PixelRefine: profile multiplier as --profile-multiplier flag; outlier rejection default off

(1) Promote the Term-2 profile-width multiplier from the PR_RMULT env knob to a real
BraggIntegrationSettings::profile_multiplier (default 6) + jfjoch_process
--profile-multiplier flag. Removes the last PR_* env knob; IndexAndRefine reads the
setting. (2) Flip the merge outlier rejection default to OFF (ScalingSettings
outlier_reject_nsigma 6 -> 0); it stays available via --reject-outliers <nsigma>, since
it helps the jet R-free but is dataset-dependent (drops crystal-2 CCref).

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

common/BraggIntegrationSettings.cpp

@@ -72,6 +72,17 @@ float BraggIntegrationSettings::GetR1() const {
     return r_1;
 }
 
+float BraggIntegrationSettings::GetProfileMultiplier() const {
+    return profile_multiplier;
+}
+
+BraggIntegrationSettings &BraggIntegrationSettings::ProfileMultiplier(float input) {
+    if (input <= 0.0f)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Profile multiplier must be positive");
+    profile_multiplier = input;
+    return *this;
+}
+
 float BraggIntegrationSettings::GetR2() const {
     return r_2;
 }

common/BraggIntegrationSettings.h

@@ -12,6 +12,10 @@ class BraggIntegrationSettings {
     float d_min_limit_A = 1.0;
     std::optional<float> fixed_profile_radius;
     float minimum_sigma_in_regards_to_i = 0.02;
+    // PixelRefine only: the measured (physical) tangential profile width is multiplied by
+    // this for the integration template, so the aperture is generous (XDS-style ~6 sigma)
+    // and tolerant of the centroid-floor scatter. Ignored by the classical integrator.
+    float profile_multiplier = 6.0;
 
 public:
     BraggIntegrationSettings& R1(float input);
@@ -19,11 +23,13 @@ public:
     BraggIntegrationSettings& R3(float input);
     BraggIntegrationSettings& DMinLimit_A(float input);
     BraggIntegrationSettings& FixedProfileRadius_recipA(std::optional<float> input);
+    BraggIntegrationSettings& ProfileMultiplier(float input);
 
 
     [[nodiscard]] float GetR1() const;
     [[nodiscard]] float GetR2() const;
     [[nodiscard]] float GetR3() const;
+    [[nodiscard]] float GetProfileMultiplier() const;
     [[nodiscard]] std::optional<float> GetFixedProfileRadius_recipA() const;
     [[nodiscard]] float GetDMinLimit_A() const;
 

common/ScalingSettings.h

@@ -23,7 +23,7 @@ class ScalingSettings {
     std::optional<double> wedge_for_scaling;
     double min_partiality = 0.02;
     double min_cc_for_image = 0.0;
-    double outlier_reject_nsigma = 6.0; // per-observation merge outlier rejection (XDS/DIALS-style); <= 0 disables
+    double outlier_reject_nsigma = 0.0; // per-observation merge outlier rejection (XDS/DIALS-style); 0 = off, e.g. 6 enables
 
     double rfree_fraction = 0.05;
     IntensityFormat intensity_format = IntensityFormat::MTZ;

image_analysis/IndexAndRefine.cpp

@@ -448,7 +448,7 @@ bool IndexAndRefine::PixelRefineIntegrate(DataMessage &msg,
 
     // Signal-box radius from the shared integration setting (same knob as BraggIntegrate2D).
     prd.shoebox_radius = static_cast<int>(std::lround(experiment.GetBraggIntegrationSettings().GetR1()));
-    if (const char *m = std::getenv("PR_RMULT")) prd.r1_multiplier = std::stod(m); // Term-2 R1 multiplier (default 6)
+    prd.r1_multiplier = experiment.GetBraggIntegrationSettings().GetProfileMultiplier();
 
     std::vector<uint8_t> buffer;
     const uint8_t *ptr = image.GetUncompressedPtr(buffer);

tools/jfjoch_process.cpp

@@ -72,7 +72,7 @@ void print_usage() {
     std::cout << "   -w, --wedge[=num]               Refine image wedge during scaling with starting wedge value" << std::endl;
     std::cout << "   --scaling-high-resolution <num> High resolution limit for spot finding (default: no limit)" << std::endl;
     std::cout << "   --min-partiality <num>          Minimum partiality to accept reflection (default: 0.02)" << std::endl;
-    std::cout << "   --reject-outliers <num>         Per-observation merge outlier rejection, N sigma from the per-reflection median (default: 6; 0 disables)" << std::endl;
+    std::cout << "   --reject-outliers <num>         Per-observation merge outlier rejection, N sigma from the per-reflection median (default: off; e.g. 6, XDS/DIALS-style)" << std::endl;
     std::cout << "   --min-image-cc <num>            Per-image CC limit in percent (default: no limit)" << std::endl;
     std::cout << "   --scaling-iterations <num>      Number of scaling iterations with no reference data (default: 3)" << std::endl;
     std::cout << "   --scaling-output <txt>              Output format for scaling results mtz|cif|txt (default: mtz)" << std::endl;
@@ -82,6 +82,7 @@ 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;
+    std::cout << "   --profile-multiplier <num>      PixelRefine: scale the measured tangential profile width R1 (default: 6; XDS-style generous aperture)" << std::endl;
     }
 
 enum {
@@ -99,7 +100,8 @@ enum {
     OPT_FORCE_ROTATION_LATTICE,
     OPT_BANDWIDTH,
     OPT_INTEGRATION_RADIUS,
-    OPT_REJECT_OUTLIERS
+    OPT_REJECT_OUTLIERS,
+    OPT_PROFILE_MULTIPLIER
 };
 
 static option long_options[] = {
@@ -138,6 +140,7 @@ static option long_options[] = {
     {"bandwidth", required_argument, nullptr, OPT_BANDWIDTH},
     {"integration-radius", required_argument, nullptr, OPT_INTEGRATION_RADIUS},
     {"reject-outliers", required_argument, nullptr, OPT_REJECT_OUTLIERS},
+    {"profile-multiplier", required_argument, nullptr, OPT_PROFILE_MULTIPLIER},
     {nullptr, 0, nullptr, 0}
 };
 
@@ -320,6 +323,7 @@ int main(int argc, char **argv) {
     std::optional<float> d_min_scale_merge;
     std::optional<std::string> integration_radius_arg; // "r1" or "r1,r2,r3"
     std::optional<double> outlier_reject_nsigma;       // merge per-observation outlier rejection
+    std::optional<float> profile_multiplier;           // PixelRefine Term-2 profile-width multiplier
 
     if (argc == 1) {
         print_usage();
@@ -515,6 +519,9 @@ int main(int argc, char **argv) {
         case OPT_REJECT_OUTLIERS:
             outlier_reject_nsigma = std::stod(optarg);
             break;
+        case OPT_PROFILE_MULTIPLIER:
+            profile_multiplier = std::stof(optarg);
+            break;
         case OPT_MIN_IMAGE_CC:
             min_image_cc = std::stod(optarg);
             break;
@@ -707,6 +714,13 @@ int main(int argc, char **argv) {
         logger.Info("Integration radii set to r1={:.1f} r2={:.1f} r3={:.1f}", r1, r2, r3);
     }
 
+    if (profile_multiplier) {
+        BraggIntegrationSettings bis = experiment.GetBraggIntegrationSettings();
+        bis.ProfileMultiplier(*profile_multiplier);
+        experiment.ImportBraggIntegrationSettings(bis);
+        logger.Info("PixelRefine profile-width multiplier set to {:.1f}", *profile_multiplier);
+    }
+
     SpotFindingSettings spot_settings;
     spot_settings.enable = true;
     spot_settings.indexing = true;