TRPipe Documentation

TRPipe is program for initial data analysis and visualisation for time-resolved experiments.

Short help can be obtained by running the command with '-h' parameter:
----
trpipe.py -h
usage: trpipe.py [-h] [-m | -u] [-df PATH] [-bf PATH] [-fb N] [-nb N] [-d]
                 sample [buffer]

        If only a sample file is given, program will analyze it without a buffer/background subtraction.
       
       Sample and buffer can be specified in three different ways:
        
        1) full path to the file: trpipe.py /path/to/my/data/file.tif
        2) relative path to the file: trpipe.py ../path/data/file.tif
        3) series number of the file: trpipe.py 6 4
            sample number can also be a range: trpipe.py 10-20 4
            for case 3), data are expected to be in ../data/ folder
        
        In case 1), results will be saved in /path/to/my/data/../analysis/automatic_analysis/
        In case 2) and 3), results will be saved in ./automatic_analysis/
    
        If option -m or --mini is specified, trpipe.py will work in 'mini mode' without atsas programs.
        
        If option -u or --micro is specified, trpipe.py will work in 'micro mode' and just run sastool without creating an html table.
        --mini and --micro options are mutualy exclusive.
    

positional arguments:
  sample                sample file path or series number
  buffer                buffer file path or series number

optional arguments:
  -h, --help            show this help message and exit
  -m, --mini            no atsas
  -u, --micro           just run sastool, don't create an html table
  -df PATH, --data_folder PATH
                        path to the data folder, used only when sample is
                        specified by series number
  -bf PATH, --buffer_folder PATH
                        path to the buffer folder if different than
                        sample/data folder, used only when sample is specified
                        by series number
  -fb N, --first_bin N  first sample for binning, default=1
  -nb N, --num_bin N    number of samples to bin, default=10
  -d, --debug           print debugging info
---------------

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.
TRPipe saves data in 'automatic_analysis' subfolder, where it creates a new folder for each sample, 'tot_files' folder which contains one averaged data file for each analyzed sample, and tr_results.html file with sample summary table.
Inside each sample subfolder is a 'sastool' folder containg all individual integrated data, and 'bin' folder where binned data are saved.

TRPipe html table output overview:

The output has the following parts:
1) Initial data collecrion information - this section includes on the data collection such as the time it was taken, the sample filename, the results of the scaling and integration of the images by sastool, and an Rg analysis.
2) Image graphs:

• a. The variance of the scaled and integrated images from the buffer and sample data collections, for rapid indentification of sample changing range
• b. A comparison of the averaged buffer and sample scattering (tot files), which allows the user to quickly see how strong the sample scatters
• c. Low q comparison of the subtracted sample scattering profiles for each image, again allowing the user to identify sample change over time
• d. A graph of the change in Rg over the image series

3) Graph of all binned data, with increased signal-to-noise ratio in respect to the individual data files, but with the lower time resolution.