From ae403871949db44cf7d04efdfb21da6f07308ff3 Mon Sep 17 00:00:00 2001
From: RealPolitiX <xrpatrick@gmail.com>
Date: Fri, 3 May 2019 01:30:10 +0200
Subject: [PATCH] Update with mpes-parser content
---
examples/mpes_metadata.json | 0
mpesparser/__init__.py | 176 +++++
{skeletonparser => mpesparser}/__main__.py | 4 +-
mpesparser/mpes.nomadmetainfo.json | 718 +++++++++++++++++++++
setup.py | 8 +-
skeletonparser/__init__.py | 96 ---
skeletonparser/skeleton.nomadmetainfo.json | 20 -
tests/example.metadata.json | 10 -
tests/mpes_data.json | 77 +++
tests/mpes_data_redacted.json | 74 +++
10 files changed, 1051 insertions(+), 132 deletions(-)
create mode 100644 examples/mpes_metadata.json
create mode 100644 mpesparser/__init__.py
rename {skeletonparser => mpesparser}/__main__.py (90%)
create mode 100644 mpesparser/mpes.nomadmetainfo.json
delete mode 100644 skeletonparser/__init__.py
delete mode 100644 skeletonparser/skeleton.nomadmetainfo.json
delete mode 100644 tests/example.metadata.json
create mode 100644 tests/mpes_data.json
create mode 100644 tests/mpes_data_redacted.json
diff --git a/examples/mpes_metadata.json b/examples/mpes_metadata.json
new file mode 100644
index 0000000..e69de29
diff --git a/mpesparser/__init__.py b/mpesparser/__init__.py
new file mode 100644
index 0000000..83158d7
--- /dev/null
+++ b/mpesparser/__init__.py
@@ -0,0 +1,176 @@
+# Copyright 2016-2018 Markus Scheidgen
+# 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.
+
+import sys
+import os.path
+import json
+import ase
+import re
+import numpy as np
+from datetime import datetime
+
+from nomadcore.simple_parser import SimpleMatcher
+from nomadcore.baseclasses import ParserInterface, AbstractBaseParser
+
+from nomad.parsing import LocalBackend
+
+
+class MPESParserInterface(ParserInterface):
+ def get_metainfo_filename(self):
+ """
+ The parser specific metainfo. To include other metadata definitions, use
+ the 'dependencies' key to refer to other local nomadmetainfo.json files or
+ to nomadmetainfo.json files that are part of the general nomad-meta-info
+ submodule (i.e. ``dependencies/nomad-meta-info``).
+ """
+ return os.path.join(os.path.dirname(__file__), 'mpes.nomadmetainfo.json')
+
+ def get_parser_info(self):
+ """ Basic info about parser used in archive data and logs. """
+ return {
+ 'name': 'mpes-parser',
+ 'version': '1.0.0'
+ }
+
+ def setup_version(self):
+ """ Can be used to call :func:`setup_main_parser` differently for different code versions. """
+ self.setup_main_parser(None)
+
+ def setup_main_parser(self, _):
+ """ Setup the actual parser (behind this interface) """
+ self.main_parser = MPESParser(self.parser_context)
+
+
+class MPESParser(AbstractBaseParser):
+
+ def parse(self, filepath):
+ backend = self.parser_context.super_backend
+
+ with open(filepath, 'rt') as f:
+ data = json.load(f)
+ # print(data)
+
+ # # You need to open sections before you can add values or sub sections to it.
+ # # The returned 'gid' can be used to reference a specific section if multiple
+ # # sections of the same type are opened.
+ root_gid = backend.openSection('section_experiment')
+ # # Values do not necessarely have to be read from the parsed file.
+ # # The backend will check the type of the given value agains the metadata definition.
+ # backend.addValue('experiment_time', int(datetime.strptime(data.get('date'), '%d.%M.%Y').timestamp()))
+ #
+ # # Read data .
