Gallery#
These demo plots and animations were created with standard postprocessing plot methods.
Particle properties#
Particle properties can easily add to computation via parameters, eg decaying concentrations, by listing in particle_properties parameters. Standard properties include, status, tide, water_depth and particle age.
Decaying particle#
Decaying particle property used to size and colour particles. decay_time_scale parameter = 3.5 hours.
particle_properties.age_decay.AgeDecaydemo60_SCHISM_3D_decaying_particle.py
json parameters
/../dev/demo_param_files/demo60_SCHISM_3D_decaying_particle.json#
{
"output_file_base": "demo60_SCHISM_3D_decaying_particle",
"debug": true,
"time_step": 120,
"NUMBA_cache_code": false,
"use_A_Z_profile": false,
"regrid_z_to_uniform_sigma_levels": true,
"reader": {
"input_dir": "C:\\Auck_work\\oceantracker\\tutorials_how_to\\demo_hindcast",
"file_mask": "demo_hindcast_schisim3D_00.nc",
"load_fields": [
"water_temperature"
]
},
"dispersion": {
"A_H": 0.2,
"A_V": 0.001
},
"release_groups": [
{
"name": "P1",
"points": [
[
1594500,
5487000,
-1
],
[
1594500,
5483000,
-1
],
[
1598000,
5486100,
-1
]
],
"pulse_size": 1,
"release_interval": 150.0,
"max_age": 17280.000000000004
}
],
"particle_properties": [
{
"name": "age_decay",
"class_name": "oceantracker.particle_properties.age_decay.AgeDecay",
"decay_time_scale": 25714.28571428571
}
]
}
yaml parameters
/../dev/demo_param_files/demo60_SCHISM_3D_decaying_particle.yaml#
NUMBA_cache_code: false
debug: true
dispersion:
A_H: 0.2
A_V: 0.001
output_file_base: demo60_SCHISM_3D_decaying_particle
particle_properties:
- class_name: oceantracker.particle_properties.age_decay.AgeDecay
decay_time_scale: 25714.28571428571
name: age_decay
reader:
file_mask: demo_hindcast_schisim3D_00.nc
input_dir: C:\Auck_work\oceantracker\tutorials_how_to\demo_hindcast
load_fields:
- water_temperature
regrid_z_to_uniform_sigma_levels: true
release_groups:
- max_age: 17280.000000000004
name: P1
points:
- - 1594500
- 5487000
- -1
- - 1594500
- 5483000
- -1
- - 1598000
- 5486100
- -1
pulse_size: 1
release_interval: 150.0
time_step: 120
use_A_Z_profile: false
Polygon aware particles#
Particles with additional inside polygon property, with optional logging of polygon entry and exit events
class:
particle_properties.inside_polygons.InsidePolygonsNonOverlapping2Dclass:
event_loggers.log_polygon_entry_and_exit.LogPolygonEntryAndExit
json parameters
/../dev/demo_param_files/demo07_inside_polygon_events.json#
{
"output_file_base": "demo07_inside_polygon_events",
"root_output_dir": "C:\\Auck_work\\oceantracker_output\\demos",
"add_date_to_run_output_dir": false,
"NUMBA_cache_code": false,
"time_buffer_size": 15,
"time_step": 600,
"debug": true,
"reader": {
"input_dir": "C:\\Auck_work\\oceantracker\\tutorials_how_to\\demo_hindcast",
"file_mask": "Random_order_*.nc"
},
"user_note": "test of notes",
"dispersion": {
"A_H": 0.1
},
"tracks_writer": {
"write_dry_cell_flag": true
},
"release_groups": [
{
"name": "P1",
"points": [
[
1594500,
5490000
],
[
1598000,
5488500
]
],
"pulse_size": 10,
"release_interval": 10800
}
],
"particle_properties": [
{
"name": "age_decay",
"class_name": "oceantracker.particle_properties.age_decay.AgeDecay",
"decay_time_scale": 86400.0
}
],
"block_dry_cells": true,
"event_loggers": [
{
"name": "in_out_poly",
