import pandas as pd import datasets import numpy as np import ast from PIL import Image class NeuripsConfig(datasets.BuilderConfig): def __init__(self, **kwargs): super(NeuripsConfig, self).__init__(**kwargs) class NeuripsDataset(datasets.GeneratorBasedBuilder): BUILDER_CONFIGS = [ NeuripsConfig( name="Kenya", version=datasets.Version("1.0.0"), description="Full dataset, combining both systematically and opportunistically sampled leaves" ), NeuripsConfig( name="South_Africa", version=datasets.Version("1.0.0"), description="Subset containing only systematically sampled leaves" ), NeuripsConfig( name="USA_Summer", version=datasets.Version("1.0.0"), description="Subset containing only opportunistically sampled leaves" ), NeuripsConfig( name="USA_Winter", version=datasets.Version("1.0.0"), description="Subset containing only opportunistically sampled leaves" ), NeuripsConfig( name="Species_ID", version=datasets.Version("1.0.0"), description="Subset containing the DataFrames allowing to link the target encounter rates to a list of species for each country" ) ] DEFAULT_CONFIG_NAME = "Kenya" def _info(self): #state,state_code,split,num_complete_checklists,target,geometry if self.config.name == "Kenya": features = datasets.Features({ "hotspot_id": datasets.Value("string"), "hotspot_name": datasets.Value("string"), "lon": datasets.Value("float32"), "lat": datasets.Value("float32"), "county": datasets.Value("string"), "county_code": datasets.Value("string"), "state": datasets.Value("string"), "state_code": datasets.Value("string"), 'sat_imagery_path': datasets.Value("string"), 'environmental_path': datasets.Value("string"), "split": datasets.Value("string"), "num_complete_checklists" : datasets.Value("int32"), "target": datasets.Sequence(feature=datasets.Value("float32"), length=1054), "geometry": datasets.Value("string") }) elif self.config.name == "South_Africa": features = datasets.Features({ "hotspot_id": datasets.Value("string"), "hotspot_name": datasets.Value("string"), "lon": datasets.Value("float32"), "lat": datasets.Value("float32"), "county": datasets.Value("string"), "county_code": datasets.Value("string"), "state": datasets.Value("string"), "state_code": datasets.Value("string"), 'sat_imagery_path': datasets.Value("string"), 'environmental_path': datasets.Value("string"), "split": datasets.Value("string"), "num_complete_checklists" : datasets.Value("int32"), "target": datasets.Sequence(feature=datasets.Value("float32"), length=1054), "geometry": datasets.Value("string") }) elif self.config.name == "USA_Summer": features = datasets.Features({ "hotspot_id": datasets.Value("string"), "hotspot_name": datasets.Value("string"), "lon": datasets.Value("float32"), "lat": datasets.Value("float32"), "county": datasets.Value("string"), "county_code": datasets.Value("string"), "state": datasets.Value("string"), "state_code": datasets.Value("string"), 'sat_imagery_path': datasets.Value("string"), 'environmental_path': datasets.Value("string"), "split": datasets.Value("string"), "num_complete_checklists" : datasets.Value("int32"), "target": datasets.Sequence(feature=datasets.Value("float32"), length=1054), "geometry": datasets.Value("string") }) elif self.config.name == "USA_Winter": features = datasets.Features({ "hotspot_id": datasets.Value("string"), "hotspot_name": datasets.Value("string"), "lon": datasets.Value("float32"), "lat": datasets.Value("float32"), "county": datasets.Value("string"), "county_code": datasets.Value("string"), "state": datasets.Value("string"), "state_code": datasets.Value("string"), 'sat_imagery_path': datasets.Value("string"), 'environmental_path': datasets.Value("string"), "split": datasets.Value("string"), "num_complete_checklists" : datasets.Value("int32"), "target": datasets.Sequence(feature=datasets.Value("float32"), length=1054), "geometry": datasets.Value("string") }) elif