Thanks John. Here they are . Seems like definite clipping going on. Would the increased mean in uncalibrated due to the hot pixels?
No, the higher mean in the uncalibrated sub is simply due to the fact that it still contains the bias offset. When you calibrate, the dark subtraction removes both the dark current and the offset that is contained in both the light and dark subs.
Adding an Output Pedestal in Image_Calibration will help keep the amount of clipping to a minimum. The Output Pedestal is limited in PI to a value of 1000 ADU. Jon Rista recommends using a value of at least 800 for many cameras. Sometimes, even the maximum value cannot prevent all clipping.
If there are any clipped pixels in the raw frames themselves, the use of an Output Pedestal in Image_Calibration may not be fully effective. In those cases, you just need to increase the camera's Offset higher so that data isn't starting out clipped. Check a few of your raw uncalibrated light frame subs to see if clipping is happening during acquisition. If you see more than a few clipped pixels in each frame, it is a good idea to raise the camera's Offset.
I regularly use a "Clipping_Checker" saved process icon in PI. To create one, you can do the following:
- Open PixelMath and enter the following equation
iif($T == 0, 0.999, 0.00)
Set PixelMath to create a new file (in the Destination Section of PM)
- Save the PixelMath process for later use. Call it Clipping_0_Checker or something similar.
To use the checker, just drag the saved process icon to the image frame to check. A new image is created. It will look black. Open up the Statistics Process and look at the statistics of the new frame. In this case, Uncheck the "Unclipped" option box. (I wrote that wrong before because I was thinking of my use of this Clipping_Checker. You want the Unclipped Option checked when looking for the minimum value in the frame. You want it unchecked when examining the output of the clipping check.) The total number of pixels that were clipped to black will be shown in the "Count (px)" field of the statistics.
Edited by jdupton, 30 September 2020 - 11:39 AM.