Mainen & Sejnowski, 1995

Laurent Perrinet

2019-05-28 10:06

In this notebook, we will go from the learning numpy and matplotlib to our first neural simulator. As a case study, we will use the work from Mainen & Sejnowski (1995). The rest of this post is in french.

Le but ici de cette première tache est de créer un "raster plot" qui montre la reproducibilité d'un train de spike avec des répétitions du même stimulus. E, particulier, nous allons essayer de répliquer la figure 1 de Mainen & Sejnowski (1995). Travail fait en collaboration avec les étudiants du L3 Sciences et Humanités Vision Lumière Couleurs d'AMU (Benjamin Chassagne, Romane Renou, Hassina Bendrer, Giulia Danielou)

Ce notebook a été élaboré lors d'un TP dans le cadre de la licence Sciences & Humanités.

Generating textures with different complexities

Laurent Perrinet

2019-01-30 10:06

Comments

This video shows different MotionClouds with different complexities, from a crystal-like Grating to textures with an incresing span of spatial frequencies (resp "Mc Narrow" and "MC Broad"). This is to illustrate the different stimuli used in this paper on the chracterization of speed-selectivity in the retina available @ https://www.nature.com/articles/s41598-018-36861-8 .

Origins of the Von Mises distribution

Laurent Perrinet

2018-12-23 20:31

Comments

The goal here is to check if the Von Mises distribution is the a priori choice to make when handling polar coordinates.

Feature vs global motion

Laurent Perrinet

2018-11-29 11:43

Comments

As we see a visual scene, there is contribution of the motion of each of the objects that constitute the visual scene into detecting its global motion. In particular, it is debatable to know which weight individual features, such as small objects in the foreground, have into this computation compared to a dense texture-like stimulus, as that of the background for instance.

Here, we design a a stimulus where we control independently these two aspects of motions to titrate their relative contribution to the detection of motion.

Can you spot the motion ? Is it more going to the upper left or to the upper right?

(For a more controlled test, imagine you fixate on the center of the movie.)

Using regex to filter an ISO8601 date

Laurent Perrinet

2018-11-14 09:36

Comments

It can be useful to find a pattern such an ISO8601-formatted date in a set of files. I discovered it is possible to do that in the atom editor:

../files/2018-11-14-regex-an-iso8601-date.png

Embedding a trajectory in noise

Laurent Perrinet

2018-11-13 11:43

Comments

MotionClouds may be considered as a control stimulus - it seems more interesting to consider more complex trajectories. Following a previous post, we design a trajectory embedded in noise.

Can you spot the motion ? from left to right or reversed ?

(For a more controlled test, imagine you fixate on the top left corner of each movie.)

(Upper row is coherent, lower row uncoherent / Left is -> Right column is <-)

Rainbow effect

Laurent Perrinet

2018-11-11 13:08

Comments

When I see a rainbow, I perceive the luminance inside the arc to be brighter than outside the arc. Is this effect percpetual (inside our head) or physical (inside each droplet in the sky). So, this is a simple notebook to show off how to synthesize the image of a rainbow on a realistic sky. TL;DR: there must be a physical reason for it.

Outline: The rainbow is a set of colors over a gradient of hues, masked for certain ones. The sky will be a gradient over blueish colors.

Statistics of the natural input to a ring model

Laurent Perrinet

2018-11-05 15:41

Comments

What does the input to a population of neurons in the primary visual cortex look like? In this post, we will try to have a feeling of the structure and statistics of the natural input to such a "ring" model.

This notebook explores this question using a retina-like temporal filtering and oriented Gabor-like filters. It produces this polar plot of the instantaneous energy in the different orientations for a natural movie :

One observes different striking features in the structure of this input to populations of V1 neurons:

input is sparse: often, a few orientations dominate - the shape of these components (bandwidth) seem to be similar,
there are many "switches": at some moments, the representations flips to another. This is due to cuts in the movie (changes from one scene to the other for instance). In a more realistic setting where we would add eye movements, these switches should also happen during saccades (but is there any knowledge of the occurence of the switch by the visual system?),
between switches, there is some coherence in amplitude (a component will slowly change its energy) but also in time (a component is more likely to have a ghradually changing oriantation, for instance when the scene rotates).

This structure is specific to the structure of natural images and to the way they transform (translations, rotations, zooms due to the motion and deformation of visual objects). This is certainly incorporated as a "prior" information in the structure of the visual cortex. As to know how and where this is implemented is an open scientific question.

This is joint work with Hugo Ladret.

extending datasets in pyTorch

Laurent Perrinet

2018-09-07 12:27

Comments

PyTorch is a great library for machine learning. You can in a few lines of codes retrieve a dataset, define your model, add a cost function and then train your model. It's quite magic to copy and paste code from the internet and get the LeNet network working in a few seconds to achieve more than 98% accuracy.

However, it can be tedious sometimes to extend existing objects and here, I will manipulate some ways to define the right dataset for your application. In particular I will modify the call to a standard dataset (MNIST) to place the characters at random places in a large image.

generating an unique seed for a given filename

Laurent Perrinet

2018-06-13 13:02

Comments

When creating large simulations, you may sometimes create unique identifiers for each of it. This is useful to cache intermediate results for instance. This is the main function of hashes. We will here create a simple one-liner function to generate one.

Testing more complex trajectories

Laurent Perrinet

2018-01-16 11:43

Comments

MotionClouds may be considered as a control stimulus - it seems more interesting to consider more complex trajectories.

predictive-coding of variable motion

Laurent Perrinet

2017-12-21 07:58

Comments

In some recent modeling work:

Laurent Perrinet, Guillaume S. Masson. Motion-based prediction is sufficient to solve the aperture problem. Neural Computation, 24(10):2726--50, 2012 https://laurentperrinet.github.io/publication/perrinet-12-pred

we study the role of transport in modifying our perception of motion. Here, we test what happens when we change the amount of noise in the stimulus.

In this script the predictive coding is done using the MotionParticles package and for a http://motionclouds.invibe.net/ within a disk aperture.

accessing the data from a pupil recording

Laurent Perrinet

2017-12-13 13:22

Comments

I am experimenting with the pupil eyetracker and could set it up (almost) smoothly on a macOS. There is an excellent documentation, and my first goal was to just record raw data and extract eye position.

In [1]:

from IPython.display import HTML
HTML('<center><video controls autoplay loop src="https://laurentperrinet.github.io/sciblog/files/2017-12-13_pupil%20test_480.mp4" width=61.8%/></center>')

Out[1]:

This video shows the world view (cranio-centric, from a head-mounted camera fixed on the frame) with overlaid the position of the (right) eye while I am configuring a text box. You see the eye fixating on the screen then jumping somewhere else on the screen (saccades) or on the keyboard / hands. Note that the screen itself shows the world view, such that this generates an self-reccurrent pattern.

For this, I could use the capture script and I will demonstrate here how to extract the raw data in a few lines of python code.

MEUL with a non-parametric homeostasis

Laurent Perrinet

2017-11-07 16:13

Comments

In this notebook, we will study how homeostasis (cooperation) may be an essential ingredient to this algorithm working on a winner-take-all basis (competition). This extension has been published as Perrinet, Neural Computation (2010) (see https://laurentperrinet.github.io/publication/perrinet-10-shl ). Compared to other posts, such as this previous post, we improve the code to not depend on any parameter (namely the Cparameter of the rescaling function). For that, we will use a non-parametric approach based on the use of cumulative histograms.

This is joint work with Victor Boutin and Angelo Francisioni. See also the other posts on unsupervised learning.

Designing a A0 poster using matplotlib

Laurent Perrinet

2017-10-25 14:05

Comments

Poster GDR Vision¶

This poster was presented in Lille at a vision workshop, check out https://laurentperrinet.github.io/publication/perrinet-17-gdr

Apart the content (which is in French) which recaps some previous work inbetween art and science, this post demonstrates how to generate a A0 poster programmatically. In particular, we will use matplotlib and some quickly forged functions to ease up the formatting.

Improving calls to the LogGabor library

Laurent Perrinet

2017-10-06 11:04

Comments

To code image as edges, for instance in the SparseEdges sparse coding scheme, we use a model of edges in images. A good model for these edges are bidimensional Log Gabor filter. This is implemented for instance in the LogGabor library. The library was designed to be precise, but not particularly for efficiency. In order to improve its speed, we demonstrate here the use of a cache to avoid redundant computations.

The fastest 2D convolution in the world

Laurent Perrinet

2017-09-20 11:13

Comments

Convolutions are essential components of any neural networks, image processing, computer vision ... but these are also a bottleneck in terms of computations... I will here benchmark different solutions using numpy, scipy or pytorch. This is work-in-progress, so that any suggestion is welcome, for instance on StackExchange or in the comments below this post.

Le jeu de l'urne

Laurent Perrinet

2017-06-15 16:42

Comments

Lors de la visite au laboratoire d'une brillante élève de seconde (salut Lena!), nous avons inventé ensemble un jeu: le jeu de l'urne. Le principe est simple: il faut deviner la couleur de la balle qu'on tire d'une urne contenant autant de balles rouges que noires - et ceci le plus tôt possible. Plus précisément, les règles sont:

On a un ensemble de balles, la motié sont rouges, l'autre moitié noires (c'est donc un nombre pair de balles qu'on appelera $N$, disons $N=8$).
Elles sont dans une urne opaque et donc on ne peut pas les voir à moins de les tirer une par une (sans remise dans l'urne). On peut tirer autant de balles qu'on veut pour les observer.
Le but est de deviner la balle qu'on va tirer. Si on gagne (on a bien prédit la couleur), alors on gagne autant de points que le nombre de balles qui étaient dans l'urne au moment de la décision. Sinon on perd autant de points que l'on en aurait gagné!
à long terme, la stratégie du jeu est de décider le meilleur moment où on est prêt à deviner la couleur de la balle qu'on va prendre et ainsi de gagner le plus de points possibles.

Nous avons d'abord créé ce jeu grâce au language de programmation Scratch sur https://scratch.mit.edu/projects/165806365/:

Ici, nous allons essayer de l'analyser plus finement.

testing COMPs-fastPcum_scripted

Laurent Perrinet

2017-05-23 16:13

Comments

In this notebook, we will study how homeostasis (cooperation) may be an essential ingredient to this algorithm working on a winner-take-all basis (competition). This extension has been published as Perrinet, Neural Computation (2010) (see https://laurentperrinet.github.io/publication/perrinet-10-shl ). Compared to the previous post, we integrated the faster code to https://github.com/bicv/SHL_scripts.

See also the other posts on unsupervised learning,

This is joint work with Victor Boutin.

testing COMPs-fastPcum

Laurent Perrinet

2017-05-23 16:13

Comments

In this notebook, we will study how homeostasis (cooperation) may be an essential ingredient to this algorithm working on a winner-take-all basis (competition). This extension has been published as Perrinet, Neural Computation (2010) (see https://laurentperrinet.github.io/publication/perrinet-10-shl ). Compared to the previous post, we optimize the code to be faster.

See also the other posts on unsupervised learning,

This is joint work with Victor Boutin.

testing COMPs-Pcum

Laurent Perrinet

2017-05-23 15:58

Comments

In this notebook, we will study how homeostasis (cooperation) may be an essential ingredient to this algorithm working on a winner-take-all basis (competition). This extension has been published as Perrinet, Neural Computation (2010) (see https://laurentperrinet.github.io/publication/perrinet-10-shl ). In particular, we will show how one can build the non-linear functions based on the activity of each filter and which implement homeostasis.

See also the other posts on unsupervised learning,

This is joint work with Victor Boutin.

A change in the definition of spatial frequency bandwidth?

