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iMars3D 3D reconstruction software for neutron imaging

Run

• Connect to cg1d-analysis2 computer:

$ ssh cg1d-analysis2.ornl.gov

• Setup software environment

$ . ~lj7/.use-imars3d

• Create a directory for the reconstruction, and cd into it

$ mkdir -p ~/recon/turbine
$ cd ~/recon/turbine

• Create a recon script:

#!/usr/bin/env python
from imars3d.CT import CT
ct = CT("PATH")
ct.recon()

Remember to replace PATH with the path to the CT data directory (which contains WB/DF/CT data) Save it as "recon.py"

• Create a "work" directory in the fast disk /SNSlocal2 (for intermediate outputs) and make a symbolic link to it in the reconstruction directory. IMPORTANT: This speeds up the recon considerably.

$ mkdir -p /SNS/local2/USERNAME/turbine
$ ln -s /SNS/local2/USERNAME/turbine work

• Run the recon script

$ python recon.py

Supported structure of data directory

Flat

* <root>
  - *CT*.fits
  - *DF*.fits
  - *OB*.fits

DF and OB in their own subdirs:

* <root>
  - *CT*.fits
  + DF/df
    - *DF*.fits
  + OB/ob
    - *OB*.fits

CT object

ct = CT(path,
    CT_subdir=None, CT_identifier=None,
    workdir='work', outdir='out', 
    parallel_preprocessing=True
    )

Workflow

• Preprocessing
  • gamma-filtering
  • normalization
  • intensity fluctuation correction
  • cropping
  • smoothing
  • tilt correction
• Reconstruction
  • build sinograms
  • find rotation center
  • reconstruct