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Robbi Bishop-Taylor robbibt

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robbibt / dea_in_r.R
Last active May 11, 2024 05:44
Loading and analysing Digital Earth Australia Sentinel-2 data in R with `rstac` and `gdalcubes`
"""
This code demonstrates how to load Digital Earth Australia Sentinel-2 Analysis Ready Data into R.
It uses `rstac` to search for available data for a time and location using DEA's STAC endpoint,
and `gdalcubes` to load and analyse the data.
Functionality includes:
* Creating a custom pixel grid to reproject data into
* Apply a cloud mask using the "s2cloudless" cloud mask
* Combine data into seasonal composites
* Create an RGB animation
@robbibt
robbibt / stac_load_from_item.py
Created April 3, 2024 03:41
Load raster data directly from a STAC item using `odc-stac`
from pystac import Item
from odc.stac import load
import rasterio
import odc.geo.xr
path = 'https://dea-public-data-dev.s3-ap-southeast-2.amazonaws.com/derivative/ga_s2ls_intertidal_cyear_3/1-0-0/x128/y165/2016--P1Y/ga_s2ls_intertidal_cyear_3_x128y165_2016--P1Y_final.stac-item.json'
# path = 'https://dea-public-data-dev.s3-ap-southeast-2.amazonaws.com/derivative/ga_s2ls_intertidal_cyear_3/1-0-0/x128/y165/2017--P1Y/ga_s2ls_intertidal_cyear_3_x128y165_2017--P1Y_final.stac-item.json'
items = [Item.from_file(path)]
data = load(items, chunks={})
@robbibt
robbibt / STAC_loading_explorer.ipynb
Created February 29, 2024 23:28
Explorer STAC loading limit issue
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@robbibt
robbibt / s3_to_vrt.py
Created February 7, 2024 03:44
Create virtual raster for files on S3
import s3fs
import pandas as pd
s3 = s3fs.S3FileSystem(anon=True)
file_list = s3.glob(
"dea-public-data-dev/derivative/ga_ls8cls9c_gm_cyear_3/4-0-0/*/*/2023--P1Y/ga_ls8cls9c_gm_cyear_3_*_2023--P1Y_final_nbart_red.tif"
)
pd.DataFrame(file_list).iloc[:, 0].str.replace(
"dea-public-data-dev/",
@robbibt
robbibt / tide_gauge_funcs.py
Created January 31, 2024 00:43
GESLA and ABSLMP tide gauge loading functions
import glob
import warnings
import datetime
from odc.geo.geom import BoundingBox
def _load_gauge_metadata(metadata_path):
# Load metadata
@robbibt
robbibt / Expanded_AOI_gridspec_tiles.ipynb
Last active January 25, 2024 03:34
Generating GridSpec summary tile grid for expanded DEA AOI
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@robbibt
robbibt / otps_tides.py
Created October 12, 2023 23:46
OTPS tide modelling function for TPXO8
import otps
import pytz
def otps_tides(lats, lons, times, timezone=None):
"""
Model tide heights for one or more locations and times using the
OTPS TPXO8 tidal model.
Parameters:
-----------
lats, lons : numeric or list of numeric values
@robbibt
robbibt / load_ls_s2.py
Last active August 14, 2023 13:10
`pc_load`: easily searching and loading data from Microsoft Planetary Computer
import numpy as np
import xarray as xr
def load_ls_s2(
x=None,
y=None,
geom=None,
start_date="2020",
end_date="2021",
@robbibt
robbibt / tide_range_constituents.py
Created June 23, 2023 03:14
Tide range from constituents
# Source: https://www.arcgis.com/home/item.html?id=d5354dea41b14f0689860bf4b2cf5e8a
# 2*(M2+S2+K1+O1)
(0.01 * 2 * (
xr.open_dataset("/var/share/tide_models/fes2014/ocean_tide/m2.nc")
+ xr.open_dataset("/var/share/tide_models/fes2014/ocean_tide/s2.nc")
+ xr.open_dataset("/var/share/tide_models/fes2014/ocean_tide/k1.nc")
+ xr.open_dataset("/var/share/tide_models/fes2014/ocean_tide/o1.nc")
)).amplitude.odc.assign_crs("EPSG:4326").plot()
@robbibt
robbibt / tide_models.py
Created June 13, 2023 07:13
Loading different tide models with `dea_tools.coastal.model_tides`
import pandas as pd
import sys
sys.path.insert(1, '../Tools/')
from dea_tools.coastal import model_tides, tidal_tag, pixel_tides, tidal_stats
# Set of times to model tides for
date_list = pd.date_range(start="2022-09-01", end="2022-09-30", freq="1H")
# Run TPXO8