def make_experimental_data(jl_dir, py_dir):
with open(py_dir + '/observable.py') as f:
lines = f.readlines()
for i, line in enumerate(lines):
if line.find('class ExperimentalData') != -1:
lines = lines[i:]
break
lines = triming_tools.replace_characters(lines)
bracket = False
for i, line in enumerate(lines):
rep_line = line
rep_line = rep_line.replace('observables.index', 'observables_index')
key = line.replace(' ', '')
if key.find('={') != -1:
rep_line = rep_line.replace('{', 'Dict(')
bracket = True
if bracket:
rep_line = rep_line.replace(':', ' =>')
if line.find('}') != -1:
rep_line = rep_line.replace('}', ')')
bracket = False
lines[i] = rep_line
experimental_data = jl_source.experimental_data_header()
experiments = triming_tools.cut_out_lines(lines,
'len(observables)',
'def get_timepoint',
mode=1)[1:-1]
for i, line in enumerate(experiments):
experimental_data += triming_tools.indent_remover(line, 1)
experimental_data += jl_source.get_timepoint_header()
get_timepoint = triming_tools.cut_out_lines(lines, 'def get_timepoint',
'return')[1:]
for i, line in enumerate(get_timepoint):
rep_line = line
rep_line = rep_line.replace('observables.index', 'observables_index')
if line.find('return') != -1:
break
if line.replace(' ', '').find('exp_t=self.') != -1:
rep_line = ''
for j in range(triming_tools.space_counter(line)):
rep_line += ' '
rep_line += line.replace(' ', '').replace('exp_t=self.', 'return ')
experimental_data += triming_tools.indent_remover(rep_line, 1)
experimental_data += jl_source.get_timepoint_footer()
with open(jl_dir + '/experimental_data.jl', mode='w') as f:
f.write(experimental_data)
def convert_search_parameter(jl_dir, py_dir):
os.makedirs(
jl_dir, exist_ok=True
)
space_num = 4
with open(py_dir+'/search_parameter.py') as f:
lines = f.readlines()
search_parameter = jl_source.header()
search_parameter += jl_source.search_idx_const_header()
search_idx_const = triming_tools.cut_out_lines(
lines, 'search_idx_const=[', ']'
)[1:]
for i, line in enumerate(search_idx_const):
search_parameter += line.replace('\\', '')
search_parameter += jl_source.search_idx_const_footer()
search_parameter += jl_source.search_idx_init_header()
search_idx_init = triming_tools.cut_out_lines(
lines, 'search_idx_init=[', ']'
)[1:]
for i, line in enumerate(search_idx_init):
search_parameter += line.replace('\\', '')
search_parameter += jl_source.search_idx_init_footer()
search_parameter += jl_source.get_search_region_header()
lines = triming_tools.convert_comment_out(lines)
lines = triming_tools.lines_triming(lines, space_num)
lines = triming_tools.insert_end(lines)
# for i,line in enumerate(lines):
# print(line.replace('\n',''))
search_region = triming_tools.cut_out_lines(
lines, 'search_region=np.zeros', 'lin2log'
)[1:]
for i,line in enumerate(search_region):
line = line.replace('for i, j', 'for (i,j)')
line = line.replace('np.', '')
line = line.replace('len', 'length')
line = line.replace('(x)', '(p)')
line = triming_tools.list_adder(line)
search_parameter += line
search_parameter += jl_source.get_search_region_footer()
search_parameter += jl_source.lin2log()
with open(jl_dir + '/search_parameter.jl', mode='w') as f:
f.write(search_parameter)
def make_param_const(jl_dir, py_dir, space_num=4):
jl_dir = jl_dir + '/model/param_const.jl'
py_dir = py_dir + '/model/param_const.py'
with open(py_dir, mode='r') as f:
lines = f.readlines()
lines = triming_tools.lines_triming(lines, space_num)
lines = triming_tools.cut_out_lines(lines, 'len_f_params', 'return x')[1:]
param_const = jl_source.param_const_header()
for i, line in enumerate(lines):
param_const += line
param_const += jl_source.param_const_footer()
with open(jl_dir, mode='w') as f:
f.write(param_const)
def make_observable(jl_dir, py_dir):
with open(py_dir + '/observable.py') as f:
lines = f.readlines()
observable = jl_source.observable_header()
observables = triming_tools.cut_out_lines(lines, 'observables=[', ']')[1:]
for i, line in enumerate(observables):
observable += line.replace(',', '').replace('\'', '\"')
