UvAGPS

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UvA-BiTS Data Model

All tables, views and functions related to UvA-BiTS are in the GPS schema in the database and begin with the prefix "uva_".

Different database tables are used depending on the version of UvA-BiTS firmware installed in the GPS device. For firmware version v0.9.3.6 till v1.0.0.X the tables UVA_ENGINEERING_DATA and UVA_TRACKING_DATA are used. But for the new firmware (versions 1.0.1.4 till 1.0.2.4) so much information was added that new tables were introduced. However for the most important tracking tables a view is created so that all similar tracking data for all types of firmware can be seen in one view. That is the UVA_TRACKING view.

Not everybody has access to all data. For most users access is limited to views with the postfix "_limited" that only give access to selected devices.

The majority of users will want to access the data found in the first five tables discussed below (uva_track_session, uva_tracking_data, uva_tracking_data101, uva_acceleration101 and uva_individual). The other tables have mainly administrative, engineering or data quality purposes.


UVA_DEVICE or UVA_DEVICE_LIMITED

To be able to track the different firmware versions and specific properties for the different devices the UVA_DEVICE table was added. This table also includes essential information needed to calibrate the accelerometers. For more information see the section below called Accelerometer calibration. Different GPS chips have been used for the tags over the years for more information see the section below called Information about GPS receivers.

Field Type Key Constraints Comments
device_info_serial integer PK NOT NULL Serial number of tag
firmware_version text NOT NULL Firmware version installed on tag
device_mass double Mass of tag (g)
x_s double Calibration sensitivity of accelerometer in the x-axis
y_s double Calibration sensitivity of accelerometer in the y-axis
z_s double Calibration sensitivity of accelerometer in the z-axis
x_o double Calibration offset of accelerometer in the x-axis
y_o double Calibration offset of accelerometer in the y-axis
z_o double Calibration offset of accelerometer in the z-axis

UVA_TRACK_SESSION or UVA_TRACK_SESSION_LIMITED

This is essential metadata about GPS tag deployment. This table includes information about each measurement session and enables inclusion of data from new species and also from the test phase of different tags. To avoid analyzing data that was collected during testing, you should always select data that coincides with the start_data of a particular track session.

Field Type Key Constraints Comments
device_info_serial int4 FK NOT NULL Serial number of GPS tag
ring_number text FK ring number of individual, link to individual table – tests do not have a ring_number
start_date timestamp Timestamp without time zone (UTC) when tracking begins yyyy-mm-dd hh:mm:ss
start_latitude float8 NOT NULL latitude where tracking begins, unit = dec degress
start_longitude float8 NOT NULL longitude where tracking begins, unit = dec degrees
end_date timestamptz Timestamp without time zone (UTC) when tracking session ends if known yyyy-mm-dd hh:mm:ss
project_leader text Project leader and point of contact for questions about data
remarks text
location geometry postgreSQL geometry


UVA_TRACKING_DATA Table or UVA_TRACKING_LIMITED View

Tracking data from UvA GPS tags for older firmware

Field Type Key Constraints Comments
device_info_serial int4 PK NOT NULL
date_time timestamp PK NOT NULL UTC
latitude float8 Decimal degrees
longitude float8 Decimal degrees
h_accuracy float8 Horizontal accuracy (m)
v_accuracy float8 Vertical accuracy (m)
altitude float8 m
x_acceleration Float8 x axis acceleration (m/s22) movement to right is + and to left is -
y_acceleration Float8 y axis acceleration (m/s22) forward movement is + and backwards is -
z_acceleration Float8 z axis acceleration (m/s22) upwards movement is + downwards is -
speed float8 m/s
course float8 Degrees
pressure float8 Pressure sensor (pascal)
temperature Float8 Degrees celcius
solar_voltage Float8 V
battery_voltage Float8 V
userflag Integer Data flagged as unacceptable by user
“"location”" geometry postgreSQL geometry


UVA_TRACKING_DATA101 Table or UVA_TRACKING_LIMITED View

The tracking data for newer firmware (V 1.0.1.4 and higher).