+ # data_gid = backend.openSection('section_data')
+ # backend.addValue('data_repository_name', 'zenodo.org')
+ # backend.addValue('data_repository_url', 'https://zenodo.org/path/to/mydata')
+ # backend.addValue('data_preview_url', 'https://www.physicsforums.com/insights/wp-content/uploads/2015/09/fem.jpg')
+ # backend.closeSection('section_data', data_gid)
+
+ # Read general experimental parameters
+ # general_gid = backend.openSection('section_experiment_general_parameters')
+ backend.addValue('general_experiment_method', data.get('experiment_method'))
+ backend.addValue('general_experiment_method_abbreviation', data.get('experiment_method_abbrv'))
+ backend.addArrayValues('general_experiment_location', np.array(re.findall(r"[\w']+", data.get('experiment_location'))))
+ backend.addValue('general_experiment_date', data.get('experiment_date'))
+ backend.addValue('general_experiment_summary', data.get('experiment_summary'))
+ backend.addValue('general_experiment_facility_institution', data.get('facility_institution'))
+ backend.addValue('general_experiment_facility_name', data.get('facility_name'))
+ backend.addValue('general_beamline', data.get('beamline'))
+ backend.addValue('general_source_pump', data.get('source_pump'))
+ backend.addValue('general_source_probe', data.get('source_probe'))
+ backend.addValue('general_equipment_description', data.get('equipment_description'))
+ backend.addValue('general_sample_description', data.get('sample_description'))
+ backend.addArrayValues('general_measurement_axis', np.array(re.findall(r"[\w']+", data.get('measurement_axis'))))
+ backend.addArrayValues('general_physical_axis', np.array(re.findall(r"[\w']+", data.get('physical_axis'))))
+
+ # Read parameters related to experimental source
+ # source_gid = backend.openSection('section_experiment_source_parameters')
+ backend.addValue('source_pump_repetition_rate', data.get('pump_rep_rate'))
+ backend.addValue('source_pump_pulse_duration', data.get('pump_pulse_duration'))
+ backend.addValue('source_pump_wavelength', data.get('pump_wavelength'))
+ backend.addArrayValues('source_pump_spectrum', np.array(data.get('pump_spectrum')))
+ backend.addValue('source_pump_photon_energy', data.get('pump_photon_energy'))
+ backend.addArrayValues('source_pump_size', np.array(data.get('pump_size')))
+ backend.addArrayValues('source_pump_fluence', np.array(data.get('pump_fluence')))
+ backend.addValue('source_pump_polarization', data.get('pump_polarization'))
+ backend.addValue('source_pump_bunch', data.get('pump_bunch'))
+ backend.addValue('source_probe_repetition_rate', data.get('probe_rep_rate'))
+ backend.addValue('source_probe_pulse_duration', data.get('probe_pulse_duration'))
+ backend.addValue('source_probe_wavelength', data.get('probe_wavelength'))
+ backend.addArrayValues('source_probe_spectrum', np.array(data.get('probe_spectrum')))
+ backend.addValue('source_probe_photon_energy', data.get('probe_photon_energy'))
+ backend.addArrayValues('source_probe_size', np.array(data.get('probe_size')))
+ backend.addArrayValues('source_probe_fluence', np.array(data.get('probe_fluence')))
+ backend.addValue('source_probe_polarization', data.get('probe_polarization'))
+ backend.addValue('source_probe_bunch', data.get('probe_bunch'))
+ backend.addValue('source_temporal_resolution', data.get('temporal_resolution'))
+
+ # Read parameters related to detector
+ # detector_gid = backend.openSection('section_experiment_detector_parameters')
+ backend.addValue('detector_extractor_voltage', data.get('extractor_voltage'))
+ backend.addValue('detector_work_distance', data.get('work_distance'))
+ backend.addArrayValues('detector_lens_names', np.array(re.findall(r"[\w']+", data.get('lens_names'))))
+ backend.addArrayValues('detector_lens_voltages', np.array(data.get('lens_voltages')))
+ backend.addValue('detector_tof_distance', data.get('tof_distance'))
+ backend.addArrayValues('detector_tof_voltages', np.array(data.get('tof_voltages')))
+ backend.addValue('detector_sample_bias', data.get('sample_bias'))
+ backend.addValue('detector_magnification', data.get('magnification'))
+ backend.addArrayValues('detector_voltages', np.array(data.get('detector_voltages')))
+ backend.addValue('detector_type', data.get('detector_type'))
+ backend.addArrayValues('detector_sensor_size', np.array(data.get('sensor_size')))
+ backend.addValue('detector_sensor_count', data.get('sensor_count'))
+ backend.addArrayValues('detector_sensor_pixel_size', np.array(data.get('sensor_pixel_size')))
+ backend.addArrayValues('detector_calibration_x_to_momentum', np.array(data.get('calibration_x_to_momentum')))
+ backend.addArrayValues('detector_calibration_y_to_momentum', np.array(data.get('calibration_y_to_momentum')))
+ backend.addArrayValues('detector_calibration_tof_to_energy', np.array(data.get('calibration_tof_to_energy')))
+ backend.addArrayValues('detector_calibration_stage_to_delay', np.array(data.get('calibration_stage_to_delay')))
+ backend.addArrayValues('detector_calibration_other_converts', np.array(data.get('calibration_other_converts')))
+ backend.addArrayValues('detector_momentum_resolution', np.array(data.get('momentum_resolution')))
+ backend.addArrayValues('detector_spatial_resolution', np.array(data.get('spatial_resolution')))
+ backend.addArrayValues('detector_energy_resolution', np.array(data.get('energy_resolution')))
+
+ # Read parameters related to sample
+ # sample_gid = backend.openSection('section_experiment_sample_parameters')
+ backend.addValue('sample_id', data.get('sample_id'))
+ backend.addValue('sample_state_of_matter', data.get('sample_state'))
+ backend.addValue('sample_purity', data.get('sample_purity'))
+ backend.addValue('sample_surface_termination', data.get('sample_surface_termination'))
+ backend.addValue('sample_layers', data.get('sample_layers'))
+ backend.addValue('sample_stacking_order', data.get('sample_stacking_order'))
+ backend.addValue('sample_space_group', data.get('sample_space_group'))
+ backend.addValue('sample_chemical_name', data.get('chemical_name'))
+ backend.addValue('sample_chemical_formula', data.get('chemical_formula'))
+ # backend.addArrayValues('sample_chemical_elements', np.array(re.findall(r"[\w']+", data.get('chemical_elements'))))
+ atoms = set(ase.Atoms(data.get('chemical_formula')).get_chemical_symbols())
+ backend.addArrayValues('sample_atom_labels', np.array(list(atoms)))
+ backend.addValue('sample_chemical_id_cas', data.get('chemical_id_cas'))
+ backend.addValue('sample_temperature', data.get('sample_temperature'))
+ backend.addValue('sample_pressure', data.get('sample_pressure'))
+ backend.addValue('sample_growth_method', data.get('growth_method'))
+ backend.addValue('sample_preparation_method', data.get('preparation_method'))
+ backend.addValue('sample_vendor', data.get('sample_vendor'))
+ backend.addValue('sample_substrate_material', data.get('substrate_material'))
+ backend.addValue('sample_substrate_state_of_matter', data.get('substrate_state'))
+ backend.addValue('sample_substrate_vendor', data.get('substrate_vendor'))
+
+ # To add arrays (vectors, matrices, etc.) use addArrayValues and provide a
+ # numpy array. The shape of the numpy array must match the shape defined in
+ # the respective metadata definition.
