====== Calibration – Generate Cal File ======
To calibrate images in Hoku, first one needs to generate a calibration file. One does this by using ReadStack to read in all of the images within a given directory that one wants to calibrate.

{{ :advanced_level:calibration:hoku_advanced_cal_1.png?nolink&100 | }}

Typically, these will be images that contain a calibration target.  As shown below, display one of the images, then draw a window on the target.
 
{{ :advanced_level:calibration:hoku_advanced_cal_2.png?nolink&350 | }}

Enter the window into Statistics, and check the ”calibration” and “verbose” flags in Statistics.  Do not check the “calibration” flag in ReadStack.
<WRAP group>
<WRAP half column>{{ :advanced_level:calibration:hoku_advanced_cal_3.png?nolink&400|}}</WRAP>
<WRAP half column>{{:advanced_level:calibration:hoku_advanced_cal_4.png?nolink&300|}}</WRAP>
</WRAP>

Now execute the program.  It will generate a display window with the statistics and ask you if you want to write out the calibration file.  Say ”yes”.  The calibration file will be written in the same directory as the images, with the name of the directory, followed by ”.cal”.