nxtomomill merge requestshttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests2022-11-22T11:48:44+01:00https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/140Merge branch 'improve_read_of_settable_params' into '0.10'2022-11-22T11:48:44+01:00paynoMerge branch 'improve_read_of_settable_params' into '0.10'h52nx: improve management of user settable parameter.
See merge request tomotools/nxtomomill!139
(cherry picked from commit 1123e6993dcd6635cff261274b12480ef9bc3d26)
b0e84b80 h52nx: improve management of user settable parameter.h52nx: improve management of user settable parameter.
See merge request tomotools/nxtomomill!139
(cherry picked from commit 1123e6993dcd6635cff261274b12480ef9bc3d26)
b0e84b80 h52nx: improve management of user settable parameter.https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/139h52nx: improve management of user settable parameter.2022-11-22T11:46:26+01:00paynoh52nx: improve management of user settable parameter.In the case the HDF5 path exists but doesn't lead to a valid dataset this can raise a TypeError which is not understandable by users.In the case the HDF5 path exists but doesn't lead to a valid dataset this can raise a TypeError which is not understandable by users.https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/138Merge branch 'fix_132' into '0.10'2022-11-22T11:19:47+01:00paynoMerge branch 'fix_132' into '0.10'h52nx: rename input option `sample-detector-distance` to...
See merge request tomotools/nxtomomill!137
(cherry picked from commit d10005fadd4c4000b2b9521cbf043816d9a8369f)
9fe64f4f h52nx: rename input option `sample-detector-distance`...h52nx: rename input option `sample-detector-distance` to...
See merge request tomotools/nxtomomill!137
(cherry picked from commit d10005fadd4c4000b2b9521cbf043816d9a8369f)
9fe64f4f h52nx: rename input option `sample-detector-distance` to...https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/137h52nx: rename input option `sample-detector-distance` to...2022-11-22T11:18:36+01:00paynoh52nx: rename input option `sample-detector-distance` to...h52nx: rename input option `sample-detector-distance` to `sample-detector-distnace-paths` which could be misleadingh52nx: rename input option `sample-detector-distance` to `sample-detector-distnace-paths` which could be misleadinghttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/136add real pixel size for HDF52022-11-17T11:15:06+01:00paynoadd real pixel size for HDF5note: For EDF as this is for backward compatibility and for esrf, fall back on magnification will be enough.note: For EDF as this is for backward compatibility and for esrf, fall back on magnification will be enough.0.11https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/135From z_stages to helical2023-02-09T15:15:27+01:00myronFrom z_stages to helicalFrom z_stages to helical
------------------------
It takes a list of nx files and obtains one whole nx scan that can be reconstructed in helical mode
--------------------------------------------------------------------------------------...From z_stages to helical
------------------------
It takes a list of nx files and obtains one whole nx scan that can be reconstructed in helical mode
--------------------------------------------------------------------------------------------------
- [x] Build a first prototype
- [x] test
- [x] integrate in nxtomomill
Example of usage
----------------
``` bash
>...: % ls /data/scisofttmp/mirone/aspect_retrieval/stages_mouton/orig/only_three_stages*.nx
/data/scisofttmp/mirone/aspect_retrieval/stages_mouton/orig/only_three_stages/HA-1100_27.73um_sheep-head_ethanol_W__0029_0001.nx
/data/scisofttmp/mirone/aspect_retrieval/stages_mouton/orig/only_three_stages/HA-1100_27.73um_sheep-head_ethanol_W__0030_0001.nx
/data/scisofttmp/mirone/aspect_retrieval/stages_mouton/orig/only_three_stages/HA-1100_27.73um_sheep-head_ethanol_W__0031_0001.nx
/data/scisofttmp/mirone/aspect_retrieval/stages_mouton/orig/only_three_stages/HA-1100_27.73um_sheep-head_ethanol_W_REF_B_0000_0001.nx
/data/scisofttmp/mirone/aspect_retrieval/stages_mouton/orig/only_three_stages/HA-1100_27.73um_sheep-head_ethanol_W_REF_E_0000_0001.nx
>...: % wd="/data/scisofttmp/mirone/aspect_retrieval/stages_mouton/orig/only_three_stages"
>...: % nxtomomill z-concatenate-scans
\--filename_template ${wd}/HA-1100\_27.73um_sheep-head_ethanol_W__XXXX_0001.nx
\--target_file concat.nx
\--total_nstages 44
\--first_stage 29
\--last_stage 31
\--cors_file cors.txt
\--pixel_size_m 0.00002737
\--flats_from_before_after yes
\--scan_before
${wd}/HA-1100\_27.73um_sheep-head_ethanol_W_REF_B_0000_0001.nx
\--scan_after
${wd}/HA-1100\_27.73um_sheep-head_ethanol_W_REF_E_0000_0001.nx
```0.12myronmyronhttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/134Merge branch 'fix_126' into '0.10'2022-11-04T12:36:34+01:00paynoMerge branch 'fix_126' into '0.10'replace some exit by raising an error
See merge request tomotools/nxtomomill!133
(cherry picked from commit d91ee751af4b6fb1ad2d5976742c75ef1ba7ff71)
