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)
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 __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()
