Add read_region function

CMakeLists.txt

@@ -21,6 +21,25 @@ include_directories("${CMAKE_SOURCE_DIR}/src/utils")
 include_directories("${CMAKE_SOURCE_DIR}/src/isyntax")
 include_directories("${CMAKE_SOURCE_DIR}/src/third_party")
 
+# Find LibTIFF library
+find_package(TIFF REQUIRED)
+if (NOT TIFF_FOUND)
+    message(WARNING "LibTIFF not found")
+    message(WARNING "Will not compile `isyntax-to-tiff` utility")
+endif()
+include_directories(${TIFF_INCLUDE_DIR})
+find_package(Threads REQUIRED)
+if (UNIX AND NOT APPLE) # needed for sem_wait, etc.
+    find_library(RT_LIBRARY rt)
+    set(EXTRA_LIBS ${RT_LIBRARY})
+elseif (APPLE)
+    # No extra libraries needed for macOS
+elseif (WIN32)
+    # No extra libraries needed for Windows
+endif ()
+
+
+
 set(LIBISYNTAX_COMMON_SOURCE_FILES
         src/libisyntax.c
         src/isyntax/isyntax.c
@@ -34,6 +53,7 @@ set(LIBISYNTAX_COMMON_SOURCE_FILES
         src/third_party/ltalloc.cc
 )
 
+
 if (WIN32)
     set(LIBISYNTAX_COMMON_SOURCE_FILES ${LIBISYNTAX_COMMON_SOURCE_FILES} src/platform/win32_utils.c)
 else()
@@ -49,9 +69,35 @@ add_executable(isyntax_example
         ${LIBISYNTAX_COMMON_SOURCE_FILES}
 )
 
+
+
+add_executable(isyntax_example2
+    src/isyntax_example2.c
+    ${LIBISYNTAX_COMMON_SOURCE_FILES}
+)
+
+if (TIFF_FOUND)
+    message(STATUS "Will compile `isyntax-to-tiff` utility")
+    add_executable(isyntax-to-tiff
+    src/isyntax_to_tiff.c
+    ${LIBISYNTAX_COMMON_SOURCE_FILES} ${TIFF_LIBRARIES})
+
+endif()
+
+target_include_directories(isyntax-to-tiff PRIVATE ${TIFF_INCLUDE_DIRS})
+
 if (WIN32)
-    target_link_libraries(libisyntax winmm)
-    target_link_libraries(isyntax_example winmm)
-else()
+    target_link_libraries(libisyntax winmm Threads::Threads)
+    target_link_libraries(isyntax_example winmm Threads::Threads)
+    target_link_libraries(isyntax_example2 winmm Threads::Threads)
+    target_link_libraries(isyntax-to-tiff winmm Threads::Threads)
 
+
+else()
+    target_link_libraries(libisyntax Threads::Threads ${EXTRA_LIBS})
+    target_link_libraries(isyntax_example Threads::Threads ${EXTRA_LIBS})
+    target_link_libraries(isyntax_example2 Threads::Threads ${EXTRA_LIBS})
+    if (TIFF_FOUND)
+        target_link_libraries(isyntax-to-tiff PRIVATE ${TIFF_LIBRARIES} Threads::Threads ${EXTRA_LIBS})
+    endif()
 endif()

src/isyntax/isyntax.c

@@ -3069,11 +3069,13 @@ bool isyntax_open(isyntax_t* isyntax, const char* filename, bool init_allocators
 						// (I guess this is related to the way the wavelet transform works.)
 						// Put another way: the highest (zoomed out levels) are shifted the to the bottom right
 						// (this is also reflected in the x and y coordinates of the codeblocks in the iSyntax header).
-						for (i32 scale = 1; scale < wsi_image->level_count; ++scale) {
-							isyntax_level_t* level = wsi_image->levels + scale;
+                        for (i32 scale = 0; scale < wsi_image->level_count; ++scale) {
+                            isyntax_level_t* level = wsi_image->levels + scale;
+                            level->origin_offset_in_pixels = ((PER_LEVEL_PADDING << wsi_image->level_count) - PER_LEVEL_PADDING) >> scale;
+                            level->width = wsi_image->width >> scale;
+                            level->height = wsi_image->height >> scale;
                             float offset_in_pixels = (float) (get_first_valid_coef_pixel(scale - 1));
-                            level->origin_offset_in_pixels = offset_in_pixels;
-							float offset_in_um_x = offset_in_pixels * wsi_image->levels[0].um_per_pixel_x;
+                            float offset_in_um_x = offset_in_pixels * wsi_image->levels[0].um_per_pixel_x;
 							float offset_in_um_y = offset_in_pixels * wsi_image->levels[0].um_per_pixel_y;
 							level->origin_offset = (v2f){offset_in_um_x, offset_in_um_y};
 						}
@@ -3297,4 +3299,40 @@ void isyntax_destroy(isyntax_t* isyntax) {
 	file_handle_close(isyntax->file_handle);
 }
 
