nxtomomill merge requestshttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests2020-11-27T18:13:53+01:00https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/28Manage id15 data2020-11-27T18:13:53+01:00paynoManage id15 dataDONE
====
- [x] try to guess if a dataset comes form 'standard' tomography or XRD-CT
- [x] insure translation for the ID15 use case
- [x] restructure code to get the two cases in parallel. Like create a '_StandardAcquisition' and a '_XR...DONE
====
- [x] try to guess if a dataset comes form 'standard' tomography or XRD-CT
- [x] insure translation for the ID15 use case
- [x] restructure code to get the two cases in parallel. Like create a '_StandardAcquisition' and a '_XRDCTAcquisition' both inheriting from '_Acquisition'
- [x] link this conversion to the existing tomoh52nx
- [x] add 'log' colormap for xrd-ct data interpretation
- [x] diode input should be normalize: diode = diode / mean(diode)
- [x] rework converter to split the Acquisition classes in a different folder
- [x] add documentation
- [x] add unit test for xrd-ct
HOW TO USE
==========
This is directly link to the `tomoh5tonx` command. And we will add two option to inform about the input format. Because we can try to guess but there is no information about it and e cannot be 100% that our guess will be correct.
* `--standard-format`: for the 'standard' format. The one we where managing until now (ID19, BM05, ID11...)
* `--xrd-ct-format`: for the format we will also manage now: ID15...
This is an example of usage:
``` bash
nxtomomill tomoh52nx /users_ext/datasets/XRD-CT/ID15/glassbeads_Cr2O3_step_scan_20um_res/glassbeads_Cr2O3_step_scan_20um_res_0001/glassbeads_Cr2O3_step_scan_20um_res_0001.h5 output_test.nx --xrd-ct-format
```0.5https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/27[tomoh5to2nx] create directories if output directories does not exists create...2020-10-12T15:13:33+02:00payno[tomoh5to2nx] create directories if output directories does not exists create it.Insure users have rights to write on files if already exists
Some PEP8 modifications too
Signed-off-by: payno <payno@linazimov.esrf.fr>Insure users have rights to write on files if already exists
Some PEP8 modifications too
Signed-off-by: payno <payno@linazimov.esrf.fr>0.4https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/26Add function redefine dark flats2020-11-10T08:23:59+01:00paynoAdd function redefine dark flatsThe goal is to provide a function able to add some darks or flats to an existing dataset.
For now we will only focus on creating a new NXTomo entry and won't manage any overwrite.
Done
====
- [x] create a generic function to insert nu...The goal is to provide a function able to add some darks or flats to an existing dataset.
For now we will only focus on creating a new NXTomo entry and won't manage any overwrite.
Done
====
- [x] create a generic function to insert numpy array or a new source to an existing Virtual dataset (at the beginning or end of the current array)
- [x] update all necessary dataset for adding a dark or flat (`instrument/detector/data`, `instrument/detector/rotation_angle`...)
- [x] insure no links are affected: for now we copy anyother data that is not 'instrument/detector/data'. Might be improved later
- [x] add tests
- [x] provide a command for it
- [x] documentation
Info
====
The command line takes a file path and a file entry as mandatory entries.
Users should provide url for darks, and flats.
This only manage 'inplace' modifications. If the users wants to have to files: one 'orginal' and one 'with the modifications' then this is up to him to first copy the file.
Example of usage:
=================
Provided API is:
```
nxtomomill patch-nx [my_file my_entry] [[--darks dark_path@dark_file --initial-flats ini_flat_path@ini_flat_file --final-flats fin_flat_path@fin_flat_file]]
```
Tested example:
```
nxtomomill patch-nx /tmp/tmpzk3v37h_/simple_case/simple_case.h5 entry --darks-at-start data2@/tmp/tmpzk3v37h_/dark.hdf5 --flats-at-start silx:///tmp/tmpzk3v37h_/simple_case/simple_case.h5?path=flat&slice=1,2
```
Note
====
for now we cannot provide any 'extra' parameter from the command line. This can only be done calling a python script.
This could be possible but some work at the command line has to be done. But I don't think this is an option 'casual' users want to have.0.4https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/17Distance to m2020-06-25T13:43:00+02:00paynoDistance to m0.2https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/9[h5tonx][converter] add a callback to set missing inputs2020-04-22T08:59:46+02:00payno[h5tonx][converter] add a callback to set missing inputs/closes #3 /closes #3 0.2https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/8Add doc2020-04-08T14:39:57+02:00paynoAdd doc0.2https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/4From v0.12020-03-12T14:45:11+01:00paynoFrom v0.10.2https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/2[tomoh5tonx] start creation of nx file from .h5.2020-03-02T14:12:47+01:00payno[tomoh5tonx] start creation of nx file from .h5.TODO
----
- [x] Read each tomo:x
- [x] create the sequence
- [x] split each sequence into a file and create a 'master file' to read them all
- [x] add `data` virtual dataset
- [x] add basic metadata (name, beam...)
- [x] add ima...TODO
----
- [x] Read each tomo:x
- [x] create the sequence
- [x] split each sequence into a file and create a 'master file' to read them all
- [x] add `data` virtual dataset
- [x] add basic metadata (name, beam...)
- [x] add image_key and image_key_control
- [x] add rotation_angle
- [x] add x_translation, y_translation, z_translation
- [x] add some progress to clarify treatment
- [x] make sure file is still valid if moved.
- [x] add count_time information
- [x] add file version (same for edftonx)
limitation from original .h5 file
---------------------------------
- image_key not register in tomo_v2_external
- some unit missing
- counter is saved as a detector. Why ? -> how to know which node contains 'camera' and which don't ?
