static gboolean
get_bounds( openslide_t *osr, VipsRect *rect )
{
static const char *openslide_names[] = {
"openslide.bounds-x",
"openslide.bounds-y",
"openslide.bounds-width",
"openslide.bounds-height"
};
static int vips_offsets[] = {
G_STRUCT_OFFSET( VipsRect, left ),
G_STRUCT_OFFSET( VipsRect, top ),
G_STRUCT_OFFSET( VipsRect, width ),
G_STRUCT_OFFSET( VipsRect, height )
};
const char *value;
int i;
for( i = 0; i < 4; i++ ) {
if( !(value = openslide_get_property_value( osr,
openslide_names[i] )) )
return( FALSE );
G_STRUCT_MEMBER( int, rect, vips_offsets[i] ) =
atoi( value );
}
return( TRUE );
}
int
vips__openslide_isslide( const char *filename )
{
openslide_t *osr;
const char *vendor;
int ok;
ok = 0;
if( (osr = openslide_open( filename )) ) {
/* Generic tiled tiff images can be opened by openslide as
* well. Only offer to load this file if it's not a generic
* tiff since we want vips_tiffload() to handle these.
*/
vendor = openslide_get_property_value( osr,
OPENSLIDE_PROPERTY_NAME_VENDOR );
if( vendor &&
strcmp( vendor, "generic-tiff" ) != 0 )
ok = 1;
openslide_close( osr );
}
VIPS_DEBUG_MSG( "vips__openslide_isslide: %s - %d\n", filename, ok );
return( ok );
}
int
vips__openslide_isslide( const char *filename )
{
#ifdef HAVE_OPENSLIDE_3_4
const char *vendor;
int ok;
vendor = openslide_detect_vendor( filename );
/* Generic tiled tiff images can be opened by openslide as well.
* Only offer to load this file if it's not a generic tiff since
* we want vips_tiffload() to handle these.
*/
ok = ( vendor &&
strcmp( vendor, "generic-tiff" ) != 0 );
VIPS_DEBUG_MSG( "vips__openslide_isslide: %s - %d\n", filename, ok );
return( ok );
#else
openslide_t *osr;
int ok;
ok = 0;
osr = openslide_open( filename );
if( osr ) {
const char *vendor;
/* Generic tiled tiff images can be opened by openslide as
* well. Only offer to load this file if it's not a generic
* tiff since we want vips_tiffload() to handle these.
*/
vendor = openslide_get_property_value( osr,
OPENSLIDE_PROPERTY_NAME_VENDOR );
/* vendor will be NULL if osr is in error state.
*/
if( vendor &&
strcmp( vendor, "generic-tiff" ) != 0 )
ok = 1;
openslide_close( osr );
}
VIPS_DEBUG_MSG( "vips__openslide_isslide: %s - %d\n", filename, ok );
return( ok );
#endif
}
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);
}
static ReadSlide *
readslide_new( const char *filename, VipsImage *out,
int level, gboolean autocrop, const char *associated )
{
ReadSlide *rslide;
int64_t w, h;
const char *error;
const char *background;
const char * const *properties;
char *associated_names;
if( level &&
associated ) {
vips_error( "openslide2vips",
"%s", _( "specify only one of level or associated "
"image" ) );
return( NULL );
}
rslide = VIPS_NEW( out, ReadSlide );
memset( rslide, 0, sizeof( *rslide ) );
g_signal_connect( out, "close", G_CALLBACK( readslide_destroy_cb ),
rslide );
rslide->level = level;
rslide->autocrop = autocrop;
rslide->associated = g_strdup( associated );
/* Non-crazy defaults, override below if we can.
*/
rslide->tile_width = 256;
rslide->tile_height = 256;
rslide->osr = openslide_open( filename );
if( rslide->osr == NULL ) {
vips_error( "openslide2vips",
"%s", _( "unsupported slide format" ) );
return( NULL );
}
error = openslide_get_error( rslide->osr );
if( error ) {
vips_error( "openslide2vips",
_( "opening slide: %s" ), error );
return( NULL );
}
if( level < 0 ||
level >= openslide_get_level_count( rslide->osr ) ) {
vips_error( "openslide2vips",
"%s", _( "invalid slide level" ) );
return( NULL );
}
if( associated &&
check_associated_image( rslide->osr, associated ) )
return( NULL );
if( associated ) {
openslide_get_associated_image_dimensions( rslide->osr,
associated, &w, &h );
vips_image_set_string( out, "slide-associated-image",
associated );
vips_image_pipelinev( out, VIPS_DEMAND_STYLE_THINSTRIP, NULL );
}
else {
char buf[256];
const char *value;
openslide_get_level_dimensions( rslide->osr,
level, &w, &h );
rslide->downsample = openslide_get_level_downsample(
rslide->osr, level );
vips_image_set_int( out, "slide-level", level );
vips_image_pipelinev( out, VIPS_DEMAND_STYLE_SMALLTILE, NULL );
/* Try to get tile width/height. An undocumented, experimental
* feature.
