def createOutputStep(self):
setEnviron() # Set the environment to access localrec modules
import localrec
import pyrelion
# return
inputSet = self._getInputParticles()
outputSet = self._createSetOfCoordinates(inputSet)
params = {
"symmetryGroup": self.symmetryGroup.get(),
"vector": self.vector.get(),
"vectorFile": self.vectorFile.get(),
"length": self.length.get(),
"unique": self.unique.get(),
"mindist": self.mindist.get(),
"side": self.side.get(),
"top": self.top.get(),
"pxSize": self.inputParticles.get().getSamplingRate(),
"dim": self.inputParticles.get().getXDim()
}
symMatrices = localrec.matrix_from_symmetry(self.symmetryGroup.get())
if self.defineVector == CMM:
cmmFn = params["vectorFile"]
vector = " "
else:
cmmFn = ""
vector = params["vector"]
subpartVectorList = localrec.load_vectors(cmmFn, vector,
params["length"],
params["pxSize"])
# Define some conditions to filter subparticles
filters = localrec.load_filters(math.radians(params["side"]),
math.radians(params["top"]),
params["mindist"])
coord = Coordinate()
for part in inputSet:
partItem = pyrelion.Item()
particleToRow(part, partItem)
subparticles = self.getSubparticles(localrec, partItem,
symMatrices, params,
subpartVectorList, filters)
for subpart in subparticles:
rowToSubcoordinate(subpart, coord, part)
coord.setObjId(None) # Force to insert as a new item
outputSet.append(coord)
if part.hasAttribute('_rlnRandomSubset'):
coord._subparticle.copyAttributes(part, '_rlnRandomSubset')
restituteRelionHome()
self._defineOutputs(outputCoordinates=outputSet)
self._defineSourceRelation(self.inputParticles, outputSet)
def createOutputStep(self):
setEnviron() # Set the environment to access localrec modules
import localrec
import pyrelion
# return
inputSet = self._getInputParticles()
outputSet = self._createSetOfCoordinates(inputSet)
params = {"symmetryGroup" : self.symmetryGroup.get(),
"vector" : self.vector.get(),
"vectorFile" : self.vectorFile.get(),
"length" : self.length.get(),
"unique" : self.unique.get(),
"mindist" : self.mindist.get(),
"side" : self.side.get(),
"top" : self.top.get(),
"pxSize" : self.inputParticles.get().getSamplingRate(),
"dim" : self.inputParticles.get().getXDim()
}
symMatrices = localrec.matrix_from_symmetry(self.symmetryGroup.get())
if self.defineVector == CMM:
cmmFn = params["vectorFile"]
vector = " "
else:
cmmFn = ""
vector = params["vector"]
subpartVectorList = localrec.load_vectors(cmmFn, vector,
params["length"],
params["pxSize"])
# Define some conditions to filter subparticles
filters = localrec.load_filters(math.radians(params["side"]),
math.radians(params["top"]),
params["mindist"])
coord = Coordinate()
for part in inputSet:
partItem = pyrelion.Item()
particleToRow(part, partItem)
subparticles = self.getSubparticles(localrec, partItem,
symMatrices, params,
subpartVectorList, filters)
for subpart in subparticles:
rowToSubcoordinate(subpart, coord, part)
coord.setObjId(None) # Force to insert as a new item
outputSet.append(coord)
if part.hasAttribute('_rlnRandomSubset'):
coord._subparticle.copyAttributes(part, '_rlnRandomSubset')
restituteRelionHome()
self._defineOutputs(outputCoordinates=outputSet)
self._defineSourceRelation(self.inputParticles, outputSet)
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
