Closed
Milestone
expired on Sep 1, 2020
ID19 restart
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
touint16
, normalization is done slice-wise instead of volume-wise. See #146. - Advanced parameters are needed (see #147, #148).
- 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)
- Auto-CoR in half tomo (important feature!)
- Account for "z series" (see minutes 05/08/2020)
- I/O: better support for tiff and jpeg2000
Unstarted Issues (open and unassigned)
0
Ongoing Issues (open and assigned)
0
Completed Issues (closed)
25
- Issue reconstructing first slices of 'bamboo'
- Print estimated parameters
- Something wrong with dataset "crayon"
- provide nabu --slice "middle" option
- Raise error if slices indices out of range
- HDF5 merge: use relative path
- convert_halftomo
- Dimensions of coeff in alignment.py
- nabu -V takes forever to return
- Alignment: missing focus calibration
- Alignment: missing camera tilt computation
- Integrate CCDCorrection in pipeline
- Watch Cuda context creation at imports
- Merge HDF5 reconstructions
- Computation of "Paganin margin"
- Double flatfield: cuda backend
- find_shift should return 2 values + poly fit
- Document CoR estimation
- Output file support: jpeg2000
- Output File support: tiff
- Center of Rotation estimation
- Sinogram builder: handle vertical shifts
- Double flat-field for rings correction
- Support half tomography
- Projections-based rings correction