circulation 0.2.0__tar.gz → 0.3.0__tar.gz

{circulation-0.2.0/src/circulation.egg-info → circulation-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: circulation
-Version: 0.2.0
+Version: 0.3.0
 Summary: Closed loop blood circulation model in FEniCS
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License-Expression: MIT

{circulation-0.2.0 → circulation-0.3.0}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=61.0.0", "wheel"]
 
 [project]
 name = "circulation"
-version = "0.2.0"
+version = "0.3.0"
 description = "Closed loop blood circulation model in FEniCS"
 authors = [{ name = "Henrik Finsberg", email = "henriknf@simula.no" }]
 license = "MIT"
@@ -116,7 +116,7 @@ tag = true
 sign_tags = false
 tag_name = "v{new_version}"
 tag_message = "Bump version: {current_version} → {new_version}"
-current_version = "0.2.0"
+current_version = "0.3.0"
 
 
 [[tool.bumpversion.files]]

circulation-0.3.0/src/circulation/__init__.py

@@ -0,0 +1,11 @@
+from . import base, log, regazzoni2020, zenker, units, time_varying_elastance, windkessel
+
+__all__ = [
+    "base",
+    "log",
+    "regazzoni2020",
+    "zenker",
+    "units",
+    "time_varying_elastance",
+    "windkessel",
+]

{circulation-0.2.0 → circulation-0.3.0}/src/circulation/base.py

@@ -267,10 +267,14 @@ class CirculationModel(ABC):
         unit_R: float = 1.0,
         unit_p: float = 1.0,
     ) -> Callable[[float, float], float]:
-        return lambda w, v: unit_R * 10.0 ** (
-            np.log10(Rmin / unit_R)
-            + (np.log10(Rmax / unit_R) - np.log10(Rmin / unit_R))
-            * smooth_heavyside((v - w) / unit_p)
+        return lambda w, v: (
+            unit_R
+            * 10.0
+            ** (
+                np.log10(Rmin / unit_R)
+                + (np.log10(Rmax / unit_R) - np.log10(Rmin / unit_R))
+                * smooth_heavyside((v - w) / unit_p)
+            )
         )
 
     def times_n_beats(self, dt: float, n: int = 1) -> np.ndarray:

{circulation-0.2.0 → circulation-0.3.0}/src/circulation/bestel.py

@@ -106,8 +106,8 @@ class BestelActivation:
 
         # print(f"Solving active stress model with parameters: {pprint.pformat(params)}")
 
-        f = (
-            lambda t: 0.25
+        f = lambda t: (
+            0.25
             * (1 + math.tanh((t - ps["t_sys"]) / ps["gamma"]))
             * (1 - math.tanh((t - ps["t_dias"]) / ps["gamma"]))
         )
@@ -286,8 +286,8 @@ class BestelPressure:
 
     def __call__(self, t, p):
         ps = self.parameters
-        f = (
-            lambda t: 0.25
+        f = lambda t: (
+            0.25
             * (1 + math.tanh((t - ps["t_sys_pre"]) / ps["gamma"]))
             * (1 - math.tanh((t - ps["t_dias_pre"]) / ps["gamma"]))
         )

{circulation-0.2.0 → circulation-0.3.0}/src/circulation/regazzoni2020.py

@@ -229,18 +229,18 @@ class Regazzoni2020(base.CirculationModel):
     @staticmethod
     def default_initial_conditions() -> dict[str, float]:
         return {
-            "V_LA": 80.0 * mL,
-            "V_LV": 110.0 * mL,
-            "V_RA": 80.0 * mL,
-            "V_RV": 110.0 * mL,
-            "p_AR_SYS": 70.0 * mmHg,
-            "p_VEN_SYS": 28.32334306787334 * mmHg,
-            "p_AR_PUL": 25.0 * mmHg,
-            "p_VEN_PUL": 20.0 * mmHg,
-            "Q_AR_SYS": 0.0 * mL / s,
-            "Q_VEN_SYS": 0.0 * mL / s,
-            "Q_AR_PUL": 0.0 * mL / s,
-            "Q_VEN_PUL": 0.0 * mL / s,
+            "V_LA": 87.183 * mL,
+            "V_LV": 118.520 * mL,
+            "V_RA": 86.833 * mL,
+            "V_RV": 166.177 * mL,
+            "p_AR_SYS": 87.675 * mmHg,
+            "p_VEN_SYS": 35.898 * mmHg,
+            "p_AR_PUL": 19.545 * mmHg,
+            "p_VEN_PUL": 15.004 * mmHg,
+            "Q_AR_SYS": 71.104 * mL / s,
+            "Q_VEN_SYS": 94.039 * mL / s,
+            "Q_AR_PUL": 94.084 * mL / s,
+            "Q_VEN_PUL": 473.279 * mL / s,
         }
 
