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support reading OpenSlide associated images

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This commit is contained in:
Benjamin Gilbert 2011-11-27 22:41:24 -05:00
parent 395d4ef067
commit 04096821aa
1 changed files with 123 additions and 25 deletions
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130
libvips/format/openslide.c
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@ -14,6 +14,7 @@
* - support reading arbitrary layers
* - use VIPS_ARRAY()
* - add helper to copy a line of pixels
* - support reading associated images
*/
/*
@ -53,9 +54,13 @@
typedef struct {
openslide_t *osr;
uint32_t background;
const char *associated;
/* Only valid if associated == NULL.
*/
int32_t layer;
double downsample;
uint32_t background;
} ReadSlide;
static void
@ -64,6 +69,19 @@ readslide_destroy_cb( VipsImage *image, ReadSlide *rslide )
VIPS_FREEF( openslide_close, rslide->osr );
}
static int
check_associated_image( openslide_t *osr, const char *name )
{
const char * const *associated;
for( associated = openslide_get_associated_image_names( osr );
*associated != NULL; associated++ )
if( strcmp( *associated, name ) == 0 )
return( 0 );
vips_error( "im_openslide2vips", _( "invalid associated image name" ));
return( -1 );
}
static ReadSlide *
readslide_new( const char *filename, VipsImage *out )
{
@ -74,6 +92,7 @@ readslide_new( const char *filename, VipsImage *out )
char *endp;
int64_t w, h;
const char * const *properties;
char *associated;
rslide = VIPS_NEW( out, ReadSlide );
memset( rslide, 0, sizeof( *rslide ));
@ -94,9 +113,10 @@ readslide_new( const char *filename, VipsImage *out )
else
rslide->background = 0xffffff;
if( mode[0] != 0 ) {
/* Parse optional mode.
*/
rslide->layer = strtol( mode, &endp, 10 );
if( *endp == 0 ) {
if( *mode != 0 && *endp == 0 ) {
/* Mode specifies slide layer.
*/
if( rslide->layer < 0 || rslide->layer >=
@ -105,15 +125,27 @@ readslide_new( const char *filename, VipsImage *out )
_( "invalid slide layer" ));
return( NULL );
}
} else {
vips_error( "im_openslide2vips",
_( "invalid file mode" ));
} else if( *mode != 0 ) {
/* Mode specifies associated image.
*/
if ( check_associated_image( rslide->osr, mode ))
return( NULL );
}
rslide->associated = vips_strdup( VIPS_OBJECT( out ), mode );
}
openslide_get_layer_dimensions( rslide->osr, rslide->layer, &w, &h );
if( w < 0 || h < 0 ) {
if( rslide->associated ) {
openslide_get_associated_image_dimensions( rslide->osr,
rslide->associated, &w, &h );
vips_image_set_string( out, "slide-associated-image",
rslide->associated );
} else {
openslide_get_layer_dimensions( rslide->osr, rslide->layer,
&w, &h );
rslide->downsample = openslide_get_layer_downsample(
rslide->osr, rslide->layer );
vips_image_set_int( out, "slide-layer", rslide->layer );
}
if( w < 0 || h < 0 || rslide->downsample < 0 ) {
vips_error( "im_openslide2vips", _( "getting dimensions: %s" ),
openslide_get_error( rslide->osr ));
return( NULL );
@ -123,8 +155,6 @@ readslide_new( const char *filename, VipsImage *out )
_( "image dimensions overflow int" ));
return( NULL );
}
rslide->downsample = openslide_get_layer_downsample( rslide->osr,
rslide->layer );
vips_image_init_fields( out, (int) w, (int) h, 4, VIPS_FORMAT_UCHAR,
VIPS_CODING_NONE, VIPS_INTERPRETATION_RGB, 1.0, 1.0 );
@ -135,7 +165,10 @@ readslide_new( const char *filename, VipsImage *out )
openslide_get_property_value( rslide->osr,
*properties ));
vips_image_set_int( out, "slide-layer", rslide->layer );
associated = g_strjoinv( ", ", (char **)
openslide_get_associated_image_names( rslide->osr ));
vips_image_set_string( out, "slide-associated-images", associated );
g_free( associated );
return( rslide );
}
@ -195,6 +228,47 @@ fill_region( VipsRegion *out, void *seq, void *_rslide, void *unused,
return( 0 );
}
static int
fill_associated( VipsImage *out, ReadSlide *rslide )
{
uint32_t *buf;
PEL *line;
int64_t w, h;
int y;
const char *error;
openslide_get_associated_image_dimensions( rslide->osr,
rslide->associated, &w, &h );
if( w == -1 || h == -1 ) {
vips_error( "im_openslide2vips", _( "getting dimensions: %s" ),
openslide_get_error( rslide->osr ));
return( -1 );
}
buf = VIPS_ARRAY( NULL, w * h, uint32_t );
line = VIPS_ARRAY( NULL, VIPS_IMAGE_SIZEOF_LINE( out ), PEL );
openslide_read_associated_image( rslide->osr, rslide->associated,
buf );
for( y = 0; y < h; y++ ) {
copy_line( rslide, buf + y * w, w, line );
if( vips_image_write_line( out, y, line )) {
vips_free( line );
vips_free( buf );
return( -1 );
}
}
vips_free( line );
vips_free( buf );
error = openslide_get_error( rslide->osr );
if( error ) {
vips_error( "im_openslide2vips",
_( "reading associated image: %s" ), error );
return( -1 );
}
return( 0 );
}
static int
openslide2vips_header( const char *filename, VipsImage *out )
{
@ -218,7 +292,9 @@ openslide2vips_header( const char *filename, VipsImage *out )
*
* By default, read the highest-resolution layer (layer 0). To read a
* different layer, specify the layer number as part of the filename
* (for example, "CMU-1.mrxs:3").
* (for example, "CMU-1.mrxs:3"). To read an associated image attached
* to the slide, specify the image's name as part of the filename (for
* example, "CMU-1.mrxs:label").
*
* See also: #VipsFormat
*
@ -230,11 +306,19 @@ im_openslide2vips( const char *filename, VipsImage *out )
ReadSlide *rslide;
rslide = readslide_new( filename, out );
if( rslide == NULL || vips_image_pio_output( out ))
if( rslide == NULL )
return( -1 );
if( rslide->associated ) {
if( vips_image_wio_output( out ))
return( -1 );
return fill_associated( out, rslide );
} else {
if( vips_image_pio_output( out ))
return( -1 );
vips_demand_hint( out, VIPS_DEMAND_STYLE_SMALLTILE, NULL );
return vips_image_generate( out, NULL, fill_region, NULL, rslide,
NULL );
return vips_image_generate( out, NULL, fill_region, NULL,
rslide, NULL );
}
}
static int
@ -265,7 +349,21 @@ isslide( const char *filename )
static VipsFormatFlags
slide_flags( const char *filename )
{
char name[FILENAME_MAX];
char mode[FILENAME_MAX];
char *endp;
vips_filename_split( filename, name, mode );
strtol( mode, &endp, 10 );
if( *mode == 0 || *endp == 0 ) {
/* Slide layer or no mode specified.
*/
return( VIPS_FORMAT_PARTIAL );
} else {
/* Associated image specified.
*/
return( 0 );
}
}
/* openslide format adds no new members.