"class_name": "oceantracker.event_loggers.log_polygon_entry_and_exit.LogPolygonEntryAndExit",
"particle_prop_to_write_list": [
"ID",
"x",
"IDrelease_group",
"status",
"age"
],
"polygon_list": [
{
"user_polygon_name": "A",
"points": [
[
1592682.1237,
5489972.7479
],
[
1593604.1667,
5490275.5488
],
[
1593886.4247,
5489464.0424
],
[
1592917.3387,
5489000.0
],
[
1592300.0,
5489000.0
],
[
1592682.1237,
5489972.7479
]
]
},
{
"user_polygon_name": "B",
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5487000
],
[
1597300,
5487000
],
[
1597682.1237,
5489972.7479
]
]
}
]
}
]
}
yaml parameters
/../dev/demo_param_files/demo07_inside_polygon_events.yaml#
NUMBA_cache_code: false
add_date_to_run_output_dir: false
block_dry_cells: true
debug: true
dispersion:
A_H: 0.1
event_loggers:
- class_name: oceantracker.event_loggers.log_polygon_entry_and_exit.LogPolygonEntryAndExit
name: in_out_poly
particle_prop_to_write_list:
- ID
- x
- IDrelease_group
- status
- age
polygon_list:
- points:
- - 1592682.1237
- 5489972.7479
- - 1593604.1667
- 5490275.5488
- - 1593886.4247
- 5489464.0424
- - 1592917.3387
- 5489000.0
- - 1592300.0
- 5489000.0
- - 1592682.1237
- 5489972.7479
user_polygon_name: A
- points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5487000
- - 1597300
- 5487000
- - 1597682.1237
- 5489972.7479
user_polygon_name: B
output_file_base: demo07_inside_polygon_events
particle_properties:
- class_name: oceantracker.particle_properties.age_decay.AgeDecay
decay_time_scale: 86400.0
name: age_decay
reader:
file_mask: Random_order_*.nc
input_dir: C:\Auck_work\oceantracker\tutorials_how_to\demo_hindcast
release_groups:
- name: P1
points:
- - 1594500
- 5490000
- - 1598000
- 5488500
pulse_size: 10
release_interval: 10800
root_output_dir: C:\Auck_work\oceantracker_output\demos
time_buffer_size: 15
time_step: 600
tracks_writer:
write_dry_cell_flag: true
user_note: test of notes
Particle Status#
Particles coloured by their status property. Status can be one of following strings
['unknown', 'bad_cord', 'cell_search_failed', 'notReleased', 'dead', 'outside_open_boundary', 'frozen', 'stranded_by_tide', 'on_bottom', 'moving']
json parameters
/../dev/demo_param_files/demo56_SCHISM_3D_resupend_crtitical_friction_vel.json#
{
"output_file_base": "demo56_SCHISM_3D_resupend_crtitical_frictn_vel",
"debug": true,
"time_step": 120,
"NUMBA_cache_code": false,
"use_A_Z_profile": false,
"regrid_z_to_uniform_sigma_levels": true,
"reader": {
"input_dir": "C:\\Auck_work\\oceantracker\\tutorials_how_to\\demo_hindcast",
"file_mask": "demo_hindcast_schisim3D_00.nc",
"load_fields": [
"water_temperature"
]
},
"dispersion": {
"A_H": 0.2,
"A_V": 0.001
},
"release_groups": [
{
"name": "poly1",
"class_name": "oceantracker.release_groups.polygon_release.PolygonRelease",
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5489000
],
[
1597300,
5489000
],
[
1597682.1237,
5489972.7479
]
],
"z_min": -1,
"z_max": -1,
"release_interval": 3660,
"start": "2017-01-01T00:31:30",
"pulse_size": 10
},
{
"name": "P1",
"points": [
[
1594500,
5487000,
-1
],
[
1594500,
5483000,
-1
],
[
1598000,
5486100,
-1
]
],
"release_interval": 3600,
"pulse_size": 10
}
],
"particle_properties": [
{
"name": "age_decay",
"class_name": "oceantracker.particle_properties.age_decay.AgeDecay",
"decay_time_scale": 86400.0
}
],
"event_loggers": [
