def getSiblingImgAssessmentStatus(imgdata): status = getImgAssessmentStatus(imgdata) if status is not None: return status siblingimgdata = apDefocalPairs.getDefocusPair(imgdata) if siblingimgdata: status = getImgAssessmentStatus(siblingimgdata) return status
def getSiblingImgAssessmentStatus(imgdata):
status = getImgAssessmentStatus(imgdata)
if status is not None:
return status
siblingimgdata = apDefocalPairs.getDefocusPair(imgdata)
if siblingimgdata:
status = getImgAssessmentStatus(siblingimgdata)
return status
def getDefocPairParticles(imgdata, selectionid, particlelabel=None):
### get defocal pair
if imgdata['preset'] is not None:
defimgdata = apDefocalPairs.getDefocusPair(imgdata)
else:
# For pairs from Leginon Manual Application
defimgdata = apDefocalPairs.getManualDefocusPair(imgdata)
if defimgdata is None:
apDisplay.printWarning(
"Could not find defocal pair for image %s (id %d)" %
(apDisplay.short(imgdata['filename']), imgdata.dbid))
return ([], {'shiftx': 0, 'shifty': 0, 'scale': 1})
apDisplay.printMsg(
"Found defocus pair %s (id %d) for image %s (id %d)" %
(apDisplay.short(defimgdata['filename']), defimgdata.dbid,
apDisplay.short(imgdata['filename']), imgdata.dbid))
### get particles
partq = appiondata.ApParticleData()
partq['image'] = defimgdata
partq['selectionrun'] = appiondata.ApSelectionRunData.direct_query(
selectionid)
if particlelabel is not None:
partq['label'] = particlelabel
partdatas = partq.query()
apDisplay.printMsg("Found %d particles for defocal pair %s (id %d)" % (
len(partdatas),
apDisplay.short(defimgdata['filename']),
defimgdata.dbid,
))
if len(partdatas) == 0:
return ([], {'shiftx': 0, 'shifty': 0, 'scale': 1})
### get shift information
has_tried = False
while True:
shiftq = appiondata.ApImageTransformationData()
shiftq['image1'] = defimgdata
shiftdatas = shiftq.query()
if shiftdatas:
shiftdata = shiftdatas[0]
apDisplay.printMsg(
"Shifting particles by %.1f,%.1f (%d X)" %
(shiftdata['shiftx'], shiftdata['shifty'], shiftdata['scale']))
break
else:
if has_tried == True:
apDisplay.printError(
"No shift inserted to database after one try")
apDisplay.printMsg("Calculating shift....")
shiftpeak = apDefocalPairs.getShift(defimgdata, imgdata)
apDefocalPairs.insertShift(defimgdata, imgdata, shiftpeak)
has_tried = True
return (partdatas, shiftdata)
def getSiblingImgCompleteStatus(imgdata):
'''
Get the assessment status for sibling. Uses getImgCompleteStatus method to include viewer_status assessment
'''
siblingimgdata = apDefocalPairs.getDefocusPair(imgdata)
if siblingimgdata:
status = getImgCompleteStatus(siblingimgdata)
else:
status = None
return status
def getSiblingImgCompleteStatus(imgdata): ''' Get the assessment status for sibling. Uses getImgCompleteStatus method to include viewer_status assessment ''' siblingimgdata = apDefocalPairs.getDefocusPair(imgdata) if siblingimgdata: status = getImgCompleteStatus(siblingimgdata) else: status = None return status
def getDefocPairParticles(imgdata, selectionid, particlelabel=None):
### get defocal pair
if imgdata['preset'] is not None:
defimgdata = apDefocalPairs.getDefocusPair(imgdata)
else:
# For pairs from Leginon Manual Application
defimgdata = apDefocalPairs.getManualDefocusPair(imgdata)
if defimgdata is None:
apDisplay.printWarning("Could not find defocal pair for image %s (id %d)"
%(apDisplay.short(imgdata['filename']), imgdata.dbid))
return ([], {'shiftx':0, 'shifty':0, 'scale':1})
apDisplay.printMsg("Found defocus pair %s (id %d) for image %s (id %d)"
%(apDisplay.short(defimgdata['filename']), defimgdata.dbid, apDisplay.short(imgdata['filename']), imgdata.dbid))
### get particles
partq = appiondata.ApParticleData()
partq['image'] = defimgdata
partq['selectionrun'] = appiondata.ApSelectionRunData.direct_query(selectionid)
if particlelabel is not None:
partq['label'] = particlelabel
partdatas = partq.query()
apDisplay.printMsg("Found %d particles for defocal pair %s (id %d)"
%(len(partdatas), apDisplay.short(defimgdata['filename']), defimgdata.dbid,))
if len(partdatas) == 0:
return ([], {'shiftx':0, 'shifty':0, 'scale':1})
### get shift information
has_tried = False
while True:
shiftq = appiondata.ApImageTransformationData()
shiftq['image1'] = defimgdata
shiftdatas = shiftq.query()
if shiftdatas:
shiftdata = shiftdatas[0]
apDisplay.printMsg("Shifting particles by %.1f,%.1f (%d X)"
%(shiftdata['shiftx'], shiftdata['shifty'], shiftdata['scale']))
break
else:
if has_tried == True:
apDisplay.printError("No shift inserted to database after one try")
apDisplay.printMsg("Calculating shift....")
