Change Log#

1.0.0: 2024/02/23#

  • app

    • add nx-copy: application to copy NXtomo contained in a file (Update relative links of the HDF5 VDS if any). (PR 188)

  • misc

    • remove ‘is_xrdct_entry’ (PR 209)

    • rework doc and move to sphinx-pydata-theme

    • move to silx 2.0

0.13.2: 2023/08/03#

  • converter
    • hdf5:

      • add bliss_orginal_files option

0.13.0: 2023/08/01#

  • converter

    • remove x and y real pixel size metadata

    • remove magnification metadata

    • edf2

      • add option output-checks: allow check on the generated volume (PR 155)

      • add option delete-edf: allow deletion of the edf input files once the conversion is done (and check if asked) (PR 155)

    • hdf5

      • benefit from ‘technique/image’ bliss metadata when possible (PR 147, 168)

      • remove plugins system as never used (PR 177)

      • improve pcotomo robustness (PR 160, PR 159)

      • estimated_cor_from_motor is now set for 360 degree scan (and not only 180) (PR 161)

      • improve robustness against cancel scan (PR 158, 165)

      • remove real pixel size and magnification

  • nexus

    • improve robustness and readibility of node name vs path handling (PR 173)

  • app

    • add edf2nx-check: application to allow check from a previous conversion and optionnaly remove EDF source files. (PR 164)

    • add split-nxfile: application to split a file containing several NXtomo into single-NXtomo files. (PR 172)

    • add z-concatenate-scans: application to concatenate a z-serie of scan into a single NXtomo (PR 174, 175).

    • zstages2nxs: add output_filename_template option (PR 176)

    • deprecate h5-quick-start in favor of h5-config (PR 166)

    • deprecate edf-quick-start in favor of edf-config (PR 166)

  • misc

    • deprecate from_dx_to_nx for from_dx_config_to_nx (PR 167)

    • replace string.format by f-strings when possible (PR 154)

    • doc: add an example of btaach processing

0.12.0: 2023/02/23#

  • app

    • zstages2nxs command added (PR 145)

  • converter
    • hdf5

      • add frame flip information (PR 109)

    • edf2nx

      • better handling of current units (PR 150)

  • misc

    • get rid of numpy distutils for packaging (PR 151)

0.11.0: 2022/12/15#

  • converter
    • hdf5:

      • handle new path with {detector_name}

      • handle flips

      • fix: was unable to find pixel position and energy for zserie

0.10.9: 2022/10/26#

  • converter

    • hdf5converter: handle EBStomo pcotomo second version

0.10.1: 2022/08/31#

  • converter

    • EDFConfig: default unit for distance, x, y and z translations from .info file is now millimeter

    • edf2nx: fix deduction of field of view.

0.10.0: 2022/08/30#

  • converter

    • remove deprecated ‘h5_to_nx’ function (deprecated since 0.5.0)

    • hdf5converter

      • add management of magnification (PR 110). Not handled for by edfconverter

      • add function to do a subselection of an NXtomo from the rotation angle and add dedicated parameter for pcotomo conversion to refine NXtomo to be created (PR 100)

    • edf2nx

      • add an option to avoid data duplication (PR 114, 115, 118)

  • nexus

    • add probe to NXsource (PR 117)

    • improve NXdetector.data setter (PR 122)

    • rename attributes unit to units

0.9.0: 2022/06/24#

  • converter
    • hdf5

      • add handling of the machine electrical current (PR 106)

      • add management of is_rearranged attribute (PR 111)

    • edf

      • add management of a configuration file (PR 104)

  • nexus

    • add Nxtomo concatenation (PR109)

0.8.0: 2021/06/04#

  • converter
    • hdf5

      • add ‘bam_single_file’ option (PR 96)

      • add pcotomo management (PR 91, 88)

  • add nexus module providing API to edit an NXtomo (PR 87)

0.7.0: 2021/01/07#

  • converter

    • hdf5: management of ExternalLink as entry (case of bliss proposal file, PR 85)

    • edf

      • fix issues with progress (PR 80)

  • patch-nx

    • add option to convert all frame of a given type (PR 84)

  • dxfile2nx

    • allow to provide pixel size as a single value (PR 77)

  • miscellaneous::

    • add some missing aliases flat/ref (PR 83)

    • benefit from validator (PR 81)

0.6.0: 2021/10/04#

  • app

    • add ‘dxfile2nx’ application. Allow to convert from dxfile format to NXtomo format

    • h52nx

      • add “duplicate_data” option to force frame duplication from the command line.

