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add fits read

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This commit is contained in:
John Cupitt 2010-10-26 15:12:49 +00:00
parent 288d8583ac
commit 57a8d8f12e
8 changed files with 477 additions and 30 deletions
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2
ChangeLog
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@ -37,6 +37,8 @@
- fix gtk-doc warnings
- small mask load/save improvements
- mask gtk-doc done
- add cfitsio dependancy
- add FITS reader
12/5/10 started 7.22.2
- the conditional image of ifthenelse can be any format, a (!=0) is added if

7
TODO
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@ -1,3 +1,10 @@
- test fits reader more ... colour?
- we get lots of valgrind errors with fits reading
- why do we read_free so often during fits read?
- are we triggering im_fits2vips() in each thread?? argh, try tracing
- maybe im_draw_smudge() is too slow :-( also, we had a sanity failure with

19
configure.in
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@ -424,6 +424,20 @@ if test x"$with_matio" != "xno"; then
])
fi
# cfitsio
AC_ARG_WITH([cfitsio],
AS_HELP_STRING([--without-cfitsio], [build without cfitsio (default: test)]))
if test x"$with_cfitsio" != "xno"; then
PKG_CHECK_MODULES(CFITSIO, cfitsio,
[AC_DEFINE(HAVE_CFITSIO,1,[define if you have cfitsio installed.])
with_cfitsio=yes
PACKAGES_USED="$PACKAGES_USED cfitsio"],
[AC_MSG_WARN([cfitsio not found; disabling cfitsio support])
with_cfitsio=no
])
fi
# pangoft2
AC_ARG_WITH([pangoft2],
AS_HELP_STRING([--without-pangoft2],
@ -556,14 +570,14 @@ fi
# Gather all up for VIPS_CFLAGS, VIPS_INCLUDES, VIPS_LIBS and VIPS_CXX_LIBS
# sort includes to get longer, more specific dirs first
# helps, for example, selecting graphicsmagick over imagemagick
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
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
do
echo $i
done | sort -ru`
VIPS_CFLAGS=`echo $VIPS_CFLAGS`
VIPS_CFLAGS="$VIPS_DEBUG_FLAGS $VIPS_CFLAGS"
VIPS_INCLUDES="$PNG_INCLUDES $TIFF_INCLUDES $ZIP_INCLUDES $JPEG_INCLUDES $FFTW_INCLUDES $LCMS_INCLUDES"
VIPS_LIBS="$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 $EXIF_LIBS -lm"
VIPS_LIBS="$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"
# need -lstdc++ for (eg.) the C++ format loaders
VIPS_CXX_LIBS="-lstdc++"
@ -649,6 +663,7 @@ file import with libMagick: $with_magick
ICC profile support with lcms: $with_lcms (version $with_lcms_ver)
file import with OpenEXR: $with_OpenEXR
file import with matio: $with_matio
file import with cfitsio: $with_cfitsio
text rendering with pangoft2: $with_pangoft2
file import/export with libpng: $with_png
file import/export with libtiff: $with_tiff

1
libvips/format/Makefile.am
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@ -21,6 +21,7 @@ libformat_la_SOURCES = \
im_vips2tiff.c \
im_vips2raw.c \
matlab.c \
fits.c \
radiance.c
INCLUDES = -I${top_srcdir}/libvips/include @VIPS_CFLAGS@ @VIPS_INCLUDES@

