File size: 15,957 Bytes
d1292d8 | 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 | """Template-backed FTIR path for the JASCO FT/IR-4700 runtime (CHEM-072).
Library (shared): ``assets/reactions/spectral_library/ir_spectra.json`` — up to four NIST WebBook IR spectra per
compound, each resampled to a 400-4000 cm^-1, 4 cm^-1 grid of absorbance normalised to 1 (null outside the measured
range) with state/sampling/resolution metadata. Since the 2026-10-14 decoder fix (scripts/spectral_library/jcamp.py)
the shared file itself carries the corrected spectra that this asset used to overlay from
``assets/reactions/jasco_ftir4700_ir_library`` (24 records: DELTAX sign, optical-constant k block, reflectance
log10(1/R)); the overlay library is retired. Corrected records are recognisable by their ``y_transform`` /
``x_step_note`` fields and are reported with ``corrected_by``.
A trusted host registers a cuvette/ATR sample as one spectral_library compound id (+ phase). ``measure`` selects a
reference spectrum whose physical state matches the sample (condensed phase: neat liquid > solution > solid;
gas: gas/vapour), broadens it to the configured resolution (Gaussian, FWHM^2 = R_req^2 - R_src^2), resamples it on
the configured range and scales the normalised band to a host-chosen peak absorbance.
NIST spectra are transmission spectra (gas cell, neat film, CCl4/CS2 solution, KBr/mull); none is an ATR spectrum and
no ATR penetration-depth correction is applied.
"""
from __future__ import annotations
import copy
import math
import re
from functools import lru_cache
from typing import Any
from scripts.basic40_templates import _analytical_common as common
LIB_REL = common.SPECTRAL + "/ir_spectra.json"
DECODER_FIX = "scripts/spectral_library/jcamp.py (2026-10-14 decoder fix; replaces the retired jasco_ftir4700_ir_library overlay)"
SOURCES = [LIB_REL]
GRID_START_CM = 400.0
GRID_STEP_CM = 4.0
CM_TO_M_INV = 100.0
PHASES = ("solid", "liquid", "gas")
MAX_PEAK_ABSORBANCE = 3.0
INTERFEROGRAM_POINTS = 257
LIMITATIONS = [
"NIST WebBook IR spectra are transmission spectra (gas cells, neat liquid films, CCl4/CS2 solutions, KBr/mull); none is an ATR spectrum and no ATR penetration-depth, refractive-index or anomalous-dispersion correction is applied, so ATR relative band intensities will differ.",
"Library absorbance is normalised to 1 at the strongest band; absolute absorbance (path length x concentration) is unknown, so the host chooses the peak absorbance (default 1.0).",
"Effective resolution is max(requested, source resolution, 4 cm^-1 library grid); finer requested resolution cannot be recovered (no deconvolution).",
"Gas-phase and condensed-phase spectra differ (rotational structure, hydrogen bonding); when no reference spectrum matches the sample phase the closest available one is used and phase_matched=false is reported.",
"Solution spectra contain CCl4/CS2 solvent-compensated regions; no noise, water-vapour/CO2 background, baseline drift or scan-averaging model.",
"Only one compound per sample; mixtures are not supported.",
]
SYNTHETIC_PARTS = ["host-chosen peak absorbance scale", "Gaussian instrument line shape", "cosine-synthesized interferogram"]
@lru_cache(maxsize=None)
def _table() -> dict[str, Any]:
"""Shared spectra; records corrected by the 2026-10-14 decoder fix are tagged with corrected_by / correction."""
table = copy.deepcopy(common.load_json(LIB_REL)["compounds"])
for spectra in table.values():
for spectrum in spectra:
note = spectrum.get("y_transform") or spectrum.get("x_step_note")
if note:
spectrum["corrected_by"] = DECODER_FIX
spectrum["correction"] = note
return table
def state_class(spectrum: dict[str, Any]) -> str:
text = (spectrum.get("state") or "").upper()
if "GAS" in text or "VAPOR" in text or "VAPOUR" in text:
return "gas"
if "SOLUTION" in text:
return "solution"
if "LIQUID" in text or "NEAT" in text:
return "liquid"
if "SOLID" in text or "KBR" in text or "MULL" in text or "NUJOL" in text:
return "solid"
return "unknown"
def source_resolution_cm(spectrum: dict[str, Any]) -> float:
match = re.search(r"[0-9]+(?:\.[0-9]+)?", str(spectrum.get("resolution") or ""))
value = float(match.group(0)) if match else GRID_STEP_CM
return max(value, GRID_STEP_CM)
PREFERENCE = {"liquid": ("liquid", "solution", "solid"), "solid": ("solid", "solution", "liquid"), "gas": ("gas",)}
def select_spectrum(substance_id: str, phase: str) -> tuple[int, dict[str, Any], bool] | None:
spectra = _table().get(substance_id) or []
if not spectra:
return None
for wanted in PREFERENCE[phase]:
for index, spectrum in enumerate(spectra):
if state_class(spectrum) == wanted:
return index, spectrum, True
return 0, spectra[0], False
def template_read(substance_id: Any) -> dict[str, Any] | None:
sid = common.resolve_compound_id(substance_id)
spectra = _table().get(sid) if sid else None
if not spectra:
return None
compound = common.compounds()[sid]
listing = []
for index, spectrum in enumerate(spectra):
values = spectrum["absorbance_normalized"]
covered = [i for i, v in enumerate(values) if v is not None]
listing.append({"index": index, "state": spectrum.get("state"), "state_class": state_class(spectrum),
"sampling": spectrum.get("sampling"), "source_resolution_m_inv": source_resolution_cm(spectrum) * CM_TO_M_INV,
"coverage_m_inv": [(GRID_START_CM + covered[0] * GRID_STEP_CM) * CM_TO_M_INV,
(GRID_START_CM + covered[-1] * GRID_STEP_CM) * CM_TO_M_INV],
"peaks_m_inv": [[p[0] * CM_TO_M_INV, p[1]] for p in spectrum.get("peaks_cm-1") or []],
"evidence": spectrum.get("evidence"), "source": spectrum.get("source"),
"corrected_by": spectrum.get("corrected_by")})
return {"substance_id": sid, "name": compound["name_en"], "name_zh": compound["name_zh"], "cas": compound["cas"],
"spectra": listing,
**common.provenance(SOURCES, "measured (NIST WebBook IR JCAMP-DX, transmission), normalised and resampled; records corrected by the 2026-10-14 decoder fix are flagged corrected_by",
SYNTHETIC_PARTS, LIMITATIONS)}
def validate_sample(substance_id: Any, *, phase: str, peak_absorbance: float = 1.0) -> dict[str, Any]:
if phase not in PHASES:
raise ValueError("phase must be solid, liquid or gas")
sid = common.resolve_compound_id(substance_id)
if sid is None or not _table().get(sid):
raise ValueError(f"{substance_id!r} has no IR spectrum in {LIB_REL}")
if not common.finite(peak_absorbance) or not 0 < peak_absorbance <= MAX_PEAK_ABSORBANCE:
raise ValueError(f"peak_absorbance must be in (0, {MAX_PEAK_ABSORBANCE}]")
index, spectrum, matched = select_spectrum(sid, phase)
return {"library": LIB_REL, "substance_id": sid, "phase": phase, "spectrum_index": index, "phase_matched": matched,
"state": spectrum.get("state"), "peak_absorbance": float(peak_absorbance)}
def _broadened(values: list[float | None], extra_fwhm_cm: float) -> tuple[list[float], float, float]:
covered = [i for i, v in enumerate(values) if v is not None]
lo, hi = covered[0], covered[-1]
data = [float(values[i]) for i in range(lo, hi + 1)]
if extra_fwhm_cm > 1e-9:
sigma = extra_fwhm_cm / (2 * math.sqrt(2 * math.log(2))) / GRID_STEP_CM
half = max(1, int(math.ceil(4 * sigma)))
kernel = [math.exp(-0.5 * (j / sigma) ** 2) for j in range(-half, half + 1)]
out = []
for i in range(len(data)):
num = den = 0.0
for j, weight in zip(range(i - half, i + half + 1), kernel):
if 0 <= j < len(data):
num += weight * data[j]
den += weight
out.append(num / den)
data = out
return data, GRID_START_CM + lo * GRID_STEP_CM, GRID_START_CM + hi * GRID_STEP_CM
def spectrum(template: dict[str, Any], state: dict[str, Any]) -> dict[str, Any] | None:
"""Agent-visible spectrum; None when the configured range does not overlap the reference coverage."""
