import builtins import json import keyword import math import re from datetime import datetime # noqa from pathlib import Path from textwrap import indent from typing import List from typing import Optional, Callable, Tuple from typing import Union, Dict, Any import numpy as np import pandas as pd import rasterio from pyproj import Geod from pyproj import Transformer from rasterio.transform import Affine from tqdm import tqdm def _nan_to_none(obj): if isinstance(obj, dict): return {k: _nan_to_none(v) for k, v in obj.items()} elif isinstance(obj, list): return [_nan_to_none(v) for v in obj] elif isinstance(obj, float) and math.isnan(obj): return None else: return obj def resolve_code(code: Any, codebook: Union[str, Dict[str, Any]], top_key: str = None, ignore_error_codes=None) -> Optional[str]: """ Resolve a hierarchical code into its labels by prefix-walking the code. - If code is in ignore_error_codes or empty -> return None silently. - If code not found in codebook and not ignored -> raise KeyError. - top_key missing is a hard error (still raises). """ # normalize ignore list ignore_error_codes = [] if ignore_error_codes is None else list(ignore_error_codes) # accept non-str inputs; only None/empty-string -> None if code is None or (isinstance(code, str) and not code.strip()): return None # normalize code to string; "3.0" -> "3" code_str = str(code).strip() try: f = float(code_str) if f.is_integer(): code_str = str(int(f)) except Exception: # keep original string if not a number pass # fast path: ignored codes if code_str in ignore_error_codes: return None # Load codebook if isinstance(codebook, str): try: with open("src/fuse_esdac/codebooks/" + codebook + ".json", "r", encoding="utf-8") as fs: codebook_dict = json.load(fs) except FileNotFoundError as e: raise FileNotFoundError(f"Codebook file not found: {codebook}") from e except json.JSONDecodeError as e: raise ValueError(f"Invalid JSON in codebook file: {codebook}") from e elif isinstance(codebook, dict): codebook_dict = codebook else: raise TypeError(f"codebook must be a file path (str) or dict, got {type(codebook).__name__}") # Pick source dict (top_key remains strict) src = codebook_dict if top_key is None else codebook_dict.get(top_key) if src is None: raise KeyError(f"top_key '{top_key}' not found in codebook") if not isinstance(src, dict): raise TypeError(f"Top-level codebook section must be a dict, got {type(src).__name__}") labels: List[str] = [] level_dict = src # progressive prefixes prefixes = [code_str[:i] for i in range(1, len(code_str) + 1)] for pref in prefixes: if not isinstance(level_dict, dict): raise ValueError(f"Invalid structure: expected dict at prefix '{pref}', got {type(level_dict).__name__}") if pref not in level_dict: break node = level_dict[pref] if isinstance(node, dict): if "value" not in node: raise KeyError(f"Missing 'value' key in node for prefix '{pref}'") if "children" not in node: raise KeyError(f"Missing 'children' key in node for prefix '{pref}'") if not isinstance(node["value"], str): raise TypeError(f"'value' for prefix '{pref}' must be a string, got {type(node['value']).__name__}") if not isinstance(node["children"], dict): raise TypeError(f"'children' for prefix '{pref}' must be a dict, got {type(node['children']).__name__}") labels.append(node["value"]) level_dict = node["children"] elif isinstance(node, str): if not node.strip(): raise ValueError(f"Empty string label for prefix '{pref}'") labels.append(node) break # leaf node, stop walking else: raise TypeError(f"Unexpected node type for prefix '{pref}': {type(node).__name__}") # post-check: no match -> ignore or raise if len(labels) == 0: if code_str in ignore_error_codes: return None raise KeyError(f"Code '{code_str}' not found in codebook") return code_str + ": " + " => ".join(labels) def as_float(number: Any, keep_str=True, ignore_substr="-999", factor=1.0) -> Optional[float]: """Convert to float; empty CSV values -> None; real errors -> raise.""" if number is None or (isinstance(number, str) and number.strip() == ""): return None if ignore_substr is not None and ignore_substr in number: return None try: return float(number) * factor except (ValueError, TypeError) as e: if keep_str: return