diff --git a/nomad/datamodel/metainfo/__init__.py b/nomad/datamodel/metainfo/__init__.py
index fc2a91d583e66578c3029d85d054d6c597ea0eeb..71b4badd91dd18ae3f173678bfbc1078f7a48862 100644
--- a/nomad/datamodel/metainfo/__init__.py
+++ b/nomad/datamodel/metainfo/__init__.py
@@ -17,3 +17,6 @@
#
from .simulation import m_env
from .material_library import m_package
+
+from .apm import m_package
+from .em_nion import m_package
diff --git a/nomad/datamodel/metainfo/apm/__init__.py b/nomad/datamodel/metainfo/apm/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e67becad427fde7e33671f41850ba22be00667dc
--- /dev/null
+++ b/nomad/datamodel/metainfo/apm/__init__.py
@@ -0,0 +1,529 @@
+#
+# 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 matplotlib.afm import CharMetrics
+import numpy as np
+import os
+
+from nomad.units import ureg
+from nomad.metainfo import (
+ MSection, Package, Quantity, SubSection, MEnum, Datetime, Section)
+from nomad.datamodel.data import EntryData
+
+
+m_package = Package(name='atom_probe_microscopy')
+
+
+class Reflectron(MSection):
+ """Details about a reflectron device at the instrument."""
+
+ has_reflectron = Quantity(
+ type=bool,
+ description='''Does the instrument have a reflectron?''',
+ a_eln=dict(component='BoolEditQuantity'))
+
+ # watch out for auto-translated keywords which become py reserved keywords
+ # nexus_string prefixing, like with nx_<<quantity_name>> comes to rescue
+ name = Quantity(
+ type=str,
+ description='''Name of the reflectron.''',
+ a_eln=dict(component='StringEditQuantity'))
+ # keyword "name" must not be used except as keyword nomad
+
+ model = Quantity(
+ type=str,
+ description='''Reflectron model.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ serial_number = Quantity(
+ type=str,
+ description='''Reflectron serial number.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ manufacturer_name = Quantity(
+ type=str,
+ description='''Reflectron manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class Detector(MSection):
+ """Details about the detector."""
+
+ description = Quantity(
+ type=str,
+ description='''
+ An (ideally globally persistent) unique identifier, link, or text
+ which gives further details.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ detector_type = Quantity(
+ type=str,
+ description='''
+ Description of the detector type. Specify if the detector is not
+ the usual type of delay-line detectors.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class Pulser(MSection):
+ """Details about the pulser (laser/high-voltage)."""
+
+ name = Quantity(
+ type=str,
+ description='''Given name.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ model = Quantity(
+ type=str,
+ description='''Given brand or model name by the manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ serial_number = Quantity(
+ type=str,
+ description='''
+ Given hardware name/serial number or hash identifier issued by
+ the manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ manufacturer_name = Quantity(
+ type=str,
+ description='''Given name of the manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ pulse_mode = Quantity(
+ type=MEnum([
+ 'laser',
+ 'high_voltage',
+ 'laser_and_high_voltage']),
+ shape=[],
+ description='''Which type of pulsing mode.''',
+ a_eln=dict(component='RadioEnumEditQuantity'))
+
+ pulse_fraction = Quantity(
+ type=np.dtype(np.float64),
+ description='''Average pulse fraction.''',
+ a_eln=dict(component='NumberEditQuantity'))
+
+ _pulse_fraction_units = Quantity(
+ type=str,
+ description='''SI unit used for pulse fraction.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class Stage(MSection):
+ """Details about the stage."""
+
+ design = Quantity(
+ type=str,
+ description='''Principal design of the stage.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ name = Quantity(
+ type=str,
+ description='''Name of the stage''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ model = Quantity(
+ type=str,
+ description='''Type of the stage''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ serial_number = Quantity(
+ type=str,
+ description='''
+ Serial number of the stage.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ manufacturer_name = Quantity(
+ type=str,
+ description='''Given name of the stage manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class InstrumentControl(MSection):
+ """Details relevant for the control of the instrument."""
