Fundus image exporting

3 files changed, 72 insertions, 12 deletions

diff --git a/src/e2e.c b/src/e2e.c
index 5ac9f6c..d842fd8 100644
--- a/src/e2e.c
+++ b/src/e2e.c
@@ -86,6 +86,12 @@ static int make_pointer(const struct e2e_data *data, const char *pos,
 static int read_fundus(struct e2e_data *data, const char *cursor,
                        struct e2e_image *image)
 {
+	if (cursor + image->width * image->height > data->end) {
+		errorf("Fundus image at %td ends past the end of file.\n",
+		        cursor - data->start);
+		return 1;
+	}
+
 	// This cast is _technically_ illegal, but I can't think of a way in
 	// which this would cause problems in practice.
 	image->fundus = (const uint8_t*)cursor;
@@ -96,6 +102,12 @@ static int read_fundus(struct e2e_data *data, const char *cursor,
 static int read_tomogram(struct e2e_data *data, const char *cursor,
                          struct e2e_image *image)
 {
+	if (cursor + image->width * image->height * 2 > data->end) {
+		errorf("Tomogram image at %td ends past the end of file.\n",
+		        cursor - data->start);
+		return 1;
+	}
+
 	image->tomogram = calloc(image->width * image->height, sizeof(float));
 	if (!image->tomogram)
 		return ENOMEM;
@@ -407,17 +419,29 @@ static int post_process(struct e2e_data *data)
 	eli_for(dir, data->dirs, data_list)
 	for (size_t i = 0; i < dir->num_entries; i++) {
 		struct e2e_entry *entry = dir->entries + i;
+		struct e2e_series *series;
 		struct e2e_slice *slice;
 
 		rv = ensure_slice(data, entry->patient_id, entry->study_id,
 		                   entry->series_id, entry->slice_id,
-		                   NULL, NULL, NULL, &slice);
+		                   NULL, NULL, &series, &slice);
 		if (rv)
 			return rv;
 
-		if (slice && entry->has_chunk
-		    && entry->chunk.type == E2E_CHUNK_IMAGE)
-			slice->image = &entry->chunk.image;
+		if (entry->has_chunk && entry->chunk.type == E2E_CHUNK_IMAGE) {
+			struct e2e_image *image = &entry->chunk.image;
+
+			if (slice &&
+			    entry->chunk.image.type == E2E_IMAGE_TOMOGRAM)
+				slice->image = image;
+
+			if (series &&
+			    entry->chunk.image.type == E2E_IMAGE_FUNDUS) {
+				eli_append(&series->fundi, image,
+				           series_fundi_list);
+				series->num_fundi++;
+			}
+		}
 	}
 
 	return 0;
diff --git a/src/e2e.h b/src/e2e.h
index 65428ea..7d3559e 100644
--- a/src/e2e.h
+++ b/src/e2e.h
@@ -15,6 +15,8 @@ struct e2e_image {
 		const uint8_t *fundus;
 		float *tomogram;
 	};
+
+	eli_header series_fundi_list;
 };
 
 #define E2E_CHUNK_IMAGE  0x40000000
@@ -69,6 +71,8 @@ struct e2e_series {
 	int id;
 
 	struct e2e_slice *slices;
+	size_t num_fundi;
+	struct e2e_image *fundi;
 
 	UT_hash_handle hh;
 };
diff --git a/src/export.c b/src/export.c
index 5a98f2d..9abd1ae 100644
--- a/src/export.c
+++ b/src/export.c
@@ -70,6 +70,34 @@ error_image3d:
 	return ENOMEM;
 }
 
+static int export_fundi(const struct e2e_series *series, matvar_t **fundi)
+{
+	size_t i, dims;
+	struct e2e_image *image;
+
+	dims = series->num_fundi;
+	*fundi = Mat_VarCreate(NULL, MAT_C_CELL, MAT_T_CELL, 1, &dims, NULL, 0);
+	if (!*fundi)
+		return ENOMEM;
+
+	i = 0;
+	eli_for(image, series->fundi, series_fundi_list) {
+		matvar_t *var;
+		size_t dims[2] = {image->width, image->height};
+
+		var = Mat_VarCreate(NULL, MAT_C_UINT8, MAT_T_UINT8, 2, dims,
+		                    (void*)image->fundus, 0);
+		if (!var) {
+			Mat_VarFree(*fundi);
+			return ENOMEM;
+		}
+
+		Mat_VarSetCell(*fundi, i++, var);
+	}
+
+	return 0;
+}
+
 static int export_series(const struct e2e_series *series, matvar_t **out)
 {
 	int rv;
@@ -89,7 +117,7 @@ static int export_series(const struct e2e_series *series, matvar_t **out)
 			"tomogram_slice_ids",
 			"fundi",
 		};
-		matvar_t *st, *id, *tomogram, *slice_ids;
+		matvar_t *st, *id, *tomogram = NULL, *slice_ids = NULL, *fundi;
 
 		st = create_struct(fields, COUNT(fields));
 		if (!st) {
@@ -103,22 +131,26 @@ static int export_series(const struct e2e_series *series, matvar_t **out)
 			goto error_id;
 		}
 
-		Mat_VarSetStructFieldByName(st, "series_id", 0, id);
 
 		if (HASH_COUNT(series1->slices)) {
 			rv = export_tomogram(series1->slices, &tomogram, &slice_ids);
 			if (rv)
 				goto error_tomogram;
-
-			Mat_VarSetStructFieldByName(st, "tomogram", 0, tomogram);
-			Mat_VarSetStructFieldByName(st, "tomogram_slice_ids", 0,
-			                            slice_ids);
 		}
-		// TODO: export fundus images
-		
+
+		rv = export_fundi(series1, &fundi);
+		if (rv)
+			goto error_fundi;
+
+		Mat_VarSetStructFieldByName(st, "tomogram", 0, tomogram);
+		Mat_VarSetStructFieldByName(st, "tomogram_slice_ids", 0,
+			                    slice_ids);
+		Mat_VarSetStructFieldByName(st, "fundi", 0, fundi);
 		Mat_VarSetCell(*out, i++, st);
 		continue;
 
+	error_fundi:
+		Mat_VarFree(tomogram);
 	error_tomogram:
 		Mat_VarFree(id);
 	error_id: