tomoscan merge requestshttps://gitlab.esrf.fr/tomotools/tomoscan/-/merge_requests2021-05-03T14:32:01+02:00https://gitlab.esrf.fr/tomotools/tomoscan/-/merge_requests/42[hdf5][tomoscan] return intrument/detector/tomo_n instead of len(projections)2021-05-03T14:32:01+02:00payno[hdf5][tomoscan] return intrument/detector/tomo_n instead of len(projections)0.6https://gitlab.esrf.fr/tomotools/tomoscan/-/merge_requests/44Fix 282021-05-18T11:19:52+02:00paynoFix 280.6https://gitlab.esrf.fr/tomotools/tomoscan/-/merge_requests/45Handle 3d xrd2021-06-10T09:45:33+02:00paynoHandle 3d xrd- [x] add HDF5XRD3DScan that can read .nx generated by `nxtomomill h5-3dxrd-2nx` and provides `base_tilt` and `rocking` properties.
- [x] extend `Frame` to also access frame `base_tilt` and `rocking`- [x] add HDF5XRD3DScan that can read .nx generated by `nxtomomill h5-3dxrd-2nx` and provides `base_tilt` and `rocking` properties.
- [x] extend `Frame` to also access frame `base_tilt` and `rocking`0.6https://gitlab.esrf.fr/tomotools/tomoscan/-/merge_requests/49[scanbase] move _FOV to public.2021-06-22T15:46:43+02:00payno[scanbase] move _FOV to public.0.6https://gitlab.esrf.fr/tomotools/tomoscan/-/merge_requests/54[hdf5tomoscan] improvement to handle different version of NXtomo (from mxtomo...2021-08-05T15:26:35+02:00payno[hdf5tomoscan] improvement to handle different version of NXtomo (from mxtomomill)- [x] add nexus_path and handling of nexus_version properties
- add missing getters
- [x] nexus_version
- [x] source attribute / class
- contains name
- contains type
- [x] instrument_name
- [ ] ~~definition ???~~...- [x] add nexus_path and handling of nexus_version properties
- add missing getters
- [x] nexus_version
- [x] source attribute / class
- contains name
- contains type
- [x] instrument_name
- [ ] ~~definition ???~~ don't see the interest to have it here. I don't think we expect to have some else than NXtomo for now at our level0.6https://gitlab.esrf.fr/tomotools/tomoscan/-/merge_requests/50first version of adding intensity normalization2021-08-24T13:57:43+02:00paynofirst version of adding intensity normalizationThis is a proposal for having some 'basic' normalization in tomoscan. At least the one common on nabu and tomwer to avoid some code duplication.
more 'constraining' use cases (using a ROI or a dataset with interaction, cuda implementati...This is a proposal for having some 'basic' normalization in tomoscan. At least the one common on nabu and tomwer to avoid some code duplication.
more 'constraining' use cases (using a ROI or a dataset with interaction, cuda implementation...) will be implemented on other projects.0.6https://gitlab.esrf.fr/tomotools/tomoscan/-/merge_requests/55Add validator2021-08-30T13:29:36+02:00paynoAdd validator# scope
Lately tomwer included a widget with some 'entry validation'. This could be extended to nabu for an application to check data prior to reconstruct them.
This could also be integrated in nxtomomill once the Nexus file is write d...# scope
Lately tomwer included a widget with some 'entry validation'. This could be extended to nabu for an application to check data prior to reconstruct them.
This could also be integrated in nxtomomill once the Nexus file is write down.
Tomwer would probably require those at the Entry level (so extra information could be provided in tooltip)
Nabu would probably need an interface like:
``` bash
nabu validator [file.h5/folder] [[entries]] [--no-phase-retrieval] [[--check-datasets]] [[--all-entries]]
```
# TODO
validators requested:
- [x] energy
- [x] distance
- [x] pixel size
- [x] darks (urls exists, check broken vds and nan)
- [x] flats (urls exists, check broken vds and nan)
- [x] projections (urls exists, check broken vds and nan)
- [x] High level validator for reconstruction (with or without phase retrieval)
- [x] improve readability
- at least adjust text on the left
- maybe we could add some icons on the terminal like 'black' for example for readability and fanciness ;)
- [x] improve vds check: look on virtual source to only check the dataset we are interested on.
# extra info
I expect the high level validator (for a reconstruction for example) to provide two 'analysis':
- summary:
```
- entryXXX@master_file.nx
- energy: valid
- darks: invalid: expected data in XXX
- projections: invalid: has broken virtualdataset link
- flats: invalid: contains nan...
- distance: valid
```
- resume:
```
- 3 issues:
- darks: invalid: expected data in XXX
- projections: invalid: has broken virtualdataset link
- flats: invalid: contains nan...
```
# API
a `single entry` validator or a `Reconstruction` validator should have the same API:
``` python
class ValidatorBase:
def is_valid(self):
...
def run(self):
...
def clear(self):
...
```
# extra info
close #35
should trigger https://gitlab.esrf.fr/tomotools/nabu/-/merge_requests/141
An example of result from nabu with source scan removed for dark and flat
![image](/uploads/6354ce32d9e896f4127d752ad8576a95/image.png)0.6paynopayno