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-rw-r--r--libcrystfel/src/index.c42
-rw-r--r--libcrystfel/src/index.h1
-rw-r--r--libcrystfel/src/stream.c20
-rw-r--r--libcrystfel/src/stream.h1
-rw-r--r--src/cell_explorer.c11
5 files changed, 70 insertions, 5 deletions
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 8ac04368..8a390d71 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -283,10 +283,13 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
}
for ( i=0; i<n; i++ ) {
- methods[i] = get_indm_from_string(method_strings[i]);
- if ( methods[i] == INDEXING_ERROR ) {
+ int err = 0;
+ methods[i] = get_indm_from_string_2(method_strings[i], &err);
+ if ( err ) {
ERROR("----- Notice -----\n");
- ERROR("The way indexing options are used has changed in this CrystFEL version.\n");
+ ERROR("The way indexing options are given has changed in this CrystFEL version.\n");
+ ERROR("The indexing method should contain only the method itself and ");
+ ERROR("prior information modifiers ('cell' or 'latt')\n");
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");
@@ -297,6 +300,7 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
free(methods);
return NULL;
}
+
}
/* No cell parameters -> no cell checking, no prior cell */
@@ -877,13 +881,15 @@ static IndexingMethod warn_method(const char *str)
}
-IndexingMethod get_indm_from_string(const char *str)
+IndexingMethod get_indm_from_string_2(const char *str, int *err)
{
int n, i;
char **bits;
IndexingMethod method = INDEXING_NONE;
int have_method = 0;
+ if ( err != NULL ) *err = 0;
+
n = assplode(str, "-", &bits, ASSPLODE_NONE);
for ( i=0; i<n; i++ ) {
@@ -945,6 +951,28 @@ IndexingMethod get_indm_from_string(const char *str)
} else if ( strcmp(bits[i], "nocell") == 0) {
method = set_nocellparams(method);
+ /* Deprecated options */
+ } else if ( strcmp(bits[i], "retry") == 0) {
+ if ( err != NULL ) *err = 1;
+ } else if ( strcmp(bits[i], "noretry") == 0) {
+ if ( err != NULL ) *err = 1;
+ } else if ( strcmp(bits[i], "multi") == 0) {
+ if ( err != NULL ) *err = 1;
+ } else if ( strcmp(bits[i], "nomulti") == 0) {
+ if ( err != NULL ) *err = 1;
+ } else if ( strcmp(bits[i], "refine") == 0) {
+ if ( err != NULL ) *err = 1;
+ } else if ( strcmp(bits[i], "norefine") == 0) {
+ if ( err != NULL ) *err = 1;
+ } else if ( strcmp(bits[i], "raw") == 0) {
+ if ( err != NULL ) *err = 1;
+ } else if ( strcmp(bits[i], "bad") == 0) {
+ if ( err != NULL ) *err = 1;
+ } else if ( strcmp(bits[i], "comb") == 0) {
+ if ( err != NULL ) *err = 1;
+ } else if ( strcmp(bits[i], "axes") == 0) {
+ if ( err != NULL ) *err = 1;
+
} else {
ERROR("Bad list of indexing methods: '%s'\n", str);
return INDEXING_ERROR;
@@ -959,3 +987,9 @@ IndexingMethod get_indm_from_string(const char *str)
return method;
}
+
+
+IndexingMethod get_indm_from_string(const char *str)
+{
+ return get_indm_from_string_2(str, NULL);
+}
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index ac386390..ae5185db 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -130,6 +130,7 @@ typedef struct _indexingprivate IndexingPrivate;
/* Convert indexing methods to/from text */
extern char *indexer_str(IndexingMethod indm);
extern IndexingMethod get_indm_from_string(const char *method);
+extern IndexingMethod get_indm_from_string_2(const char *method, int *err);
#include "detector.h"
#include "cell.h"
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index fb4b0c70..d7d997cf 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -67,8 +67,18 @@ struct _stream
int minor_version;
long long int ln;
+
+ int old_indexers; /* True if the stream reader encountered a deprecated
+ * indexing method */
};
+
+int stream_has_old_indexers(Stream *st)
+{
+ return st->old_indexers;
+}
+
+
static int read_peaks(Stream *st, struct image *image)
{
char *rval = NULL;
@@ -1196,10 +1206,14 @@ int read_chunk_2(Stream *st, struct image *image, StreamReadFlags srf)
}
if ( strncmp(line, "indexed_by = ", 13) == 0 ) {
- image->indexed_by = get_indm_from_string(line+13);
+ int err = 0;
+ image->indexed_by = get_indm_from_string_2(line+13, &err);
if ( image->indexed_by == INDEXING_ERROR ) {
ERROR("Failed to read indexer list\n");
}
+ if ( err ) {
+ st->old_indexers = 1;
+ }
}
if ( strncmp(line, "photon_energy_eV = ", 19) == 0 ) {
@@ -1327,6 +1341,7 @@ Stream *open_stream_for_read(const char *filename)
st = malloc(sizeof(struct _stream));
if ( st == NULL ) return NULL;
+ st->old_indexers = 0;
if ( strcmp(filename, "-") == 0 ) {
st->fh = stdin;
@@ -1393,6 +1408,7 @@ Stream *open_stream_fd_for_write(int fd)
st = malloc(sizeof(struct _stream));
if ( st == NULL ) return NULL;
+ st->old_indexers = 0;
st->fh = fdopen(fd, "w");
if ( st->fh == NULL ) {
@@ -1442,6 +1458,7 @@ Stream *open_stream_for_write_3(const char *filename,
st = malloc(sizeof(struct _stream));
if ( st == NULL ) return NULL;
+ st->old_indexers = 0;
st->fh = fopen(filename, "w");
if ( st->fh == NULL ) {
@@ -1493,6 +1510,7 @@ Stream *open_stream_for_write_2(const char *filename,
st = malloc(sizeof(struct _stream));
if ( st == NULL ) return NULL;
+ st->old_indexers = 0;
st->fh = fopen(filename, "w");
if ( st->fh == NULL ) {
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index 764e3e36..2ed7b050 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -106,6 +106,7 @@ extern void close_stream(Stream *st);
extern int read_chunk(Stream *st, struct image *image);
extern int read_chunk_2(Stream *st, struct image *image,
StreamReadFlags srf);
+extern int stream_has_old_indexers(Stream *st);
extern int write_chunk(Stream *st, struct image *image, struct imagefile *imfile,
int include_peaks, int include_reflections,
diff --git a/src/cell_explorer.c b/src/cell_explorer.c
index a8a8a7dc..f3ec7cb7 100644
--- a/src/cell_explorer.c
+++ b/src/cell_explorer.c
@@ -1638,6 +1638,17 @@ int main(int argc, char *argv[])
fprintf(stderr, "\n");
+ if ( stream_has_old_indexers(st) ) {
+ ERROR("----- Notice -----\n");
+ ERROR("This stream contains indexing methods specified in an old way.\n");
+ ERROR("The full indexing method names will not be shown by cell_explorer, \n");
+ ERROR("only the methods themselves and prior information modifiers ");
+ ERROR("('cell' or 'latt').\n");
+ ERROR("Similar indexing methods will be combined. For example\n");
+ ERROR("'mosflm-raw' and 'mosflm-axes' will both show up as 'mosflm'\n");
+ ERROR("To simplify matters, it's best to re-run indexamajig.\n");
+ ERROR("------------------\n");
+ }
close_stream(st);
w.cols_on[0] = 1;
generated by cgit v1.2.3 (git 2.25.1) at 2024-08-15 04:30:06 +0000