SAXSPipe: Getting Started
To run SAXSPipe from Blu-Ice after scattering images of one solution sample are collected, the user simply check the box "Use SAXSPipe" on the SolSAXS tab before the user starts the data collection.
Additionally, SAXSPipe 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:
saxspipe2.py <sample> [buffer]
If only a sample file is given, program will search for the most recent buffer file and, if found, use it for analysis. To analyze the sample without the buffer subtraction input '0' as the buffer.
If only a sample is given and the file has buffer designation (Bxxx in the filename), it will be buffer subtracted only if the found buffer file has the same sample name as the sample file. This is for the case of buffers taken during one concentration series. If the previous buffer has different name, there will be no buffer subtraction. In case that both sample and buffer are given on the command line this test is skipped.
Sample and buffer can be specified in three different ways:
1) full path to the file: saxspipe2.py /path/to/my/data/file.tif
2) relative path to the file: saxspipe2.py ../path/data/file.tif
3) series number of the file: saxspipe2.py 6
for case 3), data are expected to be in ../data/ folder
In case 1), results will be saved in /path/to/my/analysis/automatic_analysis/
In case 2) and 3), results will be saved in ./automatic_analysis/