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
GitHub
parent
ef2646ef6a
commit
7f352b3c9e
@ -18,6 +18,8 @@ master
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- threadpools size dynamically with load
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- operations can hint threadpool size
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- support for N-colour ICC profiles
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- fits load and allows many more bands
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- fits write doesn't duplicate header fields
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- add @wrap to vips_text()
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- GIF load supports truncated frames [tlsa]
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@ -33,6 +33,9 @@
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* extended filename syntax
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* 15/4/17
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* - skip HDUs with zero dimensions, thanks benepo
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* 27/10/22
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* - band interleave ourselves on read
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* - don't duplicate metadata
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*/
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/*
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@ -119,14 +122,9 @@ typedef struct {
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GMutex *lock; /* Lock fits_*() calls with this */
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/* Set this to -1 to read all bands, or a +ve int to read a specific
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* band.
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/* One line of pels ready for scatter/gather.
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*/
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int band_select;
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/* We split bands up for write into this buffer.
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*/
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VipsPel *buffer;
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VipsPel *line;
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} VipsFits;
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const char *vips__fits_suffs[] = { ".fits", ".fit", ".fts", NULL };
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@ -159,7 +157,7 @@ vips_fits_close( VipsFits *fits )
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fits->fptr = NULL;
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}
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VIPS_FREE( fits->buffer );
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VIPS_FREE( fits->line );
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}
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static void
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@ -169,7 +167,7 @@ vips_fits_close_cb( VipsImage *image, VipsFits *fits )
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}
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static VipsFits *
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vips_fits_new_read( const char *filename, VipsImage *out, int band_select )
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vips_fits_new_read( const char *filename, VipsImage *out )
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{
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VipsFits *fits;
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int status;
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@ -181,8 +179,7 @@ vips_fits_new_read( const char *filename, VipsImage *out, int band_select )
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fits->image = out;
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fits->fptr = NULL;
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fits->lock = NULL;
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fits->band_select = band_select;
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fits->buffer = NULL;
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fits->line = NULL;
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g_signal_connect( out, "close",
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G_CALLBACK( vips_fits_close_cb ), fits );
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@ -299,11 +296,6 @@ vips_fits_get_header( VipsFits *fits, VipsImage *out )
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return( -1 );
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}
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/* Are we in one-band mode?
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*/
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if( fits->band_select != -1 )
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bands = 1;
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/* Get image format. This is the equivalent format, or the format
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* stored in the file.
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*/
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@ -337,7 +329,17 @@ vips_fits_get_header( VipsFits *fits, VipsImage *out )
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width, height, bands,
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format,
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VIPS_CODING_NONE, interpretation, 1.0, 1.0 );
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if( vips_image_pipelinev( out, VIPS_DEMAND_STYLE_SMALLTILE, NULL ) )
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/* We read in lines, so SMALLTILE ends up being too small.
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*/
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if( vips_image_pipelinev( out, VIPS_DEMAND_STYLE_FATSTRIP, NULL ) )
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return( -1 );
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/* We need to be able to hold one scanline of one band for
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* scatter/gather.
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*/
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if( !(fits->line = VIPS_ARRAY( NULL,
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VIPS_IMAGE_SIZEOF_ELEMENT( out ) * out->Xsize, VipsPel )) )
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return( -1 );
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/* Read all keys into meta.
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@ -378,10 +380,16 @@ vips__fits_read_header( const char *filename, VipsImage *out )
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VIPS_DEBUG_MSG( "fits2vips_header: reading \"%s\"\n", filename );
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if( !(fits = vips_fits_new_read( filename, out, -1 )) ||
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vips_fits_get_header( fits, out ) )
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if( !(fits = vips_fits_new_read( filename, out )) )
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return( -1 );
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if( vips_fits_get_header( fits, out ) ) {
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vips_fits_close( fits );
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return( -1 );
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}
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vips_fits_close( fits );
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return( 0 );
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}
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@ -409,113 +417,96 @@ vips_fits_read_subset( VipsFits *fits,
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return( 0 );
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}
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#define SCATTER( TYPE ) { \
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TYPE *tp = (TYPE *) p; \
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TYPE *tq = ((TYPE *) q) + band; \
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\
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for( int x = 0; x < width; x++ ) { \
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*tq = tp[x]; \
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tq += bands; \
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} \
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}
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static void
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vips_fits_scatter( VipsFits *fits, VipsPel *q, VipsPel *p, int width, int band )
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{
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int bands = fits->image->Bands;
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switch( fits->image->BandFmt ) {
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case VIPS_FORMAT_UCHAR:
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case VIPS_FORMAT_CHAR:
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SCATTER( guchar );
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break;
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case VIPS_FORMAT_SHORT:
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case VIPS_FORMAT_USHORT:
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SCATTER( gushort );
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break;
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case VIPS_FORMAT_INT:
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case VIPS_FORMAT_UINT:
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case VIPS_FORMAT_FLOAT:
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SCATTER( guint );
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break;
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case VIPS_FORMAT_DOUBLE:
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SCATTER( double );
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break;
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default:
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g_assert_not_reached();
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}
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}
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static int
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fits2vips_generate( VipsRegion *out,
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vips_fits_generate( VipsRegion *out,
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void *seq, void *a, void *b, gboolean *stop )
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{
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VipsFits *fits = (VipsFits *) a;
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VipsRect *r = &out->valid;
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VipsPel *q;
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int z;
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long fpixel[MAX_DIMENSIONS];
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long lpixel[MAX_DIMENSIONS];
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long inc[MAX_DIMENSIONS];
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VIPS_DEBUG_MSG( "fits2vips_generate: "
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"generating left = %d, top = %d, width = %d, height = %d\n",
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r->left, r->top, r->width, r->height );
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/* Special case: the region we are writing to is exactly the width we
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* need, ie. we can read a rectangular area into it.
