Starting a new experiment

Last modified by sjhuotar@helsinki_fi on 2024/02/07 06:21

  1. Scotch tape a blank experiment title page to the log book. Use the left page (even page numbers). Leave a blank right page (an odd page number) on the opening before if necessary.

  2. Check the number of the last experiment, increase it by 1, and attach either your name or the name of the main collaborator to it with an underscore e.g. 1231_Doe. This is your experiment ID. Write it and other relevant info down on the title page.

  3. Open a Linux terminal

  4. Make a new data directory in a Linux shell with the command ‘mkdir /home/xasadmin/experiments/YOUR_EXP_ID’ from the Linux terminal (alternatively, if you are in the spec6 prompt, with the command ‘u mkdir /home/xasadmin/experiments/YOUR_EXP_ID’). If this fails, you have a typo in the path name.

  5. In spec6 prompt, type 'cd /home/xasadmin/experiments/YOUR_EXP_ID'
  6. Type in spec the command 'newsample'. When prompted, new file is '/home/xasadmin/data/YOUR_EXP_ID/YOUR_EXP_ID' and the last scan number 0.
  7. If you are changing also the monochromator, type in spec the command 'setmono', and type '0' to enter crystal type, and then type as prompted Si or Ge, and Miller indices h (enter) k (enter) l (enter). Follow the instructions on "how to change the monochromator".


If you are using the Amptek X-123 SDD or CdTe, follow the following instructions:

  • Setting up the MCA
    • Create a directory for MCA spectra by typing in spec 'u mkdir mca'
    • Type in spec the command 'mcasetup'
      • First question is: Acquire MCA spectrum after each ct? Answer 'y' or press enter if it YES already suggested as a default
      • Second question is: Save MCA spectra in files? Answer 'y'
        • If you answered 'y', the third question will be: MCA directory? Enter the full directory for the mca files, e.g., '/home/xasadmin/experiments/YOUR_EXP_ID/mca'
        • Fourth question is: Next MCA file number? Answer '0'
    • Open the shutter.
    • Type in spec the command 'ct'
    • If you are lucky, you will have some photons on the detector. If so, you should see the counter 'Raw in counts' having a high number (thousands or so)
    • Type 'mcaplot' and observe what is plotted on the spec6 plot
    • Depending on the reflection of the monochromator and if the detector is roughly aligned not, you may see one or several peaks in the MCA spectrum. If you see nothing, seek help. If you see one sharp peak in the MCA spectrum, that is most likely the reflection from the monochromator and you can set its position to the mca counter channels.
    • Open the mca file mca/mca_0000 with PyMCA and find the correct peak corresponding to your reflection, choose a region in channels which contains the full MCA peak and does not cut it but does not include other peaks either. For example, if the peak is centered at channel 900, you could choose the values 700 and 1100.
    • Write those channel numbers down somewhere (the logbook experiment cover page would be a good place)
    • Type in spec the command 'mcaroisetup' and when asked for ROI1 start, enter the lower channel and when asked for ROI1 end, enter the higher channel of your choice.
    • TODO FOR SIMO: RESOLVE WHY THE ROIS ARE NOT SAVED
    • Now the relevant counter to plot would be 'roi1'. Congratulations! You can check that it works by entering 'ct' as a command to spec prompt and checking that it contains counts.
    • Select which detector you wish to use for counting by typing "counters" and selecting "det" or "roi1" or the relevant detector as the detector. The monitor can be "sec"