396
libvips/format/fits.c Normal file
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@ -0,0 +1,396 @@
/* Read FITS files with cfitsio
*
* 26/10/10
* - from matlab.c
*/
/*
This file is part of VIPS.
VIPS is free software; you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
/*
These files are distributed with VIPS - http://www.vips.ecs.soton.ac.uk
*/
/*
#define DEBUG
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif /*HAVE_CONFIG_H*/
#include <vips/intl.h>
#ifdef HAVE_CFITSIO
#include <stdio.h>
#include <assert.h>
#include <stdlib.h>
#include <string.h>
#include <vips/vips.h>
#include <vips/internal.h>
#include <fitsio.h>
#ifdef WITH_DMALLOC
#include <dmalloc.h>
#endif /*WITH_DMALLOC*/
/* What we track during a cfitsio-file read.
*/
typedef struct {
char *filename;
IMAGE *out;
fitsfile *fptr;
int datatype;
} Read;
static void
read_error( int status )
{
char buf[80];
fits_get_errstatus( status, buf );
im_error( "fits", "%s", buf );
}
static void
read_destroy( Read *read )
{
IM_FREE( read->filename );
if( read->fptr ) {
int status;
if( fits_close_file( read->fptr, &status ) )
read_error( status );
read->fptr = NULL;
}
im_free( read );
}
static Read *
read_new( const char *filename, IMAGE *out )
{
Read *read;
int status;
if( !(read = IM_NEW( NULL, Read )) )
return( NULL );
read->filename = im_strdup( NULL, filename );
read->out = out;
read->fptr = NULL;
status = 0;
if( fits_open_file( &read->fptr, filename, READONLY, &status ) ) {
im_error( "fits", _( "unable to open \"%s\"" ), filename );
read_error( status );
read_destroy( read );
return( NULL );
}
return( read );
}
/* fits image types -> VIPS band formats. VIPS doesn't have 64-bit int, so no
* entry for LONGLONG_IMG (64).
*/
static int fits2vips_formats[][3] = {
{ BYTE_IMG, IM_BANDFMT_UCHAR, TBYTE },
{ SHORT_IMG, IM_BANDFMT_USHORT, TUSHORT },
{ LONG_IMG, IM_BANDFMT_UINT, TUINT },
{ FLOAT_IMG, IM_BANDFMT_FLOAT, TFLOAT },
{ DOUBLE_IMG, IM_BANDFMT_DOUBLE, TDOUBLE }
};
static int
fits2vips_get_header( Read *read )
{
int status;
int bitpix;
int naxis;
long long int naxes[3];
int width, height, bands, format, type;
int keysexist;
int morekeys;
int i;
status = 0;
if( fits_get_img_paramll( read->fptr,
3, &bitpix, &naxis, naxes, &status ) ) {
read_error( status );
return( -1 );
}
width = 1;
height = 1;
bands = 1;
switch( naxis ) {
case 3:
bands = naxes[2];
case 2:
height = naxes[1];
case 1:
width = naxes[0];
break;
default:
im_error( "fits", "bad number of axis %d", naxis );
return( -1 );
}
if( bands == 1 )
type = IM_TYPE_B_W;
else if( bands == 3 )
type = IM_TYPE_RGB;
else
type = IM_TYPE_MULTIBAND;
/* Get image format. We want the 'raw' format of the image, our caller
* can convert using the meta info if they want.
*/
for( i = 0; i < IM_NUMBER( fits2vips_formats ); i++ )
if( fits2vips_formats[i][0] == bitpix )
break;
if( i == IM_NUMBER( fits2vips_formats ) ) {
im_error( "im_fits2vips", _( "unsupported bitpix %d\n" ),
bitpix );
return( -1 );
}
format = fits2vips_formats[i][1];
read->datatype = fits2vips_formats[i][2];
im_initdesc( read->out,
width, height, bands,
im_bits_of_fmt( format ), format,
IM_CODING_NONE, type, 1.0, 1.0, 0, 0 );
/* Read all keys into meta.
*/
if( fits_get_hdrspace( read->fptr, &keysexist, &morekeys, &status ) ) {
read_error( status );
return( -1 );
}
for( i = 0; i < keysexist; i++ ) {
char key[81];
char value[81];
char comment[81];
char vipsname[100];
if( fits_read_keyn( read->fptr, i + 1,
key, value, comment, &status ) ) {
read_error( status );
return( -1 );
}
#ifdef DEBUG
printf( "fits: seen:\n" );
printf( " key == %s\n", key );
printf( " value == %s\n", value );
printf( " comment == %s\n", comment );
#endif /*DEBUG*/
im_snprintf( vipsname, 100, "fits-%s", key );
if( im_meta_set_string( read->out, vipsname, value ) )
return( -1 );
im_snprintf( vipsname, 100, "fits-%s-comment", key );
if( im_meta_set_string( read->out, vipsname, comment ) )
return( -1 );
}
return( 0 );
}
static int
fits2vips_header( const char *filename, IMAGE *out )
{
Read *read;
#ifdef DEBUG
printf( "fits2vips_header: reading \"%s\"\n", filename );
#endif /*DEBUG*/
if( !(read = read_new( filename, out )) )
return( -1 );
if( fits2vips_get_header( read ) ) {
read_destroy( read );
return( -1 );
}
read_destroy( read );
return( 0 );
}
static int
fits2vips_get_data( Read *read )
{
IMAGE *im = read->out;
const int es = IM_IMAGE_SIZEOF_ELEMENT( im );
PEL *line_buffer;
PEL *band_buffer;
PEL *p, *q;
int x, y, b, z;
int status;
status = 0;
if( !(line_buffer = IM_ARRAY( im, IM_IMAGE_SIZEOF_LINE( im ), PEL )) ||
!(band_buffer = IM_ARRAY( im, es * im->Xsize, PEL )) ||
im_outcheck( im ) ||
im_setupout( im ) )
return( -1 );
for( y = 0; y < im->Ysize; y++ ) {
long int fpixel[3];
/* Start of scanline. We have to read top-to-bottom.
*/
fpixel[0] = 1;
fpixel[1] = im->Ysize - y;
fpixel[2] = 1;
for( b = 0; b < im->Bands; b++ ) {
fpixel[2] = b + 1;
/* Read one band of one scanline, then scatter-write
* into the line buffer.
*/
if( fits_read_pix( read->fptr,
read->datatype, fpixel, im->Xsize,
NULL, band_buffer, NULL, &status ) ) {
read_error( status );
return( -1 );
}
p = band_buffer;
q = line_buffer + b * es;
for( x = 0; x < im->Xsize; x++ ) {
for( z = 0; z < es; z++ )
q[z] = p[z];
p += es;
q += im->Bands * es;
}
}
if( im_writeline( y, im, line_buffer ) )
return( -1 );
}
return( 0 );
}
/**
* im_fits2vips:
* @filename: file to load
* @out: image to write to
*
* Read a FITS image file into a VIPS image.
*
*
* See also: #VipsFormat.
*
* Returns: 0 on success, -1 on error.
*/
int
im_fits2vips( const char *filename, IMAGE *out )
{
Read *read;
#ifdef DEBUG
printf( "fits2vips: reading \"%s\"\n", filename );
#endif /*DEBUG*/
if( !(read = read_new( filename, out )) )
return( -1 );
if( fits2vips_get_header( read ) ||
fits2vips_get_data( read ) ) {
read_destroy( read );
return( -1 );
}
read_destroy( read );
return( 0 );
}
static int
isfits( const char *filename )
{
fitsfile *fptr;
int status;
status = 0;
if( fits_open_image( &fptr, filename, READONLY, &status ) ) {
#ifdef DEBUG
printf( "isfits: error reading \"%s\"\n", filename );
read_error( status );
#endif /*DEBUG*/
return( 0 );
}
fits_close_file( fptr, &status );
return( 1 );
}
static const char *fits_suffs[] = { ".fits", NULL };
/* fits format adds no new members.
*/
typedef VipsFormat VipsFormatFits;
typedef VipsFormatClass VipsFormatFitsClass;
static void
vips_format_fits_class_init( VipsFormatFitsClass *class )
{
VipsObjectClass *object_class = (VipsObjectClass *) class;
VipsFormatClass *format_class = (VipsFormatClass *) class;
object_class->nickname = "fits";
object_class->description = _( "FITS" );
format_class->is_a = isfits;
format_class->header = fits2vips_header;
format_class->load = im_fits2vips;
format_class->save = NULL;
format_class->suffs = fits_suffs;
}
static void
vips_format_fits_init( VipsFormatFits *object )
{
}
G_DEFINE_TYPE( VipsFormatFits, vips_format_fits, VIPS_TYPE_FORMAT );
#endif /*HAVE_CFITSIO*/

4
libvips/format/format.c
View File

@ -428,6 +428,10 @@ im__format_init( void )
extern GType vips_format_mat_get_type();
vips_format_mat_get_type();
#endif /*HAVE_MATIO*/
#ifdef HAVE_CFITSIO
extern GType vips_format_fits_get_type();
vips_format_fits_get_type();
#endif /*HAVE_CFITSIO*/
vips_format_rad_get_type();
#ifdef HAVE_MAGICK
extern GType vips_format_magick_get_type();

56
libvips/morphology/im_cntlines.c
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@ -1,16 +1,4 @@
/* @(#) 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 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 );

22
libvips/morphology/im_dilate.c
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@ -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 )