Tips and Tricks
Here is a collection of tips and tricks for using xpdtools.
Weak Scattering and Air Scattering
Weak scattering data benefits from image to image background subtraction.
Often for weak scattering materials the air scattering of the beamline becomes
non trivial.
At this point we need to remove the air scattering (although minimizing it on
the experimental side is preferable).
After the experiment is done one way to remove air scattering (and its shadows)
is to perform background subtraction on the images.
Since the air scattering is non azimuthally symmetric simple integration and
subtraction of the integrated background will not work, as the integration
has removed any azimuthal information from the data.
xpdtools
provides a flag, --bg_file
, to have a background image
subtracted from the foreground image.
The effect of this can be seen in the standard deviation and the z score.
Median vs. Mean masking
The automasking code has a few flags to modify its behavior, one of the most
important is --auto_type
.
This flag governs which algorithm is used to create the statistical mask.
The default is median
which does a single pass for each azimuthal ring
and finds outliers.
The flag can also be set to mean
which computes the mean for each ring
and removes a single pixel repeatidely until the all the outliers with
a z score greater than alpha
have been removed.
The mean
method is much slower, but is generally more accurate.