Fixes

image_analysis/scale_merge/ScaleAndMerge.cpp

@@ -7,7 +7,6 @@
 
 #include <thread>
 #include <iostream>
-#include <iomanip>
 #include <algorithm>
 #include <cmath>
 #include <limits>
@@ -18,7 +17,6 @@
 #include <vector>
 
 #include "../../common/ResolutionShells.h"
-#include "../../common/Logger.h"
 
 namespace {
     struct HKLKey {
@@ -237,7 +235,6 @@ namespace {
         int img_id = 0;
         int hkl_slot = -1;
         double sigma = 0.0;
-        mutable bool selected = true;
     };
 
     struct CorrectedObs {
@@ -246,103 +243,6 @@ namespace {
         double sigma_corr;
     };
 
-    void select_reflections_by_quasi_random(const std::vector<ObsRef> &obs,
-        const ScaleMergeOptions &opt,
-        std::vector<bool> &hkl_selected,
-        Logger &logger) {
-        float stat_d_min = std::numeric_limits<float>::max();
-        float stat_d_max = 0.0f;
-
-        const gemmi::SpaceGroup &sg = *opt.space_group;
-        const gemmi::GroupOps gops = sg.operations();
-        int n_operator = gops.order();
-
-        struct HKLStats {
-            int n = 0;
-            float d = std::numeric_limits<float>::max();
-            int shell_id = 0;
-        };
-        const int nhkl = static_cast<int>(hkl_selected.size());
-        std::vector<HKLStats> per_hkl(nhkl);
-        int reflection_above_cutoff = 0;
-
-        for (const auto &o: obs) {
-            if (o.r->I / o.r->sigma < opt.filter_sigma_cutoff) {
-                o.selected = false;
-                continue;
-            }
-
-            const auto d = o.r->d;
-            reflection_above_cutoff += 1;
-            if (std::isfinite(d) && d > 0.0f) {
-                if (opt.d_min_limit_A > 0.0 && d < static_cast<float>(opt.d_min_limit_A))
-                    continue;
-                stat_d_min = std::min(stat_d_min, d);
-                stat_d_max = std::max(stat_d_max, d);
-                auto &hs = per_hkl[o.hkl_slot];
-                hs.n += 1;
-                hs.d = d;
-            }
-        }
-
-        logger.Info("Reflections of I/sigma > {} : {}", opt.filter_sigma_cutoff, reflection_above_cutoff);
-        if (reflection_above_cutoff < opt.filter_min_per_bin * opt.filter_n_resolution_bins) {
-            logger.Info("No additional selection applied before scaling");
-            return;
-        }
-
-        if (stat_d_min < stat_d_max && stat_d_min > 0.0f) {
-            const float d_min_pad = stat_d_min * 0.999f;
-            const float d_max_pad = stat_d_max * 1.001f;
-            ResolutionShells scaling_shells(d_min_pad, d_max_pad, opt.filter_n_resolution_bins);
-
-            for (int h = 0; h < nhkl; ++h) {
-                const auto d = per_hkl[h].d;
-                if (std::isfinite(d) && d > 0.0f) {
-                    if (opt.d_min_limit_A > 0.0 && d < static_cast<float>(opt.d_min_limit_A))
-                        continue;
-                    auto s = scaling_shells.GetShell(d);
-                    if (s.has_value())
-                        per_hkl[h].shell_id = s.value();
-                }
-            }
-
-            // Accumulators per shell
-            struct ShellAccum {
-                int obs_unique = 0;
-                int obs_total = 0;
-                bool selected = true;
-            };
-            std::vector<ShellAccum> shell_acc(opt.filter_n_resolution_bins);
-
-            for (int h = 0; h < nhkl; ++h) {
-                auto &sa = shell_acc[per_hkl[h].shell_id];
-                if (sa.obs_unique  * n_operator  > opt.filter_min_per_bin * 1.2 || sa.obs_total > opt.filter_max_per_bin)
-                    hkl_selected[h] = false;
-                else
-                    sa.obs_unique += 1;
-                    sa.obs_total += per_hkl[h].n;
-            }
-
-            const auto shell_min_res = scaling_shells.GetShellMinRes();
-
-            logger.Info("| d-mean | n_refl_uni | n_refl_tot | selection |");
-            for (int n=0; n < opt.filter_n_resolution_bins; ++n) {
-                if (shell_acc[n].obs_unique * n_operator < opt.filter_min_per_bin)
-                    shell_acc[n].selected = false;
-                if (shell_min_res[n] <= 0.0f) continue;
-                logger.Info("| {:6.3f} | {:10d} | {:10d} | {:9d} |",
-                    shell_min_res[n], shell_acc[n].obs_unique, shell_acc[n].obs_total, shell_acc[n].selected);
-            }
-
-            for (int h = 0; h < nhkl; ++h) {
-                auto &sa = shell_acc[per_hkl[h].shell_id];
-                if (!sa.selected)
-                    hkl_selected[h] = false;
-            }
-       }
-    }
-
     void scale(const ScaleMergeOptions &opt,
                std::vector<double> &g,
                std::vector<double> &mosaicity,
@@ -350,13 +250,10 @@ namespace {
                const std::vector<uint8_t> &image_slot_used,
                bool rotation_crystallography,
                size_t nhkl,
-               const std::vector<ObsRef> &obs,
-               bool selection,
-               Logger &logger) {
+               const std::vector<ObsRef> &obs) {
         ceres::Problem problem;
 