{
"name": "inoutpoly",
"class_name": "oceantracker.event_loggers.log_polygon_entry_and_exit.LogPolygonEntryAndExit",
"particle_prop_to_write_list": [
"ID",
"x",
"IDrelease_group",
"status",
"age"
],
"polygon_list": [
{
"user_polygon_name": "A",
"points": [
[
1592682.1237,
5489972.7479
],
[
1593604.1667,
5490275.5488
],
[
1593886.4247,
5489464.0424
],
[
1592917.3387,
5489000.0
],
[
1592300.0,
5489000.0
],
[
1592682.1237,
5489972.7479
]
]
},
{
"user_polygon_name": "B",
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5487000
],
[
1597300,
5487000
],
[
1597682.1237,
5489972.7479
]
]
}
]
}
],
"particle_statistics": [
{
"name": "grid1",
"class_name": "oceantracker.particle_statistics.gridded_statistics2D.GriddedStats2D_timeBased",
"update_interval": 3600,
"particle_property_list": [
"water_depth"
],
"status_list": [
"moving"
],
"z_min": -2,
"grid_span": [
10000,
10000
],
"grid_size": [
120,
121
]
}
],
"resuspension": {
"critical_friction_velocity": 0.005
},
"velocity_modifiers": [
{
"name": "terminal_velocity",
"class_name": "oceantracker.velocity_modifiers.terminal_velocity.TerminalVelocity",
"value": -0.001
}
]
}
yaml parameters
/../dev/demo_param_files/demo56_SCHISM_3D_resupend_crtitical_friction_vel.yaml#
NUMBA_cache_code: false
debug: true
dispersion:
A_H: 0.2
A_V: 0.001
event_loggers:
- class_name: oceantracker.event_loggers.log_polygon_entry_and_exit.LogPolygonEntryAndExit
name: inoutpoly
particle_prop_to_write_list:
- ID
- x
- IDrelease_group
- status
- age
polygon_list:
- points:
- - 1592682.1237
- 5489972.7479
- - 1593604.1667
- 5490275.5488
- - 1593886.4247
- 5489464.0424
- - 1592917.3387
- 5489000.0
- - 1592300.0
- 5489000.0
- - 1592682.1237
- 5489972.7479
user_polygon_name: A
- points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5487000
- - 1597300
- 5487000
- - 1597682.1237
- 5489972.7479
user_polygon_name: B
output_file_base: demo56_SCHISM_3D_resupend_crtitical_frictn_vel
particle_properties:
- class_name: oceantracker.particle_properties.age_decay.AgeDecay
decay_time_scale: 86400.0
name: age_decay
particle_statistics:
- class_name: oceantracker.particle_statistics.gridded_statistics2D.GriddedStats2D_timeBased
grid_size:
- 120
- 121
grid_span:
- 10000
- 10000
name: grid1
particle_property_list:
- water_depth
status_list:
- moving
update_interval: 3600
z_min: -2
reader:
file_mask: demo_hindcast_schisim3D_00.nc
input_dir: C:\Auck_work\oceantracker\tutorials_how_to\demo_hindcast
load_fields:
- water_temperature
regrid_z_to_uniform_sigma_levels: true
release_groups:
- class_name: oceantracker.release_groups.polygon_release.PolygonRelease
name: poly1
points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5489000
- - 1597300
- 5489000
- - 1597682.1237
- 5489972.7479
pulse_size: 10
release_interval: 3660
start: '2017-01-01T00:31:30'
z_max: -1
z_min: -1
- name: P1
points:
- - 1594500
- 5487000
- -1
- - 1594500
- 5483000
- -1
- - 1598000
- 5486100
- -1
pulse_size: 10
release_interval: 3600
resuspension:
critical_friction_velocity: 0.005
time_step: 120
use_A_Z_profile: false
velocity_modifiers:
- class_name: oceantracker.velocity_modifiers.terminal_velocity.TerminalVelocity
name: terminal_velocity
value: -0.001
Trajectory modifiers#
Trajectory modifiers classes change the path of particles, examples from standard trajectory_modifiers classes below.
