Update the detector model after refinement in indexing. (#89)

Update the detector model after refinement to give correct indexing percentage

Output model data in same style as dials.index

Author: jbeilstenedmands

baseline/indexer/indexer.cc

@@ -20,6 +20,7 @@
 #include <mutex>
 #include <nlohmann/json.hpp>
 #include <optional>
+#include <sstream>
 #include <string>
 #include <thread>
 #include <vector>
@@ -372,14 +373,6 @@ int main(int argc, char **argv) {
     expt.set_crystal(best_xtal);
     expt.beam().set_s0(best_beam.get_s0());
     expt.detector().update(best_panel.get_d_matrix());
-    gemmi::UnitCell bestcell = best_xtal.get_unit_cell();
-    logger.info("Best cell (P1): {:.2f} {:.2f} {:.2f} {:.2f} {:.2f} {:.2f}",
-                bestcell.a,
-                bestcell.b,
-                bestcell.c,
-                bestcell.alpha,
-                bestcell.beta,
-                bestcell.gamma);
 
     // Save the indexed experiment list.
     json elist_out = expt.to_json();
@@ -396,7 +389,7 @@ int main(int argc, char **argv) {
 
         // Recalculate the rlp and s1 vectors based on the updated models.
         xyz_to_rlp_results final_results =
-          xyz_to_rlp(xyzobs_px, detector.panels()[0], expt.beam(), scan, gonio);
+          xyz_to_rlp(xyzobs_px, expt.detector().panels()[0], expt.beam(), scan, gonio);
         strong_reflections.add_column(std::string("xyzobs.mm.value"),
                                       final_results.xyzobs_mm.extent(0),
                                       3,
@@ -432,9 +425,73 @@ int main(int argc, char **argv) {
         // Index the data with the refined models.
         assign_indices_results assign_results = assign_indices_global(
           expt.crystal().get_A_matrix(), final_results.rlp, final_results.xyzobs_mm);
-        logger.info("Indexed {}/{} reflections using the refined models",
-                    assign_results.number_indexed,
-                    xyzobs_px.extent(0));
+
+        // Print useful log output of results.
+        int n_indexed = assign_results.number_indexed;
+        int n_total = xyzobs_px.extent(0);
+        double percentage_indexed = 100.0 * static_cast<double>(n_indexed) / n_total;
+        logger.info(
+          "Indexed {}/{} reflections using the refined models ({:.2f}\% indexed)",
+          n_indexed,
+          n_total,
+          percentage_indexed);
+        gemmi::UnitCell cell = expt.crystal().get_unit_cell();
+        Matrix3d U = expt.crystal().get_U_matrix();
+        Matrix3d B = expt.crystal().get_B_matrix();
+        Matrix3d A = expt.crystal().get_A_matrix();
+
+        const std::string msg = fmt::format(
+          "Crystal:\n"
+          "  Unit cell: {:.4f} {:.4f} {:.4f} {:.4f} {:.4f} {:.4f}\n"
+          "  Space group: P 1\n"
+          "  U matrix: [[{:>7.4f}, {:>7.4f}, {:>7.4f}],\n"
+          "             [{:>7.4f}, {:>7.4f}, {:>7.4f}],\n"
+          "             [{:>7.4f}, {:>7.4f}, {:>7.4f}]]\n"
+          "  B matrix: [[{:>7.4f}, {:>7.4f}, {:>7.4f}],\n"
+          "             [{:>7.4f}, {:>7.4f}, {:>7.4f}],\n"
+          "             [{:>7.4f}, {:>7.4f}, {:>7.4f}]]\n"
+          "  A = UB:   [[{:>7.4f}, {:>7.4f}, {:>7.4f}],\n"
+          "             [{:>7.4f}, {:>7.4f}, {:>7.4f}],\n"
+          "             [{:>7.4f}, {:>7.4f}, {:>7.4f}]]",
+          cell.a,
+          cell.b,
+          cell.c,
+          cell.alpha,
+          cell.beta,
+          cell.gamma,
+          U(0, 0),
+          U(0, 1),
+          U(0, 2),
+          U(1, 0),
+          U(1, 1),
+          U(1, 2),
+          U(2, 0),
+          U(2, 1),
+          U(2, 2),
+          B(0, 0),
+          B(0, 1),
+          B(0, 2),
+          B(1, 0),
+          B(1, 1),
+          B(1, 2),
+          B(2, 0),
+          B(2, 1),
+          B(2, 2),
+          A(0, 0),
+          A(0, 1),
+          A(0, 2),
+          A(1, 0),
+          A(1, 1),
+          A(1, 2),
+          A(2, 0),
+          A(2, 1),
+          A(2, 2));
+        std::istringstream iss(msg);
+        std::string line;
+        while (std::getline(iss, line)) {
+            logger.info("{}", line);
+        }
+
         strong_reflections.add_column(std::string("miller_index"),
                                       assign_results.miller_indices.extent(0),
                                       assign_results.miller_indices.extent(1),