Nabu merge requestshttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests2024-03-25T11:37:19+01:00https://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/433fix one more issue with HDF5 file2024-03-25T11:37:19+01:00paynofix one more issue with HDF5 filehttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/354Draft: Writers: clean-up2024-03-05T13:16:52+01:00Pierre PaleoDraft: Writers: clean-up## About
This MR moves code from nabu to tomoscan.
Close #421, #434
## To do
- [ ] Move features in `.vol` writer to tomoscan
- [ ] Move features in `NX` writer to tomoscan
- [x] Print full file name for non-HDF5 output (close...## About
This MR moves code from nabu to tomoscan.
Close #421, #434
## To do
- [ ] Move features in `.vol` writer to tomoscan
- [ ] Move features in `NX` writer to tomoscan
- [x] Print full file name for non-HDF5 output (close #428)
- [ ] Fix #434
- [ ] End-to-end reconstruction testshttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/399Merge branch 'fix_cor_alg_fourier_angles' into 'release_2024.1.0'2024-02-13T15:33:35+01:00Jerome LesaintMerge branch 'fix_cor_alg_fourier_angles' into 'release_2024.1.0'fourier-angles: fix taking into account the side
See merge request tomotools/nabu!396
(cherry picked from commit 605b5d97114f7855107f59adb7ec2bd02195582f)
30a68ff7 fourier-angles: fix taking into account the sidefourier-angles: fix taking into account the side
See merge request tomotools/nabu!396
(cherry picked from commit 605b5d97114f7855107f59adb7ec2bd02195582f)
30a68ff7 fourier-angles: fix taking into account the sidehttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/380Remove some deprecation warning since 'processing' module has been added2023-12-11T16:44:32+01:00paynoRemove some deprecation warning since 'processing' module has been addedhttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/353Revert "Merge branch 'fix_433_b' into 'master'"2023-12-06T16:27:46+01:00paynoRevert "Merge branch 'fix_433_b' into 'master'"I would really be in favor to revert this PR in order to avoid duplication of `ReduceMethod` should be avoid - especially to go on the `app` module (else code is duplicated, we must always use the value when communicating with tomoscan.....I would really be in favor to revert this PR in order to avoid duplication of `ReduceMethod` should be avoid - especially to go on the `app` module (else code is duplicated, we must always use the value when communicating with tomoscan... )
Maybe we should speak about the different options there to avoid loading to much stuff.https://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/317Draft: stitching: move from x_flipped, y_flipped to detector transformations2023-10-24T16:45:53+02:00paynoDraft: stitching: move from x_flipped, y_flipped to detector transformationshttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/338Add 'composite_cor_L1_norm' into 'release_2023.2.0'2023-09-28T13:40:15+02:00Pierre PaleoAdd 'composite_cor_L1_norm' into 'release_2023.2.0'Composite cor l1 norm
See merge request tomotools/nabu!319
(cherry picked from commit 02414779abe3f1f3cbbe13069208626ab9f73a1b)
24872fda L1 norm for error metric
14b05639 doc
01653600 merged with master
fa786fb5 completed the float2in...Composite cor l1 norm
See merge request tomotools/nabu!319
(cherry picked from commit 02414779abe3f1f3cbbe13069208626ab9f73a1b)
24872fda L1 norm for error metric
14b05639 doc
01653600 merged with master
fa786fb5 completed the float2inst casting
cb10cb58 one composite cor finder class with norm_order parameter
1f56eaa0 black
169032be pylint
d92a0ab6 Merge branch 'master' into composite_cor_L1_normhttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/333jp2k: rescale data before saving it2023-08-23T13:18:48+02:00paynojp2k: rescale data before saving itclose #420
https://gitlab.esrf.fr/tomotools/tomoscan/-/merge_requests/155 to be merged first and tomoscan release to be done
- [x] test on a real dataset (with default options)close #420
https://gitlab.esrf.fr/tomotools/tomoscan/-/merge_requests/155 to be merged first and tomoscan release to be done
- [x] test on a real dataset (with default options)R 2023.2.0paynopaynohttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/316Draft: Replace tomoscan flipped by detector transformations2023-08-21T11:57:36+02:00paynoDraft: Replace tomoscan flipped by detector transformationshttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/64Draft: Resolve "Alignment: focus calibration is missing some of the original ...2023-08-09T09:46:37+02:00Nicola ViganoDraft: Resolve "Alignment: focus calibration is missing some of the original features"The [focus.m](https://gitlab.esrf.fr/tomotools/octave_archive/-/blob/master/m/tomotools/focus.m) function presents more options than the simple 'std' merit function.
Mandatory features:
- [x] Implement PSD method
* [x] Implement simpl...The [focus.m](https://gitlab.esrf.fr/tomotools/octave_archive/-/blob/master/m/tomotools/focus.m) function presents more options than the simple 'std' merit function.