Laurent Perrinet

2017-05-23 11:43

Comments

Since the beginning, we have used a definition of bandwidth in the spatial frequency domain which was quite standard (see supp material for instance):

$$ \mathcal{E}(f; sf_0, B_{sf}) \propto \frac {1}{f} \cdot \exp \left( -.5 \frac {\log( \frac{f}{sf_0} ) ^2} {\log( 1 + \frac {B_sf}{sf_0} )^2 } \right) $$

This is implemented in the folowing code which reads:

env = 1./f_radius*np.exp(-.5*(np.log(f_radius/sf_0)**2)/(np.log((sf_0+B_sf)/sf_0)**2))

However the one implemented in the code looks different (thanks to Kiana for spotting this!), so that one can think that the code is using:

$$ \mathcal{E}(f; sf_0, B_{sf}) \propto \frac {1}{f} \cdot \exp \left( -.5 \frac {\log( \frac{f}{sf_0} ) ^2} {\log(( 1 + \frac {B_sf}{sf_0} )^2 ) } \right) $$

The difference is minimal, yet very important for a correct definition of the bandwidth!

Manipulating speed in motion clouds

Laurent Perrinet

2017-04-10 13:57

Comments

An essential dimension of motion is speed. However, this notion is prone to confusions as the speed that has to be measured can be relative to different object. Is it the speed of pixels? The speed of visual objects? We try to distinguish the latter two in this post.

In [1]:

%matplotlib inline
import numpy as np
np.set_printoptions(precision=3, suppress=True)
import pylab
import matplotlib.pyplot as plt

In [2]:

import os
name = '2017-04-10_physical_speed'
DOWNSCALE = 1

import MotionClouds as mc
N_X, N_Y, N_frame = mc.N_X/DOWNSCALE, mc.N_Y/DOWNSCALE, mc.N_frame/DOWNSCALE

fx, fy, ft = mc.get_grids(N_X, N_Y, N_frame)
mc.figpath = '../files/2017-04-10_physical_speed/'
if not(os.path.isdir(mc.figpath)): os.mkdir(mc.figpath)

In standard Motion Clouds, speed is that of the pixels of the textons that produce the texture. It is thus defined as a (normal) distribution of probability around the speed plane that defines the mean speed:

In [3]:

z = mc.envelope_gabor(fx, fy, ft)
name_ = name + '_vanilla' 
mc.figures(z, name_, figpath=mc.figpath)
mc.in_show_video(name_, figpath=mc.figpath)

/usr/local/lib/python3.7/site-packages/vispy/visuals/isocurve.py:22: UserWarning: VisPy is not yet compatible with matplotlib 2.2+
  warnings.warn("VisPy is not yet compatible with matplotlib 2.2+")

textures with motion parallax¶

Another way to consider speed is that of visual objects. Consider looking through the window of a train a field of similarly sized (Gabor-shaped) bushes on an infinite plane. The objects which are closer appear bigger on the retina and their speed is perceived as higher than the smaller bushes near the horizon. This relation between size and speed is linear and is called motion parallax (credit: http://www.rhsmpsychology.com/Handouts/monocular_cues_IV.htm).

In [4]:

from IPython.display import Image
Image('http://www.rhsmpsychology.com/images/monocular_IV.jpg')

Out[4]:

Such a pattern of motion distribution is highly prototypical in natural settings and it is easy to generate a texture having such a profile but with textons that are uniformly spaced in space, similar to the "Golconde" painting from Magritte (By The Shimon Yanowitz Website, Fair use, https://en.wikipedia.org/w/index.php?curid=3773027):

In [5]:

Image('https://upload.wikimedia.org/wikipedia/en/7/71/Golconde.jpg')

Out[5]:

More specifically, one finds that if we place MotionClouds on different planes perpendicular to the axis of vision, their frequency will increase as they get further , but their temporal frequency keeps constant: $$ f_0 \propto \arctan(\frac{F_0}{D}) $$ and $$ f_t \propto F_T $$

where $F_0$ is the central scale (spatial frequency) of the visual object, $f_0$ its frequency in retinal space and $D$ the distance. Compared to the classical definition of MotionClouds, this affects only the way we define the enveloppe around the speed plane. For a parallax-compatible motion, this enveloppe is on a plane around a fixed temporal frequency:

In [6]:

mc.B_sf

Out[6]:

0.1

In [7]:

def envelope_parallax_speed(fx, fy, ft, K=1., V_X=mc.V_X, V_Y=mc.V_Y,
                        B_V=mc.B_V, sf_0=mc.sf_0, B_sf=mc.B_sf, loggabor=mc.loggabor,
                        theta=mc.theta, B_theta=mc.B_theta, alpha=mc.alpha):
    """
     parallax speed envelope:
     selects a gaussian perpendicualr to the plane corresponding to the speed (V_X, V_Y) with some thickness B_V

    """


    envelope = mc.envelope_color(fx, fy, ft, alpha=alpha)
    envelope *= mc.envelope_orientation(fx, fy, ft, theta=theta, B_theta=B_theta)    
    envelope *= mc.envelope_radial(fx, fy, ft, sf_0=sf_0, B_sf=B_sf, loggabor=loggabor)
    
    f_radius = mc.frequency_radius(fx, fy, ft, ft_0=mc.ft_0, clean_division=True)
    V = np.sqrt(V_X**2 + V_Y**2)
    envelope *= np.exp(-.5*((np.sign(fx) * ft + sf_0 * V)**2/(B_V*sf_0)**2))
    # Hack to remove the other part of the envelope - use angle instead to allow for higher B_theta values
    return envelope

name_ = name + '_parallax'
opts= dict(V_X=.5, sf_0=.2, B_V=.1, B_sf=.25)
z = envelope_parallax_speed(fx, fy, ft, **opts)
mc.figures(z, name_, figpath=mc.figpath)
mc.in_show_video(name_, figpath=mc.figpath)

Let's explore what happens for different values of B_V:

In [8]:

opts_= dict(V_X=.5, sf_0=.2)
for B_V_ in np.logspace(-1, 1, 5, base=2)*opts['B_V']:
    name_ = name + '_parallax_B_V_' + str(B_V_).replace('.', '_') #os.path.join(mc.figpath, )
    z = envelope_parallax_speed(fx, fy, ft, B_V=B_V_, **opts_)
    mc.figures(z, name_, figpath=mc.figpath)
    mc.in_show_video(name_, figpath=mc.figpath)

group speed vs phase speed¶

More generally, this manipulation ---by changing the shape of the enveloppe--- changes the group vs phase speeds, as we did before with simulation of (earthly) gravitational waves. This can be done explictly by changing the shape of the enveloppe:

In [9]:

def envelope_physical_speed(fx, fy, ft, K=1., V_X=mc.V_X, V_Y=mc.V_Y,
                        B_V=mc.B_V, sf_0=mc.sf_0, B_sf=mc.B_sf, loggabor=mc.loggabor,
                        theta=mc.theta, B_theta=mc.B_theta, alpha=mc.alpha):
    """
     physical speed envelope:
     selects a gaussian perpendicualr to the plane corresponding to the speed (V_X, V_Y) with some thickness B_V

    """


    envelope = mc.envelope_color(fx, fy, ft, alpha=alpha)
    envelope *= mc.envelope_orientation(fx, fy, ft, theta=theta, B_theta=B_theta)    
    envelope *= mc.envelope_radial(fx, fy, ft, sf_0=sf_0, B_sf=B_sf, loggabor=loggabor)
    
    f_radius = mc.frequency_radius(fx, fy, ft, ft_0=mc.ft_0, clean_division=True)
    envelope *= np.exp(-.5*((ft + sf_0 * V_X - (f_radius - sf_0) / K )**2/(B_V*sf_0)**2))
    # Hack to remove the other part of the envelope - use angle instead to allow for higher B_theta values
    envelope *= fx*ft > 0

    
    return envelope

name_ = name + '_group_speed'
K = 1.
opts= dict(V_X=.5, sf_0=.2, B_V=.2)
z = envelope_physical_speed(fx, fy, ft, K=K, **opts)
mc.figures(z, name_)
mc.in_show_video(name_)

Let's explore what happens for different values of K:

In [10]:

for K_ in 1./np.linspace(0.6, 1.4, 7)*K:
    name_ = name + '_group_speed_K_' + str(K_).replace('.', '_')
    z = envelope_physical_speed(fx, fy, ft, K=K_, **opts)
    mc.figures(z, name_)
    mc.in_show_video(name_)

Extending Olshausens classical SparseNet

Laurent Perrinet

2017-03-27 10:49

Comments

In a previous notebook, we tried to reproduce the learning strategy specified in the framework of the SparseNet algorithm from Bruno Olshausen. It allows to efficiently code natural image patches by constraining the code to be sparse. In particular, we saw that in order to optimize competition, it is important to control cooperation and we implemented a heuristic to just do this.
In this notebook, we provide an extension to the SparseNet algorithm. We will study how homeostasis (cooperation) may be an essential ingredient to this algorithm working on a winner-take-all basis (competition). This extension has been published as Perrinet, Neural Computation (2010) (see https://laurentperrinet.github.io/publication/perrinet-10-shl ):

@article{Perrinet10shl,
    Title = {Role of homeostasis in learning sparse representations},
    Author = {Perrinet, Laurent U.},
    Journal = {Neural Computation},
    Year = {2010},
    Doi = {10.1162/neco.2010.05-08-795},
    Keywords = {Neural population coding, Unsupervised learning, Statistics of natural images, Simple cell receptive fields, Sparse Hebbian Learning, Adaptive Matching Pursuit, Cooperative Homeostasis, Competition-Optimized Matching Pursuit},
    Month = {July},
    Number = {7},
    Url = {https://laurentperrinet.github.io/publication/perrinet-10-shl},
    Volume = {22},
}

This is joint work with Victor Boutin.

Reproducing Olshausen's classical SparseNet (part 3)

Laurent Perrinet

2017-03-16 13:51

Comments

In this notebook, we test the convergence of SparseNet as a function of different learning parameters. This shows the relative robustness of this method according to the coding parameters, but also the importance of homeostasis to obtain an efficient set of filters:

first, whatever the learning rate, the convergence is not complete without homeostasis,
second, we achieve better convergence for similar learning rates and on a certain range of learning rates for the homeostasis
third, the smoothing parameter alpha_homeo has to be properly set to achieve a good convergence.
last, this homeostatic rule works with the different variants of sparse coding.

Reproducing Olshausens classical SparseNet (part 2)

Laurent Perrinet

2017-03-15 16:01

Comments

In a previous notebook, we tried to reproduce the learning strategy specified in the framework of the SparseNet algorithm from Bruno Olshausen. It allows to efficiently code natural image patches by constraining the code to be sparse.
However, the dictionaries are qualitatively not the same as the one from the original paper, and this is certainly due to the lack of control in the competition during the learning phase.
Herein, we re-implement the cooperation mechanism in the dictionary learning routine - this will be then proposed to the main code.

This is joint work with Victor Boutin.

Reproducing Olshausen's classical SparseNet (part 1)

Laurent Perrinet

2017-03-14 13:51

Comments

This notebook tries to reproduce the learning strategy specified in the framework of the SparseNet algorithm from Bruno Olshausen. It allows to efficiently code natural image patches by constraining the code to be sparse.
the underlying machinery uses a similar dictionary learning as used in the image denoising example from sklearn and our aim here is to show that a novel ingredient is necessary to reproduce Olshausen's results.
All these code bits is regrouped in the SHL scripts repository (where you will also find some older matlab code). You may install it using

    pip install git+https://github.com/bicv/SHL_scripts

following this failed PR to sklearn that was argued in this post (and following) the goal of this notebooks is to illustrate the simpler code implemented in the SHL scripts

This is joint work with Victor Boutin.

Some basics around probabilities

Laurent Perrinet

2017-03-09 11:41

Comments

basics of probability theory¶

In the context of a course in Computational Neuroscience, I am teaching a basic introduction in Probabilities, Bayes and the Free-energy principle.

Let's learn to use probabilities in practice by generating some "synthetic data", that is by using the computer's number generator. 2018-03-26_cours-NeuroComp_FEP

Bogacz (2017) A tutorial on free-energy

Laurent Perrinet

2017-01-15 21:41

Comments

I enjoyed reading "A tutorial on the free-energy framework for modelling perception and learning" by Rafal Bogacz, which is freely available here. In particular, the author encourages to replicate the results in the paper. He is himself giving solutions in matlab, so I had to do the same in python all within a notebook...

Resizing a bunch of files using the command-line interface

Laurent Perrinet

2016-11-29 09:08

Comments

generating databases¶

A set of bash code to resize images to a fixed size.

Problem statement: we have a set of images with heterogeneous sizes and we want to homogenize the database to avoid problems when classifying them. Solution: ImageMagick.

We first identify the size and type of images in the database. The database is a collection of folders containing each a collection of files. We thus do a nested recursive loop:

Using generators in Python

Laurent Perrinet

2016-11-24 14:22

Comments

Let's explore generators and the yield statement in the python language...

Finding extremal values in a nd-array

Laurent Perrinet

2016-11-17 09:56

Comments

Sometimes, you need to pick up the $N$-th extremal values in a mutli-dimensional matrix.

Let's suppose it is represented as a nd-array (here, I further suppose you are using the numpy library from the python language). Finding extremal values is easy with argmax, argmin or argsort but this function operated on 1d vectors... Juggling around indices is sometimes not such an easy task, but luckily, we have the unravel_index function.

For those in a hurry, one quick application is that given an np.ndarray, it's eeasy to get the index of the maximal value in that array :

In [1]:

import numpy as np
x = np.arange(2*3*4).reshape((4, 3, 2))
x = np.random.permutation(np.arange(2*3*4)).reshape((4, 3, 2))
print ('input ndarray', x)
idx = np.unravel_index(np.argmax(x.ravel()), x.shape)
print ('index of maximal value = ', idx, ' and we verify that ', x[idx], '=', x.max())

input ndarray [[[ 4  3]
  [19  7]
  [ 1 13]]

 [[ 6 12]
  [14  0]
  [16 11]]

 [[15 17]
  [20 22]
  [ 9  5]]

 [[ 8 18]
  [23 21]
  [10  2]]]
index of maximal value =  (3, 1, 0)  and we verify that  23 = 23

Let's unwrap how we found such an easy solution...

Saving and displaying movies and dynamic figures

Laurent Perrinet

2016-11-15 09:56

Comments

It is insanely useful to create movies to illustrate a talk, blog post or just to include in a notebook:

In [1]:

from IPython.display import HTML
HTML('<center><video controls autoplay loop src="../files/2016-11-15_noise.mp4" width=61.8%/></center>')

Out[1]:

For years I have used a custom made solution made around saving single frames and then calling ffmpeg to save that files to a movie file. That function (called anim_save had to be maintained accross different libraries to reflect new needs (going to WEBM and MP4 formats for instance). That made the code longer than necessary and had not its place in a scientific library.

Here, I show how to use the animation library from matplotlib to replace that

homebrew cask : creating a new cask

Laurent Perrinet

2016-11-04 09:36

Comments

A new version of https://nteract.io/ is out, I will try today to push that new infomation to http://caskroom.io/ by creating a new cask for this application. I will base things on this previous contribution where I was simply editing an existing cask.

getting the token

"$(brew --repository)/Library/Taps/caskroom/homebrew-cask/developer/bin/generate_cask_token" '/Applications/nteract.app'

set-up variables

cd "$(brew --prefix)"/Homebrew/Library/Taps/caskroom/homebrew-cask
github_user='laurentperrinet'
project='nteract'
git remote -v

A pi-pie named Monte Carlo

Laurent Perrinet

2016-10-01 14:22

Comments

A lively community of people including students, researchers and tinkerers from Marseille (France) celebrate the so-called "π-day" on the 3rd month, 14th day of each year. A nice occasion for general talks on mathematics and society in a lively athmosphere and of course to ... a pie contest!

I participated last year (in 2016) with a pie called "Monte Carlo". Herein, I give the recipe by giving some clues on its design... This page is a notebook - meaning that you can download it and re-run the analysis I do here at home (and most importantly comment or modify it and correct potential bugs...).

Une tarte au pi nommée Monte Carlo

Laurent Perrinet

2016-10-01 14:22

Comments

Une active communauté d'étudiants, chercheurs et bidouilleurs célèbrent à Marseille la "journée π" le 3ème mois, 14ème jour de chaque année. Une occasion de rêve pour en apprendre plus sur les mathématiques et la science dans une ambiance conviviale... Mais c'est aussi l'occasion d'un concours de tartes!

J'ai eu l'opportunité d'y participer l'an dernier (soit pour l'édition 2016) avec une tarte appelée "Monte Carlo". Je vais donner ici la "recette" de ma tarte, le lien avec le nombre π et quelques digressions mathématiques (notament par rapport à la présence incongrue d'un éléphant mais aussi par rapport à la démarche scientifique)... Cette page est un "notebook" - vous pouvez donc la télécharger et relancer les analyses et figures (en utilisant python + jupyter). C'est aussi un travail non figé - prière de me suggérer des corrections!

Predictive coding of motion in an aperture

Laurent Perrinet

2016-07-16 07:58

Comments

After reading the paper http://www.jneurosci.org/content/34/37/12601.full by Helena X. Wang, Elisha P. Merriam, Jeremy Freeman, and David J. Heeger (The Journal of Neuroscience, 10 September 2014, 34(37): 12601-12615; doi: 10.1523/JNEUROSCI.1034-14.2014), I was interested to test the hypothesis they raise in the discussion section :

The aperture-inward bias in V1–V3 may reflect spatial interactions between visual motion signals along the path of motion (Raemaekers et al., 2009; Schellekens et al., 2013). Neural responses might have been suppressed when the stimulus could be predicted from the responses of neighboring neurons nearer the location of motion origin, a form of predictive coding (Rao and Ballard, 1999; Lee and Mumford, 2003). Under this hypothesis, spatial interactions between neurons depend on both stimulus motion direction and the neuron's relative RF locations, but the neurons themselves need not be direction selective. Perhaps consistent with this hypothesis, psychophysical sensitivity is enhanced at locations further along the path of motion than at motion origin (van Doorn and Koenderink, 1984; Verghese et al., 1999).

Concerning the origins of aperture-inward bias, I want to test an alternative possibility. In some recent modeling work:

Laurent Perrinet, Guillaume S. Masson. Motion-based prediction is sufficient to solve the aperture problem. Neural Computation, 24(10):2726--50, 2012 https://laurentperrinet.github.io/publication/perrinet-12-pred

I was surprised to observe a similar behavior: the trailing edge was exhibiting a stronger activation (i. e. higher precision revealed by a lower variance in this probabilistic model) while I would have thought intuitively the leading edge would be more informative. In retrospect, it made sense in a motion-based prediction algorithm as information from the leading edge may propagate in more directions (135° for a 45° bar) than in the trailing edge (45°, that is a factor of 3 here). While we made this prediction we did not have any evidence for it.

In this script the predictive coding is done using the MotionParticles package and for a http://motionclouds.invibe.net/ within a disk aperture.

Static motion clouds?

Laurent Perrinet

2016-07-14 15:18

Comments

Motion Clouds were defined in the origin to define parameterized moving textures. The library in itself is also interesting in itself to generate a spatial texture. Herein I describe a solution to generate just one static frame.

compiling notebooks into a report

Laurent Perrinet

2016-06-25 07:58

Comments

For a master's project in computational neuroscience, we adopted a quite novel workflow to go all the steps from the learning of the small steps to the wrtiting of the final thesis. Though we were flexible in our method during the 6 months of this work, a simple workflow emerged that I describe here.

Compiling a set of notebook to a LaTeX document.

Compiling and using pyNN + NEST + python3

Laurent Perrinet

2016-06-01 21:21

Comments

PyNN is a neural simulation language which works well with the NEST simulator. Here I show my progress in using both with python 3 and how to show results in a notebook.

A bit more fun with gravity waves

Laurent Perrinet

2016-04-24 16:32

Comments

More fun with gravity waves¶

Motion Clouds were defined in the origin to provide a simple parameterization for textures. Thus we used a simple unimodal, normal distribution (on the log-radial frequency space to be more precise). But the larger set of Random Phase Textures may provide some interesting examples, some of them can even be fun! This is the case of this simulation of the waves you may observe on the surface on the ocean.

Main features of gravitational waves are:

longer waves travel faster (tsunami are fast and global, ripples are slow and local) - speed is linearly proportional to wavelength
phase speed (following a wave's crest) is twice as fast as group speed (following a group of waves).

More info about deep water waves : http://farside.ph.utexas.edu/teaching/336L/Fluidhtml/node122.html

IRM clouds

Laurent Perrinet

2016-04-06 15:52

Comments

A feature of MotionClouds is the ability to precisely tune the precision of information following the principal axes. One which is particularly relevant for the primary visual cortical area of primates (area V1) is to tune the otirentation mean and bandwidth.

Studying the role of contrast in V1 using MotionClouds¶

Compiling and using pyNN + NEST + python3

Laurent Perrinet

2016-02-19 14:21

Comments

PyNN is a neural simulation language which works well with the NEST simulator. Here I show my progress in using both with python 3 and how to show results in a notebook.

Mirror clouds

Laurent Perrinet

2016-01-27 15:24

Comments

An essential component of natural images is that they may contain order at large scales such as symmetries. Let's try to generate some textures with an axial (arbitrarily vertical) symmetry and take advantage of the different properties of random phase textures.

Using scratch to illustrate the Flash-Lag Effect

Laurent Perrinet

2016-01-20 11:59

Comments

Scratch (see https://scratch.mit.edu/) is a programming language aimed at introducing coding litteracy to schools and education. Yet you can implement even complex algorithms and games. It is visual, multi-platform and critically, open-source. Also, the web-site educates to sharing code and it is very easy to "fork" an existing project to change details or improve it. Openness at its best!

During a visit of a 14-year schoolboy at the lab, we used that to make a simple psychopysics experiment available at https://scratch.mit.edu/projects/92044597/ :

élasticité trames V1

Laurent Perrinet

2016-01-19 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

On va maintenant utiliser des forces elastiques pour coordonner la dynamique des lames dans la trame.

bootstraping posts for élasticité

Laurent Perrinet

2016-01-18 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

.. media:: http://vimeo.com/150813922

Ce meta-post gère la publication sur https://laurentperrinet.github.io/sciblog.

Reproducing Olshausen's classical SparseNet (part 3)

Laurent Perrinet

2015-12-11 13:51

Comments

This is an old blog post, see the newer version in this post

Reproducing Olshausen's classical SparseNet (part 4)

Laurent Perrinet

2015-12-11 13:51

Comments

This is an old blog post, see the newer version in this post and following.

homebrew cask : updating an existing cask

Laurent Perrinet

2015-12-08 13:36

Comments

A new version of owncloud is out, I will try today to push that new infomation to http://caskroom.io/
I will base things on this previous contribution

set-up variables

cd $(brew --prefix)/Library/Taps/caskroom/homebrew-cask
github_user='meduz'
project='owncloud'
git remote -v

élasticité - scénario final montage

Laurent Perrinet

2015-12-05 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

Ce post produit le montage final des séquences.

élasticité - scénario onde

Laurent Perrinet

2015-11-29 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

Ce post crée des ondes se propageant sur la série de lames.

élasticité, geometrie

Laurent Perrinet

2015-11-27 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

Ce post implémente une configuration favorisant des angles droits.

