jfjoch_process: More fixes

image_analysis/scale_merge/ScaleAndMerge.cpp

@@ -331,6 +331,8 @@ ScaleMergeResult ScaleAndMergeReflectionsCeres(const std::vector<Reflection>& ob
 
     const bool refine_partiality = opt.wedge_deg > 0.0;
 
+    std::vector<bool> is_valid_hkl_slot(nhkl, false);
+
     for (const auto& o : obs) {
         size_t mos_slot = opt.per_image_mosaicity ? o.img_slot : 0;
 
@@ -347,6 +349,7 @@ ScaleMergeResult ScaleAndMergeReflectionsCeres(const std::vector<Reflection>& ob
                                      &g[o.img_slot],
                                      &mosaicity[mos_slot],
                                      &Itrue[o.hkl_slot]);
+            is_valid_hkl_slot[o.hkl_slot] = true;
         } else {
             auto* cost = new ceres::AutoDiffCostFunction<IntensityResidual, 1, 1, 1, 1>(
                 new IntensityResidual(*o.r, o.sigma, opt.wedge_deg, refine_partiality));
@@ -356,6 +359,7 @@ ScaleMergeResult ScaleAndMergeReflectionsCeres(const std::vector<Reflection>& ob
                                      &g[o.img_slot],
                                      &mosaicity[mos_slot],
                                      &Itrue[o.hkl_slot]);
+            is_valid_hkl_slot[o.hkl_slot] = true;
         }
     }
 
@@ -363,12 +367,12 @@ ScaleMergeResult ScaleAndMergeReflectionsCeres(const std::vector<Reflection>& ob
     if (opt.log_scaling_residual) {
         for (int i = 0; i < nimg; ++i)
             problem.SetParameterLowerBound(&g[i], 0, 1e-12);
-        for (int h = 0; h < nhkl; ++h)
-            problem.SetParameterLowerBound(&Itrue[h], 0, 1e-12);
+        for (int h = 0; h < nhkl; ++h) {
+            if (is_valid_hkl_slot[h])
+                problem.SetParameterLowerBound(&Itrue[h], 0, 1e-12);
+        }
     }
 
-    // Optional Kabsch-like regularization for k
-
     // Mosaicity refinement + bounds
     if (!opt.refine_mosaicity) {
         for (int i = 0; i < nimg; ++i)