Mandatory features:
- [x] Implement PSD method
* [x] Implement simple azimuthal integration function
* [x] Implement averaging logic in frequency domain
- [ ] Create unit tests
- [x] Add documentation
Optional features:
- [x] Implement additional methods:
* [x] Gradient
* [ ] Edge
Closes #155.Nicola ViganoNicola Viganohttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/183Draft: speeding up stitching2023-08-09T09:45:42+02:00paynoDraft: speeding up stitchingimprovement of !178
TODO:
* [ ] apply shift in Fourier space
* [ ] parallelize call to `stitch_frames`
* [ ] get a clever calculation of the `data bunch` numberimprovement of !178
TODO:
* [ ] apply shift in Fourier space
* [ ] parallelize call to `stitch_frames`
* [ ] get a clever calculation of the `data bunch` numberpaynopaynohttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/325update tomoscan compatibility2023-08-03T16:23:53+02:00paynoupdate tomoscan compatibilityIn theory there is some deprecation of the x/y flipped but as handling is way different, safer to avoid 'future version'.
I think we want to avoid loosing time on this.In theory there is some deprecation of the x/y flipped but as handling is way different, safer to avoid 'future version'.
I think we want to avoid loosing time on this.R 2023.2.0https://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/281Draft: Reconstruct one slice with multiple CoR2023-07-25T16:19:53+02:00Pierre PaleoDraft: Reconstruct one slice with multiple CoR## About
This MR brings a new CLI tool to reconstruct one slice with varying centers of rotation.
## To do
- [x] Add `reset_rot_center` to `Backprojector`
- [x] Add `reset_rot_center` to `CLBackprojector`
- [ ] Implement `nabu...## About
This MR brings a new CLI tool to reconstruct one slice with varying centers of rotation.
## To do
- [x] Add `reset_rot_center` to `Backprojector`
- [x] Add `reset_rot_center` to `CLBackprojector`
- [ ] Implement `nabu-multicor` app
- [ ] Add entry point
- [ ] Testshttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/294Jonas graetz hbp2023-07-25T16:16:49+02:00myronJonas graetz hbp## About
Hierarchical back projection by Jonas Graetz algorithm
## To do
- [X] Implement feature (class and docstring)
- [X] Integrate in pipeline
- [X] End-to-end reconstruction test: just set method to HBP instead of FBP## About
Hierarchical back projection by Jonas Graetz algorithm
## To do
- [X] Implement feature (class and docstring)
- [X] Integrate in pipeline
- [X] End-to-end reconstruction test: just set method to HBP instead of FBPmyronmyronhttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/274DRAFT: produces output for z correlation and pixelsize refinement2023-07-15T10:04:20+02:00myronDRAFT: produces output for z correlation and pixelsize refinement## About
Brief description of the merge request: what it brings, why it is necessary, which issues it will close.
## To do
- [ ] Implement feature (class and docstring)
- [ ] Unit tests
- [ ] Integrate in pipeline
- [ ] End-to...## About
Brief description of the merge request: what it brings, why it is necessary, which issues it will close.
## To do
- [ ] Implement feature (class and docstring)
- [ ] Unit tests
- [ ] Integrate in pipeline
- [ ] End-to-end reconstruction test
## Notes
Additional notes, ex. implementation details.myronmyronhttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/304DRAFT: added json output for the workflow2023-07-15T09:58:29+02:00myronDRAFT: added json output for the workflow## About
if output filename has json extension the found cor's are written in json format to facilitate the workflowing
## To do
- [ ] Implement feature (class and docstring)
- [ ] test it
## Notes
Additional notes, ex. implem...## About
if output filename has json extension the found cor's are written in json format to facilitate the workflowing
## To do
- [ ] Implement feature (class and docstring)
- [ ] test it
## Notes
Additional notes, ex. implementation details.myronmyronhttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/307DRAFT:introduced fractional vertical range2023-07-15T09:53:25+02:00myronDRAFT:introduced fractional vertical range## About
Vertical range as fraction of doable range in helical
## To do
- [X ] Implement feature (class and docstring)## About
Vertical range as fraction of doable range in helical
## To do
- [X ] Implement feature (class and docstring)myronmyronhttps://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/302Draft: Fix stitching ci2023-06-14T14:39:42+02:00paynoDraft: Fix stitching ciLooks like the stitching CI was never called...Looks like the stitching CI was never called...https://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/292update metadata dict for not-hdf5 format2023-06-05T09:37:25+02:00paynoupdate metadata dict for not-hdf5 format* make sure all metadata are part of a section for metadata dump to .txt
* provide minimal metadata for tomwer volume viewer for not-hdf5 file format
Avoid to get the following kind of error when reading back the metadata with tomoscan:...* make sure all metadata are part of a section for metadata dump to .txt
* provide minimal metadata for tomwer volume viewer for not-hdf5 file format
Avoid to get the following kind of error when reading back the metadata with tomoscan:
```
'process_name = reconstruction\n' [tomoscan.esrf.volume.singleframebase](singleframebase.py:160)
2023-05-16 11:13:13,590:ERROR:tomoscan.esrf.volume.singleframebase: Failed to load metadata from /mnt/multipath-shares/tmp_14_days/payno/test_bug_920/5.06_crayon_W150_60_Al2_W0.25_xc1000_slice_0500/5.06_crayon_W150_60_Al2_W0.25_xc1000_slice_0500_infos.txt. Error is File contains no section headers.
file: '/mnt/multipath-shares/tmp_14_days/payno/test_bug_920/5.06_crayon_W150_60_Al2_W0.25_xc1000_slice_0500/5.06_crayon_W150_60_Al2_W0.25_xc1000_slice_0500_infos.txt', line: 1
'process_name = reconstruction\n'
```https://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/293Draft: attemp to fix pages2023-05-25T09:51:47+02:00paynoDraft: attemp to fix pages