Bring NXapm back that has been accepted now by the NIAC

[mkuehbach]

Summary by Sourcery

Bring back the NXapm application definition and broaden the NeXus schema with new base classes and extended process definitions for atom probe microscopy data.

New Features:

• Reintroduce the NXapm atom probe microscopy application definition in both YAML and NXDL formats.
• Add new base classes for NXimage, NXspectrum, NXinstrument_apm, and NXapm_simulation to support image, spectrum, and instrument simulation data.
• Extend the NXprocess base class by including NXparameters and NXdata groups.

Enhancements:

• Add a number_of_poles field to the NXlens_em class.
• Standardize XML/YAML formatting and update copyright years across multiple base classes and contributed definitions.
• Refine documentation strings and capitalization in several base classes (NXfabrication, NXentry, NXcomponent, etc.).

[sourcery-ai]

Reviewer's Guide

This pull request reintroduces the NXapm application definition for atom probe microscopy, restoring both YAML and NXDL files and extending several base classes (NXprocess, NXinstrument_apm, NXimage, NXspectrum, NXapm_simulation) to support detailed metadata and workflows, while also applying formatting clean-ups and year updates across various definition files.

Class diagram for the new NXapm application definition and related base classes

classDiagram
    class NXapm {
        <<application>>
        +NXentry[1..*]
    }
    class NXentry {
        +definition: NX_CHAR
        +run_number: NX_UINT
        +experiment_alias: NX_CHAR
        +experiment_description: NX_CHAR
        +start_time: NX_DATE_TIME
        +end_time: NX_DATE_TIME
        +elapsed_time: NX_FLOAT
        +operation_mode: NX_CHAR
        +userID: NXuser
        +sample: NXsample
        +specimen: NXsample
        +consistent_rotations: NXparameters
        +NAMED_reference_frame: NXcoordinate_system
        +measurement: NXapm_measurement
        +simulation: NXapm_simulation
        +atom_probeID: NXroi_process
        +profiling: NXcs_profiling
    }
    class NXapm_measurement {
        +status: NX_CHAR
        +quality: NX_CHAR
        +instrument: NXinstrument_apm
        +eventID: NXevent_data_apm
    }
    class NXinstrument_apm {
        +type: NX_CHAR
        +location: NX_CHAR
        +flight_path: NX_FLOAT
        +reflectron: NXcomponent
        +local_electrode: NXlens_em
        +ion_detector: NXdetector
        +pulser: NXcomponent
        +stage: NXmanipulator
        +analysis_chamber: NXcomponent
        +buffer_chamber: NXcomponent
        +load_lock_chamber: NXcomponent
        +getter_pump: NXpump
        +roughening_pump: NXpump
        +turbomolecular_pump: NXpump
    }
    class NXroi_process {
        +initial_specimen: NXimage
        +final_specimen: NXimage
        +raw_data: NXprocess
        +hit_finding: NXprocess
        +hit_spatial_filtering: NXprocess
        +voltage_and_bowl: NXprocess
        +mass_to_charge_conversion: NXprocess
        +reconstruction: NXapm_reconstruction
        +ranging: NXapm_ranging
    }
    class NXprocess {
        +program: NX_CHAR
        +sequence_index: NX_POSINT
        +version: NX_CHAR
        +date: NX_DATE_TIME
        +(NXnote)
        +(NXparameters)
        +(NXdata)
    }
    class NXimage {
        +image_2d: NXdata
    }
    class NXapm_simulation {
        <<group>>
    }
    class NXcs_profiling {
        +programID: NXprogram
        +environment: NXcollection
    }
    class NXcs_profiling_event {
        +start_time: NX_DATE_TIME
        +end_time: NX_DATE_TIME
        +description: NX_CHAR
        +elapsed_time: NX_NUMBER
        +max_processes: NX_UINT
        +max_threads: NX_UINT
        +max_gpus: NX_UINT
        +max_virtual_memory_snapshot: NX_NUMBER[n_processes]
        +max_resident_memory_snapshot: NX_NUMBER[n_processes]
    }
    NXapm --> NXentry
    NXentry --> NXapm_measurement
    NXentry --> NXapm_simulation
    NXentry --> NXroi_process
    NXentry --> NXcs_profiling
    NXapm_measurement --> NXinstrument_apm
    NXapm_measurement --> NXevent_data_apm
    NXroi_process --> NXimage : initial_specimen
    NXroi_process --> NXimage : final_specimen
    NXroi_process --> NXprocess : raw_data
    NXroi_process --> NXprocess : hit_finding
    NXroi_process --> NXprocess : hit_spatial_filtering
    NXroi_process --> NXprocess : voltage_and_bowl
    NXroi_process --> NXprocess : mass_to_charge_conversion
    NXroi_process --> NXapm_reconstruction : reconstruction
    NXroi_process --> NXapm_ranging : ranging
    NXcs_profiling --> NXcs_profiling_event
    NXprocess --> NXnote
    NXprocess --> NXparameters
    NXprocess --> NXdata
    NXimage --> NXdata : image_2d

Loading

Class diagram for the updated NXprocess base class

classDiagram
    class NXprocess {
        +program: NX_CHAR
        +sequence_index: NX_POSINT
        +version: NX_CHAR
        +date: NX_DATE_TIME
        +(NXnote)
        +(NXparameters)
        +(NXdata)
    }
    class NXnote {
    }
    class NXparameters {
    }
    class NXdata {
    }
    NXprocess --> NXnote
    NXprocess --> NXparameters
    NXprocess --> NXdata

