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Goret, Gael, 30/01/2015 09:07 AM

[1.1] How to Start-up the 3DRSR execution : 3DRSR_config

The configuration program for 3DRSR is made of two consecutive procedures : firstly an initial auto-assignment of the parameters from configuration file(s) inputted, then, a manual definition of all the parameters that has not been defined automatically.

3DRSR_config is launched in this way:

python Xcalibur_parameter_file.par [Inhouse_config_file.cfg]

  • Inhouse_config_file.cfg being optional

Inhouse_config_file.cfg format (without the “---” lignes):

  1. gfs1_2 - file name template
  1. 1800 - number of input files
  1. 1 - starting from number
  1. 2463 - Size-Fastest-Dimension
  1. 2527 - Size-Second-Dimension
  1. 0 - starting angle
  1. 0.1 - oscillation size in degrees
  1. 1 - apply symmetry (0/1)
  1. 53.898 - 1st tilt of U matrix
  1. 29.653 - 2nd tilt of U matrix
  1. 54.696 - 3rd tilt of U matrix

The configuration procedure start by assigning the parameter values available in the Xcalibur parameter file and (if present) in the inhouse configuration file.
Then the program display a summary of the parameters associated with their values or “None” if the program has failed to initialize one parameter.

Then the program inspect the configuration object and ask the user to set manually the value of each parameter with an undefined value.

At the end of the manual setting procedure, the program display again the list of parameter values, and write an ASCII file, named 3DRSR.conf containing all the information on parameters.

This file can be edited by any text editor in order to modify the configuration before setting the file as input of 3DRSR.

[1.2] 3DRSR : 3D Reciprocal Space Reconstruction

Once you have obtained a 3DRSR.conf file [see 1.1], you can start 3DRSR using the following syntax :

python 3DRSR.conf Filter_file images-file(s)

e.g. : python conf/3DRSR.conf mask6M ~/data/GFS/images/*


“conf/3DRSR.conf” is the path to the configuration file,

“mask6M” is the path to the filtering mask (in the example located in the current dir),

“and ~/data/GFS/images/*” is a list of X-ray detector images (given to the program by the command shell via the keyword *)

The Input file formats handled are the following : ===================
  • Bruker
      o brukerimage
      o bruker100image
      o kcdimage: Nonius KappaCCD diffractometer
  • Mar Research
      o marccd (fileformat derived from Tiff)
      o mar345 imaging plate with PCK compression
  • Dectris
      o cbfimage (implements a fast byte offset decompression scheme in python/cython)
      o pilatusimage (fileformat derived from Tiff)
  • ESRF
      o edfimage: The ESRF data Format
      o xsdimage: XML serialized image from EDNA
      o fit2dmaskimage: Fit2d Mask format
      o fit2dspreadsheetimage: Fit2d ascii tables (spread-sheet)
  • ADSC
      o adscimage
  • GE detector at APS
      o GEimage
  • PNM
      o pnmimage
  • Tiff
      o tifimage
  • D3M
      o d3mimage
  • Hamamatsu
      o HiPiCimage
  • Oxford Diffraction Sapphire 3
      o OXDimage
  • Nonius
     o KappaCCD
  • Raw Binary without compression ===================

Once 3DRSR is launched with the proper attributes, the logo is displayed, and the first question appears :


3DRSR1.png View (9.12 KB) Goret, Gael, 30/01/2015 09:14 AM

3DRSR2.png View (16.4 KB) Goret, Gael, 30/01/2015 09:14 AM