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Psocake should have generated directories and files in the experiment directory. At LCLS, all experiments are stored here: /reg/d/psdm/<instrument>/<experiment>. Let's go and see take a moment and check out our directory structure. Either open a new terminal (Remember to 'ssh psana') or use the current terminal ('Cntrl+z' to suspend psocake that is running then 'bg' to run psocake in the background), type the following command:

$ ls /reg/d/psdm/cxi/cxitut13calibcxitut13
calib  ftc  hdf5  res  scratch  usr  xtcxtc

calib: This is where all psana calibration is stored. Detector geometry, pedestals, gain, common mode constants, and bad pixelmap.

xtc: This is where all your raw data is stored. XTC is a simple and efficient format for storing large data. XTCs can be read using psana. Note you have 4 months to analyse your data before xtcs are moved off to tape.

scratch: This is where psocake saves all the files like .cxi and .stream. This directory is not backed up, so important files need to be move to /res.

res: This is the results directory which is backed up on tape. After completing your analysis, your results/data should be moved here.Open a new terminal (Remember to 'ssh psana') or escapeCntrl+z 

Mask making

In this examplesection, let's learn how to mask out pixels that should not be used for analysis (such as dead pixels), mask out the jet streak at the centre of the detector, and mask out the water ring (just for fun!).

Note: the Image Panel must be in the default "greyscale" colormap for the mask colors to display properly.

1) In the mask panel, click on "Use psana mask". This will mask out the following pixels that should not be used for analysis; calib, status, edge, central, unbonded pixels, unbonded pixel neighbor pixels. These masked pixels are shown as green on the image panel.

2) On the mask panel, click on "Use streak mask". This will mask out strong intensities originating from the edges of the central asics. The streak mask varies shot-to-shot.

3) To make a donut mask over the water ring, click on "Use user-defined mask". This will bring up a cyan circle and , cyan polygon and cyan square mask generatorgenerators.

Select "Toggle" in Masking mode. Move the cyan circle to the centre of the detector by dragging the circle. Resize the cyan circle by dragging the diamond on the perimeter. Once you are happy with the position, click "mask circular ROI" button on the mask panel.

Increase the cyan circle again by dragging the diamond on the perimeter. Click "mask circular ROI" button on the mask panel. Because we are in the "toggle" mode, the previous mask gets toggled and disappears. The area that does not overlap with the previous mask get masked out.

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