class MitosisPy(StepperPy, Field3DChangeWatcherPy):
def __init__(self, _changeWatcher):
Field3DChangeWatcherPy.__init__(self, _changeWatcher)
self.mitosisPlugin = MitosisSimplePlugin()
self.doublingVolume = 50
self.mitosisPlugin.setDoublingVolume(self.doublingVolume)
self.mitosisPlugin.init(self.changeWatcher.sim)
self.mitosisPlugin.turnOn(
) #has to be called after init to make sure vectors are allocated
self.counter = 0
self.mitosisFlag = 0
#self.childCell
#self.parentCell
def setPotts(self, potts):
self.mitosisPlugin.setPotts(potts)
def field3DChange(self):
if self.changeWatcher.newCell and self.changeWatcher.newCell.volume > self.doublingVolume:
print "BIG CELL I WILL DO MITOSIS"
self.mitosisPlugin.field3DChange(self.changeWatcher.changePoint,
self.changeWatcher.newCell,
self.changeWatcher.newCell)
self.mitosisPlugin.setMitosisFlag(1)
def step(self):
mitosisDoneFlag = False
if self.mitosisPlugin.getMitosisFlag():
self.mitosisFlag = self.mitosisPlugin.doMitosis()
self.childCell = self.mitosisPlugin.getChildCell()
self.parentCell = self.mitosisPlugin.getParentCell()
self.updateAttributes()
self.mitosisPlugin.setMitosisFlag(0)
def updateAttributes(self):
print "self.parentCell.type % 2=", self.parentCell.type % 2
if self.parentCell.type % 2:
self.childCell.type = 2
#self.childCell.type=self.parentCell.type
else:
self.childCell.type = 1
class MitosisPy (StepperPy,Field3DChangeWatcherPy):
def __init__(self,_changeWatcher):
Field3DChangeWatcherPy.__init__(self,_changeWatcher)
self.mitosisPlugin=MitosisSimplePlugin()
self.doublingVolume=50
self.mitosisPlugin.setDoublingVolume(self.doublingVolume)
self.mitosisPlugin.init(self.changeWatcher.sim)
self.mitosisPlugin.turnOn() #has to be called after init to make sure vectors are allocated
self.counter=0
self.mitosisFlag=0
#self.childCell
#self.parentCell
def setPotts(self,potts):
self.mitosisPlugin.setPotts(potts)
def field3DChange(self):
if self.changeWatcher.newCell and self.changeWatcher.newCell.volume>self.doublingVolume:
print "BIG CELL I WILL DO MITOSIS"
self.mitosisPlugin.field3DChange(self.changeWatcher.changePoint,self.changeWatcher.newCell,self.changeWatcher.newCell)
self.mitosisPlugin.setMitosisFlag(1)
def step(self):
mitosisDoneFlag=False
if self.mitosisPlugin.getMitosisFlag():
self.mitosisFlag=self.mitosisPlugin.doMitosis()
self.childCell=self.mitosisPlugin.getChildCell()
self.parentCell=self.mitosisPlugin.getParentCell()
self.updateAttributes()
self.mitosisPlugin.setMitosisFlag(0)
def updateAttributes(self):
print "self.parentCell.type % 2=",self.parentCell.type % 2
if self.parentCell.type % 2:
self.childCell.type=2
#self.childCell.type=self.parentCell.type
else:
self.childCell.type=1
class MitosisPyPluginBase(StepperPy,Field3DChangeWatcherPy):
def __init__(self,_simulator,_changeWatcherRegistry,_stepperRegistry):
Field3DChangeWatcherPy.__init__(self,_changeWatcherRegistry)
self.simulator=_simulator
self.mitosisPlugin=MitosisSimplePlugin()
self.mitosisPlugin.setPotts(self.simulator.getPotts())
self.mitosisPlugin.init(self.changeWatcher.sim)
self.mitosisPlugin.turnOn() #has to be called after init to make sure vectors are allocated
self.counter=0
self.mitosisFlag=0
_changeWatcherRegistry.registerPyChangeWatcher(self)
_stepperRegistry.registerPyStepper(self)
self.directionalMitosisFlagSet=[1,0,0]
self.useOrientationVectorMitosis=False
self.nx=1.0
self.ny=0.0
self.nz=0.0
def setPotts(self,potts):
self.mitosisPlugin.setPotts(potts)
def setDoublingVolume(self,_doublingVolume):
self.doublingVolume=_doublingVolume;
self.mitosisPlugin.setDoublingVolume(self.doublingVolume)
def setDivisionAlongMajorAxis(self):
