformat.org/) 
+  format. It is implemented as a plugin for [pynxtools](https://github.com/FAIRmat-NFDI/pynxtools) and 
+  allows to read, translate, and standardize data from Igor Pro binary waves and packed experiment files. 
+  Depending on the domain of data, pynxtools allows to ensure compliance with various NeXus application 
+  definitions.
+
+  pynxtools-igor is developed both as a standalone reader and as a tool within NOMAD, an open-source data
+  management platform for materials science ((https://nomad-lab.eu/nomad-lab/).
+
+  The work is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 460197019 (FAIRmat)
+  (https://gepris.dfg.de/gepris/projekt/460197019?language=en).
 license: Apache-2.0
diff --git a/src/pynxtools_igor/nomad/examples/Conversion of time-resolved x-ray diffraction data.ipynb b/src/pynxtools_igor/nomad/examples/Conversion of time-resolved x-ray diffraction data.ipynb
@@ -40,7 +40,7 @@
     "    \"user0/name\": \"Laurenz Rettig\",\n",
     "    \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
     "    \"instrument/beam/incident_energy\": 1187.5,\n",
-    "    \"instrument/beam/probe/pulse_duration\": 70,\n",
+    "    \"instrument/beam/probe/pulse_duration\": 70.0,\n",
     "    \"sample/chemical_formula\": \"GdIr2Si2\",\n",
     "    \"sample/name\": \"GdIr2Si2 single crystal\",\n",
     "}\n",
@@ -57,14 +57,14 @@
     "        \"metadata\": {\n",
     "            **metadata,\n",
     "            **{\n",
-    "                \"sample/temperature\": temperature,\n",
+    "                \"sample/temperature\": float(temperature),\n",
     "                \"entry_title\": f\"Resolved resonant x-ray diffraction data of GdIr2Si2 at {temperature} K\",\n",
     "            },\n",
     "        },\n",
     "    }\n",
     "\n",
     "entry_dict\n",
-    "convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
+    "convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
    ]
   },
   {
@@ -81,7 +81,7 @@
     "    \"user0/name\": \"Laurenz Rettig\",\n",
     "    \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
     "    \"instrument/beam/incident_energy\": 1187.5,\n",
-    "    \"instrument/beam/probe/pulse_duration\": 70,\n",
+    "    \"instrument/beam/probe/pulse_duration\": 70.0,\n",
     "    \"sample/chemical_formula\": \"GdCo2Si2\",\n",
     "    \"sample/name\": \"GdCo2Si2 single crystal\",\n",
     "}\n",
@@ -98,14 +98,14 @@
     "        \"metadata\": {\n",
     "            **metadata,\n",
     "            **{\n",
-    "                \"sample/temperature\": temperature,\n",
+    "                \"sample/temperature\": float(temperature),\n",
     "                \"entry_title\": f\"Resolved resonant x-ray diffraction data of GdIr2Si2 at {temperature} K\",\n",
     "            },\n",
     "        },\n",
     "    }\n",
     "\n",
     "entry_dict\n",
-    "convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
+    "convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
    ]
   },
   {
@@ -129,7 +129,7 @@
     "    \"user0/name\": \"Laurenz Rettig\",\n",
     "    \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
     "    \"instrument/beam/incident_energy\": 1187.5,\n",
-    "    \"instrument/beam/probe/pulse_duration\": 70,\n",
+    "    \"instrument/beam/probe/pulse_duration\": 70.0,\n",
     "}\n",
     "entry_dict = {}\n",
     "scans = [\n",
@@ -160,7 +160,7 @@
     "        },\n",
     "    }\n",
     "\n",
-    "convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
+    "convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
    ]
   },
   {
@@ -184,7 +184,8 @@
     "    \"user0/name\": \"Laurenz Rettig\",\n",
     "    \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
     "    \"instrument/beam/incident_energy\": 1187.5,\n",
-    "    \"instrument/beam/probe/pulse_duration\": 70,\n",
+    "    \"instrument/beam/probe/pulse_duration\": 70.0,\n",
+    "    \"sample/temperature\": 20.0,\n",
     "}\n",
     "entry_dict = {}\n",
     "scans = [\"GdRh/voigt_area\", \"GdIr/voigt_area\", \"GdCo/voigt1_area_left\"]\n",
@@ -207,7 +208,7 @@
     "        },\n",
     "    }\n",
     "\n",
-    "convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
+    "convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
    ]
   },
   {
@@ -231,10 +232,10 @@
     "    \"user0/name\": \"Laurenz Rettig\",\n",
     "    \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
     "    \"instrument/beam/incident_energy\": 1187.5,\n",
-    "    \"instrument/beam/probe/pulse_duration\": 100,\n",
+    "    \"instrument/beam/probe/pulse_duration\": 100.0,\n",
     "    \"sample/chemical_formula\": \"GdIr2Si2\",\n",
     "    \"sample/name\": \"GdIr2Si2 single crystal\",\n",
-    "    \"sample/temperature\": 20,\n",
+    "    \"sample/temperature\": 20.0,\n",
     "}\n",
     "entry_dict = {}\n",
     "scans = [\"correction_2022Jan/GdCo_amp_08\", \"GdRh_ds_030_amp\", \"GdIr_ds_0200_amp\"]\n",
@@ -260,7 +261,7 @@
     "        },\n",
     "    }\n",
     "\n",
-    "convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
+    "convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
    ]
   },
   {
@@ -277,10 +278,10 @@
     "    \"user0/name\": \"Laurenz Rettig\",\n",
     "    \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
     "    \"instrument/beam/incident_energy\": 1187.5,\n",
-    "    \"instrument/beam/probe/pulse_duration\": 100,\n",
+    "    \"instrument/beam/probe/pulse_duration\": 100.0,\n",
     "    \"sample/chemical_formula\": \"GdCo2Si2\",\n",
     "    \"sample/name\": \"GdCo2Si2 single crystal\",\n",
-    "    \"sample/temperature\": 20,\n",
+    "    \"sample/temperature\": 20.0,\n",
     "}\n",
     "entry_dict = {}\n",
     "scans = [\"02\", \"04\", \"06\", \"08\", \"12\", \"20\"]\n",
@@ -302,7 +303,7 @@
     "        },\n",
     "    }\n",
     "\n",
-    "convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
+    "convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
    ]
   },
   {
@@ -319,10 +320,10 @@
     "    \"user0/name\": \"Laurenz Rettig\",\n",
     "    \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
     "    \"instrument/beam/incident_energy\": 1187.5,\n",
-    "    \"instrument/beam/probe/pulse_duration\": 100,\n",
+    "    \"instrument/beam/probe/pulse_duration\": 100.0,\n",
     "    \"sample/chemical_formula\": \"GdRh2Si2\",\n",
     "    \"sample/name\": \"GdRh2Si2 single crystal\",\n",
-    "    \"sample/temperature\": 20,\n",
+    "    \"sample/temperature\": 20.0,\n",
     "}\n",
     "entry_dict = {}\n",
     "scans = [\"005\", \"010\", \"015\", \"020\", \"030\", \"050\"]\n",
@@ -344,7 +345,7 @@
     "        },\n",
     "    }\n",
     "\n",
-    "convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
+    "convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
    ]
   },
   {
@@ -361,10 +362,10 @@
     "    \"user0/name\": \"Laurenz Rettig\",\n",
     "    \"user0/affiliation\": \"Fritz Haber Institute of the Max Planck Society\",\n",
     "    \"instrument/beam/incident_energy\": 1187.5,\n",
-    "    \"instrument/beam/probe/pulse_duration\": 100,\n",
+    "    \"instrument/beam/probe/pulse_duration\": 100.0,\n",
     "    \"sample/chemical_formula\": \"GdIr2Si2\",\n",
     "    \"sample/name\": \"GdIr2Si2 single crystal\",\n",
-    "    \"sample/temperature\": 20,\n",
+    "    \"sample/temperature\": 20.0,\n",
     "}\n",
     "entry_dict = {}\n",
     "scans = [\"0025\", \"0050\", \"0100\", \"0150\", \"0200\", \"0300\"]\n",
@@ -386,7 +387,7 @@
     "        },\n",
     "    }\n",
     "\n",
-    "convert([configfile, infile], \"igor\", \"NXxrd\", outfile, objects=(entry_dict,))"
+    "convert([configfile, infile], \"igor\", \"NXroot\", outfile, objects=(entry_dict,))"
    ]
   },
   {

diff --git a/src/pynxtools_igor/nomad/examples/config_file.json b/src/pynxtools_igor/nomad/examples/config_file.json
@@ -3,8 +3,8 @@
     "/ENTRY/DATA[data]/@axes": "@data:dims",
     "/ENTRY/DATA[data]/AXISNAME_indices[@*_indices]": "@data:*.index",
     "/ENTRY/DATA[data]/@signal": "data",
-    "/ENTRY/DATA[data]/data": "@data:data",
-    "/ENTRY/DATA[data]/data/@units": "@data:data.units",
+    "/ENTRY/DATA[data]/DATA[data]": "@data:data",
+    "/ENTRY/DATA[data]/DATA[data]/@units": "@data:data.units",
     "/ENTRY/DATA[data]/AXISNAME[*]": "@data:*.data",
     "/ENTRY/DATA[data]/AXISNAME[*]/@units": "@data:*.units"
 }
diff --git a/src/pynxtools_igor/nomad/examples/config_file_delay_scans.json b/src/pynxtools_igor/nomad/examples/config_file_delay_scans.json
@@ -12,7 +12,7 @@
             "name": "Bessy II",
             "probe": "x-ray",
             "type": "Synchrotron X-ray Source",
-            "mode": "Slicing"
+            "mode": "Single Bunch"
         },
         "BEAM[beam_probe]": {
             "distance": 0.0,
@@ -32,36 +32,38 @@
         "BEAM[beam_pump]": {
             "distance": 0.0,
             "distance/@units": "mm",
-            "incident_energy": "1.55",
+            "incident_energy": 1.55,
             "incident_energy/@units": "eV",
-            "pulse_duration": "['@eln:/ENTRY/Instrument/Beam/Probe/pulse_duration', '50']",
+            "pulse_duration": "['@eln:/ENTRY/Instrument/Beam/Pump/pulse_duration', '50.']",
             "pulse_duration/@units": "fs",
             "incident_polarization": [1, 1, 0, 0],
             "incident_polarization/@units": "V^2/mm^2",
             "fluence": "@attrs:instrument/beam/pump/fluence",
             "fluence/@units": "mJ/cm^2"
         },
         "DETECTOR[detector]": {
-            "amplifier_type": "APD",
-            "detector_type": "APD",
-            "amplifier_voltage": 150,
-            "amplifier_voltage/@units": "V"
+            "type": "APD",
+            "acquisition_mode": "event",
+            "COLLECTION[detector_parameters]": {
+                "amplifier_voltage": 150,
+                "amplifier_voltage/@units": "V"
+            }
           }
     },
     "/ENTRY/SAMPLE[sample]": {
         "description": "['@eln:/ENTRY/Sample/description', '@attrs:sample/chemical_formula']",
         "name": "['@eln:/ENTRY/Sample/name', '@attrs:sample/name']",
         "situation": "vacuum",
-        "SUBSTANCE[substance]/molecular_formula_hill": "['@eln:/ENTRY/Sample/chemical_formula', '@attrs:sample/chemical_formula']",
+        "chemical_formula": "['@eln:/ENTRY/Sample/chemical_formula', '@attrs:sample/chemical_formula']",
         "temperature": "@attrs:sample/temperature",
         "temperature/@units": "K"
   },
   "/ENTRY/DATA[data]/@axes": "@data:dims",
   "/ENTRY/DATA[data]/@signal": "data",
   "/ENTRY/DATA[data]/AXISNAME_indices[@*_indices]": "@data:*.index",
-  "/ENTRY/DATA[data]/data": "@data:data",
-  "/ENTRY/DATA[data]/data_errors": "@data:data.errors",  
-  "/ENTRY/DATA[data]/data/@units": "@data:data.units",
+  "/ENTRY/DATA[data]/DATA[data]": "@data:data",
+  "/ENTRY/DATA[data]/FIELDNAME_errors[data_errors]": "@data:data.errors",  
+  "/ENTRY/DATA[data]/DATA[data]/@units": "@data:data.units",
   "/ENTRY/DATA[data]/AXISNAME[*]": "@data:*.data",
   "/ENTRY/DATA[data]/AXISNAME[*]/@units": "@data:*.units"
 }
diff --git a/src/pynxtools_igor/nomad/examples/config_file_energies.json b/src/pynxtools_igor/nomad/examples/config_file_energies.json
@@ -25,26 +25,27 @@
             "incident_polarization/@units": "V^2/mm^2"
         },
         "DETECTOR[detector]": {
-            "amplifier_type": "APD",
-            "detector_type": "APD",
-            "amplifier_voltage": 150,
-            "amplifier_voltage/@units": "V"
+          "type": "APD",
+          "acquisition_mode": "event",
+          "COLLECTION[detector_parameters]": {
+              "amplifier_voltage": 150,
+              "amplifier_voltage/@units": "V"
           }
+        }
     },
     "/ENTRY/SAMPLE[sample]": {
         "description": "['@eln:/ENTRY/Sample/description', '@attrs:sample/chemical_formula']",
         "name": "['@eln:/ENTRY/Sample/name', '@attrs:sample/name']",
         "situation": "vacuum",
         "chemical_formula": "['@eln:/ENTRY/Sample/chemical_formula', '@attrs:sample/chemical_formula']",
-        "temperature": "20",
+        "temperature": "@attrs:sample/temperature",
         "temperature/@units": "K"
   },
   "/ENTRY/DATA[data]/@axes": "@data:dims",
   "/ENTRY/DATA[data]/@signal": "data",
   "/ENTRY/DATA[data]/AXISNAME_indices[@*_indices]": "@data:*.index",
-  "/ENTRY/DATA[data]/data": "@data:data",
-  "/ENTRY/DATA[data]/data_errors": "@data:data.errors",  
-  "/ENTRY/DATA[data]/data/@units": "@data:data.units",
+  "/ENTRY/DATA[data]/DATA[data]": "@data:data",
+  "/ENTRY/DATA[data]/DATA[data]/@units": "@data:data.units",
   "/ENTRY/DATA[data]/AXISNAME[*]": "@data:*.data",
   "/ENTRY/DATA[data]/AXISNAME[*]/@units": "@data:*.units"
 }