template_python.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
#======================================================================
#             TITLE OF THE SCRIPT (should be representative)
#======================================================================

#@previous author: (in case of one)
#@author: name + surname(s)
#@email:  email
#updated: DD MM YYY (e.g. 28 Feb 2023) 
#status: still being developed/done 
#to-do: (optional, for keep track what needs to be improved)

#Review History
#Reviewed by Name Date (e.g. name + surname(s) DD MM YYYY)

# Description:
# - Short description of what is your code about 
#
# - Run: previous scripts that need to run these one (in case of one)
# - Input: files that are necessary to run the script
# - Output: files obtained after running the script
#-----------------------------------------------------------------------
"""

## Libraries needed, specify reason why so no extra libraries are load
import os            			    #e.g for ...
import numpy as np                 	#e.g for ... 
import nibabel as nib               #e.g for ... 
import pandas as pd               	#e.g for ... 

## Functions, please try to generalise as much as possible them 
## for not overwritting files, ... 

def create_figure(workdir, fig): 
    """ 
    Brief description of the function, input variables and output variables
    """
    return 
 
## Load data
inputdir= 

#%% (#%%) can be used for creating cells as in jupiter notebooks

#----------------------------------------------------------------------
#            SUBTITLES  (in case your code needs subdivisions)
#----------------------------------------------------------------------

# Important! Please remove any patient/subject identifier from the code.
# Please use English i.e replace comments/variables in Dutch or other languages

## If there's a clear structure use subtitles but not always are needed
## Also depending on the hierarchy of the comments use # or ## 
## Try all variable has logic names or then add comments as in the libraries
 

#----------------------------------------------------------------------
#                       References, links, others, ...   
#----------------------------------------------------------------------

# Here add links that maybe are useful or references that have to be cited 

## e.g. https://stackoverflow.com/ 
## "If you use the new robust version of SynthSeg in a publication, please cite:
## Robust Segmentation of Brain MRI in the Wild with Hierarchical CNNs and no Retraining
## B. Billot, M. Collin, S.E. Arnold, S. Das, J.E. Iglesias"