def setup_heterogeneous_progenitors(sim_dir_path):
sim_dir_path = basic.check_path(sim_dir_path)
last_path = os.path.join(sim_dir_path, 'lastIter', 'agent_State(last).xml')
output, species = results.get_single_species(last_path)
timestep = float(output.time) / float(output.iterate)
agent_State_dir = basic.unzip_files(
os.path.join(sim_dir_path, 'agent_State.zip'))
save_cells = []
for cell in species.members:
genealogy = int(cell.vars['genealogy'])
if genealogy == 1:
iter = int(float(cell.vars['birthday']) / timestep)
iter_path = os.path.join(agent_State_dir,
'agent_State(' + str(iter) + ').xml')
iter_output, iter_species = results.get_single_species(iter_path)
requirements = {'family': cell.vars['family'], 'genealogy': 0}
oldie = species.find_cells(requirements)[0]
oldie.vars['generation'] = 0
save_cells.append(oldie)
requirements['genealogy'] = 1
newbie = species.find_cells(requirements)[0]
newbie.vars['family'] = int(newbie.vars['family']) + 15
newbie.vars['generation'] = 0
newbie.vars['genealogy'] = 0
newbie.vars['birthday'] = 0.0
save_cells.append(newbie)
species.members = save_cells
species.update_agent_output()
save_path = os.path.join(sim_dir_path, 'agentS.xml')
output.write(output_path=save_path)
def setup_heterogeneous_progenitors(sim_dir_path):
sim_dir_path = basic.check_path(sim_dir_path)
last_path = os.path.join(sim_dir_path, 'lastIter', 'agent_State(last).xml')
output, species = results.get_single_species(last_path)
timestep = float(output.time) / float(output.iterate)
agent_State_dir = basic.unzip_files(os.path.join(sim_dir_path,
'agent_State.zip'))
save_cells = []
for cell in species.members:
genealogy = int(cell.vars['genealogy'])
if genealogy == 1:
iter = int( float(cell.vars['birthday']) / timestep )
iter_path = os.path.join(agent_State_dir,
'agent_State('+str(iter)+').xml')
iter_output, iter_species = results.get_single_species(iter_path)
requirements = {'family': cell.vars['family'], 'genealogy':0}
oldie = species.find_cells(requirements)[0]
oldie.vars['generation'] = 0
save_cells.append(oldie)
requirements['genealogy'] = 1
newbie = species.find_cells(requirements)[0]
newbie.vars['family'] = int(newbie.vars['family']) + 15
newbie.vars['generation'] = 0
newbie.vars['genealogy'] = 0
newbie.vars['birthday'] = 0.0
save_cells.append(newbie)
species.members = save_cells
species.update_agent_output()
save_path = os.path.join(sim_dir_path, 'agentS.xml')
output.write(output_path=save_path)
def get_first_fifteen(sim_dir_path):
sim_dir_path = basic.check_path(sim_dir_path)
last_path = os.path.join(sim_dir_path, 'lastIter', 'agent_State(last).xml')
output, species = results.get_single_species(last_path)
species.members = species.members[:15]
for i in range(15):
cell = species.members[i]
cell.vars['family'] = i + 1
cell.vars['genealogy'] = 0
cell.vars['generation'] = 0
cell.vars['birthday'] = 0.0
species.update_agent_output()
save_path = os.path.join(sim_dir_path, 'agentS.xml')
output.write(output_path=save_path)
def get_first_fifteen(sim_dir_path):
sim_dir_path = basic.check_path(sim_dir_path)
last_path = os.path.join(sim_dir_path, 'lastIter', 'agent_State(last).xml')
output, species = results.get_single_species(last_path)
species.members = species.members[:15]
for i in range(15):
cell = species.members[i]
cell.vars['family'] = i + 1
cell.vars['genealogy'] = 0
cell.vars['generation'] = 0
cell.vars['birthday'] = 0.0
species.update_agent_output()
save_path = os.path.join(sim_dir_path, 'agentS.xml')
output.write(output_path=save_path)
def process_last_iter(sim_dir_path, max_generation, use_masses=True):
sim_dir_path = basic.check_path(sim_dir_path)
last_path = os.path.join(sim_dir_path, 'lastIter', 'agent_State(last).xml')
last_path = basic.check_path(last_path)
last_output, last_species = results.get_single_species(last_path)
if use_masses:
agent_State_dir = basic.unzip_files(
os.path.join(sim_dir_path, 'agent_State.zip'))
biomass_names = ['activeBiomass', 'inactiveBiomass']
timestep = float(last_output.time) / float(last_output.iterate)
# do a first run-through
temp_cells = []
families = []
for cell in last_species.members:
family = int(cell.vars['family'])
if families.count(family) == 0:
families.append(family)
genealogy = int(cell.vars['genealogy'])
birthday = float(cell.vars['birthday'])
birth_generation = calc_birth_generation(genealogy)
for generation in range(birth_generation, max_generation + 2):
temp = LineageCell(last_species)
temp.vars['family'] = family
temp.vars['genealogy'] = genealogy
temp.vars['generation'] = generation
temp.vars['initial_time'] = birthday
if use_masses:
iter = str(int(birthday / timestep))
iter_path = os.path.join(agent_State_dir,
'agent_State(' + iter + ').xml')
iter_output, iter_species = results.get_single_species(
iter_path)
requirements = {'family': family, 'genealogy': genealogy}
iter_cell = iter_species.find_cells(requirements)[0]
