Work on cleanup branch.

czi/source_code/CMakeLists.txt

 cmake_minimum_required(VERSION 3.8.0)
 project(czi-parser VERSION 0.1.0)
 
-# include(CTest)
-# enable_testing()
-
-add_executable(czi-parser main.cpp)
+add_executable(${PROJECT_NAME} main.cpp)
 
 set(CMAKE_CXX_FLAGS "-Wall -DBZ_NO_STDIO")
 
@@ -14,30 +11,30 @@ set(Boost_USE_STATIC_RUNTIME OFF)
 find_package(Boost REQUIRED COMPONENTS filesystem locale)
 if(Boost_FOUND)
     include_directories(${Boost_INCLUDE_DIRS}) 
-    target_link_libraries(czi-parser ${Boost_LIBRARIES})
+    target_link_libraries(${PROJECT_NAME} ${Boost_LIBRARIES})
     message("LINKED BOOST")
 endif()
 
 find_package (Threads)
-    target_link_libraries (czi-parser ${CMAKE_THREAD_LIBS_INIT})
+    target_link_libraries (${PROJECT_NAME} ${CMAKE_THREAD_LIBS_INIT})
 
 find_package(ZLIB)
 if(ZLIB_FOUND)
-    target_link_libraries(czi-parser ${ZLIB_LIBRARIES})
+    target_link_libraries(${PROJECT_NAME} ${ZLIB_LIBRARIES})
     message("LINKED ZLIB")    
 endif(ZLIB_FOUND)
 
 find_package(LibLZMA)
 if (LIBLZMA_FOUND)
     include_directories(${LIBLZMA_INCLUDE_DIRS}) 
-    target_link_libraries(czi-parser ${LIBLZMA_LIBRARIES})
+    target_link_libraries(${PROJECT_NAME} ${LIBLZMA_LIBRARIES})
     message("LINKED LIBLZMA")
 endif()
 
 find_package(BZip2)
 if(BZIP2_FOUND)
     include_directories(${BZIP2_INCLUDE_DIRS})
-    target_link_libraries(czi-parser ${BZIP2_LIBRARIES})
+    target_link_libraries(${PROJECT_NAME} ${BZIP2_LIBRARIES})
     message("LINKED BZIP2")
 endif(BZIP2_FOUND)
 
@@ -49,6 +46,12 @@ if (OPENMP_FOUND)
     message("ENABLED OpenMP")
 endif()
 
+# add_subdirectory(azgra_lib)
+target_link_libraries(${PROJECT_NAME} PUBLIC 
+    azgra_lib)
+
+
+
 # add_library(BSDIFF "utilities/bsdiff/bsdiff.h" "utilities/bsdiff/bsdiff.c")
 # include_directories("utilities/bsdiff/")
 # target_link_libraries(czi-parser BSDIFF)

czi/source_code/compression/documentation.txt

-
-gzip (zlib) compress2
-	http://refspecs.linuxbase.org/LSB_3.0.0/LSB-Core-generic/LSB-Core-generic/zlib-compress2-1.html
-lzma
-	
-bzip2

czi/source_code/cont_test.csv

-filename;subblock;pixel;width;height;compression;level;originalSize;compressedSize;compressedZ;compressionRatio;compressionRatioZ;compressionTime;compressionTimeZ

czi/source_code/root/CMakeLists.txt

+cmake_minimum_required(VERSION 3.0.0)
+
+project(semestral-project)
+
+add_subdirectory(azgra_lib)
+add_subdirectory(app)
\ No newline at end of file

