Adapt_outputs.wiki

NeuroGPS' outputs saved in the treshold folder present some compatibility problems with the ground truth that have to be solved:

1. NeuroGPS' outputs are in .swc format. We need marker format to procede with testing.
2. NeuroGPS' outputs use a different reference system different from the one used in the GT. The reference systems must be the same to obtain consistent result from testing procedures.

To solve these problems we have to use the globe_marker_script.py and rename_files_script.py situated in the scripts folder. This script modified the output obtained from NeuroGPS in a GT-compatible marker file with the GT's reference system; so, the file obtained thanks to the globe_marker_script.py and rename_files_script.py is comparable with the corresponding GT's stack.

NB: In this repository, the files in treshold folder have already been processed and adapted, and are ready to be tested. For completness, in the following it's described how these files have been obtained:

1. generate all the substantial outputs for that stacks with NeuroGPS;
2. save these outputs with a name that starts with x, in a dedicated folder, specifying treshold and min radius used to obtain that output. For example, if I have a stack named x000938.tiff and I want to use NeuroGPS to find neurons in this stack with treshold = 6 and min. radius = 2, I'll save the output (specifying the route in the batch options of NeuroGPS) like this: treshold/treshold6/T6_R2/x000938.swc.
3. Run the globe_marker_script.py and rename_files_script.py, to create the markers for the tests.
4. The definitive marker files obtained with this process has a name like this: x000938_T6_R2.marker.

Note that the name of the outputs it's foundamental in the perspective of the tests.