int main(int argc, char **argv) {
if (argc!=6) {
fprintf(stderr,"Usage: %s <image file> <cancer type> <subject id> <case id> <output file>\n",argv[0]);
exit(1);
}
char *inp_file = argv[1];
char *c_type = argv[2];
char *s_id = argv[3];
char *c_id = argv[4];
char *h_name = "localhost";
FILE *fpo = fopen(argv[5],"w");
int check_ok = 1;
struct stat attrib;
stat(inp_file,&attrib);
char file_date[20];
strftime(file_date, 20, "%m-%d-%y:%H.%M.%S", localtime(&(attrib.st_ctime)));
openslide_t *osr = openslide_open(inp_file);
if (osr==NULL) {
fprintf(stderr,"Error: openslide cannot read file: %s\n",inp_file);
exit(1);
}
int64_t w,h;
openslide_get_level0_dimensions(osr,&w,&h);
if (w<=0 || h<=0) {
fprintf(stderr,"Error: openslide cannot get width (%ld) and height (%ld) from the image file: %s\n.",w,h,inp_file);
exit(1);
}
fprintf(fpo,"hostname,filename,last_modified,cancer_type,case_id,subject_id,identifier,width,height,mpp_x,mpp_y,objective,vendor,status,level_count,imageid\n");
fprintf(fpo,"%s,",h_name);
fprintf(fpo,"%s,",inp_file);
fprintf(fpo,"%s,",file_date);
fprintf(fpo,"%s,",c_type);
fprintf(fpo,"%s,",c_id);
fprintf(fpo,"%s,",s_id);
fprintf(fpo,"%s,",c_id);
fprintf(fpo,"%f,",(float)w);
fprintf(fpo,"%f,",(float)h);
/* get objective value */
char *o_val = (char*)openslide_get_property_value(osr,"openslide.objective-power");
if (o_val==NULL)
o_val = (char*)openslide_get_property_value(osr,"aperio.AppMag");
char *mpp_x = (char*)openslide_get_property_value(osr,"openslide.mpp-x");
if (mpp_x!=NULL)
fprintf(fpo,"%.8f,",atof(mpp_x));
else {
if (o_val!=NULL)
fprintf(fpo,"%f,",0.25*40.0/atof(o_val));
else {
check_ok = 0;
fprintf(fpo,"%f,",-1.0);
}
}
char *mpp_y = (char*)openslide_get_property_value(osr,"openslide.mpp-y");
if (mpp_y!=NULL)
fprintf(fpo,"%.8f,",atof(mpp_y));
else {
if (o_val!=NULL)
fprintf(fpo,"%f,",0.25*40.0/atof(o_val));
else {
check_ok = 0;
fprintf(fpo,"%f,",-1.0);
}
}
/* print objective value */
if (o_val!=NULL)
fprintf(fpo,"%f,",(float)atof(o_val));
else {
fprintf(fpo,"%f,",-1.0);
check_ok = 0;
}
char *vendor = (char*)openslide_get_property_value(osr,"openslide.vendor");
if (vendor!=NULL)
fprintf(fpo,"%s,",vendor);
else
fprintf(fpo,"no_vendor,");
if (check_ok==0) {
fprintf(fpo,"some_errors,");
fprintf(stderr,"SOME_ERRORS: %s\n",inp_file);
} else {
fprintf(fpo,"status_ok,");
fprintf(stdout,"OK: %s\n",inp_file);
}
char *level_count = (char*)openslide_get_property_value(osr,"openslide.level-count");
if (level_count!=NULL)
fprintf(fpo,"%s,",level_count);
else
fprintf(fpo,"1,");
char *image_id = (char*)openslide_get_property_value(osr,"aperio.ImageID");
if (image_id!=NULL)
fprintf(fpo,"%d\n",atoi(image_id));
else
fprintf(fpo,"-1\n");
fflush(fpo);
openslide_close(osr);
fclose(fpo);
exit(0);
}
int main(int argc, char **argv) {
if (!g_thread_supported()) {
g_thread_init(NULL);
}
if (argc != 2) {
fail("No file specified");
}
const char *path = argv[1];
if (g_str_equal(path, "--leak-check--")) {
child_check_open_fds();
return 0;
}
openslide_get_version();
if (!openslide_detect_vendor(path)) {
fail("No vendor for %s", path);
}
openslide_t *osr = openslide_open(path);
if (!osr) {
fail("Couldn't open %s", path);
}
const char *err = openslide_get_error(osr);
if (err) {
fail("Open failed: %s", err);
}
openslide_close(osr);
osr = openslide_open(path);
if (!osr || openslide_get_error(osr)) {
fail("Reopen failed");
}
int64_t w, h;
openslide_get_level0_dimensions(osr, &w, &h);
int32_t levels = openslide_get_level_count(osr);
for (int32_t i = -1; i < levels + 1; i++) {
int64_t ww, hh;
openslide_get_level_dimensions(osr, i, &ww, &hh);
openslide_get_level_downsample(osr, i);
}
openslide_get_best_level_for_downsample(osr, 0.8);
openslide_get_best_level_for_downsample(osr, 1.0);
openslide_get_best_level_for_downsample(osr, 1.5);
openslide_get_best_level_for_downsample(osr, 2.0);
openslide_get_best_level_for_downsample(osr, 3.0);
openslide_get_best_level_for_downsample(osr, 3.1);
openslide_get_best_level_for_downsample(osr, 10);
openslide_get_best_level_for_downsample(osr, 20);
openslide_get_best_level_for_downsample(osr, 25);
openslide_get_best_level_for_downsample(osr, 100);
openslide_get_best_level_for_downsample(osr, 1000);
openslide_get_best_level_for_downsample(osr, 10000);
// NULL buffer
openslide_read_region(osr, NULL, 0, 0, 0, 1000, 1000);
// empty region
openslide_read_region(osr, NULL, 0, 0, 0, 0, 0);
// read properties
const char * const *property_names = openslide_get_property_names(osr);
while (*property_names) {
const char *name = *property_names;
openslide_get_property_value(osr, name);
property_names++;
}
// read associated images
const char * const *associated_image_names =
openslide_get_associated_image_names(osr);
while (*associated_image_names) {
int64_t w, h;
const char *name = *associated_image_names;
openslide_get_associated_image_dimensions(osr, name, &w, &h);
uint32_t *buf = g_new(uint32_t, w * h);
openslide_read_associated_image(osr, name, buf);
g_free(buf);
associated_image_names++;
}
test_image_fetch(osr, -10, -10, 200, 200);
test_image_fetch(osr, w/2, h/2, 500, 500);
test_image_fetch(osr, w - 200, h - 100, 500, 400);
test_image_fetch(osr, w*2, h*2, 400, 400);
test_image_fetch(osr, w - 20, 0, 40, 100);
test_image_fetch(osr, 0, h - 20, 100, 40);
// active region
const char *bounds_x = openslide_get_property_value(osr, OPENSLIDE_PROPERTY_NAME_BOUNDS_X);
const char *bounds_y = openslide_get_property_value(osr, OPENSLIDE_PROPERTY_NAME_BOUNDS_Y);
int64_t bounds_xx = 0;
int64_t bounds_yy = 0;
if (bounds_x && bounds_y) {
bounds_xx = g_ascii_strtoll(bounds_x, NULL, 10);
bounds_yy = g_ascii_strtoll(bounds_y, NULL, 10);
test_image_fetch(osr, bounds_xx, bounds_yy, 200, 200);
}
openslide_close(osr);
check_cloexec_leaks(path, argv[0], bounds_xx, bounds_yy);
return 0;
}
