GPU analysis of converted frames: rugnux's stills spot finder

The live analysis indexed 56.3% of the frames of a serial lysozyme run where
offline rugnux indexes 59.3% of the same frames. The whole gap is the spot
finder: the broker's default fixed threshold with two-pixel minimum spots
against rugnux's adaptive threshold that keeps single-pixel spots. With
those two settings (on top of the broker's others) the live analysis
indexes 59.3% of all 24960 frames, as offline; the sustained rate is
unchanged (~1080 Hz on the workstation). The pre-pass decided the centre and
the mask with the same spot finder.

jfjoch_stills_gpu_replay analyses as the receiver does; -F keeps the
broker's fixed-threshold finder.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01UqXYdJKPUFLoeAchjzv3x4

receiver/JFJochReceiverFPGA.cpp

@@ -136,7 +136,15 @@ JFJochReceiverFPGA::JFJochReceiverFPGA(const DiffractionExperiment &in_experimen
                         SendCalibration();
                     },
                     [this](DataMessage &m, const AzimuthalIntegrationProfile &p) { GPUSink(m, p); },
-                    [this] { return GetSpotFindingSettings(); });
+                    [this] {
+                        // The broker's settings, with the spot finder rugnux uses on stills (the pre-pass
+                        // decided the centre and mask with it): adaptive threshold, single-pixel spots kept.
+                        // With the broker's default fixed threshold 3 points fewer frames index.
+                        SpotFindingSettings s = GetSpotFindingSettings();
+                        s.adaptive_threshold = true;
+                        s.min_pix_per_spot = std::nullopt;
+                        return s;
+                    });
         } else {
             SendStartMessage();
             SendCalibration();

tools/jfjoch_stills_gpu_replay.cpp

@@ -29,6 +29,7 @@ void print_usage() {
     std::cout << "   -N <num>     analysis threads (default 16)" << std::endl;
     std::cout << "   -x <px>, -y <px>  beam centre, overriding the file" << std::endl;
     std::cout << "   -C <a,b,c,alpha,beta,gamma>  unit cell of the collection" << std::endl;
+    std::cout << "   -F           the broker's default fixed-threshold spot finder (default: adaptive, as the receiver)" << std::endl;
     std::cout << "   -c           leave the file's unit cell out of the collection" << std::endl;
 }
 
@@ -44,9 +45,10 @@ int main(int argc, char **argv) {
     std::optional<float> beam_x, beam_y;
     std::optional<UnitCell> cell;
     bool no_cell = false;
+    bool fixed_threshold = false;
 
     int opt;
-    while ((opt = getopt(argc, argv, "o:s:n:r:N:x:y:C:c")) != -1) {
+    while ((opt = getopt(argc, argv, "o:s:n:r:N:x:y:C:cF")) != -1) {
         switch (opt) {
             case 'o': prefix = optarg; break;
             case 's': first = atoll(optarg); break;
@@ -56,6 +58,7 @@ int main(int argc, char **argv) {
             case 'x': beam_x = atof(optarg); break;
             case 'y': beam_y = atof(optarg); break;
             case 'c': no_cell = true; break;
+            case 'F': fixed_threshold = true; break;
             case 'C': {
                 UnitCell c{};
                 if (sscanf(optarg, "%f,%f,%f,%f,%f,%f", &c.a, &c.b, &c.c, &c.alpha, &c.beta, &c.gamma) != 6) {
@@ -104,6 +107,13 @@ int main(int argc, char **argv) {
     start.pixel_signed = stored.is_signed;
     start.pixel_mask["default"] = mask.GetMask(x);
 
+    SpotFindingSettings spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();
+    // As JFJochReceiverFPGA analyses converted frames.
+    if (!fixed_threshold) {
+        spot_finding.adaptive_threshold = true;
+        spot_finding.min_pix_per_spot = std::nullopt;
+    }
+
     IndexerThreadPool pool(x.GetIndexingSettings());
 
     std::atomic<int64_t> analysed = 0, indexed = 0;
@@ -125,7 +135,7 @@ int main(int argc, char **argv) {
                                   if (m.indexing_result.value_or(false))
                                       ++indexed;
                               },
-                              [] { return DiffractionExperiment::DefaultDataProcessingSettings(); });
+                              [&] { return spot_finding; });
 
         JFJochReaderRawImage raw;
         for (int64_t i = 0; i < n; i++) {