Field Type Key Constraints Comments
device_info_serial int4 PK NOT NULL
date_time timestamp PK NOT NULL UTC
latitude float Decimal degrees
longitude float Decimal degrees
altitude integer height above sea level (meters)
pressure integer in pascal (1mBar = 100Pa, 1pressuremeter = ~12Pa)
temperature float in celcius degrees
satellites_used smallint satellites used for fix
gps_fixtime float GpsFixTime in seconds
positiondop float Position DOP in units
h_accuracy float Horizontal accuracy (units of meter)
v_accuracy float Vertical accuracy (units of meter)
x_speed float Speed in x-axis (m/s)
y_speed float Speed in y-axis (m/s)
z_speed float Speed in z-axis (m/s)
speed_accuracy float Speed accuracy (m/s)
userflag Integer Data flagged as unacceptable by user if not 0
location geometry lat/long as PostGIS geometry


UVA_TRACKING or UVA_TRACKING_LIMITED

View to show identical fields for older and newer firmware tracking data

Field Type Key Constraints Comments
device_info_serial int4 PK NOT NULL
date_time timestamp PK NOT NULL UTC
latitude float
longitude float
altitude float
pressure integer
temperature float
h_accuracy float
v_accuracy float
x_speed float meters/second
y_speed float meters/second
z_speed float meters/second
gps_fixtime float
userflag integer Flagged as inacceptable by user if not 0
satellites_used smallint
positiondop float
speed_accuracy float
location geometry


UVA_TRACKING_SPEED or UVA_TRACKING_SPEED_LIMITED

Additional view that computes with the x_speed, y_speed and z_speed components the vnorth, veast and vdown speed components as well as the 3D speed in meters/second.

In addition to the fields in the UVA_TRACKING view this view adds :

Field Type Key Constraints Comments
vnorth float - vx * sin(lat) * cos(long) - vy * sin(lat) * sin (long) + vz * cos(lat)
veast float - vx * sin(lon) + vy * cos(lon)
vdown float - vx * cos(lat) * cos(lon) - vy * cos(lat) * sin(lon) - vz * sin(lat)
speed float sqrt(vnorth^2 + veast^2)
speed3d float sqrt(vnorth^2 + veast^2 + vdown^2)
direction float heading in degrees; 0 is north, 90 is east


UVA_ACCELERATION101 or UVA_ACCELERATION_LIMITED

Acceleration entries if accelerometer was turned on. Only for newer firmware. Actual measurements have shown that the range of values for x,y and z are larger then indicated by the manufacturer. For more information about calibration and interpretation of accelerometer data see Accelerometer calibration

Field Type Key Constraints Comments
device_info_serial int4 PK NOT NULL
date_time timestamp PK NOT NULL UTC
index smallint PK NOT NULL row index (from 0) of accelerometer measurement series
x_acceleration smallint acceleration in X-axis (-2666 till 2666)
y_acceleration smallint acceleration in Y-axis (-2666 till 2666)
z_acceleration smallint acceleration in Z-axis (-2666 till 2666)


UVA_ACC_START102 or UVA_ACC_START_LIMITED

General acceleration entry associated with a set of accelerations. Added in Firmware 1.0.2.7 because there line numbers were introduced for acceleration lines so that these lines can be tracked.

Field Type Key Constraints Comments
device_info_serial int4 PK NOT NULL
date_time timestamp PK NOT NULL
line_counter integer Number of lines associated with this set of accelerations
timesynced smallint TimeSynced (0=not synced, 1=user set, 2=Gps Synced)
accii integer Accelero measurement interval
accsn integer Number of samples (0-65536)
f smallint Accelero sample frequency (0=20Hz, 1=10Hz, 2=5Hz, 3=1Hz)


UVA_ENGINEERING_DATA

Engineering data from UvA GPS tags for older firmware (up to and including V 1.0.0.3). These tags used the UBlox gps chip LEAS4S.

