Converting Labbook AUT files to plaintext


I've already mentioned on my website that the control software for the JEOL 5800-LV scanning electron microscope I'm using for my senior thesis is frustrating: it uses its own binary file formats and doesn't provide options to convert files to more common file formats. Labbook stores locations for automated analysis in AUT files, a binary file format. In this page I'll describe AUT files and provide a Python script I've written to extract point titles and X, Y, Z coordinates from an AUT file and output them in a tab-delimited text file.

Labbook stores AUT files in C:\ISISData\USERS1\AC#\J#, where AC# and J# correspond to the analytical configuration and job number (see http://wvaughan.org/im_-to-tiff.html for more information). AUT files have a 128 byte header containing the title of the AUT file and then repeating 212 byte blocks with information about each automated analysis point. These 212 byte blocks record the title of the point; the point's X, Y, Z coordinates; the stage's rotation and tilt; the accelerating voltage, magnification, and working distance; and the beam's X and Y coordinates. Since most of these values will remain constant over an automated analysis, I only extract point titles and X, Y, Z coordinates from the AUT file. Read the script below for the details.

aut_to_plaintext.py (packed in a zip file)

To use this script, run python aut_to_plaintext.py aut-file-path plaintext-file-path from the command line.


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Will Vaughan. Last revision April 8, 2011.