Divebomb¶

Divebomb is a python package that uses pandas to divide a timeseries of depths into individual dives. The dives are profiled as a Dive or DeepDive depending on the animal. The Dive class is used for frequently surfacing animals, such as seals and whales. The DeepDive class is used for infrequently surfaceing animals, like sharks.

The dive profiles are reduced to 8 dimensions using Principal Component Analsysis. Guassian Mixed Models are generated using theses variables and the minimal Bayesian Information Criterion is used to determine the optimal number of clusters. The dives are split into the clusters using Agglomerative Hierarchical Clustering (from sklearn). The dives are then display through iPython notebooks or saved to netCDF files organized by cluster.

Dive¶

A Dive is then profiled with the following attributes:

max_depth - the max depth in the dive
dive_start - the timestamp of the first point in the dive
dive_end - the timestamp of the last point in the dive
bottom_start - the timestamp of the first point in the dive when the animal is at depth
td_bottom_duration - a timedelta object containing the duration of the time the animal is at depth in seconds
td_descent_duration - a timedelta object containing the duration of the time the animal is descending in seconds
td_ascent_duration - a timedelta object containing the duration of the time the animal is ascending in seconds
td_surface_duration - a timedelta object containing the duration of the time the animal is at the surface in seconds
bottom_variance - the variance of the depth while the animal is at the bottom of the dive
dive_variance - the variance of the depth for the entire dive.
descent_velocity - the average velocity of the descent
ascent_velocity - the average velocity of the descent
peaks - the number of peaks found in the dive profile
left_skew - a boolean of 1 or 0 indicating if the dive is left skewed
right_skew - a boolean of 1 or 0 indicating if the dive is right skewed
no_skew - a boolean of 1 or 0 indicating if the dive is not skewed

DeepDive¶

A DeepDive is then profiled with the following attributes:

max_depth - the max depth in the dive
min_depth - the max depth in the dive
dive_start - the timestamp of the first point in the dive
dive_end - the timestamp of the last point in the dive
td_total_duration - a timedelta (in seconds since 1970-01-01) containing the duration of the dive
depth_variance - the variance of the depth for the entire dive.
average_vertical_velocity - the mean velocity of the animal over the entire dive with negative value indicating upward movement
average_descent_velocity - the average velocity of any downward movement as positive value
average_ascent_velocity - the average velocity of any upward movement as positive value
number_of_descent_transitions - the number of times and animal moves descends any distance in the dive period
number_of_ascent_transitions - the number of times and animal moves ascends any distance in the dive period
total_descent_distance_traveled - the total absolute distance in meters in which the anaimal moves down
total_ascent_distance_traveled - the total absolute distance in meters in which the anaimal moves up
overall_change_in_depth - the difference between the minimum and maximum depth within the dive period
td_time_at_depth - the duration in seconds at which the animal spends in the deepest part of the vertical movement (< 85% depth)
td_time_pre_depth - the duration in seconds befor the deepest part of the vertical movement (< 85% depth)
td_time_post_depth - the duration in seconds after the deepest part of the vertical movement (< 85% depth)
peaks - the number of peaks found in the dive profile
left_skew - a boolean of 1 or 0 indicating if the dive is left skewed
right_skew - a boolean of 1 or 0 indicating if the dive is right skewed
no_skew - a boolean of 1 or 0 indicating if the dive is not skewed

Surface Thresholds¶

A surface threshold is used for surfacing animals to define a depth window for what is considered to be at surface. The surface_threshold argument defaults to 0 but can be changed in the profile_dives() function. For example surface_threshold=2 might be passed for animal that is ~2 meters long. surface_threshold is always passed in meters.

At Depth Thresholds¶

An at depth threshold is used in both the Dive and the DeepDive class. The at_depth_thresold argument is a value between 0 and 1 that determines the window for when an animal is considered to be at bottom of its dive. The default value is 0.15 which means the bottom 15% of the relative depth is considered to be at bottom. at_depth_thresold is always as value between 0 and 1 expressing a percentage.

Dive Detection¶

There are two arguments that are used to help determine dives on any animal, dive_detection_sensitivity and minimal_time_between_dives. The dive_detection_sensitivity argument is a value between 0 and 1. The default is 0.98 for surfacing animals and 0.5 for non-surfacing animals. The dive_detection_sensitivity helps determine range where dive starts can be determined. The minimal_time_between_dives is the minimum time (in seconds) that has to occur before a new dive can start. The default value for this is 10 seconds.

Skews¶

A skew is defined as any difference one way or the other in descent or ascent times for the Dive class and any difference in pre-depth or post-depth time for a DeepDive. This method was chosen as researchers found skew was most accurately represented when any difference between the values existed.

Timestamps¶

The input timestamps are expected to be in a datetime format. The output timestamps are in seconds since 1970-01-01. Every netCDF file has the time unit saved as an attribute as a reminder. All dive attributes that start with td_ are a duration in seconds. The time, dive_start, dive_end, and bottom_start will use the units mentioned above. the netCDF4 library has a num2date function that will convert the values back to a datetime object.