agencyenterprise · NewtonSander · Sep 26, 2023 · Sep 26, 2023 · Sep 26, 2023 · Sep 26, 2023
diff --git a/docs/api/scenarios.md b/docs/api/scenarios.md
@@ -12,23 +12,23 @@
     options:
       show_root_heading: true
 
-::: neurotechdevkit.scenarios.built_in.Scenario0
+::: neurotechdevkit.scenarios.built_in.ScenarioSimple
     options:
       show_root_heading: true
 
-::: neurotechdevkit.scenarios.built_in.Scenario1_2D
+::: neurotechdevkit.scenarios.built_in.ScenarioFlatSkull_2D
     options:
       show_root_heading: true
 
-::: neurotechdevkit.scenarios.built_in.Scenario1_3D
+::: neurotechdevkit.scenarios.built_in.ScenarioFlatSkull_3D
     options:
       show_root_heading: true
 
-::: neurotechdevkit.scenarios.built_in.Scenario2_2D
+::: neurotechdevkit.scenarios.built_in.ScenarioRealisticSkull_2D
     options:
       show_root_heading: true
 
-::: neurotechdevkit.scenarios.built_in.Scenario2_3D
+::: neurotechdevkit.scenarios.built_in.ScenarioRealisticSkull_3D
     options:
       show_root_heading: true
 

diff --git a/docs/examples/plot_adding_custom_source.py b/docs/examples/plot_adding_custom_source.py
@@ -37,7 +37,7 @@
     num_points=1000,
 )
 
-scenario = ndk.built_in.Scenario0()
+scenario = ndk.built_in.ScenarioSimple()
 scenario.sources = [source]
 scenario.make_grid()
 scenario.compile_problem()

diff --git a/docs/examples/plot_customized_center_frequency.py b/docs/examples/plot_customized_center_frequency.py
@@ -11,7 +11,7 @@
 
 CENTER_FREQUENCY = 6e5
 
-scenario = ndk.scenarios.built_in.Scenario0()
+scenario = ndk.scenarios.built_in.ScenarioSimple()
 
 # Customizing material properties
 scenario.material_properties = {

diff --git a/docs/examples/plot_full_scenario.py b/docs/examples/plot_full_scenario.py
@@ -7,7 +7,7 @@
     NDK and its examples are under constant development, more information
     and content will be added to this example soon!
 
-The following code is a simplified implementation of NDK's Scenario 1.
+The following code is a simplified implementation of NDK's ScenarioFlatSkull.
 """
 # %%
 # Implementing a Scenario

diff --git a/docs/examples/plot_metrics.py b/docs/examples/plot_metrics.py
@@ -14,7 +14,7 @@
 # ## Rendering scenario
 import neurotechdevkit as ndk
 
-scenario = ndk.built_in.Scenario0()
+scenario = ndk.built_in.ScenarioSimple()
 scenario.make_grid()
 scenario.compile_problem()
 result = scenario.simulate_steady_state()

diff --git a/docs/examples/plot_multiple_sources.py b/docs/examples/plot_multiple_sources.py
@@ -17,7 +17,7 @@
 # %%
 import neurotechdevkit as ndk
 
-scenario = ndk.built_in.Scenario0()
+scenario = ndk.built_in.ScenarioSimple()
 
 s1 = ndk.sources.FocusedSource2D(
     position=[0.01, 0.0],

diff --git a/docs/examples/plot_phased_array_source.py b/docs/examples/plot_phased_array_source.py
@@ -128,7 +128,7 @@
     num_points=1000,
 )
 
-scenario = ndk.scenarios.built_in.Scenario1_2D()
+scenario = ndk.scenarios.built_in.ScenarioFlatSkull_2D()
 scenario.sources = [source]
 scenario.make_grid()
 scenario.compile_problem()
@@ -142,7 +142,7 @@
 # delays are automatically computed when `focal_length` is defined. Let's explore how
 # the API looks like:
 
-scenario = ndk.scenarios.built_in.Scenario1_2D()
+scenario = ndk.scenarios.built_in.ScenarioFlatSkull_2D()
 
 phased_array = ndk.sources.PhasedArraySource2D(
     position=[0.0, 0.0],
@@ -176,7 +176,7 @@
 # In the example below we apply monotonically increasing delays to mimic a
 # counter-clockwise angle.
 
