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'''
Non-parametric computation of entropy and mutual-information

Adapted by G Varoquaux for code created by R Brette, itself
from several papers (see in the code).

These computations rely on nearest-neighbor statistics
'''
import numpy as np

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library(psych)

"
Analyze the difference between change and initial value. 

Source:
Tu, Y. K. (2016). Testing the relation between percentage change 
and baseline value. Scientific reports, 6.
"

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import numpy as np

n_stim                = 3
n_responses           = 2
trial_size            = 10
n_trials_per_stimtype = 50
n_neurons             = 84
single_trial_data = np.zeros([n_trials_per_stimtype, n_neurons, n_stim, n_responses, trial_size])
single_trial_data.fill(np.NaN)

pietromarchesi

import numpy as np

n_stim                = 3
n_responses           = 2
trial_size            = 10
n_trials_per_stimtype = 50
n_neurons             = 4
single_trial_data = np.zeros([n_trials_per_stimtype, n_neurons, n_stim, n_responses, trial_size])
single_trial_data.fill(np.NaN)

pietromarchesi

Setting up a Python environment on JULIA with virtualenvwrapper

I find the system Python I want to use by doing

$ module avail python

Then we can load Python 3.6 with

$ module load python/3.6.1

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Python environments on the JULIA system

There are different tools for managing virtual Python environments (see this answer on Stack Overflow for an overview). Here we give some instructions on how to get started using virtual environments on the JULIA system using venv (Python 3 support only) and virtualenvwrapper (an extension of the popular virtualenv, which can be used with both Python 2 and 3).

Recommended: managing environments using venv (Python 3 only)

venv is a package automatically shipped with Python 3. This method is quite straightforward, but it does not support Python 2 (for that, you can look at the second method using virtualenvwrapper which works for both Python 2 and 3).

To begin, we find the Python installation that we want to use by doing

$ module avail python

pietromarchesi

Python environments on the JULIA system

There are different tools for managing virtual Python environments (see this answer on Stack Overflow for an overview). Here we give some instructions on how to get started using virtual environments on the JULIA system using venv (Python 3 support only) and virtualenvwrapper (an extension of the popular virtualenv, which can be used with both Python 2 and 3).

Recommended: managing environments using venv (Python 3 only)

venv is a package automatically shipped with Python 3. This method is quite straightforward, but it does not support Python 2 (for that, you can look at the second method using virtualenvwrapper which works for both Python 2 and 3).

To begin, we find the Python installation that we want to use by doing

$ module avail python

pietromarchesi

import os
import luigi
import sciluigi

class MyWorkflow(sciluigi.WorkflowTask):
    runmode = luigi.Parameter()

    def workflow(self):

        if self.runmode == 'local':