Merge pull request #44 from OpenCOMPES/fixes-for-nxmpes-arpes

Update example to use NXmpes_arpes

pyproject.toml

@@ -26,12 +26,11 @@ ipywidgets = ">=7.7.1"
 matplotlib = ">=3.5.1"
 numpy = ">=1.21.6"
 opencv-python = ">=4.8.1.78"
-pynxtools-mpes = ">=0.0.1"
-pynxtools = ">=0.3.1"
+pynxtools-mpes = ">=0.1.1"
+pynxtools = ">=0.5.0"
 python-dateutil = ">=2.8.2"
 pyyaml = ">=6.0"
 xarray = ">=0.20.2"
-setuptools = ">50"
 tifffile = ">=2022.5.4"
 tqdm = ">=4.62.3"
 scipy = ">=1.8.0"

specsscan/config/NXmpes_arpes_config.json

@@ -1,8 +1,7 @@
 {
   "/@default": "entry",
   "/ENTRY[entry]/@default": "data",
-  "/ENTRY[entry]/definition": "NXmpes",
-  "/ENTRY[entry]/definition/@version": "None",
+  "/ENTRY[entry]/definition": "NXmpes_arpes",
   "/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",
@@ -15,9 +14,9 @@
   "/ENTRY[entry]/collection_time": "@attrs:metadata/timing/collection_time",
   "/ENTRY[entry]/collection_time/@units": "s",
   "/ENTRY[entry]/USER[user]": {
-    "name": "@attrs:metadata/user0/name",
+    "name": "!@attrs:metadata/user0/name",
     "role": "@attrs:metadata/user0/role",
-    "affiliation": "@attrs:metadata/user0/affiliation",
+    "affiliation": "!@attrs:metadata/user0/affiliation",
     "address": "@attrs:metadata/user0/address",
     "email": "@attrs:metadata/user0/email"
   },
@@ -70,19 +69,19 @@
     "fast_axes": "@attrs:metadata/scan_info/fast_axes",
     "slow_axes": "@attrs:metadata/scan_info/slow_axes",
     "energy_resolution": {
-      "resolution": "@attrs:metadata/instrument/electronanalyser/energy_resolution",
+      "resolution": "!@attrs:metadata/instrument/electronanalyser/energy_resolution",
       "resolution/@units": "meV",
       "physical_quantity": "energy",
       "type": "derived"
     },
     "angular_resolution": {
-      "resolution": "@attrs:metadata/instrument/electronanalyser/angular_resolution",
+      "resolution": "!@attrs:metadata/instrument/electronanalyser/angular_resolution",
       "resolution/@units": "deg",
       "physical_quantity": "angle",
       "type": "derived"
     },
     "spatial_resolution": {
-      "resolution": "@attrs:metadata/instrument/electronanalyser/spatial_resolution",
+      "resolution": "!@attrs:metadata/instrument/electronanalyser/spatial_resolution",
       "resolution/@units": "µm",
       "physical_quantity": "length",
       "type": "estimated"
@@ -135,7 +134,7 @@
     "diameter": 300.0,
     "diameter/@units": "mm",
     "entrance_slit": {
-      "shape": "curved",
+      "shape": "curved slit",
       "size": 1.0,
       "size/@units": "mm"
     },
@@ -169,7 +168,7 @@
   "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_probe]": {
     "distance": 0.0,
     "distance/@units": "mm",
-    "incident_energy": "@attrs:metadata/instrument/beam/probe/incident_energy",
+    "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",
@@ -193,7 +192,7 @@
   "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_pump]": {
     "distance": 0.0,
     "distance/@units": "mm",
-    "incident_energy": "@attrs:metadata/instrument/beam/pump/incident_energy",
+    "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",
@@ -217,7 +216,7 @@
     "temperature_sensor": {
       "name": "sample_temperature",
       "measurement": "temperature",
-      "value": "@attrs:metadata/scan_info/trARPES:Carving:TEMP_RBV",
+      "value": "!@attrs:metadata/scan_info/trARPES:Carving:TEMP_RBV",
       "value/@units": "K"
     },
     "sample_bias_voltmeter": {
@@ -229,7 +228,7 @@
     "drain_current_amperemeter": {
       "name": "drain_current",
       "measurement": "current",
-      "value": "@attrs:metadata/scan_info/trARPES:Sample:Measure",
+      "value": "!@attrs:metadata/scan_info/trARPES:Sample:Measure",
       "value/@units": "A"
     },
     "depends_on": "/entry/instrument/manipulator/transformations/trans_z",
@@ -337,13 +336,13 @@
   },
   "/ENTRY[entry]/data": {
     "@axes": "@data:dims",
-    "AXISNAME_indices[@*_indices]": "@data:*.index",
+    "@*_indices": "@data:*.index",
     "@signal": "data",
     "data": "@data:data",
     "data/@units": "counts",
-    "AXISNAME[*]": "@data:*.data",
-    "AXISNAME[*]/@units": "@data:*.unit",
-    "AXISNAME_depends[@*_depends]": "@attrs:metadata/scan_info/coordinate_depends/*",
+    "*": "@data:*.data",
+    "*/@units": "@data:*.unit",
+    "@*_depends": "@attrs:metadata/scan_info/coordinate_depends/*",
     "energy/@type": "kinetic"
   }
 }