-scenario = ndk.scenarios.built_in.Scenario1_2D()
+scenario = ndk.scenarios.built_in.ScenarioFlatSkull_2D()
 
 phased_array = ndk.sources.PhasedArraySource2D(
     position=[0.0, 0.0],
@@ -208,7 +208,7 @@
 #
 # The rest of the API is identical for both 2D and 3D scenarios.
 
-scenario_3d = ndk.scenarios.built_in.Scenario1_3D()
+scenario_3d = ndk.scenarios.built_in.ScenarioFlatSkull_3D()
 
 phased_3d = ndk.sources.PhasedArraySource3D(
     position=[0.0, 0.0, 0.0],

diff --git a/docs/examples/plot_pulsed_simulation.py b/docs/examples/plot_pulsed_simulation.py
@@ -9,7 +9,7 @@
 # %%
 import neurotechdevkit as ndk
 
-scenario = ndk.built_in.Scenario0()
+scenario = ndk.built_in.ScenarioSimple()
 scenario.make_grid()
 scenario.compile_problem()
 result = scenario.simulate_pulse()

diff --git a/docs/examples/plot_scenario2_predefined_target.py b/docs/examples/plot_scenario2_predefined_target.py
diff --git a/docs/examples/plot_scenario_predefined_target.py b/docs/examples/plot_scenario_predefined_target.py
@@ -0,0 +1,56 @@
+# -*- coding: utf-8 -*-
+"""
+
+ScenarioRealisticSkull predefined target
+====================================
+
+!!! note
+    NDK and its examples are under constant development, more information
+    and content will be added to this example soon!
+
+This example demonstrates how to use one of the predefined targets of
+ScenarioRealisticSkull.
+"""
+# %%
+# The list of supported targets is:
+import neurotechdevkit as ndk
+
+scenario_realistic_skull_2d_targets = (
+    ndk.scenarios.built_in.ScenarioRealisticSkull_2D.PREDEFINED_TARGET_OPTIONS.keys()
+)
+scenario_realistic_skull_3d_targets = (
+    ndk.scenarios.built_in.ScenarioRealisticSkull_3D.PREDEFINED_TARGET_OPTIONS.keys()
+)
+print(
+    "2D predefined targets: \n\t",
+    ", ".join(scenario_realistic_skull_2d_targets),
+    "\n\n",
+)
+print(
+    "3D predefined targets: \n\t",
+    ", ".join(scenario_realistic_skull_3d_targets),
+    "\n\n",
+)
+
+# %%
+# Using one of the predefined targets is as simple as:
+scenario = ndk.built_in.ScenarioRealisticSkull_2D()
+target_options = (
+    ndk.scenarios.built_in.ScenarioRealisticSkull_2D.PREDEFINED_TARGET_OPTIONS
+)
+scenario.target = target_options["posterior-cingulate-cortex"]
+scenario.make_grid()
+
+scenario.render_layout()
+
+# %%
+# The same can be done for the 3D:
+scenario_3d = ndk.built_in.ScenarioRealisticSkull_3D()
+target_options = (
+    ndk.scenarios.built_in.ScenarioRealisticSkull_3D.PREDEFINED_TARGET_OPTIONS
+)
+scenario_3d.target = target_options["left-temporal-lobe"]
+scenario_3d.make_grid()
+
+scenario_3d.render_layout()
+# %%
diff --git a/docs/examples/plot_scenarios.py b/docs/examples/plot_scenarios.py
@@ -20,18 +20,18 @@ def plot_scenario(chosen_scenario):
 
 
 # %%
-# Simulating scenario: scenario 0
+# Simulating scenario: scenario-simple
 # ===================================
-plot_scenario(ndk.scenarios.built_in.Scenario0)
+plot_scenario(ndk.scenarios.built_in.ScenarioSimple)
 
 # %%
-# Simulating scenario: scenario 1 2D
+# Simulating scenario: scenario-flat-skull 2D
 # ===================================
-plot_scenario(ndk.scenarios.built_in.Scenario1_2D)
+plot_scenario(ndk.scenarios.built_in.ScenarioFlatSkull_2D)
 
 # %%
-# Simulating scenario: scenario 2 2D
+# Simulating scenario: scenario-realistic-skull 2D
 # ===================================
-plot_scenario(ndk.scenarios.built_in.Scenario2_2D)
+plot_scenario(ndk.scenarios.built_in.ScenarioRealisticSkull_2D)
 
 # %%
diff --git a/docs/examples/plot_store_results.py b/docs/examples/plot_store_results.py
@@ -15,7 +15,7 @@
 # Execute the following code in a computer with ndk installed
 import neurotechdevkit as ndk
 
-scenario = ndk.built_in.Scenario0()
+scenario = ndk.built_in.ScenarioSimple()
 scenario.make_grid()
 scenario.compile_problem()
 result = scenario.simulate_steady_state()

diff --git a/docs/examples/plot_time_reverse.py b/docs/examples/plot_time_reverse.py
@@ -36,7 +36,7 @@
 # %%
 # Helper function to make the scenario with a PhasedArraySource
 def make_scenario(element_delays=None):
-    true_scenario = ndk.scenarios.built_in.Scenario2_2D()
+    true_scenario = ndk.scenarios.built_in.ScenarioRealisticSkull_2D()
 
     # define a phased-array source
     default_source = true_scenario.sources[0]
@@ -68,7 +68,7 @@ def make_scenario(element_delays=None):
 # The point source is visualized as a gray dot.
 
 # Reinitialize the scenario
-reversed_scenario = ndk.scenarios.built_in.Scenario2_2D()
+reversed_scenario = ndk.scenarios.built_in.ScenarioRealisticSkull_2D()
 # and reverse the source
 point_source = ndk.sources.PointSource2D(
     position=true_scenario.target.center,

diff --git a/docs/examples/plot_ultrasound_imaging_multiplane.py b/docs/examples/plot_ultrasound_imaging_multiplane.py
@@ -40,7 +40,7 @@
 # Imaging modules
 from neurotechdevkit.imaging import beamform, demodulate, util
 from neurotechdevkit.results import PulsedResult2D, SteadyStateResult2D
-from neurotechdevkit.scenarios.built_in import Scenario3
+from neurotechdevkit.scenarios.built_in import ScenarioUltrasoundPhantom
 from neurotechdevkit.sources import PhasedArraySource2D
 
 # %%
@@ -93,9 +93,9 @@
 # %%
 
 
-def create_scenario(tilt_angle: float = 0.0) -> Scenario3:
+def create_scenario(tilt_angle: float = 0.0) -> ScenarioUltrasoundPhantom:
     """Helper function to initialize scenario with different tilt angles."""
-    scenario = Scenario3()
+    scenario = ScenarioUltrasoundPhantom()
     scenario.center_frequency = TONE_CENTER_FREQUENCY
     source_position = [0.01, 0.0]
     unit_direction = [1.0, 0.0]
@@ -172,7 +172,7 @@ def create_scenario(tilt_angle: float = 0.0) -> Scenario3:
 # Helper functions: simulate long enough for ultrasound scattering reflection
 
 
-def calc_simulation_time(scenario: Scenario3):
+def calc_simulation_time(scenario: ScenarioUltrasoundPhantom):
     simulation_time = ndk.scenarios._time.select_simulation_time_for_pulsed(
         grid=scenario.grid,
         materials=scenario.materials,

diff --git a/docs/examples/plot_ultrasound_imaging_scanline.py b/docs/examples/plot_ultrasound_imaging_scanline.py
@@ -41,7 +41,7 @@
 # Imaging modules
 from neurotechdevkit.imaging import beamform, demodulate, util
 from neurotechdevkit.results import PulsedResult2D, SteadyStateResult2D
-from neurotechdevkit.scenarios.built_in import Scenario3
+from neurotechdevkit.scenarios.built_in import ScenarioUltrasoundPhantom
 from neurotechdevkit.sources import PhasedArraySource2D
 
 # %%
@@ -91,9 +91,9 @@
 # %%
 
 
-def create_scenario(tilt_angle: float = 0.0) -> Scenario3:
+def create_scenario(tilt_angle: float = 0.0) -> ScenarioUltrasoundPhantom:
     """Helper function to initialize scenario with different tilt angles."""
-    scenario = Scenario3()
+    scenario = ScenarioUltrasoundPhantom()
     scenario.center_frequency = TONE_CENTER_FREQUENCY
     source_position = [0.01, 0.0]
     unit_direction = [1.0, 0.0]
@@ -171,7 +171,7 @@ def create_scenario(tilt_angle: float = 0.0) -> Scenario3:
 scenario = create_scenario()
 
