Absolute package pathing (#130)

* Create pre-release v1.0.0 (#116)

* 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>

* Bump for pypi versioning (#124) (#125)

* Bump for pypi versioning

* Change authors

* Update abstract readme and authorship

* Update badge to general DOI

* Pre-release test version v2 (#127)

* Bump for pypi versioning (#124)

* Bump for pypi versioning

* Change authors

* Update abstract readme and authorship

* Update badge to general DOI

* Change pathing to absolute

* Bump versioning

---------

Co-authored-by: Vedran Kasalica <v.kasalica@esciencecenter.nl>
Co-authored-by: Peter Kok <kretep@users.noreply.github.com>
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>