def runManualPicker(self, imgdata):
#reset targets
self.targets = []
#set the assessment status
self.assessold = apDatabase.checkInspectDB(imgdata)
self.assess = self.assessold
self.app.setAssessStatus()
# useAccecepted mask is true when the assess flag is used, and an
# accepted mask is found in the indicated mask run that should be retained
# This is checked in the preLoopFunctions().
self.useAcceptedMask = False
#open new file
imgname = imgdata['filename'] + '.dwn.mrc'
imgpath = os.path.join(self.params['rundir'], imgname)
# Add this image to mask vertices file
if not self.params['checkmask']:
self.app.panel.openImageFile(imgpath)
else:
self.showAssessedMask(imgpath, imgdata)
#set vital stats
self.app.vitalstats.SetLabel(" image name: " + imgdata['filename'])
#run the picker
self.app.MainLoop()
#targets are copied to self.targets by app
#assessment is copied to self.assess by app
self.app.panel.openImageFile(None)
def runManualPicker(self, imgdata):
#reset targets
self.targets = []
#set the assessment status
self.assessold = apDatabase.checkInspectDB(imgdata)
self.assess = self.assessold
self.app.setAssessStatus()
# useAccecepted mask is true when the assess flag is used, and an
# accepted mask is found in the indicated mask run that should be retained
# This is checked in the preLoopFunctions().
self.useAcceptedMask = False
#open new file
imgname = imgdata['filename']+'.dwn.mrc'
imgpath = os.path.join(self.params['rundir'],imgname)
# Add this image to mask vertices file
if not self.params['checkmask']:
self.app.panel.openImageFile(imgpath)
else:
self.showAssessedMask(imgpath,imgdata)
#set vital stats
self.app.vitalstats.SetLabel(
" image name: "+imgdata['filename'])
#run the picker
self.app.MainLoop()
#targets are copied to self.targets by app
#assessment is copied to self.assess by app
self.app.panel.openImageFile(None)
def runManualPicker(self, imgdata):
#reset targets
self.targets = []
#set the assessment status
self.assessold = apDatabase.checkInspectDB(imgdata)
self.assess = self.assessold
# useAccecepted mask is true when the assess flag is used, and an
# accepted mask is found in the indicated mask run that should be retained
# This is checked in the preLoopFunctions().
self.useAcceptedMask = False
#open new file
imgname = imgdata['filename']+'.dwn.mrc'
maskname = imgdata['filename']+'_mask.png'
imagepath = os.path.join(self.params['rundir'],imgname)
maskpath = os.path.join(self.params['rundir'],'masks',maskname)
self.image = pyami.mrc.read(imagepath)
if not os.path.isfile(maskpath):
self.maskimg = numpy.zeros(self.image.shape)
#run the picker
self.maskimg = apImage.PngToBinarryArray(maskpath)
def runManualPicker(self, imgdata):
#reset targets
self.targets = {}
for label in self.labels:
self.app.panel.setTargets(label, [])
self.targets[label] = []
#set the assessment and viewer status
self.assessold = apDatabase.checkInspectDB(imgdata)
self.assess = self.assessold
self.app.setAssessStatus()
#open new file
imgname = imgdata['filename']+'.dwn.mrc'
imgpath = os.path.join(self.params['rundir'],imgname)
if not self.params['checkMask']:
self.app.panel.openImageFile(imgpath)
else:
self.showAssessedMask(imgpath,imgdata)
targets = self.getParticlePicks(imgdata)
if targets:
for label in targets.keys():
if label not in self.labels:
self.labels.append(label)
self.app.addLabelPicker(label)
for label in self.labels:
if label not in targets:
targets[label] = []
print "inserting ",len(targets[label]),"%s targets" % (label,)
self.app.panel.setTargets(label, targets[label])
self.app.panel.originaltargets[label] = targets[label]
# labels may have changed, default selection is the first one
if self.labels:
self.app.panel.selectiontool.setTargeting(self.labels[0], True)
#set vital stats
self.app.vitalstats.SetLabel("Vital Stats: Image "+str(self.stats['count'])
+" of "+str(self.stats['imagecount'])+", inserted "+str(self.stats['peaksum'])+" picks, "
+" image name: "+imgdata['filename'])
#run the picker
self.app.MainLoop()
#targets are copied to self.targets by app
#assessment is copied to self.assess by app
#parse and return the targets in peaktree form
self.app.panel.openImageFile(None)
peaktree=[]
for label,targets in self.targets.items():
for target in targets:
angle=None
helixnum=None
if isinstance(target, leginon.gui.wx.TargetPanelTools.StatsTarget):
t = target.stats
if t.has_key('angle'):
angle = target.stats['angle']
if t.has_key('helixnum'):
helixnum = target.stats['helixnum']
peaktree.append(self.XY2particle(target.x, target.y, angle, helixnum, label))
# if any peak has an angle, then remove all peaks that do not have an angle
#if peaktree:
# def hasangle(x):
# try:
# return 'angle' in x
# except:
# return False
# haveangles = map(hasangle, peaktree)
# anyangles = reduce(operator.or_, haveangles)
# if anyangles:
# before = len(peaktree)
# peaktree = filter(hasangle, peaktree)
# after = len(peaktree)
# diff = before - after
# apDisplay.printWarning("Removed %d particles with no angle"%(diff))
return peaktree