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Download data_utils.py from earthroverprogram/erp-gpt-eu: direct link, hf CLI and curl.
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https://huggingface.co/datasets/earthroverprogram/erp-gpt-eu/resolve/main/data_utils.py
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16.5 kB
| import json | |
| import pickle | |
| from typing import Tuple, Optional, List, Dict, Any | |
| import numpy as np | |
| import pandas as pd | |
| from geopy.distance import geodesic | |
| from gadm_utils import GADMHandler | |
| from geo_utils import resolve_place | |
| from plot_utils import scatter_plot | |
| import ast | |
| class LUCASSoilData: | |
| def __init__(self, table_path: str, dict_path: str, | |
| column_names_path: str, | |
| gadm_handler: GADMHandler) -> None: | |
| self.df = pd.read_csv(table_path, low_memory=False) | |
| self.df["LAT_LONG"] = self.df["LAT_LONG"].apply( | |
| lambda x: ast.literal_eval(x) if isinstance(x, str) else x | |
| ) | |
| with open(column_names_path, 'r') as f: | |
| self.column_names = json.load(f)["column_names"] | |
| self.property_map = {} | |
| for full_name in self.column_names: | |
| base, unit = full_name.split("(", maxsplit=1) if "(" in full_name else (full_name, None) | |
| if unit is not None: | |
| unit = unit[:-1].strip() # remove trailing ")" | |
| theme, prop = [x.strip() for x in base.split(":", 1)] | |
| self.property_map[prop] = (full_name, theme, unit) | |
| with open(dict_path, 'rb') as f: | |
| self.sample_dict = pickle.load(f) | |
| self.gadm_handler = gadm_handler | |
| def resolve_theme_property_unit(self, input_string: str) -> Tuple[str, str, str, Optional[str]]: | |
| """ | |
| Resolve and return (full_name, theme, property, unit) from a user input string. | |
| The user may provide: | |
| - full form: "theme:property (unit)" | |
| - partial form: "theme:property" | |
| - property only: "property" | |
| """ | |
| input_string = input_string.strip() | |
| # Extract unit if present | |
| if "(" in input_string: | |
| base, input_unit = input_string.split("(", maxsplit=1) | |
| input_unit = input_unit[:-1].strip() # remove trailing ")" | |
| else: | |
| base, input_unit = input_string, None | |
| # Extract theme + property | |
| if ":" in base: | |
| input_theme, input_property = [x.strip() for x in base.split(":", 1)] | |
| else: | |
| input_theme, input_property = None, base.strip() | |
| # Property must exist | |
| if input_property not in self.property_map: | |
| raise ValueError(f"Property '{input_property}' not found in dataset.") | |
| full_name, expected_theme, expected_unit = self.property_map[input_property] | |
| # Validate theme if user supplied one | |
| if input_theme is not None and input_theme != expected_theme: | |
| raise ValueError(f"Theme mismatch: expected '{expected_theme}', got '{input_theme}'.") | |
| # Validate unit if user supplied one | |
| if input_unit is not None and input_unit != expected_unit: | |
| raise ValueError(f"Unit mismatch for '{input_property}': expected '{expected_unit}', got '{input_unit}'.") | |
| return full_name, expected_theme, input_property, expected_unit | |
| def get_point(self, | |
| place: str | tuple[float, float], | |
| properties: List[str], | |
| distance_top_k: int = 20, | |
| distance_limit: float = 200000, | |
| session_name: Optional[str] = None) -> Dict[str, Any]: | |
| """ | |
| Retrieve soil data near a place, selecting the best among top-k nearest samples. | |
| Rules: | |
| 1) Find top-k nearest samples (by squared distance, then geodesic meters). | |