élasticité - scénario vague

Laurent Perrinet

2015-11-26 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

Ce post implémente une configuration implémentant une vague de propagation.

élasticité expansion en miroir - dynamique d'un point focal

Laurent Perrinet

2015-11-17 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

Ce post implémente une dynamique sur le point focal.

élasticité expansion en miroir - exploration paramètres

Laurent Perrinet

2015-11-02 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

Ce post explore les paramètres de la structure et de l'extension des reflections.

élasticité expansion en miroir - principes

Laurent Perrinet

2015-11-02 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

Ce post étudie quelques principes fondamentaux relatifs à des reflections mutliples dans des mirroirs.

Multiprocessing

Laurent Perrinet

2015-11-02 13:51

Comments

Testing some multi-threading libraries

élasticité expansion

Laurent Perrinet

2015-10-27 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

Ce post étudie commment sampler des points sur la structure.

élasticité expansion-réaction diffusion

Laurent Perrinet

2015-10-27 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

Ce post étudie une reaction de reaction diffusion sur la structure.

élasticité rapsberry pyserial

Laurent Perrinet

2015-10-27 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

Ce post étudie la connection entre le raspberry π (qui fait tourner les simulations) et les arduino (qui commandent les moteurs).

élasticité, control scenario

Laurent Perrinet

2015-10-14 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

Ce post simule une configuration de contrôle sur l'ensemble de la structure.

élasticité, Fresnel

Laurent Perrinet

2015-10-14 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

Ce post simule une configuration de type Fresnel sur l'ensemble de la structure.

élasticité, vapory and reflections

Laurent Perrinet

2015-09-30 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

Ce post simule un rendu de reflection utilisant povray.

A scene with mirrors rendered with vapory (see https://laurentperrinet.github.io/sciblog/posts/2015-01-16-rendering-3d-scenes-in-python.html )

Smooth transition between MCs

Laurent Perrinet

2015-07-02 15:06

Comments

A smooth transition of MotionClouds while smoothly changing their parameters.

homebrew cask : updating mactex

Laurent Perrinet

2015-06-12 13:36

Comments

A new version of (MacTex)[http://www.tug.org/mactex/mactex-download.html] is out, I will try today to push that new infomation to http://caskroom.io/
I will base the steps I use on this previous contribution

set-up variables

cd $(brew --prefix)/Library/Taps/caskroom/homebrew-cask
github_user='meduz'
project='mactex'
git remote -v

A simpler e-mail client: Diving into mutt

Laurent Perrinet

2015-05-29 10:55

Comments

My installation notes for mutt_+Homebrew_+gmail, based on this post by steve losh and this other post

A hitchhiker guide to Matching Pursuit

Laurent Perrinet

2015-05-22 10:59

Comments

The Matching Pursuit algorithm is popular in signal processing and applies well to digital images.

I have contributed a python implementation and we will show here how we may use that for extracting a sparse set of edges from an image.

this will be exposed in the following book chapter (see also https://laurentperrinet.github.io/publication/perrinet-15-bicv ), to be published by the end of this year:

@inbook{Perrinet15bicv,
    title = {Sparse models},
    author = {Perrinet, Laurent U.},
    booktitle = {Biologically-inspired Computer Vision},
    chapter = {13},
    editor = {Keil, Matthias and Crist\'{o}bal, Gabriel and Perrinet, Laurent U.},
    publisher = {Wiley, New-York},
    year = {2015}
}

A simple pre-processing filter for image processing

Laurent Perrinet

2015-05-21 22:01

Comments

When processing images, it is useful to avoid artifacts, in particular when you try to understand biological processes. In the past, I have used natural images (found on internet, grabbed from holiday pictures, ...) without controlling for possible problems.

In particular, digital pictures are taken on pixels which are most often placed on a rectangular grid. It means that if you rotate that image, you may lose information and distort it and thus get wrong results (even for the right algorithm!). Moreover, pictures have a border while natural scenes do not, unless you are looking at it through an aperture. Intuitively, this means that large objects would not fit on the screen and are less informative.

In computer vision, it is easier to handle these problems in Fourier space. There, an image (that we suppose square for simplicity) is transformed in a matrix of coefficients of the same size as the image. If you rotate the image, the Fourier spectrum is also rotated. But as you rotate the image, the information that was in the corners of the original spectrum may span outside the spectrum of the rotated image. Also, the information in the center of the spectrum (around low frequencies) is less relevant than the rest.

Here, we will try to keep as much information about the image as possible, while removing the artifacts related to the process of digitalizing the picture.

Extending Olshausens classical SparseNet

Laurent Perrinet

2015-05-12 10:49

Comments

This is an old blog post, see the newer version in this post

Reproducing Olshausens classical SparseNet (part 2)

Laurent Perrinet

2015-05-06 16:01

Comments

This is an old blog post, see the newer version in this post

Reproducing Olshausen's classical SparseNet (part 1)

Laurent Perrinet

2015-05-05 13:51

Comments

This is an old blog post, see the newer version in this post

trame-sensorielle

Laurent Perrinet

2015-04-30 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

Ce post utilise une image naturelle comme entrée d'une "trame sensorielle".

Moving from Mayavi to VisPy

Laurent Perrinet

2015-04-29 09:56

Comments

A long standing dependency of MotionClouds is MayaVi. While powerful, it is tedious to compile and may discourage new users. We are trying here to show some attempts to do the same with the vispy library.

In another post, we tried to use matplotlib, but this had some limitations. Let's now try vispy, a scientific visualisation library in python using opengl.

MoviePy and python3

Laurent Perrinet

2015-04-26 16:35

Comments

I was recently trying to embed a clip in a jupyter notebook using https://github.com/Zulko/moviepy, somthing that was working smoothly with python 2.7. After switching to python 3, this was not working anymore and left me scratcthing my head for a solution.

We live in a open-sourced world, so I filled an issue:

https://github.com/Zulko/moviepy/issues/160

elastic-force

Laurent Perrinet

2015-04-10 14:03

Comments

L'installation Elasticité dynamique agit comme un filtre et génère de nouveaux espaces démultipliés, comme un empilement quasi infini d'horizons. Par principe de réflexion, la pièce absorbe l'image de l'environnement et accumule les points de vue ; le mouvement permanent requalifie continuellement ce qui est regardé et entendu.

On va maintenant utiliser des forces elastiques pour coordonner la dynamique des lames dans la trame.

homebrew cask : updating an existing cask

Laurent Perrinet

2015-04-01 13:36

Comments

A new version of psychopy is out, I will try today to push that new infomation to http://caskroom.io/
I will base things on this previous contribution

set-up variables

cd $(brew --prefix)/Library/Taps/caskroom/homebrew-cask
github_user='meduz'
project='psychopy'
git remote -v

The Vancouver set

Laurent Perrinet

2015-03-26 11:06

Comments

I have heard Vancouver can get foggy and cloudy in the winter. Here, I will provide some examples of realistic simulations of it...

This stimulation was used in the following poster presented at VSS:


@article{Kreyenmeier2016,
author = {Kreyenmeier, Philipp and Fooken, Jolande and Spering, Miriam},
doi = {10.1167/16.12.457},
issn = {1534-7362},
journal = {Journal of Vision},
month = {sep},
number = {12},
pages = {457},
publisher = {The Association for Research in Vision and Ophthalmology},
title = {{Similar effects of visual context dynamics on eye and hand movements}},
url = {http://jov.arvojournals.org/article.aspx?doi=10.1167/16.12.457},
volume = {16},
year = {2016}
}

homebrew cask : updating an existing cask

Laurent Perrinet

2015-03-17 13:36

Comments

A new version of owncloud is out, I will try today to push that new infomation to http://caskroom.io/
I will base things on this previous contribution

set-up variables

cd $(brew --prefix)/Library/Taps/caskroom/homebrew-cask
github_user='meduz'
project='owncloud'
git remote -v

elastic-grids-of-edges

Laurent Perrinet

2015-02-26 14:03

Comments

Dans un notebook précédent, on a vu comment créer une grille hexagonale et comment l'animer.

On va maintenant utiliser MoviePy pour animer ces plots.

Saving files in HoloViews

Laurent Perrinet

2015-02-25 13:38

Comments

Here, we show how to save files from figures generated with HoloViews. This was thoroughly explained in this page.

An optic flow with Motion Clouds

Laurent Perrinet

2015-02-19 14:38

Comments

Horizon¶

Script done in collaboration with Jean Spezia.

Tiling Motion Clouds

Laurent Perrinet

2015-02-19 14:48

Comments

Script done in collaboration with Jean Spezia.

Creating an animation using Gizeh + MoviePy

Laurent Perrinet

2015-02-17 09:47

Comments

Gizeh (that is, Cairo for tourists) is a great interface to the Cairo drawing library.

I recently wished to make a small animation of a bar moving in the visual field and crossing a simple receptive field to illustrate some simple motions that could be captured in the primary visual cortex ansd experiments that could be done there.

homebrew cask : updating an existing cask

Laurent Perrinet

2015-02-16 13:36

Comments

A new version of owncloud is out, I will try today to push that new infomation to http://caskroom.io/
I will base things on my contribution

set-up variables

cd $(brew --prefix)/Library/Taps/caskroom/homebrew-cask
github_user='meduz'
project='owncloud'
git remote -v

Using Tikzmagic

Laurent Perrinet

2015-01-20 10:50

Comments

TIKZ is a great language for producing vector graphics. It is however a bit tedious to go over the whole $\LaTeX$-like compilation when you get used to an ipython notebooks work-flow.

I describe here how to use a cell magic implemented by http://www2.ipp.mpg.de/~mkraus/python/tikzmagic.py and a hack to use euclide within the graph (as implemented in https://github.com/laurentperrinet/ipython_magics).

Rendering 3D scenes in python

Laurent Perrinet

2015-01-16 14:36

Comments

The above snippet shows how you can create a 3D rendered scene in a few lines of codes (from http://zulko.github.io/blog/2014/11/13/things-you-can-do-with-python-and-pov-ray/):

In [1]:

import vapory

camera = vapory.Camera( 'location', [0, 2, -3], 'look_at', [0, 1, 2] )
light = vapory.LightSource( [2, 4, -3], 'color', [1, 1, 1] )
sphere = vapory.Sphere( [0, 1, 2], 2, vapory.Texture( vapory.Pigment( 'color', [1, 0, 1] )))

scene = vapory.Scene(camera = camera , # a Camera object
                     objects = [light, sphere], # POV-Ray objects (items, lights)
                     included = ["colors.inc"]) # headers that POV-Ray may need

# passing 'ipython' as argument at the end of an IPython Notebook cell
# will display the picture in the IPython notebook.
scene.render('ipython', width=900, height=500)

Out[1]:

Here are more details...

The right imports in a notebook

Laurent Perrinet

2015-01-07 14:14

Comments

Following this post http://carreau.github.io/posts/10-No-PyLab-Thanks.ipynb.html, here is ---all in one single cell--- the bits necessary to import most useful libraries in an ipython notebook:

In [1]:

# import numpy and set the printed precision to something humans can read
import numpy as np
np.set_printoptions(precision=2, suppress=True)
# set some prefs for matplotlib
import matplotlib.pyplot as plt
import matplotlib
matplotlib.rcParams.update({'text.usetex': True})
fig_width_pt = 700.  # Get this from LaTeX using \showthe\columnwidth
inches_per_pt = 1.0/72.27               # Convert pt to inches
fig_width = fig_width_pt*inches_per_pt  # width in inches
FORMATS = ['pdf', 'eps']
phi = .5*np.sqrt(5) + .5 # useful ratio for figures
# define plots to be inserted interactively
%matplotlib inline
#%config InlineBackend.figure_format='retina' # high-def PNGs, quite bad when using file versioning
%config InlineBackend.figure_format='svg'

Below, I detail some thoughts on why it is a perfect preamble for most ipython notebooks.

todo.txt

Laurent Perrinet

2015-12-29 22:05

Comments

In a previous post, I described steps to follow to live with decentralized, open-source cloud services (see here), let's focus on setting up a todo list.

