def getBestTiltTransform(imgdata):
"""
For a given image get the best tilt transform
parameters in the database
"""
transdatas = []
## case 1: check if imgdata is image1
transq = appiondata.ApImageTiltTransformData()
transq['image1'] = imgdata
transdatas1 = transq.query()
if transdatas1:
transdatas.extend(transdatas1)
## case 2: check if imgdata is image2
transq = appiondata.ApImageTiltTransformData()
transq['image2'] = imgdata
transdatas2 = transq.query()
if transdatas2:
transdatas.extend(transdatas2)
### case 1: no transformation
if len(transdatas) == 0:
apDisplay.printWarning("no transformation found for image %s" %
(apDisplay.short(imgdata['filename'])))
return None
### case 2: single transformation, no sorting required
if len(transdatas) == 1:
apDisplay.printMsg(
"single transformation found with rmsd %.2f for image %s" %
(transdatas[0]['rmsd'], apDisplay.short(imgdata['filename'])))
return transdatas[0]
### case 3: more than one transformation, get one with lowest rmsd
besttransdata = transdatas[0]
bestrmsd = transdatas[0]['rmsd']
for transdata in transdatas:
if transdata['rmsd'] > 0 and transdata['rmsd'] < bestrmsd:
besttransdata = transdata
bestrmsd = transdata['rmsd']
apDisplay.printMsg(
"returning best transformation with rmsd %.2f for image %s" %
(bestrmsd, apDisplay.short(imgdata['filename'])))
return besttransdata
def insertTiltTransform(imgdata1, imgdata2, tiltparams, params):
#First we need to sort imgdata
#'07aug30b_a_00013gr_00010sq_v01_00002sq_v01_00016en_00'
#'07aug30b_a_00013gr_00010sq_v01_00002sq_01_00016en_01'
#last two digits confer order, but then the transform changes...
bin = params['bin']
### first find the runid
runq = appiondata.ApSelectionRunData()
runq['name'] = params['runname']
runq['session'] = imgdata1['session']
rundatas = runq.query(results=1, readimages=False)
if not rundatas:
apDisplay.printError("could not find runid in database")
### the order is specified by 1,2; so don't change it let makestack figure it out
for imgdata in (imgdata1, imgdata2):
for index in ("1","2"):
transq = appiondata.ApImageTiltTransformData()
transq["image"+index] = imgdata
transq['tiltrun'] = rundatas[0]
transdata = transq.query(readimages=False)
if transdata:
apDisplay.printWarning("Transform values already in database for "+imgdata['filename'])
return transdata[0]
### prepare the insertion
transq = appiondata.ApImageTiltTransformData()
transq['image1'] = imgdata1
transq['image2'] = imgdata2
transq['tiltrun'] = rundatas[0]
dbdict = tiltPickerToDbNames(tiltparams)
if dbdict is None:
return None
#Can I do for key in appiondata.ApImageTiltTransformData() ro transq???
for key in ('image1_x','image1_y','image1_rotation','image2_x','image2_y','image2_rotation','scale_factor','tilt_angle', 'overlap'):
if key not in dbdict:
apDisplay.printError("Key: "+key+" was not found in transformation data")
for key,val in dbdict.items():
#print key
if re.match("image[12]_[xy]", key):
transq[key] = round(val*bin,2)
else:
transq[key] = val
#print i,v
### this overlap is wrong because the images are binned by 'bin' and now we give it the full image
"""
imgShape1 = numpy.asarray(imgdata1['image'].shape, dtype=numpy.int8)/params['bin']
image1 = numpy.ones(imgShape1)
imgShape2 = numpy.asarray(imgdata2['image'].shape, dtype=numpy.int8)/params['bin']
image2 = numpy.ones(imgShape2)
bestOverlap, tiltOverlap = apTiltTransform.getOverlapPercent(image1, image2, tiltparams)
print "image overlaps", bestOverlap, tiltOverlap
transq['overlap'] = round(bestOverlap,5)
"""
apDisplay.printMsg("Inserting transform between "+apDisplay.short(imgdata1['filename'])+\
" and "+apDisplay.short(imgdata2['filename'])+" into database")
transq.insert()
apDisplay.printMsg("done")
return transq
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