         std::vector<double> Itrue(nhkl, 0.0);
-        std::vector<bool> hkl_selected(nhkl, true);
 
         // Initialize Itrue from per-HKL median of observed intensities
         {
@@ -380,12 +277,8 @@ namespace {
 
         double wedge = opt.wedge_deg.value_or(0.0);
 
-        if (selection) select_reflections_by_quasi_random(obs, opt, hkl_selected, logger);
-
         std::vector<bool> is_valid_hkl_slot(nhkl, false);
         for (const auto &o: obs) {
-            if (!o.selected) continue;
-            if (!hkl_selected[o.hkl_slot]) continue;
             switch (opt.partiality_model) {
                 case ScaleMergeOptions::PartialityModel::Rotation: {
                     auto *cost = new ceres::AutoDiffCostFunction<IntensityRotResidual, 1, 1, 1, 1, 1>(
@@ -505,9 +398,8 @@ namespace {
         options.function_tolerance = 1e-4;
 
         ceres::Solver::Summary summary;
-        logger.Info("Now start the ceres-solver with residual blocks: {}", problem.NumResidualBlocks());
         ceres::Solve(options, &problem, &summary);
-        logger.Info(summary.FullReport());
+        std::cout << summary.FullReport() << std::endl;
     }
 
     void merge(size_t nhkl, ScaleMergeResult &out, const std::vector<CorrectedObs> &corr_obs) {
@@ -802,7 +694,6 @@ namespace {
                 o.img_id = img_id;
                 o.hkl_slot = hkl_slot;
                 o.sigma = sigma;
-                o.selected = true;
                 obs.push_back(o);
             }
         }
@@ -812,14 +703,10 @@ namespace {
 
 ScaleMergeResult ScaleAndMergeReflectionsCeres(const std::vector<std::vector<Reflection> > &observations,
                                                const ScaleMergeOptions &opt) {
-
-    Logger logger("ScaleAndMergeReflections");
-
     if (opt.image_cluster <= 0)
         throw std::invalid_argument("image_cluster must be positive");
 
     const bool rotation_crystallography = opt.wedge_deg.has_value();
-    const bool selection = opt.selection;
 
     size_t nrefl = 0;
     for (const auto &i: observations)
@@ -857,8 +744,7 @@ ScaleMergeResult ScaleAndMergeReflectionsCeres(const std::vector<std::vector<Ref
         }
     }
 
-    logger.Info("Now scale the reflections: {}", nrefl);
-    scale(opt, g, mosaicity, R_sq, image_slot_used, rotation_crystallography, nhkl, obs, selection, logger);
+    scale(opt, g, mosaicity, R_sq, image_slot_used, rotation_crystallography, nhkl, obs);
 
