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Configuration

You need to follow these steps to configure your RAPIDS deployment before you can extract behavioral features

  1. Verify RAPIDS can process your data streams
  2. Create your participants files
  3. Select what time segments you want to extract features on
  4. Choose the timezone of your study
  5. Configure your data streams
  6. Select what sensors and features you want to process

When you are done with this configuration, go to executing RAPIDS.

Hint

Every time you see config["KEY"] or [KEY] in these docs we are referring to the corresponding key in the config.yaml file.

Supported data streams

A data stream refers to sensor data collected using a specific type of device with a specific format and stored in a specific container. For example, the aware_mysql data stream handles smartphone data (device) collected with the AWARE Framework (format) stored in a MySQL database (container).

Check the table in introduction to data streams to know what data streams we support. If your data stream is supported, continue to the next configuration section, you will use its label later in this guide (e.g. aware_mysql). If your steam is not supported but you want to implement it, follow the tutorial to add support for new data streams and get in touch by email or in Slack if you have any questions.

Participant files

Participant files link together multiple devices (smartphones and wearables) to specific participants and identify them throughout RAPIDS. You can create these files manually or automatically. Participant files are stored in data/external/participant_files/pxx.yaml and follow a unified structure.

Remember to modify the config.yaml file with your PIDS

The list PIDS in config.yaml needs to have the participant file names of the people you want to process. For example, if you created p01.yaml, p02.yaml and p03.yaml files in /data/external/participant_files/, then PIDS should be: 

PIDS: [p01, p02, p03]

Optional: Migrating participants files with the old format

If you were using the pre-release version of RAPIDS with participant files in plain text (as opposed to yaml), you can run the following command and your old files will be converted into yaml files stored in data/external/participant_files/

python tools/update_format_participant_files.py

Structure of participants files

Example of the structure of a participant file

In this example, the participant used an android phone, an ios phone, a fitbit device, and a Empatica device throughout the study between Apr 23rd 2020 and Oct 28th 2020

If your participants didn’t use a [PHONE], [FITBIT] or [EMPATICA] device, it is not necessary to include that section in their participant file. In other words, you can analyse data from 1 or more devices per participant.

PHONE:
  DEVICE_IDS: [a748ee1a-1d0b-4ae9-9074-279a2b6ba524, dsadas-2324-fgsf-sdwr-gdfgs4rfsdf43]
  PLATFORMS: [android,ios]
  LABEL: test01
  START_DATE: 2020-04-23
  END_DATE: 2020-10-28
FITBIT:
  DEVICE_IDS: [fitbit1]
  LABEL: test01
  START_DATE: 2020-04-23
  END_DATE: 2020-10-28
EMPATICA:
  DEVICE_IDS: [empatica1]
  LABEL: test01
  START_DATE: 2020-04-23
  END_DATE: 2020-10-28
Key                      Description
[DEVICE_IDS] An array of the strings that uniquely identify each smartphone, you can have more than one for when participants changed phones in the middle of the study.
[PLATFORMS] An array that specifies the OS of each smartphone in [DEVICE_IDS] , use a combination of android or ios (we support participants that changed platforms in the middle of your study!). You can set [PLATFORMS]: [infer] and RAPIDS will infer them automatically (each phone data stream infer this differently, e.g. aware_mysql uses the aware_device table).
[LABEL] A string that is used in reports and visualizations.
[START_DATE] A string with format YYYY-MM-DD or YYYY-MM-DD HH:MM:SS. Only data collected after this date time will be included in the analysis. By default, YYYY-MM-DD is interpreted as YYYY-MM-DD 00:00:00.
[END_DATE] A string with format YYYY-MM-DD or YYYY-MM-DD HH:MM:SS. Only data collected before this date time will be included in the analysis. By default, YYYY-MM-DD is interpreted as YYYY-MM-DD 00:00:00.
Key                      Description
[DEVICE_IDS] An array of the strings that uniquely identify each Fitbit, you can have more than one in case the participant changed devices in the middle of the study.
[LABEL] A string that is used in reports and visualizations.
[START_DATE] A string with format YYYY-MM-DD or YYYY-MM-DD HH:MM:SS. Only data collected after this date time will be included in the analysis. By default, YYYY-MM-DD is interpreted as YYYY-MM-DD 00:00:00.
[END_DATE] A string with format YYYY-MM-DD or YYYY-MM-DD HH:MM:SS. Only data collected before this date time will be included in the analysis. By default, YYYY-MM-DD is interpreted as YYYY-MM-DD 00:00:00.
Key                      Description
[DEVICE_IDS] An array of the strings that uniquely identify each Empatica device used by this participant. Since the most common use case involves having multiple zip files from a single device for each person, set this device id to an arbitrary string (we usually use their pid)
[LABEL] A string that is used in reports and visualizations.
[START_DATE] A string with format YYYY-MM-DD or YYYY-MM-DD HH:MM:SS. Only data collected after this date time will be included in the analysis. By default, YYYY-MM-DD is interpreted as YYYY-MM-DD 00:00:00.
[END_DATE] A string with format YYYY-MM-DD or YYYY-MM-DD HH:MM:SS. Only data collected before this date time will be included in the analysis. By default, YYYY-MM-DD is interpreted as YYYY-MM-DD 00:00:00.

