def _startLoop(self, imgdata):
"""
initilizes several parameters for a new image
and checks if it is okay to start processing image
"""
if self.params['parallel']:
if self.lockParallel(imgdata.dbid):
apDisplay.printMsg(
'%s locked by another parallel run in the rundir' %
(imgdata['filename']))
return False
#calc images left
self.stats[
'imagesleft'] = self.stats['imagecount'] - self.stats['count']
#only if an image was processed last
if (self.stats['lastcount'] != self.stats['count']):
if self.params['background'] is False:
apDisplay.printColor(
"\nStarting image %d ( skip:%d, remain:%d ) id:%d, file: %s"
% (
self.stats['count'],
self.stats['skipcount'],
self.stats['imagesleft'],
imgdata.dbid,
imgdata['filename'],
), "green")
elif self.stats['count'] % 80 == 0:
sys.stderr.write("\n")
self.stats['lastcount'] = self.stats['count']
if apDisplay.isDebugOn():
self._checkMemLeak()
# skip if image doesn't exist:
imgpath = os.path.join(imgdata['filename'] + '.dwn.mrc')
if not os.path.isfile(imgpath):
apDisplay.printWarning(imgpath + " not found, skipping")
if self.params['parallel']:
self.unlockParallel(imgdata.dbid)
return False
# check to see if image has already been processed
if self._alreadyProcessed(imgdata):
if self.params['parallel']:
self.unlockParallel(imgdata.dbid)
return False
self.stats['waittime'] = 0
if self.reprocessImage(imgdata) is True:
if self.params['background'] is True:
sys.stderr.write(",")
else:
if self.params['background'] is True:
sys.stderr.write(".")
return True
def _startLoop(self, imgdata):
"""
initilizes several parameters for a new image
and checks if it is okay to start processing image
"""
if self.params['parallel']:
if self.lockParallel(imgdata.dbid):
apDisplay.printMsg('%s locked by another parallel run in the rundir' % (apDisplay.shortenImageName(imgdata['filename'])))
return False
#calc images left
self.stats['imagesleft'] = self.stats['imagecount'] - self.stats['count']
#only if an image was processed last
if(self.stats['lastcount'] != self.stats['count']):
if self.params['background'] is False:
apDisplay.printColor( "\nStarting image %d ( skip:%d, remain:%d ) id:%d, file: %s"
%(self.stats['count'], self.stats['skipcount'], self.stats['imagesleft'],
imgdata.dbid, apDisplay.short(imgdata['filename']),),
"green")
elif self.stats['count'] % 80 == 0:
sys.stderr.write("\n")
self.stats['lastcount'] = self.stats['count']
if apDisplay.isDebugOn():
self._checkMemLeak()
# skip if image doesn't exist:
imgpath = os.path.join(imgdata['session']['image path'], imgdata['filename']+'.mrc')
if not os.path.isfile(imgpath):
apDisplay.printWarning(imgpath+" not found, skipping")
if self.params['parallel']:
self.unlockParallel(imgdata.dbid)
return False
# check to see if image has already been processed
if self._alreadyProcessed(imgdata):
if self.params['parallel']:
self.unlockParallel(imgdata.dbid)
return False
self.stats['waittime'] = 0
if self.reprocessImage(imgdata) is True:
if self.params['background'] is True:
sys.stderr.write(",")
else:
"""apDisplay.printMsg("reprocessing "+apDisplay.shortenImageName(imgdata['filename']))"""
else:
if self.params['background'] is True:
sys.stderr.write(".")
