mda_channels,
prefix=prefix,
blacklist=wellsToSkip,
well_limit=cellsToFindPerWell,
well_count_dict=alreadyImaged,
data_dir=save_location,
stack_height=stackThickness,
slice_height=stepZ,
minAreaCOI=minAreaOfThresholdedCell,
maxAreaCOI=maxAreaOfThresholdedCell,
thresholdCOI=thresholdForOriginalCell,
visible=scan_visibility)
except:
tb=StringIO.StringIO()
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_exception(exc_type,
exc_value,
exc_traceback,
file=tb)
scan_results="There was some sort of error, "\
"your scan most likely did not finish."\
"The error was \n\n %s" % tb.getvalue()
email=EmailFromNTHAYER.email(text=str(scan_results),
TO=TO,
subject="Message about %s" % prefix,
smtp_server="zimbra.fhcrc.org")
print "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
print "######################################################"
print "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
print scan_results FROM=FROM,
### wait until next acquisition with some warning
acquisition_finish_time=time.time()
until_next=interval-(acquisition_finish_time-acquisition_start_time)
scope.move_XYstage(xnext,ynext)
scope.mmc.enableContinuousFocus(False)
while True:
current_time=time.time()
if current_time-acquisition_start_time >= interval:
break
else:
print "%s minutes remaining, %s seconds until next timepoint\r" % ((timepoints-i)*interval/60,interval-(current_time-acquisition_start_time)),
time.sleep(10)
print "Timecourse completed"
results="Scan completed"
except:
print "UH OH!"
tb=StringIO.StringIO()
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_exception(exc_type,
exc_value,
exc_traceback,
file=tb)
results="There was some sort of error, "\
"your scan most likely did not finish."\
"The error was \n\n %s" % tb.getvalue()
email=EmailFromNTHAYER.email(text=str(results),
TO="*****@*****.**",
subject="Message about your timelapse",
smtp_server="zimbra.fhcrc.org")
scan_results=plateScan(scope,
positions,
scan_illumination,
mda_channels,
prefix=prefix,
blacklist=[],
well_limit=5,
well_count_dict={},
data_dir="Z://Data\Test",
stack_height=5,
slice_height=.5)
except:
tb=StringIO.StringIO()
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_exception(exc_type,
exc_value,
exc_traceback,
file=tb)
scan_results="There was some sort of error, "\
"your scan most likely did not finish."\
"The error was \n\n %s" % tb.getvalue()
##send an email once the scan has finished
email=EmailFromNTHAYER.email(text=str(scan_results),
TO="*****@*****.**",
FROM="*****@*****.**",
subject="Message about %s" % prefix)