Loading

Class diagram for the new NXcs_profiling_event base class

classDiagram
    class NXcs_profiling_event {
        +start_time: NX_DATE_TIME
        +end_time: NX_DATE_TIME
        +description: NX_CHAR
        +elapsed_time: NX_NUMBER
        +max_processes: NX_UINT
        +max_threads: NX_UINT
        +max_gpus: NX_UINT
        +max_virtual_memory_snapshot: NX_NUMBER[n_processes]
        +max_resident_memory_snapshot: NX_NUMBER[n_processes]
    }

Loading

Class diagram for the updated NXlens_em base class

classDiagram
    class NXlens_em {
        +pole_type: NX_CHAR
        +number_of_poles: NX_UINT
    }

Loading

Class diagram for the updated NXfabrication base class

classDiagram
    class NXfabrication {
        +date: NX_DATE_TIME
        +capability: NX_CHAR
    }

Loading

Class diagram for the updated NXentry base class

classDiagram
    class NXentry {
        +entry_identifier: NX_CHAR
        +identifier_entry: NX_CHAR
    }

Loading

Class diagram for the updated NXcomponent base class

classDiagram
    class NXcomponent {
        +identifierNAME: NX_CHAR
    }

Loading

Class diagram for the updated NXcg_primitive and NXcg_roi contributed definitions

classDiagram
    class NXcg_primitive {
    }
    class NXcg_roi {
    }

Loading

Class diagram for the updated NXactuator, NXcoordinate_system, NXdata, NXhistory, NXresolution, NXroot base classes

classDiagram
    class NXactuator {
    }
    class NXcoordinate_system {
    }
    class NXdata {
    }
    class NXhistory {
    }
    class NXresolution {
    }
    class NXroot {
    }

Loading

Class diagram for the updated NXcg_face_list_data_structure, NXcg_half_edge_data_structure, NXcg_hexahedron, NXcg_parallelogram, NXcg_polygon, NXcg_polyhedron, NXcg_polyline, NXcg_tetrahedron, NXcg_triangle contributed definitions

classDiagram
    class NXcg_face_list_data_structure {
    }
    class NXcg_half_edge_data_structure {
    }
    class NXcg_hexahedron {
    }
    class NXcg_parallelogram {
    }
    class NXcg_polygon {
    }
    class NXcg_polyhedron {
    }
    class NXcg_polyline {
    }
    class NXcg_tetrahedron {
    }
    class NXcg_triangle {
    }

Loading

File-Level Changes

Change	Details	Files
Reintroduce NXapm application definition	Add complete YAML-based application definition for NXapm Add NXDL XML for NXapm with symbols, groups, and full hierarchy	applications/nyaml/NXapm.yaml applications/NXapm.nxdl.xml
Extend and clean up NXprocess base class	Enrich docstrings and formatting Add NXparameters and NXdata child groups Update copyright and XML stylesheet formatting	base_classes/nyaml/NXprocess.yaml base_classes/NXprocess.nxdl.xml
Add and refine NXinstrument_apm for dynamic/static metadata	Detail pulser, source, beamID and control fields Clean YAML quoting and NXDL formatting Support laser/voltage pulsing metadata	base_classes/nyaml/NXinstrument_apm.yaml base_classes/NXinstrument_apm.nxdl.xml
Introduce NXimage and NXspectrum definitions	Provide one-, two-, three-dimensional image/spectrum specializations Define stack variants with index dimensions Include processing metadata and axis conventions	base_classes/nyaml/NXimage.yaml base_classes/NXimage.nxdl.xml base_classes/nyaml/NXspectrum.yaml base_classes/NXspectrum.nxdl.xml
Add NXapm_simulation base class	Define simulation group with NXprogram/NXparameters/NXprocess/NXdata support Provide minimal doc and structure	base_classes/NXapm_simulation.nxdl.xml
Global formatting and copyright updates	Standardize XML stylesheet declarations Correct copyright years from 2025 to 2024 Minor docstring formatting fixes	various base_classes and contributed_definitions files

---

Tips and commands

Interacting with Sourcery

• Trigger a new review: Comment @sourcery-ai review on the pull request.
• Continue discussions: Reply directly to Sourcery's review comments.
• Generate a GitHub issue from a review comment: Ask Sourcery to create an
  issue from a review comment by replying to it. You can also reply to a
  review comment with @sourcery-ai issue to create an issue from it.
• Generate a pull request title: Write @sourcery-ai anywhere in the pull
  request title to generate a title at any time. You can also comment
  @sourcery-ai title on the pull request to (re-)generate the title at any time.
• Generate a pull request summary: Write @sourcery-ai summary anywhere in
  the pull request body to generate a PR summary at any time exactly where you
  want it. You can also comment @sourcery-ai summary on the pull request to
  (re-)generate the summary at any time.
• Generate reviewer's guide: Comment @sourcery-ai guide on the pull
  request to (re-)generate the reviewer's guide at any time.
• Resolve all Sourcery comments: Comment @sourcery-ai resolve on the
  pull request to resolve all Sourcery comments. Useful if you've already
  addressed all the comments and don't want to see them anymore.
• Dismiss all Sourcery reviews: Comment @sourcery-ai dismiss on the pull
  request to dismiss all existing Sourcery reviews. Especially useful if you
  want to start fresh with a new review - don't forget to comment
  @sourcery-ai review to trigger a new review!

Customizing Your Experience

Access your dashboard to:

• Enable or disable review features such as the Sourcery-generated pull request
  summary, the reviewer's guide, and others.
• Change the review language.
• Add, remove or edit custom review instructions.
• Adjust other review settings.

Getting Help

• Contact our support team for questions or feedback.
• Visit our documentation for detailed guides and information.
• Keep in touch with the Sourcery team by following us on X/Twitter, LinkedIn or GitHub.

[mkuehbach]

Superseeded by #400