CCPi 1 VM analysis

This document contains basic analysis of all CCPi modules, subsequent recommended actions are bellow

CCPi modules

CCPi software is maintained by CCPI group - EPSRC, STFC, University of Manchester, CoSeC http://www.ccpi.ac.uk. Preprocesing Current modules are maintained by various distinguished repositories in github:

• Preprocesing | Beam hardening removal algorithms for Xray tomography | https://cil.readthedocs.io/en/latest/preprocessing.html | https://github.com/vais-ral/CCPi-PreProcessing/releases/tag/v0.9 conda ?? |
• Reconstruction | This repository has the code for iterative reconstruction. CGLS, SIRT, MLEM. | link missing in source code https://cil.readthedocs.io/en/latest/reconstruction.html | https://github.com/vais-ral/CCPi-Reconstruction/releases/tag/v0.9 conda 0.10? | |
• Segmentation - no sources? | Segmentation is the process from which, given a 3 dimensional dataset (volume), surfaces in the volume are found at a specific value. Such surfaces are also called isosurfaces. | https://cil.readthedocs.io/en/latest/segmentation.html | conda build |
• Quantification | CCPi Quantification codes are only available as binary distribution.??? | https://cil.readthedocs.io/en/latest/quantification.html| https://github.com/vais-ral/CCPi-Quantification/releases/tag/v0.9 and conda ?? |
• CILViewer | A simple Viewer for 3D data built with VTK and Python. | https://cil.readthedocs.io/en/latest/viewer.html | https://github.com/vais-ral/CILViewer/releases/tag/v0.9 |
• Regularisation Toolkit | The CCPi-RGL software provides 2D/3D and multi-channel regularisation strategies to ensure better performance of IIR methods. | only README in source code, link to journal article | https://github.com/vais-ral/CCPi-Regularisation-Toolkit/releases/tag/v0.10.0, conda release 0.10.2 |
• Virtual Machine | VM templates - for vagrant or bootstraping VM from scratch SL7,Centos7 | only README in source code |
• FrameworkPlugins | ???? |
• Framework | Basic Python Framework for CIL | doc in README of github | https://github.com/vais-ral/CCPi-Framework/releases/tag/v0.10.0 |
• astra | A collection of Python binding for the Astra-Toolbox in the CCPi chain. | no docs at all | https://github.com/vais-ral/CCPi-astra/releases/tag/v0.10.0 |
• Apps | Simpleflex, Viewer with three different displays of the data. Main 2D slice representation, 3D view with slice and segmentation and a contour tree. Slice Viewer, Simple QT wrapping of the basic viewer with load and save toolbar items to assist in loading files. | no docs | no releases |

other repositories

• https://github.com/vais-ral/NikonCT | some .NET (C#) code, no docs, no clue |
• https://github.com/vais-ral/NikonCT-Tutorial1 |
• https://github.com/vais-ral/NikonCT-Tutorial2 |
• https://github.com/vais-ral/NikonCT-Tutorial3 |
• https://github.com/vais-ral/VirtualTomoInstrument | Virtual Tomography Instrument hall is a VR project to demonstrate a Tomography experiment hall. | | |
• https://github.com/vais-ral/SliceOPy | no description docs or release | | |
• https://github.com/vais-ral/CCPi-ML | A collection of machine learning projects. | probably self descriptive source codes | no release |
• https://github.com/vais-ral/WorkExperience | probably some demo code and data, worth to include to some demo or test | no docs | no release |
• https://github.com/vais-ral/presentation-template | template | |

summary

Important repositories are probably all in first table except CCPi-astra, FrameworkPlugins and Apps. Source codes are not provided for all modules. Binaries are distributed via: conda channel ccpi

CCPi-VirtualMachine will include all important CCPi components identified above installed from binaries and optional scripts or configuration will be made to install component from sources (if available).

Some identified challenges

• consider refactoring structure of each repository (Wrappers, Core, ... are not common place to store sources and configuration scripts together).
• consider to have convention for README should contain brief description, very brief instruction how to install and use the package and link to comprehensive documentation or article - if exists.
• consider naming convention. Some have CCPi- prefix, some demo and other stuff are without CCPi prefix
• CCPi can be as organization (multiple members can be delegated to have contributor or admin rights)