IOTA

IOTA: integration optimization, triage and analysis

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IOTA is a user-friendly front end for the cctbx.xfel suite of serial diffraction data processing programs. It is comprised of three main modules:

 1. Raw image import, conversion, pre-processing and triage
 2. Image indexing and integration using cctbx.xfel modules (with optimization of spot-finding parameters)
 3. Analysis of the integrated dataset

These modules are united by a command-line interface and are run in sequence. The user can point IOTA towards a single diffraction image, a folder of images, a list of image paths or a modified script file. If no script file is supplied, IOTA will automatically generate reasonable defaults (currently optimized for a MARCCD detector, but also usable with Pilatus detectors).

Running 'IOTA' in Auto Mode

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The simplest way to run IOTA is in Auto Mode. To do so, simply issue:

 iota.run /path/to/image/files/

The path may contain a tree of folders in any configuration. IOTA will then carry out a conversion step if the source folder contains raw diffraction images. The converted image pickles will be saved in the current folder under the subfolder "converted_pickles". Inside that folder, converted pickles will be saved separately for each IOTA run, under subfolders named "001", "002", "003", etc. Alternatively, once raw images have been successfully converted to image pickles, IOTA can be pointed to the image pickles instead, e.g.:

 iota.run ./converted_pickles/001/

Once running, IOTA will display a program logo, some information about the configuration of the run and a progress bar for each major step, e.g.:

 -bash-4.1$ iota.run converted_pickles/003/
 
 
      IIIIII            OOOOOOO        TTTTTTTTTT          A              
        II             O       O           TT             A A             
        II             O       O           TT            A   A            
 >------INTEGRATION----OPTIMIZATION--------TRIAGE-------ANALYSIS--------->
        II             O       O           TT          A       A          
        II             O       O           TT         A         A         
      IIIIII            OOOOOOO            TT        A           A   v2.23  
                                                           with CCTBX.XFEL
 
 
 Wednesday, Nov 11, 2015. 06:36 PM
 
 
 IOTA will run in AUTO mode using /net/cci-filer2/raid1/home/art/iota/test_v2.23/converted_pickles/003:
 
 Reading files from data folder -- DONE.....................................0.11s
 IMPORTING IMAGES:   9% [ -    ] [ ===>                                         ]