CompuCell3DAttachment 'CellDiffusionCalculatorSteppable.py'
Download 1 from PySteppables import *
2 import CompuCell
3 import sys
4 import time
5 from math import *
6
7
8 class CellDiffusionCalculatorSteppable(SteppablePy):
9 def __init__(self,_simulator,_frequency=1):
10 SteppablePy.__init__(self,_frequency)
11 self.simulator=_simulator
12 self.frequ=_frequency
13 #self.aa=[]
14 self.inventory=self.simulator.getPotts().getCellInventory()
15 self.cellList=CellList(self.inventory)
16 self.nTrackerPlugin=CompuCell.getNeighborTrackerPlugin()
17 self.cellFieldG=self.simulator.getPotts().getCellFieldG()
18 self.dim=self.cellFieldG.getDim()
19
20 #self.output_file = open("cellDiffusionData.txt",'w')
21
22 def start(self):
23 for cell in self.cellList:
24 if cell.type == 1 or cell.type == 2:
25 list_attrib=CompuCell.getPyAttrib(cell)
26 ptx=float(cell.xCM/float(cell.volume))
27 pty=float(cell.yCM/float(cell.volume))
28 list_attrib[0:2]=[ptx,pty]
29 import CompuCellSetup
30 self.pW=CompuCellSetup.viewManager.plotManager.getNewPlotWindow()
31 if not self.pW:
32 return
33 #Plot Title - properties
34 self.pW.setTitle("Cell Diffusion")
35 self.pW.setTitleSize(12)
36 self.pW.setTitleColor("Green")
37
38 #plot background
39 self.pW.setPlotBackgroundColor("orange")
40
41 # properties of x axis
42 self.pW.setXAxisTitle("MonteCarlo Step (MCS)")
43 self.pW.setXAxisTitleSize(10)
44 self.pW.setXAxisTitleColor("blue")
45
46 # properties of y axis
47 self.pW.setYAxisTitle("<displacement^2>/4")
48 #self.pW.setYAxisLogScale()
49 self.pW.setYAxisTitleSize(10)
50 self.pW.setYAxisTitleColor("red")
51
52 self.pW.addPlot("Non-Condensing")
53 self.pW.addPlot("Condensing")
54 # plot MCS
55 self.pW.changePlotProperty("Non-Condensing","LineWidth",1)
56 self.pW.changePlotProperty("Non-Condensing","LineColor","red")
57 # plot MCS1
58 self.pW.changePlotProperty("Condensing","LineWidth",1)
59 self.pW.changePlotProperty("Condensing","LineColor","green")
60
61
62 self.pW.addGrid()
63 #adding automatically generated legend
64 # default possition is at the bottom of the plot but here we put it at the top
65 self.pW.addAutoLegend("top")
66
67 self.pW2=CompuCellSetup.viewManager.plotManager.getNewPlotWindow()
68 if not self.pW2:
69 return
70 #Plot Title - properties
71 self.pW2.setTitle("Cell Displacement/MCS")
72 self.pW2.setTitleSize(12)
73 self.pW2.setTitleColor("Green")
74
75 #plot background
76 self.pW2.setPlotBackgroundColor("orange")
77
78 # properties of x axis
79 self.pW2.setXAxisTitle("MonteCarlo Step (MCS)")
80 self.pW2.setXAxisTitleSize(10)
81 self.pW2.setXAxisTitleColor("blue")
82
83 # properties of y axis
84 self.pW2.setYAxisTitle("<Displacement>")
85 #self.pW.setYAxisLogScale()
86 self.pW2.setYAxisTitleSize(10)
87 self.pW2.setYAxisTitleColor("red")
88
89 self.pW2.addPlot("Non-Condensing")
90 self.pW2.addPlot("Condensing")
91 # plot MCS
92 self.pW2.changePlotProperty("Non-Condensing","LineWidth",1)
93 self.pW2.changePlotProperty("Non-Condensing","LineColor","red")
94 # plot MCS1
95 self.pW2.changePlotProperty("Condensing","LineWidth",1)
96 self.pW2.changePlotProperty("Condensing","LineColor","green")
97
98
99 self.pW2.addGrid()
100 #adding automatically generated legend
101 # default possition is at the bottom of the plot but here we put it at the top
102 self.pW2.addAutoLegend("top")
103
104
105 self.pW3=CompuCellSetup.viewManager.plotManager.getNewPlotWindow()
106 if not self.pW3:
107 return
108 #Plot Title - properties
109 self.pW3.setTitle("Average Volume")
110 self.pW3.setTitleSize(12)
111 self.pW3.setTitleColor("Green")
112
113 #plot background
114 self.pW3.setPlotBackgroundColor("orange")
115
116 # properties of x axis
117 self.pW3.setXAxisTitle("MonteCarlo Step (MCS)")
118 self.pW3.setXAxisTitleSize(10)
119 self.pW3.setXAxisTitleColor("blue")
120
121 # properties of y axis
122 self.pW3.setYAxisTitle("volume")
123 #self.pW.setYAxisLogScale()
