nxtomomill merge requestshttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests2023-12-04T16:12:02+01:00https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/204Doc: rework and move to pydata_sphinx_theme2023-12-04T16:12:02+01:00paynoDoc: rework and move to pydata_sphinx_theme1.0https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/203h52nx: fix setting the instrument name. close #1622023-11-21T10:50:20+01:00paynoh52nx: fix setting the instrument name. close #1621.0paynopaynohttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/202Add fscan converter2024-01-30T13:54:50+01:00Pierre PaleoAdd fscan converter### This MR relies on tomoscan!168
Integrate an old script for converting ID15A data to NX.### This MR relies on tomoscan!168
Integrate an old script for converting ID15A data to NX.https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/201fix some application options default values2023-10-31T16:15:19+01:00paynofix some application options default values1.0https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/199NXtomo: add missing 'definition'2023-10-24T16:56:43+02:00paynoNXtomo: add missing 'definition'Note: no need to port it on the 'main' branch. Because now main relies on 'NXtomo'
Associated to commit at NXtomo level: https://gitlab.esrf.fr/tomotools/nxtomo/-/commit/f0389a8a68033fbb8e3666efa92e23e57eafe909
close #160Note: no need to port it on the 'main' branch. Because now main relies on 'NXtomo'
Associated to commit at NXtomo level: https://gitlab.esrf.fr/tomotools/nxtomo/-/commit/f0389a8a68033fbb8e3666efa92e23e57eafe909
close #160https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/198Merge branch 'correction_for_rough_voxel' into '0.13'2023-10-12T10:27:17+02:00paynoMerge branch 'correction_for_rough_voxel' into '0.13'Correction for rough voxel
See merge request tomotools/nxtomomill!189
(cherry picked from commit b3397ec86d07ef022eea2d5bc1c2cb6e9196baf8)
2ce7b501 attempt to correct the voxel size
174be748 tested
71c546d5 metersgit diff
41f084e3 bla...Correction for rough voxel
See merge request tomotools/nxtomomill!189
(cherry picked from commit b3397ec86d07ef022eea2d5bc1c2cb6e9196baf8)
2ce7b501 attempt to correct the voxel size
174be748 tested
71c546d5 metersgit diff
41f084e3 black
0d061e0a modifications for merge
a00c5801 Merge branch '0.13' into correction_for_rough_voxel
126b8d0d Merge branch '0.13' into correction_for_rough_voxel
be3e549a remove extra extra dictionarieshttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/197Merge branch 'fix_159' into '0.13'2023-10-10T16:45:24+02:00paynoMerge branch 'fix_159' into '0.13'replace 'realpath' by 'abspath'. Make it more resillient to /gpfs/data vs...
See merge request tomotools/nxtomomill!196
(cherry picked from commit 31199433b6130767634f55bdb23b9f5c8bf7473d)
4fea81ae replace 'realpath' by 'abspath'. Mak...replace 'realpath' by 'abspath'. Make it more resillient to /gpfs/data vs...
See merge request tomotools/nxtomomill!196
(cherry picked from commit 31199433b6130767634f55bdb23b9f5c8bf7473d)
4fea81ae replace 'realpath' by 'abspath'. Make it more resillient to /gpfs/data vs...https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/196replace 'realpath' by 'abspath'. Make it more resillient to /gpfs/data vs...2023-10-10T16:47:02+02:00paynoreplace 'realpath' by 'abspath'. Make it more resillient to /gpfs/data vs...replace 'realpath' by 'abspath'. Make it more resillient to /gpfs/data vs /mnt/storage ... close #159replace 'realpath' by 'abspath'. Make it more resillient to /gpfs/data vs /mnt/storage ... close #159paynopaynohttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/195Merge branch 'v0.13_adaptations_for_refs_for_helical' into '0.13'2023-10-06T09:03:34+02:00paynoMerge branch 'v0.13_adaptations_for_refs_for_helical' into '0.13'adaptations which alow to use the exact same workflow for multi-z...
See merge request tomotools/nxtomomill!190
(cherry picked from commit 9c594cbf08a1c0222a0fc096bd6c290548a4618c)
16e1cc05 adaptations which alow to use the exact same...adaptations which alow to use the exact same workflow for multi-z...
See merge request tomotools/nxtomomill!190
(cherry picked from commit 9c594cbf08a1c0222a0fc096bd6c290548a4618c)
16e1cc05 adaptations which alow to use the exact same workflow for multi-z...
