def test_particlesWithPhaseShiftToStar(self):
""" Write a SetOfParticles to Relion star input file. """
imgSet = SetOfParticles(filename=self.getOutputPath("particles_ph_sh.sqlite"))
n = 10
fn = self.getFile('particles_binary')
ctfs = [CTFModel(defocusU=10000, defocusV=15000,
defocusAngle=15, phaseShift=90),
CTFModel(defocusU=20000, defocusV=25000,
defocusAngle=25, phaseShift=60)
]
acquisition = Acquisition(magnification=60000, voltage=300,
sphericalAberration=2.,
amplitudeContrast=0.07)
imgSet.setAcquisition(acquisition)
coord = Coordinate()
coord.setMicId(1)
for i in range(n):
p = Particle()
p.setLocation(i + 1, fn)
ctf = ctfs[i % 2]
p.setCTF(ctf)
p.setAcquisition(acquisition)
p._xmipp_zScore = Float(i)
coord.setX(i * 10)
coord.setY(i * 10)
p.setCoordinate(coord)
imgSet.append(p)
fnStar = self.getOutputPath('particles_ph_sh.star')
fnStk = self.getOutputPath('particles.stk')
print (">>> Writing to file: %s" % fnStar)
relion.writeSetOfParticles(imgSet, fnStar, fnStk)
mdAll = md.MetaData(fnStar)
self.assertTrue(mdAll.containsLabel(md.RLN_IMAGE_COORD_X))
self.assertTrue(mdAll.containsLabel(md.RLN_IMAGE_COORD_Y))
self.assertFalse(mdAll.containsLabel(md.RLN_SELECT_PARTICLES_ZSCORE))
self.assertTrue(mdAll.containsLabel(md.RLN_CTF_PHASESHIFT))
def aaatest_particlesToStar(self):
""" Write a SetOfParticles to Relion star input file. """
imgSet = SetOfParticles(
filename=self.getOutputPath("particles.sqlite"))
n = 10
fn = self.particles
ctfs = [
CTFModel(defocusU=10000, defocusV=15000, defocusAngle=15),
CTFModel(defocusU=20000, defocusV=25000, defocusAngle=25)
]
acquisition = Acquisition(magnification=60000,
voltage=300,
sphericalAberration=2.,
amplitudeContrast=0.07)
imgSet.setAcquisition(acquisition)
coord = Coordinate()
coord.setMicId(1)
for i in range(n):
p = Particle()
p.setLocation(i + 1, fn)
ctf = ctfs[i % 2]
p.setCTF(ctf)
p.setAcquisition(acquisition)
p._xmipp_zScore = Float(i)
coord.setX(i * 10)
coord.setY(i * 10)
p.setCoordinate(coord)
imgSet.append(p)
fnStar = self.getOutputPath('particles.star')
fnStk = self.getOutputPath('particles.stk')
print ">>> Writing to file: %s" % fnStar
relion.writeSetOfParticles(imgSet, fnStar, fnStk)
mdAll = md.MetaData(fnStar)
self.assertTrue(mdAll.containsLabel(md.RLN_IMAGE_COORD_X))
self.assertTrue(mdAll.containsLabel(md.RLN_IMAGE_COORD_Y))
self.assertFalse(mdAll.containsLabel(md.RLN_SELECT_PARTICLES_ZSCORE))
def create_subparticles(particle, symmetry_matrices, subparticle_vector_list,
part_image_size, randomize, subparticles_total,
align_subparticles):
""" Obtain all subparticles from a given particle and set
the properties of each such subparticle. """
# Euler angles that take particle to the orientation of the model
matrix_particle = inv(particle.getTransform().getMatrix())
shifts, angles = geometryFromMatrix(matrix_particle)
subparticles = []
subparticles_total += 1
symmetry_matrix_ids = range(1, len(symmetry_matrices) + 1)
if randomize:
# randomize the order of symmetry matrices, prevents preferred views
random.shuffle(symmetry_matrix_ids)
for subparticle_vector in subparticle_vector_list:
matrix_from_subparticle_vector = subparticle_vector.get_matrix()
for symmetry_matrix_id in symmetry_matrix_ids:
# symmetry_matrix_id can be later written out to find out
# which symmetry matrix created this subparticle
symmetry_matrix = np.array(symmetry_matrices[symmetry_matrix_id -
1][0:3, 0:3])
subpart = particle.clone()
m = np.matmul(
matrix_particle[0:3, 0:3],
(np.matmul(symmetry_matrix.transpose(),
matrix_from_subparticle_vector.transpose())))
angles_org = -1.0 * np.ones(3) * euler_from_matrix(m, 'szyz')
if align_subparticles:
angles = -1.0 * np.ones(3) * euler_from_matrix(m, 'szyz')
else:
m2 = np.matmul(matrix_particle[0:3, 0:3],
symmetry_matrix.transpose())
angles = -1.0 * np.ones(3) * euler_from_matrix(m2, 'szyz')
# subparticle origin
d = subparticle_vector.get_length()
x = -m[0, 2] * d + shifts[0]
y = -m[1, 2] * d + shifts[1]
z = -m[2, 2] * d
# save the subparticle coordinates (integer part) relative to the
# user given image size and as a small shift in the origin (decimal part)
x_d, x_i = math.modf(x)
y_d, y_i = math.modf(y)
alignment = em.Transform()
alignmentOrg = em.Transform()
M = matrixFromGeometry(np.array([-x_d, -y_d, 0]), angles, True)
MOrg = matrixFromGeometry(np.array([-x_d, -y_d, 0]), angles_org,
True)
alignment.setMatrix(M)
alignmentOrg.setMatrix(MOrg)
subpart._transorg = alignmentOrg.clone()
subpart.setTransform(alignment)
coord = Coordinate()
coord.setObjId(None)
coord.setX(int(part_image_size / 2) - x_i)
coord.setY(int(part_image_size / 2) - y_i)
coord.setMicId(particle.getObjId())
if subpart.hasCTF():
ctf = subpart.getCTF()
ctf.setDefocusU(subpart.getDefocusU() + z)
ctf.setDefocusV(subpart.getDefocusV() + z)
subpart.setCoordinate(coord)
coord._subparticle = subpart.clone()
subparticles.append(subpart)
return subparticles