shiftpeak = apDefocalPairs.getShift(defimgdata, imgdata)
apDefocalPairs.insertShift(defimgdata, imgdata, shiftpeak)
has_tried = True
return (partdatas, shiftdata)
def generateParticleParams(params,modeldata,initparfile='params.0.par'):
params['inpar']=os.path.join(params['rundir'],initparfile)
apDisplay.printMsg("Creating parameter file: "+params['inpar'])
params['mode']=3
stackdata=getStackParticlesInOrder(params)
first_imageid = stackdata[0]['particle']['image'].dbid
f=open(params['inpar'],'w')
params['noClassification']=0
if params['reconiterid']:
iterdata = apRecon.getRefineIterDataFromIterationId(params['reconiterid'])
sym_name = modeldata['symmetry']['symmetry']
print "Writing out particle parameters"
if 'last' not in params:
params['last'] = len(stackdata)
for i, particle in enumerate(stackdata[:params['last']]):
# defaults
particleparams = initializeParticleParams(i)
# for helical reconstructions, film is helix number
if particle['particle']['helixnum']:
imgid=particle['particle']['image'].dbid
helix=particle['particle']['helixnum']
try:
if params['lastimgid']!=imgid or params['lasthelix']!=helix:
params['totalHelix']+=1
except:
params['totalHelix']=1
params['lastimgid']=imgid
params['lasthelix']=helix
particleparams['film']=params['totalHelix']
else:
particleparams['film']=particle['particle']['image'].dbid - first_imageid + 1
# extra particle number information not read by Frealign
particleparams['pnumber']=particle['particleNumber']
imagedata=particle['particle']['image']
if params['noctf'] is False:
if params['defocpair'] is True:
imagedata = apDefocalPairs.getDefocusPair(imagedata)
# get tilted parameters first:
if params['ctftilt'] is True:
ctfdata = ctfdb.getBestTiltCtfValueForImage(imagedata)
if ctfdata is None:
apDisplay.printError("Failed to get ctf parameters")
# get x,y coordinate of the particle
nx = particle['particle']['xcoord']
ny = particle['particle']['ycoord']
df1,df2 = ctfdb.getParticleTiltDefocus(ctfdata,imagedata,nx,ny)
# use defocus & astigmatism values
particleparams['df1']=abs(df1)
particleparams['df2']=abs(df2)
particleparams['angast']=ctfdata['angle_astigmatism']
else:
# first see if there are ctf values
ctfdata, confidence=ctfdb.getBestCtfValueForImage(imagedata, msg=False,method=params['ctfmethod'])