e62812d1 black
f2ceec2b Merge branch '0.13' into v0.13_adaptations_for_refs_for_helical
8cbeafbc tested
42f8d0e5 resolved some mess with multiple branches changing the same file
e77f573c Merge branch '0.13' into v0.13_adaptations_for_refs_for_helical
33fb3c64 testing it
03bcce85 zstages2nxs: clarify a conditionhttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/194adapted falt reducer for missing darks2023-10-03T10:39:07+02:00paynoadapted falt reducer for missing darks# Conflicts:
# nxtomomill/utils/flat_reducer.py# Conflicts:
# nxtomomill/utils/flat_reducer.pyhttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/193Merge branch 'v0.13_overwrite_in_flat_reducer_for_rerunning_wf_several_times_...2023-09-28T09:00:23+02:00paynoMerge branch 'v0.13_overwrite_in_flat_reducer_for_rerunning_wf_several_times_' into '0.13'implemented
See merge request tomotools/nxtomomill!192
(cherry picked from commit d59e5403f023eda01638ff77a3a40f2bf2e57019)
ea3fce61 implementedimplemented
See merge request tomotools/nxtomomill!192
(cherry picked from commit d59e5403f023eda01638ff77a3a40f2bf2e57019)
ea3fce61 implementedhttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/192implemented2023-09-28T08:58:09+02:00myronimplementedAllows overwriting to relaunch twice the workflow without having to cancel the generated files ( the start and end flats dark are reused, they are the one that take a long long time to be generated from projections )Allows overwriting to relaunch twice the workflow without having to cancel the generated files ( the start and end flats dark are reused, they are the one that take a long long time to be generated from projections )myronmyronhttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/191V0.13 missing darks for reducer2023-10-03T10:32:29+02:00myronV0.13 missing darks for reducerWhen no dark is present in th bliss files, adds a default one with value 300. This is good for bm18. May be should be setted by some parameter, which one? is there already a parameter for that?When no dark is present in th bliss files, adds a default one with value 300. This is good for bm18. May be should be setted by some parameter, which one? is there already a parameter for that?myronmyronhttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/190adaptations which alow to use the exact same workflow for multi-z...2023-10-06T09:00:23+02:00myronadaptations which alow to use the exact same workflow for multi-z...adaptations which alow to use the exact same workflow for multi-z multi-reference scans also for one helical scan with external referenceadaptations which alow to use the exact same workflow for multi-z multi-reference scans also for one helical scan with external referencemyronmyronhttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/189Correction for rough voxel2023-10-12T10:24:03+02:00myronCorrection for rough voxelit can save the day when the bliss pixel is really wrong, so wrong that the pixel refinement is meaningless.
This occurs tipically when a binning factor in the macro is not accountedit can save the day when the bliss pixel is really wrong, so wrong that the pixel refinement is meaningless.
This occurs tipically when a binning factor in the macro is not accountedmyronmyronhttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/188Add a 'nx-copy' application2023-10-23T11:33:04+02:00paynoAdd a 'nx-copy' application# TODO
- [x] Add application to copy an NXtomo from one file to another (or to a folder)
- [x] add a simple option to remove link and embed all in the NXtomo (loading it all in memory for now). If some more advanced option is requir...# TODO
- [x] Add application to copy an NXtomo from one file to another (or to a folder)
- [x] add a simple option to remove link and embed all in the NXtomo (loading it all in memory for now). If some more advanced option is required will be done in another PR
- [x] Add test
- [x] Add doc
- [x] Update tomwer doc once done (user corner / python script - how to copy an NXtomo)
# API
copy a single file (with potentially several NXtomo):
```
nxtomomill nx-copy /path/to/nxomofile.nx .
nxtomomill nx-copy /path/to/nxomofile.nx new.nx
```
copy a single NXtomo (potentially contained in a file with several NXtomo):
```
nxtomomill nx-copy /path/to/nxomofile.nx --entry entry0000 .
nxtomomill nx-copy /path/to/nxomofile.nx --entries entry0000,entry0001 .
```
copy a set of file:
```
for file in *.nx
do
nxtomomill nx-copy "$file" /new/path/"$file"
done
```
To replace HDF5 virtual datasets by a standard dataset you can also use the `--remove-vds` option. In this case the full dataset will be load in memory before dumping it.
related to https://gitlab.esrf.fr/tomotools/nxtomo/-/merge_requests/81.0https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/187replace silx deprecation warning by nxtomomill deprecation warning2023-08-28T12:02:03+02:00paynoreplace silx deprecation warning by nxtomomill deprecation warninghttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/186Merge branch 'make_PROCESSED_DATA_default' into '0.13'2023-08-17T11:15:18+02:00paynoMerge branch 'make_PROCESSED_DATA_default' into '0.13'Take into accound 'RAW_DATA' and 'PROCESSED_DATA'
See merge request tomotools/nxtomomill!183
(cherry picked from commit 0fcb00347db684b6375d0d8a417597f633993bec)
f79c62e6 h52nx: update default output file path in the case file is cont...Take into accound 'RAW_DATA' and 'PROCESSED_DATA'
See merge request tomotools/nxtomomill!183
(cherry picked from commit 0fcb00347db684b6375d0d8a417597f633993bec)
f79c62e6 h52nx: update default output file path in the case file is contained in 'RAW_DATA'
e336e612 h52nx: update test_simple_conversion to have it with 'RAW_DATA' vs 'PROCESSED_DATA'
86a54087 h52nx: add message on conversion start
57a9d6b0 rename test file for pytesthttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/185move doc to 1.02023-08-16T09:58:27+02:00paynomove doc to 1.0https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/184improve documentation2023-08-16T09:49:02+02:00paynoimprove documentation