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LevanBokeriaLevanBokeria
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adding back models under development
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‎src/ModularCirc/Models/KPat5MixedModel.py

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from .OdeModel import OdeModel
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from .KorakianitisModel_parameters import KorakianitisModel_parameters as k2006
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from .ParametersObject import ParametersObject as po
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from ..Components import Rlc_component, Valve_simple_bernoulli, HC_mixed_elastance
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FULL_NAMES =[
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'LeftA',
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'MiValve',
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'LeftV',
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'AoV',
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'SysAoSin',
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'SysArt',
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'SysVen',
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'RightA',
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'TriValve',
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'RightV',
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'PulV',
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'PulArtSin',
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'PulArt0',
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'PulArt1',
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'PulArt2',
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'PulArt3',
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'PulArt4',
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'PulVen',
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]
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class KPat5MixedModel(OdeModel):
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def __init__(self, time_setup_dict, parobj:po=k2006, suppress_printing:bool=False) -> None:
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super().__init__(time_setup_dict)
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self.name = 'KorakianitisModel'
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if not suppress_printing: print(parobj)
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# The components...
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for key, name in zip(parobj.components.keys(), FULL_NAMES):
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if key in parobj._vessels:
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class_ = Rlc_component
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elif key in parobj._valves:
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class_ = Valve_simple_bernoulli
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elif key in parobj._chambers:
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class_ = HC_mixed_elastance
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else:
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raise Exception(f'Component name {key} not in the model list.')
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self.components[key] = class_(name=name,
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time_object=self.time_object,
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**parobj[key].to_dict())
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if key not in parobj._valves:
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self.set_v_sv(key)
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# else:
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# self.set_phi_sv(key)
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self.components[key].setup()
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self.connect_modules(self.components['lv'],
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self.components['ao'],
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plabel='p_lv',
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qlabel='q_ao')
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self.connect_modules(self.components['ao'],
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self.components['sas'],
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plabel='p_sas',
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qlabel='q_ao')
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self.connect_modules(self.components['sas'],
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self.components['sat'],
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plabel='p_sat',
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qlabel='q_sas')
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self.connect_modules(self.components['sat'],
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self.components['svn'],
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plabel='p_svn',
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qlabel='q_sat')
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self.connect_modules(self.components['svn'],
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self.components['ra'],
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plabel='p_ra',
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qlabel='q_svn')
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self.connect_modules(self.components['ra'],
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self.components['ti'],
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plabel='p_ra',
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qlabel='q_ti')
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self.connect_modules(self.components['ti'],
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self.components['rv'],
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plabel='p_rv',
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qlabel='q_ti')
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self.connect_modules(self.components['rv'],
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self.components['po'],
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plabel='p_rv',
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qlabel='q_po')
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self.connect_modules(self.components['po'],
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self.components['pas'],
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plabel='p_pas',
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qlabel='q_po')
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############################################
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self.connect_modules(self.components['pas'],
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self.components['pat0'],
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plabel='p_pat0',
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qlabel='q_pas')
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self.connect_modules(self.components['pat0'],
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self.components['pat1'],
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plabel='p_pat1',
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qlabel='q_pat0')
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self.connect_modules(self.components['pat1'],
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self.components['pat2'],
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plabel='p_pat2',
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qlabel='q_pat1')
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self.connect_modules(self.components['pat2'],
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self.components['pat3'],
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plabel='p_pat3',
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qlabel='q_pat2')
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self.connect_modules(self.components['pat3'],
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self.components['pat4'],
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plabel='p_pat4',
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qlabel='q_pat3')
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############################################
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self.connect_modules(self.components['pat4'],
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self.components['pvn'],
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plabel='p_pvn',
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qlabel='q_pat4')
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############################################
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self.connect_modules(self.components['pvn'],
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self.components['la'],
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plabel='p_la',
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qlabel='q_pvn')
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self.connect_modules(self.components['la'],
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self.components['mi'],
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plabel='p_la',
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qlabel='q_mi')
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self.connect_modules(self.components['mi'],
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self.components['lv'],
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plabel='p_lv',
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qlabel='q_mi')
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for component in self.components.values():
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component.setup()
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# def set_phi_sv(self, comp_key:str) -> None:
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# phi_key = 'phi_' + comp_key
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# self._state_variable_dict[phi_key] = self.components[comp_key]._PHI
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# self._state_variable_dict[phi_key].set_name(phi_key)
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# self.all_sv_data[phi_key] = self.components[comp_key].PHI