+
+
+ # Close sections in the reverse order
+ # backend.closeSection('section_data', data_gid)
+ backend.closeSection('section_experiment', root_gid)
+ # backend.closeSection('section_experiment_general_parameters', general_gid)
+ # backend.closeSection('section_experiment_source_parameters', source_gid)
+ # backend.closeSection('section_experiment_detector_parameters', detector_gid)
+ # backend.closeSection('section_experiment_sample_parameters', sample_gid)
diff --git a/skeletonparser/__main__.py b/mpesparser/__main__.py
similarity index 90%
rename from skeletonparser/__main__.py
rename to mpesparser/__main__.py
index d393f8d..02973c9 100644
--- a/skeletonparser/__main__.py
+++ b/mpesparser/__main__.py
@@ -14,11 +14,11 @@
import sys
from nomad.parsing import LocalBackend
-from skeletonparser import SkeletonParserInterface
+from mpesparser import MPESParserInterface
if __name__ == "__main__":
# instantiate the parser via its interface with a LocalBackend
- parser = SkeletonParserInterface(backend=LocalBackend)
+ parser = MPESParserInterface(backend=LocalBackend)
# call the actual parsing with the given mainfile
parser.parse(sys.argv[1])
# print the results stored in the LocalBackend
diff --git a/mpesparser/mpes.nomadmetainfo.json b/mpesparser/mpes.nomadmetainfo.json
new file mode 100644
index 0000000..10fe096
--- /dev/null
+++ b/mpesparser/mpes.nomadmetainfo.json
@@ -0,0 +1,718 @@
+{
+ "type": "nomad_meta_info_1_0",
+ "description": "Metadata a multidimensional photoemission spectroscopy experiment.",
+ "dependencies": [
+ {
+ "metainfoPath":"general.nomadmetainfo.json"
+ },
+ {
+ "metainfoPath":"general.experimental.nomadmetainfo.json"
+ }
+ ],
+ "metaInfos": [
+ {
+ "description": "Name of the city and country the experiment took place, format 'Country, City'",
+ "name": "data_repository_name",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Name of the city and country the experiment took place, format 'Country, City'",
+ "name": "data_repository_url",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Name of the city and country the experiment took place, format 'Country, City'",
+ "name": "data_preview_url",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Shape of the None/Null object",
+ "name": "none_shape",
+ "dtypeStr": "i",
+ "kindStr": "type_dimension",
+ "shape": [],
+ "superNames": ["section_experiment"]
+ },
+ {
+ "description": "Full name of the experimental method in use",
+ "name": "general_experiment_method",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Abbreviated name (e.g. acronym) of the experimental method",
+ "name": "general_experiment_method_abbreviation",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Number of name segments in the experiment location",
+ "name": "number_of_location_names",
+ "dtypeStr": "i",
+ "kindStr": "type_dimension",
+ "shape": [],
+ "superNames": ["section_experiment"]
+ },
+ {
+ "description": "Name of the city and country the experiment took place, format 'Country, City'",
+ "name": "general_experiment_location",
+ "dtypeStr": "C",
+ "shape": ["number_of_location_names"],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Start and end dates of the experiment, format 'DD.MM.YYYY - DD.MM.YYYY'",
+ "name": "general_experiment_date",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "C"
+ },
+ {
+ "description": "Descriptive summary of the content of the experiment.",
+ "name": "general_experiment_summary",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Name of the institution hosting the experimental facility (e.g. in an acronym).",
+ "name": "general_experiment_facility_institution",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Name of the experimental facility (e.g. in an acronym).",
+ "name": "general_experiment_facility_name",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Name of the beamline the experiment took place.",
+ "name": "general_beamline",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Name or model of the pump light source.",
+ "name": "general_source_pump",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Name or model of the probe light source.",
+ "name": "general_source_probe",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Name or model of the equipment (e.g. in an acronym).",
+ "name": "general_equipment_description",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Description of the sample used in the experiment.",
+ "name": "general_sample_description",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Number of axes in the measurement hardware.",
+ "name": "number_of_axes",
+ "dtypeStr": "i",
+ "kindStr": "type_dimension",
+ "shape": [],
+ "superNames": ["section_experiment"]
+ },
+ {
+ "description": "Names of the axes in the measurement hardware.",
+ "name": "general_measurement_axis",
+ "dtypeStr": "C",
+ "shape": ["number_of_axes"],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Names of the axes in physical terms.",
+ "name": "general_physical_axis",
