def preLoopFunctions(self):
self.powerspecdir = os.path.join(self.params['rundir'], "opimages")
apParam.createDirectory(self.powerspecdir, warning=False)
self.acerunq = None
self.params['matdir'] = os.path.join(self.params['rundir'], "matfiles")
self.params['tempdir'] = os.path.join(self.params['rundir'], "temp")
apParam.createDirectory(os.path.join(self.params['matdir']),
warning=False)
apParam.createDirectory(os.path.join(self.params['tempdir']),
warning=False)
if self.params['sessionname'] is not None:
self.params['outtextfile'] = os.path.join(
self.params['rundir'], self.params['sessionname'] + ".txt")
if self.params['xvfb'] is True:
apParam.resetVirtualFrameBuffer()
apMatlab.checkMatlabPath(self.params)
acepath = os.path.join(os.getcwd(), self.functionname + ".py")
#if not os.path.isfile(acepath):
# apDisplay.printWarning("'"+self.functionname+".py' usually needs to be run in the "+\
# "same directory as all of its matlab files")
print "Connecting to matlab ... "
if self.params['xvfb'] is True:
apParam.resetVirtualFrameBuffer()
try:
self.matlab = pymat.open()
#self.matlab = pymat.open('matlab -nodisplay')
except:
apDisplay.environmentError()
raise
apMatlab.setAceConfig(self.matlab, self.params)
def checkMatlabPath(params=None):
'''
Return immediately if MATLABPATH environment variable is already set.
Searches for ace.m and adds its directory to matlab path.
'''
if os.environ.get("MATLABPATH") is None:
#TRY LOCAL DIRECTORY FIRST
matlabpath = os.path.abspath(".")
if os.path.isfile(os.path.join(matlabpath,"ace.m")):
updateMatlabPath(matlabpath)
return
#TRY APPIONDIR/ace
if params is not None and 'appiondir' in params:
matlabpath = os.path.join(params['appiondir'],"ace")
if os.path.isdir(matlabpath) and os.path.isfile(os.path.join(matlabpath,"ace.m")):
updateMatlabPath(matlabpath)
return
#TRY sibling dir of this script
libdir = os.path.dirname(__file__)
libdir = os.path.abspath(libdir)
appiondir = os.path.dirname(libdir)
acedir = os.path.join(appiondir, 'ace')
if os.path.isdir(acedir) and os.path.isfile(os.path.join(acedir,"ace.m")):
updateMatlabPath(acedir)
return
apDisplay.environmentError()
raise RuntimeError('Could not find ace.m. Check MATLABPATH environment variable.')
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, conf = ctfdb.getBestCtfValueForImage(imgdict)
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 preLoopFunctions(self):
self.powerspecdir = os.path.join(self.params['rundir'], "opimages")
apParam.createDirectory(self.powerspecdir, warning=False)
self.acerunq = None
self.params['matdir'] = os.path.join(self.params['rundir'],"matfiles")
self.params['tempdir'] = os.path.join(self.params['rundir'],"temp")
apParam.createDirectory(os.path.join(self.params['matdir']), warning=False)
apParam.createDirectory(os.path.join(self.params['tempdir']), warning=False)
if self.params['sessionname'] is not None:
self.params['outtextfile']=os.path.join(self.params['rundir'], self.params['sessionname']+".txt")
if self.params['xvfb'] is True:
apParam.resetVirtualFrameBuffer()
apMatlab.checkMatlabPath(self.params)
acepath = os.path.join(os.getcwd(), self.functionname+".py")
#if not os.path.isfile(acepath):
# apDisplay.printWarning("'"+self.functionname+".py' usually needs to be run in the "+\
# "same directory as all of its matlab files")
print "Connecting to matlab ... "
if self.params['xvfb'] is True:
apParam.resetVirtualFrameBuffer()
try:
self.matlab = pymat.open()
#self.matlab = pymat.open('matlab -nodisplay')
except:
apDisplay.environmentError()
raise
apMatlab.setAceConfig(self.matlab, self.params)
def checkMatlabPath(params=None):
'''
Return immediately if MATLABPATH environment variable is already set.
Searches for ace.m and adds its directory to matlab path.
'''
if os.environ.get("MATLABPATH") is None:
#TRY LOCAL DIRECTORY FIRST
matlabpath = os.path.abspath(".")
if os.path.isfile(os.path.join(matlabpath,"ace.m")):
updateMatlabPath(matlabpath)
return
#TRY APPIONDIR/ace
if params is not None and 'appiondir' in params:
matlabpath = os.path.join(params['appiondir'],"ace")
if os.path.isdir(matlabpath) and os.path.isfile(os.path.join(matlabpath,"ace.m")):
updateMatlabPath(matlabpath)
return
#TRY sibling dir of this script
libdir = os.path.dirname(__file__)
libdir = os.path.abspath(libdir)
appiondir = os.path.dirname(libdir)
acedir = os.path.join(appiondir, 'ace')
if os.path.isdir(acedir) and os.path.isfile(os.path.join(acedir,"ace.m")):
updateMatlabPath(acedir)
return
apDisplay.environmentError()
raise RuntimeError('Could not find ace.m. Check MATLABPATH environment variable.')
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
