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revise fitsload (#3120) 

* compiles

* note changelog

and switch to FATSTRIP (much quicker)

* don't duplicate header fields in fitssave

be careful not to set records twice in save

see https://github.com/libvips/libvips/issues/3113

* tiny polish
This commit is contained in:
John Cupitt 2022-11-13 18:52:28 +00:00 committed by GitHub
parent ef2646ef6a
commit 7f352b3c9e
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2 changed files with 120 additions and 152 deletions
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2
ChangeLog
View File

@ -18,6 +18,8 @@ master
- threadpools size dynamically with load
- operations can hint threadpool size
- support for N-colour ICC profiles
- fits load and allows many more bands
- fits write doesn't duplicate header fields
- add @wrap to vips_text()
- GIF load supports truncated frames [tlsa]

270
libvips/foreign/fits.c
View File

@ -33,6 +33,9 @@
* extended filename syntax
* 15/4/17
* - skip HDUs with zero dimensions, thanks benepo
* 27/10/22
* - band interleave ourselves on read
* - don't duplicate metadata
*/
/*
@ -119,14 +122,9 @@ typedef struct {
GMutex *lock; /* Lock fits_*() calls with this */
/* Set this to -1 to read all bands, or a +ve int to read a specific
* band.
/* One line of pels ready for scatter/gather.
*/
int band_select;
/* We split bands up for write into this buffer.
*/
VipsPel *buffer;
VipsPel *line;
} VipsFits;
const char *vips__fits_suffs[] = { ".fits", ".fit", ".fts", NULL };
@ -159,7 +157,7 @@ vips_fits_close( VipsFits *fits )
fits->fptr = NULL;
}
VIPS_FREE( fits->buffer );
VIPS_FREE( fits->line );
}
static void
@ -169,7 +167,7 @@ vips_fits_close_cb( VipsImage *image, VipsFits *fits )
}
static VipsFits *
vips_fits_new_read( const char *filename, VipsImage *out, int band_select )
vips_fits_new_read( const char *filename, VipsImage *out )
{
VipsFits *fits;
int status;
@ -181,8 +179,7 @@ vips_fits_new_read( const char *filename, VipsImage *out, int band_select )
fits->image = out;
fits->fptr = NULL;
fits->lock = NULL;
fits->band_select = band_select;
fits->buffer = NULL;
fits->line = NULL;
g_signal_connect( out, "close",
G_CALLBACK( vips_fits_close_cb ), fits );
@ -299,11 +296,6 @@ vips_fits_get_header( VipsFits *fits, VipsImage *out )
return( -1 );
}
/* Are we in one-band mode?
*/
if( fits->band_select != -1 )
bands = 1;
/* Get image format. This is the equivalent format, or the format
* stored in the file.
*/
@ -337,7 +329,17 @@ vips_fits_get_header( VipsFits *fits, VipsImage *out )
width, height, bands,
format,
VIPS_CODING_NONE, interpretation, 1.0, 1.0 );
if( vips_image_pipelinev( out, VIPS_DEMAND_STYLE_SMALLTILE, NULL ) )
/* We read in lines, so SMALLTILE ends up being too small.
*/
if( vips_image_pipelinev( out, VIPS_DEMAND_STYLE_FATSTRIP, NULL ) )
return( -1 );
/* We need to be able to hold one scanline of one band for
* scatter/gather.
*/
if( !(fits->line = VIPS_ARRAY( NULL,
VIPS_IMAGE_SIZEOF_ELEMENT( out ) * out->Xsize, VipsPel )) )
return( -1 );
/* Read all keys into meta.
@ -378,10 +380,16 @@ vips__fits_read_header( const char *filename, VipsImage *out )
VIPS_DEBUG_MSG( "fits2vips_header: reading \"%s\"\n", filename );
if( !(fits = vips_fits_new_read( filename, out, -1 )) ||
vips_fits_get_header( fits, out ) )
if( !(fits = vips_fits_new_read( filename, out )) )
return( -1 );
if( vips_fits_get_header( fits, out ) ) {
vips_fits_close( fits );
return( -1 );
}
vips_fits_close( fits );
return( 0 );
}
