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 dispense(self,tipMask,volume,src):
self.evapcheck('dispense')
if self.plate.curloc=='PTC':
logging.error("Dispense to PTC!, loc=(%d,%d)"%(self.plate.grid,self.plate.pos))
if volume<0.1:
logging.warning("attempt to dispense only %.1f ul to %s ignored"%(volume,self.name))
return
if self.volume+volume < MINDEPOSITVOLUME:
logging.warning("Dispense of %.1ful into %s results in total of %.1ful which is less than minimum deposit volume of %.1f ul"%(volume,self.name,self.volume+volume,MINDEPOSITVOLUME))
#well=[self.well if self.well!=None else 2**(tipMask-1)-1 ]
well=[self.well if self.well!=None else int(math.log(tipMask,2)) ]
if self.well is None:
logging.warning("Dispense with well is None, not sure what right logic is..., using well=%d"%well[0])
if self.volume+volume > self.plate.maxVolume:
logging.error("Dispense of %.1ful into %s results in total of %.1ful which is more than the maximum volume of %.1f ul"%(volume,self.name,self.volume+volume,self.plate.maxVolume))
if self.hasBeads and self.plate.curloc=="Magnet":
worklist.dispense(tipMask,well,self.beadsLC,volume,self.plate)
elif self.volume>=MINLIQUIDDETECTVOLUME:
worklist.dispense(tipMask,well,self.inliquidLC,volume,self.plate)
elif self.volume+volume>=MINSIDEDISPENSEVOLUME:
worklist.dispense(tipMask,well,self.bottomSideLC,volume,self.plate)
else:
worklist.dispense(tipMask,well,self.bottomLC,volume,self.plate)
# Assume we're diluting the contents
if self.conc is None and src.conc is None:
pass
elif src.conc is None or volume==0:
if self.volume==0:
self.conc=None
else:
self.conc=self.conc.dilute((self.volume+volume)/self.volume)
elif self.conc is None or self.volume==0 or self.conc.final is None or src.conc.final is None:
self.conc=src.conc.dilute((self.volume+volume)/volume)
else:
# Both have concentrations, they should match
c1=self.conc.dilute((self.volume+volume)/self.volume)
c2=src.conc.dilute((self.volume+volume)/volume)
if abs(c1.stock/c1.final-c2.stock/c2.final)>.01:
logging.warning("Dispense of %.1ful of %s@%.2fx into %.1ful of %s@%.2fx does not equalize concentrations"%(volume,src.name,src.conc.dilutionneeded(),self.volume,self.name,self.conc.dilutionneeded()))
#assert abs(c1.stock/c1.final-c2.stock/c2.final)<.01
self.conc=None
else:
self.conc=Concentration(c1.stock/c1.final,1.0,'x') # Since there are multiple ingredients express concentration as x
# Set to not mixed after second ingredient added
if self.volume>0:
self.lastMixed=None
self.wellMixed=False
if src.hasBeads and src.plate.curloc!="Magnet":
#print "Set %s to have beads since %s does\n"%(self.name,src.name)
self.hasBeads=True
self.volume=self.volume+volume
self.emptied=False
#self.addhistory("%06x %s"%(self.getHash(w)&0xffffff,src.name),volume,tipMask)
self.addhistory(src.name,volume,tipMask)
self.addingredients(src,volume)
import worklist
import plate
#aspirate(1,"LC",[1,3,4],1,2,3,"wells")
plate1=plate.Plate("Samples",4,3,12,8)
worklist.aspirate(7,['B3','D3','E3'],"Water",[10,20,30],plate1)
worklist.aspirate(7,['B4','D4','F4'],"Water",[10,20,30],plate1)
worklist.aspirate(1,['B1'],"Water",[10],plate1)
worklist.dispense(2,['B1'],"Water",[10],plate1)
worklist.mix(2,['B1'],"Water",[10],plate1,7)
worklist.vector("ROMAVector",plate1,worklist.SAFETOEND,True,worklist.OPEN,worklist.CLOSE)
worklist.execute("python test",True,"result")
worklist.userprompt("Script done")
worklist.dump()
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
def dispense(self, tipMask, volume, src):