Automatic creation of participant files

You can use a CSV file with a row per participant to automatically create participant files.

AWARE_DEVICE_TABLE was deprecated

In previous versions of RAPIDS, you could create participant files automatically using the aware_device table. We deprecated this option but you can still achieve the same results if you export the output of the following SQL query as a CSV file and follow the instructions below:

SELECT device_id, device_id as fitbit_id, CONCAT("p", _id) as empatica_id, CONCAT("p", _id) as pid, if(brand = "iPhone", "ios", "android") as platform, CONCAT("p", _id)  as label, DATE_FORMAT(FROM_UNIXTIME((timestamp/1000)- 86400), "%Y-%m-%d") as start_date, CURRENT_DATE as end_date from aware_device order by _id;

In your config.yaml:

  1. Set CSV_FILE_PATH to a CSV file path that complies with the specs described below
  2. Set the devices (PHONE, FITBIT, EMPATICA) [ADD] flag to TRUE depending on what devices you used in your study.
CREATE_PARTICIPANT_FILES:
  CSV_FILE_PATH: "your_path/to_your.csv"
  PHONE_SECTION:
    ADD: TRUE # or FALSE
    IGNORED_DEVICE_IDS: []
  FITBIT_SECTION:
    ADD: TRUE # or FALSE
    IGNORED_DEVICE_IDS: []
  EMPATICA_SECTION:
    ADD: TRUE # or FALSE
    IGNORED_DEVICE_IDS: []

Your CSV file ([CSV_FILE_PATH]) should have the following columns (headers) but the values within each column can be empty:

Column Description
device_id Phone device id. Separate multiple ids with ;
fitbit_id Fitbit device id. Separate multiple ids with ;
empatica_id Empatica device id. Since the most common use case involves having multiple zip files from a single device for each person, set this device id to an arbitrary string (we usually use their pid)
pid Unique identifiers with the format pXXX (your participant files will be named with this string)
platform Use android, ios or infer as explained above, separate values with ;
label A human readable string that is used in reports and visualizations.
start_date A string with format YYY-MM-DD or YYYY-MM-DD HH:MM:SS. By default, YYYY-MM-DD is interpreted as YYYY-MM-DD 00:00:00.
end_date A string with format YYY-MM-DD or YYYY-MM-DD HH:MM:SS. By default, YYYY-MM-DD is interpreted as YYYY-MM-DD 00:00:00.

Example

We added white spaces to this example to make it easy to read but you don’t have to.

device_id                                                                ,fitbit_id, empatica_id ,pid ,label ,platform    ,start_date ,end_date
a748ee1a-1d0b-4ae9-9074-279a2b6ba524;dsadas-2324-fgsf-sdwr-gdfgs4rfsdf43 ,fitbit1  , p01         ,p01 ,julio ,android;ios ,2020-01-01 ,2021-01-01
4c4cf7a1-0340-44bc-be0f-d5053bf7390c                                     ,fitbit2  , p02         ,p02 ,meng  ,ios         ,2021-01-01 ,2022-01-01

Then run 

snakemake -j1 create_participants_files

Time Segments

Time segments (or epochs) are the time windows on which you want to extract behavioral features. For example, you might want to process data on every day, every morning, or only during weekends. RAPIDS offers three categories of time segments that are flexible enough to cover most use cases: frequency (short time windows every day), periodic (arbitrary time windows on any day), and event (arbitrary time windows around events of interest). See also our examples.

These segments are computed on every day and all have the same duration (for example 30 minutes). Set the following keys in your config.yaml

TIME_SEGMENTS: &time_segments
  TYPE: FREQUENCY
  FILE: "data/external/your_frequency_segments.csv"
  INCLUDE_PAST_PERIODIC_SEGMENTS: FALSE

The file pointed by [TIME_SEGMENTS][FILE] should have the following format and can only have 1 row.

Column Description
label A string that is used as a prefix in the name of your time segments
length An integer representing the duration of your time segments in minutes

Example

label,length
thirtyminutes,30

This configuration will compute 48 time segments for every day when any data from any participant was sensed. For example:

start_time,length,label
00:00,30,thirtyminutes0000
00:30,30,thirtyminutes0001
01:00,30,thirtyminutes0002
01:30,30,thirtyminutes0003
...

These segments can be computed every day, or on specific days of the week, month, quarter, and year. Their minimum duration is 1 minute but they can be as long as you want. Set the following keys in your config.yaml.

TIME_SEGMENTS: &time_segments
  TYPE: PERIODIC
  FILE: "data/external/your_periodic_segments.csv"
  INCLUDE_PAST_PERIODIC_SEGMENTS: FALSE # or TRUE

If [INCLUDE_PAST_PERIODIC_SEGMENTS] is set to TRUE, RAPIDS will consider instances of your segments back enough in the past as to include the first row of data of each participant. For example, if the first row of data from a participant happened on Saturday March 7th 2020 and the requested segment duration is 7 days starting on every Sunday, the first segment to be considered would start on Sunday March 1st if [INCLUDE_PAST_PERIODIC_SEGMENTS] is TRUE or on Sunday March 8th if FALSE.

The file pointed by [TIME_SEGMENTS][FILE] should have the following format and can have multiple rows.

Column Description
label A string that is used as a prefix in the name of your time segments. It has to be unique between rows
start_time A string with format HH:MM:SS representing the starting time of this segment on any day
length A string representing the length of this segment.It can have one or more of the following strings XXD XXH XXM XXS to represent days, hours, minutes and seconds. For example 7D 23H 59M 59S
repeats_on One of the follow options every_day, wday, qday, mday, and yday. The last four represent a week, quarter, month and year day
repeats_value An integer complementing repeats_on. If you set repeats_on to every_day set this to 0, otherwise 1-7 represent a wday starting from Mondays, 1-31 represent a mday, 1-91 represent a qday, and 1-366 represent a yday

Example

label,start_time,length,repeats_on,repeats_value
daily,00:00:00,23H 59M 59S,every_day,0
morning,06:00:00,5H 59M 59S,every_day,0
afternoon,12:00:00,5H 59M 59S,every_day,0
evening,18:00:00,5H 59M 59S,every_day,0
night,00:00:00,5H 59M 59S,every_day,0

This configuration will create five segments instances (daily, morning, afternoon, evening, night) on any given day (every_day set to 0). The daily segment will start at midnight and will last 23:59:59, the other four segments will start at 6am, 12pm, 6pm, and 12am respectively and last for 05:59:59.

These segments can be computed before or after an event of interest (defined as any UNIX timestamp). Their minimum duration is 1 minute but they can be as long as you want. The start of each segment can be shifted backwards or forwards from the specified timestamp. Set the following keys in your config.yaml.

TIME_SEGMENTS: &time_segments
  TYPE: EVENT
  FILE: "data/external/your_event_segments.csv"
  INCLUDE_PAST_PERIODIC_SEGMENTS: FALSE # or TRUE

The file pointed by [TIME_SEGMENTS][FILE] should have the following format and can have multiple rows.

Column Description
label A string that is used as a prefix in the name of your time segments. If labels are unique, every segment is independent; if two or more segments have the same label, their data will be grouped when computing auxiliary data for features like the most frequent contact for calls (the most frequent contact will be computed across all these segments). There cannot be two overlaping event segments with the same label (RAPIDS will throw an error)
event_timestamp A UNIX timestamp that represents the moment an event of interest happened (clinical relapse, survey, readmission, etc.). The corresponding time segment will be computed around this moment using length, shift, and shift_direction
length A string representing the length of this segment. It can have one or more of the following keys XXD XXH XXM XXS to represent a number of days, hours, minutes, and seconds. For example 7D 23H 59M 59S
shift A string representing the time shift from event_timestamp. It can have one or more of the following keys XXD XXH XXM XXS to represent a number of days, hours, minutes and seconds. For example 7D 23H 59M 59S. Use this value to change the start of a segment with respect to its event_timestamp. For example, set this variable to 1H to create a segment that starts 1 hour from an event of interest (shift_direction determines if it’s before or after).
shift_direction An integer representing whether the shift is before (-1) or after (1) an event_timestamp
device_id The device id (smartphone or fitbit) to whom this segment belongs to. You have to create a line in this event segment file for each event of a participant that you want to analyse. If you have participants with multiple device ids you can choose any of them

