def templatePick(self, diam=256, thresh=0.5, maxthresh=0.8, maxsize=0.05, lowpass=25, bin=4, rangelist="0,360,15x"):
runnum = apParticle.getNumSelectionRunsFromSession(self.sessionname)
tmplname = "tmplrun%d-%s"%(runnum+1, self.timestamp)
templateids = self.getMostRecentTemplates(3)
script = os.path.join(self.appiondir, "bin", "templateCorrelator.py ")
params = (" --runname=%s --projectid=%d --session=%s --diam=%d --thresh=%.2f --maxthresh=%.2f --invert --no-wait --planereg --maxsize=%.2f --lowpass=%d --bin=%d --thread-findem "
%(tmplname, self.params['projectid'], self.sessionname, diam, thresh, maxthresh, maxsize, lowpass, bin))
# TODO: what should these lists be set to?
tmplliststr = " --template-list="
rangeliststr = " --range-list="
for templateid in templateids:
tmplliststr += "%d,"%(templateid)
#rangeliststr += "%d,%d,%dx"%(0,360,15)
rangeliststr += rangelist
params += tmplliststr[:-1]
params += rangeliststr[:-1]
# Add appion flags
params += self.appionFlags
self.runCommand(script+" "+params)
return tmplname
def templatePick(self):
runnum = apParticle.getNumSelectionRunsFromSession(self.sessionname)
tmplname = "tmplrun%d-%s" % (runnum + 1, self.timestamp)
templateids = self.getMostRecentTemplates(3)
script = os.path.join(self.appiondir, "bin", "templateCorrelator.py ")
params = (
" --runname=%s --projectid=%d --session=%s --diam=%d --thresh=%.2f --maxthresh=%.2f --invert --no-wait --planereg --maxsize=%.2f --lowpass=%d --bin=%d --thread-findem "
% (tmplname, self.params["projectid"], self.sessionname, 256, 0.5, 0.8, 0.05, 25, 4)
)
tmplliststr = " --template-list="
rangeliststr = " --range-list="
for templateid in templateids:
tmplliststr += "%d," % (templateid)
rangeliststr += "%d,%d,%dx" % (0, 360, 15)
params += tmplliststr[:-1]
params += rangeliststr[:-1]
if self.params["commit"] is True:
params += " --commit "
else:
params += " --no-commit "
self.runCommand(script + " " + params)
return tmplname
def dogPicker(self):
runnum = apParticle.getNumSelectionRunsFromSession(self.sessionname)
dogname = "dogrun%d-%s"%(runnum+1, self.timestamp)
script = os.path.join(self.appiondir, "bin", "dogPicker.py ")
params = (" --runname=%s --projectid=%d --session=%s --diam=%d --thresh=%.2f --maxthresh=%.2f --invert --no-wait --planereg --maxsize=%.2f --numslices=%d --sizerange=%d --bin=%d "
%(dogname, self.params['projectid'], self.sessionname, 150, 0.42, 0.8, 0.5, 3, 50, 4))
if self.params['commit'] is True:
params += " --commit "
else:
params += " --no-commit "
self.runCommand(script+" "+params)
return dogname
def dogPicker(self):
runnum = apParticle.getNumSelectionRunsFromSession(self.sessionname)
dogname = "dogrun%d-%s"%(runnum+1, self.timestamp)
script = os.path.join(self.appiondir, "bin", "dogPicker.py ")
params = (" --runname=%s --projectid=%d --session=%s --diam=%d --thresh=%.2f --maxthresh=%.2f --invert --no-wait --planereg --maxsize=%.2f --numslices=%d --sizerange=%d --bin=%d "
%(dogname, self.params['projectid'], self.sessionname, 150, 0.42, 0.8, 0.5, 3, 50, 4))
if self.params['commit'] is True:
params += " --commit "
else:
params += " --no-commit "
self.runCommand(script+" "+params)
return dogname
def dogPicker(self, diam=150, thresh=0.42, maxthresh=0.8, peaktype='centerofmass', median=2, lowpass=15, highpass=0, maxsize=0.5, numslices=3, pixlimit=4.0, sizerange=50, bin=4 ):
runnum = apParticle.getNumSelectionRunsFromSession(self.sessionname)
dogname = "dogrun%d-%s"%(runnum+1, self.timestamp)
# Build the command
script = os.path.join(self.appiondir, "bin", "dogPicker.py ")
params = (" --runname=%s --projectid=%d --session=%s --diam=%d --thresh=%.2f --maxthresh=%.2f --invert --no-wait --peaktype=%s --median=%d --lowpass=%d --highpass=%d --planereg --maxsize=%.2f --numslices=%d --pixlimit=%.2f --sizerange=%d --bin=%d"
%(dogname, self.params['projectid'], self.sessionname, diam, thresh, maxthresh, peaktype, median, lowpass, highpass, maxsize, numslices, pixlimit, sizerange, bin ))
# Add appion flags
params += self.appionFlags
# Run the command
self.runCommand(script+" "+params)
return dogname
def templatePick(self):
runnum = apParticle.getNumSelectionRunsFromSession(self.sessionname)
tmplname = "tmplrun%d-%s"%(runnum+1, self.timestamp)
templateids = self.getMostRecentTemplates(3)
script = os.path.join(self.appiondir, "bin", "templateCorrelator.py ")
params = (" --runname=%s --projectid=%d --session=%s --diam=%d --thresh=%.2f --maxthresh=%.2f --invert --no-wait --planereg --maxsize=%.2f --lowpass=%d --bin=%d --thread-findem "
%(tmplname, self.params['projectid'], self.sessionname, 256, 0.5, 0.8, 0.05, 25, 4))
tmplliststr = " --template-list="
rangeliststr = " --range-list="
for templateid in templateids:
tmplliststr += "%d,"%(templateid)
rangeliststr += "%d,%d,%dx"%(0,360,15)
params += tmplliststr[:-1]
params += rangeliststr[:-1]
if self.params['commit'] is True:
params += " --commit "
else:
params += " --no-commit "
self.runCommand(script+" "+params)
return tmplname