def dispense(self, tip, reactive, vol=None): # OK coordinate with robot
"""
Dispense vol with ONE tip to reactive
:param tip:
:param reactive:
:param vol:
"""
vol = vol or reactive.minVol() # really ?? # todo: revise !!
reactive.autoselect() # reactive.labware.selectOnly([reactive.pos])
v = [0] * self.robot.curArm().nTips
v[tip] = vol
Itr.dispense(Rbt.tipMask[tip], reactive.defLiqClass, v, reactive.labware).exec()
def dispensemultiwells(self, tips, liq_class, labware, vol):
""" One dispense of multitip in multiwell with different vol
:param tips:
:param liq_class:
:param labware:
:param vol:
"""
if not isinstance(vol, list):
vol = [vol] * tips
om = Rbt.tipsMask[tips]
# Rbt.Robot.current.curArm().dispense(vol, om)
Itr.dispense(om, liq_class, vol, labware).exec()
def dispensemultiwells(tips, liq_class, labware, vol):
""" One dispense of multitip in multiwell with different vol
:param tips:
:param liq_class:
:param labware:
:param vol:
"""
if not isinstance(vol, list):
vol = [vol] * tips
om = Rbt.tipsMask[tips]
# Rbt.Robot.current.curArm().dispense(vol, om)
Itr.dispense(om, liq_class, vol, labware).exec()
def dispense(tip, reactive, vol=None): # OK coordinate with robot
"""
Dispense vol with ONE tip to reactive
:param tip:
:param reactive:
:param vol:
"""
vol = vol or reactive.minVol() # really ??
reactive.autoselect() # reactive.labware.selectOnly([reactive.pos])
v = [0] * Rbt.Robot.current.curArm().nTips
v[tip] = vol
Itr.dispense(Rbt.tipMask[tip], reactive.defLiqClass, v,
reactive.labware).exec()
def multidispense_in_replicas(self, tip, reactive, vol):
""" Multi-dispense of the content of ONE tip into the reactive replicas
:param tip:
:param reactive:
:param vol:
"""
assert isinstance(vol, list)
re = reactive.Replicas
assert len(vol) <= len(re)
for v, w in zip(vol, re): # zip continues until the shortest iterable is exhausted
Itr.dispense(Rbt.tipMask[tip], self.robot.curArm().Tips[tip].origin.reactive.defLiqClass,
# reactive.defLiqClass,
v, w.labware.selectOnly([w.offset])).exec()
def multidispense_in_replicas(tip, reactive, vol):
""" Multi-dispense of the content of ONE tip into the reactive replicas
:param tip:
:param reactive:
:param vol:
"""
assert isinstance(vol, list)
re = reactive.Replicas
assert len(vol) == len(re)
for v, w in zip(vol, re):
Itr.dispense(
Rbt.tipMask[tip],
Rbt.Robot.current.curArm().Tips[tip].origin.reactive.defLiqClass,
# reactive.defLiqClass,
v,
w.labware.selectOnly([w.offset])).exec()
def waste(self, from_labware_region=None, using_liquid_class=None, volume=None, to_waste_labware=None, optimize=True):
"""
:param from_labware_region:
:param using_liquid_class:
:param volume:
:param to_waste_labware:
:param optimize:
:return:
"""
to_waste_labware = to_waste_labware or self.worktable.def_WashWaste
assert isinstance(from_labware_region, Lab.Labware), 'A Labware expected in from_labware_region to transfer'
if not volume or volume< 0.0 : volume = 0.0
assert isinstance(volume, (int, float))
oriSel = from_labware_region.selected()
nt = self.robot.curArm().nTips # the number of tips to be used in each cycle of pippeting
if not oriSel:
oriSel = range(Rtv.NumOfSamples)
if optimize:
oriSel = from_labware_region.parallelOrder(nt, oriSel)
NumSamples = len(oriSel)
SampleCnt = NumSamples
if nt > SampleCnt:
nt = SampleCnt
tm = Rbt.tipsMask[nt]
nt = to_waste_labware.autoselect(maxTips=nt)
mV = self.worktable.def_DiTi.maxVol # todo revise !! What tip tp use !
