Removing 'scenario_id' attribute

agencyenterprise · Jul 31, 2023 · 0f80407 · 0f80407
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diff --git a/docs/api/make.md b/docs/api/make.md
diff --git a/docs/api/scenarios.md b/docs/api/scenarios.md
@@ -15,32 +15,22 @@
 ::: neurotechdevkit.scenarios.Scenario0
     options:
       show_root_heading: true
-      members:
-        - scenario_id
 
 ::: neurotechdevkit.scenarios.Scenario1_2D
     options:
       show_root_heading: true
-      members:
-        - scenario_id
 
 ::: neurotechdevkit.scenarios.Scenario1_3D
     options:
       show_root_heading: true
-      members:
-        - scenario_id
 
 ::: neurotechdevkit.scenarios.Scenario2_2D
     options:
       show_root_heading: true
-      members:
-        - scenario_id
 
 ::: neurotechdevkit.scenarios.Scenario2_3D
     options:
       show_root_heading: true
-      members:
-        - scenario_id
 
 ::: neurotechdevkit.scenarios.Target
     options:

diff --git a/docs/examples/plot_adding_custom_source.py b/docs/examples/plot_adding_custom_source.py
@@ -39,7 +39,7 @@
     num_points=1000,
 )
 
-scenario = ndk.make("scenario-0-v0")
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_0.value()
 scenario.sources.clear()
 scenario.add_source(source)
 scenario.compile_problem(center_frequency=5e5)

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.make("scenario-0-v0")
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_0.value()
 
 # using default material layers
 scenario.material_layers = ["water", "cortical_bone", "brain", "tumor"]

diff --git a/docs/examples/plot_full_scenario.py b/docs/examples/plot_full_scenario.py
@@ -29,7 +29,6 @@ class FullScenario(Scenario2D):
     https://asa.scitation.org/doi/pdf/10.1121/10.0013426
     """
 
-    scenario_id = "the_id_for_this_scenario"
     """
     Target attributes:
         target_id: the string id of the target.

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.make("scenario-0-v0")
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_0.value()
 scenario.compile_problem(center_frequency=5e5)
 result = scenario.simulate_steady_state()
 assert isinstance(result, ndk.results.SteadyStateResult2D)

diff --git a/docs/examples/plot_multiple_sources.py b/docs/examples/plot_multiple_sources.py
@@ -19,7 +19,7 @@
 
 import neurotechdevkit as ndk
 
-scenario = ndk.make("scenario-0-v0")
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_0.value()
 
 s1 = ndk.sources.FocusedSource2D(
     position=np.array([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.make("scenario-1-2d-v0")
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_1_2D.value()
 scenario.sources = [source]
 scenario.compile_problem(center_frequency=5e5)
 result = scenario.simulate_steady_state()
@@ -141,7 +141,7 @@
 # delays are automatically computed when `focal_length` is defined. Let's explore how
 # the API looks like:
 
-scenario = ndk.make("scenario-1-2d-v0")
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_1_2D.value()
 
 phased_array = ndk.sources.PhasedArraySource2D(
     position=np.array([0.0, 0.0]),
@@ -175,7 +175,7 @@
 # In the example below we apply monotonically increasing delays to mimic a
 # counter-clockwise angle.
 
-scenario = ndk.make("scenario-1-2d-v0")
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_1_2D.value()
 
 phased_array = ndk.sources.PhasedArraySource2D(
     position=np.array([0.0, 0.0]),
@@ -207,7 +207,7 @@
 #
 # The rest of the API is identical for both 2D and 3D scenarios.
 
-scenario = ndk.make("scenario-1-3d-v0")
+scenario_3d = ndk.BUILTIN_SCENARIOS.SCENARIO_1_3D.value()
 
 phased_3d = ndk.sources.PhasedArraySource3D(
     position=np.array([0.0, 0.0, 0.0]),
@@ -220,10 +220,10 @@
     tilt_angle=30,
     height=5.0e-3,
 )
-scenario.sources.clear()
-scenario.add_source(phased_3d)
-scenario.compile_problem(center_frequency=5e5)
-results = scenario.simulate_steady_state()
+scenario_3d.sources.clear()
+scenario_3d.add_source(phased_3d)
+scenario_3d.compile_problem(center_frequency=5e5)
+results = scenario_3d.simulate_steady_state()
 assert isinstance(results, ndk.results.SteadyStateResult3D)
 results.render_steady_state_amplitudes()
 