Example

label,event_timestamp,length,shift,shift_direction,device_id
stress1,1587661220000,1H,5M,1,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
stress2,1587747620000,4H,4H,-1,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
stress3,1587906020000,3H,5M,1,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
stress4,1584291600000,7H,4H,-1,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
stress5,1588172420000,9H,5M,-1,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
mood,1587661220000,1H,0,0,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
mood,1587747620000,1D,0,0,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
mood,1587906020000,7D,0,0,a748ee1a-1d0b-4ae9-9074-279a2b6ba524

This example will create eight segments for a single participant (a748ee1a...), five independent stressX segments with various lengths (1,4,3,7, and 9 hours). Segments stress1, stress3, and stress5 are shifted forwards by 5 minutes and stress2 and stress4 are shifted backwards by 4 hours (that is, if the stress4 event happened on March 15th at 1pm EST (1584291600000), the time segment will start on that day at 9am and end at 4pm).

The three mood segments are 1 hour, 1 day and 7 days long and have no shift. In addition, these mood segments are grouped together, meaning that although RAPIDS will compute features on each one of them, some necessary information to compute a few of such features will be extracted from all three segments, for example the phone contact that called a participant the most or the location clusters visited by a participant.

Date time labels of event segments

In the final feature file, you will find a row per event segment. The local_segment column of each row has a label, a start date-time string, and an end date-time string.

weeklysurvey2060#2020-09-12 01:00:00,2020-09-18 23:59:59

All sensor data is always segmented based on timestamps, and the date-time strings are attached for informative purposes. For example, you can plot your features based on these strings.

When you configure RAPIDS to work with a single time zone, such tz code will be used to convert start/end timestamps (the ones you typed in the event segments file) into start/end date-time strings. However, when you configure RAPIDS to work with multiple time zones, RAPIDS will use the most common time zone across all devices of every participant to do the conversion. The most common time zone is the one in which a participant spent the most time.

In practical terms, this means that the date-time strings of event segments that happened in uncommon time zones will have shifted start/end date-time labels. However, the data within each segment was correctly filtered based on timestamps.

Segment Examples

Use the following Frequency segment file to create 288 (12 * 60 * 24) 5-minute segments starting from midnight of every day in your study 

label,length
fiveminutes,5

Use the following Periodic segment file to create daily segments starting from midnight of every day in your study 

label,start_time,length,repeats_on,repeats_value
daily,00:00:00,23H 59M 59S,every_day,0

Use the following Periodic segment file to create morning segments starting at 06:00:00 and ending at 11:59:59 of every day in your study 

label,start_time,length,repeats_on,repeats_value
morning,06:00:00,5H 59M 59S,every_day,0

Use the following Periodic segment file to create overnight segments starting at 20:00:00 and ending at 07:59:59 (next day) of every day in your study 

label,start_time,length,repeats_on,repeats_value
morning,20:00:00,11H 59M 59S,every_day,0

Use the following Periodic segment file to create non-overlapping weekly segments starting at midnight of every Monday in your study 

label,start_time,length,repeats_on,repeats_value
weekly,00:00:00,6D 23H 59M 59S,wday,1
Use the following Periodic segment file to create overlapping weekly segments starting at midnight of every day in your study 
label,start_time,length,repeats_on,repeats_value
weekly,00:00:00,6D 23H 59M 59S,every_day,0

Use the following Periodic segment file to create week-end segments starting at midnight of every Saturday in your study 

label,start_time,length,repeats_on,repeats_value
weekend,00:00:00,1D 23H 59M 59S,wday,6

Use the following Event segment file to create two 2-hour segments that start 1 hour before surveys answered by 3 participants 

label,event_timestamp,length,shift,shift_direction,device_id
survey1,1587661220000,2H,1H,-1,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
survey2,1587747620000,2H,1H,-1,a748ee1a-1d0b-4ae9-9074-279a2b6ba524
survey1,1587906020000,2H,1H,-1,rqtertsd-43ff-34fr-3eeg-efe4fergregr
survey2,1584291600000,2H,1H,-1,rqtertsd-43ff-34fr-3eeg-efe4fergregr
survey1,1588172420000,2H,1H,-1,klj34oi2-8frk-2343-21kk-324ljklewlr3
survey2,1584291600000,2H,1H,-1,klj34oi2-8frk-2343-21kk-324ljklewlr3

Timezone of your study

Single timezone

If your study only happened in a single time zone or you want to ignore short trips of your participants to different time zones, select the appropriate code form this list and change the following config key. Double-check your timezone code pick, for example, US Eastern Time is America/New_York not EST

TIMEZONE: 
    TYPE: SINGLE
    TZCODE: America/New_York

Multiple timezones

If your participants lived in different time zones or they traveled across time zones, and you know when participants’ devices were in a specific time zone, RAPIDS can use this data to process your data streams with the correct date-time. You need to provide RAPIDS with the time zone data in a CSV file ([TZCODES_FILE]) in the format described below.

TIMEZONE: 
    TYPE: MULTIPLE
    SINGLE:
      TZCODE: America/New_York
    MULTIPLE:
      TZCODES_FILE: path_to/time_zones_csv.file
      IF_MISSING_TZCODE: STOP
      DEFAULT_TZCODE: America/New_York
      FITBIT: 
        ALLOW_MULTIPLE_TZ_PER_DEVICE: False
        INFER_FROM_SMARTPHONE_TZ: False

Parameters for [TIMEZONE]

Parameter                                                            Description
[TYPE] Either SINGLE or MULTIPLE as explained above
[SINGLE][TZCODE] The time zone code from this list to be used across all devices
[MULTIPLE][TZCODES_FILE] A CSV file containing the time zones in which participants’ devices sensed data (see the required format below). Multiple devices can be linked to the same person, read more in Participants Files
[MULTIPLE][IF_MISSING_TZCODE] When a device is missing from [TZCODES_FILE] Set this flag to STOP to stop RAPIDS execution and show an error, or to USE_DEFAULT to assign the time zone specified in [DEFAULT_TZCODE] to any such devices
[MULTIPLE][FITBIT][ALLOW_MULTIPLE_TZ_PER_DEVICE] You only need to care about this flag if one or more Fitbit devices sensed data in one or more time zones, and you want RAPIDS to take into account this in its feature computation. Read more in “How does RAPIDS handle Fitbit devices?” below.
[MULTIPLE][FITBIT][INFER_FROM_SMARTPHONE_TZ] You only need to care about this flag if one or more Fitbit devices sensed data in one or more time zones, and you want RAPIDS to take into account this in its feature computation. Read more in “How does RAPIDS handle Fitbit devices?” below.
Format of TZCODES_FILE

TZCODES_FILE has three columns and a row for each time zone a device visited (a device can be a smartphone or wearable (Fitbit/Empatica)):

Column Description
device_id A string that uniquely identifies a smartphone or wearable
tzcode A string with the appropriate code from this list that represents the time zone where the device sensed data
timestamp A UNIX timestamp indicating when was the first time this device_id sensed data in tzcode 
device_id,                            tzcode,              timestamp
13dbc8a3-dae3-4834-823a-4bc96a7d459d, America/New_York,     1587500000000
13dbc8a3-dae3-4834-823a-4bc96a7d459d, America/Mexico_City,  1587600000000
13dbc8a3-dae3-4834-823a-4bc96a7d459d, America/Los_Angeles,  1587700000000
65sa66a5-2d2d-4524-946v-44ascbv4sad7, Europe/Amsterdam,     1587100000000
65sa66a5-2d2d-4524-946v-44ascbv4sad7, Europe/Berlin,        1587200000000
65sa66a5-2d2d-4524-946v-44ascbv4sad7, Europe/Amsterdam,     1587300000000

Using this file, RAPDIS will create time zone intervals per device, for example for 13dbc8a3-dae3-4834-823a-4bc96a7d459d:

  • Interval 1 [1587500000000, 1587599999999] for America/New_York
  • Interval 2 [1587600000000, 1587699999999] for America/Mexico_City
  • Interval 3 [1587700000000, now] for America/Los_Angeles

Any sensor data row from a device will be assigned a timezone if it falls within that interval, for example:

  • A screen row sensed at 1587533333333 will be assigned to America/New_York because it falls within Interval 1
  • A screen row sensed at 1587400000000 will be discarded because it was logged outside any interval.
Can I get the TZCODES_FILE from the time zone table collected automatically by the AWARE app?

