def _waitForMoreSeries(self,timeout_min=180):
"""
pauses wait_time mins and then checks for more series to process
"""
### SKIP MESSAGE
if(self.stats['skipcount'] > 0):
apDisplay.printWarning("Series already processed and were therefore skipped (total "+str(self.stats['skipcount'])+" skipped).")
apDisplay.printMsg("to process them again, remove \'continue\' option and run "+self.functionname+" again.")
self.stats['skipcount'] = 0
### SHOULD IT WAIT?
if self.params['wait'] is False:
return False
if self.params["mrcnames"] is not None:
return False
if self.params["limit"] is not None:
return False
### CHECK FOR IMAGES, IF MORE THAN 10 JUST GO AHEAD
apDisplay.printMsg("Finished all series, checking for more\n")
self._getAllSeries()
### reset counts
self.stats['seriescount'] = len(self.seriestree)
self.stats['seriesleft'] = self.stats['seriescount'] - self.stats['count']
if self.stats['seriesleft'] > 0:
return True
### WAIT
timeout_sec = timeout_min * 60
# self.stats['waittime'] is in minutes
if(self.stats['waittime'] > timeout_min):
timeout_hr = timeout_min / 60.0
apDisplay.printWarning("waited longer than %.1f hours for new series with no results, so I am quitting" % timeout_hr)
return False
apParam.closeFunctionLog(functionname=self.functionname, logfile=self.logfile, msg=False, stats=self.stats)
twait0 = time.time()
# Wait at least 30 sec and at most 5 % of timeout before checking for new tilt series
dot_wait = 30
timecheck_sec = max(timeout_sec/20,dot_wait*2)
wait_step = max(1,int(round(timecheck_sec * 1.0 / dot_wait)))
sys.stderr.write("\nAll Series processed. Waiting %.1f minutes for new Series (waited %.1f min so far" % (timecheck_sec / 60.0, self.stats['waittime']))
for i in range(wait_step):
time.sleep(dot_wait)
#print a dot every 30 seconds
sys.stderr.write(".")
self.stats['waittime'] += round((time.time()-twait0)/60.0,2)
sys.stderr.write("\n")
### GET NEW IMAGES
self._getAllSeries()
### reset counts
self.stats['seriescount'] = len(self.seriestree)
self.stats['seriesleft'] = self.stats['seriescount'] - self.stats['count']
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"))
apDisplay.printMsg("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 _waitForMoreImages(self):
"""
pauses 10 mins and then checks for more images to process
"""
### SKIP MESSAGE
if(self.stats['skipcount'] > 0):
apDisplay.printWarning("Images already processed and were therefore skipped (total "+str(self.stats['skipcount'])+" skipped).")
apDisplay.printMsg("to process them again, remove \'continue\' option and run "+self.functionname+" again.")
self.stats['skipcount'] = 0
### SHOULD IT WAIT?
if self.params['wait'] is False:
return False
if self.params["mrcnames"] is not None:
return False
if self.params["limit"] is not None:
return False
### CHECK FOR IMAGES, IF MORE THAN self.process_batch_count (default 10) JUST GO AHEAD
apDisplay.printMsg("Finished all images, checking for more\n")
self._getAllImages()
### reset counts
self.stats['imagecount'] = len(self.imgtree)
self.stats['imagesleft'] = self.stats['imagecount'] - self.stats['count']
### Not sure this really works since imagesleft appears to be negative value AC
if self.stats['imagesleft'] > self.process_batch_count:
return True
### WAIT
if(self.stats['waittime'] > 180):
apDisplay.printWarning("waited longer than three hours for new images with no results, so I am quitting")
return False
apParam.closeFunctionLog(functionname=self.functionname, logfile=self.logfile, msg=False, stats=self.stats)
sys.stderr.write("\nAll images processed. Waiting %d minutes for new images (waited %.2f min so far)." % (int(self.sleep_minutes),float(self.stats['waittime'])))
twait0 = time.time()
repeats = int(self.sleep_minutes * 60 / 20)
for i in range(repeats):
apDisplay.printMsg("Sleeping 20 seconds")
time.sleep(20)
#print a dot every 30 seconds
sys.stderr.write(".")
self.stats['waittime'] += round((time.time()-twait0)/60.0,2)
sys.stderr.write("\n")
### GET NEW IMAGES
self._getAllImages()
### reset counts
self.stats['imagecount'] = len(self.imgtree)
self.stats['imagesleft'] = self.stats['imagecount'] - self.stats['count']
return True
def _waitForMoreImages(self):
"""
pauses 10 mins and then checks for more images to process
"""
### SKIP MESSAGE
if (self.stats['skipcount'] > 0):
apDisplay.printWarning(
"Images already processed and were therefore skipped (total " +
str(self.stats['skipcount']) + " skipped).")
apDisplay.printMsg(
"to process them again, remove \'continue\' option and run " +
self.functionname + " again.")
self.stats['skipcount'] = 0
### SHOULD IT WAIT?
if self.params['wait'] is False:
return False
if self.params["mrcnames"] is not None:
return False
if self.params["limit"] is not None:
return False
### CHECK FOR IMAGES, IF MORE THAN self.process_batch_count (default 10) JUST GO AHEAD
apDisplay.printMsg("Finished all images, checking for more\n")
self._getAllImages()
### reset counts
self.stats['imagecount'] = len(self.imgtree)
self.stats[
'imagesleft'] = self.stats['imagecount'] - self.stats['count']
### Not sure this really works since imagesleft appears to be negative value AC
if self.stats['imagesleft'] > self.process_batch_count:
return True
### WAIT
if (self.stats['waittime'] > 180):
apDisplay.printWarning(
"waited longer than three hours for new images with no results, so I am quitting"
)
return False
apParam.closeFunctionLog(functionname=self.functionname,
logfile=self.logfile,
msg=False,
stats=self.stats)
sys.stderr.write(
"\nAll images processed. Waiting %d minutes for new images (waited %.2f min so far)."
% (int(self.sleep_minutes), float(self.stats['waittime'])))
twait0 = time.time()
repeats = int(self.sleep_minutes * 60 / 20)
for i in range(repeats):
time.sleep(20)
#print a dot every 30 seconds
sys.stderr.write(".")
self.stats['waittime'] += round((time.time() - twait0) / 60.0, 2)
sys.stderr.write("\n")
### GET NEW IMAGES
self._getAllImages()
### reset counts
self.stats['imagecount'] = len(self.imgtree)
self.stats[
'imagesleft'] = self.stats['imagecount'] - self.stats['count']
return True