Skip to content

Update biv docs #170

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
finsberg merged 1 commit into from
Apr 27, 2026
Merged

Update biv docs #170

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Binary file modified _static/pv_loop_time_dependent_land_circ_biv.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified _static/time_dependent_bestel_biv.mp4
View file
Open in desktop
Binary file not shown.
Binary file modified _static/time_dependent_land_circ_biv.mp4
View file
Open in desktop
Binary file not shown.
64 changes: 4 additions & 60 deletions demo/geometries/biv_ellipsoid.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,41 +44,28 @@
#
# We generate the mesh and fibers if they don't already exist.
#
# ### 1. Mesh Generation
# `cardiac_geometries.mesh.biv_ellipsoid` creates the mesh with markers for:
# * **LV_ENDO_FW**: LV Endocardium Free Wall
# * **LV_SEPTUM**: LV Septum
# * **RV_ENDO_FW**: RV Endocardium Free Wall
# * **RV_SEPTUM**: RV Septum
# * **LV_EPI_FW**: LV Epicardium Free Wall
# * **RV_EPI_FW**: RV Epicardium Free Wall
# * **BASE**: Base
#
# ### 2. Fiber Generation (LDRB)
# The LDRB algorithm solves Laplace equations to define transmural and apicobasal coordinates.
# Based on these coordinates, it assigns fiber angles (e.g., +60 to -60 degrees transmurally).

outdir = Path("biv_ellipsoid")
outdir.mkdir(parents=True, exist_ok=True)
geodir = outdir / "geometry"

if not geodir.exists():
# Generate mesh
geo = cardiac_geometries.mesh.biv_ellipsoid(outdir=geodir)

# Map mesh markers to the format expected by LDRB
markers = cardiac_geometries.mesh.transform_biv_markers(geo.markers)

# Run LDRB algorithm
system = ldrb.dolfinx_ldrb(
mesh=geo.mesh,
ffun=geo.ffun,
markers=markers,
markers=geo.markers,
alpha_endo_lv=60, # Fiber angle at LV endocardium
alpha_epi_lv=-60, # Fiber angle at LV epicardium
beta_endo_lv=0, # Sheet angle (0 for now)
beta_epi_lv=0,
fiber_space="P_2",
create_fibers=True,
)

# Save microstructure to XDMF/H5
Expand All @@ -94,49 +81,6 @@
folder=geodir,
)

# ### Marker Consolidation
# We group the detailed surface markers into broader categories for applying boundary conditions.
#
# * **ENDO_LV**: All LV endocardial surfaces (Free Wall + Septum).
# * **ENDO_RV**: All RV endocardial surfaces (Free Wall + Septum).
# * **EPI**: All epicardial surfaces.
# * **BASE**: The base.

markers = {"ENDO_LV": [1, 2], "ENDO_RV": [2, 2], "BASE": [3, 2], "EPI": [4, 2]}

# Create a new marker array based on the old one
marker_values = geo.ffun.values.copy()
marker_indices = geo.ffun.indices

# Helper to update markers
def update_marker(old_name, new_id):
old_id = geo.markers[old_name][0]
marker_values[np.isin(marker_indices, geo.ffun.find(old_id))] = new_id

# Update LV Endo
update_marker("LV_ENDO_FW", markers["ENDO_LV"][0])
update_marker("LV_SEPTUM", markers["ENDO_LV"][0])

# Update RV Endo
update_marker("RV_ENDO_FW", markers["ENDO_RV"][0])
update_marker("RV_SEPTUM", markers["ENDO_RV"][0])

# Update Base
update_marker("BASE", markers["BASE"][0])

# Update Epi
update_marker("LV_EPI_FW", markers["EPI"][0])
update_marker("RV_EPI_FW", markers["EPI"][0])

# Assign back to geometry object
geo.markers = markers
geo.ffun = dolfinx.mesh.meshtags(
geo.mesh,
geo.ffun.dim,
geo.ffun.indices,
marker_values,
)

# Scale the geometry from mm to meters (approximate scale factor)
geo.mesh.geometry.x[:] *= 1.4e-2

Expand Down Expand Up @@ -195,10 +139,10 @@ def update_marker(old_name, new_id):
# * $P_{RV}$ on $\Gamma_{endo, RV}$

lvp = dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(0.0))
neumann_lv = pulse.NeumannBC(traction=lvp, marker=geometry.markers["ENDO_LV"][0])
neumann_lv = pulse.NeumannBC(traction=lvp, marker=geometry.markers["LV"][0])

rvp = dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(0.0))
neumann_rv = pulse.NeumannBC(traction=rvp, marker=geometry.markers["ENDO_RV"][0])
neumann_rv = pulse.NeumannBC(traction=rvp, marker=geometry.markers["RV"][0])

