Less logging in demos

demo/benchmark/problem2.py

@@ -33,6 +33,7 @@
 import pulse
 
 logging.basicConfig(level=logging.INFO)
+logging.getLogger("scifem").setLevel(logging.WARNING)
 
 # ## 1. Geometry
 #
@@ -66,6 +67,7 @@
 )
 
 # We convert to `pulse.Geometry`. We assume the mesh units are mm (consistent with parameters).
+
 geometry = pulse.Geometry.from_cardiac_geometries(geo, metadata={"quadrature_degree": 4})
 
 # ## 2. Constitutive Model
@@ -74,6 +76,7 @@
 # By setting $b_f = b_t = b_{fs} = 1.0$, the exponent $Q$ becomes $Q = (E_{11}^2 + E_{22}^2 + E_{33}^2 + 2E_{12}^2 + \dots) = \text{tr}(\mathbf{E}^2)$, making the model isotropic.
 # For an isotropic material, the fiber direction vectors don't affect the energy (as b parameters are equal),
 # but the class requires them. We can use dummy fields or the ones from the mesh.
+
 material = pulse.Guccione(
     C=pulse.Variable(dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(10.0)), "kPa"),
     bf=pulse.Variable(dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(1.0)), "dimensionless"),

demo/benchmark/problem3.py

@@ -37,7 +37,7 @@
 import cardiac_geometries
 import pulse
 
-log.set_log_level(log.LogLevel.INFO)
+# log.set_log_level(log.LogLevel.INFO)
 
 # ## 1. Geometry and Fibers
 # We regenerate the mesh with the specific fiber angles required for Problem 3 ($+90^\circ$ to $-90^\circ$).

demo/biv_ellipsoid.py

@@ -43,7 +43,7 @@
 
 # We enable info logging to track solver progress.
 
-log.set_log_level(log.LogLevel.INFO)
+# log.set_log_level(log.LogLevel.INFO)
 
 # ## Geometry and Microstructure
 #

demo/lv_ellipsoid.py

@@ -157,10 +157,6 @@
     parameters={"base_bc": pulse.BaseBC.fixed},
 )
 
-# We initialize the solver log level to INFO to track convergence.
-
-log.set_log_level(log.LogLevel.INFO)
-
 # ### Phase 1: Passive Inflation
 # We first solve the passive mechanics by increasing the endocardial pressure.
 # We initialize a VTX writer to save the displacement field for visualization.

demo/lv_ellipsoid_fixed_x.py

@@ -29,6 +29,7 @@
 # (Holzapfel-Ogden with Active Stress) as in the [base example](lv_ellipsoid.ipynb).
 
 # 1. Generate Mesh
+
 outdir = Path("lv_ellipsoid_custom_bcs")
 outdir.mkdir(parents=True, exist_ok=True)
 geodir = outdir / "geometry"
@@ -41,13 +42,15 @@
     )
 
 # 2. Load Geometry
+
 geo = cardiac_geometries.geometry.Geometry.from_folder(
     comm=MPI.COMM_WORLD,
     folder=geodir,
 )
 geometry = pulse.Geometry.from_cardiac_geometries(geo, metadata={"quadrature_degree": 4})
 
 # 3. Define Constitutive Model
+
 material_params = pulse.HolzapfelOgden.transversely_isotropic_parameters()
 material = pulse.HolzapfelOgden(f0=geo.f0, s0=geo.s0, **material_params)
 

demo/maths.py

@@ -20,8 +20,10 @@
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger("pulse")
+for lib in ["trame_server", "wslink"]:
+    logging.getLogger(lib).setLevel(logging.WARNING)
 logger.setLevel(logging.DEBUG)
-dolfinx.log.set_log_level(dolfinx.log.LogLevel.INFO)
+# dolfinx.log.set_log_level(dolfinx.log.LogLevel.INFO)
 