number.strip() raise ValueError(f"as_float: cannot convert {number!r}") from e def as_int_id(number: Any, allow_letters: bool = False) -> Optional[str]: """ Convert to integer-like string. If allow_letters is True, allow prefix/suffix letters around digits (e.g., 'AA024322BB'), but reject strings with interleaved letters (e.g., 'A2323B232C'). """ if number is None: raise ValueError("as_int_id: input is None") s = str(number).strip() if not allow_letters: try: return str(int(float(s))) except (ValueError, TypeError) as e: raise ValueError(f"as_int_id: cannot convert {number!r}") from e else: # Allow only prefix/suffix letters, core must be digits m = re.fullmatch(r"[A-Za-z]*([0-9]+)[A-Za-z]*", s) if not m: raise ValueError(f"as_int_id: invalid alphanumeric format {number!r}") return m.group(1) def _sanitize_identifier(name: str, used: set) -> str: """Convert arbitrary string to a unique, valid Python identifier.""" # Replace non-identifier chars with underscores and strip leading/trailing underscores ident = re.sub(r'\W+', '_', str(name)).strip('_') # Empty or starts with digit -> prefix with underscore if not ident or ident[0].isdigit(): ident = f"_{ident}" if ident else "_arg" # Avoid keywords and builtins if keyword.iskeyword(ident) or ident in dir(builtins): ident += "_" # Ensure uniqueness base = ident i = 1 while ident in used: ident = f"{base}_{i}" i += 1 used.add(ident) return ident def make_callable(expr: str, returns_str: bool = False) -> Union[Callable, Tuple[Callable, str]]: """ Compile an expression string with placeholders into a callable. Placeholders of the form 【name】 are replaced by valid Python parameter names, preserving order and uniqueness. A mapping from safe names to original placeholders is attached to the returned function as `_arg_map` and `_arg_order`. Args: expr: Expression string containing placeholders. returns_str: If True, return (callable, function_definition_str); otherwise return callable. Returns: Callable or (Callable, str): The compiled function, and optionally the source code. """ # find placeholders orig_vars = re.findall(r'【(.*?)】', expr) orig_vars = list(dict.fromkeys(orig_vars)) # dedupe preserving order # build safe arg names + mapping used = set() safe_args = [] arg_map = {} for v in orig_vars: s = _sanitize_identifier(v, used) safe_args.append(s) arg_map[s] = v # replace placeholders in expression with safe arg names body_expr = expr for s in safe_args: orig = arg_map[s] body_expr = body_expr.replace(f"【{orig}】", s) # define function text args_str = ", ".join(safe_args) func_str = f"def func({args_str}):\n" func_str += indent(f"return {body_expr}", " ") # exec in isolated globals that still see current globals exec_globals = globals().copy() local_vars = {} exec(func_str, exec_globals, local_vars) fn = local_vars["func"] # attach mapping for callers setattr(fn, "_arg_map", arg_map) # safe -> original setattr(fn, "_arg_order", tuple(safe_args)) # ordered safe args if returns_str: return fn, func_str return fn def _eval_expr(expr: str, row: Dict[str, Any]) -> Any: """ Evaluate a schema expression against a CSV row. - If any referenced CSV value is empty/None -> return None (no noise). - Otherwise: print detailed error and return None. """ if expr is None: return None try: fn, func_src = make_callable(expr, returns_str=True) kwargs = {} had_empty_input = False for safe in getattr(fn, "_arg_order", []): orig = fn._arg_map[safe] raw = row.get(orig, None) # normalize to str or None; treat "" as empty if raw is None: had_empty_input = True kwargs[safe] = None else: s = str(raw) if s == "": had_empty_input = True kwargs[safe] = None else: kwargs[safe] = s return fn(**kwargs) except Exception as e: if 'had_empty_input' in locals() and had_empty_input: return None print("=== EVAL ERROR ===") print("expr:", expr) try: print("compiled:\n", func_src) except Exception: pass try: print("kwargs:", kwargs) except Exception: pass print("error:", repr(e)) print("==================") return None def _labels_to_list(s: Optional[str]) -> list: if not isinstance(s, str): return [] parts = [p.strip() for p in s.split(",")] return [p for p in parts if p] def fuse_csv( source_file: Union[str, Path], schema: Dict[str, Any], source_name: str, current_dict: Dict[str, Any], ) -> Dict[str, Any]: """ Fuse CSV rows into hierarchical dict. New convention: - Thematic sections map var_name -> expression directly. - Units parsed from "(...)" in var_name. - SHARED merged into every variable. - ENTRY_KEY handling: * If ENTRY_KEY starts with '^', treat as regex to match existing keys (never create new). * Otherwise, treat as literal key (create new if not present). """ df = pd.read_csv(source_file, dtype=str, keep_default_na=False, na_values=[]) out_dict = dict(current_dict) if current_dict else {} CONTROL_KEYS = {"ENTRY_KEY", "LAT_LONG", "COUNTRY_CODE", "SAMPLE_DATE", "SAMPLE_DEPTH_RANGE_CM", "SHARED"} thematic_keys = [k for k in schema.keys() if k not in CONTROL_KEYS] filename_for_bar = Path(source_file).name if isinstance(source_file, (str, Path)) else str(source_file) for _, row in tqdm(df.iterrows(), total=len(df), desc=filename_for_bar): row_dict = row.to_dict() entry_key_expr = schema.get("ENTRY_KEY") entry_key_val = _eval_expr(entry_key_expr, row_dict) if entry_key_val in (None, ""): continue lat_long = _eval_expr(schema.get("LAT_LONG"), row_dict) country_code = _eval_expr(schema.get("COUNTRY_CODE"), row_dict) sample_date = _eval_expr(schema.get("SAMPLE_DATE"), row_dict) sample_depth_range_cm = _eval_expr(schema.get("SAMPLE_DEPTH_RANGE_CM"), row_dict) # Shared metadata shared_evaluated = {sk: _eval_expr(sv, row_dict) for sk, sv in (schema.get("SHARED", {}) or {}).items()} shared_evaluated["source_dataset"] = source_name if "distance_to_grid (m)" not in shared_evaluated: shared_evaluated["distance_to_grid (m)"] = 0.0 # Step 1. Resolve target entries if str(entry_key_val).startswith("^"): # regex matching pattern = re.compile(str(entry_key_val)) targets = [k for k in out_dict.keys() if pattern.search(k)] is_new_sample = False # never create new else: # exact match if lat_long is None: continue if lat_long[0] is None or lat_long[1] is None: continue if entry_key_val not in out_dict: out_dict[entry_key_val] = {} targets = [entry_key_val] is_new_sample = True # Step 2. Apply update for key in targets: sample = out_dict[key] if is_new_sample: assert lat_long is not None sample["LAT_LONG"] = lat_long assert country_code is not None sample["COUNTRY_CODE"] = country_code assert sample_date is not None sample["SAMPLE_DATE"] = sample_date assert sample_depth_range_cm is not None sample["SAMPLE_DEPTH_RANGE_CM"] = sample_depth_range_cm assert source_name is not None sample["SAMPLE_SOURCE_DATASET"] = source_name for sec_name in thematic_keys: sec_schema = schema.get(sec_name, {}) or {} section_data = {} for var_name, expr in sec_schema.items(): value = _eval_expr(expr, row_dict) m = re.match(r"^([^\s()]+)\s*\((.+)\)\s*$", var_name) if m: clean_name = m.group(1).strip() unit = m.group(2).strip() else: clean_name, unit = var_name.strip(), None leaf = {"value": value} if unit: leaf["unit"] = unit leaf.update(shared_evaluated) section_data[clean_name] = leaf existing_section = sample.get(sec_name, {}) merged_section = dict(existing_section) for var_name, leaf in section_data.items(): if var_name not in merged_section: merged_section[var_name] = leaf # only add if missing sample[sec_name] = merged_section return out_dict def fuse_tif( source_file: Union[str, Path], schema: Dict[str, Any], source_name: str, current_dict: Dict[str, Any], ) -> Dict[str, Any]: out_dict = dict(current_dict) if current_dict else {} CONTROL_KEYS = {"CRS_STRING"} thematic_keys = [k for k in schema.keys() if k not in CONTROL_KEYS] keys, lats, lons = [], [], [] for k, s in out_dict.items(): if "LAT_LONG" in s and s["LAT_LONG"] not in (None, "", "null"): lat, lon = s["LAT_LONG"] keys.append(k) lats.append(lat) lons.append(lon) if not keys: return out_dict keys = np.array(keys) lats = np.array(lats, dtype=float) lons = np.array(lons, dtype=float) tif_dir = Path(source_file) geod = Geod(ellps="WGS84") def _sample_one_entry(tif_entry): value_map = None scale_factor = 1.0 if isinstance(tif_entry, list): if len(tif_entry) == 2: if isinstance(tif_entry[1], dict): tif_key, value_map = tif_entry elif isinstance(tif_entry[1], (int, float)): tif_key, scale_factor = tif_entry else: raise ValueError( f"Error parsing entry {tif_entry}: second item