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IOTA: integration optimization, triage and analysis

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: Auto Mode

The simplest way to run IOTA is in Auto Mode. To do so, simply issue: /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.: ./converted_pickles/001/

Alternatively, if a list of images exists, IOTA can accept that list of images as input (IOTA creates the input list automatically and saves it under ./integration/###/input_images.lst): ./integration/001/input_images.lst

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$ converted_pickles/003/
      IIIIII            OOOOOOO        TTTTTTTTTT          A              
        II             O       O           TT             A A             
        II             O       O           TT            A   A            
        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% [ -    ] [ ===>                                         ]

IOTA will automatically create two script files: iota.param (which contains settings for running IOTA) and target.phil (a cctbx.xfel target file), which can be modified by a user to fine-tune various settings. The output will be collected in the folder named "integration", which will contain subfolders for each integration run, titled "001", "002", "003", etc. Each run generates a folder named "final" with the final integrated pickles as well as individual cctbx.xfel logs for each image. Furthermore, lists of files that have been successfully integrated (integrated.lst), failed integration (not_integrated.lst), etc. can be found there. Finally, a pre-populated script for PRIME (prime.phil) can be found there as well. (Currently, the user must manually edit prime.phil to specify the number of residues - "n_residues" - in order to run PRIME successfully.)

Running IOTA: Script Mode

IOTA can be run using a script file, e.g.: script.param

The script contains settings in PHIL format, e.g.:

 description = "IOTA run #5, with some modified settings"
 input = "/path/to/raw/images/"
 target = "target.phil"
 cctbx {
   grid_search {
     type = None *brute_force smart
     area_median = 5
     area_range = 2
     height_median = 4
     height_range = 2
     sig_height_search = False
   selection {
     select_only {
       flag_on = False
       grid_search_path = None
     min_sigma = 5
     select_by = *epv mosaicity
     prefilter {
       flag_on = False
       target_pointgroup = None
       target_unit_cell = None
       target_uc_tolerance = 0.05
       min_reflections = 0
       min_resolution = None

The script can be auto-generated (with an accompanying target.phil file with some default cctbx.xfel settings) via a "dry run" by issuing -d

The same "-d" command-line option will print to terminal the full IOTA script file with help statements (which will also be included at the end of this page).

Additionally, IOTA settings can be modified by command-line statements, e.g.: script.param cctbx.grid_search.type=smart cctbx.grid_search.area_median=7

Running IOTA: Single-Image Mode

IOTA can accept a single image as input: images/img_00001.pickle 

Alternatively, IOTA can be run in bare-bones "single-image mode"

 iota.single_image images/img_00001.pickle 

These options are best for testing purposes.

Running IOTA: Command-line Options

In addition to a command script, IOTA runs can be modified by command-line options:

 -h, --help                   show help message and exit
 --version                    Prints version info
 -l, --list                   Output a file (input_images.lst) with input image paths and exit
 -c, --convert                Convert raw images to pickles and exit
 -d, --default                Generate default iota.param and target.phil files and exit
 -p PREFIX, --prefix PREFIX   Specify custom prefix for converted pickles (e.g. -p user)
 -s, --select                 Selection only, no grid search
 -r RANDOM                    Run IOTA with a random subset of images, e.g. "-r 5"
 -n NPROC                     Specify a number of cores for a multiprocessor run"
 --mpi [MPI]                  Specify stage of process - for MPI only
 --analyze [ANALYZE]          Use for analysis only; specify run number or folder with results

These options can be shown by issuing: -h

Perhaps the most useful of these are -r and -n options, as they allow the user to adjust an IOTA run in Auto-mode on the fly. Alternatively, both of these settings can be changed within the script file.

All of the options in the script can be introduced as command-line statements by using a "compressed" PHIL format. Thus:

 cctbx {
   grid_search {
     type = None *brute_force smart

translates into script.param cctbx.grid_search.type=brute_force

IOTA Output

Due to IOTA's flexibility, there are several types of output that co-exist simultaneously and can be somewhat disconnected from one another. It helps to think of them as three separate stages of the process: pre-processing, grid-search / integration, and post-processing / analysis.

In pre-processing, raw images are read in and converted to cctbx.xfel "pickle" format (i.e. pickled arrays of pixel intensity values). These are saved under the "converted_pickles" folder in the format <prefix>_<run_no>_<#####>.pickle; each cycle of pre-processing is assigned a run number (e.g. "001", "002", "003", etc.). Pre-processing is only triggered if a) the read-in image is not already in pickle format or b) the image has to be modified in some way (e.g. override beamXY coordinates, change detector distance, etc.). Thus, if converted and modified pickles are submitted to IOTA, the "converted_pickles" folder will not be created. The purpose of this is to allow the user to experiment with image modification, then subsequently select the converted pickles that best fit the user's needs.

The output of the other two steps (grid-search / integration and post-processing / analysis) can be found under the "integration" folder. The grid-search results are saved to the "integration/###/image_objects" folder in the format <filename>.int. These are pickled dictionaries which contain all the information about the individual images (without the pixel values or integrated intensities), such as raw image filename, converted pickle filename, the details of the grid search, etc. These can be used for some of the advanced options, such as experimentation with the selection process without repeating the grid search.

The integrated pickles are collected under "integration/###/final" folder, in the format int_<filename>.pickle. Only successfully integrated images are saved this way. For each of the input images, however, a log of cctbx.xfel output is saved in the same folder, in the format <filename>.log. This log documents each integration attempt from the grid-search, with the final integration attempt at the end, and can be used for troubleshooting.

If the user chooses to output any charts (e.g. grid-search heatmap, beam center plot, image visualization, etc.), these will be found under "integration/###/visualization" folder.

Finally, the "integration/###" folder itself contains text files with lists of images, e.g. input images, all integrated images, all images that failed integration, major clusters from the unit cell-clustering module, etc. The main logfile (iota.log) is also found here, as is the default input file for PRIME (prime.phil).