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Remove Nexus file before rereating it.
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@RubelMozumder
RubelMozumder committed Dec 19, 2024
1 parent df4c741 commit ec860a2
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Showing 2 changed files with 40 additions and 39 deletions.
70 changes: 36 additions & 34 deletions src/nomad_measurements/utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@
)

import h5py
import copy
import numpy as np
import pint
from nomad.datamodel.hdf5 import HDF5Reference
Expand Down Expand Up @@ -334,18 +335,17 @@ def write_file(self):
main archive file (e.g. HDF5, NeXus).
"""
if self.nexus:
self._write_nx_file()
# try:
# self._write_nx_file()
# except Exception as e:
# self.nexus = False
# self.logger.warning(
# f'Encountered "{e}" error while creating nexus file. '
# 'Creating h5 file instead.'
# )
# self._write_hdf5_file()
# else:
# self._write_hdf5_file()
try:
self._write_nx_file()
except Exception as e:
self.nexus = False
self.logger.warning(
f'Encountered "{e}" error while creating nexus file. '
'Creating h5 file instead.'
)
self._write_hdf5_file()
else:
self._write_hdf5_file()

def _write_nx_file(self):
"""
Expand All @@ -364,57 +364,59 @@ def _write_nx_file(self):
populate_nx_dataset_and_attribute(
archive=self.archive, attr_dict=attr_dict, dataset_dict=dataset_dict
)
for nx_path, dset in list(self._hdf5_datasets.items()) + list(
for nx_path, dset_ori in list(self._hdf5_datasets.items()) + list(
dataset_dict.items()
):
dset = copy.deepcopy(dset_ori)
if dset.internal_reference:
# convert to the nexus type link
dset.data = {'link': self._remove_nexus_annotations(dset.data)}

try:
template[nx_path] = dset.data
except KeyError:
template['optional'][nx_path] = dset.data

hdf_path = self._remove_nexus_annotations(nx_path)
hdf5_path = self._remove_nexus_annotations(nx_path)
self._set_hdf5_reference(
self.archive,
dset.archive_path,
f'/uploads/{self.archive.m_context.upload_id}/raw'
f'/{self.data_file}#{hdf_path}',
)
self.archive,
dset.archive_path,
f'/uploads/{self.archive.m_context.upload_id}/raw'
f'/{self.data_file}#{hdf5_path}',
)
for nx_path, attr_d in list(self._hdf5_attributes.items()) + list(
attr_dict.items()
):
# hdf5_path = self._remove_nexus_annotations(nx_path)
for attr_k, attr_v in attr_d.items():
if attr_k:
if attr_v != 'dimensionless' and attr_v:
try:
template[f'{nx_path}/@{attr_k}'] = attr_v
except KeyError:
template['optional'][f'{nx_path}/@{attr_k}'] = attr_v
try:
nx_full_path = os.path.join(
nx_full_file_path = os.path.join(
self.archive.m_context.raw_path(), self.data_file
)
if self.archive.m_context.raw_path_exists(self.data_file):
os.remove(nx_full_file_path)

pynxtools_writer(
data=template, nxdl_f_path=nxdl_f_path, output_path=nx_full_path
data=template, nxdl_f_path=nxdl_f_path, output_path=nx_full_file_path
).write()

# entry_list = Entry.objects(
# upload_id=self.archive.m_context.upload_id, mainfile=self.data_file
# )
# if not entry_list:
# self.archive.m_context.process_updated_raw_file(self.data_file)
entry_list = Entry.objects(
upload_id=self.archive.m_context.upload_id, mainfile=self.data_file
)
if not entry_list:
self.archive.m_context.process_updated_raw_file(self.data_file)

except Exception as exc:
if os.path.exists(self.data_file):
os.remove(self.data_file)
self.data_file = self.data_file.rsplit(os.pathsep, 1)[-1]
raise Exception('NeXus file can not be generated.') from exc

# raise NotImplementedError('Method `write_nx_file` is not implemented.')
# TODO add archive data to `hdf5_data_dict` before creating the nexus file. Use
# `populate_hdf5_data_dict` method for each quantity that is needed in .nxs
# file. Create a NeXus file with the data in `hdf5_data_dict`.
# One issue here is as we populate the `hdf5_data_dict` with the archive data,
# we will always have to over write the nexus file

def _write_hdf5_file(self): # noqa: PLR0912
"""
Method for creating an HDF5 file.
Expand Down
9 changes: 4 additions & 5 deletions src/nomad_measurements/xrd/nx.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -50,20 +50,19 @@


CONCEPT_MAP = {
'/ENTRY[entry]/@default': 'experiment_result',
'/ENTRY[entry]/definition': 'NXxrd_pan',
'/ENTRY[entry]/method': 'archive.data.method',
'/ENTRY[entry]/measurement_type': 'archive.data.diffraction_method_name',
'/ENTRY[entry]/experiment_result/@signal': 'intensity',
'/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/scan_axis': 'archive.data.results[0].scan_axis',
'/ENTRY[entry]/experiment_config/count_time': 'archive.data.results[0].integration_time',
'/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',
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/xray_tube_voltage': 'archive.data.xrd_settings.source.xray_tube_voltage',
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_one': 'archive.data.xrd_settings.source.kalpha_one',
'/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_two': 'archive.data.xrd_settings.source.kalpha_two',
'/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',
'/ENTRY[entry]/@default': 'experiment_result',
'/ENTRY[entry]/experiment_result/@signal': 'intensity',
'/ENTRY[entry]/definition': 'NXxrd_pan',
}


Expand Down Expand Up @@ -116,7 +115,7 @@ def populate_nx_dataset_and_attribute(
)

if isinstance(data, pint.Quantity):
if str(data.units) != 'unitless' and str(data.units):
if str(data.units) != 'dimensionless' and str(data.units):
attr_tmp = {nx_path: dict(units=str(data.units))}
attr_dict.update(attr_tmp)
# attr_dict[nx_path].update({'units': str(data.units)})
Expand Down

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