def REMOVE_DC_FROM_DISCRETE_GRID(dcoord_vec, dCellNum, occupiedPositions):
for p in range(3):
p -= 1
if (dcoord_vec[0] + p >= numPositions):
break
elif dcoord_vec[0] + p < 0:
continue
for q in range(3):
q -= 1
if dcoord_vec[1] + q >= numPositions:
break
elif dcoord_vec[1] + q < 0:
continue
for r in range(3):
r -= 1
if dcoord_vec[2] + r >= numPositions:
break
elif dcoord_vec[2] + r < 0:
continue
# now clear this particular dCellNum from the position in the occupiedPositions array
nearbyDCs = occupiedPositions[threed_to_1d(
dcoord_vec + np.asarray([p, q, r]), numPositions)]
nearbyDCs = np.delete(nearbyDCs,
np.where(nearbyDCs == dCellNum))
occupiedPositions[threed_to_1d(
dcoord_vec + np.asarray([p, q, r]),
numPositions)] = nearbyDCs
def CHECK_CONTACT_WITH_DENDRITES_DC(posn_vec, inContact, dCellList,
occupiedPositions):
coord_vec = set_coordinates(posn_vec, radius, cellSide)
nearbyDCs = occupiedPositions[threed_to_1d(coord_vec, numPositions)]
if isinstance(nearbyDCs, float):
pass
else:
for j in nearbyDCs:
cell = dCellList[int(j)]
dend_vec = cell.posn
diff_vec = posn_vec - dend_vec
if diff_vec.dot(diff_vec) <= contactRadius**2:
inContact = 1
break
return inContact
def PLACE_DC_ON_GRID(i, dCellList, occupiedPositions):
cell = dCellList[i]
cellStatus = False
while (cellStatus == False):
# let's generate potential coordinates
posn_vec = np.random.uniform(-1, 1, 3) * radius
if inside_sphere(posn_vec, radius):
# we need to check it's not touching any other DCs now
inContact = 0
inContact = CHECK_CONTACT_WITH_DENDRITES_DC(
posn_vec, inContact, dCellList, occupiedPositions)
if inContact == 1:
continue
else:
cell.posn = posn_vec
cellStatus = True
else:
continue
# better update the occupied positions list
coord_vec = set_coordinates(posn_vec, radius, cellSide)
if occupiedPositions[threed_to_1d(coord_vec, numPositions)] == 0.0:
occupiedPositions[threed_to_1d(coord_vec, numPositions)] = [i]
else:
occupiedPositions[threed_to_1d(coord_vec, numPositions)].append(i)
def GET_CONTACTING_DC_COORDS_AND_NUM(posn_vec, dCellList, tCellList, tCellNum,
occupiedPositions):
coord_vec = set_coordinates(posn_vec, radius, cellSide)
nearbyDCs = occupiedPositions[threed_to_1d(coord_vec, numPositions)]
if isinstance(nearbyDCs, float):
pass
else:
for j in nearbyDCs:
cell = dCellList[int(j)]
if (HAS_CONTACTED_DC(tCellNum, j, tCellList)):
continue
dend_vec = cell.posn
diff_vec = posn_vec - dend_vec
if diff_vec.dot(diff_vec) <= contactRadius**2:
cont_vec = dend_vec
contNum = j
break
return [cont_vec, contNum]