# Un-hardwrap a text file

I made a python script that un-hardwraps text, and put it up on github:

https://github.com/johnflux/unhardwrap

Take a txt file that has been hard-wrapped and remove the hardwrapping.

Use like:

./unhardwrap.py < example_in.txt > example_out.txt


This takes text, for example: (line numbers added for clarity)

1. Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor
2. incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
3. nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
4. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu
5. fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in
6. culpa qui officia deserunt mollit anim id est laborum.


And produces output without the hardwrapped newlines, like: (line numbers added for clarity)

1. Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
2. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.


The rules are:

• Two adjacent lines are considered to have been hardwrapped and should be remerged, if the first line ends with a letter, comma or hyphen.
• But don’t merge if the second line starts with a space or utf8 opening quote.
• Everything between utf8 speechmarks “..” will be treated as one line.

# Mars Rover Robot

This is an ongoing multi-year project.  I need to write this up properly, but I’ve got so much stuff that I’m going to attack this in stages.

# Current Status

14 motors, controlled by a raspberry pi.  Arm doesn’t quite work yet.  Everything else works.

Front end – I wrote this in ReactJS, and it communicates with the robot via a websocket to RobotOS, using ‘rosbridge’.  Sorry it’s so pink – it uses infrared LEDs to work at night, but they are kinda overpowering.  Also sorry for the mess – I have two children…

In the top left, the green circle is a ‘nipple’ – to let you move the rover about via webpage. Either via mouse or finger press.

In the top right, the xbox controller image shows what buttons are being pressed on an xbox controller, to control the robot. The xbox controller can either be connected to the rover, or connected to the PC / mobile phone – the webpage relays controller commands through to the rover.

Beneath the xbox controller is the list of running processes (“ros nodes”), with cpu and mem information.

Below that is the error messages etc.

# Console UI

I’m strong believer in trying to make my projects ‘transparent’ – as in, when you connect, it should be obvious what is going on, and how to do things.

With that in mind, I always create nice colored scripts that show the current status.

Below is the output when I ssh into the raspberry pi.  It shows:

– Wifi status and IP address
– Currently running ROS Node processes, and their mem and cpu status.  Colored Green for good, Red for stopped/crashed.
– Show that ‘rosmon’ is running on ‘screen’ and how to connect to it.
– The command line shows the current git status

I put this script in git in two parts – the first is a bash script to source from bash, and the second is a python script to use ros to get the current status.

See those links for the source code.  I think that every ROS project can benefit from these.

# Ultrasonic Sensor

I played about with making a robot face.  I combined a Ultrasonic Sensor (HC-SR04) and NeoPixel leds.  The leds reflect the distance – one pixel per 10 of cm.

I’m wondering if I can do SLAM – Simultaneous Location And Mapping  with a single (or a few) very-cheap ultrasonic sensor. Well, the answer is almost certainly no, but I’m very curious to see how far I can get.

NOTE: This is an old design – from more than two years ago

# Laplace Transform – visualized

The Laplace Transform is a particular tool that is used in mathematics, science, engineering and so on.  There are many books, web pages, and so on about it.

My animations are now on Wikipedia: https://en.wikipedia.org/wiki/Laplace_transform

And yet I cannot find a single decent visualization of it!  Not a single person that I can find appears to have tried to actually visualize what it is doing.  There are plenty of animations for the Fourier Transform like:

But nothing for Laplace Transform that I can find.

So, I will attempt to fill that gap.

# What is the Laplace Transform?

It’s a way to represent a function that is 0 for time < 0 (typically) as a sum of many waves that look more like:

Graph of $e^t cos(10t)$

Note that what I just said isn’t entirely true, because there’s an imaginary component here too, and we’re actually integrating.  So take this as a crude idea just to get started, and let’s move onto the math to get a better idea:

# Math

The goal of this is to visualize how the Laplace Transform works:

$\displaystyle\mathscr{L}\{f(t)\}=F(s)$

To do this, we need to look at the definition of the inverse Laplace Transform:

$\displaystyle f(t) = \mathscr{L}^{-1}\{F(s)\}=\frac{1}{2\pi j}\int^{c+j\infty}_{c-j\infty} F(s)e^{st}\mathrm{d}s$

While pretty, it’s not so nice to work with, so let’s make the substitution:

$\displaystyle s := c+jr$

so that our new limits are just $\infty$ to $-\infty$, and $\mathrm{d}s/\mathrm{d}r = j$ giving:

$\displaystyle f(t) = \mathscr{L}^{-1}\{F(s)\}=\frac{1}{2\pi j}\int^{\infty}_{-\infty} F(c+jr)e^{(c+jr)t}j\mathrm{d}r$

$\displaystyle = \frac{1}{2\pi}\int^{\infty}_{-\infty} F(c+jr)e^{(c+jr)t}\mathrm{d}r$

Which we will now approximate as:

$\displaystyle \approx \frac{1}{2\pi}\sum^{n}_{i=-n} F(c+jr_i)e^{(c+jr_i)t}\Delta r_i$

# Code

The code turned out to be a bit too large for a blog post, so I’ve put it here:

https://github.com/johnflux/laplace-transform-visualized/blob/master/Laplace%20Transform.ipynb

# Results

Note: The graphs say “Next frequency to add: … where $s = c+rj$“, but really it should be “Next two frequencies to add: … where $s = c\pm rj$” since we are adding two frequencies at a time, in such a way that their imaginary parts cancel out, allowing us to keep everything real in the plots.  I fixed this comment in the code, but didn’t want to rerender all the videos.

A cubic polynomial:

A cosine wave:

Now a square wave.  This has infinities going to infinity, so it’s not technically possible to plot.  But I tried anyway, and it seems to visually work:

Note the overshoot ‘ringing’ at the corners in the square wave. This is the Gibbs phenomenon and occurs in Fourier Transforms as well. See that link for more information.

Now some that it absolutely can’t handle, like: $\delta(t)$.  (A function that is 0 everywhere, except a sharp peak at exactly time = 0).  In the S domain, this is a constant, meaning that we never converge.  But visually it’s still cool.

Note that this never ‘settles down’ (converges) because the frequency is constantly increasing while the magnitude remains constant.

There is visual ‘aliasing’ (like how a wheel can appear to go backwards as its speed increases). This is not “real” – it is an artifact of trying to render high frequency waves. If we rendered (and played back) the video at a higher resolution, the effect would disappear.

At the very end, it appears as if the wave is just about to converge. This is not a coincidence and it isn’t real. It happens because the frequency of the waves becomes too high so that we just don’t see them, making the line appear to go smooth, when in reality the waves are just too close together to see.

The code is automatically calculating this point and setting our time step such that it only breaksdown at the very end of the video. If make the timestep smaller, this effect would disappear.

And a simple step function:

A sawtooth:

# Worst/Trickiest code I have ever seen

It’s easy to write bad code, but it takes a real genius to produce truly terrible code.  And the guys who wrote the python program hyperopt were clearly very clever.

Have a look at this function:  (don’t worry about what it is doing) from tpe.py

# These produce conditional estimators for various prior distributions
@adaptive_parzen_sampler('uniform')
def ap_uniform_sampler(obs, prior_weight, low, high, size=(), rng=None):
prior_mu = 0.5 * (high + low)
prior_sigma = 1.0 * (high - low)
weights, mus, sigmas = scope.adaptive_parzen_normal(obs,
prior_weight, prior_mu, prior_sigma)
return scope.GMM1(weights, mus, sigmas, low=low, high=high, q=None,
size=size, rng=rng)


The details don’t matter here, but clearly it’s calling some function “adaptive_parzen_normal”  which returns three values, then it passes that to another function called “GMM1”  and returns the result.

Pretty straight forward?  With me so far?  Great.

Now here is some code that calls this function:

fn = adaptive_parzen_samplers[node.name]
named_args = [[kw, memo[arg]] for (kw, arg) in node.named_args]
a_args = [obs_above, prior_weight] + aa
a_post = fn(*a_args, **dict(named_args))


Okay this is getting quite messy, but with a bit of thinking we can understand it.  It’s just calling the  ‘ap_uniform_sampler’  function, whatever that does, but letting us pass in parameters in some funky way.

So a_post is basically whatever “GMM1” returns  (which is a list of numbers, fwiw)

Okay, let’s continue!

fn_lpdf = getattr(scope, a_post.name + '_lpdf')
a_kwargs = dict([(n, a) for n, a in a_post.named_args if n not in ('rng', 'size')])
above_llik = fn_lpdf(*([b_post] + a_post.pos_args), **a_kwargs)


and that’s it.  There’s no more code using a_post.

This took me a whole day to figure out what on earth is going on.  But I’ll give you, the reader, a hint.  This is not running any algorithm – it’s constructing an Abstract Syntax Tree and manipulating it.

If you want, try and see if you can figure out what it’s doing.

Answer: Continue reading

# Tensorflow for Neurobiologists

I couldn’t find anyone else that has done this, so I made this really quick guide.  This uses tensorflow which is a complete overkill for this specific problem, but I figure that a simple example is much easier to follow.

Install and run python3 notebook, and tensorflow.  In Linux, as a user without using sudo:

$pip3 install --upgrade --user ipython[all] tensorflow matplotlib$ ipython3  notebook


Then in the notebook window, do New->Python 3

Here’s an example I made earlier. You can download the latest version on github here: https://github.com/johnflux/Spike-Triggered-Average-in-TensorFlow

# Spike Triggered Average in TensorFlow

The data is an experimentally recorded set of spikes recorded from the famous H1 motion-sensitive neuron of the fly (Calliphora vicina) from the lab of Dr Robert de Ruyter van Steveninck.

This is a complete rewrite of non-tensorflow code in the Coursera course Computational Neuroscience by University of Washington. I am thoroughly enjoying this course!

Here we use TensorFlow to find out how the neuron is reacting to the data, to see what causes the neuron to trigger.

%matplotlib inline
import pickle
import matplotlib.pyplot as plt
import numpy as np
import tensorflow as tf
sess = tf.InteractiveSession()

FILENAME = 'data.pickle'

with open(FILENAME, 'rb') as f:
data = pickle.load(f)

stim = tf.constant(data['stim'])
rho = tf.constant(data['rho'])
sampling_period = 2 # The data was sampled at 500hz = 2ms
window_size = 150 # Let's use a 300ms / sampling_period sliding window


We now have our data loaded into tensorflow as a constant, which means that we can easily ‘run’ our tensorflow graph. For example, let’s examine stim and rho:

print("Spike-train time-series =", rho.eval(),
"\nStimulus time-series     =", stim.eval())

Spike-train time-series = [0 0 0 ..., 0 0 0]
Stimulus time-series    = [-111.94824219  -81.80664062
10.21972656 ...,  9.78515625 24.11132812 50.25390625]


rho is an binary array where a 1 indicates a spike. Let’s turn that into an array of indices of where the value is 1, but ignoring the first window_size elements.

Note: We can use the [] and + operations on a tensorflow variable, and it correctly adds those operations to the graph. This is equivalent to using the tf.slice and tf.add operations.

spike_times = tf.where(tf.not_equal(rho[window_size:-1], 0)) + window_size
print("Time indices where there is a spike:\n", spike_times.eval())

Time indices where there is a spike:
[[   158]
[   160]
[   162]
...,
[599936]
[599941]
[599947]]
def getStimWindow(index):
i = tf.cast(index, tf.int32)
return stim[i-window_size+1:i+1]
stim_windows = tf.map_fn(lambda x: getStimWindow(x[0]), spike_times, dtype=tf.float64)
spike_triggered_average = tf.reduce_mean(stim_windows, 0).eval()
print("Spike triggered averaged is:", spike_triggered_average[0:5], "(truncated)")

Spike triggered averaged is: [-0.33083048 -0.29083503 -0.23076012 -0.24636984 -0.10962767] (truncated)

Now let’s plot this!

time = (np.arange(-window_size, 0) + 1) * sampling_period
plt.plot(time, spike_triggered_average)
plt.xlabel('Time (ms)')
plt.ylabel('Stimulus')
plt.title('Spike-Triggered Average')

plt.show()


It’s… beautiful!

What we are looking at here, is that we’ve discovered that our neuron is doing a leaky integration of the stimulus. And when that integration adds up to a certain value, it triggers.

Do see the github repo for full source: https://github.com/johnflux/Spike-Triggered-Average-in-TensorFlow

Update: I was curious how much noise there was. There’s a plot with 1 standard deviation in light blue:

mean, var = tf.nn.moments(stim_windows,axes=[0])
plt.errorbar(time, spike_triggered_average, yerr=tf.sqrt(var).eval(), ecolor="#0000ff33")


Yikes!  This is why the input signal MUST be Gaussian, and why we need lots of data to average over.  For this, we’re averaging over 53583 thousand windows.