alphacsc 0.4.0

Installation

To install this package, the easiest way is using pip. It will install this package and its dependencies. The setup.py depends on numpy and cython for the installation so it is advised to install them beforehand. To install this package, please run one of the two commands:

(Latest stable version)

pip install alphacsc

(Development version)

pip install git+https://github.com/alphacsc/alphacsc.git#egg=alphacsc

(Dicodile backend)

pip install numpy cython
pip install alphacsc[dicodile]

To use dicodile backend, do not forget to set MPI_HOSTFILE environment variable.

If you do not have admin privileges on the computer, use the --user flag with pip. To upgrade, use the --upgrade flag provided by pip.

To check if everything worked fine, you can run:

python -c 'import alphacsc'

and it should not give any error messages.

Quickstart

Here is an example to present briefly the API:

import numpy as np
import matplotlib.pyplot as plt
from alphacsc import BatchCDL

# Define the different dimensions of the problem
n_atoms = 10
n_times_atom = 50
n_channels = 5
n_trials = 10
n_times = 1000

# Generate a random set of signals
X = np.random.randn(n_trials, n_channels, n_times)

# Learn a dictionary with batch algorithm and rank1 constraints.
cdl = BatchCDL(n_atoms, n_times_atom, rank1=True)
cdl.fit(X)

# Display the learned atoms
fig, axes = plt.subplots(n_atoms, 2, num="Dictionary")
for k in range(n_atoms):
    axes[k, 0].plot(cdl.u_hat_[k])
    axes[k, 1].plot(cdl.v_hat_[k])

axes[0, 0].set_title("Spatial map")
axes[0, 1].set_title("Temporal map")
for ax in axes.ravel():
    ax.set_xticklabels([])
    ax.set_yticklabels([])

plt.show()

Dicodile backend

AlphaCSC can use a dicodile-based backend to perform sparse encoding in parallel.

To install dicodile, run pip install alphacsc[dicodile].

Bug reports

Use the github issue tracker to report bugs.

Cite our work

If you use this code in your project, please consider citing our work: