Change Log#
1.1.0: 2024/12/06#
- h52nx
add ‘–no-master-file’ option (PR 272)
fix cropping of machine current points (PR 177)
fix motor geometry (PR 195)
add source to sample distance (PR 202)
improve machine electric current deduction (PR 179)
add ROI (PR 172)
- edf2nx
add an option ‘using the real angle values’ (PR 181)
- misc
move progress to tqdm (PR 187)
remove ‘3D-XRD’, ‘XRD-CT’ classes (PR 196)
remove ‘require_x_translation’, ‘require_z_translation’ (PR 199)
remove usage of ‘scan_numbers’ (PR 173)
move to ‘__future__’ annotations (PR 166)
move sources to ‘src’ (PR 130)
1.0.11: 2024/10/07#
h52nx: modify bliss file scan ordering (based on each scan ‘start_time’ when existing)
1.0.9: 2024/08/27#
h52nx: handle z-series v 3 (PR 258)
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’ …)