     ScaleMergeResult out;
 

image_analysis/scale_merge/ScaleAndMerge.h

@@ -50,12 +50,6 @@ struct ScaleMergeOptions {
 
     bool refine_wedge = false;
 
-    bool selection = true;
-    double filter_sigma_cutoff = 1.0;
-    int filter_min_per_bin = 10000; // needs optimization
-    int filter_max_per_bin = 80000;
-    int filter_n_resolution_bins = 20;
-
     enum class PartialityModel {Fixed, Rotation, Unity, Still} partiality_model = PartialityModel::Fixed;
 };
 

tools/jfjoch_process.cpp

@@ -2,7 +2,6 @@
 // SPDX-License-Identifier: GPL-3.0-only
 
 #include <iostream>
-#include <iomanip>
 #include <vector>
 #include <string>
 #include <unistd.h>
@@ -45,15 +44,12 @@ void print_usage(Logger &logger) {
     logger.Info("   -d<num>    High resolution limit for spot finding (default: 1.5)");
     logger.Info("   -D<num>    High resolution limit for scaling/merging (default: 0.0; no limit)");
     logger.Info("   -S<num>    Space group number");
-    logger.Info("   -M[num]    Scale and merge (refine mosaicity) and write scaled.hkl + image.dat, unless indexing rate is below threshold (default: 0.5)");
+    logger.Info("   -M         Scale and merge (refine mosaicity) and write scaled.hkl + image.dat");
     logger.Info("   -P<txt>    Partiality refinement fixed|rot|unity (default: fixed)");
     logger.Info("   -A         Anomalous mode (don't merge Friedel pairs)");
     logger.Info("   -C<cell>   Fix reference unit cell: -C\"a,b,c,alpha,beta,gamma\" (comma-separated, no spaces; quotes optional)");
     logger.Info("   -c<num>    Max spot count (default: 250)");
-    logger.Info("   -W<txt>    HDF5 file with analysis results is written. 'l' or 'light' deactivates image-output");
-    logger.Info("   -T<num>    Noise sigma level for spot finding (default: 3.0)");
-    logger.Info("   -m<num>    Min unique reflections per bin used for scaling. Use all when no value is specified (default: 10000)");
-    logger.Info("   -w         Refine wedge in scaling (default: false)");
+    logger.Info("   -W         HDF5 file with analysis results is written");
 }
 
 void trim_in_place(std::string& t) {
@@ -64,36 +60,6 @@ void trim_in_place(std::string& t) {
     t = t.substr(b, e - b);
 };
 
-void print_statistics(Logger &logger, const MergeStatistics &stats) {
-    logger.Info("");
-    logger.Info("  {:>8s} {:>8s} {:>8s} {:>8s} {:>8s} {:>10s}",
-                "d_min", "N_obs", "N_uniq", "Rmeas", "<I/sig>", "Complete");
-    logger.Info("  {:->8s} {:->8s} {:->8s} {:->8s} {:->8s} {:->10s}",
-                "", "", "", "", "", "");
-    for (const auto &sh: stats.shells) {
-        if (sh.unique_reflections == 0)
-            continue;
-        std::string compl_str = (sh.completeness > 0.0)
-                                    ? fmt::format("{:8.1f}%", sh.completeness * 100.0)
-                                    : "      N/A";
-        logger.Info("  {:8.2f} {:8d} {:8d} {:8.3f}% {:8.1f} {:>10s}",
-                    sh.d_min, sh.total_observations, sh.unique_reflections,
-                    sh.rmeas * 100, sh.mean_i_over_sigma, compl_str);
-    }
-    {
-        const auto &ov = stats.overall;
-        logger.Info("  {:->8s} {:->8s} {:->8s} {:->8s} {:->8s} {:->10s}",
-                    "", "", "", "", "", "");
-        std::string compl_str = (ov.completeness > 0.0)
-                                    ? fmt::format("{:8.1f}%", ov.completeness * 100.0)
-                                    : "      N/A";
-        logger.Info("  {:>8s} {:8d} {:8d} {:8.3f}% {:8.1f} {:>10s}",
-                    "Overall", ov.total_observations, ov.unique_reflections,
-                    ov.rmeas * 100, ov.mean_i_over_sigma, compl_str);
-    }
-    logger.Info("");
-}
-
 std::optional<UnitCell> parse_unit_cell_arg(const char* arg)  {
     if (!arg)
         return std::nullopt;
@@ -166,14 +132,8 @@ int main(int argc, char **argv) {
     std::optional<int> space_group_number;
     std::optional<UnitCell> fixed_reference_unit_cell;
     bool write_output = false;
-    bool write_output_noimage = false;
-    bool filtering = true;
-    std::optional<int16_t> filter_min_per_bin;
     std::optional<int64_t> max_spot_count_override;
-    float sigma_spot_finding = 3.0;
-    std::optional<float> merging_threshold;
     IndexingAlgorithmEnum indexing_algorithm = IndexingAlgorithmEnum::Auto;
-    bool refine_wedge = false;
 