 
-def calc_simulation_time(scenario: Scenario3):
+def calc_simulation_time(scenario: ScenarioUltrasoundPhantom):
     simulation_time = ndk.scenarios._time.select_simulation_time_for_pulsed(
         grid=scenario.grid,
         materials=scenario.materials,

diff --git a/docs/index.md b/docs/index.md
@@ -49,7 +49,7 @@ To install and run **neurotechdevkit** locally check the [installation](http://n
 ```python
 import neurotechdevkit as ndk
 
-scenario = ndk.scenarios.built_in.Scenario0()
+scenario = ndk.scenarios.built_in.ScenarioSimple()
 scenario.make_grid()
 scenario.compile_problem()
 result = scenario.simulate_steady_state()

diff --git a/docs/usage/defining_sources.md b/docs/usage/defining_sources.md
@@ -5,7 +5,7 @@ Users can specify the parameters and placement of sources, and add them to their
 import neurotechdevkit as ndk
 import numpy as np
 
-scenario = ndk.scenarios.built_in.Scenario2_2D()
+scenario = ndk.scenarios.built_in.ScenarioRealisticSkull_2D()
 
 source = ndk.sources.FocusedSource2D(
     position=np.array([0.19, 0.07]),
@@ -50,7 +50,7 @@ The 2D sources are for 2D scenarios and the 3D sources for 3D scenarios. The par
 import neurotechdevkit as ndk
 import numpy as np
 
-scenario = ndk.scenarios.built_in.Scenario2_2D()
+scenario = ndk.scenarios.built_in.ScenarioRealisticSkull_2D()
 
 source_position = np.array([0.19, 0.07])
 source = ndk.sources.PlanarSource2D(

diff --git a/docs/usage/gpu.md b/docs/usage/gpu.md
@@ -14,7 +14,7 @@ Now when running NDK simulations you should be able to see `platform=nvidiaX` in
 ```py
 import neurotechdevkit as ndk
 
-scenario = ndk.scenarios.built_in.Scenario2_2D()
+scenario = ndk.scenarios.built_in.ScenarioRealisticSkull_2D()
 scenario.make_grid()
 scenario.compile_problem()
 result = scenario.simulate_steady_state()

diff --git a/docs/usage/loading_scenarios.md b/docs/usage/loading_scenarios.md
@@ -9,17 +9,17 @@ The following is all that's needed to load a pre-defined scenario:
 ```py
 import neurotechdevkit as ndk
 
-scenario = ndk.scenarios.built_in.Scenario2_2D()
+scenario = ndk.scenarios.built_in.ScenarioRealisticSkull_2D()
 scenario.make_grid()
 ```
 
-The existing scenarios are:
+The existing scenarios include:
 
-- `SCENARIO_0` (2D) - a simple quickstart toy scenario that enables users to dive in and experiment with their first simulation immediately.
-- `SCENARIO_1_3D` (3D) - a scenario containing a flat 3-layer bone covered by skin, with water above the skin and brain below the bone. This is based on benchmark 4 of [Jean-Francois Aubry, et al.](https://doi.org/10.1121/10.0013426).
-- `SCENARIO_2_3D` (3D) - a scenario containing a full skull and brain mesh immersed in water. This is based on benchmark 8 of [Jean-Francois Aubry, et al.](https://doi.org/10.1121/10.0013426).
-- `SCENARIO_1_2D` (2D) - a 2D version of scenario 1.
-- `SCENARIO_2_2D` (2D) - a 2D version of scenario 2.
+- `SCENARIO_SIMPLE` (2D) - a simple quick-start toy scenario that enables users to dive in and experiment with their first simulation immediately.
+- `SCENARIO_FLAT_SKULL_3D` (3D) - a scenario containing a flat 3-layer bone covered by skin, with water above the skin and brain below the bone. This is based on benchmark 4 of [Jean-Francois Aubry, et al.](https://doi.org/10.1121/10.0013426).
+- `SCENARIO_REALISTIC_SKULL_3D` (3D) - a scenario containing a full skull and brain mesh immersed in water. This is based on benchmark 8 of [Jean-Francois Aubry, et al.](https://doi.org/10.1121/10.0013426).
+- `SCENARIO_FLAT_SKULL_2D` (2D) - a 2D version of `SCENARIO_FLAT_SKULL`.
+- `SCENARIO_REALISTIC_SKULL_2D` (2D) - a 2D version of `SCENARIO_REALISTIC_SKULL`.
 
 All of these scenarios are immediately ready for visualization and simulation, with appropriate default parameters used where needed.