-
+void bgra_to_rgba(uint32_t *pixels, int tile_width, int tile_height) {
+    int num_pixels = tile_width * tile_height;
+    int num_pixels_aligned = (num_pixels / 4) * 4;
+
+#if defined(__ARM_NEON)
+    for (int i = 0; i < num_pixels_aligned; i += 4) {
+        uint32x4_t bgra = vld1q_u32(pixels + i);
+        uint32x4_t b_mask = vdupq_n_u32(0x000000FF);
+        uint32x4_t r_mask = vdupq_n_u32(0x00FF0000);
+        uint32x4_t b = vandq_u32(bgra, b_mask);
+        uint32x4_t r = vandq_u32(bgra, r_mask);
+        uint32x4_t br_swapped = vorrq_u32(vshlq_n_u32(b, 16), vshrq_n_u32(r, 16));
+        uint32x4_t ga_alpha_mask = vdupq_n_u32(0xFF00FF00);
+        uint32x4_t ga_alpha = vandq_u32(bgra, ga_alpha_mask);
+        uint32x4_t rgba = vorrq_u32(ga_alpha, br_swapped);
+        vst1q_u32(pixels + i, rgba);
+    }
+#elif defined(__SSE2__)
+    for (int i = 0; i < num_pixels_aligned; i += 4) {
+        __m128i bgra = _mm_loadu_si128((__m128i*)(pixels + i));
+        __m128i b_mask = _mm_set1_epi32(0x000000FF);
+        __m128i r_mask = _mm_set1_epi32(0x00FF0000);
+        __m128i b = _mm_and_si128(bgra, b_mask);
+        __m128i r = _mm_and_si128(bgra, r_mask);
+        __m128i br_swapped = _mm_or_si128(_mm_slli_epi32(b, 16), _mm_srli_epi32(r, 16));
+        __m128i ga_alpha_mask = _mm_set1_epi32(0xFF00FF00);
+        __m128i ga_alpha = _mm_and_si128(bgra, ga_alpha_mask);
+        __m128i rgba = _mm_or_si128(ga_alpha, br_swapped);
+        _mm_storeu_si128((__m128i*)(pixels + i), rgba);
+    }
+#else
+    for (int i = num_pixels_aligned; i < num_pixels; ++i) {
+        uint32_t val = pixels[i];
+        pixels[i] = ((val & 0xff) << 16) | (val & 0x00ff00) | ((val & 0xff0000) >> 16) | (val & 0xff000000);
+    }
+#endif
+}

src/isyntax/isyntax.h

@@ -275,13 +275,15 @@ typedef struct isyntax_level_t {
 	i32 scale;
 	i32 width_in_tiles;
 	i32 height_in_tiles;
+    u64 width;
+    u64 height;
 	float downsample_factor;
 	float um_per_pixel_x;
 	float um_per_pixel_y;
 	float x_tile_side_in_um;
 	float y_tile_side_in_um;
 	u64 tile_count;
-	float origin_offset_in_pixels;
+	i32 origin_offset_in_pixels;
 	v2f origin_offset;
 	isyntax_tile_t* tiles;
 	bool is_fully_loaded;

src/isyntax_example.c

@@ -6,13 +6,8 @@
 #define STB_IMAGE_WRITE_IMPLEMENTATION
 #include "third_party/stb_image_write.h"  // for png export
 
-
-
 #define LOG_VAR(fmt, var) printf("%s: %s=" fmt "\n", __FUNCTION__, #var, var)
 
