Zulko

## dna_chisel_animation.py
# Warning: quick and dirty code.

import dnachisel as dc
import proglog
proglog.notebook()
import matplotlib.pyplot as plt
from dna_features_viewer import BiopythonTranslator, GraphicFeature

counter = [0]

## ddeint.py
# REQUIRES PACKAGES Numpy AND Scipy INSTALLED
import numpy as np
import scipy.integrate
import scipy.interpolate

class ddeVar:
    """ special function-like variables for the integration of DDEs """

    def __init__(self,g,tc=0):
        """ g(t) = expression of Y(t) for t<tc """

## awkward.py
# Code for this GIF:
# http://imgur.com/gallery/pTypr1Y

# This demonstrates how to freeze a region with MoviePy

from moviepy.editor import *

clip = (VideoFileClip("the_fault_in_our_stars.mp4")
        .subclip("00:59:48.4","00:59:49.6")
        .resize(width=600)

## zombie_france.py
"""
Model of a Zombie outbreak in France, starting in Grenoble

This is a rewrite from this blog post by Max Berrgren:

http://maxberggren.github.io/2014/11/27/model-of-a-zombie-outbreak/

with a different country, a slightly different model, and different
libraries. The map of population density is taken from Wikimedia Commons

## graph_editor.py
import matplotlib.pyplot as plt
import numpy as np

def graph_editor(grid=True, grid_N = 12):
    """
    This function enables to draw a graph manually using
    Matplotlib's interactive plotting capabilites.

    In a first phase you are asked to place the nodes
    (left-click to place a node, right-click to remove

## entwin.py
"""
Provides a naive solution to the following problem:

Given a couple (a,b), use the transformations

L: (a,b)->( 2a, b+1 )
R: (a,b)->( a+1, 2b )

to come to two equal integers.

## cube_solver.py
import numpy as np

segments_lengths = [3, 2, 2, 2, 1, 1, 1, 2, 2, 1, 1, 2, 1, 2, 1, 1, 2]
assert sum(segments_lengths) == 27

def solve(cube, position, direction, segment_number):
    if segment_number == len(segments_lengths):
        return cube
    x, y, z = direction
    a1, a2 = np.array([y, z, x]), np.array([z, x, y])

## bacterial_growth_animation.py
"""
This script produces a video analysis proving for the first time in history
that bacterial populations grow exponentially. See the result here:
http://i.imgur.com/uoITKiA.gif

We proceed as follows:

- Download a video of bacteria growing under a microscope.
- Cut the video to keep only the first 7 seconds.
- Threshold each frame to find where the bacteria are, and compute the

## Eugene_hey.py
# Result: http://i.imgur.com/thrh1TU.gif

from moviepy.editor import *

# We start with a looping gif, and we will add some text
clip = VideoFileClip("eugene.gif").speedx(0.7) # slow down a little

txt = (TextClip("Hey", fontsize=78, font='Impact-Normal',
                     color='yellow', stroke_color='black',
                     stroke_width=3, kerning=1.5)

## param_curves.py
# IMPORTS: THIS SCRIPT REQUIRES THE PACKAGES PYLAB AND MOVIEPY
# It produces this gif: http://i.imgur.com/LbU55oK.gif

from pylab import *
import moviepy.editor as mp
from moviepy.video.io.bindings import mplfig_to_npimage


# PARAMETERS OF THE CURVE AND THE GIF
	# Warning: quick and dirty code.

	import dnachisel as dc
	import proglog
	proglog.notebook()
	import matplotlib.pyplot as plt
	from dna_features_viewer import BiopythonTranslator, GraphicFeature

	counter = [0]
	# REQUIRES PACKAGES Numpy AND Scipy INSTALLED
	import numpy as np
	import scipy.integrate
	import scipy.interpolate

	class ddeVar:
	""" special function-like variables for the integration of DDEs """

	def __init__(self,g,tc=0):
	""" g(t) = expression of Y(t) for t<tc """
	# Code for this GIF:
	# http://imgur.com/gallery/pTypr1Y

	# This demonstrates how to freeze a region with MoviePy

	from moviepy.editor import *

	clip = (VideoFileClip("the_fault_in_our_stars.mp4")
	.subclip("00:59:48.4","00:59:49.6")
	.resize(width=600)
	"""
	Model of a Zombie outbreak in France, starting in Grenoble

	This is a rewrite from this blog post by Max Berrgren:

	http://maxberggren.github.io/2014/11/27/model-of-a-zombie-outbreak/

	with a different country, a slightly different model, and different
	libraries. The map of population density is taken from Wikimedia Commons
	import matplotlib.pyplot as plt
	import numpy as np

	def graph_editor(grid=True, grid_N = 12):
	"""
	This function enables to draw a graph manually using
	Matplotlib's interactive plotting capabilites.

	In a first phase you are asked to place the nodes
	(left-click to place a node, right-click to remove
	"""
	Provides a naive solution to the following problem:

	Given a couple (a,b), use the transformations

	L: (a,b)->( 2a, b+1 )
	R: (a,b)->( a+1, 2b )

	to come to two equal integers.
	import numpy as np

	segments_lengths = [3, 2, 2, 2, 1, 1, 1, 2, 2, 1, 1, 2, 1, 2, 1, 1, 2]
	assert sum(segments_lengths) == 27

	def solve(cube, position, direction, segment_number):
	if segment_number == len(segments_lengths):
	return cube
	x, y, z = direction
	a1, a2 = np.array([y, z, x]), np.array([z, x, y])
	"""
	This script produces a video analysis proving for the first time in history
	that bacterial populations grow exponentially. See the result here:
	http://i.imgur.com/uoITKiA.gif

	We proceed as follows:

	- Download a video of bacteria growing under a microscope.
	- Cut the video to keep only the first 7 seconds.
	- Threshold each frame to find where the bacteria are, and compute the
	# Result: http://i.imgur.com/thrh1TU.gif

	from moviepy.editor import *

	# We start with a looping gif, and we will add some text
	clip = VideoFileClip("eugene.gif").speedx(0.7) # slow down a little

	txt = (TextClip("Hey", fontsize=78, font='Impact-Normal',
	color='yellow', stroke_color='black',
	stroke_width=3, kerning=1.5)
	# IMPORTS: THIS SCRIPT REQUIRES THE PACKAGES PYLAB AND MOVIEPY
	# It produces this gif: http://i.imgur.com/LbU55oK.gif

	from pylab import *
	import moviepy.editor as mp
	from moviepy.video.io.bindings import mplfig_to_npimage


	# PARAMETERS OF THE CURVE AND THE GIF