# ### Robin BC: Pericardial Constraint
# We model the pericardium as a spring-like boundary condition on the epicardium.
Expand Down
31 changes: 5 additions & 26 deletions demo/time_dependent/time_dependent_bestel_biv.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -53,31 +53,10 @@

geo.mesh.geometry.x[:] *= 1.5e-2

# Now we need to redefine the markers to have so that facets on the endo- and epicardium combine both
# free wall and the septum.

markers = {"ENDO_LV": [1, 2], "ENDO_RV": [2, 2], "BASE": [3, 2], "EPI": [4, 2]}
marker_values = geo.ffun.values.copy()
marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["LV_ENDO_FW"][0]))] = markers["ENDO_LV"][0]
marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["LV_SEPTUM"][0]))] = markers["ENDO_LV"][0]
marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["RV_ENDO_FW"][0]))] = markers["ENDO_RV"][0]
marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["RV_SEPTUM"][0]))] = markers["ENDO_RV"][0]
marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["BASE"][0]))] = markers["BASE"][0]
marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["LV_EPI_FW"][0]))] = markers["EPI"][0]
marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["RV_EPI_FW"][0]))] = markers["EPI"][0]
geo.markers = markers
ffun = dolfinx.mesh.meshtags(
geo.mesh,
geo.ffun.dim,
geo.ffun.indices,
marker_values,
)
geo.ffun = ffun

# We create the geometry object and print the volumes of the LV and RV cavities

geometry = pulse.HeartGeometry.from_cardiac_geometries(geo, metadata={"quadrature_degree": 6})
print(geometry.volume("ENDO_LV") * 1e6, geometry.volume("ENDO_RV") * 1e6)
print(geometry.volume("LV") * 1e6, geometry.volume("RV") * 1e6)

material_params = pulse.HolzapfelOgden.orthotropic_parameters()
material = pulse.HolzapfelOgden(f0=geo.f0, s0=geo.s0, **material_params) # type: ignore
Expand All @@ -96,10 +75,10 @@
# One difference with the LV example is that we now have two different pressure boundary conditions, one for the LV and one for the RV

traction_lv = pulse.Variable(dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(0.0)), "Pa")
neumann_lv = pulse.NeumannBC(traction=traction_lv, marker=geometry.markers["ENDO_LV"][0])
neumann_lv = pulse.NeumannBC(traction=traction_lv, marker=geometry.markers["LV"][0])

traction_rv = pulse.Variable(dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(0.0)), "Pa")
neumann_rv = pulse.NeumannBC(traction=traction_rv, marker=geometry.markers["ENDO_RV"][0])
neumann_rv = pulse.NeumannBC(traction=traction_rv, marker=geometry.markers["RV"][0])

# Otherwize we have the same Robin boundary conditions as in the LV example

Expand Down Expand Up @@ -204,8 +183,8 @@
vtx.write(0.0)

volume_form = geometry.volume_form(u=problem.u)
lv_volume_form = dolfinx.fem.form(volume_form * geometry.ds(geometry.markers["ENDO_LV"][0]))
rv_volume_form = dolfinx.fem.form(volume_form * geometry.ds(geometry.markers["ENDO_RV"][0]))
lv_volume_form = dolfinx.fem.form(volume_form * geometry.ds(geometry.markers["LV"][0]))
rv_volume_form = dolfinx.fem.form(volume_form * geometry.ds(geometry.markers["RV"][0]))

lv_volumes = []
rv_volumes = []
Expand Down
55 changes: 10 additions & 45 deletions demo/time_dependent/time_dependent_land_circ_biv.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,43 +61,8 @@
folder=geodir,
)
# Scale the geometry to meters and adjust the size so that LV and RV volumes are reasonable
geo.mesh.geometry.x[:] *= 1.5e-2

# Now we need to redefine the markers to have so that facets on the endo- and epicardium combine both
# free wall and the septum.

