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All modifications related to HDF Reference implementation.
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@RubelMozumder
RubelMozumder committed Aug 29, 2024
1 parent 8bf889f commit fbba60f
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Showing 2 changed files with 352 additions and 149 deletions.
197 changes: 187 additions & 10 deletions src/nomad_measurements/xrd/nx.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
# limitations under the License.
#
from typing import TYPE_CHECKING
from nomad_measurements import xrd
from pynxtools.nomad.dataconverter import populate_nexus_subsection
from pynxtools import dataconverter

Expand All @@ -25,7 +26,7 @@


# source_peak_wavelength
def connect_concepts(template, archive: 'EntryArchive', scan_type: str):
def connect_concepts_from_archive(archive: 'EntryArchive', template, scan_type: str):
"""Connect the concepts between ELNXrayDiffraction and NXxrd_pan schema."""

# Genneral concepts
Expand Down Expand Up @@ -229,36 +230,212 @@ def connect_concepts(template, archive: 'EntryArchive', scan_type: str):
"link": "/ENTRY[entry]/experiment_result/q_perpendicular"
}

# source_peak_wavelength
def connect_concepts_from_dict(xrd_dict, archive: 'EntryArchive', template, scan_type: str):
"""Connect the concepts between ELNXrayDiffraction and NXxrd_pan schema."""

eln_dict = xrd_dict['eln_dict']
# Genneral concepts
template['/ENTRY[entry]/definition'] = 'NXxrd_pan'

try:
print(' #################### ', eln_dict)

template['/ENTRY[entry]/method'] = eln_dict['method']
print(' #################### ')
except KeyError as e:
pass

try:
template['/ENTRY[entry]/measurement_type'] = eln_dict['diffraction_method_name']
except KeyError as e:
pass

# Source
try:
template[
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_material'
] = eln_dict['xray_tube_material']
except KeyError as e:
pass

try:
template[
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_current'
] = eln_dict['xray_tube_current']
template[
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_current/@units'
] = eln_dict['xray_tube_current/unit']
except KeyError as e:
pass

try:
template[
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_voltage'
] = eln_dict['xray_tube_voltage']
template[
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_voltage/@units'
] = eln_dict['xray_tube_voltage/unit']
except KeyError as e:
pass

try:
template[
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_one'
] = eln_dict['kalpha_one']
template[
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_one/@units'
] = eln_dict['kalpha_one/unit']
except KeyError as e:
pass

try:
template[
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_two'
] = eln_dict['kalpha_two']
template[
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_two/@units'
] = eln_dict['kalpha_two/unit']
except KeyError as e:
pass

try:
template[
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/ratio_k_alphatwo_k_alphaone'
] = eln_dict['ratio_kalphatwo_kalphaone']
except KeyError as e:
pass

try:
template['/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/kbeta'] = eln_dict['kbeta']
template[
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/kbeta/@units'
] = eln_dict['kbeta/unit']
except KeyError as e:
pass

# Result or scattering data
try:
template['/ENTRY[entry]/experiment_result/intensity'] = xrd_dict['intensity']
template['/ENTRY[entry]/experiment_result/intensity/@units'] = 'counts per second'
except KeyError as e:
pass

try:
template['/ENTRY[entry]/experiment_result/two_theta'] = xrd_dict['2Theta']
template['/ENTRY[entry]/experiment_result/two_theta/@units'] = 'deg'
except KeyError as e:
pass

try:
template['/ENTRY[entry]/experiment_result/omega'] = xrd_dict['Omega'],
template['/ENTRY[entry]/experiment_result/omega/@units'] = 'deg'
except KeyError as e:
pass

try:
template['/ENTRY[entry]/experiment_result/chi'] = xrd_dict['Chi']
template['/ENTRY[entry]/experiment_result/chi/@units'] = 'deg'
except KeyError as e:
pass

try:
template['/ENTRY[entry]/experiment_result/phi'] = xrd_dict['Phi']
template['/ENTRY[entry]/experiment_result/phi/@units'] = 'deg'
except KeyError as e:
pass

try:
template[
'/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/scan_axis'
] = xrd_dict['metadata']['scan_axis']
except KeyError as e:
pass

try:
template['/ENTRY[entry]/experiment_config/count_time'] = xrd_dict['countTime']
template['/ENTRY[entry]/experiment_config/count_time/@units'] = 's'
except KeyError as e:
pass
try:
template['/ENTRY[entry]/experiment_result/q_norm'] = xrd_dict['q_norm']
template['/ENTRY[entry]/experiment_result/q_norm/@units'] = '1/m'
except KeyError as e:
pass


if scan_type == 'line':
pass
# rsm
elif scan_type == 'rsm':
try:
template['/ENTRY[entry]/experiment_result/q_parallel'] = xrd_dict['q_parallel']
template['/ENTRY[entry]/experiment_result/q_parallel/@units'] = '1/m'
except KeyError as e:
pass

try:
template['/ENTRY[entry]/experiment_result/q_perpendicular'] = xrd_dict['q_perpendicular']
template['/ENTRY[entry]/experiment_result/q_perpendicular/@units'] = '1/m'
except KeyError as e:
pass


# 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/experiment_result/q_norm"
}
template["/ENTRY[entry]/q_data/intensity"] = {
"link": "/entry/experiment_result/intensity"
}
template["/ENTRY[entry]/q_data/q_parallel"] = {
"link": "/entry/experiment_result/q_parallel"
}
template["/ENTRY[entry]/q_data/q_perpendicular"] = {
"link": "/entry/experiment_result/q_perpendicular"
}


def write_nx_section_and_create_file(archive: 'EntryArchive',
logger: 'BoundLogger',
generate_nexus_file,
nxs_as_entry):
nx_file,
nxs_as_entry,
scan_type,
xrd_dict = None,
):
'''
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.
nx_file (str): The name of the .nxs file to be generated
nxs_as_entry (boolean): If True, the function will generate a .nxs file
as a nomad entry.
scan_type (str): The type of scan, either 'line' or 'rsm'
xrd_dict (dict): A dictionary containing the data from experiment file and
eln data under the key 'eln_dict
'''
entry_type = archive.metadata.entry_type
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='line')
archive_name = archive.metadata.mainfile.split('.')[0]
nexus_output = f'{archive_name}_output.nxs'
# connect_concepts_from_archive(archive, template, scan_type='line')
connect_concepts_from_dict(xrd_dict=xrd_dict,
archive=archive,
template=template,
scan_type=scan_type)

populate_nexus_subsection(
template=template,
app_def="NXxrd_pan",
archive=archive,
logger=logger,
output_file_path=nexus_output,
on_temp_file=generate_nexus_file,
output_file_path=nx_file,
on_temp_file=False,
nxs_as_entry=nxs_as_entry
)
archive.metadata.entry_type = entry_type

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