def runpgm(self,pgm,duration,waitForCompletion=True,volume=10,hotlidmode="TRACKING",hotlidtemp=1):
if self.ptcrunning:
logging.error("Attempt to start a progam on PTC when it is already running")
if len(pgm)>8:
logging.error("PTC program name (%s) too long (max is 8 char)"%pgm)
# move to thermocycler
worklist.flushQueue()
self.lihahome()
cmt="run %s"%pgm
worklist.comment(cmt)
#print "*",cmt
worklist.pyrun("PTC\\ptclid.py OPEN")
self.moveplate(decklayout.SAMPLEPLATE,"PTC")
worklist.vector("Hotel 1 Lid",decklayout.HOTELPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
worklist.vector("PTC200lid",decklayout.PTCPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
worklist.romahome()
worklist.pyrun("PTC\\ptclid.py CLOSE")
# pgm="PAUSE30" # For debugging
assert hotlidmode=="TRACKING" or hotlidmode=="CONSTANT"
assert (hotlidmode=="TRACKING" and hotlidtemp>=0 and hotlidtemp<=45) or (hotlidmode=="CONSTANT" and hotlidtemp>30)
worklist.pyrun('PTC\\ptcrun.py %s CALC %s,%d %d'%(pgm,hotlidmode,hotlidtemp,volume))
self.pgmStartTime=clock.pipetting
self.pgmEndTime=duration*60+clock.pipetting
self.ptcrunning=True
Sample.addallhistory("{%s}"%pgm,addToEmpty=False,onlyplate=decklayout.SAMPLEPLATE.name)
if waitForCompletion:
self.waitpgm()
def waitpgm(self, sanitize=True):
if not self.ptcrunning:
return
#print "* Wait for PTC to finish"
if sanitize:
self.sanitize() # Sanitize tips before waiting for this to be done
worklist.comment("Wait for PTC")
while self.pgmEndTime-clock.pipetting > 120:
# Run any idle programs
oldElapsed=clock.pipetting
for ip in self.idlePgms:
if self.pgmEndTime-clock.pipetting > 120:
#print "Executing idle program with %.0f seconds"%(self.pgmEndTime-clock.pipetting)
ip(self.pgmEndTime-clock.pipetting-120)
if oldElapsed==clock.pipetting:
# Nothing was done
break
worklist.flushQueue() # Just in case
clock.pipandthermotime+=(clock.pipetting-self.pgmStartTime)
clock.thermotime+=(self.pgmEndTime-clock.pipetting)
clock.pipetting=self.pgmStartTime
#print "Waiting for PTC with %.0f seconds expected to remain"%(self.pgmEndTime-clock.pipetting)
self.lihahome()
worklist.pyrun('PTC\\ptcwait.py')
worklist.pyrun("PTC\\ptclid.py OPEN")
# worklist.pyrun('PTC\\ptcrun.py %s CALC ON'%"COOLDOWN")
# worklist.pyrun('PTC\\ptcwait.py')
worklist.vector("PTC200lid",decklayout.PTCPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
worklist.vector("Hotel 1 Lid",decklayout.HOTELPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
worklist.vector("PTC200WigglePos",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.CLOSE,True)
worklist.vector("PTC200Wiggle",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.OPEN,True)
worklist.vector("PTC200WigglePos",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle2Pos",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle2",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.CLOSE,True)
worklist.vector("PTC200Wiggle2",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.OPEN,True)
worklist.vector("PTC200Wiggle2Pos",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200WigglePos",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.CLOSE,True)
worklist.vector("PTC200Wiggle",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.OPEN,True)
worklist.vector("PTC200WigglePos",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
self.ptcrunning=False
self.moveplate(decklayout.SAMPLEPLATE,"Home")
# Mark all samples on plate as unmixed (due to condensation)
Sample.notMixed(decklayout.SAMPLEPLATE.name)
