f043d1fa
 David Mayerich
first commit
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#include <iostream>
#include <string>
#include <openslide/openslide.h>
#include <opencv2/opencv.hpp>
#include <stim/parser/arguments.h>
stim::arglist args;
int32_t level = 0;
int64_t x = 0;
int64_t y = 0;
int64_t sx, sy;
openslide_t* slide = NULL;
std::string infile;
std::string outfile;
void openSlide() {
slide = openslide_open(infile.c_str()); //open the slide file
if (slide == NULL) { //if the slide wasn't opened
throw std::runtime_error("ERROR: unable to open file");
}
}
void closeSlide() {
openslide_close(slide); //close the slide file
}
//this function displays details about the specified image
void dispDetails() {
std::cout << "OpenSlide version: " << openslide_get_version() << std::endl;
openSlide();
std::cout << "Details for slide file: " << infile << std::endl;
int32_t levels = openslide_get_level_count(slide);
int64_t w, h;
std::cout << "level sizes (in pixels):" << std::endl;
std::cout << "-------------------------------------" << std::endl;
for (int32_t l = 0; l < levels; l++) {
std::cout << "level " << l;
openslide_get_level_dimensions(slide, l, &w, &h);
std::cout << " [" << w << " x " << h << "]" << std::endl;
}
closeSlide();
}
void addArguments() {
args.add("help", "prints this help");
args.add("level", "specify the level to output", "", "integer value between 0 and max");
args.add("region", "region to save", "", "x-pos y-pos x-size y-size");
}
void readArguments() {
if (args.nargs() > 0) infile = args.arg(0); //store the file name
if (args.nargs() > 1) outfile = args.arg(1); //store the output file name
if (args["level"]) {
level = args["level"].as_int(); //store the desired level to extract
}
else { //if the desired level isn't set, default to the smallest resolution image
openSlide();
int32_t levels = openslide_get_level_count(slide);
level = levels - 1;
closeSlide();
}
if (args["region"]) {
if (args["region"].nargs() == 4) {
x = args["region"].as_int(0);
y = args["region"].as_int(1);
sx = args["region"].as_int(2);
sy = args["region"].as_int(3);
}
else {
throw std::runtime_error("ERROR: --region requires 4 parameters");
}
}
else {
openSlide();
openslide_get_level_dimensions(slide, level, &sx, &sy);
closeSlide();
}
}
int main(int argc, char** argv) {
addArguments();
args.parse(argc, argv);
readArguments();
if (args.nargs() == 0 || args["help"]) { //if the user requests help or doesn't do anything, show usage
std::cout << "OpenSlide version: " << openslide_get_version() << std::endl;
std::cout << "Usage----------------" << std::endl;
std::cout << "save the full image at the lowest resolution: slideconvert slidefile.ndpi output.bmp" << std::endl;
std::cout << "save the level-3 (3x downsampling) image: slideconvert slidefile.ndpi output.bmp --level 3" << std::endl;
std::cout << "save a 1024x1024 region at full-resolution: slideconvert slidefile.ndpi output.bmp --level 0 --region 10000 15000 1024 1024" << std::endl;
std::cout << args.str(); //if no arguments are provided, show usage
return 0;
}
else if (args.nargs() == 1) { //if one argument is provided, display file information
dispDetails();
return 0;
}
else if (args.nargs() == 2) { //if two arguments are provided, save the specified region
openSlide();
cv::Mat I(sy, sx, CV_8UC4); //allocate an OpenCV image array
openslide_read_region(slide, (uint32_t*)I.data, x, y, level, sx, sy);
cv::imwrite(outfile, I);
closeSlide();
}
}
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