124 self.pW3.setYAxisTitleSize(10)
125 self.pW3.setYAxisTitleColor("red")
126
127 self.pW3.addPlot("Non-Condensing")
128 self.pW3.addPlot("Condensing")
129 # plot MCS
130 self.pW3.changePlotProperty("Non-Condensing","LineWidth",1)
131 self.pW3.changePlotProperty("Non-Condensing","LineColor","red")
132 # plot MCS1
133 self.pW3.changePlotProperty("Condensing","LineWidth",1)
134 self.pW3.changePlotProperty("Condensing","LineColor","green")
135
136
137 self.pW3.addGrid()
138 #adding automatically generated legend
139 # default possition is at the bottom of the plot but here we put it at the top
140 self.pW3.addAutoLegend("top")
141
142 self.pW4=CompuCellSetup.viewManager.plotManager.getNewPlotWindow()
143 if not self.pW4:
144 return
145 #Plot Title - properties
146 self.pW4.setTitle("Average Surface Area")
147 self.pW4.setTitleSize(12)
148 self.pW4.setTitleColor("Green")
149
150 #plot background
151 self.pW4.setPlotBackgroundColor("orange")
152
153 # properties of x axis
154 self.pW4.setXAxisTitle("MonteCarlo Step (MCS)")
155 self.pW4.setXAxisTitleSize(10)
156 self.pW4.setXAxisTitleColor("blue")
157
158 # properties of y axis
159 self.pW4.setYAxisTitle("Surface Area")
160 #self.pW.setYAxisLogScale()
161 self.pW4.setYAxisTitleSize(10)
162 self.pW4.setYAxisTitleColor("red")
163
164 self.pW4.addPlot("Non-Condensing")
165 self.pW4.addPlot("Condensing")
166 # plot MCS
167 self.pW4.changePlotProperty("Non-Condensing","LineWidth",1)
168 self.pW4.changePlotProperty("Non-Condensing","LineColor","red")
169 # plot MCS1
170 self.pW4.changePlotProperty("Condensing","LineWidth",1)
171 self.pW4.changePlotProperty("Condensing","LineColor","green")
172
173
174 self.pW4.addGrid()
175 #adding automatically generated legend
176 # default possition is at the bottom of the plot but here we put it at the top
177 self.pW4.addAutoLegend("top")
178
179
180
181 def step(self,mcs):
182 self.Potts=self.simulator.getPotts()
183 cell_counter1=0
184 cell_counter2=0
185 d2_CON=0
186 d2_NONCON=0
187 d_CON=0
188 d_NONCON=0
189 t1_volume=0
190 t2_volume=0
191 t1_surface=0
192 t2_surface=0
193
194
195 for cell in self.cellList:
196 if cell.type == 1:
197 list_attrib=CompuCell.getPyAttrib(cell)
198 cell_counter1+=1;
199 ptx=float(cell.xCM/float(cell.volume))
200 pty=float(cell.yCM/float(cell.volume))
201 pt2x=list_attrib[0]
202 pt2y=list_attrib[1]
203 dx2=(ptx-pt2x)**2
204 dy2=(pty-pt2y)**2
205 d2_CON+=(dx2+dy2)
206 d_CON+=(dx2+dy2)**(0.5)
207 list_attrib[0]=ptx
208 list_attrib[1]=pty
209 t1_volume += cell.volume
210 t1_surface += cell.surface
211
212 if cell.type == 2:
213 list_attrib=CompuCell.getPyAttrib(cell)
214 cell_counter2+=1;
215 ptx=float(cell.xCM/float(cell.volume))
216 pty=float(cell.yCM/float(cell.volume))
217 pt2x=list_attrib[0]
218 pt2y=list_attrib[1]
219 dx2=(ptx-pt2x)**2
220 dy2=(pty-pt2y)**2
221 d2_NONCON+=(dx2+dy2)
222 d_NONCON+=(dx2+dy2)**(0.5)
223 list_attrib[0]=ptx
224 list_attrib[1]=pty
225 t2_volume += cell.volume
226 t2_surface += cell.surface
227
228
229
230 AVE_d2_CON=d2_CON/cell_counter1/self.frequ
231 AVE_d2_NONCON=d2_NONCON/cell_counter2/self.frequ
232 AVE_d_CON=d_CON/cell_counter1/self.frequ
233 AVE_d_NONCON=d_NONCON/cell_counter2/self.frequ
234 if mcs%50==0:
235 self.pW.addDataPoint("Condensing",mcs,AVE_d2_CON/4)
236 self.pW.addDataPoint("Non-Condensing",mcs,AVE_d2_NONCON/4)
237 self.pW.showAllPlots()
238 self.pW2.addDataPoint("Condensing",mcs,AVE_d_CON)
239 self.pW2.addDataPoint("Non-Condensing",mcs,AVE_d_NONCON)
240 self.pW2.showAllPlots()
241 self.pW3.addDataPoint("Condensing",mcs,t1_volume/cell_counter1)
242 self.pW3.addDataPoint("Non-Condensing",mcs,t2_volume/cell_counter2)
243 self.pW3.showAllPlots()
244 self.pW4.addDataPoint("Condensing",mcs,t1_surface/cell_counter1)
245 self.pW4.addDataPoint("Non-Condensing",mcs,t2_surface/cell_counter2)
246 self.pW4.showAllPlots()
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