Classifier package ppg #109
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… into heart_rate_estimation
… into heart_rate_estimation
… into heart_rate_estimation
… into heart_rate_estimation
… into heart_rate_estimation
…rkinson/paradigma into pandas-to-numpy-ppg
… into pandas-to-numpy-ppg
…arkinson/paradigma into pandas-to-numpy-ppg
… into pandas-to-numpy-ppg
… into classifier-package-ppg
… into classifier-package-ppg
… into classifier-package-ppg
Erikpostt
reviewed
Jan 16, 2025
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| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "execution_count": 1, |
Erikpostt
reviewed
Jan 16, 2025
src/paradigma/config.py
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| @@ -244,7 +244,7 @@ def __init__(self, step: str | None = None) -> None: | |||
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| class HeartRateConfig(PPGConfig): | |||
| def __init__(self, sensor: str = 'ppg', min_window_length: float = 10) -> None: | |||
| def __init__(self, sensor: str = 'ppg', min_window_length: int = 30) -> None: | |||
There was a problem hiding this comment.
You might want to rename it to min_window_length_s to clarify the units.
Erikpostt
approved these changes
Jan 16, 2025
|
@Erikpostt implemented the suggestions and will merge it now |
KarsVeldkamp
added a commit
that referenced
this pull request
Jan 17, 2025
* change test output * Update tremor_analysis.ipynb * add documentation * fix bug * remove irrelevant config * resolved comments PR reviewer * remove data type since it causes pytype error * Simplify * Updating Poetry * clear execution count * Remove angle and velocity from preprocessing * import heart_rate_estimation * Change rotation axes * Adjust parameters segmentation * Add flexibility for pathing * Return a Series instead of df * ensure features dont scale when storing * Update tabulate windows * Heart rate estimation (#85) * Start heart rate estimation including tfd * stash updates * update based on merge conflicts * update hr main function * update minor stuff matlab files * change tfd parameters to dict * Finalizing heart rate pipeline plus renaming preprocessing to acc instead of imu * setting execution count to null * fix output types * fixing pytype due to old configs * fix min_hr_samples pytype error * remove irrelevant config * resolved comments PR reviewer * remove data type since it causes pytype error * clear execution count * clear execution counts * execution counts + indentation + short documentation * update final comments + small matlab changes * merge updates * Solve pytype issue * Solve pytype issue * added suggestions * remove execution counts * update ppg_analysis * test update notebook * execution counts * Vectorize merging of predictions with timestamps * Add flexibility to filtering gait parameters * Remove redundant cells in notebooks * Solve bugs * Solve conflict * Continue process when dataframe is empty * Modify quantification * Modify quantification * Typo * Add flexibility for pred proba to merging * Add flexibility for pred proba to merging * Add flexibility for pred proba to merging * Solve numpy/list bug * Solve numpy/list bug * Solve numpy/list bug * Solve numpy/list bug * Start catching errors * Start catching errors * Fix np.nan issue * Fix np.nan issue * Reduce memory reqs * Temp for debugging * Temp for debugging * Typo * replace df to numpy arrays * fix notebook * adding accelerometer feature * fix type error list vs float * Expand feature extraction docs * change notebook accordingly * Update notebooks * Add '1' to MFCC filter points * implement accelerometer feature * update matlab file based on refactoring * fixing types, docstrings and readibility * adding documentation acc feature * add documentation of autocorrelation * Pandas to numpy ppg (#93) * Start heart rate estimation including tfd * stash updates * update based on merge conflicts * update hr main function * update minor stuff matlab files * change tfd parameters to dict * First steps to refactoring to numpy * Finalizing heart rate pipeline plus renaming preprocessing to acc instead of imu * setting execution count to null * fix output types * fixing pytype due to old configs * fix min_hr_samples pytype error * remove irrelevant config * resolved comments PR reviewer * remove data type since it causes pytype error * clear execution count * import heart_rate_estimation * merge updates * update ppg_analysis * replace df to numpy arrays * fix notebook * fix type error list vs float * fixing types, docstrings and readibility * add documentation of autocorrelation --------- Co-authored-by: Erikpostt <erik_post_6@hotmail.com> * Modify test data * Change mfcc param * Change mfcc param * Structure * Reset legacy for the time being * Adjust test scripts to changes * Adjust tremor to changes * structure docstrings * Improve consistency of docstrings * Structure testing * Update test data * Resolve pytype error * Adjust tabulate_windows to new version * Ensure first column is returned for PPG * modify mfcc calculation and update classifier * Made requested changes * fix config * modify test data * Adding accelerometer to ppg (#95) * Start heart rate estimation including tfd * stash updates * update based on merge conflicts * update hr main function * update minor stuff matlab files * change tfd parameters to dict * First steps to refactoring to numpy * Finalizing heart rate pipeline plus renaming preprocessing to acc instead of imu * setting execution count to null * fix output types * fixing pytype due to old configs * fix min_hr_samples pytype error * remove irrelevant config * resolved comments PR reviewer * remove data type since it causes pytype error * clear execution count * import heart_rate_estimation * merge updates * update ppg_analysis * replace df to numpy arrays * fix notebook * adding accelerometer feature * fix type error list vs float * implement accelerometer feature * update matlab file based on refactoring * fixing types, docstrings and readibility * adding documentation acc feature * add documentation of autocorrelation * Made requested changes * fix config --------- Co-authored-by: Erikpostt <erik_post_6@hotmail.com> * add tutorial * Solve issues raised by reviewer * Rerun notebooks ppg * Change scalers, classifiers and thresholds * Update test files * Add aggregation of quantification * modified tutorial * update tutorial * remove execution counts * Add ability to create classifier objects * Test to remove rom features * Test to remove rom features * adding aggregation heart rate * Adjust functions to classification package * Update package loading * Adjust gait pipeline to classifier packages * added suggestions * Change test data with new classifier * Adjust tests and ensure Path used in notebooks * Change pathing to fix poetry pytest * restructure functions * update test data * update tutorial * fixed typo's * Merge with main * update aggregates * remove config * Add files via upload * add start tutorial * aggregation implementation with dictionary * add lines for consistency * Add user guides for coordinate system and update index of docs * moved windoweddataextractor to segmenting * Displays outputs of data preparation tutorial * Heart rate aggregation (#102) * Start heart rate estimation including tfd * stash updates * update based on merge conflicts * update hr main function * update minor stuff matlab files * change tfd parameters to dict * First steps to refactoring to numpy * Finalizing heart rate pipeline plus renaming preprocessing to acc instead of imu * setting execution count to null * fix output types * fixing pytype due to old configs * fix min_hr_samples pytype error * remove irrelevant config * resolved comments PR reviewer * remove data type since it causes pytype error * clear execution count * import heart_rate_estimation * merge updates * update ppg_analysis * replace df to numpy arrays * fix notebook * adding accelerometer feature * fix type error list vs float * implement accelerometer feature * update matlab file based on refactoring * fixing types, docstrings and readibility * adding documentation acc feature * add documentation of autocorrelation * Made requested changes * fix config * adding aggregation heart rate * update aggregates * remove config * aggregation implementation with dictionary * add lines for consistency * moved windoweddataextractor to segmenting * updates based on review --------- Co-authored-by: Erikpostt <erik_post_6@hotmail.com> * resolve merge conflict * add tremor classifier package * update notebook * remove execution counts * Modify according to feedback of reviewer * update test function * Concat forward & backward pav to allow for dataframes * Renaming functions * Add error messages when df is empty * Print -> Raise eerror messages when df is empty * Also raise when no gait without other arm activity * Remove irrelevant test files and raise valuerrors * Reset to io wrappers * Update docstrings * update loading + preprocessing with seperate functionality * update tutorial notebook and corresponding notebook * change path usage * Update test to io function * Update README.md * print notebook output * change total psd * add function links * Faster computation using any() * Remove unnecessary improts * Tutorial ppg (#106) * Start heart rate estimation including tfd * stash updates * update based on merge conflicts * update hr main function * update minor stuff matlab files * change tfd parameters to dict * First steps to refactoring to numpy * Finalizing heart rate pipeline plus renaming preprocessing to acc instead of imu * setting execution count to null * fix output types * fixing pytype due to old configs * fix min_hr_samples pytype error * remove irrelevant config * resolved comments PR reviewer * remove data type since it causes pytype error * clear execution count * import heart_rate_estimation * merge updates * update ppg_analysis * replace df to numpy arrays * fix notebook * adding accelerometer feature * fix type error list vs float * implement accelerometer feature * update matlab file based on refactoring * fixing types, docstrings and readibility * adding documentation acc feature * add documentation of autocorrelation * Made requested changes * fix config * adding aggregation heart rate * update aggregates * remove config * add start tutorial * aggregation implementation with dictionary * add lines for consistency * moved windoweddataextractor to segmenting * resolve merge conflict * update loading + preprocessing with seperate functionality * update tutorial notebook and corresponding notebook * Update test to io function * update tutorial and notebook with simplified loading of the data * Reset execution counts in notebook cells * update execution_counts and output * Updates from PR feedback * fix type error * made final feedback --------- Co-authored-by: Erikpostt <erik_post_6@hotmail.com> Co-authored-by: Erik Post <57133568+Erikpostt@users.noreply.github.com> * Resolve merge conflict * add suggestions * Move notebooks to parent directory and remove subdirectories * change total_psd_calculation