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| 1 | +++ a/CMakeLists.txt | |
| 1 | +#Specify the version being used aswell as the language | |
| 2 | +cmake_minimum_required(VERSION 3.12) | |
| 3 | +cmake_policy(SET CMP0074 NEW) | |
| 4 | + | |
| 5 | +#Name your project here | |
| 6 | +project(slideconvert) | |
| 7 | + | |
| 8 | +#set the module directory | |
| 9 | +set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}") | |
| 10 | + | |
| 11 | +#default to release mode | |
| 12 | +if(NOT CMAKE_BUILD_TYPE) | |
| 13 | + set(CMAKE_BUILD_TYPE Release) | |
| 14 | +endif(NOT CMAKE_BUILD_TYPE) | |
| 15 | + | |
| 16 | +#build the executable in the binary directory on MS Visual Studio | |
| 17 | +if ( MSVC ) | |
| 18 | + SET( CMAKE_RUNTIME_OUTPUT_DIRECTORY_DEBUG "${OUTPUT_DIRECTORY}") | |
| 19 | + SET( CMAKE_RUNTIME_OUTPUT_DIRECTORY_RELEASE "${OUTPUT_DIRECTORY}") | |
| 20 | + SET( LIBRARY_OUTPUT_DIRECTORY_DEBUG "${OUTPUT_DIRECTORY}") | |
| 21 | + SET( LIBRARY_OUTPUT_DIRECTORY_RELEASE "${OUTPUT_DIRECTORY}") | |
| 22 | + add_definitions(-D_CRT_SECURE_NO_WARNINGS) | |
| 23 | + add_definitions(-D_SCL_SECURE_NO_WARNINGS) | |
| 24 | +endif ( MSVC ) | |
| 25 | +#MAYBE REMOVE----------------- | |
| 26 | +#set C++11 flags if using GCC | |
| 27 | +if( CMAKE_COMPILER_IS_GNUCC ) | |
| 28 | + SET( CMAKE_CXX_FLAGS "-std=c++11") | |
| 29 | + SET( CUDA_NVCC_FLAGS "-std=c++11") | |
| 30 | +endif( CMAKE_COMPILER_IS_GNUCC ) | |
| 31 | +#----------------------------- | |
| 32 | + | |
| 33 | +#find packages----------------------------------- | |
| 34 | + | |
| 35 | +find_package(OpenCV REQUIRED) | |
| 36 | +add_definitions(-DUSING_OPENCV) | |
| 37 | + | |
| 38 | +#find the pthreads package | |
| 39 | +find_package(Threads) | |
| 40 | + | |
| 41 | +#find the X11 package | |
| 42 | +find_package(X11) | |
| 43 | + | |
| 44 | +#find the STIM library | |
| 45 | +find_package(STIM REQUIRED) | |
| 46 | + | |
| 47 | +find_package(OpenSlide REQUIRED) | |
| 48 | + | |
| 49 | +add_executable(slideconvert | |
| 50 | + main.cpp | |
| 51 | +) | |
| 52 | + | |
| 53 | +#include include directories | |
| 54 | +include_directories(${OpenSlide_INCLUDE_DIRS} | |
| 55 | + ${OpenCV_INCLUDE_DIRS} | |
| 56 | + ${STIM_INCLUDE_DIRS} | |
| 57 | +) | |
| 58 | + | |
| 59 | +target_link_libraries(slideconvert | |
| 60 | + ${OpenSlide_LIBRARIES} | |
| 61 | + ${OpenCV_LIBS} | |
| 62 | +) | |
| 0 | 63 | \ No newline at end of file | ... | ... |
| 1 | +++ a/FindOpenSlide.cmake | |
| 1 | +# A CMake find module for the OpenSlide microscopy file reader library. | |
| 2 | +# | |
| 3 | +# http://openslide.org | |
| 4 | +# | |
| 5 | +# Once done, this module will define | |
| 6 | +# OpenSlide_FOUND - system has OpenSlide | |
| 7 | +# OpenSlide_INCLUDE_DIRS - the OpenSlide include directory | |
| 8 | +# OpenSlide_LIBRARIES - link to these to use OpenSlide | |
| 9 | + | |
| 10 | +set(OpenSlide_ROOT $ENV{OpenSlide_ROOT}) | |
| 11 | +IF(NOT OpenSlide_ROOT) | |
| 12 | + MESSAGE("ERROR: OpenSlide_ROOT must be set!") | |
| 13 | +ENDIF(NOT OpenSlide_ROOT) | |
| 14 | + | |
| 15 | +FIND_PATH(OpenSlide_INCLUDE_DIRS DOC "Path to OpenSlide include directory." | |
| 16 | + NAMES openslide/openslide.h | |
| 17 | + PATHS ${OpenSlide_ROOT}/include) | |
| 18 | + | |
