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 fil