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  • ID19 restart

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 to uint16, 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
  • Issues 25
  • Merge Requests 13
  • Participants 2
  • Labels 8
Unstarted Issues (open and unassigned)
0
Ongoing Issues (open and assigned)
0
Completed Issues (closed)
25
  • Issue reconstructing first slices of 'bamboo'
    #165 BUG Pipeline
  • Print estimated parameters
    #152 Improvement Pipeline
  • Something wrong with dataset "crayon"
    #151 BUG Pipeline
  • provide nabu --slice "middle" option
    #150 Improvement User interface
  • Raise error if slices indices out of range
    #149 Improvement User interface
  • HDF5 merge: use relative path
    #144 I/O
  • convert_halftomo
    #143 Improvement Sinogram processing
  • Dimensions of coeff in alignment.py
    #142 BUG Radios Processing
  • nabu -V takes forever to return
    #139 Improvement
  • Alignment: missing focus calibration
    #135
  • Alignment: missing camera tilt computation
    #134
  • Integrate CCDCorrection in pipeline
    #133
  • Watch Cuda context creation at imports
    #132 BUG
  • Merge HDF5 reconstructions
    #131 I/O
  • Computation of "Paganin margin"
    #122 Radios Processing
  • Double flatfield: cuda backend
    #117
  • find_shift should return 2 values + poly fit
    #116 Improvement
  • Document CoR estimation
    #113 Nabu project
  • Output file support: jpeg2000
    #105 I/O
  • Output File support: tiff
    #104 I/O
  • Center of Rotation estimation
    #97
  • Sinogram builder: handle vertical shifts
    #96
  • Double flat-field for rings correction
    #94
  • Support half tomography
    #92
  • Projections-based rings correction
    #60
100% complete
100%
Start date
No start date
Until
Sep 1 2020
Due date
Sep 1, 2020 (Past due)
25
Issues 25 New issue
Open: 0 Closed: 25
13
Merge requests 13
Open: 0 Closed: 0 Merged: 13
0
Releases
None
Reference: tomotools/nabu%"ID19 restart"