Fixes NXsensor_scan and axes attribute error (#237)

* Updates definitions * Fix reading of items over the length of the axes array * Update nexus version file * Updates reference files * Updates eln schema file
FAIRmat-NFDI · Feb 13, 2024 · ea64cbf · ea64cbf
1 parent 62afeb7
commit ea64cbf
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Showing 6 changed files with 14 additions and 9 deletions.
diff --git a/pynxtools/definitions b/pynxtools/definitions
diff --git a/pynxtools/nexus-version.txt b/pynxtools/nexus-version.txt
@@ -1 +1 @@
-v2020.10-1452-gd2fdad4f
+v2020.10-1459-g364a77d1
diff --git a/pynxtools/nexus/nexus.py b/pynxtools/nexus/nexus.py
@@ -2,12 +2,12 @@
 """Read files from different format and print it in a standard NeXus format
 """
 
+import logging
 import os
-
 import sys
-import logging
-import h5py
+
 import click
+import h5py
 
 from pynxtools.nexus.nxdl_utils import *  # pylint: disable=wildcard-import, unused-wildcard-import
 
@@ -560,7 +560,9 @@ def get_single_or_multiple_axes(nxdata, ax_datasets, a_item, ax_list):
                 if ind and isinstance(ind, int):
                     if ind == a_item:
                         ax_list.append(nxdata[aax])
-            if not ax_list:  # positional determination of the dimension number
+            if not ax_list and a_item < len(
+                ax_datasets
+            ):  # positional determination of the dimension number
                 ax_list.append(nxdata[ax_datasets[a_item]])
     except KeyError:
         pass

diff --git a/tests/data/dataconverter/readers/mpes/Ref_nexus_mpes.log b/tests/data/dataconverter/readers/mpes/Ref_nexus_mpes.log
@@ -2111,8 +2111,11 @@ DEBUG - ===== FIELD (//entry/instrument/electronanalyser/collectioncolumn/lens_m
 DEBUG - value: b'6kV_kmodem2.0_30VTOF_MoTe2_2340VMCP.sav' 
 DEBUG - classpath: ['NXentry', 'NXinstrument', 'NXelectronanalyser', 'NXcollectioncolumn', 'NX_CHAR']
 DEBUG - classes:
+NXmpes.nxdl.xml:/ENTRY/INSTRUMENT/ELECTRONANALYSER/COLLECTIONCOLUMN/lens_mode
 NXcollectioncolumn.nxdl.xml:/lens_mode
-DEBUG - <<OPTIONAL>>
+DEBUG - <<RECOMMENDED>>
+DEBUG - documentation (NXmpes.nxdl.xml:/ENTRY/INSTRUMENT/ELECTRONANALYSER/COLLECTIONCOLUMN/lens_mode):
+DEBUG - 
 DEBUG - documentation (NXcollectioncolumn.nxdl.xml:/lens_mode):
 DEBUG - 
              Labelling of the lens setting in use.

diff --git a/tests/data/eln_mapper/eln.yaml b/tests/data/eln_mapper/eln.yaml
@@ -9,7 +9,7 @@ Instrument:
         vendor: null
       field_aperture: null
       iris: null
-      mode: null
+      lens_mode: null
       projection: null
       scheme: null
       spatial_acceptance: null

diff --git a/tests/data/eln_mapper/mpes.scheme.archive.yaml b/tests/data/eln_mapper/mpes.scheme.archive.yaml
@@ -350,7 +350,7 @@ definitions:
                                 component: StringEditQuantity
                                 defaultDisplayUnit: <No Default unit>
                             description: ' Scheme of the electron collection column. '
-                          mode:
+                          lens_mode:
                             type: str
                             m_annotations:
                               eln:
+6 −0		contributed_definitions/NXelectronanalyser.nxdl.xml
+0 −7		contributed_definitions/NXenergydispersion.nxdl.xml
+1 −2		contributed_definitions/NXmpes.nxdl.xml
+6 −6		contributed_definitions/NXsensor_scan.nxdl.xml
+12 −1		contributed_definitions/nyaml/NXelectronanalyser.yaml
+1 −14		contributed_definitions/nyaml/NXenergydispersion.yaml
+3 −6		contributed_definitions/nyaml/NXmpes.yaml
+1 −1		contributed_definitions/nyaml/NXsensor_scan.yaml
+0 −1		dev_tools/docs/xsd_units.py
+1 −1		dev_tools/globals/urls.py
+1 −0		dev_tools/tests/test_nxdl_utils.py
+2 −2		manual/source/conf.py
+1 −1		requirements.txt