def calc_mean_attribute(sim_dir_path, attribute, output_type, file_process,
starting_time=2400):
attributes = {'name':attribute,
'starting_time':str(starting_time),
'header':'mean,std'}
sim_dir_path = basic.check_path(sim_dir_path)
results_file_path = os.path.join(sim_dir_path, 'results.xml')
results_output = results.ResultsOutput(path=results_file_path)
result_set = results.ResultSet(results_output, attributes)
if len(result_set.members) > 0:
result = result_set.members[0]
return float(result.vars['mean']), float(result.vars['std'])
values = []
file_dir = os.path.join(sim_dir_path, output_type)
basic.unzip_files(file_dir+'.zip')
file_list = basic.file_list(file_dir)
for filename in file_list:
args = [attribute, filename]
val = file_process(*args)
# If output.time < starting_time, None will be returned
if not val == None:
values.append(val)
single_result = results.SingleResult()
mean_value = numpy.mean(values)
std_value = numpy.std(values)
single_result.vars['mean'] = mean_value
single_result.vars['std'] = std_value
result_set.members.append(single_result)
result_set.update_results_output()
results_output.write(results_file_path)
basic.rm_dir(file_dir)
return mean_value, std_value
def get_all_cells_location(sim_dir_path, iternum=480):
sim_dir_path = basic.check_path(sim_dir_path)
attributes = {'name':'locations', 'header':'X,Y'}
results_file_path = os.path.join(sim_dir_path, 'cell_locations.xml')
results_output = results.ResultsOutput(path=results_file_path)
result_set = results.ResultSet(results_output, attributes)
#requirements = {'family':'', 'genealogy':''}
file_dir = os.path.join(sim_dir_path, 'agent_State')
basic.unzip_files(file_dir+'.zip')
file_list = basic.file_list(file_dir)
for filename in file_list:
output = results.AgentOutput(path=filename)
if output.iterate == iternum:
output = results.AgentOutput(path=filename)
cells = output.get_all_cells()
#species = results.SpeciesOutput(output)
#cells = species.find_cells(requirements)
for cell in cells:
single_result = results.SingleResult()
single_result.vars['X'] = cell.vars['locationX']
single_result.vars['Y'] = cell.vars['locationY']
result_set.members.append(single_result)
result_set.update_results_output()
results_output.write(results_file_path)
basic.rm_dir(file_dir)
return result_set
#sim_dir_path = sys.argv[1]
#get_grid_size(sim_dir_path)
#get_all_cells_location(sim_dir_path)
def build_population_structure(sim_dir_path, attribute,
bins=numpy.linspace(0, 0.6, 121), starting_time=2400,
biomass_names=['activeBiomassGrowth', 'activeBiomassRepair', 'inactiveBiomassGrowth', 'activeBiomassRepair']):
attributes = {'name':attribute+' population structure',
'starting_time':str(starting_time),
'header':'bin,frequency'}
sim_dir_path = basic.check_path(sim_dir_path)
results_file_path = os.path.join(sim_dir_path, 'results.xml')
results_output = results.ResultsOutput(path=results_file_path)
result_set = results.ResultSet(results_output, attributes)
if len(result_set.members) > 0:
return result_set.members
attr_values = []
total_pop = 0.0
file_dir = os.path.join(sim_dir_path, 'agent_State')
basic.unzip_files(file_dir+'.zip')
file_list = basic.file_list(file_dir)
for filename in file_list:
output = results.AgentOutput(path=filename)
if output.time >= starting_time:
species = results.SpeciesOutput(output)
species.set_biomass_names(biomass_names)
attr_values.extend(species.get_attribute_values(attribute))
total_pop += species.population()
hist, bin_edges = numpy.histogram(attr_values, bins)
for i in range(len(hist)):
single_result = results.SingleResult()
single_result.vars['bin'] = str(bins[i+1])+'-'+str(bins[i])
single_result.vars['frequency'] = str(float(hist[i])/total_pop)
result_set.members.append(single_result)