Particle behaviour#
Particles with a random fraction temporarily frozen on a polygon shaped reef.
class:
trajectory_modifiers.settlement_in_polygon.SettleInPolygon
json parameters
/../dev/demo_param_files/demo06_reefstranding.json#
{
"output_file_base": "demo06_reefstranding",
"root_output_dir": "C:\\Auck_work\\oceantracker_output\\demos",
"add_date_to_run_output_dir": false,
"NUMBA_cache_code": false,
"time_buffer_size": 15,
"time_step": 600,
"debug": true,
"reader": {
"input_dir": "C:\\Auck_work\\oceantracker\\tutorials_how_to\\demo_hindcast",
"file_mask": "Random_order_*.nc"
},
"user_note": "test of notes",
"dispersion": {
"A_H": 0.1
},
"tracks_writer": {
"write_dry_cell_flag": true
},
"release_groups": [
{
"name": "P1",
"points": [
[
1594500,
5482700
],
[
1598000,
5486100
],
[
1595500,
5489700
]
],
"pulse_size": 10,
"release_interval": 10800
},
{
"name": "poly1",
"class_name": "oceantracker.release_groups.polygon_release.PolygonRelease",
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5489000
],
[
1597300,
5489000
],
[
1597682.1237,
5489972.7479
]
],
"pulse_size": 1,
"release_interval": 0
}
],
"particle_properties": [
{
"name": "Oxygen",
"class_name": "AgeDecay",
"decay_time_scale": 86400.0,
"initial_value": 20.0
},
{
"name": "distance_travelled",
"class_name": "DistanceTravelled"
},
{
"name": "age_decay",
"class_name": "AgeDecay",
"decay_time_scale": 86400.0
},
{
"name": "my_constant_prop",
"class_name": "ParticleLoad",
"initial_value": 100
}
],
"block_dry_cells": true,
"trajectory_modifiers": [
{
"name": "settle_in_polygon",
"class_name": "oceantracker.trajectory_modifiers.settle_in_polygon.SettleInPolygon",
"polygon": {
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5489000
],
[
1597300,
5489000
],
[
1597682.1237,
5489972.7479
]
]
},
"probability_of_settlement": 0.1,
"settlement_duration": 10800.0
}
],
"backtracking": true,
"particle_statistics": [
{
"name": "polystats1",
"class_name": "oceantracker.particle_statistics.polygon_statistics.PolygonStats2D_timeBased",
"update_interval": 1800,
"particle_property_list": [
"water_depth"
],
"use_release_group_polygons": true,
"polygon_list": [
{
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5489000
],
[
1597300,
5489000
],
[
1597682.1237,
5489972.7479
]
]
}
]
}
]
}
yaml parameters
/../dev/demo_param_files/demo06_reefstranding.yaml#
NUMBA_cache_code: false
add_date_to_run_output_dir: false
backtracking: true
block_dry_cells: true
debug: true
dispersion:
A_H: 0.1
output_file_base: demo06_reefstranding
particle_properties:
- class_name: AgeDecay
decay_time_scale: 86400.0
initial_value: 20.0
name: Oxygen
- class_name: DistanceTravelled
name: distance_travelled
- class_name: AgeDecay
decay_time_scale: 86400.0
name: age_decay
- class_name: ParticleLoad
initial_value: 100
name: my_constant_prop
particle_statistics:
- class_name: oceantracker.particle_statistics.polygon_statistics.PolygonStats2D_timeBased
name: polystats1
particle_property_list:
- water_depth
polygon_list:
- points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5489000
- - 1597300
- 5489000
- - 1597682.1237
- 5489972.7479
update_interval: 1800
use_release_group_polygons: true
reader:
file_mask: Random_order_*.nc
input_dir: C:\Auck_work\oceantracker\tutorials_how_to\demo_hindcast
release_groups:
- name: P1
points:
- - 1594500
- 5482700
- - 1598000
- 5486100
- - 1595500
- 5489700
pulse_size: 10
release_interval: 10800
- class_name: oceantracker.release_groups.polygon_release.PolygonRelease
name: poly1
points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5489000
- - 1597300
- 5489000
- - 1597682.1237
- 5489972.7479
pulse_size: 1
release_interval: 0
root_output_dir: C:\Auck_work\oceantracker_output\demos
time_buffer_size: 15
time_step: 600
tracks_writer:
write_dry_cell_flag: true
trajectory_modifiers:
- class_name: oceantracker.trajectory_modifiers.settle_in_polygon.SettleInPolygon
name: settle_in_polygon
polygon:
points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5489000
- - 1597300
- 5489000
- - 1597682.1237
- 5489972.7479
probability_of_settlement: 0.1
settlement_duration: 10800.0
user_note: test of notes
Resuspension#
Particles with fall velocity and resuspension based on critical friction velocity.
class
trajectory_modifiers.resuspension.BasicResuspension
Vertical slice showing one example of a falling particle and resuspension, with particle on bottom during low flows around low and high tides. Blue line is particle status, 10= moving, 6 = on the bottom.
json parameters
/../dev/demo_param_files/demo58_bottomBounce.json#
{
"output_file_base": "demo58_bottomBounce",
"debug": true,
"time_step": 120,
"NUMBA_cache_code": false,
"use_A_Z_profile": false,
"regrid_z_to_uniform_sigma_levels": true,
"reader": {
"input_dir": "C:\\Auck_work\\oceantracker\\tutorials_how_to\\demo_hindcast",
"file_mask": "demo_hindcast_schisim3D_00.nc",
"load_fields": [
"water_temperature"
]
},
"dispersion": {
"A_H": 0.1,
"A_V": 0.005
},
"release_groups": [
{
"name": "P11",
"pulse_size": 10,
"release_interval": 0,
"points": [
[
1593000.0,
5486000.0,
-1
]
],
"release_at_surface": true
}
],
"particle_properties": [
{
"name": "age_decay",
"class_name": "oceantracker.particle_properties.age_decay.AgeDecay",
"decay_time_scale": 86400.0
}
],
"event_loggers": [
{
"name": "inoutpoly",
"class_name": "oceantracker.event_loggers.log_polygon_entry_and_exit.LogPolygonEntryAndExit",
"particle_prop_to_write_list": [
"ID",
"x",
"IDrelease_group",
"status",
"age"
],
"polygon_list": [
{
"user_polygon_name": "A",
"points": [
[
1592682.1237,
5489972.7479
],
[
1593604.1667,
5490275.5488
],
[
1593886.4247,
5489464.0424
],
[
1592917.3387,
5489000.0
],
[
1592300.0,
5489000.0
],
[
1592682.1237,
5489972.7479
]
]
},
{
"user_polygon_name": "B",
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5487000
],
[
1597300,
5487000
],
[
1597682.1237,
5489972.7479
]
]
}
]
}
],
"particle_statistics": [
{
"name": "grid1",
"class_name": "oceantracker.particle_statistics.gridded_statistics2D.GriddedStats2D_timeBased",
"update_interval": 3600,
"particle_property_list": [
"water_depth"
],
"status_list": [
"moving"
],
"z_min": -2,
"grid_span": [
10000,
10000
],
"grid_size": [
120,
121
]
}
],
"resuspension": {
"critical_friction_velocity": 0.005
},
"velocity_modifiers": [
{
"name": "terminal_velocity",
"class_name": "oceantracker.velocity_modifiers.terminal_velocity.TerminalVelocity",
