def recruit_new(self, rec_rate_ph, rec_r, p_rec_r, tissue, grid, cyto):
num_reps = rec_rate_ph # maximum number of macrophages recruited per time step
cyto_index = np.argwhere(
np.logical_and(tissue == TissueType.BLOOD.value, cyto >= rec_r))
if len(cyto_index) == 0:
# nowhere to place cells
return
for _ in range(num_reps):
if p_rec_r > rg.random():
ii = rg.integers(cyto_index.shape[0])
point = Point(
x=grid.x[cyto_index[ii, 2]],
y=grid.y[cyto_index[ii, 1]],
z=grid.z[cyto_index[ii, 0]],
)
# Do we really want these things to always be in the exact center of the voxel?
# No we do not. Should not have any effect on model, but maybe some on
# visualization.
perturbation = rg.multivariate_normal(mean=[0.0, 0.0, 0.0],
cov=[[0.25, 0.0, 0.0],
[0.0, 0.25, 0.0],
[0.0, 0.0, 0.25]])
perturbation_magnitude = np.linalg.norm(perturbation)
perturbation /= max(1.0, perturbation_magnitude)
point += perturbation
self.append(MacrophageCellData.create_cell(point=point))
def recruit_new(self, rec_rate_ph, rec_r, granule_count, neutropenic, time, grid, tissue, cyto):
num_reps = 0
if not neutropenic:
num_reps = rec_rate_ph # number of neutrophils recruited per time step
elif neutropenic and 48 <= time <= 96:
# TODO: relate 3 to Algorithm S3.14 and rec_rate_ph or introduce neutropenic parameter
# In S3.14: num_reps = 6 and int( (time-48)/ 8), both are 1/3 values here
num_reps = int((time - 48) / 8) * 3
if num_reps <= 0:
return
cyto_index = np.argwhere(np.logical_and(tissue == TissueType.BLOOD.value, cyto >= rec_r))
if len(cyto_index) <= 0:
# nowhere to place cells
return
for _ in range(num_reps):
ii = rg.integers(cyto_index.shape[0])
point = Point(
x=grid.x[cyto_index[ii, 2]],
y=grid.y[cyto_index[ii, 1]],
z=grid.z[cyto_index[ii, 0]],
)
self.append(
NeutrophilCellData.create_cell(
point=point,
status=NeutrophilCellData.Status.NONGRANULATING,
granule_count=granule_count,
)
)
def remove_if_sporeless(self, val):
living = self.alive()
living_len = len(living)
num = int(val * living_len)
if num == 0 and living_len > 0:
num = 1
for _ in range(num):
r = rg.integers(living_len)
self.cell_data[living[r]]['dead'] = True