reference = _table()[template["substance_id"]][template["spectrum_index"]]
requested_cm = state["method.resolution_m_inv"] / CM_TO_M_INV
source_cm = source_resolution_cm(reference)
effective_cm = max(requested_cm, source_cm)
extra = math.sqrt(max(0.0, effective_cm ** 2 - source_cm ** 2))
data, first_cm, last_cm = _broadened(reference["absorbance_normalized"], extra)
start_cm = max(state["method.start_wavenumber_m_inv"] / CM_TO_M_INV, first_cm)
stop_cm = min(state["method.stop_wavenumber_m_inv"] / CM_TO_M_INV, last_cm)
step_cm = max(GRID_STEP_CM, effective_cm / 2)
if stop_cm - start_cm < step_cm:
return None
count = int(math.floor((stop_cm - start_cm) / step_cm + 1e-9)) + 1
grid_cm = [first_cm + i * GRID_STEP_CM for i in range(len(data))]
top = max(data) or 1.0
axis, absorbance = [], []
for i in range(count):
x = start_cm + i * step_cm
value = common.interp(x, grid_cm, data)
axis.append(x * CM_TO_M_INV)
absorbance.append(max(0.0, value) / top * template["peak_absorbance"])
transmittance = [10.0 ** -a for a in absorbance]
top_m = axis[-1]
opd = [(index - (INTERFEROGRAM_POINTS - 1) // 2) / (2 * top_m) for index in range(INTERFEROGRAM_POINTS)]
interferogram = [sum(t * math.cos(2 * math.pi * nu * path) for nu, t in zip(axis, transmittance)) / len(axis) for path in opd]
return {"wavenumber_m_inv": axis, "absorbance": absorbance, "transmittance": transmittance,
"interferogram": {"optical_path_difference_m": opd, "relative_intensity": interferogram, "synthetic": True,
"axis_unit": "m", "signal_unit": "1"},
"reported_mode": state["method.output_mode"], "quality": "estimated", "axis_unit": "m^-1", "signal_unit": "1",
"resolution_m_inv": state["method.resolution_m_inv"], "effective_resolution_m_inv": effective_cm * CM_TO_M_INV,
"point_spacing_m_inv": step_cm * CM_TO_M_INV, "scan_count": state["method.scan_count"],
"spectral_resolution_applied": True, "scan_averaging_applied": False, "measurement_duration_s": None,
"requested_range_m_inv": [state["method.start_wavenumber_m_inv"], state["method.stop_wavenumber_m_inv"]],
"coverage_m_inv": [axis[0], axis[-1]], "reference_state": template["state"], "phase_matched": template["phase_matched"],
"accessory_mode": state["accessory.mode"], "atr_correction_applied": False,
**common.provenance(SOURCES, "measured (NIST WebBook IR, transmission) -> normalised, broadened to the configured resolution and resampled",
SYNTHETIC_PARTS, LIMITATIONS)}
def spectrum_schema() -> dict[str, Any]:
n, obj, nullable = common.number, common.obj, common.nullable
series = lambda unit, minimum=None: {"type": "array", "items": n(unit, minimum), "minItems": 2, "maxItems": 901}
pair = lambda unit: {"type": "array", "items": n(unit, 0), "minItems": 2, "maxItems": 2}
interferogram = obj({"optical_path_difference_m": {"type": "array", "items": n("m"), "minItems": INTERFEROGRAM_POINTS, "maxItems": INTERFEROGRAM_POINTS},
"relative_intensity": {"type": "array", "items": n("1"), "minItems": INTERFEROGRAM_POINTS, "maxItems": INTERFEROGRAM_POINTS},
"synthetic": {"type": "boolean", "const": True}, "axis_unit": {"type": "string", "const": "m"},
"signal_unit": {"type": "string", "const": "1"}})
return obj({"wavenumber_m_inv": series("m^-1", 0), "absorbance": series("1", 0), "transmittance": series("1", 0),
"interferogram": interferogram,
"reported_mode": {"type": "string", "enum": ["absorbance", "transmittance", "interferogram"]},
