nimbalwear 0.21.8

NiMBaLWear wearable device data processing pipeline.

nimbalwear

nimbalwear is an open source toolkit for processing data from wearable sensors.

Contents

• Under construction

Installation

To install the latest release of nimbalwear directly from GitHub using pip, run the following line in terminal or console:

pip install git+https://github.com/nimbal/nimbalwear

To install a specific release, insert M.m after the repository name to install from the branch associated with that minor release. For example:

pip install git+https://github.com/nimbal/nimbalwear@0.21

Package Dependency

To include the latest release of nimbalwear as a dependency in your Python package, include the following line in setup.py or include the string within the list alongside your other dependencies:

install_requires=['nimbalwear@git+https://github.com/nimbal/nimbalwear@[version]']

To include a specific release, replace [version] with the branch associated with that minor release.

Changes by version

v0.21.8

• update version dependencies for numpy < 2, matplotlib < 3.9
• bug fix: resolved start_time inaccuracy for Axivity devices when using fractional timestamps

v0.21.7

• bug fix: resolved error in collection report if no sync events
• bug fix: resolved sync event naming issue based on device location in collection report
• bug fix: fixed logic for including supp_info files with or without password protection
• updated to require numba v0.59.0 or higher for Python 3.12 compatibility
• added "create" parameter to Study to give option to create new study folder
• added Study.sync_raw() method to sync files from raw_source_dir folder
• moved supp_pwd parameter from Study.__init__() to Study.run_pipeline()

v0.21.6

• bug fix: resolve error in collection report when not all possible device locations collected

v0.21.5

• add collection report
• change vertdetach references to nimbaldetach
• bug fix: remove all Nonin file capabilities to resolve textract/six issues with Python 3.12

v0.21.4

• add get_timestamps method to Device object
• bug fix: error when dataframes not created if data does not exist
• bug fix: error creating nonwear bouts dataframe if no nonwear detected
• bug fix: dropping rejected syncs if none detected

v0.21.3

• update vertdetach version
• update compatibility with pyedflib v1.0.34 (sex header field and sample_frequency)
• bug fix: datetime conversion when reading nonwear csv
• bug fix: add flatten-dict to setup.cfg

v0.21.2

• bug fix: indexing issue caused states to sometimes be skipped
• bug fix: start date calculation for multiple gait devices

v0.21.1

• fixed MANIFEST.in bug

v0.21.0

• reorganized gait module code

v0.20.1

• adjust start time moved to before sync

v0.20.0

• add autocal offset and scale outputs
• option to save separate sensor EDF files after data prep
• move settings dump from log into separate file
• rename Pipeline class to Study
• separate default, study, and custom pipeline settings
• some missing data handled and reported as warning instead of raising exception
• bug fix: all filters now dual pass
• separate sync event and segments into separate folders
• syncs detected from any axis rather than choosing those from one axis
• include config sync in sync list
• add ref device type and location to sync output

v0.19.8

• bug fix: properly handles Axivity devices with no gyro collected

v0.19.7

• bug fix: instead of error, sync returns empty DataFrame when no syncs detected or matched
• bug fix: fix bug where sync plots aren't displayed

v0.19.6

• bug fix: ensure physical_min < physical_max when writing edf

v0.19.5

• bug fix: properly detects sleep bouts when entire SPTW is sleep

v0.19.4

• added utility to read password protected excel files

v0.19.3

• bug fix: adjust filter order in activity module
• bug fix: fix error when trying to run activity module with no sleep detected

v0.19.2

• bug fix: properly calculates sample indices to be removed - no longer attempts to remove sample beyond end of window

v0.19.1

• add minimum correlation option for sync
• bug fix: references to settings.json instead of settings.toml on install

v0.19.0

• subjects.csv renamed to collections.csv and coll_id column added
• settings.toml replaces settings.json
• moved config_time check to only occur on first device in sync and display appropriately in log
• activity analysis now done for all wrist devices available with options to select cutpoints
• Pipeline.add_custom_events() provides ability to add or replace custom events from csv
• can specify separate non-wear detection parameters for ankle, wrist, and trunk devices

v0.18.3

• change search radius to minutes
• fix bug in plot if sync is near end of sync radius
• fix assignment bug if search radius is not set

v0.18.2

• fix bug where pipeline tries to autocalibrate data from file that wasn't found

v0.18.1

• fix bug when sync search radius falls outside target collection time

v0.18.0

• insert wear bouts between nonwear bouts (added event column)

v0.17.3

• fixed bug excluding sleep windows to exclude from activity

v0.17.2

• accel step detection uses gait_stats for summary

v0.17.1

• rename start_timestamp and end_timestamp to start_time and end_time in gait

v0.17.0

• rename "feedback report"
• add daily non-wear summary
• crop non-wear from start of collection
• separate sedentary detected from wrist data while walking from other sedentary
• option to classify sptw and sleep bouts as 'overnight'

v0.16.3

• handle Bittium file import if header is imperfect
• add sync search radius

v0.16.2

• activity fixes
  • output 1-second avm
  • fix hard-coded epoch_length

v0.16.1

• add accel_std_thresh_mg as nonwear setting in JSON file
• check for accelerometer signals before autocal
• fix Nonin device data import bugs
• fix missing gait pushoff data bug

