int
vips__openslide_read_associated( const char *filename, VipsImage *out,
const char *associated )
{
ReadSlide *rslide;
VipsImage *raw;
const char *error;
VIPS_DEBUG_MSG( "vips__openslide_read_associated: %s %s\n",
filename, associated );
/* Memory buffer. Get associated directly to this, then copy to out.
*/
raw = vips_image_new_buffer();
vips_object_local( out, raw );
if( !(rslide = readslide_new( filename, raw, 0, associated )) ||
vips_image_write_prepare( raw ) )
return( -1 );
openslide_read_associated_image( rslide->osr, rslide->associated,
(uint32_t *) VIPS_IMAGE_ADDR( raw, 0, 0 ) );
error = openslide_get_error( rslide->osr );
if( error ) {
vips_error( "openslide2vips",
_( "reading associated image: %s" ), error );
return( -1 );
}
if( vips_image_write( raw, out ) )
return( -1 );
return( 0 );
}
static void test_image_fetch(openslide_t *osr,
int64_t x, int64_t y,
int64_t w, int64_t h) {
uint32_t *buf = g_new(uint32_t, w * h);
for (int32_t level = 0; level < openslide_get_level_count(osr); level++) {
openslide_read_region(osr, buf, x, y, level, w, h);
}
g_free(buf);
const char *err = openslide_get_error(osr);
if (err) {
fail("Read failed: %"G_GINT64_FORMAT" %"G_GINT64_FORMAT
" %"G_GINT64_FORMAT" %"G_GINT64_FORMAT": %s", x, y, w, h, err);
}
}
static int
vips__openslide_generate( VipsRegion *out,
void *seq, void *_rslide, void *unused, gboolean *stop )
{
ReadSlide *rslide = _rslide;
VipsRect *r = &out->valid;
const char *error;
int x, y;
VIPS_DEBUG_MSG( "vips__openslide_generate: %dx%d @ %dx%d\n",
r->width, r->height, r->left, r->top );
/* Fill in tile-sized chunks. Some versions of OpenSlide can fail for
* very large requests.
*/
for( y = 0; y < r->height; y += TILE_HEIGHT )
for( x = 0; x < r->width; x += TILE_WIDTH ) {
int w = VIPS_MIN( TILE_WIDTH, r->width - x );
int h = VIPS_MIN( TILE_HEIGHT, r->height - y );
openslide_read_region( rslide->osr,
(uint32_t *) VIPS_REGION_ADDR( out,
r->left + x, r->top + y ),
(r->left + x) * rslide->downsample,
(r->top + y) * rslide->downsample,
rslide->layer,
w, h );
}
error = openslide_get_error( rslide->osr );
if( error ) {
vips_error( "openslide2vips",
_( "reading region: %s" ), error );
return( -1 );
}
return( 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 void aperio_tiff_tilereader(openslide_t *osr,
TIFF *tiff,
uint32_t *dest,
int64_t x, int64_t y,
int32_t w, int32_t h) {
// which compression?
uint16_t compression_mode;
TIFFGetField(tiff, TIFFTAG_COMPRESSION, &compression_mode);
// not for us? fallback
if ((compression_mode != APERIO_COMPRESSION_JP2K_YCBCR) &&
(compression_mode != APERIO_COMPRESSION_JP2K_RGB)) {
_openslide_generic_tiff_tilereader(osr, tiff, dest, x, y, w, h);
return;
}
// else, JPEG 2000!
opj_cio_t *stream = NULL;
opj_dinfo_t *dinfo = NULL;
opj_image_t *image = NULL;
opj_image_comp_t *comps = NULL;
// note: don't use info_handler, it outputs lots of junk
opj_event_mgr_t event_callbacks = {
.error_handler = error_callback,
.warning_handler = warning_callback,
};
// get tile number
ttile_t tile_no = TIFFComputeTile(tiff, x, y, 0, 0);
// g_debug("aperio reading tile_no: %d", tile_no);
// get tile size
toff_t *sizes;
if (TIFFGetField(tiff, TIFFTAG_TILEBYTECOUNTS, &sizes) == 0) {
_openslide_set_error(osr, "Cannot get tile size");
return; // ok, haven't allocated anything yet
}
tsize_t tile_size = sizes[tile_no];
// a slide with zero-length tiles has been seen in the wild
if (!tile_size) {
// fill with transparent
memset(dest, 0, w * h * 4);
//g_debug("skipping tile %d", tile_no);
return; // ok, haven't allocated anything yet
}
// get raw tile
tdata_t buf = g_slice_alloc(tile_size);
tsize_t size = TIFFReadRawTile(tiff, tile_no, buf, tile_size);
if (size == -1) {
_openslide_set_error(osr, "Cannot get raw tile");
goto DONE;
}
// init decompressor
opj_dparameters_t parameters;
dinfo = opj_create_decompress(CODEC_J2K);
opj_set_default_decoder_parameters(¶meters);
opj_setup_decoder(dinfo, ¶meters);
stream = opj_cio_open((opj_common_ptr) dinfo, buf, size);
opj_set_event_mgr((opj_common_ptr) dinfo, &event_callbacks, osr);
// decode
image = opj_decode(dinfo, stream);
// check error
if (openslide_get_error(osr)) {
goto DONE;
}
comps = image->comps;
// sanity check
if (image->numcomps != 3) {
_openslide_set_error(osr, "image->numcomps != 3");
goto DONE;
}
// TODO more checks?
copy_aperio_tile(compression_mode, comps, dest,
w, h,
w / comps[0].w, h / comps[0].h,
w / comps[1].w, h / comps[1].h,
w / comps[2].w, h / comps[2].h);
DONE:
// erase
g_slice_free1(tile_size, buf);
if (image) opj_image_destroy(image);
if (stream) opj_cio_close(stream);
if (dinfo) opj_destroy_decompress(dinfo);
}
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);
}
