app def missing. (#108)

* Implement write nexus section based on the populated nomad archive * app def missing. * mapping nomad_measurement. * All concept are connected, creates nexus file and subsection. * adding links in hdf5 file. * Remove the nxs file. * back to the previous design. * Include pynxtools plugins in nomad.yaml and extend dependencies including pynxtools ans pnxtools-xrd. * PR review correction. * Remove the entry_type overwtitten. * Remove comments. * Replace __str__ function. * RUFF * Update pyproject.toml Co-authored-by: Sarthak Kapoor <[email protected]> * Update src/nomad_measurements/xrd/schema.py Co-authored-by: Sarthak Kapoor <[email protected]> * Update src/nomad_measurements/xrd/nx.py * Replace Try-block. --------- Co-authored-by: Sarthak Kapoor <[email protected]> Co-authored-by: Sarthak Kapoor <[email protected]>
FAIRmat-NFDI · Aug 28, 2024 · 6588892 · 6588892
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diff --git a/pyproject.toml b/pyproject.toml
@@ -32,7 +32,7 @@ dependencies = [
     "nomad-lab>=1.3.4dev", 
     "xmltodict==0.13.0",
     "fairmat-readers-xrd~=0.0.3",
-    "pynxtools", 
+    "pynxtools>=0.6.1",
 ]
 [project.urls]
 "Homepage" = "https://github.com/FAIRmat-NFDI/nomad-measurements"

