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-rw-r--r--libcrystfel/src/stream.c120
1 files changed, 49 insertions, 71 deletions
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index e767b59f..f1f2173c 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -148,8 +148,7 @@ static ImageFeatureList *read_peaks(Stream *st, struct image *image)
ERROR("Failed to convert peak coords\n");
} else {
image_add_feature(features, x, y,
- pn, image, intensity,
- NULL);
+ pn, intensity, NULL);
}
}
@@ -200,7 +199,7 @@ static int write_peaks(const struct image *image,
}
-static RefList *read_stream_reflections_2_3(Stream *st)
+static RefList *read_stream_reflections_2_3(Stream *st, double kpred)
{
char *rval = NULL;
int first = 1;
@@ -268,6 +267,7 @@ static RefList *read_stream_reflections_2_3(Stream *st)
set_mean_bg(refl, bg);
set_redundancy(refl, 1);
set_symmetric_indices(refl, h, k, l);
+ set_kpred(refl, kpred);
}
} while ( rval != NULL );
@@ -339,11 +339,9 @@ static int num_integrated_reflections(RefList *list)
}
-static int write_crystal(Stream *st, Crystal *cr,
- int include_reflections)
+static int write_crystal(Stream *st, Crystal *cr, RefList *reflist)
{
UnitCell *cell;
- RefList *reflist;
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
@@ -390,7 +388,6 @@ static int write_crystal(Stream *st, Crystal *cr,
fprintf(st->fh, "predict_refine/det_shift x = %.3f y = %.3f mm\n",
det_shift_x*1e3, det_shift_y*1e3);
- reflist = crystal_get_reflections(cr);
if ( reflist != NULL ) {
fprintf(st->fh, "diffraction_resolution_limit"
@@ -407,20 +404,17 @@ static int write_crystal(Stream *st, Crystal *cr,
}
- if ( include_reflections ) {
-
- if ( reflist != NULL ) {
+ if ( reflist != NULL ) {
- fprintf(st->fh, STREAM_REFLECTION_START_MARKER"\n");
- ret = write_stream_reflections(st->fh, reflist,
- st->dtempl_write);
- fprintf(st->fh, STREAM_REFLECTION_END_MARKER"\n");
+ fprintf(st->fh, STREAM_REFLECTION_START_MARKER"\n");
+ ret = write_stream_reflections(st->fh, reflist,
+ st->dtempl_write);
+ fprintf(st->fh, STREAM_REFLECTION_END_MARKER"\n");
- } else {
+ } else {
- fprintf(st->fh, "No integrated reflections.\n");
+ fprintf(st->fh, "No integrated reflections.\n");
- }
}
fprintf(st->fh, STREAM_CRYSTAL_END_MARKER"\n");
@@ -454,7 +448,7 @@ int stream_write_chunk(Stream *st, const struct image *i,
fprintf(st->fh, "hit = %i\n", i->hit);
indexer = indexer_str(i->indexed_by);
fprintf(st->fh, "indexed_by = %s\n", indexer);
- free(indexer);
+ cffree(indexer);
if ( i->indexed_by != INDEXING_NONE ) {
fprintf(st->fh, "n_indexing_tries = %i\n", i->n_indexing_tries);
}
@@ -513,11 +507,11 @@ int stream_write_chunk(Stream *st, const struct image *i,
}
for ( j=0; j<i->n_crystals; j++ ) {
- if ( crystal_get_user_flag(i->crystals[j]) ) {
+ if ( crystal_get_user_flag(i->crystals[j].cr) ) {
continue;
}
- ret = write_crystal(st, i->crystals[j],
- srf & STREAM_REFLECTIONS);
+ ret = write_crystal(st, i->crystals[j].cr,
+ srf & STREAM_REFLECTIONS ? i->crystals[j].refls : NULL);
}
fprintf(st->fh, STREAM_CHUNK_END_MARKER"\n");
@@ -565,8 +559,7 @@ static void read_crystal(Stream *st, struct image *image,
char unique_axis = '*';
LatticeType lattice_type = L_TRICLINIC;
Crystal *cr;
- int n;
