jfjoch_process/scale: default to mmCIF, auto-detect rotation, rot3d partiality

- Default reflection format is now mmCIF (ScalingSettings.h, the single source of
  truth). jfjoch_process and jfjoch_scale no longer hard-code a local MTZ default;
  they override only when --scaling-output is given. jfjoch_viewer inherits this.
- A dataset with a rotation goniometer axis is processed as rotation data (two-pass
  indexing) by default; add --process-as-stills to force per-frame stills. -R still
  tunes the first-pass image count.
- rot3d is the default partiality model for rotation processing (fixed for stills)
  when no explicit -P is given.
- Update docs/JFJOCH_PROCESS.md: new de-novo rotation/stills examples, corrected
  -R/-P/--scaling-output defaults, --process-as-stills, and a real Integration table.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

tools/jfjoch_process.cpp

@@ -45,7 +45,9 @@ void print_usage() {
     std::cout << std::endl;
 
     std::cout << "  Indexing" << std::endl;
-    std::cout << "   -R, --two-pass-rotation[=num]    Two-pass offline rotation indexing (optional: number of images, default: 100)" << std::endl;
+    std::cout << "   (A dataset with a rotation goniometer axis is processed as rotation data by default; use --process-as-stills to override)" << std::endl;
+    std::cout << "   --process-as-stills              Process a rotation (goniometer) dataset as independent stills instead of rotation" << std::endl;
+    std::cout << "   -R, --two-pass-rotation[=num]    Two-pass offline rotation indexing (default for goniometer data; optional first-pass image count, default: 100)" << std::endl;
     std::cout << "   --single-pass-rotation[=num]     Use online-like single-pass rotation indexing (optional: min angular range deg)" << std::endl;
     std::cout << "   --redo-rotation-spots            Redo spot finding for two-pass rotation indexing" << std::endl;
     std::cout << "   --force-rotation-lattice <vec>   Force rotation indexer with external lattice (in Angstrom) : \"a0x,a0y,a0z,a1x,a1y,a1z,a2x,a2y,a2z\" (9 floats, skips first pass)" << std::endl;
@@ -62,7 +64,7 @@ void print_usage() {
     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[=deg]                rot3d: smooth per-frame scale G over a deg-degree rotation range (XDS DELPHI-like) before the combine (default: 5 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 << "   -P, --partiality <txt>          Partiality model fixed|rot|rot3d|unity (default: rot3d for rotation data, fixed for stills). rot3d = rot + 3D combine of per-frame partials" << std::endl;
     std::cout << "   -A, --anomalous                 Anomalous mode (don't merge Friedel pairs)" << std::endl;
     std::cout << "   -B, --refine-bfactor            Refine per image B-factor" << std::endl;
     std::cout << "   -w, --wedge[=num]               Refine image wedge during scaling with starting wedge value" << std::endl;
@@ -74,7 +76,7 @@ void print_usage() {
     std::cout << "   --reject-delta-cchalf <num>     Per-crystal CC1/2-delta rejection: drop images with deltaCChalf below mean - N*stddev (default: off; e.g. 2.5)" << 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;
+    std::cout << "   --scaling-output <txt>              Output format for scaling results mtz|cif|txt (default: cif)" << std::endl;
     std::cout << "   -z, --reference-mtz <file>      Reference MTZ file" << std::endl;
     std::cout << "   --reference-column <label>      Reference MTZ column to use (default: auto - F-model, else IMEAN/I/...)" << std::endl;
     std::cout << std::endl;
@@ -114,7 +116,8 @@ enum {
     OPT_DETECT_ICE_RINGS,
     OPT_NO_SCALE_FULLS,
     OPT_WRITE_PROCESS_H5,
-    OPT_ABSORPTION
+    OPT_ABSORPTION,
+    OPT_PROCESS_AS_STILLS
 };
 
 static option long_options[] = {
@@ -144,6 +147,7 @@ static option long_options[] = {
 
     {"two-pass-rotation", optional_argument, nullptr, 'R'},
     {"single-pass-rotation", optional_argument, nullptr, OPT_SINGLE_PASS_ROTATION},
+    {"process-as-stills", no_argument, nullptr, OPT_PROCESS_AS_STILLS},
     {"redo-rotation-spots", no_argument, nullptr, OPT_REDO_ROTATION_SPOTS},
     {"force-rotation-lattice", required_argument, nullptr, OPT_FORCE_ROTATION_LATTICE},
 
@@ -297,6 +301,7 @@ int main(int argc, char **argv) {
 
     bool verbose = false;
     bool rotation_indexing = false;
+    bool process_as_stills = false;     // --process-as-stills: force per-frame stills on a rotation dataset
     bool two_pass_rotation = true;
     bool reuse_rotation_spots = true;
     int rotation_indexing_image_count = 100;
@@ -331,8 +336,9 @@ int main(int argc, char **argv) {
     IndexingAlgorithmEnum indexing_algorithm = IndexingAlgorithmEnum::Auto;
     GeomRefinementAlgorithmEnum refinement_algorithm = GeomRefinementAlgorithmEnum::BeamCenter;
 
-    IntensityFormat intensity_format = IntensityFormat::MTZ;
+    std::optional<IntensityFormat> intensity_format;   // --scaling-output override; default lives in ScalingSettings (mmCIF)
     PartialityModel partiality_model = PartialityModel::Fixed;
+    bool partiality_explicit = false;   // true once -P is given, so the rotation/stills default does not override it
     bool combine_3d = false;   // -P rot3d: weight-sum per-frame partials into fulls before merging
 
     float d_min_spot_finding = 1.5;
@@ -515,6 +521,7 @@ int main(int argc, char **argv) {
                 print_usage();
                 exit(EXIT_FAILURE);
             }
+            partiality_explicit = true;
             break;
         case OPT_SPOT_SIGMA:
             sigma_spot_finding = atof(optarg);
@@ -601,6 +608,9 @@ int main(int argc, char **argv) {
                 exit(EXIT_FAILURE);
             }
             break;
+        case OPT_PROCESS_AS_STILLS:
+            process_as_stills = true;
+            break;
         case OPT_SCALING_ITERATIONS:
             scaling_iter = atoi(optarg);
             if (scaling_iter <= 0) {
@@ -753,6 +763,32 @@ int main(int argc, char **argv) {
     if (experiment.GetBandwidthFWHM())
         logger.Info("X-ray bandwidth FWHM set to {:.4f}", experiment.GetBandwidthFWHM().value());
 
+    // Rotation vs stills. A dataset collected on a rotation goniometer is processed as rotation data
+    // (two-pass indexing) by default; --process-as-stills forces per-frame stills. The rotation flags
+    // (-R / --single-pass-rotation / --force-rotation-lattice) still request rotation explicitly and
+    // choose the pass/lattice; at this point they show up as rotation_indexing already being set.
+    const bool has_goniometer = experiment.GetGoniometer().has_value();
+    if (process_as_stills) {
+        if (rotation_indexing) {
+            logger.Error("--process-as-stills conflicts with -R / --single-pass-rotation / --force-rotation-lattice");
+            exit(EXIT_FAILURE);
+        }
+        if (has_goniometer)
+            logger.Info("--process-as-stills: treating the rotation dataset as independent stills");
+    } else if (!rotation_indexing && has_goniometer) {
+        rotation_indexing = true;
+        two_pass_rotation = true;
+        logger.Info("Dataset has a rotation goniometer axis: processing as rotation data (two-pass "
+                    "indexing). Use --process-as-stills to treat it as stills.");
+    }
+
+    // Default partiality model: rot3d for rotation processing (Rotation partiality + 3D combine of the
+    // per-frame partials into fulls), fixed for stills. An explicit -P always wins.
+    if (!partiality_explicit && rotation_indexing) {
+        partiality_model = PartialityModel::Rotation;
+        combine_3d = true;   // rot3d
+    }
+
     // Configure Indexing
     IndexingSettings indexing_settings;
     indexing_settings.Algorithm(indexing_algorithm);
@@ -791,7 +827,8 @@ int main(int argc, char **argv) {
     scaling_settings.MinCCForImage(min_image_cc / 100.0);   // --min-image-cc is in percent; the setting is a fraction
     scaling_settings.OutlierRejectNsigma(
         outlier_reject_nsigma.value_or(combine_3d ? REJECT_OUTLIERS_DEFAULT_NSIGMA : 0.0));
-    scaling_settings.FileFormat(intensity_format);
+    if (intensity_format)
+        scaling_settings.FileFormat(intensity_format.value());
 
     experiment.ImportScalingSettings(scaling_settings);