Walter Simson

Migrate Examples to Jupyter Notebook

1

Vision here is to have something like the k-Wave-example pages in Jupyter notebooks.

Use nbconvert to test notebooks in the GitHub CI

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[nbconvert](https://nbconvert.readthedocs.io/en/latest/) would allow auto-running notebooks and using output as readme for example See blog post: https://innerjoin.bit.io/automate-jupyter-notebooks-on-github-9d988ecf96a6

**Describe the example** Include the benchmark examples from transcranial simulations as scripts as well as notebooks. - [ ] 1 - [ ] 2 - [x] 3 - [x] 4...

It seems there is quite a bit of repeated logic in kSpaceFirstOrder{2,3}D. It would be great if we could consolidate the logic here

**Describe the bug** I have encountered an execution error likely related to the cross-compilation compatibility of the CPU binaries. When running a simple example with: ```python execution_options = SimulationExecutionOptions(is_gpu_simulation=False) ```...

Refactor package file layout

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Some classes are hidden in subdirectories, leading to difficulty finding them and lengthy import statements (c.f. [here](https://github.com/waltsims/k-wave-python/blob/8e9385ab67076e16686650b56000d9129f1a6e32/tests/matlab_test_data_collectors/python_testers/test_linear_array_transducer.py#L1)). We should work to refactor this moving forward to improve usability.

Create a results object to encapsulate simulation results and logic

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**Is your feature request related to a problem? Please describe.** kWaveFirstOrder returns a variety of values depending on the simulation configuration. The logic of which values are returned, how they...