add OpenSlide VipsFormat
Don't export im_openslide2vips, since there's no point in creating new deprecated API.
This commit is contained in:
Benjamin Gilbert
parent
1078c2a7fb
commit
25733e7bb7
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@ -22,6 +22,7 @@ libformat_la_SOURCES = \
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im_vips2raw.c \
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matlab.c \
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fits.c \
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radiance.c
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radiance.c \
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openslide.c
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INCLUDES = -I${top_srcdir}/libvips/include @VIPS_CFLAGS@ @VIPS_INCLUDES@
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@ -464,6 +464,10 @@ im__format_init( void )
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extern GType vips_format_exr_get_type();
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vips_format_exr_get_type();
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#endif /*HAVE_OPENEXR*/
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#ifdef HAVE_OPENSLIDE
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extern GType vips_format_openslide_get_type();
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vips_format_openslide_get_type();
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#endif /*HAVE_OPENSLIDE*/
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#ifdef HAVE_MATIO
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extern GType vips_format_mat_get_type();
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vips_format_mat_get_type();
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@ -0,0 +1,247 @@
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/* Read a virtual microscope slide using OpenSlide.
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*
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* Benjamin Gilbert
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*
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* Copyright (c) 2011 Carnegie Mellon University
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*
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* 26/11/11
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* - initial version
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*/
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/*
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This file is part of VIPS.
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VIPS is free software; you can redistribute it and/or modify
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it under the terms of the GNU Lesser General Public License as published by
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the Free Software Foundation; either version 2 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU Lesser General Public License for more details.
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You should have received a copy of the GNU Lesser General Public License
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along with this program; if not, write to the Free Software
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Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*/
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#ifdef HAVE_CONFIG_H
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#include <config.h>
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#endif /*HAVE_CONFIG_H*/
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#ifdef HAVE_OPENSLIDE
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#include <string.h>
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#include <stdint.h>
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#include <limits.h>
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#include <openslide.h>
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#include <vips/vips.h>
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#include <vips/intl.h>
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static void
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close_slide( VipsImage *image, openslide_t *osr )
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{
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openslide_close( osr );
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}
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static int
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load_header( openslide_t *osr, VipsImage *out )
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{
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int64_t w, h;
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openslide_get_layer0_dimensions( osr, &w, &h );
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if( w < 0 || h < 0 ) {
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vips_error( "im_openslide2vips", _( "getting dimensions: %s" ),
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openslide_get_error( osr ));
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return( -1 );
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}
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if( w > INT_MAX || h > INT_MAX ) {
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vips_error( "im_openslide2vips",
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_( "image dimensions overflow int" ));
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return( -1 );
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}
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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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return( 0 );
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}
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static int
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fill_region( VipsRegion *out, void *seq, void *_osr, void *unused,
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gboolean *stop )
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{
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openslide_t *osr = _osr;
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uint32_t *buf;
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const char *error;
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PEL *pel;
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uint32_t sample;
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uint8_t a;
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int x, y;
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buf = vips_malloc( NULL, out->valid.width * out->valid.height *
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sizeof( *buf ));
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openslide_read_region( osr, buf, out->valid.left, out->valid.top,
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0, out->valid.width, out->valid.height );
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for( y = 0; y < out->valid.height; y++ ) {
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for( x = 0; x < out->valid.width; x++ ) {
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/* Convert from ARGB to RGBA and undo
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* premultiplication.
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*/
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sample = buf[y * out->valid.height + x];
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a = sample >> 24;
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if( a == 0 ) {
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/* R, G, B should also be zero, so we just
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* need to avoid the zero divide.
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*/
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a = 1;
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}
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pel = VIPS_REGION_ADDR( out, out->valid.left + x,
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out->valid.top + y );
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pel[0] = 255 * ((sample >> 16) & 255) / a;
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pel[1] = 255 * ((sample >> 8) & 255) / a;
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pel[2] = 255 * (sample & 255) / a;
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pel[3] = a;
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}
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}
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vips_free( buf );
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error = openslide_get_error( osr );
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if( error ) {
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vips_error( "im_openslide2vips", _( "reading region: %s" ),
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error );
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/* OpenSlide handle is now in error state.
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*/
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*stop = TRUE;
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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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openslide_t *osr;
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int ret;
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osr = openslide_open( filename );
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if( osr == NULL ) {
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vips_error( "im_openslide2vips", _( "failure opening slide" ));
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return( -1 );
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}
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ret = load_header( osr, out );
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openslide_close( osr );
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return( ret );
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}
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/**
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* im_openslide2vips:
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* @filename: file to load
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* @out: image to write to
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*
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* Read a virtual slide supported by the OpenSlide library into a VIPS image.
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* OpenSlide supports images in Aperio, Hamamatsu VMS, Hamamatsu VMU, MIRAX,
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* and Trestle formats. It also supports generic tiled TIFF images, but
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* im_openslide2vips() does not.
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*
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* Currently, only layer 0 (the highest-resolution slide layer) is used.
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*
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* See also: #VipsFormat
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*
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* Returns: 0 on success, -1 on error.
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*/
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static int
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im_openslide2vips( const char *filename, VipsImage *out )
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{
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openslide_t *osr;
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osr = openslide_open( filename );
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if( osr == NULL ) {
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vips_error( "im_openslide2vips", _( "failure opening slide" ));
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return( -1 );
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}
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g_signal_connect( out, "close", G_CALLBACK( close_slide ), osr );
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if( load_header( osr, out ) || 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, osr, NULL );
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}
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static int
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isslide( const char *filename )
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{
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openslide_t *osr;
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const char *vendor;
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int ok;
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ok = 1;
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osr = openslide_open(filename);
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if( osr != NULL ) {
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/* If this is a generic tiled TIFF image, decline to support
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* it, since im_tiff2vips can do better.
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*/
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vendor = openslide_get_property_value( osr,
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OPENSLIDE_PROPERTY_NAME_VENDOR );
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if( vendor == NULL ||
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strcmp( vendor, "generic-tiff" ) == 0 )
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ok = 0;
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openslide_close( osr );
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} else {
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ok = 0;
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}
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return( ok );
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}
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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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}
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/* openslide format adds no new members.
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*/
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typedef VipsFormat VipsFormatOpenslide;
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typedef VipsFormatClass VipsFormatOpenslideClass;
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static const char *slide_suffs[] = {
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".svs", /* Aperio */
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".vms", ".vmu", /* Hamamatsu */
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".mrxs", /* MIRAX */
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".tif", /* Trestle */
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NULL
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};
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static void
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vips_format_openslide_class_init( VipsFormatOpenslideClass *class )
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{
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VipsObjectClass *object_class = (VipsObjectClass *) class;
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VipsFormatClass *format_class = (VipsFormatClass *) class;
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object_class->nickname = "openslide";
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object_class->description = _( "OpenSlide-supported" );
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format_class->is_a = isslide;
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format_class->header = openslide2vips_header;
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format_class->load = im_openslide2vips;
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format_class->get_flags = slide_flags;
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format_class->suffs = slide_suffs;
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/* Some TIFF files are virtual slides with odd vendor extensions
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* (or outright format violations!). Ensure we look at them before
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* im_tiff2vips does. OpenSlide tries very hard to reject files it
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* doesn't understand, so this should be safe.
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*/
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format_class->priority = 100;
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}
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static void
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vips_format_openslide_init( VipsFormatOpenslide *object )
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{
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}
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G_DEFINE_TYPE( VipsFormatOpenslide, vips_format_openslide, VIPS_TYPE_FORMAT );
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#endif /*HAVE_OPENSLIDE*/
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