Geometry overhaul (+tests), update all notebooks

[jadball]

• Refactor of ImageD11.sinograms.geometry
  • Now tested in test/test_geometry.py
  • Updated ImageD11.sinograms.point_by_point accordingly
    • This has been validated against lab geometry and sinograms method for the Al foil + wire sample
  • Demonstration notebook available in sandbox/scanning_geometry.ipynb
• Added get_cf_3d_from_disk() method to ImageD11.sinograms.dataset
• Updated shift mechanics in run_iradon() and run_mlem() inside ImageD11.sinograms.roi_iradon
  • Replaced y0 parameter with shift (because we don't shift by y0 anyway)
  • Removed errant negative sign in the shift call
  • Updated ImageD11.sinograms.sinogram to match this
• Fixed some HDF5 IO bugs in ImageD11.sinograms.sinogram

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[jonwright]

I will merge, but there are some things to look at. In point_by_point it was intentional to precompute the cos/sin omega before doing the dtymask selection for each point...