"value": -0.002,
"variance": 0.0002
}
],
"backtracking": false
}
yaml parameters
/../dev/demo_param_files/demo58_bottomBounce.yaml#
NUMBA_cache_code: false
backtracking: false
debug: true
dispersion:
A_H: 0.1
A_V: 0.005
event_loggers:
- class_name: oceantracker.event_loggers.log_polygon_entry_and_exit.LogPolygonEntryAndExit
name: inoutpoly
particle_prop_to_write_list:
- ID
- x
- IDrelease_group
- status
- age
polygon_list:
- points:
- - 1592682.1237
- 5489972.7479
- - 1593604.1667
- 5490275.5488
- - 1593886.4247
- 5489464.0424
- - 1592917.3387
- 5489000.0
- - 1592300.0
- 5489000.0
- - 1592682.1237
- 5489972.7479
user_polygon_name: A
- points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5487000
- - 1597300
- 5487000
- - 1597682.1237
- 5489972.7479
user_polygon_name: B
output_file_base: demo58_bottomBounce
particle_properties:
- class_name: oceantracker.particle_properties.age_decay.AgeDecay
decay_time_scale: 86400.0
name: age_decay
particle_statistics:
- class_name: oceantracker.particle_statistics.gridded_statistics2D.GriddedStats2D_timeBased
grid_size:
- 120
- 121
grid_span:
- 10000
- 10000
name: grid1
particle_property_list:
- water_depth
status_list:
- moving
update_interval: 3600
z_min: -2
reader:
file_mask: demo_hindcast_schisim3D_00.nc
input_dir: C:\Auck_work\oceantracker\tutorials_how_to\demo_hindcast
load_fields:
- water_temperature
regrid_z_to_uniform_sigma_levels: true
release_groups:
- name: P11
points:
- - 1593000.0
- 5486000.0
- -1
pulse_size: 10
release_at_surface: true
release_interval: 0
resuspension:
critical_friction_velocity: 0.005
time_step: 120
use_A_Z_profile: false
velocity_modifiers:
- class_name: oceantracker.velocity_modifiers.terminal_velocity.TerminalVelocity
name: terminal_velocity
value: -0.002
variance: 0.0002
Splitting particles#
Particles with splitting in two every 6 hours and a 5% chance of dying every 6 hours.
class:
trajectory_modifiers.split_particles.SplitParticlesclass:
trajectory_modifiers.cull_particles.CullParticles
json parameters
/../dev/demo_param_files/demo08_particle_splitting.json#
{
"output_file_base": "demo08_particle_splitting",
"root_output_dir": "C:\\Auck_work\\oceantracker_output\\demos",
"add_date_to_run_output_dir": false,
"NUMBA_cache_code": false,
"time_buffer_size": 15,
"time_step": 600,
"debug": true,
"reader": {
"input_dir": "C:\\Auck_work\\oceantracker\\tutorials_how_to\\demo_hindcast",
"file_mask": "Random_order_*.nc"
},
"user_note": "test of notes",
"dispersion": {
"A_H": 0.1
},
"tracks_writer": {
"write_dry_cell_flag": true
},
"release_groups": [
{
"name": "P1",
"points": [
[
1594500,
5483500
],
[
1594500,
5486500
]
],
"pulse_size": 1,
"release_interval": 0
}
],
"particle_properties": [
{
"name": "age_decay",
"class_name": "oceantracker.particle_properties.age_decay.AgeDecay",
"decay_time_scale": 86400.0
}
],
"block_dry_cells": true,
"event_loggers": [
{
"name": "in_out_poly",
"class_name": "oceantracker.event_loggers.log_polygon_entry_and_exit.LogPolygonEntryAndExit",
"particle_prop_to_write_list": [
"ID",
"x",
"IDrelease_group",
"status",
"age"
],
"polygon_list": [
{
"user_polygon_name": "A",
"points": [
