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SECPipe Documentations

SECPipe is an automated SEC-SAXS data real-time processing and analyzing pipeline. It requires no user intervention and creates a current sample folder inside the analysis folder with following data:
- 'sastool' folder - here is the output os sastool folder, containing individual scattering curves.
- 'average' folder - scattering data averaged in sets of 5
- 'plots' folder - plots showing Rg, I0, Iqmin and UV data during the elution. The data to re-create these graphs is also saved and can also be opened with bl42-dat program.
- <sample_name_number>.bip - this file is used by Blu-Ice to display real-time Rg, I0 and Iqmin data during the experiment.

SECPipe can be run from a command line, giving a possibility to re-analyze data after the experiment.
If run without any parameters, it will output a basic how-to:
        <path to the first sample> <num buf> <end num> <wait time [s]> [<shut cl start> <shut cl end>]
<path to the first sample> - path to the first sample for the SECSaxs experiment
<num buf> - number of images to use for buffer subtraction
<end num> - total number of images
<wait time [s]> - this is useful during real-time analysis as it sets the time to wait for a new image before exiting the pipeline. Waiting time is 120 seconds plus the command line parameter.
<shut cl start> <shut cl end> - in case the x-ray shutter was closed for the part of the experiment, that data will not be evaluated. This parameters are not required.

The pipeline is written in Python2 and uses analysis software from the ATSAS package by Dimitri Svergun’s group at Hamburg and our in-house image scaling and integration software SasTool. The software has been designed to be modular and easily adaptable, allowing the easy addition of new software tools as they arise. SECPipe is now regularly used during SEC-SAXS experiments to help users analyze their data.