def geometryFromMatrix(matrix):
from pwem.convert.transformations import euler_from_matrix
matrix = inv(matrix)
angles = -rad2deg(euler_from_matrix(matrix, axes='szyz'))
return angles
def prepareObj(self, index, halfString, doAlign, objType):
shiftX, shiftY, shiftZ, rotMatrix = self.readVector(index)
rot, tilt, psi = np.rad2deg(
euler_from_matrix(rotMatrix.transpose(), 'szyz'))
# Window the sub-volume to the output volume size
objWin = self._getFileName(objType, 'windowed', index + 1, halfString)
if objType == 'mask':
objMasked = self._getFileName('mask', index + 1)
else:
objMasked = self._getFileName(objType, 'masked', index + 1,
halfString)
program = 'xmipp_transform_window'
args = '-i %s --size %d -o %s' % (objMasked, self.outDim, objWin)
self.runJob(program, args)
# If sub-particles are aligned along z
if doAlign:
program = 'xmipp_transform_geometry'
args = '-i %s --rotate_volume euler %f %f %f -o %s' \
% (objWin, -rot, -tilt, -psi, objWin)
self.runJob(program, args)
# Shift the sub-volume to its center in the volume
objShifted = self._getFileName(objType, 'shifted', index + 1,
halfString)
program = 'xmipp_transform_geometry'
args = (
'-i %s --shift %f %f %f -o %s --dont_wrap --interp %s' %
(objWin, shiftX, shiftY, shiftZ, objShifted, self.interpString))
self.runJob(program, args)
def _align2DToRow(self, alignment, row):
matrix = alignment.getMatrix()
shifts = tfs.translation_from_matrix(matrix)
shifts *= self._pixelSize
angles = -np.rad2deg(tfs.euler_from_matrix(matrix, axes='szyz'))
row['rlnOriginXAngst'], row['rlnOriginYAngst'] = shifts[:2]
row['rlnAnglePsi'] = -(angles[0] + angles[2])
def _alignProjToRow(self, alignment, row):
matrix = np.linalg.inv(alignment.getMatrix())
shifts = -tfs.translation_from_matrix(matrix)
shifts *= self._pixelSize
angles = -np.rad2deg(tfs.euler_from_matrix(matrix, axes='szyz'))
row['rlnOriginXAngst'], row['rlnOriginYAngst'], row[
'rlnOriginZAngst'] = shifts
row['rlnAngleRot'], row['rlnAngleTilt'], row['rlnAnglePsi'] = angles
def geometryFromMatrix(matrix, inverseTransform):
if inverseTransform:
matrix = numpy.linalg.inv(matrix)
shifts = -transformations.translation_from_matrix(matrix)
else:
shifts = transformations.translation_from_matrix(matrix)
angles = -numpy.rad2deg(
transformations.euler_from_matrix(matrix, axes='szyz'))
return shifts, angles
def geometryFromMatrix(matrix, inverseTransform):
from pwem.convert.transformations import translation_from_matrix, euler_from_matrix
if inverseTransform:
from numpy.linalg import inv
matrix = inv(matrix)
shifts = -translation_from_matrix(matrix)
else:
shifts = translation_from_matrix(matrix)
angles = -numpy.rad2deg(euler_from_matrix(matrix, axes='szyz'))
return shifts, angles
def convertInputStep(self):
inputParts = self.inputParticles.get()
self.rotDict, self.tiltDict, self.psiDict = {}, {}, {}
for part in inputParts:
alignment = part.getTransform()
matrix = np.linalg.inv(alignment.getMatrix())
angles = -np.rad2deg(tfs.euler_from_matrix(matrix, axes='szyz'))
self.rotDict[part.getObjId()] = angles[0]
self.tiltDict[part.getObjId()] = angles[1]
self.psiDict[part.getObjId()] = angles[2]
def geometryFromMatrix(matrix):
""" Convert the transformation matrix to shifts and angles.
:param matrix: input matrix
:return: two lists, shifts and angles
"""
matrix = np.linalg.inv(matrix)
shifts = -transformations.translation_from_matrix(matrix)
angles = -np.rad2deg(transformations.euler_from_matrix(matrix,
axes='szyz'))
return shifts, angles
def geometryFromMatrix(matrix, inverseTransform):
""" Convert the transformation matrix to shifts and angles.
:param matrix: input matrix
:return: two lists, shifts and angles
"""
from pwem.convert.transformations import translation_from_matrix, euler_from_matrix
if inverseTransform:
from numpy.linalg import inv
matrix = inv(matrix)
shifts = -translation_from_matrix(matrix)
else:
shifts = translation_from_matrix(matrix)
angles = -numpy.rad2deg(euler_from_matrix(matrix, axes='szyz'))
return shifts, angles
def _getTransformInfoFromSubtomo(subtomo, calcInv=True):
angles = [0, 0, 0]
shifts = [0, 0, 0]
T = subtomo.getTransform()
if T: # Alignment performed before
M = subtomo.getTransform().getMatrix()
shifts = translation_from_matrix(M)
if calcInv:
shifts = -shifts
M = np.linalg.inv(M)
angles = -np.rad2deg(euler_from_matrix(M, axes='szyz'))
return angles, shifts
def geometryFromMatrix(matrix):
from pwem.convert.transformations import translation_from_matrix, euler_from_matrix
shifts = -1.0 * translation_from_matrix(matrix)
angles = -1.0 * np.ones(3) * euler_from_matrix(matrix, axes='szyz')
return shifts, angles
def create_subparticles(particle, symmetry_matrices, subparticle_vector_list,
part_image_size, randomize, subparticles_total,
align_subparticles, handness, angpix):
""" 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.objects.data.Transform()
alignmentOrg = em.objects.data.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():
# Pixel to Angstrom
z_ang = z * angpix
if not handness:
z_ang *= -1
ctf = subpart.getCTF()
ctf.setDefocusU(subpart.getCTF().getDefocusU() + z_ang)
ctf.setDefocusV(subpart.getCTF().getDefocusV() + z_ang)
subpart.setCoordinate(coord)
coord._subparticle = subpart.clone()
subparticles.append(subpart)
return subparticles