Esteban, I can not help you much with mencoder or GStreamer, but I did not understand - what exactly does your program need? Just to make sure you are not streaming the video and them extract individual images from the stream.
Image server (imgsrv) that listens on camera port 8081 (i.e. http:/// 192.168.0.9:8081) is optimized for providing individual images to be processed on the host computer. In the case you need exact measurements I would recommend using jp46 format - and the program similar to the one we provide as plugin to ImageJ program ( http://elphel.git.sourceforge.net/git/gitweb.cgi?p=elphel/ImageJ-Elphel;a=blob;f=JP46_Reader_camera.java) - it can process either recorded images or get them directly from the camera. The code processes image Exif headers and extracts information about the gamma-correction, gains and orientation of the image, then un-applies it to the data providing floating-point pixel values. It is written in Java, you may either incorporate it into you program or just use the algorithms to implement in your code. Andrey
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