Field Type Key Constraints Comments
device_info_serial int4 PK NOT NULL
date_time timestamp PK NOT NULL UTC
t_syncsts smallint 0: not synced, 1: user synced, 2: Gps synced
t_entzt smallint 0: UCT time,1: TZT time (timezone time)
gzp_currentrategps int4
gzp_currentratecom int4
gzp_currentratepwr int4
sbm_voltagesolarpanel float8
sbm_voltagebattery float8
sbm_chargemode int2
egzp_mainrategps integer
egzp_mainratecom integer
egzp_mainratepwr integer
smg_on text
smg_off text
smg_esavegpsrate integer
smz_on text
smz_off text
smz_esavecomrate integer
gpsnavigationmode smallint This is the Kalman filter used for GPS navigation mode often called the "Dynamic platform model". The following codes are provided by the GPS chip manufacturer for UBlox chip LEAS4S: 1 = stationary, 2 = pedestrian, 3 = automotive, 4 = sea, 5 = airborne 1G, 6 = airborne 2G, 7 = airborne 3G
gpsfixtimeout smallint
eh text


UVA_COMM101 or UVA_COMM_LIMITED

Communication table indicates status and result of communications with ground stations. Only for newer firmware (V 1.0.1.4 and higher).

Field Type Key Constraints Comments
device_info_serial integer PK NOT NULL
date_time timestamp PK NOT NULL timestamp of start communication
date_time_end timestamp timestamp of end communication
date_time_utc timestamp date_time in utc (if available)
date_time_end_utc timestamp date_time_end in utc (if available)
action text JOINED / RESCHEDULE  ??
bytes_communicated integer Number of bytes communicated (total of all bytes per DATA line)
status text READY, TIMEOUT, LOWPOWER, MISSING
network_join_time integer milliseconds
number_identical_lines integer Number identical lines in data block. Gives indication
non_ascii_char integer Number of non ascii characters (indicated by question-mark ?)
sts_time timestamp derived from S0 hh,mi
timesynced smallint TimeSynced (0=not sy:wnced, 1=user set, 2=Gps Synced)
devicemode smallint DeviceMode (0-99). This describes whether the device is in a special operational mode. 0 = normal operational mode; 80 hex = Memory save mode (memory is almost full and all activity is drastically reduced so the circular memory probably won't be overwritten or, if it does, it will be kept to a minimum)
vbat float Battery voltage in V (0-~4.200V)
logb integer logged bytes, waiting for download (0-4Mbyte)
logp smallint Logged percentage (units 0.1%) of memory waiting to be downloaded (0-1000)
gpsii integer GpsIval, current (0-65535)
comii integer ComIval, current (0-65535)
accii integer AcceleroIval, current (0-65535)
swddd integer User switches, current (0-65535)
last_gps_fix timestamp timestamp of last fix
latitude float Latitude of last fix. Decimal degrees
longitude float Longitude of last fix. Decimal degrees


UVA_SETTINGS101 or UVA_SETTINGS_LIMITED

Settings are either from C0-C1-C9 lines or parsed from uplink communication lines If C0-C1 is parsed its values are compared with the previous value and if the settings are the same no new records needs to be added If uplink settings are parsed wait till the last setting has been seen, (DL command or EOF) then store all the new settings in one record. Only for newer firmware.

Field Type Key Constraints Comments
device_info_serial int4 PK NOT NULL
date_time timestamp PK NOT NULL Derive timestamp from Hh:mi fields in C0 combined with computer timestamp in JOINED line
timesynced smallint
timezone_time smallint
swddd integer SpecialUserSwitches
gpsnavmode smallint GpsNavMode 0-8. This is the Kalman filter used for GPS navigation mode often called the "Dynamic platform model". The following codes are provided by the GPS chip manufacturer for the UBlox GPS chip LEAS4S: 1 = stationary, 2 = pedestrian, 3 = automotive, 4 = sea, 5 = airborne 1G, 6 = airborne 2G, 7 = airborne 3G. The UBlox GPS chip LEAS6S uses the following codes: 0 = portable, 2 = stationary, 3 = pedestrian, 4 = automotive, 5 = sea, 6 = airborne with < 1g acceleration, 7 = airborne with < 2g acceleration, 8 = airborne with < 4g acceleration
gpsreceivermode smallint GpsReceiverNode 0-3
gpsfixtime smallint GpsFixTime 0-255
gps_ivaln_on_h smallint hours Gps IvalN on
gps_ivaln_on_m smallint minutes Gps IvalN on
gps_ivaln integer GpsIvalN (0-65530)
gps_ivale_on_h smallint hours Gps IvalE on
gps_ivale_on_m smallint minutes GpS IvalE on
gps_ivale integer GpsIvalE
com_ivaln_on_h smallint hours Com IvalN on
com_ivaln_on_m smallint minutes Com IvalN on
com_ivaln integer ComIvalN (0-65530)
com_ivale_on_h smallint hours Com IvalE on
com_ivale_on_m smallint minutes Com IvalE on
com_ivale integer ComIvalE
accii integer Accelero measurement interval
accbn integer Accelero number of blocks
accsn integer Accelero number of samples (0-65536)
f smallint Accelero sample frequency (0=20Hz, 1=10Hz, 2=5Hz, 3=1Hz)
pdp smallint PdopMsk (3-250)
pac smallint PaccMsk (10-100)
tdp smallint TdopMsk (3-250)
tac smallint TaccMsk (30-300)
ga smallint Additional Fixes GpsIval mode (3-25) before interval fix is logged
aol smallint AccMemOffLev (100 - 950) units 0.1%; if Memfull above this level all Accelero activity will be overruled and switched off untill MemFull < level - 5
eventnum text 12 eventnumbers (0-0xff) only printed if not zero, therfore converted to text