Sure. You can put your timezone table (timezone.csv) collected by the AWARE app under data/external folder and run: 

python tools/create_multi_timezones_file.py
The TZCODES_FILE will be saved as data/external/multiple_timezones.csv file.

What happens if participant X lives in Los Angeles but participant Y lives in Amsterdam and they both stayed there during my study?

Add a row per participant and set timestamp to 0: 

device_id,                            tzcode,              timestamp
13dbc8a3-dae3-4834-823a-4bc96a7d459d, America/Los_Angeles,  0
65sa66a5-2d2d-4524-946v-44ascbv4sad7, Europe/Amsterdam,     0

What happens if I forget to add a timezone for one or more devices?

It depends on [IF_MISSING_TZCODE].

If [IF_MISSING_TZCODE] is set to STOP, RAPIDS will stop its execution and show you an error message.

If [IF_MISSING_TZCODE] is set to USE_DEFAULT, it will assign the time zone specified in [DEFAULT_TZCODE] to any devices with missing time zone information in [TZCODES_FILE]. This is helpful if only a few of your participants had multiple timezones and you don’t want to specify the same time zone for the rest.

How does RAPIDS handle Fitbit devices?

Fitbit devices are not time zone aware and they always log data with a local date-time string.

  • When none of the Fitbit devices in your study changed time zones (e.g., p01 was always in New York and p02 was always in Amsterdam), you can set a single time zone per Fitbit device id along with a timestamp 0 (you can still assign multiple time zones to smartphone device ids) 

    device_id, tzcode,              timestamp
fitbit123, America/New_York,     0
fitbit999, Europe/Amsterdam,     0

  • On the other hand, when at least one of your Fitbit devices changed time zones AND you want RAPIDS to take into account these changes, you need to set [ALLOW_MULTIPLE_TZ_PER_DEVICE] to True. You have to manually allow this option because you need to be aware it can produce inaccurate features around the times when time zones changed. This is because we cannot know exactly when the Fitbit device detected and processed the time zone change.

    If you want to ALLOW_MULTIPLE_TZ_PER_DEVICE you will need to add any time zone changes per device in the TZCODES_FILE as explained above. You could obtain this data by hand but if your participants also used a smartphone during your study, you can use their time zone logs. Recall that in RAPIDS every participant is represented with a participant file pXX.yaml, this file links together multiple devices and we will use it to know what smartphone time zone data should be applied to Fitbit devices. Thus set INFER_FROM_SMARTPHONE_TZ to TRUE, if you have included smartphone time zone data in your TZCODE_FILE and you want to make a participant’s Fitbit data time zone aware with their respective smartphone data.

Data Stream Configuration

Modify the following keys in your config.yaml depending on the data stream you want to process.

Set [PHONE_DATA_STREAMS][TYPE] to the smartphone data stream you want to process (e.g. aware_mysql) and configure its parameters (e.g. [DATABASE_GROUP]). Ignore the parameters of streams you are not using (e.g. [FOLDER] of aware_csv).

PHONE_DATA_STREAMS:
  USE: aware_mysql

  # AVAILABLE:
  aware_mysql:
    DATABASE_GROUP: MY_GROUP

  aware_csv:
    FOLDER: data/external/aware_csv
Key Description
[DATABASE_GROUP] A database credentials group. Read the instructions below to set it up
Setting up a DATABASE_GROUP and its connection credentials.

  1. If you haven’t done so, create an empty file called credentials.yaml in your RAPIDS root directory:

  2. Add the following lines to credentials.yaml and replace your database-specific credentials (user, password, host, and database):

    MY_GROUP:
  database: MY_DATABASE
  host: MY_HOST
  password: MY_PASSWORD
  port: 3306
  user: MY_USER

  3. Notes

    1. The label [MY_GROUP] is arbitrary but it has to match the [DATABASE_GROUP] attribute of the data stream you choose to use.

    2. Indentation matters

    3. You can have more than one credentials group in credentials.yaml

Upgrading from ./.env from RAPIDS 0.x

In RAPIDS versions 0.x, database credentials were stored in a ./.env file. If you are migrating from that type of file, you have two options:

  1. Migrate your credentials by hand:

    [MY_GROUP]
user=MY_USER
password=MY_PASSWORD
host=MY_HOST
port=3306
database=MY_DATABASE

    MY_GROUP:
  user: MY_USER
  password: MY_PASSWORD
  host: MY_HOST
  port: 3306
  database: MY_DATABASE

  2. Use the migration script we provide (make sure your conda environment is active):

    python tools/update_format_env.py
Connecting to localhost (host machine) from inside our docker container.