‎src/ModularCirc/Models/KPat5MixedModel_parameters.py

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from ..HelperRoutines import activation_function_2, activation_function_3
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from .ParametersObject import ParametersObject
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import pandas as pd
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KKPat10_COMPONENTS = [
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'la', # left atrium
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'mi', # mitral valve
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'lv', # left ventricle
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'ao', # aortic valve
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'sas', # systemic aortic sinus
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'sat', # systemic artery
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'svn', # systemic vein
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'ra', # right atrium
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'ti', # tricuspid vale
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'rv', # right ventricle
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'po', # pulmonary valve
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'pas', # pulmonary artery sinus
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###############################
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'pat0', # pulmonary artery
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'pat1', # pulmonary artery
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'pat2', # pulmonary artery
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'pat3', # pulmonary artery
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'pat4', # pulmonary artery
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###############################
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'pvn' # pulmonary vein
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]
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VESSELS = ['sas', 'sat', 'svn', 'pas', 'pat0', 'pat1', 'pat2', 'pat3', 'pat4', 'pvn']
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VESSELS_PAR = ['r', 'c', 'l', 'v_ref', 'v', 'p']
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VALVES = ['mi', 'ao', 'ti', 'po']
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VALVES_PAR = ['CQ', 'RRA']
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CHAMBERS = ['la', 'lv', 'ra', 'rv']
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CHAMBERS_PAR = ['E_pas', 'E_act', 'v_ref', 'k_pas', 'af', 'v', 'p', 'tr', 'td', 'delay', 'tpww', 'tpwb']
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class KPat5MixedModel_parameters(ParametersObject):
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"""
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Intro
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-----
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Model Parameters based on Korakianitis and Shi (2006)
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"""
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def __init__(self, name='Korakianitis 2006') -> None:
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super().__init__(name=name)
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self.components = {key : None for key in KKPat10_COMPONENTS}
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for type_, type_var in [[VESSELS, VESSELS_PAR], [VALVES, VALVES_PAR], [CHAMBERS, CHAMBERS_PAR]]:
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for key in type_:
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self[key] = pd.Series(index=type_var, dtype=object)
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self._vessels = VESSELS
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self._valves = VALVES
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self._chambers= CHAMBERS
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self.set_chamber_comp('lv', E_pas= 0.1, k_pas=0.01, E_act= 2.5, v_ref=50.0, tr = 0.30, td = 0.450, v=100.)
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self.set_chamber_comp('la', E_pas= 0.15, k_pas=0.01, E_act= 0.25, v_ref=10.0, tpwb = 0.0, tpww = 0.09, delay=0.08, v=0.0)
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self.set_chamber_comp('rv', E_pas= 0.1, k_pas=0.01, E_act= 1.15, v_ref=50., tr=0.30, td=0.45, v=100.)
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self.set_chamber_comp('ra', E_pas= 0.15, k_pas=0.01, E_act= 0.25, v_ref=10., tpwb=0.0, tpww=0.09, delay=0.08, v=0.0)
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self.set_activation_function('lv', af=activation_function_2)
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self.set_activation_function('rv', af=activation_function_2)
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self.set_activation_function('la', af=activation_function_3)
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self.set_activation_function('ra', af=activation_function_3)
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# systemic circulation
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self.set_rlc_comp('sas', r=0.003, c=0.08, l=0.000062, v=0.0, v_ref=0.0)
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self.set_rlc_comp('sat', r=(0.05 + 0.5 + 0.52), c=1.6 , l=0.0017 , v=550.0, v_ref=0.0)
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self.set_rlc_comp('svn', r=0.075, c=20.5, v=0.0, v_ref=0.0)
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# pulmonary circulation
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self.set_rlc_comp('pas', r=0.002 , c=0.18, l=0.000052, v=0.0, v_ref=0.0)
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#############################################################################################
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self.set_rlc_comp('pat0', r=(0.01/5.), c=(3.8/5.) , l=(0.0017/5.) , v=0.0, v_ref=0.0)
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self.set_rlc_comp('pat1', r=(0.01/5.), c=(3.8/5.) , l=(0.0017/5.) , v=0.0, v_ref=0.0)
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self.set_rlc_comp('pat2', r=(0.01/5.), c=(3.8/5.) , l=(0.0017/5.) , v=0.0, v_ref=0.0)
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self.set_rlc_comp('pat3', r=(0.01/5.), c=(3.8/5. ), l=(0.0017/5. ) , v=0.0, v_ref=0.0)
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self.set_rlc_comp('pat4', r=(0.01/5.+0.05+0.25), c=(3.8/5.) , l=(0.0017/5.), v=0.0, v_ref=0.0)
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#############################################################################################
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self.set_rlc_comp('pvn', r=0.006 , c=20.5 , v=0.0, v_ref=0.0)
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# valves
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self.set_valve_comp('ao', CQ=350., RRA=0.0)
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self.set_valve_comp('mi', CQ=400., RRA=0.0)
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self.set_valve_comp('po', CQ=350., RRA=0.0)
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self.set_valve_comp('ti', CQ=400., RRA=0.0)
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def set_chamber_comp(self, key, **kwargs):
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self._set_comp(key=key, set=CHAMBERS, **kwargs)
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def set_activation_function(self, key, af):
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self._set_comp(key, set=CHAMBERS, af=af)
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def set_rlc_comp(self, key, **kwargs):
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self._set_comp(key=key, set=VESSELS, **kwargs)
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def set_valve_comp(self, key, **kwargs):
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self._set_comp(key=key, set=VALVES, **kwargs)
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def set(self, key, **kwargs):
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if key in CHAMBERS:
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self._set_comp(key=key, set=CHAMBERS, **kwargs)
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if key in VESSELS:
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self._set_comp(key=key, set=VESSELS, **kwargs)
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if key in VALVES:
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self._set_comp(key=key, set=VALVES, **kwargs)