     ScaleMergeOptions::PartialityModel partiality_model = ScaleMergeOptions::PartialityModel::Fixed;
 
@@ -186,7 +146,7 @@ int main(int argc, char **argv) {
     }
 
     int opt;
-    while ((opt = getopt(argc, argv, "o:N:s:e:vc:R::FX:xd:S:M::P:AD:C:T:W:m::w")) != -1) {
+    while ((opt = getopt(argc, argv, "o:N:s:e:vc:R::FX:xd:S:MP:AD:C:W")) != -1) {
         switch (opt) {
             case 'o':
                 output_prefix = optarg;
@@ -202,10 +162,6 @@ int main(int argc, char **argv) {
                 break;
             case 'W':
                 write_output = true;
-                if (strcmp(optarg, "light") == 0 || strcmp(optarg, "l") == 0) {
-                    write_output_noimage = true;
-                    logger.Warning("Image data will not be saved.");
-                }
                 break;
             case 'v':
                 verbose = true;
@@ -248,14 +204,6 @@ int main(int argc, char **argv) {
             case 'x':
                 refine_beam_center = false;
                 break;
-            case 'm':
-                filtering = false;
-                if (optarg)
-                    filter_min_per_bin = atoi(optarg);
-                break;
-            case 'w':
-                refine_wedge = true;
-                break;
             case 'D':
                 d_min_scale_merge = atof(optarg);
                 logger.Info("High resolution limit for scaling/merging set to {:.2f} A", d_min_spot_finding);
@@ -265,15 +213,10 @@ int main(int argc, char **argv) {
                 break;
             case 'M':
                 run_scaling = true;
-                if (optarg) merging_threshold = atof(optarg);
                 break;
             case 'A':
                 anomalous_mode = true;
                 break;
-            case 'T':
-                sigma_spot_finding = atof(optarg);
-                logger.Info("Noise threshold level for spot finding set to {:.2f} sigma", sigma_spot_finding);
-                break;
             case 'C': {
                 auto uc = parse_unit_cell_arg(optarg);
                 if (!uc.has_value()) {
@@ -353,11 +296,8 @@ int main(int argc, char **argv) {
     experiment.OverwriteExistingFiles(true);
     experiment.PolarizationFactor(0.99);
 
-    if (fixed_reference_unit_cell.has_value()) {
+    if (fixed_reference_unit_cell.has_value())
         experiment.SetUnitCell(*fixed_reference_unit_cell);
-    } else {
-        experiment.SetUnitCell({});
-    }
 
     if (max_spot_count_override.has_value()) {
         experiment.MaxSpotCount(max_spot_count_override.value());
@@ -368,8 +308,6 @@ int main(int argc, char **argv) {
     IndexingSettings indexing_settings;
     indexing_settings.Algorithm(indexing_algorithm);
     indexing_settings.RotationIndexing(rotation_indexing);
-    if (rotation_indexing)
-        logger.Info("Rotation indexing is activated.");
     if (rotation_indexing_range.has_value())
         indexing_settings.RotationIndexingMinAngularRange_deg(rotation_indexing_range.value());
 