+ "dtypeStr": "C",
+ "shape": ["number_of_axes"],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Repetition rate of the pump source.",
+ "name": "source_pump_repetition_rate",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "Hz"
+ },
+ {
+ "description": "Pulse duration of the pump source.",
+ "name": "source_pump_pulse_duration",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "fs"
+ },
+ {
+ "description": "Center wavelength of the pump source.",
+ "name": "source_pump_wavelength",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "nm"
+ },
+ {
+ "description": "Spectrum of the pump source.",
+ "name": "source_pump_spectrum",
+ "dtypeStr": "f",
+ "shape": ["length_of_spectrum"],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Photon energy of the pump source.",
+ "name": "source_pump_photon_energy",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "eV"
+ },
+ {
+ "description": "Full-width at half-maximum size of the pump source at or closest to the sample position.",
+ "name": "source_pump_size",
+ "dtypeStr": "f",
+ "shape": ["none_shape"],
+ "superNames": ["section_experiment"],
+ "units": "mm**2"
+ },
+ {
+ "description": "Fluence of the pump source at or closest to the sample position.",
+ "name": "source_pump_fluence",
+ "dtypeStr": "f",
+ "shape": ["none_shape"],
+ "superNames": ["section_experiment"],
+ "units": "mJ/mm**2"
+ },
+ {
+ "description": "Polarization of the pump source.",
+ "name": "source_pump_polarization",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Total bunch number of the pump source.",
+ "name": "source_pump_bunch",
+ "dtypeStr": "i",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Repetition rate of the probe source.",
+ "name": "source_probe_repetition_rate",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "Hz"
+ },
+ {
+ "description": "Pulse duration of the probe source.",
+ "name": "source_probe_pulse_duration",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "fs"
+ },
+ {
+ "description": "Center wavelength of the probe source.",
+ "name": "source_probe_wavelength",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "nm"
+ },
+ {
+ "description": "Number of pixel elements in the spectrum.",
+ "name": "length_of_spectrum",
+ "dtypeStr": "i",
+ "kindStr": "type_dimension",
+ "shape": [],
+ "superNames": ["section_experiment"]
+ },
+ {
+ "description": "Spectrum of the probe source.",
+ "name": "source_probe_spectrum",
+ "dtypeStr": "f",
+ "shape": ["length_of_spectrum"],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Photon energy of the probe source.",
+ "name": "source_probe_photon_energy",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "eV"
+ },
+ {
+ "description": "Full-width at half-maximum size of the probe source at or closest to the sample position.",
+ "name": "source_probe_size",
+ "dtypeStr": "f",
+ "shape": ["none_shape"],
+ "superNames": ["section_experiment"],
+ "units": "mm**2"
+ },
+ {
+ "description": "Fluence of the probe source at or closest to the sample position.",
+ "name": "source_probe_fluence",
+ "dtypeStr": "f",
+ "shape": ["none_shape"],
+ "superNames": ["section_experiment"],
+ "units": "mJ/mm**2"
+ },
+ {
+ "description": "Polarization of the probe source.",
+ "name": "source_probe_polarization",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Total bunch number of the probe source.",
+ "name": "source_probe_bunch",
+ "dtypeStr": "i",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Full-width at half-maximum of the pump-probe cross-correlation function.",
+ "name": "source_temporal_resolution",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "fs"
+ },
+ {
+ "description": "Voltage between the extractor and the sample.",
+ "name": "detector_extractor_voltage",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "V"
+ },
+ {
+ "description": "Distance between the sample and the detector entrance.",
+ "name": "detector_work_distance",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "mm"
+ },
+ {
+ "description": "Number of electron lenses in the electron detector.",
+ "name": "number_of_lenses",
+ "dtypeStr": "i",
+ "kindStr": "type_dimension",
+ "shape": [],
+ "superNames": ["section_experiment"]
+ },
+ {
+ "description": "Set of names for the electron-optic lenses.",
+ "name": "detector_lens_names",
+ "dtypeStr": "C",
+ "shape": ["number_of_lenses"],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Set of electron-optic lens voltages.",
+ "name": "detector_lens_voltages",
+ "dtypeStr": "f",
+ "shape": ["number_of_lenses"],
+ "superNames": ["section_experiment"],
+ "units": "V"
+ },
+ {
+ "description": "Drift distance of the time-of-flight tube.",
+ "name": "detector_tof_distance",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "m"
+ },
+ {
+ "description": "Number of time-of-flight (TOF) drift tube voltage values in the electron detector.",
+ "name": "number_of_tof_voltages",
+ "dtypeStr": "i",
+ "kindStr": "type_dimension",
+ "shape": [],
+ "superNames": ["section_experiment"]
+ },
+ {
+ "description": "Voltage applied to the time-of-flight tube.",
+ "name": "detector_tof_voltages",
+ "dtypeStr": "f",
+ "shape": ["number_of_tof_voltages"],
+ "superNames": ["section_experiment"],
+ "units": "V"
+ },
+ {
+ "description": "Voltage bias applied to sample.",
+ "name": "detector_sample_bias",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "V"
+ },
+ {
+ "description": "Detector magnification.",
+ "name": "detector_magnification",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Number of detector voltage settings in the electron detector.",
+ "name": "number_of_detector_voltages",
+ "dtypeStr": "i",
+ "kindStr": "type_dimension",
+ "shape": [],
+ "superNames": ["section_experiment"]
+ },
+ {
+ "description": "Voltage applied to detector.",
+ "name": "detector_voltages",
+ "dtypeStr": "f",
+ "shape": ["number_of_detector_voltages"],
+ "superNames": ["section_experiment"],
+ "units": "V"
+ },
+ {
+ "description": "Description of the detector type (e.g. ‘MCP’, ‘CCD’, ‘CMOS’, etc.).",
+ "name": "detector_type",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Number of detector sensor size dimensions (depending on the number of sensors).",
+ "name": "number_of_sensor_sizes",
+ "dtypeStr": "i",
+ "kindStr": "type_dimension",
+ "shape": [],
+ "superNames": ["section_experiment"]
+ },
+ {
+ "description": "Size of each of the imaging sensor chip on the detector.",
+ "name": "detector_sensor_size",
+ "dtypeStr": "f",
+ "shape": ["number_of_sensor_sizes"],
+ "superNames": ["section_experiment"],
+ "units": "mm"
+ },
+ {
+ "description": "Number of imaging sensor chips on the detector.",
+ "name": "detector_sensor_count",
+ "dtypeStr": "i",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Pixel size of the imaging sensor chip on the detector.",
+ "name": "detector_sensor_pixel_size",
+ "dtypeStr": "f",
+ "shape": ["none_shape"],
+ "superNames": ["section_experiment"],
+ "units": "um"
+ },
+ {
+ "description": "Number of the momentum calibration parameters for the detector.",
+ "name": "number_of_momentum_calibration_coefficients",
+ "dtypeStr": "i",
+ "kindStr": "type_dimension",
+ "shape": [],
+ "superNames": ["section_experiment"]
+ },
+ {
+ "description": "Pixel x axis to kx momentum calibration.",
+ "name": "detector_calibration_x_to_momentum",
+ "dtypeStr": "f",
+ "shape": ["number_of_momentum_calibration_coefficients"],
+ "superNames": ["section_experiment"],
+ "units": "AA**-1"
+ },
+ {
+ "description": "Pixel y axis to ky momentum calibration.",
+ "name": "detector_calibration_y_to_momentum",
+ "dtypeStr": "f",
+ "shape": ["number_of_momentum_calibration_coefficients"],
+ "superNames": ["section_experiment"],
+ "units": "AA**-1"
+ },
+ {
+ "description": "Number of the energy calibration parameters for the detector.",
+ "name": "number_of_energy_calibration_coefficients",
+ "dtypeStr": "i",
+ "kindStr": "type_dimension",
+ "shape": [],
+ "superNames": ["section_experiment"]
+ },
+ {
+ "description": "Time-of-flight to energy calibration.",
+ "name": "detector_calibration_tof_to_energy",
+ "dtypeStr": "f",
+ "shape": ["number_of_energy_calibration_coefficients"],
+ "superNames": ["section_experiment"],
+ "units": "eV"
+ },
+ {
+ "description": "Translation stage delay to pump-probe delay calibration.",
+ "name": "detector_calibration_stage_to_delay",
+ "dtypeStr": "f",
+ "shape": ["number_of_delay_calibration_coefficients"],
+ "superNames": ["section_experiment"],
+ "units": "fs"
+ },
+ {
+ "description": "Number of the other calibration parameters for the detector.",
+ "name": "number_of_other_calibration_coefficients",
+ "dtypeStr": "i",
+ "kindStr": "type_dimension",
+ "shape": [],
+ "superNames": ["section_experiment"]
+ },
+ {
+ "description": "Conversion factor between other measured and physical axes.",
+ "name": "detector_calibration_other_converts",
+ "dtypeStr": "f",
+ "shape": ["number_of_other_calibration_coefficients"],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Momentum resolution of the detector.",
+ "name": "detector_momentum_resolution",
+ "dtypeStr": "f",
+ "shape": ["none_shape"],
+ "superNames": ["section_experiment"],
+ "units": "AA**-1"
+ },
+ {
+ "description": "Spatial resolution of the source.",
+ "name": "detector_spatial_resolution",
+ "dtypeStr": "f",
+ "shape": ["none_shape"],
+ "superNames": ["section_experiment"],
+ "units": "um"
+ },
+ {
+ "description": "Energy resolution of the detector.",
+ "name": "detector_energy_resolution",
+ "dtypeStr": "f",
+ "shape": ["none_shape"],
+ "superNames": ["section_experiment"],
+ "units": "eV"
+ },
+ {
+ "description": "Identification number or signatures of the sample used.",
+ "name": "sample_id",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Physical state of the sample.",
+ "name": "sample_state_of_matter",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Chemical purity of the sample.",
+ "name": "sample_purity",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Surface termination of the sample (if crystalline).",
