dxfile2nx tutorial

10 min read

the dxfile2nx application is used to convert an acquisition stored with the dxfile format to the NXTomo format.

To call this application you can call directly

nxtomomill dxfile2nx [input_file] [output_file] [[options]]

You can access help by calling

$ nxtomomill dxfile2nx --help
usage: nxtomomill dxfile2nx [-h] [--input_entry INPUT_ENTRY]
                            [--output_entry OUTPUT_ENTRY]
                            [--file_extension FILE_EXTENSION]
                            [--scan-range SCAN_RANGE]
                            [--pixel-size PIXEL_SIZE] [--fov FIELD_OF_VIEW]
                            [--distance DISTANCE] [--energy ENERGY]
                            [--overwrite] [--no-data-copy]
                            input_file output_file

convert acquisition contained in provided dx file to NXTomo entry

positional arguments:
  input_file            master file of the acquisition
  output_file           output .nx or .h5 file

optional arguments:
  -h, --help            show this help message and exit
  --input_entry INPUT_ENTRY
                        h5py group path to be converted
  --output_entry OUTPUT_ENTRY
                        h5py group path to store the NXTomo
  --file_extension FILE_EXTENSION
                        extension of the output file. Valid values are
                        .h5/.hdf5/.nx
  --scan-range SCAN_RANGE
                        scan range of the projections. Dark and flat will
                        always be considered with rotation angle ==
                        scan_range[0]
  --pixel-size PIXEL_SIZE
                        pixel size in meter as (x pixel size, y pixel size)
  --fov FIELD_OF_VIEW, --field-of-view FIELD_OF_VIEW
                        pixel size in meter as (x pixel size, y pixel size)
  --distance DISTANCE, --detector-sample-distance DISTANCE
                        sample to detector distance (in meter)
  --energy ENERGY, --incident-beam-energy ENERGY
                        incident beam energy in keV
  --overwrite           Do not ask for user permission to overwrite output
                        files
  --no-data-copy        Avoid creating any symbolic link between input and
                        output fileand duplicate the frame datasets to have a
                        'all-in-one' output file.

Here is an example on how to convert a dxfile. For it we downloaded the tomo_00068 dataset

To convert it we simply go for

nxtomomill dxfile2nx tomo_00068.h5 tomo_00068.nx

Here the conversion will set default values to parameters that are not recorded in the dxfile but that tomography software mights need. Such as beam energy … Here is an example of providing more information to the converter and requesting the converter to overwrite the output NXtomo entry if it exists

nxtomomill dxfile2nx tomo_00068.h5 tomo_00068.nx --scan-range 0,180 --distance 0.15 --energy 14 --overwrite

Here is an example of the NXTomo entry generated:

From it you can use several tomography tool like nabu and / or tomwer.

Warning

to have a complete usage of tomwer you will also have to provide the field of view of the detector (Full or Half)

Example of the reconstruction of the middle slice using nabu: