Changelog#

All notable changes to this project will be documented in this file.

The format follows the Keep a Changelog conventions and this project adheres to Semantic Versioning 2.0.0.

[Unreleased]#

Added#

  • h52nx

    • Handle rotation_is_clockwise.

    • Allow users to provide mechanical flips.

    • Try to deduce scan category/type from technique / scan_category.

  • Save NXtomo according to McStats (a flip between x, y and z axes is now supported).

Fixed#

  • h52nx – Improve robustness to invalid unit.

Misc#

  • The minimum Python version required is now 3.10.

[1.2.7] - 2025-09-22#

Fixed#

  • h52nx – Read optic_pixel_size first to determine detector/pixel size (PR 337).

[1.2.6] - 2025-09-19#

Fixed#

  • h52nx – Fix execution from the configuration file (PR 334).

[1.2.5] - 2025-07-29#

Fixed#

  • h52nx – Improve robustness if the camera is defined but no dataset is created (PR 328).

[1.2.4] - 2025-07-29#

Removed#

  • h52nx – Remove bam_single_file option (PR 324).

  • Applications – Remove configuration-level option (PR 324).

Changed#

  • Move config files to pydantic (PR 324).

[1.2.3] - 2025-07-21#

Fixed#

  • h52nx – Fix performance issues from deduce_machine_current (PR 320).

[1.2.0] - 2025‑07‑18#

Changed#

  • Refactored acquisition handling: added _AcquisitionConstructor classes (PR 313).

  • pcotomo deprecated in favour of multitomo.

  • Renamed machine_electric_current → machine_current (PR 305, 285).

  • Switched from pyunit to pint for units handling (PR 310, 309, 306, 294).

  • Documentation

    • Use program-output (PR 299, 293).

Added#

  • h52nx

    • --with-master-file option (replaces the old --no-master-file flag).

    • Propagation distance, sample‑to‑source distance, and sample pixel size handling.

    • Bliss “back‑and‑forth” sequence handling.

    • sequence_number handling.

Fixed#

  • Silx deprecation warning removed (PR 315).

Misc#

  • Minimum supported Python version is now 3.9.

  • Added Bandit to the CI pipeline.

[1.1.0] - 2024‑12‑06#

Added#

  • h52nx

    • --no-master-file option (PR 272).

    • Cropping fix for machine‑current points (PR 177).

    • Motor geometry fix (PR 195).

    • Source‑to‑sample distance handling (PR 202).

    • Region‑of‑interest (ROI) support (PR 172).

  • edf2nx

    • Option to use real angle values (PR 181).

Changed#

  • h52nx

    • Improved machine‑current deduction (PR 179).

Misc#

  • Progress reporting moved to tqdm (PR 187).

  • Removed legacy 3D‑XRD and XRD‑CT classes (PR 196).

  • Dropped require_x_translation and require_z_translation (PR 199).

  • Removed scan_numbers usage (PR 173).

  • Updated to __future__ annotations (PR 166).

  • Sources moved to the src directory (PR 130).

[1.0.11] - 2024‑10‑07#

Changed#

  • h52nx – Modified Bliss file scan ordering to use each scan’s start_time when present.

[1.0.9] - 2024‑08‑27#

Added#

  • h52nx – Added handling for Z‑series version 3 (PR 258).

[1.0.0] - 2024‑02‑23#

Added#

  • app

    • nx-copy – Copies an NXtomo and updates relative HDF5 VDS links (PR 188).

Removed#

  • Removed is_xrdct_entry (PR 209).

Misc#

  • Documentation rebuilt with sphinx‑pydata‑theme.

  • Upgraded to silx 2.0.

[0.13.2] - 2023‑08‑03#

Added#

  • converter → hdf5

    • bliss_original_files option.

[0.13.0] - 2023‑08‑01#

Changed#

  • hdf5

    • Uses technique/image Bliss metadata when available (PR 147, 168).

    • Improved multi‑tomo (pcotomo) robustness (PR 160, 159).

    • estimated_cor_from_motor now set for 360° scans (PR 161).

    • Better handling of cancelled scans (PR 158, 165).

    • Removed real pixel size and magnification fields.

  • nexus

    • Strengthened node‑name vs‑path handling robustness (PR 173).

  • app

    • edf2nx-check – Verify previous conversions and optionally delete EDF sources (PR 164).

    • split-nxfile – Split a file containing multiple NXtomo entries (PR 172).

    • z-concatenate-scans – Concatenate a Z‑series into a single NXtomo (PR 174, 175).

    • Deprecated h5-quick-start → h5-config and edf-quick-start → edf-config (PR 166).

  • misc

    • Deprecated from_dx_to_nx → from_dx_config_to_nx (PR 167).

    • Replaced str.format with f‑strings where possible (PR 154).

    • Added batch‑processing example to docs.

Added#

  • edf2

    • output-checks option to validate generated volumes (PR 155).

    • delete-edf option to delete source EDF files after conversion (PR 155).

    • zstages2nxs – Added output_filename_template option (PR 176).

Removed#

  • converter

    • Removed x/y real‑pixel‑size and magnification metadata.

      • hdf5

      • Removed unused plugins system (PR 177).

[0.12.0] - 2023‑02‑23#

Added#

  • app

    • zstages2nxs command (PR 145).

  • converter → hdf5

    • Frame‑flip information (PR 109).

Changed#

  • converter → edf2nx

    • Better handling of current units (PR 150).

misc#

  • Dropped numpy.distutils for packaging (PR 151).

[0.11.0] - 2022‑12‑15#

Added#

  • converter → hdf5

    • Support for {detector_name} placeholders in paths.

    • Flip handling.

