From f87a4b45a879bf7f8bf7578247eb5f6e4e5695d0 Mon Sep 17 00:00:00 2001
From: James Beilsten-Edmands
 <30625594+jbeilstenedmands@users.noreply.github.com>
Date: Mon, 23 Oct 2023 16:41:09 +0100
Subject: [PATCH] Fix some tests

---
 src/dials/algorithms/indexing/indexer.py   |  4 ++++
 tests/algorithms/indexing/test_index.py    | 13 ++++++++++---
 tests/algorithms/indexing/test_phi_scan.py | 12 ++++++------
 3 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/src/dials/algorithms/indexing/indexer.py b/src/dials/algorithms/indexing/indexer.py
index 8bdfa828e5..0b3928ab09 100644
--- a/src/dials/algorithms/indexing/indexer.py
+++ b/src/dials/algorithms/indexing/indexer.py
@@ -691,6 +691,10 @@ def index(self):
                         refined_reflections.unset_flags(
                             sel.iselection(), refined_reflections.flags.indexed
                         )
+                        self.unindexed_reflections.extend(
+                            refined_reflections.select(sel)
+                        )
+                        refined_reflections.del_selected(sel)
                         break
 
                 self._unit_cell_volume_sanity_check(experiments, refined_experiments)
diff --git a/tests/algorithms/indexing/test_index.py b/tests/algorithms/indexing/test_index.py
index a1d8dedc2c..39a39a225e 100644
--- a/tests/algorithms/indexing/test_index.py
+++ b/tests/algorithms/indexing/test_index.py
@@ -68,12 +68,17 @@ def run_indexing(
     assert out_refls.is_file()
 
     experiments_list = load.experiment_list(out_expts, check_format=False)
-    assert len(experiments_list.crystals()) == n_expected_lattices
+    assert (
+        len([c for c in experiments_list.crystals() if c is not None])
+        == n_expected_lattices
+    )
     indexed_reflections = flex.reflection_table.from_file(out_refls)
     indexed_reflections.assert_experiment_identifiers_are_consistent(experiments_list)
     rmsds = None
 
-    for i, experiment in enumerate(experiments_list):
+    for experiment in experiments_list:
+        if experiment.crystal is None:
+            continue
         assert unit_cells_are_similar(
             experiment.crystal.get_unit_cell(),
             expected_unit_cell,
@@ -88,7 +93,9 @@ def run_indexing(
             sg.type().hall_symbol(),
             expected_hall_symbol,
         )
-        reflections = indexed_reflections.select(indexed_reflections["id"] == i)
+        reflections = indexed_reflections.select_on_experiment_identifiers(
+            [experiment.identifier]
+        )
         mi = reflections["miller_index"]
         assert (mi != (0, 0, 0)).count(False) == 0
         reflections = reflections.select(mi != (0, 0, 0))
diff --git a/tests/algorithms/indexing/test_phi_scan.py b/tests/algorithms/indexing/test_phi_scan.py
index 3bfdc95488..ad673468d7 100644
--- a/tests/algorithms/indexing/test_phi_scan.py
+++ b/tests/algorithms/indexing/test_phi_scan.py
@@ -97,9 +97,9 @@ def test_run(dials_data, tmp_path):
 
     assert result_old.rmsds == pytest.approx(result_new.rmsds, abs=1e-6)
     assert result_old.experiments[
-        0
+        1
     ].crystal.get_unit_cell().parameters() == pytest.approx(
-        result_new.experiments[0].crystal.get_unit_cell().parameters(), abs=1e-6
+        result_new.experiments[1].crystal.get_unit_cell().parameters(), abs=1e-6
     )
 
     # Now test refinement gradients are correct
@@ -110,9 +110,9 @@ def test_run(dials_data, tmp_path):
                 detector=imageset_old.get_detector(),
                 goniometer=gonio_old,
                 scan=imageset_old.get_scan(),
-                crystal=result_old.experiments[0].crystal,
+                crystal=result_old.experiments[1].crystal,
                 imageset=None,
-                identifier=result_old.experiments[0].identifier,
+                identifier=result_old.experiments[1].identifier,
             )
         ]
     )
@@ -123,9 +123,9 @@ def test_run(dials_data, tmp_path):
                 detector=imageset_new.get_detector(),
                 goniometer=gonio_new,
                 scan=imageset_new.get_scan(),
-                crystal=result_new.experiments[0].crystal,
+                crystal=result_new.experiments[1].crystal,
                 imageset=None,
-                identifier=result_new.experiments[0].identifier,
+                identifier=result_new.experiments[1].identifier,
             )
         ]
     )