py_eddy_tracker.observations.tracking.TrackEddiesObservations

class py_eddy_tracker.observations.tracking.TrackEddiesObservations(*args, **kwargs)

Bases: GroupEddiesObservations

Class to practice Tracking on observations

Methods

add_distance	Add a field of distance (m) between two consecutive observations, 0 for the last observation of each track
add_fields	Add a new field.
add_rotation_type
align_on	Align the variable indices of two datasets.
append	Merge.
basic_formula_ellipse_major_axis	Give major axis in km with a given latitude
bins_stat	param str,array xname variable to compute stats on
box_display	Return values evenly spaced with few numbers
build_var_list
circle_contour	Set contours as circles from radius and center data.
close_tracks	Get close trajectories from another atlas.
coherence	Check coherence between two datasets.
compare_units
compute_index	If obs are not sorted by track, __first_index_of_track will be unusable
concatenate
contains	Return index of contour containing (x,y)
copy
copy_data_to_zarr	Copy with buffer for zarr.
cost_function	Return the cost function between two obs.
cost_function_common_area	How does it work on x bound ?
count_by_track	Count by track
create_particles	Create particles inside contour (Default : speed contour).
create_variable
create_variable_zarr
display	Plot the speed and effective (dashed) contour of the eddies
display_color	Plot colored contour of eddies
display_shape	This function draws the shape of each trajectory
distance	Use haversine distance for distance matrix between every self and other eddies.
distance_to_next	return array of distance in m, 0 when next obs is from another track
empty_dataset
extract_first_obs_in_box
extract_ids
extract_in_direction
extract_longer_eddies	Select the trajectories longer than nb_min
extract_toward_direction	Get trajectories going in the same direction
extract_with_area	Extract geographically with a bounding box.
extract_with_length	Return the observations within trajectories lasting between [b0:b1]
extract_with_mask	Extract a subset of observations
extract_with_period	Extract within a time period
field_table	Produce description table of the fields available in this object
fill_coherence	_summary_
filled	param matplotlib.axes.Axes ax matplotlib axe used to draw
filled_by_interpolation	Fill selected values by interpolation
first_obs	Get first obs of each trajectory.
fix_next_previous_obs	Function used after 'insert_virtual', to correct next_obs and previous obs.
fixed_ellipsoid_mask
follow_obs	Associate the observations to the segments
format_label
from_array
from_netcdf
from_zarr
get_azimuth	Return azimuth for each track.
get_color	Return colors as a cyclic list
get_filters_zarr	Get filters to store in zarr for known variable
get_infos
get_mask_from_id
get_missing_indices	Find indices where observations are missing.
get_next_obs	Forward association of observations to the segments
get_previous_obs	Backward association of observations to the segments
grid_box_stat	Get percentile of eddies in each bin
grid_count	Count the eddies in each bin (use all pixels in each contour)
grid_stat	Return the mean of the eddies' variable in each bin
hist	Build histograms.
index	Return obs from self at the index.
insert_observations	Insert other obs in self at the given index.
insert_virtual	Insert virtual observations on segments where observations are missing
inside	True for each point inside the effective contour of an eddy
intern
interp_grid	Interpolate a grid on a center or contour with mean, min or max method
is_convex	Get flag of the eddy's convexity
iter_on	Yield observation group for each bin.
iter_track	Yield track
keep_tracks_by_date	Find tracks that exist at date date and lasted at least nb_days after.
last_obs	Get Last obs of each trajectory.
load_file	Load the netcdf or the zarr file.
load_from_netcdf	Load data from netcdf.
load_from_zarr	Load data from zarr.
loess_filter
mask_from_polygons	Return mask for all observations in one of polygons list
mask_function
match	Return index and score computed on the effective contour.
median_filter
merge	Merge two datasets.
merge_filters	Compute an intersection between all filters after to evaluate each of them
merge_particle_result	Copy local result in merged result with global indexation
needed_variable
netcdf_create_dimensions
new_like
normalize_longitude	Normalize all longitudes
obs_dimension
parse_varname
particle_candidate_atlas	Select particles within eddies, advect them, return target observation and associated percentages
plot	This function will draw path of each trajectory
position_filter
post_process_link
propagate	Fill virtual obs (C).
re_reference_index	Shift index with ref
remove_fields	Copy with fields listed remove
reset
scatter	Scatter data.
set_global_attr_netcdf	Set global attributes
set_global_attr_zarr
set_tracks	Split one group (network) in segments
shape_polygon	Get the polygon enclosing each trajectory.
shifted_ellipsoid_degrees_mask
solve_conflict
solve_first
solve_function
solve_simultaneous	Deduce link from cost matrix.
split_network	Return each group (network) divided in segments
time_sub_sample	Time sub sampling
to_netcdf
to_zarr
track_slice
tracking	Track obs between self and other
write_file	Write a netcdf or zarr with eddy obs.
zarr_dimension

Attributes

COLORS
ELEMENTS
NB_COLORS
NOGROUP
age	Return age in % for each observation, will be [0:100]
array_variables
dtype	Return dtype to build numpy array.
elements	Return all the names of the variables.
fields
global_attr
index_from_track
lifetime	Return lifetime for each observation
nb_days	Return period in days covered by the dataset
nb_obs_by_track
nb_tracks	Count and return number of track
obs	Return observations.
observations
only_variables
period	Give the time coverage.
period_
raw_data
shape
sign_legend
sign_type
track_array_variables
track_extra_variables
tracks

ELEMENTS = ['lon', 'lat', 'radius_s', 'radius_e', 'speed_area', 'effective_area', 'amplitude', 'speed_average', 'time', 'shape_error_e', 'shape_error_s', 'nb_contour_selected', 'num_point_e', 'num_point_s', 'height_max_speed_contour', 'height_external_contour', 'height_inner_contour', 'cost_association']

NOGROUP = 0

add_distance()

Add a field of distance (m) between two consecutive observations, 0 for the last observation of each track

property age

Return age in % for each observation, will be [0:100]

close_tracks(other, nb_obs_min=10, **kwargs)

Get close trajectories from another atlas.

