T239 wavelength independent volume creation #240
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TomTomRixRix
requested changes
Sep 19, 2023
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When I run the optical_and_acoustic_simulation.py example it crashes in the k-Wave adapter with this trace:
Traceback (most recent call last):
File "/home/tom/dev/new_simpa/simpa/simpa_examples/optical_and_acoustic_simulation.py", line 188, in <module>
sp.simulate(SIMULATION_PIPELINE, settings, device)
File "/home/tom/dev/simpa/.venv-simpa/lib/python3.10/site-packages/simpa/core/simulation.py", line 79, in simulate
pipeline_element.run(digital_device_twin)
File "/home/tom/dev/simpa/.venv-simpa/lib/python3.10/site-packages/simpa/core/simulation_modules/acoustic_forward_module/__init__.py", line 68, in run
time_series_data = self.forward_model(_device)
File "/home/tom/dev/simpa/.venv-simpa/lib/python3.10/site-packages/simpa/core/simulation_modules/acoustic_forward_module/acoustic_forward_module_k_wave_adapter.py", line 118, in forward_model
data_dict[Tags.DATA_FIELD_INITIAL_PRESSURE] = np.rot90(data_dict[Tags.DATA_FIELD_INITIAL_PRESSURE]
KeyError: 700| for data_field in data_fields: | ||
| if (data_field in TissueProperties.wavelength_independent_properties |
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Having a comment of what happens in these lines would be super helpful for reading. E.g. for wavelength-independent data field skip all wavelengths except of the last one and only crop it then
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| volume_path = generate_dict_path(Tags.SIMULATION_PROPERTIES, self.global_settings[Tags.WAVELENGTH]) | ||
| save_hdf5(save_volumes, self.global_settings[Tags.SIMPA_OUTPUT_PATH], file_dictionary_path=volume_path) | ||
| if (key in TissueProperties.wavelength_independent_properties |
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here the same comment would make the code more readable
| @@ -90,6 +90,9 @@ def create_simulation_volume(self) -> dict: | |||
| for key in volumes.keys(): | |||
| if structure_properties[key] is None: | |||
| continue | |||
| if (key in TissueProperties.wavelength_independent_properties | |||
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here an explaining comment would be nice
TomTomRixRix
approved these changes
Sep 19, 2023
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optical_and_acoustic_simulation.pywith spacing 0.1 and 5 wavelengths 122s ➡️ 110sPlease check the following before creating the pull request (PR):
Provide issue / feature request fixed by this PR
Fixes #239