Rest = 50 # the volume we cannot more aspire with liquid detection, to small, collisions
RestPlus = 50
CtrVol = 0.5
if volume:
v = volume
else:
v = from_labware_region.Wells[oriSel[0]].vol
Asp = Itr.aspirate(tm, Te_Mag_LC, volume, from_labware_region)
# Asp = Itr.aspirate(tm, using_liquid_class[0], volume, from_labware_region)
Dst = Itr.dispense(tm, using_liquid_class, volume, to_waste_labware)
# Ctr = Itr.moveLiha(Itr.moveLiha.y_move, Itr.moveLiha.z_start, 3.0, 2.0, tm, from_labware_region)
lf = from_labware_region
msg = "Waste: {v:.1f} µL of {n:s}".format(v=v, n=lf.label)
with group(msg):
msg += " [grid:{fg:d} site:{fs:d}] in order:".format(fg=lf.location.grid, fs=lf.location.site+1) \
+ str([i+1 for i in oriSel])
Itr.comment(msg).exec()
while SampleCnt:
curSample = NumSamples - SampleCnt
if nt > SampleCnt:
nt = SampleCnt
tm = Rbt.tipsMask[nt]
Asp.tipMask = tm
Dst.tipMask = tm
sel = oriSel[curSample:curSample + nt]
spl = range(curSample, curSample + nt)
Asp.labware.selectOnly(sel)
if volume:
r = volume # r: Waste_available yet; volume: to be Waste
else:
vols = [w.vol for w in Asp.labware.selected_wells()]
r_min, r_max = min(vols), max(vols)
assert r_min == r_max
r = r_max
if not using_liquid_class:
if sel:
Dst.liquidClass = Asp.labware.selected_wells()[0].reactive.defLiqClass
with self.tips(tm, drop=True, preserve=False, selected_samples=spl):
while r > Rest: # dont aspire Rest with these Liq Class (Liq Detect)
dV = r if r < mV else mV
if dV < Rest: break # ??
dV -= Rest # the last Rest uL have to be aspired with the other Liq Class
Asp.volume = dV # with Liq Class with Detect: ">> AVR-Serum 1000 << 365"
Dst.volume = dV
Asp.liquidClass = Te_Mag_LC # ">> AVR-Serum 1000 << 365" # "No Liq Detect"
Asp.exec()
Asp.volume = CtrVol
Asp.liquidClass = Te_Mag_Centre
with self.tips(allow_air=CtrVol):
Asp.exec()
if dV + Rest + RestPlus + 2*CtrVol > mV:
Dst.exec()
r -= dV
Dst.volume = 0
else:
break
Asp.volume = Rest
Asp.liquidClass = Te_Mag_Rest # ">> AVR-Serum 1000 << 367" # "No Liq Detect"
with self.tips(allow_air=Rest):
Asp.exec()
Asp.volume = CtrVol
Asp.liquidClass = Te_Mag_Force_Centre
with self.tips(allow_air=CtrVol):
Asp.exec()
Asp.volume = RestPlus
Asp.liquidClass = Te_Mag_RestPlus # ">> AVR-Serum 1000 << 369" # "No Liq Detect"
with self.tips(allow_air=RestPlus):
Asp.exec()
#Ctr.exec()
Asp.volume = CtrVol
Asp.liquidClass = Te_Mag_Force_Centre
Dst.volume += Rest + RestPlus
with self.tips(allow_air=CtrVol):
Asp.exec()
with self.tips(allow_air=Rest + RestPlus):
Dst.exec()
SampleCnt -= nt
Asp.labware.selectOnly(oriSel)
Itr.wash_tips(wasteVol=4).exec()
return oriSel
def transfer(self, from_labware_region, to_labware_region, volume, using_liquid_class=None,
optimizeFrom=True, optimizeTo=True, NumSamples=None):
"""
:param NumSamples: Priorized !!!! If true reset the selection
:param from_reactive: Reagent to spread
:param to_labware_region: Labware in which the destine well are selected
:param volume: if not, volume is set from the default of the source reactive
:param optimize: minimize zigzag of multipippeting
"""
assert isinstance(from_labware_region, Lab.Labware), 'A Labware expected in from_labware_region to transfer'
assert isinstance(to_labware_region, Lab.Labware), 'A Labware expected in to_labware_region to transfer'
# assert isinstance(using_liquid_class, tuple)
nt = self.robot.curArm().nTips # the number of tips to be used in each cycle of pippeting