-> have to filter the 'detector name'
- rotation is sometime named srot, sometime hrsrot !!! (and for projection both are recorded !!!!) So in **this case the order of checking key matter !!!**
- for reference: several frame, one srot value !!!
0.2https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/226Merge branch 'rework_hdf5' into '1.0'2024-03-21T05:39:58+01:00paynoMerge branch 'rework_hdf5' into '1.0'get rid of the HDF5File when try to read (and use silx.io.utils.open instead)
See merge request tomotools/nxtomomill!225
(cherry picked from commit e0fa48071cfdb5a0727fcc3cf328248678a46cb2)
bf81e88a get rid of the HDF5File when try to...get rid of the HDF5File when try to read (and use silx.io.utils.open instead)
See merge request tomotools/nxtomomill!225
(cherry picked from commit e0fa48071cfdb5a0727fcc3cf328248678a46cb2)
bf81e88a get rid of the HDF5File when try to read (and use silx.io.utils.open instead)
9aafa5c2 update requirementshttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/225get rid of the HDF5File when try to read (and use silx.io.utils.open instead)2024-03-21T05:36:33+01:00paynoget rid of the HDF5File when try to read (and use silx.io.utils.open instead)https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/224Doc: fix warnings2024-03-15T11:45:50+01:00paynoDoc: fix warningshttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/222Merge branch 'modify_swmr_mode' into '1.0'2024-02-22T15:21:23+01:00paynoMerge branch 'modify_swmr_mode' into '1.0'get swmr from get_swmr_mode
See merge request tomotools/nxtomomill!221
(cherry picked from commit d5903219bc57de2f50b0dcb0d8140ce0b2beeb13)
51c95f9e get swmr from get_swmr_mode
982b0397 update requirements
bad65916 fix 51c95f9e8c5c5cb...get swmr from get_swmr_mode
See merge request tomotools/nxtomomill!221
(cherry picked from commit d5903219bc57de2f50b0dcb0d8140ce0b2beeb13)
51c95f9e get swmr from get_swmr_mode
982b0397 update requirements
bad65916 fix 51c95f9e8c5c5cbc15f9f6221e8e6d0410708b52
91f13408 edfconverter: fix, close the grp before checking the
e4c350a5 swmr: safer layout
5b124ae6 fix bad6591632503137ec0268726e361bb68bc3018c
411c3c97 CI: force installation of fix_h5py_file
b0555e27 TestStandardAcqConversionWithExternalUrls: fix self-referencing dataset.
f4c7a649 Revert "CI: force installation of fix_h5py_file"
be6fb952 requirements: upgrade nxtomo and tomoscan version to safely handle VDShttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/221get swmr from get_swmr_mode2024-02-22T15:18:52+01:00paynoget swmr from get_swmr_modehttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/220Merge branch 'fix_patch_nx' into '1.0'2024-02-20T13:17:41+01:00paynoMerge branch 'fix_patch_nx' into '1.0'Fix patch nx
See merge request tomotools/nxtomomill!219
(cherry picked from commit ca5ceac6fee2fce3cac2c7df84b8f639a9d8053e)
8b97907f Doc: fix typo on patch-nx
57a57739 is_nx_tomo_entry: fix deprecation warning
06cdecdd Doc: patch-nx:...Fix patch nx
See merge request tomotools/nxtomomill!219
(cherry picked from commit ca5ceac6fee2fce3cac2c7df84b8f639a9d8053e)
8b97907f Doc: fix typo on patch-nx
57a57739 is_nx_tomo_entry: fix deprecation warning
06cdecdd Doc: patch-nx: rename 'simple_case.h5' to 'my_nxtomo.nx' which is more indicativehttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/218Merge branch 'fix_config_handler' into '1.0'2024-02-20T10:09:24+01:00paynoMerge branch 'fix_config_handler' into '1.0'h52nx: add information on default values being None instead of False
See merge request tomotools/nxtomomill!217
(cherry picked from commit 7408230453c9f5af93ce1e77c890dbcfc761fb3d)
0381a7ab Revert "h52nx: fix several incoherent defaul...h52nx: add information on default values being None instead of False
See merge request tomotools/nxtomomill!217
(cherry picked from commit 7408230453c9f5af93ce1e77c890dbcfc761fb3d)
0381a7ab Revert "h52nx: fix several incoherent default values. close #158"
473920d2 h52nx: add comments to the default values being None instead of Falsehttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/216Merge branch 'improve_robustness_hdf5config' into '1.0'2024-02-15T15:53:14+01:00paynoMerge branch 'improve_robustness_hdf5config' into '1.0'hdf5config: improve robust to realpath
See merge request tomotools/nxtomomill!215
(cherry picked from commit cfd7182a73e0bc2e65334d133218f9249f1ea68b)
21ad7198 hdf5config: improve robust to realpathhdf5config: improve robust to realpath
See merge request tomotools/nxtomomill!215
(cherry picked from commit cfd7182a73e0bc2e65334d133218f9249f1ea68b)
21ad7198 hdf5config: improve robust to realpathhttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/215hdf5config: improve robust to realpath2024-02-15T15:45:59+01:00paynohdf5config: improve robust to realpathhttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/214Doc: add autodoc-hints2024-02-07T15:25:58+01:00paynoDoc: add autodoc-hintshttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/206Fix doc2023-12-18T16:55:09+01:00paynoFix dochttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/205Doc: rework - add a development section and link to change log2023-12-14T11:55:48+01:00paynoDoc: rework - add a development section and link to change log