# Verify plate is in place
worklist.vector(decklayout.SAMPLEPLATE.vectorName,decklayout.SAMPLEPLATE,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.CLOSE)
worklist.vector(decklayout.SAMPLEPLATE.vectorName,decklayout.SAMPLEPLATE,worklist.ENDTOSAFE,False,worklist.OPEN,worklist.DONOTMOVE)
worklist.romahome()
#worklist.userprompt("Plate should be back on deck. Press return to continue")
# Wash tips again to remove any drips that may have formed while waiting for PTC
worklist.wash(15,1,5,True)
def moveplate(self,plate,dest="Home",returnHome=True):
if self.ptcrunning and plate==decklayout.SAMPLEPLATE:
self.waitpgm()
# move to given destination (one of "Home","Magnet","Shaker","PTC" )
if plate!=decklayout.SAMPLEPLATE and plate!=decklayout.DILPLATE:
print "Only able to move %s or %s plates, not %s"%(decklayout.SAMPLEPLATE.name,decklayout.DILPLATE.name,plate.name)
assert False
if plate.curloc==dest:
#print "Plate %s is already at %s"%(plate.name,dest)
return
#print "Move plate %s from %s to %s"%(plate.name,plate.curloc,dest)
worklist.flushQueue()
self.lihahome()
cmt="moveplate %s %s"%(plate.name,dest)
worklist.comment(cmt)
if plate.curloc=="Home":
worklist.vector(plate.vectorName,plate,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
elif plate.curloc=="Magnet":
worklist.vector("Magplate",decklayout.MAGPLATELOC,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
elif plate.curloc=="Shaker":
worklist.vector("Shaker",decklayout.SHAKERPLATELOC,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
elif plate.curloc=="PTC":
worklist.vector("PTC200",decklayout.PTCPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
else:
print "Plate %s is in unknown location: %s"%(plate.name,plate.curloc)
assert False
if dest=="Home":
plate.movetoloc(dest)
worklist.vector(plate.vectorName,plate,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
elif dest=="Magnet":
plate.movetoloc(dest,decklayout.MAGPLATELOC)
worklist.vector("Magplate",decklayout.MAGPLATELOC,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
elif dest=="Shaker":
plate.movetoloc(dest,decklayout.SHAKERPLATELOC)
worklist.vector("Shaker",decklayout.SHAKERPLATELOC,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
elif dest=="PTC":
plate.movetoloc(dest,decklayout.PTCPOS)
worklist.vector("PTC200",decklayout.PTCPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
else:
print "Attempt to move plate %s to unknown location: %s"%(plate.name,dest)
assert False
Sample.addallhistory("{->%s}"%dest,onlyplate=plate.name)
if returnHome:
worklist.romahome()
def runpgm(self,
pgm,
duration,
waitForCompletion=True,
volume=10,
hotlidmode="TRACKING",
hotlidtemp=1):
if self.ptcrunning:
logging.error(
"Attempt to start a progam on PTC when it is already running")
if len(pgm) > 8:
logging.error("PTC program name (%s) too long (max is 8 char)" %
pgm)
# move to thermocycler
worklist.flushQueue()
self.lihahome()
cmt = "run %s" % pgm
worklist.comment(cmt)
#print "*",cmt
worklist.pyrun("PTC\\ptclid.py OPEN")
self.moveplate(decklayout.SAMPLEPLATE, "PTC")
worklist.vector("Hotel 1 Lid", decklayout.HOTELPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.CLOSE)
worklist.vector("PTC200lid", decklayout.PTCPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.OPEN)
worklist.romahome()
worklist.pyrun("PTC\\ptclid.py CLOSE")
# pgm="PAUSE30" # For debugging
assert hotlidmode == "TRACKING" or hotlidmode == "CONSTANT"
assert (hotlidmode == "TRACKING" and hotlidtemp >= 0
and hotlidtemp <= 45) or (hotlidmode == "CONSTANT"
and hotlidtemp > 30)
worklist.pyrun('PTC\\ptcrun.py %s CALC %s,%d %d' %
(pgm, hotlidmode, hotlidtemp, volume))