if NumSamples: # OK? select convenient def
oriSel = range(NumSamples)
dstSel = range(NumSamples)
else:
oriSel = to_labware_region.selected()
dstSel = from_labware_region.selected()
if not dstSel:
if not oriSel:
oriSel = range(Rtv.NumOfSamples)
dstSel = range(Rtv.NumOfSamples)
else:
dstSel = oriSel
else:
if not oriSel:
oriSel = dstSel
else:
l = min(len(oriSel), len(dstSel)) # todo transfer the minimun of the selected ???? Best reise error
oriSel = oriSel[:l]
dstSel = dstSel[:l]
if optimizeFrom: oriSel = from_labware_region.parallelOrder(nt, oriSel)
if optimizeTo: dstSel = to_labware_region.parallelOrder(nt, dstSel)
NumSamples = len(dstSel)
SampleCnt = NumSamples
assert isinstance(volume, (int, float))
if nt > SampleCnt: nt = SampleCnt
lf = from_labware_region
lt = to_labware_region
Asp = Itr.aspirate(Rbt.tipsMask[nt], volume=volume, labware=from_labware_region)
Dst = Itr.dispense(Rbt.tipsMask[nt], volume=volume, labware=to_labware_region)
msg = "Transfer: {v:.1f} µL of {n:s}".format(v=volume, n=lf.label)
with group(msg):
msg += " [grid:{fg:d} site:{fs:d}] in order {oo:s} into {to:s}[grid:{tg:d} site:{ts:d}] in order {do:s}:" \
.format(fg =lf.location.grid,
fs =lf.location.site+1,
oo =str([i+1 for i in oriSel]),
do =str([i+1 for i in dstSel]),
to =lt.label,
tg =lt.location.grid,
ts =lt.location.site+1)
Itr.comment(msg).exec()
while SampleCnt:
curSample = NumSamples - SampleCnt
if nt > SampleCnt:
nt = SampleCnt
Asp.tipMask = Rbt.tipsMask[nt]
Dst.tipMask = Rbt.tipsMask[nt]
src = oriSel[curSample:curSample + nt]
trg = dstSel[curSample:curSample + nt]
spl = range(curSample, curSample + nt)
sw = Asp.labware.selected_wells()
if isinstance(using_liquid_class, tuple):
if using_liquid_class[0]:
Asp.liquidClass = using_liquid_class[0]
else:
Asp.liquidClass = sw[0].reactive.defLiqClass
if using_liquid_class[1]:
Dst.liquidClass = using_liquid_class[1]
else:
Dst.liquidClass = sw[0].reactive.defLiqClass
else:
Asp.liquidClass = sw[0].reactive.defLiqClass
Dst.liquidClass = sw[0].reactive.defLiqClass
with self.tips(Rbt.tipsMask[nt], selected_samples=spl): # todo what if volume > maxVol_tip ?
Asp.labware.selectOnly(src)
Asp.exec()
Dst.labware.selectOnly(trg)
Dst.exec()
for s, d in zip(Asp.labware.selected_wells(), Dst.labware.selected_wells()):
d.track = s.track
SampleCnt -= nt
Asp.labware.selectOnly(oriSel)
Dst.labware.selectOnly(dstSel)
return oriSel, dstSel
def waste(from_labware_region=None,
using_liquid_class=None,
volume=None,
to_waste_labware=None,
optimize=True):
"""
:param from_labware_region:
:param using_liquid_class:
:param volume:
:param to_waste_labware:
:param optimize:
:return:
"""
to_waste_labware = to_waste_labware or Lab.def_WashWaste
assert isinstance(
from_labware_region,
Lab.Labware), 'A Labware expected in from_labware_region to transfer'
if not volume or volume < 0.0: volume = 0.0
assert isinstance(volume, (int, float))
oriSel = from_labware_region.selected()
nt = Rbt.Robot.current.curArm(
).nTips # the number of tips to be used in each cycle of pippeting
if not oriSel:
oriSel = range(Rtv.NumOfSamples)
if optimize:
oriSel = from_labware_region.parallelOrder(nt, oriSel)
NumSamples = len(oriSel)
SampleCnt = NumSamples
if nt > SampleCnt:
nt = SampleCnt
tm = Rbt.tipsMask[nt]
nt = to_waste_labware.autoselect(maxTips=nt)
mV = Lab.def_DiTi.maxVol # todo revise !! What tip tp use !
