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-rw-r--r--libcrystfel/src/peaks.c32
-rw-r--r--libcrystfel/src/reax.c7
-rw-r--r--src/indexamajig.c154
3 files changed, 142 insertions, 51 deletions
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index ffe77290..047bac34 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -160,6 +160,8 @@ static int *make_BgMask(struct image *image, struct panel *p,
mask = calloc(w*h, sizeof(int));
if ( mask == NULL ) return NULL;
+ if ( image->reflections == NULL ) return mask;
+
/* Loop over all reflections */
for ( refl = first_refl(image->reflections, &iter);
refl != NULL;
@@ -278,17 +280,26 @@ static int integrate_peak(struct image *image, int cfs, int css,
/* It must have all the "good" bits to be valid */
if ( !((flags & image->det->mask_good)
- == image->det->mask_good) ) return 1;
+ == image->det->mask_good) ) {
+ free(bgPkMask);
+ return 1;
+ }
/* If it has any of the "bad" bits, reject */
- if ( flags & image->det->mask_bad ) return 1;
+ if ( flags & image->det->mask_bad ) {
+ free(bgPkMask);
+ return 1;
+ }
}
val = image->data[idx];
/* Veto peak if it contains saturation in bg region */
- if ( use_max_adu && (val > p->max_adu) ) return 1;
+ if ( use_max_adu && (val > p->max_adu) ) {
+ free(bgPkMask);
+ return 1;
+ }
bg_tot += val;
bg_tot_sq += pow(val, 2.0);
@@ -330,17 +341,26 @@ static int integrate_peak(struct image *image, int cfs, int css,
/* It must have all the "good" bits to be valid */
if ( !((flags & image->det->mask_good)
- == image->det->mask_good) ) return 1;
+ == image->det->mask_good) ) {
+ free(bgPkMask);
+ return 1;
+ }
/* If it has any of the "bad" bits, reject */
- if ( flags & image->det->mask_bad ) return 1;
+ if ( flags & image->det->mask_bad ) {
+ free(bgPkMask);
+ return 1;
+ }
}
val = image->data[idx] - bg_mean;
/* Veto peak if it contains saturation */
- if ( use_max_adu && (image->data[idx] > p->max_adu) ) return 1;
+ if ( use_max_adu && (image->data[idx] > p->max_adu) ) {
+ free(bgPkMask);
+ return 1;
+ }
pk_counts++;
pk_total += val;
diff --git a/libcrystfel/src/reax.c b/libcrystfel/src/reax.c
index 58dce40a..3124a77c 100644
--- a/libcrystfel/src/reax.c
+++ b/libcrystfel/src/reax.c
@@ -348,6 +348,7 @@ static double iterate_refine_vector(double *x, double *y, double *z,
gsl_matrix_free(C);
gsl_vector_free(A);
+ gsl_vector_free(t);
return dtmax;
}
@@ -1019,6 +1020,7 @@ void reax_index(IndexingPrivate *pp, struct image *image, UnitCell *cell)
fftw_complex *fft_out;
double pmax;
struct reax_search *s;
+ int i;
assert(pp->indm == INDEXING_REAX);
p = (struct reax_private *)pp;
@@ -1045,6 +1047,11 @@ void reax_index(IndexingPrivate *pp, struct image *image, UnitCell *cell)
assemble_cells_from_candidates(image, s, cell);
+ for ( i=0; i<s->n_search; i++ ) {
+ free(s->search[i].cand);
+ }
+ free(s->search);
+ free(s);
fftw_free(fft_in);
fftw_free(fft_out);
}
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 1db8b353..33caddfa 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -99,14 +99,12 @@ struct index_args
int cellr;
float tols[4];
struct beam_params *beam;
- const char *element;
- const char *hdf5_peak_path;
+ char *element;
+ char *hdf5_peak_path;
double ir_inn;
double ir_mid;
double ir_out;
-
- /* Output stream */
- const struct copy_hdf5_field *copyme;
+ struct copy_hdf5_field *copyme;
};
@@ -366,11 +364,8 @@ static void process_image(const struct index_args *iargs,
case PEAK_ZAEF:
search_peaks(&image, iargs->threshold,
- iargs->min_gradient,
- iargs->min_snr,
- iargs->ir_inn,
- iargs->ir_mid,
- iargs->ir_out);
+ iargs->min_gradient, iargs->min_snr,
+ iargs->ir_inn, iargs->ir_mid, iargs->ir_out);
break;
}
@@ -483,9 +478,20 @@ static void run_work(const struct index_args *iargs,
free(line);
}
+
/* close my pipes */
fclose(fh);
close(results_pipe);
+
+ cleanup_indexing(iargs->ipriv);
+ free(iargs->indm);
+ free(iargs->ipriv);
+ free_detector_geometry(iargs->det);
+ free(iargs->beam);
+ free(iargs->element);
+ free(iargs->hdf5_peak_path);
+ free_copy_hdf5_field_list(iargs->copyme);
+ cell_free(iargs->cell);
}
@@ -616,10 +622,13 @@ static void run_reader(int *stream_pipe_read, int n_proc, FILE *ofh)
if ( feof(fhs[i]) ) {
/* Process died */
finished[i] = 1;
+ ERROR("EOF during chunk\n");
} else {
ERROR("fgets() failed: %s\n",
strerror(errno));
}
+ fprintf(ofh, "Chunk is unfinished!\n");
+ chunk_finished = 1;
continue;
}
@@ -646,6 +655,9 @@ static void run_reader(int *stream_pipe_read, int n_proc, FILE *ofh)
