def evapcheck(self, op, thresh=0.20):
'Update amount of evaporation and check for issues'
if self.plate.name == "Samples":
dt = clock.pipetting - self.lastevapupdate # Assume no evaporation while in PTC
if dt < -0.1:
# This may happen during thermocycler operation since pipetting while thermocycling is moved to pipthermotime after waitpgm() is called
logging.notice(
"%s: clock went backwards: pipetting=%f, lastevapupdate=%f, dt=%f -- probably OK due to counting pipetting time during PTC operation"
% (self.name, clock.pipetting, self.lastevapupdate, dt))
else:
dt = clock.elapsed() - self.lastevapupdate
if dt < -0.1:
logging.error(
"%s: clock went backwards: elapsed=%f, lastevapupdate=%f, dt=%f"
% (self.name, clock.elapsed(), self.lastevapupdate, dt))
if dt <= 0.1:
return
for i in range(
10): # Break it into smaller steps since volume affects rate
evaprate = self.plate.getevaprate(max(0, self.volume - self.evap))
self.evap += evaprate * dt / 3600 / 10
if op == 'aspirate' and self.evap > thresh * self.volume and self.evap > 2.0 and self.volume > 0:
pctevap = self.evap / self.volume * 100
logging.warning(
" %s (%s.%s, vol=%.1f ul) may have %.1f ul of evaporation (%.0f%%)"
% (self.name, str(self.plate), self.plate.wellname(
self.well), self.volume, self.evap, pctevap))
if "evap" in __historyOptions:
self.history = self.history + (' [Evap: %0.1f ul]' %
(self.evap))
self.lastevapupdate += dt
def savesummary(self, filename, settings=None):
# Print amount of samples needed
fd = open(filename, "w")
# print >>fd,"Deck layout:"
# print >>fd,decklayout.REAGENTPLATE
# print >>fd,decklayout.SAMPLEPLATE
# print >>fd,decklayout.QPCRPLATE
# print >>fd,decklayout.WATERLOC
# print >>fd,decklayout.WASTE
# print >>fd,decklayout.BLEACHLOC
# print >>fd,decklayout.WASHLOC
# print >>fd
#print >>fd,"DiTi usage:",worklist.getDITIcnt()
#print >>fd
print >> fd, "Generated %s (%s-%s pyTecan-%s)" % (
datetime.now().ctime(), sys.argv[0], self.checksum, self.gitlabel)
rtime = "Run time: %d (pipetting only) + %d (thermocycling only) + %d (both) = %d minutes (%.1f hours)\n" % (
clock.pipetting / 60.0, clock.thermotime / 60,
clock.pipandthermotime / 60, clock.elapsed() / 60,
clock.elapsed() / 3600.0)
print rtime
print >> fd, rtime
reagents.printprep(fd)
Sample.printallsamples("All Samples:", fd, w=worklist)
liquidclass.LC.printalllc(fd)
if settings is not None:
pprint(settings, stream=fd)
fd.close()
def shaken(plate,speed):
'Called after shaking to mark all samples as mixed'
for s in __allsamples:
if plate==s.plate.name and s.volume>0:
[minx,maxx]=s.plate.getmixspeeds(s.volume,s.volume)
s.wellMixed=s.wellMixed or speed>=minx
s.lastMixed=clock.elapsed()
def shaken(plate, speed):
'Called after shaking to mark all samples as mixed'
for s in __allsamples:
if plate == s.plate.name and s.volume > 0:
[minx, maxx] = s.plate.getmixspeeds(s.volume, s.volume)
s.wellMixed = s.wellMixed or speed >= minx
s.lastMixed = clock.elapsed()
def shaken(plate, speed):
'Called after shaking to mark all samples as mixed'
for s in __allsamples:
if plate == s.plate.name and s.volume > 0:
if not s.wellMixed:
(minx, maxx) = s.getmixspeeds()
s.wellMixed = speed >= minx - 1
s.lastMixed = clock.elapsed()
def isMixed(self):
'Check if sample is currently mixed'
if self.lastMixed is None:
return False
elif not self.hasBeads:
return True
else:
return clock.elapsed() - self.lastMixed < BEADSETTLINGTIME
def isMixed(self):
'Check if sample is currently mixed'
if self.lastMixed is None:
return False
elif not self.hasBeads:
return True
else:
return clock.elapsed()-self.lastMixed < BEADSETTLINGTIME
def shaken(plate,speed):
'Called after shaking to mark all samples as mixed'
for s in __allsamples:
if plate==s.plate.name and s.volume>0:
if not s.wellMixed:
(minx,maxx)=s.getmixspeeds()
s.wellMixed=speed>=minx-1
s.lastMixed=clock.elapsed()
def evapcheck(self,op,thresh=0.20):
'Update amount of evaporation and check for issues'
if self.plate.name=="Samples":
dt=clock.pipetting-self.lastevapupdate # Assume no evaporation while in PTC
else:
dt=clock.elapsed()-self.lastevapupdate
if dt<-0.1:
print "***ERROR*** -- clock went backwards: elapsed=",clock.elapsed(),", lastevapupdate=",self.lastevapupdate,", dt=",dt
assert False
if dt<=0.1:
return
for i in range(10): # Break it into smaller steps since volume affects rate
evaprate=self.plate.getevaprate(max(0,self.volume-self.evap))
self.evap+=evaprate*dt/3600/10
if op=='aspirate' and self.evap>thresh*self.volume and self.evap>2.0 and self.volume>0:
pctevap=self.evap/self.volume*100
print "WARNING: %s (%s.%s, vol=%.1f ul) may have %.1f ul of evaporation (%.0f%%)"%(self.name,str(self.plate),self.plate.wellname(self.well),self.volume,self.evap,pctevap)
