def rowToAlignment(alignmentRow, alignType):
"""
is2D == True-> matrix is 2D (2D images alignment)
otherwise matrix is 3D (3D volume alignment or projection)
invTransform == True -> for xmipp implies projection
"""
is2D = alignType == em.ALIGN_2D
inverseTransform = True #alignType == em.ALIGN_PROJ
if alignmentRow.containsAny(ALIGNMENT_DICT):
alignment = em.Transform()
angles = numpy.zeros(3)
shifts = numpy.zeros(3)
angles[2] = alignmentRow.getValue(md.RLN_ORIENT_PSI, 0.)
shifts[0] = alignmentRow.getValue(md.RLN_ORIENT_ORIGIN_X, 0.)
shifts[1] = alignmentRow.getValue(md.RLN_ORIENT_ORIGIN_Y, 0.)
if not is2D:
angles[0] = alignmentRow.getValue(md.RLN_ORIENT_ROT, 0.)
angles[1] = alignmentRow.getValue(md.RLN_ORIENT_TILT, 0.)
shifts[2] = alignmentRow.getValue(md.RLN_ORIENT_ORIGIN_Z, 0.)
M = matrixFromGeometry(shifts, angles, inverseTransform)
alignment.setMatrix(M)
else:
alignment = None
return alignment
def createOutputStep(self):
vols = []
for vol in self._iterInputVolumes():
outVol = em.Volume()
outVol.setLocation(vol.outputName)
outVol.setObjLabel(vol.getObjLabel())
outVol.setObjComment(vol.getObjComment())
#set transformation matrix
volId = vol.getObjId()
fhInputTranMat = self._getExtraPath('transformation-matrix_vol%06d.txt'%volId)
transMatFromFile = np.loadtxt(fhInputTranMat)
transformationMat = np.reshape(transMatFromFile,(4,4))
transform = em.Transform()
transform.setMatrix(transformationMat)
outVol.setTransform(transform)
vols.append(outVol)
if len(vols) > 1:
volSet = self._createSetOfVolumes()
volSet.setSamplingRate(self.inputReference.get().getSamplingRate())
for vol in vols:
volSet.append(vol)
outputArgs = {'outputVolumes': volSet}
else:
vols[0].setSamplingRate(self.inputReference.get().getSamplingRate())
outputArgs = {'outputVolume': vols[0]}
self._defineOutputs(**outputArgs)
for pointer in self.inputVolumes:
self._defineSourceRelation(pointer, outputArgs.values()[0])
def createOutputStep(self):
outVolFn = self._getExtraPath("inputVolumeAligned.vol")
outVol = em.Volume()
outVol.setLocation(outVolFn)
#set transformation matrix
fhInputTranMat = self._getExtraPath('transformation-matrix.txt')
transMatFromFile = np.loadtxt(fhInputTranMat)
transformationMat = np.reshape(transMatFromFile, (4, 4))
transform = em.Transform()
transform.setMatrix(transformationMat)
outVol.setTransform(transform)
outVol.setSamplingRate(self.inputVolume.get().getSamplingRate())
outputArgs = {'outputVolume': outVol}
self._defineOutputs(**outputArgs)
self._defineSourceRelation(self.inputVolume, outVol)
#particles....
outParticlesFn = self._getExtraPath('outputParticles.xmd')
outputParticles = self._createSetOfParticles()
outputParticles.copyInfo(self.inputParticles.get())
outputParticles.setAlignmentProj()
readSetOfParticles(outParticlesFn, outputParticles)
outputArgs = {'outputParticles': outputParticles}
self._defineOutputs(**outputArgs)
self._defineSourceRelation(self.inputParticles, outputParticles)
def rowToAlignment(subpart):
inverseTransform = True
alignment = em.Transform()
angles = numpy.zeros(3)
shifts = numpy.zeros(3)
shifts[0] = subpart.rlnOriginX
shifts[1] = subpart.rlnOriginY
shifts[2] = subpart.rlnOriginZ or 0
angles[0] = subpart.rlnAngleRot
angles[1] = subpart.rlnAngleTilt
angles[2] = subpart.rlnAnglePsi
M = matrixFromGeometry(shifts, angles, inverseTransform)
alignment.setMatrix(M)
return alignment
def rowToAlignment(alignmentRow, samplingRate):
"""
Return an Transform object representing the Alignment
from a given parFile row.
