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’
-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

$ pyFAI-average --help
usage: pyFAI-average [options] [options] -o output.edf file1.edf file2.edf ...

This tool can be 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)

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.