def run(self):
t0 = time.time()
imgarray = self.openFile()
self.imgshape = imgarray.shape
self.printImageInfo(imgarray)
coordlist = self.setupCoordList()
ctfdict = {}
self.count = 0
### process image pieces
print "processing %d image pieces" % (len(coordlist))
keys = coordlist.keys()
keys.sort()
for key in keys:
(xstr, ystr) = key.split('x')
x = int(xstr)
y = int(ystr)
self.count += 1
subarray = self.getSubImage(imgarray, x, y)
#self.printImageInfo(subarray)
imgfile = "splitimage-" + key + ".dwn.mrc"
mrc.write(subarray, imgfile)
ctfvalues = None
reproc = 0
edgeblur = 8
while ctfvalues is None and reproc < 3:
ctfvalues = self.processImage(imgfile, edgeblur)
reproc += 1
edgeblur += 2
if ctfvalues is not None:
sys.stderr.write("#")
else:
sys.stderr.write("!")
ctfdict[key] = ctfvalues
apFile.removeFilePattern(imgfile + "*", False)
sys.stderr.write("\n")
### calculate ctf parameters
self.fitPlaneToCtf(ctfdict)
apDisplay.printMsg("Time: %s" %
(apDisplay.timeString(time.time() - t0)))
def run(self):
t0 = time.time()
imgarray = self.openFile()
self.imgshape = imgarray.shape
self.printImageInfo(imgarray)
coordlist = self.setupCoordList()
ctfdict = {}
self.count = 0
### process image pieces
print "processing %d image pieces"%(len(coordlist))
keys = coordlist.keys()
keys.sort()
for key in keys:
(xstr,ystr) = key.split('x')
x = int(xstr)
y = int(ystr)
self.count += 1
subarray = self.getSubImage(imgarray, x, y)
#self.printImageInfo(subarray)
imgfile = "splitimage-"+key+".dwn.mrc"
mrc.write(subarray, imgfile)
ctfvalues = None
reproc = 0
edgeblur = 8
while ctfvalues is None and reproc < 3:
ctfvalues = self.processImage(imgfile, edgeblur)
reproc += 1
edgeblur += 2
if ctfvalues is not None:
sys.stderr.write("#")
else:
sys.stderr.write("!")
ctfdict[key] = ctfvalues
apFile.removeFilePattern(imgfile+"*", False)
sys.stderr.write("\n")
### calculate ctf parameters
self.fitPlaneToCtf(ctfdict)
apDisplay.printMsg("Time: %s"%(apDisplay.timeString(time.time()-t0)))
def processImage(self, imgfile, edgeblur=8, msg=False):
### make command line
acecmd = ("%s -i %s -c %.2f -k %d -a %.3f -e %d,0.001 -b 1" %
(self.ace2exe, imgfile, self.params['cs'], self.params['kv'],
self.params['apix'], edgeblur))
### run ace2
aceoutf = open("ace2.stdout", "w")
#print acecmd
ace2proc = subprocess.Popen(acecmd,
shell=True,
stdout=aceoutf,
stderr=aceoutf)
ace2proc.wait()
### check if ace2 worked
imagelog = imgfile + ".ctf.txt"
if not os.path.isfile(imagelog) and self.count <= 1:
### ace2 always crashes on first image??? .fft_wisdom file??
time.sleep(1)
ace2proc = subprocess.Popen(acecmd,
shell=True,
stdout=aceoutf,
stderr=aceoutf)
ace2proc.wait()
aceoutf.close()
### die
if not os.path.isfile(imagelog):
apDisplay.printError("ace2 did not run")
### parse log file
ctfvalues = {}
logf = open(imagelog, "r")
for line in logf:
sline = line.strip()
if re.search("^Final Defocus:", sline):
parts = sline.split()
ctfvalues['defocus1'] = float(parts[2])
ctfvalues['defocus2'] = float(parts[3])
### convert to degrees
ctfvalues['angle_astigmatism'] = math.degrees(float(parts[4]))
elif re.search("^Amplitude Contrast:", sline):
parts = sline.split()
ctfvalues['amplitude_contrast'] = float(parts[2])
elif re.search("^Confidence:", sline):
parts = sline.split()
ctfvalues['confidence'] = float(parts[1])
ctfvalues['confidence_d'] = float(parts[1])
logf.close()
### summary stats
avgdf = (ctfvalues['defocus1'] + ctfvalues['defocus2']) / 2.0
ampconst = 100.0 * ctfvalues['amplitude_contrast']
pererror = 100.0 * (ctfvalues['defocus1'] -
ctfvalues['defocus2']) / avgdf
if msg is True:
apDisplay.printMsg("============")
apDisplay.printMsg("Defocus: %.3f x %.3f um (%.2f percent error)" %
(ctfvalues['defocus1'] * 1.0e6,
ctfvalues['defocus2'] * 1.0e6, pererror))
apDisplay.printMsg("Angle astigmatism: %.2f degrees" %
(ctfvalues['angle_astigmatism']))
apDisplay.printMsg("Amplitude contrast: %.2f percent" % (ampconst))
apDisplay.printMsg("Final confidence: %.3f" %
(ctfvalues['confidence']))
### double check that the values are reasonable
if avgdf < -1.0e-3 or avgdf > -1.0e-9:
apDisplay.printWarning(
"bad defocus estimate, not committing values to database")
return None
if ampconst < -0.01 or ampconst > 80.0:
apDisplay.printWarning(
"bad amplitude contrast, not committing values to database")
return None
if ctfvalues['confidence'] < 0.6:
sys.stderr.write("c")
#apDisplay.printWarning("bad confidence")
return None
return ctfvalues
def processImage(self, imgfile, edgeblur=8, msg=False):
### make command line
acecmd = ("%s -i %s -c %.2f -k %d -a %.3f -e %d,0.001 -b 1"
%(self.ace2exe, imgfile, self.params['cs'], self.params['kv'], self.params['apix'], edgeblur))
### run ace2
aceoutf = open("ace2.stdout", "w")
#print acecmd
ace2proc = subprocess.Popen(acecmd, shell=True, stdout=aceoutf, stderr=aceoutf)
ace2proc.wait()
### check if ace2 worked
imagelog = imgfile+".ctf.txt"
if not os.path.isfile(imagelog) and self.count <= 1:
### ace2 always crashes on first image??? .fft_wisdom file??
time.sleep(1)
ace2proc = subprocess.Popen(acecmd, shell=True, stdout=aceoutf, stderr=aceoutf)
ace2proc.wait()
aceoutf.close()
### die
if not os.path.isfile(imagelog):
apDisplay.printError("ace2 did not run")
### parse log file
ctfvalues = {}
logf = open(imagelog, "r")
for line in logf:
sline = line.strip()
if re.search("^Final Defocus:", sline):
parts = sline.split()
ctfvalues['defocus1'] = float(parts[2])
ctfvalues['defocus2'] = float(parts[3])
### convert to degrees
ctfvalues['angle_astigmatism'] = math.degrees(float(parts[4]))
elif re.search("^Amplitude Contrast:",sline):
parts = sline.split()
ctfvalues['amplitude_contrast'] = float(parts[2])
elif re.search("^Confidence:",sline):
parts = sline.split()
ctfvalues['confidence'] = float(parts[1])
ctfvalues['confidence_d'] = float(parts[1])
logf.close()
### summary stats
avgdf = (ctfvalues['defocus1']+ctfvalues['defocus2'])/2.0
ampconst = 100.0*ctfvalues['amplitude_contrast']
pererror = 100.0 * (ctfvalues['defocus1']-ctfvalues['defocus2']) / avgdf
if msg is True:
apDisplay.printMsg("============")
apDisplay.printMsg("Defocus: %.3f x %.3f um (%.2f percent error)"%
(ctfvalues['defocus1']*1.0e6, ctfvalues['defocus2']*1.0e6, pererror ))
apDisplay.printMsg("Angle astigmatism: %.2f degrees"%(ctfvalues['angle_astigmatism']))
apDisplay.printMsg("Amplitude contrast: %.2f percent"%(ampconst))
apDisplay.printMsg("Final confidence: %.3f"%(ctfvalues['confidence']))
### double check that the values are reasonable
if avgdf < -1.0e-3 or avgdf > -1.0e-9:
apDisplay.printWarning("bad defocus estimate, not committing values to database")
return None
if ampconst < -0.01 or ampconst > 80.0:
apDisplay.printWarning("bad amplitude contrast, not committing values to database")
return None
if ctfvalues['confidence'] < 0.6:
sys.stderr.write("c")
#apDisplay.printWarning("bad confidence")
return None
return ctfvalues
