def dispose(self, volume, src, mix=False, getDITI=True, dropDITI=True):
'Dispose of a given volume by aspirating and not dispensing (will go to waste during next wash)'
if self.ptcrunning and src.plate==decklayout.SAMPLEPLATE:
self.waitpgm()
if volume>self.MAXVOLUME:
reuseTip=False # Since we need to wash to get rid of it
print "Splitting large transfer of %.1f ul into smaller chunks < %.1f ul "%(volume,self.MAXVOLUME),
if reuseTip:
print "with tip reuse"
else:
print "without tip reuse"
self.dispose(self.MAXVOLUME,src,mix,getDITI,dropDITI)
self.dispose(volume-self.MAXVOLUME,src,False,getDITI,dropDITI)
return
cmt="Remove and dispose of %.1f ul from %s"%(volume, src.name)
ditivolume=volume+src.inliquidLC.singletag
if mix and not src.isMixed():
cmt=cmt+" with src mix"
ditivolume=max(ditivolume,src.volume)
if self.useDiTis:
tipMask=4
if getDITI:
worklist.getDITI(tipMask&self.DITIMASK,ditivolume)
else:
tipMask=self.cleantip()
#print "*",cmt
worklist.comment(cmt)
if mix and not src.isMixed():
src.mix(tipMask)
src.aspirate(tipMask,volume)
if self.useDiTis and dropDITI:
worklist.dropDITI(tipMask&self.DITIMASK,decklayout.WASTE)
def multitransfer(self, volumes, src, dests,mix=(True,False),getDITI=True,dropDITI=True,ignoreContents=False,extraFrac=0.05):
'Multi pipette from src to multiple dest. mix is (src,dest) mixing -- only mix src if needed though'
#print "multitransfer(",volumes,",",src,",",dests,",",mix,",",getDITI,",",dropDITI,")"
if self.ptcrunning and (src.plate==decklayout.SAMPLEPLATE or len([1 for d in dests if d.plate==decklayout.SAMPLEPLATE])>0):
self.waitpgm()
if isinstance(volumes,(int,long,float)):
# Same volume for each dest
volumes=[volumes for i in range(len(dests))]
assert len(volumes)==len(dests)
# if len([d.volume for d in dests if d.conc!=None])==0:
if len([dests[i].volume for i in range(0,len(dests)) if dests[i].conc != None and volumes[i]>0.01])==0:
maxval=0
else:
maxval=max([dests[i].volume for i in range(0,len(dests)) if dests[i].conc != None and volumes[i]>0.01])
# maxval=max([d.volume for d in dests if d.conc != None])
#print "volumes=",[d.volume for d in dests],", conc=",[str(d.conc) for d in dests],", maxval=",maxval
if not mix[1] and len(volumes)>1 and ( maxval<.01 or ignoreContents):
if sum(volumes)*(1+extraFrac)>self.MAXVOLUME:
#print "sum(volumes)=%.1f, MAXVOL=%.1f"%(sum(volumes),self.MAXVOLUME)
for i in range(1,len(volumes)):
if sum(volumes[0:i+1])*(1+extraFrac)>self.MAXVOLUME:
destvol=max([d.volume for d in dests[0:i]])
reuseTip=destvol<=0
# print "Splitting multi with total volume of %.1f ul into smaller chunks < %.1f ul after %d dispenses "%(sum(volumes),self.MAXVOLUME,i),
# if reuseTip:
# print "with tip reuse"
# else:
# print "without tip reuse"
self.multitransfer(volumes[0:i],src,dests[0:i],mix,getDITI,not reuseTip,extraFrac=extraFrac)
self.multitransfer(volumes[i:],src,dests[i:],(False,mix[1]),not reuseTip,dropDITI,extraFrac=extraFrac)
return
if self.useDiTis:
tipMask=4
