PretextView 1.0.3

.gitignore

@@ -3,9 +3,38 @@ app/
 ascii.dSYM/
 build_cmake/
 builddir/
-.DS_Store
+*.DS_Store
+__pycache__/
+*.pyc
+.idea/          # JetBrains IDE
+.vscode/        # Visual Studio Code
+*.suo           # VS Code user settings
+*.swp           # Vim swap files
+*.log          
+*.tmp          
+*.bak           # backup files
+venv/           # 
+env/            # 
+*.egg-info/     # Python egg files
+*.eggs/
 
-python/
+python/comparison_fig/
+python/test_data_from_openglbuffer/
+python/graphData_constructor.py
+python/open_plot_saved_compressed_extension.py
+python/open_plot_saved_compressed_hic.py
+python/open_plot_saved_textures.py
+python/test_cal_mass_center.py
+python/test_compresed_data.py
+python/test.py
+python/compressed_data_test/
+python/autoCut/models/cfgs/error_model.pth
+python/autoCut/models/cfgs/chr_model.pth
+python/autoCut/models/swin/mmdet.egg-info/*
+python/classic_cut/show_hic_density.py
+python/colormap_colorblind/*
+python/greedy_topo_sort_test/*
+python/linear_weight_test/*
 
 subprojects/eigen
 subprojects/glfw
@@ -36,6 +65,7 @@ logs/
 .gitignore
 
 ico_design/icon_design.ai
+ico_design/icon_v1.iconset/
 include/GLFW/glfw3.h
 include/GLFW/glfw3native.h
 include/libdeflate.h
@@ -45,3 +75,10 @@ PretextViewAI.zip
 
 test_data/
 subprojects/libtorch(not needed in this version)/
+
+hic_figures/
+auto_cut_output/
+python/autoCut/models/swin/README.md
+python/autoCut/models/swin/mmcv_custom/
+
+yahs_archive/

.gitmodules

@@ -14,3 +14,7 @@
 [submodule "subprojects/pytorch_scatter"]
 	path = subprojects/pytorch_scatter
 	url = https://github.com/guanshaoheng/pytorch_scatter.git 
+
+[submodule "subprojects/fmt"]
+	path = subprojects/fmt
+	url = https://github.com/fmtlib/fmt.git

CMakeLists.txt

@@ -1,10 +1,12 @@
 cmake_minimum_required(VERSION 3.17)
-project(PretextView VERSION "1.0.1")
+project(PretextView VERSION "1.0.3")
 
 
-option(FORCE_MAC_X86 "Force macOS x86_64 build" OFF)  
+option(FORCE_MAC_X86 "Force macOS x86_64 build" OFF)
 option(BUILD_UNIVERSAL "Build macOS universal binary" OFF) 
 option(WITH_TORCH "Find and link torch lib" OFF)
+option(DEBUG_OUTPUT_LIKELIHOOD_TABLE "Output likelihood table to file" OFF)
+option(DEBUG_OUTPUT_PIXEL_CUT_FILE "Output the pixel cut files" OFF)
 
 set(CMAKE_C_STANDARD 17)   
 set(CMAKE_CXX_STANDARD 17)   
@@ -14,7 +16,6 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(target_name PretextViewAI)
 
 if (APPLE)
-
     if(FORCE_MAC_X86) 
         message(STATUS "Forcing x86_64 architecture build")
         set(CMAKE_OSX_ARCHITECTURES "x86_64" CACHE STRING "Build architectures" FORCE)
@@ -55,6 +56,9 @@ else()
     endif()
 endif()
 
+if (MSVC)
+    add_compile_options(/utf-8)  # force MSVC to use UTF-8 
+endif()
 
 message(STATUS "Install path: ${CMAKE_INSTALL_PREFIX}")
 
@@ -76,11 +80,26 @@ include_directories(
     subprojects/glfw/include
     subprojects/libdeflate
     subprojects/glm
+    subprojects/fmt/include
 )
 
 add_subdirectory(subprojects/glfw)
 add_subdirectory(subprojects/glm)
 
+find_library(
+    lib_fmt
+    NAMES fmt libfmt
+    PATHS 
+        subprojects/fmt/build 
+        subprojects/fmt/build/debug 
+        subprojects/fmt/build/Release
+        subprojects/fmt/build/release)
+if(NOT lib_fmt)
+    message(FATAL_ERROR "lib_fmt not found")
+else()
+    message(STATUS "lib_fmt found: ${lib_fmt}")
+endif()
+
 
 find_library(
     lib_deflate_static 
@@ -96,6 +115,9 @@ else()
     message(STATUS "lib_deflate_static found: ${lib_deflate_static}")
 endif()
 
+add_library(lib_yahs STATIC 
+    src/yahs_sort.cpp
+)
 
 # set(CMAKE_PREFIX_PATH "subprojects/libtorch/share/cmake/Torch")
 if (WITH_TORCH)
@@ -111,14 +133,16 @@ if (WITH_TORCH)
     target_link_libraries(
         sortlib PUBLIC 
         ${TORCH_LIBRARIES} 
-        ${torchscatter})
+        ${torchscatter} 
+        lib_yahs)
 else()
     message(STATUS "Libtorch: Build without libtorch")
     add_library(sortlib STATIC src/frag_sort.cpp )
+    target_link_libraries(sortlib PRIVATE lib_yahs)
 endif()
 
 
-add_library(glad STATIC glad.c)
+add_library(glad STATIC src/glad.c)
 add_library(utilsPretextView STATIC src/utilsPretextView.cpp)
 add_library(copy_texture STATIC src/copy_texture.cpp)
 # target_link_libraries(copy_texture PRIVATE Eigen3::Eigen)
@@ -141,6 +165,7 @@ else()
         MACOSX_BUNDLE_INFO_PLIST "${CMAKE_SOURCE_DIR}/Info.plist"
     )
 endif()
+
 target_compile_definitions(${target_name} PRIVATE PV=${PROJECT_VERSION})
 if (CMAKE_BUILD_TYPE STREQUAL "Debug")
     target_compile_definitions(${target_name} PRIVATE DEBUG)
@@ -149,16 +174,23 @@ if (CMAKE_BUILD_TYPE STREQUAL "Debug")
 else()
     message(STATUS "Release version: flag (${CMAKE_BUILD_TYPE}) without DEBUG")
 endif()
+if (DEBUG_OUTPUT_LIKELIHOOD_TABLE)
+    message(STATUS "Debug version: flag (${CMAKE_BUILD_TYPE}) with DEBUG_OUTPUT_LIKELIHOOD_TABLE")
+    target_compile_definitions(${target_name} PRIVATE DEBUG_OUTPUT_LIKELIHOOD_TABLE)
+endif()
+
 target_link_libraries(
     ${target_name} PRIVATE 
     ${lib_deflate_static} 
+    ${lib_fmt}
     sortlib 
     glm 
     glad 
     utilsPretextView 
     copy_texture 
     imgui 
     glfw 
+    lib_yahs
 )   
 
 if (APPLE)

Info.plist

@@ -13,7 +13,7 @@
   <key>CFBundleIconFile</key>
   <string>icon.icns</string>
   <key>CFBundleShortVersionString</key>
-  <string>1.0.1</string>
+  <string>1.0.3</string>
   <key>CFBundleInfoDictionaryVersion</key>
   <string>6.0</string>
   <key>CFBundlePackageType</key>