self.directionalMitosisFlagSet=[0,1,0]
def setDivisionAlongMinorAxis(self):
self.directionalMitosisFlagSet=[0,0,1]
def setNondirectionalDivision(self):
self.directionalMitosisFlagSet=[1,0,0]
def setMitosisOrientationVector(self,_nx,_ny,_nz):
self.useOrientationVectorMitosis=True
self.nx=_nx
self.ny=_ny
self.nz=_nz
def unsetMitosisOrientationVector(self):
self.useOrientationVectorMitosis=False
# these functions show how to extract semiminor axis. MItosis can be done along major, minor or user specified axis
# once you know directions of principal axec of cells you may do custom mitosis along vector derived using principal orientation vectors
def getSemiminorVectorXY(self):
orientationVectors=self.mitosisPlugin.getOrientationVectorsMitosis2D_xy(self.changeWatcher.newCell)
print "orientationVectors.semiminorVec=",orientationVectors.semiminorVec.x,",",orientationVectors.semiminorVec.y,",",orientationVectors.semiminorVec.z
print "orientationVectors.semimajorVec=",orientationVectors.semimajorVec.x,",",orientationVectors.semimajorVec.y,",",orientationVectors.semimajorVec.z
return orientationVectors.semiminorVec
def getSemiminorVectorXY(self):
orientationVectors=self.mitosisPlugin.getOrientationVectorsMitosis2D_xy(self.changeWatcher.newCell)
print "orientationVectors.semiminorVec=",orientationVectors.semiminorVec.x,",",orientationVectors.semiminorVec.y,",",orientationVectors.semiminorVec.z
print "orientationVectors.semimajorVec=",orientationVectors.semimajorVec.x,",",orientationVectors.semimajorVec.y,",",orientationVectors.semimajorVec.z
return orientationVectors.semimajorVec
def field3DChange(self):
self.newCell=self.changeWatcher.getNewCell()
if self.newCell and self.newCell.volume>self.doublingVolume:
self.changePoint=self.changeWatcher.getChangePoint()
self.mitosisPlugin.field3DChange(self.changePoint, \
self.newCell, \
self.newCell)
self.mitosisPlugin.setMitosisFlag(1)
def step(self):
mitosisDoneFlag=False
if self.mitosisPlugin.getMitosisFlag():
if self.useOrientationVectorMitosis:
mitosisDoneFlag=self.mitosisPlugin.doDirectionalMitosisOrientationVectorBased(self.nx,self.ny,self.nz)
else:
if self.directionalMitosisFlagSet[0]:
mitosisDoneFlag=self.mitosisPlugin.doMitosis()
if self.directionalMitosisFlagSet[1]:#do mitosis along major Axis
self.mitosisPlugin.setDivideAlongMajorAxis()
# right before doing mitosis you may want to calculate division axis based on orientatin of principal axes. This is the place where you would do these calculations
# self.getSemiminorVectorXY()
mitosisDoneFlag=self.mitosisPlugin.doDirectionalMitosis()
if self.directionalMitosisFlagSet[2]:#do mitosis along minor Axis
self.mitosisPlugin.setDivideAlongMinorAxis()
mitosisDoneFlag=self.mitosisPlugin.doDirectionalMitosis()
self.childCell=self.mitosisPlugin.getChildCell()
self.parentCell=self.mitosisPlugin.getParentCell()
if mitosisDoneFlag:
self.updateAttributes()
self.mitosisPlugin.setMitosisFlag(0)
def updateAttributes(self):
self.childCell.targetVolume=self.parentCell.targetVolume
self.childCell.lambdaVolume=self.parentCell.lambdaVolume
self.childCell.type=self.parentCell.type
class MitosisPyPluginBase(StepperPy, Field3DChangeWatcherPy):
def __init__(self, _simulator, _changeWatcherRegistry, _stepperRegistry):
Field3DChangeWatcherPy.__init__(self, _changeWatcherRegistry)
self.simulator = _simulator
self.mitosisPlugin = MitosisSimplePlugin()
self.mitosisPlugin.setPotts(self.simulator.getPotts())
self.mitosisPlugin.init(self.changeWatcher.sim)
self.mitosisPlugin.turnOn(
) #has to be called after init to make sure vectors are allocated
self.counter = 0
self.mitosisFlag = 0