Everything revolves under the http://todotxt.com/ specifications -- all in one, simple todo.txt file

Bib Cloud

Laurent Perrinet

2015-12-29 15:48

Comments

I always used a single babel.bib BibTex file to keep a record of all my readings. Great. Then I managed it using a VCS (first SVN, then git). Super great. But at the same time, resources like CiteUlike or Mendeley (but also other services like orcid) allow for cloud-like services of having this data everywhere, anytime. Super super great!

But this fails if you have no connection to internet (remote conference, ...) or more importantly if these services change their policy (mendeley to citeulike sync disappeared at a sudden). The work you provide is not yours. These are mostly commercial services while all the open-source tools are there. Most importantly, the multiplicity of tools makes it difficult to share bibliographic data easily, while if we would have a tool to translate between them this would make it possible (without changing your habits).

Can we live without Google and co?

Laurent Perrinet

2014-12-18 16:27

Comments

The tools offered by so-called "cloud services" are useful but most often rely on the capacity to lock you in. Without leaving them completely, is there an alternative?

In a previous post on how to live with open-source cloud services and to not depend on centralized private cloud services (see here), let's focus on an install on a empty android phone.

Recruiting different population ratios in V1 using orientation components: defining a protocol

Laurent Perrinet

2014-12-10 10:56

Comments

A feature of MotionClouds is the ability to precisely tune the precision of information following the principal axes. One which is particularly relevant for the primary visual cortical area of primates (area V1) is to tune the otirentation mean and bandwidth.

This is part of a larger study to tune orientation bandwidth.

summary of the electro-physiology protocol¶

Polar bar plots

Laurent Perrinet

2014-12-09 13:57

Comments

I needed to show prior information for the orientation of contours in natural images showing a preference for cardinal axis. A polar plot showing seemed to be a natural choice for showing the probability distribution function. However, this seems visually flawed...

Can we live without Google and co?

Laurent Perrinet

2014-12-07 16:27

Comments

The tools offered by so-called "cloud services" are useful but most often there is a (natural) tendency for these services to make you use their tools (youtube for google, iphone for apple). Why do we need to be locked to these services when open-source alternatives abound?

paramétrer l'e-mail à l'INT

Laurent Perrinet

2014-12-04 13:36

Comments

paramétrer un nouveau compte avec son adresse lolo.toto@univ-amu.fr
indiquer les parametres:
1. en entrant, serveur IMAP imap.univ-amu.fr avec SSL (port 993) et l'authentification est par mot de passe
2. en sortant, serveur SMTP smtp.univ-amu.fr en STARTTLS, port 587 et l'authentification est par mot de passe
3. attention, en entrant et en sortant, comme identifiant, l'identifiant univ-amu (de la forme toto.l)

Reading KML My Tracks files in ipython

Laurent Perrinet

2014-11-22 14:24

Comments

It's easy to record tracks (for instance while running) using the "My tracks" app on android systems. What about being able to re-use them?

In :doc:2014-11-22-reading-kml-my-tracks-files-in-ipython we reviewed different approches. Let's now try to use this data.

Reading KML My Tracks files in ipython

Laurent Perrinet

2014-11-15 14:38

Comments

It's easy to record tracks (for instance while running) using the "My tracks" app (see https://play.google.com/store/apps/details?id=com.google.android.maps.mytracks) on android systems. What about being able to re-use them?

Here, I am reviewing some methods to read a KML file, including fastkml, pykml, to finally opt for a custom method with the xmltodict package.

homebrew cask : updating an existing cask

Laurent Perrinet

2014-11-12 13:36

Comments

A new version of owncloud is out, I will try today to push that new infomation to http://caskroom.io/
I will base things on :doc:`my contribution <2013-11-08-homebrew-cask-(level-0)-contributing-a-new-cask>`,

System Message: ERROR/3 (<string>, line 4); backlink

"2013-11-08-homebrew-cask-level-0-contributing-a-new-cask" slug doesn't exist.

though now phinze-cask paths are now brew-cask.

set-up variables

cd $(brew --prefix)/Library/Taps/caskroom/homebrew-cask
github_user='meduz'
project='owncloud'
git remote -v

Reverse-phi and Asymmetry of ON and OFF responses

Laurent Perrinet

2014-11-10 11:03

Comments

We test Reverse-phi motion and the Asymmetry of ON and OFF responses using MotionClouds.

Recruiting different population ratios in V1 using orientation components

Laurent Perrinet

2014-11-10 10:56

Comments

A feature of MotionClouds is the ability to precisely tune the precision of information following the principal axes. One which is particularly relevant for the primary visual cortical area of primates (area V1) is to tune the orientation mean and bandwidth.

Recruiting different population ratios in V1 using orientation components: a biphoton study

Laurent Perrinet

2014-11-10 10:56

Comments

A feature of MotionClouds is the ability to precisely tune the precision of information following the principal axes. One which is particularly relevant for the primary visual cortical area of primates (area V1) is to tune the otirentation mean and bandwidth.

To install the necessary libraries, check out the documentation.

summary of the biphoton protocol¶

For the biphoton experiment:

The refresh rate of the screen is 70Hz and stimulation for 5 times 1s, which makes 350 images.
for the spatial frequency 0.125 cyc/deg is optimal (between 0.01 and 0.16).
for the temporal frequency 2 cyc/sec is optimal (between 0.8 and 4 sic/sec), we manipulate $B_V$ to get a qualitative estimate.

A bit of fun with gravity waves

Laurent Perrinet

2014-10-24 16:32

Comments

A bit of fun with gravity waves¶

Motion Clouds were defined in the origin to provide a simple parameterization for textures. Thus we used a simple unimodal, normal distribution (on the log-radial frequency space to be more precise). But the larger set of Random Phase Textures may provide some interesting examples, some of them can even be fun! This is the case of this simulation of the waves you may observe on the surface on the ocean.

In [1]:

from IPython.display import HTML
HTML('<center><video controls autoplay loop src="../files/2014-10-24_waves/waves.mp4" width=61.8%/></center>')

Out[1]:

Main features of gravitational waves are:

longer waves travel faster (tsunami are fast and global, ripples are slow and local) - speed is linearly proportional to wavelength
phase speed (following a wave's crest) is twice as fast as group speed (following a group of waves).

More info about deep water waves : http://farside.ph.utexas.edu/teaching/336L/Fluidhtml/node122.html

Statistics of time-varying images

Laurent Perrinet

2014-10-21 13:36

Comments

In this notebook, we are interested in replicating the results from Dong and Attick (1995).

Motion Plaid

Laurent Perrinet

2014-10-20 17:50

Comments

MotionPaids : from MotionClouds components to a plaid-like stimulus¶

In [1]:

import numpy as np
import MotionClouds as mc
downscale = 2
fx, fy, ft = mc.get_grids(mc.N_X/downscale, mc.N_Y/downscale, mc.N_frame/downscale)
name = 'MotionPlaid'

mc.figpath = '../files/2014-10-20_MotionPlaids'
import os
if not(os.path.isdir(mc.figpath)): os.mkdir(mc.figpath)

Plaids are usually created by adding two moving gratings (the components) to form a new simulus (the pattern). Such stimuli are crucial to understand how for instance information about motion is represented and processed and its neural mechanisms have been extensively studied notably by Anthony Movshon at the NYU. One shortcomming is the fact that these are created by components which created interference patterns when they are added (as in a Moiré pattern). The question remains to know if everything that we know about components vs pattern processing comes from these interference patterns or reaaly by the processing of the two componenents as a whole. As such, Motion Clouds are ideal candidates because they are generated with random phases: by construction, there should not be any localized interference between components. Let's verfy that:

Defintion of parameters:

In [2]:

theta1, theta2, B_theta = np.pi/4., -np.pi/4., np.pi/32

This figure shows how one can create MotionCloud stimuli that specifically target component and pattern cell. We show in the different lines of this table respectively: Top) one motion cloud component (with a strong selectivity toward the orientation perpendicular to direction) heading in the upper diagonal Middle) a similar motion cloud component following the lower diagonal Bottom) the addition of both components: perceptually, the horizontal direction is predominant.

In [3]:

print( mc.in_show_video.__doc__)


    Columns represent isometric projections of a cube. The left column displays
    iso-surfaces of the spectral envelope by displaying enclosing volumes at 5
    different energy values with respect to the peak amplitude of the Fourier spectrum.
    The middle column shows an isometric view of the faces of the movie cube.
    The first frame of the movie lies on the x-y plane, the x-t plane lies on the
    top face and motion direction is seen as diagonal lines on this face (vertical
    motion is similarly see in the y-t face). The third column displays the actual
    movie as an animation.

    Given a name, displays the figures corresponding to the Fourier spectra, the
    stimulus cubes and movies within the notebook.

Component one:

In [ ]:

diag1 = mc.envelope_gabor(fx, fy, ft, theta=theta1, V_X=np.cos(theta1), V_Y=np.sin(theta1), B_theta=B_theta)
name_ = name + '_comp1'
mc.figures(diag1, name_, seed=12234565, figpath=mc.figpath)
mc.in_show_video(name_, figpath=mc.figpath)

/usr/local/lib/python3.7/site-packages/vispy/visuals/isocurve.py:22: UserWarning: VisPy is not yet compatible with matplotlib 2.2+
  warnings.warn("VisPy is not yet compatible with matplotlib 2.2+")

Component two:

In [ ]:

diag2 = mc.envelope_gabor(fx, fy, ft, theta=theta2, V_X=np.cos(theta2), V_Y=np.sin(theta2), B_theta=B_theta)
name_ = name + '_comp2'
mc.figures(diag2, name_, seed=12234565, figpath=mc.figpath)
mc.in_show_video(name_, figpath=mc.figpath)

The pattern is the sum of the two components:

In [ ]:

name_ = name
mc.figures(diag1 + diag2, name, seed=12234565, figpath=mc.figpath)
mc.in_show_video(name_, figpath=mc.figpath)

A grid of plaids shows switch from transparency to pattern motion¶

Script done in collaboration with Jean Spezia.

In [ ]:

import os
import numpy as np
import MotionClouds as mc

name = 'MotionPlaid_9x9'
if mc.check_if_anim_exist(name):
    B_theta = np.pi/32
    N_orient = 9
    downscale = 4
    fx, fy, ft = mc.get_grids(mc.N_X//downscale, mc.N_Y//downscale, mc.N_frame//downscale)
    mov = mc.np.zeros(((N_orient*mc.N_X//downscale), (N_orient*mc.N_X//downscale), mc.N_frame//downscale))
    i = 0
    j = 0
    for theta1 in np.linspace(0, np.pi/2, N_orient)[::-1]:
        for theta2 in np.linspace(0, np.pi/2, N_orient):
            diag1 = mc.envelope_gabor(fx, fy, ft, theta=theta1, V_X=np.cos(theta1), V_Y=np.sin(theta1), B_theta=B_theta)
            diag2 = mc.envelope_gabor(fx, fy, ft, theta=theta2, V_X=np.cos(theta2), V_Y=np.sin(theta2), B_theta=B_theta)
            mov[(i)*mc.N_X//downscale:(i+1)*mc.N_X//downscale, (j)*mc.N_Y//downscale : (j+1)*mc.N_Y//downscale, :] = mc.random_cloud(diag1 + diag2, seed=1234)
            j += 1
        j = 0
        i += 1
    mc.anim_save(mc.rectif(mov, contrast=.99), os.path.join(mc.figpath, name))

In [ ]:

mc.in_show_video(name, figpath=mc.figpath)

As in (Rust, 06) we show in this table the concatenation of a table of 9x9 MotionPlaids where the angle of the components vary on respectively the horizontal and vertical axes.
The diagonal from the bottom left to the top right corners show the addition of two component MotionClouds of similar direction: They are therefore also intance of the same Motion Clouds and thus consist in a single component.
As one gets further away from this diagonal, the angle between both component increases, as can be seen in the figure below. Note that first and last column are different instance of similar MotionClouds, just as first and last lines in in the table.

