Description / Goal
Insure translation from dxfile to NXtomo.
add an application to convert from dxfile to NXTomo
add a function to do conversion from a script
insure version is stored
test on several dxfile
test tomwer / nabu can handle the file for a processing
INFO (how to use...)
Example of usage:
- 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...)
nxtomomill dxfile2nx tomo_00022.h5 tomo_00022.nx --overwrite --scan-range 0,180
We can now try nabu on it
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
note: note sure at all about nabu reconstruction parameters, cor value... but at least it processes it.
close to the tomo_00022. This time we avoid data duplication
nxtomomill dxfile2nx tomo_00024.h5 tomo_00024.nx --overwrite --no-data-copy
This time we test tomwer on it (with nabu)
We need to specify the field of fiew to provide it to nabu so we need to add the
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.
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
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 ?