     @staticmethod

circulation-0.3.0/src/circulation/windkessel.py

@@ -0,0 +1,120 @@
+from . import base
+from . import units
+
+mL = units.ureg("mL")
+mmHg = units.ureg("mmHg")
+s = units.ureg("s")
+
+
+class ThreeElementWindkessel(base.CirculationModel):
+    """
+    A 0D model of the Left Ventricle coupled to a 3-Element Windkessel system.
+
+    The 3-Element Windkessel (WK3) models the systemic arterial tree using:
+    - R_c: Characteristic resistance (proximal aortic impedance)
+    - C: Arterial compliance (vessel elasticity)
+    - R_p: Peripheral resistance (microcirculation)
+    """
+
+    def __init__(self, parameters=None, p_LV_func=None, **kwargs):
+        super().__init__(parameters, **kwargs)
+
+        if p_LV_func is not None:
+            self.p_LV_func = p_LV_func
+            self._E_LV = lambda t: 1.0  # Dummy function, not used
+        else:
+            # Use default time-varying elastance model if no custom mechanics are provided
+            self._E_LV = self.time_varying_elastance(**self.parameters["chambers"]["LV"])
+            self.p_LV_func = lambda V, t: (
+                self._E_LV(t) * (V - self.parameters["chambers"]["LV"]["V0"])
+            )
+
+        self._initialize()
+
+    @property
+    def HR(self) -> float:
+        return self.parameters["HR"]
+
+    @staticmethod
+    def default_parameters():
+        return {
+            "HR": 1.25 * units.ureg("Hz"),  # Heart rate in Hz (75 BPM)
+            "R_c": 0.05 * mmHg * s / mL,  # Characteristic resistance (mmHg*s/mL)
+            "R_p": 1.05 * mmHg * s / mL,  # Peripheral resistance (mmHg*s/mL)
+            "C": 1.3 * mL / mmHg,  # Arterial compliance (mL/mmHg)
+            "P_venous": 8.0 * mmHg,  # Preload / Left Atrial Pressure (mmHg)
+            "R_mitral": 0.01 * mmHg * s / mL,  # Mitral valve resistance
+            "R_aortic": 0.01 * mmHg * s / mL,  # Aortic valve resistance
+            "chambers": {
+                "LV": {
+                    "EA": 2.5 * mmHg / mL,  # Max elastance (mmHg/mL)
+                    "EB": 0.08 * mmHg / mL,  # Min elastance (mmHg/mL)
+                    "TC": 0.25 * s,  # Contraction duration (s)
+                    "TR": 0.15 * s,  # Relaxation duration (s)
+                    "tC": 0.0 * s,  # Time of contraction onset (s)
+                    "V0": 15.0 * mL,  # Unstressed volume (mL)
+                }
+            },
+        }
+
+    @staticmethod
+    def default_initial_conditions() -> dict:
+        return {
+            "V_LV": 140.0 * mL,  # Initial left ventricular volume
+            "p_c": 80.0 * mmHg,  # Pressure in the arterial compliance capacitor
+        }
+
+    @staticmethod
+    def state_names() -> list:
+        return ["V_LV", "p_c"]
+
+    @staticmethod
+    def var_names() -> list:
+        return ["p_LV", "p_ao", "Q_in", "Q_out", "Q_p"]
+
+    def update_static_variables(self, t, y):
+        V_LV = y[0]
+        p_c = y[1]
+
+        p_LV = self.p_LV_func(V_LV, t)
+
+        P_venous = self.parameters["P_venous"]
+        R_mitral = self.parameters["R_mitral"]
+        R_aortic = self.parameters["R_aortic"]
+        R_c = self.parameters["R_c"]
+        R_p = self.parameters["R_p"]
+
+        # 1. Mitral Flow (Diastolic Filling)
+        Q_in = max(0.0, (P_venous - p_LV) / R_mitral)
+
+        # 2. Aortic Flow (Systolic Ejection)
+        # In a WK3 model, aortic pressure P_ao = p_c + Q_out * R_c
+        # If the valve is open (p_LV > p_ao), we substitute P_ao and solve for Q_out
+        if p_LV > p_c:
+            Q_out = (p_LV - p_c) / (R_aortic + R_c)
+        else:
+            Q_out = 0.0
+
+        # 3. Pressures and Peripheral Flow
+        p_ao = p_c + Q_out * R_c
+        Q_p = p_c / R_p  # Discharge to venous pool (assumed 0 mmHg pressure drop reference)
+
+        var = self._get_var(t)
+        var[0] = p_LV
+        var[1] = p_ao
+        var[2] = Q_in
+        var[3] = Q_out
+        var[4] = Q_p
+        return var
+
+    def rhs(self, t, y):
+        var = self.update_static_variables(t, y)
+        Q_in = var[2]
+        Q_out = var[3]
+        Q_p = var[4]
+        C = self.parameters["C"]
+
+        self.dy[0] = Q_in - Q_out
+        self.dy[1] = (Q_out - Q_p) / C
+
+        return self.dy