| 19 | +FIND_LIBRARY(OpenSlide_LIBRARIES DOC "Absolute path to OpenSlide library." | |
| 20 | + NAMES libopenslide.lib | |
| 21 | + PATHS ${OpenSlide_ROOT}/lib) | |
| 22 | +include(FindPackageHandleStandardArgs) | |
| 23 | +find_package_handle_standard_args(OpenSlide DEFAULT_MSG OpenSlide_LIBRARIES OpenSlide_INCLUDE_DIRS) | |
| 24 | + | |
| 25 | +mark_as_advanced(OpenSlide_INCLUDE_DIRS OpenSlide_LIBRARIES) | |
| 0 | 26 | \ No newline at end of file | ... | ... |
| 1 | +++ a/FindSTIM.cmake | |
| 1 | +# finds the STIM library (downloads it if it isn't present) | |
| 2 | +# set STIMLIB_PATH to the directory containing the stim subdirectory (the stim repository) | |
| 3 | + | |
| 4 | +include(FindPackageHandleStandardArgs) | |
| 5 | + | |
| 6 | +set(STIM_ROOT $ENV{STIM_ROOT}) | |
| 7 | + | |
| 8 | +IF(NOT UNIX) | |
| 9 | + IF(NOT STIM_ROOT) | |
| 10 | + MESSAGE("ERROR: STIM_ROOT environment variable must be set!") | |
| 11 | + ENDIF(NOT STIM_ROOT) | |
| 12 | + | |
| 13 | + FIND_PATH(STIM_INCLUDE_DIRS DOC "Path to GLFW include directory." | |
| 14 | + NAMES stim/image/image.h | |
| 15 | + PATHS ${STIM_ROOT}) | |
| 16 | +ENDIF(NOT UNIX) | |
| 17 | + | |
| 18 | +find_package_handle_standard_args(STIM DEFAULT_MSG STIM_INCLUDE_DIRS) | |
| 19 | + | |
| 20 | +if(STIM_FOUND) | |
| 21 | + set(STIM_INCLUDE_DIRS ${STIM_INCLUDE_DIRS}) | |
| 22 | +elseif(STIM_FOUND) | |
| 23 | + message("STIM library not found. Set the STIM_ROOT environment variable to the STIM location.") | |
| 24 | + message("STIMLIB can be found here: https://git.stim.ee.uh.edu/codebase/stimlib") | |
| 25 | +endif(STIM_FOUND) | |
| 26 | + | |
| 27 | +find_package_handle_standard_args(STIM DEFAULT_MSG STIM_INCLUDE_DIRS) | ... | ... |
| 1 | +++ a/main.cpp | |
| 1 | +#include <iostream> | |
| 2 | +#include <string> | |
| 3 | +#include <openslide/openslide.h> | |
| 4 | +#include <opencv2/opencv.hpp> | |
| 5 | +#include <stim/parser/arguments.h> | |
| 6 | + | |
| 7 | +stim::arglist args; | |
| 8 | +int32_t level = 0; | |
| 9 | +int64_t x = 0; | |
| 10 | +int64_t y = 0; | |
| 11 | +int64_t sx, sy; | |
| 12 | +openslide_t* slide = NULL; | |
| 13 | + | |
| 14 | +std::string infile; | |
| 15 | +std::string outfile; | |
| 16 | + | |
| 17 | +void openSlide() { | |
| 18 | + slide = openslide_open(infile.c_str()); //open the slide file | |
| 19 | + if (slide == NULL) { //if the slide wasn't opened | |
| 20 | + throw std::runtime_error("ERROR: unable to open file"); | |
| 21 | + } | |
| 22 | +} | |
| 23 | +void closeSlide() { | |
| 24 | + openslide_close(slide); //close the slide file | |
| 25 | +} | |
| 26 | +//this function displays details about the specified image | |
| 27 | +void dispDetails() { | |
| 28 | + std::cout << "OpenSlide version: " << openslide_get_version() << std::endl; | |
| 29 | + openSlide(); | |
| 30 | + std::cout << "Details for slide file: " << infile << std::endl; | |
| 31 | + int32_t levels = openslide_get_level_count(slide); | |
| 32 | + int64_t w, h; | |
| 33 | + std::cout << "level sizes (in pixels):" << std::endl; | |
| 34 | + std::cout << "-------------------------------------" << std::endl; | |
| 35 | + for (int32_t l = 0; l < levels; l++) { | |
| 36 | + std::cout << "level " << l; | |
