Helical Pipeline

The helical pipeline is invoked with the following command, which takes as argument the name of a configuration file

    nabu-helical nabu_config_file.cfg

Helical Specific Parameters

the config file is mainly the same as for the standard pipeline with few exceptions. Here we list them, for each section of the configuration file

  • preproc section

    • processes_file this file is expected to contain the map of weights, of the same shape as the detector, and the double flatfield, which can possibly be equal to one everywhere, but is needed nonetheless. A default file can be created with the nabu-helical-prepare-weights-double command

      nabu-helical-prepare-weights-double  name_of_tomomilled_file.nx entry0000

      where the second argument is the entry name for desired scan. This command creates a file name double.h5.

      • example for setting the processes_file parameter in the preproc section

        processes_file =  map_and_doubleff.h5

    • double_flatfield_enabled = 1 always enable this. If you dont have any double-flat provide as a fallback solution a completely flat double_field, everywhere equal to 1.

    • flatfield=1 Always enable flat-field. If you dont have one provide a uniform flat-field.

  • reconstruction section

    • enable_halftomo nabu-helical applies the same treatment for half-tomo as for full-tomo. Always let this key to zero

      enable_halftomo = 0

    • start_z, end_z, start_z_mm, end_z_mm these parameters determine the, vertically, reconstructed region. if they are not set, they take their default values, which triggers the reconstruction of the whole reconstructable region. Such default values are:

      start_z = 0
end_z =   -1
start_z_mm = 0
end_z_mm =   0

      These parameters offer two alternative methods to specify the reconstruction range :

      • if both start_z_mm and end_z_mm are identical to zero, then the recontruction range is determined on the basis of start_z and end_z. Use positive integers, with start_z < end_z, strictly, unless you use the default values which trigger the whole reconstruction. The reconstructed vertical region will be performed form slice start = first doable + start_z until slice end = first doable + end_z. If necessary the range will be clipped, if the given region exceed the doable range. example:

      start_z = 10
end_z = 20

      for reconstructing 10 slices close to scan start. NOTE: we are proceeding in the direction of the scan so that, in the laboratory reference system the start may be above or below the end, depending on the direction of the scan.

      • If one of start_z_mm end_z_mm or both ar different from zero, the reconstruction range is the one comprised between these two values, interpreted as heights, in millimiters, above the sample stage.

    • use_hbp this parameter is by default set to 0. If it is set to 1, and IF the package is available (not available in the public branch yet) the hyerarchical backpropagation algorithm (Jonatz Graetz 2021) is used. Default is :

      use_hbp = 0

    • redundancy_angle_deg this parameter has its role in the criteria used to establish wether a given slice is reconstructable or not. By default the minimal required span is 360 degree. When dead zones in the detector exists, instead, ( dead zones are tagged with zero weight in the weight field) the minimal required span is increased by 2*redundancy_angle_deg. Default is : redundancy_angle_deg = 0

    • angular_tolerance_steps the angular tolerance, an angular width expressed in units of an angular step, which is tolerated in the criteria for deciding if a slice is reconstructable or not. Its defult is zero. This tolerance can be used to reconstruct non helical scan which cover slightly less then 360 degrees.

Concerning the output

if tiff format is chosed, the slices will be written separately, one per file, and the name of the file will be postpended, just before the file extension (.tiff), with the height in millimiters that the slice has above the sample stage. This value is written with a fixed number of digits, with the dot of the floating point number replaced by the letter p. The total lenght of the file name being thus constant for all the slices.

Full list of helical specific parameters.

we have given here the most commonly used parameters. The full list of available parameters, comprising also the one very seldomly used, can be found in the file nabu/pipeline/helical/nabu_config.py