aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--libcrystfel/src/index.c6
-rw-r--r--libcrystfel/src/mosflm.h4
-rw-r--r--libcrystfel/src/peaks.c10
-rw-r--r--libcrystfel/src/stream.c18
-rw-r--r--libcrystfel/src/stream.h10
-rw-r--r--src/im-sandbox.c50
-rw-r--r--src/im-sandbox.h2
-rw-r--r--src/indexamajig.c10
8 files changed, 55 insertions, 55 deletions
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 821be39a..cd6628e9 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -68,7 +68,6 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
IndexingPrivate **iprivs;
while ( indm[nm] != INDEXING_NONE ) nm++;
- STATUS("Preparing %i indexing method%s.\n", nm, maybes(nm));
iprivs = malloc((nm+1) * sizeof(IndexingPrivate *));
for ( n=0; n<nm; n++ ) {
@@ -76,12 +75,13 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
switch ( indm[n] & INDEXING_METHOD_MASK ) {
case INDEXING_DIRAX :
- iprivs[n] = dirax_prepare(indm[nm], cell, filename, det,
+ iprivs[n] = dirax_prepare(indm[n], cell, filename, det,
beam, ltl);
break;
case INDEXING_MOSFLM :
- iprivs[n] = NULL;
+ iprivs[n] = mosflm_prepare(indm[n], cell, filename, det,
+ beam, ltl);
break;
case INDEXING_REAX :
diff --git a/libcrystfel/src/mosflm.h b/libcrystfel/src/mosflm.h
index 1d296cb7..65aeb631 100644
--- a/libcrystfel/src/mosflm.h
+++ b/libcrystfel/src/mosflm.h
@@ -40,5 +40,9 @@
extern int run_mosflm(struct image *image, IndexingPrivate *ipriv);
+extern IndexingPrivate *mosflm_prepare(IndexingMethod indm, UnitCell *cell,
+ const char *filename,
+ struct detector *det,
+ struct beam_params *beam, float *ltl);
#endif /* MOSFLM_H */
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 08595ef5..54ba6468 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -148,7 +148,7 @@ static int cull_peaks(struct image *image)
static void add_crystal_to_mask(struct image *image, struct panel *p,
- double ir_out, double ir_inn, int w, int h,
+ double ir_inn, int w, int h,
int *mask, Crystal *cr)
{
Reflection *refl;
@@ -200,8 +200,7 @@ static void add_crystal_to_mask(struct image *image, struct panel *p,
/* cfs, css relative to panel origin */
-static int *make_BgMask(struct image *image, struct panel *p,
- double ir_out, double ir_inn)
+static int *make_BgMask(struct image *image, struct panel *p, double ir_inn)
{
int *mask;
int w, h;
@@ -215,7 +214,7 @@ static int *make_BgMask(struct image *image, struct panel *p,
if ( image->crystals == NULL ) return mask;
for ( i=0; i<image->n_crystals; i++ ) {
- add_crystal_to_mask(image, p, ir_inn, ir_out,
+ add_crystal_to_mask(image, p, ir_inn,
w, h, mask, image->crystals[i]);
}
@@ -860,8 +859,7 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
}
for ( i=0; i<image->det->n_panels; i++ ) {
int *mask;
- mask = make_BgMask(image, &image->det->panels[i],
- ir_out, ir_inn);
+ mask = make_BgMask(image, &image->det->panels[i], ir_inn);
if ( mask == NULL ) {
ERROR("Couldn't create background mask.\n");
return;
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 113dc359..fbcbaf2e 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -52,16 +52,6 @@
#define LATEST_MAJOR_VERSION (2)
#define LATEST_MINOR_VERSION (1)
-#define CHUNK_START_MARKER "----- Begin chunk -----"
-#define CHUNK_END_MARKER "----- End chunk -----"
-#define PEAK_LIST_START_MARKER "Peaks from peak search"
