Merge pull request #6 from bgilbert/openslide
Support reading virtual slide files with OpenSlide
This commit is contained in:
John Cupitt
commit
9d8f0188d2
4
README
4
README
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@ -140,6 +140,10 @@ OpenEXR
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if available, libvips will directly read (but not write, sadly)
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OpenEXR images
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OpenSlide
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if available, libvips can load OpenSlide-supported virtual slide
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files: Aperio, Hamamatsu VMS and VMU, MIRAX, and Trestle
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swig
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python
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python-dev
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19
configure.in
19
configure.in
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@ -438,6 +438,20 @@ if test x"$with_OpenEXR" != "xno"; then
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])
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fi
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# OpenSlide
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AC_ARG_WITH([openslide],
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AS_HELP_STRING([--without-openslide], [build without OpenSlide (default: test)]))
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if test x"$with_openslide" != "xno"; then
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PKG_CHECK_MODULES(OPENSLIDE, openslide >= 3.2.0,
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[AC_DEFINE(HAVE_OPENSLIDE,1,[define if you have OpenSlide >= 3.2.0 installed.])
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with_openslide=yes
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PACKAGES_USED="$PACKAGES_USED openslide"],
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[AC_MSG_WARN([OpenSlide >= 3.2.0 not found; disabling virtual slide support])
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with_openslide=no
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])
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fi
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# matio
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AC_ARG_WITH([matio],
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AS_HELP_STRING([--without-matio], [build without matio (default: test)]))
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@ -598,14 +612,14 @@ fi
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# Gather all up for VIPS_CFLAGS, VIPS_INCLUDES, VIPS_LIBS and VIPS_CXX_LIBS
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# sort includes to get longer, more specific dirs first
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# helps, for example, selecting graphicsmagick over imagemagick
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VIPS_CFLAGS=`for i in $VIPS_CFLAGS $GTHREAD_CFLAGS $REQUIRED_CFLAGS $PANGOFT2_CFLAGS $FFTW3_CFLAGS $MAGICK_CFLAGS $PNG_CFLAGS $EXIF_CFLAGS $MATIO_CFLAGS $CFITSIO_CFLAGS $OPENEXR_CFLAGS $ORC_CFLAGS
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VIPS_CFLAGS=`for i in $VIPS_CFLAGS $GTHREAD_CFLAGS $REQUIRED_CFLAGS $PANGOFT2_CFLAGS $FFTW3_CFLAGS $MAGICK_CFLAGS $PNG_CFLAGS $EXIF_CFLAGS $MATIO_CFLAGS $CFITSIO_CFLAGS $OPENEXR_CFLAGS $OPENSLIDE_CFLAGS $ORC_CFLAGS
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do
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echo $i
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done | sort -ru`
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VIPS_CFLAGS=`echo $VIPS_CFLAGS`
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VIPS_CFLAGS="$VIPS_DEBUG_FLAGS $VIPS_CFLAGS"
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VIPS_INCLUDES="$PNG_INCLUDES $TIFF_INCLUDES $ZIP_INCLUDES $JPEG_INCLUDES $FFTW_INCLUDES $LCMS_INCLUDES"
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VIPS_LIBS="$MAGICK_LIBS $PNG_LIBS $TIFF_LIBS $ZIP_LIBS $JPEG_LIBS $GTHREAD_LIBS $REQUIRED_LIBS $PANGOFT2_LIBS $FFTW3_LIBS $FFTW_LIBS $ORC_LIBS $LCMS_LIBS $OPENEXR_LIBS $CFITSIO_LIBS $MATIO_LIBS $EXIF_LIBS -lm"
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VIPS_LIBS="$MAGICK_LIBS $PNG_LIBS $TIFF_LIBS $ZIP_LIBS $JPEG_LIBS $GTHREAD_LIBS $REQUIRED_LIBS $PANGOFT2_LIBS $FFTW3_LIBS $FFTW_LIBS $ORC_LIBS $LCMS_LIBS $OPENEXR_LIBS $OPENSLIDE_LIBS $CFITSIO_LIBS $MATIO_LIBS $EXIF_LIBS -lm"
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# we need this to generate paths in swig/python/setup.py.in
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AC_SUBST(top_srcdir)
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@ -681,6 +695,7 @@ accelerate loops with orc: $with_orc
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(requires orc-0.4.11 or later)
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ICC profile support with lcms: $with_lcms (version $with_lcms_ver)
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file import with OpenEXR: $with_OpenEXR
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file import with OpenSlide: $with_openslide
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file import with matio: $with_matio
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file import with cfitsio: $with_cfitsio
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text rendering with pangoft2: $with_pangoft2
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@ -22,6 +22,7 @@ libformat_la_SOURCES = \
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im_vips2raw.c \
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matlab.c \
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fits.c \
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radiance.c
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radiance.c \
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openslide.c
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INCLUDES = -I${top_srcdir}/libvips/include @VIPS_CFLAGS@ @VIPS_INCLUDES@
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@ -57,7 +57,7 @@
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* transparently supported by im_open().