@@ -379,27 +317,10 @@ int main(int argc, char **argv) {
         indexing_settings.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::None);
     experiment.ImportIndexingSettings(indexing_settings);
 
-    switch (experiment.GetIndexingAlgorithm()) {
-        case IndexingAlgorithmEnum::FFBIDX:
-            logger.Info("Indexer used: FFBIDX");
-            break;
-        case IndexingAlgorithmEnum::FFTW:
-            logger.Info("Indexer used: FFTW");
-            break;
-        case IndexingAlgorithmEnum::FFT:
-            logger.Info("Indexer used: FFT (CUDA)");
-            break;
-        case IndexingAlgorithmEnum::None:
-            logger.Warning("Indexer not defined!");
-            return 0;
-        default: ;
-    }
-
     SpotFindingSettings spot_settings;
     spot_settings.enable = true;
     spot_settings.indexing = true;
     spot_settings.high_resolution_limit = d_min_spot_finding;
-    spot_settings.signal_to_noise_threshold = sigma_spot_finding;
     if (d_min_scale_merge > 0)
         spot_settings.high_resolution_limit = d_min_spot_finding;
 
@@ -475,10 +396,6 @@ int main(int argc, char **argv) {
         compressed_buffer.resize(MaxCompressedSize(experiment.GetCompressionAlgorithm(),
                                                    experiment.GetPixelsNum(),
                                                    experiment.GetByteDepthImage()));
-        auto size = compressor.Compress(compressed_buffer.data(),
-                            compressed_buffer.data(),
-                            experiment.GetPixelsNum(),
-                            sizeof(uint8_t));
 
         // Thread-local analysis resources
         MXAnalysisWithoutFPGA analysis(experiment, mapping, pixel_mask, indexer);
@@ -529,11 +446,10 @@ int main(int argc, char **argv) {
             auto image_end_time = std::chrono::high_resolution_clock::now();
             std::chrono::duration<float> image_duration = image_end_time - image_start_time;
 
-            if (!write_output_noimage)
-                size = compressor.Compress(compressed_buffer.data(),
-                                                img->Image().data(),
-                                                experiment.GetPixelsNum(),
-                                                sizeof(int32_t));
+            auto size = compressor.Compress(compressed_buffer.data(),
+                                            img->Image().data(),
+                                            experiment.GetPixelsNum(),
+                                            sizeof(int32_t));
 
             msg.image = CompressedImage(compressed_buffer.data(),
                                         size, experiment.GetXPixelsNum(),
@@ -566,7 +482,7 @@ int main(int argc, char **argv) {
             }
 
             // Progress log
-            if ((current_idx_offset > 0 && (current_idx_offset+1) % 100 == 0) || image_idx == end_image - 1) {
+            if (current_idx_offset > 0 && current_idx_offset % 100 == 0) {
                 std::optional<float> indexing_rate;
                 {
                     std::lock_guard<std::mutex> lock(plots_mutex);
@@ -575,21 +491,11 @@ int main(int argc, char **argv) {
 
                 if (indexing_rate.has_value()) {
                     logger.Info("Processed {} / {} images (indexing rate {:.1f}%)",
-                                current_idx_offset+1, images_to_process,
+                                current_idx_offset, images_to_process,
                                 indexing_rate.value() * 100.0f);
                 } else {
                     logger.Info("Processed {} / {} images (indexing rate N/A)",
-                                current_idx_offset+1, images_to_process);
-                }
-                if (image_idx == end_image - 1) {
-                    if (!merging_threshold.has_value()) merging_threshold = 0.5f;
-                    if (!indexing_rate.has_value()) {
-                        run_scaling = false;
-                    } else if (indexing_rate.value() < merging_threshold) {
-                        run_scaling = false;
-                        logger.Warning("Not proceed to scale and merge with lower indexing rate: {:.1f}%",
-                            indexing_rate.value()*100.0f);
-                    }
+                                current_idx_offset, images_to_process);
                 }
             }
         }
@@ -641,6 +547,7 @@ int main(int argc, char **argv) {
         logger.Info("Rotation Indexing found lattice");
     }
 