_changeWatcherRegistry.registerPyChangeWatcher(self)
_stepperRegistry.registerPyStepper(self)
self.directionalMitosisFlagSet = [1, 0, 0]
self.useOrientationVectorMitosis = False
self.nx = 1.0
self.ny = 0.0
self.nz = 0.0
def setPotts(self, potts):
self.mitosisPlugin.setPotts(potts)
def setDoublingVolume(self, _doublingVolume):
self.doublingVolume = _doublingVolume
self.mitosisPlugin.setDoublingVolume(self.doublingVolume)
def setDivisionAlongMajorAxis(self):
self.directionalMitosisFlagSet = [0, 1, 0]
def setDivisionAlongMinorAxis(self):
self.directionalMitosisFlagSet = [0, 0, 1]
def setNondirectionalDivision(self):
self.directionalMitosisFlagSet = [1, 0, 0]
def setMitosisOrientationVector(self, _nx, _ny, _nz):
self.useOrientationVectorMitosis = True
self.nx = _nx
self.ny = _ny
self.nz = _nz
def unsetMitosisOrientationVector(self):
self.useOrientationVectorMitosis = False
# these functions show how to extract semiminor axis. MItosis can be done along major, minor or user specified axis
# once you know directions of principal axec of cells you may do custom mitosis along vector derived using principal orientation vectors
def getSemiminorVectorXY(self):
orientationVectors = self.mitosisPlugin.getOrientationVectorsMitosis2D_xy(
self.changeWatcher.newCell)
print "orientationVectors.semiminorVec=", orientationVectors.semiminorVec.x, ",", orientationVectors.semiminorVec.y, ",", orientationVectors.semiminorVec.z
print "orientationVectors.semimajorVec=", orientationVectors.semimajorVec.x, ",", orientationVectors.semimajorVec.y, ",", orientationVectors.semimajorVec.z
return orientationVectors.semiminorVec
def getSemiminorVectorXY(self):
orientationVectors = self.mitosisPlugin.getOrientationVectorsMitosis2D_xy(
self.changeWatcher.newCell)
print "orientationVectors.semiminorVec=", orientationVectors.semiminorVec.x, ",", orientationVectors.semiminorVec.y, ",", orientationVectors.semiminorVec.z
print "orientationVectors.semimajorVec=", orientationVectors.semimajorVec.x, ",", orientationVectors.semimajorVec.y, ",", orientationVectors.semimajorVec.z
return orientationVectors.semimajorVec
def field3DChange(self):
self.newCell = self.changeWatcher.getNewCell()
if self.newCell and self.newCell.volume > self.doublingVolume:
self.changePoint = self.changeWatcher.getChangePoint()
self.mitosisPlugin.field3DChange(self.changePoint, \
self.newCell, \
self.newCell)
self.mitosisPlugin.setMitosisFlag(1)
def step(self):
mitosisDoneFlag = False
if self.mitosisPlugin.getMitosisFlag():
if self.useOrientationVectorMitosis:
mitosisDoneFlag = self.mitosisPlugin.doDirectionalMitosisOrientationVectorBased(
self.nx, self.ny, self.nz)
else:
if self.directionalMitosisFlagSet[0]:
mitosisDoneFlag = self.mitosisPlugin.doMitosis()
if self.directionalMitosisFlagSet[
1]: #do mitosis along major Axis
self.mitosisPlugin.setDivideAlongMajorAxis()
# right before doing mitosis you may want to calculate division axis based on orientatin of principal axes. This is the place where you would do these calculations
# self.getSemiminorVectorXY()
mitosisDoneFlag = self.mitosisPlugin.doDirectionalMitosis()
if self.directionalMitosisFlagSet[
2]: #do mitosis along minor Axis
self.mitosisPlugin.setDivideAlongMinorAxis()
mitosisDoneFlag = self.mitosisPlugin.doDirectionalMitosis()
self.childCell = self.mitosisPlugin.getChildCell()
self.parentCell = self.mitosisPlugin.getParentCell()
if mitosisDoneFlag:
self.updateAttributes()
self.mitosisPlugin.setMitosisFlag(0)
def updateAttributes(self):
self.childCell.targetVolume = self.parentCell.targetVolume
self.childCell.lambdaVolume = self.parentCell.lambdaVolume
self.childCell.type = self.parentCell.type