UVA_ENERGY101 or UVA_ENERGY_LIMITED

Only for newer firmware.

Field Type Key Constraints Comments
device_info_serial int4 PK NOT NULL
date_time timestamp PK NOT NULL
timesynced smallint TimeSynced (0=not synced, 1=user set, 2=Gps synced)
devicemode smallint (0-99)
vsll float Solar Voltage during charging in mV (0-~2500)
vbat float Battery Voltage in V (0-~4.200)
ssw smallint Solar Cell Switches ... (0-255) fw1022 and up
extended fields if special user switch is on
vsoo float Solar voltage open in V (0-~2.500)
vdrf float reference voltage Dac in V (0-~2.435)
vchr float charge current voltage
g smallint Gps battery threshold OK
c smallint Com battery threshold OK
m smallint Charge Mode (0,1,2 Com battery threshold OK
pressure integer in pascal (1mBar = 100Pa, 1pressuremeter = ~12Pa)
temperature float in celcius degrees


UVA_WARNING102 or UVA_WARNING_LIMITED

Since firmware version 1.0.2.7 this table was added as catchall for tags that do not occur very often (C10, C20) or errors that occur during parsing. For example all CRC failures can be selected with : 

 select * from gps.uva_warning102 
 where warning = 'CRC8 failure'
 order by device_info_serial;
Field Type Key Constraints Comments
device_info_serial integer PK NOT NULL
filename text PK NOT NULL UvAGPS log filename
linenumber integer PK NOT NULL linenumber in file
warning text The warming message or tag
line text The actual line in the file


UVA_INDIVIDUAL or UVA_INDIVIDUAL_LIMITED

Table includes important information used to identify an individual tracked with a GPS tag. Remarks can also include a URL linking to a file with additional information about the individual (eg additional biometric measurements)

Field Type Key Constraints Comments
ring_number text PK NOT NULL metal ring number
color_ring text code for color ring without punctuation
species text NOT NULL Scientific name of species
sex text update if or when known
mass float mass of bird at start of tracking session
Remarks text If additional information of this individual is available please provide the file with relevant data (eg biometric data). This field should include the file name and extension


UVA_NEST or UVA_NEST_LIMITED

Table includes information, if available, used to identify the nest of an individual tracked with a GPS tag.

Field Type Key Constraints Comments
ring_number text FK NOT NULL metal ring number
nest_id text FK individual code for nest or territory
date_time timestamp Timestamp without time zone (UTC) when nest first marked yyyy-mm-dd hh:mm:ss
latitude float latitude of nest or territory (decimal degrees)
longitude float longitude of nest or territory (decimal degrees)
Remarks text If additional breeding information is available please provide the file with relevant data. This field should include the file name and extension

UvAGPS functions

get_uvagps_track_speed

Compute distance (meters), time-interval (time stamp hh:mm:ss), speed (meters/second) and heading (degrees) for a series of subsequent tracking entries with specific device_info_serial. For the first entry in the sequence these values will always be missing because they are computed as the difference between subsequent rows.

