DiamondLightSource/Savu: Version 2.4

Core updates:

• Adds singularity recipe and conda recipes for hdf5, h5py, openmpi and fftw
• Reverts axis labels to correct length after temporary reduction of frames (plugin previewing)
• Updates astra install to dev version
• Fixes incorrect numbering in process lists when nplugins > 9
• Stops GPU check from failing when no GPU processes are requested
• Converts data transfer bounds from frames to bytes
• Speed improvements:
  • Allows a wider variety of mft for data with dim > 3
  • Improves mft calculations for data with multiple slice dimensions
  • Improves chunking for > 3D datasets
• Allows input OR output datasets with different slice lengths
• Fixes inconsistent mft for in/out datasets with different dtypes
• Resets process frames counter for compatibility with parameter tuning
• dls cluster launcher script updates:
  • Adds auto-deletion of intermediate files when tmp directory is passed to dls launcher script
  • Rewrites savu_launcher.sh for compatibility with Science cluster and Hamilton
  • Integrates developer launcher script with standard launcher script

Plugin updates:

• Simplifies accessing current frame index from plugins
• Fixes initial volume in reconstruction
• Fixes initial volume in reconstruction
• Fixes problem in yaml converter when "savu" is in the file path
• Fixes but when outputting and reloading dictionary entries in meta data
• Fixes mrc loader to be compatible with checkpointing
• Fixes dark and flat previewing for tomo data with no image key
• Reconstruction COR updates:
  • Allows manual input as COR (as dict)
  • Allows COR as dataset
• Updates citation information for DistortionCorrection plugin
• Replaces C-wrapped DistortionCorrection plugin with python implemention
• Corrects the use of angles parameters in CameraRotCorrection to allow for parameter tuning
• Allows different angles per scan in NxtomoLoader
• Allows ImageLoader without dark field data
• Further improvements to auto-centering method

New plugins added:

• basic_operations:
  • arithmetic_operations.py
  • data_rescale.py
  • get_data_statistics.py
• corrections:
  • convert_360_180_sinogram.py
• filters:
  • ccpi_denoising_cpu.py
  • ccpi_denoising_gpu.py
  • fresnel_filter.py
  • hilbert_filter.py
• reconstructions:
  • tomobar_recon.py
  • tomobar_recon_3D.py
  • tomobar_recon_cpu.py
  • visual_hulls_recon.py
• reshape:
  • mipmap.py
• ring_removal:
  • remove_all_rings.py
  • remove_large_rings.py
  • remove_unresponsive_and_fluctuating_rings.py
  • ring_removal_filtering.py
  • ring_removal_fitting.py
  • ring_removal_regularization.py
  • ring_removal_sorting.py
• savers:
  • image_saver.py
• stats:
  • min_and_max.py
• visualisation:
  • ortho_slice.py
• segmentation:
  • geo_distance.py
  • gmm_segment3D.py
  • mask_evolve.py
  • mask_initialiser.py
  • morph_snakes.py
  • morph_snakes3D.py
  • morphological_operations/morph_proc.py
  • thresh_segm.py
  • i23segmentation:
    • final_segment_i23.py
    • i23_segment.py
    • i23_segment3D.py