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, 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