if getDITI:
ditivol=sum(volumes)*(1+extraFrac)+src.inliquidLC.multicond+src.inliquidLC.multiexcess
worklist.getDITI(tipMask&self.DITIMASK,min(self.MAXVOLUME,ditivol),True,True)
else:
tipMask=self.cleantip()
cmt="Multi-add %s to samples %s"%(src.name,",".join("%s[%.1f]"%(dests[i].name,volumes[i]) for i in range(len(dests))))
#print "*",cmt
worklist.comment(cmt)
if mix[0] and not src.isMixed():
if src.plate==decklayout.SAMPLEPLATE or src.plate==decklayout.DILPLATE:
self.shakeSamples([src])
else:
src.mix(tipMask)
src.aspirate(tipMask,sum(volumes)*(1+extraFrac),True) # Aspirate extra
for i in range(len(dests)):
if volumes[i]>0.01:
dests[i].dispense(tipMask,volumes[i],src)
if self.useDiTis and dropDITI:
worklist.dropDITI(tipMask&self.DITIMASK,decklayout.WASTE)
else:
for i in range(len(dests)):
if volumes[i]>0.01:
self.transfer(volumes[i],src,dests[i],(mix[0] and i==0,mix[1]),getDITI,dropDITI)
def transfer(self,
volume,
src,
dest,
mix=(True, False),
getDITI=True,
dropDITI=True):
if self.ptcrunning and (src.plate == decklayout.SAMPLEPLATE
or dest.plate == decklayout.SAMPLEPLATE) > 0:
self.waitpgm()
if volume > self.MAXVOLUME:
destvol = dest.volume
reuseTip = destvol <= 0
print "Splitting large transfer of %.1f ul into smaller chunks < %.1f ul " % (
volume, self.MAXVOLUME),
if reuseTip:
print "with tip reuse"
else:
print "without tip reuse"
self.transfer(self.MAXVOLUME, src, dest, mix, getDITI, False)
self.transfer(volume - self.MAXVOLUME, src, dest,
(mix[0] and not reuseTip, mix[1]), False, dropDITI)
return
cmt = "Add %.1f ul of %s to %s" % (volume, src.name, dest.name)
ditivolume = volume + src.inliquidLC.singletag
if mix[0] and not src.isMixed():
cmt = cmt + " with src mix"
ditivolume = max(ditivolume, src.volume)
if mix[1] and dest.volume > 0 and not src.isMixed():
cmt = cmt + " with dest mix"
ditivolume = max(ditivolume, volume + dest.volume)
# print "Mix volume=%.1f ul"%(ditivolume)
if self.useDiTis:
tipMask = 4
if getDITI:
worklist.getDITI(tipMask & self.DITIMASK, ditivolume)
else:
tipMask = self.cleantip()
#print "*",cmt
worklist.comment(cmt)
if mix[0] and not src.isMixed():
if src.plate == decklayout.SAMPLEPLATE or src.plate == decklayout.DILPLATE:
self.shakeSamples([src])
else:
src.mix(tipMask)
src.aspirate(tipMask, volume)
dest.dispense(tipMask, volume, src)
if mix[1]:
dest.mix(tipMask, True)
if self.useDiTis and dropDITI:
worklist.dropDITI(tipMask & self.DITIMASK, decklayout.WASTE)
def transfer(self, volume, src, dest, mix=(True,False), getDITI=True, dropDITI=True):
if self.ptcrunning and (src.plate==decklayout.SAMPLEPLATE or dest.plate==decklayout.SAMPLEPLATE)>0:
self.waitpgm()
if volume>self.MAXVOLUME:
destvol=dest.volume
reuseTip=destvol<=0
msg="Splitting large transfer of %.1f ul into smaller chunks < %.1f ul "%(volume,self.MAXVOLUME)
if reuseTip:
msg+= "with tip reuse"
else:
msg+= "without tip reuse"
logging.notice(msg)
self.transfer(self.MAXVOLUME,src,dest,mix,getDITI,False)
