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Goret, Gael, 30/01/2015 09:17 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:

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

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

where,

“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 :

Internally, 3DRSR is composed by two distinct procedures :
The reconstruction of the whole reciprocal space binned into a 3D Cartesian grid.
Or, the reconstruction of an image corresponding to a slice of this volume.
Depending of what you want to do, type key “v” or “s”, then press Enter.

[1.2.1] Volumetric reconstruction

From a series of diffraction images taken in rotation (with different tilt angles along one axis), the program back-project each image on the Ewald sphere, and thanks to the diffractometer parameters (goniometer angles, crystal orientation, ... ) the given curved image is binned into a 3D grid. The intensities contained in each image (the value of each pixel) are summed-up, symmetrized, and finally averaged to give the final reconstruction.

Once the type of reconstruction is chosen, the program display the minimal list of generators necessary to compute, by combination, the symmetry operator list of all the point groups.

If you want that 3DRSR symmetrized the computed reconstruction, you can defined a list of generators adapted to you case.

e.g. :
P6mmm → 2(z),3(z),m(x),m(y),m(z)
m4m → 1~,2(y),2(z),2(110),3(111)

If you prefer computing a volume without symmetry applications, juste press the key Enter, “no symmetry” is the default choice.

The application of symmetry operations are computed on the 3D massif at the end of the reconstruction

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