Integration radius: default r1=4, CLI flag, PixelRefine shares the knob

Bumped the default signal-box radius to r1=4 (r2=6, r3=8): on the lysozyme jet
(1% DMM) it lifts CCref 50.1->52.2% and CC1/2 90.8->92.5% (its broadened spots
spill past a radius-3 box), is neutral on the mono crystal and on the classical
integrator. Added 'jfjoch_process --integration-radius <r1|r1,r2,r3>' (a single
value derives r2=r1+2, r3=r1+4) and wired PixelRefine's shoebox radius to
BraggIntegrationSettings::GetR1() so it shares the classical integrator's knob.

(Explored but rejected: an elliptical/anisotropic Term-2 profile. The jet's
tangential spots are mildly anisotropic - axis ratio 1.15->1.44 low->high res,
azimuthal mosaic, separate from the radial DMM bandwidth - but using the measured
2x2 covariance as the profile DEGRADED the jet, CC1/2 92.5->83.5: the tight
measured width loses to a generous aperture, same lesson as the radius bump.)

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

common/BraggIntegrationSettings.h

@@ -6,8 +6,8 @@
 #include <optional>
 
 class BraggIntegrationSettings {
-    float r_1 = 3;
-    float r_2 = 5;
+    float r_1 = 4;
+    float r_2 = 6;
     float r_3 = 8;
     float d_min_limit_A = 1.0;
     std::optional<float> fixed_profile_radius;

image_analysis/IndexAndRefine.cpp

@@ -446,6 +446,9 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
     if (const auto bw = experiment.GetBandwidthFWHM())
         prd.bandwidth = bw.value() / 2.3548; // FWHM -> sigma
 
+    // Signal-box radius from the shared integration setting (same knob as BraggIntegrate2D).
+    prd.shoebox_radius = static_cast<int>(std::lround(experiment.GetBraggIntegrationSettings().GetR1()));
+
     std::vector<uint8_t> buffer;
     const uint8_t *ptr = image.GetUncompressedPtr(buffer);
     switch (image.GetMode()) {

tools/jfjoch_process.cpp

@@ -80,6 +80,7 @@ void print_usage() {
 
     std::cout << "  Pixel refinement (experimental, select via -r pixelrefine, needs --reference-mtz)" << std::endl;
     std::cout << "   --bandwidth <num>               Relative X-ray bandwidth FWHM (e.g. 0.01 for 1% DMM); default from file or 0" << std::endl;
+    std::cout << "   --integration-radius <r>        Signal-box radius r1, or r1,r2,r3 (px). One value => r2=r1+2, r3=r1+4" << std::endl;
     }
 
 enum {
@@ -95,7 +96,8 @@ enum {
     OPT_SINGLE_PASS_ROTATION,
     OPT_REDO_ROTATION_SPOTS,
     OPT_FORCE_ROTATION_LATTICE,
-    OPT_BANDWIDTH
+    OPT_BANDWIDTH,
+    OPT_INTEGRATION_RADIUS
 };
 
 static option long_options[] = {
@@ -132,6 +134,7 @@ static option long_options[] = {
     {"scaling-high-resolution", required_argument, nullptr, OPT_SCALING_HIGH_RESOLUTION},
     {"scaling-output", required_argument, nullptr, OPT_SCALING_OUTPUT},
     {"bandwidth", required_argument, nullptr, OPT_BANDWIDTH},
+    {"integration-radius", required_argument, nullptr, OPT_INTEGRATION_RADIUS},
     {nullptr, 0, nullptr, 0}
 };
 
@@ -312,6 +315,7 @@ int main(int argc, char **argv) {
 
     float d_min_spot_finding = 1.5;
     std::optional<float> d_min_scale_merge;
+    std::optional<std::string> integration_radius_arg; // "r1" or "r1,r2,r3"
 
     if (argc == 1) {
         print_usage();
@@ -501,6 +505,9 @@ int main(int argc, char **argv) {
         case OPT_MIN_PARTIALITY:
             min_partiality = std::stod(optarg);
             break;
+        case OPT_INTEGRATION_RADIUS:
+            integration_radius_arg = optarg;
+            break;
         case OPT_MIN_IMAGE_CC:
             min_image_cc = std::stod(optarg);
             break;
@@ -671,6 +678,26 @@ int main(int argc, char **argv) {
 
     experiment.ImportScalingSettings(scaling_settings);
 
+    // Integration radii: r1 (signal box), r2/r3 (background annulus). PixelRefine reads
+    // r1 as its shoebox radius; the classical integrator uses all three.
+    if (integration_radius_arg) {
+        std::vector<float> rr;
+        std::stringstream ss(*integration_radius_arg);
+        std::string tok;
+        while (std::getline(ss, tok, ',')) {
+            trim_in_place(tok);
+            if (!tok.empty()) rr.push_back(std::stof(tok));
+        }
+        float r1, r2, r3;
+        if (rr.size() == 1) { r1 = rr[0]; r2 = r1 + 2.0f; r3 = r1 + 4.0f; }
+        else if (rr.size() == 3) { r1 = rr[0]; r2 = rr[1]; r3 = rr[2]; }
+        else { logger.Error("--integration-radius expects r1 or r1,r2,r3"); return 1; }
+        BraggIntegrationSettings bis = experiment.GetBraggIntegrationSettings();
+        bis.R1(r1).R2(r2).R3(r3);
+        experiment.ImportBraggIntegrationSettings(bis);
+        logger.Info("Integration radii set to r1={:.1f} r2={:.1f} r3={:.1f}", r1, r2, r3);
+    }
+
     SpotFindingSettings spot_settings;
     spot_settings.enable = true;
     spot_settings.indexing = true;