def validateAndInsertCTFData(imgdata,
ctfvalues,
rundata,
rundir,
fftpath=None,
fftfreq=None):
"""
function to insert CTF values in database
"""
apDisplay.printMsg("Committing ctf parameters for " +
apDisplay.short(imgdata['filename']) + " to database")
if ctfvalues is None or not 'defocus2' in ctfvalues:
apDisplay.printWarning("No ctf values")
return False
### convert to common convention
ctfvalues = convertDefociToConvention(ctfvalues)
### check to make sure parameters are valid
isvalid = checkParams(ctfvalues)
if isvalid is False:
apDisplay.printWarning("Bad CTF values, insert but not create images")
### run the main CTF display program
opimagedir = os.path.join(rundir, "opimages")
if isvalid is True:
oldctfvalues = ctfvalues.copy()
ctfvalues = runCTFdisplayTools(imgdata, ctfvalues, opimagedir, fftpath,
fftfreq)
# check if image creation failed
if ctfvalues is None:
ctfvalues = oldctfvalues
### clean rundir from all entries:
if not rundir.endswith("/"):
rundir += "/"
for key in ctfvalues.keys():
if isinstance(ctfvalues[key],
str) and ctfvalues[key].startswith(rundir):
ctfvalues[key] = ctfvalues[key].replace(rundir, "")
### time to insert
ctfq = appiondata.ApCtfData()
ctfq['acerun'] = rundata
ctfq['image'] = imgdata
if debug is True:
apDisplay.printMsg("CTF data values")
print ctfvalues
for key in ctfq.keys():
if key in ctfvalues:
ctfq[key] = ctfvalues[key]
if debug is True:
apDisplay.printMsg("%s :: %s" % (key, ctfvalues[key]))
elif debug is True:
apDisplay.printMsg("SKIPPING %s :: %s" % (key, ctfvalues[key]))
ctfdb.printCtfData(ctfq)
ctfq.insert()
return
def validateAndInsertCTFData(imgdata, ctfvalues, rundata, rundir, fftpath=None, fftfreq=None):
"""
function to insert CTF values in database
"""
apDisplay.printMsg("Committing ctf parameters for "
+apDisplay.short(imgdata['filename'])+" to database")
if ctfvalues is None or not 'defocus2' in ctfvalues:
apDisplay.printWarning("No ctf values")
return False
### convert to common convention
ctfvalues = convertDefociToConvention(ctfvalues)
### check to make sure parameters are valid
isvalid = checkParams(ctfvalues)
if isvalid is False:
apDisplay.printWarning("Bad CTF values, insert but not create images")
### run the main CTF display program
opimagedir = os.path.join(rundir, "opimages")
if isvalid is True:
oldctfvalues = ctfvalues.copy()
ctfvalues = runCTFdisplayTools(imgdata, ctfvalues, opimagedir, fftpath, fftfreq)
# check if image creation failed
if ctfvalues is None:
ctfvalues = oldctfvalues
### clean rundir from all entries:
if not rundir.endswith("/"):
rundir += "/"
for key in ctfvalues.keys():
if isinstance(ctfvalues[key], str) and ctfvalues[key].startswith(rundir):
ctfvalues[key] = ctfvalues[key].replace(rundir, "")
### time to insert
ctfq = appiondata.ApCtfData()
ctfq['acerun'] = rundata
ctfq['image'] = imgdata
if debug is True:
apDisplay.printMsg("CTF data values")
print ctfvalues
for key in ctfq.keys():
if key in ctfvalues:
ctfq[key] = ctfvalues[key]
if debug is True:
apDisplay.printMsg("%s :: %s"%(key, ctfvalues[key]))
elif debug is True:
apDisplay.printMsg("SKIPPING %s :: %s"%(key, ctfvalues[key]))
ctfdb.printCtfData(ctfq)
ctfq.insert()
return
def convertDefociToConvention(self, ctfdata):
ctfdb.printCtfData(ctfdata)
initdefocusratio = ctfdata['defocus2']/ctfdata['defocus1']
# program specific corrections?
self.angle = ctfdata['angle_astigmatism']
#angle = round(self.angle/2.5,0)*2.5
#by convention: abs(ctfdata['defocus1']) < abs(ctfdata['defocus2'])
if abs(ctfdata['defocus1']) > abs(ctfdata['defocus2']):
# incorrect, need to shift angle by 90 degrees
apDisplay.printWarning("|def1| > |def2|, flipping defocus axes")
self.defocus1 = ctfdata['defocus2']
self.defocus2 = ctfdata['defocus1']
self.angle += 90
else:
# correct, ratio > 1
self.defocus1 = ctfdata['defocus1']
self.defocus2 = ctfdata['defocus2']
if self.defocus1 < 0 and self.defocus2 < 0:
apDisplay.printWarning("Negative defocus values, taking absolute value")
self.defocus1 = abs(self.defocus1)
self.defocus2 = abs(self.defocus2)
self.defdiff = self.defocus1 - self.defocus2
#elliptical ratio is ratio of zero locations NOT defocii
self.defocusratio = self.defocus2/self.defocus1
self.ellipratio = ctftools.defocusRatioToEllipseRatio(self.defocus1, self.defocus2,
self.initfreq, self.cs, self.volts, self.ampcontrast)
# get angle within range -90 < angle <= 90
while self.angle > 90:
self.angle -= 180
while self.angle < -90:
self.angle += 180
apDisplay.printColor("Final params: def1: %.2e | def2: %.2e | angle: %.1f | defratio %.2f"%
(self.defocus1, self.defocus2, self.angle, self.defocusratio), "cyan")
perdiff = abs(self.defocus1-self.defocus2)/abs(self.defocus1+self.defocus2)
apDisplay.printMsg("Defocus Astig Percent Diff %.2f -- %.3e, %.3e"
%(perdiff*100,self.defocus1,self.defocus2))
return
