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
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)
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 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 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)
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()