v1.0.0-rc.178 (#88)

* Rugnux: Processes serial crystallography data from XFELs - SACLA (MPCCD), PAL-XFEL and European XFEL (CXI), LCLS (XTC) and SwissFEL Alvra (JUNGFRAU with a CrystFEL module geometry) - with several files or Jungfraujoch master files merged in one run (`rugnux *_master.h5`).
* Rugnux: Stills processing takes a known unit cell and space group as a starting point, finds the beam centre (and, with a cell, the detector distance) from the images, detects the saturation level in other facilities' files and refines the placement of individual detector panels.
* Rugnux: The stills report gives R_split and CC1/2 from frame half-sets, comparable with CrystFEL.
* jfjoch_viewer: Opens the same XFEL file formats.
* Validation: A stills battery checks Rugnux against deposited structures from SACLA, PAL-XFEL, LCLS, European XFEL and SwissFEL.
* Rugnux: More reliable convergence of rotation scaling, and live molecular replacement starts as soon as the model is uploaded.
* jfjoch_broker: Initialize clears the previous dataset's bearer tokens, image buffer and live Rugnux status, and a slow CUDA JIT cache is reported at start.

Reviewed-on: #88
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

image_analysis/structure_refinement/ModelStructureFactorsGPU.cu

@@ -280,7 +280,7 @@ void ModelStructureFactorsGPUEngine::Compute(const std::vector<ModelDensityAtom>
                                  cudaMemcpyHostToDevice, e.stream));
 
     e.density->Compute(e.pos, e.grid);
-    cufft_err(cufftExecR2C(e.forward, e.grid, reinterpret_cast<cufftComplex *>(e.spectrum.get())));
+    cufft_err(e.forward.R2C(e.grid, reinterpret_cast<cufftComplex *>(e.spectrum.get())));
     if (rows > 0) {
         compose_kernel<<<blocks(rows), THREADS, 0, e.stream>>>(e.spectrum, e.Norm(), g.nu, g.nv, g.nw, e.ops,
                                                                static_cast<int>(e.setup.sym_ops.size()), e.setup.den,
@@ -289,7 +289,7 @@ void ModelStructureFactorsGPUEngine::Compute(const std::vector<ModelDensityAtom>
     }
 
     e.mask->Compute(e.mask_atoms, static_cast<int>(mask_atoms.size()), e.grid);
-    cufft_err(cufftExecR2C(e.forward, e.grid, reinterpret_cast<cufftComplex *>(e.spectrum.get())));
+    cufft_err(e.forward.R2C(e.grid, reinterpret_cast<cufftComplex *>(e.spectrum.get())));
     if (rows > 0) {
         fmask_kernel<<<blocks(rows), THREADS, 0, e.stream>>>(e.spectrum, e.Norm(), e.row_hkl, rows, g.nu, g.nv, g.nw,
                                                              e.fmask);
@@ -320,7 +320,7 @@ void ModelStructureFactorsGPUEngine::Map(int nu, int nv, int nw, double volume,
                              e.stream));
     conjugate_kernel<<<blocks(complex_points), THREADS, 0, e.stream>>>(e.spectrum, complex_points);
     cuda_err(cudaGetLastError());
-    cufft_err(cufftExecC2R(plan, reinterpret_cast<cufftComplex *>(e.spectrum.get()),
+    cufft_err(plan.C2R(reinterpret_cast<cufftComplex *>(e.spectrum.get()),
                            reinterpret_cast<cufftReal *>(e.spectrum.get())));
     transpose_kernel<<<blocks(points), THREADS, 0, e.stream>>>(reinterpret_cast<const float *>(e.spectrum.get()),
                                                                nu, nv, nw, static_cast<float>(1.0 / volume), e.grid);