result_set.update_results_output()
results_output.write(results_file_path)
basic.rm_dir(file_dir)
return result_set
def build_life_history(sim_dir_path, attribute, cell_id=(1,0),
biomass_names=['activeBiomass', 'inactiveBiomass']):
sim_dir_path = basic.check_path(sim_dir_path)
attributes = {'name':attribute, 'header':'time,value'}
results_file_path = os.path.join(sim_dir_path, 'results.xml')
results_output = results.ResultsOutput(path=results_file_path)
result_set = results.ResultSet(results_output, attributes)
if len(result_set.members) > 0:
return result_set.members
requirements = {'family':str(cell_id[0]), 'genealogy':str(cell_id[1])}
file_dir = os.path.join(sim_dir_path, 'agent_State')
basic.unzip_files(file_dir+'.zip')
file_list = basic.file_list(file_dir)
for filename in file_list:
output = results.AgentOutput(path=filename)
species = results.SpeciesOutput(output)
cells = species.find_cells(requirements)
cell = cells[0]
single_result = results.SingleResult()
single_result.vars['time'] = output.time
if attribute == 'specific growth rate':
single_result.vars['value'] = \
cell.get_specific_growth_rate(biomass_names)
else:
single_result.vars['value'] = cell.vars[attribute]
result_set.members.append(single_result)
result_set.update_results_output()
results_output.write(results_file_path)
basic.rm_dir(file_dir)
return result_set
def build_population_structure(sim_dir_path,
attribute='specific growth rate',
bins=numpy.linspace(0, 0.6, 90),
starting_time=2400,
biomass_names=[
'activeBiomassGrowth',
'activeBiomassRepair',
'inactiveBiomassGrowth',
'inactiveBiomassRepair'
]):
sim_dir_path = os.path.join(
'/Volumes/Robyn_W_2/july_2018/paper/comparison_clegg/' + sim_dir_path +
'/')
attr_values = []
total_pop = 0.0
file_dir = os.path.join(sim_dir_path, 'agent_State')
basic.unzip_files(file_dir + '.zip')
file_list = basic.file_list(file_dir)
all_growth = []
for filename in file_list:
output = results.AgentOutput(path=filename)
if output.time >= starting_time:
species = results.SpeciesOutput(output)
species.set_biomass_names(biomass_names)
attr_values.extend(species.get_attribute_values(attribute))
all_growth.append(species.get_attribute_values(attribute))
total_pop += species.population()
hist, bin_edges = numpy.histogram(attr_values, bins)
bin_using, frequencies = [], []
for i in range(len(hist)):
bin_using.append((bins[i + 1] + bins[i]) / 2)
frequencies.append(float(hist[i] / total_pop))
basic.rm_dir(file_dir)
return bin_using, frequencies, all_growth
def get_biomass(sim_dir_path, a):
times1, biomass1, population1, growthrate1 = [], [], [], []
times2, biomass2, population2, growthrate2 = [], [], [], []
file_path = '/Volumes/Robyn_W_2/july_2018/paper/' + sim_dir_path
file_dir = file_path + '/agent_sum'
basic.unzip_files(file_dir + '.zip')
file_list = basic.file_list(file_dir)
for filename in file_list:
output = results.AgentOutput(path=filename)
species1 = results.SpeciesOutput(output, 'OldieA')
requirements = {}
cells = species1.find_cells(requirements)
times1.append(float(output.time))
if len(cells) == 0:
continue
cell = cells[0]
population1.append(float(cell.vars['population']))
biomass1.append(float(cell.vars['mass']))
growthrate1.append(float(cell.vars['growthRate']))
species2 = results.SpeciesOutput(output, 'OldieB')
cells = species2.find_cells(requirements)
times2.append(float(output.time))
if len(cells) == 0:
continue
cell = cells[0]
population2.append(float(cell.vars['population']))
biomass2.append(float(cell.vars['mass']))
growthrate2.append(float(cell.vars['growthRate']))
basic.rm_dir(file_dir)
lists_a, lists_b = [population1, biomass1,
growthrate1], [population2, biomass2, growthrate2]
t_a1, t_b1 = times1, times2
for i in range(3):
list1, list2, list3, list4 = t_a1, lists_a[i], t_b1, lists_b[i]
t_a, lists_a[i] = (list(x) for x in zip(
*sorted(zip(list1, list2), key=itemgetter(0))))
t_b, lists_b[i] = (list(x) for x in zip(
*sorted(zip(list3, list4), key=itemgetter(0))))
biomass_ratio, population_ratio, growthrate_ratio = [], [], []
for j in range(len(lists_a[1])):
if lists_a[1][j] == 0 and lists_b[1][j] == 0 or lists_a[1][
j] == 0 and lists_b[1][j] != 0 or lists_a[1][
j] != 0 and lists_b[1][j] == 0:
biomass_ratio.append(0)
else:
biomass_ratio.append(numpy.log(lists_a[1][j] / lists_b[1][j]))
if lists_a[0][j] == 0 and lists_b[0][j] == 0 or lists_a[0][
j] == 0 and lists_b[0][j] != 0 or lists_a[0][
j] != 0 and lists_b[0][j] == 0:
population_ratio.append(0)
else:
population_ratio.append(lists_a[0][j] / lists_b[0][j])
if lists_a[2][j] == 0 and lists_b[2][j] == 0 or lists_a[2][
j] == 0 and lists_b[2][j] != 0 or lists_a[2][
j] != 0 and lists_b[2][j] == 0:
growthrate_ratio.append(0)
else:
growthrate_ratio.append(lists_a[2][j] / lists_b[2][j])
return t_a, biomass_ratio, population_ratio, growthrate_ratio
def clean_up(self):
"""
if os.path.isdir( self.env_Sum ):
toolbox_basic.rm_dir(self.env_Sum)
if os.path.isdir( self.env_State ):
toolbox_basic.rm_dir(self.env_State)
if os.path.isdir( self.agent_Sum ):
toolbox_basic.rm_dir(self.agent_Sum)
"""
if os.path.isdir( self.agent_State ):
toolbox_basic.rm_dir(self.agent_State)
"""
def clean_up(self):
if os.path.isdir( self.env_Sum ):
toolbox_basic.rm_dir(self.env_Sum)
if os.path.isdir( self.env_State ):
toolbox_basic.rm_dir(self.env_State)
if os.path.isdir( self.agent_Sum ):
toolbox_basic.rm_dir(self.agent_Sum)
if os.path.isdir( self.agent_State ):
toolbox_basic.rm_dir(self.agent_State)
"""
def build_life_history(
sim_dir_path,
attribute1,
attribute2,
cell_id=(1, 0),
biomass_names=["activeBiomassGrowth", "activeBiomassRepair", "inactiveBiomassGrowth", "inactiveBiomassRepair"],
):
sim_dir_path = basic.check_path(sim_dir_path)
# this must be value and not value1 for the first value so that the plotting
# script can also plot older results at the same time
attributes = {"name": attribute1, "name2": attribute2, "name3": "generation", "header": "time,value,value2,value3"}
results_file_path = os.path.join(sim_dir_path, "life_history_results.xml")
results_output = results.ResultsOutput(path=results_file_path)
result_set = results.ResultSet(results_output, attributes)
if len(result_set.members) > 0:
return result_set.members
requirements = {"family": str(cell_id[0]), "genealogy": str(cell_id[1])}
file_dir = os.path.join(sim_dir_path, "agent_State")
basic.unzip_files(file_dir + ".zip")
file_list = basic.file_list(file_dir)
for filename in file_list:
output = results.AgentOutput(path=filename)
species = results.SpeciesOutput(output)
cells = species.find_cells(requirements)
single_result = results.SingleResult()
single_result.vars["time"] = output.time
if len(cells) == 0:
continue
cell = cells[0]
single_result.vars["value3"] = cell.vars["generation"]
if attribute1 == "specific growth rate":
single_result.vars["value"] = cell.get_specific_growth_rate(biomass_names)
else:
single_result.vars["value"] = cell.vars[attribute1]
if attribute2 == "specific growth rate":
single_result.vars["value2"] = cell.get_specific_growth_rate(biomass_names)
else:
single_result.vars["value2"] = cell.vars[attribute2]
result_set.members.append(single_result)
result_set.update_results_output()
results_output.write(results_file_path)
basic.rm_dir(file_dir)
return result_set
def build_population_structure(
sim_dir_path,
attribute,
bins=numpy.linspace(0, 0.6, 90),
starting_time=2400,
biomass_names=["activeBiomassGrowth", "activeBiomassRepair", "inactiveBiomassGrowth", "inactiveBiomassRepair"],
):
attributes = {