for ( i=0; i<n_proc; i++ ) {
fclose(fhs[i]);
}
+ free(fhs);
+
+ if ( ofh != stdout ) fclose(ofh);
}
@@ -892,16 +904,14 @@ int main(int argc, char *argv[])
free(filename);
if ( outfile == NULL ) {
- outfile = strdup("-");
- }
- if ( strcmp(outfile, "-") == 0 ) {
ofh = stdout;
} else {
ofh = fopen(outfile, "w");
- }
- if ( ofh == NULL ) {
- ERROR("Failed to open output file '%s'\n", outfile);
- return 1;
+ if ( ofh == NULL ) {
+ ERROR("Failed to open output file '%s'\n", outfile);
+ return 1;
+ }
+ free(outfile);
}
if ( hdf5_peak_path == NULL ) {
@@ -1064,6 +1074,7 @@ int main(int argc, char *argv[])
prepare_line = tmp;
}
snprintf(prepare_filename, 1023, "%s%s", prefix, prepare_line);
+ free(prepare_line);
/* Prepare the indexer */
if ( indm != NULL ) {
@@ -1144,12 +1155,6 @@ int main(int argc, char *argv[])
return 1;
}
- finished = calloc(n_proc, sizeof(int));
- if ( finished == NULL ) {
- ERROR("Couldn't allocate memory for process flags.\n");
- return 1;
- }
-
for ( i=0; i<n_proc; i++ ) {
int stream_pipe[2];
@@ -1170,7 +1175,44 @@ int main(int argc, char *argv[])
return 1;
}
- if ( pr == 0 ) run_reader(stream_pipe_read, n_proc, ofh);
+ if ( pr == 0 ) {
+
+ /* Free resources not needed by reader
+ * (but which will be needed by worker or master) */
+ for ( i=0; i<n_proc; i++ ) {
+ close(stream_pipe_write[i]);
+ }
+ free(prefix);
+ free(use_this_one_instead);
+ free(filename_pipes);
+ free(result_fhs);
+ free(stream_pipe_write);
+ cleanup_indexing(ipriv);
+ free(indm);
+ free(ipriv);
+ free_detector_geometry(det);
+ free(beam);
+ free(element);
+ free(hdf5_peak_path);
+ free_copy_hdf5_field_list(copyme);
+ cell_free(cell);
+ free(pids);
+ fclose(fh);
+
+ run_reader(stream_pipe_read, n_proc, ofh);
+
+ free(stream_pipe_read);
+
+ exit(0);
+
+ }
+
+ /* Free resources needed by reader only */
+ if ( ofh != stdout ) fclose(ofh);
+ for ( i=0; i<n_proc; i++ ) {
+ close(stream_pipe_read[i]);
+ }
+ free(stream_pipe_read);
/* Fork the right number of times */
for ( i=0; i<n_proc; i++ ) {
@@ -1197,19 +1239,34 @@ int main(int argc, char *argv[])
if ( p == 0 ) {
- FILE *fh;
+ FILE *sfh;
+ int j;
+
+ /* Free resources which will not be needed by worker */
+ for ( j=0; j<n_proc; j++ ) {
+ if ( i != j ) close(stream_pipe_write[j]);
+ }
+ free(prefix);
+ free(use_this_one_instead);
+ free(filename_pipes);
+ free(result_fhs);
+ fclose(fh);
+ free(pids);
/* Child process gets the 'read' end of the filename
* pipe, and the 'write' end of the result pipe. */
close(filename_pipe[1]);
close(result_pipe[0]);
- fh = fdopen(stream_pipe_write[i], "w");
+ sfh = fdopen(stream_pipe_write[i], "w");
run_work(&iargs, filename_pipe[0], result_pipe[1],
- fh, i);
- fclose(fh);
+ sfh, i);
+ fclose(sfh);
+
+ free(stream_pipe_write);
exit(0);
+
}
/* Parent process gets the 'write' end of the filename pipe
@@ -1227,6 +1284,21 @@ int main(int argc, char *argv[])
}
+ /* Free resources which will not be used by the main thread */
+ cleanup_indexing(ipriv);
+ free(indm);
+ free(ipriv);
+ free_detector_geometry(det);
+ free(beam);
+ free(element);
+ free(hdf5_peak_path);
+ free_copy_hdf5_field_list(copyme);
+ cell_free(cell);
+ for ( i=0; i<n_proc; i++ ) {
+ close(stream_pipe_write[i]);
+ }
+ free(stream_pipe_write);
+
/* Send first image to all children */
for ( i=0; i<n_proc; i++ ) {
@@ -1251,6 +1323,12 @@ int main(int argc, char *argv[])
}
+ finished = calloc(n_proc, sizeof(int));
+ if ( finished == NULL ) {
+ ERROR("Couldn't allocate memory for process flags.\n");
+ return 1;
+ }
+
allDone = 0;
while ( !allDone ) {
@@ -1361,6 +1439,8 @@ int main(int argc, char *argv[])
}
+ fclose(fh);
+
for ( i=0; i<n_proc; i++ ) {
int status;
waitpid(pids[i], &status, 0);
@@ -1371,28 +1451,12 @@ int main(int argc, char *argv[])
fclose(result_fhs[i]);
}
+ free(prefix);
free(filename_pipes);
free(result_fhs);
- free(stream_pipe_read);
- free(stream_pipe_write);
free(pids);
free(finished);
- cleanup_indexing(ipriv);
-
- free(indm);
- free(ipriv);
- free(prefix);
- free_detector_geometry(det);
- free(beam);
- free(element);
- free(hdf5_peak_path);
- free_copy_hdf5_field_list(copyme);
- cell_free(cell);
- free(use_this_one_instead);
- if ( fh != stdin ) fclose(fh);
- if ( ofh != stdout ) fclose(ofh);
-
STATUS("There were %i images, of which %i could be indexed.\n",
n_processed, n_indexable);
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-15 06:42:44 +0000