def gotran2latex(filename, params):
"""
Create LaTeX code from a gotran model
"""
if not params.sympy_contraction:
# A hack to avoid sympy contractions
# import gotran.codegeneration.avoidsympycontractions
pass
# Load Gotran model
ode = load_ode(filename)
# Check for completeness
# TODO: Should raise a more descriptive exception?
if not ode.is_complete:
raise Exception("Incomplete ODE")
params.output = (
params.output or Path(filename).with_name(f"{ode.name}.tex").as_posix()
)
# Create a gotran -> LaTeX document generator
gen = LatexCodeGenerator(ode, params)
info("")
info(f"Generating LaTeX files for the {ode.name} ode...")
with open(gen.output_file, "w") as f:
f.write(gen.generate())
info(" done.")
def gotran2dolfin(filename, params):
"""
Create ufl code from a gotran model
"""
# Load Gotran model
ode = load_ode(filename)
# Create a ufl based model code generator
code_gen = DOLFINCodeGenerator(params)
output = params.output
if output:
if not output.endswith(".py"):
output += ".py"
else:
output = filename.replace(".ode", "") + ".py"
f = open(output, "w")
f.write("from __future__ import division\n\n")
f.write(code_gen.init_states_code(ode) + "\n\n")
f.write(code_gen.init_parameters_code(ode) + "\n\n")
f.write(
code_gen.function_code(
rhs_expressions(ode, params=code_gen.params.code)) + "\n", )
def gotran2matlab(filename, params):
"""
Create a matlab code from a gotran model
"""
timer = Timer(f"Generate Matlab code from {filename}") # noqa: F841
# Load Gotran model
ode = load_ode(filename)
gen = MatlabCodeGenerator(params)
info("")
info(f"Generating Matlab files for the {ode.name} ode...")
# Collect monitored
if params.functions.monitored.generate:
monitored = [expr.name for expr in ode.intermediates + ode.state_expressions]
else:
monitored = None
for function_name, code in list(gen.code_dict(ode, monitored).items()):
open(f"{ode.name}_{function_name}.m", "w").write(code)
info(" done.")
def gotran2cuda(filename, params):
"""
Create a CUDA file from a gotran model
"""
# Load Gotran model
ode = load_ode(filename)
# Create a C code generator
gen = CUDACodeGenerator(params)
output = params.output
if output:
if not output.endswith(".cu"):
output += ".cu"
else:
output = filename.replace(".ode", "") + ".cu"
info("")
info(f"Generating CUDA code for the {ode.name} ode...")
code = gen.module_code(ode)
info(" done.")
with open(output, "w") as f:
if params.system_headers:
f.write("#include <math.h>\n")
f.write("#include <string.h>\n")
f.write(code)
if params.list_timings:
list_timings()
def gotranprobe(filename, params):
set_log_level(WARNING)
ode = load_ode(filename)
set_log_level(INFO)
if params.flat_view:
print()
print(f" Components({len(ode.components)}):")
print(join_indent_and_split([comp.name for comp in ode.components]))
print()
print(f" States({len(ode.full_states)}):")
print(join_indent_and_split([state.name for state in ode.full_states]))
if len(ode.parameters) > 0:
print()
print(f" Parameters({len(ode.parameters)}):")
print(join_indent_and_split([param.name for param in ode.parameters]))
print()
print(f" Intermediates({len(ode.intermediates)}): ")
print(
join_indent_and_split(
[interm.name for interm in ode.intermediates]))
else:
for comp in ode.components:
if comp.states or comp.parameters or comp.intermediates:
print(f"\n {comp.name}:")
if comp.full_states:
print(
" States: ",
", ".join(state.name for state in comp.full_states),
)
if comp.parameters:
print(
" Parameters: ",
", ".join(param.name for param in comp.parameters),
)
if comp.intermediates:
print(
" Intermediates: ",
", ".join(interm.name
for interm in comp.intermediates),
)
print(
" Dependencies: ",
", ".join(
set(dep.name for interm in comp.intermediates
for dep in ode.expression_dependencies[interm]
if not isinstance(dep, Comment) and dep not in
comp.full_states + comp.parameters), ),
)
def gotran2py(filename, params):
"""
Create a c header file from a gotran model
"""
timer = Timer(f"Generate Python code from {filename}")
# Load Gotran model
ode = load_ode(filename)
# Collect monitored
if params.functions.monitored.generate:
monitored = [
expr.name for expr in ode.intermediates + ode.state_expressions
]
else:
monitored = None
# Create a Python code generator
gen = PythonCodeGenerator(
params,
ns=params.namespace,
import_inside_functions=params.import_inside_functions,
)
output = params.output
if output:
if not output.endswith(".py"):
output += ".py"
else:
output = filename.replace(".ode", "") + ".py"
info("")
info(f"Generating Python code for the {ode.name} ode...")
