Hot pixels and intermodulus ones are automatically masked out by pilatus giving them the value of -2. Usually we create manually a mask (at beginning of a run) to take away other 'invalid' pixels, mainly thouse shadowed or perturbed by the beamstop in the beam. However, it can be use for any kind of unwanted features (as a crazy pixel or mysterious cloud suddenly appering in a part of detector area) which can appear any time for various reason. How to proceed to create a new mask:

  • take a 2D image (for example test) and look on it in 2D tab of BsxCuBE;
  • click on monkey icon: dialogue open, choice polygone (better for irregular shape of beamstop) or rectangle (andvantage of it is the possibility to drug it outside detector area to prevent any pixel from the border to be skipped) tool;
  • delimit manualy beamstop shadow on 2D image (draw polygone) and save (in bm29/archive/CALIBRATIONS/Mask/BM29/Originals/raw_DAY_MONTH_YEAR_msk.edf) once happy (you can add/remote variouse bits = polygones, rectangles = until good);
  • open an X-term window and go to the directory where you have saved it;
  • write "mask_conversion raw_test_ msk.edf Pcon_test_msk.edf" this will convert the file from Oxidis logics to a format which data processing will recognise as a mask (-1);
  • in BsxCuBE "Beamline parameters" change the mask file to the new one (you should be in expert mode);
  • redo a Collect and check if better (on 1D curves) if not, excercise with monkey again.