| 2) Exclude samples farther than `distance_limit` (meters). | |
| 3) From remaining samples, choose the one with the most valid properties. | |
| (valid = property exists AND sample[...] has non-None "value"). | |
| Tie-break: smaller distance wins. | |
| 4) If all survivors have zero valid properties, return Failed. | |
| 5) Resolver is strict: if user requests an unknown property, immediate Failed. | |
| Output always contains `query_input` and `query_status`. Sample data is | |
| included only for success or partial success cases. | |
| """ | |
| # always include input record in response | |
| query_input = { | |
| "place": place, | |
| "properties": properties, | |
| "distance_limit": distance_limit, | |
| "distance_top_k": distance_top_k, | |
| } | |
| # ---------- Resolve place → (lat, lon) ---------- | |
| try: | |
| if isinstance(place, str): | |
| if place not in self.gadm_handler.tree: | |
| resolved = resolve_place(place, session_name=session_name, gadm_handler=self.gadm_handler) | |
| gid = resolved.get("gid") | |
| if gid is None: | |
| return { | |
| "query_input": query_input, | |
| "query_status": f"Failed. Cannot resolve place: {place}", | |
| "query_output": {} | |
| } | |
| else: | |
| gid = place | |
| geom_info = self.gadm_handler.get_geometry_info(gid) | |
| if geom_info is None: | |
| return { | |
| "query_input": query_input, | |
| "query_status": f"Failed. Cannot get geometry for place (GID): {place} ({gid})", | |
| "query_output": {} | |
| } | |
| lat, lon = geom_info["latitude"], geom_info["longitude"] | |
| else: | |
| lat, lon = place | |
| except Exception as e: | |
| return { | |
| "query_input": query_input, | |
| "query_status": f"Failed. {str(e)}", | |
| "query_output": {} | |
| } | |
| # ---------- Strict property resolution (fail if any invalid) ---------- | |
| resolved_props = [] | |
| try: | |
| for input_prop in properties: | |
| full_name, theme, prop, unit = self.resolve_theme_property_unit(input_prop) | |
| resolved_props.append((theme, prop, input_prop)) | |
| except Exception as e: | |
| return { | |
| "query_input": query_input, | |
| "query_status": f"Failed. {str(e)}", | |
| "query_output": {} | |
| } | |
| # ---------- Find top-k nearest candidates ---------- | |
| try: | |
| latlon = np.vstack(self.df["LAT_LONG"].values).astype(float) # (N, 2) | |
| d2 = (latlon[:, 0] - lat) ** 2 + (latlon[:, 1] - lon) ** 2 | |
| k = max(1, min(distance_top_k, len(d2))) | |
| idx_k = np.argpartition(d2, kth=k - 1)[:k] | |
| candidates = [] | |
| for idx in idx_k: | |
| sample_lat, sample_lon = latlon[idx] | |
| dist_m = geodesic((lat, lon), (sample_lat, sample_lon)).meters | |
| candidates.append((idx, dist_m)) | |
| survivors = [(idx, dist_m) for (idx, dist_m) in candidates if dist_m <= distance_limit] | |
| if not survivors: | |
| return { | |
| "query_input": query_input, | |
| "query_status": f"Failed. No nearby samples within {distance_limit:g} m.", | |
| "query_output": {} | |
| } | |
| except Exception as e: | |
| return { | |
| "query_input": query_input, | |
| "query_status": f"Failed. Error during nearest-point search: {str(e)}", | |
| "query_output": {} | |
| } | |
| # ---------- Score survivors by valid property count, then distance ---------- | |
| def count_valid(idx: int) -> int: | |
| row = self.df.iloc[idx] | |
| src = self.sample_dict.get(row["id"], {}) | |
| valid = 0 | |
| for theme, prop, _orig in resolved_props: | |
| try: | |
| val = src[theme][prop]["value"] | |
| if val is not None: | |
| valid += 1 | |
| except Exception: | |
| pass | |
| return valid | |
