add fits read
This commit is contained in:
John Cupitt
parent
288d8583ac
commit
57a8d8f12e
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@ -37,6 +37,8 @@
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- fix gtk-doc warnings
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- small mask load/save improvements
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- mask gtk-doc done
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- add cfitsio dependancy
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- add FITS reader
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12/5/10 started 7.22.2
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- the conditional image of ifthenelse can be any format, a (!=0) is added if
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7
TODO
7
TODO
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@ -1,3 +1,10 @@
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- test fits reader more ... colour?
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- we get lots of valgrind errors with fits reading
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- why do we read_free so often during fits read?
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- are we triggering im_fits2vips() in each thread?? argh, try tracing
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- maybe im_draw_smudge() is too slow :-( also, we had a sanity failure with
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19
configure.in
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configure.in
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@ -424,6 +424,20 @@ if test x"$with_matio" != "xno"; then
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])
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fi
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# cfitsio
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AC_ARG_WITH([cfitsio],
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AS_HELP_STRING([--without-cfitsio], [build without cfitsio (default: test)]))
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if test x"$with_cfitsio" != "xno"; then
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PKG_CHECK_MODULES(CFITSIO, cfitsio,
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[AC_DEFINE(HAVE_CFITSIO,1,[define if you have cfitsio installed.])
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with_cfitsio=yes
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PACKAGES_USED="$PACKAGES_USED cfitsio"],
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[AC_MSG_WARN([cfitsio not found; disabling cfitsio support])
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with_cfitsio=no
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])
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fi
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# pangoft2
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AC_ARG_WITH([pangoft2],
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AS_HELP_STRING([--without-pangoft2],
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@ -556,14 +570,14 @@ 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 $OPENEXR_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
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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 $LCMS_LIBS $OPENEXR_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 $LCMS_LIBS $OPENEXR_LIBS $CFITSIO_LIBS $MATIO_LIBS $EXIF_LIBS -lm"
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# need -lstdc++ for (eg.) the C++ format loaders
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VIPS_CXX_LIBS="-lstdc++"
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@ -649,6 +663,7 @@ file import with libMagick: $with_magick
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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 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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file import/export with libpng: $with_png
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file import/export with libtiff: $with_tiff
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@ -21,6 +21,7 @@ libformat_la_SOURCES = \
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im_vips2tiff.c \
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im_vips2raw.c \
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matlab.c \
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fits.c \
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radiance.c
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INCLUDES = -I${top_srcdir}/libvips/include @VIPS_CFLAGS@ @VIPS_INCLUDES@
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@ -0,0 +1,396 @@
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/* Read FITS files with cfitsio
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*
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* 26/10/10
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* - from matlab.c
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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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These files are distributed with VIPS - http://www.vips.ecs.soton.ac.uk
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*/
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/*
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#define 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_CFITSIO
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#include <stdio.h>
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#include <assert.h>
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#include <stdlib.h>
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#include <string.h>
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#include <vips/vips.h>
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#include <vips/internal.h>
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#include <fitsio.h>
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#ifdef WITH_DMALLOC
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#include <dmalloc.h>
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#endif /*WITH_DMALLOC*/
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/* What we track during a cfitsio-file read.
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*/
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typedef struct {
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char *filename;
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IMAGE *out;
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fitsfile *fptr;
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int datatype;
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} Read;
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static void
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read_error( int status )
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{
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char buf[80];
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fits_get_errstatus( status, buf );
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im_error( "fits", "%s", buf );
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}
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static void
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read_destroy( Read *read )
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{
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IM_FREE( read->filename );
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if( read->fptr ) {
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int status;
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if( fits_close_file( read->fptr, &status ) )
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read_error( status );
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read->fptr = NULL;
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}
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im_free( read );
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}
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static Read *
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read_new( const char *filename, IMAGE *out )
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{
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Read *read;
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int status;
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if( !(read = IM_NEW( NULL, Read )) )
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return( NULL );
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read->filename = im_strdup( NULL, filename );
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read->out = out;
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read->fptr = NULL;
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status = 0;
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if( fits_open_file( &read->fptr, filename, READONLY, &status ) ) {
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im_error( "fits", _( "unable to open \"%s\"" ), filename );
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read_error( status );
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read_destroy( read );
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return( NULL );
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}
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return( read );
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}
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/* fits image types -> VIPS band formats. VIPS doesn't have 64-bit int, so no
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* entry for LONGLONG_IMG (64).