+
+ base_temperature = Quantity(
+ type=np.dtype(np.float64),
+ unit='kelvin',
+ description='''
+ Average temperature at the specimen base, i.e. base temperature,
+ during the measurement.''',
+ a_eln=dict(component='NumberEditQuantity'))
+
+ _base_temperature_units = Quantity(
+ type=str,
+ description='''
+ Unit used for the average temperature at the specimen base.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ pressure = Quantity(
+ type=np.dtype(np.float64),
+ unit='pascal',
+ description='''Average pressure in the analysis chamber.''',
+ a_eln=dict(component='NumberEditQuantity'))
+
+ _pressure_units = Quantity(
+ type=str,
+ description='''Average pressure in the analysis chamber.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ program = Quantity(
+ type=str,
+ description='''
+ Given name of the program that was used to control the experiment.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ _program_version = Quantity(
+ type=str,
+ description='''
+ Ideally program version plus build number, or commit hash or
+ description of ever persistent resources where the source code of the
+ program and build instructions can be found so that the program can
+ be configured ideally in such a manner that the result of this
+ computational process is recreatable
+ in the same deterministic manner.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class Instrument(MSection):
+ """Details about the atom probe microscope, components, and software."""
+
+ name = Quantity(
+ type=str,
+ description='''
+ Given name of the microscope, e.g Oxcart, One atom at a time.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ location = Quantity(
+ type=str,
+ description='''
+ Geographic coordinates of the lab or the place where the instrument
+ is installed using GEOREF geocodes ideally.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ instrument_manufacturer = Quantity(
+ type=str,
+ description='''
+ Manufacturer of the entire instrument (e.g. AMETEK/Cameca) to enable
+ e.g. queries in materials database systems for instrument
+ manufacturers. Usually more technical details are needed though to
+ specify the instrument, these should be written into instrument_model
+ and instrument_capabilities.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ instrument_model = Quantity(
+ type=str,
+ description='''
+ Manufacturer brand/model to enable e.g. queries about
+ microscope models (e.g. LEAP3000XS).''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ instrument_identifier = Quantity(
+ type=str,
+ description='''
+ Hardware name/serial number or hash identifier given by the
+ manufacturer to identify the instrument.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ instrument_capability = Quantity(
+ type=str,
+ description='''Free-text list possibly multiple terms of
+ functionalities which the instrument provides.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ flight_path_length = Quantity(
+ type=np.dtype(np.float64),
+ unit='meter',
+ description='''
+ The space inside the atom probe that ions pass through when they
+ leave the specimen and travel to the detector.''',
+ a_eln=dict(component='NumberEditQuantity'))
+
+ _flight_path_length_units = Quantity(
+ type=str,
+ description='''
+ The space inside the atom probe that ions pass through when they
+ leave the specimen and travel to the detector.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ reflectron = SubSection(section_def=Reflectron)
+ detector = SubSection(section_def=Detector)
+ pulser = SubSection(section_def=Pulser)
+ control = SubSection(section_def=InstrumentControl)
+
+
+class Operator(MSection):
+ """Contact information of at least the user of the instrument.
+
+ Or the investigator who performed this experiment.
+ Adding multiple users if relevant is recommended.
+ """
+
+ m_def = Section(a_eln=dict())
+
+ name = Quantity(
+ type=str,
+ description='''
+ Given (first) name and surname of the user.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ affiliation = Quantity(
+ type=str,
+ description='''
+ Name of the affiliation of the user at the point in time
+ when the experiment was performed.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ address = Quantity(
+ type=str,
+ description='''Postal address of the affiliation.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ email = Quantity(
+ type=str,
+ description='''
+ Email address of the user at the point in time
+ when the experiment was performed.
+ Giving the most permanently used email is recommended.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ orcid = Quantity(
+ type=str,
+ description='''
+ Globally unique identifier of the user as offers
+ by services like ORCID or Researcher ID.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ telephone_number = Quantity(
+ type=str,
+ description='''
+ (Business) (tele)phone number of the user at the point
+ in time when the experiment was performed.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ role = Quantity(
+ type=str,
+ description='''
+ Which role does the user have in the place, and at the point in time
+ when, the experiment was performed (e.g. technician operating the
+ microscope, student, postdoc, principal investigator, guest ...)''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class Sample(MSection):
+ """Properties of the specimen, its history."""
+
+ name = Quantity(
+ type=str,
+ description='''
+ Descriptive name or identifier with which to distinguish the specimen
+ from all others and especially the parts from where it was cut.
+ In cases where the specimen was e.g. site-specifically cut from
+ samples or in cases of an instrument session during which multiple
+ specimens are loaded, the name has to be descriptive enough to resolve
+ which specimen on e.g. the microtip array was taken. The user is
+ advised to store the details how specimens were cut/prepared from
+ samples in the sample history.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ sample_history = Quantity(
+ type=str,
+ description='''
+ Ideally, a reference to the location of or a (globally persistent)
+ unique identifier of e.g. another file which should document ideally
+ as many details as possible of the material, its microstructure, and
+ its thermo-chemo-mechanical processing/preparation history.
+ In the case that such a detailed history of the sample/specimen is not
+ available, use this field as a free-text description to specify a sub-
+ set of the entire sample history, i.e. what you would consider being
+ the key steps and relevant information about the specimen, its
+ material, microstructure, thermo-chemo-mechanical processing state,
+ and details of the preparation.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ preparation_date = Quantity(
+ type=Datetime,
+ description='''
+ ISO8601 date and time with local time zone offset to UTC included
+ when the specimen was prepared. Ideally report the end of the
+ preparation, i.e. the last known time the measured specimen surface
+ was actively prepared. Knowing when the specimen was exposed to e.g.
+ specific atmosphere is especially required for environmentally
+ sensitive material such as hydrogen-charged specimens or experiments
+ including tracers with a short half-time. The user is advised to
+ include these temporal details in the sample_history.''',
+ a_eln=dict(component='DateTimeEditQuantity'))
+
+ atom_types = Quantity(
+ type=str,
+ description='''
+ Use Hill's system for listing elements of the periodic table which
+ are inside or attached to the surface of the specimen and thus
+ considered relevant from a scientific point. The purpose of the field
+ is to offer materials database systems an opportunity to parse the
+ relevant elements without having to interpret these
+ from the sample history.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class AtomProbeMicroscopy(EntryData):
+ """Application definition describing atom probe experiments.
+
+ The here specified ELN is a proof-of-concept whose scope is to provide
+ a mechanism to inject additional pieces of information to create a NeXus
+ file that matches a:
+ - particular version of the NXapm.nxdl.xml appdef
+ - https://github.com/FAIRmat-Experimental/nexus_definitions/commit/
+ - 1d46b94dc36a42225ad247cc763277a47dcd30d4
+ - working with experiments as a pair of APT/RNG or APT/RRNG files,
+ - specifically with these file formats being interpretable as with the
+ - following so-called apm dataconverter (see commit below).
+ The ELN returns a json file that is to be used to inject the
+ here collected pieces of information in a
+ - specifically-versioned dataconverter apm
+ - https://github.com/nomad-coe/nomad-parser-nexus/commit/
+ - 47bc4f9724b8e980bd41d0fca3a663c0b79a7fb1
+ """
+
+ start_time = Quantity(
+ type=Datetime,
+ description='''
+ ISO 8601 formatted time code with local time zone offset to UTC
+ information included when the experiment started.
+ If the application demands that time codes in this section of the
+ application definition should only be used for specifying when the
+ experiment was performed - and the exact duration is not relevant
+ - this start time field should be used. Often though it is useful to
+ specify a time interval with specifying both start_time and end_time
+ to allow for more detailed bookkeeping and interpretation of the
+ experiment. The user should be aware that even with having both time
+ instances specified it may not be advisable to infer how long the
+ experiment took or for how long data were acquired. More detailed
+ timing data over the course of the experiment have to be collected.''',
+ a_eln=dict(component='DateTimeEditQuantity'))
+
+ end_time = Quantity(
+ type=Datetime,
+ description='''
+ ISO 8601-formatted time code with local time zone offset to UTC
+ included when the experiment ended.''',
+ a_eln=dict(component='DateTimeEditQuantity'))
+
+ run_number = Quantity(
+ type=str,
+ description='''
+ Not the specimen name or the experiment identifier but the identifier
+ through which the experiment is referred to in the control software.
