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authorThomas White <taw@physics.org>2018-04-20 11:27:07 +0200
committerThomas White <taw@physics.org>2018-04-20 17:36:40 +0200
commit7c0a1228c1254db06e0f5956cdc9691e86033cda (patch)
treed732530d017b621966abde70aca4b2aaf50311e5
parent8314534edc2f5076239d2ee39833d84df2b8be9c (diff)
Restore peak alignment check and unset multi-lattice indexing as default
Unfortunately, they seem to be severely reducing data quality. Partially reverts 60c48f3876b0d3c30bf729ce691dbd3f56665c4c
-rw-r--r--libcrystfel/src/index.c4
-rw-r--r--src/indexamajig.c13
2 files changed, 10 insertions, 7 deletions
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index a62dfcf1..b20c689a 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -316,9 +316,9 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
ERROR("To disable prediction refinement ('norefine'), use --no-refine.\n");
ERROR("To check cell axes only ('axes'), use --no-cell-combinations.\n");
ERROR("To disable all unit cell checks ('raw'), use --no-check-cell.\n");
+ ERROR("To disable peak alignment check ('bad'), use --no-check-peaks.\n");
ERROR("To disable indexing retry ('noretry'), use --no-retry.\n");
- ERROR("Multi-lattice indexing ('multi') is now the default: "
- "use --no-multi to disable it.\n");
+ ERROR("To enable multi-lattice indexing by 'delete and retry', use --multi\n");
ERROR("------------------\n");
free(methods);
return NULL;
diff --git a/src/indexamajig.c b/src/indexamajig.c
index a6651497..3cfe2c6e 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -124,11 +124,11 @@ static void show_help(const char *s)
" --no-check-cell Don't check lattice parameters against input cell\n"
" --no-cell-combinations\n"
" Don't use axis combinations when checking cell\n"
-" --no-multi Don't repeat indexing to index multiple hits\n"
+" --multi Repeat indexing to index multiple hits\n"
" --no-retry Don't repeat indexing to increase indexing rate\n"
" --no-refine Skip the prediction refinement step\n"
-" --check-peaks Check that most of the peaks can be accounted for\n"
-" by the indexing solution\n"
+" --no-check-peaks Don't check that most of the peaks can be accounted\n"
+" for by the indexing solution\n"
"\n"
" --taketwo-member-threshold\n"
" Minimum number of members in network\n"
@@ -239,8 +239,8 @@ int main(int argc, char *argv[])
int if_refine = 1;
int if_nocomb = 0;
int if_nocheck = 0;
- int if_peaks = 0;
- int if_multi = 1;
+ int if_peaks = 1;
+ int if_multi = 0;
int if_retry = 1;
int serial_start = 1;
@@ -343,8 +343,11 @@ int main(int argc, char *argv[])
{"no-check-cell", 0, &if_nocheck, 1},
{"no-cell-check", 0, &if_nocheck, 1},
{"check-peaks", 0, &if_peaks, 1},
+ {"no-check-peaks", 0, &if_peaks, 0},
{"no-retry", 0, &if_retry, 0},
+ {"retry", 0, &if_retry, 1},
{"no-multi", 0, &if_multi, 0},
+ {"multi", 0, &if_multi, 1},
{"overpredict", 0, &iargs.overpredict, 1},
/* Long-only options which don't actually do anything */