def listenShowJ(self):
self.serversocket = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
self.serversocket.bind(('', self.showjPort))
#become a server socket
self.serversocket.listen(1)
while True:
try:
(clientsocket, address) = self.serversocket.accept()
msg = clientsocket.recv(
1024) #should be a single message, so no loop
tokens = shlex.split(msg)
cmd = tokens[0]
if cmd == 'rotate':
rot = float(tokens[1])
tilt = float(tokens[2])
psi = float(tokens[3])
matrix = xmipp.Euler_angles2matrix(rot, tilt, psi)
elif cmd == 'rotate_matrix':
matrixString = tokens[1]
matrix = ast.literal_eval(matrixString)
matrix = [matrix[0][:3], matrix[1][:3], matrix[2][:3]]
self.client.send('rotate')
self.client.send(matrix)
clientsocket.close()
except EOFError:
print('Lost connection to client')
def listenShowJ(self):
"""This function with a very confusing name send messages to
the chimera server"""
while True:
try:
(clientsocket, address) = self.serversocket.accept()
msg = clientsocket.recv(
1024) #should be a single message, so no loop
tokens = shlex.split(msg)
cmd = tokens[0]
if cmd == 'rotate':
rot = float(tokens[1])
tilt = float(tokens[2])
psi = float(tokens[3])
matrix = xmipp.Euler_angles2matrix(rot, tilt, psi)
elif cmd == 'rotate_matrix':
matrixString = tokens[1]
matrix = ast.literal_eval(matrixString)
matrix = [matrix[0][:3], matrix[1][:3], matrix[2][:3]]
self.client.send('rotate')
self.client.send(matrix)
clientsocket.close()
except EOFError:
print('Lost connection to client')
def _getTransformation(self, md, objId):
rot = md.getValue(xmipp.MDL_ANGLE_ROT, objId) or 0.
tilt = md.getValue(xmipp.MDL_ANGLE_TILT, objId) or 0.
psi = md.getValue(xmipp.MDL_ANGLE_PSI, objId) or 0.
tMatrix = xmipp.Euler_angles2matrix(rot, tilt, psi)
x = md.getValue(xmipp.MDL_SHIFT_X, objId) or 0.
y = md.getValue(xmipp.MDL_SHIFT_Y, objId) or 0.
z = md.getValue(xmipp.MDL_SHIFT_Z, objId) or 0.
matrix = [
tMatrix[0][0], tMatrix[0][1], tMatrix[0][2], x, tMatrix[1][0],
tMatrix[1][1], tMatrix[1][2], y, tMatrix[2][0], tMatrix[2][1],
tMatrix[2][2], z
]
return matrix
def _showProjMatchLibAndImages(self, paramName=None):
from numpy import array, dot
#map stack position with ref number
imgAndClasses = []
mdIn = xmipp.MetaData()
mdOut = xmipp.MetaData()
mdTmp = xmipp.MetaData()
for ref3d in self._refsList:
for it in self._iterations:
convert_refno_to_stack_position = {}
file_name = self.protocol._getFileName(
'projectLibrarySampling', iter=it, ref=ref3d)
file_nameReferences = 'projectionDirections@' + file_name
if exists(file_name):
#last reference name
mdReferences = xmipp.MetaData(file_nameReferences)
mdReferencesSize = mdReferences.size()
for id in mdReferences:
convert_refno_to_stack_position[mdReferences.getValue(
xmipp.MDL_NEIGHBOR, id)] = id
file_nameImages = "ctfGroup[0-9][0-9][0-9][0-9][0-9][0-9]@" + self.protocol._getFileName(
'docfileInputAnglesIters', iter=it)
mdTmp.read(file_nameImages) #query with ref3D
mdIn.importObjects(mdTmp,
xmipp.MDValueEQ(xmipp.MDL_REF3D, ref3d))
mdOut.clear()
for i in mdIn:
id1 = mdOut.addObject()
mdOut.setValue(xmipp.MDL_IMAGE,
mdIn.getValue(xmipp.MDL_IMAGE, i), id1)
psi = -1. * mdIn.getValue(xmipp.MDL_ANGLE_PSI, i)
flip = mdIn.getValue(xmipp.MDL_FLIP, i)
if (flip):
psi = -psi
eulerMatrix = xmipp.Euler_angles2matrix(0., 0., psi)
x = mdIn.getValue(xmipp.MDL_SHIFT_X, i)
y = mdIn.getValue(xmipp.MDL_SHIFT_Y, i)
shift = array([x, y, 0])
shiftOut = dot(eulerMatrix, shift)
[x, y, z] = shiftOut
if flip:
x = -x
mdOut.setValue(xmipp.MDL_ANGLE_PSI, psi, id1)
mdOut.setValue(xmipp.MDL_SHIFT_X, x, id1)
mdOut.setValue(xmipp.MDL_SHIFT_Y, y, id1)
mdOut.setValue(xmipp.MDL_FLIP, flip, id1)
ref2D = mdIn.getValue(xmipp.MDL_REF, i)
file_references = self.protocol._getFileName(
'projectLibraryStk', iter=it, ref=ref3d)
file_reference = xmipp.FileName()
file_reference.compose(
convert_refno_to_stack_position[ref2D],
file_references)
id2 = mdOut.addObject()
mdOut.setValue(xmipp.MDL_IMAGE, file_reference, id2)
mdOut.setValue(xmipp.MDL_ANGLE_PSI, 0., id2)
if mdOut.size() == 0:
print "Empty metadata"
else:
file_nameReferences = self.protocol._getFileName(
'projectLibrarySampling', iter=it, ref=ref3d)
sfn = createUniqueFileName(file_nameReferences)
file_nameReferences = 'projectionDirections@' + sfn
mdOut.write(file_nameReferences)
imgAndClasses.append(
self.createDataView(file_nameReferences))
else:
print "File %s does not exist" % file_name
return imgAndClasses