support reading OpenSlide associated images
This commit is contained in:
Benjamin Gilbert
parent
395d4ef067
commit
04096821aa
@ -14,6 +14,7 @@
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* - support reading arbitrary layers
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* - use VIPS_ARRAY()
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* - add helper to copy a line of pixels
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* - support reading associated images
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*/
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/*
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@ -53,9 +54,13 @@
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typedef struct {
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openslide_t *osr;
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uint32_t background;
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const char *associated;
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/* Only valid if associated == NULL.
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*/
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int32_t layer;
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double downsample;
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uint32_t background;
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} ReadSlide;
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static void
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@ -64,6 +69,19 @@ readslide_destroy_cb( VipsImage *image, ReadSlide *rslide )
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VIPS_FREEF( openslide_close, rslide->osr );
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}
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static int
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check_associated_image( openslide_t *osr, const char *name )
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{
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const char * const *associated;
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for( associated = openslide_get_associated_image_names( osr );
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*associated != NULL; associated++ )
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if( strcmp( *associated, name ) == 0 )
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return( 0 );
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vips_error( "im_openslide2vips", _( "invalid associated image name" ));
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return( -1 );
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}
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static ReadSlide *
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readslide_new( const char *filename, VipsImage *out )
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{
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@ -74,6 +92,7 @@ readslide_new( const char *filename, VipsImage *out )
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char *endp;
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int64_t w, h;
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const char * const *properties;
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char *associated;
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rslide = VIPS_NEW( out, ReadSlide );
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memset( rslide, 0, sizeof( *rslide ));
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@ -94,26 +113,39 @@ readslide_new( const char *filename, VipsImage *out )
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else
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rslide->background = 0xffffff;
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if( mode[0] != 0 ) {
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rslide->layer = strtol( mode, &endp, 10 );
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if( *endp == 0 ) {
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/* Mode specifies slide layer.
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*/
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if( rslide->layer < 0 || rslide->layer >=
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openslide_get_layer_count( rslide->osr )) {
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vips_error( "im_openslide2vips",
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_( "invalid slide layer" ));
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return( NULL );
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}
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} else {
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/* Parse optional mode.
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*/
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rslide->layer = strtol( mode, &endp, 10 );
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if( *mode != 0 && *endp == 0 ) {
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/* Mode specifies slide layer.
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*/
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if( rslide->layer < 0 || rslide->layer >=
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openslide_get_layer_count( rslide->osr )) {
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vips_error( "im_openslide2vips",
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_( "invalid file mode" ));
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_( "invalid slide layer" ));
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return( NULL );
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}
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} else if( *mode != 0 ) {
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/* Mode specifies associated image.
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*/
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if ( check_associated_image( rslide->osr, mode ))
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return( NULL );
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rslide->associated = vips_strdup( VIPS_OBJECT( out ), mode );
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}
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openslide_get_layer_dimensions( rslide->osr, rslide->layer, &w, &h );
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if( w < 0 || h < 0 ) {
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if( rslide->associated ) {
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openslide_get_associated_image_dimensions( rslide->osr,
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rslide->associated, &w, &h );
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vips_image_set_string( out, "slide-associated-image",
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rslide->associated );
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} else {
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openslide_get_layer_dimensions( rslide->osr, rslide->layer,
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&w, &h );
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rslide->downsample = openslide_get_layer_downsample(
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rslide->osr, rslide->layer );
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vips_image_set_int( out, "slide-layer", rslide->layer );
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}
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if( w < 0 || h < 0 || rslide->downsample < 0 ) {
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vips_error( "im_openslide2vips", _( "getting dimensions: %s" ),
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openslide_get_error( rslide->osr ));
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return( NULL );
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@ -123,8 +155,6 @@ readslide_new( const char *filename, VipsImage *out )
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_( "image dimensions overflow int" ));
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return( NULL );
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}
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rslide->downsample = openslide_get_layer_downsample( rslide->osr,
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rslide->layer );
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vips_image_init_fields( out, (int) w, (int) h, 4, VIPS_FORMAT_UCHAR,
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VIPS_CODING_NONE, VIPS_INTERPRETATION_RGB, 1.0, 1.0 );
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@ -135,7 +165,10 @@ readslide_new( const char *filename, VipsImage *out )
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openslide_get_property_value( rslide->osr,
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*properties ));
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vips_image_set_int( out, "slide-layer", rslide->layer );
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associated = g_strjoinv( ", ", (char **)
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openslide_get_associated_image_names( rslide->osr ));
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vips_image_set_string( out, "slide-associated-images", associated );
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g_free( associated );
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return( rslide );
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}
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@ -195,6 +228,47 @@ fill_region( VipsRegion *out, void *seq, void *_rslide, void *unused,
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return( 0 );
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}
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static int
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fill_associated( VipsImage *out, ReadSlide *rslide )
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{
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uint32_t *buf;
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PEL *line;
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int64_t w, h;
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int y;
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const char *error;
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openslide_get_associated_image_dimensions( rslide->osr,
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rslide->associated, &w, &h );
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if( w == -1 || h == -1 ) {
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vips_error( "im_openslide2vips", _( "getting dimensions: %s" ),
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openslide_get_error( rslide->osr ));
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return( -1 );
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}
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buf = VIPS_ARRAY( NULL, w * h, uint32_t );
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line = VIPS_ARRAY( NULL, VIPS_IMAGE_SIZEOF_LINE( out ), PEL );
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openslide_read_associated_image( rslide->osr, rslide->associated,
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buf );
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for( y = 0; y < h; y++ ) {
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copy_line( rslide, buf + y * w, w, line );
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if( vips_image_write_line( out, y, line )) {
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vips_free( line );
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vips_free( buf );
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return( -1 );
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}
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}
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vips_free( line );
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vips_free( buf );
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error = openslide_get_error( rslide->osr );
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if( error ) {
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vips_error( "im_openslide2vips",
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_( "reading associated image: %s" ), error );
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return( -1 );
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}
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return( 0 );
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}
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static int
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openslide2vips_header( const char *filename, VipsImage *out )
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{
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@ -218,7 +292,9 @@ openslide2vips_header( const char *filename, VipsImage *out )
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*
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* By default, read the highest-resolution layer (layer 0). To read a
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* different layer, specify the layer number as part of the filename
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* (for example, "CMU-1.mrxs:3").
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* (for example, "CMU-1.mrxs:3"). To read an associated image attached
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* to the slide, specify the image's name as part of the filename (for
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* example, "CMU-1.mrxs:label").
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*
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* See also: #VipsFormat
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*
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@ -230,11 +306,19 @@ im_openslide2vips( const char *filename, VipsImage *out )
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ReadSlide *rslide;
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rslide = readslide_new( filename, out );
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if( rslide == NULL || vips_image_pio_output( out ))
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if( rslide == NULL )
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return( -1 );
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vips_demand_hint( out, VIPS_DEMAND_STYLE_SMALLTILE, NULL );
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return vips_image_generate( out, NULL, fill_region, NULL, rslide,
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NULL );
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if( rslide->associated ) {
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if( vips_image_wio_output( out ))
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return( -1 );
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return fill_associated( out, rslide );
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} else {
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if( vips_image_pio_output( out ))
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return( -1 );
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vips_demand_hint( out, VIPS_DEMAND_STYLE_SMALLTILE, NULL );
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return vips_image_generate( out, NULL, fill_region, NULL,
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rslide, NULL );
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}
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}
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static int
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@ -265,7 +349,21 @@ isslide( const char *filename )
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static VipsFormatFlags
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slide_flags( const char *filename )
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{
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return( VIPS_FORMAT_PARTIAL );
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char name[FILENAME_MAX];
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char mode[FILENAME_MAX];
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char *endp;
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vips_filename_split( filename, name, mode );
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strtol( mode, &endp, 10 );
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if( *mode == 0 || *endp == 0 ) {
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/* Slide layer or no mode specified.
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*/
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return( VIPS_FORMAT_PARTIAL );
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} else {
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/* Associated image specified.
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*/
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return( 0 );
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}
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}
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/* openslide format adds no new members.
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