Parameters

• other (self) – Atlas to compare

• nb_obs_min (int) – Minimal number of overlap for one trajectory

• kwargs (dict) – keyword arguments for match function

Returns

return other atlas reduced to common trajectories with self

Warning

It could be a costly operation for huge dataset

compute_index()

If obs are not sorted by track, __first_index_of_track will be unusable

classmethod concatenate(observations)

count_by_track(mask)

Count by track

Parameters

mask (array[bool]) – Mask of boolean count +1 if true

Returns

Return count by track

Return type

array

display_shape(ax, ref=None, intern=False, **kwargs)

This function draws the shape of each trajectory

Parameters

• ax (matplotlib.axes.Axes) – ax to draw

• ref (float,int) – if defined, all coordinates are wrapped with ref as western boundary

• intern (bool) – If True use speed contour instead of effective contour

• kwargs (dict) – keyword arguments for Axes.plot

Returns

matplotlib mappable

distance_to_next()

Returns

array of distance in m, 0 when next obs is from another track

Return type

array

property elements

Return all the names of the variables.

extract_first_obs_in_box(res)

extract_ids(tracks)

extract_in_direction(direction, value=0)

extract_longer_eddies(nb_min, nb_obs, compress_id=True)

Select the trajectories longer than nb_min

extract_toward_direction(west=True, delta_lon=None)

Get trajectories going in the same direction

Parameters

• west (bool) – Only eastward eddies if True return westward

• delta_lon (None,float) – Only eddies with more than delta_lon span in longitude

Returns

Only eastern eddy

Return type

__class__

extract_with_length(bounds)

Return the observations within trajectories lasting between [b0:b1]

Parameters

bounds ((int,int)) – length min and max of the desired trajectories, if -1 this bound is not used

Returns

Return all trajectories having length between bounds

Return type

TrackEddiesObservations

Display fields

Display fields

Display Tracks

Display Tracks

extract_with_mask(mask, full_path=False, remove_incomplete=False, compress_id=False, reject_virtual=False)

Extract a subset of observations

Parameters

• mask (array(bool)) – mask to select observations

• full_path (bool) – extract the full trajectory if only one part is selected

• remove_incomplete (bool) – delete trajectory if not fully selected

• compress_id (bool) – resample trajectory number to use a smaller range

• reject_virtual (bool) – if only virtuals are selected, the trajectory is removed

Returns

same object with the selected observations

Return type

self.__class__

extract_with_period(period, **kwargs)

Extract within a time period

Parameters

• period ((int,int)) – two dates to define the period, must be specified from 1/1/1950

• kwargs (dict) – look at extract_with_mask()

Returns

Return all eddy tracks in period

Return type

TrackEddiesObservations

fix_next_previous_obs()

Function used after ‘insert_virtual’, to correct next_obs and previous obs.

classmethod follow_obs(i_next, track_id, used, ids, *args, **kwargs)

Associate the observations to the segments

format_label(label)

get_azimuth(equatorward=False)

Return azimuth for each track.

Azimuth is computed with first and last observations

Parameters

equatorward (bool) – If True, Poleward is positive and Equatorward negative

Return type

array

get_mask_from_id(tracks)

get_missing_indices(dt)

Find indices where observations are missing.

Parameters

dt (int,float) – theorical delta time between 2 observations

static get_next_obs(i_current, ids, x, y, time_s, time_e, time_ref, window, min_overlap=0.2, **kwargs)

Forward association of observations to the segments

static get_previous_obs(i_current, ids, x, y, time_s, time_e, time_ref, window, min_overlap=0.2, **kwargs)

Backward association of observations to the segments

property index_from_track

iter_track()

Yield track

property lifetime

Return lifetime for each observation

loess_filter(half_window, xfield, yfield, inplace=True)

median_filter(half_window, xfield, yfield, inplace=True)

property nb_obs_by_track

property nb_tracks

Count and return number of track

normalize_longitude()

Normalize all longitudes

Normalize longitude field and in the same range : - longitude_max - contour_lon_e (how to do if in raw) - contour_lon_s (how to do if in raw)

plot(ax, ref=None, **kwargs)

This function will draw path of each trajectory

Parameters

• ax (matplotlib.axes.Axes) – ax to draw

• ref (float,int) – if defined, all coordinates are wrapped with ref as western boundary

• kwargs (dict) – keyword arguments for Axes.plot

Returns

matplotlib mappable

position_filter(median_half_window, loess_half_window)

set_global_attr_netcdf(h_nc)

Set global attributes

set_tracks(x, y, ids, window, **kwargs)

Split one group (network) in segments

Parameters

• x (array) – coordinates of group

• y (array) – coordinates of group

• ids (ndarray) – several fields like time, group, …

• window (int) – number of days where observations could missed

shape_polygon(intern=False)

Get the polygon enclosing each trajectory.

The polygon merges the non-overlapping bounds of the specified contours

Parameters

intern (bool) – If True use speed contour instead of effective contour

Return type

list(array, array)

split_network(intern=True, **kwargs)

Return each group (network) divided in segments

track_slice(track)