Draft: cast_volume: add an option to apply percentiles only on positive values.
The initial goal of this PR was to ignore (on user request) negative values when computing percentiles during volume-cast.
But it turned out there was some scores here and there that should be fixed on this PR.
It also intend to generalize PartialHistogram
for any type of volume (defined in tomoscan at least). this is why the signature of PartialHistogram has been changed to work on a volume instead of an HDF5 url.
At the end it is sadly way more complex than expected. @paleo if you want we can have a look together might be simpler.
TODO
-
add option to compute percentiles on positive value only -
rework VolumeHistogram to generalize it for any tomoscan volume -
add test -
add documentation
close #446
Signed-off-by: payno henri.payno@esrf.fr
Merge request reports
Activity
added 21 commits
- 2d8cc99e...5dcd383c - 11 earlier commits
- 43887311 - Add offset_x in roll() and revert()
- 1b47d194 - fftshift.cl: rename, comment, and add out-of-place fftshift
- eb244cda - Adapt OpenCLFFTShft and add unit test
- aa0e5716 - Move roll() related code
- 69374b69 - move test_roll
- 2551d8f6 - Bump changelog
- dcbbb430 - pylint fix
- b05e29c9 - Fix (?) test execution on machines without opencl
- caa11926 - cast_volume: add an option to apply percentiles only on positive values.
- 38e4c3c0 - cast-volume application: provide more aliases for options
Toggle commit listadded 110 commits
-
38e4c3c0...41544e2c - 108 commits from branch
master
- e078e9f3 - cast_volume: add an option to apply percentiles only on positive values.
- f404227e - cast-volume application: provide more aliases for options
-
38e4c3c0...41544e2c - 108 commits from branch
added 1 commit
- 1a666eb5 - nabu.processing.histogram.VolumeHistogram: rework to make compatible with any kind of volume
added 1 commit
- 1658c878 - VolumesHistogram: adapt to using a Volume instead of an HDF5 file + data_path
added 124 commits
-
b1de2476...4ee6aee5 - 117 commits from branch
master
- 7cf0b914 - cast_volume: add an option to apply percentiles only on positive values.
- a2d12258 - cast-volume application: provide more aliases for options
- 27fe1251 - nabu.processing.histogram.VolumeHistogram: rework to make compatible with any kind of volume
- 78901cb2 - VolumesHistogram: adapt to using a Volume instead of an HDF5 file + data_path
- a87f6a14 - cast_colume: rename 'filter_neg_val_for_percentiles' for 'filter_negative' and...
- e154c02b - Cast volume: improve handling of histogram in the case data is already loaded...
- a5902a37 - cast_volume: clamp before rescale, safer and more logical.
Toggle commit list-
b1de2476...4ee6aee5 - 117 commits from branch
added 1 commit
- 78c285b3 - cast_volume: clamp before rescale, safer and more logical.
added 1 commit
- 9836878c - cast_volume: clamp before rescale, safer and more logical.
added 1 commit
- 24dd5b54 - requirements: increase tomoscan to 2.0.0a9. Need Rawvolume.get_colume_shape to be implemented
- Resolved by Pierre Paleo
added 1 commit
- a5922ebd - Fix get_histogram_single_volume: better handling of the case where the...
mentioned in merge request !390 (merged)
added 1 commit
- 4ee20ae8 - histogram: look to open histogram file only if exists