+ For LEAP instruments it is recommended to use the IVAS/AP Suite run
+ number. For other instruments, such as the one from Stuttgart or Oxcart
+ from Erlangen, or the instruments in Rouen, use the identifier that is
+ closest in meaning to the LEAP run number. As a destructive microscopy
+ method, a run can be performed only once. It is possible, however,
+ to interrupt a run and restart, still all using the same specimen.
+ In this case, each evaporation run needs to be distinguished with
+ different run numbers. This is how most atom probe groups handle
+ it across the globe.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ operation_mode = Quantity(
+ type=MEnum([
+ 'leap',
+ 'apt',
+ 'fim',
+ 'apt_and_fim']),
+ shape=[],
+ description='''
+ What type of atom probe microscope experiment is performed.
+ This field can be used e.g. by materials database systems to
+ qualitatively filter experiments.''',
+ a_eln=dict(component='RadioEnumEditQuantity'))
+
+ sample = SubSection(section_def=Sample)
+ operator = SubSection(section_def=Operator, repeats=True)
+ instrument = SubSection(section_def=Instrument)
+
+ reconstruction_file = Quantity(
+ type=str,
+ description='''
+ Vendor/community-specific file (APT, POS, ePOS are supported)
+ which contains reconstructed ion positions and other data.''',
+ a_eln=dict(component='FileEditQuantity'),
+ a_browser=dict(adaptor='RawFileAdaptor'))
+
+ ranging_file = Quantity(
+ type=str,
+ description='''
+ Vendor/community-specific file (RNG, RRNG are supported)
+ which contains ranging definitions.''',
+ a_eln=dict(component='FileEditQuantity'),
+ a_browser=dict(adaptor='RawFileAdaptor'))
+
+ # maybe a database dump file from IVAS/APSuite
+
+ def normalize(self, archive, logger):
+ """Normalize data."""
+ # store content of the above ELN entries into a dictionary
+ # data = self.m_to_dict()
+
+ # map paths in this dictionary on paths as expected by apm reader
+ # for instance by storing flattened data key value pairs in a json
+ # file
+
+ # remains to be implemented
+
+# runner = CliRunner()
+# converter_args = ['--input-file', self.reconstruction_file,
+# '--input-file', self.ranging_file,
+# '--input-file',
+# os.path.join(filepath, 'eln.apm.json'),
+# '--reader', 'apm',
+# '--nxdl', 'NXapm',
+# '--output', os.path.join(filepath, \
+# 'apm.test.nxs')]
+# runner.invoke(convert, converter_args)
+
+ pass
+
+# =============================================================================
+# import yaml
+# from nomad.datamodel.metainfo.ellipsometry.dict_flattener \
+# import dict_flatten, dict_key_cut
+# from nexusparser.tools.dataconverter.convert import convert
+# from click.testing import CliRunner
+#
+# data = self.m_to_dict()
+# data.update(data.pop('data_file'))
+# dict_flatten(data)
+# dict_key_cut(data)
+#
+# kl = list(data.keys())
+# for k in kl:
+# if '/_' in k:
+# data[k.replace('/_', r"/\@")] = data.pop(k)
+# dict_key_cut(data, '/', 1, '@')
+# data['definition'] = 'NXellipsometry'
+# data[r"definition/\@version"] = '0.0.1'
+# data[r"definition/\@url"] = 'https://'
+#
+# with archive.m_context.raw_file('eln.apm.json', 'w') as outfile:
+# yaml.dump(data, outfile, default_flow_style=False)
+# filepath = os.path.dirname(outfile.name)
+# =============================================================================
+
+
+m_package.__init_metainfo__()
diff --git a/nomad/datamodel/metainfo/em_nion/__init__.py b/nomad/datamodel/metainfo/em_nion/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..9ba4fd24a00f1d5b087c56b59c2e0787e97e3d50
--- /dev/null
+++ b/nomad/datamodel/metainfo/em_nion/__init__.py
@@ -0,0 +1,599 @@
+#
+# 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 matplotlib.afm import CharMetrics
+import numpy as np
+import os
+
+from nomad.units import ureg
+from nomad.metainfo import (
+ MSection, Package, Quantity, SubSection, MEnum, Datetime, Section)
+from nomad.datamodel.data import EntryData
+
+
+m_package = Package(name='electron_microscopy_nion')
+
+
+class ElectronGun(MSection):
+ """Details the electron gun."""