| scored = [(idx, dist, count_valid(idx)) for idx, dist in survivors] | |
| scored.sort(key=lambda x: (-x[2], x[1])) # most valid props, then nearest | |
| best_idx, best_dist, best_valid = scored[0] | |
| if best_valid == 0: | |
| return { | |
| "query_input": query_input, | |
| "query_status": ( | |
| "Failed. No sample within " | |
| f"{distance_limit:g} m contains any of the requested properties." | |
| ), | |
| "query_output": {} | |
| } | |
| # ---------- Build result for best candidate ---------- | |
| try: | |
| row = self.df.iloc[best_idx] | |
| source = self.sample_dict[row["id"]] | |
| except Exception: | |
| return { | |
| "query_input": query_input, | |
| "query_status": f"Failed. Sample data missing for best candidate.", | |
| "query_output": {} | |
| } | |
| result = {} | |
| for key in ["LAT_LONG", "GADM_IDS", "GADM_NAMES", "COUNTRY_CODE", | |
| "SAMPLE_DATE", "SAMPLE_DEPTH_RANGE_CM", "SAMPLE_SOURCE_DATASET"]: | |
| result[key] = source.get(key) | |
| failed_props = [] | |
| for theme, prop, original_input in resolved_props: | |
| try: | |
| val = source[theme][prop]["value"] | |
| if val is not None: | |
| if theme not in result: | |
| result[theme] = {} | |
| result[theme][prop] = val | |
| else: | |
| failed_props.append(original_input) | |
| except Exception: | |
| failed_props.append(original_input) | |
| if failed_props and len(failed_props) < len(resolved_props): | |
| status = ( | |
| "Partial success. Some properties were not available: " | |
| + ", ".join(failed_props) | |
| + f". Distance to nearest sample (m): {best_dist:.1f}." | |
| ) | |
| else: | |
| status = f"Success. Distance to nearest sample (m): {best_dist:.1f}." | |
| result["entry_key"] = row["id"] | |
| return { | |
| "query_output": result, | |
| "query_input": query_input, | |
| "query_status": status, | |
| } | |
| def get_map(self, | |
| place: str | tuple[float, float, float], | |
| properties: List[str], | |
| session_name: Optional[str] = None, | |
| **kwargs) -> Dict[str, Any]: | |
| """ | |
| Generate scatter plots for the specified properties around a GADM region. | |
| Returns: | |
| { | |
| "query_output": { "<full_name>": "<url or warning string>", ... }, | |
| "query_input": { "place": ..., "properties": [...] }, | |
| "query_status": "Success. N plot(s) generated." | "Failed. <reason>" | |
| } | |
| """ | |
| # Always include the input | |
| query_input = {"place": place, "properties": properties} | |
| # ---------- Resolve place → gid (and lat/lon if needed) ---------- | |
| try: | |
| if isinstance(place, str): | |
| if place not in self.gadm_handler.tree: | |
| resolved = resolve_place(place, session_name=session_name, gadm_handler=self.gadm_handler) | |
| gid = resolved.get("gid") | |
| if gid is None: | |
| return {"query_input": query_input, | |
| "query_status": f"Failed. Cannot resolve place: {place}", | |
| "query_output": {}} | |
| else: | |
| gid = place | |
| else: | |
| # tuple expected: (lat, lon, bbox_area) | |
| if len(place) != 3: | |
| return {"query_input": query_input, | |
| "query_status": "Failed. Tuple `place` must be (lat, lon, bbox_area).", | |
| "query_output": {}} | |
| lat, lon, bbox_area = place | |
| gid = self.gadm_handler.find_gid(lat, lon, bbox_area) | |
| if gid is None: | |
| return {"query_input": query_input, | |
| "query_status": "Failed. No matching GADM region found for given coordinates.", | |
| "query_output": {}} | |
| geom_info = self.gadm_handler.get_geometry_info(gid) | |
| if geom_info is None: | |
| return {"query_input": query_input, | |
| "query_status": f"Failed. Cannot get geometry for place (GID): {gid}", | |
