update C++ codebase for handling of feature dependencies [vcs: #minor] #334
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@@ -21,4 +21,4 @@ bin | |
| *.ipynb_checkpoints | ||
| lib | ||
| fllog.txt | ||
| *.DS_Store | ||
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| @@ -0,0 +1,21 @@ | ||
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| # Changelog | ||
| All notable changes to this project will be documented in this file. | ||
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| The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), | ||
| and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | ||
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| ## [5.4.0] - 2024-01 | ||
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| ### C++ changes | ||
| - New C++ function `getFeatures` replaced `getVec`. | ||
| - `getFeatures` automatically handles failures & distinguishes empty results from failures. | ||
| - Centralized error handling in `getFeatures` shortens the code by removing repetitions. | ||
| - C++ features' access is restricted. Read-only references are marked `const`. | ||
| - Removed wildcard features from C++ API. Use of Python is encouraged for that purpose. | ||
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| ### Python changes | ||
| - `bpap_attenuation` feature is added to the Python API. | ||
| - `Spikecount`, `Spikecount_stimint`, `burst_number`, `strict_burst_number` and `trace_check` features migrated to Python from C++. | ||
| - `check_ais_initiation` is added to the Python API. |
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@@ -15,6 +15,8 @@ Submodules | |
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| api | ||
| io | ||
| pyfeatures.multitrace | ||
| pyfeatures.pyfeatures | ||
| pyfeatures.validation | ||
| units | ||
| settings | ||
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@@ -150,19 +150,21 @@ time from stimulus start to last spike | |
| else: | ||
| time_to_last_spike = 0 | ||
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| `Python efeature`_ : spike_count | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
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| number of spikes in the trace, including outside of stimulus interval | ||
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| - **Required features**: LibV1:peak_indices | ||
| - **Units**: constant | ||
| - **Pseudocode**: :: | ||
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| spike_count = len(peak_indices) | ||
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| **Note**: In the future this feature will be called "spike_count". | ||
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| `Python efeature`_ : spike_count_stimint | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
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| number of spikes inside the stimulus interval | ||
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@@ -171,7 +173,9 @@ number of spikes inside the stimulus interval | |
| - **Pseudocode**: :: | ||
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| peaktimes_stimint = numpy.where((peak_time >= stim_start) & (peak_time <= stim_end)) | ||
| spike_count_stimint = len(peaktimes_stimint) | ||
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| **Note**: In the future this feature will be called "spike_count_stimint". | ||
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| `LibV5`_ : number_initial_spikes | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
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@@ -343,23 +347,6 @@ The adaptation index is zero for a constant firing rate and bigger than zero for | |
| ISI_sub = ISI_values[1:] - ISI_values[:-1] | ||
| adaptation_index = numpy.mean(ISI_sum / ISI_sub) | ||
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There was a problem hiding this comment. It would be nice to keep this feature. Some users have used it before: There was a problem hiding this comment. This is reimplemented as a Python function. |
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| `LibV1`_ : burst_mean_freq | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
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@@ -419,8 +406,8 @@ The burst detection can be fine-tuned by changing the setting strict_burst_facto | |
| ) | ||
| ) | ||
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| `Python efeature`_ : burst_number | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
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| The number of bursts | ||
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@@ -430,8 +417,8 @@ The number of bursts | |
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| burst_number = len(burst_mean_freq) | ||
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| `Python efeature`_ : strict_burst_number | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
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| The number of bursts | ||
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@@ -1287,98 +1274,6 @@ Slope of the V, dVdt phasespace plot at the beginning of every spike | |
| range_min_idxs = AP_begin_indices - AP_phseslope_range | ||
| AP_phaseslope = (dvdt[range_max_idxs] - dvdt[range_min_idxs]) / (v[range_max_idxs] - v[range_min_idxs]) | ||
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| Voltage features | ||
| ---------------- | ||
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@@ -2007,7 +1902,7 @@ Computes the impedance given a ZAP current input and its voltage response. | |
| It will return the frequency at which the impedance is maximal, in the range (0, impedance_max_freq] Hz, | ||
| with impedance_max_freq being a setting with 50.0 as a default value. | ||
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| - **Required features**: current, spike_count, LibV5:voltage_base, LibV5:current_base | ||
| - **Units**: Hz | ||
| - **Pseudocode**: :: | ||
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Could you please tell in the note that this feature replaces Spikecount, that Spikecount is deprecated, but can still be used for the moment?
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Ah yes, I also noticed I forgot to update this one. Done in the last commit. 👍