@ -409,113 +417,96 @@ vips_fits_read_subset( VipsFits *fits,
return( 0 );
}
#define SCATTER( TYPE ) { \
TYPE *tp = (TYPE *) p; \
TYPE *tq = ((TYPE *) q) + band; \
\
for( int x = 0; x < width; x++ ) { \
*tq = tp[x]; \
tq += bands; \
} \
}
static void
vips_fits_scatter( VipsFits *fits, VipsPel *q, VipsPel *p, int width, int band )
{
int bands = fits->image->Bands;
switch( fits->image->BandFmt ) {
case VIPS_FORMAT_UCHAR:
case VIPS_FORMAT_CHAR:
SCATTER( guchar );
break;
case VIPS_FORMAT_SHORT:
case VIPS_FORMAT_USHORT:
SCATTER( gushort );
break;
case VIPS_FORMAT_INT:
case VIPS_FORMAT_UINT:
case VIPS_FORMAT_FLOAT:
SCATTER( guint );
break;
case VIPS_FORMAT_DOUBLE:
SCATTER( double );
break;
default:
g_assert_not_reached();
}
}
static int
fits2vips_generate( VipsRegion *out,
vips_fits_generate( VipsRegion *out,
void *seq, void *a, void *b, gboolean *stop )
{
VipsFits *fits = (VipsFits *) a;
VipsRect *r = &out->valid;
VipsPel *q;
int z;
long fpixel[MAX_DIMENSIONS];
long lpixel[MAX_DIMENSIONS];
long inc[MAX_DIMENSIONS];
VIPS_DEBUG_MSG( "fits2vips_generate: "
"generating left = %d, top = %d, width = %d, height = %d\n",
r->left, r->top, r->width, r->height );
/* Special case: the region we are writing to is exactly the width we
* need, ie. we can read a rectangular area into it.
*/
if( VIPS_REGION_LSKIP( out ) == VIPS_REGION_SIZEOF_LINE( out ) ) {
VIPS_DEBUG_MSG( "fits2vips_generate: block read\n" );
vips__worker_lock( fits->lock );
for( z = 0; z < MAX_DIMENSIONS; z++ )
fpixel[z] = 1;
fpixel[0] = r->left + 1;
fpixel[1] = r->top + 1;
fpixel[2] = fits->band_select + 1;
for( int w = 0; w < out->im->Bands; w++ ) {
for( int y = r->top; y < VIPS_RECT_BOTTOM( r ); y++ ) {
long fpixel[MAX_DIMENSIONS];
long lpixel[MAX_DIMENSIONS];
long inc[MAX_DIMENSIONS];
for( z = 0; z < MAX_DIMENSIONS; z++ )
lpixel[z] = 1;
lpixel[0] = VIPS_RECT_RIGHT( r );
lpixel[1] = VIPS_RECT_BOTTOM( r );
lpixel[2] = fits->band_select + 1;
for( z = 0; z < MAX_DIMENSIONS; z++ )
inc[z] = 1;
q = VIPS_REGION_ADDR( out, r->left, r->top );
vips__worker_lock( fits->lock );
if( vips_fits_read_subset( fits, fpixel, lpixel, inc, q ) ) {
g_mutex_unlock( fits->lock );
return( -1 );
}
g_mutex_unlock( fits->lock );
}
else {
int y;
for( y = r->top; y < VIPS_RECT_BOTTOM( r ); y ++ ) {
for( z = 0; z < MAX_DIMENSIONS; z++ )
for( int z = 0; z < MAX_DIMENSIONS; z++ )
fpixel[z] = 1;
fpixel[0] = r->left + 1;
fpixel[1] = y + 1;
fpixel[2] = fits->band_select + 1;
fpixel[2] = w + 1;
for( z = 0; z < MAX_DIMENSIONS; z++ )
for( int z = 0; z < MAX_DIMENSIONS; z++ )
lpixel[z] = 1;
lpixel[0] = VIPS_RECT_RIGHT( r );
lpixel[1] = y + 1;
lpixel[2] = fits->band_select + 1;
lpixel[2] = w + 1;
for( z = 0; z < MAX_DIMENSIONS; z++ )
for( int z = 0; z < MAX_DIMENSIONS; z++ )
inc[z] = 1;
q = VIPS_REGION_ADDR( out, r->left, y );
vips__worker_lock( fits->lock );
/* We're inside a lock, so it's OK to write to ->line.
*/
if( vips_fits_read_subset( fits,
fpixel, lpixel, inc, q ) ) {
fpixel, lpixel, inc, fits->line ) ) {
g_mutex_unlock( fits->lock );
return( -1 );
}
g_mutex_unlock( fits->lock );
vips_fits_scatter( fits,
VIPS_REGION_ADDR( out, r->left, y ), fits->line,
r->width, w );
}
}
return( 0 );
}
static int
fits2vips( const char *filename, VipsImage *out, int band_select )
{
VipsFits *fits;
/* The -1 mode is just for reading the header.
*/
g_assert( band_select >= 0 );
if( !(fits = vips_fits_new_read( filename, out, band_select )) )
return( -1 );
if( vips_fits_get_header( fits, out ) ||
vips_image_generate( out,
NULL, fits2vips_generate, NULL, fits, NULL ) ) {