diff --git a/src/nomad_measurements/xrd/nx.py b/src/nomad_measurements/xrd/nx.py
@@ -0,0 +1,182 @@
+#
+# 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.
+#
+from typing import TYPE_CHECKING
+
+from pynxtools import dataconverter
+from pynxtools.nomad.dataconverter import populate_nexus_subsection
+
+if TYPE_CHECKING:
+    from nomad.datamodel.datamodel import EntryArchive
+    from structlog.stdlib import (
+        BoundLogger,
+    )
+
+
+def walk_through_object(parent_obj, attr_chain, default=None):
+    """
+    Walk though the object until reach the leaf.
+
+    Args:
+        parent_obj: This is a python obj.
+        attr_chain: Dot separated obj chain.
+        default: A value to be returned by default, if not data is found.
+    """
+    expected_parts = 2
+    if isinstance(attr_chain, str):
+        parts = attr_chain.split('.', 1)
+
+        if len(parts) == expected_parts:
+            child_nm, rest_part = parts
+            if '[' in child_nm:
+                child_nm, index = child_nm.split('[')
+                index = int(index[:-1])
+                child_obj = getattr(parent_obj, child_nm)[index]
+            else:
+                child_obj = getattr(parent_obj, child_nm)
+            return walk_through_object(child_obj, rest_part, default=default)
+        else:
+            return getattr(parent_obj, attr_chain, default)
+
+
+def connect_concepts(template, archive: 'EntryArchive', scan_type: str):  # noqa: PLR0912
+    """
+    Connect the concepts between `ELNXrayDiffraction` and `NXxrd_pan` schema.
+
+    Args:
+        template (Template): The pynxtools template, a inherited class from python dict.
+        archive (EntryArchive): Nomad archive contains secttions, subsections and
+            quantities.
+        scan_type (str): Name of the scan type such as line and RSM.
+    """
+
+    # General concepts
+    # ruff: noqa: E501
+    concept_map = {
+        '/ENTRY[entry]/method': 'archive.data.method',
+        '/ENTRY[entry]/measurement_type': 'archive.data.diffraction_method_name',
+        '/ENTRY[entry]/experiment_result/intensity': 'archive.data.results[0].intensity.magnitude',
+        '/ENTRY[entry]/experiment_result/two_theta': 'archive.data.results[0].two_theta.magnitude',
+        '/ENTRY[entry]/experiment_result/two_theta/@units': 'archive.data.results[0].two_theta.units',
+        '/ENTRY[entry]/experiment_result/omega': 'archive.data.results[0].omega.magnitude',
+        '/ENTRY[entry]/experiment_result/omega/@units': 'archive.data.results[0].omega.units',
+        '/ENTRY[entry]/experiment_result/chi': 'archive.data.results[0].chi.magnitude',
+        '/ENTRY[entry]/experiment_result/chi/@units': 'archive.data.results[0].chi.units',
+        '/ENTRY[entry]/experiment_result/phi': 'archive.data.results[0].phi.magnitude',
+        '/ENTRY[entry]/experiment_result/phi/@units': 'archive.data.results[0].phi.units',
+        '/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/scan_axis': 'archive.data.results[0].scan_axis',
+        '/ENTRY[entry]/experiment_config/count_time': 'archive.data.results[0].count_time.magnitude',
+        'line': '',  # For future implementation
+        'rsm': {
+            '/ENTRY[entry]/experiment_result/q_parallel': 'archive.data.results[0].q_parallel',
+            '/ENTRY[entry]/experiment_result/q_parallel/@units': 'archive.data.results[0].q_parallel.units',
+            '/ENTRY[entry]/experiment_result/q_perpendicular': 'archive.data.results[0].q_perpendicular.magnitude',
+            '/ENTRY[entry]/experiment_result/q_perpendicular/@units': 'archive.data.results[0].q_perpendicular.units',
+            '/ENTRY[entry]/experiment_result/q_norm': 'archive.data.results[0].q_norm.magnitude',
+            '/ENTRY[entry]/experiment_result/q_norm/@units': 'archive.data.results[0].q_norm.units',
+        },
+        # Source
+        '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_material': 'archive.data.xrd_settings.source.xray_tube_material',
+        '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_current': 'archive.data.xrd_settings.source.xray_tube_current.magnitude',
+        '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_current/@units': 'archive.data.xrd_settings.source.xray_tube_current.units',
+        '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_voltage': 'archive.data.xrd_settings.source.xray_tube_voltage.magnitude',
+        '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_voltage/@units': 'archive.data.xrd_settings.source.xray_tube_voltage.units',
+        '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_one': 'archive.data.xrd_settings.source.kalpha_one.magnitude',
+        '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_one/@units': 'archive.data.xrd_settings.source.kalpha_one.units',
+        '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_two': 'archive.data.xrd_settings.source.kalpha_two.magnitude',
+        '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_two/@units': 'archive.data.xrd_settings.source.kalpha_two.units',
+        '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/ratio_k_alphatwo_k_alphaone': 'archive.data.xrd_settings.source.ratio_kalphatwo_kalphaone',
+        '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/kbeta': 'archive.data.xrd_settings.source.kbeta.magnitude',
+        '/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/kbeta/@units': 'archive.data.xrd_settings.source.kbeta.units',
+    }
+
+    for key, archive_concept in concept_map.items():
+        if isinstance(archive_concept, dict):
+            if key == scan_type:
+                for sub_key, sub_archive_concept in archive_concept.items():
+                    _, arch_attr = sub_archive_concept.split('.', 1)
+                    value = None
+                    try:
+                        value = walk_through_object(archive, arch_attr)
+                    except (AttributeError, IndexError, KeyError, ValueError):
+                        pass
+                    finally:
+                        if value is not None:
+                            template[sub_key] = (
+                                str(value) if sub_key.endswith('units') else value
+                            )
+            else:
+                continue
+        elif archive_concept:
+            _, arch_attr = archive_concept.split('.', 1)
+            value = None
+            try:
+                value = walk_through_object(archive, arch_attr)
+            # Use multiple excepts to avoid catching all exceptions
+            except (AttributeError, IndexError, KeyError, ValueError):
+                pass
+            finally:
+                if value is not None:
+                    template[key] = str(value) if key.endswith('units') else value
+
+    template['/ENTRY[entry]/definition'] = 'NXxrd_pan'
+
+    # Links to the data and concepts
+    template['/ENTRY[entry]/@default'] = 'experiment_result'
+    template['/ENTRY[entry]/experiment_result/@signal'] = 'intensity'
+    template['/ENTRY[entry]/experiment_result/@axes'] = 'two_theta'
+    template['/ENTRY[entry]/q_data/q'] = {
+        'link': '/ENTRY[entry]/experiment_result/q_norm'
+    }
+    template['/ENTRY[entry]/q_data/intensity'] = {
+        'link': '/ENTRY[entry]/experiment_result/intensity'
+    }
+    template['/ENTRY[entry]/q_data/q_parallel'] = {
+        'link': '/ENTRY[entry]/experiment_result/q_parallel'
+    }
+    template['/ENTRY[entry]/q_data/q_perpendicular'] = {
+        'link': '/ENTRY[entry]/experiment_result/q_perpendicular'
+    }
+
+
+def write_nx_section_and_create_file(
+    archive: 'EntryArchive', logger: 'BoundLogger', scan_type: str = 'line'
+):
+    """
+    Uses the archive to generate the NeXus section and .nxs file.
+
+    Args:
+        archive (EntryArchive): The archive containing the section.
+        logger (BoundLogger): A structlog logger.
+        generate_nexus_file (boolean): If True, the function will generate a .nxs file.
+        nxs_as_entry (boolean): If True, the function will generate a .nxs file
+                as a nomad entry.
+    """
+    nxdl_root, _ = dataconverter.helpers.get_nxdl_root_and_path('NXxrd_pan')
+    template = dataconverter.template.Template()
+    dataconverter.helpers.generate_template_from_nxdl(nxdl_root, template)
+    connect_concepts(template, archive, scan_type=scan_type)
+    archive_name = archive.metadata.mainfile.split('.')[0]
+    nexus_output = f'{archive_name}.nxs'
+
+    populate_nexus_subsection(
+        template=template,
+        app_def='NXxrd_pan',
+        archive=archive,
+        logger=logger,
+        output_file_path=nexus_output,
+    )
diff --git a/src/nomad_measurements/xrd/schema.py b/src/nomad_measurements/xrd/schema.py
@@ -68,20 +68,17 @@
     NOMADMeasurementsCategory,
 )
 from nomad_measurements.utils import get_bounding_range_2d, merge_sections
+from nomad_measurements.xrd.nx import write_nx_section_and_create_file
 