self.pgmStartTime = clock.pipetting
self.pgmEndTime = duration * 60 + clock.pipetting
self.ptcrunning = True
Sample.addallhistory("{%s}" % pgm,
addToEmpty=False,
onlyplate=decklayout.SAMPLEPLATE.name,
type="ptc")
if waitForCompletion:
self.waitpgm()
def sanitize(self,nmix=1,deepvol=20,force=False):
'Deep wash including RNase-Away treatment'
fixedTips=(~self.DITIMASK)&15
worklist.flushQueue()
if not force and fixedTips==self.cleanTips:
# print no sanitize needed
worklist.comment("Sanitize not needed cleanTips=%d"%self.cleanTips)
return
worklist.comment("Sanitize (cleanTips=%d)"%self.cleanTips)
worklist.wash(15,1,2)
fixedWells=[]
if not self.overrideSanitize:
for i in range(4):
if (fixedTips & (1<<i)) != 0:
fixedWells.append(i)
decklayout.BLEACH.addhistory("SANITIZE",0,1<<i)
worklist.mix(fixedTips,fixedWells,decklayout.BLEACH.mixLC,200,decklayout.BLEACH.plate,nmix,False)
worklist.wash(fixedTips,1,deepvol,True)
self.cleanTips|=fixedTips
# print "* Sanitize"
worklist.comment(clock.statusString())
def sanitize(self, nmix=1, deepvol=20, force=False):
'Deep wash including RNase-Away treatment'
fixedTips = (~self.DITIMASK) & 15
worklist.flushQueue()
if not force and fixedTips == self.cleanTips:
# print no sanitize needed
worklist.comment("Sanitize not needed cleanTips=%d" %
self.cleanTips)
return
worklist.comment("Sanitize (cleanTips=%d)" % self.cleanTips)
worklist.wash(15, 1, 2)
fixedWells = []
if not self.overrideSanitize:
for i in range(4):
if (fixedTips & (1 << i)) != 0:
fixedWells.append(i)
decklayout.BLEACH.addhistory("SANITIZE", 0, 1 << i)
worklist.mix(fixedTips, fixedWells, decklayout.BLEACH.mixLC, 200,
decklayout.BLEACH.plate, nmix, False)
worklist.wash(fixedTips, 1, deepvol, True)
self.cleanTips |= fixedTips
# print "* Sanitize"
worklist.comment(clock.statusString())
def savegem(self, filename):
worklist.flushQueue()
worklist.savegem(decklayout.headerfile, filename)
def waitpgm(self, sanitize=True):
if not self.ptcrunning:
return
#print "* Wait for PTC to finish"
if sanitize:
self.sanitize() # Sanitize tips before waiting for this to be done
worklist.comment("Wait for PTC")
while self.pgmEndTime - clock.pipetting > 120:
# Run any idle programs
oldElapsed = clock.pipetting
for ip in self.idlePgms:
if self.pgmEndTime - clock.pipetting > 120:
#print "Executing idle program with %.0f seconds"%(self.pgmEndTime-clock.pipetting)
ip(self.pgmEndTime - clock.pipetting - 120)
if oldElapsed == clock.pipetting:
# Nothing was done
break
worklist.flushQueue() # Just in case
clock.pipandthermotime += (clock.pipetting - self.pgmStartTime)
clock.thermotime += (self.pgmEndTime - clock.pipetting)
clock.pipetting = self.pgmStartTime
#print "Waiting for PTC with %.0f seconds expected to remain"%(self.pgmEndTime-clock.pipetting)
worklist.pyrun('PTC\\ptcwait.py')
worklist.pyrun("PTC\\ptclid.py OPEN")
# worklist.pyrun('PTC\\ptcrun.py %s CALC ON'%"COOLDOWN")
# worklist.pyrun('PTC\\ptcwait.py')
worklist.vector("PTC200lid", decklayout.PTCPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.CLOSE)
worklist.vector("Hotel 1 Lid", decklayout.HOTELPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.OPEN)
worklist.vector("PTC200WigglePos", decklayout.PTCPOS,
worklist.SAFETOEND, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle", decklayout.PTCPOS, worklist.SAFETOEND,
False, worklist.DONOTMOVE, worklist.CLOSE, True)
worklist.vector("PTC200Wiggle", decklayout.PTCPOS, worklist.ENDTOSAFE,
False, worklist.DONOTMOVE, worklist.OPEN, True)
worklist.vector("PTC200WigglePos", decklayout.PTCPOS,