if params.class_code:
code = gen.class_code(ode, monitored=monitored)
else:
code = gen.module_code(ode, monitored=monitored)
info(" done.")
with open(output, "w") as f:
f.write(code)
del timer
if params.list_timings:
list_timings()
def gotranexport(filename, params):
if len(params.components) == 1 and params.components[0] == "":
error("Expected at least 1 component.")
if params.name == "":
error("Expected a name of the exported ODE.")
if params.name in params.components:
error(
"Expected the name of the ODE to be different from the components."
)
sub_ode = ODE(params.name)
sub_ode.import_ode(load_ode(filename), components=params.components)
sub_ode.finalize()
sub_ode.save()
def gotran2md(filename):
filename = Path(filename)
ode = load_ode(filename)
parameters = make_table(
[[f"${format_expr(p.name)}$", f"{p._repr_latex_()}"] for p in ode.parameters],
header_names=["Name", "Value"],
)
states = make_table(
[[f"${format_expr(p.name)}$", f"{p._repr_latex_()}"] for p in ode.states],
header_names=["Name", "Value"],
)
expr = "\n\n".join(
[
f"$$\n{p._repr_latex_name()} = {p._repr_latex_expr()}\n$$"
for p in ode.intermediates
],
)
state_expr = "\n\n".join(
[
f"$$\n{p._repr_latex_name()} = {p._repr_latex_expr()}\n$$"
for p in ode.state_expressions
],
)
mdname = filename.with_suffix(".md")
with open(mdname, "w") as f:
f.write(
_template.format(
name=ode.name,
parameters=parameters,
states=states,
expr=expr,
state_expr=state_expr,
),
)
print(f"Saved to {mdname}")
def gotran2cpp(filename, params):
"""
Create a C++ header file from a gotran model
"""
timer = Timer(f"Generate C++ code from {filename}")
# Load Gotran model
ode = load_ode(filename)
# Create a C code generator
gen = CppCodeGenerator(params)
output = params.output
if output:
if not (output.endswith(".cpp") or output.endswith(".h")):
output += ".h"
else:
output = filename.replace(".ode", "") + ".h"
info("")
info(f"Generating C++ code for the {ode.name} ode...")
if params.class_code:
code = gen.class_code(ode)
else:
code = gen.module_code(ode)
info(" done.")
with open(output, "w") as f:
if params.system_headers:
f.write("#include <cmath>\n")
f.write("#include <cstring>\n")
f.write("#include <stdexcept>\n")
f.write(code)
del timer
if params.list_timings:
list_timings()
def gotran2julia(filename, params):
"""
Create a c header file from a gotran model
"""
timer = Timer(f"Generate Julia code from {filename}")
# Load Gotran model
ode = load_ode(filename)
# Collect monitored
if params.functions.monitored.generate:
monitored = [
expr.name for expr in ode.intermediates + ode.state_expressions
]
else:
monitored = None
# Create a C code generator
gen = JuliaCodeGenerator(params)
output = params.output
if output:
if not output.endswith(".jl"):
output += ".jl"
else:
output = filename.replace(".ode", "") + ".jl"
info("")
info(f"Generating Julia code for the {ode.name} ode...")
code = gen.module_code(ode, monitored=monitored)
info(" done.")
with open(output, "w") as f:
f.write(code)
del timer
if params.list_timings:
list_timings()
def create_module(ode, path="../ode/"):
"""
Compile a gotran ode and return the module and
corresponding forward method.
