def runpgm(self,pgm,duration,waitForCompletion=True,volume=10,hotlidmode="TRACKING",hotlidtemp=1):
if self.ptcrunning:
logging.error("Attempt to start a progam on PTC when it is already running")
if len(pgm)>8:
logging.error("PTC program name (%s) too long (max is 8 char)"%pgm)
# move to thermocycler
worklist.flushQueue()
self.lihahome()
cmt="run %s"%pgm
worklist.comment(cmt)
#print "*",cmt
worklist.pyrun("PTC\\ptclid.py OPEN")
self.moveplate(decklayout.SAMPLEPLATE,"PTC")
worklist.vector("Hotel 1 Lid",decklayout.HOTELPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
worklist.vector("PTC200lid",decklayout.PTCPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
worklist.romahome()
worklist.pyrun("PTC\\ptclid.py CLOSE")
# pgm="PAUSE30" # For debugging
assert hotlidmode=="TRACKING" or hotlidmode=="CONSTANT"
assert (hotlidmode=="TRACKING" and hotlidtemp>=0 and hotlidtemp<=45) or (hotlidmode=="CONSTANT" and hotlidtemp>30)
worklist.pyrun('PTC\\ptcrun.py %s CALC %s,%d %d'%(pgm,hotlidmode,hotlidtemp,volume))
self.pgmStartTime=clock.pipetting
self.pgmEndTime=duration*60+clock.pipetting
self.ptcrunning=True
Sample.addallhistory("{%s}"%pgm,addToEmpty=False,onlyplate=decklayout.SAMPLEPLATE.name)
if waitForCompletion:
self.waitpgm()
def shake(self,plate,dur=60,speed=None,accel=5,returnPlate=True,samps=None,force=False):
if self.ptcrunning and plate==decklayout.SAMPLEPLATE:
self.waitpgm()
# Move the plate to the shaker, run for the given time, and bring plate back
allsamps=Sample.getAllOnPlate(plate)
if samps is None:
samps=allsamps
if all([x.isMixed() for x in samps]) and not force:
logging.notice( "No need to shake "+plate.name+", but doing so anyway.")
minspeed=0
maxspeed=2000
for x in samps:
(a,b)=x.getmixspeeds()
minspeed=max([a,minspeed])
maxspeed=min([b,maxspeed])
if speed is None:
if minspeed<maxspeed:
speed=max((maxspeed+minspeed)/2,maxspeed-50) # Mix as fast as safely possible (but always above minspeed)
else:
speed=maxspeed
if speed<minspeed-2 or speed>maxspeed+2:
others=""
for x in allsamps:
(a,b)=x.getmixspeeds()
if b<minspeed or a>maxspeed:
if a is not None and a>0:
others+=" {%s: %.1ful,G=%.2f%%,min=%.0f,max=%.0f}"%(x.name,x.volume,x.glycerolfrac()*100,a,b)
else:
others+=" {%s: %.1ful,G=%.2f%%,max=%.0f}"%(x.name,x.volume,x.glycerolfrac()*100,b)
logging.mixwarning("Mixing %s at %.0f RPM; minspeed(%.0f) > maxspeed(%.0f), limits=[%s]"%(plate.name,speed,minspeed,maxspeed,others))
else:
logging.notice("Mixing %s at %.0f RPM ( min RPM=%.0f, max RPM=%.f)"%(plate.name, speed, minspeed, maxspeed))
oldloc=plate.curloc
self.moveplate(plate,"Shaker",returnHome=False)
global __shakerActive
__shakerActive=True
worklist.pyrun("BioShake\\bioexec.py setElmLockPos")
worklist.pyrun("BioShake\\bioexec.py setShakeTargetSpeed%d"%speed)
worklist.pyrun("BioShake\\bioexec.py setShakeAcceleration%d"%accel)
worklist.pyrun("BioShake\\bioexec.py shakeOn")
self.starttimer()
Sample.shaken(plate.name,speed)
Sample.addallhistory("(S%d@%.0f)"%(dur,speed),onlyplate=plate.name)
self.waittimer(dur)
worklist.pyrun("BioShake\\bioexec.py shakeOff")
self.starttimer()
self.waittimer(accel+4)
worklist.pyrun("BioShake\\bioexec.py setElmUnlockPos")
