Preparatory steps pyana version

The CS-PAD detector at LCLS is sensitive to temperature distortions and is not automatically dark-subtracted, like images from a synchrotron source. Because of this it is necessary to periodically collect a dark run with the shutters closed during an LCLS experiment. The dark run should contain on the order of X images. Before an experimental run can be processed, this dark must be averaged, so that subsequent experimental data can have it subtracted. Further, events during collection can necessitate a new dark, such as ice in the beam oversaturating creating dead pixels.

In addition, inactive and non-bonded pixels, as well as hypersensitive pixels and any beam stop (if used) should be masked out.

Finally, averaging a light run in general is a useful tool for examining diffraction throughout a data collection run. This tutorial covers averaging, dark subtraction and masking.