    • Fixed inability to locate pixel position & energy for Z‑series.

[0.10.9] - 2022‑10‑26#

Added#

  • converter → hdf5converter

    • Support for EBStomo pcotomo second version.

[0.10.1] - 2022‑08‑31#

Fixed#

  • converter

    • Default distance, X/Y/Z translation units set to millimeter in EDFConfig.

    • Fixed field‑of‑view deduction in edf2nx.

[0.10.0] - 2022‑08‑30#

Added#

  • converter

    • hdf5converter

      • Added magnification management (PR 110).

      • Added sub‑selection of NXtomo by rotation angle and pcotomo‑specific parameters (PR 100).

    • edf2nx

      • Added option to avoid data duplication (PR 114, 115, 118).

  • nexus

    • Added probe to NXsource (PR 117).

Changed#

  • converter

    • Improved NXdetector.data setter (PR 122).

    • Renamed attribute unit → units.

Removed#

  • converter

    • Removed deprecated h5_to_nx (since 0.5.0).

[0.9.0] - 2022‑06‑24#

Added#

  • converter → hdf5

    • Machine electrical current handling (PR 106).

    • is_rearranged attribute management (PR 111).

  • converter → edf

    • Configuration‑file support (PR 104).

  • nexus

    • Added Nxtomo concatenation (PR 109).

[0.8.0] - 2021‑06‑04#

Added#

  • converter → hdf5

    • bam_single_file option (PR 96).

    • pcotomo management (PR 91, 88).

  • Added nexus module exposing an API to edit an NXtomo (PR 87).

[0.7.0] - 2021‑01‑07#

Added#

  • converter → hdf5

    • ExternalLink handling for Bliss proposal files (PR 85).

  • converter → edf

    • Fixed progress‑bar issues (PR 80).

  • patch‑nx

    • Option to convert all frames of a given type (PR 84).

  • dxfile2nx

    • Single‑value pixel‑size support (PR 77).

  • miscellaneous

    • Added missing aliases flat/ref (PR 83).

    • Integrated validator (PR 81).

[0.6.0] - 2021‑10‑04#

Added#

  • app

    • dxfile2nx – Convert DX‑files to NXtomo.

    • h52nx – New duplicate_data flag to force frame duplication.

    • h5-3dxrd-2nx – Convert Bliss‑HDF5 3D‑XRD to enhanced NXtomo (updates VDS links).

  • converter

    • Added dxfileconverter.

[0.5.0] - 2021‑04‑20#

Fixed#

  • utils

    • Fixed negative‑index handling.

Added#

  • converter → hdf5

    • Added start_time & end_time fields.

    • Full configuration‑file support (HDF5Config, HDF5ConfigHandler).

    • ignore_sub_entries to skip specific scans.

  • app

    • patch-nx – Added --embed-data flag.

    • Added --ignore-sub-entries option.

Changed#

  • converter → hdf5

    • Reworked virtual‑dataset creation.

    • Enforced projection count consistency (tomo_n).

    • Improved key/path discovery logic.

    • Warning when no acquisitions are found.

  • utils

    • Refactored _insert_frame_data into _FrameAppender class.

  • app

    • Renamed tomoh52nx → h52nx (deprecating former).

    • Renamed tomoedf2nx → edf2nx (deprecating former).

    • h52nx now accepts a configuration file (--config).

[0.4.0] - 2020‑11‑09#

Added#

  • utils

    • change_image_key_control – Modify frame type in‑place.

    • add_dark_flat_nx_file – Insert dark/flat series into an existing NXtomo.

  • converter → h5_to_nx

    • Proposal‑file handling (External/SoftLink).

    • Saved discovered magnified/sample pixel size as pixel_size.

    • Optional display_advancement flag.

    • Z‑series split by Z value.

    • Added NXdata for root‑level detector/image display.

  • app

    • tomoh52nx – Added warnings for files already containing NXtomo entries, auto‑creates output directories, checks write permissions, splits Z‑series.

Changed#

  • app

    • patch-nx – Modify existing NXtomo (add dark/flat, change frame type).

  • converter → h5_to_nx

    • Enforced relative paths for output files.

Misc#

  • Minimum required h5py ≥ 3.

  • Adopted black code‑style formatting.

[0.3.4] - 2020‑10‑05#

Fixed#

  • Logging issues in the converter.

[0.3.3] - 2020‑08‑26#

Added#

  • h5_to_nx

    • set-param option to pre‑define parameters (e.g., energy) and avoid interactive prompts.

  • io

    • Support for HDF5 files via tomoscan.io.HDF5File.

[0.3.1] - 2020‑08‑19#

Added#

  • field_of_view parameter.

  • Plugin system allowing users to define motor positions from a Python script (PR !19).

[0.3.0] - 2020‑03‑20#

Added#

  • app

    • Various options to set titles.

  • h5_to_nx

    • Plugin support for custom motor positions.

    • Distances now expressed in metres.

  • edf_to_nx

    • Distances now expressed in metres.

[0.2.0] - 2020‑04‑22#

Added#

  • Entry point on __main__.

  • converter → h5_to_nx

    • Optional callback for input handling.

  • doc

    • API documentation.

    • Tutorials for tomoedf2nx and tomoh5tonx.

[0.1.0] - 2020‑03‑12#

Added#

  • app

    • tomoedf2nx – Convert Bliss + EDF acquisitions to HDF5/NXtomo.

    • tomoh5tonx – Convert Bliss/HDF5 acquisitions to NXtomo.

  • converter

    • h5_to_nx – Core conversion function from Bliss HDF5 to NXtomo.

    • get_bliss_tomo_entries – Retrieve Bliss “roor” entries (e.g., tomo:basic, tomo:fullturn).

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