First we should mention that this calibration step is the only one which has to be done on a regular basis (several times per day, ideally). It can be done most easily by clicking the "Calibrate Now" button in SM_GUI (or by calling the appropriate command in sm_script), but if you are doing the full calibration in IDL, you should do this step in IDL as well to make sure you get the calibration parameters into detcal_gui. Also, the detailed noise analysis as described in the next section can only be done here.
The calibration constants (u0_mvolts) and (c_idark_mvolts_per_ms) are obtained by applying a linear fit to detector output voltage versus pixel dwell time from a number of dark scans, as mentioned above. It is absolutely crucial that these scans were recorded with the x-ray shutter closed and the microscope chamber shielded from visible light (the latter has to be the case all the time if you want to obtain meaningful data).
Click the "Dark Current Correction" button. A window will pop up in which you have to select all dark scan files. In Microsoft Windows, you can select consecutive files by holding the "Shift" button while selecting, or you can choose separate files by holding the "Ctrl" button.
As soon as you select the files (and if there is no error), the linear fit will be applied. IDL will write a postscript file into the current working directory with "dark_current.ps" appended to the file name of the last dark scan file. Look at the IDL output log to see where the file was written. Take a look at the file and make sure all fits look nice.