tem op• Data kinds: image2d → table
• Call: import fullseye as fs; fs.ledger.tem_ctf_estimate(image, pixel_A=1.0, kv=300.0, cs_mm=2.7, amplitude_contrast=0.07, phase_shift_deg=0.0, defocus_min_A=3000.0, defocus_max_A=50000.0, k_min=0.03333333333333333, k_max=None, tile=None, overlap=0.5, astigmatism=True, min_rings=3, min_peak_z=8.0, on_fail='raise') (to call the implementation directly, import temsim; temsim.tem_ctf_estimate(image, pixel_A=1.0, kv=300.0, cs_mm=2.7, amplitude_contrast=0.07, phase_shift_deg=0.0, defocus_min_A=3000.0, defocus_max_A=50000.0, k_min=0.03333333333333333, k_max=None, tile=None, overlap=0.5, astigmatism=True, min_rings=3, min_peak_z=8.0, on_fail='raise'); from the registry, opsoptics.get("tem_ctf_estimate"))
Estimate defocus (and astigmatism) from the Thon rings in the power spectrum of a micrograph (table).
> The detailed description below is the original text — the summary and the headings are translated.
手順: (1) タイルの平均のパワースペクトル(tem_power_spectrum と同じ)→ 振幅スペクトル √PS。
(2) 動径平均を k について等間隔に取り、k² について不等間隔の標本に Lomb–Scargle(mathspectral)を掛けて
リングの周期 1/(λΔf) から初期値。(3) 背景 = u = k² の上でリング 1 周期の移動平均、振れ幅で割って平坦にする。
(4) Δf を格子で掃き(位相が k_max で π/8 ずつ動く刻み)、CTF² との正規化相互相関(CTFFIND4 の採点の考え方)が
最大の所を有界の 1 次元探索で詰める。(5) astigmatism=True なら 2-D の環の上で (Δf_u, Δf_v, θ) を Nelder–Mead で詰める(決まった 4 方向から出発、乱数なし)。(6) 不確かさ = タイルを 8 組に分けた jackknife の標準誤差(Δf の平均)。
拒否(on_fail="raise" で ValueError、"report" で accepted=False の表): 相関の最大が掃いた格子の中央値から MAD の min_peak_z 倍に届かない(リングが雑音に埋もれた)、帯域 [k_min, k_max] に零点が min_rings 個無い(周期が決まらない)、最大が探索範囲の端(範囲の外にある疑い)。
返り値: defocus_A(平均)/ defocus_u_A ≥ defocus_v_A / astig_angle_deg(Δf_u の軸、0〜180)/ defocus_sigma_A(jackknife)/ score(2-D の相関)/ score_1d / peak_z / n_rings / fit_resolution_A(局所の相関が 0.3 を下回る最初の周波数の逆数)/ initial_lomb_A / accepted / reason / 曲線 k と flat(平坦にした動径平均)と model。
Every optics op validates its input before computing (nothing slips through silently):
• Units are baked into the argument name — _mm / _um / _deg / _mrad. Confusing mm with µm does not crash; it yields a plausible-looking wrong answer, so the name prevents it. Nothing here guesses the unit from the magnitude.
• Strings raise ValueError — float('50') succeeds, so an unparsed configuration value would slip through as a length (measured: thin_lens('50', '200') returned a plausible 66.667 mm). bool is refused too, as the implicit promotion True == 1.
• complex / masked arrays raise ValueError (real-valued slots only; silently dropping the imaginary part or peeling off the mask is refused). NaN/Inf raises ValueError on every input.
• Division by zero and its relatives are refused by name: focal length 0, radius of curvature 0, refractive index <= 0, a fully opaque aperture (all zeros, so the normalisation is 0/0), a PSF whose sum is <= 0, a Stokes vector with S0 = 0, and an object sitting at the front focal point (the image is at infinity).
• Only two ops return a non-finite value, and both state it as a contract: depth_of_field returns far_mm = inf beyond the hyperfocal distance (that is what the hyperfocal distance means), and gaussian_beam returns wavefront_radius_mm = inf at the waist (the radius of curvature of a plane wavefront). Both also return a finite companion (far_is_infinite / curvature_per_mm). Any other silent NaN/Inf is detected internally and raises ValueError — "float64 overflowed" and "the answer is infinite" are different claims, so the first is never returned wearing the face of the second.
• Size caps: generated grids are capped by optics.MAX_GRID (4096); supplied fields/PSFs/apertures by optics.MAX_FIELD_ELEMENTS (2^24); ABCD element chains by optics.MAX_SYSTEM_ELEMENTS (1024); Zernike by MAX_ZERNIKE_TERMS (512) / MAX_ZERNIKE_ORDER (40) / MAX_ZERNIKE_BASIS (2^25). This closes, fail-closed, the paths where a small argument triggers a huge internal allocation (measured: n_max=40 × 4096² needs 108 GB).
• Physically impossible states are refused too: a Stokes vector with degree of polarisation > 1, negative transmittance, negative intensity, and invalid Zernike indices such as n-|m| odd.
• Sample-data catalog (download URLs / licences) — 2-D uses skimage.data (BSD/public domain) plus synthetic images; 3-D lists download URLs for real data sources (Stanford, PDS, …).
• Operator provenance and references — the sources of the research/methods this op family came from.
• The canonical algorithm (author, year) and its uses are named in the family usage guide above.
• poc_tem_ctf_thon_rings — py -3.11 examples/poc_tem_ctf_thon_rings.py
table as input)abcd_matrix · wavefront_stats · sfr_from_edge · paraxial_trace · seidel_coefficients · spot_stats · tolerance_analysis · wavefront_from_opd
tem)tem_wavelength · tem_scherzer · tem_ctf · tem_ctf_profile · tem_projected_potential · tem_amorphous_film · tem_image_weak_phase · tem_multislice
*Provenance: temsim.py — OPTICS operator registry. This per-op note is generated by tools/opdocs.py md (do not hand-edit).*
© 2026 Kazufumi Furuse — Fullseye operator documentation. Licensed under Apache-2.0.