def getStackParticleEulersForIteration(self, stackPart):
"""
find the eulers assigned to a stack particle
during a refinement. This function will first
find the particle id for the given stack particle,
then find its position in the reference stack, and
will get the eulers for that particle in the recon
assumes recon with FREALIGN
"""
# get stack particle id
stackPartId = stackPart.dbid
partId = stackPart['particle'].dbid
# find particle in reference stack
refStackId = apStack.getStackIdFromIterationId(self.params['reconiterid'], msg=False)
refStackPart = apStack.getStackParticleFromParticleId(partId, refStackId)
if not refStackPart:
apDisplay.printWarning('No classification for stack particle %d in reconstruction iteration id: %d' % (refStackId, self.params['reconiterid']))
self.noClassification += 1
if self.noClassification > (float(params['last'])*0.10):
apDisplay.printError('More than 10% of the particles have no classification, use a different reference reconstruction')
eulerDict = {
'psi': 0.0,
'theta': 0.0,
'phi': 0.0,
'shiftx': 0.0,
'shifty': 0.0,
}
return eulerDict
refIterData = appiondata.ApRefineIterData.direct_query(self.params['reconiterid'])
if refStackPart.dbid != stackPartId:
self.mismatch += 1
refinePartQuery = appiondata.ApRefineParticleData()
refinePartQuery['particle'] = refStackPart
refinePartQuery['refineIter'] = refIterData
refinePartDatas = refinePartQuery.query()
refinePartData = refinePartDatas[0]
emanEulerDict = {
'alt': refinePartData['euler1'],
'az': refinePartData['euler2'],
'phi': refinePartData['euler3'],
'shiftx': refinePartData['shiftx'],
'shifty': refinePartData['shifty'],
'mirror': refinePartData['mirror'],
}
eulerDict = apFrealign.convertAppionEmanEulersToFrealign(emanEulerDict, self.symmetryName)
eulerDict['shiftx'] = emanEulerDict['shiftx']*self.params['bin']
eulerDict['shifty'] = emanEulerDict['shifty']*self.params['bin']
if refinePartData['mirror'] is True:
eulerDict['shiftx'] *= -1
return eulerDict
def getStackParticleEulersForIteration(params, pnum):
"""
find the eulers assigned to a stack particle
during a refinement. This function will first
find the particle id for the given stack particle,
then find its position in the reference stack, and
will get the eulers for that particle in the recon
"""
# get stack particle id
stackp = apStack.getStackParticle(params['stackid'], pnum)
particleid = stackp['particle'].dbid
# find particle in reference stack
refstackid = apStack.getStackIdFromIterationId(params['reconiterid'],
msg=False)
refstackp = apStack.getStackParticleFromParticleId(particleid,
refstackid,
nodie=True)
if not refstackp:
apDisplay.printWarning(
'No classification for stack particle %d in reconstruction iteration id: %d'
% (pnum, params['reconiterid']))
params['noClassification'] += 1
if params['noClassification'] > (float(params['last']) * 0.10):
apDisplay.printError(
'More than 10% of the particles have no classification, use a different reference reconstruction'
)
pclass = {}
pclass['eulers'] = {}
pclass['eulers']['euler1'] = 0.0
pclass['eulers']['euler2'] = 0.0
pclass['inplane_rotation'] = 0.0
pclass['mirror'] = False
pclass['shiftx'] = 0.0
pclass['shifty'] = 0.0
else:
pclassq = appiondata.ApRefineParticleData()
pclassq['particle'] = refstackp
pclassq['refineIter'] = appiondata.ApRefineIterData.direct_query(
params['reconiterid'])
pclass = pclassq.query()
pclass = pclass[0]
params['eman_orient'] = {}
params['eman_orient']['alt'] = pclass['euler1']
params['eman_orient']['az'] = pclass['euler2']
params['eman_orient']['phi'] = pclass['euler3']
params['eman_orient']['mirror'] = pclass['mirror']
params['eman_orient']['shiftx'] = pclass['shiftx']
params['eman_orient']['shifty'] = pclass['shifty']
return params
def getStackParticleEulersForIteration(params,pnum):
"""
find the eulers assigned to a stack particle
during a refinement. This function will first
find the particle id for the given stack particle,
then find its position in the reference stack, and
will get the eulers for that particle in the recon
"""
# get stack particle id
stackp = apStack.getStackParticle(params['stackid'],pnum)
particleid = stackp['particle'].dbid
# find particle in reference stack
refstackid = apStack.getStackIdFromIterationId(params['reconiterid'],msg=False)
refstackp = apStack.getStackParticleFromParticleId(particleid,refstackid, nodie=True)