else:
"""apDisplay.printMsg("processing "+apDisplay.shortenImageName(imgdata['filename']))"""
return True
def close(self):
self.onClose()
# loadavg = os.getloadavg()[0]
# if loadavg > 2.0:
# apDisplay.printMsg("Load average is high "+str(round(loadavg,2)))
# time.sleep(loadavg**2)
apParam.closeFunctionLog(functionname=self.functionname,
logfile=self.logfile, msg=(not self.quiet))
if self.quiet is False:
apDisplay.printMsg("Ended at "+time.strftime("%a, %d %b %Y %H:%M:%S"))
if apDisplay.isDebugOn():
apDisplay.printDebug("Memory increase during run: %.3f MB"%((mem.active()-self.startmem)/1024.0))
apDisplay.printColor("Total run time:\t"+apDisplay.timeString(time.time()-self.t0),"green")
def close(self):
self.onClose()
# loadavg = os.getloadavg()[0]
# if loadavg > 2.0:
# apDisplay.printMsg("Load average is high "+str(round(loadavg,2)))
# time.sleep(loadavg**2)
apParam.closeFunctionLog(functionname=self.functionname,
logfile=self.logfile,
msg=(not self.quiet))
if self.quiet is False:
apDisplay.printMsg("Ended at " +
time.strftime("%a, %d %b %Y %H:%M:%S"))
if apDisplay.isDebugOn():
apDisplay.printDebug("Memory increase during run: %.3f MB" %
((mem.active() - self.startmem) / 1024.0))
apDisplay.printColor(
"Total run time:\t" +
apDisplay.timeString(time.time() - self.t0), "green")
def _startLoop(self, info):
"""
appionLoop OVERRIDE
initilizes several parameters for a new image
and checks if it is okay to start processing image
"""
if info is None:
self.stats['lastimageskipped'] = True
self.stats['skipcount'] += 1
return False
name = info['filename']
# check to see if image of the same name is already in leginon
imgq = leginon.leginondata.AcquisitionImageData(session=self.session,
filename=name)
results = imgq.query(readimages=False)
if results:
apDisplay.printWarning("File %s.mrc exists at the destination" %
name)
apDisplay.printWarning("Skip Uploading")
self.stats['lastimageskipped'] = True
self.stats['skipcount'] += 1
return False
#calc images left
self.stats[
'imagesleft'] = self.stats['imagecount'] - self.stats['count']
#only if an image was processed last
if (self.stats['lastcount'] != self.stats['count']):
apDisplay.printColor( "\nStarting image "+str(self.stats['count'])\
+" ( skip:"+str(self.stats['skipcount'])+", remain:"\
+str(self.stats['imagesleft'])+" ) file: "\
+apDisplay.short(name), "green")
self.stats['lastcount'] = self.stats['count']
if apDisplay.isDebugOn():
self._checkMemLeak()
# check to see if image has already been processed
if self._alreadyProcessed(info):
return False
self.stats['waittime'] = 0
return True
def _startLoop(self, info):
"""
appionLoop OVERRIDE
initilizes several parameters for a new image
and checks if it is okay to start processing image
"""
if info is None:
self.stats['lastimageskipped'] = True
self.stats['skipcount'] += 1
return False
name = info['filename']
# check to see if image of the same name is already in leginon
imgq = leginon.leginondata.AcquisitionImageData(session=self.session, filename=name)
results = imgq.query(readimages=False)
if results:
apDisplay.printWarning("File %s.mrc exists at the destination" % name)
apDisplay.printWarning("Skip Uploading")
self.stats['lastimageskipped'] = True
self.stats['skipcount'] += 1
return False
#calc images left
self.stats['imagesleft'] = self.stats['imagecount'] - self.stats['count']
#only if an image was processed last
if(self.stats['lastcount'] != self.stats['count']):
apDisplay.printColor( "\nStarting image "+str(self.stats['count'])\
+" ( skip:"+str(self.stats['skipcount'])+", remain:"\
+str(self.stats['imagesleft'])+" ) file: "\
+apDisplay.short(name), "green")
self.stats['lastcount'] = self.stats['count']
if apDisplay.isDebugOn():
self._checkMemLeak()
# check to see if image has already been processed
if self._alreadyProcessed(info):
return False
self.stats['waittime'] = 0
return True