self.history= self.history + (' [Evap: %0.1f ul]'%(self.evap))
self.lastevapupdate+=dt
def evapcheck(self, op, thresh=0.20):
'Update amount of evaporation and check for issues'
if self.plate.name == "Samples":
dt = clock.pipetting - self.lastevapupdate # Assume no evaporation while in PTC
else:
dt = clock.elapsed() - self.lastevapupdate
if dt < -0.1:
print "***ERROR*** -- clock went backwards: elapsed=", clock.elapsed(
), ", lastevapupdate=", self.lastevapupdate, ", dt=", dt
assert False
if dt <= 0.1:
return
for i in range(
10): # Break it into smaller steps since volume affects rate
evaprate = self.plate.getevaprate(max(0, self.volume - self.evap))
self.evap += evaprate * dt / 3600 / 10
if op == 'aspirate' and self.evap > thresh * self.volume and self.evap > 2.0 and self.volume > 0:
pctevap = self.evap / self.volume * 100
print "WARNING: %s (%s.%s, vol=%.1f ul) may have %.1f ul of evaporation (%.0f%%)" % (
self.name, str(self.plate), self.plate.wellname(
self.well), self.volume, self.evap, pctevap)
self.history = self.history + (' [Evap: %0.1f ul]' % (self.evap))
self.lastevapupdate += dt
def savesummary(self, filename):
# Print amount of samples needed
fd = open(filename, "w")
# print >>fd,"Deck layout:"
# print >>fd,decklayout.REAGENTPLATE
# print >>fd,decklayout.SAMPLEPLATE
# print >>fd,decklayout.QPCRPLATE
# print >>fd,decklayout.WATERLOC
# print >>fd,decklayout.WASTE
# print >>fd,decklayout.BLEACHLOC
# print >>fd,decklayout.WASHLOC
# print >>fd
#print >>fd,"DiTi usage:",worklist.getDITIcnt()
#print >>fd
rtime = "Run time: %d (pipetting only) + %d (thermocycling only) + %d (both) = %d minutes\n" % (
clock.pipetting / 60.0, clock.thermotime / 60,
clock.pipandthermotime / 60, clock.elapsed() / 60)
print rtime
print >> fd, rtime
reagents.printprep(fd)
Sample.printallsamples("All Samples:", fd, w=worklist)
liquidclass.LC.printalllc("All LC:", fd)
fd.close()
def __init__(self,
name,
plate,
well=None,
conc=None,
volume=0,
hasBeads=False,
extraVol=50,
mixLC=liquidclass.LCMixBottom,
firstWell=None,
extrainfo=[],
ingredients=None,
atEnd=False):
while True:
# wrap with a loop to allow use of backupPlate
# If firstWell is not None, then it is a hint of the first well position that should be used
if well != None and well != -1:
if not isinstance(well, int):
well = plate.wellnumber(well)
if well not in plate.wells:
logging.warning(
"Attempt to assign sample %s to well %d (%s) which is not legal on plate %s"
% (name, well, plate.wellname(well), plate.name))
for s in __allsamples:
if s.well == well and s.plate == plate:
logging.warning(
"Attempt to assign sample %s to plate %s, well %s that already contains %s"
% (name, str(plate), plate.wellname(well), s.name))
if firstWell is None:
firstWell = well
well = None
break
if well is None:
# Find first unused well
found = False
if firstWell is not None:
# First check only wells>=firstWell
for well in plate.wells:
if well < firstWell:
continue
found = True
for s in __allsamples:
if s.plate == plate and s.well == well:
well = well + 1
found = False
break
if found:
break
if not found:
well = max(plate.wells) if atEnd else min(plate.wells)
while (well >= 0) if atEnd else (well <= max(plate.wells)):
found = True
for s in __allsamples:
if s.plate == plate and s.well == well:
well = well + (-1 if atEnd else 1)
found = False
break
if found:
break
elif well == -1:
well = None
if well >= plate.nx * plate.ny:
# Overflow
if plate.backupPlate is not None:
# Overflow onto backup plate
logging.warning(
"Overflow of %s plate, moving %s to %s plate -- verify carefully!"
% (plate.name, name, plate.backupPlate.name))
plate = plate.backupPlate
well = None
continue
else:
logging.error("Overflow of plate %s while adding %s" %
(str(plate), name))
break
for s in __allsamples:
if s.plate == plate and s.well == well:
logging.error(
"Attempt to assign sample %s to plate %s, well %s that already contains %s"
% (name, str(plate), plate.wellname(well), s.name))
if name in [s.name for s in __allsamples]:
while name in [s.name for s in __allsamples]:
name = name + "#"
logging.notice("renaming sample to %s" % name)
self.name = name
self.plate = plate
self.well = well
if isinstance(conc, Concentration) or conc is None:
self.conc = conc
else:
self.conc = Concentration(conc)
self.volume = volume
self.initVol = volume
if volume > 0:
if ingredients is None:
self.ingredients = {name: volume}
else:
self.ingredients = ingredients.copy()
total = sum([v for v in ingredients.values()])
for k in self.ingredients:
self.ingredients[k] = self.ingredients[k] * volume / total
self.lastvolcheck = None
else:
self.ingredients = {}
self.lastvolcheck = 0 # Assume that it has already been checked for 0 (since it can't be any less...)