+ "name": "sample_surface_termination",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Sample layer or bulk structure.",
+ "name": "sample_layers",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Stacking order of the solid surface (if crystalline).",
+ "name": "sample_stacking_order",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Space group of the sample compound (if crystalline).",
+ "name": "sample_space_group",
+ "dtypeStr": "i",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Chemical name of the sample.",
+ "name": "sample_chemical_name",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Chemical formula of the sample.",
+ "name": "sample_chemical_formula",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Number of distinct chemical elements in the sample.",
+ "name": "number_of_elements",
+ "dtypeStr": "i",
+ "kindStr": "type_dimension",
+ "shape": [],
+ "superNames": ["section_experiment"]
+ },
+ {
+ "description": "Symbols of the chemical elements contained in the sample.",
+ "name": "sample_atom_labels",
+ "dtypeStr": "C",
+ "shape": ["number_of_elements"],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "CAS registry number of the sample’s chemical content.",
+ "name": "sample_chemical_id_cas",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Temperature of the sample at the time of measurement.",
+ "name": "sample_temperature",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "K"
+ },
+ {
+ "description": "Pressure surrounding the sample at the time of measurement.",
+ "name": "sample_pressure",
+ "dtypeStr": "f",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": "Pa"
+ },
+ {
+ "description": "Sample growth method.",
+ "name": "sample_growth_method",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Sample preparation method.",
+ "name": "sample_preparation_method",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Name of the sample vendor.",
+ "name": "sample_vendor",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Material of the substrate the sample has immediate contact with.",
+ "name": "sample_substrate_material",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "State of matter of the substrate material.",
+ "name": "sample_substrate_state_of_matter",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ },
+ {
+ "description": "Name of the substrate vendor.",
+ "name": "sample_substrate_vendor",
+ "dtypeStr": "C",
+ "shape": [],
+ "superNames": ["section_experiment"],
+ "units": ""
+ }
+ ]
+}
diff --git a/setup.py b/setup.py
index 89a925c..d669a95 100644
--- a/setup.py
+++ b/setup.py
@@ -16,14 +16,14 @@ from setuptools import setup, find_packages
def main():
setup(
- name='skeletonparser', # replace with new name for parser's python package
+ name='mpesparser',
version='0.1',
- description='A skeleton NOMAD parser implementation.', # change accordingly
- author='', # add your names
+ description='NOMAD parser implementation for multidimensional photoemission spectroscopy data.',
+ author='R. Patrick Xian',
license='APACHE 2.0',
packages=find_packages(),
package_data={
- 'skeletonparser': ['*.json']
+ 'mpesparser': ['*.json']
},
install_requires=[
'nomadcore'
diff --git a/skeletonparser/__init__.py b/skeletonparser/__init__.py
deleted file mode 100644
index b7f0fd6..0000000
--- a/skeletonparser/__init__.py
+++ /dev/null
@@ -1,96 +0,0 @@
-# Copyright 2016-2018 Markus Scheidgen
-# 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.
-
-import sys
-import os.path
-import json
-import ase
-import numpy as np
-from datetime import datetime
-
-from nomadcore.simple_parser import SimpleMatcher
-from nomadcore.baseclasses import ParserInterface, AbstractBaseParser
-
-from nomad.parsing import LocalBackend
-
-
-class SkeletonParserInterface(ParserInterface):
-
- def get_metainfo_filename(self):
- """
- The parser specific metainfo. To include other metadata definitions, use
- the 'dependencies' key to refer to other local nomadmetainfo.json files or
- to nomadmetainfo.json files that are part of the general nomad-meta-info
- submodule (i.e. ``dependencies/nomad-meta-info``).
- """
- return os.path.join(os.path.dirname(__file__), 'skeleton.nomadmetainfo.json')
-
- def get_parser_info(self):
- """ Basic info about parser used in archive data and logs. """
- return {
- 'name': 'you parser name',
- 'version': '1.0.0'
- }
-
- def setup_version(self):
- """ Can be used to call :func:`setup_main_parser` differently for different code versions. """
- self.setup_main_parser(None)
-
- def setup_main_parser(self, _):
- """ Setup the actual parser (behind this interface) """
- self.main_parser = SkeletonParser(self.parser_context)
-
-
-class SkeletonParser(AbstractBaseParser):
- def parse(self, filepath):
- backend = self.parser_context.super_backend
-
- with open(filepath, 'rt') as f:
- data = json.load(f)
-
- # You need to open sections before you can add values or sub sections to it.