- Crystal **crystals_new;
+ RefList *reflist = NULL;
double shift_x, shift_y;
as.u = 0.0; as.v = 0.0; as.w = 0.0;
@@ -665,18 +658,13 @@ static void read_crystal(Stream *st, struct image *image,
if ( (strcmp(line, STREAM_REFLECTION_START_MARKER) == 0)
&& (srf & STREAM_REFLECTIONS) )
{
-
- RefList *reflist;
- reflist = read_stream_reflections_2_3(st);
+ reflist = read_stream_reflections_2_3(st, 1.0/image->lambda);
if ( reflist == NULL ) {
ERROR("Failed while reading reflections\n");
ERROR("Filename = %s\n", image->filename);
ERROR("Event = %s\n", image->ev);
break;
}
-
- crystal_set_reflections(cr, reflist);
-
}
if ( strcmp(line, STREAM_CRYSTAL_END_MARKER) == 0 ) break;
@@ -714,17 +702,7 @@ static void read_crystal(Stream *st, struct image *image,
/* Unused at the moment */
crystal_set_mosaicity(cr, 0.0);
- /* Add crystal to the list for this image */
- n = image->n_crystals+1;
- crystals_new = realloc(image->crystals, n*sizeof(Crystal *));
-
- if ( crystals_new == NULL ) {
- ERROR("Failed to expand crystal list!\n");
- } else {
- image->crystals = crystals_new;
- image->crystals[image->n_crystals++] = cr;
- }
-
+ image_add_crystal_refls(image, cr, reflist);
}
@@ -734,7 +712,7 @@ static void parse_header(const char *line_in, struct image *image,
char *line;
char *pos;
- line = strdup(line_in);
+ line = cfstrdup(line_in);
chomp(line);
pos = strchr(line, ' ');
@@ -817,12 +795,12 @@ struct image *stream_read_chunk(Stream *st, StreamFlags srf)
chomp(line);
if ( strncmp(line, "Image filename: ", 16) == 0 ) {
- image->filename = strdup(line+16);
+ image->filename = cfstrdup(line+16);
have_filename = 1;
}
if ( strncmp(line, "Event: ", 7) == 0 ) {
- image->ev = strdup(line+7);
+ image->ev = cfstrdup(line+7);
}
if ( strncmp(line, "hdf5/", 5) == 0 ) {
@@ -929,7 +907,7 @@ struct image *stream_read_chunk(Stream *st, StreamFlags srf)
char *stream_audit_info(Stream *st)
{
if ( st->audit_info == NULL ) return NULL;
- return strdup(st->audit_info);
+ return cfstrdup(st->audit_info);
}
@@ -946,7 +924,7 @@ static int read_geometry_file(Stream *st)
const size_t max_geom_len = 1024*1024;
char *geom;
- geom = malloc(max_geom_len);
+ geom = cfmalloc(max_geom_len);
if ( geom == NULL ) {
ERROR("Failed to allocate memory for geometry file\n");
return 1;
@@ -963,7 +941,7 @@ static int read_geometry_file(Stream *st)
if ( rval == NULL ) {
ERROR("Failed to read stream geometry file.\n");
stream_close(st);
- free(geom);
+ cffree(geom);
return 1;
}
@@ -976,7 +954,7 @@ static int read_geometry_file(Stream *st)
if ( len > max_geom_len-1 ) {
ERROR("Stream's geometry file is too long (%li > %i).\n",
(long)len, (int)max_geom_len);
- free(geom);
+ cffree(geom);
return 1;
} else {
strcat(geom, line);
@@ -995,7 +973,7 @@ static int read_headers(Stream *st)
int done = 0;
size_t len = 0;
- st->audit_info = malloc(4096);
+ st->audit_info = cfmalloc(4096);
if ( st->audit_info == NULL ) {
ERROR("Failed to allocate memory for audit information\n");
return 1;
@@ -1042,7 +1020,7 @@ Stream *stream_open_for_read(const char *filename)
{
Stream *st;
- st = malloc(sizeof(struct _stream));
+ st = cfmalloc(sizeof(struct _stream));
if ( st == NULL ) return NULL;
st->old_indexers = 0;
st->audit_info = NULL;