self.checkingredients()
if plate.pierce:
self.bottomLC = liquidclass.LCWaterPierce
self.bottomSideLC = self.bottomLC # Can't use side with piercing
self.inliquidLC = self.bottomLC # Can't use liquid detection when piercing
else:
self.bottomLC = liquidclass.LCWaterBottom
self.bottomSideLC = liquidclass.LCWaterBottomSide
self.inliquidLC = liquidclass.LCWaterInLiquid
self.beadsLC = liquidclass.LCWaterBottomBeads
self.mixLC = mixLC
self.airLC = liquidclass.LCAir
# Same as bottom for now
self.emptyLC = self.bottomLC
self.history = ""
__allsamples.append(self)
if hasBeads:
self.lastMixed = None
else:
self.lastMixed = clock.elapsed(
) - 20 * 60 # Assume it was last mixed an 20 min before start of run
self.wellMixed = True
self.initHasBeads = hasBeads
self.hasBeads = hasBeads # Setting this to true overrides the manual conditioning
self.extraVol = extraVol # Extra volume to provide
self.evap = 0 # Amount that has evaporated
if self.plate.name == "Samples":
self.lastevapupdate = clock.pipetting
else:
self.lastevapupdate = clock.elapsed()
self.extrainfo = extrainfo
self.emptied = False
def mix(self,tipMask,preaspirateAir=False,nmix=4):
if self.isMixed() and self.wellMixed:
logging.notice( "mix() called for sample %s, which is already mixed"%self.name)
return False
logging.mixwarning("Pipette mixing of %s may introduce bubbles"%self.name)
self.volcheck(tipMask,[self.well],0)
blowvol=5
mstr=""
extraspace=blowvol+0.1
if preaspirateAir:
extraspace+=5
mixvol=self.volume # -self.plate.unusableVolume; # Can mix entire volume, if air is aspirated, it will just be dispensed first without making a bubble
if self.volume>MAXVOLUME-extraspace:
mixvol=MAXVOLUME-extraspace
logging.mixwarning("Mix of %s limited to %.0f ul instead of full volume of %.0ful"%(self.name,mixvol,self.volume))
well=[self.well if self.well!=None else 2**(tipMask-1)-1 ]
mixprefillvol=5
if mixvol<self.plate.unusableVolume-mixprefillvol:
logging.notice("Not enough volume in sample %s (%.1f) to mix"%(self.name,self.volume))
self.history+="(UNMIXED)"
return False
else:
if preaspirateAir:
# Aspirate some air to avoid mixing with excess volume aspirated into pipette from source in previous transfer
self.aspirateAir(tipMask,5)
if False: # this results in losing mixprefillvol of sample which was not mixed; remainder has different concentration than planned
worklist.aspirateNC(tipMask,well,self.inliquidLC,mixprefillvol,self.plate)
self.volume-=mixprefillvol
self.addhistory("(PRE)",-mixprefillvol,tipMask)
worklist.mix(tipMask,well,self.mixLC,mixvol,self.plate,nmix)
mstr="(MB)"
elif False: # self.volume>=MINLIQUIDDETECTVOLUME: # Another short-lived strategy
worklist.mix(tipMask,well,self.inliquidLC,mixvol,self.plate,nmix)
self.history+="(MLD)"
else:
height=self.plate.getliquidheight(self.volume)
if height is None:
worklist.mix(tipMask,well,self.mixLC,mixvol,self.plate,nmix)
mstr="(MB)"
else:
mixheight=math.floor(height-1) # At least 1mm below liquid height
if mixheight<2:
mixheight=2
# print 'Vol=%.1f ul, height=%.1f mm, mix=%d, blow=%d'%(self.volume,height,mixheight,blowheight)
mixLC=liquidclass.LCMix[min(12,mixheight)]
if blowvol>0:
blowoutLC=liquidclass.LCBlowoutLD
worklist.aspirateNC(tipMask,well,self.airLC,(blowvol+0.1),self.plate)
if self.volume<30:
worklist.mix(tipMask,well,self.mixLC,mixvol,self.plate,nmix)
mstr="(MB)"
else:
for _ in range(nmix):
worklist.aspirateNC(tipMask,well,mixLC,mixvol,self.plate)
worklist.dispense(tipMask,well,mixLC,mixvol,self.plate)
mstr="(M@%d)"%(mixheight)
if blowvol>0:
worklist.dispense(tipMask,well,blowoutLC,blowvol,self.plate)
worklist.dispense(tipMask,well,liquidclass.LCDip,0.1,self.plate)
self.volume-=MIXLOSS
self.addhistory(mstr,-MIXLOSS,tipMask)
self.lastMixed=clock.elapsed()
self.wellMixed=True
return True
def __init__(self,name,plate,well=None,conc=None,volume=0,hasBeads=False,extraVol=50,mixLC=liquidclass.LCMixBottom,firstWell=None,extrainfo=[],ingredients=None,atEnd=False):
# If firstWell is not None, then it is a hint of the first well position that should be used
if well!=None and well!=-1:
if not isinstance(well,int):
well=plate.wellnumber(well)
if well not in plate.wells:
logging.warning("Attempt to assign sample %s to well %d (%s) which is not legal on plate %s"%(name,well,plate.wellname(well),plate.name))
for s in __allsamples:
if s.well==well and s.plate==plate:
logging.warning("Attempt to assign sample %s to plate %s, well %s that already contains %s"%(name,str(plate),plate.wellname(well),s.name))
well=None
break
if well is None:
# Find first unused well
found=False
if firstWell is not None:
# First check only wells>=firstWell
for well in plate.wells:
if well<firstWell:
continue
found=True
for s in __allsamples:
if s.plate==plate and s.well==well:
well=well+1
found=False
break
if found:
break
if not found:
well=max(plate.wells) if atEnd else min(plate.wells)
while (well>=0) if atEnd else (well<=max(plate.wells)):
found=True
for s in __allsamples:
if s.plate==plate and s.well==well:
well=well+(-1 if atEnd else 1)
found=False
break
if found:
break
elif well==-1:
well=None
for s in __allsamples:
if s.plate==plate and s.well==well:
logging.error("Attempt to assign sample %s to plate %s, well %s that already contains %s"%(name,str(plate),plate.wellname(well),s.name))
if name in [s.name for s in __allsamples]:
while name in [s.name for s in __allsamples]:
name=name+"#"
logging.notice("renaming sample to %s"%name)
self.name=name
self.plate=plate
if well>=plate.nx*plate.ny:
logging.error("Overflow of plate %s while adding %s"%(str(plate),name))
self.well=well
if isinstance(conc,Concentration) or conc is None:
self.conc=conc
else:
self.conc=Concentration(conc)
self.volume=volume
self.initVol=volume
if volume>0:
if ingredients is None:
self.ingredients={name:volume}
else:
self.ingredients=ingredients
total=sum([v for v in ingredients.values()])
for k in self.ingredients:
self.ingredients[k]=self.ingredients[k]*volume/total
self.lastvolcheck=None
else:
self.ingredients={}
self.lastvolcheck=0 # Assume that it has already been checked for 0 (since it can't be any less...)
if plate.pierce:
self.bottomLC=liquidclass.LCWaterPierce
self.bottomSideLC=self.bottomLC # Can't use side with piercing
self.inliquidLC=self.bottomLC # Can't use liquid detection when piercing
else:
self.bottomLC=liquidclass.LCWaterBottom
self.bottomSideLC=liquidclass.LCWaterBottomSide
self.inliquidLC=liquidclass.LCWaterInLiquid
self.beadsLC=liquidclass.LCWaterBottomBeads
self.mixLC=mixLC
self.airLC=liquidclass.LCAir
# Same as bottom for now
self.emptyLC=self.bottomLC
self.history=""
__allsamples.append(self)
if hasBeads:
self.lastMixed=None
else:
self.lastMixed=clock.elapsed()-20*60 # Assume it was last mixed an 20 min before start of run
self.wellMixed=True
self.initHasBeads=hasBeads
self.hasBeads=hasBeads # Setting this to true overrides the manual conditioning
self.extraVol=extraVol # Extra volume to provide
self.evap=0 # Amount that has evaporated
if self.plate.name=="Samples":
self.lastevapupdate=clock.pipetting
else:
self.lastevapupdate=clock.elapsed()
self.extrainfo=extrainfo
self.emptied=False
def aspirate(self,tipMask,volume,multi=False):
self.evapcheck('aspirate')
if self.plate.curloc=='PTC':
logging.error( "Aspirate from PTC!, loc=%d,%d"%(self.plate.grid,self.plate.pos))
removeAll=volume==self.volume
if removeAll:
logging.notice("Removing all contents (%.1ful) from %s"%(volume,self.name))
if volume<0.1:
logging.warning("attempt to aspirate only %.1f ul from %s ignored"%(volume,self.name))
return
if volume<2 and not multi and self.name!="Water":
logging.warning("Inaccurate for < 2ul: attempting to aspirate %.1f ul from %s"%(volume,self.name))
if volume>self.volume and self.volume>0:
logging.error("Attempt to aspirate %.1f ul from %s that contains only %.1f ul"%(volume, self.name, self.volume))
if not self.isMixed() and self.plate.curloc!="Magnet":
if self.hasBeads and self.lastMixed is not None:
logging.mixwarning("Aspirate %.1f ul from sample %s that has beads and has not been mixed for %.0f sec. "%(volume,self.name,clock.elapsed()-self.lastMixed))
else:
logging.mixwarning("Aspirate %.1f ul from unmixed sample %s. "%(volume,self.name))
if not self.wellMixed and self.plate.curloc!="Magnet":
logging.mixwarning("Aspirate %.1f ul from poorly mixed sample %s (shake speed was too low). "%(volume,self.name))
if self.well is None:
well=[]
for i in range(4):
if (tipMask & (1<<i)) != 0:
well.append(i)
else:
well=[self.well]
lc=self.chooseLC(volume)
self.volcheck(tipMask,well,volume)
if (self.hasBeads and self.plate.curloc=="Magnet") or removeAll:
# With beads don't do any manual conditioning and don't remove extra (since we usually want to control exact amounts left behind, if any)
worklist.aspirateNC(tipMask,well,lc,volume,self.plate)
remove=lc.volRemoved(volume,multi=False)
if self.volume==volume:
# Removing all, ignore excess remove
remove=self.volume-0.1 # Leave behind enough to be able to keep track of ingredients
self.emptied=True
else:
worklist.aspirate(tipMask,well,lc,volume,self.plate)
