Merge CIL recon #1034
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Merge CIL recon #1034
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numpy.typing is new in 1.20
Note, need to roll back to numpy 1.18 for now
New reconstruction algorithm using CIL Changes to integrate CILRecon into the GUI
Also fix some varaible name issues
CIL and tomopy pass the full dataset, so need to apply the negative log operation themselves.
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DolicaAkelloEgwel
approved these changes
Jul 8, 2021
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Issue
Closes #1025
Description
Merge initial version of CIL algorithm. This is not complete, but sufficient to do a simple reconstruction.
This also rolls numpy back to 1.18, the newest supported by current CIL.
Testing
After checking out the branch, you will need a new dev environment with CIL libraries and an older numpy
python3 setup.py create_dev_envAcceptance Criteria
Docker tests are expected to fail, as they will not have the correct libraries. Conda tests should pass.
It should be possible to perform a reconstruction with the CIL algorithm, with the IMAT00010675 , no preprocessing and number of iterations set to 2. With just 2 iterations the output is very soft but you can see the rough shape. (takes about 5 mins to run, peaks at ~30GB RAM)
Documentation
Release notes