def start(self):
"""
this is the main component of the script
where all the processing is done
"""
imgarray = mrc.read(self.params['image'])
if self.params['invert'] is True:
imgarray = -1.0*imgarray
dogmaps = apDog.diffOfGaussParam(imgarray, self.params)
rootname = os.path.splitext(self.params['image'])[0]
pixdiam = self.params['diam']/self.params['apix']
pixrad = pixdiam/2.0
peaktreelist = []
count = 0
for dogmap in dogmaps:
count += 1
### threshold maps and extract peaks
peaktree = apPeaks.findPeaksInMap(dogmap, thresh=self.params['thresh'],
pixdiam=pixdiam, count=count, olapmult=self.params["overlapmult"],
maxpeaks=self.params["maxpeaks"], maxsizemult=self.params["maxsizemult"],
msg=True, bin=1)
### remove peaks from areas near the border of the image
peaktree = apPeaks.removeBorderPeaks(peaktree, pixdiam,
dogmap.shape[0], dogmap.shape[1])
### create a nice image of pick locations
mapfile = "%s-map%02d.jpg"%(rootname, count)
apPeaks.createPeakMapImage(peaktree, dogmap, imgname=mapfile, pixrad=pixrad)
imgfile = "%s-picks%02d.jpg"%(rootname, count)
apPeaks.subCreatePeakJpeg(imgarray, peaktree, pixrad, imgfile, bin=1)
peaktreelist.append(peaktree)
### merge list in a single set of particle picks
imgdata = { 'filename': self.params['image'], }
peaktree = apPeaks.mergePeakTrees(imgdata, peaktreelist, self.params, pikfile=False)
### throw away particles above maxthresh
precount = len(peaktree)
peaktree = apPeaks.maxThreshPeaks(peaktree, self.params['maxthresh'])
postcount = len(peaktree)
apDisplay.printMsg("Filtered %d particles above max threshold %.2f"
%(precount-postcount,self.params['maxthresh']))
### create final images with pick locations
mapfile = "%s-finalmap.jpg"%(rootname)
apPeaks.createPeakMapImage(peaktree, dogmap, imgname=mapfile, pixrad=pixrad)
imgfile = "%s-finalpicks.jpg"%(rootname)
apPeaks.subCreatePeakJpeg(imgarray, peaktree, pixrad, imgfile, bin=1)
### write output file
self.writeTextFile(peaktree)
def findPeaks(imgdict, maplist, params, pikfile=True):
#modeified from apPeaks.findPeaks to read peaks from box file per ccmap
peaktreelist = []
count = 0
imgname = imgdict['filename']
mapdir = os.path.join(params['rundir'], "maps")
bin = int(params["bin"])
diam = float(params["diam"])
apix = float(params["apix"])
olapmult = float(params["overlapmult"])
maxthresh = params["maxthresh"]
maxsizemult = float(params["maxsize"])
msg = not params['background']
tmpldbid = None
for imgmap in maplist:
count += 1
if 'templateIds' in params:
#template correlator
tmpldbid = params['templateIds'][count - 1]
peaktree = getPeaksFromBoxFile(imgmap)
newpeaktree = []
for peakdict in peaktree:
peakdict = apPeaks.attachTemplateLabel(peakdict, count, tmpldbid,
diam)
newpeaktree.append(peakdict)
peaktree = newpeaktree
#write pikfile
if pikfile is True:
apPeaks.peakTreeToPikFile(peaktree, imgname, count,
params['rundir'])
#append to complete list of peaks
peaktreelist.append(peaktree)
peaktree = apPeaks.mergePeakTrees(imgdict,
peaktreelist,
params,
msg,
pikfile=pikfile)
#max threshold
if maxthresh is not None:
precount = len(peaktree)
peaktree = apPeaks.maxThreshPeaks(peaktree, maxthresh)
postcount = len(peaktree)
#if precount != postcount:
apDisplay.printMsg("Filtered %d particles above threshold %.2f" %
(precount - postcount, maxthresh))
return peaktree
def findPeaks(imgdict, maplist, params,pikfile=True):
#modeified from apPeaks.findPeaks to read peaks from box file per ccmap
peaktreelist = []
count = 0
imgname = imgdict['filename']
mapdir = os.path.join(params['rundir'], "maps")
bin = int(params["bin"])
diam = float(params["diam"])
apix = float(params["apix"])
olapmult = float(params["overlapmult"])
maxthresh = params["maxthresh"]
maxsizemult = float(params["maxsize"])
msg = not params['background']
tmpldbid = None
for imgmap in maplist:
count += 1
if 'templateIds' in params:
#template correlator
tmpldbid = params['templateIds'][count-1]
peaktree = getPeaksFromBoxFile(imgmap)
newpeaktree = []
for peakdict in peaktree:
peakdict = apPeaks.attachTemplateLabel(peakdict,count,tmpldbid,diam)
newpeaktree.append(peakdict)
peaktree = newpeaktree
#write pikfile
if pikfile is True:
apPeaks.peakTreeToPikFile(peaktree, imgname, count, params['rundir'])
#append to complete list of peaks
peaktreelist.append(peaktree)
peaktree = apPeaks.mergePeakTrees(imgdict, peaktreelist, params, msg, pikfile=pikfile)
#max threshold
if maxthresh is not None:
precount = len(peaktree)
peaktree = apPeaks.maxThreshPeaks(peaktree, maxthresh)
postcount = len(peaktree)
#if precount != postcount:
apDisplay.printMsg("Filtered %d particles above threshold %.2f"%(precount-postcount,maxthresh))
return peaktree