A parametric exploration on MotionPlaids¶

In [ ]:

N_orient = 8
downscale = 2
fx, fy, ft = mc.get_grids(mc.N_X/downscale, mc.N_Y/downscale, mc.N_frame)
theta = 0
for dtheta in np.linspace(0, np.pi/2, N_orient):
    name_ = name + 'dtheta_' + str(dtheta).replace('.', '_')
    diag1 = mc.envelope_gabor(fx, fy, ft, theta=theta + dtheta, V_X=np.cos(theta + dtheta), V_Y=np.sin(theta + dtheta), B_theta=B_theta)
    diag2 = mc.envelope_gabor(fx, fy, ft, theta=theta - dtheta, V_X=np.cos(theta - dtheta), V_Y=np.sin(theta - dtheta), B_theta=B_theta)
    mc.figures(diag1 + diag2, name_, seed=12234565, figpath=mc.figpath)
    mc.in_show_video(name_, figpath=mc.figpath)

For clarity, we display MotionPlaids as the angle between both component increases from 0 to pi/2.
Left column displays iso-surfaces of the spectral envelope by displaying enclosing volumes at 5 different energy values with respect to the peak amplitude of the Fourier spectrum.
Right column of the table displays the actual movie as an animation.

Aperture Problem

Laurent Perrinet

2014-10-20 17:19

Comments

SlippingClouds: MotionClouds for exploring the aperture problem¶

Animation in a notebook using holoviews

Laurent Perrinet

2014-10-20 14:03

Comments

An easy way to include movie in a notebook using Holoviews.

Chi distribution

Laurent Perrinet

2014-10-20 13:47

Comments

When studying a multi-dimensional random variable, if these are guassian the norm if the vector follows a $\chi$ distribution (see http://en.m.wikipedia.org/wiki/Chi_distribution).

How can I display an image in the terminal?

Laurent Perrinet

2014-10-16 09:17

Comments

Trying to answer the question in http://stackoverflow.com/questions/12233105/how-can-i-display-an-image-in-the-terminal/22537549?noredirect=1#comment41404352_22537549 :

Is there any sort of utility I can use to convert an image to ASCII and then print it in my terminal? I looked for one but couldn't seem to find any.

Trying to include javascript in a notebook

Laurent Perrinet

2014-10-15 14:45

Comments

Trying to include javascript in a notebook¶

Following http://nbviewer.ipython.org/github/ipython/ipython/blob/1.x/examples/notebooks/Part%205%20-%20Rich%20Display%20System.ipynb and http://nbviewer.ipython.org/gist/fonnesbeck/ad091b81bffda28fd657 , let's try to integrate an interactive D3 plot within a notebook.

Setting options in holoviews

Laurent Perrinet

2014-10-15 14:35

Comments

using holoviews : setting display options¶

Holoviews is a nice framework to extend pyplot capacities.

2014-10-08_Moving from Mayavi to Matplotlib

Laurent Perrinet

2014-10-08 12:44

Comments

A long standing dependency of MotionClouds is MayaVi. While powerful, it is tedious to compile and may discourage new users. We are trying here to show some attempts to do the same with matplotlib or any other library.

transferring (lots of) files to a remote server + saving space

Laurent Perrinet

2014-07-07 10:31

Comments

I have recently been asked how to transfer lots of file from a backup server to a local disk. The context is that

the backup is an archive to be put on an external hard drive and then in a closet for future use,
the transfer line is not quite reliable and transfers may stop (for instance if it is mounted as a samba / windows / applefile share)

animation-in-a-notebook

Laurent Perrinet

2014-06-25 14:03

Comments

animation in a notebook¶

Dans le notebook précédent, on a vu comment créer

la grille rectangulaire puis hexagonale,
les lames autour de ces points - puis un fonction pour les représenter.

On va maintenant utiliser:

http://matplotlib.org/api/animation_api.html

http://jakevdp.github.io/blog/2012/08/18/matplotlib-animation-tutorial/

... pour créer des animations de ces lames.

grille-hexagonale

Laurent Perrinet

2014-06-25 14:03

Comments

Positionnement des lames¶

on définit des configurations pour la position des lames

[Stage M1] Chloé Pasturel : week 6

Laurent Perrinet

2014-06-18 12:58

Comments

Nous allons simuler un ring avec en entrée une courbe représentant des stimuli "naturels"

simulations center-surround
synthèse
écriture poster en latex

[Stage M1] Chloé Pasturel : week 5

Laurent Perrinet

2014-06-18 11:20

Comments

Loi de Von mises :¶

La densité est définie sur $[0, 2\pi[$ par $ f(x) = \frac {e^{\kappa cos(\theta - m)}}{2 \pi I_{0}(\kappa)} ~$
avec $~ \kappa = \frac {1}{\sigma^{2}} $

L'orientation est définie sur $[0, \pi[$ par un remplaçant de la variable $~ (\theta_d - m) ~$ par $~ 2(\theta_o - m)$

nous obtenons alors la densité pour $\theta_o$: $ f(x) = \frac{1}{2 \pi I_{0}(\kappa)} \cdot {e^{\frac{cos(2(\theta - m))}{\sigma^{2}}}}$ et $~ p = \frac {1} {2\pi \sigma_1 \sigma_2} \cdot e^{- 2 \frac{(m_2-m_1)^{2}}{\sigma_{1}^{2} + \sigma_{2}^{2}}}$

car avec le changement de variable : $ \varepsilon(x) = \frac {1} {\sigma_{1} \sqrt{2\pi}} \cdot e^{\frac {-(2(x-m_{1}))^{2}} {2\sigma_{1}^{2}}} $ et $\gamma (x) = \frac {1} {\sigma_2 \sqrt{2\pi}} \cdot e^{\frac {-(2(x-m_2))^{2}} {2\sigma_{2}^{2}}} $

donc $\varepsilon(x) \cdot \gamma(x) = \frac {1}{2\pi \sigma_{1} \sigma_{2}} \cdot e^{-2(\frac {(x-m_{1})^{2}}{\sigma_{1}^{2}} + \frac{(x-m_{2})^{2}}{\sigma_{2}^{2}})} = \frac {1} {2\pi \sigma_1 \sigma_2} \cdot e^{- 2 \frac{(m_2-m_1)^{2}}{\sigma_{1}^{2} + \sigma_{2}^{2}}}$

[Stage M1] Chloé Pasturel : week 4

Laurent Perrinet

2014-06-18 11:20

Comments

simulations avec différents MCs
ring avec représentation de la vitesse angulaire

[Stage M1] Chloé Pasturel : week 3

Laurent Perrinet

2014-06-18 11:20

Comments

Travail sur les Motion Clouds et observation des différents changement de paramètre particulièrement B_sf

introduction aux motions clouds: installation et display dans un notebook
synthèse de clouds avec différents theta
synthèse avec différents B_theta (V=0)
utilisation du trick dans http://motionclouds.invibe.net/posts/smooth-transition-between-mcs.html pour créer un stimulus pour lequel l'orientation tourne de 0 à 2*pi
proposer une façon simple de passer de ce signal à une entré pour le ring (un peu de maths? un MC est une texture définie en fourier, une cellule simple fait une convolution dans l'espace, donc une multiplication dans Fourier: on pourrait avoir la sortie linéaire du neurone de V1 directement ...)

http://neuralensemble.github.io/MotionClouds/

https://invibe.net/LaurentPerrinet/TagMotionClouds

[Stage M1] Chloé Pasturel : week 2

Laurent Perrinet

2014-06-18 11:20

Comments

Simulation d'un ring model grâce au programme brian et observation des conséquences du changement de différents paramêtres

simulation d'un ring par l'intermédiaire de brian http://briansimulator.org/
courbe de sélectivité en fonction des parametres
courbe de sélectivité à différents contrastes

[Stage M1] Chloé Pasturel : plan du stage

Laurent Perrinet

2014-06-18 11:10

Comments

Modele d'une entrée naturelle à un modèle de selectivité à l'orientation¶

Stage M1 de Chloé Pasturel, encadrée par Laurent Perrinet (INT, CNRS)

Contexte du stage¶

(importé depuis https://invibe.net/LaurentPerrinet/TagAnrBalaV1 )

[Stage M1] Chloé Pasturel : week 1

Laurent Perrinet

2014-06-18 11:10

Comments

définition du sujet - lecture Hansel
mise en place du python notebook
demos de brian

installation des outils¶

virtual box
VM ubuntu
<<< guest additions + clone
neurodebian

    wget -O- http://neuro.debian.net/lists/trusty.de-md.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
    sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9
    sudo apt-get update

install on ubuntu

sudo apt-get install aptitude
sudo aptitude install ipython-notebook
sudo aptitude install python-matplotlib
sudo aptitude install python-brian 
sudo aptitude install texlive-full


sudo aptitude install python-pynn 
pip install --user neurotools

Vim commands for moving around

Laurent Perrinet

2014-05-15 11:20

Comments

Basics commands in Vim

Sometimes, it's good to go back to the basics.

In command mode, typing :help usr_02.txt (or simplier something like :h usr_<TAB>02<TAB><ENTER>), you learn the letters for navigating a file:

these letters are HJKL - glad it works on an international keyboard.
letters on the borders (HL) are for horizontal movements- obviously H for left, L for right
letters on the inside are for vertical movements - J for down, K for up; a nice feature is that these keys are now quite widely used in the community, take for example in the gmail interface when switching to the next message.

I was still using the arrows keys, but taking this habit makes thinks easier, especially when switching often keyboards.

Simalarly, to scroll the text - you can use:

<CTRL-U> to scroll a half-page up
<CTRL-D> to scroll a half-page down

Here, the :h ctrl-u page will give you more info (or :help usr_03.txt).

Note that to follow a link (think "searching a tag"), you can press * (or # to go backwards).

Batch removing files on a FTP server

Laurent Perrinet

2014-02-28 09:33

Comments

In a previous post, I have shown how to convert MoinMoin pages to this blog (Nikola angine). Let's now tidy up the place and remove obsolete pages.

Pages that were succesfully converted:

Converting moinmoin pages to nikola

Laurent Perrinet

2014-02-15 15:09

Comments

nikolFrom a previous post, we have this function to import a page from moinmoin, convert it and publish:

Converting MoinMoin pages to Nikola

Laurent Perrinet

2014-02-11 16:07

Comments

I have another wiki to take notes. These are written using the MoinMoin syntax, which is nice, but I found no converter from MoinMoin to anything compatible with Nikola.

Following this post http://carreau.github.io/posts/06-NBconvert-Doc-Draft.html , I thought I might give it a try using ipython within nikola:

In [1]:

URL = 'https://invibe.net/cgi-bin/index.cgi/SciBlog/2005-10-29?action=print'

NOTE: this should not be tried with these URLS as they do not exist anymore...

SSH says 'Read from socket failed: Operation timed out'

Laurent Perrinet

2014-02-10 14:38

Comments

While SSH is rock solid, we stumbled on a strange bug while trying to establish a connection:

$ ssh myname@myserver.fr -vvv

OpenSSH_6.2p2, OSSLShim 0.9.8r 8 Dec 2011

(...)

