Quick Start

Start analyzing data

You may test if everything is working by telling NEMS to download some sample auditory stimulus-response data, use a simple linear-nonlinear model (which should taking about 2 minutes to fit), and then save the results locally:

python demo_script.py

Or open demo_script.py in an editor to work through each step of the fit.

I just want to analyze data! Where should I put my script?

If you are just hacking around, please put your code in the scripts directory – it’s for any one-off analysis or snippet of code that isn’t yet ready for reuse by other people. We recommend using scripts/demo_script.py as a guide for the types of operations that you may find useful.

There is an xforms system for batching and saving analyses in a way that you can reload later; this was what we used in the scripts/fit_model.py command. We also have a good tutorial/template at scripts/demo_script.py. We recommend beginners make a copy of it and edit it as needed. You can run it with:

python scripts/demo_script.py

Where should I put my data? Where should I save my results?

Input Data

If your data is in Recording format, put it in the recordings directory. If it is not yet in recording form, you may want to make a conversion script in scripts that is able convert your data from your custom format into Signals and Recordings.

Below is some pseudocode for a script that converts your data from a custom format and then saves it as a Signal to make it easier for other people to use.

from nems.signal import Signal

numpy_array = load_my_custom_data_format(...)
sig = Signal(data=numpy_array,
             name='mysignal',
             recording='some-string',
             fs=200  # Hz
             )
sig.save('recordings/my-new-recording/my-new-signal')

Output Results

Once you have fit a model to a recording, you can save the resulting files either locally in your NEMS/results directory, or to a remote database server.