def printCtfData(self, ctfvalue):
if ctfvalue is None:
return
defocusratio = ctfvalue['defocus2']/ctfvalue['defocus1']
if 'acerun' in ctfvalue:
method = getCtfMethod(ctfvalue)
runname = ctfvalue['acerun']['name']
sys.stderr.write("[%s] method: %s | runname %s\n"%
(apDisplay.colorString("CTF run", "blue"), method, runname))
sys.stderr.write("[%s] def1: %.2e | def2: %.2e | angle: %.1f | ampcontr %.2f | defratio %.3f\n"%
(apDisplay.colorString("CTF param", "blue"), ctfvalue['defocus1'],
ctfvalue['defocus2'], ctfvalue['angle_astigmatism'],
ctfvalue['amplitude_contrast'], defocusratio))
if 'resolution_80_percent' in ctfvalue.keys() and ctfvalue['resolution_80_percent'] is not None:
sys.stderr.write("[%s] conf_30-10: %s | conf_5peak: %s | res_0.8: %.1fA | res_0.5 %.1fA\n"%
(apDisplay.colorString("CTF stats", "blue"),
apDisplay.colorProb(ctfvalue['confidence_30_10']),
apDisplay.colorProb(ctfvalue['confidence_5_peak']),
ctfvalue['resolution_80_percent'], ctfvalue['resolution_50_percent']))
#sys.stderr.write("[%s] conf: %s | conf_d: %s\n"%
# (apDisplay.colorString("CTF stats", "blue"), apDisplay.colorProb(ctfvalue['confidence']),
# apDisplay.colorProb(ctfvalue['confidence_d'])))
#apDisplay.colorProb(numlist[i])
#time.sleep(3)
return
def printCtfData(ctfvalue):
if ctfvalue is None:
return
defocusratio = ctfvalue['defocus2'] / ctfvalue['defocus1']
method = getCtfMethod(ctfvalue)
if 'acerun' in ctfvalue:
method = getCtfMethod(ctfvalue)
runname = ctfvalue['acerun']['name']
sys.stderr.write(
"[%s] method: %s | runname %s\n" %
(apDisplay.colorString("CTF run", "blue"), method, runname))
sys.stderr.write(
"[%s] def1: %.2e | def2: %.2e | angle: %.1f | ampcontr %.2f | defratio %.3f\n"
% (apDisplay.colorString("CTF param", "blue"), ctfvalue['defocus1'],
ctfvalue['defocus2'], ctfvalue['angle_astigmatism'],
ctfvalue['amplitude_contrast'], defocusratio))
if 'resolution_80_percent' in ctfvalue.keys(
) and ctfvalue['resolution_80_percent'] is not None:
sys.stderr.write(
"[%s] conf_30-10: %s | conf_5peak: %s | res_0.8: %.1fA | res_0.5 %.1fA\n"
% (apDisplay.colorString("CTF stats", "blue"),
apDisplay.colorProb(ctfvalue['confidence_30_10']),
apDisplay.colorProb(ctfvalue['confidence_5_peak']),
ctfvalue['resolution_80_percent'],
ctfvalue['resolution_50_percent']))
#sys.stderr.write("[%s] conf: %s | conf_d: %s\n"%
# (apDisplay.colorString("CTF stats", "blue"), apDisplay.colorProb(ctfvalue['confidence']),
# apDisplay.colorProb(ctfvalue['confidence_d'])))
#apDisplay.colorProb(numlist[i])
#time.sleep(3)
return
def runAce(matlab, imgdata, params, showprev=True):
imgname = imgdata['filename']
if showprev is True:
bestctfvalue, bestconf = ctfdb.getBestCtfValueForImage(imgdata)
if bestctfvalue:
print ( "Prev best: '"+bestctfvalue['acerun']['name']+"', conf="+
apDisplay.colorProb(bestconf)+", defocus="+str(round(-1.0*abs(bestctfvalue['defocus1']*1.0e6),2))+
" microns" )
if params['uncorrected']:
tmpname='temporaryCorrectedImage.mrc'
imgarray = apDBImage.correctImage(imgdata)
imgpath = os.path.join(params['rundir'],tmpname)
apImage.arrayToMrc(imgarray, imgpath)
print "processing", imgpath
else:
imgpath = os.path.join(imgdata['session']['image path'], imgname+'.mrc')
nominal = None
if params['nominal'] is not None:
nominal=params['nominal']
elif params['newnominal'] is True:
nominal = ctfdb.getBestDefocusForImage(imgdata, msg=True)
if nominal is None:
nominal = imgdata['scope']['defocus']
if nominal is None or nominal > 0 or nominal < -15e-6:
apDisplay.printWarning("Nominal should be of the form nominal=-1.2e-6"+\
" for -1.2 microns NOT:"+str(nominal))
#Neil's Hack
#if 'autosample' in params and params['autosample']:
# x = abs(nominal*1.0e6)
# val = 1.585 + 0.057587 * x - 0.044106 * x**2 + 0.010877 * x**3
# resamplefr_override = round(val,3)
# print "resamplefr_override=",resamplefr_override
# pymat.eval(matlab, "resamplefr="+str(resamplefr_override)+";")
pymat.eval(matlab,("dforig = %e;" % nominal))
if params['stig'] == 0:
plist = (imgpath, params['outtextfile'], params['display'], params['stig'],\
params['medium'], -nominal, params['tempdir']+"/")
acecmd = makeMatlabCmd("ctfparams = ace(",");",plist)
else:
plist = (imgname, imgpath, params['outtextfile'], params['opimagedir'], \
params['matdir'], params['display'], params['stig'],\
params['medium'], -nominal, params['tempdir']+"/", params['resamplefr'])
acecmd = makeMatlabCmd("ctfparams = measureAstigmatism(",");",plist)
#print acecmd
pymat.eval(matlab,acecmd)
matfile = os.path.join(params['matdir'], imgname+".mrc.mat")
if params['stig']==0:
savematcmd = "save('"+matfile+"','ctfparams','scopeparams', 'dforig');"
pymat.eval(matlab,savematcmd)
ctfvalue = pymat.get(matlab, 'ctfparams')
ctfvalue=ctfvalue[0]
ctfdb.printResults(params, nominal, ctfvalue)
return ctfvalue
def runAce(matlab, imgdata, params, showprev=True):
imgname = imgdata['filename']
if showprev is True:
bestctfvalue = ctfdb.getBestCtfByResolution(imgdata)
if bestctfvalue:
bestconf = ctfdb.calculateConfidenceScore(bestctfvalue)
print ( "Prev best: '"+bestctfvalue['acerun']['name']+"', conf="+
apDisplay.colorProb(bestconf)+", defocus="+str(round(-1.0*abs(bestctfvalue['defocus1']*1.0e6),2))+
" microns" )
if params['uncorrected']:
tmpname='temporaryCorrectedImage.mrc'
imgarray = apDBImage.correctImage(imgdata)
imgpath = os.path.join(params['rundir'],tmpname)
apImage.arrayToMrc(imgarray, imgpath)
print "processing", imgpath
else:
imgpath = os.path.join(imgdata['session']['image path'], imgname+'.mrc')
nominal = None
if params['nominal'] is not None:
nominal=params['nominal']
elif params['newnominal'] is True:
bestctfvalue = ctfdb.getBestCtfByResolution(imgdata)
nominal = bestctfvalue['defocus1']
if nominal is None:
nominal = imgdata['scope']['defocus']
if nominal is None or nominal > 0 or nominal < -15e-6:
apDisplay.printWarning("Nominal should be of the form nominal=-1.2e-6"+\
" for -1.2 microns NOT:"+str(nominal))
#Neil's Hack
#if 'autosample' in params and params['autosample']:
# x = abs(nominal*1.0e6)
# val = 1.585 + 0.057587 * x - 0.044106 * x**2 + 0.010877 * x**3
# resamplefr_override = round(val,3)
# print "resamplefr_override=",resamplefr_override
# pymat.eval(matlab, "resamplefr="+str(resamplefr_override)+";")
pymat.eval(matlab,("dforig = %e;" % nominal))
if params['stig'] == 0:
plist = (imgpath, params['outtextfile'], params['display'], params['stig'],\
params['medium'], -nominal, params['tempdir']+"/")
acecmd = makeMatlabCmd("ctfparams = ace(",");",plist)
else:
plist = (imgname, imgpath, params['outtextfile'], params['opimagedir'], \
params['matdir'], params['display'], params['stig'],\
params['medium'], -nominal, params['tempdir']+"/", params['resamplefr'])
acecmd = makeMatlabCmd("ctfparams = measureAstigmatism(",");",plist)
#print acecmd
pymat.eval(matlab,acecmd)
matfile = os.path.join(params['matdir'], imgname+".mrc.mat")
if params['stig']==0:
savematcmd = "save('"+matfile+"','ctfparams','scopeparams', 'dforig');"
pymat.eval(matlab,savematcmd)
ctfvalue = pymat.get(matlab, 'ctfparams')
ctfvalue=ctfvalue[0]
printResults(params, nominal, ctfvalue)
return ctfvalue