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.make("scenario-0-v0")
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_0.value()
 scenario.compile_problem(center_frequency=5e5)
 result = scenario.simulate_pulse()
 assert isinstance(result, ndk.results.PulsedResult2D)

diff --git a/docs/examples/plot_scenarios.py b/docs/examples/plot_scenarios.py
@@ -12,16 +12,16 @@
 
 def plot_scenario(scenario_id):
     print(f"Simulating scenario: {scenario_id}")
-    scenario = ndk.make(scenario_id)
+    scenario = ndk.BUILTIN_SCENARIOS[scenario_id].value()
     scenario.compile_problem(center_frequency=5e5)
     result = scenario.simulate_steady_state()
     result.render_steady_state_amplitudes(show_material_outlines=False)
 
 
 # %%
-# Simulating scenario: scenario-0-v0
+# Simulating scenario: scenario-0
 # ===================================
-plot_scenario("scenario-0-v0")
+plot_scenario("scenario-0")
 
 # %%
 # Simulating scenario: scenario-1-2d-v0

diff --git a/docs/examples/plot_store_results.py b/docs/examples/plot_store_results.py
@@ -15,10 +15,10 @@
 # Execute the following code in a computer with ndk installed
 import neurotechdevkit as ndk
 
-scenario = ndk.make("scenario-0-v0")
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_0.value()
 scenario.compile_problem(center_frequency=5e5)
 result = scenario.simulate_steady_state()
-result.save_to_disk("scenario-0-v0-results.tar.gz")
+result.save_to_disk("scenario-0-results.tar.gz")
 
 
 # %%
@@ -27,7 +27,7 @@
 # be loaded running the following code:
 import neurotechdevkit as ndk  # noqa: E402
 
-result2 = ndk.load_result_from_disk("scenario-0-v0-results.tar.gz")
+result2 = ndk.load_result_from_disk("scenario-0-results.tar.gz")
 assert isinstance(result2, ndk.results.SteadyStateResult2D)
 result2.render_steady_state_amplitudes(show_material_outlines=False)
 # %%
diff --git a/docs/examples/plot_time_reverse.py b/docs/examples/plot_time_reverse.py
@@ -28,16 +28,15 @@
 import neurotechdevkit as ndk
 
 # Parameters
-SCENARIO_NAME = "scenario-2-2d-v0"
 CENTER_FREQUENCY = 5e5
 NUM_ELEMENTS = 20
 ELEMENT_WIDTH = 1.2e-3
 
 
 # %%
 # Helper function to make the scenario with a PhasedArraySource
-def make_scenario(element_delays=None) -> ndk.scenarios.Scenario:
-    true_scenario = ndk.make(SCENARIO_NAME)
+def make_scenario(element_delays=None):
+    true_scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_2_2D.value()
 
     # define a phased-array source
     default_source = true_scenario.sources[0]
@@ -58,7 +57,6 @@ def make_scenario(element_delays=None) -> ndk.scenarios.Scenario:
 # %%
 # ## Set up and visualize the forward scenario
 true_scenario = make_scenario()
-assert isinstance(true_scenario, ndk.scenarios.Scenario2D)
 true_scenario.compile_problem(center_frequency=CENTER_FREQUENCY)
 true_scenario.render_layout()
 
@@ -69,14 +67,13 @@ def make_scenario(element_delays=None) -> ndk.scenarios.Scenario:
 # The point source is visualized as a gray dot.
 
 # Reinitialize the scenario
-reversed_scenario = ndk.make(SCENARIO_NAME)
+reversed_scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_2_2D.value()
 # and reverse the source
 point_source = ndk.sources.PointSource2D(
     position=true_scenario.target.center,
 )
 reversed_scenario.add_source(point_source)
 
-assert isinstance(reversed_scenario, ndk.scenarios.Scenario2D)
 reversed_scenario.compile_problem(center_frequency=CENTER_FREQUENCY)
 reversed_scenario.render_layout()
 

diff --git a/docs/index.md b/docs/index.md
@@ -22,23 +22,25 @@ You can run `neurotechdevkit` inside a docker container with just a couple of st
 
 1. Run the following command:
 
-    ```
-    docker run -p 8888:8888 -it ghcr.io/agencyenterprise/neurotechdevkit:latest
-    ```
+   ```
+   docker run -p 8888:8888 -it ghcr.io/agencyenterprise/neurotechdevkit:latest
+   ```
 
-    The command above will start a [Jupyter notebook](https://jupyterlab.readthedocs.io/en/stable/getting_started/overview.html) server with example notebooks you can use to explore `neurotechdevkit`. Use the printed URL to open it in your browser or connect to it using your IDE.
+   The command above will start a [Jupyter notebook](https://jupyterlab.readthedocs.io/en/stable/getting_started/overview.html) server with example notebooks you can use to explore `neurotechdevkit`. Use the printed URL to open it in your browser or connect to it using your IDE.
 
