A Sentinel-2 multi-year, multi-country benchmark dataset for crop classification and segmentation with deep learning
Contributors: Sykas D., Zografakis D., Sdraka M.
Supplementary repo with DL experiments using the Sen4AgriNet dataset: Sen4AgriNet-Models.
This repository provides a native PyTorch Dataset Class for Sen4AgriNet dataset (patches_dataset.py). Should work with any new version of PyTorch1.7.1+ and Python3.8.5+.
Dataset heavily relies on cocoapi for dataloading and indexing, therefore make sure you have it installed:
pip3 install pycocotoolsThen make sure every other requirement is installed:
pip3 install -r requirements.txtIn order to use the provided PyTroch Dataset class, the required netCDF files of Sen4AgriNet must be downloaded and placed inside the dataset/netcdf/ folder. These files are available for download at Dropbox, Google Drive and HuggingFace Hub (experimental).
Then, three separate COCO files must be created: one for training, one for validation and one for testing.
After this initial setup, patches_dataset.py can be used in a PyTorch deep learning pipeline to load, prepare and return patches from the dataset according to the split dictated by the COCO files. This Dataset class has the following features:
- Reads the netCDF files of the dataset containing the Sentinel-2 observations over time and the corresponding labels.
- Isolates the Sentinel-2 bands requested by the user.
- Computes the median Sentinel-2 image on a given frequency, e.g. monthly (or loads precomputed medians, if any).
- Returns the timeseries of median images inside a predefined window.
- Normalizes the images.
- Returns hollstein masks for clouds, cirrus, shadow or snow.
- Returns a parcel mask: 1 for parcel, 0 for non-parcel.
- Can alternatively return binary labels: 1 for crops, 0 for non-crops.
This is roughly the way that our patches_dataset.py works. The whole procedure is also described in the provided notebook.
- Open a netCDF file for exploration.
import netCDF4
from pathlib import Path
patch = netCDF4.Dataset(Path('data/2020_31TCG_patch_14_14.nc'), 'r')
patchOutputs
"""
<class 'netCDF4._netCDF4.Dataset'>
root group (NETCDF4 data model, file format HDF5):
title: S4A Patch Dataset
authors: Papoutsis I., Sykas D., Zografakis D., Sdraka M.
patch_full_name: 2020_31TCG_patch_14_14
patch_year: 2020
patch_name: patch_14_14
patch_country_code: ES
patch_tile: 31TCG
creation_date: 27 Apr 2021
references: Documentation available at .
institution: National Observatory of Athens.
version: 21.03
_format: NETCDF4
_nco_version: netCDF Operators version 4.9.1 (Homepage = https://nco.sf.net, Code = https://github.com/nco/nco)
_xarray_version: 0.17.0
dimensions(sizes):
variables(dimensions):
groups: B01, B02, B03, B04, B05, B06, B07, B08, B09, B10, B11, B12, B8A, labels, parcels
"""- Visualize a single timestamp.
import xarray as xr
band_data = xr.open_dataset(xr.backends.NetCDF4DataStore(patch['B02']))
band_data.B02.isel(time=0).plot()
- Visualize the labels:
labels = xr.open_dataset(xr.backends.NetCDF4DataStore(patch['labels']))
labels.labels.plot()
- Visualize the parcels:
parcels = xr.open_dataset(xr.backends.NetCDF4DataStore(patch['parcels']))
parcels.parcels.plot()
- Plot the median of observations for each month:
import pandas as pd
# Or maybe aggregate based on a given frequency
# Refer to
# https://pandas.pydata.org/pandas-docs/stable/user_guide/timeseries.html#timeseries-offset-aliases
group_freq = '1MS'
# Grab year from netcdf4's global attribute
year = patch.patch_year
# output intervals
date_range = pd.date_range(start=f'{year}-01-01', end=f'{int(year) + 1}-01-01', freq=group_freq)
# Aggregate based on given frequency
band_data = band_data.groupby_bins(
'time',
bins=date_range,
right=True,
include_lowest=False,
labels=date_range[:-1]
).median(dim='time')If you plot right now, you might notice that some months are empty:
(Optional) Fill in empty months:
import matplotlib.pyplot as plt
band_data = band_data.interpolate_na(dim='time_bins', method='linear', fill_value='extrapolate')
fig, axes = plt.subplots(nrows=3, ncols=4, figsize=(18, 12))
for i, season in enumerate(band_data.B02):
ax = axes.flat[i]
cax = band_data.B02.isel(time_bins=i).plot(ax=ax)
for i, ax in enumerate(axes.flat):
ax.axes.get_xaxis().set_ticklabels([])
ax.axes.get_yaxis().set_ticklabels([])
ax.axes.axis('tight')
ax.set_xlabel('')
ax.set_ylabel('')
ax.set_title(f'Month: {i+1}')
plt.tight_layout()
plt.show()
Please refer to the provided notebook for a detailed usage example of the provided PatchesDataset.
- Read the COCO file to be used.
from pathlib import Path
from pycocotools.coco import COCO
root_path_coco = Path('coco_files/')
coco_train = COCO(root_path_coco / 'coco_example.json')- Initialize the PatchesDataset.
from torch.utils.data import DataLoader
from patches_dataset import PatchesDataset
from utils.config import LINEAR_ENCODER
root_path_netcdf = Path('dataset/netcdf') # Path to the netCDF files
dataset_train = PatchesDataset(root_path_netcdf=root_path_netcdf,
coco=coco_train,
group_freq='1MS',
prefix='test_patchesdataset',
bands=['B02', 'B03', 'B04'],
linear_encoder=LINEAR_ENCODER,
saved_medians=False,
window_len=6,
requires_norm=False,
return_masks=False,
clouds=False,
cirrus=False,
shadow=False,
snow=False,
output_size=(183, 183)
)- Initialize the Dataloader.
dataloader_train = DataLoader(dataset_train,
batch_size=1,
shuffle=True,
num_workers=4,
pin_memory=True
)- Get a batch.
batch = next(iter(dataloader_train))The batch variable is a dictionary containing the keys: medians, labels, idx.
batch['medians'] contains a pytorch tensor of size [1, 6, 3, 183, 183] where:
- batch size: 1
- timestamps: 6
- bands: 3
- height: 183
- width: 183
batch['labels'] contains the corresponding labels of the medians, which is a pytorch tensor of size [1, 183, 183] where:
- batch size: 1
- height: 183
- width: 183
batch['idx'] contains the index of the returned timeseries.
Dataset Webpage: https://www.sen4agrinet.space.noa.gr/
Please visit Sen4AgriNet-Models for a complete experimentation pipeline using the Sen4AgriNet dataset.
To cite please use:
@ARTICLE{
9749916,
author={Sykas, Dimitrios and Sdraka, Maria and Zografakis, Dimitrios and Papoutsis, Ioannis},
journal={IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing},
title={A Sentinel-2 multi-year, multi-country benchmark dataset for crop classification and segmentation with deep learning},
year={2022},
doi={10.1109/JSTARS.2022.3164771}
}