Marco/dev

[bommaritom]

This pull request implements laminography methods as a wrapper on top of the 'master' branch of mbircone.

Updates include:

• A new module 'mbircone/laminography.py' containing two methods:
  • 'recon_lamino' runs a qGGMRF reconstruction using laminography geometry.
  • 'project_lamino' runs a forward projection using laminography geometry.
• A new demo file 'demo_laminography.py', which does the following:
  • Generates a 3D laminography sample phantom.
  • Generates synthetic laminography data by forward projecting the phantom.
  • Performs a 3D qGGMRF reconstruction in laminography coordinates.
  • Displays the results.
• Add the method 'gen_lamino_sample_3d' to 'phantom.py' that generates a thin phantom for use in laminography.
• Boilerplate updates for laminography:
  • Update 'docs/source/api.rst' to include docstrings for laminography.py
  • Add 'docs/source/laminography.rst' to the readthedocs file
  • Add import statement in 'init.py' to import laminography.py functions
• Change 'svmbir' to 'mbircone' in one location in 'clean_install.rst'

Laminography methods have been tested in a small test suite. See files 'test_project_lamino.py' and 'test_recon_lamino.py': https://github.com/bommaritom/mbircone/tree/test/lamino_features

The tests suite mentioned above, as well as the results of 'demo_laminography', are documented in the attached slides: Tests-Laminography.pptx

The following demo files have been tested (will update as I test):

• demo_laminography.py
• demo_3D_shepp_logan.py