temp.vars['initial_mass'] = iter_cell.get_total_biomass(
biomass_names)
requirements['genealogy'] = genealogy - 2**(generation - 1)
sibling = iter_species.find_cells(requirements)
if len(sibling) == 1:
temp.sibling_mass = sibling[0].get_total_biomass(
biomass_names)
temp_cells.append(temp)
print(
str(len(temp_cells)) + ' cells in ' + str(len(families)) + ' families')
# then filter
last_species.members = []
for family in families:
members = [c for c in temp_cells if c.vars['family'] == family]
next_gen = [c for c in members if c.vars['generation'] == 0]
for generation in range(max_generation + 1):
current_gen = next_gen
next_gen = [
c for c in members if c.vars['generation'] == generation + 1
]
for cell in current_gen:
genealogy = cell.vars['genealogy']
# find my baby
baby_genealogy = genealogy + 2**generation
possibles = [
c for c in next_gen
if c.vars['genealogy'] == baby_genealogy
]
if len(possibles) == 1:
baby = possibles[0]
baby_bday = baby.vars['initial_time']
cell.vars['division_time'] = baby_bday
if use_masses:
total_mass = baby.vars[
'initial_mass'] + baby.sibling_mass
cell.vars['division_mass'] = total_mass
possibles = [
c for c in next_gen if c.vars['genealogy'] == genealogy
]
if len(possibles) == 1:
me_next = possibles[0]
me_next.vars['initial_time'] = baby_bday
if use_masses:
me_next.vars['initial_mass'] = baby.sibling_mass
cell.set_growth_rate()
last_species.members.append(cell)
print(str(len(last_species.members)) + ' cells remain')
#for cell in temp_cells.members:
header = 'family,genealogy,generation,initial_time,division_time,'
header += 'initial_mass,division_mass,growth_rate'
last_species.change_header(header)
last_species.update_agent_output()
save_path = os.path.join(sim_dir_path, 'lineage_results.xml')
last_output.write(output_path=save_path)
def process_last_iter(sim_dir_path, max_generation, use_masses=True):
sim_dir_path = basic.check_path(sim_dir_path)
last_path = os.path.join(sim_dir_path, 'lastIter', 'agent_State(last).xml')
last_path = basic.check_path(last_path)
last_output, last_species = results.get_single_species(last_path)
if use_masses:
agent_State_dir = basic.unzip_files(os.path.join(sim_dir_path, 'agent_State.zip'))
biomass_names = ['activeBiomass','inactiveBiomass']
timestep = float(last_output.time) / float(last_output.iterate)
# do a first run-through
temp_cells = []
families = []
for cell in last_species.members:
family = int(cell.vars['family'])
if families.count(family) == 0:
families.append(family)
genealogy = int(cell.vars['genealogy'])
birthday = float(cell.vars['birthday'])
birth_generation = calc_birth_generation(genealogy)
for generation in range(birth_generation, max_generation+2):
temp = LineageCell(last_species)
temp.vars['family'] = family
temp.vars['genealogy'] = genealogy
temp.vars['generation'] = generation
temp.vars['initial_time'] = birthday
if use_masses:
iter = str(int( birthday / timestep ))
iter_path = os.path.join(agent_State_dir,
'agent_State('+iter+').xml')
iter_output, iter_species = results.get_single_species(iter_path)
requirements = {'family':family, 'genealogy':genealogy}
iter_cell = iter_species.find_cells(requirements)[0]
temp.vars['initial_mass'] = iter_cell.get_total_biomass(biomass_names)
requirements['genealogy'] = genealogy - 2**(generation-1)
sibling = iter_species.find_cells(requirements)
if len(sibling) == 1:
temp.sibling_mass = sibling[0].get_total_biomass(biomass_names)
temp_cells.append(temp)
print(str(len(temp_cells))+' cells in '+str(len(families))+' families')
# then filter
last_species.members = []
for family in families:
members = [c for c in temp_cells if c.vars['family'] == family]
next_gen = [c for c in members if c.vars['generation'] == 0]
for generation in range(max_generation + 1):
current_gen = next_gen
next_gen = [c for c in members if
c.vars['generation'] == generation+1]
for cell in current_gen:
genealogy = cell.vars['genealogy']
# find my baby
baby_genealogy = genealogy + 2**generation
possibles = [c for c in next_gen if
c.vars['genealogy'] == baby_genealogy]
if len(possibles) == 1:
baby = possibles[0]
baby_bday = baby.vars['initial_time']
cell.vars['division_time'] = baby_bday
if use_masses:
total_mass = baby.vars['initial_mass'] + baby.sibling_mass
cell.vars['division_mass'] = total_mass
possibles = [c for c in next_gen if
c.vars['genealogy'] == genealogy]
if len(possibles) == 1:
me_next = possibles[0]
me_next.vars['initial_time'] = baby_bday
if use_masses:
me_next.vars['initial_mass'] = baby.sibling_mass
cell.set_growth_rate()
last_species.members.append(cell)
print(str(len(last_species.members))+' cells remain')
#for cell in temp_cells.members:
header = 'family,genealogy,generation,initial_time,division_time,'
header += 'initial_mass,division_mass,growth_rate'
last_species.change_header(header)
last_species.update_agent_output()
save_path = os.path.join(sim_dir_path, 'lineage_results.xml')
last_output.write(output_path=save_path)