def commitToDatabase(self, imgdata):
"""
Uses the appionLoop commit
"""
imgassess = apDatabase.getImgCompleteStatus(imgdata)
tiltdata = apTiltPair.getTiltPair(imgdata)
msg = not self.params['background']
if tiltdata is None:
if imgassess is not False:
apDisplay.printColor("\nrejecting unpaired image: "+apDisplay.short(imgdata['filename']), "red")
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runid'], False, msg=msg)
self.reject+=1
return
if self.params['background'] is False:
apDisplay.printMsg("tiltpair: "+apDisplay.short(tiltdata['filename']))
tiltassess = apDatabase.getImgCompleteStatus(tiltdata)
if imgassess is False or tiltassess is False:
if imgassess is not False:
apDisplay.printColor("\nrejecting bad tilt images: "+apDisplay.short(imgdata['filename']), "magenta")
if tiltassess is not False:
apDisplay.printColor("\nrejecting bad tilt images: "+apDisplay.short(tiltdata['filename']), "magenta")
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runid'], False, msg=msg)
apDatabase.insertImgAssessmentStatus(tiltdata, self.params['runid'], False, msg=msg)
self.reject+=2
if self.params['background'] is False:
print "Assessment:", imgassess, tiltassess
return
def commitToDatabase(self, imgdata):
"""
Uses the appionLoop commit
"""
imgassess = apDatabase.getImgCompleteStatus(imgdata)
tiltdata = apTiltPair.getTiltPair(imgdata)
msg = not self.params['background']
if tiltdata is None:
if imgassess is not False:
apDisplay.printColor("\nrejecting unpaired image: "+apDisplay.short(imgdata['filename']), "red")
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runid'], False, msg=msg)
self.reject+=1
return
if self.params['background'] is False:
apDisplay.printMsg("tiltpair: "+apDisplay.short(tiltdata['filename']))
tiltassess = apDatabase.getImgCompleteStatus(tiltdata)
if imgassess is False or tiltassess is False:
if imgassess is not False:
apDisplay.printColor("\nrejecting bad tilt images: "+apDisplay.short(imgdata['filename']), "magenta")
if tiltassess is not False:
apDisplay.printColor("\nrejecting bad tilt images: "+apDisplay.short(tiltdata['filename']), "magenta")
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runid'], False, msg=msg)
apDatabase.insertImgAssessmentStatus(tiltdata, self.params['runid'], False, msg=msg)
self.reject+=2
if self.params['background'] is False:
print "Assessment:", imgassess, tiltassess
return
def getTiltAssess(self, imgdata, tiltdata): ass1 = apDatabase.getImgCompleteStatus(imgdata) ass2 = apDatabase.getImgCompleteStatus(tiltdata) if ass1 is False or ass2 is False: return False if ass1 is True and ass2 is True: return True return None
def loopCheckAndProcess(self):
allfiles = self.getAllFiles()
images = []
for filename in allfiles:
if os.path.isfile(filename) and '_st.mrc' in filename and self.rundata['session']['name'] in filename:
try:
imagedata = leginondata.AcquisitionImageData(session=self.rundata['session'],filename=filename[:-7]).query()[0]
except:
continue
images.append(imagedata)
self.num_stacks = len(images)
for imagedata in images:
if self.params['limit'] > 0:
if self.success_count >= self.params['limit']:
return True
# Avoid hidden and trash images
if apDatabase.getImgCompleteStatus(imagedata) == False:
apDisplay.printMsg('---------------------------------------------------------')
apDisplay.printMsg(' Skipping hidden/trashed %s' % imagedata['filename'])
apDisplay.printMsg('---------------------------------------------------------')
continue
apDisplay.printMsg('---------------------------------------------------------')
apDisplay.printMsg(' Processing %s' % imagedata['filename'])
apDisplay.printMsg('---------------------------------------------------------')
self.processImage(imagedata)
if self.params['commit']:
self.commitToDatabase(imagedata)
apDisplay.printMsg('\n')
return False
def skipTestOnImage(self, imgdata):
imgname = imgdata['filename']
skip = False
reason = None
#tiltskip is default to None since it might not need evaluation
tiltskip = None
if imgname in self.donedict:
skip = True
reason = 'done'
elif self.reprocessImage(imgdata) is False:
self._writeDoneDict(imgname)
reason = 'reproc'
skip = True
if skip is True:
return skip, reason
else:
# image not done or reprocessing allowed
# check sibling status instead if wanted
if self.params['sibassess'] is True:
status = apDatabase.getSiblingImgCompleteStatus(imgdata)
else:
status = apDatabase.getImgCompleteStatus(imgdata)
if self.params['norejects'] is True and status is False:
reason = 'reject'
skip = True
elif self.params['bestimages'] is True and status is not True:
reason = 'reject'
skip = True
elif (self.params['tiltangle'] is not None
or self.params['tiltangle'] != 'all'):
tiltangle = apDatabase.getTiltAngleDeg(imgdata)
tiltangle = apDatabase.getTiltAngleDeg(imgdata)
if (self.params['tiltangle'] == 'notilt'