worklist.ENDTOSAFE, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle2Pos", decklayout.PTCPOS,
worklist.SAFETOEND, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle2", decklayout.PTCPOS, worklist.SAFETOEND,
False, worklist.DONOTMOVE, worklist.CLOSE, True)
worklist.vector("PTC200Wiggle2", decklayout.PTCPOS, worklist.ENDTOSAFE,
False, worklist.DONOTMOVE, worklist.OPEN, True)
worklist.vector("PTC200Wiggle2Pos", decklayout.PTCPOS,
worklist.ENDTOSAFE, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200WigglePos", decklayout.PTCPOS,
worklist.SAFETOEND, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle", decklayout.PTCPOS, worklist.SAFETOEND,
False, worklist.DONOTMOVE, worklist.CLOSE, True)
worklist.vector("PTC200Wiggle", decklayout.PTCPOS, worklist.ENDTOSAFE,
False, worklist.DONOTMOVE, worklist.OPEN, True)
worklist.vector("PTC200WigglePos", decklayout.PTCPOS,
worklist.ENDTOSAFE, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
self.ptcrunning = False
self.moveplate(decklayout.SAMPLEPLATE, "Home")
# Mark all samples on plate as unmixed (due to condensation)
Sample.notMixed(decklayout.SAMPLEPLATE.name)
# Verify plate is in place
worklist.vector(decklayout.SAMPLEPLATE.vectorName,
decklayout.SAMPLEPLATE, worklist.SAFETOEND, False,
worklist.DONOTMOVE, worklist.CLOSE)
worklist.vector(decklayout.SAMPLEPLATE.vectorName,
decklayout.SAMPLEPLATE, worklist.ENDTOSAFE, False,
worklist.OPEN, worklist.DONOTMOVE)
worklist.romahome()
#worklist.userprompt("Plate should be back on deck. Press return to continue")
# Wash tips again to remove any drips that may have formed while waiting for PTC
worklist.wash(15, 1, 5, True)
def moveplate(self, plate, dest="Home", returnHome=True):
if self.ptcrunning and plate == decklayout.SAMPLEPLATE:
self.waitpgm()
# move to given destination (one of "Home","Magnet","Shaker","PTC" )
if plate != decklayout.SAMPLEPLATE and plate != decklayout.DILPLATE:
print "Only able to move %s or %s plates, not %s" % (
decklayout.SAMPLEPLATE.name, decklayout.DILPLATE.name,
plate.name)
assert False
if plate.curloc == dest:
#print "Plate %s is already at %s"%(plate.name,dest)
return
#print "Move plate %s from %s to %s"%(plate.name,plate.curloc,dest)
worklist.flushQueue()
self.lihahome()
cmt = "moveplate %s %s" % (plate.name, dest)
worklist.comment(cmt)
if plate.curloc == "Home":
worklist.vector(plate.vectorName, plate, worklist.SAFETOEND, True,
worklist.DONOTMOVE, worklist.CLOSE)
elif plate.curloc == "Magnet":
worklist.vector("Magplate", decklayout.MAGPLATELOC,
worklist.SAFETOEND, True, worklist.DONOTMOVE,
worklist.CLOSE)
elif plate.curloc == "Shaker":
worklist.vector("Shaker", decklayout.SHAKERPLATELOC,
worklist.SAFETOEND, True, worklist.DONOTMOVE,
worklist.CLOSE)
elif plate.curloc == "PTC":
worklist.vector("PTC200", decklayout.PTCPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.CLOSE)
else:
print "Plate %s is in unknown location: %s" % (plate.name,
plate.curloc)
assert False
if dest == "Home":
plate.movetoloc(dest)
worklist.vector(plate.vectorName, plate, worklist.SAFETOEND, True,
worklist.DONOTMOVE, worklist.OPEN)
elif dest == "Magnet":
plate.movetoloc(dest, decklayout.MAGPLATELOC)
worklist.vector("Magplate", decklayout.MAGPLATELOC,
worklist.SAFETOEND, True, worklist.DONOTMOVE,
worklist.OPEN)
elif dest == "Shaker":
plate.movetoloc(dest, decklayout.SHAKERPLATELOC)
worklist.vector("Shaker", decklayout.SHAKERPLATELOC,
worklist.SAFETOEND, True, worklist.DONOTMOVE,
worklist.OPEN)
elif dest == "PTC":
plate.movetoloc(dest, decklayout.PTCPOS)
worklist.vector("PTC200", decklayout.PTCPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.OPEN)