self.evapcheck('dispense')
if self.plate.curloc == 'PTC':
logging.error("Dispense to PTC!, loc=(%d,%d)" %
(self.plate.grid, self.plate.pos))
if volume < 0.1:
logging.warning("attempt to dispense only %.1f ul to %s ignored" %
(volume, self.name))
return
if self.volume + volume < MINDEPOSITVOLUME:
logging.warning(
"Dispense of %.1ful into %s results in total of %.1ful which is less than minimum deposit volume of %.1f ul"
% (volume, self.name, self.volume + volume, MINDEPOSITVOLUME))
#well=[self.well if self.well!=None else 2**(tipMask-1)-1 ]
well = [self.well if self.well != None else int(math.log(tipMask, 2))]
if self.well is None:
logging.warning(
"Dispense with well is None, not sure what right logic is..., using well=%d"
% well[0])
if self.volume + volume > self.plate.maxVolume:
logging.error(
"Dispense of %.1ful into %s results in total of %.1ful which is more than the maximum volume of %.1f ul"
% (volume, self.name, self.volume + volume,
self.plate.maxVolume))
if self.hasBeads and self.plate.curloc == "Magnet":
worklist.dispense(tipMask, well, self.beadsLC, volume, self.plate)
elif self.volume >= MINLIQUIDDETECTVOLUME:
worklist.dispense(tipMask, well, self.inliquidLC, volume,
self.plate)
elif self.volume + volume >= MINSIDEDISPENSEVOLUME:
worklist.dispense(tipMask, well, self.bottomSideLC, volume,
self.plate)
else:
worklist.dispense(tipMask, well, self.bottomLC, volume, self.plate)
# Assume we're diluting the contents
if self.conc is None and src.conc is None:
pass
elif src.conc is None or volume == 0:
if self.volume == 0:
self.conc = None
else:
self.conc = self.conc.dilute(
(self.volume + volume) / self.volume)
elif self.conc is None or self.volume == 0 or self.conc.final is None or src.conc.final is None:
self.conc = src.conc.dilute((self.volume + volume) / volume)
else:
# Both have concentrations, they should match
c1 = self.conc.dilute((self.volume + volume) / self.volume)
c2 = src.conc.dilute((self.volume + volume) / volume)
if abs(c1.stock / c1.final - c2.stock / c2.final) > .01:
logging.warning(
"Dispense of %.1ful of %s@%.2fx into %.1ful of %s@%.2fx does not equalize concentrations"
% (volume, src.name, src.conc.dilutionneeded(),
self.volume, self.name, self.conc.dilutionneeded()))
#assert abs(c1.stock/c1.final-c2.stock/c2.final)<.01
self.conc = None
else:
self.conc = Concentration(
c1.stock / c1.final, 1.0, 'x'
) # Since there are multiple ingredients express concentration as x
# Set to not mixed after second ingredient added
if self.volume > 0:
self.lastMixed = None
self.wellMixed = False
if src.hasBeads and src.plate.curloc != "Magnet":
#print "Set %s to have beads since %s does\n"%(self.name,src.name)
self.hasBeads = True
self.volume = self.volume + volume
self.emptied = False
#self.addhistory("%06x %s"%(self.getHash(w)&0xffffff,src.name),volume,tipMask)
self.addhistory(src.name, volume, tipMask)
self.addingredients(src, volume)
import worklist
import plate
#aspirate(1,"LC",[1,3,4],1,2,3,"wells")
plate1 = plate.Plate("Samples", 4, 3, 12, 8)
worklist.aspirate(7, ['B3', 'D3', 'E3'], "Water", [10, 20, 30], plate1)
worklist.aspirate(7, ['B4', 'D4', 'F4'], "Water", [10, 20, 30], plate1)
worklist.aspirate(1, ['B1'], "Water", [10], plate1)
worklist.dispense(2, ['B1'], "Water", [10], plate1)
worklist.mix(2, ['B1'], "Water", [10], plate1, 7)
worklist.vector("ROMAVector", plate1, worklist.SAFETOEND, True, worklist.OPEN,
worklist.CLOSE)
worklist.execute("python test", True, "result")
worklist.userprompt("Script done")
worklist.dump()
