from PySteppables import * import CompuCell import sys import time from math import * class CellDiffusionCalculatorSteppable(SteppablePy): def __init__(self,_simulator,_frequency=1): SteppablePy.__init__(self,_frequency) self.simulator=_simulator self.frequ=_frequency #self.aa=[] self.inventory=self.simulator.getPotts().getCellInventory() self.cellList=CellList(self.inventory) self.nTrackerPlugin=CompuCell.getNeighborTrackerPlugin() self.cellFieldG=self.simulator.getPotts().getCellFieldG() self.dim=self.cellFieldG.getDim() #self.output_file = open("cellDiffusionData.txt",'w') def start(self): for cell in self.cellList: if cell.type == 1 or cell.type == 2: list_attrib=CompuCell.getPyAttrib(cell) ptx=float(cell.xCM/float(cell.volume)) pty=float(cell.yCM/float(cell.volume)) list_attrib[0:2]=[ptx,pty] import CompuCellSetup self.pW=CompuCellSetup.viewManager.plotManager.getNewPlotWindow() if not self.pW: return #Plot Title - properties self.pW.setTitle("Cell Diffusion") self.pW.setTitleSize(12) self.pW.setTitleColor("Green") #plot background self.pW.setPlotBackgroundColor("orange") # properties of x axis self.pW.setXAxisTitle("MonteCarlo Step (MCS)") self.pW.setXAxisTitleSize(10) self.pW.setXAxisTitleColor("blue") # properties of y axis self.pW.setYAxisTitle("/4") #self.pW.setYAxisLogScale() self.pW.setYAxisTitleSize(10) self.pW.setYAxisTitleColor("red") self.pW.addPlot("Non-Condensing") self.pW.addPlot("Condensing") # plot MCS self.pW.changePlotProperty("Non-Condensing","LineWidth",1) self.pW.changePlotProperty("Non-Condensing","LineColor","red") # plot MCS1 self.pW.changePlotProperty("Condensing","LineWidth",1) self.pW.changePlotProperty("Condensing","LineColor","green") self.pW.addGrid() #adding automatically generated legend # default possition is at the bottom of the plot but here we put it at the top self.pW.addAutoLegend("top") self.pW2=CompuCellSetup.viewManager.plotManager.getNewPlotWindow() if not self.pW2: return #Plot Title - properties self.pW2.setTitle("Cell Displacement/MCS") self.pW2.setTitleSize(12) self.pW2.setTitleColor("Green") #plot background self.pW2.setPlotBackgroundColor("orange") # properties of x axis self.pW2.setXAxisTitle("MonteCarlo Step (MCS)") self.pW2.setXAxisTitleSize(10) self.pW2.setXAxisTitleColor("blue") # properties of y axis self.pW2.setYAxisTitle("") #self.pW.setYAxisLogScale() self.pW2.setYAxisTitleSize(10) self.pW2.setYAxisTitleColor("red") self.pW2.addPlot("Non-Condensing") self.pW2.addPlot("Condensing") # plot MCS self.pW2.changePlotProperty("Non-Condensing","LineWidth",1) self.pW2.changePlotProperty("Non-Condensing","LineColor","red") # plot MCS1 self.pW2.changePlotProperty("Condensing","LineWidth",1) self.pW2.changePlotProperty("Condensing","LineColor","green") self.pW2.addGrid() #adding automatically generated legend # default possition is at the bottom of the plot but here we put it at the top self.pW2.addAutoLegend("top") self.pW3=CompuCellSetup.viewManager.plotManager.getNewPlotWindow() if not self.pW3: return #Plot Title - properties self.pW3.setTitle("Average Volume") self.pW3.setTitleSize(12) self.pW3.setTitleColor("Green") #plot background self.pW3.setPlotBackgroundColor("orange") # properties of x axis self.pW3.setXAxisTitle("MonteCarlo Step (MCS)") self.pW3.setXAxisTitleSize(10) self.pW3.setXAxisTitleColor("blue") # properties of y axis