__shakerActive=False
if returnPlate:
self.moveplate(plate,oldloc)
def moveplate(self,plate,dest="Home",returnHome=True):
if self.ptcrunning and plate==decklayout.SAMPLEPLATE:
self.waitpgm()
# move to given destination (one of "Home","Magnet","Shaker","PTC" )
if plate!=decklayout.SAMPLEPLATE and plate!=decklayout.DILPLATE:
print "Only able to move %s or %s plates, not %s"%(decklayout.SAMPLEPLATE.name,decklayout.DILPLATE.name,plate.name)
assert False
if plate.curloc==dest:
#print "Plate %s is already at %s"%(plate.name,dest)
return
#print "Move plate %s from %s to %s"%(plate.name,plate.curloc,dest)
worklist.flushQueue()
self.lihahome()
cmt="moveplate %s %s"%(plate.name,dest)
worklist.comment(cmt)
if plate.curloc=="Home":
worklist.vector(plate.vectorName,plate,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
elif plate.curloc=="Magnet":
worklist.vector("Magplate",decklayout.MAGPLATELOC,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
elif plate.curloc=="Shaker":
worklist.vector("Shaker",decklayout.SHAKERPLATELOC,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
elif plate.curloc=="PTC":
worklist.vector("PTC200",decklayout.PTCPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
else:
print "Plate %s is in unknown location: %s"%(plate.name,plate.curloc)
assert False
if dest=="Home":
plate.movetoloc(dest)
worklist.vector(plate.vectorName,plate,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
elif dest=="Magnet":
plate.movetoloc(dest,decklayout.MAGPLATELOC)
worklist.vector("Magplate",decklayout.MAGPLATELOC,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
elif dest=="Shaker":
plate.movetoloc(dest,decklayout.SHAKERPLATELOC)
worklist.vector("Shaker",decklayout.SHAKERPLATELOC,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
elif dest=="PTC":
plate.movetoloc(dest,decklayout.PTCPOS)
worklist.vector("PTC200",decklayout.PTCPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
else:
print "Attempt to move plate %s to unknown location: %s"%(plate.name,dest)
assert False
Sample.addallhistory("{->%s}"%dest,onlyplate=plate.name)
if returnHome:
worklist.romahome()
def runpgm(self,
pgm,
duration,
waitForCompletion=True,
volume=10,
hotlidmode="TRACKING",
hotlidtemp=1):
if self.ptcrunning:
logging.error(
"Attempt to start a progam on PTC when it is already running")
if len(pgm) > 8:
logging.error("PTC program name (%s) too long (max is 8 char)" %
pgm)
# move to thermocycler
worklist.flushQueue()
self.lihahome()
cmt = "run %s" % pgm
worklist.comment(cmt)
#print "*",cmt
worklist.pyrun("PTC\\ptclid.py OPEN")
self.moveplate(decklayout.SAMPLEPLATE, "PTC")
worklist.vector("Hotel 1 Lid", decklayout.HOTELPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.CLOSE)
worklist.vector("PTC200lid", decklayout.PTCPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.OPEN)
worklist.romahome()
worklist.pyrun("PTC\\ptclid.py CLOSE")
# pgm="PAUSE30" # For debugging
assert hotlidmode == "TRACKING" or hotlidmode == "CONSTANT"
assert (hotlidmode == "TRACKING" and hotlidtemp >= 0
and hotlidtemp <= 45) or (hotlidmode == "CONSTANT"
and hotlidtemp > 30)
worklist.pyrun('PTC\\ptcrun.py %s CALC %s,%d %d' %
