Skip to content

Commit c05641f

Browse files
aranasjemrobinson
aranas
and
jemrobinson
authored
Whale corridors visualisation (#96)
* set-up data config for whale corridor viz * add and update dataset configs add dataset configs for three key years and for whale point-based dataset * add notebook for whale viz * clean up notebook imports * clear notebook outputs * move ipynb into notebook folder * fix hardcoded paths for exec from notebooks folder * add missing dataset specs to whale_viz config * improve notebook instructions re data download * removing hardcoded path and fix linting error * fix linting error * 🚨 Autoformatted notebook * 📝 More explicit statement that whale data should be downloaded by the user * ⚰️ Remove unused file * 🚚 Move config files to nested structure * 🔧 Small notebook fixes/updates * 🚨 Fixed YAML linting * 📝 Added note to README about how to run notebooks --------- Co-authored-by: James Robinson <james.em.robinson@gmail.com>
1 parent 0c3ec7a commit c05641f

10 files changed

Lines changed: 840 additions & 2 deletions

‎README.md‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -137,3 +137,8 @@ Pros:
137137
Cons:
138138
- input variables have been transformed into latent space
139139
- time-step information has been compressed into the latent space
140+
141+
## Jupyter notebooks
142+
143+
There are various demonstrator Jupyter notebooks in the `notebooks` folder.
144+
You can run these with `uv run --group notebooks jupyter notebook`.

‎ice_station_zebra/config/datasets/osisaf-sic-north-2003-08-24h-v1.yaml‎

Lines changed: 19 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,19 @@
1+
osisaf-sic-north-2003-08-24h-v1:
2+
name: osisaf-sic-north-2003-08-24h-v1
3+
group_as: osisaf-north
4+
description: OSISAF sea ice concentration for northern hemisphere - Summer 2003 (August-September)
5+
attribution: EUMETSAT
6+
licence: CC-BY-4.0
7+
8+
dates:
9+
start: '2003-08-01T00:00:00'
10+
end: '2003-09-30T23:00:00'
11+
frequency: 24h
12+
13+
preprocessor:
14+
type: IceNetSIC
15+
hemisphere: north
16+
17+
input:
18+
netcdf:
19+
path: ${base_path}/data/preprocessing/${...preprocessor.type}/data/osisaf/${...preprocessor.hemisphere}/siconca/2003.nc

‎ice_station_zebra/config/datasets/osisaf-sic-north-2010-08-24h-v1.yaml‎

Lines changed: 19 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,19 @@
1+
osisaf-sic-north-2010-08-24h-v1:
2+
name: osisaf-sic-north-2010-08-24h-v1
3+
group_as: osisaf-north
4+
description: OSISAF sea ice concentration for northern hemisphere - Summer 2010 (August-September)
5+
attribution: EUMETSAT
6+
licence: CC-BY-4.0
7+
8+
dates:
9+
start: '2010-08-01T00:00:00'
10+
end: '2010-09-30T23:00:00'
11+
frequency: 24h
12+
13+
preprocessor:
14+
type: IceNetSIC
15+
hemisphere: north
16+
17+
input:
18+
netcdf:
19+
path: ${base_path}/data/preprocessing/${...preprocessor.type}/data/osisaf/${...preprocessor.hemisphere}/siconca/2010.nc

‎ice_station_zebra/config/datasets/osisaf-sic-north-2018-08-24h-v1.yaml‎

Lines changed: 19 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,19 @@
1+
osisaf-sic-north-2018-08-24h-v1:
2+
name: osisaf-sic-north-2018-08-24h-v1
3+
group_as: osisaf-north
4+
description: OSISAF sea ice concentration for northern hemisphere - Summer 2018 (August-September)
5+
attribution: EUMETSAT
6+
licence: CC-BY-4.0
7+
8+
dates:
9+
start: '2018-08-01T00:00:00'
10+
end: '2018-09-30T23:00:00'
11+
frequency: 24h
12+
13+
preprocessor:
14+
type: IceNetSIC
15+
hemisphere: north
16+
17+
input:
18+
netcdf:
19+
path: ${base_path}/data/preprocessing/${...preprocessor.type}/data/osisaf/${...preprocessor.hemisphere}/siconca/2018.nc

‎ice_station_zebra/config/notebooks/whale_telemetry_csv.yaml‎

Lines changed: 38 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,38 @@
1+
whale_telemetry:
2+
name: whale_telemetry
3+
group_as: whale_data
4+
description: Whale telemetry data for West Greenland/Canadian Arctic region
5+
attribution: Philippine Chambault et al. (2022, Science Advances)
6+
licence: CC-BY-4.0
7+
8+
# Data source
9+
input:
10+
csv:
11+
path: ${base_path}/data/notebooks/whale_corridors/Locations_3species_West-East_Greenland.csv
12+
separator: ";"
13+
14+
# Column mapping
15+
columns:
16+
id: id
17+
timestamp: dateTime
18+
longitude: lon
19+
latitude: lat
20+
month: month
21+
year: year
22+
species: species
23+
side: side
24+
25+
# Filtering criteria
26+
filters:
27+
side: West
28+
species: Bw
29+
30+
# Coordinate system
31+
input_crs: EPSG:4326 # WGS84
32+
target_crs: AEQD # Azimuthal Equidistant
33+
34+
# Date filtering (applied after loading all data)
35+
date_filter:
36+
start_month: 7 # July
37+
end_month: 9 # September
38+
target_years: [2003, 2010, 2018]

‎ice_station_zebra/config/notebooks/whale_visualisation.yaml‎

Lines changed: 50 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,50 @@
1+
visualization:
2+
# Spatial extent for West Greenland/Canadian Arctic (configurable bbox)
3+
spatial_extent:
4+
north: 85.0 # Northern boundary
5+
south: 60.0 # Southern boundary
6+
east: -30.0 # Eastern boundary (Greenland)
7+
west: -120.0 # Western boundary (Canadian Arctic)
8+
9+
# Sea ice visualization settings
10+
sea_ice:
11+
# Ice edge threshold
12+
ice_edge_threshold: 0.15 # 15% concentration
13+
14+
# Colormap
15+
colormap: "Blues_r" # Blue to white
16+
17+
# Missing data color
18+
missing_color: "orange"
19+
20+
# Whale track visualization
21+
whale_tracks:
22+
# Line thickness
23+
line_width: 2.0
24+
25+
# Color scheme
26+
color_scheme: "tab10" # Distinct colors per whale
27+
28+
# Track smoothing
29+
smooth_tracks: true
30+
31+
# Date stamp format
32+
date_format: "%Y-%m-%d"
33+
34+
# Animation settings
35+
animation:
36+
frame_rate: 24 # FPS
37+
duration: 10 # seconds
38+
resolution: [1920, 1080]
39+
40+
# Frame generation
41+
weekly_frames: true
42+
frame_interval: "7D" # Weekly intervals
43+
44+
# Output settings
45+
output:
46+
directory: plots/
47+
save_intermediate: true
48+
format: "png" # For static plots
49+
video_format: "mp4"
50+
video_codec: "H.264"

‎ice_station_zebra/config/whale_corridors.yaml‎

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,10 @@
1+
defaults:
2+
- base
3+
- datasets:
4+
- osisaf-sic-north-2003-08-24h-v1
5+
- osisaf-sic-north-2010-08-24h-v1
6+
- osisaf-sic-north-2018-08-24h-v1
7+
- notebooks:
8+
- whale_telemetry_csv
9+
- whale_visualisation
10+
- _self_

0 commit comments

Comments
 (0)