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Taxonomic Hierarchy Engine for Western Australia Flora.
Builds and maps Species -> Genus -> Family for hierarchical multi-task classification.
"""
import pandas as pd
from pathlib import Path
# Common WA Flora Genus -> Family mapping dictionary
GENUS_TO_FAMILY = {
# Proteaceae
"Banksia": "Proteaceae", "Grevillea": "Proteaceae", "Hakea": "Proteaceae",
"Dryandra": "Proteaceae", "Adenanthos": "Proteaceae", "Isopogon": "Proteaceae",
"Petrophile": "Proteaceae", "Synaphea": "Proteaceae", "Conospermum": "Proteaceae",
"Lambertia": "Proteaceae", "Persoonia": "Proteaceae", "Xylomelum": "Proteaceae",
"Franklandia": "Proteaceae", "Stirlingia": "Proteaceae",
# Myrtaceae
"Eucalyptus": "Myrtaceae", "Corymbia": "Myrtaceae", "Melaleuca": "Myrtaceae",
"Verticordia": "Myrtaceae", "Calothamnus": "Myrtaceae", "Darwinia": "Myrtaceae",
"Chamelaucium": "Myrtaceae", "Thryptomene": "Myrtaceae", "Beaufortia": "Myrtaceae",
"Baeckea": "Myrtaceae", "Regelia": "Myrtaceae", "Calytrix": "Myrtaceae",
"Eremaea": "Myrtaceae", "Kunzea": "Myrtaceae", "Micromyrtus": "Myrtaceae",
"Hypocalymma": "Myrtaceae", "Scholtzia": "Myrtaceae", "Phymatocarpus": "Myrtaceae",
"Leptospermum": "Myrtaceae", "Astartea": "Myrtaceae", "Taxandria": "Myrtaceae",
# Fabaceae (Legumes)
"Acacia": "Fabaceae", "Gastrolobium": "Fabaceae", "Daviesia": "Fabaceae",
"Jacksonia": "Fabaceae", "Bossiaea": "Fabaceae", "Hovea": "Fabaceae",
"Kennedia": "Fabaceae", "Hardenbergia": "Fabaceae", "Gompholobium": "Fabaceae",
"Mirbelia": "Fabaceae", "Chorizema": "Fabaceae", "Pultenaea": "Fabaceae",
"Isotropis": "Fabaceae", "Swainsona": "Fabaceae", "Senna": "Fabaceae",
"Indigofera": "Fabaceae", "Templetonia": "Fabaceae", "Latrobea": "Fabaceae",
# Orchidaceae (Orchids)
"Caladenia": "Orchidaceae", "Thelymitra": "Orchidaceae", "Diuris": "Orchidaceae",
"Pterostylis": "Orchidaceae", "Drakaea": "Orchidaceae", "Microtis": "Orchidaceae",
"Prasophyllum": "Orchidaceae", "Cyanicula": "Orchidaceae", "Ericksonella": "Orchidaceae",
"Leporella": "Orchidaceae", "Paracaleana": "Orchidaceae", "Pyrorchis": "Orchidaceae",
"Cryptostylis": "Orchidaceae", "Elythranthera": "Orchidaceae", "Spiculaea": "Orchidaceae",
# Haemodoraceae (Kangaroo Paws)
"Anigozanthos": "Haemodoraceae", "Macropidia": "Haemodoraceae", "Conostylis": "Haemodoraceae",
"Tribonanthes": "Haemodoraceae", "Haemodorum": "Haemodoraceae", "Phlebocarya": "Haemodoraceae",
# Ericaceae / Epacridaceae (Heaths)
"Leucopogon": "Ericaceae", "Astroloma": "Ericaceae", "Lysinema": "Ericaceae",
"Conostephium": "Ericaceae", "Andersonia": "Ericaceae", "Sphenotoma": "Ericaceae",
"Styphelia": "Ericaceae", "Cosmelia": "Ericaceae",
# Goodeniaceae
"Goodenia": "Goodeniaceae", "Dampiera": "Goodeniaceae", "Scaevola": "Goodeniaceae",
"Lechenaultia": "Goodeniaceae", "Velleia": "Goodeniaceae", "Anthotium": "Goodeniaceae",
# Stylidiaceae (Triggerplants)
"Stylidium": "Stylidiaceae", "Levenhookia": "Stylidiaceae",
# Droseraceae (Sundews / Carnivorous)
"Drosera": "Droseraceae",
# Asteraceae (Daisies)
"Rhodanthe": "Asteraceae", "Waitzia": "Asteraceae", "Schoenia": "Asteraceae",
"Podolepis": "Asteraceae", "Olearia": "Asteraceae", "Senecio": "Asteraceae",
"Brachyscome": "Asteraceae", "Lawrencella": "Asteraceae", "Xerochrysum": "Asteraceae",
# Xanthorrhoeaceae / Asphodelaceae
"Xanthorrhoea": "Asphodelaceae",
# Dasypogonaceae
"Kingia": "Dasypogonaceae", "Dasypogon": "Dasypogonaceae", "Calectasia": "Dasypogonaceae",
