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Growing bacteria with population size analysis (Matplotlib/MoviePy)
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""" | |
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 | |
total number of pixels that they occupy | |
- Make an animated plot of the number of pixels occupied versus time | |
- Assemble the original video, the thresholded version, and the plot, | |
and write everything to a file. | |
I don't know the source of the original video so I can't give credits, | |
sorry guys ! | |
""" | |
import numpy as np | |
import matplotlib.pyplot as plt | |
from moviepy.video.io.bindings import mplfig_to_npimage | |
from moviepy.editor import VideoFileClip, VideoClip, clips_array | |
# DOWLOAD THE VIDEO Requires Youtube-dl installed. | |
import os | |
os.system("youtube-dl gEwzDydciWc -o growth.mp4") # requires Youtube-dl | |
# LOAD THE VIDEO, SELECT THE EXCERPT BETWEEN t=0-7 seconds | |
video = VideoFileClip("growth.mp4", audio=False).subclip(0,7) | |
# THRESHOLD THE FRAMES TO GET THE POPULATION AREA | |
# We normalize each frame by the luminosity of its upper left corner | |
# to correct for the changing luminosity of the video | |
thresholder = lambda im: ( 1.0*im[:,:,1]/np.mean(im[:50,:50]) ) < 0.8 | |
thresholded = video.fl_image(thresholder) | |
thresholded_RGB = thresholded.set_ismask(True).to_RGB() # RGB Version for movie | |
areas = [(t,frame.sum()) | |
for (t,frame) in thresholded.iter_frames(with_times=True)] | |
# ESTIMATE THE GROWTH RATE | |
tt, aa = [np.array(e) for e in zip(*areas)] # times and areas | |
gr_rate, a0 = np.polyfit(tt, np.log(aa),1) | |
# PLOT THE FIGURE | |
fig, ax = plt.subplots(1, figsize=(3,2.5), facecolor=(1,1,1)) | |
ax.plot(tt, np.exp(a0+gr_rate*tt), lw=2, ls='--', c='k', label = r"$Ae^{rt}$") | |
l, = ax.plot(tt, aa, lw=3, c='r') | |
ax.set_ylabel("Pop. surface (pixels)") | |
ax.set_xlabel("time (unit unknown)") | |
ax.legend(loc=2) | |
fig.tight_layout() # <- I love this function :D | |
# ANIMATE THE FIGURE WITH MOVIEPY | |
def plot_until_t(t): | |
tt, aa = zip(*[(t_,v) for (t_,v) in areas if t_<=t]) | |
l.set_xdata(tt) | |
l.set_ydata(aa) | |
return mplfig_to_npimage(fig) | |
plotclip = VideoClip(plot_until_t, duration=video.duration) | |
# ASSEMBLE ALL THE CLIPS, WRITE TO A FILE | |
final_clip = clips_array([[clip.margin(2, color=[255,255,255]) for clip in | |
[video.resize(.6), thresholded_RGB.resize(.6), plotclip]]], | |
bg_color=[255,255,255]) | |
final_clip.write_videofile('growth2.mp4', fps=15) | |
#final_clip.write_gif('growth.gif', fps=15, opt="OptimizeTransparency", fuzz=10) |
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Any chance this would work with GreenScreen?
I'm failing to find any moviepy green screen tips....