must be a dict (codebook) or a number (scale factor)" ) elif len(tif_entry) == 1 and isinstance(tif_entry[0], str): # simple single-item list, same as plain string tif_key = tif_entry[0] else: # multi-entry list → likely a profile list, handle outside raise ValueError( f"Error parsing entry {tif_entry}: unexpected list form (did you mean a profile list?)" ) else: tif_key = tif_entry tif_path = tif_dir / f"{tif_key}.standardized.tif" with rasterio.open(tif_path) as ds: arr = ds.read(1) nodata = ds.nodata inv_affine: Affine = ~ds.transform if "CRS_STRING" in schema: crs = rasterio.crs.CRS.from_string(schema["CRS_STRING"]) else: crs = ds.crs if crs is None or "LOCAL_CS" in crs.to_wkt(): raise ValueError(f"{tif_key}.standardized.tif: CRS not available. Please provide CRS_STRING") transformer = Transformer.from_crs("EPSG:4326", crs, always_xy=True) xs, ys = transformer.transform(lons, lats) cols, rows = inv_affine * (xs, ys) rows = np.round(rows).astype(int) cols = np.round(cols).astype(int) in_bounds = (rows >= 0) & (rows < ds.height) & (cols >= 0) & (cols < ds.width) values = np.empty(len(keys), dtype=object) values[:] = np.nan dists = np.full(len(keys), np.nan, dtype=float) if np.any(in_bounds): r = rows[in_bounds] c = cols[in_bounds] raw_vals = arr[r, c] x_centers, y_centers = ds.transform * (c, r) lats_geo = lats[in_bounds] lons_geo = lons[in_bounds] if crs.is_geographic: _, _, d_valid = geod.inv(lons_geo, lats_geo, x_centers, y_centers) else: xs_valid = xs[in_bounds] ys_valid = ys[in_bounds] d_valid = np.sqrt((xs_valid - x_centers) ** 2 + (ys_valid - y_centers) ** 2) if nodata is not None: nd_mask = np.isclose(raw_vals, nodata, equal_nan=True) else: nd_mask = np.zeros_like(raw_vals, dtype=bool) out_vals = [] for rv, is_nd in zip(raw_vals, nd_mask): if is_nd: out_vals.append(np.nan) else: if value_map is not None: try: code_str = str(int(round(float(rv)))) except Exception: code_str = str(int(round(rv))) out_vals.append(code_str + ": " + str(value_map.get(code_str, "Unknown"))) else: out_vals.append(float(rv) * scale_factor) values[in_bounds] = out_vals d_valid = np.array(d_valid, dtype=float) d_valid[nd_mask] = np.nan dists[in_bounds] = d_valid return values, dists, in_bounds all_vars = [] for sec_name in thematic_keys: for var_name, tif_entry in schema[sec_name].items(): all_vars.append((sec_name, var_name, tif_entry)) for sec_name, var_name, tif_entry in tqdm(all_vars, desc=f"Processing variables in {tif_dir.name}"): m = re.match(r"^(.*)\s+\(([^()]*)\)$", var_name) if m: clean_name, unit = m.group(1).strip(), m.group(2).strip() else: clean_name, unit = var_name.strip(), None is_profile = ( isinstance(tif_entry, list) and not ( len(tif_entry) == 2 and isinstance(tif_entry[1], (dict, int, float)) ) ) if is_profile: per_entry_values = [] per_entry_dists = [] union_in_bounds = np.zeros(len(keys), dtype=bool) for entry in tif_entry: vals, dists, in_bounds = _sample_one_entry(entry) per_entry_values.append(vals) per_entry_dists.append(dists) union_in_bounds |= in_bounds for idx, key in enumerate(keys): if not union_in_bounds[idx]: continue sample = out_dict[key] section = sample.setdefault(sec_name, {}) if clean_name in section: continue value_list = [vals[idx] for vals in per_entry_values] dist_candidates = [] for d in per_entry_dists: di = d[idx] if not (isinstance(di, float) and np.isnan(di)): dist_candidates.append(float(di)) dist_reduced = (max(dist_candidates) if dist_candidates else None) leaf = { "value": value_list, **({"unit": unit} if unit else {}), "distance_to_grid (m)": dist_reduced, "source_dataset": source_name } leaf = _nan_to_none(leaf) section[clean_name] = leaf else: vals, dists, in_bounds = _sample_one_entry(tif_entry) ib_idx = np.where(in_bounds)[0] for ii in ib_idx: key = keys[ii] sample = out_dict[key] section = sample.setdefault(sec_name, {}) if clean_name in section: continue raw_val = vals[ii] val = None if (isinstance(raw_val, float) and np.isnan(raw_val)) else raw_val dist_val = float(dists[ii]) if not np.isnan(dists[ii]) else np.nan leaf = { "value": val, **({"unit": unit} if unit else {}), "distance_to_grid (m)": dist_val, "source_dataset": source_name } leaf = _nan_to_none(leaf) section[clean_name] = leaf return out_dict