-    All changes you make to these files will be lost once you stop the docker container.
+   All changes you make to these files will be lost once you stop the docker container.
 
 > **Note**:
 >
->    You can have persisting [Jupyter notebooks](https://jupyterlab.readthedocs.io/en/stable/getting_started/overview.html) by running
->    ```
->    docker run -p 8888:8888  -v $(pwd)/notebooks:/ndk/notebooks -it ghcr.io/agencyenterprise/neurotechdevkit:latest
->    ```
->    The command above will create a folder `notebooks` in your current directory where you can put your jupyter notebooks.
+> You can have persisting [Jupyter notebooks](https://jupyterlab.readthedocs.io/en/stable/getting_started/overview.html) by running
 >
->    We recommend downloading the `.zip` file with example notebooks from this [link](https://agencyenterprise.github.io/neurotechdevkit/generated/gallery/gallery_jupyter.zip), and extracting it into your local `notebooks` folder so you can access them from the docker.
+> ```
+> docker run -p 8888:8888  -v $(pwd)/notebooks:/ndk/notebooks -it ghcr.io/agencyenterprise/neurotechdevkit:latest
+> ```
+>
+> The command above will create a folder `notebooks` in your current directory where you can put your jupyter notebooks.
+>
+> We recommend downloading the `.zip` file with example notebooks from this [link](https://agencyenterprise.github.io/neurotechdevkit/generated/gallery/gallery_jupyter.zip), and extracting it into your local `notebooks` folder so you can access them from the docker.
 
 ### Local installation
 
@@ -49,7 +51,7 @@ To install and run **neurotechdevkit** locally check the [installation](https://
 ```python
 import neurotechdevkit as ndk
 
-scenario = ndk.make('scenario-0-v0')
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_0.value()
 result = scenario.simulate_steady_state()
 result.render_steady_state_amplitudes(show_material_outlines=False)
 ```

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.make('scenario-2-2d-v0')
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_2_2D.value()
 
 source = ndk.sources.FocusedSource2D(
     position=np.array([0.19, 0.07]),
@@ -49,7 +49,7 @@ 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.make('scenario-2-2d-v0')
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_2_2D.value()
 
 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.make('scenario-2-2d-v0')
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_2_2D.value()
 result = scenario.simulate_steady_state()
 result.render_steady_state_amplitudes()
 ```

diff --git a/docs/usage/loading_scenarios.md b/docs/usage/loading_scenarios.md
@@ -9,16 +9,16 @@ The following is all that's needed to load a pre-defined scenario:
 ```py
 import neurotechdevkit as ndk
 
-scenario = ndk.make('scenario-2-2d-v0')
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_2_2D.value()
 ```
 
 The existing scenario ids are:
 
-- `scenario-0-v0` (2D) - a simple quickstart toy scenario that enables users to dive in and experiment with their first simulation immediately.
-- `scenario-1-3d-v0` (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-v0` (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-v0` (2D) - a 2D version of scenario 1.
-- `scenario-2-2d-v0` (2D) - a 2D version of scenario 2.
+- `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.
 
 All of these scenarios are immediately ready for visualization and simulation, with appropriate default parameters used where needed.
 

diff --git a/docs/usage/running_simulation.md b/docs/usage/running_simulation.md
@@ -5,7 +5,7 @@ Running a simulation takes just a single function call.
 ```py
 import neurotechdevkit as ndk
 
-scenario = ndk.make('scenario-2-2d-v0')
+scenario = ndk.BUILTIN_SCENARIOS.SCENARIO_2_2D.value()
 result = scenario.simulate_steady_state()
 result.render_steady_state_amplitudes()
 ```

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -36,7 +36,6 @@ nav:
       - Troubleshooting: usage/troubleshooting.md
       - GPU support: usage/gpu.md
   - API:
-      - Make: api/make.md
       - Scenarios: api/scenarios.md
       - Utils: api/utils.md
       - Sources: api/sources.md