"""
angles = np.zeros(3)
shifts = np.zeros(3)
alignment = em.Transform()
# PSI THETA PHI SHX SHY
angles[0] = float(alignmentRow.get('PSI'))
angles[1] = float(alignmentRow.get('THETA'))
angles[2] = float(alignmentRow.get('PHI'))
shifts[0] = float(alignmentRow.get('SHX')) / samplingRate
shifts[1] = float(alignmentRow.get('SHY')) / samplingRate
M = matrixFromGeometry(shifts, angles)
alignment.setMatrix(M)
return alignment
def rowToAlignment(alignmentList, alignType):
"""
is2D == True-> matrix is 2D (2D images alignment)
otherwise matrix is 3D (3D volume alignment or projection)
invTransform == True -> for xmipp implies projection
"""
is2D = alignType == em.ALIGN_2D
inverseTransform = alignType == em.ALIGN_PROJ
alignment = em.Transform()
angles = numpy.zeros(3)
shifts = numpy.zeros(3)
shifts[0] = alignmentList[3]
shifts[1] = alignmentList[4]
if not is2D:
angles[0] = alignmentList[0]
angles[1] = alignmentList[1]
shifts[2] = 0
angles[2] = alignmentList[2]
else:
psi = alignmentList[0]
rot = alignmentList[1]
if rot !=0. and psi !=0:
print "HORROR rot and psi are different from zero"
angles[0] = alignmentList[0] + alignmentList[1]
#if alignment
matrix = matrixFromGeometry(shifts, angles, inverseTransform)
alignment.setMatrix(matrix)
#FIXME: now are also storing the alignment parameters since
# the conversions to the Transform matrix have not been extensively tested.
# After this, we should only keep the matrix
#for paramName, label in ALIGNMENT_DICT.iteritems():
# if alignmentRow.hasLabel(label):
# setattr(alignment, paramName, alignmentRow.getValueAsObject(label))
return alignment
def rowToAlignment(alignmentList, alignType):
"""
is2D == True-> matrix is 2D (2D images alignment)
otherwise matrix is 3D (3D volume alignment or projection)
invTransform == True -> for xmipp implies projection
"""
# use all angles in 2D since we might have mirrors
# is2D = alignType == em.ALIGN_2D
inverseTransform = alignType == em.ALIGN_PROJ
alignment = em.Transform()
angles = numpy.zeros(3)
shifts = numpy.zeros(3)
shifts[0] = alignmentList[3]
shifts[1] = alignmentList[4]
shifts[2] = 0
angles[0] = alignmentList[0]
angles[1] = alignmentList[1]
angles[2] = alignmentList[2]
matrix = matrixFromGeometry(shifts, angles, inverseTransform)
alignment.setMatrix(matrix)
return alignment
def alignParticlesStep(self):
fhInputTranMat = self._getExtraPath('transformation-matrix.txt')
outParticlesFn = self._getExtraPath('outputParticles.xmd')
transMatFromFile = np.loadtxt(fhInputTranMat)
transformationMat = np.reshape(transMatFromFile, (4, 4))
transform = em.Transform()
transform.setMatrix(transformationMat)
resultMat = Transform()
outputParts = md.MetaData()
mdToAlign = md.MetaData(self.imgsInputFn)
for row in md.iterRows(mdToAlign):
inMat = rowToAlignment(row, ALIGN_PROJ)
partTransformMat = inMat.getMatrix()
partTransformMatrix = np.matrix(partTransformMat)
newTransformMatrix = np.matmul(transformationMat,
partTransformMatrix)
resultMat.setMatrix(newTransformMatrix)
rowOut = md.Row()
rowOut.copyFromRow(row)
alignmentToRow(resultMat, rowOut, ALIGN_PROJ)
rowOut.addToMd(outputParts)
outputParts.write(outParticlesFn)
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