- # The returned 'gid' can be used to reference a specific section if multiple
- # sections of the same type are opened.
- root_gid = backend.openSection('section_experiment')
- # Values are added to the open section of the given metadata definitions. In
- # the following case 'experiment_location' is a quantity of 'section_experiment'.
- # When multiple sections of the same type (e.g. 'section_experiment') are open,
- # you can use the 'gid' as an additional argument.
- backend.addValue('experiment_location', data.get('location'))
- # Values do not necessarely have to be read from the parsed file.
- backend.addValue('experiment_method_name', data.get('method', 'Bare eyes'))
- # The backend will check the type of the given value agains the metadata definition.
- backend.addValue('experiment_time', int(datetime.strptime(data.get('date'), '%d.%M.%Y').timestamp()))
-
- # Subsections work like before. The parent section must still be open.
- data_gid = backend.openSection('section_data')
- backend.addValue('data_repository_name', 'zenedo.org')
- backend.addValue('data_repository_url', 'https://zenedo.org/path/to/mydata')
- backend.addValue('data_preview_url', 'https://www.physicsforums.com/insights/wp-content/uploads/2015/09/fem.jpg')
- backend.closeSection('section_data', data_gid)
-
- # Subsections work like before. The parent section must still be open.
- sample_gid = backend.openSection('section_sample')
- backend.addValue('sample_chemical_name', data.get('sample_chemical'))
- backend.addValue('sample_chemical_formula', data.get('sample_formula'))
- backend.addValue('sample_temperature', data.get('sample_temp'))
-
- atoms = set(ase.Atoms(data.get('sample_formula')).get_chemical_symbols())
- # To add arrays (vectors, matrices, etc.) use addArrayValues and provide a
- # numpy array. The shape of the numpy array must match the shape defined in
- # the respective metadata definition.
- backend.addArrayValues('sample_atom_labels', np.array(list(atoms)))
-
- # Close sections in the reverse order.
- backend.closeSection('section_sample', sample_gid)
- backend.closeSection('section_experiment', root_gid)
diff --git a/skeletonparser/skeleton.nomadmetainfo.json b/skeletonparser/skeleton.nomadmetainfo.json
deleted file mode 100644
index 6720cef..0000000
--- a/skeletonparser/skeleton.nomadmetainfo.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "type": "nomad_meta_info_1_0",
- "description": "Parser specific metadata definitions.",
- "dependencies":[
- {
- "metainfoPath":"general.nomadmetainfo.json"
- },
- {
- "metainfoPath":"general.experimental.nomadmetainfo.json"
- }
- ],
- "metaInfos": [
- {
- "description": "Contains information relating to an archive.",
- "name": "experiment_location",
- "dtypeStr": "C",
- "superNames": ["section_experiment"]
- }
- ]
-}
diff --git a/tests/example.metadata.json b/tests/example.metadata.json
deleted file mode 100644
index 22933e8..0000000
--- a/tests/example.metadata.json
+++ /dev/null
@@ -1,10 +0,0 @@
-{
- "type":"skeleton experimental metadata format 1.0",
- "date":"24.12.2018",
- "location":"Northpole",
- "sample_formula":"H2O",
- "sample_chemical":"Ice",
- "sample_state":"Frozen",
- "result":"https://bitcoinist.com/wp-content/uploads/2018/08/shutterstock_764225425.jpg",
- "sample_temp":384
-}
\ No newline at end of file
diff --git a/tests/mpes_data.json b/tests/mpes_data.json
new file mode 100644
index 0000000..8bc30b5
--- /dev/null
+++ b/tests/mpes_data.json
@@ -0,0 +1,77 @@
+{"GeneralParameters":
+ {"experiment_location": "Hamburg, Germany",
+ "experiment_date": "04.2018 - 05.2018",
+ "experiment_summary": "Characterization of excited-state circular dichroism of WSe2",
+ "institution": "DESY",
+ "facility": "FLASH",
+ "beamline": "PG-2",
+ "source_pump": "Free electron laser",
+ "source_probe": "Femtosecond laser",
+ "equipment": "HEXTOF detector",
+ "sample": "Bulk tungsten diselenide",
+ "measurement_axis": ["X", "Y", "t", "ADC"],
+ "physical_axis": ["kx", "ky", "E", "tpp"]},
+"SourceParameters":
+ {"pump_rep_rate": 1000,
+ "pump_pulse_duration": 100,
+ "pump_wavelength": 800,
+ "pump_spectrum": [],