*/
vips_snprintf( buf, 256,
"openslide.level[%d].tile-width", level );
if( (value = openslide_get_property_value( rslide->osr, buf )) )
rslide->tile_width = atoi( value );
vips_snprintf( buf, 256,
"openslide.level[%d].tile-height", level );
if( (value = openslide_get_property_value( rslide->osr, buf )) )
rslide->tile_height = atoi( value );
if( value )
VIPS_DEBUG_MSG( "readslide_new: found tile-size\n" );
/* Some images have a bounds in the header. Crop to
* that if autocrop is set.
*/
if( rslide->autocrop )
if( !get_bounds( rslide->osr, &rslide->bounds ) )
rslide->autocrop = FALSE;
if( rslide->autocrop ) {
VipsRect image;
rslide->bounds.left /= rslide->downsample;
rslide->bounds.top /= rslide->downsample;
rslide->bounds.width /= rslide->downsample;
rslide->bounds.height /= rslide->downsample;
/* Clip against image size.
*/
image.left = 0;
image.top = 0;
image.width = w;
image.height = h;
vips_rect_intersectrect( &rslide->bounds, &image,
&rslide->bounds );
/* If we've clipped to nothing, ignore bounds.
*/
if( vips_rect_isempty( &rslide->bounds ) )
rslide->autocrop = FALSE;
}
if( rslide->autocrop ) {
w = rslide->bounds.width;
h = rslide->bounds.height;
}
}
rslide->bg = 0xffffff;
if( (background = openslide_get_property_value( rslide->osr,
OPENSLIDE_PROPERTY_NAME_BACKGROUND_COLOR )) )
rslide->bg = strtoul( background, NULL, 16 );
if( w <= 0 ||
h <= 0 ||
rslide->downsample < 0 ) {
vips_error( "openslide2vips", _( "getting dimensions: %s" ),
openslide_get_error( rslide->osr ) );
return( NULL );
}
if( w > INT_MAX ||
h > INT_MAX ) {
vips_error( "openslide2vips",
"%s", _( "image dimensions overflow int" ) );
return( NULL );
}
if( !rslide->autocrop ) {
rslide->bounds.left = 0;
rslide->bounds.top = 0;
rslide->bounds.width = w;
rslide->bounds.height = h;
}
vips_image_init_fields( out, w, h, 4, VIPS_FORMAT_UCHAR,
VIPS_CODING_NONE, VIPS_INTERPRETATION_RGB, 1.0, 1.0 );
for( properties = openslide_get_property_names( rslide->osr );
*properties != NULL; properties++ )
vips_image_set_string( out, *properties,
openslide_get_property_value( rslide->osr,
*properties ) );
associated_names = g_strjoinv( ", ", (char **)
openslide_get_associated_image_names( rslide->osr ) );
vips_image_set_string( out,
"slide-associated-images", associated_names );
VIPS_FREE( associated_names );
return( rslide );
}
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;
}
static ReadSlide *
readslide_new( const char *filename, VipsImage *out,
int layer, const char *associated )
{
ReadSlide *rslide;
int64_t w, h;
const char *background;
const char * const *properties;
rslide = VIPS_NEW( out, ReadSlide );
memset( rslide, 0, sizeof( *rslide ) );
g_signal_connect( out, "close", G_CALLBACK( readslide_destroy_cb ),
rslide );
rslide->layer = layer;
rslide->associated = g_strdup( associated );
rslide->osr = openslide_open( filename );
if( rslide->osr == NULL ) {
vips_error( "openslide2vips",
"%s", _( "failure opening slide" ) );
return( NULL );
}
if( layer < 0 ||
layer >= openslide_get_layer_count( rslide->osr ) ) {
vips_error( "openslide2vips",
"%s", _( "invalid slide level" ) );
return( NULL );
}
if( associated &&
check_associated_image( rslide->osr, associated ) )
return( NULL );
if( associated ) {
openslide_get_associated_image_dimensions( rslide->osr,
associated, &w, &h );
vips_image_set_string( out, "slide-associated-image",
associated );
vips_demand_hint( out, VIPS_DEMAND_STYLE_THINSTRIP, NULL );
}
else {
openslide_get_layer_dimensions( rslide->osr,
layer, &w, &h );
rslide->downsample = openslide_get_layer_downsample(
rslide->osr, layer );
vips_image_set_int( out, "slide-level", layer );
vips_demand_hint( out, VIPS_DEMAND_STYLE_SMALLTILE, NULL );
}
/* This tag is used by argb2rgba() to paint fully-transparent pixels.
*/
background = openslide_get_property_value( rslide->osr,
OPENSLIDE_PROPERTY_NAME_BACKGROUND_COLOR );
if( background != NULL )
vips_image_set_int( out,
VIPS_META_BACKGROUND_RGB,
strtoul( background, NULL, 16 ) );
else
vips_image_set_int( out, VIPS_META_BACKGROUND_RGB, 0xffffff );
if( w < 0 || h < 0 || rslide->downsample < 0 ) {
vips_error( "openslide2vips", _( "getting dimensions: %s" ),
openslide_get_error( rslide->osr ) );
return( NULL );
}
if( w > INT_MAX ||
h > INT_MAX ) {
vips_error( "openslide2vips",
"%s", _( "image dimensions overflow int" ) );
return( NULL );
}
vips_image_init_fields( out, w, h, 4, VIPS_FORMAT_UCHAR,
VIPS_CODING_NONE, VIPS_INTERPRETATION_RGB, 1.0, 1.0 );
for( properties = openslide_get_property_names( rslide->osr );
*properties != NULL; properties++ )
vips_image_set_string( out, *properties,
openslide_get_property_value( rslide->osr,
*properties ) );
associated = g_strjoinv( ", ", (char **)
openslide_get_associated_image_names( rslide->osr ) );
vips_image_set_string( out, "slide-associated-images", associated );
return( rslide );
}
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
/*variables*/
char *buffer; /*array for input string*/
int32_t levels; /*number of levels*/
int64_t w, h; /*width, height of each level*/
double *dims, *ds; /*pointers to outputs - for convenience*/
const char *objective, *mppx, *mppy;
openslide_t *slide; /*openslide struct*/
int i; /*loop iterator*/
/*check input arguments*/
if(nrhs != 1) {
mexErrMsgTxt("'openslide_check_levels.m' requires one input argument.");
}
if(nlhs > 5) {
mexErrMsgTxt("'openslide_check_levels.m' produces two outputs.");
}
/*check input type*/
if(!mxIsChar(prhs[0]) || (mxGetM(prhs[0]) != 1)) {
mexErrMsgTxt("Input must be character array.");
}
/*copy*/
buffer = mxArrayToString(prhs[0]);
/*copy input*/
if(openslide_can_open(buffer) == 1) {
/*open*/
slide = openslide_open(buffer);
/*check for error*/
if(openslide_get_error(slide) != NULL) {
mexErrMsgTxt("'openslide_check_levels.m' cannot open slide.");
}
else {
/*get # of levels*/
levels = openslide_get_layer_count(slide);
/*allocate arrays*/
plhs[0] = mxCreateDoubleMatrix((mwSize)levels, 2, mxREAL);
plhs[1] = mxCreateDoubleMatrix((mwSize)levels, 1, mxREAL);
/*get output addresses*/
dims = mxGetPr(plhs[0]);
ds = mxGetPr(plhs[1]);
/*loop through levels, get dimensions/downsample factor of each*/
for(i = 0; i < levels; i++) {
/*get level info*/
openslide_get_layer_dimensions(slide, (int32_t)i, &w, &h);
*ds = openslide_get_layer_downsample(slide, (int32_t)i);
ds = ds + 1;
/*copy dimensions to outputs*/
*dims = (double)h;
*(dims+levels) = (double)w;
dims = dims + 1;
}
/*get properties*/
objective = openslide_get_property_value(slide, OPENSLIDE_PROPERTY_NAME_OBJECTIVE_POWER);
mppx = openslide_get_property_value(slide, OPENSLIDE_PROPERTY_NAME_MPP_X);
mppy = openslide_get_property_value(slide, OPENSLIDE_PROPERTY_NAME_MPP_Y);
/*assign properties to outputs*/
plhs[2] = mxCreateString(objective);
plhs[3] = mxCreateString(mppx);
plhs[4] = mxCreateString(mppy);
}
}
else{ /*can't open slide*/
mexErrMsgTxt("'openslide_check_levels.m' cannot open slide.");
}
/*free input buffer copy*/
mxFree(buffer);
}