# Manual conditioning handled in worklist
remove=lc.volRemoved(volume,multi=True)
if self.volume<remove+0.1 and self.volume>0:
logging.warning("Removing all contents (%.1f from %.1ful) from %s"%(remove,self.volume,self.name))
remove=self.volume-0.1 # Leave residual
for k in self.ingredients:
self.ingredients[k] *= (self.volume-remove)/self.volume
self.volume=self.volume-remove
if self.volume+.001<self.plate.unusableVolume and self.volume+remove>0 and not (self.hasBeads and self.plate.curloc=='Magnet') and not removeAll:
logging.warning("Aspiration of %.1ful from %s brings volume down to %.1ful which is less than its unusable volume of %.1f ul"%(remove,self.name,self.volume,self.plate.unusableVolume))
self.addhistory("",-remove,tipMask)
def aspirate(self, tipMask, volume, multi=False):
self.evapcheck('aspirate')
if self.plate.curloc == 'PTC':
print "Aspirate from PTC!, loc=", self.plate.grid, ",", self.plate.pos
assert False
if volume < 0.1:
print "WARNING: attempt to aspirate only %.1f ul from %s ignored" % (
volume, self.name)
return
if volume < 2 and not multi and self.name != "Water":
print "WARNING: Inaccurate for < 2ul: attempting to aspirate %.1f ul from %s" % (
volume, self.name)
if volume > self.volume and self.volume > 0:
print "ERROR:Attempt to aspirate %.1f ul from %s that contains only %.1f ul" % (
volume, self.name, self.volume)
if not self.isMixed() and self.plate.curloc != "Magnet":
if self.hasBeads and self.lastMixed is not None:
print "WARNING: Aspirate %.1f ul from sample %s that has beads and has not been mixed for %.0f sec. " % (
volume, self.name, clock.elapsed() - self.lastMixed)
else:
print "WARNING: Aspirate %.1f ul from unmixed sample %s. " % (
volume, self.name)
if not self.wellMixed:
print "WARNING: Aspirate %.1f ul from poorly mixed sample %s (shake speed was too low). " % (
volume, self.name)
if self.well is None:
well = []
for i in range(4):
if (tipMask & (1 << i)) != 0:
well.append(i)
else:
well = [self.well]
lc = self.chooseLC(volume)
if self.hasBeads and self.plate.curloc == "Magnet":
# With beads don't do any manual conditioning and don't remove extra (since we usually want to control exact amounts left behind, if any)
worklist.aspirateNC(tipMask, well, lc, volume, self.plate)
remove = lc.volRemoved(volume, multi=False)
if self.volume == volume:
# Removing all, ignore excess remove
remove = self.volume
self.ingredients = {}
else:
worklist.aspirate(tipMask, well, lc, volume, self.plate)
# Manual conditioning handled in worklist
remove = lc.volRemoved(volume, multi=True)
if self.volume < remove and self.volume > 0:
print "WARNING: Removing all contents (%.1f from %.1ful) from %s" % (
remove, self.volume, self.name)
remove = self.volume
self.ingredients = {}
for k in self.ingredients:
if self.plate.curloc == "Magnet" and k == 'BIND':
pass
else:
self.ingredients[k] *= (self.volume - remove) / self.volume
self.volume = self.volume - remove
if self.volume + .001 < self.plate.unusableVolume and self.volume + remove > 0 and not (
self.hasBeads and self.plate.curloc == 'Magnet'):
print "WARNING: Aspiration of %.1ful from %s brings volume down to %.1ful which is less than its unusable volume of %.1f ul" % (
remove, self.name, self.volume, self.plate.unusableVolume)
self.addhistory("", -remove, tipMask)
def __init__(self,name,plate,well=None,conc=None,volume=0,hasBeads=False,extraVol=50,mixLC=liquidclass.LCMixBottom):
if well!=None and well!=-1:
if not isinstance(well,int):
well=plate.wellnumber(well)
if well not in plate.wells:
print "Attempt to assign sample %s to well %d (%s) which is not legal on plate %s"%(name,well,plate.wellname(well),plate.name)
for s in __allsamples:
if s.well==well and s.plate==plate:
print "Attempt to assign sample %s to plate %s, well %s that already contains %s"%(name,str(plate),plate.wellname(well),s.name)
well=None
break
if well is None:
# Find first unused well
found=False
for well in plate.wells:
found=True
for s in __allsamples:
if s.plate==plate and s.well==well:
well=well+1
found=False
break
if found:
break
elif well==-1:
well=None
for s in __allsamples:
if s.plate==plate and s.well==well:
print "Attempt to assign sample %s to plate %s, well %s that already contains %s"%(name,str(plate),plate.wellname(well),s.name)
# print "Aliasing %s as %s"%(s.name,name)
assert False
if name in [s.name for s in __allsamples]:
while name in [s.name for s in __allsamples]:
name=name+"#"
print "NOTICE: renaming sample to %s"%name
self.name=name
self.plate=plate
if well>=plate.nx*plate.ny:
print "Overflow of plate %s"%str(plate)
for s in __allsamples:
if s.plate==plate:
print s
assert False
self.well=well
if isinstance(conc,Concentration) or conc is None:
self.conc=conc
else:
self.conc=Concentration(conc)
self.volume=volume
if volume>0:
self.ingredients={name:volume}
else:
self.ingredients={}
if plate.pierce:
self.bottomLC=liquidclass.LCWaterPierce
self.bottomSideLC=self.bottomLC # Can't use side with piercing
self.inliquidLC=self.bottomLC # Can't use liquid detection when piercing
else:
self.bottomLC=liquidclass.LCWaterBottom
self.bottomSideLC=liquidclass.LCWaterBottomSide
self.inliquidLC=liquidclass.LCWaterInLiquid
self.beadsLC=liquidclass.LCWaterBottomBeads
self.mixLC=mixLC
self.airLC=liquidclass.LCAir
# Same as bottom for now
self.emptyLC=self.bottomLC
self.history=""
__allsamples.append(self)
if hasBeads:
self.lastMixed=None
else:
self.lastMixed=clock.elapsed()-20*60 # Assume it was last mixed an 20 min before start of run
self.wellMixed=True
self.initHasBeads=hasBeads
self.hasBeads=hasBeads # Setting this to true overrides the manual conditioning
self.extraVol=extraVol # Extra volume to provide
self.evap=0 # Amount that has evaporated
if self.plate.name=="Samples":
self.lastevapupdate=clock.pipetting
else:
self.lastevapupdate=clock.elapsed()
def __init__(self,
name,
plate,
well=None,
conc=None,
volume=0,
hasBeads=False,
extraVol=50,
mixLC=liquidclass.LCMixBottom):
if well != None and well != -1:
if not isinstance(well, int):
well = plate.wellnumber(well)
if well not in plate.wells:
print "Attempt to assign sample %s to well %d (%s) which is not legal on plate %s" % (
name, well, plate.wellname(well), plate.name)
for s in __allsamples:
if s.well == well and s.plate == plate:
print "Attempt to assign sample %s to plate %s, well %s that already contains %s" % (
name, str(plate), plate.wellname(well), s.name)
well = None
break
if well is None:
# Find first unused well
found = False
for well in plate.wells:
found = True
for s in __allsamples:
if s.plate == plate and s.well == well:
well = well + 1
found = False
break
if found:
break
elif well == -1:
well = None
for s in __allsamples:
if s.plate == plate and s.well == well:
print "Attempt to assign sample %s to plate %s, well %s that already contains %s" % (
name, str(plate), plate.wellname(well), s.name)
# print "Aliasing %s as %s"%(s.name,name)
assert False
if name in [s.name for s in __allsamples]:
while name in [s.name for s in __allsamples]:
name = name + "#"
print "NOTICE: renaming sample to %s" % name
self.name = name
self.plate = plate
if well >= plate.nx * plate.ny:
print "Overflow of plate %s" % str(plate)
for s in __allsamples:
if s.plate == plate:
print s
assert False
self.well = well
if isinstance(conc, Concentration) or conc is None:
self.conc = conc
else:
self.conc = Concentration(conc)
self.volume = volume
if volume > 0:
self.ingredients = {name: volume}
else:
self.ingredients = {}
if plate.pierce:
self.bottomLC = liquidclass.LCWaterPierce
self.bottomSideLC = self.bottomLC # Can't use side with piercing
self.inliquidLC = self.bottomLC # Can't use liquid detection when piercing
else:
self.bottomLC = liquidclass.LCWaterBottom
self.bottomSideLC = liquidclass.LCWaterBottomSide
self.inliquidLC = liquidclass.LCWaterInLiquid
self.beadsLC = liquidclass.LCWaterBottomBeads
self.mixLC = mixLC
self.airLC = liquidclass.LCAir
# Same as bottom for now
self.emptyLC = self.bottomLC
self.history = ""
__allsamples.append(self)
if hasBeads:
self.lastMixed = None
else:
self.lastMixed = clock.elapsed(
) - 20 * 60 # Assume it was last mixed an 20 min before start of run
self.wellMixed = True
self.initHasBeads = hasBeads
self.hasBeads = hasBeads # Setting this to true overrides the manual conditioning
self.extraVol = extraVol # Extra volume to provide
self.evap = 0 # Amount that has evaporated
if self.plate.name == "Samples":
self.lastevapupdate = clock.pipetting
else:
self.lastevapupdate = clock.elapsed()
def savesummary(self,filename):
# Print amount of samples needed
fd=open(filename,"w")
# print >>fd,"Deck layout:"
# print >>fd,decklayout.REAGENTPLATE
# print >>fd,decklayout.SAMPLEPLATE
# print >>fd,decklayout.QPCRPLATE
# print >>fd,decklayout.WATERLOC
# print >>fd,decklayout.WASTE
# print >>fd,decklayout.BLEACHLOC
# print >>fd,decklayout.WASHLOC
# print >>fd
#print >>fd,"DiTi usage:",worklist.getDITIcnt()
#print >>fd
rtime="Run time: %d (pipetting only) + %d (thermocycling only) + %d (both) = %d minutes\n"%(clock.pipetting/60.0,clock.thermotime/60, clock.pipandthermotime/60, clock.elapsed()/60)