{circulation-0.2.0 → circulation-0.3.0/src/circulation.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: circulation
-Version: 0.2.0
+Version: 0.3.0
 Summary: Closed loop blood circulation model in FEniCS
 Author-email: Henrik Finsberg <henriknf@simula.no>
 License-Expression: MIT

{circulation-0.2.0 → circulation-0.3.0}/src/circulation.egg-info/SOURCES.txt

@@ -8,6 +8,7 @@ src/circulation/log.py
 src/circulation/regazzoni2020.py
 src/circulation/time_varying_elastance.py
 src/circulation/units.py
+src/circulation/windkessel.py
 src/circulation/zenker.py
 src/circulation.egg-info/PKG-INFO
 src/circulation.egg-info/SOURCES.txt
@@ -16,4 +17,5 @@ src/circulation.egg-info/requires.txt
 src/circulation.egg-info/top_level.txt
 tests/test_bestel.py
 tests/test_initialization.py
-tests/test_models.py
+tests/test_models.py
+tests/test_regazzoni_steady_state.py

{circulation-0.2.0 → circulation-0.3.0}/tests/test_models.py

@@ -24,3 +24,15 @@ def test_Regazzoni2020():
     for k, v in model.default_initial_conditions().items():
         assert k in results
         assert results[k][0] == v.magnitude
+
+
+def test_ThreeElementWindkessel():
+    model = circulation.windkessel.ThreeElementWindkessel()
+    results = model.solve(T=1.0, dt=1e-3, dt_eval=0.1)
+
+    for k, v in results.items():
+        assert len(v) == len(results["time"]), k
+
+    for k, v in model.default_initial_conditions().items():
+        assert k in results
+        assert results[k][0] == v.magnitude

circulation-0.3.0/tests/test_regazzoni_steady_state.py

@@ -0,0 +1,15 @@
+import numpy as np
+from circulation import regazzoni2020
+
+
+def test_regazzoni_steady_state():
+    """
+    Test that the default initial state is close to the limit cycle.
+    We run the model for ten beats and check that the state hasn't drifted much.
+    """
+    model = regazzoni2020.Regazzoni2020()
+    initial_state = model.state.copy()
+    model.solve(num_beats=10)
+    final_state = model.state
+
+    np.testing.assert_allclose(final_state, initial_state, rtol=1e-2, verbose=True)

circulation-0.2.0/src/circulation/__init__.py

@@ -1,3 +0,0 @@
-from . import base, log, regazzoni2020, zenker, units, time_varying_elastance
-
-__all__ = ["base", "log", "regazzoni2020", "zenker", "units", "time_varying_elastance"]