## Do we really want value from any method if it is specified?
if ctfdata is None:
ctfdata, confidence=ctfdb.getBestCtfValueForImage(imagedata, msg=False)
if ctfdata is not None:
# use defocus & astigmatism values
particleparams['df1']=abs(ctfdata['defocus1']*1e10)
particleparams['df2']=abs(ctfdata['defocus2']*1e10)
particleparams['angast']=ctfdata['angle_astigmatism']
# if using parameters from previous reconstruction
if params['reconiterid'] is not None:
params['mode']=1
getStackParticleEulersForIteration(params,particle['particleNumber'])
fr_eulers = convertAppionEmanEulersToFrealign(params['eman_orient'],sym_name)
particleparams['psi'] = fr_eulers['psi']
particleparams['theta'] = fr_eulers['theta']
particleparams['phi'] = fr_eulers['phi']
particleparams['shx']=-params['eman_orient']['shiftx']
particleparams['shy']=-params['eman_orient']['shifty']
if params['eman_orient']['mirror'] is True:
particleparams['shx']*=-1
writeParticleParamLine(particleparams,f)
f.close()
def generateParticleParams(params, modeldata, initparfile='params.0.par'):
params['inpar'] = os.path.join(params['rundir'], initparfile)
apDisplay.printMsg("Creating parameter file: " + params['inpar'])
params['mode'] = 3
stackdata = getStackParticlesInOrder(params)
first_imageid = stackdata[0]['particle']['image'].dbid
f = open(params['inpar'], 'w')
params['noClassification'] = 0
if params['reconiterid']:
iterdata = apRecon.getRefineIterDataFromIterationId(
params['reconiterid'])
sym_name = modeldata['symmetry']['symmetry']
print "Writing out particle parameters"
if 'last' not in params:
params['last'] = len(stackdata)
for i, particle in enumerate(stackdata[:params['last']]):
# defaults
particleparams = initializeParticleParams(i)
# for helical reconstructions, film is helix number
if particle['particle']['helixnum']:
imgid = particle['particle']['image'].dbid
helix = particle['particle']['helixnum']
try:
if params['lastimgid'] != imgid or params['lasthelix'] != helix:
params['totalHelix'] += 1
except:
params['totalHelix'] = 1
params['lastimgid'] = imgid
params['lasthelix'] = helix
particleparams['film'] = params['totalHelix']
else:
particleparams['film'] = particle['particle'][
'image'].dbid - first_imageid + 1
# extra particle number information not read by Frealign
particleparams['pnumber'] = particle['particleNumber']
imagedata = particle['particle']['image']
if params['noctf'] is False:
if params['defocpair'] is True:
imagedata = apDefocalPairs.getDefocusPair(imagedata)
# get tilted parameters first:
if params['ctftilt'] is True:
ctfdata = ctfdb.getBestTiltCtfValueForImage(imagedata)
if ctfdata is None:
apDisplay.printError("Failed to get ctf parameters")
# get x,y coordinate of the particle
nx = particle['particle']['xcoord']
ny = particle['particle']['ycoord']
df1, df2 = ctfdb.getParticleTiltDefocus(
ctfdata, imagedata, nx, ny)
# use defocus & astigmatism values
particleparams['df1'] = abs(df1)
particleparams['df2'] = abs(df2)
particleparams['angast'] = ctfdata['angle_astigmatism']
else:
# first see if there are ctf values
ctfdata, confidence = ctfdb.getBestCtfValueForImage(
imagedata, msg=False, method=params['ctfmethod'])
## Do we really want value from any method if it is specified?
if ctfdata is None:
ctfdata, confidence = ctfdb.getBestCtfValueForImage(
imagedata, msg=False)
if ctfdata is not None:
# use defocus & astigmatism values
particleparams['df1'] = abs(ctfdata['defocus1'] * 1e10)
particleparams['df2'] = abs(ctfdata['defocus2'] * 1e10)
particleparams['angast'] = ctfdata['angle_astigmatism']
# if using parameters from previous reconstruction
if params['reconiterid'] is not None:
params['mode'] = 1
getStackParticleEulersForIteration(params,
particle['particleNumber'])
fr_eulers = convertAppionEmanEulersToFrealign(
params['eman_orient'], sym_name)
particleparams['psi'] = fr_eulers['psi']
particleparams['theta'] = fr_eulers['theta']
particleparams['phi'] = fr_eulers['phi']
particleparams['shx'] = -params['eman_orient']['shiftx']
particleparams['shy'] = -params['eman_orient']['shifty']
if params['eman_orient']['mirror'] is True:
particleparams['shx'] *= -1
writeParticleParamLine(particleparams, f)
f.close()
