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Commit 849df8b6 authored by Thomas White's avatar Thomas White
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Fix a load of memory leaks

parent 0fe63533
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Inline Side-by-side
libcrystfel/src/peaks.c
View file @ 849df8b6
......@@ -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;
......
libcrystfel/src/reax.c
View file @ 849df8b6
......@@ -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);
}
......
src/indexamajig.c
View file @ 849df8b6
......@@ -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);
......
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