specsscan/config/example_config_FHI.yaml

@@ -55,7 +55,7 @@ nexus:
   # the reader to use
   reader: "mpes"
   # the NeXus definition to use
-  definition: "NXmpes"
+  definition: "NXmpes_arpes"
   # additional input files, e.g. config and ELN files
   input_files: ["../specsscan/config/NXmpes_arpes_config.json"]
 

tests/test_specsscan.py

@@ -4,6 +4,7 @@
 
 import numpy as np
 import pytest
+from pynxtools.dataconverter.convert import ValidationFailed
 
 import specsscan
 from specsanalyzer.core import create_fft_params
@@ -323,8 +324,8 @@ def test_conversion_and_save_to_nexus():
         sps.save("result.tiff")
     sps.save("result.tiff", alias_dict={"X": "angular0", "Y": "angular1"})
     sps.save("result.h5")
-    # with pytest.raises(LookupError):
-    #    sps.save("result.nxs")
+    with pytest.raises(ValidationFailed):
+        sps.save("result.nxs", fail=True)
 
     metadata = {}
     # General
@@ -345,6 +346,10 @@ def test_conversion_and_save_to_nexus():
     metadata["instrument"]["beam"]["probe"] = {}
     metadata["instrument"]["beam"]["probe"]["incident_energy"] = 21.7
 
+    # 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
@@ -357,4 +362,4 @@ def test_conversion_and_save_to_nexus():
         collect_metadata=True,
     )
 
-    sps.save("result.nxs")
+    sps.save("result.nxs", fail=True)

tutorial/3_specsscan_conversion_to_NeXus.ipynb

@@ -124,7 +124,7 @@
    },
    "outputs": [],
    "source": [
-    "config = {\"nexus\":{\"definition\": \"NXmpes\"}, \"spa_params\":{\"crop\":True, \"ek_range_min\":0.07597844332538181, \"ek_range_max\":0.9117413199045858, \"ang_range_min\":0.16453159041394336, \"ang_range_max\":0.8840087145969499,}}\n",
+    "config = {\"nexus\":{\"definition\": \"NXmpes_arpes\"}, \"spa_params\":{\"crop\":True, \"ek_range_min\":0.07597844332538181, \"ek_range_max\":0.9117413199045858, \"ang_range_min\":0.16453159041394336, \"ang_range_max\":0.8840087145969499,}}\n",
     "sps = SpecsScan(config=config, user_config=\"../specsscan/config/example_config_FHI.yaml\")\n",
     "path = \"../tests/data/\" # Path to the test data set"
    ]