Skip to content

Version 3.0
Compare
Choose a tag to compare
@nicwade nicwade released this 18 Dec 14:34
· 2243 commits to master since this release
v3.0
86619a7
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

Core updates:

  • Ports Savu to Python 3
  • Fixes dosna transport
  • Restructures experiment collection and plugin runner to reduce the number of plugin load repetitions
  • Fixes 4D processing problems, including chunks not set
  • Fixes incorrect dimension error when fixing nFrames to be an integer
  • Fixes error in choosing first slice dimension
  • Fixes incorrect nxentry group name
  • Adds VOLUME_3D pattern
  • Adds sinomovie pattern
  • Fixes volume patterns for data with no y axis (single entry)
  • Adds option to "getall" of a pattern of lower dimensions than the one requested

Plugin updates:

  • First data simulation plugin via TomoPhantom integration
  • Faster Astra toolbox reconstruction using vector geometry
  • GPU implementations of median_filter and dezinger plugins
  • Large field of view experiment integration
  • Improves MinAndMax plugin used for ImageSaver
  • Improves ImageSaver: save 8-bit, 16-bit tiff; manually select global min-max
  • Fixes DarkFlatFieldCorrection SINOGRAM processing
  • Updates the Fresnel filter for projection or sinogram processing
  • Adds novel modifications to tomobar plugins fully based on vector Astra geometry
  • Fixes error in base_recon when previewing reconstruction methods
  • Mrc loader update
  • Fixes nxtomo_loader not using image_key_path parameter
  • Allows user to set a value of the outer circle mask in both Tomopy_recon and Astra_recon
  • Fixes error in base_recon when previewing reconstruction methods
  • Fixes incorrect slicing in mipmap plugin
  • Correction to faulty flats averaging
  • Adds getall flag option to plugin_data

Configurator updates:

  • Adds error message when loading a module that exists but failed on import
  • Replaces Gnureadline with readline
  • Adds examples flag option to include plugin templates
  • Amends mutations to check process list version number
  • Adds option to output error messages when loading modules via -e flag

Other updates:

  • Updates profiler
  • Adds iterative plugin templates
  • Adds savu-lite conda installation for local PC
  • Adds savu tools to easily extract parameter information from process lists and loader yaml templates
  • Adds zocalo qsub and new JSV to fix variable nodes error in launcher script
  • Adds keep flag to launcher script for option to not delete data when passing an intermediate folder
  • Improves tests
  • Refines savu installer

New Plugins added:

  • basic_operations:
    • data_threshold.py
    • elementwise_arrays_arithmetics.py
    • value_mask_replacement.py
  • corrections:
    • mtf_deconvolution.py
  • filters:
    • denoising:
      • ccpi_denoising_cpu.py
      • ccpi_denoising_cpu_3D.py
      • ccpi_denoising_gpu.py
      • ccpi_denoising_gpu_3D.py
  • loaders:
    • full_field_loaders:
      • lfov_loader.py
  • reshape:
    • image_stitching.py
  • ring_removal:
    • ring_removal_interpolation.py
  • segmentation:
    • evolving_contours:
      • region_grow.py
      • region_grow3D.py
    • geo_distance:
      • geo_distance3D.py
    • morphological_operations:
      • morph_proc_line3D.py
      • morph_remove_objects.py
  • simulation:
    • tomo_phantom.py
    • tomo_phantom_quantification.py

Plugin Replacements:

  • dezinger => dezinger, dezinger_gpu
  • median_filter => median_filter, median_filter_gp
  • AstraReconGpu (new vectorised geometry)

Deprecated plugins:

  • dezinger
  • dezinger_simple
  • dezinger_sinogram
  • median_filter

Removed plugins:

  • base_fluo_fitter.py
  • fastxrf_fitting.py
  • simple_fit_xrf.py
  • base_i18_multi_modal_loader.py
  • i18_fluo_loader.py
  • i18_mm_loader.py
  • i18_monitor_loader.py
  • i18_stxm_loader.py
  • i18_xrd_loader.py
Assets 2
Loading