observable += jl_source.observable_body()
with open(jl_dir + '/observable.jl', mode='w') as f:
f.write(observable)
def make_initial_condition(jl_dir, py_dir, space_num=4):
jl_dir = jl_dir + '/model/initial_condition.jl'
py_dir = py_dir + '/model/initial_condition.py'
with open(py_dir, mode='r') as f:
lines = f.readlines()
lines = triming_tools.lines_triming(lines, space_num)
lines = triming_tools.cut_out_lines(lines, 'len_f_vars', 'return y0')[1:]
initial_condition = jl_source.initial_condition_header()
for i, line in enumerate(lines):
initial_condition += line
initial_condition += jl_source.initial_condition_footer()
with open(jl_dir, mode='w') as f:
f.write(initial_condition)
def make_variables(jl_dir, py_dir, space_num=4):
jl_dir = jl_dir + '/model/name2idx/variables.jl'
py_dir = py_dir + '/model/name2idx/variables.py'
with open(py_dir, mode='r') as f:
lines = f.readlines()
lines = triming_tools.lines_triming(lines, space_num)
lines = triming_tools.cut_out_lines(lines, 'var_names', 'len_f_vars')[1:]
variables = jl_source.variables_header()
for i, line in enumerate(lines):
variables += line
variables = variables + jl_source.variables_footer()
with open(jl_dir, mode='w') as f:
f.write(variables)
def make_parameters(jl_dir, py_dir, space_num=4):
jl_dir = jl_dir + '/model/name2idx/parameters.jl'
py_dir = py_dir + '/model/name2idx/parameters.py'
with open(py_dir, mode='r') as f:
lines = f.readlines()
lines = triming_tools.lines_triming(lines, space_num)
lines = triming_tools.cut_out_lines(lines, 'param_names',
'len_f_params')[1:]
parameters = jl_source.parameters_header()
for i, line in enumerate(lines):
parameters += line
parameters = parameters + jl_source.parameters_footer()
with open(jl_dir, mode='w') as f:
f.write(parameters)
def make_simulation(jl_dir, py_dir):
with open(py_dir + '/observable.py') as f:
lines = f.readlines()
lines = triming_tools.cut_out_lines(lines, 'class NumericalSimulation',
'class ExperimentalData')
lines = triming_tools.lines_triming(lines)
for i, line in enumerate(lines):
lines[i] = triming_tools.copy_list(line)
simulation = jl_source.simulation_header()
line_tspan = triming_tools.cut_out_line(lines, 'tspan=')
line_tspan = line_tspan.replace('[', '(').replace(']', ')')
line_tspan = triming_tools.indent_remover(line_tspan, 1)
line_t = triming_tools.cut_out_line(lines, 't=')
simulation += triming_tools.insert_after_indent(line_tspan, 'const ')
if line_t.find('/') != -1:
line_t = line_t[line_t.find('/') + 1:]
simulation += 'const t = collect(tspan[1]:1.0:tspan[end])./' + \
line_t + '\n'
else:
line_t = line_t[line_t.find(')') + 1:]
simulation += 'const t = collect(tspan[1]:1.0:tspan[end])' + \
line_t + '\n'
line_conditions = triming_tools.cut_out_line(lines, 'conditions=')
simulation += triming_tools.indent_remover(
triming_tools.insert_after_indent(line_conditions, 'const ') + '\n', 1)
simulation += jl_source.simulation_body1()
conditions1 = triming_tools.cut_out_lines(lines, 'def simulate(',
'steady_state')[1:]
conditions2 = triming_tools.cut_out_lines(lines,
'=copy',
'solveode',
mode=1)[1:]
conditions2 = triming_tools.insert_end(conditions2)[:-2]
for i, line in enumerate(conditions1):
simulation += line
simulation += jl_source.simulation_body2()
for i, line in enumerate(conditions2):
simulation += line
simulation += jl_source.simulation_body3()
get_timepoint = triming_tools.cut_out_lines(lines,
'simulations[',
'class ExperimentalData',
mode=1)
for i, line in enumerate(get_timepoint):
rep_line = line
if rep_line.find('class ExperimentalData') != -1:
break
rep_line = rep_line.replace('self.', '')
rep_line = rep_line.replace('observables.index', 'observables_index')
if rep_line.find('Y[:, ') != -1:
rep_line = rep_line.replace('Y[:, ', 'sol.u[j][')
else:
rep_line = rep_line.replace('Y[:,', 'sol.u[j][')
if rep_line.find('simulations[') != -1:
rep_line = rep_line.replace(':,', 'j,')
simulation += rep_line
simulation += jl_source.simulation_footer()
with open(jl_dir + '/simulation.jl', mode='w') as f:
f.write(simulation)