‎src/ModularCirc/Models/KorakianitisMaynardModel.py

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from .OdeModel import OdeModel
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from .KorakianitisModel_parameters import KorakianitisModel_parameters as k2006
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from .ParametersObject import ParametersObject as po
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from ..Components import Rlc_component, Valve_maynard, HC_constant_elastance
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FULL_NAMES =[
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'LeftA',
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'MiValve',
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'LeftV',
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'AoV',
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'SysAoSin',
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'SysArt',
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'SysVen',
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'RightA',
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'TriValve',
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'RightV',
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'PulV',
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'PulArtSin',
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'PulArt',
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'PulVen',
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]
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class KorakianitisMaynardModel(OdeModel):
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def __init__(self, time_setup_dict, parobj:po=k2006) -> None:
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super().__init__(time_setup_dict)
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self.name = 'KorakianitisModel'
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print(parobj)
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# The components...
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for key, name in zip(parobj.components.keys(), FULL_NAMES):
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if key in parobj._vessels:
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class_ = Rlc_component
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elif key in parobj._valves:
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class_ = Valve_maynard
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elif key in parobj._chambers:
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class_ = HC_constant_elastance
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else:
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raise Exception(f'Component name {key} not in the model list.')
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self.components[key] = class_(name=name,
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time_object=self.time_object,
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**parobj[key].to_dict())
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if key not in parobj._valves:
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self.set_v_sv(key)
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else:
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self.set_phi_sv(key)
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self.components[key].setup()
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self.connect_modules(self.components['lv'],
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self.components['ao'],
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plabel='p_lv',
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qlabel='q_ao')
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self.connect_modules(self.components['ao'],
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self.components['sas'],
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plabel='p_sas',
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qlabel='q_ao')
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self.connect_modules(self.components['sas'],
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self.components['sat'],
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plabel='p_sat',
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qlabel='q_sas')
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self.connect_modules(self.components['sat'],
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self.components['svn'],
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plabel='p_svn',
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qlabel='q_sat')
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self.connect_modules(self.components['svn'],
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self.components['ra'],
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plabel='p_ra',
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qlabel='q_svn')
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self.connect_modules(self.components['ra'],
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self.components['ti'],
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plabel='p_ra',
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qlabel='q_ti')
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self.connect_modules(self.components['ti'],
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self.components['rv'],
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plabel='p_rv',
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qlabel='q_ti')
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self.connect_modules(self.components['rv'],
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self.components['po'],
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plabel='p_rv',
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qlabel='q_po')
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self.connect_modules(self.components['po'],
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self.components['pas'],
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plabel='p_pas',
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qlabel='q_po')
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self.connect_modules(self.components['pas'],
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self.components['pat'],
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plabel='p_pat',
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qlabel='q_pas')
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self.connect_modules(self.components['pat'],
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self.components['pvn'],
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plabel='p_pvn',
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qlabel='q_pat')
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self.connect_modules(self.components['pvn'],
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self.components['la'],
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plabel='p_la',
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qlabel='q_pvn')
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self.connect_modules(self.components['la'],
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self.components['mi'],
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plabel='p_la',
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qlabel='q_mi')
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self.connect_modules(self.components['mi'],
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self.components['lv'],
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plabel='p_lv',
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qlabel='q_mi')
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for component in self.components.values():
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component.setup()
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def set_phi_sv(self, comp_key:str) -> None:
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phi_key = 'phi_' + comp_key
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self._state_variable_dict[phi_key] = self.components[comp_key]._PHI
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self._state_variable_dict[phi_key].set_name(phi_key)
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self.all_sv_data[phi_key] = self.components[comp_key].PHI
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self.components[comp_key]._PHI._u = self.all_sv_data[phi_key]

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