Meeting 09 12 2018

During Meeting

Looked at: https://github.com/ActiveBrainAtlas/MouseBrainAtlas_dev/blob/master/doc/running_scripts/DemoComplete.md

Our goal is to extract the structure of the file names and directories. We do this through the following steps:

1. define environmental variables that point to the specific dir/files currently processed. (these will be put into a configuration files).
2. define a schema which describes the breakdown of the file names.
3. define regular expressions for parsing the file names.

The cleaned documentation will have several separate files:

1. definitions 1,2,3 above.
2. A page that describes the steps: feature detection, registration, visualization, building atlas that are to be executed assuming the env. variables are set correctly. Based on yuncong's description with the following changes:

• No explicit filenames of directories - all based on env variables.
• include the argparse help (-h) before the call to the script.

3. A page for describing pre-processing.