+
+ emitter_type = Quantity(
+ type=str,
+ description='''
+ Emitter type used to create the beam.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ description = Quantity(
+ type=str,
+ description='''
+ Ideally a reference to (another) file (ideally formatted using also an
+ an application definition) via a link, name, or a (globally persistent)
+ unique identifier to give further details about the electron gun.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ name = Quantity(
+ type=str,
+ description='''Given name.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ model = Quantity(
+ type=str,
+ description='''Given brand or model name by the manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ serial_number = Quantity(
+ type=str,
+ description='''
+ Given hardware name/serial number or hash identifier issued by the
+ manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class Aperture(MSection):
+ """Details about an aperture."""
+
+ name = Quantity(
+ type=str,
+ description='''Given name.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ model = Quantity(
+ type=str,
+ description='''Given brand or model name by the manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ serial_number = Quantity(
+ type=str,
+ description='''
+ Given hardware name/serial number or hash identifier issued by the
+ manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ manufacturer_name = Quantity(
+ type=str,
+ description='''Given name of the manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ value = Quantity(
+ type=np.dtype(np.float64),
+ description='''
+ Relevant value from the control software as this is not always just
+ the diameter of (not even in the case) of a circular aperture but a
+ rather a value from a list of predefined ones in the control software.
+ Which actual settings are behind these should be Details which choice
+ was made should be explained under description.''',
+ a_eln=dict(component='NumberEditQuantity'))
+
+ _value_units = Quantity(
+ type=str,
+ description='''
+ Relevant value from the control software as this is not always just
+ the diameter of (not even in the case) of a circular aperture but
+ a rather a value from a list of predefined ones in the control
+ software. Which actual settings are behind these should be detailed and
+ which choices were made should be explained under description.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ description = Quantity(
+ type=str,
+ description='''
+ An (ideally globally persistent) unique identifier, link, or text
+ which gives further details.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class Lens(MSection):
+ """Details about a lens."""
+
+ name = Quantity(
+ type=str,
+ description='''Given name.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ model = Quantity(
+ type=str,
+ description='''Given brand or model name by the manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ serial_number = Quantity(
+ type=str, description='''Given hardware name/serial number or
+ hash identifier issued by the manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ manufacturer_name = Quantity(
+ type=str, description='''Given name of the manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class Detector(MSection):
+ """Details about the detector."""
+
+ name = Quantity(
+ type=str,
+ description='''Given name.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ model = Quantity(
+ type=str,
+ description='''Given brand or model name by the manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ serial_number = Quantity(
+ type=str, description='''
+ Given hardware name/serial number or hash identifier issued
+ by the manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ manufacturer_name = Quantity(
+ type=str,
+ description='''Given name of the manufacturer.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ sensor_material = Quantity(
+ type=str,
+ description=''' ''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ bit_depth_readout = Quantity(
+ type=np.dtype(np.int64),
+ description=''' ''',
+ a_eln=dict(component='NumberEditQuantity'))
+
+ _bit_depth_readout_units = Quantity(
+ type=str,
+ description=''' ''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ number_of_cycles = Quantity(
+ type=np.dtype(np.int64),
+ description=''' ''',
+ a_eln=dict(component='NumberEditQuantity'))
+
+ _number_of_cycles_units = Quantity(
+ type=str,
+ description=''' ''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ x_pixel_size = Quantity(
+ type=np.dtype(np.float64),
+ unit='meter',
+ description='''Physical distance represented by
+ the edge of the pixel along the x direction.''',
+ a_eln=dict(component='NumberEditQuantity'))
+
+ _x_pixel_size_units = Quantity(
+ type=str,
+ description=''' ''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ y_pixel_size = Quantity(
+ type=np.dtype(np.float64),
+ unit='meter',
+ description='''Physical distance represented by
+ the edge of the pixel along the y direction.''',
+ a_eln=dict(component='NumberEditQuantity'))
+
+ _y_pixel_size_units = Quantity(
+ type=str,
+ description=''' ''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ flatfield_applied = Quantity(
+ type=bool,
+ description=''' ''',
+ a_eln=dict(component='BoolEditQuantity'))
+
+ flatfield = Quantity(
+ type=np.dtype(np.float64),
+ description=''' ''',
+ a_eln=dict(component='NumberEditQuantity'))
+
+ _flatfield_units = Quantity(
+ type=str,
+ description=''' ''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ description = Quantity(
+ type=str,
+ description='''
+ Free text option to write further details about the detector.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class InstrumentControl(MSection):
+ """Details relevant for the control of the instrument."""