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*/
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static int fits2vips_formats[][3] = {
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{ BYTE_IMG, IM_BANDFMT_UCHAR, TBYTE },
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{ SHORT_IMG, IM_BANDFMT_USHORT, TUSHORT },
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{ LONG_IMG, IM_BANDFMT_UINT, TUINT },
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{ FLOAT_IMG, IM_BANDFMT_FLOAT, TFLOAT },
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{ DOUBLE_IMG, IM_BANDFMT_DOUBLE, TDOUBLE }
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};
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static int
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fits2vips_get_header( Read *read )
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{
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int status;
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int bitpix;
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int naxis;
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long long int naxes[3];
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int width, height, bands, format, type;
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int keysexist;
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int morekeys;
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int i;
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status = 0;
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if( fits_get_img_paramll( read->fptr,
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3, &bitpix, &naxis, naxes, &status ) ) {
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read_error( status );
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return( -1 );
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}
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width = 1;
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height = 1;
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bands = 1;
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switch( naxis ) {
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case 3:
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bands = naxes[2];
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case 2:
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height = naxes[1];
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case 1:
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width = naxes[0];
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break;
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default:
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im_error( "fits", "bad number of axis %d", naxis );
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return( -1 );
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}
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if( bands == 1 )
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type = IM_TYPE_B_W;
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else if( bands == 3 )
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type = IM_TYPE_RGB;
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else
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type = IM_TYPE_MULTIBAND;
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/* Get image format. We want the 'raw' format of the image, our caller
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* can convert using the meta info if they want.
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*/
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for( i = 0; i < IM_NUMBER( fits2vips_formats ); i++ )
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if( fits2vips_formats[i][0] == bitpix )
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break;
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if( i == IM_NUMBER( fits2vips_formats ) ) {
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im_error( "im_fits2vips", _( "unsupported bitpix %d\n" ),
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bitpix );
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return( -1 );
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}
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format = fits2vips_formats[i][1];
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read->datatype = fits2vips_formats[i][2];
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im_initdesc( read->out,
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width, height, bands,
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im_bits_of_fmt( format ), format,
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IM_CODING_NONE, type, 1.0, 1.0, 0, 0 );
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/* Read all keys into meta.
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*/
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if( fits_get_hdrspace( read->fptr, &keysexist, &morekeys, &status ) ) {
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read_error( status );
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return( -1 );
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}
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for( i = 0; i < keysexist; i++ ) {
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char key[81];
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char value[81];
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char comment[81];
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char vipsname[100];
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if( fits_read_keyn( read->fptr, i + 1,
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key, value, comment, &status ) ) {
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read_error( status );
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return( -1 );
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}
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#ifdef DEBUG
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printf( "fits: seen:\n" );
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printf( " key == %s\n", key );
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printf( " value == %s\n", value );
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printf( " comment == %s\n", comment );
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#endif /*DEBUG*/
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im_snprintf( vipsname, 100, "fits-%s", key );
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if( im_meta_set_string( read->out, vipsname, value ) )
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return( -1 );
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im_snprintf( vipsname, 100, "fits-%s-comment", key );
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if( im_meta_set_string( read->out, vipsname, comment ) )
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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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fits2vips_header( const char *filename, IMAGE *out )
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{
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Read *read;
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#ifdef DEBUG
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printf( "fits2vips_header: reading \"%s\"\n", filename );
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#endif /*DEBUG*/
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if( !(read = read_new( filename, out )) )
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return( -1 );
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if( fits2vips_get_header( read ) ) {
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read_destroy( read );
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return( -1 );
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}
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read_destroy( read );
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return( 0 );
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}
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static int
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fits2vips_get_data( Read *read )
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{
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IMAGE *im = read->out;
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const int es = IM_IMAGE_SIZEOF_ELEMENT( im );
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PEL *line_buffer;
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PEL *band_buffer;
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PEL *p, *q;
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int x, y, b, z;
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int status;
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status = 0;
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if( !(line_buffer = IM_ARRAY( im, IM_IMAGE_SIZEOF_LINE( im ), PEL )) ||
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!(band_buffer = IM_ARRAY( im, es * im->Xsize, PEL )) ||
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im_outcheck( im ) ||
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im_setupout( im ) )
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return( -1 );
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for( y = 0; y < im->Ysize; y++ ) {
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long int fpixel[3];
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/* Start of scanline. We have to read top-to-bottom.
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*/
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fpixel[0] = 1;
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fpixel[1] = im->Ysize - y;
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fpixel[2] = 1;
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for( b = 0; b < im->Bands; b++ ) {
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fpixel[2] = b + 1;
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/* Read one band of one scanline, then scatter-write
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* into the line buffer.
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*/
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if( fits_read_pix( read->fptr,
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read->datatype, fpixel, im->Xsize,
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NULL, band_buffer, NULL, &status ) ) {
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read_error( status );
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return( -1 );
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}
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p = band_buffer;
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q = line_buffer + b * es;
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for( x = 0; x < im->Xsize; x++ ) {
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for( z = 0; z < es; z++ )
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q[z] = p[z];
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p += es;
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q += im->Bands * es;
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}
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}
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if( im_writeline( y, im, line_buffer ) )
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return( -1 );
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}
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return( 0 );
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}
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/**
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* im_fits2vips:
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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 FITS image file into a VIPS image.
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*
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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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int
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im_fits2vips( const char *filename, IMAGE *out )
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{
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Read *read;
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#ifdef DEBUG
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printf( "fits2vips: reading \"%s\"\n", filename );
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#endif /*DEBUG*/
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if( !(read = read_new( filename, out )) )
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return( -1 );
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if( fits2vips_get_header( read ) ||
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fits2vips_get_data( read ) ) {
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read_destroy( read );
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return( -1 );
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}
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read_destroy( read );
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return( 0 );
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}
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static int
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isfits( const char *filename )
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{
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fitsfile *fptr;
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int status;
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status = 0;
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if( fits_open_image( &fptr, filename, READONLY, &status ) ) {
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#ifdef DEBUG
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printf( "isfits: error reading \"%s\"\n", filename );
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read_error( status );
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#endif /*DEBUG*/
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return( 0 );
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}
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fits_close_file( fptr, &status );
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return( 1 );
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}
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static const char *fits_suffs[] = { ".fits", NULL };
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/* fits format adds no new members.
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*/
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typedef VipsFormat VipsFormatFits;
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typedef VipsFormatClass VipsFormatFitsClass;
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static void
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vips_format_fits_class_init( VipsFormatFitsClass *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 = "fits";
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object_class->description = _( "FITS" );
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format_class->is_a = isfits;
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format_class->header = fits2vips_header;
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format_class->load = im_fits2vips;
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format_class->save = NULL;
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format_class->suffs = fits_suffs;
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}
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static void
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vips_format_fits_init( VipsFormatFits *object )
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{
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}
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G_DEFINE_TYPE( VipsFormatFits, vips_format_fits, VIPS_TYPE_FORMAT );
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#endif /*HAVE_CFITSIO*/
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@ -428,6 +428,10 @@ im__format_init( void )
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extern GType vips_format_mat_get_type();
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vips_format_mat_get_type();
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#endif /*HAVE_MATIO*/
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#ifdef HAVE_CFITSIO
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extern GType vips_format_fits_get_type();
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vips_format_fits_get_type();
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#endif /*HAVE_CFITSIO*/
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vips_format_rad_get_type();
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#ifdef HAVE_MAGICK
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extern GType vips_format_magick_get_type();
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@ -1,16 +1,4 @@
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/* @(#) Function which calculates the number of transitions
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* @(#) between black and white for the horizontal or the vertical
|
||||
* @(#) direction of an image. black<128 , white>=128
|
||||
* @(#) The function calculates the number of transitions for all
|
||||
* @(#) Xsize or Ysize and returns the mean of the result
|
||||
* @(#) Input should be binary one channel
|
||||
* @(#)
|
||||
* @(#) int im_cntlines(im, nolines, flag)
|
||||
* @(#) IMAGE *im;
|
||||
* @(#) float *nolines;
|
||||
* @(#) int flag; 0 to cnt horizontal and 1 to count vertical lines
|
||||
* @(#)
|
||||
* @(#) Returns 0 on success and -1 on error
|
||||
/* count lines
|
||||
*
|
||||
* Copyright: 1990, N. Dessipris.
|
||||
*
|
||||
|
|
@ -20,6 +8,8 @@
|
|||
*
|
||||
* 19/9/95 JC
|
||||
* - tidied up
|
||||
* 23/10/10
|
||||
* - gtk-doc
|
||||
*/
|
||||
|
||||
/*
|
||||
|
|
@ -61,6 +51,23 @@
|
|||
#include <dmalloc.h>
|
||||
#endif /*WITH_DMALLOC*/
|
||||
|
||||
/**
|
||||
* im_cntlines:
|
||||
* @im: input #IMAGE
|
||||
* @nolines: output average number of lines
|
||||
* @flag: 0 horizontal, 1 vertical
|
||||
*
|
||||
* Function which calculates the number of transitions
|
||||
* between black and white for the horizontal or the vertical
|
||||
* direction of an image. black<128 , white>=128
|
||||
* The function calculates the number of transitions for all
|
||||
* Xsize or Ysize and returns the mean of the result
|
||||
* Input should be one band, 8-bit.