vips_fits_close( fits );
return( -1 );
}
/* Don't vips_fits_close(), we need it to stick around for the
* generate.
*/
g_mutex_unlock( fits->lock );
return( 0 );
}
@ -523,59 +514,15 @@ fits2vips( const char *filename, VipsImage *out, int band_select )
int
vips__fits_read( const char *filename, VipsImage *out )
{
VipsImage *t;
int bands;
VipsInterpretation interpretation;
VipsFits *fits;
VIPS_DEBUG_MSG( "fits2vips: reading \"%s\"\n", filename );
/* fits is naturally a band-separated format. For single-band images
* we can just read out. For many bands we read each band out
* separately then join them.
*/
t = vips_image_new();
if( vips__fits_read_header( filename, t ) ) {
g_object_unref( t );
if( !(fits = vips_fits_new_read( filename, out )) )
return( -1 );
if( vips_fits_get_header( fits, out ) ||
vips_image_generate( out,
NULL, vips_fits_generate, NULL, fits, NULL ) ) {
vips_fits_close( fits );
return( -1 );
}
bands = t->Bands;
interpretation = t->Type;
g_object_unref( t );
if( bands == 1 ) {
if( fits2vips( filename, out, 0 ) )
return( -1 );
}
else {
VipsImage **x;
VipsImage **y;
int i;
t = vips_image_new();
x = (VipsImage **) vips_object_local_array( VIPS_OBJECT( t ),
bands );
y = (VipsImage **) vips_object_local_array( VIPS_OBJECT( t ),
3 );
for( i = 0; i < bands; i++ ) {
x[i] = vips_image_new();
if( fits2vips( filename, x[i], i ) ) {
g_object_unref( t );
return( -1 );
}
}
if( vips_bandjoin( x, &y[0], bands, NULL ) ||
vips_copy( y[0], &y[1],
"interpretation", interpretation,
NULL ) ||
vips_image_write( y[1], out ) ) {
g_object_unref( t );
return( -1 );
}
g_object_unref( t );
}
return( 0 );
@ -619,8 +566,7 @@ vips_fits_new_write( VipsImage *in, const char *filename )
fits->image = in;
fits->fptr = NULL;
fits->lock = NULL;
fits->band_select = -1;
fits->buffer = NULL;
fits->line = NULL;
g_signal_connect( in, "close",
G_CALLBACK( vips_fits_close_cb ), fits );
@ -629,7 +575,7 @@ vips_fits_new_write( VipsImage *in, const char *filename )
/* We need to be able to hold one scanline of one band.
*/
if( !(fits->buffer = VIPS_ARRAY( NULL,
if( !(fits->line = VIPS_ARRAY( NULL,
VIPS_IMAGE_SIZEOF_ELEMENT( in ) * in->Xsize, VipsPel )) )
return( NULL );
@ -651,6 +597,20 @@ vips_fits_new_write( VipsImage *in, const char *filename )
return( fits );
}
/* Header fields which cfitsio 4.1 writes for us start like this.
*/
const char *vips_fits_basic[] = {
"SIMPLE ",
"BITPIX ",
"NAXIS ",
"NAXIS1 ",
"NAXIS2 ",
"NAXIS3 ",
"EXTEND ",
"COMMENT FITS (Fl",
"COMMENT and Astro",
};
static void *
vips_fits_write_meta( VipsImage *image,
const char *field, GValue *value, void *a )
@ -672,6 +632,12 @@ vips_fits_write_meta( VipsImage *image,
*/
value_str = vips_value_get_ref_string( value, NULL );
/* We don't want fields which cfitsio will have already written for us.
*/
for( int i = 0; i < VIPS_NUMBER( vips_fits_basic ); i++ )
if( vips_isprefix( vips_fits_basic[i], value_str ) )
return( NULL );
VIPS_DEBUG_MSG( "vips_fits_write_meta: setting meta on fits image:\n" );
VIPS_DEBUG_MSG( " value == \"%s\"\n", value_str );
@ -758,7 +724,7 @@ vips_fits_write( VipsRegion *region, VipsRect *area, void *a )
long fpixel[3];
p1 = p + b * es;
q = fits->buffer;
q = fits->line;
for( x = 0; x < area->width; x++ ) {
for( k = 0; k < es; k++ )
@ -776,7 +742,7 @@ vips_fits_write( VipsRegion *region, VipsRect *area, void *a )
*/
if( fits_write_pix( fits->fptr, fits->datatype,
fpixel, area->width, fits->buffer,
fpixel, area->width, fits->line,
&status ) ) {
vips_fits_error( status );
return( -1 );