+
+ camera_length = Quantity(
+ type=np.dtype(np.float64),
+ unit='meter',
+ description='''Exact definition as understood by HU colleagues
+ remains to be communicated.''',
+ a_eln=dict(component='NumberEditQuantity'))
+
+ _camera_length_units = Quantity(
+ type=str,
+ description='''Exact definition as understood by HU colleagues
+ remains to be communicated.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ magnification = Quantity(
+ type=np.dtype(np.float64),
+ description='''
+ Exact definition as understood by HU colleagues
+ remains to be communicated.''',
+ a_eln=dict(component='NumberEditQuantity'))
+
+ _magnification_units = Quantity(
+ type=str,
+ description='''
+ Exact definition as understood by HU colleagues
+ remains to be communicated.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class Stage(MSection):
+ """Details about the stage."""
+
+ design = Quantity(
+ type=str,
+ description=''' ''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ name = Quantity(
+ type=str,
+ description=''' ''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ model = Quantity(
+ type=str,
+ description=''' ''', a_eln=dict(component='StringEditQuantity'))
+
+ serial_number = Quantity(
+ type=str,
+ description=''' ''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ manufacturer_name = Quantity(
+ type=str,
+ description=''' ''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ description = Quantity(
+ type=str,
+ description=''' ''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class Instrument(MSection):
+ """Details about the electron microscope, its components, and software."""
+
+ name = Quantity(
+ type=str,
+ description='''
+ Given name of the microscope, e.g NionHermes.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ location = Quantity(
+ type=str,
+ description='''
+ Geographic coordinates of the lab or the place where the instrument
+ is installed using GEOREF geocodes ideally.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ instrument_manufacturer = Quantity(
+ type=str,
+ description='''
+ Manufacturer of the entire instrument (e.g. Nion, FEI, Zeiss,
+ Thermofisher) to enable e.g. queries in materials
+ database systems for instrument manufacturers.
+ Usually more technical details are needed though to specify the
+ instrument, these should be written into instrument_model and
+ instrument_capabilities.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ instrument_model = Quantity(
+ type=str,
+ description='''
+ Manufacturer brand/model to enable e.g. queries about
+ microscope models.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ instrument_identifier = Quantity(
+ type=str,
+ description='''
+ Hardware name/serial number or hash identifier given by the
+ manufacturer to identify the instrument.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ instrument_capability = Quantity(
+ type=str,
+ description='''Free-text list possibly multiple terms of
+ functionalities which the instrument provides.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ electron_gun = SubSection(section_def=ElectronGun)
+ aperture = SubSection(section_def=Aperture, repeats=True)
+ lens = SubSection(section_def=Lens, repeats=True)
+ stage = SubSection(section_def=Stage)
+ detector = SubSection(section_def=Detector)
+ control = SubSection(section_def=InstrumentControl)
+
+
+class Operator(MSection):
+ """Contact information of at least the user of the instrument.
+
+ Or the investigator who performed this experiment.
+ Adding multiple users if relevant is recommended.
