Pathta

Description

After a long hesitation between "Pathta" and "Tapath", I decided to call this incredibly complex toolbox "Pathta" given that I made a Postdoc surrounded by Italians. "Pathta" contains the world "Path" which is relatively natural since the goal of this incredibly complex toolbox is to manage path to files belonging to different research studies. Then there's the remaining "ta". I'm still not very sure what it means but someone suggested "to architecture". As a result, "Pathta" stands for "Path to architecture", which means nothing but sounds semi-professional. This incredibly complex toolbox can also be used to avoid setting paths between different systems (e.g. local computing and distant servers, collaborations between it-aliens etc.).

In case you asked, here's the logo :

https://github.com/EtienneCmb/pathta/blob/master/docs/source/_static/PATHTA.png

Created by Etienne Combrithon, Ruggero Bathanithi

Installing Pathta

To install Pathta, clone the repository, go inside it and run :

python setup.py develop

Then wait for 10 minutes for al dente. Don't use cream.

Usage

Creation of a study

Define a new study :

from pathta import Study

# define the name of your study
stname = "MyStudy"
# define the root path where to save this study
path = "/home/thteven/research"
# create the study
st = Study(stname)
# add it
st.add(path)

Managing files of this study

Once your study is created, you can reload it :

from pathta import Study

st = Study('MyStudy')

# create a 'conn' folder
path_to_conn = st.add_folder(folder='conn')

# get the path to a folder and create it if it doesn't exist
path_to_corr = st.path_to_folder(folder='corr', force=True)

# join a file name to an existing folder
path_to_file = st.join("my_file.xlsx", folder='excel', force=True)

# search for files containing words "subject_1", "stats"
is_files = st.search("subject_1", "stats", folder='conn')

Managing configuration files and python scripts

Pathta lets you create configuration files :

from pathta import Study

st = Study('MyStudy')

# create a configuration file
cfg = {'bad_channels': [0, 1, 2], "subject_name": "Thteven"}
st.save_config("preprocessing.json", cfg)

# reload a configuration
cfg = st.load_config("preprocessing.json")

You can also load python scripts :

from pathta import Study

st = Study('MyStudy')
script = st.load_script("my_python_file.py")
script.my_function(x=1)

Measures execution time

Finally, you can measures the execution time of script relatively easily :

from pathta import Study

st = Study('MyStudy')
st.runtime()

# do a lot a complicate stuffs
x = 0
x += 1
x -= 1

st.runtime()

The results are stored in path_to_MyStudy/cache/runtime.txt

EtienneCmb/pathta