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 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 runChimeraScript(chimscript, xvfb=False):
if not chimscript or not os.path.isfile(chimscript):
print chimscript
apDisplay.printError("Could not find file: apChimSnapshot.py")
#apDisplay.printColor("Trying to use chimera for model imaging","cyan")
if xvfb is True:
port = apParam.resetVirtualFrameBuffer()
time.sleep(1)
if 'CHIMERA' in os.environ and os.path.isdir(os.environ['CHIMERA']):
chimpath = os.environ['CHIMERA']
os.environ['CHIMERA'] = chimpath
os.environ['CHIMERAPATH'] = os.path.join(chimpath,"share")
os.environ['LD_LIBRARY_PATH'] = os.path.join(chimpath,"lib")+":"+os.environ['LD_LIBRARY_PATH']
chimexe = os.path.join(chimpath,"bin/chimera")
if not os.path.isfile(chimexe):
apDisplay.printWarning("Could not find chimera at: "+chimexe)
else:
chimpath = None
chimexe = "chimera"
#apDisplay.printWarning("'CHIMERA' environmental variable is unset")
rendercmd = (chimexe+" --debug python:"+chimscript)
logf = open("chimeraRun.log", "a")
apDisplay.printColor("running Chimera:\n "+rendercmd, "cyan")
if xvfb is True:
print "import -verbose -display :%d -window root screencapture.png"%(port)
proc = subprocess.Popen(rendercmd, shell=True, stdout=logf, stderr=logf)
proc.wait()
logf.close()
if xvfb is True:
apParam.killVirtualFrameBuffer(port)
return
def runChimeraScript(chimscript, xvfb=False):
if not chimscript or not os.path.isfile(chimscript):
print chimscript
apDisplay.printError("Could not find file: apChimSnapshot.py")
#apDisplay.printColor("Trying to use chimera for model imaging","cyan")
if xvfb is True:
port = apParam.resetVirtualFrameBuffer()
time.sleep(1)
if 'CHIMERA' in os.environ and os.path.isdir(os.environ['CHIMERA']):
chimpath = os.environ['CHIMERA']
os.environ['CHIMERA'] = chimpath
os.environ['CHIMERAPATH'] = os.path.join(chimpath, "share")
os.environ['LD_LIBRARY_PATH'] = os.path.join(
chimpath, "lib") + ":" + os.environ['LD_LIBRARY_PATH']
chimexe = os.path.join(chimpath, "bin/chimera")
if not os.path.isfile(chimexe):
apDisplay.printWarning("Could not find chimera at: " + chimexe)
else:
chimpath = None
chimexe = "chimera"
#apDisplay.printWarning("'CHIMERA' environmental variable is unset")
rendercmd = (chimexe + " --debug python:" + chimscript)
logf = open("chimeraRun.log", "a")
apDisplay.printColor("running Chimera:\n " + rendercmd, "cyan")
if xvfb is True:
print "import -verbose -display :%d -window root screencapture.png" % (
port)
proc = subprocess.Popen(rendercmd, shell=True, stdout=logf, stderr=logf)
proc.wait()
logf.close()
if xvfb is True:
apParam.killVirtualFrameBuffer(port)
return