If you are using RAPIDS’ docker container and Docker-for-mac or Docker-for-Windows 18.03+, you can connect to a MySQL database in your host machine using host.docker.internal instead of 127.0.0.1 or localhost. In a Linux host, you need to run our docker container using docker run --network="host" -d moshiresearch/rapids:latest and then 127.0.0.1 will point to your host machine.

Key Description
[FOLDER] Folder where you have to place a CSV file per phone sensor. Each file has to contain all the data from every participant you want to process.

Set [FITBIT_DATA_STREAMS][TYPE] to the Fitbit data stream you want to process (e.g. fitbitjson_mysql) and configure its parameters (e.g. [DATABASE_GROUP]). Ignore the parameters of the other streams you are not using (e.g. [FOLDER] of aware_csv).

Warning

You will probably have to tell RAPIDS the name of the columns where you stored your Fitbit data. To do this, modify your chosen stream’s format.yaml column mappings to match your raw data column names.

FITBIT_DATA_STREAMS:
  USE: fitbitjson_mysql

  # AVAILABLE:
  fitbitjson_mysql:
    DATABASE_GROUP: MY_GROUP
    SLEEP_SUMMARY_EPISODE_DAY_ANCHOR: False

  fitbitjson_csv:
    FOLDER: data/external/fitbit_csv
    SLEEP_SUMMARY_EPISODE_DAY_ANCHOR: False

  fitbitparsed_mysql:
    DATABASE_GROUP: MY_GROUP
    SLEEP_SUMMARY_EPISODE_DAY_ANCHOR: False

  fitbitparsed_csv:
    FOLDER: data/external/fitbit_csv
    SLEEP_SUMMARY_EPISODE_DAY_ANCHOR: False

This data stream process Fitbit data inside a JSON column as obtained from the Fitbit API and stored in a MySQL database. Read more about its column mappings and mutations in fitbitjson_mysql.

Key Description
[DATABASE_GROUP] A database credentials group. Read the instructions below to set it up
[SLEEP_SUMMARY_EPISODE_DAY_ANCHOR] One of start or end. Summary sleep episodes are considered as events based on either the start timestamp or end timestamp (they will belong to the day where they start or end).
Setting up a DATABASE_GROUP and its connection credentials.

  1. If you haven’t done so, create an empty file called credentials.yaml in your RAPIDS root directory:

  2. Add the following lines to credentials.yaml and replace your database-specific credentials (user, password, host, and database):

    MY_GROUP:
  database: MY_DATABASE
  host: MY_HOST
  password: MY_PASSWORD
  port: 3306
  user: MY_USER

  3. Notes

    1. The label [MY_GROUP] is arbitrary but it has to match the [DATABASE_GROUP] attribute of the data stream you choose to use.

    2. Indentation matters

    3. You can have more than one credentials group in credentials.yaml

Upgrading from ./.env from RAPIDS 0.x

In RAPIDS versions 0.x, database credentials were stored in a ./.env file. If you are migrating from that type of file, you have two options:

  1. Migrate your credentials by hand:

    [MY_GROUP]
user=MY_USER
password=MY_PASSWORD
host=MY_HOST
port=3306
database=MY_DATABASE

    MY_GROUP:
  user: MY_USER
  password: MY_PASSWORD
  host: MY_HOST
  port: 3306
  database: MY_DATABASE

  2. Use the migration script we provide (make sure your conda environment is active):

    python tools/update_format_env.py
Connecting to localhost (host machine) from inside our docker container.

If you are using RAPIDS’ docker container and Docker-for-mac or Docker-for-Windows 18.03+, you can connect to a MySQL database in your host machine using host.docker.internal instead of 127.0.0.1 or localhost. In a Linux host, you need to run our docker container using docker run --network="host" -d moshiresearch/rapids:latest and then 127.0.0.1 will point to your host machine.

This data stream process Fitbit data inside a JSON column as obtained from the Fitbit API and stored in a CSV file. Read more about its column mappings and mutations in fitbitjson_csv.