else:
print "Attempt to move plate %s to unknown location: %s" % (
plate.name, dest)
assert False
Sample.addallhistory("{->%s}" % dest, onlyplate=plate.name)
if returnHome:
worklist.romahome()
def volcheck(self,tipMask,well,volToRemove):
'''Check if the well contains the expected volume'''
if self.lastvolcheck is not None:
# Decide if a volume check is needed
if volToRemove==0:
# No need to check if not removing anything and it has been checked previously (i.e. lastvolcheck is not None)
return
if self.volume-volToRemove > max(30,self.lastvolcheck-200) or self.volume-volToRemove>200:
# Not needed
return
self.lastvolcheck=self.volume
height=self.plate.getliquidheight(self.volume)
gemvol=self.plate.getgemliquidvolume(height) # Volume that would be reported by Gemini for this height
if gemvol is None:
logging.warning( "No volume equation for %s, skipping initial volume check"%self.name)
return
volwarn=self.volume*0.80
heightwarn=min(self.plate.getliquidheight(volwarn),height-1.0) # threshold is lower of 1mm or 80%
gemvolwarn=self.plate.getgemliquidvolume(heightwarn) # Volume that would be reported by Gemini for this height
volcrit=self.plate.unusableVolume*0.8+volToRemove
heightcrit=self.plate.getliquidheight(volcrit)
gemvolcrit=self.plate.getgemliquidvolume(heightcrit) # Volume that would be reported by Gemini for this height
worklist.flushQueue()
worklist.comment( "Check that %s contains %.1f ul (warn< %.1f, crit<%.1f), (gemvol=%.1f (warn<%.1f,crit<%.1f); height=%.1f (>%.1f) )"%(self.name,self.volume,volwarn,volcrit,gemvol,gemvolwarn,gemvolcrit,height,heightwarn))
tipnum=0
tm=tipMask
while tm>0:
tm=tm>>1
tipnum+=1
volvar='detected_volume_%d'%tipnum
worklist.variable(volvar,-2)
worklist.detectLiquid(tipMask,well,self.inliquidLC,self.plate)
doneLabel=worklist.getlabel()
worklist.condition(volvar,">",gemvolwarn,doneLabel)
ptmp=clock.pipetting;
warnLabel=worklist.getlabel()
worklist.condition(volvar,">",gemvolcrit,warnLabel)
worklist.moveliha(worklist.WASHLOC) # Get LiHa out of the way
msg="Failed volume check of %s - should have %.0f ul (gemvol=~%s~, crit=%.0f)"%(self.name,self.volume,volvar,gemvolcrit)
worklist.email(dest='*****@*****.**',subject=msg)
worklist.stringvariable("response","retry",msg+" Enter 'ignore' to ignore and continue, otherwise will retry.")
worklist.condition("response","==","ignore",doneLabel)
# Retry
worklist.detectLiquid(tipMask,well,self.inliquidLC,self.plate)
worklist.condition(volvar,">",gemvolcrit,doneLabel)
worklist.stringvariable("response","retry","Still have <%.0f. Enter 'ignore' to ignore and continue, otherwise will retry."%self.volume)
worklist.condition("response","==","ignore",doneLabel)
# Retry again
worklist.detectLiquid(tipMask,well,self.inliquidLC,self.plate)
worklist.condition(volvar,">",gemvolcrit,doneLabel)
worklist.stringvariable("response","ignore","Still have <%.0f. Will continue regardless."%self.volume)
worklist.condition("response","!=","warn",doneLabel)
worklist.comment(warnLabel)
msg="Warning: volume check of %s - should have %.0f ul (gemvol=~%s~, warn=%.0f, crit=%.0f)"%(self.name,self.volume,volvar,gemvolwarn,gemvolcrit)
worklist.email(dest='*****@*****.**',subject=msg)
worklist.comment(doneLabel)
clock.pipetting=ptmp # All the retries don't usually happen, so don't count in total time
self.addhistory("LD",0,tipMask)
def savegem(self,filename):
worklist.comment("Completed (%s-%s)"%(sys.argv[0],self.checksum))
worklist.flushQueue()
worklist.savegem(decklayout.headerfile,filename)
