# ----------------------------------------------------------------------
# RTD without units
# ----------------------------------------------------------------------

"""PVL perfusion sampling model."""
from sbmlutils.cytoscape import visualize_sbml
from sbmlutils.factory import *
from sbmlutils.metadata import *



mid = "RTD"
version = 1

_m = Model(
    sid=f"{mid}",
    name="RTD",
    notes=f"""
    <a href="http://sbml.org">SBML</a> format. 

    **version:** {version}

    ## Changelog

    **version 1**

    - initial
    """,
    creators=[
        Creator(
            familyName="Höpfl",
            givenName="Sebastian",
            email="sebastian.hoepfl@isa.uni-stuttgart.de",
            organization="University of Stuttgart, Institute for Stochastics and Applications",
        )
    ]
    
)
_m.functions = [
    Function(
        sid="time_trafo",
        name="Time transformation for the retarded response",
        value="lambda(time, Tshift, Trange, "
              "1 * (log(power(10, (time*10 /Trange)) + power(10, Tshift/1))"
              " - log(1 + power(10, Tshift/1))))",
        sboTerm=SBO.SBO_0000474
    )
]

_m.parameters.extend([
    Parameter(sid="Asus", value=1.0),
    Parameter(sid="Atrans", value=1.0),
    Parameter(sid="t1", value=1.0),
    Parameter(sid="t11", value=1.0),
    Parameter(sid="t2", value=3.0),
    Parameter(sid="p0", value=0.1),
    Parameter(sid="Tshift", value=-2.0),
    Parameter(sid="Trange", value=5.0)
])

_m.rules.extend([
    AssignmentRule(
        "y",
        value="Asus  * (1 - exp(-time_trafo(time, Tshift, Trange)/t1)) "
              "+ Atrans * (1 - exp(-time_trafo(time, Tshift, Trange)/t11)) * exp(-time_trafo(time, Tshift, Trange)/t2)"
              " + p0",
        name="response",
    )
])


if __name__ == "__main__":

    results = create_model(
        filepath= f"{mid}.xml",
        model=[
            _m,
        ],
        sbml_level=3, sbml_version=2,
        validation_options=ValidationOptions(units_consistency=False)
    )
    visualize_sbml(results.sbml_path, delete_session=False)