Read from socket failed: Operation timed out

Nothing worked. The usual check of keys, encodings, permissions gave nothing.

Vim folding commands

Laurent Perrinet

2014-01-15 11:20

Comments

Using folds in Vim

Folds are useful when having long files to have a good perspective on its structure. Especially useful in LaTeX mode.

To install, I recommend using the python-mode described in http://unlogic.co.uk/2013/02/08/vim-as-a-python-ide/

The magical shortcut all begin with z. Type :hep fold to learn more about them.

Trying out ipython blogging

Laurent Perrinet

2014-01-14 10:37

Comments

How to easily publish an ipython notebook?¶

installing the appropriate plugins¶

Here, we will need to install additions to the nikola publishing tool: a rendering machine + a theme. Using homebrew in mcosx, this looks like:

brew install npm
npm install -g less

and

nikola install_theme zen-ipython

Once this was done, one could tune conf.py and then issue:

nikola new_post -f ipynb

Finally, one needs to build (nikola build) and publish (nikola deploy)

example¶

In [1]:

plot(rand(50))

Out[1]:

[<matplotlib.lines.Line2D at 0x10ab2d1d0>]

Bootstrapping Nikola

Laurent Perrinet

2014-01-04 14:15

Comments

Nikola Tesla Corner by nicwest, on Flickr

I have managed to install Nikola, and build a site using it using this code:

install-nikola.sh (Source)

git clone git://github.com/getnikola/nikola.git
cd nikola
pip install -r requirements-full.txt
pip install .
nikola init --demo invibe
nikola build
nikola serve

Pretty simple, congratulations to the developpers!

More info:

You can read the manual here
You can see a demo photo gallery here
You can learn more about Nikola at http://getnikola.com

How Airplanes Fly: A Physical Description of Lift

Laurent Perrinet

2014-01-01 13:36

Comments

see http://www.allstar.fiu.edu/aero/airflylvl3.htm

homebrew cask (level 1): correcting a pull request

Laurent Perrinet

2013-11-09 13:36

Comments

I mistyped :doc:`my contribution <2013-11-08-homebrew-cask-(level-0)-contributing-a-new-cask>`, so I have to modify my pull request

System Message: ERROR/3 (<string>, line 2); backlink

"2013-11-08-homebrew-cask-level-0-contributing-a-new-cask" slug doesn't exist.

set-up variables

cd $(brew --prefix)/Library/Taps/phinze-cask
github_user='meduz'
project='texshop'
git remote -v

homebrew cask (level 0): contributing a new cask

Laurent Perrinet

2013-11-08 13:36

Comments

homebrew casks are a friendly homebrew-style CLI workflow for the administration of Mac applications distributed as binaries. Something I always needed, hoped to get with the app store, frowned when openoffice or vlc were absent, and here they are!
see my list of casks I currently use (it is also a script to install them)

SparkleShare on a QNAP

Laurent Perrinet

2013-11-04 13:36

Comments

SparkleShare is a great alternative to DropBox

Fetch the Dazzle script on https://github.com/hbons/Dazzle

curl https://raw.github.com/hbons/Dazzle/master/dazzle.sh   --output /usr/bin/dazzle && chmod +x /usr/bin/dazzle

Meshnet

Laurent Perrinet

2013-10-26 13:36

Comments

New Scientist : Meshnet activists rebuilding the internet from scratch. http://google.com/producer/s/CBIw8NukjwE
https://projectmeshnet.org/‎
routing uses http://cjdns.info/

Useful numbers

Laurent Perrinet

2013-07-08 13:36

Comments

adapted from http://www.stanford.edu/group/vista/cgi-bin/wandell/a-brief-organized-list/

updating to mactex (texlive for mac), version 2013

Laurent Perrinet

2013-06-12 13:36

Comments

mactex is not there yet, but pre-relaeses are.

dropping owncloud

Laurent Perrinet

2013-05-14 13:36

Comments

since about 6 months, I was using ownCloud as a remplacement of dropbox, but I had unfortunately lots of problems and finally decided to drop wasting time on maintaining it.

using tabs in vim

Laurent Perrinet

2013-03-25 13:36

Comments

call vim to open more files
```
vim -p file1 file2 file3
```

upgrading owncloud to 5.0.0

Laurent Perrinet

2013-03-23 13:36

Comments

from http://doc.owncloud.org/server/5.0/admin_manual/maintenance/update.html

backup

rsync -a owncloud/ owncloud_bkp`date +"%Y%m%d"`/

Completely disable quarantine of downloaded files

Laurent Perrinet

2013-03-13 13:36

Comments

Starting in Leopard (I believe) when you open a file downloaded from the web, OS X asks if you really mean it. While it is intended to stop maliciousness, it is only a source of aggravation for me. While there are some hints here on working around it, it turns out that you can disable it completely using a Terminal command:

defaults write com.apple.LaunchServices LSQuarantine -bool NO

shortcut to put the display to sleep

Laurent Perrinet

2013-03-13 13:36

Comments

⇧⌃⏏ (shift+control+eject)

setting some conventions common in Bibdesk (to work with bibtex, citeUlike)

Laurent Perrinet

2013-03-06 13:36

Comments

I found this set useful to collaborate:
- citekey `` %a1%y%u0 ``
- rangement semi-automatique papiers: `` %f{Cite Key}%n0%e ``
- Topic = use citekey of related papers
- Comment (instead annote) to put... comments (as annote gets printed in the manuscript that would use the entry)

removing files based on their date

Laurent Perrinet

2013-02-20 16:18

Comments

Everything (almost) can be done by the find command:

finding in the current directory (.) all files containing a lock pattern:
find . -name *lock*

WP5 Year 2 report: contribution of CNRS-INT (Institut de Neurosciences de la Timone)

Laurent Perrinet

2013-02-04 13:36

Comments

During the first year of BrainScaleS, we have concentrated on disseminating our work on the role of motion-based prediction in motion detection. This led to a publication on the hypothesis that this prior expectation may explain some phenomena explained otherwise by complex arrangements of mechanisms, namely that motion-based prediction is sufficient to solve the aperture problem (Perrinet and Masson, 2012). During the second year, we extended this hypothesis to other types of problems linked to the detection of motion. In particular, we focused on the case were the stimulus is transiently and unexpectedly blanked, a physiologically very relevant constraint occurring for instances during blinks of the eye. For this, we have used the same theoretical framework based on a Bayesian formulation and implemented using a particle filtering scheme, but used a different experimental protocol inspired by behavioral experiments conducted in the laboratory by CNRS-INT (Bogadhi, 2012). This is an important aspect as it allows to better understand the dynamics of the neural representation without sensory input and more generally to understand the interaction of the sensory flow with an internal neural representation of the environment.

How To Change Your Time Machine Backup Interval

Laurent Perrinet

2013-02-02 13:36

Comments

tl;dr `` sudo /usr/libexec/PlistBuddy -c 'set :LaunchEvents:com.apple.time:"Backup Interval":Interval 86400' /System/Library/LaunchDaemons/com.apple.backupd-auto.plist ``

summarizing the instructions in http://maketecheasier.com/change-your-time-machine-backup-interval/2009/06/05 :

(re)moving lots of file containing a similar pattern

Laurent Perrinet

2013-01-31 13:36

Comments

I use ownCloud as a remplacement of dropbox, but I had unfortunately lots of conflicts files (on client and server)

these contain the _conflict- pattern, so a solution is to move all of them to a backup folder:

cd /share/DriveOne/Web/owncloud/data/admin/files
find . -name *_conflict-* -exec mv {} /share/Backups/backups/duplicate-photos/ \;

WP4 report : NeuroTools support for the synthesis of random textured dynamical stimuli

Laurent Perrinet

2013-01-16 13:36

Comments

In the context of BrainScales, we have developed a library to synthesize stimuli targeted at the characterization of motion perception. This process took the following steps:

setting the umask to define default permissions for created files

Laurent Perrinet

2012-11-28 13:36

Comments

the parameter to use is umask https://en.wikipedia.org/wiki/Umask

craac 2012

Laurent Perrinet

2012-11-07 13:36

Comments

Compte rendu annuel d'activité des chercheurs du CNRSAnnée 2011 - 2012

discover ports on MacOSX

Laurent Perrinet

2012-09-30 13:36

Comments

the network utility GUI is useful, but you may get the same results via the command line:

installing linux on imac hardware

Laurent Perrinet

2012-09-09 13:36

Comments

on a 2007 imac that will slow to a crawl since mountain lion, I have installed linux mint (why not debian?)

connecting a linux client to a QNAP's LDAP server

Laurent Perrinet

2012-09-04 13:36

Comments

after installing a linux client, you usually wish to have the same users as on your QNAP server. A LDAP server is one useful solution.

installing Dovecot on QNAP

Laurent Perrinet

2012-08-27 13:36

Comments

master howto: http://forum.qnap.com/viewtopic.php?f=143&t=33376&start=30

István Orosz

Laurent Perrinet

2012-08-19 13:36

Comments

discovered this by looking to nemo > outis > http://en.wikipedia.org/wiki/Istv%C3%A1n_Orosz

Make PDF files searchable and copyable

Laurent Perrinet

2012-07-24 13:36

Comments

The cmap package is intended to make the PDF files generated by pdflatex "searchable and copyable" in acrobat reader and other compliant PDF viewers.

using and re-using metadata in LaTeX

Laurent Perrinet

2012-07-10 13:36

Comments

Introduire des metas / Include meta keywords

2013-11-12 craac

Laurent Perrinet

2012-07-09 22:28

Comments

craac 2013

Compte rendu annuel d'activité des chercheurs du CNRSAnnée 2012 - 2013

racourci pour accéder à une page INIST

Laurent Perrinet

2012-06-12 13:36

Comments

dans un journal qui nécessite un abonnement pour accéder au contenu, il faut passer par le serveur de l'INIST.

rotating a video using ffmpeg

Laurent Perrinet

2012-04-30 13:36

Comments

Easy transformations of videos:

turn to the right

ffmpeg  -i  2012-04-29\ 19.31.32.mov  -vf "transpose=1" -sameq -y 2012-04-29\ 19.31.32_right.mov

Converting FLAC to AAC (or MP3 to OGG etc...)

Laurent Perrinet

2012-04-22 13:36

Comments

the solution is http://audiotools.sourceforge.net/

transition from movie15.sty to media9.sty

Laurent Perrinet

2012-04-17 13:36

Comments

recently, a message popped-up :

Package movie15 Warning: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
(movie15)                @@ Package `movie15' is obsolete and @@
(movie15)                @@ superseded by `media9'.           @@
(movie15)                @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@.

managing defaults on MacOsX

Laurent Perrinet

2012-04-05 13:36

Comments

when managing multiple machines, it is sometimes a pain to reset all default parameters. Still you want the same behaviour everywhere...

going back to simplicity: duckduckgo

Laurent Perrinet

2012-03-25 13:36

Comments

duckduckgo is a search engine as google was.
add to firefox : https://addons.mozilla.org/en-US/firefox/addon/duckduckgo-ssl/

Type your paths directly

Laurent Perrinet

2012-03-24 13:36

Comments

from http://apple.blogoverflow.com/2012/03/open-and-save-like-a-pro-secrets-of-opensave-dialogs/ :

Let’s move on to a more advanced feature: the Go to Folder dialog. Like in Finder, you can access a prompt for typing a path by pressing ⇧+⌘+G. If you love the keyboard, you’ll love this dialog; frequently, the fastest way to get to where you want to go is by typing its path. This is especially true because the Go to Folder dialog features tab autocompletion: type the beginning of the name of a file or folder and hit tab to fill in the rest of the name automatically. My favorite part about the Go to Folder dialog is that it appears automatically whenever you begin typing a path (/ or ~). When saving, the desired filename can even be included in the path.

how to leave iphoto

Laurent Perrinet

2012-03-22 13:36

Comments

iphoto.app is certainly a nice tool, but it is also
1. slow, unresponsive and locks you in some ugly closed-source format.
2. also, try to look in forums when you want to share pictures on different {computers / OSs / iphoto versions / places / users} = nightmare!
3. on top of that, the *cloud stuff is intellectually just very corrupted...
4. what decided me to drop it entirely was a sudden corruption of the library. It took 2 days to recover my files and re-rotate correctly all pictures...
5. last nail in the coffin was the fact that libraries are not backward compatible : you have to upgrade to the new product.

installing Dovecot on MacOsX using HomeBrew

Laurent Perrinet

2012-03-21 13:36

Comments

master howto: https://trac.macports.org/wiki/howto/SetupDovecot

Creating a bootable Debian USB flash drive on MacOsX

Laurent Perrinet

2012-03-16 13:36

Comments

largely adapted from https://help.ubuntu.com/community/Installation/FromUSBStick#From_Mac_OSX

Moving Time Machine to a New Hard Drive

Laurent Perrinet

2012-03-13 13:36

Comments

There exist some solution to move a time machine data folder to a new drive by making a clone of the drive. My problem is that I already have data on the new drive and that this data can difficultly be moved.

