nxtomomill merge requestshttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests2022-01-04T09:29:59+01:00https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/84[patch-nx] add an option to convert automatically all frame of a given type...2022-01-04T09:29:59+01:00payno[patch-nx] add an option to convert automatically all frame of a given type...[patch-nx] add an option to convert automatically all frame of a given type (dark, flat, projection...)
close #82[patch-nx] add an option to convert automatically all frame of a given type (dark, flat, projection...)
close #820.7https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/83[h52nx] rename some remaining `ref_titles` to `flat_titles`.2021-12-06T11:01:40+01:00payno[h52nx] rename some remaining `ref_titles` to `flat_titles`.Insure backward compatibility by adding aliases for the `flat_titles` key.Insure backward compatibility by adding aliases for the `flat_titles` key.0.7https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/82rename some remaining `ref_titles` to `flat_titles`2021-12-06T09:42:18+01:00paynorename some remaining `ref_titles` to `flat_titles`0.7https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/81benefit from validator and improve tests2021-11-30T09:56:29+01:00paynobenefit from validator and improve tests0.7https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/80edf2nx: fix issues with the progress.2021-11-29T15:27:46+01:00paynoedf2nx: fix issues with the progress.flat and projections can be write `interlace` and reseting the progress was a mess.
Simply avoid reseting the progress and only update advancement when write projection.flat and projections can be write `interlace` and reseting the progress was a mess.
Simply avoid reseting the progress and only update advancement when write projection.0.7https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/79edfconverter: improve file closing management2021-11-22T15:58:53+01:00paynoedfconverter: improve file closing managementclose #80close #800.7https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/77[app][dxfile2nx] allow to provide pixel size as a single value2021-10-04T10:23:30+02:00payno[app][dxfile2nx] allow to provide pixel size as a single valueclose #66close #660.7https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/73modification for format 1.12021-08-04T14:27:55+02:00paynomodification for format 1.1- reorder datasets:
- sample/sample_name -> sample/name
- sample/name -> title
- add NxSource information
- contains name and type- reorder datasets:
- sample/sample_name -> sample/name
- sample/name -> title
- add NxSource information
- contains name and type0.6https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/72[h52nx][converter] group several call to `_generic_path_getter`2021-08-02T16:59:59+02:00payno[h52nx][converter] group several call to `_generic_path_getter`Description / Goal
------------------
Several modifications to the Nexus output:
- add title
- move beam to an NXbeam and save it under NXinstrument
TODO list
---------
- [x] add title
- [x] refactoring: group several dataset getter #...Description / Goal
------------------
Several modifications to the Nexus output:
- add title
- move beam to an NXbeam and save it under NXinstrument
TODO list
---------
- [x] add title
- [x] refactoring: group several dataset getter #75
- [x] add NXbeam class (under NXsample probably ?)
- [x] keep compatibility with the previous beam thing
- [x] add test
INFO (how to use...)
--------------------
- close #75
- a pre-release wheel should be done for it0.6https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/70[setup] move to setup.cfg2021-07-27T08:35:38+02:00payno[setup] move to setup.cfg0.8https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/69Fix patch nx translation2021-07-13T16:15:21+02:00paynoFix patch nx translation0.6https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/68[app][h52nx] add option '--copy-data' to enforce data duplication inside the ...2021-07-09T11:37:01+02:00payno[app][h52nx] add option '--copy-data' to enforce data duplication inside the fileclose #72close #720.6https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/673dxrd improvements2022-03-14T16:58:35+01:00Julia Garriga Ferrer3dxrd improvementsDescription / Goal
------------------
Add management of 3d-xrd dataset in nxtomomill.
TODO list
---------
- handle HDF5
- [ ] ~~add a Mock up class for 3D XRD~~ to be done in another PR
- [x] add unittest
- [x] add a new appl...Description / Goal
------------------
Add management of 3d-xrd dataset in nxtomomill.
TODO list
---------
- handle HDF5
- [ ] ~~add a Mock up class for 3D XRD~~ to be done in another PR
- [x] add unittest
- [x] add a new application to handle 3d-xrd
- [x] save motor position for 'rocking'
- handle EDF
- [ ] ~~rework EDF converter~~ might be done in another PR. No the prioroty at this point.
INFO (how to use...)
--------------------
some example of usage:
* without a configuration file
```
nxtomomill h5-3dxrd-2nx bassanite_Bassanite_start_1_4.h5 test_julia_no_cfg.nx --single-file
```
* with a configuration file
```
nxtomomill h5-3dxrd-2nx --config xrd_3d_config.cfg
```
an example of a configuration file: [xrd_3d_config.cfg](/uploads/dc42b3546e28919978f9bd01ce19988f/xrd_3d_config.cfg)
Any warning ?
-------------
associated materials (screenshot, test scripts...)
--------------------------------------------------0.8Julia Garriga FerrerJulia Garriga Ferrerhttps://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/64[app][dxfile2nx] convert dxfile to NXTomo2021-12-16T11:37:00+01:00payno[app][dxfile2nx] convert dxfile to NXTomo# Description / Goal
Insure translation from dxfile to NXtomo.
# TODO list
- [x] add an application to convert from dxfile to NXTomo
- [x] add a function to do conversion from a script
- [x] doc
- [x] general information
- [x] a...# Description / Goal
Insure translation from dxfile to NXtomo.
# TODO list
- [x] add an application to convert from dxfile to NXTomo
- [x] add a function to do conversion from a script
- [x] doc
- [x] general information
- [x] add tutorial
- [x] add tests
- [x] insure version is stored
- [x] test on several dxfile
- [x] tomo_00022
- [x] tomo_00024
- [x] tomo_00068
- [x] tomo_00076
- [x] test tomwer / nabu can handle the file for a processing
# INFO (how to use...)
Example of usage:
### *tomo_00022 case*
- x rotation angle "theta" are not take into account for now. Might evolve with time. But in this case we might expect rotation angle for all dark, flat and projection not only projection. For now users must provide a scan range (0,180) in this case:
- other mandatory parameters are converted (pixel size, distance, energy...)
``` bash
nxtomomill dxfile2nx tomo_00022.h5 tomo_00022.nx --overwrite --scan-range 0,180
```
We can now try nabu on it
``` bash
nabu-config
```
This generate a nabu.conf file that we have to set up. Adding dataset location (generated .nx file), rotation_axis_position=auto, enable_halftomo=0, output location, Paganin ? ...
Once done we can call nabu with it.
```
nabu nabu.conf --slice middle
```
![Nxtomo - tomo_00022.nx](/uploads/a771d99ff0d08cf80db707eef659dc52/image.png)
![dxfile - tomo_00022.h5](/uploads/446a74522fd5df9f7ec80974d7572cde/image.png)
![nabu reconstruction](/uploads/8c9830923f26e34bea7b5ff90bb0b23a/image.png)
note: note sure at all about nabu reconstruction parameters, cor value... but at least it processes it.
### *tomo_00024 case*
close to the *tomo_00022*. This time we avoid data duplication
``` bash
nxtomomill dxfile2nx tomo_00024.h5 tomo_00024.nx --overwrite --no-data-copy
```
This time we test tomwer on it (with nabu)
```
tomwer canvas
```
We need to specify the field of fiew to provide it to nabu so we need to add the `--field-of-view` option
``` bash
nxtomomill dxfile2nx tomo_00024.h5 tomo_00024.nx --overwrite --no-data-copy --field-of-view full
```
Again not sure at all by the reconstruction parameters. I guess the provided .tiff does not help much.
![image](/uploads/7bcc349f3cd34edad90c3c605675edfb/image.png)
### *tomo_00068 case*
test file conversion providing distance and energy + test it with nabu (no paganin)
```
nxtomomill dxfile2nx tomo_00068.h5 tomo_00068.nx --overwrite --no-data-copy --energy 20 --distance 0.36
```
![nabu middle slice - tomo_00068](/uploads/5684b477ef5edbed20c927f6deb04b79/image.png)
### *tomo_00071 case*
simply test file conversion
Any warning ?
-------------
* several "core" information are not provided by dxfile as rotation angle, detector-sample distance, pixel size.
Some "default" values are provided but might need to be provided during conversion.
* alignment projection are not handled
* it look like dxfile contains one acquisition per file. If not users will have to call several time the converter and providing the *input_entry* parameter
* to call nabu from tomwer the field of view need to be provided. Maybe we will also create a default value ?
associated materials (screenshot, test scripts...)
--------------------------------------------------
![dxfile](/uploads/7884c69f3ce90d862bef3a0980433725/image.png)
![converted nxtomo file](/uploads/5d59f7ddf208eb6451c7c3d6035fe11d/image.png)0.6https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/63Improve ci2021-05-18T09:54:14+02:00paynoImprove ci0.6https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/62clean up format2021-05-18T08:22:21+02:00paynoclean up format0.6https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/61update documentation and add documentation on design2021-05-12T13:57:48+02:00paynoupdate documentation and add documentation on design0.6https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/60Add 3d xrd (third PR)2021-06-09T16:45:44+02:00paynoAdd 3d xrd (third PR)Description / Goal
------------------
Include management of 3d-xrd dataset in nxtomomill.
TODO list
---------
- handle HDF5
- [x] add a `3DXRD` inheriting from BaseAcquisition for 3DXRD.
- [x] add a `3DXRDH5Config` or a `3DXRDCo...Description / Goal
------------------
Include management of 3d-xrd dataset in nxtomomill.
TODO list
---------
- handle HDF5
- [x] add a `3DXRD` inheriting from BaseAcquisition for 3DXRD.
- [x] add a `3DXRDH5Config` or a `3DXRDConfig`
- [ ] ~~add a Mock up class for 3D XRD~~
- [ ] ~~add unittest~~
- [x] add an application to handle it
- handle EDF
- [ ] ~~rework EDF converter ?~~
- [ ] ~~handle EDF to work with urls if necessary~~
- [ ] ~~create external storage for EDF~~
- [ ] ~~create virtual dataset from external storage for the `data` dataset~~
- [ ] ~~add an application to handle it~~
- [ ] ~~add deprecation warning for API modifications (settings, HDF5Config class...)~~
INFO (how to use...)
--------------------
some example of usage:
* without a configuration file
```
nxtomomill h5-3dxrd-2nx bassanite_Bassanite_start_1_4.h5 test_julia_no_cfg.nx --single-file
```
* with a configuration file
```
nxtomomill h5-3dxrd-2nx --config xrd_3d_config.cfg
```
an example of a configuration file: [xrd_3d_config.cfg](/uploads/18865262b5fbc13ff06e033f89311592/xrd_3d_config.cfg)
Any warning ?
-------------
associated materials (screenshot, test scripts...)
--------------------------------------------------0.6https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/59[hdf5] read rotation motor from "technique/scan/motor"2021-05-04T09:06:29+02:00payno[hdf5] read rotation motor from "technique/scan/motor"- to activate this option the H5_ROT_ANGLE_KEYS should be set to None- to activate this option the H5_ROT_ANGLE_KEYS should be set to None0.6https://gitlab.esrf.fr/tomotools/nxtomomill/-/merge_requests/58[converter][hdf5] save tomo_n2021-05-03T14:33:24+02:00payno[converter][hdf5] save tomo_n0.6