One gain mechanism: frames analysed in their own units, the gain applied where a photon count is assumed

The gain of an input in detector units (SMV, marCCD, XTC, the XFEL formats) is measured once, before
anything reads the frames (RugnuxMeasureGain: photon-peak spacing and background variance per unit
mean), or given with --gain, and handed to the integration and the spot finding by one function
(ApplyRugnuxPixelGain). The rotation pre-scan no longer measures it, and the stills reader no longer
converts frames of a detector whose photons are not resolved: SACLA MPCCD, Rayonix and CCD frames are
integrated in ADU at the gain, rotation and stills alike.

Where a photon count was assumed, it is now taken at the gain (bit-identical at gain 1):
- integration: the background clip's one-photon floor, the sigma floor (one photon), the profile fit's
  background floor (0.01 photon), and a still's overload kept as a lower bound, which was left in ADU
  while every other reflection left the integrator in photons - the cause of the earlier loss of the
  engine route on clipped CCD stills (merged low resolution inflated by the gain, the rocking-width
  fit's bandwidth collapsing); CPU and CUDA, Metal through the shared CPU code;
- the adaptive spot threshold (Poisson arm and its one-photon floor), CPU and GPU;
- the pre-scan spot-width measurement (strong-spot SNR, the ring clip) behind the stills bandwidth and
  the rotation signal radius;
- the hot/dead pixel tests, CPU and GPU; the empty-aperture ring clip.
BackgroundPixelGain is gone: one pixel_gain.

A detector whose background resolves single photons (photon peaks: JUNGFRAU in keV, AGIPD) is a photon
counter and its frames are still counted in whole photons as read: analysed in keV at the gain instead,
a photon-counting still set lost 0.008 R-free (fewer spots, a noisier beam-centre trial) - the rounding
is the detector's own discrimination. --gain sets the value, the background still says which kind.

Validation, against rc178: photon-counting and g<=1 rotation p.hkl md5-identical (lyso, thau, cytc,
myob, insu, a small-molecule set, 5reo, 6cee, 6i3j, 2xfw, 6s1u, 8v4j); CCD g>1 at or within noise of rc178 (5uth
R_meas 0.113 -> 0.108). Stills R-free (0-cycle REFMAC): MPCCD sets 0.184 -> 0.185 and 0.199 -> 0.196,
Rayonix identical, photon-resolving sets back on their rc178 numbers.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit da8dbfc8147354b63e375f2d9521dffb80938b6d)

viewer/JFJochProcessController.cpp

@@ -8,6 +8,7 @@
 #include "../reader/JFJochHDF5Reader.h"
 #include "../rugnux/ResultReport.h"
 #include "../rugnux/RugnuxOutputFiles.h"
+#include "../rugnux/RugnuxDefaults.h"
 
 #include <QElapsedTimer>
 #include <QMetaType>
@@ -67,16 +68,20 @@ void JFJochProcessController::run_(QString file_path, DiffractionExperiment expe
         } else if (JFJochMarCCDReader::CanRead(path)) {
             marccd_reader.ReadFiles(path);
             reader_ptr = &marccd_reader;
-            config.counts_in_adu = true;   // a CCD: pixel values are ADU, as for rugnux
         } else if (JFJochSMVReader::CanRead(path)) {
             smv_reader.ReadFiles(path);
             reader_ptr = &smv_reader;
-            config.counts_in_adu = true;
         } else {
             hdf5_reader.ReadFile(path);
             reader_ptr = &hdf5_reader;
         }
         JFJochReader &reader = *reader_ptr;
+        // A CCD's pixel values are ADU: analysed at the gain its background shows, as rugnux does.
+        if (reader_ptr == &marccd_reader || reader_ptr == &smv_reader) {
+            const RugnuxMeasuredGain g = RugnuxMeasureGain(reader);
+            const std::optional<float> gain = g.peaks ? std::optional<float>(g.peaks->gain) : g.variance;
+            ApplyRugnuxPixelGain(experiment, config.spot_finding, gain.value_or(1.0f));
+        }
 
         // Seed the live dataset with the experiment so the chart has geometry context; per-image
         // results are filled in by OnImageProcessed as the run progresses.