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)