def __init__(self,
xLength=150, yLength=200, zLength=1,
voxelDensity=1,
initNutrientDiffusion = False,
MCSperDay=500,
simDurationDays=720,
sampleIntervalInDays=0.5,
fluctuationAmplitude=10.0,
flip2DimRatio=0.5,
neighborOrder=1,
boundary_x="Periodic",
debugOutputFrequency=50000,
SEED=-1):
"""
:param xLength:
:param yLength:
:param zLength:
:param voxelDensity:
:param MCSperDay: MC steps per Day. Default is 500, i.e. 500 MCS = 1 day.
:param simDurationDays:
:param fluctuationAmplitude:
:param flip2DimRatio:
:param neighborOrder:
:param boundary_x:
:param debugOutputFrequency:
:param SEED:
:return:
"""
self.xLength = xLength
self.yLength = yLength
self.zLength = zLength
self.voxelDensity = voxelDensity # 1 voxel / 1 mu
self.initNutrientDiffusion = initNutrientDiffusion
self.dimensions = 2 if zLength <= 0 else 3
self.xDimension = self.calcPixelFromMuMeter(xLength)
self.yDimension = self.calcPixelFromMuMeter(yLength)
self.zDimension = 1 if self.dimensions == 2 else self.calcPixelFromMuMeterMin1(zLength)
self.latticeSizeInVoxel = self.xDimension * self.yDimension * self.zDimension
self.MCSperDay = MCSperDay
self.simDurationDays = simDurationDays
self.sampleIntervalInDays = sampleIntervalInDays
self.sampleIntervalInMCS = self.calcMCSfromDays(sampleIntervalInDays)
self.maxSteps = self.calcMCSfromDays(simDurationDays)
self.fluctuationAmplitude = fluctuationAmplitude
self.flip2DimRatio = flip2DimRatio
self.neighborOrder = neighborOrder
self.boundary_x = boundary_x
self.debugOutputFrequency = debugOutputFrequency
# TODO: change the seed value of every random number used in Moduro project
self.SEED = (int(round(time.time() * 1000)) % 9999) if SEED < 0 else SEED
self.__cc3d = None
self.parameterStore = ParameterStore()
self.parameterStore.addObj(self)
class ExecConfig(object):
def __init__(self,
xLength=150, yLength=200, zLength=1,
voxelDensity=1,
initNutrientDiffusion = False,
MCSperDay=500,
simDurationDays=720,
sampleIntervalInDays=0.5,
fluctuationAmplitude=10.0,
flip2DimRatio=0.5,
neighborOrder=1,
boundary_x="Periodic",
debugOutputFrequency=50000,
SEED=-1):
"""
:param xLength:
:param yLength:
:param zLength:
:param voxelDensity:
:param MCSperDay: MC steps per Day. Default is 500, i.e. 500 MCS = 1 day.
:param simDurationDays:
:param fluctuationAmplitude:
:param flip2DimRatio:
:param neighborOrder:
:param boundary_x:
:param debugOutputFrequency:
:param SEED:
:return:
"""
self.xLength = xLength
self.yLength = yLength
self.zLength = zLength
self.voxelDensity = voxelDensity # 1 voxel / 1 mu
self.initNutrientDiffusion = initNutrientDiffusion
self.dimensions = 2 if zLength <= 0 else 3
self.xDimension = self.calcPixelFromMuMeter(xLength)
self.yDimension = self.calcPixelFromMuMeter(yLength)
self.zDimension = 1 if self.dimensions == 2 else self.calcPixelFromMuMeterMin1(zLength)
self.latticeSizeInVoxel = self.xDimension * self.yDimension * self.zDimension
self.MCSperDay = MCSperDay
self.simDurationDays = simDurationDays
self.sampleIntervalInDays = sampleIntervalInDays
self.sampleIntervalInMCS = self.calcMCSfromDays(sampleIntervalInDays)
self.maxSteps = self.calcMCSfromDays(simDurationDays)
self.fluctuationAmplitude = fluctuationAmplitude
self.flip2DimRatio = flip2DimRatio
self.neighborOrder = neighborOrder
self.boundary_x = boundary_x
self.debugOutputFrequency = debugOutputFrequency
# TODO: change the seed value of every random number used in Moduro project
self.SEED = (int(round(time.time() * 1000)) % 9999) if SEED < 0 else SEED
self.__cc3d = None
self.parameterStore = ParameterStore()
self.parameterStore.addObj(self)
def initPotts(self):
self.__cc3d = ElementCC3D("CompuCell3D", {"version": "3.7.3"})
potts = self.__cc3d.ElementCC3D("Potts")
potts.ElementCC3D("Dimensions", {"x": self.xDimension, "y": self.yDimension, "z": self.zDimension})
potts.ElementCC3D("Steps", {}, self.maxSteps)
potts.ElementCC3D("FluctuationAmplitude", {}, self.fluctuationAmplitude)
potts.ElementCC3D("Flip2DimRatio", {}, self.flip2DimRatio)
potts.ElementCC3D("NeighborOrder", {}, self.neighborOrder)
potts.ElementCC3D("Boundary_x", {}, self.boundary_x)
potts.ElementCC3D("DebugOutputFrequency", {}, self.debugOutputFrequency)
potts.ElementCC3D("RandomSeed", {}, self.SEED)
def initCellTypes(self, cellTypes):
PluginElmnt = self.__cc3d.ElementCC3D("Plugin", {"Name": "CellType"})
for i in range(cellTypes.__len__()):
if cellTypes[i].frozen:
PluginElmnt.ElementCC3D("CellType", {"Freeze": "",
"TypeId": cellTypes[i].id,
"TypeName": cellTypes[i].name})
else:
PluginElmnt.ElementCC3D("CellType", {"TypeId": cellTypes[i].id,
"TypeName": cellTypes[i].name})
def initEnergyMatrix(self, cellTypes, energyMatrix, adhFactor):
contact = self.__cc3d.ElementCC3D("Plugin", {"Name": "Contact"})
for i in range(cellTypes.__len__()):
for j in range(i, cellTypes.__len__()):
contact.ElementCC3D("Energy", {"Type1": cellTypes[i].name,
"Type2": cellTypes[j].name},
adhFactor * energyMatrix[i][j])
def initPlugins(self, *args):
for a in args:
self.__cc3d.ElementCC3D("Plugin", {"Name": a})
def initDiffusion(self, cellType, secretionRateNutr, decayConstantNutr):
SteppableElmnt = self.__cc3d.ElementCC3D("Steppable", {"Type": "FlexibleDiffusionSolverFE"})
DiffusionFieldElmnt = SteppableElmnt.ElementCC3D("DiffusionField")
DiffusionDataElmnt = DiffusionFieldElmnt.ElementCC3D("DiffusionData")
DiffusionDataElmnt.ElementCC3D("FieldName", {}, "Nutrients")
DiffusionDataElmnt.ElementCC3D("DiffusionConstant", {}, secretionRateNutr)
DiffusionDataElmnt.ElementCC3D("DecayConstant", {}, decayConstantNutr)
SecretionDataElmnt = DiffusionFieldElmnt.ElementCC3D("SecretionData")
SecretionDataElmnt.ElementCC3D("Secretion", {"Type": cellType.name}, secretionRateNutr)
def getCC3D(self):
return self.__cc3d
def calculateLatticeSize(self):
return self.xDimension * self.yDimension * self.zDimension
def interuptMCS(self, mcs):
return (mcs == 0) or (mcs % self.sampleIntervalInMCS == 0)
def addParameter(self, key, value):
# TODO: ghj
return None
def calcPixelFromMuMeter(self, mum):
"""
Convert a length in micro meter to a pixel length.
This is influenced by the voxelDensity.
:param mum:
:return:
"""
#python has approximation errors when casted into int with long number of .99999999
return int(self.voxelDensity * mum + 0.000001)
def calcPixelFromMuMeterMin1(self, mum):
"""
Convert a length in micro meter to a pixel length.
This is influenced by the voxelDensity.
:param mum:
:return:
"""
return self.__truncate(self.voxelDensity * mum)
def calculateVolume(self, diameter):
if self.dimensions == 2:
return PI * (diameter / 2.0) ** 2 # Area
else:
return 4.0 / 3.0 * PI * (diameter / 2.0) ** 3 # Volume
def calculateSurface(self, diameter):
if self.dimensions == 2:
return 2 * PI * (diameter / 2.0) # Circumference
else:
return 4 * PI * (diameter / 2.0) ** 2 # Surface
def calcVoxelVolumeFromVolume(self, volume):
"""
Calculates the voxel volume from a physical volume. The results
depends on the dimension of the simulation (2D or 3D).
The scaling is influenced by the voxelDensity.
:param volume: physical volume in mu m^3.
:return: Voxel volume.
"""
r = (3 * volume / (4.0 * PI)) ** (1.0 / 3.0) # Radius of a sphere with known volume.
rDimension = self.calcPixelFromMuMeter(r) # Convert it to a pixel unit.
if self.dimensions == 2:
# a = self.__truncateToVoxel(PI * (rDimension ** 2))
# if volume > 0:
# print "volume=", volume, ", rDim=", rDimension, ", r=", r, ", A=", a
return self.__truncate(PI * (rDimension ** 2)) # Area of a circle.
else:
return self.__truncate(4.0 / 3.0 * PI * (rDimension ** 3)) # Volume of a sphere.
def calcVoxelSurfaceFromVoxelVolume(self, voxelVolume):
"""
Calculates the voxel surface from a voxel volume. The results
depends on the dimension of the simulation (2D or 3D).
:param voxelVolume: volume (in pixel^3).
:return: Surface in pixel^2 ^(3D) or pixel (2).
"""
if self.dimensions == 2:
# some fractal factor!
return self.__truncate(1.5 * 2 * (PI * voxelVolume) ** (1.0 / 2.0)) # Circumference.
else:
return self.__truncate(2.0 * 4 * PI * (3 * voxelVolume / (4 * PI)) ** (2.0 / 3.0)) # Surface.
def __truncate(self, value):
res = int(value + 0.00001)
if res <= 1:
return 1 # Ensure that size is at least 1.
else:
return res
def calcMCSfromDays(self, days):
"""
Convert the time scale days into MC steps.
:param days:
:return:
"""
return self.__truncate(self.MCSperDay * days)
def calcDaysFromMCS(self, mcs):
"""
Convert the MCS number into days.
:param mcs:
:return:
"""
return mcs / (1.0 * self.MCSperDay)
def calcHoursFromMCS(self, mcs):
"""
Convert the MCS number into hours.
:param mcs:
:return:
"""
return mcs / (1.0 * self.MCSperDay) * 24.0
def calcSurLambdaFromSurFit(self, surFit):
return 0.05 * surFit
def calcVolLambdaFromVolFit(self, volFit):
return 1.0 * volFit