[
1592682.1237,
5489972.7479
],
[
1593604.1667,
5490275.5488
],
[
1593886.4247,
5489464.0424
],
[
1592917.3387,
5489000.0
],
[
1592300.0,
5489000.0
],
[
1592682.1237,
5489972.7479
]
]
},
{
"user_polygon_name": "B",
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5487000
],
[
1597300,
5487000
],
[
1597682.1237,
5489972.7479
]
]
}
]
}
],
"max_particles": 1000,
"trajectory_modifiers": [
{
"name": "part_spliting",
"class_name": "oceantracker.trajectory_modifiers.split_particles.SplitParticles",
"interval": 21600,
"statuses": [
"moving"
]
},
{
"name": "part_culling",
"class_name": "oceantracker.trajectory_modifiers.cull_particles.CullParticles",
"interval": 21600,
"statuses": [
"moving"
],
"probability": 0.05
}
]
}
yaml parameters
/../dev/demo_param_files/demo08_particle_splitting.yaml#
NUMBA_cache_code: false
add_date_to_run_output_dir: false
block_dry_cells: true
debug: true
dispersion:
A_H: 0.1
event_loggers:
- class_name: oceantracker.event_loggers.log_polygon_entry_and_exit.LogPolygonEntryAndExit
name: in_out_poly
particle_prop_to_write_list:
- ID
- x
- IDrelease_group
- status
- age
polygon_list:
- points:
- - 1592682.1237
- 5489972.7479
- - 1593604.1667
- 5490275.5488
- - 1593886.4247
- 5489464.0424
- - 1592917.3387
- 5489000.0
- - 1592300.0
- 5489000.0
- - 1592682.1237
- 5489972.7479
user_polygon_name: A
- points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5487000
- - 1597300
- 5487000
- - 1597682.1237
- 5489972.7479
user_polygon_name: B
max_particles: 1000
output_file_base: demo08_particle_splitting
particle_properties:
- class_name: oceantracker.particle_properties.age_decay.AgeDecay
decay_time_scale: 86400.0
name: age_decay
reader:
file_mask: Random_order_*.nc
input_dir: C:\Auck_work\oceantracker\tutorials_how_to\demo_hindcast
release_groups:
- name: P1
points:
- - 1594500
- 5483500
- - 1594500
- 5486500
pulse_size: 1
release_interval: 0
root_output_dir: C:\Auck_work\oceantracker_output\demos
time_buffer_size: 15
time_step: 600
tracks_writer:
write_dry_cell_flag: true
trajectory_modifiers:
- class_name: oceantracker.trajectory_modifiers.split_particles.SplitParticles
interval: 21600
name: part_spliting
statuses:
- moving
- class_name: oceantracker.trajectory_modifiers.cull_particles.CullParticles
interval: 21600
name: part_culling
probability: 0.05
statuses:
- moving
user_note: test of notes
Particle Statistics#
Heat maps#
Heatmaps built on the fly with no particle tracks recorded. Options for both time and aged based gridded heatmaps
class:
particle_statistics.gridded_statistics.GriddedStats2D_timeBasedclass:
particle_statistics.gridded_statistics.GriddedStats2D_agedBased
along with counts of particles inside polygons
class:
particle_statistics.polygon_statistics.PolygonStats2D_timeBasedclass:
particle_statistics.polygon_statistics.PolygonStats2D_ageBased
json parameters
/../dev/demo_param_files/demo03_heatmaps.json#
{
"output_file_base": "demo03_heatmaps",
"root_output_dir": "C:\\Auck_work\\oceantracker_output\\demos",
"add_date_to_run_output_dir": false,
"NUMBA_cache_code": false,
"time_buffer_size": 15,
"time_step": 900,
"debug": true,
"reader": {
"input_dir": "C:\\Auck_work\\oceantracker\\tutorials_how_to\\demo_hindcast",