-#define PEAK_LIST_END_MARKER "End of peak list"
-#define CRYSTAL_START_MARKER "--- Begin crystal"
-#define CRYSTAL_END_MARKER "--- End crystal"
-#define REFLECTION_START_MARKER "Reflections measured after indexing"
-/* REFLECTION_END_MARKER is over in reflist-utils.h because it is also
- * used to terminate a standalone list of reflections */
-
struct _stream
{
@@ -184,8 +174,6 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
if ( include_reflections ) {
- fprintf(st->fh, "\n");
-
if ( reflist != NULL ) {
fprintf(st->fh, REFLECTION_START_MARKER"\n");
@@ -199,7 +187,7 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
}
}
- fprintf(st->fh, CRYSTAL_START_MARKER"\n\n");
+ fprintf(st->fh, CRYSTAL_END_MARKER"\n");
}
@@ -226,19 +214,17 @@ void write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
copy_hdf5_fields(hdfile, i->copyme, st->fh);
if ( include_peaks ) {
- fprintf(st->fh, "\n");
write_peaks(i, st->fh);
}
fprintf(st->fh, "photon_energy_eV = %f\n",
J_to_eV(ph_lambda_to_en(i->lambda)));
- fprintf(st->fh, "\n");
for ( j=0; j<i->n_crystals; j++ ) {
write_crystal(st, i->crystals[j], include_reflections);
}
- fprintf(st->fh, CHUNK_END_MARKER"\n\n");
+ fprintf(st->fh, CHUNK_END_MARKER"\n");
fflush(st->fh);
}
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index 4d561cd2..cdce0ea2 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -38,6 +38,16 @@
struct image;
struct hdfile;
+#define CHUNK_START_MARKER "----- Begin chunk -----"
+#define CHUNK_END_MARKER "----- End chunk -----"
+#define PEAK_LIST_START_MARKER "Peaks from peak search"
+#define PEAK_LIST_END_MARKER "End of peak list"
+#define CRYSTAL_START_MARKER "--- Begin crystal"
+#define CRYSTAL_END_MARKER "--- End crystal"
+#define REFLECTION_START_MARKER "Reflections measured after indexing"
+/* REFLECTION_END_MARKER is over in reflist-utils.h because it is also
+ * used to terminate a standalone list of reflections */
+
typedef struct _stream Stream;
extern Stream *open_stream_for_read(const char *filename);
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 825f2d6a..d476c72d 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -305,6 +305,8 @@ static void process_image(const struct index_args *iargs,
/* Index the pattern */
index_pattern(&image, indm, iargs->ipriv);
+ pargs->n_crystals = image.n_crystals;
+
/* Default beam parameters */
image.div = image.beam->divergence;
image.bw = image.beam->bandwidth;
@@ -328,22 +330,20 @@ static void process_image(const struct index_args *iargs,
crystal_set_reflections(image.crystals[i], reflections);
- if ( reflections != NULL ) {
-
- integrate_reflections(&image,
- iargs->config_closer,
- iargs->config_bgsub,
- iargs->min_int_snr,
- iargs->ir_inn,
- iargs->ir_mid,
- iargs->ir_out,
- iargs->integrate_saturated);
- }
-
}
- write_chunk(st, &image, hdfile, iargs->include_peaks,
- iargs->include_reflections);
+ /* Integrate all the crystals at once - need all the crystals so that
+ * overlaps can be detected. */
+ integrate_reflections(&image, iargs->config_closer,
+ iargs->config_bgsub,
+ iargs->min_int_snr,
+ iargs->ir_inn,
+ iargs->ir_mid,
+ iargs->ir_out,
+ iargs->integrate_saturated);
+
+ write_chunk(st, &image, hdfile,
+ iargs->include_peaks, iargs->include_reflections);
for ( i=0; i<image.n_crystals; i++ ) {
crystal_free(image.crystals[i]);