 if TYPE_CHECKING:
     import pint
     from nomad.datamodel.datamodel import (
         EntryArchive,
     )
-    from pynxtools.dataconverter.template import Template
     from structlog.stdlib import (
         BoundLogger,
     )
-    import pint
 
-from pynxtools.nomad.dataconverter import populate_nexus_subsection
-from pynxtools import dataconverter
 
 from nomad.config import config
 
@@ -862,6 +859,7 @@ class ELNXRayDiffraction(XRayDiffraction, EntryData, PlotSection):
     generate_nexus_file = Quantity(
         type=bool,
         description='Whether or not to generate a NeXus output file (if possible).',
+        default=True,
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.BoolEditQuantity,
             label='Generate NeXus file',
@@ -957,41 +955,6 @@ def write_xrd_data(
         )
         merge_sections(self, xrd, logger)
 
-    def write_nx_section_and_create_file(
-        self, archive: 'EntryArchive', logger: 'BoundLogger'
-    ):
-        """
-        Uses the archive to generate the NeXus section and .nxs file.
-
-        Args:
-            archive (EntryArchive): The archive containing the section.
-            logger (BoundLogger): A structlog logger.
-        """
-        nxdl_root, _ = dataconverter.helpers.get_nxdl_root_and_path('NXxrd_pan')
-        template = dataconverter.template.Template()
-        dataconverter.helpers.generate_template_from_nxdl(nxdl_root, template)
-
-        template['/ENTRY[entry]/2theta_plot/intensity'] = archive.data.results[
-            0
-        ].intensity.magnitude
-        template['/ENTRY[entry]/2theta_plot/two_theta'] = archive.data.results[
-            0
-        ].two_theta.magnitude
-        template['/ENTRY[entry]/2theta_plot/two_theta/@units'] = str(
-            archive.data.results[0].two_theta.units
-        )
-        archive_name = archive.metadata.mainfile.split('.')[0]
-        nexus_output = f'{archive_name}_output.nxs'
-
-        populate_nexus_subsection(
-            template=template,
-            app_def='NXxrd_pan',
-            archive=archive,
-            logger=logger,
-            output_file_path=nexus_output,
-            on_temp_file=self.generate_nexus_file,
-        )
-
     def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger'):
         """
         The normalize function of the `ELNXRayDiffraction` section.
@@ -1014,7 +977,11 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger'):
         super().normalize(archive, logger)
         if not self.results:
             return
-        self.write_nx_section_and_create_file(archive, logger)
+
+        scan_type = xrd_dict.get('metadata', {}).get('scan_type', None)
+        if self.generate_nexus_file and self.data_file is not None:
+            write_nx_section_and_create_file(archive, logger, scan_type=scan_type)
+
         self.figures = self.results[0].generate_plots(archive, logger)
 
 

diff --git a/tests/test_parser.py b/tests/test_parser.py
@@ -47,8 +47,9 @@ def parsed_archive(request):
 
     yield measurement_archive
 
-    if os.path.exists(measurement):
-        os.remove(measurement)
+    for file_path in [measurement, measurement.replace('archive.json', 'nxs')]:
+        if os.path.exists(file_path):
+            os.remove(file_path)
 
 
 def test_normalize_all(parsed_archive):