def runAceCorrect(imgdict,params):
imgname = imgdict['filename']
imgpath = os.path.join(imgdict['session']['image path'], imgname+'.mrc')
voltage = (imgdict['scope']['high tension'])
apix = apDatabase.getPixelSize(imgdict)
ctfvalues = ctfdb.getBestCtfByResolution(imgdata)
conf = ctfdb.calculateConfidenceScore(bestctfvalue)
ctdimname = imgname
ctdimpath = os.path.join(params['rundir'],ctdimname)
print "Corrected Image written to " + ctdimpath
#pdb.set_trace()
acecorrectcommand=("ctfcorrect1('%s', '%s', '%.32f', '%.32f', '%f', '%f', '%f');" % \
(imgpath, ctdimpath, ctfvalues['defocus1'], ctfvalues['defocus2'], -ctfvalues['angle_astigmatism'], voltage, apix))
print acecorrectcommand
try:
matlab = pymat.open("matlab -nosplash")
except:
apDisplay.environmentError()
raise
pymat.eval(matlab, acecorrectcommand)
pymat.close(matlab)
return
def phaseFlipAceTwo(self, inimgpath, imgdata):
apix = apDatabase.getPixelSize(imgdata)
bestctfvalue = self.getBestCtfValue(imgdata, True)
if bestctfvalue is None:
apDisplay.printWarning("No ctf estimation for current image")
self.badprocess = True
return None
if bestctfvalue['acerun'] is None:
apDisplay.printWarning("No ctf runid for current image")
self.badprocess = True
return None
if bestctfvalue['ctfvalues_file'] is None:
# Since method = ace2 requires a ctfvalues_file,
# create file from database values
### cannot use ACE2 correction without CS value in database
if not 'cs' in bestctfvalue:
apDisplay.printMsg('No spherical abberation value in database, skipping image')
self.badprocess = True
return None
# create ctfvalues_file from ctf run
ctfvaluesfile = "tmp_ctfvaluesfile.txt"
if abs(bestctfvalue['defocus1']) < abs(bestctfvalue['defocus2']):
## this is the canonical form
df1 = abs(bestctfvalue['defocus1'])
df2 = abs(bestctfvalue['defocus2'])
angast = bestctfvalue['angle_astigmatism']
else:
apDisplay.printWarning("|def1| > |def2|, flipping defocus axes")
df1 = abs(bestctfvalue['defocus2'])
df2 = abs(bestctfvalue['defocus1'])
angast = bestctfvalue['angle_astigmatism'] + 90
amp = bestctfvalue['amplitude_contrast']
kv = imgdata['scope']['high tension']/1000
cs = self.getCS(bestctfvalue)/1000
conf = ctfdb.calculateConfidenceScore(bestctfvalue)
if os.path.isfile(ctfvaluesfile):
os.remove(ctfvaluesfile)
f = open(ctfvaluesfile,'w')
f.write("\tFinal Params for image: %s.mrc\n"%imgdata['filename'])
# acecorrect definition is opposite to database
f.write("\tFinal Defocus (m,m,deg): %.6e %.6e %.6f\n"%(df1,df2,-angast))
f.write("\tAmplitude Contrast: %.6f\n"%amp)
f.write("\tVoltage (kV): %.6f\n"%kv)
f.write("\tSpherical Aberration (mm): %.6e\n"%cs)
f.write("\tAngstroms per pixel: %.6e\n"%apix)
f.write("\tConfidence: %.6e\n"%conf)
f.close()
# use ace2 ctfvalues file
else:
ctfvaluesfile = os.path.join(bestctfvalue['acerun']['path']['path'], bestctfvalue['ctfvalues_file'])
ctfvaluesfilesplit = os.path.splitext(ctfvaluesfile)
while ctfvaluesfilesplit[1] != '.mrc':
ctfvaluesfilesplit = os.path.splitext(ctfvaluesfilesplit[0])
ctfvaluesfile = ctfvaluesfilesplit[0]+".mrc.ctf.txt"
defocus1 = bestctfvalue['defocus1']
defocus2 = bestctfvalue['defocus2']
defocus = (defocus1+defocus2)/2.0*1.0e6
apDisplay.printMsg("using ctfvaluesfile: "+ctfvaluesfile)
if not os.path.isfile(ctfvaluesfile):
apDisplay.printError("ctfvaluesfile does not exist")
ace2exe = self.getACE2Path()
outfile = os.path.join(os.getcwd(),imgdata['filename']+".mrc.corrected.mrc")
ace2cmd = (ace2exe+" -ctf %s -apix %.3f -img %s -out %s" % (ctfvaluesfile, apix, inimgpath,outfile))
if self.params['fliptype'] == "ace2image":
ace2cmd += " -wiener 0.1"
apDisplay.printMsg("ace2 command: "+ace2cmd)
apDisplay.printMsg("phaseflipping entire micrograph with defocus "+str(round(defocus,3))+" microns")
#apEMAN.executeEmanCmd(ace2cmd, showcmd = True)
if self.params['verbose'] is True:
ace2proc = subprocess.Popen(ace2cmd, shell=True)
else:
aceoutf = open("ace2.out", "a")
aceerrf = open("ace2.err", "a")
ace2proc = subprocess.Popen(ace2cmd, shell=True, stderr=aceerrf, stdout=aceoutf)
ace2proc.wait()
if self.stats['count'] <= 1:
### ace2 always crashes on first image??? .fft_wisdom file??
time.sleep(0.1)
if self.params['verbose'] is True:
ace2proc = subprocess.Popen(ace2cmd, shell=True)
else:
aceoutf = open("ace2.out", "a")
aceerrf = open("ace2.err", "a")
ace2proc = subprocess.Popen(ace2cmd, shell=True, stderr=aceerrf, stdout=aceoutf)
ace2proc.wait()
if self.params['verbose'] is False:
aceoutf.close()
aceerrf.close()
if not os.path.isfile(outfile):
apDisplay.printError("ACE 2 failed to create image file:\n%s" % outfile)
return outfile
def checkCtfParams(self, imgdata):
shortname = apDisplay.short(imgdata['filename'])
ctfvalue = self.getBestCtfValue(imgdata)
### check if we have values and if we care
if ctfvalue is None:
return not self.checkRequireCtf()
### check that CTF estimation is above confidence threshold
conf = ctfdb.calculateConfidenceScore(ctfvalue)
if self.params['ctfcutoff'] and conf < self.params['ctfcutoff']:
apDisplay.printColor(shortname+" is below confidence threshold (conf="+str(round(conf,3))+")\n","cyan")
return False
### check resolution requirement for CTF fit at 0.8 threshold
if self.params['ctfres80min'] is not None or self.params['ctfres80max'] is not None:
if not 'resolution_80_percent' in ctfvalue.keys() or ctfvalue['resolution_80_percent'] is None:
apDisplay.printColor("%s: no 0.8 resolution found"%(shortname), "cyan")
return False
if self.params['ctfres80max'] and ctfvalue['resolution_80_percent'] > self.params['ctfres80max']:
apDisplay.printColor("%s is above resolution threshold %.2f > %.2f"
%(shortname, ctfvalue['resolution_80_percent'], self.params['ctfres80max']), "cyan")
return False
if self.params['ctfres80min'] and ctfvalue['resolution_80_percent'] < self.params['ctfres80min']:
apDisplay.printColor("%s is below resolution threshold %.2f > %.2f"
%(shortname, ctfvalue['resolution_80_percent'], self.params['ctfres80min']), "cyan")
return False
### check resolution requirement for CTF fit at 0.5 threshold
if self.params['ctfres50min'] is not None or self.params['ctfres50max'] is not None:
if not 'resolution_50_percent' in ctfvalue.keys() or ctfvalue['resolution_50_percent'] is None:
apDisplay.printColor("%s: no 0.5 resolution found"%(shortname), "cyan")
return False
if self.params['ctfres50max'] and ctfvalue['resolution_50_percent'] > self.params['ctfres50max']:
apDisplay.printColor("%s is above resolution threshold %.2f > %.2f"
%(shortname, ctfvalue['resolution_50_percent'], self.params['ctfres50max']), "cyan")
return False
if self.params['ctfres50min'] and ctfvalue['resolution_50_percent'] < self.params['ctfres50min']:
apDisplay.printColor("%s is below resolution threshold %.2f > %.2f"
%(shortname, ctfvalue['resolution_50_percent'], self.params['ctfres50min']), "cyan")
return False
if self.params['mindefocus'] is not None or self.params['maxdefocus'] is not None:
### get best defocus value
### defocus should be in negative meters
if ctfvalue['defocus2'] is not None and ctfvalue['defocus1'] != ctfvalue['defocus2']:
defocus = (ctfvalue['defocus1'] + ctfvalue['defocus2'])/2.0
else:
defocus = ctfvalue['defocus1']
defocus = -1.0*abs(defocus)
### assume defocus values are ALWAYS negative but mindefocus is greater than maxdefocus
if self.params['mindefocus']:
self.params['mindefocus'] = -abs( self.params['mindefocus'] )
if self.params['maxdefocus']:
self.params['maxdefocus'] = -abs( self.params['maxdefocus'] )
if self.params['mindefocus'] and self.params['maxdefocus']:
if self.params['maxdefocus'] > self.params['mindefocus']:
mindef = self.params['mindefocus']
maxdef = self.params['maxdefocus']
self.params['mindefocus'] = maxdef
self.params['maxdefocus'] = mindef
### skip micrograph that have defocus above or below min & max defocus levels
if self.params['mindefocus'] and defocus > self.params['mindefocus']:
#apDisplay.printColor(shortname+" defocus ("+str(round(defocus*1e6,2))+\
# " um) is less than mindefocus ("+str(self.params['mindefocus']*1e6)+" um)\n","cyan")
return False
if self.params['maxdefocus'] and defocus < self.params['maxdefocus']:
#apDisplay.printColor(shortname+" defocus ("+str(round(defocus*1e6,2))+\
# " um) is greater than maxdefocus ("+str(self.params['maxdefocus']*1e6)+" um)\n","cyan")
return False
return True
def checkCtfParams(self, imgdata):
shortname = apDisplay.short(imgdata['filename'])
ctfvalue = self.getBestCtfValue(imgdata)
### check if we have values and if we care
if ctfvalue is None:
return not self.checkRequireCtf()
### check that CTF estimation is above confidence threshold
conf = ctfdb.calculateConfidenceScore(ctfvalue)
if self.params['ctfcutoff'] and conf < self.params['ctfcutoff']:
apDisplay.printColor(
shortname + " is below confidence threshold (conf=" +
str(round(conf, 3)) + ")\n", "cyan")
return False
### check resolution requirement for CTF fit at 0.8 threshold
if self.params['ctfres80min'] is not None or self.params[
'ctfres80max'] is not None:
if not 'resolution_80_percent' in ctfvalue.keys(
) or ctfvalue['resolution_80_percent'] is None:
apDisplay.printColor(
"%s: no 0.8 resolution found" % (shortname), "cyan")
return False
if self.params['ctfres80max'] and ctfvalue[
'resolution_80_percent'] > self.params['ctfres80max']:
apDisplay.printColor(
"%s is above resolution threshold %.2f > %.2f" %
(shortname, ctfvalue['resolution_80_percent'],
self.params['ctfres80max']), "cyan")
return False
if self.params['ctfres80min'] and ctfvalue[
'resolution_80_percent'] < self.params['ctfres80min']:
apDisplay.printColor(
"%s is below resolution threshold %.2f > %.2f" %
(shortname, ctfvalue['resolution_80_percent'],
self.params['ctfres80min']), "cyan")
return False
### check resolution requirement for CTF fit at 0.5 threshold
if self.params['ctfres50min'] is not None or self.params[
'ctfres50max'] is not None:
if not 'resolution_50_percent' in ctfvalue.keys(
) or ctfvalue['resolution_50_percent'] is None:
apDisplay.printColor(
"%s: no 0.5 resolution found" % (shortname), "cyan")
return False
if self.params['ctfres50max'] and ctfvalue[
'resolution_50_percent'] > self.params['ctfres50max']:
apDisplay.printColor(
"%s is above resolution threshold %.2f > %.2f" %
(shortname, ctfvalue['resolution_50_percent'],
self.params['ctfres50max']), "cyan")
return False
if self.params['ctfres50min'] and ctfvalue[
'resolution_50_percent'] < self.params['ctfres50min']:
apDisplay.printColor(
"%s is below resolution threshold %.2f > %.2f" %
(shortname, ctfvalue['resolution_50_percent'],
self.params['ctfres50min']), "cyan")
return False
if self.params['mindefocus'] is not None or self.params[
'maxdefocus'] is not None:
### get best defocus value
### defocus should be in negative meters
if ctfvalue['defocus2'] is not None and ctfvalue[
'defocus1'] != ctfvalue['defocus2']:
defocus = (ctfvalue['defocus1'] + ctfvalue['defocus2']) / 2.0
else:
defocus = ctfvalue['defocus1']
defocus = -1.0 * abs(defocus)
### assume defocus values are ALWAYS negative but mindefocus is greater than maxdefocus
if self.params['mindefocus']:
self.params['mindefocus'] = -abs(self.params['mindefocus'])
if self.params['maxdefocus']:
self.params['maxdefocus'] = -abs(self.params['maxdefocus'])
if self.params['mindefocus'] and self.params['maxdefocus']:
if self.params['maxdefocus'] > self.params['mindefocus']:
mindef = self.params['mindefocus']
maxdef = self.params['maxdefocus']
self.params['mindefocus'] = maxdef
self.params['maxdefocus'] = mindef
### skip micrograph that have defocus above or below min & max defocus levels
if self.params[
'mindefocus'] and defocus > self.params['mindefocus']:
#apDisplay.printColor(shortname+" defocus ("+str(round(defocus*1e6,2))+\
# " um) is less than mindefocus ("+str(self.params['mindefocus']*1e6)+" um)\n","cyan")
return False
if self.params[
'maxdefocus'] and defocus < self.params['maxdefocus']:
#apDisplay.printColor(shortname+" defocus ("+str(round(defocus*1e6,2))+\
# " um) is greater than maxdefocus ("+str(self.params['maxdefocus']*1e6)+" um)\n","cyan")
return False
return True
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