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v4.2

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@dkazanc dkazanc released this 25 Jul 09:40
v4.2
2e6a3a0

Savu Version 4.2

Core

  • Statistics class:
    • Stats relating to the data calculated alongside each plugin.
    • Can be accessed in Savu for use in plugins.
    • Collated and saved as a table, graphs and a .h5 file for inspection after a run (found in the 'stats' folder).
    • Use option --stats and parse arguments on or off to set stats on or off for a run (on by defualt).
    • MinAndMax plugin is now deprecated (use statistics class instead).
  • Iterative plugins (A capability to enable some plugins to be iterative):
    • iterate command to enable control over iterative plugins (see iterate -h for help)

Existing Plugins

Alignment

  • For the case of projection_2d_alignment creating an output dataset that
    contains the shifted projections, preview information about this dataset
    is provided to the experimental metadata.

Centering

  • Modify vo_centering to enable its use in the iterative alignment
    implementation which shifts the projections.

Simulation

  • A sub-pixel misalignment simulation for projections from TomoPhantom
  • Various Tomoloader fixes. Closing of the linked nxs file with MPI fixed.

Reconstruction

  • AstraReconGPU, 3D GPU methods are added (BP3D_CUDA, CGLS3D_CUDA, SIRT3D_CUDA)
  • FBP3D_CUDA method added (filtering before backprojection with BP3D_CUDA)
  • ForwardProjector works with the 3D geometry
  • 3D geometries can accept metadata for x-y shifts and correct the misalignment
  • ToMoBAR (3d version) has got different methods (FBP3D, CGLS3D, FISTA3D) working well with iterative alignment
  • GPU memory usage check for tomobar_recon_3D plugin to avoid CUDA error
  • tomobar_recon_3D access to regularisation using Wavelets, try set regularisation method e.g. to 'PD_TV_WAVELETS'
  • SWLS, PWLS methods for data fidelities are enabled in tomobar_recon_3D
  • GPU device indices are controlled through ToMoBAR iterative methods and regularisation

Filters

  • GPU memory usage check for ccpi_denoising_gpu_3D plugin to avoid CUDA error
  • DezingerSinogram changed to utilise new statistics class.
  • DownsampleFiler changed to utilise new statistics class.

Savers

  • ImageSaver changed to utilise new statistics class.

New plugins

Alignment

  • projection_2d_alignment - works with 2 sets of 3D projection data by comparing projection images and estimating vertical-horizontal shifts in data. The vector shifts then stored in experimental data to be used later in 3D vector geometry.

Filters

  • wavelet_denoising_gpu - a GPU plugin for denoising using Wavelets. Highly optimised for GPU performance.

Corrections

  • phase_unwrapping - a plugin for unwrapping phase-retrieved images

Centering

  • 360_centering - a plugin to calculate centre of rotation.

Updated and new packages as dependencies

  • A new pypwt GPU wavelet package added through Jenkins build and savu-dep channel
  • ToMoBAR and TomoPhantom packages have been updated

Configurator

  • Allow a list as a single dimension input to the preview parameter
  • Allow a start keyword inside the preview parameter
  • Allow a parameter to be a directory path within the Savu folder
  • Asterix line added to indicate the start and end of the process list
  • Line separator added to indicate an iterative plugin loop
  • Include a link to relevant online plugin guides
  • Warning added when loading plugins from a user directory
  • First dataset passed by default to the next plugin

New Commands

  • savu_mod - a way to modify one parameter present in a plugin list.
  • mod -g parameter - a way to modify a parameter in the process list globally (for all plugins)

Documentation

  • Plugin API moved to dropdown boxes on every plugin documentation page
  • Plugin template links updated
  • Video demos added

BUGS

  • res_norm bug when using AstaReconGPU with CGLS_CUDA
  • Fix indentation for the plugin_generator command
  • Allow saving to inner plugin directories when using the plugin_generator command
  • Plugin number and order error fixed

Other

  • The test dataset 24737.nxs has been changed to tomo-standard.nxs
  • The synthetic test data has been added
  • Environment variable type is replaced with GPUarch_nodes
  • savu_mod - Modify one parameter present in a plugin list.
  • Save the job command to a log file
  • Save the directory the command was run to a log file
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