+ """
+
+ m_def = Section(a_eln=dict())
+
+ name = Quantity(
+ type=str,
+ description='''
+ Given (first) name and surname of the user.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ affiliation = Quantity(
+ type=str,
+ description='''
+ Name of the affiliation of the user at the point in time
+ when the experiment was performed.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ address = Quantity(
+ type=str,
+ description='''Postal address of the affiliation.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ email = Quantity(
+ type=str,
+ description='''
+ Email address of the user at the point in time
+ when the experiment was performed.
+ Giving the most permanently used email is recommended.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ orcid = Quantity(
+ type=str,
+ description='''
+ Globally unique identifier of the user as offered
+ by services like ORCID or ResearcherID.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ telephone_number = Quantity(
+ type=str,
+ description='''
+ (Business) (tele)phone number of the user at the point
+ in time when the experiment was performed.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ role = Quantity(
+ type=str,
+ description='''
+ Which role does the user have in the place, and at the point in time
+ when, the experiment was performed (e.g. technician operating the
+ microscope, student, postdoc, principal investigator, guest ...)''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class Sample(MSection):
+ """Properties of the specimen, its history."""
+
+ name = Quantity(
+ type=str,
+ description='''
+ Descriptive name or identifier with which to distinguish the specimen
+ from all others and especially the parts from where it was cut.
+ In cases where the specimen was e.g. site-specifically cut from
+ samples or in cases of an instrument session during which multiple
+ specimens are loaded, the name has to be descriptive enough to resolve
+ which specimen on e.g. the microtip array was taken. The user is
+ advised to store the details how specimens were cut/prepared from
+ samples in the sample history.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ sample_history = Quantity(
+ type=str,
+ description='''
+ Ideally, a reference to the location of or a (globally persistent)
+ unique identifier of e.g. another file which should document ideally
+ as many details as possible of the material, its microstructure, and
+ its thermo-chemo-mechanical processing/preparation history.
+ In the case that such a detailed history of the sample/specimen is not
+ available, use this field as a free-text description to specify a sub-
+ set of the entire sample history, i.e. what you would consider being
+ the key steps and relevant information about the specimen, its
+ material, microstructure, thermo-chemo-mechanical processing state,
+ and details of the preparation.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ preparation_date = Quantity(
+ type=Datetime,
+ description='''
+ ISO8601 date and time with local time zone offset to UTC included
+ when the specimen was prepared. Ideally report the end of the
+ preparation, i.e. the last known time the measured specimen surface
+ was actively prepared. Knowing when the specimen was exposed to e.g.
+ specific atmosphere is especially required for environmentally
+ sensitive material such as hydrogen-charged specimens or experiments
+ including tracers with a short half-time. The user is advised to
+ include these temporal details in the sample_history.''',
+ a_eln=dict(component='DateTimeEditQuantity'))
+
+ atom_types = Quantity(
+ type=str,
+ description='''
+ Use Hill's system for listing elements of the periodic table which
+ are inside or attached to the surface of the specimen and thus
+ considered relevant from a scientific point. The purpose of the field
+ is to offer materials database systems an opportunity to parse the
+ relevant elements without having to interpret these
+ from the sample history.''',
+ a_eln=dict(component='StringEditQuantity'))
+
+ thickness = Quantity(
+ type=np.dtype(np.float64),
+ unit='meter',
+ description='''Sample thickness''',
+ a_eln=dict(component='NumberEditQuantity'))
+
+ _thickness_units = Quantity(
+ type=str,
+ description='''Sample thickness''',
+ a_eln=dict(component='StringEditQuantity'))
+
+
+class ElectronMicroscopyNion(EntryData):
+ """Application definition describing electron microscope experiments.
+
+ Applies when working with a Nion microscope using NXem_nion.nxdl.xml.
+ The here specified ELN is a proof-of-concept whose scope is to provide
+ a mechanism to inject additional pieces of information to create a NeXus
+ file that matches a:
+ - particular version of the NXem_nion.nxdl.xml appdef
+ - https://github.com/FAIRmat-Experimental/nexus_definitions/commit/
+ - 1d46b94dc36a42225ad247cc763277a47dcd30d4
+ - working with experiments as a pair of Numpy NPY binary and Nion
+ - metadata JSON file. Specifically with these file formats being
+ - interpretable with the following, so-called em_nion dataconverter
+ - (see commit below).