+ "pump_photon_energy": 1.55,
+ "pump_size": "",
+ "pump_fluence": 1.5,
+ "pump_polarization": "linear",
+ "pump_bunch": 400,
+ "probe_rep_rate": 1000,
+ "probe_pulse_duration": 100,
+ "probe_wavelength": 800,
+ "probe_spectrum": [],
+ "probe_photon_energy": 109,
+ "probe_size": "",
+ "probe_fluence": "",
+ "probe_polarization": "circular",
+ "probe_bunch": 400,
+ "temporal_resolution": 100},
+"DetectorParameters":
+ {"extractor_voltage": 6000,
+ "work_distance": 4,
+ "lens_names": ["A", "B", "C", "D", "E", "F", "G", "H"],
+ "lens_voltages": [],
+ "tof_distance": 0.9,
+ "tof_voltages": 30,
+ "sample_bias": 15,
+ "magnification": [],
+ "detector_voltage": [],
+ "detector_type": "MCP",
+ "sensor_size": [],
+ "sensor_count": 4,
+ "sensor_pixel_size": [],
+ "x_to_momentum": [],
+ "y_to_momentum": [],
+ "tof_to_energy": [],
+ "stage_to_delay": [],
+ "other_converts": [],
+ "momentum_resolution": 0.01,
+ "spatial_resolution": "",
+ "energy_resolution": ""},
+"SampleParameters":
+ {"sample_id": "000",
+ "sample_state": "solid",
+ "sample_purity": 0.99,
+ "sample_surface_term": "",
+ "sample_layer": "bulk",
+ "sample_stacking": "2H",
+ "sample_space_group": 194,
+ "chem_formula": "WSe2",
+ "chem_elements": ["W", "Se"],
+ "chem_name": "tungsten diselenide",
+ "chem_id_cas": "12067-46-8",
+ "sample_temp": 300,
+ "sample_pressure": 1e-11,
+ "growth_method": "chemical vaport transport",
+ "preparation_method": "in-vacuum cleaving",
+ "sample_vendor": "HQ Graphene",
+ "substrate_material": "copper",
+ "substrate_state": "solid",
+ "substrate_vendor": "custom"
+ }
+}
diff --git a/tests/mpes_data_redacted.json b/tests/mpes_data_redacted.json
new file mode 100644
index 0000000..30e619f
--- /dev/null
+++ b/tests/mpes_data_redacted.json
@@ -0,0 +1,74 @@
+{
+ "experiment_method": "multidimensional photoemission spectroscopy",
+ "experiment_method_abbrv": "MPES",
+ "experiment_location": "Hamburg, Germany",
+ "experiment_date": "04.2018 05.2018",
+ "experiment_summary": "Characterization of excited-state circular dichroism of WSe2",
+ "facility_institution": "DESY",
+ "facility_name": "FLASH",
+ "beamline": "PG-2",
+ "source_pump": "Free electron laser",
+ "source_probe": "Femtosecond laser",
+ "equipment_description": "HEXTOF detector",
+ "sample_description": "Bulk tungsten diselenide",
+ "measurement_axis": "X, Y, TOF, ADC",
+ "physical_axis": "kx, ky, E, tpp",
+ "pump_rep_rate": 1000,
+ "pump_pulse_duration": 100,
+ "pump_wavelength": 800,
+ "pump_spectrum": [],
+ "pump_photon_energy": 1.55,
+ "pump_size": [],
+ "pump_fluence": [],
+ "pump_polarization": "linear",
+ "pump_bunch": 400,
+ "probe_rep_rate": 1000,
+ "probe_pulse_duration": 100,
+ "probe_wavelength": 800,
+ "probe_spectrum": [],
+ "probe_photon_energy": 36.4970,
+ "probe_size": [],
+ "probe_fluence": [],
+ "probe_polarization": "circular",
+ "probe_bunch": 400,
+ "temporal_resolution": 100,
+ "extractor_voltage": 6030,
+ "work_distance": 4,
+ "lens_names": "A, B, C, D, E, F, G, H, I",
+ "lens_voltages": [],
+ "tof_distance": 0.9,
+ "tof_voltages": [20],
+ "sample_bias": 29,
+ "magnification": [-1.5],
+ "detector_voltages": [],
+ "detector_type": "MCP",
+ "sensor_size": [],
+ "sensor_count": 4,
+ "sensor_pixel_size": [],
+ "calibration_x_to_momentum": [],
+ "calibration_y_to_momentum": [],
+ "calibration_tof_to_energy": [],
+ "calibration_stage_to_delay": [],
+ "calibration_other_converts": [],
+ "momentum_resolution": [0.01],
+ "spatial_resolution": [],
+ "energy_resolution": [],
+ "sample_id": "000",
+ "sample_state": "solid",
+ "sample_purity": 0.99,
+ "sample_surface_termination": "0001",
+ "sample_layers": "bulk",
+ "sample_stacking_order": "2H",
+ "sample_space_group": 194,
+ "chemical_name": "tungsten diselenide",
+ "chemical_formula": "WSe2",
+ "chemical_id_cas": "12067-46-8",
+ "sample_temperature": 300,
+ "sample_pressure": 3.85e-10,
+ "growth_method": "chemical vaport transport",
+ "preparation_method": "in-vacuum cleaving",
+ "sample_vendor": "HQ Graphene",
+ "substrate_material": "copper",
+ "substrate_state": "solid",
+ "substrate_vendor": "custom"
+}
--
GitLab