|
||||
*
|
||||
* See also: im_erode().
|
||||
*
|
||||
* Returns: 0 on success, -1 on error.
|
||||
*/
|
||||
int
|
||||
im_cntlines( IMAGE *im, double *nolines, int flag )
|
||||
{
|
||||
|
|
@ -68,16 +75,11 @@ im_cntlines( IMAGE *im, double *nolines, int flag )
|
|||
PEL *line;
|
||||
int cnt;
|
||||
|
||||
/* Is im valid?
|
||||
*/
|
||||
if( im_incheck( im ) )
|
||||
if( im_incheck( im ) ||
|
||||
im_check_uncoded( "im_cntlines", im ) ||
|
||||
im_check_mono( "im_cntlines", im ) ||
|
||||
im_check_format( "im_cntlines", im, IM_BANDFMT_UCHAR ) )
|
||||
return( -1 );
|
||||
if( im->Coding != IM_CODING_NONE || im->BandFmt != IM_BANDFMT_UCHAR ||
|
||||
im->Bands != 1 ) {
|
||||
im_error( "im_cntlines", "%s",
|
||||
_( "1-band uchar uncoded only" ) );
|
||||
return( -1 );
|
||||
}
|
||||
if( flag != 0 && flag != 1 ) {
|
||||
im_error( "im_cntlines", "%s",
|
||||
_( "flag should be 0 (horizontal) or 1 (vertical)" ) );
|
||||
|
|
@ -92,9 +94,9 @@ im_cntlines( IMAGE *im, double *nolines, int flag )
|
|||
PEL *p = line;
|
||||
|
||||
for( x = 0; x < im->Xsize - 1; x++ ) {
|
||||
if( p[0] < (PEL)128 && p[1] >= (PEL)128 )
|
||||
if( p[0] < 128 && p[1] >= 128 )
|
||||
cnt++;
|
||||
else if( p[0] >= (PEL)128 && p[1] < (PEL)128 )
|
||||
else if( p[0] >= 128 && p[1] < 128 )
|
||||
cnt++;
|
||||
|
||||
p++;
|
||||
|
|
@ -113,9 +115,9 @@ im_cntlines( IMAGE *im, double *nolines, int flag )
|
|||
PEL *p2 = line + im->Xsize;
|
||||
|
||||
for( x = 0; x < im->Xsize; x++ ) {
|
||||
if( *p1 < (PEL)128 && *p2 >= (PEL)128 )
|
||||
if( *p1 < 128 && *p2 >= 128 )
|
||||
cnt++;
|
||||
else if( *p1 >= (PEL)128 && *p2 < (PEL)128 )
|
||||
else if( *p1 >= 128 && *p2 < 128 )
|
||||
cnt++;
|
||||
|
||||
p1++;
|
||||
|
|
@ -125,7 +127,7 @@ im_cntlines( IMAGE *im, double *nolines, int flag )
|
|||
line += im->Xsize;
|
||||
}
|
||||
|
||||
*nolines = (float)cnt / (2.0 * im->Xsize);
|
||||
*nolines = (float) cnt / (2.0 * im->Xsize);
|
||||
}
|
||||
|
||||
return( 0 );
|
||||
|
|
|
|||
|
|
@ -308,7 +308,27 @@ im_dilate_raw( IMAGE *in, IMAGE *out, INTMASK *m )
|
|||
return( 0 );
|
||||
}
|
||||
|
||||
/* The above, with a border to make out the same size as in.
|
||||
|
||||
/**
|
||||
* im_dilate:
|
||||
* @in: input image
|
||||
* @out: output image
|
||||
* @m: dilate mask
|
||||
*
|
||||
* Dilate an image with a mask.
|
||||
* The mask coefficients are either 255 (object) or 0 (black) or 128 (don't
|
||||
* care).
|
||||
* Input image are binary images with either 0 or 255 values, one channel
|
||||
* only. The program dilates a white object on a black background.
|
||||
* The center of the mask is at location (m->xsize/2, m->ysize/2)
|
||||
* integer division. The mask is expected to have an odd width and
|
||||
* height.
|
||||
|
||||
sets pixels in the output if
|
||||
*
|
||||
* See also: im_erode().
|
||||
*
|
||||
* Returns: 0 on success, -1 on error
|
||||
*/
|
||||
int
|
||||
im_dilate( IMAGE *in, IMAGE *out, INTMASK *m )
|
||||
|
|
|
|||
Loading…
Reference in New Issue