diff --git a/README.md b/README.md index 75b1493..7220d08 100644 --- a/README.md +++ b/README.md @@ -4,9 +4,9 @@ CropHarvest is an open source remote sensing dataset for agriculture with benchm Spatial distribution of labels -The dataset consists of **90,480** datapoints, of which **30,899** (34.2%) have multiclass labels. All other datapoints only have binary crop / non-crop labels. +The dataset consists of **95,186** datapoints, of which **33,205** (35%) have multiclass labels. All other datapoints only have binary crop / non-crop labels. -**65,690** (73%) of these labels are paired with remote sensing and climatology data, specifically [Sentinel-2](https://sentinel.esa.int/web/sentinel/missions/sentinel-2), [Sentinel-1](https://sentinel.esa.int/web/sentinel/missions/sentinel-1/), the [SRTM Digital Elevation Model](https://cgiarcsi.community/data/srtm-90m-digital-elevation-database-v4-1/) and [ERA 5 climatology data](https://www.ecmwf.int/en/forecasts/datasets/reanalysis-datasets/era5). +**70,213** (74%) of these labels are paired with remote sensing and climatology data, specifically [Sentinel-2](https://sentinel.esa.int/web/sentinel/missions/sentinel-2), [Sentinel-1](https://sentinel.esa.int/web/sentinel/missions/sentinel-1/), the [SRTM Digital Elevation Model](https://cgiarcsi.community/data/srtm-90m-digital-elevation-database-v4-1/) and [ERA 5 climatology data](https://www.ecmwf.int/en/forecasts/datasets/reanalysis-datasets/era5). 21 datasets are aggregated into CropHarvest - these are documented [here](https://github.com/nasaharvest/cropharvest/blob/main/datasets.md). @@ -40,13 +40,105 @@ pip install cropharvest ``` ### Getting started [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/nasaharvest/cropharvest/blob/main/demo.ipynb) -See the [`demo.ipynb`](https://github.com/nasaharvest/cropharvest/blob/main/demo.ipynb) notebook for an example on how to download the data from [Zenodo](https://zenodo.org/record/5828893) and train a random forest against this data. +See the [`demo.ipynb`](https://github.com/nasaharvest/cropharvest/blob/main/demo.ipynb) notebook for an example on how to download the data from [Zenodo](https://zenodo.org/record/7257688) and train a random forest against this data. For more examples of models trained against this dataset, see the [benchmarks](https://github.com/nasaharvest/cropharvest/blob/main/benchmarks). ### Contributing If you would like to contribute a dataset, please see the [contributing readme](https://github.com/nasaharvest/cropharvest/blob/main/contributing.md). +### ~~FAQ~~ Questions asked at least once + +
+How do I use CropHarvest for a specific geography? + +All the data is accessible through the `cropharvest.datasets.CropHarvest` object. The main parameters which you might be interested in manipulating are controllable through a `cropharvest.datasets.Task`, which takes as input the following parameters: +- A bounding box, which defines the spatial boundaries of the labels retrieves +- A target label, which defines the class of the positive labels (if this is left to `None`, then the positive class will be crops and the negative class will be non-crops) +- A boolean defining whether or not to balance the crops and non-crops in the negative class +- A test_identifier string, which tells the dataset whether or not to retrieve a file from the `test_features` folder and return it as the test data. + +So if I wanted to use this to train a model to identify crop vs. non crop in France, I might do it like this: + +```python +from sklearn.ensemble import RandomForestClassifier + +from cropharvest.datasets import Task, CropHarvest +from cropharvest.countries import get_country_bbox + +# folder into which the data will be downloaded / already exists +data_dir = "data" + +# get_country_bbox returns a list of bounding boxes. +# the one representing Metropolitan France is the 2nd box +metropolitan_france_bbox = get_country_bbox("France")[1] + +task = Task(bounding_box=metropolitan_france_bbox, normalize=True) + +my_dataset = CropHarvest(data_dir, task) + +X, y = my_dataset.as_array(flatten_x=True) +model = RandomForestClassifier(random_state=0) +model.fit(X, y) +``` +
+ +
+How do I load a specific pixel timeseries? + +The specific use case here is to retrieve NDVI values for a specific row in the `labels.geojson`. Here is how you might go about doing that: + +Firstly, I will load the geosjon. I'll do it through a `CropHarvestLabels` object, which is just a wrapper around the geojson but provides some nice utility functions. +```python +>>> from cropharvest.datasets import CropHarvestLabels +>>> +>>> labels = CropHarvestLabels("cropharvest/data") +>>> labels_geojson = labels.as_geojson() +>>> labels_geojson.head() + harvest_date planting_date ... is_test geometry +0 None None ... False POLYGON ((37.08252 10.71274, 37.08348 10.71291... +1 None None ... False POLYGON ((37.08721 10.72398, 37.08714 10.72429... +2 None None ... False POLYGON ((37.08498 10.71371, 37.08481 10.71393... +3 None None ... False POLYGON ((37.09021 10.71320, 37.09014 10.71341... +4 None None ... False POLYGON ((37.08307 10.72160, 37.08281 10.72197... + +[5 rows x 13 columns] +``` + +Now, I can use the `labels` object to retrieve the filepath of the processed satellite data for each row in the labels geojson: +```python +>>> path_to_file = labels._path_from_row(labels_geojson.iloc[0]) +``` +This processed satellite data is stored as `h5py` files, so I can load it up as follows: +```python +>>> import h5py +>>> h5py_file = h5py.File(path_to_file, "r") +>>> x = h5py_file.get("array")[:] +>>> x.shape +(12, 18) +``` +The shape of `x` represents 12 timesteps and 18 bands. To retrieve the band I am interested in: +```python +>>> from cropharvest.bands import BANDS +>>> x[:, BANDS.index("NDVI")] +array([0.28992072, 0.28838343, 0.26833579, 0.22577633, 0.27138986, + 0.06584114, 0.498998 , 0.50147203, 0.50437743, 0.44326343, + 0.33735849, 0.28375967]) +``` +These are 12 NDVI values, corresponding to the 12 months captured in this timeseries. To find out exactly which month each timestep represents, I can do +```python +>>> labels_geojson.iloc[0].export_end_date +'2021-02-01T00:00:00' +``` +Wich tells me that the last timestep represents January 2021. I can work backwards from there. + +
+ +
+What is the data format? +The structure of the different data files is now described in depth in the data folder's [Readme](https://github.com/nasaharvest/cropharvest/blob/main/data/README.md) +
+ ### License CropHarvest has a [Creative Commons Attribution-ShareAlike 4.0 International](https://github.com/nasaharvest/cropharvest/blob/main/LICENSE.txt) license. diff --git a/cropharvest/config.py b/cropharvest/config.py index 203e1e7..e5d1f61 100644 --- a/cropharvest/config.py +++ b/cropharvest/config.py @@ -16,7 +16,7 @@ EXPORT_END_MONTH = 2 EXPORT_END_DAY = 1 -DATASET_VERSION_ID = 6985649 +DATASET_VERSION_ID = 7257688 DATASET_URL = f"https://zenodo.org/record/{DATASET_VERSION_ID}" LABELS_FILENAME = "labels.geojson" FEATURES_DIR = "features" diff --git a/setup.py b/setup.py index 1f87a54..2235426 100644 --- a/setup.py +++ b/setup.py @@ -15,7 +15,7 @@ author="Gabriel Tseng", author_email="gabrieltseng95@gmail.com", url="https://github.com/nasaharvest/cropharvest", - version="0.5.0", + version="0.6.0", classifiers=[ "Programming Language :: Python :: 3", "License :: Other/Proprietary License",