@@ -1059,7 +1037,7 @@ Stream *stream_open_for_read(const char *filename)
}
if ( st->fh == NULL ) {
- free(st);
+ cffree(st);
return NULL;
}
@@ -1109,7 +1087,7 @@ Stream *stream_open_fd_for_write(int fd, const DataTemplate *dtempl)
{
Stream *st;
- st = malloc(sizeof(struct _stream));
+ st = cfmalloc(sizeof(struct _stream));
if ( st == NULL ) return NULL;
st->old_indexers = 0;
st->audit_info = NULL;
@@ -1121,7 +1099,7 @@ Stream *stream_open_fd_for_write(int fd, const DataTemplate *dtempl)
st->fh = fdopen(fd, "w");
if ( st->fh == NULL ) {
- free(st);
+ cffree(st);
return NULL;
}
@@ -1166,7 +1144,7 @@ Stream *stream_open_for_write(const char *filename,
{
Stream *st;
- st = malloc(sizeof(struct _stream));
+ st = cfmalloc(sizeof(struct _stream));
if ( st == NULL ) return NULL;
st->old_indexers = 0;
st->audit_info = NULL;
@@ -1179,7 +1157,7 @@ Stream *stream_open_for_write(const char *filename,
st->fh = fopen(filename, "w");
if ( st->fh == NULL ) {
ERROR("Failed to open stream.\n");
- free(st);
+ cffree(st);
return NULL;
}
@@ -1210,11 +1188,11 @@ int stream_get_fd(Stream *st)
void stream_close(Stream *st)
{
if ( st == NULL ) return;
- free(st->audit_info);
- free(st->geometry_file);
+ cffree(st->audit_info);
+ cffree(st->geometry_file);
data_template_free(st->dtempl_read);
fclose(st->fh);
- free(st);
+ cffree(st);
}
@@ -1339,9 +1317,9 @@ struct _streamindex
void stream_index_free(StreamIndex *index)
{
if ( index == NULL ) return;
- free(index->keys);
- free(index->ptrs);
- free(index);
+ cffree(index->keys);
+ cffree(index->ptrs);
+ cffree(index);
}
@@ -1352,7 +1330,7 @@ static char *make_key(const char *filename,
if ( ev == NULL ) ev = "//";
- key = malloc(strlen(filename)+strlen(ev)+2);
+ key = cfmalloc(strlen(filename)+strlen(ev)+2);
if ( key == NULL ) return NULL;
strcpy(key, filename);
@@ -1399,14 +1377,14 @@ static void add_index_record(StreamIndex *index,
char **new_keys;
long int *new_ptrs;
- new_keys = realloc(index->keys,
- new_max_keys*sizeof(char *));
+ new_keys = cfrealloc(index->keys,
+ new_max_keys*sizeof(char *));
if ( new_keys == NULL ) return;
- new_ptrs = realloc(index->ptrs,
- new_max_keys*sizeof(long int));
+ new_ptrs = cfrealloc(index->ptrs,
+ new_max_keys*sizeof(long int));
if ( new_ptrs == NULL ) {
- free(new_keys);
+ cffree(new_keys);
return;
}
@@ -1437,7 +1415,7 @@ StreamIndex *stream_make_index(const char *filename)
fh = fopen(filename, "r");
if ( fh == NULL ) return NULL;
- index = malloc(sizeof(StreamIndex));
+ index = cfmalloc(sizeof(StreamIndex));
if ( index == NULL ) {
fclose(fh);
return NULL;
@@ -1468,11 +1446,11 @@ StreamIndex *stream_make_index(const char *filename)
}
if ( strncmp(line, "Image filename: ", 16) == 0 ) {
- last_filename = strdup(line+16);
+ last_filename = cfstrdup(line+16);
}
if ( strncmp(line, "Event: ", 7) == 0 ) {
- last_ev = strdup(line+7);
+ last_ev = cfstrdup(line+7);
}
if ( strcmp(line, STREAM_CHUNK_END_MARKER) == 0 ) {
@@ -1484,8 +1462,8 @@ StreamIndex *stream_make_index(const char *filename)
last_filename,
last_ev);
}
- free(last_filename);
- free(last_ev);
+ cffree(last_filename);
+ cffree(last_ev);
last_start_pos = 0;
last_filename = NULL;
last_ev = NULL;
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-17 20:04:56 +0000