 # %% [markdown]
 # ## 1. Geometry and Mesh

demo/prestress_biv.py

@@ -71,13 +71,14 @@
 
 comm = MPI.COMM_WORLD
 logging.basicConfig(level=logging.INFO)
-dolfinx.log.set_log_level(dolfinx.log.LogLevel.INFO)
+logging.getLogger("scifem").setLevel(logging.WARNING)
 
 # ## 1. Geometry Generation (Target Configuration)
 #
-# We generate an idealized Bi-Ventricular (BiV) geometry using `cardiac-geometries` which represents our **target**
-# geometry (e.g., the end-diastolic state). This includes both the Left Ventricle (LV) and Right Ventricle (RV).
-# We also generate the fiber architecture.
+# We generate an Bi-Ventricular (BiV) geometry using `cardiac-geometries` which represents our **target**
+# geometry (e.g., the end-diastolic state). This geometry is generated from the mean shape of an
+# [atlas from the UK Biobank](https://github.com/ComputationalPhysiology/ukb-atlas).
+# We also generate the fiber architecture using a [rule-based method](https://github.com/finsberg/fenicsx-ldrb).
 
 mode = -1
 std = 0

demo/prestress_fixedpoint_unloader.py

@@ -8,7 +8,8 @@
 # acquired geometry and the known end-diastolic pressure. This process is often called "pre-stressing" or
 # "inverse mechanics".
 #
-# In this demo, we solve the inverse problem using a **Fixed-Point Iteration** (also known as the Backward Displacement Method).
+# In this demo, we solve the inverse problem using a **Fixed-Point Iteration** (also known as the Backward Displacement Method o
+# Sellier's method) {cite}`SELLIER20111461`.
 # Unlike the Inverse Elasticity Problem (IEP) which formulates equilibrium on the target configuration, this method
 # iteratively updates the reference coordinates $\mathbf{X}$ by subtracting the displacement $\mathbf{u}$ computed from a
 # forward solve.
@@ -23,7 +24,7 @@
 # 2. For iteration $k=0, 1, \dots$:
 #    a. Solve the **Forward** mechanics problem on the geometry defined by $\mathbf{X}_k$ to get displacement $\mathbf{u}_k$.
 #    b. Update the reference geometry:
-#       $$ \mathbf{X}_{k+1} = \mathbf{x}_{target} - \mathbf{u}_k $$
+#       $ \mathbf{X}_{k+1} = \mathbf{x}_{target} - \mathbf{u}_k $
 #    c. Check convergence: $||\mathbf{X}_{k+1} - \mathbf{X}_k|| < \text{tol}$.
 #
 # In `fenicsx-pulse`, the `FixedPointUnloader` class automates this iterative process.

demo/time_dependent_bestel_biv.py

@@ -25,6 +25,7 @@
 
 
 logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger("pulse")
 comm = MPI.COMM_WORLD
 
 outdir = Path("time-dependent-bestel-biv")
@@ -124,7 +125,7 @@
 problem = pulse.problem.DynamicProblem(model=model, geometry=geometry, bcs=bcs)
 
 
-log.set_log_level(log.LogLevel.INFO)
+# log.set_log_level(log.LogLevel.INFO)
 problem.solve()
 
 dt = problem.parameters["dt"].to_base_units()

demo/time_dependent_bestel_lv.py

@@ -199,6 +199,7 @@
 # Next we set up the logging and the MPI communicator
 
 logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger("pulse")
 comm = MPI.COMM_WORLD
 
 # and create an output directory
@@ -277,11 +278,11 @@
 #
 
 alpha_epi = pulse.Variable(
-        dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(1e8)), "Pa / m",
+    dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(1e8)), "Pa / m",
 )
 robin_epi_u = pulse.RobinBC(value=alpha_epi, marker=geometry.markers["EPI"][0])
 beta_epi = pulse.Variable(
-        dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(5e3)), "Pa s/ m",
+    dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(5e3)), "Pa s/ m",
 )
 robin_epi_v = pulse.RobinBC(value=beta_epi, marker=geometry.markers["EPI"][0], damping=True)
 