czi/source_code/root/app/CMakeLists.txt

+cmake_minimum_required(VERSION 3.8.0)
+
+project(czi)
+
+add_executable(${PROJECT_NAME} main.cpp
+    src/czi/czi_file.cpp
+    src/czi/czi_parser.cpp
+    src/image/image_matrix.cpp
+    src/compression/benchmark.cpp
+    )
+
+include_directories(${PROJECT_SOURCE_DIR}/include)
+
+target_link_libraries(${PROJECT_NAME} sub::azgra)
+
+
+set(CMAKE_CXX_FLAGS "-Wall -DBZ_NO_STDIO")
+
+set(Boost_USE_MULTITHREADED ON)  
+set(Boost_USE_STATIC_RUNTIME OFF) 
+find_package(Boost REQUIRED COMPONENTS filesystem locale)
+if(Boost_FOUND)
+    include_directories(${Boost_INCLUDE_DIRS}) 
+    target_link_libraries(${PROJECT_NAME} ${Boost_LIBRARIES})
+    message("LINKED BOOST")
+endif()
+
+find_package (Threads REQUIRED)
+    target_link_libraries (${PROJECT_NAME} ${CMAKE_THREAD_LIBS_INIT})
+
+find_package(ZLIB)
+if(ZLIB_FOUND)
+    target_link_libraries(${PROJECT_NAME} ${ZLIB_LIBRARIES})
+    message("LINKED ZLIB")    
+endif(ZLIB_FOUND)
+
+find_package(LibLZMA)
+if (LIBLZMA_FOUND)
+    include_directories(${LIBLZMA_INCLUDE_DIRS}) 
+    target_link_libraries(${PROJECT_NAME} ${LIBLZMA_LIBRARIES})
+    message("LINKED LIBLZMA")
+endif()
+
+find_package(BZip2)
+if(BZIP2_FOUND)
+    include_directories(${BZIP2_INCLUDE_DIRS})
+    target_link_libraries(${PROJECT_NAME} ${BZIP2_LIBRARIES})
+    message("LINKED BZIP2")
+endif(BZIP2_FOUND)
+
+find_package(OpenMP)
+if (OPENMP_FOUND)
+    set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+    set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+    message("ENABLED OpenMP")
+endif()
+
+# set(CPACK_PROJECT_NAME ${PROJECT_NAME})
+# set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})
+# include(CPack)
\ No newline at end of file

czi/source_code/utilities/api_bsdiff.h → czi/source_code/root/app/include/bsdiff/api_bsdiff.h

@@ -4,10 +4,10 @@
 namespace _bsdiff
 {
 #define new _new
-#include "lib_bsdiff/bsdiff.h"
-#include "lib_bsdiff/bsdiff.c"
-#include "lib_bsdiff/bspatch.h"
-#include "lib_bsdiff/bspatch.c"
+#include "bsdiff.h"
+#include "bsdiff.c"
+#include "bspatch.h"
+#include "bspatch.c"
 #undef new
 
 struct bsdiff_read_info

czi/source_code/compression/benchmark.h → czi/source_code/root/app/include/compression/benchmark.h

 #pragma once
 #include "compressors.h"
-#include "../czi_file.h"
-#include "../file_system.h"
-#include "../stream/memory_bit_stream.h"
+
+#include <czi/czi_file.h>
+#include <filesystem/file_system.h>
+#include <azgra/stream/memory_bit_stream.h>
+#include <bsdiff/api_bsdiff.h>
 #include <iomanip>
 #include <thread>
-#include "../utilities/api_bsdiff.h"
 
 struct BaseBenchmarkRecord
 {
@@ -89,8 +90,8 @@ struct DiffBenchmarkRecord : BaseBenchmarkRecord
 };
 
 // Raw Compression benchmark functions.
-static void write_compression_report(const std::vector<BaseBenchmarkRecord> &results, const std::string &reportFile);
-static void compression_thread_work(const ByteArray &data, CompressionMethod method, int compressionLevel, CompressionResult &result, const char *info);
+void write_compression_report(const std::vector<BaseBenchmarkRecord> &results, const std::string &reportFile);
+void compression_thread_work(const ByteArray &data, CompressionMethod method, int compressionLevel, CompressionResult &result, const char *info);
 static std::vector<BaseBenchmarkRecord> benchmark_continuos_compression_one_level(const ByteArray &data, const ByteArray &zOrderedData, int compressionLevel);
 void benchmark_continuos_compression(CziFile &cziFile, const std::string &reportFile, bool verbose, int level = -1);
 void benchmark_compression(CziFile &cziFile, const std::string &reportFile, bool verbose, int level = -1);
@@ -101,6 +102,4 @@ void value_diff_by_prev_frame_benchmark(CziFile &cziFile, const std::string &rep
 
 void bsdiff_by_prev_frame_benchmark(CziFile &cziFile, const std::string &reportFile, bool verbose, CompressionMethod cm, int level, bool firstFrameDiff);
 
