def lihahome(self):
'Move LiHa to left of deck'
worklist.moveliha(decklayout.WASHLOC)
def lihahome(self):
'Move LiHa to left of deck'
worklist.moveliha(decklayout.WASHLOC)
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 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")