def moveCell(self, cell, shiftVector):
#we have to make two list of pixels :
pixelsToDelete=[] #used to hold pixels to delete
pixelsToMove=[] #used to hold pixels to move
# If we try to reassign pixels in the loop where we iterate over pixel data we will corrupt the container so in the loop below all we will do is to populate the two list mentioned above
pixelList=self.getCellPixelList(cell)
pt=CompuCell.Point3D()
print " Moving ",pixelList.numberOfPixels()," pixels of cell.id=",cell.id," . Shift vector=",shiftVector
for pixelTrackerData in pixelList:
pt.x = pixelTrackerData.pixel.x + shiftVector.x
pt.y = pixelTrackerData.pixel.y + shiftVector.y
pt.z = pixelTrackerData.pixel.z + shiftVector.z
# here we are making a copy of the cell
print "adding pt=",pt
pixelsToDelete.append(CompuCell.Point3D(pixelTrackerData.pixel))
if self.checkIfInTheLattice(pt):
pixelsToMove.append(CompuCell.Point3D(pt))
# self.cellField.set(pt,cell)
# Now we will move cell
for pixel in pixelsToMove:
# self.cellField.set(pixel,cell)
self.cellField[pixel.x,pixel.y,pixel.z]=cell
# Now we will delete old pixels
pixelList=self.getCellPixelList(cell)
pt=CompuCell.Point3D()
self.mediumCell=CompuCell.getMediumCell()
print " Deleting ",len(pixelsToDelete)," pixels of cell.id=",cell.id
for pixel in pixelsToDelete:
self.cellField[pixel.x,pixel.y,pixel.z]=self.mediumCell
def moveCell(self, cell, shiftVector):
#we have to make two list of pixels :
pixelsToDelete = [] #used to hold pixels to delete
pixelsToMove = [] #used to hold pixels to move
# If we try to reassign pixels in the loop where we iterate over pixel data we will corrupt the container so in the loop below all we will do is to populate the two list mentioned above
pixelList = self.getCellPixelList(cell)
pt = CompuCell.Point3D()
print " Moving ", pixelList.numberOfPixels(
), " pixels of cell.id=", cell.id, " . Shift vector=", shiftVector
for pixelTrackerData in pixelList:
pt.x = pixelTrackerData.pixel.x + shiftVector.x
pt.y = pixelTrackerData.pixel.y + shiftVector.y
pt.z = pixelTrackerData.pixel.z + shiftVector.z
# here we are making a copy of the cell
print "adding pt=", pt
pixelsToDelete.append(CompuCell.Point3D(pixelTrackerData.pixel))
if self.checkIfInTheLattice(pt):
pixelsToMove.append(CompuCell.Point3D(pt))
# self.cellField.set(pt,cell)
# Now we will move cell
for pixel in pixelsToMove:
# self.cellField.set(pixel,cell)
self.cellField[pixel.x, pixel.y, pixel.z] = cell
# Now we will delete old pixels
pixelList = self.getCellPixelList(cell)
pt = CompuCell.Point3D()
self.mediumCell = CompuCell.getMediumCell()
print " Deleting ", len(pixelsToDelete), " pixels of cell.id=", cell.id
for pixel in pixelsToDelete:
self.cellField[pixel.x, pixel.y, pixel.z] = self.mediumCell
def deleteCell(self,cell):
# pixelsToDelete=self.getCopyOfCellPixels(cell,SteppableBasePy.CC3D_FORMAT) # returns list of Point3D
pixelsToDelete=self.getCopyOfCellPixels(cell,SteppableBasePy.TUPLE_FORMAT) # returns list of tuples
self.mediumCell=CompuCell.getMediumCell()
for pixel in pixelsToDelete:
print "CELL.volume=",cell.volume
self.cellField[pixel[0],pixel[1],pixel[2]]=self.mediumCell
def deleteCell(self, cell):
# pixelsToDelete=self.getCopyOfCellPixels(cell,SteppableBasePy.CC3D_FORMAT) # returns list of Point3D
pixelsToDelete = self.getCopyOfCellPixels(
cell, SteppableBasePy.TUPLE_FORMAT) # returns list of tuples
self.mediumCell = CompuCell.getMediumCell()
for pixel in pixelsToDelete:
print "CELL.volume=", cell.volume
self.cellField[pixel[0], pixel[1], pixel[2]] = self.mediumCell
def cut(self,x0,y0,dx,dy):
medium=CompuCell.getMediumCell() #get medium
deleteCells = []
for xx in range(int(dx)):
x = int(x0-dx/2 + xx + .5)
for yy in range(int(dy)):
y = int(y0-dy/2 + yy + .5)
for z in range(self.dim.z):
cell=self.cellField[x,y,z]
if cell:
cell.targetVolume-=1 #decrease cell target volume by 1
if (-1<cell.targetVolume<0): deleteCells.append(cell)
self.cellField[x,y,z]=medium #replacing cell pixel by medium
for cell in deleteCells: #making sure cells are deleted
self.deleteCell(cell)
#
#
##
def start(self):
radi = self.dim.x/2
# Assign Property for Cell ID = 1
cells_to_die=[]
for cell in self.cellListByType(1):
cell.targetVolume = tVol
cell.lambdaVolume = 5
# Basal Membrane Generation
radi = int(self.dim.x/2)
pt=CompuCell.Point3D(0,0,0)
Wall = self.potts.createCellG(pt) # the arguments are (type,pt,xSize,ySize,zSize)
Wall.type = 2
