def produce_projection_image(a=0, b=0, c=0, mrc_file='./zika_153.mrc'):
"""
mrc_file: string of MRC file name
a: rotation about x-axis (in degrees)
b: rotation about y-axis (in degrees)
c: rotation about z-axis (in degrees)
"""
cos = math.cos
sin = math.sin
f = MRCFile(mrc_file)
f.load_all_slices()
# ar stands for degree in radian
ar = a * math.pi / 180
br = b * math.pi / 180
cr = c * math.pi / 180
Ra = [[1, 0, 0],
[0, cos(ar), -sin(ar)],
[0, sin(ar), cos(ar)]]
Rb = [[cos(br), 0, sin(br)],
[0, 1, 0],
[-sin(br), 0, cos(br)]]
Rc = [[cos(cr), -sin(cr), 0],
[sin(cr), cos(cr), 0],
[0, 0, 1]]
R = np.dot(np.dot(Ra, Rb), Rc)
I = project_fst(f.slices, R)
return I, R
def main():
f = MRCFile('zika_153.mrc')
f.load_all_slices()
r = np.array([[0.25581, -0.77351, 0.57986], [-0.85333, -0.46255, -0.24057],
[0.45429, -0.43327, -0.77839]])
molecule = f.slices[:, :, :]
middle_slice = fft.ifftn(
fft.ifftshift(fft.fftshift(fft.fftn(molecule))[:, :, 76]))
# middle_slice = middle_slice.real
# print(middle_slice)
# plt.imshow(middle_slice)
# plt.show()
middle_back_proj = b(middle_slice)
middle_back_proj = middle_back_proj.real[:, :, 76]
plt.imshow(middle_back_proj)
plt.show()
def main():
f = MRCFile('zika_153.mrc')
f.load_all_slices()
r = np.array([[0.25581, -0.77351, 0.57986],
[-0.85333, -0.46255, -0.24057],
[0.45429, -0.43327, -0.77839]])
molecule = f.slices[:, :, :]
middle_slice = fft.ifftn(fft.ifftshift(fft.fftshift(fft.fftn(molecule))[:, :, 76]))
# middle_slice = middle_slice.real
# print(middle_slice)
# plt.imshow(middle_slice)
# plt.show()
middle_back_proj = b(middle_slice)
middle_back_proj = middle_back_proj.real[:, :, 76]
plt.imshow(middle_back_proj)
plt.show()
from back_projection import back_project
from sim_image import project_fst
from MRCFile import MRCFile
from vanheel import random_rotation_matrix
import numpy as np
import sys
if len(sys.argv) != 3:
print "please call with an mrc file as argument 1, and number of rotations as argument 2"
else:
f = MRCFile(sys.argv[1])
f.load_all_slices()
images = []
images_noisy = []
Rs = [random_rotation_matrix() for i in xrange(int(sys.argv[2]))]
# TODO here we can make many images later
for R in Rs:
image = project_fst(f.slices, R)
images.append(image)
noise = np.random.normal(0.0, 20 * np.mean(image), image.shape)
images_noisy.append(image + noise)
data = zip(images, Rs)
noisy_data = zip(images_noisy, Rs)
f.slices = back_project(data, use_filter=False)
f.write_file("#nofilter.mrc", overwrite=True)
f.slices = back_project(data)
f.write_file("filter.mrc", overwrite=True)
f.slices = back_project(noisy_data, use_filter=False)
f.write_file("#nofilter_noise.mrc", overwrite=True)
f.slices = back_project(noisy_data)
f.write_file("filter_noise.mrc", overwrite=True)
from MRCFile import MRCFile
from sim_image import project_fst
import matplotlib.pyplot as plt
from vanheel import random_rotation_matrix
zika_153 = MRCFile('zika_153.mrc')
zika_153.load_all_slices()
mol = zika_153.slices
# image = project_fst(mol, np.eye(3))
image = project_fst(mol, random_rotation_matrix())
plt.imshow(image)
plt.show()
