Merge pull request #86 from pinton-lab/develop

v1.1.0

Author: MasashiSode

.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "1.0.20"
+current_version = "1.1.0"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.

examples/linear_transducer/linear_transducer_abdominal_wall.py

@@ -149,16 +149,22 @@ def main() -> None:  # noqa: PLR0915
     )
 
     # define scatterer
-    scatterer = presets.ScattererDomain(
+
+    rng = np.random.default_rng(seed=42)
+
+    csr = 0.05
+    ratio_scatterer_to_total_grid = 0.38
+
+    scatterer, _ = fullwave.utils.generate_scatterer(
         grid=grid,
-        num_scatterer=18,
-        ncycles=2,
+        # ratio_scatterer_to_total_grid=0.38,
+        ratio_scatterer_to_total_grid=ratio_scatterer_to_total_grid,
+        scatter_value_std=csr / 2,
+        rng=rng,
     )
 
-    # scatterer will be applied to density directly, instead of registering as a domain
-    csr = 0.035
-    background.density -= scatterer.density * csr
-    abdominal_wall.density -= scatterer.density * csr
+    background.density *= scatterer
+    abdominal_wall.density *= scatterer
 
     # register the domains to MediumBuilder
     mb = MediumBuilder(
@@ -170,7 +176,7 @@ def main() -> None:  # noqa: PLR0915
     # mb.register_domain(simple_domain_2)
 
     # we can plot to see the current registered domains
-    mb.plot_current_map(export_path=work_dir / "medium.png")
+    mb.plot_current_map(export_path=work_dir / "medium.svg")
 
     # generate medium for simulation
     medium = mb.run()
@@ -200,17 +206,18 @@ def main() -> None:  # noqa: PLR0915
     )
     propagation_map = np.nan_to_num(propagation_map, 0, posinf=p_max, neginf=-p_max)
 
-    p_max_plot = np.abs(propagation_map).max().item() / 2
+    p_max_plot = np.abs(propagation_map).max().item() / 8
 
-    time_step = propagation_map.shape[0] // 3 * 2
+    time_step = propagation_map.shape[0] // 50 * 37
     plot_utils.plot_wave_propagation_snapshot(
         propagation_map=propagation_map[time_step],
         c_map=medium.sound_speed,
         rho_map=medium.density,
-        export_name=work_dir / "wave_propagation_snapshot_1.png",
+        export_name=work_dir / "wave_propagation_snapshot_1.svg",
         vmin=-p_max_plot,
         vmax=p_max_plot,
         turn_off_axes=True,
+        figsize=(6, 6),
     )
 
     plot_utils.plot_wave_propagation_with_map(

fullwave/__init__.py

@@ -60,7 +60,7 @@
     __version__ = version("fullwave")
 except PackageNotFoundError:
     # Update via bump-my-version, not manually
-    __version__ = "1.0.20"
+    __version__ = "1.1.0"
 
 VERSION = __version__  # for convenience
 logger.info("Fullwave version: %s", __version__)

fullwave/medium.py

@@ -777,7 +777,7 @@ def __init__(
         / "solver"
         / "bins"
         / "database"
-        / "relaxation_params_database_num_relax=2_20251027_1437.mat",
+        / "relaxation_params_database_num_relax=2_20260113_0957.mat",
         n_relaxation_mechanisms: int = 2,
         attenuation_builder: str = "lookup",
         use_isotropic_relaxation: bool = True,

fullwave/medium_builder/domain.py

@@ -40,7 +40,7 @@ def __init__(
         / "solver"
         / "bins"
         / "database"
-        / "relaxation_params_database_num_relax=2_20251027_1437.mat",
+        / "relaxation_params_database_num_relax=2_20260113_0957.mat",
         n_relaxation_mechanisms: int = 2,
     ) -> None:
         """Initialize the Domain class.

fullwave/medium_builder/medium_builder.py

@@ -32,7 +32,7 @@ def __init__(
         / "solver"
         / "bins"
         / "database"
-        / "relaxation_params_database_num_relax=2_20251027_1437.mat",
+        / "relaxation_params_database_num_relax=2_20260113_0957.mat",
         n_relaxation_mechanisms: int = 2,
         attenuation_builder: str = "lookup",
     ) -> None:

fullwave/medium_builder/presets/domain_abdominal_wall.py

@@ -174,7 +174,7 @@ def __init__(
         / "solver"
         / "bins"
         / "database"
-        / "relaxation_params_database_num_relax=2_20251027_1437.mat",
+        / "relaxation_params_database_num_relax=2_20260113_0957.mat",
         n_relaxation_mechanisms: int = 2,
         transducer_surface: NDArray[np.float64] | None = None,
     ) -> None:
@@ -222,7 +222,7 @@ def __init__(
             Defaults to
             Path(__file__).parent.parent / "solver" / "bins"
             / "database"
-            / "relaxation_params_database_num_relax=2_20251027_1437.mat",
+            / "relaxation_params_database_num_relax=2_20260113_0957.mat",
         n_relaxation_mechanisms: int, optional
             The number of relaxation mechanisms.
             Defaults to 4.

fullwave/medium_builder/presets/domain_background.py

@@ -24,7 +24,7 @@ def __init__(
         / "solver"
         / "bins"
         / "database"
-        / "relaxation_params_database_num_relax=2_20251027_1437.mat",
+        / "relaxation_params_database_num_relax=2_20260113_0957.mat",
         n_relaxation_mechanisms: int = 2,
     ) -> None:
         """Initialize a Background instance.

fullwave/medium_builder/presets/domain_scatterer.py

@@ -26,7 +26,7 @@ def __init__(
         / "solver"
         / "bins"
         / "database"
-        / "relaxation_params_database_num_relax=2_20251027_1437.mat",
+        / "relaxation_params_database_num_relax=2_20260113_0957.mat",
         n_relaxation_mechanisms: int = 2,
         seed: int | None = None,
     ) -> None:

fullwave/medium_builder/presets/domain_simple.py

@@ -25,7 +25,7 @@ def __init__(
         / "bins"
         / "database"
         / "database"
-        / "relaxation_params_database_num_relax=2_20251027_1437.mat",
+        / "relaxation_params_database_num_relax=2_20260113_0957.mat",
         n_relaxation_mechanisms: int = 2,
     ) -> None:
         """Initialize a SimpleDomain.