create image with atlas

[rmarabini]

The first step in automatic data collection in cryoEM is to image the entire grid and ascertain the location and quality of potential squares available for data collection. Many automation software packages (EM-TOOLS, EPU, JADAS, Leginon, SerialEM, TOM2) provide the option of automatically collecting such a map of the entire grid, often referred to as an atlas. With an atlas for reference, suitable squares for imaging are selected.

I attach a script that uses as input a mdoc file (and the corresponding mrc stack) and creates a large image (one per grid square) showing the atlas. I just release this script with the idea that some people may find in useful. I also attach the mdoc dile used as input

mdoc.py.txt
composite.py.txt
hex.mrc.mdoc.txt