743bd45f replace some exit by raising an errorreplace some exit by raising an error
See merge request tomotools/nxtomomill!133
(cherry picked from commit d91ee751af4b6fb1ad2d5976742c75ef1ba7ff71)
743bd45f replace some exit by raising an errorhttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/133replace some exit by raising an error2022-11-04T12:34:26+01:00paynoreplace some exit by raising an error0.10https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/132Merge branch 'create_pcotomo_v2' into 'master'2022-10-26T11:13:57+02:00paynoMerge branch 'create_pcotomo_v2' into 'master'update pcotomo - use nb_turns
See merge request tomotools/nxtomomill!131
(cherry picked from commit 70d978eed2541985edb6fa0e61cca4afff90b483)
c8ccc921 NXSplitter: add control to split
5183a2b1 settings: add Y pixel size
34481687 updat...update pcotomo - use nb_turns
See merge request tomotools/nxtomomill!131
(cherry picked from commit 70d978eed2541985edb6fa0e61cca4afff90b483)
c8ccc921 NXSplitter: add control to split
5183a2b1 settings: add Y pixel size
34481687 update PCOTOMO init title and replace in by a 'startswith'
9c540d0f update pcotomo:0.10https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/131update pcotomo - use nb_turns2022-10-26T11:11:46+02:00paynoupdate pcotomo - use nb_turns* handle several paths in `technique`
* handle second version of pcotomo storing (using nb_turns now* handle several paths in `technique`
* handle second version of pcotomo storing (using nb_turns now0.10https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/130Tomo helical title2022-09-12T14:46:16+02:00myronTomo helical titleAdds title for helical scan in setting.py
-----------------------------------------
TODO list
---------
- [x] Add the title in the list
- [x] test itAdds title for helical scan in setting.py
-----------------------------------------
TODO list
---------
- [x] Add the title in the list
- [x] test itpaynopaynohttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/129NXtomo: improvement saving data as a virtual dataset2022-09-12T14:38:51+02:00paynoNXtomo: improvement saving data as a virtual dataset0.10https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/128several small fix for 0.102022-09-12T10:58:35+02:00paynoseveral small fix for 0.10fix _generic_path_getter: url can be None and entry provided (if configuration provided from a configuration file)fix _generic_path_getter: url can be None and entry provided (if configuration provided from a configuration file)0.10https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/127Merge branch 'fixes_post_visit_id16b' into '0.10'2022-09-09T08:21:00+02:00paynoMerge branch 'fixes_post_visit_id16b' into '0.10'fixes bug found in edf2nx after some time on ID16b
See merge request tomotools/nxtomomill!126
(cherry picked from commit 4c7b75f6031d9f60e559919ff04686a073d11a4c)
684dc2cf remove useless print
04a3910c nexus: nxobject: fix: __str__ wa...fixes bug found in edf2nx after some time on ID16b
See merge request tomotools/nxtomomill!126
(cherry picked from commit 4c7b75f6031d9f60e559919ff04686a073d11a4c)
684dc2cf remove useless print
04a3910c nexus: nxobject: fix: __str__ was not returning a string
de6339fe raise an error is scan_range or tomo_n is None (fail to discover .info file)
70c6d5a3 edf2nx: fix computing rotation angle when no key in the header
d2947e44 edf2nx: rework rotation angle creation when forced.https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/126fixes bug found in edf2nx after some time on ID16b2022-09-09T08:18:39+02:00paynofixes bug found in edf2nx after some time on ID16bupdate post id16bupdate post id16b0.10https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/125edfconverter: fix: handle x, y and z translation unit2022-09-05T08:23:54+02:00paynoedfconverter: fix: handle x, y and z translation unit- [x] fix: check default of the distance
- [x] add unit test for the unit of ditance, x, y and z translations- [x] fix: check default of the distance
- [x] add unit test for the unit of ditance, x, y and z translations0.10https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/124Improve nexus compatibility2022-09-01T15:59:22+02:00paynoImprove nexus compatibility0.10https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/123edf2nx configuration: set default distance and translation to millimeter2022-08-31T13:12:34+02:00paynoedf2nx configuration: set default distance and translation to millimeterclose #113close #1130.10https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/122rework NXdetector setter to accept 1D numpy array containing Union[DataUrl, V...2022-08-30T15:31:34+02:00paynorework NXdetector setter to accept 1D numpy array containing Union[DataUrl, VirtualSource, VDSmap]close #112
Signed-off-by: Henri Payno <henri.payno@gmail.com>close #112
Signed-off-by: Henri Payno <henri.payno@gmail.com>0.10https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/121Clean2022-08-30T15:31:41+02:00paynoClean0.10