Doing a red-lined article file from two versions of a paper in LaTeX

Laurent Perrinet

2012-03-12 13:36

Comments

The editor of our submitted paper asked for a red-lined article file. Using latexdiff makes this task very easy: Simply grab the 2 versions of your manuscript and issue

Read more…

Stop Bonjour from broadcasting ssh and sftp

Laurent Perrinet

2012-03-11 13:36

Comments

largely a copy-and-paste from http://hints.macworld.com/article.php?story=20070622210507844 ; Jun 25, '07 07:30:00AM • Contributed by: delight1

After doing a backup, edit the following file:

sudo vim /System/Library/LaunchDaemons/ssh.plist

Completely disable quarantine of downloaded files

Laurent Perrinet

2012-03-05 13:36

Comments

copy and paste from http://hints.macworld.com/article.php?story=20091208050655947

Starting in Leopard when you open a file downloaded from the web, OS X asks if you really mean it. While it is intended to stop maliciousness, it is only a source of aggravation for me. While there are some hints here on working around it, it turns out that you can disable it completely using a Terminal command:

access spawn

Laurent Perrinet

2012-02-22 13:36

Comments

Finder / Pomme-K / smb://10.164.0.66

paramétrer l'e-mail à l'INT

Laurent Perrinet

2012-02-17 13:36

Comments

paramétrer un nouveau compte avec son adresse lolo.toto@univ-amu.fr

Tropique :-intervention Enghien

Laurent Perrinet

2012-02-16 13:36

Comments

An experimentation and meeting about Tropique of Etienne Rey

neurosciences?

Mon projet scientifique s'intéresse aux mécanismes computationnels qui sous-tendent la cognition. C'est-à-dire que l'on sait où se produisent ces mécanismes définissant la système nerveux central en un réseau de neurones connectés par des synapses et qu'ils sont supportés par des signaux électro-chimiques entre ces noeuds, mais on ne connaît pas encore totalement comment l'information qui semble être portée ces signaux peut être interprété. Ce décodage, qui est le fond de notre travail en neurosciences, à un "Graal" qui est la découverte d'un hypothétique "code neural", c'est-à-dire du langage qui est utilisé dans notre cerveau. On ne sait si cette découverte est possible; la question se pose: peut-il exister une connaissance globale du cerveau à la manière d'autres disciplines scientifiques (par exemple, la trajectoire d'une planète avec les lois de Newton?). Il est clair que le cerveau de chaque humain n'est pas assez complexe pour en délimiter la complexité, même les cerveaux mis en réseau avec toutes les communautés neuro-scientifiques, artistiques vont nous permettre dans le futur de mieux comprendre cet objet...

installing Dovecot on debian

Laurent Perrinet

2012-02-08 13:36

Comments

master howto: https://trac.macports.org/wiki/howto/SetupDovecot
Install
```
sudo aptitude install dovecot
```

Compiling pyglet on MacOsX

Laurent Perrinet

2012-01-18 13:36

Comments

you may get errors if trying to install pyglet using the traditional way, using pip for instance (was my case on MacOs X Lion 10.7.0 + python 64bits from EPD or homebrew). in cause is the carbon code that has been abandonned in the 64bits libraries that come with the OS

installing MoinMoin on a OVH server

Laurent Perrinet

2012-01-07 13:36

Comments

due to a disruption on my previous server, I had to move in a rush to a new server.

computational and theoretical neuroscience

Laurent Perrinet

2011-07-25 13:36

Comments

the poll

On april 1st, 2011, I sent the following message to the comp-neuro and connectionists lists: (see http://www.neuroinf.org/pipermail/comp-neuro/2011-April/002613.html

mounting filesystems using SSH

Laurent Perrinet

2011-07-10 13:36

Comments

install on ubuntu

mercurial & LaTeX

Laurent Perrinet

2011-07-08 13:36

Comments

using a versioning system

Laurent Perrinet

2011-07-07 13:36

Comments

scripting MoinMoin to get, change or rename pages

Laurent Perrinet

2011-07-06 13:36

Comments

MoinMoin is hugely useful for day to day use. Scripting is even better. Here, I show how to get, edit and rename pages on your wiki. To avoid bad surprise, this is based on a copy of the remote server using a local server with a wikiconfig.py script.

Publications 2006-2010

Laurent Perrinet

2011-07-05 13:36

Comments

articles

HomeBrew: compiling a python toolchain

Laurent Perrinet

2011-05-04 13:36

Comments

SpikeStream & Nemo

Laurent Perrinet

2011-03-10 13:36

Comments

SpikeStream & Nemo are (ultra fast) neural simulation frameworks. cool. but how to compile on ubuntu?

Ermentrout : "Double or Nothing: Phosphenes and the periodic driving of cortex"

Laurent Perrinet

2011-03-09 13:36

Comments

GATSBY UNIT EXTERNAL SEMINAR

Bard Ermentrout
Department of Mathematics
University of Pittsburgh

Wednesday 9 March 2011, 16:00

Seminar Room, Wellcome Trust Centre for Neuroimaging (FIL)
12 Queen Square, London, WC1N 3AR

Title:

Double or Nothing: Phosphenes and the periodic driving of cortex

Abstract:

In this talk, I examine two different types of phosphenes - patterns in the visual systems evoked from within it. I first study contour phosphenes in which direct stimulation of the eyeball coupled with a moving bar in the visual field produces slowly propagating waves. The mechanism appears to be due to period doubling which produces an intrinsic bistability. Using averaging, I analyze the dynamics of a one-dimensional analog. In the second part of the talk, I study flicker-induced hallucinations in which diffuse stroboscopic light is capable of  evoking spatial patterns in the visual field. I use Floquet theory and symmetric bifurcation theory to explain experiments that indicate different patterns are seen with different temporal frequencies.

Change User ID and Group ID in Snow Leopard

Laurent Perrinet

2011-02-22 13:36

Comments

find source and traget UID / GID using the id command on unix and dscllocalhostread/Local/Default/Users/lup in MacOsX

Ubuntu 10.10 64bit AHCI hosted on a dell T3500

Laurent Perrinet

2011-02-21 13:36

Comments

Warning

This post is certainly obsolete...

quoting http://ubuntuforums.org/showpost.php?p=10189331&postcount=35 : "For those (like me) who aren't familiar with grub tampering, here's what I did to make the change automatic:"

Read more…

pmset: selecting the sleep mode in Mac Os X

Laurent Perrinet

2011-02-09 13:36

Comments

Warning

This post is certainly obsolete...

from http://www.fscklog.com/2008/02/schnellschlaf-s.html:

To select one of the different sleep modes of the Mac use the command-line tool pmset:

handling processes in bash

Laurent Perrinet

2011-01-29 13:36

Comments

Give detailed information on all python processes:
```
ps -fp $(pgrep -d, -x python)
```

python in user space

Laurent Perrinet

2011-01-26 13:36

Comments

with a setup.py package, http://docs.python.org/install/index.html
```
python setup.py install --home=$HOME/Python2.6
```

Finder Shortcuts in MacOsX

Laurent Perrinet

2011-01-25 13:36

Comments

⇧⌘C: Computer
⇧⌘H: Home
⇧⌘D: Desktop
⇧⌘K: Network
⌥⌘L: Downloads
⇧⌘A: Applications
⇧⌘O: Documents
⇧⌘U: Utilities

inverting colors in MacOsX

Laurent Perrinet

2011-01-19 13:36

Comments

during a presentation, a figure may reveal more readable if you invert colors and luminance: black gets white and reverse, red becomes cyan and so on.

ubuntu : starting sshd at boot

Laurent Perrinet

2011-01-18 13:36

Comments

ssh server installed but not starting at boot (I certainly messed up something):

$ ls -l /etc/init.d/*ssh*
-rwxr-xr-x 1 root root 3704 2010-09-14 19:20 /etc/init.d/ssh
$ ls -l /etc/rc2.d/*ssh*
ls: cannot access /etc/rc2.d/*ssh*: No such file or directory
$ ls -l /etc/rc1.d/*ssh*

how to find stuff

Laurent Perrinet

2010-12-27 13:36

Comments

the most simple command is locate :
```
locate Python.h
```
; it is based on a database updated regulalry (most often daily).

Caps Lock, what a useless key

Laurent Perrinet

2010-12-20 13:36

Comments

[Ubuntu / gnome] You should be disable it do this with System->Preferences->Keyboard->Layouts->Options...->CapsLockkeybehavior
[MacosX] Open SystemPreferences, select the Keyboard pane. Within here, click the ModifierKeys… button at the bottom. To disable the Caps Lock key, pull down the associated menu and select NoAction.

CRAAC: Compte rendu annuel d'activité des chercheurs du CNRS. Année 2010

Laurent Perrinet

2010-12-08 13:36

Comments

2010-12-08 10:56:10

Compte rendu annuel d'activité des chercheurs du CNRS Année 2009 - 2010

ignoring a folder in SVN

Laurent Perrinet

2010-11-27 13:36

Comments

simply issue
```
svn propset svn:ignore '*' data/
```

Password-less logins with OpenSSH

Laurent Perrinet

2010-11-15 13:36

Comments

from http://www.debian-administration.org/articles/152

Because OpenSSH allows you to run commands on remote systems, showing you the results directly, as well as just logging in to systems it's ideal for automating common tasks with shellscripts and cronjobs. One thing that you probably won't want is to do though is store the remote system's password in the script. Instead you'll want to setup SSH so that you can login securely without having to give a password.

Instinct Paradise :-journée IMERA du 9 nov 2010

Laurent Perrinet

2010-11-09 13:36

Comments

journée IMERA du 9/11/2010

Mon projet scientifique s'intéresse aux mécanismes computationnels qui sous-tendent la cognition. C'est-à-dire que l'on sait que l'on sait où se produisent ces mécanismes définissant la système nerveux central en un réseau de neurones connectés par des synapses et qu'ils sont supportés par des signaux électro-chimiques entre ces noeuds, mais on ne connaît pas encore totalement comment l'information qui semble être portée ces signaux peut être interprété. Ce "Graal" est la découverte du "code neural" c'est-à-dire du langage qui est utilisé dans notre cerveau. On ne sait si cette découverte est possible: peut-il exister une connaissance globale du cerveau comme on peut deviner la trajectoire d'une planète avec les lois de Newton? Peut-etre le cerveau lui-même n'est pas assez complexe, même mis en réseau avec tous les neuro-scientifiques du monde entier, pour se laisser deviner... Mais il y a de nombreuses perspectives à le découvrir progressivement: