From 04096821aa205d79ddcee4e82f0aea57cbf5450e Mon Sep 17 00:00:00 2001 From: Benjamin Gilbert Date: Sun, 27 Nov 2011 22:41:24 -0500 Subject: [PATCH] support reading OpenSlide associated images --- libvips/format/openslide.c | 148 ++++++++++++++++++++++++++++++------- 1 file changed, 123 insertions(+), 25 deletions(-) diff --git a/libvips/format/openslide.c b/libvips/format/openslide.c index f7bb53f0..5da10c55 100644 --- a/libvips/format/openslide.c +++ b/libvips/format/openslide.c @@ -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 )); @@ -94,26 +113,39 @@ readslide_new( const char *filename, VipsImage *out ) else rslide->background = 0xffffff; - if( mode[0] != 0 ) { - rslide->layer = strtol( mode, &endp, 10 ); - if( *endp == 0 ) { - /* Mode specifies slide layer. - */ - if( rslide->layer < 0 || rslide->layer >= - openslide_get_layer_count( rslide->osr )) { - vips_error( "im_openslide2vips", - _( "invalid slide layer" )); - return( NULL ); - } - } else { + /* Parse optional mode. + */ + rslide->layer = strtol( mode, &endp, 10 ); + if( *mode != 0 && *endp == 0 ) { + /* Mode specifies slide layer. + */ + if( rslide->layer < 0 || rslide->layer >= + openslide_get_layer_count( rslide->osr )) { vips_error( "im_openslide2vips", - _( "invalid file mode" )); + _( "invalid slide layer" )); return( NULL ); } + } 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 ); - vips_demand_hint( out, VIPS_DEMAND_STYLE_SMALLTILE, NULL ); - return vips_image_generate( out, NULL, fill_region, NULL, rslide, - NULL ); + 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 ); + } } static int @@ -265,7 +349,21 @@ isslide( const char *filename ) static VipsFormatFlags slide_flags( const char *filename ) { - return( VIPS_FORMAT_PARTIAL ); + 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.