- block stitching code, aligned to zarr block dimensions, seems to be…

… working

- cleanup example2.c according to review
- cleanup tests according to review and fix a bunch of improper memory handling
- add small logging functonality to vesuvius-c.h
- add more thorough logging to chunk grafting and vs_vol_get_chunk

CMakeLists.txt

@@ -7,6 +7,7 @@ list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 add_executable(vesuvius_example example.c)
 add_executable(vesuvius_example2 example2.c)
 add_executable(vesuvius_tests runtests.c)
+add_executable(vesuvius_tests_sanitizer runtests.c)
 
 include_directories(third-party/json.h)
 
@@ -19,11 +20,13 @@ if(UNIX)
     target_link_options(vesuvius_example PUBLIC -rdynamic)
     target_link_options(vesuvius_example2 PUBLIC -rdynamic)
     target_link_options(vesuvius_tests PUBLIC -rdynamic)
+    target_link_options(vesuvius_tests_sanitizer PUBLIC -rdynamic)
 endif()
 
 target_link_libraries(vesuvius_example PUBLIC -lm)
 target_link_libraries(vesuvius_example2 PUBLIC -lm)
 target_link_libraries(vesuvius_tests PUBLIC -lm)
+target_link_libraries(vesuvius_tests_sanitizer PUBLIC -lm)
 
 find_package(Blosc2 REQUIRED)
 find_package(CURL REQUIRED)
@@ -34,7 +37,7 @@ if(Blosc2_FOUND)
     target_link_libraries(vesuvius_example PUBLIC Blosc2::Blosc2)
     target_link_libraries(vesuvius_example2 PUBLIC Blosc2::Blosc2)
     target_link_libraries(vesuvius_tests PUBLIC Blosc2::Blosc2)
-    add_compile_definitions(VESUVIUS_ZARR_IMPL)
+    target_link_libraries(vesuvius_tests_sanitizer PUBLIC Blosc2::Blosc2)
 else()
     message(FATAL_ERROR "Blosc2 not found, please install blosc2")
 endif()
@@ -44,9 +47,10 @@ if(CURL_FOUND)
     target_link_libraries(vesuvius_example PUBLIC CURL::libcurl)
     target_link_libraries(vesuvius_example2 PUBLIC CURL::libcurl)
     target_link_libraries(vesuvius_tests PUBLIC CURL::libcurl)
-    add_compile_definitions(VESUVIUS_CURL_IMPL)
+    target_link_libraries(vesuvius_tests_sanitizer PUBLIC CURL::libcurl)
 else()
     message(FATAL_ERROR "CURL not found, please install curl")
 endif()
 
-
+target_compile_options(vesuvius_tests_sanitizer PUBLIC -fsanitize=address -fno-omit-frame-pointer)
+target_link_options(vesuvius_tests_sanitizer PUBLIC -fsanitize=address)

example2.c

@@ -3,36 +3,41 @@
 #include "vesuvius-c.h"
 