@@ -290,7 +291,7 @@
 )
 robin_base_u = pulse.RobinBC(value=alpha_base, marker=geometry.markers["BASE"][0])
 beta_base = pulse.Variable(
-        dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(5e3)), "Pa s/ m",
+    dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(5e3)), "Pa s/ m",
 )
 robin_base_v = pulse.RobinBC(value=beta_base, marker=geometry.markers["BASE"][0], damping=True)
 
@@ -305,7 +306,7 @@
 
 # Note that we also specify that the base is free to move, meaning that there will be no Dirichlet boundary conditions on the base. Now we can do an initial solve the problem
 
-log.set_log_level(log.LogLevel.INFO)
+# log.set_log_level(log.LogLevel.INFO)
 problem.solve()
 
 # The next step is to get the activation and pressure as a function of time. For this we use the time step from the problem parameters
@@ -357,13 +358,13 @@
 
 volume_form = dolfinx.fem.form(geometry.volume_form(u=problem.u) * geometry.ds(geometry.markers["ENDO"][0]))
 initial_volume = geo.mesh.comm.allreduce(dolfinx.fem.assemble_scalar(volume_form))
-print(f"Initial volume: {initial_volume}")
+logger.info(f"Initial volume: {initial_volume}")
 
 # and then loop over the time steps and solve the problem for each time step
 
 volumes = []
 for i, (tai, pi, ti) in enumerate(zip(activation, pressure, times)):
-    print(f"Solving for time {ti}, activation {tai}, pressure {pi}")
+    logger.info(f"Solving for time {ti}, activation {tai}, pressure {pi}")
     traction.assign(pi)
     Ta.assign(tai)
     problem.solve()

demo/time_dependent_land_circ_biv.py

@@ -131,7 +131,6 @@
 rv_cavity = pulse.problem.Cavity(marker="ENDO_RV", volume=rv_volume)
 
 
-
 cavities = [lv_cavity, rv_cavity]
 
 
@@ -147,7 +146,7 @@
 
 # Now we can solve the problem
 
-log.set_log_level(log.LogLevel.INFO)
+# log.set_log_level(log.LogLevel.INFO)
 problem.solve()
 
 dt = 0.001
@@ -196,8 +195,9 @@ def solve_beat(times, states, dt, p, V_index, Ca_index, Vs, Cais, Tas):
     Vs = np.zeros(len(times) * nbeats)
     Cais = np.zeros(len(times) * nbeats)
     Tas = np.zeros(len(times) * nbeats)
+    logger.debug(f"Starting to solve {nbeats} beats of the cell model")
     for beat in range(nbeats):
-        print(f"Solving beat {beat}")
+        logger.debug(f"Solving beat {beat}")
         V_tmp = Vs[beat * len(times) : (beat + 1) * len(times)]
         Cai_tmp = Cais[beat * len(times) : (beat + 1) * len(times)]
         Ta_tmp = Tas[beat * len(times) : (beat + 1) * len(times)]
@@ -308,9 +308,9 @@ def callback(model, i: int, t: float, save=True):
 # 4.  **Output**: We retrieve the Lagrange multipliers for both LV and RV cavities (indices 0 and 1 in `problem.cavity_pressures`), convert them to mmHg, and return them.
 
 def p_BiV_func(V_LV, V_RV, t):
-    print("Calculating pressure at time", t)
+    logger.debug("Calculating pressure at time %f", t)
     value = get_activation(t)
-    print("Time", t, "Activation", value)
+    logger.debug("Time %f Activation %f", t, value)
 
     logger.debug(f"Time{t} with activation: {value}")
     Ta.assign(value)

demo/time_dependent_land_circ_lv.py

@@ -62,6 +62,8 @@
 # Next we set up the logging and the MPI communicator
 
 circulation.log.setup_logging(logging.INFO)
+logging.getLogger("scifem").setLevel(logging.WARNING)
+logger = logging.getLogger("pulse")
 comm = MPI.COMM_WORLD
 
