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Jungfraujoch/image_analysis/geom_refinement/BeamCenterFFTCPU.cpp
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v1.0.0-rc.169 (#79)
* Building Jungfraujoch no longer needs zlib or Eigen installed on the machine, and the dependencies the build fetches are pinned and updated to current releases.
* rugnux: improvements in indexing, lattice selection and geometry post-refinement, which index crystals that previously returned no lattice and keep the better of the two geometries a run measures.
* rugnux: improvements in beam-centre measurement, beam-stop detection and space-group determination.
* rugnux: the unit cell reported with a determined space group now obeys that group - a cell whose symmetry was confirmed from the intensities is re-refined under it, and a cell the group cannot describe is reported with a warning rather than as it stands.
* rugnux drops the stretches of a rotation sweep whose removal measurably improves the merged intensities and reports what became of every frame, and decides the resolution cut on the crystal's own diffraction rather than on its ice rings.
* The rugnux results report is machine-readable - every line that is not `KEY= value` data starts with `#` - and states the build it was written by, its authorship and its terms of use (`REPORT_VERSION= 8`).
* `jfjoch_viewer`: improvements in the file manager (CBF frames beside HDF5 datasets, a remembered root), the dataset plots, the inspector and the image statistics, plus a settable font size, a view of the rugnux results report, usable performance over a remote display (`ssh -X`) and a reset of all settings to defaults; the reciprocal-space window is removed.
* Broker fixes around DECTRIS collections and dark-mask calibration: re-initialising after a run that never started no longer freezes the broker, a cancelled calibration is abandoned instead of reported as done, and a collection whose start message never arrives ends by itself.

Reviewed-on: #79
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-09-15 17:09:31 +02:00