+ The ELN returns a json file that is to be used to inject the
+ here collected pieces of information in a
+ - specifically-versioned dataconverter em_nion
+ - https://github.com/nomad-coe/nomad-parser-nexus/commit/
+ 47bc4f9724b8e980bd41d0fca3a663c0b79a7fb1
+ """
+
+ start_time = Quantity(
+ type=Datetime,
+ description='''
+ ISO 8601 formatted time code with local time zone offset to UTC
+ information included when the experiment started. If the application
+ demands that time codes in this section of the application definition
+ should only be used for specifying when the experiment was performed -
+ and the exact duration is not relevant - this start time field
+ should be used. Often though it is useful to specify a time interval
+ with specifying both start_time and end_time to allow for more
+ detailed bookkeeping and interpretation of the experiment. The user
+ should be aware that even with having both time instances specified
+ it may not be advisable to infer how long the experiment took or
+ for how long data were acquired. More detailed timing data over
+ the course of the experiment have to be collected.''',
+ a_eln=dict(component='DateTimeEditQuantity'))
+
+ end_time = Quantity(
+ type=Datetime,
+ description='''
+ ISO 8601-formatted time code with local time zone offset to UTC
+ included when the experiment ended.''',
+ a_eln=dict(component='DateTimeEditQuantity'))
+
+ sample = SubSection(section_def=Sample)
+ operator = SubSection(section_def=Operator, repeats=True)
+ instrument = SubSection(section_def=Instrument)
+
+ nionswift_data_npy_file = Quantity(
+ type=str,
+ description='''
+ Numpy data file as exported from NionSwift''',
+ a_eln=dict(component='FileEditQuantity'),
+ a_browser=dict(adaptor='RawFileAdaptor'))
+
+ nionswift_metadata_json_file = Quantity(
+ type=str,
+ description='''
+ Json file with metadata as exported from NionSwift''',
+ a_eln=dict(component='FileEditQuantity'),
+ a_browser=dict(adaptor='RawFileAdaptor'))
+
+ # maybe a database dump file from e.g. NionSwift or microscope control
+ # software in general
+
+ def normalize(self, archive, logger):
+ """Normalize data."""
+ # store content of the above ELN entries into a dictionary
+ # data = self.m_to_dict()
+
+ # map paths in this dictionary on paths as expected by apm reader
+ # for instance by storing flattened data key value pairs in a json
+ # file
+
+ # remains to be implemented
+
+# runner = CliRunner()
+# converter_args = ['--input-file', self.nionswift_data_npy_file,
+# '--input-file', self.nionswift_metadata_json_file,
+# '--input-file',
+# os.path.join(filepath, 'eln.em_nion.json'),
+# '--reader', 'em_nion',
+# '--nxdl', 'NXem_nion',
+# '--output', os.path.join(filepath, \
+# 'em_nion.test.nxs')]
+# runner.invoke(convert, converter_args)
+
+ pass
+
+# =============================================================================
+# import yaml
+# from nomad.datamodel.metainfo.ellipsometry.dict_flattener \
+# import dict_flatten, dict_key_cut
+# from nexusparser.tools.dataconverter.convert import convert
+# from click.testing import CliRunner
+#
+# data = self.m_to_dict()
+# data.update(data.pop('data_file'))
+# dict_flatten(data)
+# dict_key_cut(data)
+#
+# kl = list(data.keys())
+# for k in kl:
+# if '/_' in k:
+# data[k.replace('/_', r"/\@")] = data.pop(k)
+# dict_key_cut(data, '/', 1, '@')
+# data['definition'] = 'NXellipsometry'
+# data[r"definition/\@version"] = '0.0.1'
+# data[r"definition/\@url"] = 'https://'
+#
+# with archive.m_context.raw_file('eln.apm.json', 'w') as outfile:
+# yaml.dump(data, outfile, default_flow_style=False)
+# filepath = os.path.dirname(outfile.name)
+# =============================================================================
+
+
+m_package.__init_metainfo__()