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Let’s start by reviewing some basic coding principles that might help you get familiar with NeuroKit
If you are reading this, it could be because you don’t feel comfortable enough with Python and NeuroKit (yet), and you impatiently want to get to know it in order to start looking at your data.
“Tous les chemins mènent à Rome” (all roads lead to Rome)
Let me start by saying that there are multiple ways you’ll be able to access the documentation in order to get to know different functions, follow examples and other tutorials. So keep in mind that you will eventually find your own workflow, and that these tricks are shared simply to help you get to know your options.
You probably already saw the README file that shows up on NeuroKit’s Github home page (right after the list of directories). It contains a brief overview of the project, some examples and figures. But, most importantly, there are the links that will take you to the Documentation.
Documentation basically means code explanations, references and examples.
In the Documentation section of the README, you’ll find links to the readthedocs website like this one :
Did you know that you can access the documentation website using the
rtfd domain name
https://neurokit2.rtfd.io/, which stands for READ THE F**** DOCS 😏
And a link to the API (or Application Program Interface, containing the list of functions) like this one:
All the info you will see on that webpage is rendered directly from the code, meaning that the website reads the code and generates a HTML page from it. That’s why it’s important to structure your code in a standard manner (You can learn how to contribute here).
The API is organized by types of signals. You’ll find that each function has a description, and that most of them refer to peer-reviewed papers or other GitHub repositories. Also, for each function, parameters are described in order. Some of them will take many different options and all of them should be described as well.
If the options are not explained, they should be.
It’s not your fault you don’t understand. That’s why we need you to contribute.
In the ECG section, the ecg_findpeaks function takes 4 parameters. One of them is method: each method refers to a peer-reviewed paper that published a peak detection algorithm. You can also see what the function returns and what type of data has been returned (integers and floating point numbers, strings, etc). Additionally, you can find related functions in the See also part. An small example of the function should also be found. You can copy paste it in your Python kernel, or in a Jupyter Notebook, to see what it does.
2. The code on Github¶
Now that you’re familiar with readthedocs website, let’s go back to the repo. What you have to keep in mind is that everything you saw in the previous section is in the Github repository. The website pages, the lines that you are currently reading, are stored in the repository, which is then automatically uploaded to the website. Everything is cross-referenced, everything relates to the core which can be found in the repo. If you got here, you probably already know that a repository is like a tree containing different branches or directories that eventually lead you to a script, in which you can find a function.
Ready for inception ? let’s find the location of the file you’re currently reading. Go under
docs and find it by yourself… it should be straight-forward.
As you can see, there are several sections (see the Table of Content on the left), and we are in the tutorials section. So you might want to look into the tutorials folder :)
See! It’s super handy because you can visit the scripts without downloading it. Github also renders Jupyter Notebook quite well, so you can not only see the script, but also figures and markdown sections where the coder discusses results.
3. The code on YOUR machine¶
Now, you’re probably telling yourself :
If I want to use these functions, they should be somewhere on my computer!
For that, I encourage you to visit the installation page if you didn’t already. Once Python is installed, its default pathway should be :
(if the directory doesn’t match, just search for the folder name
Or, if you’re using WinPython it should be in the folder of its installation (e.g.,
Linux users should know that already
Environment and NeuroKit directory¶
NeuroKit, along with all the other packages, are located in the python directory in the
site-package folder (itself in the
Lib folder). It should be located under the environment where you installed it (if you didn’t do it already, set a computing environment. Otherwise, you can run into problems when running your code). The directory should look like this:
Or, if you’re using WinPython:
Take the ECG again :
From the specified directory, I can note that the different folders are arranged in the same way as in the readthedocs website.
Let’s say I want to go back to the same function ecg_findpeaks(): I’d click on
ecg folder, and from there I can see the source code for the function under ; ecg_findpeaks.py.