totalNumOfSeg = 15
segm = []
cellsToDelete=[]
for pty in range(0,self.dim.y):
for ptx in range(0,self.dim.x):
for ptz in range(0,self.dim.z):
pt.y=pty
pt.x=ptx
pt.z=ptz
# Generate Tube structure
if pty>= radi:
if ((ptx-radi)**2+(ptz-radi)**2)<=radi**2 and ((ptx-radi)**2+(ptz-radi)**2)>=(radi-5)**2:
overwrittenCell=self.cellField.get(pt)
self.cellField.set(pt,Wall)
self.cleanDeadCells()
ang = math.atan2(ptx-radi,ptz-radi)*(180./math.pi)+180
segN= int(ang/(360/totalNumOfSeg))
if segN ==15:
segN = 0
segm.append([segN,pt])
elif ((ptx-radi)**2+(ptz-radi)**2)>radi**2:
self.cellField.set(pt,CompuCell.getMediumCell())
self.cleanDeadCells()
# Generate Semi-Sphere Sturcture ((Bottom of the crypt)
elif pty < radi:
if ((ptx-radi)**2+(pty-radi)**2+(ptz-radi)**2)<=radi**2 and ((ptx-radi)**2+(pty-radi)**2+(ptz-radi)**2)>=(radi-5)**2:
self.cellField.set(pt,Wall)
self.cleanDeadCells()
elif ((ptx-radi)**2+(pty-radi)**2+(ptz-radi)**2)>radi**2:
overwrittenCell=self.cellField.get(pt)
if pt.x!=0 and pt.y!=0 and pt.z!=0: # this line is essential because you do not wan to remove wall cell which sits at (0,0,0)
self.cellField.set(pt,CompuCell.getMediumCell())
self.cleanDeadCells()
# now we can overwrite (0,0,0) with medium
pt.x=0
pt.y=0
pt.z=0
self.cellField.set(pt,CompuCell.getMediumCell())
self.divideCellOrientationVectorBased(Wall,0,0,1)
for divN in range(0,3):
cell_to_divide=[]
# iterating over cells of type 2
for cell in self.cellListByType(2):
cell_to_divide.append(cell)
for cell in cell_to_divide:
DiviVectorX = (cell.xCOM-radi)
DiviVectorZ = (cell.zCOM-radi)
self.divideCellOrientationVectorBased(cell,-DiviVectorZ,0,DiviVectorX)
for divN in range(0,4):
cell_to_divide=[]
# iterating over cells of type 2
for cell in self.cellListByType(2):
cell_to_divide.append(cell)
for cell in cell_to_divide:
self.divideCellOrientationVectorBased(cell,0,1,0)
# Assign property for Cell type = 2
for cell in self.cellListByType(2):
cell.targetVolume = cell.volume
cell.lambdaVolume = 10000000
cells_to_die=[]
for cell in self.cellList:
if cell.type == 1:
# Program Cell Death
# Set up threshold to kill cells when cells go above the threshold
if cell.yCOM > self.dim.y-10:
cells_to_die.append(cell)
cellNeighborList=self.getCellNeighbors(cell) # generates list of neighbors of cell 'cell'
wallflag=0
# Kill cells when the cells not touching BM
for neighbor in cellNeighborList:
# neighborSurfaceData.neighborAddress is a pointer to one of 'cell' neighbors stired in cellNeighborList
#IMPORTANT: cell may have Medium (NULL pointer) as a neighbor. therefore before accessing neighbor we first check if it is no Medium
if neighbor.neighborAddress:
# Detect the cells touching BM
if neighbor.neighborAddress.type == 2:
wallflag=1
if wallflag==0:
# Delete the cells without contacting BM
cells_to_die.append(cell)
# Cell Killing program
for cell in cells_to_die:
cell.targetVolume = 0
self.deleteCell(cell)
# The next line araises the dead cell register
self.cleanDeadCells()
self.BreakCells()# call new BreakCells() to generate apical and basal cells from Epi cells
#Cell type-id and type-name:
self.typeIdTypeNameDict # {0:"Medium", 1:"CELL_TYPE_1", ...}
self.typeIdTypeNameDict[cell.type] # current cell's type name
len(self.typeIdTypeNameDict) # number of cell types + medium
#Cell from id:
cell=self.inventory.attemptFetchingCellById(id)
#Distance between cells:
D = self.distanceBetweenCells(cell,cell2) # D = sqrt(dx**2+dy**2+dz**2)
V = self.distanceVectorBetweenCells(cell,cell2) # [dx,dy,dz]
#
Access/Modify Cell Lattice:
pt=CompuCell.Point3D(x,y,z) # defines a lattice vector
medium=CompuCell.getMediumCell() #get Medium cell
cell=self.cellField.get(pt) # get cell that is on pt [self.cellField.get(pt.x,pt.y,pt.z)]
cell=self.cellField[x,y,0]
# to create a brand new cell
newcell=self.potts.createCellG(pt)
newcell.type=1 # don’t forget to assign a type to the new cell
cell=self.potts.createCell()
self.cellField.set(pt,cell) # to create an extension of that cell
self.cellField[x:x+4,y:y+4,0]=cell
#
SBML solver:
#Loading/adding SBML
self.addSBMLToCellTypes(_modelFile='',_modelName='',_types=[],_stepSize=1.0,_initialConditions={})
def start(self):
self.pixelAssigned=False
self.mediumCell=CompuCell.getMediumCell()
self.boundaryArray=self.boundaryMonitorPlugin.getBoundaryArray()
print 'self.boundaryArray=',self.boundaryArray
print 'dir(self.boundaryArray)=',dir(self.boundaryArray)
