DiamondLightSource/Savu: v4.2

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