"name": attribute + " population structure",
"starting_time": str(starting_time),
"header": "bin,frequency",
}
print sim_dir_path
sim_dir_path = basic.check_path(sim_dir_path)
results_file_path = os.path.join(sim_dir_path, "results.xml")
results_output = results.ResultsOutput(path=results_file_path)
result_set = results.ResultSet(results_output, attributes)
if len(result_set.members) > 0:
return result_set.members
attr_values = []
total_pop = 0.0
file_dir = os.path.join(sim_dir_path, "agent_State")
basic.unzip_files(file_dir + ".zip")
file_list = basic.file_list(file_dir)
for filename in file_list:
output = results.AgentOutput(path=filename)
if output.time >= starting_time:
species = results.SpeciesOutput(output)
species.set_biomass_names(biomass_names)
attr_values.extend(species.get_attribute_values(attribute))
total_pop += species.population()
hist, bin_edges = numpy.histogram(attr_values, bins)
for i in range(len(hist)):
single_result = results.SingleResult()
single_result.vars["bin"] = str(bins[i + 1]) + "-" + str(bins[i])
single_result.vars["frequency"] = str(float(hist[i]) / total_pop)
result_set.members.append(single_result)
result_set.update_results_output()
results_output.write(results_file_path)
basic.rm_dir(file_dir)
return result_set
def build_life_history(sim_dir_path,
attribute1='specific growth rate',
attribute2='age',
cell_id=(1, 0),
biomass_names=[
'activeBiomassGrowth', 'activeBiomassRepair',
'inactiveBiomassGrowth', 'inactiveBiomassRepair'
]):
sim_dir_path = os.path.join(
'//Volumes/Robyn_W_2/july_2018/paper/comparison_clegg/' +
sim_dir_path + '/')
time, generation, spec_growth, age, inact_rep, act_rep, inact_gro, act_gro, total_biomass = [], [], [], [], [], [], [], [], []
requirements = {'family': str(cell_id[0]), 'genealogy': str(cell_id[1])}
file_dir = os.path.join(sim_dir_path, 'agent_State')
basic.unzip_files(file_dir + '.zip')
file_list = basic.file_list(file_dir)
for filename in file_list:
#print filename
output = results.AgentOutput(path=filename)
species = results.SpeciesOutput(output)
cells = species.find_cells(requirements)
time.append(output.time)
if len(cells) == 0:
continue
cell = cells[0]
generation.append(cell.vars['generation'])
ar = cell.vars['activeBiomassRepair']
act_rep.append(ar)
ir = cell.vars['inactiveBiomassRepair']
inact_rep.append(ir)
ag = cell.vars['activeBiomassGrowth']
act_gro.append(ag)
ig = cell.vars['inactiveBiomassGrowth']
inact_gro.append(ig)
total_biomass.append(ar + ir + ag + ig)
spec_growth.append(cell.get_specific_growth_rate(biomass_names))
age.append(cell.vars[attribute2])
basic.rm_dir(file_dir)
return time, generation, spec_growth, age, inact_rep, act_rep, inact_gro, act_gro
type="int", help="number of images per second")
parser.add_option("-r", "--ResultsDir", dest="results_dir",
default=os.getcwd(), help="path to results directory")
parser.add_option("-s", "--SoluteName", dest="solute_name", default="none",
help="name of the solute to be plotted behind cells")
(options, args) = parser.parse_args()
sim = toolbox_idynomics.SimulationDirectory(options.results_dir)
save_name = 'biofilm_'+options.solute_name
file_list = toolbox_basic.file_list(sim.figures_dir, save_name+'*.png')
num_digits = len(str(len(file_list)))
temp_dir = os.path.join(os.path.abspath(sim.movies_dir), 'temp')
toolbox_basic.make_dir(temp_dir)
for i, filename in enumerate(file_list):
save_num = str(i)
link_name = 'img' + (num_digits-len(save_num))*'0' + save_num + '.png'
link_name = os.path.join(temp_dir, link_name)
toolbox_basic.make_symbolic_link(filename, link_name)
cmd = "ffmpeg -framerate "+str(options.frame_rate)+" -i '"
cmd += os.path.join(temp_dir, "img%"+str(num_digits)+"d.png'")
cmd += " -pix_fmt yuv420p -r 24 '"
