v1.0.0-rc.148 (#58)

This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144.

* jfjoch_broker: Improve azimuthal integration (add <I^2> calculation)
* jfjoch_broker: Fixes around indexing, aiming to handle multi-lattice crystals (work in progress, it is not fully integrated)
* jfjoch_writer: Save mean(I), stddev(I), and count(I) for each azimuthal bin

Reviewed-on: #58

writer/HDF5DataFilePluginMX.cpp

@@ -46,7 +46,9 @@ inline std::string to_bravais_code(const std::optional<LatticeMessage> &lm_opt)
 }
 
 HDF5DataFilePluginMX::HDF5DataFilePluginMX(const StartMessage &msg)
-    : max_spots(msg.max_spot_count), indexing(msg.indexing_algorithm != IndexingAlgorithmEnum::None) {
+    : max_spots(msg.max_spot_count),
+      max_extra_lattices(msg.max_extra_lattices),
+      indexing(msg.indexing_algorithm != IndexingAlgorithmEnum::None) {
 }
 
 void HDF5DataFilePluginMX::OpenFile(HDF5File &data_file, const DataMessage &msg, size_t images_per_file) {
@@ -58,26 +60,18 @@ void HDF5DataFilePluginMX::OpenFile(HDF5File &data_file, const DataMessage &msg,
     spot_x.reserve(max_spots * images_per_file);
     spot_y.reserve(max_spots * images_per_file);
     spot_int.reserve(max_spots * images_per_file);
-    spot_indexed.reserve(max_spots * images_per_file);
     spot_ice_ring.reserve(max_spots * images_per_file);
     spot_h.reserve(max_spots * images_per_file);
     spot_k.reserve(max_spots * images_per_file);
     spot_l.reserve(max_spots * images_per_file);
     spot_dist_ewald.reserve(max_spots * images_per_file);
 
-    spot_x.reserve(max_spots * images_per_file);
-    spot_y.reserve(max_spots * images_per_file);
-    spot_int.reserve(max_spots * images_per_file);
-    spot_ice_ring.reserve(max_spots * images_per_file);
-    spot_h.reserve(max_spots * images_per_file);
-    spot_k.reserve(max_spots * images_per_file);
-    spot_l.reserve(max_spots * images_per_file);
-    spot_dist_ewald.reserve(max_spots * images_per_file);
-    if (indexing)
+    if (indexing) {
         spot_indexed.reserve(max_spots * images_per_file);
-    if (indexing)
+        spot_lattice.reserve(max_spots * images_per_file);
         indexed_lattice.reserve(images_per_file * 9);
-
+        extra_lattices.reserve(images_per_file * max_extra_lattices * 9);
+    }
     beam_corr_x.reserve(images_per_file);
     beam_corr_y.reserve(images_per_file);
 
@@ -118,12 +112,14 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
         spot_h.resize(max_spots * (max_image_number + 1));
         spot_k.resize(max_spots * (max_image_number + 1));
         spot_l.resize(max_spots * (max_image_number + 1));
-        spot_dist_ewald.resize(max_spots * (max_image_number + 1));
+        spot_lattice.resize(max_spots * (max_image_number + 1), -1);
+        spot_dist_ewald.resize(max_spots * (max_image_number + 1), NAN);
 
-        if (indexing)
+        if (indexing) {
             spot_indexed.resize(max_spots * (max_image_number + 1));
-        if (indexing)
             indexed_lattice.resize((max_image_number + 1) * 9, NAN);
+           extra_lattices.resize((max_image_number + 1) * max_extra_lattices * 9, NAN);
+        }
     }
 
     uint32_t spot_cnt = std::min(msg.spots.size(), max_spots);
@@ -134,6 +130,7 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
         spot_int[max_spots * image_number + i] = msg.spots[i].intensity;
         if (indexing) {
             spot_indexed[max_spots * image_number + i] = msg.spots[i].indexed;
+            spot_lattice[max_spots * image_number + i] = msg.spots[i].lattice;
             spot_h[max_spots * image_number + i] = msg.spots[i].h;
             spot_k[max_spots * image_number + i] = msg.spots[i].k;
             spot_l[max_spots * image_number + i] = msg.spots[i].l;
@@ -150,6 +147,8 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
 
     if (indexing) {
         indexed[image_number] = msg.indexing_result.value_or(0);
+        // Fallback value is indexing result (1 or 0 lattices)
+        indexing_lattice_count[image_number] = msg.indexing_lattice_count.value_or(indexed[image_number]);
         profile_radius[image_number] = msg.profile_radius.value_or(NAN);
         mosaicity_deg[image_number] = msg.mosaicity_deg.value_or(NAN);
         b_factor[image_number] = msg.b_factor.value_or(NAN);
@@ -169,6 +168,18 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
                 indexed_lattice[image_number * 9 + i] = NAN;
         }
 
+        for (size_t li = 0; li < max_extra_lattices; li++) {
+            const size_t base = (image_number * max_extra_lattices + li) * 9;
+            if (li < msg.indexing_extra_lattices.size()) {
+                auto tmp = msg.indexing_extra_lattices[li].GetVector();
+                for (int i = 0; i < 9; i++)
+                    extra_lattices[base + i] = tmp[i];
+            } else {
+                for (int i = 0; i < 9; i++)
+                    extra_lattices[base + i] = NAN;
+            }
+        }
+
         if (msg.lattice_type) {
             bravais_lattice[image_number] = to_bravais_code(msg.lattice_type);
             niggli_class[image_number] = msg.lattice_type->niggli_class;
@@ -204,6 +215,7 @@ void HDF5DataFilePluginMX::WriteFinal(HDF5File &data_file) {
             data_file.SaveVector("/entry/MX/peakDistEwaldSphere", spot_dist_ewald,
                                  {(hsize_t) (max_image_number + 1), max_spots});
             data_file.SaveVector("/entry/MX/peakIndexed", spot_indexed, {(hsize_t) (max_image_number + 1), max_spots});
+            data_file.SaveVector("/entry/MX/peakLattice", spot_lattice, {(hsize_t) (max_image_number + 1), max_spots});
         }
     }
 
@@ -221,9 +233,16 @@ void HDF5DataFilePluginMX::WriteFinal(HDF5File &data_file) {
 
     if (!indexed.empty())
         data_file.SaveVector("/entry/MX/imageIndexed", indexed.vec());
+    if (!indexing_lattice_count.empty())
+        data_file.SaveVector("/entry/MX/indexingLatticeCount", indexing_lattice_count.vec());
     if (!indexed_lattice.empty())
         data_file.SaveVector("/entry/MX/latticeIndexed", indexed_lattice, {(hsize_t) (max_image_number + 1), 9})
                 ->Units("Angstrom");
+    if (!extra_lattices.empty())
+        data_file.SaveVector("/entry/MX/latticeIndexedExtra", extra_lattices,
+                             {(hsize_t) (max_image_number + 1), (hsize_t) max_extra_lattices, 9})
+                ->Units("Angstrom");
+
     if (!bkg_estimate.empty())
         data_file.SaveVector("/entry/MX/bkgEstimate", bkg_estimate.vec());
     if (!profile_radius.empty())