| "query_output": {}} | |
| except Exception as e: | |
| return {"query_input": query_input, "query_status": f"Failed. {str(e)}", | |
| "query_output": {}} | |
| # ---------- Strict property resolution (fail if any invalid) ---------- | |
| resolved = [] | |
| try: | |
| for input_prop in properties: | |
| full_name, theme, prop, unit = self.resolve_theme_property_unit(input_prop) | |
| resolved.append((full_name, theme, prop, unit)) | |
| except Exception as e: | |
| return {"query_input": query_input, "query_status": f"Failed. {str(e)}", "query_output": {}} | |
| if len(resolved) > 5: | |
| return {"query_input": query_input, | |
| "query_status": "Failed. API does not accept more than 5 properties.", | |
| "query_output": {}} | |
| # ---------- Compute map extent using gid + siblings ---------- | |
| try: | |
| siblings = self.gadm_handler.get_tree_info(gid)["siblings"] | |
| gids = [gid] + siblings | |
| polygon = self.gadm_handler.get_polygon(gid) | |
| minx, miny, maxx, maxy = polygon.bounds | |
| # 100% margin | |
| dlat = (maxy - miny) or 1.0 | |
| dlon = (maxx - minx) or 1.0 | |
| lat_min, lat_max = miny - dlat, maxy + dlat | |
| lon_min, lon_max = minx - dlon, maxx + dlon | |
| except Exception as e: | |
| return {"query_input": query_input, "query_status": f"Failed. {str(e)}", "query_output": {}} | |
| # ---------- Region filter using LAT_LONG ---------- | |
| try: | |
| latlon = np.vstack(self.df["LAT_LONG"].values).astype(float) # shape (N,2) | |
| lats, lons = latlon[:, 0], latlon[:, 1] | |
| mask = (lats >= lat_min) & (lats <= lat_max) & (lons >= lon_min) & (lons <= lon_max) | |
| df_region = self.df[mask] | |
| except Exception as e: | |
| return {"query_input": query_input, "query_status": f"Failed. {str(e)}", "query_output": {}} | |
| # ---------- Plot helper (returns URL or warning string) ---------- | |
| def plot_one(full_name: str, prop: str) -> str: | |
| try: | |
| if full_name not in df_region.columns: | |
| return "Skipped. No valid data." | |
| # Build [lat, lon, value] | |
| values = pd.to_numeric(df_region[full_name], errors="coerce") | |
| ok = values.notna() | |
| if not ok.any(): | |
| return "Skipped. No valid data." | |
| # extract lat/lon for the same rows | |
| latlon_sub = np.vstack(df_region.loc[ok, "LAT_LONG"].values).astype(float) | |
| data = np.column_stack([latlon_sub[:, 0], latlon_sub[:, 1], values.loc[ok].astype(float).values]) | |
| # numeric vs categorical: if after coercion we have floats, treat as numeric. | |
| # If you need categorical, you can branch by dtype before coercion. | |
| img_path = scatter_plot( | |
| gadm_handler=self.gadm_handler, | |
| data=data, | |
| is_categorical=False, | |
| short_name=prop, | |
| long_name=full_name, | |
| map_boundary_gadm_gids=gids, | |
| map_limits="gadm_first", | |
| session_name=session_name, | |
| **kwargs | |
| ) | |
| return img_path | |
| except Exception: | |
| return "Skipped. No valid data." | |
| # ---------- Generate outputs (flat) ---------- | |
| query_output: Dict[str, str] = {} | |
| for full_name, theme, prop, unit in resolved: | |
| query_output[full_name] = plot_one(full_name, prop) | |
| # ---------- Status ---------- | |
| n_plots = sum(1 for v in query_output.values() if isinstance(v, str) and v.endswith(".png")) | |
| if n_plots >= 1: | |
| status = f"Success. {n_plots} plot{'s' if n_plots != 1 else ''} generated." | |
| else: | |
| status = "Failed. No plots generated." | |
| return { | |
| "query_output": query_output, | |
| "query_input": query_input, | |
| "query_status": status, | |
| } | |