@@ -485,15 +485,17 @@ static int pump_chunk(FILE *fh, FILE *ofh)
}
- if ( strcmp(line, "END\n") == 0 ) {
+ fprintf(ofh, "%s", line);
+
+ if ( strcmp(line, CHUNK_END_MARKER"\n") == 0 ) {
chunk_finished = 1;
- } else {
+ }
+ if ( strcmp(line, CHUNK_START_MARKER"\n") == 0 ) {
chunk_started = 1;
- fprintf(ofh, "%s", line);
}
- } while ( !chunk_finished );
+ } while ( !chunk_finished );
return 0;
}
@@ -711,7 +713,7 @@ static void handle_zombie(struct sandbox *sb)
void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
int config_basename, FILE *fh, char *use_this_one_instead,
- Stream *st)
+ FILE *ofh)
{
int i;
int allDone;
@@ -738,6 +740,7 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
pthread_mutex_init(&sb->lock, NULL);
+ sb->ofh = ofh;
sb->stream_pipe_read = calloc(n_proc, sizeof(int));
sb->stream_pipe_write = calloc(n_proc, sizeof(int));
if ( sb->stream_pipe_read == NULL ) {
@@ -950,15 +953,12 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
tNow = get_monotonic_seconds();
if ( tNow >= sb->t_last_stats+STATS_EVERY_N_SECONDS ) {
- STATUS("Total so far: %i images processed, "
+ STATUS("%i images processed so far, "
"%i had crystals, %i crystals overall. "
- "Since the last message: %i images processed,"
- "%i had crystals, %i crystals overall.\n",
+ "%i images processed since the last message\n",
sb->n_processed, sb->n_hadcrystals,
sb->n_crystals,
- sb->n_processed - sb->n_processed_last_stats,
- sb->n_hadcrystals - sb->n_hadcrystals_last_stats,
- sb->n_crystals - sb->n_crystals_last_stats);
+ sb->n_processed - sb->n_processed_last_stats);
sb->n_processed_last_stats = sb->n_processed;
sb->n_hadcrystals_last_stats = sb->n_hadcrystals;
diff --git a/src/im-sandbox.h b/src/im-sandbox.h
index 176bfde0..96311056 100644
--- a/src/im-sandbox.h
+++ b/src/im-sandbox.h
@@ -76,4 +76,4 @@ struct index_args
extern void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
int config_basename, FILE *fh,
- char *use_this_one_instead, Stream *st);
+ char *use_this_one_instead, FILE *stream);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 3076ea86..5d57d336 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -180,7 +180,7 @@ int main(int argc, char *argv[])
char *filename = NULL;
char *outfile = NULL;
FILE *fh;
- Stream *st;
+ FILE *ofh;
char *rval = NULL;
int config_noindex = 0;
int config_cmfilter = 0;
@@ -264,6 +264,7 @@ int main(int argc, char *argv[])
{"peaks", 1, NULL, 2},
{"cell-reduction", 1, NULL, 3},
{"min-gradient", 1, NULL, 4},
+ {"record", 1, NULL, 5},
{"cpus", 1, NULL, 6},
{"cpugroup", 1, NULL, 7},
{"cpuoffset", 1, NULL, 8},
@@ -352,6 +353,7 @@ int main(int argc, char *argv[])
case 5 :
ERROR("The option '--record' is no longer used.\n");
+ /* FIXME: Translate to new style */
break;
case 6 :
@@ -526,8 +528,8 @@ int main(int argc, char *argv[])
cell = NULL;
}
- st = open_stream_for_write(outfile);
- if ( st == NULL ) {
+ ofh = fopen(outfile, "w");
+ if ( ofh == NULL ) {
ERROR("Failed to open stream '%s'\n", outfile);
return 1;
}
@@ -600,7 +602,7 @@ int main(int argc, char *argv[])
iargs.include_reflections = 1; /* FIXME! */
create_sandbox(&iargs, n_proc, prefix, config_basename, fh,
- use_this_one_instead, st);
+ use_this_one_instead, ofh);
free(prefix);
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-19 17:02:13 +0000