Fixes from main branch#35
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Pull request overview
This PR syncs fixes from the main branch by centralizing state-array allocation in the core CardiacModel.initialize() and updating CPU-wave model initializers accordingly, while also re-enabling/refreshing the 2D propagation regression tests with a lighter stimulation protocol.
Changes:
- Move
_allocate_state_arrays()intofinitewave.core.model.CardiacModel.initialize(). - Remove redundant
_allocate_state_arrays()calls from multiple CPU-wave modelinitialize()implementations (and add short docstrings in a few). - Replace the previously commented-out 2D propagation test module with active propagation tests and updated expected speeds.
Reviewed changes
Copilot reviewed 10 out of 10 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/test_propagation_2d.py | Re-enables 2D propagation tests and introduces shared helpers for model setup, run, and wave-speed estimation. |
| finitewave/core/model/cardiac_model.py | Centralizes state-array allocation in the base model initialization flow. |
| finitewave/cpuwave/model/aliev_panfilov.py | Removes redundant state allocation in initialize() after base initialization change. |
| finitewave/cpuwave/model/barkley.py | Removes redundant state allocation in initialize() and adds a short initialize() docstring. |
| finitewave/cpuwave/model/bueno_orovio.py | Removes redundant state allocation in initialize(). |
| finitewave/cpuwave/model/courtemanche.py | Removes redundant state allocation in initialize() and adds a short initialize() docstring. |
| finitewave/cpuwave/model/fenton_karma.py | Removes redundant state allocation in initialize(). |
| finitewave/cpuwave/model/luo_rudy_91.py | Removes redundant state allocation in initialize() and adds a short initialize() docstring. |
| finitewave/cpuwave/model/mitchell_schaeffer.py | Removes redundant state allocation in initialize(). |
| finitewave/cpuwave/model/ten_tusscher_panfilov_2006.py | Removes redundant state allocation in initialize() and adds a short initialize() docstring. |
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| import os | ||
| import shutil |
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| t_calc : float | ||
| Time after the last preconditioning beat to continue recording (ms or model units). | ||
| t_prebeats : float | ||
| Interval between preconditioning stimuli (ms or model units). | ||
| dt : float |
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| model = model_class() | ||
| model.dt = dt | ||
| model.dr = dr | ||
| model.t_max = 1*t_prebeats + t_calc | ||
| model.cardiac_tissue = tissue | ||
| model.stim_sequence = stim_sequence |
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| Returns | ||
| ------- | ||
| output : np.ndarray | ||
| Time series of membrane potential for a specific cell. | ||
| """ |
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| time_diffs = np.diff(activation_times, axis=0) | ||
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| assert np.all(np.isfinite(time_diffs)), "Activation times contain NaN or inf" |
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