Output Format

The output format is determined by the OUTPUT_FILE input variable

The following documentation has been generated automatically from the comments found in the code.

class Parameters_module.Parameters

The input variables are read from the input file. The input file is written with python syntax. The Input file is interpreted as python after a preprocessing The preprocessing was introduced at the time of HST-> PYHST transition to maintaing compatibility with:

  • NO/YES meaning 0/1

  • items containing FILE in their name can be initialized without using the “” which are otherwise necessary for strings

The input file has to set (some of) the following variables. To setup easily an input file you are suggested to start from one of the examples given in the doc.


Set this to 1 to write preprocessed projection after Paganin. Each projection will be written to an edf file whose prefix is given by OUTPUT_PAGANIN_FILE input variable. No further processing is done when this option is on. To use properly this option the best way is selecting just the middle slice for reconstruction and then setting a high PAGANIN_MARGE marge such to encompass a whole radiography plus a margin for the paganin kernel. The output is the data after Paganin, before logarithm and before interpolation for longitudinal correction.

OUTPUT_FILE = 'dum.vol'

Choice of the output format

  • if OUTPUT_FILE has postfix .vol then the reconstructed volume is written in binary form, as an array of float32s to the specified file, with z being the slowest dimension, x the fastest

  • if OUTPUT_FILE has postfix .edf, or no postfix then each slice is written separately to an edf file, numbered with the z coordinate.

besides this, at the end of the calculation, two info files are written : OUTPUT_FILE.info and OUTPUT_FILE.xml, both containing basically the same informations : NUM_X, NUM_Y, NUM_Z, voxelSize, BYTEORDER, ValMin, ValMax, s1, s2, S1, S2. An histogram, on (10)^6 bins is written to histogram_OUTPUT_FILE.edf ( in edf format )

s1 and s2 are the minimum and maximum values of the range that excludes 0.001% of the voxels on both sides of the histo. S1 and S2, instead, exclude 0.2% on both sides


if set to 1, no reconstruction is done but a sinogram is outputted per each slice in an edf file ( the edf output will countain the sinogram instead than the slice )