def __isShortTiltSeries(self, tiltseriesdata):
imgtree = apDatabase.getImagesFromTiltSeries(tiltseriesdata,False)
imagelimit = self.params['imagelimit']
is_short = len(imgtree) < imagelimit
if is_short:
apDisplay.printWarning("Tilt series has less than %d images" % imagelimit)
return is_short
def _startLoop(self, tiltseriesdata):
"""
initilizes several parameters for a new series
and checks if it is okay to start processing series
"""
#calc series left
self.stats[
'seriesleft'] = self.stats['seriescount'] - self.stats['count']
if self.params['background'] is False:
apDisplay.printColor(
"\nStarting series %d ( skip:%d, remain:%d ) id:%d" % (
tiltseriesdata['number'],
self.stats['skipcount'],
self.stats['seriesleft'],
tiltseriesdata.dbid,
), "green")
#only if a series was processed last
if (self.stats['lastcount'] != self.stats['count']):
sys.stderr.write("\n")
self.stats['lastcount'] = self.stats['count']
self._checkMemLeak()
# skip if last image belong to the series doesn't exist:
imgtree = apDatabase.getImagesFromTiltSeries(tiltseriesdata, False)
imgpath = os.path.join(tiltseriesdata['session']['image path'],
imgtree[0]['filename'] + '.mrc')
if not os.path.isfile(imgpath):
apDisplay.printWarning(imgpath + " not found, skipping")
return False
# skip if there are some problem with the series
if self.__isShortTiltSeries(tiltseriesdata) or self.isBadTiltSeries(
tiltseriesdata):
apDisplay.printWarning(
"Series %d is not good enough for processing, skipping" %
(tiltseriesdata['number']))
seriesname = "series%3d" % (tiltseriesdata['number'])
self._writeDoneDict(seriesname)
self.stats['count'] += 1
return False
# check to see if series has already been processed
if self._alreadyProcessed(tiltseriesdata):
return False
self.stats['waittime'] = 0
if self.reprocessSeries(tiltseriesdata) is True:
if self.params['background'] is True:
sys.stderr.write(",")
else:
"""apDisplay.printMsg("reprocessing series %d" % (tiltseriesdata['number']))"""
else:
if self.params['background'] is True:
sys.stderr.write(".")
else:
"""apDisplay.printMsg("processing series %d" % (tiltseriesdata['number']))"""
return True
def processTiltSeries(self, tiltseriesdata): """ Call your processing command from here per tilt series Here we just print out the filenames of the images in the tilt series """ print "Tiltseries %d -------------------" % tiltseriesdata['number'] imgtree = apDatabase.getImagesFromTiltSeries(tiltseriesdata,True) for imagedata in imgtree: print imagedata['filename']
def _startLoop(self, tiltseriesdata):
"""
initilizes several parameters for a new series
and checks if it is okay to start processing series
"""
#calc series left
self.stats['seriesleft'] = self.stats['seriescount'] - self.stats['count']
if self.params['background'] is False:
apDisplay.printColor( "\nStarting series %d ( skip:%d, remain:%d ) id:%d"
%(tiltseriesdata['number'], self.stats['skipcount'], self.stats['seriesleft'],
tiltseriesdata.dbid,),
"green")
#only if a series was processed last
if(self.stats['lastcount'] != self.stats['count']):
sys.stderr.write("\n")
self.stats['lastcount'] = self.stats['count']
self._checkMemLeak()
# skip if last image belong to the series doesn't exist:
imgtree = apDatabase.getImagesFromTiltSeries(tiltseriesdata,False)
imgpath = os.path.join(tiltseriesdata['session']['image path'], imgtree[0]['filename']+'.mrc')
if not os.path.isfile(imgpath):
apDisplay.printWarning(imgpath+" not found, skipping")
return False
# skip if there are some problem with the series
if self.__isShortTiltSeries(tiltseriesdata) or self.isBadTiltSeries(tiltseriesdata):
apDisplay.printWarning("Series %d is not good enough for processing, skipping" % (tiltseriesdata['number']))
seriesname = "series%3d" % (tiltseriesdata['number'])
self._writeDoneDict(seriesname)
self.stats['count'] += 1
return False
# check to see if series has already been processed
if self._alreadyProcessed(tiltseriesdata):
return False
self.stats['waittime'] = 0
if self.reprocessSeries(tiltseriesdata) is True:
if self.params['background'] is True:
sys.stderr.write(",")
else:
"""apDisplay.printMsg("reprocessing series %d" % (tiltseriesdata['number']))"""
else:
if self.params['background'] is True:
sys.stderr.write(".")
else:
"""apDisplay.printMsg("processing series %d" % (tiltseriesdata['number']))"""
return True
def run(self):
"""
processes all series
"""
### get tilt series from database
self._getAllSeries()
os.chdir(self.params['rundir'])
self.preLoopFunctions()
### start the loop
self.notdone=True
self.badprocess = False
self.stats['startloop'] = time.time()
while self.notdone:
apDisplay.printColor("\nBeginning Main Loop", "green")
seriesnum = 0
while seriesnum < len(self.seriestree) and self.notdone is True:
self.stats['startseries'] = time.time()
tiltseriesdata = self.seriestree[seriesnum]
seriesnum += 1
### CHECK IF IT IS OKAY TO START PROCESSING IMAGE
if not self._startLoop(tiltseriesdata):
continue
### set the pixel size
imgtree = apDatabase.getImagesFromTiltSeries(tiltseriesdata,False)
self.params['apix'] = apDatabase.getPixelSize(imgtree[0])
if not self.params['background']:
apDisplay.printMsg("Pixel size: "+str(self.params['apix']))
### START any custom functions HERE:
results = self.loopProcessTiltSeries(tiltseriesdata)
### WRITE db data
if self.badprocess is False:
if self.params['commit'] is True:
if not self.params['background']:
apDisplay.printColor(" ==== Committing data to database ==== ", "blue")
self.loopCommitToDatabase(tiltseriesdata)
self.commitResultsToDatabase(tiltseriesdata, results)
else:
apDisplay.printWarning("not committing results to database, all data will be lost")
apDisplay.printMsg("to preserve data start script over and add 'commit' flag")
self.writeResultsToFiles(tiltseriesdata, results)
else:
apDisplay.printWarning("IMAGE FAILED; nothing inserted into database")
self.badprocess = False
self.stats['lastpeaks'] = 0
### FINISH with custom functions
seriesname = "series%3d" % (tiltseriesdata['number'])
self._writeDoneDict(seriesname)
loadavg = os.getloadavg()[0]
if loadavg > 2.0:
apDisplay.printMsg("Load average is high "+str(round(loadavg,2)))
loadsquared = loadavg*loadavg
time.sleep(loadsquared)
apDisplay.printMsg("New load average "+str(round(os.getloadavg()[0],2)))
self._printSummary()
if self.params['limit'] is not None and self.stats['count'] > self.params['limit']:
apDisplay.printWarning("reached series limit of "+str(self.params['limit'])+"; now stopping")
#END LOOP OVER IMAGES
if self.notdone is True:
self.notdone = self._waitForMoreSeries(timeout_min=self.params['timeout'])
#END NOTDONE LOOP
self.postLoopFunctions()
self.close()