self.config.name == "Species_ID": features = datasets.Features({ "scientific_name": datasets.Value("string"), "ebird_code": datasets.Value("string"), "inat_preview": datasets.Image(), "target_value_index" : datasets.Value("int32"), }) else: raise ValueError(f"Unsupported config: {self.config.name}") return datasets.DatasetInfo( description="The SITTELLE Benchmark Dataset", features=features, supervised_keys=None, homepage="https://huggingface.co/datasets/imageomics/invasive_plants_hawaii", license="MIT", ) def _split_generators(self, dl_manager): if self.config.name == "Kenya": train_csv = "Kenya/train_split.csv" test_csv = "Kenya/test_split.csv" val_csv = "Kenya/valid_split.csv" return [ datasets.SplitGenerator(name="train", gen_kwargs={"filepath": train_csv}), datasets.SplitGenerator(name="val", gen_kwargs={"filepath": test_csv}), datasets.SplitGenerator(name="test", gen_kwargs={"filepath": val_csv}), ] elif self.config.name == "South_Africa": train_csv = "Kenya/train_split.csv" test_csv = "Kenya/test_split.csv" val_csv = "Kenya/valid_split.csv" return [ datasets.SplitGenerator(name="train", gen_kwargs={"filepath": train_csv}), datasets.SplitGenerator(name="val", gen_kwargs={"filepath": test_csv}), datasets.SplitGenerator(name="test", gen_kwargs={"filepath": val_csv}), ] elif self.config.name == "USA_Summer": train_csv = "Kenya/train_split.csv" test_csv = "Kenya/test_split.csv" val_csv = "Kenya/valid_split.csv" return [ datasets.SplitGenerator(name="train", gen_kwargs={"filepath": train_csv}), datasets.SplitGenerator(name="val", gen_kwargs={"filepath": test_csv}), datasets.SplitGenerator(name="test", gen_kwargs={"filepath": val_csv}), ] elif self.config.name == "USA_Winter": train_csv = "Kenya/train_split.csv" test_csv = "Kenya/test_split.csv" val_csv = "Kenya/valid_split.csv" return [ datasets.SplitGenerator(name="train", gen_kwargs={"filepath": train_csv}), datasets.SplitGenerator(name="val", gen_kwargs={"filepath": test_csv}), datasets.SplitGenerator(name="test", gen_kwargs={"filepath": val_csv}), ] elif self.config.name == "Species_ID": kenya_csv = "Kenya/species_id_kenya.csv" southafrica_csv = "Kenya/species_id_kenya.csv" usasummer_csv = "Kenya/species_id_kenya.csv" usawinter_csv = "Kenya/species_id_kenya.csv" return [ datasets.SplitGenerator(name="Kenya", gen_kwargs={"filepath": kenya_csv}), datasets.SplitGenerator(name="South_Africa", gen_kwargs={"filepath": southafrica_csv}), datasets.SplitGenerator(name="USA_Summer", gen_kwargs={"filepath": usasummer_csv}), datasets.SplitGenerator(name="USA_Winter", gen_kwargs={"filepath": usawinter_csv}), ] else: raise ValueError(f"Unknown config: {self.config.name}") def _generate_examples(self, filepath): if self.config.name in ["Kenya", "South_Africa", "USA_Summer", "USA_Winter"]: df_metadata = pd.read_csv(filepath) df_metadata["target"] = df_metadata["target"].apply(ast.literal_eval).apply(lambda x: list(map(float, x))) for idx in range(len(df_metadata)): row = df_metadata.iloc[idx] yield idx, { "hotspot_id": row['hotspot_id'], "hotspot_name": row['hotspot_name'], "lon": row['lon'], "lat": row['lat'], "county": row['county'], "county_code": row['county_code'], "state": row['state'], "state_code": row['state_code'], 'sat_imagery_path': row['sat_imagery_path'], 'environmental_path': row['environmental_path'], "split": row['split'], "num_complete_checklists" : row['num_complete_checklists'], "target": row['target'], "geometry": row['geometry'] } if self.config.name == "Species_ID": df_metadata = pd.read_csv(filepath) for idx in range(len(df_metadata)): row = df_metadata.iloc[idx] yield idx, { "scientific_name": row['scientific_name'], "ebird_code": row['ebird_code'], "inat_preview": row['inat_preview'], "target_value_index" : row['target_value_index'], }