(pgm, hotlidmode, hotlidtemp, volume))
self.pgmStartTime = clock.pipetting
self.pgmEndTime = duration * 60 + clock.pipetting
self.ptcrunning = True
Sample.addallhistory("{%s}" % pgm,
addToEmpty=False,
onlyplate=decklayout.SAMPLEPLATE.name,
type="ptc")
if waitForCompletion:
self.waitpgm()
def pause(self, duration):
self.starttimer()
self.waittimer(duration)
Sample.addallhistory("(%ds)" % duration)
def shake(self,
plate,
dur=60,
speed=None,
accel=5,
returnPlate=True,
samps=None):
if self.ptcrunning and plate == decklayout.SAMPLEPLATE:
self.waitpgm()
# Move the plate to the shaker, run for the given time, and bring plate back
allsamps = Sample.getAllOnPlate(plate)
if samps is None:
samps = allsamps
if all([x.isMixed() for x in samps]):
print "No need to shake ", plate
maxvol = max([x.volume for x in allsamps])
minvol = min([x.volume for x in samps if not x.isMixed()] + [200])
(minspeed, maxspeed) = plate.getmixspeeds(
minvol * 0.95, maxvol + 5) # Assume volumes could be off
if minspeed > maxspeed:
print "minspeed(", minspeed, ") > maxspeed (", maxspeed, ")"
if speed is None:
if minspeed < maxspeed:
speed = (maxspeed + minspeed) / 2
else:
speed = maxspeed
warned = False
if speed > maxspeed:
print "WARNING: %s plate contains wells with up to %.2f ul, which may spill at %d RPM: " % (
plate.name, maxvol, speed),
for x in samps:
tmp = plate.getmixspeeds(x.volume, x.volume)
if tmp[1] < speed:
print "%s[%.1ful, max=%.0f RPM] " % (x.name, x.volume,
tmp[1]),
print
warned = True
if globals.verbose and speed < minspeed:
print "NOTICE: %s plate contains unmixed wells that may not be mixed at %d RPM: " % (
plate.name, speed),
for x in samps:
if x.isMixed():
continue
tmp = plate.getmixspeeds(x.volume * 0.95, x.volume + 5)
if speed < tmp[0]:
print "%s[%.1ful, min=%.0f RPM, max=%.0f RPM] " % (
x.name, x.volume, tmp[0], tmp[1]),
print
warned = True
if warned or globals.verbose:
print " Mixing %s at %.0f RPM (min unmixed vol=%.0ful -> min RPM=%.0f; max vol=%.0ful -> max RPM=%.f)" % (
plate.name, speed, minvol, minspeed, maxvol, maxspeed)
oldloc = plate.curloc
self.moveplate(plate, "Shaker", returnHome=False)
global __shakerActive
__shakerActive = True
worklist.pyrun("BioShake\\bioexec.py setElmLockPos")
worklist.pyrun("BioShake\\bioexec.py setShakeTargetSpeed%d" % speed)
worklist.pyrun("BioShake\\bioexec.py setShakeAcceleration%d" % accel)
worklist.pyrun("BioShake\\bioexec.py shakeOn")
self.starttimer()
Sample.shaken(plate.name, speed)
Sample.addallhistory("(S%d@%.0f)" % (dur, speed), onlyplate=plate.name)
self.waittimer(dur)
worklist.pyrun("BioShake\\bioexec.py shakeOff")
self.starttimer()
self.waittimer(accel + 4)
worklist.pyrun("BioShake\\bioexec.py setElmUnlockPos")
__shakerActive = False
if returnPlate:
self.moveplate(plate, oldloc)
def moveplate(self, plate, dest="Home", returnHome=True):
if self.ptcrunning and plate == decklayout.SAMPLEPLATE:
self.waitpgm()
# move to given destination (one of "Home","Magnet","Shaker","PTC" )
if plate != decklayout.SAMPLEPLATE and plate != decklayout.DILPLATE:
print "Only able to move %s or %s plates, not %s" % (
decklayout.SAMPLEPLATE.name, decklayout.DILPLATE.name,
plate.name)