if not refstackp:
apDisplay.printWarning('No classification for stack particle %d in reconstruction iteration id: %d' % (pnum, params['reconiterid']))
params['noClassification']+=1
if params['noClassification'] > (float(params['last'])*0.10):
apDisplay.printError('More than 10% of the particles have no classification, use a different reference reconstruction')
pclass={}
pclass['eulers']={}
pclass['eulers']['euler1']=0.0
pclass['eulers']['euler2']=0.0
pclass['inplane_rotation']=0.0
pclass['mirror']=False
pclass['shiftx']=0.0
pclass['shifty']=0.0
else:
pclassq = appiondata.ApRefineParticleData()
pclassq['particle'] = refstackp
pclassq['refineIter'] = appiondata.ApRefineIterData.direct_query(params['reconiterid'])
pclass = pclassq.query()
pclass=pclass[0]
params['eman_orient']={}
params['eman_orient']['alt']=pclass['euler1']
params['eman_orient']['az']=pclass['euler2']
params['eman_orient']['phi']=pclass['euler3']
params['eman_orient']['mirror']=pclass['mirror']
params['eman_orient']['shiftx']=pclass['shiftx']
params['eman_orient']['shifty']=pclass['shifty']
return params
def setupParticleParams(self):
if self.params["reconiterid"] is not None:
### use parameters from previous reconstruction
self.iflag = 1
self.oldreconstackid = apStack.getStackIdFromIterationId(self.params["reconiterid"])
elif self.params["dang"] is not None:
### use slow projection matching search to determine initial Eulers
self.iflag = 3
"""
if self.params['inpar'] is not None and os.path.isfile(self.params['inpar']):
### use specified parameter file
paramfile = self.params['inpar']
apDisplay.printMsg("Using parameter file: "+paramfile)
return paramfile
"""
paramfile = self.generateParticleParams()
return paramfile
def setupParticleParams(self):
if self.params['reconiterid'] is not None:
### use parameters from previous reconstruction
self.iflag = 1
self.oldreconstackid = apStack.getStackIdFromIterationId(
self.params['reconiterid'])
elif self.params['dang'] is not None:
### use slow projection matching search to determine initial Eulers
self.iflag = 3
"""
if self.params['inpar'] is not None and os.path.isfile(self.params['inpar']):
### use specified parameter file
paramfile = self.params['inpar']
apDisplay.printMsg("Using parameter file: "+paramfile)
return paramfile
"""
paramfile = self.generateParticleParams()
return paramfile
def getStackParticleEulersForIteration(self, stackPart):
"""
find the eulers assigned to a stack particle
during a refinement. This function will first
find the particle id for the given stack particle,
then find its position in the reference stack, and
will get the eulers for that particle in the recon
assumes recon with FREALIGN
"""
# get stack particle id
stackPartId = stackPart.dbid
partId = stackPart['particle'].dbid
# find particle in reference stack
refStackId = apStack.getStackIdFromIterationId(
self.params['reconiterid'], msg=False)
refStackPart = apStack.getStackParticleFromParticleId(
partId, refStackId)
if not refStackPart:
apDisplay.printWarning(
'No classification for stack particle %d in reconstruction iteration id: %d'
% (refStackId, self.params['reconiterid']))
self.noClassification += 1
if self.noClassification > (float(params['last']) * 0.10):
apDisplay.printError(
'More than 10% of the particles have no classification, use a different reference reconstruction'
)
eulerDict = {
'psi': 0.0,
'theta': 0.0,
'phi': 0.0,
'shiftx': 0.0,
'shifty': 0.0,
}
return eulerDict
refIterData = appiondata.ApRefineIterData.direct_query(
self.params['reconiterid'])
if refStackPart.dbid != stackPartId:
self.mismatch += 1
refinePartQuery = appiondata.ApRefineParticleData()
refinePartQuery['particle'] = refStackPart
refinePartQuery['refineIter'] = refIterData
refinePartDatas = refinePartQuery.query()
refinePartData = refinePartDatas[0]
emanEulerDict = {
'alt': refinePartData['euler1'],
'az': refinePartData['euler2'],
'phi': refinePartData['euler3'],
'shiftx': refinePartData['shiftx'],
'shifty': refinePartData['shifty'],
'mirror': refinePartData['mirror'],
}
eulerDict = apFrealign.convertAppionEmanEulersToFrealign(
emanEulerDict, self.symmetryName)
eulerDict['shiftx'] = emanEulerDict['shiftx'] * self.params['bin']
eulerDict['shifty'] = emanEulerDict['shifty'] * self.params['bin']
if refinePartData['mirror'] is True:
eulerDict['shiftx'] *= -1
return eulerDict