def _openFile(self):
try:
import CompuCellSetup
fileHandle, fullFileName = CompuCellSetup.openFileInSimulationOutputDirectory(self._fileName, "a")
except IOError:
print "Could not open file ", self._fileName, " for writing. Check if you have necessary permissions."
return fileHandle
def __openParameterfile(self, filename):
"""
Writes all parameters to a file.
:param filename:
:return:
"""
#TODO: change from pure text file to xml?
try:
import CompuCellSetup
self.__fileHandle, self.__fullFileName = CompuCellSetup.openFileInSimulationOutputDirectory(filename, "a")
except IOError:
print "Could not open file ", filename, \
" for writing. Check if you have necessary permissions."
def step(self,mcs):
fileName="diffusion_output/FGF_"+str(mcs)+".dat"
field=CompuCell.getConcentrationField(self.simulator,"FGF")
if field:
try:
import CompuCellSetup
fileHandle,fullFileName=CompuCellSetup.openFileInSimulationOutputDirectory(fileName,"w")
except IOError:
print "Could not open file ", fileName," for writing. Check if you have necessary permissions"
for i,j,k in self.everyPixel():
fileHandle.write("%d\t%d\t%d\t%f\n"%(i,j,k,field[i,j,k]))
fileHandle.close()
def step(self, mcs):
if self.execConfig.interuptMCS(mcs):
sumFitness_a = []
totalVolume = 0
umbrellaVolume = 0
intermediateVolume = 0
basalStemVolume = 0
mediumVolume = self.latticeSize
for cell in self.cellList:
if cell.type == self.BASALMEMBRANE:
mediumVolume -= cell.volume
if cell.type > self.BASALMEMBRANE:
totalVolume += cell.volume
if cell.type == self.UMBRELLA:
umbrellaVolume += cell.volume
mediumVolume -= cell.volume
elif cell.type == self.INTERMEDIATE:
intermediateVolume += cell.volume
mediumVolume -= cell.volume
else:
basalStemVolume += cell.volume
mediumVolume -= cell.volume
if totalVolume == 0 or mediumVolume == 0:
fitness_v = 0.0
# print "No more cell in simulation"
self.stopSimulation()
else:
fitness_v = (
(
self.latticeSize
/ ((float(self.idealUmbrellaCellsVol) - float(umbrellaVolume)) ** 2.0 / 3.0 + self.latticeSize)
)
+ (
self.latticeSize
/ (
(float(self.idealIntermediateCellsVol) - float(intermediateVolume)) ** 2.0 / 3.0
+ self.latticeSize
)
)
+ (
self.latticeSize
/ (
(float(self.idealBasalStemCellsVol) - float(basalStemVolume)) ** 2.0 / 3.0
+ self.latticeSize
)
)
) / 3.0
for x in xrange(13, self.execConfig.xDimension, 20):
swaps = 0
layers = 0
cells_in_order = []
for y in xrange(3, self.execConfig.yDimension, 7):
# Gives the mode of a cell ID in a 5x3 pixels rectangle
mode_of_cellIDs = []
for width in xrange(0, 2, 1):
for height in xrange(0, 2, 1):
if self.cellField[x + width, y + height, 0] is not None:
mode_of_cellIDs.append(self.cellField[x + width, y + height, 0].id)
# If mode ID exists and in not already in cell_in_order list it will be added
if len(mode_of_cellIDs) > 0:
cellToCheck = self.attemptFetchingCellById(self.mode(mode_of_cellIDs))
exist = False
for cell in cells_in_order:
if cellToCheck.id == cell.id:
exist = True
if not exist:
cells_in_order.append(cellToCheck)
layers = len(cells_in_order)
if layers == 0:
fitness_a = 0
else:
if cells_in_order[layers - 1].type == self.UMBRELLA:
lastLayer = 1
layers -= 1
else:
lastLayer = 0
if cells_in_order[0].type == self.STEM or cells_in_order[0].type == self.BASAL:
firstLayer = 1
layers -= 1
else:
firstLayer = 0
layersInBetween = layers
for x in range(firstLayer, len(cells_in_order) - 1 - lastLayer, 1):
if cells_in_order[x].type != self.INTERMEDIATE:
layersInBetween -= 1
fitness_a = 1.0 / (
(1.0 - float(firstLayer)) + (1.0 - float(lastLayer)) + (layers - layersInBetween) + 1.0
)
sumFitness_a.append(fitness_a)
if len(sumFitness_a) == 0:
self.optimum.append(0 + 1.0 / 2.0 * fitness_v)
else:
fitness_a = sum(sumFitness_a) / len(sumFitness_a)
self.optimum.append(1.0 / 2.0 * fitness_a + 1.0 / 2.0 * fitness_v)
if len(self.optimum) == 0:
fitness = 0
else:
fitness = sum(self.optimum) / len(self.optimum)
fileName = "FitnessPlot.dat"
try:
import CompuCellSetup
fileHandle, fullFileName = CompuCellSetup.openFileInSimulationOutputDirectory(fileName, "a")
except IOError:
print "Could not open file ", fileName, " for writing. Check if you have necessary permissions"
fileHandle.write("%s " % (float(mcs) / 1440.0))
fileHandle.write("%s " % (fitness))
fileHandle.write("\n")
fileHandle.close()
fileName = "FitnessArrangement.dat"
try:
import CompuCellSetup
fileHandle, fullFileName = CompuCellSetup.openFileInSimulationOutputDirectory(fileName, "a")
except IOError:
print "Could not open file ", fileName, " for writing. Check if you have necessary permissions"
fileHandle.write("%s " % (float(mcs) / 1440.0))
fileHandle.write("%s " % (fitness_a))
fileHandle.write("\n")
fileHandle.close()
fileName = "FitnessVolume.dat"
try:
import CompuCellSetup
fileHandle, fullFileName = CompuCellSetup.openFileInSimulationOutputDirectory(fileName, "a")
except IOError:
print "Could not open file ", fileName, " for writing. Check if you have necessary permissions"
fileHandle.write("%s " % (float(mcs) / 1440.0))
fileHandle.write("%s " % (fitness_v))
fileHandle.write("\n")
fileHandle.close()
del self.optimum[:]
