NiPyとmatplotlibで、脳機能画像のアニメーション

NiPyとmatplotlibで、脳機能画像のアニメーション

NiPyとmatplotlibで、脳機能画像のアニメーションを作っていきます。

Axial画像

import nipy
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation


def input_files(data_path):
    img = nipy.load_image(data_path)
    data = img.get_data()
    
    return img, data

#(x,y,z,t)の4D-NIfTIファイル
img, data = input_files(data_path)

fig = plt.figure()
ims = []

for i in range(data.shape[2]):
    im = plt.imshow(data[:, :, i, 1].T, cmap='gray', animated=True)
    plt.gca().invert_yaxis()
    ims.append([im])
ani = animation.ArtistAnimation(fig, ims, interval=100)
ani.save('Axial.gif' ,writer = 'imagemagick')

Saggital画像

import nipy
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation


def input_files(data_path):
    img = nipy.load_image(data_path)
    data = img.get_data()
    
    return img, data

#(x,y,z,t)の4D-NIfTIファイル
img, data = input_files(data_path)

fig = plt.figure()
ims = []

for i in range(data.shape[0]):
    im = plt.imshow(data[i, :, : , 1].T, cmap='gray', animated=True)
    plt.gca().invert_yaxis()
    ims.append([im])
ani = animation.ArtistAnimation(fig, ims, interval=100)
ani.save('Saggital.gif' ,writer = 'imagemagick')

Coronal画像

import nipy
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation


def input_files(data_path):
    img = nipy.load_image(data_path)
    data = img.get_data()
    
    return img, data

#(x,y,z,t)の4D-NIfTIファイル
img, data = input_files(data_path)

fig = plt.figure()
ims = []

for i in range(data.shape[1]):
    im = plt.imshow(data[:, i, : , 1].T, cmap='gray', animated=True)
    plt.gca().invert_yaxis()
    ims.append([im])
ani = animation.ArtistAnimation(fig, ims, interval=100)
ani.save('Coronal.gif' ,writer = 'imagemagick')