File size: 6,479 Bytes
ae853c1 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 | """Science Lab Mode — a BrAPI-inspired germplasm/speciation surface over the
session catalog. Pure functions: build germplasm records, facets, a Newick
pedigree export, and a Monte-Carlo cross predictor from the real genetics.
"""
import colorsys
from collections import defaultdict
from breeder import _recombine, _avg_stabilities
from phenotype_pipeline import generate_phenotype
# Trait ontology (BrAPI ObservationVariable = Trait + Method + Scale).
TRAIT_VARIABLES = [
{"key": "THC", "label": "THC", "unit": "%", "min": 0, "max": 35, "scale": "numeric"},
{"key": "CBD", "label": "CBD", "unit": "%", "min": 0, "max": 20, "scale": "numeric"},
{"key": "Yield", "label": "Yield", "unit": "g", "min": 30, "max": 140, "scale": "numeric"},
{"key": "GrowTime", "label": "Grow Time", "unit": "d", "min": 40, "max": 80, "scale": "numeric"},
{"key": "BudHue", "label": "Bud Hue", "unit": "deg", "min": 0, "max": 360, "scale": "circular"},
{"key": "LeafHue", "label": "Leaf Hue", "unit": "deg", "min": 0, "max": 360, "scale": "circular"},
{"key": "Stability", "label": "Stability", "unit": "", "min": 0, "max": 1, "scale": "numeric"},
]
def _hue(rgb):
return round(colorsys.rgb_to_hsv(*[c / 255.0 for c in rgb])[0] * 360, 1)
def color_family(hue):
if hue < 15 or hue >= 330:
return "red"
if hue < 40:
return "orange"
if hue < 70:
return "yellow"
if hue < 160:
return "green"
if hue < 200:
return "cyan"
if hue < 260:
return "blue"
if hue < 290:
return "purple"
return "magenta"
def _generation(seed, by_id, cache):
if seed.seed_id in cache:
return cache[seed.seed_id]
p1, p2 = (seed.lineage or (None, None))
gens = [_generation(by_id[p], by_id, cache) for p in (p1, p2) if p in by_id]
gen = (max(gens) + 1) if gens else 0
cache[seed.seed_id] = gen
return gen
def _pedigree_str(seed, by_id):
p1, p2 = (seed.lineage or (None, None))
n1 = by_id[p1].strain_name if p1 in by_id else None
n2 = by_id[p2].strain_name if p2 in by_id else None
if n1 and n2:
return f"{n1} / {n2}"
if n1:
return f"{n1} (clone)"
return "founder"
def _mean_stability(seed):
vals = [v for v in seed.stabilities.values() if isinstance(v, (int, float))]
return round(sum(vals) / len(vals), 3) if vals else 0.0
def germplasm_records(seeds):
by_id = {s.seed_id: s for s in seeds}
cache = {}
records = []
for s in seeds:
bud_hue, leaf_hue = _hue(s.bud_color), _hue(s.leaf_color)
records.append({
"germplasmDbId": s.seed_id,
"germplasmName": s.strain_name,
"germplasmType": s.type,
"generation": _generation(s, by_id, cache),
"pedigree": _pedigree_str(s, by_id),
"parents": list(s.lineage or (None, None)),
"isStarter": s.is_starter,
"stage": s.growth_stage.name,
"THC": s.thc,
"CBD": s.cbd,
"Yield": s.yield_,
"GrowTime": s.grow_time,
"BudHue": bud_hue,
"LeafHue": leaf_hue,
"Stability": _mean_stability(s),
"budColor": list(s.bud_color),
"leafColor": list(s.leaf_color),
"budFamily": color_family(bud_hue),
"alleles": s.alleles,
"attemptsUsed": s.attempts_used,
"maxAttempts": s.max_attempts,
"canAttempt": s.can_attempt(),
})
return records
def facets(records):
def count(key):
d = defaultdict(int)
for r in records:
d[str(r[key])] += 1
return dict(sorted(d.items()))
return {
"germplasmType": count("germplasmType"),
"generation": count("generation"),
"stage": count("stage"),
"budFamily": count("budFamily"),
}
def lab_payload(seeds):
records = germplasm_records(seeds)
return {
"variables": TRAIT_VARIABLES,
"records": records,
"facets": facets(records),
"count": len(records),
}
def predict_cross(parent1, parent2, n=200):
"""Monte-Carlo the real breeding rules N times (no state mutation) and
return predicted offspring trait distributions + a progeny color cloud."""
thc, cbd, yld, grow = [], [], [], []
bud_pts, leaf_pts = [], []
for _ in range(n):
alleles = _recombine(parent1.alleles, parent2.alleles)
stab = _avg_stabilities(parent1.stabilities, parent2.stabilities)
ph = generate_phenotype(alleles, stab)
thc.append(round(ph["thc"], 2))
cbd.append(round(ph["cbd"], 2))
yld.append(round(ph["yield"], 1))
grow.append(round(ph["growtime"], 1))
bud_pts.append(ph["budcolor_rgb"])
leaf_pts.append(ph["leafcolor_rgb"])
def summary(arr):
s = sorted(arr)
return {
"min": s[0], "max": s[-1],
"mean": round(sum(s) / len(s), 2),
"median": s[len(s) // 2],
"values": arr,
}
return {
"n": n,
"parents": [parent1.strain_name, parent2.strain_name],
"THC": summary(thc),
"CBD": summary(cbd),
"Yield": summary(yld),
"GrowTime": summary(grow),
"budCloud": bud_pts,
"leafCloud": leaf_pts,
}
def to_newick(seeds):
"""Reticulate pedigree as an Extended-Newick-style string (crosses appear
under each parent; founders are leaves). Rooted at the newest specimens."""
by_id = {s.seed_id: s for s in seeds}
children = defaultdict(list)
has_parent = set()
for s in seeds:
for p in (s.lineage or (None, None)):
if p in by_id:
children[p].append(s.seed_id)
has_parent.add(s.seed_id)
def safe(name):
return name.replace(",", "_").replace("(", "[").replace(")", "]").replace(":", "-")
seen = set()
def render(node_id):
node = by_id[node_id]
kids = [k for k in children.get(node_id, []) if k not in seen]
for k in kids:
seen.add(k)
label = f"{safe(node.strain_name)}#{node_id[:6]}"
if not kids:
return label
inner = ",".join(render(k) for k in kids)
return f"({inner}){label}"
roots = [s.seed_id for s in seeds if s.seed_id not in has_parent]
parts = [render(r) for r in roots if r not in seen or not seen.add(r)]
return "(" + ",".join(parts) + ");"
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