jfjoch_process: optional absorption surface for rot3d scaling (--absorption)

Adds an opt-in smooth absorption correction for rotation scaling. After the
rot3d fulls are scaled, --absorption[=num] fits a multiplicative surface
A(s1_crystal) - a degree<=4 monomial basis (real spherical harmonics up to l=4,
as XDS/DIALS) of the diffracted-beam direction in the crystal/goniometer frame,
by ridge-regularized log-linear least-squares of I_scaled/I_ref weighted by
(I/sigma)^2, over num iterations (default 3); the surface divides image_scale_corr
and the fulls are re-merged.

Off by default and a no-op without rot3d. On the test panel (~13 keV, thin
crystals) it is metric-neutral - fitted rms(log A) ~3-4%, ISa/CC1/2 unchanged -
because absorption is negligible there and the per-frame scale G(phi) already
absorbs the angular part. It is kept as a lever for low-energy data (e.g. 6 keV)
where absorption becomes significant. Stored as ScalingSettings::absorption_iter.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

tools/jfjoch_process.cpp

@@ -52,6 +52,7 @@ void print_usage() {
     std::cout << "   --scale-fulls                   After -P rot3d combine, refit a per-frame scale on the fulls (XDS order, Unity model); implies -M. Default ON for rot3d" << std::endl;
     std::cout << "   --no-scale-fulls                Disable the rot3d scale-fulls refit (it is on by default for rot3d)" << std::endl;
     std::cout << "   --write-process-h5              Also write the (large) _process.h5 when merging (default: only .mtz/.cif when merging)" << std::endl;
+    std::cout << "   --absorption[=num]              rot3d: fit a smooth absorption surface on the fulls over num iterations (default 3; off by default; matters at low energy)" << std::endl;
     std::cout << "   --smooth-g[=num]                rot3d: smooth per-frame scale G over a num-frame window before the combine (default: 9 for rot3d; 0 = off)" << std::endl;
     std::cout << "   -P, --partiality <txt>          Partiality model fixed|rot|rot3d|unity (default: fixed). rot3d = rot + 3D combine of per-frame partials" << std::endl;
     std::cout << "   -A, --anomalous                 Anomalous mode (don't merge Friedel pairs)" << std::endl;
@@ -103,7 +104,8 @@ enum {
     OPT_SMOOTH_G,
     OPT_RECIPROCAL_PROFILE,
     OPT_NO_SCALE_FULLS,
-    OPT_WRITE_PROCESS_H5
+    OPT_WRITE_PROCESS_H5,
+    OPT_ABSORPTION
 };
 
 static option long_options[] = {
@@ -127,6 +129,7 @@ static option long_options[] = {
     {"scale-fulls", no_argument, nullptr, OPT_SCALE_FULLS},
     {"no-scale-fulls", no_argument, nullptr, OPT_NO_SCALE_FULLS},
     {"write-process-h5", no_argument, nullptr, OPT_WRITE_PROCESS_H5},
+    {"absorption", optional_argument, nullptr, OPT_ABSORPTION},
     {"smooth-g", optional_argument, nullptr, OPT_SMOOTH_G},
     {"refine", required_argument, nullptr, 'r'},
 
@@ -291,6 +294,7 @@ int main(int argc, char **argv) {
     bool run_scaling = false;
     std::optional<bool> scale_fulls_arg;   // --scale-fulls / --no-scale-fulls; default on for rot3d
     bool write_process_h5_flag = false;    // --write-process-h5; also write _process.h5 when merging
+    int absorption_iter = 0;               // --absorption[=n]; rot3d absorption-surface iterations (0 = off)
     std::optional<int> smooth_g_window_arg;   // --smooth-g[=window]; default 9 for rot3d, 0 (off) otherwise
     bool anomalous_mode = false;
     std::optional<int64_t> space_group_number;
@@ -531,6 +535,10 @@ int main(int argc, char **argv) {
         case OPT_WRITE_PROCESS_H5:
             write_process_h5_flag = true;
             break;
+        case OPT_ABSORPTION:
+            absorption_iter = optarg ? std::stoi(optarg) : 3;
+            run_scaling = true;
+            break;
         case OPT_SMOOTH_G:
             smooth_g_window_arg = optarg ? std::stoi(optarg) : 9;
             break;
@@ -748,6 +756,7 @@ int main(int argc, char **argv) {
     scaling_settings.SetPartialityModel(partiality_model);
     scaling_settings.Combine3D(combine_3d);
     scaling_settings.ScaleFulls(scale_fulls);
+    scaling_settings.AbsorptionIter(absorption_iter);
     scaling_settings.SmoothGWindow(smooth_g_window_arg.value_or(combine_3d ? 9 : 0));
     if (d_min_scale_merge)
         scaling_settings.HighResolutionLimit_A(d_min_scale_merge.value());