"file_mask": "Random_order_*.nc"
},
"user_note": "test of notes",
"dispersion": {
"A_H": 0.1
},
"tracks_writer": {
"turn_on_write_particle_properties_list": [
"n_cell"
],
"write_dry_cell_flag": true
},
"release_groups": [
{
"name": "myP1",
"points": [
[
1596000,
5486000
]
],
"pulse_size": 2000,
"release_interval": 7200,
"release_radius": 100.0
},
{
"name": "myP2",
"points": [
[
1596000,
5490000
]
],
"pulse_size": 3000,
"release_interval": 3600
}
],
"particle_properties": [
{
"name": "Oxygen",
"class_name": "AgeDecay",
"decay_time_scale": 86400.0,
"initial_value": 20.0
},
{
"name": "distance_travelled",
"class_name": "DistanceTravelled"
},
{
"name": "age_decay",
"class_name": "AgeDecay",
"decay_time_scale": 86400.0
},
{
"name": "my_constant_prop",
"class_name": "ParticleLoad",
"initial_value": 100
}
],
"particle_statistics": [
{
"name": "gridstats1",
"class_name": "oceantracker.particle_statistics.gridded_statistics2D.GriddedStats2D_timeBased",
"update_interval": 1800,
"particle_property_list": [
"water_depth"
],
"grid_span": [
10000,
10000
],
"grid_size": [
220,
221
]
},
{
"name": "polystats1",
"class_name": "oceantracker.particle_statistics.polygon_statistics.PolygonStats2D_timeBased",
"update_interval": 1800,
"particle_property_list": [
"water_depth"
],
"polygon_list": [
{
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5489000
],
[
1597300,
5489000
],
[
1597682.1237,
5489972.7479
]
]
}
]
}
],
"particle_buffer_initial_size": 20000,
"write_tracks": false,
"max_run_duration": 259200
}
yaml parameters
/../dev/demo_param_files/demo03_heatmaps.yaml#
NUMBA_cache_code: false
add_date_to_run_output_dir: false
debug: true
dispersion:
A_H: 0.1
max_run_duration: 259200
output_file_base: demo03_heatmaps
particle_buffer_initial_size: 20000
particle_properties:
- class_name: AgeDecay
decay_time_scale: 86400.0
initial_value: 20.0
name: Oxygen
- class_name: DistanceTravelled
name: distance_travelled
- class_name: AgeDecay
decay_time_scale: 86400.0
name: age_decay
- class_name: ParticleLoad
initial_value: 100
name: my_constant_prop
particle_statistics:
- class_name: oceantracker.particle_statistics.gridded_statistics2D.GriddedStats2D_timeBased
grid_size:
- 220
- 221
grid_span:
- 10000
- 10000
name: gridstats1
particle_property_list:
- water_depth
update_interval: 1800
- class_name: oceantracker.particle_statistics.polygon_statistics.PolygonStats2D_timeBased
name: polystats1
particle_property_list:
- water_depth
polygon_list:
- points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5489000
- - 1597300
- 5489000
- - 1597682.1237
- 5489972.7479
update_interval: 1800
reader:
file_mask: Random_order_*.nc
input_dir: C:\Auck_work\oceantracker\tutorials_how_to\demo_hindcast
release_groups:
- name: myP1
points:
- - 1596000
- 5486000
pulse_size: 2000
release_interval: 7200
release_radius: 100.0
- name: myP2
points:
- - 1596000
- 5490000
pulse_size: 3000
release_interval: 3600
root_output_dir: C:\Auck_work\oceantracker_output\demos
time_buffer_size: 15
time_step: 900
tracks_writer:
turn_on_write_particle_properties_list:
- n_cell
write_dry_cell_flag: true
user_note: test of notes
write_tracks: false