Rest = 50 # the volume we cannot more aspire with liquid detection, to small, collisions
RestPlus = 50
CtrVol = 0.5
if volume:
v = volume
else:
v = from_labware_region.Wells[oriSel[0]].vol
Asp = Itr.aspirate(tm, Te_Mag_LC, volume, from_labware_region)
# Asp = Itr.aspirate(tm, using_liquid_class[0], volume, from_labware_region)
Dst = Itr.dispense(tm, using_liquid_class, volume, to_waste_labware)
# Ctr = Itr.moveLiha(Itr.moveLiha.y_move, Itr.moveLiha.z_start, 3.0, 2.0, tm, from_labware_region)
lf = from_labware_region
msg = "Waste: {v:.1f} µL of {n:s}".format(v=v, n=lf.label)
with group(msg):
msg += " [grid:{fg:d} site:{fs:d}] in order:".format(fg=lf.location.grid, fs=lf.location.site+1) \
+ str([i+1 for i in oriSel])
Itr.comment(msg).exec()
while SampleCnt:
curSample = NumSamples - SampleCnt
if nt > SampleCnt:
nt = SampleCnt
tm = Rbt.tipsMask[nt]
Asp.tipMask = tm
Dst.tipMask = tm
sel = oriSel[curSample:curSample + nt]
spl = range(curSample, curSample + nt)
Asp.labware.selectOnly(sel)
if volume:
r = volume # r: Waste_available yet; volume: to be Waste
else:
vols = [w.vol for w in Asp.labware.selected_wells()]
r_min, r_max = min(vols), max(vols)
assert r_min == r_max
r = r_max
if not using_liquid_class:
if sel:
Dst.liquidClass = Asp.labware.selected_wells(
)[0].reactive.defLiqClass
with tips(tm, drop=True, preserve=False, selected_samples=spl):
while r > Rest: # dont aspire Rest with these Liq Class (Liq Detect)
dV = r if r < mV else mV
if dV < Rest: break # ??
dV -= Rest # the last Rest uL have to be aspired with the other Liq Class
Asp.volume = dV # with Liq Class with Detect: ">> AVR-Serum 1000 << 365"
Dst.volume = dV
Asp.liquidClass = Te_Mag_LC # ">> AVR-Serum 1000 << 365" # "No Liq Detect"
Asp.exec()
Asp.volume = CtrVol
Asp.liquidClass = Te_Mag_Centre
with tips(allow_air=CtrVol):
Asp.exec()
if dV + Rest + RestPlus + 2 * CtrVol > mV:
Dst.exec()
r -= dV
Dst.volume = 0
else:
break
Asp.volume = Rest
Asp.liquidClass = Te_Mag_Rest # ">> AVR-Serum 1000 << 367" # "No Liq Detect"
with tips(allow_air=Rest):
Asp.exec()
Asp.volume = CtrVol
Asp.liquidClass = Te_Mag_Force_Centre
with tips(allow_air=CtrVol):
Asp.exec()
Asp.volume = RestPlus
Asp.liquidClass = Te_Mag_RestPlus # ">> AVR-Serum 1000 << 369" # "No Liq Detect"
with tips(allow_air=RestPlus):
Asp.exec()
#Ctr.exec()
Asp.volume = CtrVol
Asp.liquidClass = Te_Mag_Force_Centre
Dst.volume += Rest + RestPlus
with tips(allow_air=CtrVol):
Asp.exec()
with tips(allow_air=Rest + RestPlus):
Dst.exec()
SampleCnt -= nt
Asp.labware.selectOnly(oriSel)
Itr.wash_tips(wasteVol=4).exec()
return oriSel
def transfer(from_labware_region,
to_labware_region,
volume,
using_liquid_class=None,
optimizeFrom=True,
optimizeTo=True,
NumSamples=None):
"""
:param NumSamples: Priorized !!!! If true reset the selection
:param from_reactive: Reactive to spread
:param to_labware_region: Labware in which the destine well are selected
