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 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 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()
# 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 get_encapsulation(elements):