 # ## 1. Geometry Generation
@@ -159,7 +161,7 @@
 
 # Now we can solve the problem
 
-log.set_log_level(log.LogLevel.INFO)
+# log.set_log_level(log.LogLevel.INFO)
 problem.solve()
 
 # We also use the time step from the problem to set the time step for the 0D cell model
@@ -222,8 +224,9 @@ def solve_beat(times, states, dt, p, V_index, Ca_index, Vs, Cais, Tas):
     Vs = np.zeros(len(times) * nbeats)
     Cais = np.zeros(len(times) * nbeats)
     Tas = np.zeros(len(times) * nbeats)
+    logger.info(f"Starting to solve {nbeats} beats of the cell model")
     for beat in range(nbeats):
-        print(f"Solving beat {beat}")
+        logger.debug(f"Solving beat {beat}")
         V_tmp = Vs[beat * len(times) : (beat + 1) * len(times)]
         Cai_tmp = Cais[beat * len(times) : (beat + 1) * len(times)]
         Ta_tmp = Tas[beat * len(times) : (beat + 1) * len(times)]
@@ -321,7 +324,7 @@ def callback(model, i: int, t: float, save=True):
             for axi in [ax2, ax3, ax4]:
                 axi.set_xlabel("Time [s]")
 
-            print(f"Saving figure to {outdir / 'pv_loop_incremental.png'}")
+            logger.debug(f"Saving figure to {outdir / 'pv_loop_incremental.png'}")
             fig.savefig(outdir / "pv_loop_incremental.png")
             plt.close(fig)
             # fig, ax = plt.subplots(4, 1)
@@ -349,9 +352,9 @@ def callback(model, i: int, t: float, save=True):
 # 4.  **Output**: The Lagrange multiplier associated with the volume constraint is the cavity pressure. We return this pressure (converted to mmHg) to the circulation model.
 
 def p_LV_func(V_LV, t):
-    print("Calculating pressure at time", t)
+    logger.debug("Calculating pressure at time %f", t)
     value = get_activation(t)
-    print("Time", t, "Activation", value)
+    logger.debug("Time %f Activation %f", t, value)
     Ta.assign(value)
     Volume.value = V_LV * 1e-6
     problem.solve()
@@ -371,7 +374,7 @@ def p_LV_func(V_LV, t):
 add_units = False
 surface_area = geometry.surface_area("ENDO")
 initial_volume = geo.mesh.comm.allreduce(geometry.volume("ENDO", u=problem.u), op=MPI.SUM) * 1e6
-print(f"Initial volume: {initial_volume}")
+logger.info(f"Initial volume: {initial_volume}")
 init_state = {"V_LV": initial_volume * mL}
 
 

src/pulse/cardiac_model.py

@@ -47,7 +47,7 @@ def S(self, C: ufl.core.expr.Expr) -> ufl.core.expr.Expr: ...
 class ViscoElasticity(Protocol):
     def strain_energy(self, C_dot: ufl.core.expr.Expr) -> ufl.core.expr.Expr: ...
 
-    def P(self, F: ufl.core.expr.Expr) -> ufl.core.expr.Expr: ...
+    def P(self, F_dot: ufl.core.expr.Expr) -> ufl.core.expr.Expr: ...
 
     def S(self, C_dot: ufl.core.expr.Expr) -> ufl.core.expr.Expr: ...
 

src/pulse/unloading.py

@@ -108,7 +108,7 @@ def _update_model_fields(self, u: dolfinx.fem.Function) -> None:
                     )
                     logger.warning(msg)
                     continue
-                logger.info(f"Deforming field '{fieldname}' of model '{model_name}'.")
+                logger.debug(f"Deforming field '{fieldname}' of model '{model_name}'.")
                 deformed_field = map_vector_field(
                     f=f,
                     u=u,
@@ -159,7 +159,7 @@ def unload(self) -> dolfinx.fem.Function:
                         msg = f"Ramping {name} traction to {value:.4f}"
                     else:
                         msg = f"Ramping traction to {value:.4f}"
-                    logger.info(msg)
+                    logger.debug(msg)
                 problem.solve()
             u = problem.u