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 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):
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)