"""
generation = parameters.generation.copy()
for what_not in [
"componentwise_rhs_evaluation", "forward_backward_subst",
"linearized_rhs_evaluation", "lu_factorization", "jacobian"
]:
generation.functions[what_not].generate = False
solver = "rush_larsen"
generation.solvers[solver].generate = True
if isinstance(ode, str):
ode = load_ode(path + ode)
module = compile_module(ode, "c", [], generation)
forward = getattr(module, "forward_" + solver)
return module, forward
extract_equations = []
change_state_names = []
# params = CellMLParser.default_parameters()
# parser = CellMLParser(model, params=params)
# open(parser.name+".ode", "w").write(parser.to_gotran())
# ode = load_ode(parser.name+".ode")
for f in glob.glob("*.cellml"):
# print
# print f
params = CellMLParser.default_parameters()
parser = CellMLParser(f, params=params)
open(parser.name + ".ode", "w").write(parser.to_gotran())
try:
ode = load_ode(parser.name + ".ode")
except Exception as e:
print("***Error: Could not load gotran model", parser.name, e)
print()
list_timings()
clear_timings()
print()
mathmlparser = parser.mathmlparser
parsed_components = parser.components
cellml = parser.cellml
cellml_namespace = cellml.tag.split("}")[0] + "}"
# Grab encapsulation grouping
encapsulations = {}
def gotranrun(filename, params):
# Copy of default parameters
generation = parameters.generation.copy()
# Set body parameters
generation.code.body.representation = params.code.body_repr
generation.code.body.use_cse = params.code.use_cse
generation.code.body.optimize_exprs = params.code.optimize_exprs
# Set what code we are going to generate and not
for what_not in [
"componentwise_rhs_evaluation",
"forward_backward_subst",
"linearized_rhs_evaluation",
"lu_factorization",
"jacobian",
]:
generation.functions[what_not].generate = False
# Always generate code for monitored expressions
generation.functions.monitored.generate = True
# If scipy is used to solve we generate RHS and potentially a jacobian
if params.solver == "scipy":
generation.functions.rhs.generate = True
generation.functions.jacobian.generate = params.code.generate_jacobian
else:
generation.solvers[params.solver].generate = True
# Compile executeable code from gotran ode
model_arguments = params.model_arguments
if len(model_arguments) == 1 and model_arguments[0] == "":
model_arguments = []
if len(model_arguments) % 2 != 0:
error("Expected an even number of values for 'model_arguments'")
arguments = dict()
for arg_name, arg_value in [
(model_arguments[i * 2], model_arguments[i * 2 + 1])
for i in range(int(len(model_arguments) / 2))
]:
arguments[arg_name] = arg_value
ode = load_ode(filename, **arguments)
# Check for DAE
if ode.is_dae:
error(
"Can only integrate pure ODEs. {0} includes algebraic states "
"and is hence a DAE.".format(ode.name),
)
# Get monitored and plot states
plot_states = params.plot_y
# Get x_values
x_name = params.plot_x
state_names = [state.name for state in ode.full_states]
monitored_plot = [
plot_states.pop(plot_states.index(name))
for name in plot_states[:]
if name not in state_names
]
monitored = []
all_monitored_names = []
for expr in sorted(ode.intermediates + ode.state_expressions):
if expr.name not in monitored:
monitored.append(expr.name)
all_monitored_names.append(expr.name)
# Check valid monitored plot
for mp in monitored_plot:
if mp not in monitored:
error(f"{mp} is not a state or intermediate in this ODE")
# Check x_name
if x_name not in ["time"] + monitored + state_names:
error(