| 37 | + openslide_get_level_dimensions(slide, l, &w, &h); | |
| 38 | + std::cout << " [" << w << " x " << h << "]" << std::endl; | |
| 39 | + } | |
| 40 | + closeSlide(); | |
| 41 | +} | |
| 42 | + | |
| 43 | +void addArguments() { | |
| 44 | + args.add("help", "prints this help"); | |
| 45 | + args.add("level", "specify the level to output", "", "integer value between 0 and max"); | |
| 46 | + args.add("region", "region to save", "", "x-pos y-pos x-size y-size"); | |
| 47 | +} | |
| 48 | + | |
| 49 | +void readArguments() { | |
| 50 | + | |
| 51 | + if (args.nargs() > 0) infile = args.arg(0); //store the file name | |
| 52 | + | |
| 53 | + if (args.nargs() > 1) outfile = args.arg(1); //store the output file name | |
| 54 | + | |
| 55 | + if (args["level"]) { | |
| 56 | + level = args["level"].as_int(); //store the desired level to extract | |
| 57 | + } | |
| 58 | + else { //if the desired level isn't set, default to the smallest resolution image | |
| 59 | + openSlide(); | |
| 60 | + int32_t levels = openslide_get_level_count(slide); | |
| 61 | + level = levels - 1; | |
| 62 | + closeSlide(); | |
| 63 | + } | |
| 64 | + if (args["region"]) { | |
| 65 | + if (args["region"].nargs() == 4) { | |
| 66 | + x = args["region"].as_int(0); | |
| 67 | + y = args["region"].as_int(1); | |
| 68 | + sx = args["region"].as_int(2); | |
| 69 | + sy = args["region"].as_int(3); | |
| 70 | + } | |
| 71 | + else { | |
| 72 | + throw std::runtime_error("ERROR: --region requires 4 parameters"); | |
| 73 | + } | |
| 74 | + } | |
| 75 | + else { | |
| 76 | + openSlide(); | |
| 77 | + openslide_get_level_dimensions(slide, level, &sx, &sy); | |
| 78 | + closeSlide(); | |
| 79 | + } | |
| 80 | +} | |
| 81 | + | |
| 82 | +int main(int argc, char** argv) { | |
| 83 | + addArguments(); | |
| 84 | + args.parse(argc, argv); | |
| 85 | + readArguments(); | |
| 86 | + if (args.nargs() == 0 || args["help"]) { //if the user requests help or doesn't do anything, show usage | |
| 87 | + std::cout << "OpenSlide version: " << openslide_get_version() << std::endl; | |
| 88 | + std::cout << "Usage----------------" << std::endl; | |
| 89 | + std::cout << "save the full image at the lowest resolution: slideconvert slidefile.ndpi output.bmp" << std::endl; | |
| 90 | + std::cout << "save the level-3 (3x downsampling) image: slideconvert slidefile.ndpi output.bmp --level 3" << std::endl; | |
| 91 | + std::cout << "save a 1024x1024 region at full-resolution: slideconvert slidefile.ndpi output.bmp --level 0 --region 10000 15000 1024 1024" << std::endl; | |
| 92 | + std::cout << args.str(); //if no arguments are provided, show usage | |
| 93 | + return 0; | |
| 94 | + } | |
| 95 | + else if (args.nargs() == 1) { //if one argument is provided, display file information | |
| 96 | + dispDetails(); | |
| 97 | + return 0; | |
| 98 | + } | |
| 99 | + else if (args.nargs() == 2) { //if two arguments are provided, save the specified region | |
| 100 | + openSlide(); | |
| 101 | + cv::Mat I(sy, sx, CV_8UC4); //allocate an OpenCV image array | |
| 102 | + openslide_read_region(slide, (uint32_t*)I.data, x, y, level, sx, sy); | |
| 103 | + cv::imwrite(outfile, I); | |
| 104 | + closeSlide(); | |
| 105 | + } | |
| 106 | +} | |
| 0 | 107 | \ No newline at end of file | ... | ... |