+    // --- Optional: run scaling (mosaicity refinement) on accumulated reflections ---
     // --- Optional: run scaling (mosaicity refinement) on accumulated reflections ---
     if (run_scaling) {
         logger.Info("Running scaling (mosaicity refinement) ...");
@@ -651,15 +558,6 @@ int main(int argc, char **argv) {
         scale_opts.max_solver_time_s = 240.0; // generous cutoff for now
         scale_opts.merge_friedel = !anomalous_mode;
         scale_opts.d_min_limit_A = d_min_scale_merge.value_or(0.0);
-        scale_opts.refine_wedge = refine_wedge;
-        if (filter_min_per_bin.has_value()) {
-            scale_opts.selection = true;
-            scale_opts.filter_min_per_bin = filter_min_per_bin.value();
-        } else {
-            scale_opts.selection = filtering;
-        }
-        if (rotation_indexing)
-            scale_opts.filter_min_per_bin = scale_opts.filter_min_per_bin * 0.25;
 
         const bool fixed_space_group = space_group || experiment.GetGemmiSpaceGroup().has_value();
 
@@ -667,17 +565,12 @@ int main(int argc, char **argv) {
             scale_opts.space_group = *space_group;
         else
             scale_opts.space_group = experiment.GetGemmiSpaceGroup();
-        if (scale_opts.space_group->number == 0) scale_opts.space_group = *gemmi::find_spacegroup_by_number(1);
 
-        logger.Info("Starting SG-no.: {}", scale_opts.space_group->number);
         auto scale_start = std::chrono::steady_clock::now();
         auto scale_result = indexer.ScaleRotationData(scale_opts);
         auto scale_end = std::chrono::steady_clock::now();
         double scale_time = std::chrono::duration<double>(scale_end - scale_start).count();
 
-        if (scale_result) print_statistics(logger, scale_result->statistics);
-//        if (scale_opts.wedge_deg.has_value()) logger.Info("Refined wedge: {:.3f}", scale_opts.wedge_deg.value());
-
         if (scale_result && !fixed_space_group) {
             logger.Info("Searching for space group from P1-merged reflections ...");
 
@@ -686,16 +579,13 @@ int main(int argc, char **argv) {
             sg_opts.centering = '\0';
             sg_opts.merge_friedel = !anomalous_mode;
             sg_opts.d_min_limit_A = d_min_scale_merge.value_or(0.0);
-            sg_opts.min_i_over_sigma = 4.0; // 0.0; follows the DIALS's default
+            sg_opts.min_i_over_sigma = 0.0;
             sg_opts.min_operator_cc = 0.80;
             sg_opts.min_pairs_per_operator = 20;
             sg_opts.min_total_compared = 100;
             sg_opts.test_systematic_absences = true;
 
-            auto sg_search_start = std::chrono::steady_clock::now();
             const auto sg_search = SearchSpaceGroup(scale_result->merged, sg_opts);
-            auto sg_search_end = std::chrono::steady_clock::now();
-            double sg_search_time = std::chrono::duration<double>(sg_search_end - sg_search_start).count();
 
             logger.Info("");
             {
@@ -709,24 +599,17 @@ int main(int argc, char **argv) {
             logger.Info("");
 
             if (sg_search.best_space_group.has_value()) {
-                logger.Info("SG-search wall-clock time: {:.2f} s", sg_search_time);
-                if (sg_search.best_space_group->number != 0) {
-                    if (sg_search.best_space_group->number != scale_opts.space_group->number) {
-                        logger.Info("Re-running scaling in detected space group {}", sg_search.best_space_group->short_name());
+                logger.Info("Re-running scaling in detected space group {}", sg_search.best_space_group->short_name());
 
-                        scale_opts.space_group = *sg_search.best_space_group;
+                scale_opts.space_group = *sg_search.best_space_group;
 
-                        auto rescale_start = std::chrono::steady_clock::now();
-                        auto refined_scale_result = indexer.ScaleRotationData(scale_opts);
-                        auto rescale_end = std::chrono::steady_clock::now();
+                auto rescale_start = std::chrono::steady_clock::now();
+                auto refined_scale_result = indexer.ScaleRotationData(scale_opts);
+                auto rescale_end = std::chrono::steady_clock::now();
 