    • add ‘h5-3dxrd-2nx’: convert from to 3D XRD - bliss-hdf5 to (enhance) NXtomo Format .

  • converter

    • add dxfileconverter

0.5.0: 2021/04/20#

  • converter
    • hdf5

      • rework virtual dataset creation

      • insure the number of projection found is that same as the expected number of projection (tomo_n)

      • add start_time and end_time

      • handle configuration file

        • add HDF5config and HDF5ConfigHandler

      • improve research of keys / path. First try to retrieve a dataset with the expected number of elements. If fail return the first dataset fitting a path.

      • add ignore_sub_entries to skip some scan

      • add a warning if no acquisition are found

    • utils

      • rework _insert_frame_data to use a class instead _FrameAppender

      • fix management of negative indexing

  • app
    • patch-nx

      • add an option –embed-data

    • rename tomoh52nx to h52nx. Deprecate tomoh52nx.

    • rename tomoedf2nx to edf2nx. Deprecate tomoedf2nx.

    • h52nx

      • can now take a configuration file in parameter (“–config” option)

      • add option –ignore-sub-entries

0.4.0: 2020/11/09#

  • requires h5py >= 3

  • utils:

    • add change_image_key_control function to modify frame type inplace

    • add add_dark_flat_nx_file function to add dark or flat in an existing NXTomo entry

    • converter
      • h5_to_nx:

        • add management of ‘proposal file’: handle External / SoftLink

        • insure relative path is given when converting the file

        • magnified_pixel_size will not be write anymore. If a magnified / sample pixel size is discover then this will be saved as the ‘pixel_size’.

        • add an option to display_advancement or not.

        • split “zseries” according to z value

        • add NXdata information to display detector/data from root as image

      • move format version to 1.0

  • app:
    • add patch-nx application to modify an existing NXTomo

      • add dark or flat series

      • modify frame type

    • tomoh52nx:

      • warning if we try to convert a file containing some NXTomo entry

      • create directories for output file if necessary

      • check write rights on output file

      • split “zseries” according to z value

  • miscellaneous::

    • adopt ‘black’ coding style

0.3.4: 2020/10/05#

  • converter: fix log

0.3.3: 2020/08/26#

  • h5_to_nx:

    • add set-param option to let the user define some parameters values like energy if he knows it is missing (and avoid asking him n times).

  • io: add management of hdf5 files from tomoscan.io.HDF5File

0.3.1: 2020/08/19#

  • add field_of_view parameter

  • add plugin management (allows user to define motor position value from a python script) - PR !19

0.3.0: 2020/03/20#

  • app: add several option to define titles

  • h5_to_nx:

    • add possibility to add plugins for defining new motor position

    • units: move distances to meter

  • edf_to_nx:

    • units: move distances to meter

0.2.0: 2020/22/04#

  • setup: add entry point on __main__

  • converter

    • h5_to_nx: add a possible callback to give input

  • doc

    • add API documentation

    • add tutorials for tomoedf2nx and tomoh5tonx

0.1.0: 2020/03/12#

  • app

    • add application tomoedf2nx: convert acquisition using old bliss and EDF to .hdf5 file format, nexus (NXtomo) compliant format.

    • add application tomoh5tonx: convert acquisition using bliss/hdf5 to a nexus (NXtomo) compliant format.

  • converter

    • add h5_to_nx function to convert from bliss .hdf5 to nexus (NXtomo) compliant format.

    • add get_bliss_tomo_entries function to return the bliss ‘roor’ entries (for now named ‘tomo:basic’, ‘tomo:fullturn’ …)