print rtime
print >>fd,rtime
reagents.printprep(fd)
Sample.printallsamples("All Samples:",fd,w=worklist)
liquidclass.LC.printalllc("All LC:",fd)
fd.close()
def aspirate(self,tipMask,volume,multi=False):
self.evapcheck('aspirate')
if self.plate.curloc=='PTC':
print "Aspirate from PTC!, loc=",self.plate.grid,",",self.plate.pos
assert False
if volume<0.1:
print "WARNING: attempt to aspirate only %.1f ul from %s ignored"%(volume,self.name)
return
if volume<2 and not multi and self.name!="Water":
print "WARNING: Inaccurate for < 2ul: attempting to aspirate %.1f ul from %s"%(volume,self.name)
if volume>self.volume and self.volume>0:
print "ERROR:Attempt to aspirate %.1f ul from %s that contains only %.1f ul"%(volume, self.name, self.volume)
if not self.isMixed() and self.plate.curloc!="Magnet":
if self.hasBeads and self.lastMixed is not None:
print "WARNING: Aspirate %.1f ul from sample %s that has beads and has not been mixed for %.0f sec. "%(volume,self.name,clock.elapsed()-self.lastMixed)
else:
print "WARNING: Aspirate %.1f ul from unmixed sample %s. "%(volume,self.name)
if not self.wellMixed:
print "WARNING: Aspirate %.1f ul from poorly mixed sample %s (shake speed was too low). "%(volume,self.name)
if self.well is None:
well=[]
for i in range(4):
if (tipMask & (1<<i)) != 0:
well.append(i)
else:
well=[self.well]
lc=self.chooseLC(volume)
if self.hasBeads and self.plate.curloc=="Magnet":
# With beads don't do any manual conditioning and don't remove extra (since we usually want to control exact amounts left behind, if any)
worklist.aspirateNC(tipMask,well,lc,volume,self.plate)
remove=lc.volRemoved(volume,multi=False)
if self.volume==volume:
# Removing all, ignore excess remove
remove=self.volume
self.ingredients={}
else:
worklist.aspirate(tipMask,well,lc,volume,self.plate)
# Manual conditioning handled in worklist
remove=lc.volRemoved(volume,multi=True)
if self.volume<remove and self.volume>0:
print "WARNING: Removing all contents (%.1f from %.1ful) from %s"%(remove,self.volume,self.name)
remove=self.volume
self.ingredients={}
for k in self.ingredients:
if self.plate.curloc=="Magnet" and k=='BIND':
pass
else:
self.ingredients[k] *= (self.volume-remove)/self.volume
self.volume=self.volume-remove
if self.volume+.001<self.plate.unusableVolume and self.volume+remove>0 and not (self.hasBeads and self.plate.curloc=='Magnet'):
print "WARNING: Aspiration of %.1ful from %s brings volume down to %.1ful which is less than its unusable volume of %.1f ul"%(remove,self.name,self.volume,self.plate.unusableVolume)
self.addhistory("",-remove,tipMask)
def aspirate(self, tipMask, volume, multi=False):
self.evapcheck('aspirate')
if self.plate.curloc == 'PTC':
logging.error("Aspirate from PTC!, loc=%d,%d" %
(self.plate.grid, self.plate.pos))
removeAll = volume == self.volume
if removeAll:
logging.notice("Removing all contents (%.1ful) from %s" %
(volume, self.name))
if volume < 0.1:
logging.warning(
"attempt to aspirate only %.1f ul from %s ignored" %
(volume, self.name))
return
if volume < 2 and not multi and self.name != "Water":
logging.warning(
"Inaccurate for < 2ul: attempting to aspirate %.1f ul from %s"
% (volume, self.name))
if volume > self.volume and self.volume > 0:
logging.error(
"Attempt to aspirate %.1f ul from %s that contains only %.1f ul"
% (volume, self.name, self.volume))
if not self.isMixed() and self.plate.curloc != "Magnet":
if self.hasBeads and self.lastMixed is not None:
logging.mixwarning(
"Aspirate %.1f ul from sample %s that has beads and has not been mixed for %.0f sec. "
% (volume, self.name, clock.elapsed() - self.lastMixed))
else:
logging.mixwarning(
"Aspirate %.1f ul from unmixed sample %s. " %
(volume, self.name))
if not self.wellMixed and self.plate.curloc != "Magnet":
logging.mixwarning(
"Aspirate %.1f ul from poorly mixed sample %s (shake speed was too low). "
% (volume, self.name))
if self.well is None:
well = []
for i in range(4):
if (tipMask & (1 << i)) != 0:
well.append(i)
else:
well = [self.well]
lc = self.chooseLC(volume)
self.volcheck(tipMask, well, volume)
if (self.hasBeads and self.plate.curloc == "Magnet") or removeAll:
# With beads don't do any manual conditioning and don't remove extra (since we usually want to control exact amounts left behind, if any)
worklist.aspirateNC(tipMask, well, lc, volume, self.plate)
remove = lc.volRemoved(volume, multi=False)
if self.volume == volume:
# Removing all, ignore excess remove
remove = self.volume - 0.1 # Leave behind enough to be able to keep track of ingredients