self.transfer(volume-self.MAXVOLUME,src,dest,(mix[0] and not reuseTip,mix[1]),False,dropDITI)
return
cmt="Add %.1f ul of %s to %s"%(volume, src.name, dest.name)
ditivolume=volume+src.inliquidLC.singletag
if mix[0] and not src.isMixed():
cmt=cmt+" with src mix"
ditivolume=max(ditivolume,src.volume)
if mix[1] and dest.volume>0 and not src.isMixed():
cmt=cmt+" with dest mix"
ditivolume=max(ditivolume,volume+dest.volume)
# print "Mix volume=%.1f ul"%(ditivolume)
if mix[0] and not src.isMixed() and (src.plate==decklayout.SAMPLEPLATE or src.plate==decklayout.DILPLATE):
worklist.comment("shaking for src mix of "+src.name)
self.shakeSamples([src]) # Need to do this before allocating a tip since washing during this will modify the tip clean states
if self.useDiTis:
tipMask=4
if getDITI:
worklist.getDITI(tipMask&self.DITIMASK,ditivolume)
else:
tipMask=self.cleantip()
#print "*",cmt
worklist.comment(cmt)
if mix[0] and (not src.isMixed() or not src.wellMixed):
if (src.plate==decklayout.SAMPLEPLATE or src.plate==decklayout.DILPLATE):
logging.notice("Forcing pipette mix of "+src.name)
worklist.comment("pipette mix for src mix of "+src.name)
src.mix(tipMask) # Manual mix (after allocating a tip for this)
src.aspirate(tipMask,volume)
dest.dispense(tipMask,volume,src)
if mix[1]:
dest.mix(tipMask,True)
if self.useDiTis and dropDITI:
worklist.dropDITI(tipMask&self.DITIMASK,decklayout.WASTE)
def transfer(self, volume, src, dest, mix=(True,False), getDITI=True, dropDITI=True):
if self.ptcrunning and (src.plate==decklayout.SAMPLEPLATE or dest.plate==decklayout.SAMPLEPLATE)>0:
self.waitpgm()
if volume>self.MAXVOLUME:
destvol=dest.volume
reuseTip=destvol<=0
print "Splitting large transfer of %.1f ul into smaller chunks < %.1f ul "%(volume,self.MAXVOLUME),
if reuseTip:
print "with tip reuse"
else:
print "without tip reuse"
self.transfer(self.MAXVOLUME,src,dest,mix,getDITI,False)
self.transfer(volume-self.MAXVOLUME,src,dest,(mix[0] and not reuseTip,mix[1]),False,dropDITI)
return
cmt="Add %.1f ul of %s to %s"%(volume, src.name, dest.name)
ditivolume=volume+src.inliquidLC.singletag
if mix[0] and not src.isMixed():
cmt=cmt+" with src mix"
ditivolume=max(ditivolume,src.volume)
if mix[1] and dest.volume>0 and not src.isMixed():
cmt=cmt+" with dest mix"
ditivolume=max(ditivolume,volume+dest.volume)
# print "Mix volume=%.1f ul"%(ditivolume)
if self.useDiTis:
tipMask=4
if getDITI:
worklist.getDITI(tipMask&self.DITIMASK,ditivolume)
else:
tipMask=self.cleantip()
#print "*",cmt
worklist.comment(cmt)
if mix[0] and not src.isMixed():
if src.plate==decklayout.SAMPLEPLATE or src.plate==decklayout.DILPLATE:
self.shakeSamples([src])
else:
src.mix(tipMask)
src.aspirate(tipMask,volume)
dest.dispense(tipMask,volume,src)
if mix[1]:
dest.mix(tipMask,True)
if self.useDiTis and dropDITI:
worklist.dropDITI(tipMask&self.DITIMASK,decklayout.WASTE)
def dispose(self, volume, src, mix=False, getDITI=True, dropDITI=True):
'Dispose of a given volume by aspirating and not dispensing (will go to waste during next wash)'
