viewer: control _process.h5 and merged .mtz/.cif output independently

The 'Save _process.h5' checkbox drove output_prefix, so unchecking it also
suppressed the merged .mtz/.cif, and there was no way to run for the ISa/R-meas
numbers only. Split it into two checkboxes wired to independent flags:
- Save _process.h5  -> ProcessConfig::write_process_h5 (also drives the viewer
  snapshot, so unchecking it means the viewer is not updated with spots/results)
- Write merged .mtz/.cif -> new ProcessConfig::write_merged

output_prefix is set when either is wanted; both off = process for stats only.
Scaling/merge statistics (hence the ISa/R-meas window) are independent of file
writing, so they show in every case. RugnuxCommandLine now emits
--write-process-h5 so a copied command matches the GUI's choice.

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

rugnux/Rugnux.cpp

@@ -831,7 +831,7 @@ ProcessResult Rugnux::Run(RugnuxObserver *observer) {
         result.merge_statistics = sm.statistics;
         result.has_reference = !config_.reference_data.empty();
 
-        if (result.consensus_cell && write_files) {
+        if (result.consensus_cell && write_files && config_.write_merged) {
             phase("Writing reflections");
             WriteReflections(sm.merged, *result.consensus_cell, experiment_, sm.statistics,
                              result.error_model_isa > 0 ? fmt::format("{:.2f}", result.error_model_isa) : "?",

rugnux/Rugnux.h

@@ -46,6 +46,11 @@ struct ProcessConfig {
     // (the .mtz/.cif is the wanted output and the h5 is large) unless --write-process-h5 is given.
     bool write_process_h5 = true;
 
+    // Write the merged reflections (.mtz/.cif). Defaults true (the CLI always writes them when
+    // merging); the viewer can turn them off independently of the _process.h5 (e.g. a quick run that
+    // only wants the ISa/R-meas numbers). Only relevant to FullAnalysis with scaling.
+    bool write_merged = true;
+
     SpotFindingSettings spot_finding;   // FullAnalysis spot finding
 
     // Rotation indexing (FullAnalysis)

rugnux/RugnuxCommandLine.cpp

@@ -127,6 +127,11 @@ std::string RugnuxCommandLine(const ProcessConfig &config,
                 args.emplace_back("-A");
             if (sc.GetRefineB())
                 args.emplace_back("-B");
+            // When merging, the CLI skips the large _process.h5 unless asked; emit the flag when it is
+            // wanted so a copied command matches the GUI's "Save _process.h5" choice. (write_merged has
+            // no CLI equivalent - the CLI always writes the .mtz/.cif when merging.)
+            if (config.write_process_h5)
+                args.emplace_back("--write-process-h5");
         } else {
             args.emplace_back("--no-merge");
         }

viewer/windows/JFJochProcessingJobsWindow.cpp

@@ -138,8 +138,15 @@ int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec
     threads->setRange(1, 256);
     threads->setValue(default_threads());
 
-    auto *save = new QCheckBox("Save _process.h5", &dlg);
-    save->setChecked(true);
+    // Two independent outputs: the large per-image _process.h5 (updates the viewer with spots/results)
+    // and the small merged .mtz/.cif. Either can be turned off; the ISa/R-meas window is shown
+    // regardless (it needs only the in-memory merge statistics), so a stats-only run turns both off.
+    auto *save_h5 = new QCheckBox("Save _process.h5 (per-image results; updates viewer)", &dlg);
+    save_h5->setChecked(true);
+
+    auto *save_merged = new QCheckBox("Write merged .mtz/.cif", &dlg);
+    save_merged->setChecked(true);
+    save_merged->setEnabled(!azint);   // no merged output in azimuthal-integration mode
 
     // Default the output next to the input file, not the viewer's working directory (the viewer starts
     // wherever it was installed). This is an absolute path; Rugnux writes it via the trusted setter,
@@ -160,7 +167,8 @@ int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec
     form->addRow("Start image", start_image);
     form->addRow("End image", end_image);
     form->addRow("Threads", threads);
-    form->addRow(save);
+    form->addRow(save_h5);
+    form->addRow(save_merged);
     form->addRow("Output prefix", prefix);
     form->addRow(scaling);
 
@@ -189,7 +197,8 @@ int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec
         spec.start_image = start_image->value();
         spec.end_image = end_image->value();
         spec.threads = threads->value();
-        spec.save = save->isChecked();
+        spec.save_h5 = save_h5->isChecked();
+        spec.save_merged = save_merged->isEnabled() && save_merged->isChecked();
         spec.prefix = prefix->text();
         spec.scaling = scaling->isEnabled() && scaling->isChecked();
     }
@@ -202,7 +211,11 @@ ProcessConfig JFJochProcessingJobsWindow::buildConfig(const JobSpec &spec, const
     config.nthreads = spec.threads;
     config.start_image = spec.start_image;
     config.end_image = spec.end_image > 0 ? spec.end_image : -1;   // 0 => to the end
-    config.output_prefix = spec.save ? spec.prefix.toStdString() : std::string();
+    // Files land at output_prefix; leave it empty (write nothing, stats only) when neither output is
+    // wanted. The two flags then select which files are actually written there.
+    config.output_prefix = (spec.save_h5 || spec.save_merged) ? spec.prefix.toStdString() : std::string();
+    config.write_process_h5 = spec.save_h5;
+    config.write_merged = spec.save_merged;
     config.spot_finding = inputs.spot_finding;
     if (spec.mode == ProcessMode::FullAnalysis) {
         // Rotation indexing follows the panel's "Process as stills" (= the experiment's indexing
@@ -256,7 +269,7 @@ void JFJochProcessingJobsWindow::newJob(bool azint) {
     JobInfo info;
     info.id = id;
     info.label = label;
-    if (spec.save)
+    if (spec.save_h5)
         info.snapshot_path = QString::fromStdString(config.output_prefix) + "_process.h5";
 
     const int row = table_->rowCount();

viewer/windows/JFJochProcessingJobsWindow.h

@@ -71,7 +71,8 @@ private:
         int start_image = 0;
         int end_image = 0;       // 0 == to the end
         int threads = 4;
-        bool save = true;
+        bool save_h5 = true;        // write the per-image _process.h5 (also drives the viewer snapshot)
+        bool save_merged = true;    // write the merged .mtz/.cif
         QString prefix;
         bool rotation = false;
         int rotation_images = 30;   // images used to find the rotation lattice (first pass)