and abs(tiltangle) > 3.0):
skip = True
elif (self.params['tiltangle'] == 'hightilt'
and abs(tiltangle) < 30.0):
skip = True
elif (self.params['tiltangle'] == 'lowtilt'
and abs(tiltangle) >= 30.0):
skip = True
### the reason why -2.0 and 2.0 are used is because the tilt angle is saved as 0 +/- a small amount
elif (self.params['tiltangle'] == 'minustilt'
and tiltangle > -2.0):
skip = True
elif (self.params['tiltangle'] == 'plustilt'
and tiltangle < 2.0):
skip = True
if skip == True:
reason = 'tilt'
return skip, reason
def rejectTiltPairs(self, imgdata):
tiltdata = apTiltPair.getTiltPair(imgdata)
if tiltdata is None:
apDisplay.printColor("\nrejecting unpaired image: "+apDisplay.short(imgdata['filename']), "red")
return False
tiltassess = apDatabase.getImgCompleteStatus(tiltdata)
if tiltassess is False:
apDisplay.printColor("\nrejecting bad tilt images: "+apDisplay.short(imgdata['filename']), "magenta")
return False
return True
def skipTestOnImage(self,imgdata):
imgname = imgdata['filename']
skip = False
reason = None
#tiltskip is default to None since it might not need evaluation
tiltskip = None
if imgname in self.donedict:
skip = True
reason = 'done'
elif self.reprocessImage(imgdata) is False:
self._writeDoneDict(imgname)
reason = 'reproc'
skip = True
if skip is True:
return skip, reason
else:
# image not done or reprocessing allowed
# check sibling status instead if wanted
if self.params['sibassess'] is True:
status=apDatabase.getSiblingImgCompleteStatus(imgdata)
else:
status=apDatabase.getImgCompleteStatus(imgdata)
if self.params['norejects'] is True and status is False:
reason = 'reject'
skip = True
elif self.params['bestimages'] is True and status is not True:
reason = 'reject'
skip = True
elif ( self.params['tiltangle'] is not None or self.params['tiltangle'] != 'all' ):
tiltangle = apDatabase.getTiltAngleDeg(imgdata)
tiltangle = apDatabase.getTiltAngleDeg(imgdata)
if (self.params['tiltangle'] == 'notilt' and abs(tiltangle) > 3.0 ):
skip = True
elif (self.params['tiltangle'] == 'hightilt' and abs(tiltangle) < 30.0 ):
skip = True
elif (self.params['tiltangle'] == 'lowtilt' and abs(tiltangle) >= 30.0 ):
skip = True
### the reason why -2.0 and 2.0 are used is because the tilt angle is saved as 0 +/- a small amount
elif (self.params['tiltangle'] == 'minustilt' and tiltangle > -2.0 ):
skip = True
elif (self.params['tiltangle'] == 'plustilt' and tiltangle < 2.0 ):
skip = True
if skip == True:
reason = 'tilt'
return skip, reason
def rejectTiltPairs(self, imgdata):
tiltdata = apTiltPair.getTiltPair(imgdata)
if tiltdata is None:
apDisplay.printColor(
"\nrejecting unpaired image: " +
apDisplay.short(imgdata['filename']), "red")
return False
tiltassess = apDatabase.getImgCompleteStatus(tiltdata)
if tiltassess is False:
apDisplay.printColor(
"\nrejecting bad tilt images: " +
apDisplay.short(imgdata['filename']), "magenta")
return False
return True
def chooseValidResultImageInDDAlignPairs(self, alldata):
'''
Return the first non-rejected result image
'''
if not alldata:
# no data
return False
for pairdata in alldata:
if apDatabase.getImgCompleteStatus(pairdata['result']) is False:
# bad status
continue
# good status
return pairdata['result']
# no data with valid image status
return False
def chooseValidResultImageInDDAlignPairs(self, alldata): ''' Return the first non-rejected result image ''' if not alldata: # no data return False for pairdata in alldata: if apDatabase.getImgCompleteStatus(pairdata['result']) is False: # bad status continue # good status return pairdata['result'] # no data with valid image status return False
def loopCheckAndProcess(self):
allfiles = self.getAllFiles()
images = []
for filename in allfiles:
if os.path.isfile(
filename) and '_st.mrc' in filename and self.rundata[
'session']['name'] in filename:
try:
imagedata = leginondata.AcquisitionImageData(
session=self.rundata['session'],
filename=filename[:-7]).query()[0]
except:
continue
images.append(imagedata)
self.num_stacks = len(images)
for imagedata in images:
if self.params['limit'] > 0:
if self.success_count >= self.params['limit']:
return True
# Avoid hidden and trash images
if apDatabase.getImgCompleteStatus(imagedata) == False:
apDisplay.printMsg(
'---------------------------------------------------------'
)
apDisplay.printMsg(' Skipping hidden/trashed %s' %
imagedata['filename'])
apDisplay.printMsg(
'---------------------------------------------------------'
)
continue
apDisplay.printMsg(
'---------------------------------------------------------')
apDisplay.printMsg(' Processing %s' % imagedata['filename'])
apDisplay.printMsg(
'---------------------------------------------------------')
self.processImage(imagedata)
if self.params['commit']:
self.commitToDatabase(imagedata)
apDisplay.printMsg('\n')
return False