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Jungfraujoch/gemmi_gph/gemmi/bessel.hpp
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v1.0.0-rc.159 (#69)
This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use.

* rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell.
* rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged.
* rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set.
* rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme.
* rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free.
* rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry.
* Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md.
* Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #69

Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-07-13 13:54:03 +02:00

129 lines
3.9 KiB
C++

// Functions derived from modified Bessel functions I1(x) and I0(x).
//
// Crystallographic codes (including Refmac and cctbx) often use polynomial
// approximation of I0 and I1 from p. 378 of Abramowitz and Stegun.
// Gemmi uses approximation based on polynomial coefficients from bessel_i0
// and bessel_i1(float) from Boost.Math:
// https://www.boost.org/doc/libs/1_76_0/libs/math/doc/html/math_toolkit/bessel/mbessel.html
// This approximation was derived in 2017 by John Maddock,
// building on the work of Pavel Holoborodko:
// https://www.advanpix.com/2015/11/11/rational-approximations-for-the-modified-bessel-function-of-the-first-kind-i0-computations-double-precision/
// The efficiency is similar to that of scitbx.math.bessel_i1_over_i0.
// Using std::cyl_bessel_if was not considered, because it requires C++17,
#ifndef GEMMI_BESSEL_HPP_
#define GEMMI_BESSEL_HPP_
#include <cmath>
namespace gemmi {
template<int N>
inline double evaluate_polynomial(const double(&poly)[N], double x) {
static_assert(N > 1, "");
double result = poly[N-1];
for (int i = N-2; i >= 0; --i)
result = result * x + poly[i];
return result;
}
template<class Dummy>
struct BesselTables_
{
static const double P1[8];
static const double Q1[9];
static const double P2[5];
static const double Q2[5];
static const double Q3[3];
};
template<class Dummy> const double BesselTables_<Dummy>::P1[8] = {
8.333333221e-02,
6.944453712e-03,
3.472097211e-04,
1.158047174e-05,
2.739745142e-07,
5.135884609e-09,
5.262251502e-11,
1.331933703e-12
};
template<class Dummy> const double BesselTables_<Dummy>::Q1[9] = {
1.00000003928615375e+00,
2.49999576572179639e-01,
2.77785268558399407e-02,
1.73560257755821695e-03,
6.96166518788906424e-05,
1.89645733877137904e-06,
4.29455004657565361e-08,
3.90565476357034480e-10,
1.48095934745267240e-11
};
template<class Dummy> const double BesselTables_<Dummy>::P2[5] = {
3.98942115977513013e-01,
-1.49581264836620262e-01,
-4.76475741878486795e-02,
-2.65157315524784407e-02,
-1.47148600683672014e-01
};
template<class Dummy> const double BesselTables_<Dummy>::Q2[5] = {
3.98942651588301770e-01,
4.98327234176892844e-02,
2.91866904423115499e-02,
1.35614940793742178e-02,
1.31409251787866793e-01
};
template<class Dummy> const double BesselTables_<Dummy>::Q3[3] = {
3.98942391532752700e-01,
4.98455950638200020e-02,
2.94835666900682535e-02
};
inline double bessel_i1_over_i0(double x) {
using B = BesselTables_<void>;
if (x < 0)
return -bessel_i1_over_i0(-x);
if (x < 7.75) {
double a = x * x / 4;
double bessel0 = a * evaluate_polynomial(B::Q1, a) + 1;
double R[3] = { 1, 0.5f, evaluate_polynomial(B::P1, a) };
double bessel1 = x * evaluate_polynomial(R, a) / 2;
return bessel1 / bessel0;
}
double p = evaluate_polynomial(B::P2, 1 / x);
double q = x < 50 ? evaluate_polynomial(B::Q2, 1 / x)
: evaluate_polynomial(B::Q3, 1 / x);
return p / q;
}
// Simplified function from Boost.Math.
// Similar to std::cyl_bessel_i(0, x), but much faster, less exact and doesn't
// throw out_of_range on negative argument. Relative error < 5.02e-08.
inline double bessel_i0(double x) {
using B = BesselTables_<void>;
x = std::fabs(x);
if (x < 7.75) {
double a = x * x / 4;
return a * evaluate_polynomial(B::Q1, a) + 1;
}
if (x < 50)
return std::exp(x) * evaluate_polynomial(B::Q2, 1 / x) / std::sqrt(x);
double ex = std::exp(x / 2);
return ex * evaluate_polynomial(B::Q3, 1 / x) / std::sqrt(x) * ex;
}
// Relative error < 4e-08.
inline double log_bessel_i0(double x) {
using B = BesselTables_<void>;
x = std::fabs(x);
if (x < 7.75) {
double a = x * x / 4;
return std::log1p(a * evaluate_polynomial(B::Q1, a));
}
double q = x < 50 ? evaluate_polynomial(B::Q2, 1 / x)
: evaluate_polynomial(B::Q3, 1 / x);
return x + std::log(q / std::sqrt(x));
}
} // namespace gemmi
#endif