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pandas as pd +import rasterio +from pyproj import Transformer + +# NLCD Land Cover Classification Dictionary +NLCD_CLASSES = { + 11: "Open Water", + 12: "Perennial Ice/Snow", + 21: "Developed, Open Space", + 22: "Developed, Low Intensity", + 23: "Developed, Medium Intensity", + 24: "Developed, High Intensity", + 31: "Barren Land", + 41: "Deciduous Forest", + 42: "Evergreen Forest", + 43: "Mixed Forest", + 51: "Dwarf Scrub", + 52: "Shrub/Scrub", + 71: "Grassland/Herbaceous", + 72: "Sedge/Herbaceous", + 73: "Lichens", + 74: "Moss", + 81: "Pasture/Hay", + 82: "Cultivated Crops", + 90: "Woody Wetlands", + 95: "Emergent Herbaceous Wetlands" +} +# Path to the NLCD .img file +nlcd_file = "../downloads/NLCD_2016_Land_Cover_AK_20200724.img" + +# Path to the TSV file containing coordinates +tsv_file = "../downloads/Marina Nieto-Caballero air study proposed local scale - merged and curated (1).tsv" + +output_filename = "../local/nlcd_land_cover_results.tsv" + +# Read the TSV file +df = pd.read_csv(tsv_file, sep='\t') + +# Open the NLCD .img file +with rasterio.open(nlcd_file) as src: + # Initialize coordinate transformer + transformer = Transformer.from_crs("EPSG:4326", src.crs, always_xy=True) + + # Prepare lists to collect results + sample_names = [] + nlcd_codes = [] + nlcd_descriptions = [] + + # Iterate over the DataFrame rows + for _, row in df.iterrows(): + lon, lat = row['lon val'], row['lat val'] + sample_name = row['sample name'] + + # Transform coordinates to raster CRS + transformed_coord = transformer.transform(lon, lat) + + # Extract NLCD land cover class + land_cover_value = [val for val in src.sample([transformed_coord])][0][0] + land_cover_description = NLCD_CLASSES.get(land_cover_value, "Unknown Class") + + # Store the results + sample_names.append(sample_name) + nlcd_codes.append(land_cover_value) + nlcd_descriptions.append(land_cover_description) + +# Create a results DataFrame +results_df = pd.DataFrame({ + 'Sample Name': sample_names, + 'NLCD Code': nlcd_codes, + 'NLCD Description': nlcd_descriptions +}) + +# Save results to a new TSV file +results_df.to_csv(output_filename, sep='\t', index=False) + +print(f"Land cover classification completed. Results saved to '{output_filename}'.") diff --git a/sample_annotator/alaska_air_osm.py b/sample_annotator/alaska_air_osm.py new file mode 100644 index 0000000..30bbb45 --- /dev/null +++ b/sample_annotator/alaska_air_osm.py @@ -0,0 +1,119 @@ +import osmnx as ox +import pandas as pd +import time +from typing import List, Dict, Any + +# Path to the TSV file containing coordinates +tsv_file: str = "../downloads/Marina Nieto-Caballero air study proposed local scale - merged and curated (1).tsv" + +output_filename: str = "../local/osm_all_features_results.tsv" + +# Threshold for flagging uncommon features (e.g., less than 20% of samples) +uncommon_threshold: float = 0.2 + +# Read the TSV file +df: pd.DataFrame = pd.read_csv(tsv_file, sep='\t') + + +def fetch_osm_features(lat: float, lon: float, dist: int = 1000) -> pd.DataFrame: + """ + Fetch OpenStreetMap (OSM) features near a specified latitude and longitude. + + Args: + lat (float): Latitude of the location. + lon (float): Longitude of the location. + dist (int): Search radius in meters (default is 1000). + + Returns: + pd.DataFrame: A DataFrame containing the fetched OSM features. + """ + tags: Dict[str, bool] = { + 'aeroway': True, + 'amenity': True, + 'barrier': True, + 'boundary': True, + 'building': True, + 'emergency': True, + 'geological': True, + 'highway': True, + 'historic': True, + 'landuse': True, + 'leisure': True, + 'man_made': True, + 'military': True, + 'natural': True, + 'place': True, + 'surface': True, + 'tourism': True, + 'water': True, + 'waterway': True, + 'wetland': True + } + features: pd.DataFrame = ox.features_from_point((lat, lon), tags=tags, dist=dist) + return features + + +# Prepare a list to collect results +results: List[Dict[str, Any]] = [] + +# Iterate over each coordinate and fetch OSM features +for idx, row in df.iterrows(): + lat, lon = row['lat val'], row['lon val'] + sample_name = row['sample name'] + + print(f"Processing {idx + 1}/{len(df)}: Sample '{sample_name}' at ({lat}, {lon})") + + try: + features: pd.DataFrame = fetch_osm_features(lat, lon) + + if features.empty: + print(f"No features found for Sample '{sample_name}' at ({lat}, {lon})") + results.append({ + 'sample_name': sample_name, + 'latitude': lat, + 'longitude': lon, + 'feature_info': 'No features found' + }) + else: + for _, feature in features.iterrows(): + feature_info: str = ", ".join( + f"{k}: {v}" for k, v in feature.items() + if pd.notnull(v) and k != 'geometry' and ( + k in ['name', 'name:en', 'old_name', 'old_name:en'] or ( + not k.startswith('name:') and not k.startswith('old_name:') + ) + ) + ) + results.append({ + 'sample_name': sample_name, + 'latitude': lat, + 'longitude': lon, + 'feature_info': feature_info if feature_info else 'No English name found' + }) + except Exception as e: + print(f"Error fetching data for Sample '{sample_name}': {e}") + results.append({ + 'sample_name': sample_name, + 'latitude': lat, + 'longitude': lon, + 'feature_info': f"Error fetching data: {e}" + }) + + time.sleep(1) # 1-second delay between requests + +# Convert results to DataFrame +results_df: pd.DataFrame = pd.DataFrame(results) + +# Identify and flag uncommon features across samples +feature_counts: pd.Series = results_df['feature_info'].value_counts() +total_samples: int = len(df) + +dynamic_column_name: str = f"lt_{int(uncommon_threshold * 100)}_pct_of_samples" +results_df[dynamic_column_name] = results_df['feature_info'].apply( + lambda x: True if feature_counts[x] / total_samples < uncommon_threshold else False +) + +# Save the results to a TSV file +results_df.to_csv(output_filename, sep='\t', index=False) + +print(f"OSM feature extraction completed. Results saved to '{output_filename}'.")