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Switches to use Nexus Template for common data model
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@sherjeelshabih
sherjeelshabih committed Apr 15, 2024
1 parent 53472ae commit 4e6c8a8
Showing 1 changed file with 108 additions and 80 deletions.
188 changes: 108 additions & 80 deletions src/nomad_measurements/xrd/schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,8 +58,9 @@
PlotSection,
PlotlyFigure,
)
# from nomad.datamodel.metainfo.eln.nexus_data_converter import populate_nexus_subsection
from pynxtools.dataconverter import convert as dataconverter
from pynxtools.dataconverter.template import Template
from pynxtools_xrd.reader import XRDReader
from pynxtools_xrd.read_file_formats import read_file
from pynxtools_xrd.utils import merge_sections, get_bounding_range_2d
from nomad_measurements import (
Expand All @@ -75,52 +76,9 @@
BoundLogger,
)
import pint
from pynxtools.dataconverter.template import Template

m_package = Package(name='nomad_xrd')


def populate_nexus_subsection(**kwargs):
raise NotImplementedError

def handle_nexus_subsection(
xrd_template: 'Template',
nexus_out: str,
archive: 'EntryArchive',
logger: 'BoundLogger'
):
'''
Function for populating the NeXus section from the xrd_template.
Args:
xrd_template (Template): The xrd data in a NeXus Template.
nexus_out (str): The name of the optional NeXus output file.
archive (EntryArchive): The archive containing the section.
logger (BoundLogger): A structlog logger.
'''
nxdl_name = 'NXxrd_pan'
if nexus_out:
if not nexus_out.endswith('.nxs'):
nexus_out = nexus_out + '.nxs'
populate_nexus_subsection(
template=xrd_template,
app_def=nxdl_name,
archive=archive,
logger=logger,
output_file_path=nexus_out,
on_temp_file=False,
)
else:
populate_nexus_subsection(
template=xrd_template,
app_def=nxdl_name,
archive=archive,
logger=logger,
output_file_path=nexus_out,
on_temp_file=True,
)


def calculate_two_theta_or_q(
wavelength: 'pint.Quantity',
q: 'pint.Quantity'=None,
Expand Down Expand Up @@ -707,56 +665,113 @@ class ELNXRayDiffraction(XRayDiffraction, EntryData, PlotSection):

def write_xrd_data(
self,
xrd_dict: Dict[str, Any],
xrd_dict: Template,
archive: 'EntryArchive',
logger: 'BoundLogger',
) -> None:
'''
Write method for populating the `ELNXRayDiffraction` section from a dict.
Args:
xrd_dict (Dict[str, Any]): A dictionary with the XRD data.
xrd_dict (Template): A NeXus Dataconverter Template with the XRD data.
archive (EntryArchive): The archive containing the section.
logger (BoundLogger): A structlog logger.
'''
metadata_dict: dict = xrd_dict.get('metadata', {})
source_dict: dict = metadata_dict.get('source', {})

scan_type = metadata_dict.get('scan_type', None)
scan_type = xrd_dict.get("/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/scan_mode")
if scan_type == 'line':
result = XRDResult1D(
intensity=xrd_dict.get('intensity', None),
two_theta=xrd_dict.get('2Theta', None),
omega=xrd_dict.get('Omega', None),
chi=xrd_dict.get('Chi', None),
phi=xrd_dict.get('Phi', None),
scan_axis=metadata_dict.get('scan_axis', None),
integration_time=xrd_dict.get('countTime', None),
intensity=xrd_dict.get(
'/ENTRY[entry]/2theta_plot/intensity',
None,
),
two_theta=xrd_dict.get(
'/ENTRY[entry]/2theta_plot/two_theta',
None,
),
omega=xrd_dict.get(
'/ENTRY[entry]/2theta_plot/omega',
None,
),
chi=xrd_dict.get(
'/ENTRY[entry]/2theta_plot/chi',
None),
phi=xrd_dict.get(
'/ENTRY[entry]/2theta_plot/phi',
None,
),
scan_axis=xrd_dict.get(
'/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/scan_axis',
None,
),
integration_time=xrd_dict.get(
'/ENTRY[entry]/COLLECTION[collection]/count_time',
None
),
)
result.normalize(archive, logger)

elif scan_type == 'rsm':
result = XRDResultRSM(
intensity=xrd_dict.get('intensity', None),
two_theta=xrd_dict.get('2Theta', None),
omega=xrd_dict.get('Omega', None),
chi=xrd_dict.get('Chi', None),
phi=xrd_dict.get('Phi', None),
scan_axis=metadata_dict.get('scan_axis', None),
integration_time=xrd_dict.get('countTime', None),
intensity=xrd_dict.get(
'/ENTRY[entry]/2theta_plot/intensity',
None,
),
two_theta=xrd_dict.get(
'/ENTRY[entry]/2theta_plot/two_theta',
None,
),
omega=xrd_dict.get(
'/ENTRY[entry]/2theta_plot/omega',
None,
),
chi=xrd_dict.get(
'/ENTRY[entry]/2theta_plot/chi',
None),
phi=xrd_dict.get(
'/ENTRY[entry]/2theta_plot/phi',
None,
),
scan_axis=xrd_dict.get(
'/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/scan_axis',
None,
),
integration_time=xrd_dict.get(
'/ENTRY[entry]/COLLECTION[collection]/count_time',
None
),
)
result.normalize(archive, logger)
else:
raise NotImplementedError(f'Scan type `{scan_type}` is not supported.')

source = XRayTubeSource(
xray_tube_material=source_dict.get('anode_material', None),
kalpha_one=source_dict.get('kAlpha1', None),
kalpha_two=source_dict.get('kAlpha2', None),
ratio_kalphatwo_kalphaone=source_dict.get('ratioKAlpha2KAlpha1', None),
kbeta=source_dict.get('kBeta', None),
xray_tube_voltage=source_dict.get('voltage', None),
xray_tube_current=source_dict.get('current', None),
xray_tube_material=xrd_dict.get(
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_material',
None,
),
kalpha_one=xrd_dict.get(
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_one',
None,
),
kalpha_two=xrd_dict.get(
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_two',
None,
),
ratio_kalphatwo_kalphaone=xrd_dict.get(
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/ratio_k_alphatwo_k_alphaone',
None,
),
kbeta=xrd_dict.get(
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/kbeta',
None,
),
xray_tube_voltage=xrd_dict.get(
'ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_voltage',
None
),
xray_tube_current=xrd_dict.get(
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_current',
None,
),
)
source.normalize(archive, logger)

Expand All @@ -766,7 +781,7 @@ def write_xrd_data(
xrd_settings.normalize(archive, logger)

sample = CompositeSystemReference(
lab_id=metadata_dict.get('sample_id', None),
lab_id=xrd_dict.get('/ENTRY[entry]/SAMPLE[sample]/sample_id', None),
)
sample.normalize(archive, logger)

Expand All @@ -777,11 +792,21 @@ def write_xrd_data(
)
merge_sections(self, xrd, logger)

if self.generate_nexus_file:
archive_name = archive.metadata.mainfile.split('.')[0]
nexus_output = f'{archive_name}_output.nxs'
dataconverter.logger = logger
dataconverter.convert(input_file=[], output="todo-add_name_for_this_file.nxs", reader="xrd", nxdl="NXxrd_pan", objects=(xrd_dict,))

archive_name = archive.metadata.mainfile.split('.')[0]
nexus_output = f'{archive_name}.nxs'
dataconverter.logger = logger
with archive.m_context.raw_file(self.data_file) as file:
dataconverter.convert(input_file=[file.name], output=nexus_output, reader="xrd", nxdl="NXxrd_pan", skip_verify=True)
# TODO: Need to check what NeXus definitions version can parse this NXxrd_pan
# from nomad.parsing.nexus.nexus import NexusParser
# nexus_parser = NexusParser()
# nexus_parser.parse(mainfile=nexus_output, archive=archive, logger=logger)
if not self.generate_nexus_file:
import os
with archive.m_context.raw_file(nexus_output) as file:
os.remove(file.name)


def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger'):
"""
Expand All @@ -794,8 +819,11 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger'):
"""
if self.data_file is not None:
with archive.m_context.raw_file(self.data_file) as file:
xrd_dict = read_file(file.name)
self.write_xrd_data(xrd_dict, archive, logger)
nxdl_root, nxdl_f_path = dataconverter.get_nxdl_root_and_path("NXxrd_pan")
template = Template()
dataconverter.helpers.generate_template_from_nxdl(nxdl_root, template)
filled_template = XRDReader().read(template, [file.name])
self.write_xrd_data(filled_template, archive, logger)
super().normalize(archive, logger)
self.figures = self.results[0].generate_plots(archive, logger)

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