assert False
if plate.curloc == dest:
#print "Plate %s is already at %s"%(plate.name,dest)
return
#print "Move plate %s from %s to %s"%(plate.name,plate.curloc,dest)
worklist.flushQueue()
self.lihahome()
cmt = "moveplate %s %s" % (plate.name, dest)
worklist.comment(cmt)
if plate.curloc == "Home":
worklist.vector(plate.vectorName, plate, worklist.SAFETOEND, True,
worklist.DONOTMOVE, worklist.CLOSE)
elif plate.curloc == "Magnet":
worklist.vector("Magplate", decklayout.MAGPLATELOC,
worklist.SAFETOEND, True, worklist.DONOTMOVE,
worklist.CLOSE)
elif plate.curloc == "Shaker":
worklist.vector("Shaker", decklayout.SHAKERPLATELOC,
worklist.SAFETOEND, True, worklist.DONOTMOVE,
worklist.CLOSE)
elif plate.curloc == "PTC":
worklist.vector("PTC200", decklayout.PTCPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.CLOSE)
else:
print "Plate %s is in unknown location: %s" % (plate.name,
plate.curloc)
assert False
if dest == "Home":
plate.movetoloc(dest)
worklist.vector(plate.vectorName, plate, worklist.SAFETOEND, True,
worklist.DONOTMOVE, worklist.OPEN)
elif dest == "Magnet":
plate.movetoloc(dest, decklayout.MAGPLATELOC)
worklist.vector("Magplate", decklayout.MAGPLATELOC,
worklist.SAFETOEND, True, worklist.DONOTMOVE,
worklist.OPEN)
elif dest == "Shaker":
plate.movetoloc(dest, decklayout.SHAKERPLATELOC)
worklist.vector("Shaker", decklayout.SHAKERPLATELOC,
worklist.SAFETOEND, True, worklist.DONOTMOVE,
worklist.OPEN)
elif dest == "PTC":
plate.movetoloc(dest, decklayout.PTCPOS)
worklist.vector("PTC200", decklayout.PTCPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.OPEN)
else:
print "Attempt to move plate %s to unknown location: %s" % (
plate.name, dest)
assert False
Sample.addallhistory("{->%s}" % dest, onlyplate=plate.name)
if returnHome:
worklist.romahome()
def pause(self,duration):
self.starttimer()
self.waittimer(duration)
Sample.addallhistory("(%ds)"%duration)
def shake(self,plate,dur=60,speed=None,accel=5,returnPlate=True,samps=None):
if self.ptcrunning and plate==decklayout.SAMPLEPLATE:
self.waitpgm()
# Move the plate to the shaker, run for the given time, and bring plate back
allsamps=Sample.getAllOnPlate(plate)
if samps is None:
samps=allsamps
if all([x.isMixed() for x in samps]):
print "No need to shake ",plate
maxvol=max([x.volume for x in allsamps])
minvol=min([x.volume for x in samps if not x.isMixed() ]+[200])
(minspeed,maxspeed)=plate.getmixspeeds(minvol*0.95,maxvol+5) # Assume volumes could be off
if minspeed>maxspeed:
print "minspeed(",minspeed,") > maxspeed (",maxspeed,")"
if speed is None:
if minspeed<maxspeed:
speed=(maxspeed+minspeed)/2
else:
speed=maxspeed
warned=False
if speed>maxspeed:
print "WARNING: %s plate contains wells with up to %.2f ul, which may spill at %d RPM: "%(plate.name, maxvol, speed),
for x in samps:
tmp=plate.getmixspeeds(x.volume,x.volume)
if tmp[1]<speed:
print "%s[%.1ful, max=%.0f RPM] "%(x.name,x.volume,tmp[1]),
print
warned=True
if globals.verbose and speed<minspeed:
print "NOTICE: %s plate contains unmixed wells that may not be mixed at %d RPM: "%(plate.name, speed),
for x in samps:
if x.isMixed():
continue
tmp=plate.getmixspeeds(x.volume*0.95,x.volume+5)