Key Description
[FOLDER] Folder where you have to place a CSV file per Fitbit sensor. Each file has to contain all the data from every participant you want to process.
[SLEEP_SUMMARY_EPISODE_DAY_ANCHOR] One of start or end. Summary sleep episodes are considered as events based on either the start timestamp or end timestamp (they will belong to the day where they start or end).

This data stream process Fitbit data stored in multiple columns after being parsed from the JSON column returned by Fitbit API and stored in a MySQL database. Read more about its column mappings and mutations in fitbitparsed_mysql.

Key Description
[DATABASE_GROUP] A database credentials group. Read the instructions below to set it up
[SLEEP_SUMMARY_EPISODE_DAY_ANCHOR] One of start or end. Summary sleep episodes are considered as events based on either the start timestamp or end timestamp (they will belong to the day where they start or end).
Setting up a DATABASE_GROUP and its connection credentials.

  1. If you haven’t done so, create an empty file called credentials.yaml in your RAPIDS root directory:

  2. Add the following lines to credentials.yaml and replace your database-specific credentials (user, password, host, and database):

    MY_GROUP:
  database: MY_DATABASE
  host: MY_HOST
  password: MY_PASSWORD
  port: 3306
  user: MY_USER

  3. Notes

    1. The label [MY_GROUP] is arbitrary but it has to match the [DATABASE_GROUP] attribute of the data stream you choose to use.

    2. Indentation matters

    3. You can have more than one credentials group in credentials.yaml

Upgrading from ./.env from RAPIDS 0.x

In RAPIDS versions 0.x, database credentials were stored in a ./.env file. If you are migrating from that type of file, you have two options:

  1. Migrate your credentials by hand:

    [MY_GROUP]
user=MY_USER
password=MY_PASSWORD
host=MY_HOST
port=3306
database=MY_DATABASE

    MY_GROUP:
  user: MY_USER
  password: MY_PASSWORD
  host: MY_HOST
  port: 3306
  database: MY_DATABASE

  2. Use the migration script we provide (make sure your conda environment is active):

    python tools/update_format_env.py
Connecting to localhost (host machine) from inside our docker container.

If you are using RAPIDS’ docker container and Docker-for-mac or Docker-for-Windows 18.03+, you can connect to a MySQL database in your host machine using host.docker.internal instead of 127.0.0.1 or localhost. In a Linux host, you need to run our docker container using docker run --network="host" -d moshiresearch/rapids:latest and then 127.0.0.1 will point to your host machine.

This data stream process Fitbit data stored in multiple columns (plain text) after being parsed from the JSON column returned by Fitbit API and stored in a CSV file. Read more about its column mappings and mutations in fitbitparsed_csv.

Key Description
[FOLDER] Folder where you have to place a CSV file per Fitbit sensor. Each file has to contain all the data from every participant you want to process.
[SLEEP_SUMMARY_EPISODE_DAY_ANCHOR] One of start or end. Summary sleep episodes are considered as events based on either the start timestamp or end timestamp (they will belong to the day where they start or end).

Set [USE] to the Empatica data stream you want to use; see the table in introduction to data streams. Configure any parameters as indicated below.

EMPATICA_DATA_STREAMS:
  USE: empatica_zip

  # AVAILABLE:
  empatica_zip: 
    FOLDER: data/external/empatica
Key Description
[FOLDER] The relative path to a folder containing one subfolder per participant. The name of a participant folder should match their device_id assigned in their participant file. Each participant folder can have one or more zip files with any name; in other words, the sensor data in those zip files belong to a single participant. The zip files are automatically generated by Empatica and have a CSV file per sensor (ACC, HR, TEMP, EDA, BVP, TAGS). All CSV files of the same type contained in one or more zip files are uncompressed, parsed, sorted by timestamp, and joined together.
Example of an EMPATICA FOLDER

In the file tree below, we want to process three participants’ data: p01, p02, and p03. p01 has two zip files, p02 has only one zip file, and p03 has three zip files. Each zip has a CSV file per sensor that are joined together and processed by RAPIDS.

data/ # this folder exists in the root RAPIDS folder
  external/
    empatica/
      p01/
        file1.zip
        file2.zip
      p02/
        aaaa.zip
      p03/
        t1.zip
        t2.zip
        t3.zip

Sensor and Features to Process

Finally, you need to modify the config.yaml section of the sensors you want to extract behavioral features from. All sensors follow the same naming nomenclature (DEVICE_SENSOR) and parameter structure which we explain in the Behavioral Features Introduction.

Done

Head over to Execution to learn how to execute RAPIDS.

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