-static void write_diff_report(const std::vector<DiffBenchmarkRecord> &results, const std::string &reportFile);
-
-#include "benchmark.cpp"
\ No newline at end of file
+void write_diff_report(const std::vector<DiffBenchmarkRecord> &results, const std::string &reportFile);

czi/source_code/compression/compressors.h → czi/source_code/root/app/include/compression/compressors.h

 #pragma once
-#include "../custom_types.h"
-#include "../utilities/vector_utilities.h"
-#include "../image/z_order.h"
-#include "../utilities/Stopwatch.h"
+#include <azgra/utilities/vector_utilities.h>
+#include <azgra/utilities/z_order.h>
+#include <azgra/utilities/Stopwatch.h>
+#include <custom_types.h>
 
 namespace library_zlib
 {

czi/source_code/root/app/include/custom_types.h

+#pragma once
+#include <azgra/azgra.h>
+
+// Define to 1 or true to enable very verbose logging of parser.
+#define VERBOSE_PARSER 0
+
+constexpr bool NOT_IMPLEMENTED_YET = false;
+#define MUST_BE_IMPLEMENTED always_assert(false);
+
+#define TagType std::string, std::string
+typedef std::pair<TagType> Tag;
+
+constexpr char GZIP_NAME[] = "GZIP";
+constexpr char LZMA_NAME[] = "LZMA";
+constexpr char BZIP2_NAME[] = "BZIP2";
\ No newline at end of file

czi/source_code/czi_file.h → czi/source_code/root/app/include/czi/czi_file.h

 #pragma once
+
 #include <map>
-#include "czi_parts/segments.h"
-#include "utilities/type_mapper.h"
-#include "stream/binary_file_stream.h"
-#include "stream/binary_writer.h"
-#include "image/image_matrix.h"
-#include "image/z_order.h"
-#include "compression/compressors.h"
-#include "file_system.h"
+
+#include <czi/czi_parts/segments.h>
+#include <azgra/utilities/type_mapper.h>
+#include <azgra/stream/binary_file_stream.h>
+#include <azgra/stream/binary_writer.h>
+#include <image/image_matrix.h>
+#include <azgra/utilities/z_order.h>
+#include <compression/compressors.h>
+#include <filesystem/file_system.h>
 
 //TODO: Handle multi-file scenarios.
 class CziFile
@@ -53,6 +55,4 @@ public:
   void test_compression(CompressionMethod method, bool verbose, int compressionLevel) const;
   // Get subblocks grouped by their channels.
   std::vector<std::pair<uint, std::vector<uint>>> get_subblocks_grouped_by_channels() const;
-};
-
-#include "czi_file.cpp"
\ No newline at end of file
+};
\ No newline at end of file

czi/source_code/czi_parser.h → czi/source_code/root/app/include/czi/czi_parser.h

 #pragma once
 #include "czi_file.h"
-#include "stream/binary_file_stream.h"
-#include "stream/buffered_binary_stream.h"
-#include "utilities/xml_parser.h"
+#include <azgra/stream/binary_file_stream.h>
+#include <azgra/stream/buffered_binary_stream.h>
 
 class CziParser
 {
@@ -27,6 +26,4 @@ public:
   CziParser(bool parseMetadata = true);
   ~CziParser();
   CziFile parse_czi_file(const std::string &file);
-};
-
-#include "czi_parser.cpp"
\ No newline at end of file
+};
\ No newline at end of file