Features scope

From Nabu minutes on 20/02/2020:

• Simple flat-fielding
• Absorption linearization (-log)
• Projection-based ring correction (e.g. double flat-fielding)
• Paganin filtering with modifications (unsharp mask)
• Simple rotation-axis finding algorithms (global, accurate, near, manual)
• Sample shifts for correction sample motion, reducing ring artifacts (aka. correct motion)
• Handling half-acquisition
• Data conversion (8/16 TIFF)

State on 03/08/2020

Done

• Simple flat-fielding
• Absorption linearization (-log)
• Projection-based ring correction (e.g. double flat-fielding)
• Paganin filtering with modifications (unsharp mask)
• Handling half-acquisition
• Simple rotation axis finding
• "Sample shifts" (horizontal/vertical)

Note: "sample shifts" is implemented, but we need a real test dataset.

Left for later

• Rotation axis estimation: need more robust methods, and a method working with half-tomo
• Half-tomo when CoR is on the left

Notes

Support for tiff and jpeg2000 is incomplete:

• When data is cast from float32 to uint16, normalization is done slice-wise instead of volume-wise. See #146 (closed).
• Advanced parameters are needed (see #147, #148 (closed)).
• The nabu configuration is not exported

Post-release

After this milestone: what to do ? When ?

In my opinion the things to do straight after the release are the following:

• Fix subvolumes stitching when binning_z is activated (#160)
• Fix binning_z on small subvolumes (#167, #168)
• Halftomo: support CoR on the left (#145 (closed))
• Auto-CoR in half tomo (important feature!)
• Account for "z series" (see minutes 05/08/2020)
• I/O: better support for tiff and jpeg2000