"quality": {"type": "string", "const": "estimated"}, "axis_unit": {"type": "string", "const": "m^-1"},
"signal_unit": {"type": "string", "const": "1"}, "resolution_m_inv": n("m^-1", 40),
"effective_resolution_m_inv": n("m^-1", 400), "point_spacing_m_inv": n("m^-1", 400),
"scan_count": {"type": "integer", "minimum": 1, "maximum": 1024, "x-unit": "1"},
"spectral_resolution_applied": {"type": "boolean", "const": True},
"scan_averaging_applied": {"type": "boolean", "const": False}, "measurement_duration_s": {"type": "null"},
"requested_range_m_inv": pair("m^-1"), "coverage_m_inv": pair("m^-1"), "reference_state": nullable(common.TEXT),
"phase_matched": {"type": "boolean"}, "accessory_mode": {"type": "string", "enum": ["atr", "transmission"]},
"atr_correction_applied": {"type": "boolean", "const": False}, **common.provenance_schema()})
def template_read_schema() -> dict[str, Any]:
n, obj, nullable = common.number, common.obj, common.nullable
item = obj({"index": {"type": "integer", "minimum": 0, "x-unit": "1"}, "state": nullable(common.TEXT),
"state_class": {"type": "string", "enum": ["gas", "solution", "liquid", "solid", "unknown"]},
"sampling": nullable(common.TEXT), "source_resolution_m_inv": n("m^-1", 0),
"coverage_m_inv": {"type": "array", "items": n("m^-1", 0), "minItems": 2, "maxItems": 2},
"peaks_m_inv": {"type": "array", "items": {"type": "array", "items": n("1"), "minItems": 2, "maxItems": 2}},
"evidence": common.TEXT, "source": common.TEXT, "corrected_by": nullable(common.TEXT)})
return obj({"substance_id": common.TEXT, "name": common.TEXT, "name_zh": common.TEXT, "cas": nullable(common.TEXT),
"spectra": {"type": "array", "items": item, "minItems": 1}, **common.provenance_schema()})
def extend_metadata(metadata: dict[str, Any]) -> dict[str, Any]:
legacy = metadata["capabilities"]["measure"]["output_schema"]["properties"]["spectrum"]
template = spectrum_schema()
metadata["capabilities"]["measure"]["output_schema"]["properties"]["spectrum"] = {"anyOf": [legacy, template]}
metadata["capabilities"]["measure"]["preconditions"] = metadata["capabilities"]["measure"]["preconditions"] + [
"Template-backed sample only: the configured wavenumber range must overlap the reference spectrum coverage by at least one output step."]
metadata["state_slots"]["measurement.spectrum"]["value_schema"] = {"anyOf": [legacy, template, {"type": "null"}]}
cap = common.template_read_capability(
"JascoFTIR4700", "ethyl_acetate", template_read_schema(), ["optical_module"],
"spectral_library compound id (NIST IR reference spectra); does not refer to the loaded sample")
cap["errors"] = ["UNKNOWN_INSTANCE", "UNKNOWN_CAPABILITY", "INVALID_ARGUMENT", "REQUEST_CONFLICT"]
metadata["capabilities"]["template.read"] = cap
metadata["parameters"]["template_library"] = {"value": SOURCES, "unit": "1", "evidence": "measured",
"conditions": "NIST WebBook IR transmission spectra, normalised absorbance on a 400-4000 cm^-1, 4 cm^-1 grid; not ATR"}
metadata["parameters"]["template_grid_step_m_inv"] = {"value": GRID_STEP_CM * CM_TO_M_INV, "unit": "m^-1", "evidence": "derived",
"conditions": "library resampling grid; output spacing = max(grid, effective resolution / 2)"}
metadata["limits"] = metadata["limits"] + [
"Template-backed samples (host register_template_sample) return NIST transmission IR spectra broadened to the configured resolution; no ATR correction. The synthetic Gaussian fixture path is unchanged and remains the default."]
return metadata
|