self.emptied = True
else:
worklist.aspirate(tipMask, well, lc, volume, self.plate)
# Manual conditioning handled in worklist
remove = lc.volRemoved(volume, multi=True)
if self.volume < remove + 0.1 and self.volume > 0:
logging.warning(
"Removing all contents (%.1f from %.1ful) from %s" %
(remove, self.volume, self.name))
remove = self.volume - 0.1 # Leave residual
self.removeVolume(remove)
if self.volume + .001 < self.plate.unusableVolume and self.volume + remove > 0 and not (
self.hasBeads
and self.plate.curloc == 'Magnet') and not removeAll:
logging.warning(
"Aspiration of %.1ful from %s brings volume down to %.1ful which is less than its unusable volume of %.1f ul"
% (remove, self.name, self.volume, self.plate.unusableVolume))
self.addhistory("", -remove, tipMask)
def savesummary(self,filename):
# Print amount of samples needed
fd=open(filename,"w")
# print >>fd,"Deck layout:"
# print >>fd,decklayout.REAGENTPLATE
# print >>fd,decklayout.SAMPLEPLATE
# print >>fd,decklayout.QPCRPLATE
# print >>fd,decklayout.WATERLOC
# print >>fd,decklayout.WASTE
# print >>fd,decklayout.BLEACHLOC
# print >>fd,decklayout.WASHLOC
# print >>fd
#print >>fd,"DiTi usage:",worklist.getDITIcnt()
#print >>fd
print >>fd,"Generated %s (%s-%s pyTecan-%s)"%(datetime.now().ctime(),sys.argv[0],self.checksum,self.gitlabel)
rtime="Run time: %d (pipetting only) + %d (thermocycling only) + %d (both) = %d minutes (%.1f hours)\n"%(clock.pipetting/60.0,clock.thermotime/60, clock.pipandthermotime/60, clock.elapsed()/60, clock.elapsed()/3600.0)
print rtime
print >>fd,rtime
reagents.printprep(fd)
Sample.printallsamples("All Samples:",fd,w=worklist)
liquidclass.LC.printalllc(fd)
fd.close()
def mix(self, tipMask, preaspirateAir=False, nmix=4):
if self.isMixed() and self.wellMixed:
logging.notice(
"mix() called for sample %s, which is already mixed" %
self.name)
return False
logging.mixwarning("Pipette mixing of %s may introduce bubbles" %
self.name)
self.volcheck(tipMask, [self.well], 0)
blowvol = 5
mstr = ""
extraspace = blowvol + 0.1
if preaspirateAir:
extraspace += 5
mixvol = self.volume # -self.plate.unusableVolume; # Can mix entire volume, if air is aspirated, it will just be dispensed first without making a bubble
if self.volume > MAXVOLUME - extraspace:
mixvol = MAXVOLUME - extraspace
logging.mixwarning(
"Mix of %s limited to %.0f ul instead of full volume of %.0ful"
% (self.name, mixvol, self.volume))
well = [self.well if self.well != None else 2**(tipMask - 1) - 1]
mixprefillvol = 5
if mixvol < self.plate.unusableVolume - mixprefillvol:
logging.notice("Not enough volume in sample %s (%.1f) to mix" %
(self.name, self.volume))
self.history += "(UNMIXED)"
return False
else:
if preaspirateAir:
# Aspirate some air to avoid mixing with excess volume aspirated into pipette from source in previous transfer
self.aspirateAir(tipMask, 5)
if False: # this results in losing mixprefillvol of sample which was not mixed; remainder has different concentration than planned
worklist.aspirateNC(tipMask, well, self.inliquidLC,
mixprefillvol, self.plate)
self.removeVolume(mixprefillvol)
self.addhistory("(PRE)", -mixprefillvol, tipMask)
worklist.mix(tipMask, well, self.mixLC, mixvol, self.plate,
nmix)
mstr = "(MB)"
elif False: # self.volume>=MINLIQUIDDETECTVOLUME: # Another short-lived strategy
worklist.mix(tipMask, well, self.inliquidLC, mixvol,
self.plate, nmix)
self.history += "(MLD)"
else:
height = self.plate.getliquidheight(self.volume)
if height is None:
worklist.mix(tipMask, well, self.mixLC, mixvol, self.plate,
nmix)
mstr = "(MB)"
else:
mixheight = math.floor(
height - 1) # At least 1mm below liquid height
if mixheight < 2:
mixheight = 2
# print 'Vol=%.1f ul, height=%.1f mm, mix=%d, blow=%d'%(self.volume,height,mixheight,blowheight)
mixLC = liquidclass.LCMix[min(12, mixheight)]
if blowvol > 0:
blowoutLC = liquidclass.LCBlowoutLD
worklist.aspirateNC(tipMask, well, self.airLC,
(blowvol + 0.1), self.plate)
if self.volume < 30:
worklist.mix(tipMask, well, self.mixLC, mixvol,
self.plate, nmix)
mstr = "(MB)"
else:
for _ in range(nmix):
worklist.aspirateNC(tipMask, well, mixLC, mixvol,
self.plate)
worklist.dispense(tipMask, well, mixLC, mixvol,
self.plate)
mstr = "(M@%d)" % (mixheight)
if blowvol > 0:
worklist.dispense(tipMask, well, blowoutLC, blowvol,
self.plate)
worklist.dispense(tipMask, well, liquidclass.LCDip,
0.1, self.plate)
self.removeVolume(MIXLOSS)
self.addhistory(mstr, -MIXLOSS, tipMask)
self.lastMixed = clock.elapsed()
self.wellMixed = True
return True