self.pW3.setYAxisTitle("volume") #self.pW.setYAxisLogScale() self.pW3.setYAxisTitleSize(10) self.pW3.setYAxisTitleColor("red") self.pW3.addPlot("Non-Condensing") self.pW3.addPlot("Condensing") # plot MCS self.pW3.changePlotProperty("Non-Condensing","LineWidth",1) self.pW3.changePlotProperty("Non-Condensing","LineColor","red") # plot MCS1 self.pW3.changePlotProperty("Condensing","LineWidth",1) self.pW3.changePlotProperty("Condensing","LineColor","green") self.pW3.addGrid() #adding automatically generated legend # default possition is at the bottom of the plot but here we put it at the top self.pW3.addAutoLegend("top") self.pW4=CompuCellSetup.viewManager.plotManager.getNewPlotWindow() if not self.pW4: return #Plot Title - properties self.pW4.setTitle("Average Surface Area") self.pW4.setTitleSize(12) self.pW4.setTitleColor("Green") #plot background self.pW4.setPlotBackgroundColor("orange") # properties of x axis self.pW4.setXAxisTitle("MonteCarlo Step (MCS)") self.pW4.setXAxisTitleSize(10) self.pW4.setXAxisTitleColor("blue") # properties of y axis self.pW4.setYAxisTitle("Surface Area") #self.pW.setYAxisLogScale() self.pW4.setYAxisTitleSize(10) self.pW4.setYAxisTitleColor("red") self.pW4.addPlot("Non-Condensing") self.pW4.addPlot("Condensing") # plot MCS self.pW4.changePlotProperty("Non-Condensing","LineWidth",1) self.pW4.changePlotProperty("Non-Condensing","LineColor","red") # plot MCS1 self.pW4.changePlotProperty("Condensing","LineWidth",1) self.pW4.changePlotProperty("Condensing","LineColor","green") self.pW4.addGrid() #adding automatically generated legend # default possition is at the bottom of the plot but here we put it at the top self.pW4.addAutoLegend("top") def step(self,mcs): self.Potts=self.simulator.getPotts() cell_counter1=0 cell_counter2=0 d2_CON=0 d2_NONCON=0 d_CON=0 d_NONCON=0 t1_volume=0 t2_volume=0 t1_surface=0 t2_surface=0 for cell in self.cellList: if cell.type == 1: list_attrib=CompuCell.getPyAttrib(cell) cell_counter1+=1; ptx=float(cell.xCM/float(cell.volume)) pty=float(cell.yCM/float(cell.volume)) pt2x=list_attrib[0] pt2y=list_attrib[1] dx2=(ptx-pt2x)**2 dy2=(pty-pt2y)**2 d2_CON+=(dx2+dy2) d_CON+=(dx2+dy2)**(0.5) list_attrib[0]=ptx list_attrib[1]=pty t1_volume += cell.volume t1_surface += cell.surface if cell.type == 2: list_attrib=CompuCell.getPyAttrib(cell) cell_counter2+=1; ptx=float(cell.xCM/float(cell.volume)) pty=float(cell.yCM/float(cell.volume)) pt2x=list_attrib[0] pt2y=list_attrib[1] dx2=(ptx-pt2x)**2 dy2=(pty-pt2y)**2 d2_NONCON+=(dx2+dy2) d_NONCON+=(dx2+dy2)**(0.5) list_attrib[0]=ptx list_attrib[1]=pty t2_volume += cell.volume t2_surface += cell.surface AVE_d2_CON=d2_CON/cell_counter1/self.frequ AVE_d2_NONCON=d2_NONCON/cell_counter2/self.frequ AVE_d_CON=d_CON/cell_counter1/self.frequ AVE_d_NONCON=d_NONCON/cell_counter2/self.frequ if mcs%50==0: self.pW.addDataPoint("Condensing",mcs,AVE_d2_CON/4) self.pW.addDataPoint("Non-Condensing",mcs,AVE_d2_NONCON/4) self.pW.showAllPlots() self.pW2.addDataPoint("Condensing",mcs,AVE_d_CON) self.pW2.addDataPoint("Non-Condensing",mcs,AVE_d_NONCON) self.pW2.showAllPlots() self.pW3.addDataPoint("Condensing",mcs,t1_volume/cell_counter1) self.pW3.addDataPoint("Non-Condensing",mcs,t2_volume/cell_counter2) self.pW3.showAllPlots() self.pW4.addDataPoint("Condensing",mcs,t1_surface/cell_counter1) self.pW4.addDataPoint("Non-Condensing",mcs,t2_surface/cell_counter2) self.pW4.showAllPlots()