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*
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* VIPS comes with VipsFormat for TIFF, JPEG, PNG, Analyze, PPM, OpenEXR, CSV,
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* Matlab, Radiance, RAW, VIPS and one that wraps libMagick.
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* Matlab, Radiance, RAW, VIPS and ones that wrap libMagick and OpenSlide.
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*/
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/**
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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 +1,435 @@
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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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#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 <stdlib.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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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", _( "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", _( "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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_( "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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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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}
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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( 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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} 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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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, 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( 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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ReadSlide *rslide;
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rslide = readslide_new( filename, out );
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if( rslide == NULL )
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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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rslide = readslide_new( filename, out );
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if( rslide == NULL )
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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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return fill_associated( out, rslide );
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||||
} else {
|
||||
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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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;
|
||||
|
||||
ok = 1;
|
||||
osr = openslide_open(filename);
|
||||
if( osr != NULL ) {
|
||||
/* If this is a generic tiled TIFF image, decline to support
|
||||
* it, since im_tiff2vips can do better.
|
||||
*/
|
||||
vendor = openslide_get_property_value( osr,
|
||||
OPENSLIDE_PROPERTY_NAME_VENDOR );
|
||||
if( vendor == NULL ||
|
||||
strcmp( vendor, "generic-tiff" ) == 0 )
|
||||
ok = 0;
|
||||
openslide_close( osr );
|
||||
} else {
|
||||
ok = 0;
|
||||
}
|
||||
return( ok );
|
||||
}
|
||||
|
||||
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 );
|
||||
}
|
||||
}
|
||||
|
||||
static void
|
||||
error_handler( const char *domain, GLogLevelFlags level, const char *message,
|
||||
void *data )
|
||||
{
|
||||
vips_error( "im_openslide2vips", "%s", message );
|
||||
}
|
||||
|
||||
/* openslide format adds no new members.
|
||||
*/
|
||||
typedef VipsFormat VipsFormatOpenslide;
|
||||
typedef VipsFormatClass VipsFormatOpenslideClass;
|
||||
|
||||
static const char *slide_suffs[] = {
|
||||
".svs", /* Aperio */
|
||||
".vms", ".vmu", /* Hamamatsu */
|
||||
".mrxs", /* MIRAX */
|
||||
".tif", /* Trestle */
|
||||
NULL
|
||||
};
|
||||
|
||||
static void
|
||||
vips_format_openslide_class_init( VipsFormatOpenslideClass *class )
|
||||
{
|
||||
VipsObjectClass *object_class = (VipsObjectClass *) class;
|
||||
VipsFormatClass *format_class = (VipsFormatClass *) class;
|
||||
|
||||
object_class->nickname = "openslide";
|
||||
object_class->description = _( "OpenSlide-supported" );
|
||||
|
||||
format_class->is_a = isslide;
|
||||
format_class->header = openslide2vips_header;
|
||||
format_class->load = im_openslide2vips;
|
||||
format_class->get_flags = slide_flags;
|
||||
format_class->suffs = slide_suffs;
|
||||
|
||||
/* Some TIFF files are virtual slides with odd vendor extensions
|
||||
* (or outright format violations!). Ensure we look at them before
|
||||
* im_tiff2vips does. OpenSlide tries very hard to reject files it
|
||||
* doesn't understand, so this should be safe.
|
||||
*/
|
||||
format_class->priority = 100;
|
||||
|
||||
g_log_set_handler( "Openslide",
|
||||
G_LOG_LEVEL_CRITICAL | G_LOG_LEVEL_WARNING,
|
||||
error_handler, NULL );
|
||||
}
|
||||
|
||||
static void
|
||||
vips_format_openslide_init( VipsFormatOpenslide *object )
|
||||
{
|
||||
}
|
||||
|
||||
G_DEFINE_TYPE( VipsFormatOpenslide, vips_format_openslide, VIPS_TYPE_FORMAT );
|
||||
|
||||
#endif /*HAVE_OPENSLIDE*/
|
||||
Loading…
Reference in New Issue