if self.ptcrunning and src.plate == decklayout.SAMPLEPLATE:
self.waitpgm()
if volume > self.MAXVOLUME:
reuseTip = False # Since we need to wash to get rid of it
msg = "Splitting large transfer of %.1f ul into smaller chunks < %.1f ul " % (
volume, self.MAXVOLUME),
if reuseTip:
msg += "with tip reuse"
else:
msg += "without tip reuse"
logging.notice(msg)
self.dispose(self.MAXVOLUME, src, mix, getDITI, dropDITI)
self.dispose(volume - self.MAXVOLUME, src, False, getDITI,
dropDITI)
return
cmt = "Remove and dispose of %.1f ul from %s" % (volume, src.name)
ditivolume = volume + src.inliquidLC.singletag
if mix and not src.isMixed():
cmt = cmt + " with src mix"
ditivolume = max(ditivolume, src.volume)
if self.useDiTis:
tipMask = 4
if getDITI:
worklist.getDITI(tipMask & self.DITIMASK, ditivolume)
else:
tipMask = self.cleantip()
#print "*",cmt
worklist.comment(cmt)
if mix and not src.isMixed():
src.mix(tipMask)
src.aspirate(tipMask, volume)
if self.useDiTis and dropDITI:
worklist.dropDITI(tipMask & self.DITIMASK, decklayout.WASTE)
def multitransfer(self,
volumes,
src,
dests,
mix=(True, False),
getDITI=True,
dropDITI=True,
ignoreContents=False,
extraFrac=0.05):
'Multi pipette from src to multiple dest. mix is (src,dest) mixing -- only mix src if needed though'
#print "multitransfer(",volumes,",",src,",",dests,",",mix,",",getDITI,",",dropDITI,")"
if self.ptcrunning and (src.plate == decklayout.SAMPLEPLATE or len(
[1 for d in dests if d.plate == decklayout.SAMPLEPLATE]) > 0):
self.waitpgm()
if isinstance(volumes, (int, long, float)):
# Same volume for each dest
volumes = [volumes for i in range(len(dests))]
assert len(volumes) == len(dests)
# if len([d.volume for d in dests if d.conc!=None])==0:
if len([
dests[i].volume for i in range(0, len(dests))
if dests[i].conc != None and volumes[i] > 0.01
]) == 0:
maxval = 0
else:
maxval = max([
dests[i].volume for i in range(0, len(dests))
if dests[i].conc != None and volumes[i] > 0.01
])
# maxval=max([d.volume for d in dests if d.conc != None])
#print "volumes=",[d.volume for d in dests],", conc=",[str(d.conc) for d in dests],", maxval=",maxval
if not mix[1] and len(volumes) > 1 and (maxval < .01
or ignoreContents):
if sum(volumes) * (1 + extraFrac) > self.MAXVOLUME:
#print "sum(volumes)=%.1f, MAXVOL=%.1f"%(sum(volumes),self.MAXVOLUME)
for i in range(1, len(volumes)):
if sum(volumes[0:i + 1]) * (1 +
extraFrac) > self.MAXVOLUME:
destvol = max([d.volume for d in dests[0:i]])
reuseTip = destvol <= 0
# print "Splitting multi with total volume of %.1f ul into smaller chunks < %.1f ul after %d dispenses "%(sum(volumes),self.MAXVOLUME,i),
# if reuseTip:
# print "with tip reuse"
# else:
# print "without tip reuse"
self.multitransfer(volumes[0:i],
src,
dests[0:i],
mix,
getDITI,
not reuseTip,
extraFrac=extraFrac)
self.multitransfer(volumes[i:],
src,
dests[i:], (False, mix[1]),
not reuseTip,
dropDITI,
extraFrac=extraFrac)
return
if self.useDiTis:
tipMask = 4