# Casuarinaceae (Sheoaks)
"Allocasuarina": "Casuarinaceae", "Casuarina": "Casuarinaceae",
# Pittosporaceae
"Marianthus": "Pittosporaceae", "Billardiera": "Pittosporaceae", "Pittosporum": "Pittosporaceae",
"Cheiranthera": "Pittosporaceae",
# Restionaceae (Rushes / Sedges)
"Desmocladus": "Restionaceae", "Alexgeorgea": "Restionaceae", "Loxocarya": "Restionaceae",
"Chordifex": "Restionaceae", "Lyginia": "Restionaceae",
# Chenopodiaceae / Amaranthaceae
"Atriplex": "Amaranthaceae", "Maireana": "Amaranthaceae", "Tecticornia": "Amaranthaceae",
"Ptilotus": "Amaranthaceae",
# Malvaceae
"Alyogyne": "Malvaceae", "Thomasia": "Malvaceae", "Guichenotia": "Malvaceae",
"Lasiopetalum": "Malvaceae", "Seringia": "Malvaceae", "Androcalva": "Malvaceae",
# Rutaceae (Boronias / Waxflowers)
"Boronia": "Rutaceae", "Philotheca": "Rutaceae", "Diplolaena": "Rutaceae",
"Correa": "Rutaceae", "Crowea": "Rutaceae", "Geleznowia": "Rutaceae",
"Asterolasia": "Rutaceae", "Eriostemon": "Rutaceae",
# Loranthaceae (Mistletoes / Christmas Tree)
"Nuytsia": "Loranthaceae", "Amyema": "Loranthaceae", "Lysiana": "Loranthaceae",
}
class TaxonomyHierarchy:
"""Manages species -> genus -> family indices and mappings."""
def __init__(self, species_list: list[str]):
self.species_list = sorted(list(set(s for s in species_list if isinstance(s, str) and s.strip())))
# 1. Species Index
self.species_to_idx = {s: i for i, s in enumerate(self.species_list)}
self.idx_to_species = {i: s for s, i in self.species_to_idx.items()}
self.n_species = len(self.species_list)
# 2. Genus Index
self.species_to_genus = {}
genera_set = set()
for s in self.species_list:
genus = s.split()[0] if s else "Unknown"
self.species_to_genus[s] = genus
genera_set.add(genus)
self.genus_list = sorted(list(genera_set))
self.genus_to_idx = {g: i for i, g in enumerate(self.genus_list)}
self.idx_to_genus = {i: g for g, i in self.genus_to_idx.items()}
self.n_genera = len(self.genus_list)
# 3. Family Index
# FIX: avoid synthetic per-genus families (previous f"{g}_Family" exploded to ~250 singletons).
# Unknown genera now collapsed to a single "Unknown_Family" bucket to keep loss meaningful.
self.genus_to_family = {}
families_set = set()
unknown_genera: list[str] = []
for g in self.genus_list:
fam = GENUS_TO_FAMILY.get(g)
if fam is None:
fam = "Unknown_Family"
unknown_genera.append(g)
self.genus_to_family[g] = fam
families_set.add(fam)
if unknown_genera:
print(
f"[taxonomy] {len(unknown_genera)}/{len(self.genus_list)} genera fallback to Unknown_Family "
f"(e.g. {unknown_genera[:5]})",
flush=True,
)
self.family_list = sorted(list(families_set))
self.family_to_idx = {f: i for i, f in enumerate(self.family_list)}
self.idx_to_family = {i: f for f, i in self.family_to_idx.items()}
self.n_families = len(self.family_list)
# Precompute lookup tables
self.species_idx_to_genus_idx = [
self.genus_to_idx[self.species_to_genus[self.idx_to_species[i]]]
for i in range(self.n_species)
]
self.species_idx_to_family_idx = [
self.family_to_idx[self.genus_to_family[self.species_to_genus[self.idx_to_species[i]]]]
for i in range(self.n_species)
]
def get_taxonomy_indices(self, species_name: str) -> tuple[int, int, int]:
"""Returns (species_idx, genus_idx, family_idx)."""
s_idx = self.species_to_idx.get(species_name, -1)
if s_idx == -1:
return -1, -1, -1
return s_idx, self.species_idx_to_genus_idx[s_idx], self.species_idx_to_family_idx[s_idx]
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