v0.16.0

• updated filtering and vm calculation for activity calculation (faster)
• renamed Data object to Device
• added autocalibration of accelerometers
• added relevant functions from nwdata, nwnonwear, nwgait, nwsleep, nwactivity, and nwapp as data.py, nonwear.py, gait.py, sleep.py, activity.py and app.py modules
• tidy sync outputs
• add option to provide alternative settings.json file
• new processing log for each collection
• output settings to log

v0.15.2

• update to nwdata v0.9.2 (much faster file reading and writing)
• update to nwgait v0.4.2
• new processing log for each run call

v0.15.1

• fix package setup files

v0.15.0

• add option to adjust start time of device on convert
• update to nwnonwear v0.2.0 that uses vertdetach package
• allow choice between accel and gyro step detection
• update pandas append to concat

v0.14.2

• bug fix: non-wear end detection windows in proper direction (nwnonwear v0.1.3)
• bug fix: non-wear detection accounts for temperature frequency in rate of change (nwnonwearv0.1.3)

v0.14.1

• add option to lowpass data before activity calculations (nwactivity v0.2.1)
• bug fix: does not count activity during nonwear or sleep (nwactivity v0.3.0)

v0.14.0

• add option to synchronize devices on convert (nwdata v0.9.0)
• select activity cutpoints based on age (nwactivty v0.2.0)
• bug fix: dominant hand from subjects.csv no longer case sensitive

v0.13.0

• gyro step detection for gait

v0.12.0

• nwdata v0.8.0 update
  • add option to crop NWData inplace
  • add read_header method to CWAFile
  • add rotate_z method to rotate accelerometer and gyroscope data around z axis
  • adjust Bittium accelerometer signals to g instead of mg
  • restructure NWData header

v0.11.1

• create separate file for rejected steps
• bug fix: only include single device in cropped nonwear csv
• bug fix: report correct steps detected in log file
• bug fix: do not allow sleep and nonwear to overlap (nwsleep v0.3.1)
• bug fix: dedicated logger based on study code

v0.11.0

• reorganized Pipeline and Collection classes
• moved many settings to settings.json file
• read and convert split so convert can be tracked by status
• update to nwdata v0.7.2
• adjust gait algorithm and vertical axis detection (nwgait v0.3.0)
• bug fix: quiet variable is passed to edf export function

v0.10.0

• modify collection loop to only perform collections included in device list
• create cropped non-wear time file
• bug fix: file duration calculation while cropping (nwdata v0.7.1)

v0.9.0

• updated to nwdata v0.7.0 to incorporate multiple changes
  • convert to ndarray before write with pyedflib (bug)
  • handle Bittium Faros 360 and variable signals
  • update device type codes
• Modify device and sensor logic to match nwdata v0.7.0
• bug fix: axis selection during gait detection (nwgait v0.1.4)

v0.8.0

• add option to run daily sleep stats on all sptw that contain sleep (nwsleep v0.3.0)

v0.7.2

• add option to select axis used to detect gait
• add daily_all sleep stats output
• bug fix: convert device locations to upper case when selecting devices
• bug fix: add column names to steps table if none found (workaround)
• bug fix: check for minimum usable data and candidate sptw and sleep bouts before continuing processing (nwsleep v0.2.2)

v0.7.1

• update pyedflib for all required packages

v0.7.0

• add mechanism to add data dictionaries to output folders
• ignore non-wear when detecting sleep period time windows (nwsleep v0.2.0)
• run t5a5 and t8a4 sleep bout detection
• require pyedflib v0.1.22

v0.6.0

• add non-wear detection for Axivity devices (AXV6) (nwnonwear v0.1.2)
• interpolate inserted values when correcting clock drift or sample rate (nwdata v0.5.0)
• faster GENEActiv read and progress bars on clock drift correct (nwdata v0.6.0)
• adjust device selection logic for activity, gait, sleep analytics

v0.5.0

• update nwdata to require v0.4.0
  • fixes bug where startdate not updated when cropping NWData
  • adds method to get day indices of a signal
• add subjects.csv
• add sleep detection and analysis (nwsleep v0.1.0)
• fix bug where errors during collection not logged correctly

v0.4.0

• update nwactivity to require v0.1.1 (remove mvpa from daily summary)
• update nwgait to require v0.1.2 (add daily gait summary)
• add daily gait summary output
• add pipeline status tracking
• renames EDF files to standard names based on information from devices.csv
• loads data only required devices for single stage
• add support for Axivity AX6 devices (update nwdata to require v0.3.0)

v0.3.0

• add gait processing (nwgait v0.1.0)
• add unexpected error handling with traceback output to log
• add activity processing (nwactivity v0.1.0)
• add study_code as an identifier for all generated data
• add nonwear_bout_id to nonwear output (nwnonwear v0.1.1)

v0.2.0

• add nonwear processing (nwnonwear v0.1.0)
• add option to process only a single stage of the pipeline

v0.1.1

• update nwdata to require v0.1.2