Python Flipbook Movies
In my Looking at Co-registered Brain Data post, I showed a movie of different subjects brain data. Here is how I created that movie.
I wrote a quick bit of python code that will show slice 136 of dimension 2 (in this case sagittal) and write out a movie named t1.mp4 at 5 frames a second, from the subjects listed in t1*.nii.
drawASlice.py 136 2 t1.mp4 5 t1*.nii
This code was used to create this movie.
Here is the full bit of code.
#!/usr/bin/env python
# import alot of libraries...
# If these aren't installed, you will have to install them. :-/
import sys
import os
import nibabel as nib
import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import subprocess
def main(argv):
sliceNum = argv[1]
dim = int(argv[2])
outf = argv[3]
rate = int(argv[4])
in_files = argv[5:]
# Prepare to pipe to ffmpeg
cmdstring = ('ffmpeg',
'-y',
'-f','image2pipe',
'-r', '%d' % rate,
'-vcodec', 'png',
'-s', '320x280',
'-i', 'pipe:', outf
)
# setup a ffmpeg pipe...
p = subprocess.Popen(cmdstring, stdin=subprocess.PIPE)
# setup a the fig and main axis to plot on
fig = plt.figure(facecolor='black', figsize=(4, 3), dpi=80)
ax = plt.Axes(fig, [0., 0., 1., 1.])
ax.set_axis_off()
fig.add_axes(ax)
# for each image in the input list
for i, f in enumerate(in_files):
# read the image
img = nib.load(f)
img_data = img.get_data()
# find the right slice to draw
if dim==1:
toDraw = img_data[:,sliceNum,:];
elif dim==2:
toDraw = img_data[sliceNum,:,:];
elif dim==3:
toDraw = img_data[:,:,sliceNum];
# orient appropriately?
toDraw=np.rot90(toDraw)
# show the image
im = ax.imshow(toDraw, cmap = cm.Greys_r, interpolation='nearest')
plt.show()
# write to the pipe...
plt.savefig(p.stdin, format='png', facecolor=fig.get_facecolor(), edgecolor='none', dpi=(80) )
if __name__ == '__main__':
main(sys.argv)
I also use this technique to verify that my clusters are where I claim they are in each participant. :-D