def plot_circle_in_micrograph(micrograph_2d, coordinate, particle_size, filename, color = 'white'):
"""plot the particle circle in micrograph image
Based on the coordinate of particle, plot circles of the particles in the micrograph.
And save the ploted image in filename.
Args:
micrograph_2d: numpy.array,it is a 2D numpy array.
coordinate: list, it is a 2D list, the shape is (num_particle, 2).
particle_size: int, the value of the particle size
filename: the filename of the image to be save.
color: define the color of the circle
Raises:
pass
"""
micrograph_2d = micrograph_2d.reshape(micrograph_2d.shape[0], micrograph_2d.shape[1])
fig = plt.figure()
ax = fig.add_subplot(111)
plt.axis('off')
plt.gray()
plt.imshow(micrograph_2d)
radius = particle_size/2
i = 0
while True:
if i >= len(coordinate):
break
coordinate_x = coordinate[i][0]
coordinate_y = coordinate[i][1]
cir1 = Circle(xy = (coordinate_x, coordinate_y), radius = radius, alpha = 0.5, color = color, fill = False)
ax.add_patch(cir1)
# extract the particles
i = i + 1
plt.savefig(filename)
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