Accelerometer

Minor bug fixes:
- 83d07c6025a55dd1211f7b33241768c2cf946b3b improve collate json and fix future regex bug. Closes 178
- 426a057aae1209a603b76c6b4ed25c6f02ebd8d9 fix file extension case sensitive
- 1a520f97569c272cf914795891c1b1bb8268eed6 fix folder writable assertion. Closes 182
- 46572c7e13f201073c866705ece877b2a71c7395 fix nan wrongly imputed
- 5d1d7c2ca29f9d744f8a82d20693382c89a0b818 fix impute plot

What's Changed
* Setup for packaging (PyPI, Conda) by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/177
* Major flake8 refactoring + GitHub workflows by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/179
* Fixes and improvements: d61d86ff23d49600c2963b872510ed6d2ac52af2, aacd87fd860cd4c88bfe092931d1a80f50f762de, 582c0b2238728e33881e2c1b1c37acf79c319c9a

What's Changed
* add --timeZoneOffset argument for cwa cwa.gz files; expose csv arguments to python script by xiangnandang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/21
* fix minor issue in accUtils.loadTimeSeriesCSV for --timeSeriesDataCol… by xiangnandang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/23
* Circadian analysis including PSD, Relative Amplitude and Fourier Frequency by R-Walmsley in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/26
* Gt3v2 support round 1 by angerhang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/24
* Major fixes and improvements in the Java feature extraction code by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/28
* Gt3v2 fix get device id method by angerhang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/29
* Document by angerhang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/30
* fix lowpass cutoff to be capped by Nyquist freq by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/31
* fix sampleRate not passed for calibration by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/32
* fix rounding errors in integer divisions by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/33
* fix convert pandas to numpy before numpy call by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/34
* fix FFT and entropy normalization by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/36
* hotfix to allow sampleRate of 25Hz by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/39
* propagate verbose argument to CsvReader.java by xiangnandang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/41
* Arm angel by angerhang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/42
* allow display of activity classification during imputed period of time by xiangnandang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/47
* allow daylight savings crossover check from different timezones by xiangnandang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/48
* timeZone for check_daylight_savings_crossover by xiangnandang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/51
* fix small bug: missing field in summary.json by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/54
* Native DST crossover correction for CWA files by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/55
* fix minor issue: arm angle result was in integer, corrected to double by xiangnandang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/57
* make use of cutpoint based definitions explicit by R-Walmsley in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/59
* fix bug in get_interrupts, wrong index slicing by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/61
* change dir structure when process multiple files by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/60
* autogenerate folder names to avoid default errors by R-Walmsley in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/63
* add junit framework by angerhang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/67
* Fix startTime and endTime comparison in summariseEpoch by angerhang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/74
* fix start/endTime flag time zone by angerhang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/76
* add clipsBefore/AfterCalibr and total reads to the summary. by R-Walmsley in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/82
* Add regression test; Add data quality outputs in summary by R-Walmsley in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/85
* Fixed gt3x v1 and v2 parsing with ci tests by angerhang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/70
* Update default activity classification model to Walmsley 2020 by aidendoherty in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/88
* Fix sklearn dependency problem and new tests for python and java builds on macos and linux by aidendoherty in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/89
* avoid error message when epoch folder manually changed by R-Walmsley in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/95
* fix bug in get_clips and get_total_reads by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/91
* handle potential nan in correlation features by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/56
* fix bug in interrupts; deprecation; refactor by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/99
* fix hrLabels missing last tick; also use 24 format by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/104
* Changes to use scikit-learn 0.24.0 by R-Walmsley in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/108
* Update reference epoch.csv to reflect changes introduced in 2fabe36 by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/112
* Implement installation with requirements.txt by R-Walmsley in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/109
* fix 'imputed' column in timeSeries file by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/105
* fix NA for avgArmAngelAbsDiff with epoch size 5sec by angerhang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/113
* update installation instructions addressing 114 by R-Walmsley in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/123
* add feature set used in model Walmsley et al 2020 and remove old files by R-Walmsley in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/118
* add CONTRIBUTING.md by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/125
* fix install doc by angerhang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/129
* Suggestion in CONTRIBUTING.md to checkout PR locally for review by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/141
* add support for nearest neighbor resampling by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/140
* Bump urllib3 from 1.26.2 to 1.26.4 by dependabot in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/143
* Bump pillow from 8.1.0 to 8.1.1 by angerhang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/138
* Bump jinja2 from 2.11.2 to 2.11.3 by angerhang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/135
* fix warning pandas keep_tz by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/142
* update github badges by angerhang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/149
* add to installation instructions; update version to current tag by R-Walmsley in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/148
* fix small bug in calibration rmse calculation by chanshing in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/160
* Bump urllib3 from 1.26.4 to 1.26.5 by dependabot in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/163
* Bump pillow from 8.1.1 to 8.2.0 by dependabot in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/164
* Plot update by aidendoherty in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/166
* fix bug which before read the packetLength field rather than the device… by aidendoherty in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/171
* Fall back for downloadDataModel by angerhang in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/172
* new feature to flexibly read in raw .csv files by aidendoherty in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/165
* update citation by R-Walmsley in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/176
* Bump pillow from 8.2.0 to 8.3.2 by dependabot in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/175

New Contributors
* chanshing made their first contribution in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/28
* aidendoherty made their first contribution in https://github.com/activityMonitoring/biobankAccelerometerAnalysis/pull/88

**Full Changelog**: https://github.com/activityMonitoring/biobankAccelerometerAnalysis/compare/v2.3.0...v3.2

This stable release contains a number of major updates including:
- Complete rewrite of underlying java codebase
- Fixing a number of minor issues in extracting frequency domain features (thanks chanshing)
- Retraining of machine learning activity models (consistent with fixed features and now using n=100 trees in Random Forest)
- Support for Actigraph gt3x files, both versions 1 and 2 (thanks angerhang)
- Support for circadian rhythm analysis (thanks Alaina121, R-Walmsley, and chanshing)

Other updates include:
- Resampling of signal now possible (thanks chanshing)
- Timezone parameterisation (thanks xiangnandang)
- Improved plotting capabilities (thanks xiangnandang)
- New arm angle features (thanks angerhang)

Major refactor to improve checks, prints, and cleanup (thanks chanshing)
- Rename variable 'rawFile' to 'inputFile' so that we dont confuse it with 'rawOutputFile', which is now named 'rawFile'. Similarly 'npyOutputFile' is now simply 'npyFile'. Method 'processRawFile' is now called
'processInputFile'.
- Use Python 'assert' to perform checks. Also simplify some checks, e.g. ArgumentParser automatically checks for missing arguments.
- Add new argument 'accProcess.py --npyFolder' for consistency.
- Use 'os.path.join' to create paths. This properly handles both cases whether a directory name is provided with or without the trailing slash '/'.
- Use 'atexit' to schedule deletion of intermediate files. This has the benefit that it will still run if the code exits prematurely. Some exceptions apply.
- Slightly improve prints.

Other updates:
- Filtering now correctly activated (thanks chanshing)