markers = {"ENDO_LV": [1, 2], "ENDO_RV": [2, 2], "BASE": [3, 2], "EPI": [4, 2]}
marker_values = geo.ffun.values.copy()
marker_values[
np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["LV_ENDO_FW"][0]))
] = markers["ENDO_LV"][0]
marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["LV_SEPTUM"][0]))] = (
markers["ENDO_LV"][0]
)
marker_values[
np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["RV_ENDO_FW"][0]))
] = markers["ENDO_RV"][0]
marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["RV_SEPTUM"][0]))] = (
markers["ENDO_RV"][0]
)
marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["BASE"][0]))] = (
markers["BASE"][0]
)
marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["LV_EPI_FW"][0]))] = (
markers["EPI"][0]
)
marker_values[np.isin(geo.ffun.indices, geo.ffun.find(geo.markers["RV_EPI_FW"][0]))] = (
markers["EPI"][0]
)
geo.mesh.geometry.x[:] *= 1.6e-2

geo.markers = markers
ffun = dolfinx.mesh.meshtags(
geo.mesh,
geo.ffun.dim,
geo.ffun.indices,
marker_values,
)
geo.ffun = ffun

geometry = pulse.HeartGeometry.from_cardiac_geometries(
geo, metadata={"quadrature_degree": 6},
Expand Down Expand Up @@ -131,7 +96,7 @@
)

alpha_epi = pulse.Variable(
dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(1e8)),
dolfinx.fem.Constant(geometry.mesh, dolfinx.default_scalar_type(1e6)),
"Pa / m",
)
robin_epi = pulse.RobinBC(value=alpha_epi, marker=geometry.markers["EPI"][0])
Expand All @@ -142,17 +107,17 @@
robin_base = pulse.RobinBC(value=alpha_base, marker=geometry.markers["BASE"][0])


lvv_initial = geo.mesh.comm.allreduce(geometry.volume("ENDO_LV"), op=MPI.SUM)
lvv_initial = geo.mesh.comm.allreduce(geometry.volume("LV"), op=MPI.SUM)
lv_volume = dolfinx.fem.Constant(
geometry.mesh, dolfinx.default_scalar_type(lvv_initial),
)
lv_cavity = pulse.problem.Cavity(marker="ENDO_LV", volume=lv_volume)
lv_cavity = pulse.problem.Cavity(marker="LV", volume=lv_volume)

rvv_initial = geo.mesh.comm.allreduce(geometry.volume("ENDO_RV"), op=MPI.SUM)
rvv_initial = geo.mesh.comm.allreduce(geometry.volume("RV"), op=MPI.SUM)
rv_volume = dolfinx.fem.Constant(
geometry.mesh, dolfinx.default_scalar_type(rvv_initial),
)
rv_cavity = pulse.problem.Cavity(marker="ENDO_RV", volume=rv_volume)
rv_cavity = pulse.problem.Cavity(marker="RV", volume=rv_volume)


cavities = [lv_cavity, rv_cavity]
Expand Down Expand Up @@ -284,7 +249,7 @@ def get_activation(t: float):

def callback(model, i: int, t: float, save=True):
Ta_history.append(get_activation(t))
if save and i % 100 == 0:
if save and i % 10 == 0:
io4dolfinx.write_function(filename, problem.u, time=t, name="displacement")
vtx.write(t)

Expand Down Expand Up @@ -363,19 +328,18 @@ def p_BiV_func(V_LV, V_RV, t):
mL = circulation.units.ureg("mL")
add_units = False
lvv_init = (
geo.mesh.comm.allreduce(geometry.volume("ENDO_LV", u=problem.u), op=MPI.SUM)
geo.mesh.comm.allreduce(geometry.volume("LV", u=problem.u), op=MPI.SUM)
* 1e6
* 1.0
) # Increase the volume by 5%
rvv_init = (
geo.mesh.comm.allreduce(geometry.volume("ENDO_RV", u=problem.u), op=MPI.SUM)
geo.mesh.comm.allreduce(geometry.volume("RV", u=problem.u), op=MPI.SUM)
* 1e6
* 1.0
) # Increase the volume by 5%
logger.info(f"Initial volume (LV): {lvv_init} mL and (RV): {rvv_init} mL")
init_state = {"V_LV": lvv_initial * 1e6 * mL, "V_RV": rvv_initial * 1e6 * mL}


circulation_model_3D = circulation.regazzoni2020.Regazzoni2020(
add_units=add_units,
callback=callback,
Expand All @@ -385,6 +349,7 @@ def p_BiV_func(V_LV, V_RV, t):
outdir=outdir,
initial_state=init_state,
)
# exit()
# Set end time for early stopping if running in CI
end_time = 2 * dt if os.getenv("CI") else None
circulation_model_3D.solve(
Expand Down
Loading