From 1a37de5cce5c2df83e37fb189409659299594b1b Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Wed, 22 Oct 2014 17:50:37 +0200
Subject: Fix a load of memory leaks

---
 libcrystfel/src/detector.c    |  1 +
 libcrystfel/src/dirax.c       |  2 ++
 libcrystfel/src/events.c      | 11 ++++-------
 libcrystfel/src/events.h      |  2 +-
 libcrystfel/src/integration.c |  1 +
 libcrystfel/src/stream.c      |  3 +++
 src/im-sandbox.c              |  8 +++++---
 src/indexamajig.c             |  2 ++
 src/process_image.c           |  7 +------
 9 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index 4a202f2e..683fdd49 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -1333,6 +1333,7 @@ void free_detector_geometry(struct detector *det)
 
 	for ( i=0; i<det->n_panels; i++ ) {
 		free(det->panels[i].clen_from);
+		free_dim_structure(det->panels[i].dim_structure);
 	}
 
 	free(det->panels);
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c
index 0a137784..a48cf2e8 100644
--- a/libcrystfel/src/dirax.c
+++ b/libcrystfel/src/dirax.c
@@ -255,6 +255,8 @@ static void dirax_parseline(const char *line, struct image *image,
 			dirax->success = 1;
 		}
 
+		cell_free(cell);
+
 		return;
 
 	}
diff --git a/libcrystfel/src/events.c b/libcrystfel/src/events.c
index 6e52f6cd..19d69b81 100644
--- a/libcrystfel/src/events.c
+++ b/libcrystfel/src/events.c
@@ -238,12 +238,13 @@ void free_event_list(struct event_list *el)
 
 void free_filename_plus_event(struct filename_plus_event *fpe)
 {
-
 	free(fpe->filename);
 
 	if ( fpe->ev != NULL ) {
 		free_event(fpe->ev);
 	}
+
+	free(fpe);
 }
 
 
@@ -622,12 +623,8 @@ struct dim_structure *default_dim_structure()
 
 void free_dim_structure(struct dim_structure *hsd)
 {
-	int di;
-
-	for ( di=0; di<hsd->num_dims; di++ ) {
-		free (hsd->dims);
-		free (hsd);
-	}
+	free(hsd->dims);
+	free(hsd);
 }
 
 
diff --git a/libcrystfel/src/events.h b/libcrystfel/src/events.h
index e6e5d840..ee47c5a5 100644
--- a/libcrystfel/src/events.h
+++ b/libcrystfel/src/events.h
@@ -103,6 +103,6 @@ extern int set_dim_structure_entry(struct dim_structure *hsd,
                                    const char *string_dim,
                                    const char *val_string);
 extern void free_dim_structure_entry(struct dim_structure *hsd);
-
+extern void free_dim_structure(struct dim_structure *hsd);
 
 #endif	/* EVENTS_H */
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 34bde83a..55adf287 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -641,6 +641,7 @@ static void delete_box(struct intcontext *ic, struct peak_box *bx)
 	}
 
 	free(bx->bm);
+	gsl_matrix_free(bx->bgm);
 
 	memmove(&ic->boxes[i], &ic->boxes[i+1],
 	        (ic->n_boxes-i-1)*sizeof(struct peak_box));
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 519a1ca9..c1b32a4f 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -1304,6 +1304,9 @@ void write_geometry_file(Stream *st, const char *geom_filename) {
 		rval = fgets(line, 1023, geom_fh);
 		fputs(line, st->fh);
 	} while ( rval != NULL );
+
+	fclose(geom_fh);
+
 	fprintf(st->fh, GEOM_END_MARKER"\n");
 	fflush(st->fh);
 }
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 45a058ba..6970a14f 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -476,10 +476,10 @@ static void run_work(const struct index_args *iargs,
 				ERROR("write P0\n");
 			}
 
-			free_filename_plus_event(pargs.filename_p_e);
-
 		}
 
+		free_filename_plus_event(pargs.filename_p_e);
+
 	}
 
 	free(bd.line);
@@ -780,7 +780,7 @@ static void start_worker_process(struct sandbox *sb, int slot)
 		free(sb->filename_pipes);
 		free(sb->result_fhs);
 		free(sb->pids);
-		/* Also prefix, use_this_one_instead and fh */
+		/* Also prefix, tempdir, */
 
 		/* Child process gets the 'read' end of the filename
 		 * pipe, and the 'write' end of the result pipe. */
@@ -795,6 +795,8 @@ static void start_worker_process(struct sandbox *sb, int slot)
 		//close(filename_pipe[0]);
 		close(result_pipe[1]);
 
+		free(sb);
+
 		exit(0);
 
 	}
diff --git a/src/indexamajig.c b/src/indexamajig.c
index b139f299..cb4ee084 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -679,6 +679,8 @@ int main(int argc, char *argv[])
 	free(prefix);
 	free(tempdir);
 	free_detector_geometry(iargs.det);
+	close_stream(st);
+	cleanup_indexing(indm, ipriv);
 
 	return 0;
 }
diff --git a/src/process_image.c b/src/process_image.c
index 68708fd7..807facd9 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -164,12 +164,6 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 
 	mark_resolution_range_as_bad(&image, iargs->highres, +INFINITY);
 
-	hdfile = hdfile_open(image.filename);
-	if ( hdfile == NULL ) {
-		ERROR("Couldn't open file %s.\n", image.filename);
-		return;
-	}
-
 	switch ( iargs->peaks ) {
 
 		case PEAK_HDF5:
@@ -224,6 +218,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		hdfile_close(hdfile);
 		return;
 	}
+	free(rn);
 
 	pargs->n_crystals = image.n_crystals;
 	for ( i=0; i<image.n_crystals; i++ ) {
-- 
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