"Expected plot_x to be either 'time' or one of the plotable "
"variables, got {}".format(x_name),
)
# Logic if x_name is not 'time' as we then need to add the name to
# either plot_states or monitored_plot
if x_name != "time":
if x_name in state_names:
plot_states.append(x_name)
else:
monitored_plot.append(x_name)
module = compile_module(ode, params.code.language, monitored, generation)
parameter_values = params.parameters
init_conditions = params.init_conditions
if len(parameter_values) == 1 and parameter_values[0] == "":
parameter_values = []
if len(init_conditions) == 1 and init_conditions[0] == "":
init_conditions = []
if len(parameter_values) % 2 != 0:
error("Expected an even number of values for 'parameters'")
if len(init_conditions) % 2 != 0:
error("Expected an even number of values for 'initial_conditions'")
user_params = dict()
for param_name, param_value in [
(parameter_values[i * 2], parameter_values[i * 2 + 1])
for i in range(int(len(parameter_values) / 2))
]:
user_params[param_name] = float(param_value)
user_ic = dict()
for state_name, state_value in [
(init_conditions[i * 2], init_conditions[i * 2 + 1])
for i in range(int(len(init_conditions) / 2))
]:
user_ic[state_name] = float(state_value)
# Use scipy to integrate model
t0 = 0.0
t1 = params.tstop
dt = params.dt
rhs = module.rhs
jac = module.compute_jacobian if params.code.generate_jacobian else None
y0 = module.init_state_values(**user_ic)
model_params = module.init_parameter_values(**user_params)
# Check for steady state solve
if params.steady_state.solve and root:
result = root(
rhs,
y0,
args=(0.0, model_params),
jac=jac,
method=params.steady_state.method,
tol=params.steady_state.tol,
)
if result.success:
y0 = result.x
print(
"Found stead state:",
", ".join(
f"{state.name}: {value:e}"
for value, state in zip(y0, ode.full_states)
),
)
else:
warning(result.message)
tsteps = np.linspace(t0, t1, int(t1 / dt) + 1)
# What solver should we use
if params.solver == "scipy":
try:
from scipy.integrate import odeint
except Exception as e:
error(f"Problem importing scipy.integrate.odeint. {e}")
results = odeint(rhs, y0, tsteps, Dfun=jac, args=(model_params,))
else:
# Get generated forward method
forward = getattr(module, "forward_" + params.solver)
results = [y0]
states = y0.copy()
# Integrate solution using generated forward method
for ind, t in enumerate(tsteps[:-1]):
# Step solver
forward(states, t, dt, model_params)
results.append(states.copy())
# Plot results
if not (plot_states or monitored or params.save_results):
return
# allocate memory for saving results
if params.save_results:
save_results = np.zeros(
(len(results), 1 + len(state_names) + len(all_monitored_names)),
)
all_monitor_inds = np.array(
[monitored.index(monitor) for monitor in all_monitored_names],
dtype=int,
)
all_results_header = ", ".join(["time"] + state_names + all_monitored_names)
plot_inds = [module.state_indices(state) for state in plot_states]
monitor_inds = np.array(
[monitored.index(monitor) for monitor in monitored_plot],
dtype=int,
)
monitored_get_values = np.zeros(len(monitored), dtype=np.float_)
# Allocate memory
plot_values = np.zeros((len(plot_states) + len(monitored_plot), len(results)))
for ind, (time, res) in enumerate(zip(tsteps, results)):
if plot_states:
plot_values[: len(plot_states), ind] = res[plot_inds]
if monitored_plot or params.save_results:
module.monitor(res, time, model_params, monitored_get_values)
if monitored_plot:
plot_values[len(plot_states) :, ind] = monitored_get_values[monitor_inds]
if params.save_results:
save_results[ind, 0] = time
save_results[ind, 1 : len(state_names) + 1] = res
save_results[ind, len(state_names) + 1 :] = monitored_get_values[
all_monitor_inds
]
# Save data
if params.save_results:
np.savetxt(
f"{params.basename}.csv",
save_results,
header=all_results_header,
delimiter=", ",
)
# Plot data
if not (plot_states + monitored_plot):
return
# Fixes for derivatives
monitored_plot_updated = []
for monitor in monitored_plot:
expr, what = special_expression(monitor, ode)
if what == DERIVATIVE_EXPRESSION:
var, dep = expr.groups()
if var in ode.present_ode_objects and dep in ode.present_ode_objects:
monitored_plot_updated.append(f"d{var}/d{dep}")
else:
monitored_plot_updated.append(monitor)
else:
monitored_plot_updated.append(monitor)
plot_items = plot_states + monitored_plot
if x_name != "time":
x_values = plot_values[plot_items.index(x_name)]
else:
x_values = tsteps
plt.rcParams["lines.linewidth"] = 2
# line_styles = cycle([c+s for s in ["-", "--", "-.", ":"]
# for c in plt.rcParams["axes.color_cycle"]])
line_styles = cycle(
[
c + s
for s in ["-", "--", "-.", ":"]
for c in ["b", "g", "r", "c", "m", "y", "k"]
],
)
plotted_items = 0
for what, values in zip(plot_items, plot_values):
if what == x_name:
continue
plotted_items += 1
plt.plot(x_values, values, next(line_styles))
if plotted_items > 1:
plt.legend([f"$\\mathrm{{{latex(value)}}}$" for value in plot_items])
elif plot_items:
plt.ylabel(f"$\\mathrm{{{latex(plot_items[0])}}}$")
plt.xlabel(f"$\\mathrm{{{latex(x_name)}}}$")
plt.title(ode.name.replace("_", "\\_"))
plt.show()
def import_ode(self, ode, prefix="", components=None, **arguments):
"""
Import a Model into the present Model
Arguments
---------
ode : str, gotran.ODE
The ode which should be added. If ode is a str an
ODE stored in that file will be loaded. If it is an ODE it will be
added directly to the present ODE.
prefix : str (optional)
A prefix which all state, parameters and intermediates are
prefixed with.
components : list, tuple of str (optional)
A list of components which will either be extracted or excluded
from the imported model. If not given the whole ODE will be imported.
arguments : dict (optional)
Optional arguments which can control loading of model
"""
timer = Timer("Import ode") # noqa: F841
components = components or []
check_arg(ode, (str, Path, ODE), 0, context=ODE.import_ode)
check_arg(prefix, str, 1, context=ODE.import_ode)
check_arg(components, list, 2, context=ODE.import_ode, itemtypes=str)
# If ode is given directly
if isinstance(ode, (str, Path)):
# If not load external ODE
from gotran.model.loadmodel import load_ode
ode = load_ode(ode, **arguments)
# Postfix prefix with "_" if prefix is not ""
if prefix and prefix[-1] != "_":
prefix += "_"
# If extracting only a certain components
if components:
ode = ode.extract_components(ode.name, *components)
# Subs for expressions
subs = {}
old_new_map = {ode: self}
def add_comp_and_children(added, comp):
"Help function to recursively add components to ode"
# Add states and parameters
for obj in comp.ode_objects:
# Check if obj already excists as a ODE parameter
old_obj = self.present_ode_objects.get(str(obj))
if old_obj and self.object_component[old_obj] == self:
new_name = obj.name
else:
new_name = prefix + obj.name
if isinstance(obj, State):
subs[obj.sym] = added.add_state(new_name, obj.param)
elif isinstance(obj, Parameter):
# If adding an ODE parameter
if comp == ode:
# And parameter name already excists in the present ODE
if str(obj) in self.present_ode_objects:
# Skip it and add the registered symbol for
# substitution
subs[obj.sym] = self.present_ode_objects[str(
obj)].sym
else:
# If not already present just add unprefixed name
subs[obj.sym] = added.add_parameter(
obj.name, obj.param)
else:
subs[obj.sym] = added.add_parameter(
new_name, obj.param)
# Add child components
for child in list(comp.children.values()):
added_child = added.add_component(child.name)
# Get corresponding component in present ODE
old_new_map[child] = added_child
add_comp_and_children(added_child, child)
# Recursively add states and parameters
add_comp_and_children(self, ode)
# Iterate over all components to add expressions
for comp_name in ode.all_expr_components_ordered:
comp = ode.all_components[comp_name]
comp_comment = f"Expressions for the {comp.name} component"
# Get corresponding component in new ODE
added = old_new_map[comp]
# Iterate over all objects of the component and save only expressions
# and comments
for obj in comp.ode_objects:
# If saving an expression
if isinstance(obj, Expression):
# The new sympy expression
new_expr = obj.expr.xreplace(subs)
# If the component is a Markov model
if comp.rates:
# Do not save State derivatives
if isinstance(obj, StateDerivative):
continue
# Save rate expressions slightly different
elif isinstance(obj, RateExpression):
states = obj.states
added._add_single_rate(
subs[states[0].sym],
subs[states[1].sym],
new_expr,
)
continue
# If no prefix we just add the expression by using setattr
# magic
if prefix == "":
setattr(added, str(obj), new_expr)
subs[obj.sym] = added.ode_objects.get(obj.name).sym
elif isinstance(obj, (StateExpression, StateSolution)):
state = subs[obj.state.sym]
if isinstance(obj, AlgebraicExpression):
subs[obj.sym] = added.add_algebraic(
state, new_expr)
elif isinstance(obj, StateDerivative):
subs[obj.sym] = added.add_derivative(
state,
added.t,
new_expr,
)
elif isinstance(obj, StateSolution):
subs[obj.sym] = added.add_state_solution(
state, new_expr)
print(repr(obj), obj.sym)
else:
error("Should not reach here...")
# Derivatives are tricky. Here the der expr and dep var
# need to be registered in the ODE already. But they can
# be registered with and without prefix, so we need to
# check that.
elif isinstance(obj, Derivatives):
# Get der_expr
der_expr = self.root.present_ode_objects.get(
obj.der_expr.name)
if der_expr is None:
# If not found try prefixed version
der_expr = self.root.present_ode_objects.get(
prefix + obj.der_expr.name, )
if der_expr is None:
if prefix:
error(
"Could not find expression: "
"({0}){1} while adding "
"derivative".format(
prefix, obj.der_expr), )
else:
error(
"Could not find expression: "
"{0} while adding derivative".format(
obj.der_expr, ), )
dep_var = self.root.present_ode_objects.get(
obj.dep_var.name)
if isinstance(dep_var, Time):
dep_var = self._time
elif dep_var is None:
# If not found try prefixed version
dep_var = self.root.present_ode_objects.get(
prefix + obj.dep_var.name, )
if dep_var is None:
if prefix:
error(
"Could not find expression: "
"({0}){1} while adding "
"derivative".format(
prefix, obj.dep_var), )
else:
error(
"Could not find expression: "
"{0} while adding derivative".format(
obj.dep_var, ), )
subs[obj.sym] = added.add_derivative(
der_expr,
dep_var,
new_expr,
)
elif isinstance(obj, Intermediate):
subs[obj.sym] = added.add_intermediate(
prefix + obj.name,
new_expr,
)
else:
error("Should not reach here!")
# If saving a comment
elif isinstance(obj, Comment) and str(obj) != comp_comment:
added.add_comment(str(obj))