if getDITI:
ditivol = sum(volumes) * (
1 + extraFrac
) + src.inliquidLC.multicond + src.inliquidLC.multiexcess
worklist.getDITI(tipMask & self.DITIMASK,
min(self.MAXVOLUME, ditivol), True, True)
else:
tipMask = self.cleantip()
cmt = "Multi-add %s to samples %s" % (src.name, ",".join(
"%s[%.1f]" % (dests[i].name, volumes[i])
for i in range(len(dests))))
#print "*",cmt
worklist.comment(cmt)
if mix[0] and not src.isMixed():
if src.plate == decklayout.SAMPLEPLATE or src.plate == decklayout.DILPLATE:
self.shakeSamples([src])
else:
src.mix(tipMask)
src.aspirate(tipMask,
sum(volumes) * (1 + extraFrac),
True) # Aspirate extra
for i in range(len(dests)):
if volumes[i] > 0.01:
dests[i].dispense(tipMask, volumes[i], src)
if self.useDiTis and dropDITI:
worklist.dropDITI(tipMask & self.DITIMASK, decklayout.WASTE)
else:
for i in range(len(dests)):
if volumes[i] > 0.01:
self.transfer(volumes[i], src, dests[i],
(mix[0] and i == 0, mix[1]), getDITI,
dropDITI)
def transfer(self,
volume,
src,
dest,
mix=(True, False),
getDITI=True,
dropDITI=True):
if self.ptcrunning and (src.plate == decklayout.SAMPLEPLATE
or dest.plate == decklayout.SAMPLEPLATE) > 0:
self.waitpgm()
if volume > self.MAXVOLUME:
destvol = dest.volume
reuseTip = destvol <= 0
msg = "Splitting large transfer of %.1f ul into smaller chunks < %.1f ul " % (
volume, self.MAXVOLUME)
if reuseTip:
msg += "with tip reuse"
else:
msg += "without tip reuse"
logging.notice(msg)
self.transfer(self.MAXVOLUME, src, dest, mix, getDITI, False)
self.transfer(volume - self.MAXVOLUME, src, dest,
(mix[0] and not reuseTip, mix[1]), False, dropDITI)
return
cmt = "Add %.1f ul of %s to %s" % (volume, src.name, dest.name)
ditivolume = volume + src.inliquidLC.singletag
if mix[0] and not src.isMixed():
cmt = cmt + " with src mix"
ditivolume = max(ditivolume, src.volume)
if mix[1] and dest.volume > 0 and not src.isMixed():
cmt = cmt + " with dest mix"
ditivolume = max(ditivolume, volume + dest.volume)
# print "Mix volume=%.1f ul"%(ditivolume)
if mix[0] and not src.isMixed() and (
src.plate == decklayout.SAMPLEPLATE
or src.plate == decklayout.DILPLATE):
worklist.comment("shaking for src mix of " + src.name)
self.shakeSamples(
[src]
) # Need to do this before allocating a tip since washing during this will modify the tip clean states
if self.useDiTis:
tipMask = 4
if getDITI:
worklist.getDITI(tipMask & self.DITIMASK, ditivolume)
else:
tipMask = self.cleantip()
#print "*",cmt
worklist.comment(cmt)
if mix[0] and (not src.isMixed() or not src.wellMixed):
if (src.plate == decklayout.SAMPLEPLATE
or src.plate == decklayout.DILPLATE):
logging.notice("Forcing pipette mix of " + src.name)
worklist.comment("pipette mix for src mix of " + src.name)
src.mix(tipMask) # Manual mix (after allocating a tip for this)
src.aspirate(tipMask, volume)
dest.dispense(tipMask, volume, src)
if mix[1]:
dest.mix(tipMask, True)
if self.useDiTis and dropDITI:
worklist.dropDITI(tipMask & self.DITIMASK, decklayout.WASTE)