CHANGELOG.rst

Change Log

2.1.1: 2024/11/28

• volume:

  • VolumeSingleFrameBase: add cleaning of possible remaining files from previous save (PR 243)

2.1.0: 2024/11/22

• scan

  • remove 'HDF5XRD3DScan' and 'XRD3DFrame' classes

• series

  • deprecate tomoscan.serie.serie (PR 236)

2.0.0: 2024/02/07

• scan:

  • NXtomo: replace x_flipped and y_flipped by NXtransformations (PR 145)
  • deprecate tomoscan.esrf.scan.hdf5scan.HDF5TomoScan in favor of tomoscan.esrf.scan.nxtomo.NXtomoScan
  • deprecate tomoscan.esrf.scan.mock.MockHDF5 in favor of tomoscan.esrf.scan.mock.MockNXtomo
  • deprecate tomoscan.test.utils.HDF5MockContext in favor of tomoscan.test.utils.NXtomoMockContext
  • add 'build_drac_metadata' function
  • NXtomoScan.flat_n: change behavior: return the number of flat per series (like for EDFTomoScan) instead of the total number of (raw) flats

• add dependancy to nxtomo and move all nexus path to it.

1.3.2: 2023/08/23

• volume

  • jp2k: rescale data if cast it to uint16 by default

1.3.0: 2023/08/01

• identifier

  • replace data_path request by path to be closer to silx API (PR 144)

• volume

  • replace pixel_size-scalar by voxel_size-tuple. (PR 139)
  • get_bounding_box: remove API allowing to provide axis as 'x', 'y', 'z' and only tolerate integers (PR 138)
  • guess_volumes: add filtering of nabu histograms (8444be27)

• scan:

  • HDF5TomoScan:

    • modify NXtomo behavior when no image_key_control: previously it was trying to get some 'return' projections from rotation angle. This was a non sense. It has been removed.
    • check detector dataset - log warning if virtual dataset is broken or appear to contain more external file than the OS can handle (PR 147)

• misc

  • increase usage of f-strings when possible (PR 71)

1.2.0: 2023/02/23

• volume:

  • single frame per file volume (edf, jp2k) default digit number moved from 4 to 6 (reading still compatible - PR 336)

• frame reducer

  • overwrite existing dataset when possible (PR 128)

• scan

  • rework get_short_description: compress file name if too long (PR 129)

• misc

  • remove distutils for packaging (PR 126)

1.1.2: 2023/01/10

• volume:

  • add RawVolume (legacy for some processing pipeline - PR 123)

1.1.0: 2022/12/15

• scan: add metadata for stitching (!118)
• misc: add pylint

1.0.0: 2022/08/30

• handle source probe (PR 80)

• volume:

  • add browse_data_urls function (PR 83)
  • add browse_data_files and browse_metadata_files functions (PR 82)
  • create output directories for single files if doesn't exists (PR 81)
  • add utils function (guess_volumes, guess_hdf5_volume_data_paths...) (PR 85, PR 89)
  • HDF5 Volume: add browse_slices and load_chink functions (PR 96)

• reduced frames

  • add metadata to reduced frames (PR 92)
  • add copy_darks_to and copy_flats_to functions (PR 90)
  • add utils to handle relative reduced frame indices (PR 99)

• validator

  • use tomo_n when possible on NXtomo validity check (PR 97)

• misc

  • rename exposure_time to count_time (PR 98)

0.9.0: 2022/06/19

• EDFScan: add dataset_basename and scan_info to the constructor (PR 77)

  • dataset_basename is used to determine the projection files. If not provided fall back on folder name (as it was the case previously. Insure compatibility if not provided)
  • scan_info: users can provide .info file to be used to retrieve metadata. If not provided uses datasaet_basename.info. If not provided insure to have the same behavior as previously.

• add machine current (PR 78)

  • goes to nexus_path.ELECTRIC_CURRENT_PATH for HDF5 / nexus
  • goes to nexus_path.ELECTRIC_CURRENT_PATH for HDF5 / nexus

0.8.0: 2022/02/05

• add nexus module: module dedicated to defines nexus path (PR 73)

• unitsystem

  • add timesystem. Module dedicated to time system (PR 72)

• improve management of a series (PR 67)
• add the volume of concept inside tomoscan (PR 70)

0.7.0: 2022/01/04

• esrf

  • add default methods to load and save darks / flats according to the file format (hdf5, edf): PR 65
  • improve mock class: PR 57

  • hdf5scan

    • add possibility to provide the nexus version on the constructor to insure backward compatibility: PR 58

  • add 'get_relative_file' helper.

• Miscellaneous

  • move documentation to autosummary: PR 56
  • replace some 'ref' by 'flat': PR 60

0.6.0: 2021/08/31

• add validator: helper function to parse input file and look for some missing dataset, invalid values or broken link

• esrf

  • TomoScanBase

    • add a first version of the intensity normalization
    • add property intensity_monitor to read diode for example
    • add property exposure_time to get frame exposure time

  • add Source class
  • move _FOV to public

  • HDF5TomoScan

    • adapt to read from various version of nexus version

      • add _NEXUS_PATHS class to keep trace of the path through history and simplify reading from a specific version

    • tomo_n now return the value from instrument/detector/tomo_n instead of len(projections)

  • utils

    • get_compacted_dataslices: preserve defined scheme

  • add HDF5XRD3DScan class to handle XRD-3D data

• Miscellaneous

  • move to setup.cfg

0.5.0: 2021/04/20

• esrf

  • TomoScanBase

    • add sequence_name, sample_name and group_size properties
    • add start_time and end_time properties
    • add x_translation, y_translation and z_translation properties (Not handled by EDFTomoScan for now)

    • HDF5TomoScan

      • speed up sinogram generation

    EDFTomoscan

    • improve lazy loading

  • utils: add the concept of groups. A group for example is a set of sequences defining a zseries

0.4.0: 2020/11/09

• esrf

  • HDF5TomoScan & EDFTomoScan add ignore_projections in the constructor

  • add properties to scanBase.TomoScanBase class:

    • alignment_projections
    • estimated_cor_frm_motor

  • add flat_field_correction function
  • move h5py dependency to 3.x

• Miscellaneous: add 'black' format

0.3.2: 2020/08/26

• HDF5TomoScan

  • manage hdf5 files using the HDFFile Class in order to avoid any file corruption.

0.3.1: 2020/08/19

• TomoScanBase

  • add field_of_view

• notebooks: rework notebooks

0.3.0: 2020/06/26

• move default distance units to meter
• open with swmr mode by default

• utils:

  • add get_compacted_dataslices
  • rework HDF5 mock class

0.2.0: 2020/03/09

• add some cache

• TomoScanBase

  • add distance
  • add energy

• EDFTomoScan

  • rework guess_index_frm_file_name

• HDF5TomoScan

  • add entry (one master file can have several sequence so several HDF5TomoScan)
  • add image_key (projection, dark...)
  • adapt to latest bliss file (bamboo)
  • add return_projs
  • add rotation_angle
  • add magnified pixel size
  • add frames

• rework UnitSystem

0.1.0: 2020/02/11

• add tomoscan.esrf.edfscan
• add tomoscan.esrf.hdf5scan