def volcheck(self, tipMask, well, volToRemove):
'''Check if the well contains the expected volume'''
if self.lastvolcheck is not None:
# Decide if a volume check is needed
if volToRemove == 0:
# No need to check if not removing anything and it has been checked previously (i.e. lastvolcheck is not None)
return
if self.volume - volToRemove > max(
30, self.lastvolcheck -
200) or self.volume - volToRemove > 200:
# Not needed
return
self.lastvolcheck = self.volume
height = self.plate.getliquidheight(self.volume)
gemvol = self.plate.getgemliquidvolume(
height) # Volume that would be reported by Gemini for this height
if gemvol is None:
logging.warning(
"No volume equation for %s, skipping initial volume check" %
self.name)
return
volcrit = self.plate.unusableVolume * 0.8 + volToRemove
volwarn = min(volcrit, self.volume * 0.80)
heightwarn = min(self.plate.getliquidheight(volwarn),
height - 1.0) # threshold is lower of 1mm or 80%
gemvolwarn = self.plate.getgemliquidvolume(
heightwarn
) # Volume that would be reported by Gemini for this height
heightcrit = self.plate.getliquidheight(volcrit)
gemvolcrit = self.plate.getgemliquidvolume(
heightcrit
) # Volume that would be reported by Gemini for this height
worklist.flushQueue()
worklist.comment(
"Check that %s contains %.1f ul (warn< %.1f, crit<%.1f), (gemvol=%.1f (warn<%.1f,crit<%.1f); height=%.1f (>%.1f) )"
% (self.name, self.volume, volwarn, volcrit, gemvol, gemvolwarn,
gemvolcrit, height, heightwarn))
tipnum = 0
tm = tipMask
while tm > 0:
tm = tm >> 1
tipnum += 1
volvar = 'detected_volume_%d' % tipnum
worklist.variable(volvar, -2)
worklist.detectLiquid(tipMask, well, self.inliquidLC, self.plate)
doneLabel = worklist.getlabel()
worklist.condition(volvar, ">", gemvolwarn, doneLabel)
ptmp = clock.pipetting
warnLabel = worklist.getlabel()
worklist.condition(volvar, ">", gemvolcrit, warnLabel)
worklist.moveliha(worklist.WASHLOC) # Get LiHa out of the way
msg = "Failed volume check of %s - should have %.0f ul (gemvol=~%s~, crit=%.0f)" % (
self.name, self.volume, volvar, gemvolcrit)
worklist.email(dest='*****@*****.**', subject=msg)
worklist.stringvariable(
"response", "retry", msg +
" Enter 'ignore' to ignore and continue, otherwise will retry.")
worklist.condition("response", "==", "ignore", doneLabel)
# Retry
worklist.detectLiquid(tipMask, well, self.inliquidLC, self.plate)
worklist.condition(volvar, ">", gemvolcrit, doneLabel)
worklist.stringvariable(
"response", "retry",
"Still have <%.0f. Enter 'ignore' to ignore and continue, otherwise will retry."
% self.volume)
worklist.condition("response", "==", "ignore", doneLabel)
# Retry again
worklist.detectLiquid(tipMask, well, self.inliquidLC, self.plate)
worklist.condition(volvar, ">", gemvolcrit, doneLabel)
worklist.stringvariable(
"response", "ignore",
"Still have <%.0f. Will continue regardless." % self.volume)
worklist.condition("response", "!=", "warn", doneLabel)
worklist.comment(warnLabel)
msg = "Warning: volume check of %s - should have %.0f ul (gemvol=~%s~, warn=%.0f, crit=%.0f)" % (
self.name, self.volume, volvar, gemvolwarn, gemvolcrit)
worklist.email(dest='*****@*****.**', subject=msg)
worklist.comment(doneLabel)
clock.pipetting = ptmp # All the retries don't usually happen, so don't count in total time
self.addhistory("LD", 0, tipMask, "detect")
def savegem(self,filename):
worklist.flushQueue()
worklist.savegem(decklayout.headerfile,filename)
def savegem(self, filename):
worklist.comment("Completed (%s-%s)" % (sys.argv[0], self.checksum))
worklist.flushQueue()
worklist.savegem(decklayout.headerfile, filename)