199 lines
8.5 KiB
C++

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "BeamCenterFFTCPU.h"
#include <algorithm>
#include <complex>
#include <cstring>
#include <mutex>
#include <stdexcept>
#include <fftw3.h>
namespace {
// FFTW planning is not thread-safe (execution is); same idiom as FFTIndexerCPU.
std::mutex &FftwPlanMutex() {
static std::mutex m;
return m;
}
// One real-to-complex 2D FFT workspace of fixed padded size, reused for every forward transform.
class Rfft2 {
int64_t ny, nx, nxc;
std::vector<float> real;
fftwf_plan fwd = nullptr;
fftwf_plan bwd = nullptr;
public:
std::vector<std::complex<float>> spectrum;
Rfft2(int64_t ny_, int64_t nx_) : ny(ny_), nx(nx_), nxc(nx_ / 2 + 1) {
real.resize(static_cast<size_t>(ny * nx));
spectrum.resize(static_cast<size_t>(ny * nxc));
std::unique_lock lock(FftwPlanMutex());
fwd = fftwf_plan_dft_r2c_2d(static_cast<int>(ny), static_cast<int>(nx), real.data(),
reinterpret_cast<fftwf_complex *>(spectrum.data()),
FFTW_ESTIMATE);
bwd = fftwf_plan_dft_c2r_2d(static_cast<int>(ny), static_cast<int>(nx),
reinterpret_cast<fftwf_complex *>(spectrum.data()),
real.data(), FFTW_ESTIMATE);
if (!fwd || !bwd)
throw std::runtime_error("BeamCenterFFT: fftwf plan failed");
}
Rfft2(const Rfft2 &) = delete;
Rfft2 &operator=(const Rfft2 &) = delete;
~Rfft2() {
std::unique_lock lock(FftwPlanMutex());
if (fwd)
fftwf_destroy_plan(fwd);
if (bwd)
fftwf_destroy_plan(bwd);
}
// Zero-pad `src` (height x width) into the workspace and return its spectrum.
std::vector<std::complex<float>> Forward(const std::vector<float> &src, int64_t height,
int64_t width) {
std::fill(real.begin(), real.end(), 0.0f);
for (int64_t y = 0; y < height; y++)
std::memcpy(&real[static_cast<size_t>(y * nx)], &src[static_cast<size_t>(y * width)],
sizeof(float) * static_cast<size_t>(width));
fftwf_execute(fwd);
return spectrum; // copy: the workspace is reused
}
// Inverse-transform the elementwise product u*v, normalised, cropped to out_h x out_w.
std::vector<float> InverseProduct(const std::vector<std::complex<float>> &u,
const std::vector<std::complex<float>> &v, int64_t out_h,
int64_t out_w) {
const float norm = 1.0f / (static_cast<float>(ny) * static_cast<float>(nx));
for (size_t i = 0; i < spectrum.size(); i++)
spectrum[i] = u[i] * v[i];
fftwf_execute(bwd);
std::vector<float> out(static_cast<size_t>(out_h * out_w));
for (int64_t y = 0; y < out_h; y++)
for (int64_t x = 0; x < out_w; x++)
out[static_cast<size_t>(y * out_w + x)] =
real[static_cast<size_t>(y * nx + x)] * norm;
return out;
}
};
std::vector<float> Transpose(const std::vector<float> &src, int64_t h, int64_t w) {
std::vector<float> out(src.size());
for (int64_t y = 0; y < h; y++)
for (int64_t x = 0; x < w; x++)
out[static_cast<size_t>(x * h + y)] = src[static_cast<size_t>(y * w + x)];
return out;
}
} // namespace
BeamCenterConvSurfaces2D BeamCenterFFTCPU::PointSurfaces(const std::vector<float> &a,
const std::vector<float> &m, int64_t h,
int64_t w) {
Rfft2 fft(BeamCenterFFTPadSize(2 * h), BeamCenterFFTPadSize(2 * w));
const auto A = fft.Forward(a, h, w);
const auto M = fft.Forward(m, h, w);
std::vector<float> a2(a.size());
for (size_t i = 0; i < a2.size(); i++)
a2[i] = a[i] * a[i];
const auto A2 = fft.Forward(a2, h, w);
BeamCenterConvSurfaces2D out;
out.C = fft.InverseProduct(A, A, 2 * h, 2 * w);
out.S = fft.InverseProduct(A, M, 2 * h, 2 * w);
out.Q = fft.InverseProduct(A2, M, 2 * h, 2 * w);
out.D = fft.InverseProduct(M, M, 2 * h, 2 * w);
return out;
}
// Each sequence is correlated with its own mirror and the four accumulators are summed over the
// other coordinate in double complex (the same cancellation argument as the 2D surface), so only
// four inverse transforms are needed however many sequences there are.
BeamCenterConvSurfaces1D BeamCenterFFTCPU::LineSurfaces(const std::vector<float> &a_in,
const std::vector<float> &m_in, int64_t h,
int64_t w, BeamCenterMirror mirror) {
// Mirroring the column coordinate is the same computation on the transposed image.
const std::vector<float> at = mirror == BeamCenterMirror::Rows ? std::vector<float>()
: Transpose(a_in, h, w);
const std::vector<float> mt = mirror == BeamCenterMirror::Rows ? std::vector<float>()
: Transpose(m_in, h, w);
const std::vector<float> &a = mirror == BeamCenterMirror::Rows ? a_in : at;
const std::vector<float> &m = mirror == BeamCenterMirror::Rows ? m_in : mt;
const int64_t nseq = mirror == BeamCenterMirror::Rows ? h : w;
const int64_t nbatch = mirror == BeamCenterMirror::Rows ? w : h;
const int64_t nfft = BeamCenterFFTPadSize(2 * nseq);
const int64_t nc = nfft / 2 + 1;
std::vector<float> in(static_cast<size_t>(nfft));
std::vector<std::complex<float>> A(static_cast<size_t>(nc)), M(static_cast<size_t>(nc)),
A2(static_cast<size_t>(nc));
std::vector<std::complex<double>> accC(static_cast<size_t>(nc)), accS(static_cast<size_t>(nc)),
accQ(static_cast<size_t>(nc)), accD(static_cast<size_t>(nc));
fftwf_plan fwd, bwd;
{
std::unique_lock lock(FftwPlanMutex());
fwd = fftwf_plan_dft_r2c_1d(static_cast<int>(nfft), in.data(),
reinterpret_cast<fftwf_complex *>(A.data()), FFTW_ESTIMATE);
bwd = fftwf_plan_dft_c2r_1d(static_cast<int>(nfft),
reinterpret_cast<fftwf_complex *>(A.data()), in.data(),
FFTW_ESTIMATE);
}
if (!fwd || !bwd)
throw std::runtime_error("BeamCenterFFT: fftwf 1D plan failed");
auto forward_into = [&](auto value_of, std::vector<std::complex<float>> &dst) {
for (int64_t y = 0; y < nseq; y++)
in[static_cast<size_t>(y)] = value_of(y);
std::fill(in.begin() + nseq, in.end(), 0.0f);
fftwf_execute_dft_r2c(fwd, in.data(), reinterpret_cast<fftwf_complex *>(A.data()));
dst = A;
};
for (int64_t x = 0; x < nbatch; x++) {
forward_into([&](int64_t y) { return a[static_cast<size_t>(y * nbatch + x)]; }, A2);
std::swap(A, A2); // A = spectrum of the sequence of a
std::vector<std::complex<float>> Acol = A;
forward_into([&](int64_t y) { return m[static_cast<size_t>(y * nbatch + x)]; }, M);
forward_into(
[&](int64_t y) {
const float v = a[static_cast<size_t>(y * nbatch + x)];
return v * v;
},
A2);
for (int64_t i = 0; i < nc; i++) {
const std::complex<double> ca(Acol[i]), cm(M[i]), ca2(A2[i]);
accC[i] += ca * ca;
accS[i] += ca * cm;
accQ[i] += ca2 * cm;
accD[i] += cm * cm;
}
}
const double norm = 1.0 / static_cast<double>(nfft);
auto inverse = [&](const std::vector<std::complex<double>> &acc) {
for (int64_t i = 0; i < nc; i++)
A[i] = std::complex<float>(acc[i]);
fftwf_execute_dft_c2r(bwd, reinterpret_cast<fftwf_complex *>(A.data()), in.data());
std::vector<double> out(static_cast<size_t>(2 * nseq));
for (int64_t i = 0; i < 2 * nseq; i++)
out[static_cast<size_t>(i)] = in[static_cast<size_t>(i)] * norm;
return out;
};
BeamCenterConvSurfaces1D out;
out.C = inverse(accC);
out.S = inverse(accS);
out.Q = inverse(accQ);
out.D = inverse(accD);
{
std::unique_lock lock(FftwPlanMutex());
fftwf_destroy_plan(fwd);
fftwf_destroy_plan(bwd);
}
return out;
}