 int test_volume_load() {
-    chunk* mychunk;
-
+    const char* zarray_url = "https://dl.ash2txt.org/full-scrolls/Scroll1/PHercParis4.volpkg/volumes_zarr_standardized/54keV_7.91um_Scroll1A.zarr/0/.zarray";
+    const char* zarr_block_url = "https://dl.ash2txt.org/full-scrolls/Scroll1/PHercParis4.volpkg/volumes_zarr_standardized/54keV_7.91um_Scroll1A.zarr/0/50/30/30";
     void* metadata_buf;
-    char url[1024] = "https://dl.ash2txt.org/full-scrolls/Scroll1/PHercParis4.volpkg/volumes_zarr_standardized/54keV_7.91um_Scroll1A.zarr/0/.zarray";
-    if (vs_download(url, &metadata_buf) <= 0) {
+    printf("downloading %s\n",zarray_url);
+    if (vs_download(zarray_url, &metadata_buf) <= 0) {
         return 1;
     }
+
     zarr_metadata metadata;
+    printf("parsing zarr metadata\n");
     if (vs_zarr_parse_metadata(metadata_buf, &metadata)) {
         return 1;
     }
+
     void* compressed_buf;
-    strncpy(url,"https://dl.ash2txt.org/full-scrolls/Scroll1/PHercParis4.volpkg/volumes_zarr_standardized/54keV_7.91um_Scroll1A.zarr/0/50/30/30",1023);
     long compressed_size;
-    if ((compressed_size = vs_download(url, &compressed_buf)) <= 0) {
+    printf("downloading %s\n",zarr_block_url);
+    if ((compressed_size = vs_download(zarr_block_url, &compressed_buf)) <= 0) {
         return 1;
     }
-    mychunk = vs_zarr_decompress_chunk(compressed_size, compressed_buf,metadata);
+    printf("decompressing zarr chunk\n");
+    chunk* mychunk = vs_zarr_decompress_chunk(compressed_size, compressed_buf,metadata);
     if (mychunk == NULL) {
         return 1;
     }
+    printf("rescaling zarr chunk\n");
     chunk* rescaled = vs_normalize_chunk(mychunk);
     s32 vertex_count, index_count;
     f32 *vertices;
     s32 *indices;
-
-    if (vs_march_cubes(mychunk->data,mychunk->dims[0],mychunk->dims[1],mychunk->dims[2],.5f,&vertices,&indices,&vertex_count,&index_count)) {
+    printf("marching cubes on rescaled chunk\n");
+    if (vs_march_cubes(rescaled->data,rescaled->dims[0],rescaled->dims[1],rescaled->dims[2],.5f,&vertices,&indices,&vertex_count,&index_count)) {
         return 1;
     }
-
+    printf("writing mesh to out_vol.ply\n");
     if (vs_ply_write("out_vol.ply",vertices,NULL,indices,vertex_count,index_count)) {
         return 1;
     }
@@ -41,36 +46,42 @@ int test_volume_load() {
 }
 
 int test_fiber_load() {
+    const char* zarray_url = "https://dl.ash2txt.org/community-uploads/bruniss/Fiber-and-Surface-Models/GP-Predictions/updated_zarrs/mask-2ext-surface_ome.zarr/0/.zarray";
+    const char* zarr_block_url = "https://dl.ash2txt.org/community-uploads/bruniss/Fiber-and-Surface-Models/GP-Predictions/updated_zarrs/mask-2ext-surface_ome.zarr/0/50/30/30";
+
     chunk* mychunk;
 
     void* metadata_buf;
-    char url[1024] = "https://dl.ash2txt.org/community-uploads/bruniss/Fiber-and-Surface-Models/GP-Predictions/updated_zarrs/mask-2ext-surface_ome.zarr/0/.zarray";
-    if (vs_download(url, &metadata_buf) <= 0) {
+    printf("downloading %s\n",zarray_url);
+    if (vs_download(zarray_url, &metadata_buf) <= 0) {
         return 1;
     }
     zarr_metadata metadata;
+    printf("parsing zarray metadata\n");
     if (vs_zarr_parse_metadata(metadata_buf, &metadata)) {
         return 1;
     }
     void* compressed_buf;
-    strncpy(url,"https://dl.ash2txt.org/community-uploads/bruniss/Fiber-and-Surface-Models/GP-Predictions/updated_zarrs/mask-2ext-surface_ome.zarr/0/50/30/30",1023);
     long compressed_size;
-    if ((compressed_size = vs_download(url, &compressed_buf)) <= 0) {
+    printf("downloading %s\n",zarr_block_url);
+    if ((compressed_size = vs_download(zarr_block_url, &compressed_buf)) <= 0) {
         return 1;
     }
+    printf("decompressing zarr chunk\n");
     mychunk = vs_zarr_decompress_chunk(compressed_size, compressed_buf,metadata);
     if (mychunk == NULL) {
         return 1;
     }
+    printf("rescaling zarr chunk\n");
     chunk* rescaled = vs_normalize_chunk(mychunk);
     s32 vertex_count, index_count;
     f32 *vertices;
     s32 *indices;
-
-    if (vs_march_cubes(mychunk->data,mychunk->dims[0],mychunk->dims[1],mychunk->dims[2],.5f,&vertices,&indices,&vertex_count,&index_count)) {
+    printf("marching cubes on rescaled chunk\n");
+    if (vs_march_cubes(rescaled->data,rescaled->dims[0],rescaled->dims[1],rescaled->dims[2],.5f,&vertices,&indices,&vertex_count,&index_count)) {
         return 1;
     }
-
+    printf("writing mesh to out_surface.ply\n");
     if (vs_ply_write("out_surface.ply",vertices,NULL,indices,vertex_count,index_count)) {
         return 1;
     }