-                        if (refined_scale_result) {
-                            scale_result = std::move(refined_scale_result);
-                            scale_time += std::chrono::duration<double>(rescale_end - rescale_start).count();
-                        }
-                    } else {
-                        logger.Info("No space group update indicated.");
-                    }
+                if (refined_scale_result) {
+                    scale_result = std::move(refined_scale_result);
+                    scale_time += std::chrono::duration<double>(rescale_end - rescale_start).count();
                 }
             } else {
                 logger.Warning("No space group accepted; keeping P1-merged result");
@@ -740,7 +623,36 @@ int main(int argc, char **argv) {
                         scale_time, scale_result->merged.size());
 
             // Print resolution-shell statistics table
-            print_statistics(logger, scale_result->statistics);
+            {
+                const auto &stats = scale_result->statistics;
+                logger.Info("");
+                logger.Info("  {:>8s} {:>8s} {:>8s} {:>8s} {:>8s} {:>10s}",
+                            "d_min", "N_obs", "N_uniq", "Rmeas", "<I/sig>", "Complete");
+                logger.Info("  {:->8s} {:->8s} {:->8s} {:->8s} {:->8s} {:->10s}",
+                            "", "", "", "", "", "");
+                for (const auto &sh: stats.shells) {
+                    if (sh.unique_reflections == 0)
+                        continue;
+                    std::string compl_str = (sh.completeness > 0.0)
+                                                ? fmt::format("{:8.1f}%", sh.completeness * 100.0)
+                                                : "      N/A";
+                    logger.Info("  {:8.2f} {:8d} {:8d} {:8.3f}% {:8.1f} {:>10s}",
+                                sh.d_min, sh.total_observations, sh.unique_reflections,
+                                sh.rmeas * 100, sh.mean_i_over_sigma, compl_str);
+                }
+                {
+                    const auto &ov = stats.overall;
+                    logger.Info("  {:->8s} {:->8s} {:->8s} {:->8s} {:->8s} {:->10s}",
+                                "", "", "", "", "", "");
+                    std::string compl_str = (ov.completeness > 0.0)
+                                                ? fmt::format("{:8.1f}%", ov.completeness * 100.0)
+                                                : "      N/A";
+                    logger.Info("  {:>8s} {:8d} {:8d} {:8.3f}% {:8.1f} {:>10s}",
+                                "Overall", ov.total_observations, ov.unique_reflections,
+                                ov.rmeas * 100, ov.mean_i_over_sigma, compl_str);
+                }
+                logger.Info("");
+            }
 
             {
                 const std::string img_path = output_prefix + "_image.dat";
@@ -786,8 +698,6 @@ int main(int argc, char **argv) {
                         cif_meta.unit_cell = rotation_indexer_ret->lattice.GetUnitCell();
                     } else if (experiment.GetUnitCell().has_value()) {
                         cif_meta.unit_cell = experiment.GetUnitCell().value();
-                    } else {
-                        logger.Warning("No UnitCell output");
                     }
 
                     if (scale_opts.space_group.has_value()) {
@@ -835,11 +745,12 @@ int main(int argc, char **argv) {
     double frame_rate = static_cast<double>(images_to_process) / processing_time;
 
     logger.Info("");
-    logger.Info("Processing time (excl. scaling): {:8.2f} s", processing_time);
-    logger.Info("Frame rate:                      {:8.2f} Hz", frame_rate);
-    logger.Info("Total throughput:                {:8.2f} MB/s", throughput_MBs);
+    logger.Info("Processing time: {:.2f} s", processing_time);
+    logger.Info("Frame rate:      {:.2f} Hz", frame_rate);
+    logger.Info("Total throughput:{:.2f} MB/s", throughput_MBs);
+
     // Print extended stats similar to Receiver
-    if (end_msg.indexing_rate.has_value()) {
+    if (!end_msg.indexing_rate.has_value()) {
         logger.Info("Indexing rate:   {:.2f}%", end_msg.indexing_rate.value() * 100.0);
     }