Added xraydb to get all X-ray emission lines

dev-requirements.txt

@@ -108,6 +108,8 @@ gitdb==4.0.11
     # via gitpython
 gitpython==3.1.40
     # via pynxtools (pyproject.toml)
+greenlet==3.0.3
+    # via sqlalchemy
 h5py==3.10.0
     # via
     #   fabio
@@ -297,6 +299,7 @@ numpy==1.24.4
     #   tables
     #   tifffile
     #   xarray
+    #   xraydb
     #   zarr
 numpy-quaternion==2022.4.3
     # via orix
@@ -319,6 +322,7 @@ packaging==23.2
     #   scikit-image
     #   tables
     #   xarray
+    #   xraydb
 pandas==2.0.3
     # via
     #   ifes-apt-tc-data-modeling
@@ -352,6 +356,7 @@ platformdirs==4.0.0
     #   pooch
     #   pylint
     #   requests-cache
+    #   xraydb
 pluggy==1.3.0
     # via pytest
 ply==3.11
@@ -470,6 +475,7 @@ scipy==1.9.1
     #   scikit-image
     #   scikit-learn
     #   sparse
+    #   xraydb
 silx==1.1.2
     # via pyfai
 six==1.16.0
@@ -482,6 +488,8 @@ smmap==5.0.1
     # via gitdb
 sparse==0.14.0
     # via hyperspy
+sqlalchemy==2.0.25
+    # via xraydb
 stack-data==0.6.3
     # via ipython
 structlog==23.2.0
@@ -555,6 +563,7 @@ typing-extensions==4.8.0
     #   astroid
     #   cattrs
     #   mypy
+    #   sqlalchemy
 tzdata==2023.3
     # via
     #   pandas
@@ -582,6 +591,8 @@ xarray==2023.1.0
     # via pynxtools (pyproject.toml)
 xmltodict==0.13.0
     # via pynxtools (pyproject.toml)
+xraydb==4.5.4
+    # via pynxtools (pyproject.toml)
 zarr==2.16.1
     # via hyperspy
 zipp==3.17.0

pynxtools/dataconverter/readers/em/concepts/nxs_concepts.py

@@ -17,7 +17,7 @@
 #
 """Implement NeXus-specific groups and fields to document software and versions used."""
 
-# pylint: disable=no-member
+# pylint: disable=no-member,too-few-members
 
 from typing import List
 from pynxtools.dataconverter.readers.em.concepts.concept_mapper \
@@ -59,3 +59,13 @@ def parse(self, template: dict, entry_id: int = 1, cmd_line_args: List = []) ->
             template["/cs_profiling/@NX_class"] = "NXcs_profiling"
             template["/cs_profiling/command_line_call"] = cmd_line_args
         return template
+
+
+class NxConcept():
+    """"Define a NeXus concept object to handle paths.
+
+    """
+    def __init__(self, hdf_paths: List = []):
+        # TODO::remove redundant code for instantiating specific NxConcepts like
+        # NxSpectrum, NxImageRealSpaceSet, NxEmEdsIndexing
+        pass

pynxtools/dataconverter/readers/em/concepts/nxs_em_eds_indexing.py

@@ -0,0 +1,54 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+"""NXem_eds indexing instance data."""
+
+from typing import Dict, List
+
+from pynxtools.dataconverter.readers.em.concepts.nxs_object import NxObject
+
+
+NX_EM_EDS_INDEXING_HDF_PATH = ["indexing-group",
+                               "indexing/element_names-field",
+                               "indexing/IMAGE_R_SET-group",
+                               "indexing/IMAGE_R_SET/PROCESS-group",
+                               "indexing/IMAGE_R_SET/PROCESS/peaks-field",
+                               "indexing/IMAGE_R_SET/PROCESS/weights-field",
+                               "indexing/PEAK-group",
+                               "indexing/PEAK/ION-group",
+                               "indexing/PEAK/ION/energy-field",
+                               "indexing/PEAK/ION/energy_range-field",
+                               "indexing/PEAK/ION/iupac_line_names-field",
+                               "indexing/PROGRAM-group",
+                               "indexing/summary-group",
+                               "indexing/summary/axis_energy-field",
+                               "indexing/summary/axis_energy@long_name-attribute",
+                               "indexing/summary/intensity-field",
+                               "indexing/summary/intensity@long_name-attribute"]
+
+
+class NxEmEdsIndexing():
+    def __init__(self):
+        self.tmp: Dict = {}
+        self.tmp["source"] = None
+        for entry in NX_EM_EDS_INDEXING_HDF_PATH:
+            if entry.endswith("-field") is True:
+                self.tmp[entry[0:len(entry) - len("-field")]] = NxObject(eqv_hdf="dataset")
+            elif entry.endswith("-attribute") is True:
+                self.tmp[entry[0:len(entry) - len("-attribute")]] = NxObject(eqv_hdf="attribute")
+            else:
+                self.tmp[entry[0:len(entry) - len("-group")]] = NxObject(eqv_hdf="group")

pynxtools/dataconverter/readers/em/concepts/nxs_image_r_set.py

@@ -17,9 +17,6 @@
 #
 """NXem spectrum set (element of a labelled property graph) to store instance data."""
 
-# pylint: disable=no-member,too-few-public-methods
-
-
 from typing import Dict
 
 from pynxtools.dataconverter.readers.em.concepts.nxs_object import NxObject

pynxtools/dataconverter/readers/em/concepts/nxs_spectrum_set.py

@@ -17,9 +17,6 @@
 #
 """NXem spectrum set (element of a labelled property graph) to store instance data."""
 
-# pylint: disable=no-member,too-few-public-methods
-
-
 from typing import Dict, List
 
 from pynxtools.dataconverter.readers.em.concepts.nxs_object import NxObject

pynxtools/dataconverter/readers/em/subparsers/hfive_apex.py

@@ -201,6 +201,11 @@ def parse_and_normalize(self):
                                         h5r, f"/{grp_nm}/{sub_grp_nm}/{sub_sub_grp_nm}/{area_grp_nm}", ckey)
                                     cache_id += 1
 
+                                    ckey = self.init_named_cache(f"eds_map{cache_id}")
+                                    self.parse_and_normalize_eds_rois(
+                                        h5r, f"/{grp_nm}/{sub_grp_nm}/{sub_sub_grp_nm}/{area_grp_nm}", ckey)
+                                    cache_id += 1
+
     def parse_and_normalize_group_ebsd_header(self, fp, ckey: str):
         # no official documentation yet from EDAX/APEX, deeply nested, chunking, virtual ds
         if f"{self.prfx}/EBSD/ANG/DATA/DATA" not in fp:
@@ -581,3 +586,7 @@ def parse_and_normalize_eds_lsd(self, fp, src: str, ckey: str):
         for key, val in self.tmp[ckey].tmp.items():
             if key.startswith("spectrum_oned"):
                 print(f"spectrum_oned, key: {key}, val: {val}")
+
+    def parse_and_normalize_eds_rois(self, fp, src: str, ckey: str):
+        """Normalize and scale APEX-specific EDS element emission line maps to NeXus."""
+

pyproject.toml

@@ -30,9 +30,10 @@ dependencies = [
     "pandas>=1.3.2",
     "odfpy>=1.4.1",
     "ase>=3.19.0",
-    "flatdict>=4.0.1",
-    "hyperspy>=1.7.6",
-    "rosettasciio>=0.2",
+    "flatdict",
+    "hyperspy",
+    "rosettasciio",
+    "xraydb",
     "ifes_apt_tc_data_modeling>=0.1",
     "gitpython>=3.1.24",
     "pytz>=2021.1",