again * Modify structure of files * Update classifier, update test data, update dependencies, update testing gait pipeline * Update dtypes heart rate pipeline * Reset scikit version, update tremor values * Remove notebook temporarily to pass tests * Reduce no. of configs and change notebooks accordingly * Update test data * Remove redundant files * final suggestions * Modify tremor low freq power and slightly adjust tutorial * Change git attributes to ensure output in tutorials * Test displaying output tutorials * Test displaying output tutorials * Test II * Update config and remove nbstripout from gitattributes * Add tutorial outputs other domains * Merge conflict heart rate pipeline * Merge conflicts gait pipeline * Merge conflicts gait pipeline * Update notebooks * Revert time to first binary file * Add suggestions * Iterate on tutorial gait * Complete gait pipeline * Classifier package ppg (#109) * Start heart rate estimation including tfd * stash updates * update based on merge conflicts * update hr main function * update minor stuff matlab files * change tfd parameters to dict * First steps to refactoring to numpy * Finalizing heart rate pipeline plus renaming preprocessing to acc instead of imu * setting execution count to null * fix output types * fixing pytype due to old configs * fix min_hr_samples pytype error * remove irrelevant config * resolved comments PR reviewer * remove data type since it causes pytype error * clear execution count * import heart_rate_estimation * merge updates * update ppg_analysis * replace df to numpy arrays * fix notebook * adding accelerometer feature * fix type error list vs float * implement accelerometer feature * update matlab file based on refactoring * fixing types, docstrings and readibility * adding documentation acc feature * add documentation of autocorrelation * Made requested changes * fix config * adding aggregation heart rate * update aggregates * remove config * add start tutorial * aggregation implementation with dictionary * add lines for consistency * moved windoweddataextractor to segmenting * resolve merge conflict * update loading + preprocessing with seperate functionality * update tutorial notebook and corresponding notebook * Update test to io function * update tutorial and notebook with simplified loading of the data * Reset execution counts in notebook cells * update execution_counts and output * Updates from PR feedback * fix type error * remove unneccessary matlab files * update merge conflicts * update using classifier package * fix pkl feature names in scaler and delete old classifier files * renaming ppg to heart rate * rename files ppg to heart_rate * remove legacy classification * renaming clf_package * modify tutorial * update abs stats * update tutorial based on abs stats output * Remove redundant stuff from notebook * remove tremor txt files * update tutorial based on right config settings * type error fix * fix type error * update based on suggestions --------- Co-authored-by: Erikpostt <erik_post_6@hotmail.com> Co-authored-by: Erik Post <57133568+Erikpostt@users.noreply.github.com> * Add tutorial data * Update tutorial per reviewers remarks * Remove output notebooks * Update docs * DRAFT: Update sync functions (#115) * Start heart rate estimation including tfd * stash updates * update based on merge conflicts * update hr main function * update minor stuff matlab files * change tfd parameters to dict * First steps to refactoring to numpy * Finalizing heart rate pipeline plus renaming preprocessing to acc instead of imu * setting execution count to null * fix output types * fixing pytype due to old configs * fix min_hr_samples pytype error * remove irrelevant config * resolved comments PR reviewer * remove data type since it causes pytype error * clear execution count * import heart_rate_estimation * merge updates * update ppg_analysis * replace df to numpy arrays * fix notebook * adding accelerometer feature * fix type error list vs float * implement accelerometer feature * update matlab file based on refactoring * fixing types, docstrings and readibility * adding documentation acc feature * add documentation of autocorrelation * Made requested changes * fix config * adding aggregation heart rate * update aggregates * remove config * add start tutorial * aggregation implementation with dictionary * add lines for consistency * moved windoweddataextractor to segmenting * resolve merge conflict * update loading + preprocessing with seperate functionality * update tutorial notebook and corresponding notebook * Update test to io function * Update notebook with functional links * move scan_and_sync_segments to util with corresponding functions * remove ppp functionalities from util * Correct implementation of the extract_overlapping_segments * update tests without scan_and_sync_segments * updates based on suggestions * fix type error --------- Co-authored-by: Erikpostt <erik_post_6@hotmail.com> * Major reshuffling of files and directories * Adding nbsphinx * update tutorials functional links + preprocessing * Update readme contact (#119) --------- Co-authored-by: nienketimmermans <65012819+nienketimmermans@users.noreply.github.com> Co-authored-by: KarsVeldkamp <veldkampkars@gmail.com> Co-authored-by: KarsVeldkamp <105375796+KarsVeldkamp@users.noreply.github.com>
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In this PR I have added the classifier package of PPG but also:
@Erikpostt Most of the adjustments are clean-up and almost all relevant additions are in heart_rate_analysis.py