:param volume: if not, volume is set from the default of the source reactive
:param optimize: minimize zigzag of multipippeting
"""
assert isinstance(
from_labware_region,
Lab.Labware), 'A Labware expected in from_labware_region to transfer'
assert isinstance(
to_labware_region,
Lab.Labware), 'A Labware expected in to_labware_region to transfer'
# assert isinstance(using_liquid_class, tuple)
nt = Rbt.Robot.current.curArm(
).nTips # the number of tips to be used in each cycle of pippeting
if NumSamples: # OK? select convenient def
oriSel = range(NumSamples)
dstSel = range(NumSamples)
else:
oriSel = to_labware_region.selected()
dstSel = from_labware_region.selected()
if not dstSel:
if not oriSel:
oriSel = range(Rtv.NumOfSamples)
dstSel = range(Rtv.NumOfSamples)
else:
dstSel = oriSel
else:
if not oriSel:
oriSel = dstSel
else:
l = min(
len(oriSel), len(dstSel)
) # todo transfer the minimun of the selected ???? Best reise error
oriSel = oriSel[:l]
dstSel = dstSel[:l]
if optimizeFrom: oriSel = from_labware_region.parallelOrder(nt, oriSel)
if optimizeTo: dstSel = to_labware_region.parallelOrder(nt, dstSel)
NumSamples = len(dstSel)
SampleCnt = NumSamples
assert isinstance(volume, (int, float))
if nt > SampleCnt: nt = SampleCnt
lf = from_labware_region
lt = to_labware_region
Asp = Itr.aspirate(Rbt.tipsMask[nt],
volume=volume,
labware=from_labware_region)
Dst = Itr.dispense(Rbt.tipsMask[nt],
volume=volume,
labware=to_labware_region)
msg = "Transfer: {v:.1f} µL of {n:s}".format(v=volume, n=lf.label)
with group(msg):
msg += " [grid:{fg:d} site:{fs:d}] in order {oo:s} into {to:s}[grid:{tg:d} site:{ts:d}] in order {do:s}:" \
.format(fg=lf.location.grid, fs=lf.location.site+1, oo=str([i+1 for i in oriSel]),
do=str([i+1 for i in dstSel]), to=lt.label, tg=lt.location.grid, ts=lt.location.site+1)
Itr.comment(msg).exec()
while SampleCnt:
curSample = NumSamples - SampleCnt
if nt > SampleCnt:
nt = SampleCnt
Asp.tipMask = Rbt.tipsMask[nt]
Dst.tipMask = Rbt.tipsMask[nt]
src = oriSel[curSample:curSample + nt]
trg = dstSel[curSample:curSample + nt]
spl = range(curSample, curSample + nt)
sw = Asp.labware.selected_wells()
if isinstance(using_liquid_class, tuple):
if using_liquid_class[0]:
Asp.liquidClass = using_liquid_class[0]
else:
Asp.liquidClass = sw[0].reactive.defLiqClass
if using_liquid_class[1]:
Dst.liquidClass = using_liquid_class[1]
else:
Dst.liquidClass = sw[0].reactive.defLiqClass
else:
Asp.liquidClass = sw[0].reactive.defLiqClass
Dst.liquidClass = sw[0].reactive.defLiqClass
with tips(Rbt.tipsMask[nt], selected_samples=spl
): # todo what if volume > maxVol_tip ?
Asp.labware.selectOnly(src)
Asp.exec()
Dst.labware.selectOnly(trg)
Dst.exec()
for s, d in zip(Asp.labware.selected_wells(),
Dst.labware.selected_wells()):
d.track = s.track
SampleCnt -= nt
Asp.labware.selectOnly(oriSel)
Dst.labware.selectOnly(dstSel)
return oriSel, dstSel