try a tile cache for openslide read
This commit is contained in:
John Cupitt
parent
21781b9f0f
commit
cace9d5da8
4
TODO
4
TODO
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@ -2,6 +2,10 @@
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also, cairo fails for very long lines, fill piecewise
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tried with a tile cache and performance is pretty bad
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try just piecewise fill?
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- vipsimage should be cached too, eg.
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@ -0,0 +1,463 @@
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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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* 27/11/11
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* - fix black background in transparent areas
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* - no need to set *stop on fill_region() error return
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* - add OpenSlide properties to image metadata
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* - consolidate setup into one function
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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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* 7/12/11
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* - redirect OpenSlide error logging to vips_error()
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* 8/12/11
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* - add more exposition to documentation
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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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/*
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#define VIPS_DEBUG
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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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#include <vips/intl.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 <stdlib.h>
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#include <limits.h>
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#include <vips/vips.h>
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#include <vips/debug.h>
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#include <openslide.h>
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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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} ReadSlide;
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static void
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readslide_destroy_cb( VipsImage *image, ReadSlide *rslide )
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{
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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",
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"%s", _( "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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ReadSlide *rslide;
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char name[FILENAME_MAX];
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char mode[FILENAME_MAX];
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const char *background;
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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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g_signal_connect( out, "close", G_CALLBACK( readslide_destroy_cb ),
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rslide );
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vips_filename_split( filename, name, mode );
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rslide->osr = openslide_open( name );
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if( rslide->osr == NULL ) {
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vips_error( "im_openslide2vips",
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"%s", _( "failure opening slide" ) );
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return( NULL );
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}
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background = openslide_get_property_value( rslide->osr,
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OPENSLIDE_PROPERTY_NAME_BACKGROUND_COLOR );
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if( background != NULL )
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rslide->background = strtoul( background, NULL, 16 );
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else
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rslide->background = 0xffffff;
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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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"%s", _( "invalid slide layer" ) );
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return( NULL );
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}
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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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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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}
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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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}
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if( w > INT_MAX || h > INT_MAX ) {
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vips_error( "im_openslide2vips",
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"%s", _( "image dimensions overflow int" ) );
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return( NULL );
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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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for( properties = openslide_get_property_names( rslide->osr );
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*properties != NULL; properties++ )
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vips_image_set_string( out, *properties,
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openslide_get_property_value( rslide->osr,
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*properties ) );
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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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static void
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copy_line( ReadSlide *rslide, uint32_t *in, int count, PEL *out )
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{
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uint8_t a;
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int i;
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for( i = 0; i < count; i++ ) {
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/* Convert from ARGB to RGBA and undo premultiplication.
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*/
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a = in[i] >> 24;
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if( a != 0 ) {
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out[4 * i + 0] = 255 * ((in[i] >> 16) & 255) / a;
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out[4 * i + 1] = 255 * ((in[i] >> 8) & 255) / a;
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out[4 * i + 2] = 255 * (in[i] & 255) / a;
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}
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else {
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/* Use background color.
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*/
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out[4 * i + 0] = (rslide->background >> 16) & 255;
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out[4 * i + 1] = (rslide->background >> 8) & 255;
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out[4 * i + 2] = rslide->background & 255;
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}
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out[4 * i + 3] = a;
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}
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}
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static int
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fill_region( VipsRegion *out, void *seq, void *_rslide, void *unused,
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gboolean *stop )
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{
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ReadSlide *rslide = _rslide;
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uint32_t *buf;
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const char *error;
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int y;
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VIPS_DEBUG_MSG( "openslide.c:fill_region: %d x %d @ %d x %d\n",
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out->valid.width, out->valid.height,
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out->valid.left, out->valid.top );
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/* We should really not alloc in the render thread. But
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* openslide_read_region() does a lot of allocing anyway, so we might
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* as well too.
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*/
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buf = VIPS_ARRAY( NULL, out->valid.width * out->valid.height,
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uint32_t );
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openslide_read_region( rslide->osr, buf,
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out->valid.left * rslide->downsample,
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out->valid.top * rslide->downsample, rslide->layer,
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out->valid.width, out->valid.height );
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for( y = 0; y < out->valid.height; y++ )
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copy_line( rslide, buf + y * out->valid.width,
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out->valid.width,
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VIPS_REGION_ADDR_TOPLEFT( out ) +
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y * VIPS_REGION_LSKIP( out ) );
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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", _( "reading region: %s" ),
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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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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( out, w * h, uint32_t );
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line = VIPS_ARRAY( out, 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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return( -1 );
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}
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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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ReadSlide *rslide;
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if( !(rslide = readslide_new( filename, out )) )
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return( -1 );
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return( 0 );
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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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* To facilitate zooming, virtual slide formats include multiple scaled-down
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* versions of the high-resolution image. These are typically called
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* "levels", though OpenSlide and im_openslide2vips() call them "layers".
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* By default, im_openslide2vips() reads the highest-resolution layer
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* (layer 0). To read a different layer, specify the layer number as part
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* of the filename (for example, "CMU-1.mrxs:3").
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*
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* In addition to the slide image itself, virtual slide formats sometimes
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* include additional images, such as a scan of the slide's barcode.
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* OpenSlide calls these "associated images". To read an associated image,
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* specify the image's name as part of the filename (for example,
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* "CMU-1.mrxs:label"). A slide's associated images are listed in the
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* "slide-associated-images" metadata item.
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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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ReadSlide *rslide;
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VIPS_DEBUG_MSG( "im_openslide2vips: %s\n", filename );
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if( !(rslide = readslide_new( filename, out )) )
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return( -1 );
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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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VIPS_DEBUG_MSG( "fill_associated:\n" );
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return( fill_associated( out, rslide ) );
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}
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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,
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NULL, fill_region, NULL, rslide, NULL ) );
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}
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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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}
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else
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ok = 0;
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VIPS_DEBUG_MSG( "isslide: %s - %d\n", filename, ok );
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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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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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static void
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error_handler( const char *domain, GLogLevelFlags level, const char *message,
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void *data )
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{
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vips_error( "im_openslide2vips", "%s", message );
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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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g_log_set_handler( "Openslide",
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G_LOG_LEVEL_CRITICAL | G_LOG_LEVEL_WARNING,
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error_handler, NULL );
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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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@ -19,6 +19,8 @@
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* - redirect OpenSlide error logging to vips_error()
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* 8/12/11
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* - add more exposition to documentation
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* 9/12/11
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* - unpack to a tile cache
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*/
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/*
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@ -189,6 +191,22 @@ readslide_new( const char *filename, VipsImage *out )
|
|||
return( rslide );
|
||||
}
|
||||
|
||||
/* The maximum size of the tiles we read from OpenSlide. It can fail with
|
||||
* very large tile shapes (eg. 78000 x 1). Also, limiting the tile size means
|
||||
* we can have a per-thread buffer for unpacking.
|
||||
*/
|
||||
#define TILE_WIDTH (256)
|
||||
#define TILE_HEIGHT (256)
|
||||
|
||||
/* Allocate a per-thread tile buffer.
|
||||
*/
|
||||
static void *
|
||||
seq_start( VipsImage *out, void *a, void *b )
|
||||
{
|
||||
return( (void *) VIPS_ARRAY( NULL,
|
||||
TILE_WIDTH * TILE_HEIGHT, uint32_t ) );
|
||||
}
|
||||
|
||||
static void
|
||||
copy_line( ReadSlide *rslide, uint32_t *in, int count, PEL *out )
|
||||
{
|
||||
|
|
@ -220,30 +238,37 @@ fill_region( VipsRegion *out, void *seq, void *_rslide, void *unused,
|
|||
gboolean *stop )
|
||||
{
|
||||
ReadSlide *rslide = _rslide;
|
||||
uint32_t *buf;
|
||||
uint32_t *buf = (uint32_t *) seq;
|
||||
VipsRect *r = &out->valid;
|
||||
|
||||
const char *error;
|
||||
int y;
|
||||
int x, y, z;
|
||||
|
||||
VIPS_DEBUG_MSG( "openslide.c:fill_region: %d x %d @ %d x %d\n",
|
||||
out->valid.width, out->valid.height,
|
||||
out->valid.left, out->valid.top );
|
||||
VIPS_DEBUG_MSG( "fill_region: %dx%d @ %dx%d\n",
|
||||
r->width, r->height, r->left, r->top );
|
||||
|
||||
/* We should really not alloc in the render thread. But
|
||||
* openslide_read_region() does a lot of allocing anyway, so we might
|
||||
* as well too.
|
||||
/* Loop over the region to be filled calling openslide_read_region().
|
||||
*/
|
||||
buf = VIPS_ARRAY( NULL, out->valid.width * out->valid.height,
|
||||
uint32_t );
|
||||
openslide_read_region( rslide->osr, buf,
|
||||
out->valid.left * rslide->downsample,
|
||||
out->valid.top * rslide->downsample, rslide->layer,
|
||||
out->valid.width, out->valid.height );
|
||||
for( y = 0; y < out->valid.height; y++ )
|
||||
copy_line( rslide, buf + y * out->valid.width,
|
||||
out->valid.width,
|
||||
VIPS_REGION_ADDR_TOPLEFT( out ) +
|
||||
y * VIPS_REGION_LSKIP( out ) );
|
||||
vips_free( buf );
|
||||
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,
|
||||
buf,
|
||||
(r->left + x) * rslide->downsample,
|
||||
(r->top + y) * rslide->downsample,
|
||||
rslide->layer,
|
||||
w, h );
|
||||
|
||||
for( z = 0; z < h; z++ )
|
||||
copy_line( rslide,
|
||||
buf + z * w,
|
||||
w,
|
||||
VIPS_REGION_ADDR( out,
|
||||
r->left + x,
|
||||
r->top + y + z ) );
|
||||
}
|
||||
|
||||
error = openslide_get_error( rslide->osr );
|
||||
if( error ) {
|
||||
|
|
@ -255,6 +280,14 @@ fill_region( VipsRegion *out, void *seq, void *_rslide, void *unused,
|
|||
return( 0 );
|
||||
}
|
||||
|
||||
static int
|
||||
seq_stop( void *seq, void *a, void *b )
|
||||
{
|
||||
vips_free( seq );
|
||||
|
||||
return( 0 );
|
||||
}
|
||||
|
||||
static int
|
||||
fill_associated( VipsImage *out, ReadSlide *rslide )
|
||||
{
|
||||
|
|
@ -335,28 +368,48 @@ static int
|
|||
im_openslide2vips( const char *filename, VipsImage *out )
|
||||
{
|
||||
ReadSlide *rslide;
|
||||
VipsImage *raw;
|
||||
|
||||
VIPS_DEBUG_MSG( "im_openslide2vips: %s\n", filename );
|
||||
|
||||
if( !(rslide = readslide_new( filename, out )) )
|
||||
/* Tile cache: keep enough for two complete rows of tiles.
|
||||
* This lets us do (smallish) area ops, like im_conv(), while
|
||||
* still only hitting each tile once.
|
||||
*/
|
||||
if( !(raw = im_open_local( out, "cache", "p" )) )
|
||||
return( -1 );
|
||||
|
||||
if( !(rslide = readslide_new( filename, raw )) )
|
||||
return( -1 );
|
||||
|
||||
if( rslide->associated ) {
|
||||
if( vips_image_wio_output( out ) )
|
||||
return( -1 );
|
||||
|
||||
VIPS_DEBUG_MSG( "fill_associated:\n" );
|
||||
|
||||
return( fill_associated( out, rslide ) );
|
||||
if( vips_image_wio_output( raw ) )
|
||||
return( -1 );
|
||||
|
||||
if( fill_associated( raw, rslide ) )
|
||||
return( -1 );
|
||||
}
|
||||
else {
|
||||
if( vips_image_pio_output( out ) )
|
||||
if( vips_image_pio_output( raw ) )
|
||||
return( -1 );
|
||||
vips_demand_hint( out, VIPS_DEMAND_STYLE_SMALLTILE, NULL );
|
||||
vips_demand_hint( raw, VIPS_DEMAND_STYLE_SMALLTILE, NULL );
|
||||
|
||||
return( vips_image_generate( out,
|
||||
NULL, fill_region, NULL, rslide, NULL ) );
|
||||
if( vips_image_generate( raw,
|
||||
seq_start, fill_region, seq_stop, rslide, NULL ) )
|
||||
return( -1 );
|
||||
}
|
||||
|
||||
/* Copy to out, adding a cache. Enough tiles for two complete
|
||||
* rows.
|
||||
*/
|
||||
if( im_tile_cache( raw, out,
|
||||
TILE_WIDTH, TILE_HEIGHT,
|
||||
2 * (1 + raw->Xsize / TILE_WIDTH) ) )
|
||||
return( -1 );
|
||||
|
||||
return( 0 );
|
||||
}
|
||||
|
||||
static int
|
||||
|
|
|
|||
Loading…
Reference in New Issue