if speed<tmp[0]:
print "%s[%.1ful, min=%.0f RPM, max=%.0f RPM] "%(x.name,x.volume,tmp[0],tmp[1]),
print
warned=True
if warned or globals.verbose:
print " Mixing %s at %.0f RPM (min unmixed vol=%.0ful -> min RPM=%.0f; max vol=%.0ful -> max RPM=%.f)"%(plate.name, speed, minvol, minspeed, maxvol, maxspeed)
oldloc=plate.curloc
self.moveplate(plate,"Shaker",returnHome=False)
global __shakerActive
__shakerActive=True
worklist.pyrun("BioShake\\bioexec.py setElmLockPos")
worklist.pyrun("BioShake\\bioexec.py setShakeTargetSpeed%d"%speed)
worklist.pyrun("BioShake\\bioexec.py setShakeAcceleration%d"%accel)
worklist.pyrun("BioShake\\bioexec.py shakeOn")
self.starttimer()
Sample.shaken(plate.name,speed)
Sample.addallhistory("(S%d@%.0f)"%(dur,speed),onlyplate=plate.name)
self.waittimer(dur)
worklist.pyrun("BioShake\\bioexec.py shakeOff")
self.starttimer()
self.waittimer(accel+4)
worklist.pyrun("BioShake\\bioexec.py setElmUnlockPos")
__shakerActive=False
if returnPlate:
self.moveplate(plate,oldloc)
def shake(self,
plate,
dur=60,
speed=None,
accel=5,
returnPlate=True,
samps=None,
force=False):
if self.ptcrunning and plate == decklayout.SAMPLEPLATE:
self.waitpgm()
# Move the plate to the shaker, run for the given time, and bring plate back
allsamps = Sample.getAllOnPlate(plate)
if samps is None:
samps = allsamps
if all([x.isMixed() for x in samps]) and not force:
logging.notice("No need to shake " + plate.name +
", but doing so anyway.")
minspeed = 0
maxspeed = 2000
for x in samps:
(a, b) = x.getmixspeeds()
minspeed = max([a, minspeed])
for x in allsamps:
(a, b) = x.getmixspeeds()
maxspeed = min([b, maxspeed])
if speed is None:
if minspeed < maxspeed:
speed = max(
(maxspeed + minspeed) / 2, maxspeed - 50
) # Mix as fast as safely possible (but always above minspeed)
else:
speed = maxspeed
if speed < minspeed - 2 or speed > maxspeed + 2:
others = ""
for x in allsamps:
(a, b) = x.getmixspeeds()
if b < minspeed or a > maxspeed:
if a is not None and a > 0:
others += " {%s: %.1ful,G=%.2f%%,min=%.0f,max=%.0f}" % (
x.name, x.volume, x.glycerolfrac() * 100, a, b)
else:
others += " {%s: %.1ful,G=%.2f%%,max=%.0f}" % (
x.name, x.volume, x.glycerolfrac() * 100, b)
logging.mixwarning(
"Mixing %s at %.0f RPM; minspeed(%.0f) > maxspeed(%.0f), limits=[%s]"
% (plate.name, speed, minspeed, maxspeed, others))
else:
logging.notice(
"Mixing %s at %.0f RPM ( min RPM=%.0f, max RPM=%.f)" %
(plate.name, speed, minspeed, maxspeed))
oldloc = plate.curloc
self.moveplate(plate, "Shaker", returnHome=False)
global __shakerActive
__shakerActive = True
worklist.pyrun("BioShake\\bioexec.py setElmLockPos")
worklist.pyrun("BioShake\\bioexec.py setShakeTargetSpeed%d" % speed)
worklist.pyrun("BioShake\\bioexec.py setShakeAcceleration%d" % accel)
worklist.pyrun("BioShake\\bioexec.py shakeOn")
self.starttimer()
Sample.shaken(plate.name, speed)
Sample.addallhistory("(S%d@%.0f)" % (dur, speed),
onlyplate=plate.name,
type="shake")
self.waittimer(dur)
worklist.pyrun("BioShake\\bioexec.py shakeOff")
self.starttimer()
self.waittimer(accel + 4)
worklist.pyrun("BioShake\\bioexec.py setElmUnlockPos")
__shakerActive = False
if returnPlate:
self.moveplate(plate, oldloc)
