def getTiltTransformFromParticle(partdata):
t0 = time.time()
### figure out if its particle 1 or 2
tiltpartq1 = appiondata.ApTiltParticlePairData()
tiltpartq1['particle1'] = partdata
tiltpartdatas1 = tiltpartq1.query(results=1, readimages=False)
tiltpartq2 = appiondata.ApTiltParticlePairData()
tiltpartq2['particle2'] = partdata
tiltpartdatas2 = tiltpartq2.query(results=1, readimages=False)
if tiltpartdatas1 and not tiltpartdatas2:
imgnum = 1
transformdata = tiltpartdatas1[0]['transform']
otherpartdata = tiltpartdatas1[0]['particle2']
elif not tiltpartdatas1 and tiltpartdatas2:
imgnum = 2
transformdata = tiltpartdatas2[0]['transform']
otherpartdata = tiltpartdatas2[0]['particle1']
else:
print partdata
print tiltpartdatas1
print tiltpartdatas2
apDisplay.printError("failed to get tilt pair data")
if time.time()-t0 > 1.0:
apDisplay.printMsg("long getTiltTransFromPart1 "+apDisplay.timeString(time.time()-t0))
return imgnum, transformdata, otherpartdata
def getStackParticleTiltPair(stackid, partnum, tiltstackid=None):
"""
takes a stack id and particle number (1+) spider-style
returns the stack particle number for the tilt pair
"""
#print stackid, partnum
if tiltstackid is None:
tiltstackid = stackid
t0 = time.time()
stackpartdata1 = apStack.getStackParticle(stackid, partnum)
partdata = stackpartdata1['particle']
### figure out if its particle 1 or 2
tiltpartq1 = appiondata.ApTiltParticlePairData()
tiltpartq1['particle1'] = partdata
tiltpartdatas1 = tiltpartq1.query(results=1, readimages=False)
tiltpartq2 = appiondata.ApTiltParticlePairData()
tiltpartq2['particle2'] = partdata
tiltpartdatas2 = tiltpartq2.query(results=1, readimages=False)
if not tiltpartdatas1 and tiltpartdatas2:
#print "image1"
otherpart = tiltpartdatas2[0]['particle1']
elif tiltpartdatas1 and not tiltpartdatas2:
#print "image2"
otherpart = tiltpartdatas1[0]['particle2']
else:
print partdata
print tiltpartdatas1
print tiltpartdatas2
apDisplay.printError("failed to get tilt pair data")
### get tilt stack particle
tiltstackdata = apStack.getOnlyStackData(tiltstackid, msg=False)
stackpartq = appiondata.ApStackParticleData()
stackpartq['stack'] = tiltstackdata
stackpartq['particle'] = otherpart
stackpartdatas2 = stackpartq.query(results=1, readimages=False)
if not stackpartdatas2:
#print otherpart.dbid
#apDisplay.printError("particle "+str(partnum)+" has no tilt pair in stackid="+str(tiltstackid))
return None
stackpartdata = stackpartdatas2[0]
#print partnum,"-->",stackpartnum
if time.time() - t0 > 1.0:
apDisplay.printMsg("long getStackPartTiltPair " +
apDisplay.timeString(time.time() - t0))
return stackpartdata
def insertParticlePeakPairs(peaktree1, peaktree2, peakerrors, imgdata1,
imgdata2, transdata, runname):
"""
takes both image data (imgdata) and inserts particle pairs into DB from peaktrees
"""
#INFO
sessiondata = imgdata1['session']
legimgid1 = int(imgdata1.dbid)
legimgid2 = int(imgdata2.dbid)
imgname1 = imgdata1['filename']
imgname2 = imgdata2['filename']
#CHECK ARRAY LENGTHS
len1 = len(peaktree1)
len2 = len(peaktree2)
len3 = len(peakerrors)
if len1 != len2 or len2 != len3:
apDisplay.printError("insertParticlePeakPairs particle arrays must have the same length "+\
str(len1)+" "+str(len2)+" "+str(len3))
#GET RUN DATA
runq = appiondata.ApSelectionRunData()
runq['name'] = runname
runq['session'] = sessiondata
selectionruns = runq.query(results=1)
if not selectionruns:
apDisplay.printError("could not find selection run in database")
#GET TRANSFORM DATA
transq = appiondata.ApImageTiltTransformData()
transq['image1'] = imgdata1
transq['image2'] = imgdata2
transq['tiltrun'] = selectionruns[0]
transids = transq.query(results=1)
if not transids:
apDisplay.printError("could not find transform id in database")
### WRITE PARTICLES TO DATABASE
count = 0
t0 = time.time()
last50 = time.time()
apDisplay.printMsg("looping over " + str(len(peaktree1)) + " particles")
for i in range(len(peaktree1)):
remaining_peaks = len(peaktree1) - count
if count and remaining_peaks and remaining_peaks % 50 == 0:
#sys.stderr.write("<"+str(len(peaktree1)-count))
print(
"%d particles remain, %s time remains, %s per particle, %s last 50 particles"
% (
len(peaktree1) - count,
apDisplay.timeString(
(time.time() - t0) / count * (remaining_peaks)),
apDisplay.timeString((time.time() - t0) / count),
apDisplay.timeString(time.time() - last50),
))
last50 = time.time()
peakdict1 = peaktree1[i]
peakdict2 = peaktree2[i]
error = peakerrors[i]
partq1 = appiondata.ApParticleData()
partq1['selectionrun'] = selectionruns[0]
partq1['image'] = imgdata1
partq1['xcoord'] = peakdict1['xcoord']
partq1['ycoord'] = peakdict1['ycoord']
partq1['peakarea'] = 1
partq2 = appiondata.ApParticleData()
partq2['selectionrun'] = selectionruns[0]
partq2['image'] = imgdata2
partq2['xcoord'] = peakdict2['xcoord']
partq2['ycoord'] = peakdict2['ycoord']
partq2['peakarea'] = 1
# I do NOT have to check if particles already exist, because this is a NEW selectionrun
partpairq = appiondata.ApTiltParticlePairData()
partpairq['particle1'] = partq1
partpairq['particle2'] = partq2
#NEED TO LOOK UP TRANSFORM DATA
partpairq['transform'] = transdata
#NEED TO CALCULATE ERROR, ALWAYS POSITIVE
partpairq['error'] = error
#presult = partpairq.query()
#if not presult:
count += 1
partq1.insert(force=True)
partq2.insert(force=True)
partpairq.insert(force=True)
apDisplay.printMsg("inserted " + str(count) + " of " +
str(len(peaktree1)) + " peaks into database" + " in " +
apDisplay.timeString(time.time() - t0))
return