cmd += os.path.join(os.path.abspath(sim.movies_dir), save_name+".mp4'")
os.system(cmd)
toolbox_basic.rm_dir(temp_dir)
def get_all(folder, f):
sim_dir_path = basic.check_path(folder + f + '/')
file_dir = os.path.join(sim_dir_path, 'agent_Sum')
basic.unzip_files(file_dir + '.zip')
file_list = basic.file_list(file_dir)
t_a, population_a, biomass_a, growthrate_a = [], [], [], []
t_b, population_b, biomass_b, growthrate_b = [], [], [], []
last_pop_a, last_biomass_a, last_growthrate_a = [], [], []
last_pop_b, last_biomass_b, last_growthrate_b = [], [], []
for filename in file_list:
output = results.AgentOutput(path=filename)
species = results.SpeciesOutput(output, 'OldieA')
requirements = {}
cells = species.find_cells(requirements)
#single_result = results.SingleResult()
t_a.append(float(output.time))
if len(cells) == 0:
continue
cell = cells[0]
population_a.append(float(cell.vars['population']))
biomass_a.append(float(cell.vars['mass']))
growthrate_a.append(float(cell.vars['growthRate']))
species = results.SpeciesOutput(output, 'OldieB')
requirements = {}
cells = species.find_cells(requirements)
#single_result = results.SingleResult()
t_b.append(float(output.time))
if len(cells) == 0:
continue
cell = cells[0]
population_b.append(float(cell.vars['population']))
biomass_b.append(float(cell.vars['mass']))
growthrate_b.append(float(cell.vars['growthRate']))
basic.rm_dir(file_dir)
lists_a, lists_b = [population_a, biomass_a,
growthrate_a], [population_b, biomass_b, growthrate_b]
t_a1, t_b1 = t_a, t_b
for i in range(3):
list1, list2, list3, list4 = t_a1, lists_a[i], t_b1, lists_b[i]
t_a, lists_a[i] = (list(x) for x in zip(
*sorted(zip(list1, list2), key=itemgetter(0))))
t_b, lists_b[i] = (list(x) for x in zip(
*sorted(zip(list3, list4), key=itemgetter(0))))
biomass_ratio, population_ratio, growthrate_ratio = [], [], []
for j in range(len(lists_a[1])):
biomass_ratio.append(numpy.log(lists_a[1][j] / lists_b[1][j]))
population_ratio.append(numpy.log(lists_a[0][j] / lists_b[0][j]))
if lists_a[2][j] == 0 and lists_b[2][j] == 0:
growthrate_ratio.append(0)
elif lists_a[2][j] == 0:
lists_b[2][j] = abs(1 / (lists_b[2][j]))
growthrate_ratio.append(numpy.log(lists_b[2][j]))
elif lists_b[2][j] == 0:
lists_a[2][j] = abs((lists_a[2][j]) / 1)
growthrate_ratio.append(numpy.log(lists_a[2][j]))
else:
growthrate_ratio.append(
abs(numpy.log(lists_a[2][j] / lists_b[2][j])))
if j == len(lists_a[1]) - 1:
last_pop_a.append(lists_a[0][j])
last_pop_b.append(lists_b[0][j])
last_biomass_a.append(lists_a[1][j])
last_biomass_b.append(lists_b[1][j])
last_growthrate_a.append(lists_a[2][j])
last_growthrate_b.append(lists_b[2][j])
return t_a, [biomass_ratio, population_ratio, growthrate_ratio]
help="path to results directory")
parser.add_option("-s",
"--SoluteName",
dest="solute_name",
default="none",
help="name of the solute to be plotted behind cells")
(options, args) = parser.parse_args()
sim = toolbox_idynomics.SimulationDirectory(options.results_dir)
save_name = 'biofilm_' + options.solute_name
file_list = toolbox_basic.file_list(sim.figures_dir, save_name + '*.png')
num_digits = len(str(len(file_list)))
temp_dir = os.path.join(os.path.abspath(sim.movies_dir), 'temp')
toolbox_basic.make_dir(temp_dir)
for i, filename in enumerate(file_list):
save_num = str(i)
link_name = 'img' + (num_digits - len(save_num)) * '0' + save_num + '.png'
link_name = os.path.join(temp_dir, link_name)
toolbox_basic.make_symbolic_link(filename, link_name)
cmd = "ffmpeg -framerate " + str(options.frame_rate) + " -i '"
cmd += os.path.join(temp_dir, "img%" + str(num_digits) + "d.png'")
cmd += " -pix_fmt yuv420p -r 24 '"
cmd += os.path.join(os.path.abspath(sim.movies_dir), save_name + ".mp4'")
os.system(cmd)
toolbox_basic.rm_dir(temp_dir)