Usage examples : 

select * from gps.get_uvagps_track_speed(119, '2008-01-01 00:00:00', '2010-01-01 00:00:00');

select * from gps.get_uvagps_track_speed(119);

select t.*, a.distance, a.interval, a.speed, a.direction 
from gps.get_uvagps_track_speed(119, '2008-01-01 00:00:00', '2010-01-01 00:00:00') a 
join gps.uva_tracking t using(device_info_serial, date_time);

Distances and heading are calculated with spherical correction with the Haversine formula as described here. The heading is the initial heading. PostGIS does not calculate the heading, so therefore we don't use PostGIS.

In these functions the records that have been flagged as invalid by setting the userflag to 1 are not taken into account and discarded. If speed calculations are required for all records an additional boolean argument get raw data can be given. i.e. 

select * from gps.get_uvagps_track_speed(119, '2008-01-01 00:00:00', '2010-01-01 00:00:00', true);

select * from gps.get_uvagps_track_speed(119, true);

get_uvagps_track_distance

Compute distance (meters) for UvAGPS tracks to arbitrary point in lat/long or geometry location

Example usage : 

select * from gps.get_uvagps_track_distance(119, 52.1897017, 6.1996606); 

select * from gps.get_uvagps_track_distance(119, (select location from gps.uva_tracking where device_info_serial = 119 and date_time = '2009-05-07 19:55:08'));

Here the distance is calculated with the PostGIS distance_sphere function which uses spherical correction.

get_uvagps_track_distance_direction

Compute distance (meters) and direction (degrees) for UvAGPS tracks from arbitrary point in lat/long or geometry location

Example usage: 

select * from gps.get_uvagps_track_distance_direction(119, 52.1897017, 6.1996606);

Distances and direction are calculated with spherical correction with the Haversine formula as described here. The direction is the direction from the given point.

In this function the records where the userflag has been set are discarded. To see these records a additional boolean argument for show raw data should be added like : 

select * from gps.get_uvagps_track_distance_direction(119, 52.1897017, 6.1996606, true);

Accelerometer calibration

The accelerometer measures the acceleration in 3D (20 times per second). Acceleration is caused by gravity (static component) and by a change in speed (dynamic component). When the logger is static in horizontal position (solar cells up), gravity (green arrow) shows a heave (vertical acceleration, z) of +1 g (1 g = 9.81 m.s-2) while surge and heave are both 0. When the front of the logger is vertically pointing down (forward acceleration, x), surge is +1g and when it is rolled to the right (sidewards acceleration, y) sway is +1g. Due to gravity, the pitch of a logger is thus translated into the values of heave, surge and sway (or z, x, y).

However, the values are measured in mV instead of g. Before delivering the GPS-loggers, they have been calibrated at UvA. The acceleration (A) expressed in g is calculated from the measured value (M) and the calibration factors offset (O) and sensitivity (S).

Thus acceleration for heave (z), surge (x) and sway (y) is calculated as: Az = (Mz-Oz)/Sz ; Ax = (Mx-Ox)/Sx; Ay = (My-Oy)/Sy ;

The values of O (in general ranging from 0-60, sometimes even 300) and S (ranging from 1300-1450) are available in the device table of the data base. If not available, use the factory defaults O = 0 and S = 1365.

Accelero1.png Accelero2.png|

In the figure above heave (z) is shown in green, surge(x) in red and sway (y) in blue, all values are expressed in g (on the y-axis).


Data processing and filtering

The raw log files are processed before being entered into the database. Each firmware version has a dedicated parser for the task. In certain cases data that is found in the log files is not stored in the database. This can occur for two reasons:

1. The data did not pass the CRC8 checksum (cyclic redundancy check). This is a standard procedure designed to detect accidental changes to raw computer data.

2. If the data has an invalid signature. For example, if a certain data format (eg numeric) or number of values (eg 4 digits) is expected but not returned, this record is not stored in the database.

When a line is deleted, the log file name, line number and the type of error is stored in the table gps.uva_warning102


Information about GPS receivers

The first series of tags used the UBlox LEAS4S chip (~up to tag 541), newer tags use UBlox LEAS6S. The series developed in 2012 will use the Max6G receivers. From 2012 receiver versions will be stored in the database. The UBX protocol is used for programming firmware, packaging and processing data. For more information about the receivers themselves see the ublox documentation. Ublox 4 Protocol specification [1] Ublox 6 Protocol specification [2]

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