-uint32_t bgra_to_rgba(uint32_t val) {
-    return ((val & 0xff) << 16) | (val & 0x00ff00) | ((val & 0xff0000) >> 16) | (val & 0xff000000);
-}
 
 void print_isyntax_levels(isyntax_t* isyntax) {
     int wsi_image_idx = libisyntax_get_wsi_image_index(isyntax);
@@ -74,9 +69,8 @@ int main(int argc, char** argv) {
         assert(libisyntax_tile_read(isyntax, isyntax_cache, level, tile_x, tile_y, &pixels) == LIBISYNTAX_OK);
 
         // convert data to the correct pixel format (bgra->rgba).
-        for (int i = 0; i < tile_height * tile_width; ++i) {
-            pixels[i] = bgra_to_rgba(pixels[i]);
-        }
+        bgra_to_rgba(pixels, tile_width, tile_height);
+
         printf("Writing %s...\n", output_png);
         stbi_write_png(output_png, tile_width, tile_height, 4, pixels, tile_width * 4);
         printf("Done writing %s.\n", output_png);
@@ -87,4 +81,4 @@ int main(int argc, char** argv) {
 
     libisyntax_close(isyntax);
     return 0;
-}
+}

src/isyntax_example2.c

@@ -0,0 +1,69 @@
+#include "libisyntax.h"
+#include <stdint.h>
+#include <assert.h>
+
+#define STB_IMAGE_WRITE_IMPLEMENTATION
+
+#include "third_party/stb_image_write.h"  // for png export
+
+#define LOG_VAR(fmt, var) printf("%s: %s=" fmt "\n", __FUNCTION__, #var, var)
+
+
+int main(int argc, char **argv) {
+
+    if (argc <= 7) {
+        printf("Usage: %s <isyntax_file> <level> <x_coord> <y_coord> <width> <height> <output.png> - write a tile to output.png",
+               argv[0], argv[0]);
+        return 0;
+    }
+
+    char *filename = argv[1];
+
+    libisyntax_init();
+
+    isyntax_t *isyntax;
+    if (libisyntax_open(filename, /*is_init_allocators=*/0, &isyntax) != LIBISYNTAX_OK) {
+        printf("Failed to open %s\n", filename);
+        return -1;
+    }
+    printf("Successfully opened %s\n", filename);
+
+    int32_t level = atoi(argv[2]);
+    int32_t x_coord = atoi(argv[3]);
+    int32_t y_coord = atoi(argv[4]);
+    int32_t region_width = atoi(argv[5]);
+    int32_t region_height = atoi(argv[6]);
+    const char *output_png = argv[7];
+
+    LOG_VAR("%d", level);
+    LOG_VAR("%d", x_coord);
+    LOG_VAR("%d", y_coord);
+    LOG_VAR("%d", region_width);
+    LOG_VAR("%d", region_height);
+    LOG_VAR("%s", output_png);
+
+    int32_t tile_width = libisyntax_get_tile_width(isyntax);
+    int32_t tile_height = libisyntax_get_tile_height(isyntax);
+    LOG_VAR("%d", tile_width);
+    LOG_VAR("%d", tile_height);
+
+    isyntax_cache_t *isyntax_cache = NULL;
+    assert(libisyntax_cache_create("example cache", 2000, &isyntax_cache) == LIBISYNTAX_OK);
+    assert(libisyntax_cache_inject(isyntax_cache, isyntax) == LIBISYNTAX_OK);
+
+    uint32_t *pixels = NULL;
+    assert(libisyntax_read_region(isyntax, isyntax_cache, level, x_coord, y_coord, region_width, region_height, &pixels) ==
+           LIBISYNTAX_OK);
+
+    // convert data to the correct pixel format (bgra->rgba).
+    bgra_to_rgba(pixels, region_width, region_height);
+
+    printf("Writing %s...\n", output_png);
+    stbi_write_png(output_png, region_width, region_height, 4, pixels, region_width * 4);
+    printf("Done writing %s.\n", output_png);
+
+    libisyntax_tile_free_pixels(pixels);
+    libisyntax_cache_destroy(isyntax_cache);
+    libisyntax_close(isyntax);
+    return 0;
+}