Preprocessing tool: pyFAI-average

Purpose

This tool is used to average out a set of dark current images using mean or median filter (along the image stack). One can also reject outliers be specifying a cutoff (remove cosmic rays / zingers from dark)

It can also be used to merge many images from the same sample when using a small beam and reduce the spotty-ness of Debye-Scherrer rings. In this case the “max-filter” is usually recommended.

Options:

Usage: pyFAI-average [options] -o output.edf file1.edf file2.edf …

positional arguments:

FILE Files to be processed

optional arguments:

-h, --help

show this help message and exit

-V, --version

show program’s version number and exit

-o OUTPUT, --output OUTPUT

Output/ destination of average image

-m METHOD, --method METHOD

Method used for averaging, can be ‘mean’ (default) or ‘min’, ‘max’, ‘median’, ‘sum’, ‘quantiles’ , ‘cutoff’, ‘std’. Multiple filters can be defined with ‘,’ separator.

-c CUTOFF, --cutoff CUTOFF

Take the mean of the average +/- cutoff * std_dev.

-F FORMAT, --format FORMAT

Output file/image format (by default EDF)

-d DARK, --dark DARK

Dark noise to be subtracted

-f FLAT, --flat FLAT

Flat field correction

-v, --verbose

switch to verbose/debug mode

-q QUANTILES, --quantiles QUANTILES

average out between two quantiles -q 0.20-0.90

--monitor-name MONITOR_KEY

Name of the monitor in the header of each input files. If defined the contribution of each input file is divided by the monitor. If the header does not contain or contains a wrong value, the contribution of the input file is ignored. On EDF files, values from ‘counter_pos’ can accessed by using the expected mnemonic. For example ‘counter/bmon’.

--quiet

Only error messages are printed out

It can also be used to merge many images from the same sample when using a small beam and reduce the spotty-ness of Debye-Sherrer rings. In this case the “max-filter” is usually recommended.