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*/
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if( VIPS_REGION_LSKIP( out ) == VIPS_REGION_SIZEOF_LINE( out ) ) {
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VIPS_DEBUG_MSG( "fits2vips_generate: block read\n" );
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vips__worker_lock( fits->lock );
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for( z = 0; z < MAX_DIMENSIONS; z++ )
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fpixel[z] = 1;
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fpixel[0] = r->left + 1;
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fpixel[1] = r->top + 1;
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fpixel[2] = fits->band_select + 1;
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for( int w = 0; w < out->im->Bands; w++ ) {
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for( int y = r->top; y < VIPS_RECT_BOTTOM( r ); y++ ) {
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long fpixel[MAX_DIMENSIONS];
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long lpixel[MAX_DIMENSIONS];
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long inc[MAX_DIMENSIONS];
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for( z = 0; z < MAX_DIMENSIONS; z++ )
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lpixel[z] = 1;
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lpixel[0] = VIPS_RECT_RIGHT( r );
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lpixel[1] = VIPS_RECT_BOTTOM( r );
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lpixel[2] = fits->band_select + 1;
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for( z = 0; z < MAX_DIMENSIONS; z++ )
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inc[z] = 1;
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q = VIPS_REGION_ADDR( out, r->left, r->top );
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vips__worker_lock( fits->lock );
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if( vips_fits_read_subset( fits, fpixel, lpixel, inc, q ) ) {
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g_mutex_unlock( fits->lock );
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return( -1 );
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}
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g_mutex_unlock( fits->lock );
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}
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else {
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int y;
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for( y = r->top; y < VIPS_RECT_BOTTOM( r ); y ++ ) {
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for( z = 0; z < MAX_DIMENSIONS; z++ )
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for( int z = 0; z < MAX_DIMENSIONS; z++ )
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fpixel[z] = 1;
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fpixel[0] = r->left + 1;
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fpixel[1] = y + 1;
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fpixel[2] = fits->band_select + 1;
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fpixel[2] = w + 1;
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for( z = 0; z < MAX_DIMENSIONS; z++ )
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for( int z = 0; z < MAX_DIMENSIONS; z++ )
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lpixel[z] = 1;
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lpixel[0] = VIPS_RECT_RIGHT( r );
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lpixel[1] = y + 1;
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lpixel[2] = fits->band_select + 1;
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lpixel[2] = w + 1;
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for( z = 0; z < MAX_DIMENSIONS; z++ )
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for( int z = 0; z < MAX_DIMENSIONS; z++ )
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inc[z] = 1;
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q = VIPS_REGION_ADDR( out, r->left, y );
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vips__worker_lock( fits->lock );
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/* We're inside a lock, so it's OK to write to ->line.
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*/
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if( vips_fits_read_subset( fits,
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fpixel, lpixel, inc, q ) ) {
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fpixel, lpixel, inc, fits->line ) ) {
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g_mutex_unlock( fits->lock );
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return( -1 );
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}
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g_mutex_unlock( fits->lock );
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vips_fits_scatter( fits,
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VIPS_REGION_ADDR( out, r->left, y ), fits->line,
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r->width, w );
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}
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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( const char *filename, VipsImage *out, int band_select )
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{
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VipsFits *fits;
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/* The -1 mode is just for reading the header.
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*/
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g_assert( band_select >= 0 );
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if( !(fits = vips_fits_new_read( filename, out, band_select )) )
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return( -1 );
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if( vips_fits_get_header( fits, out ) ||
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vips_image_generate( out,
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NULL, fits2vips_generate, NULL, fits, NULL ) ) {
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vips_fits_close( fits );
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return( -1 );
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}
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/* Don't vips_fits_close(), we need it to stick around for the
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* generate.
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*/
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g_mutex_unlock( fits->lock );
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return( 0 );
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}
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@ -523,59 +514,15 @@ fits2vips( const char *filename, VipsImage *out, int band_select )
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int
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vips__fits_read( const char *filename, VipsImage *out )
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{
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VipsImage *t;
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int bands;
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VipsInterpretation interpretation;
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VipsFits *fits;
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VIPS_DEBUG_MSG( "fits2vips: reading \"%s\"\n", filename );
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/* fits is naturally a band-separated format. For single-band images
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* we can just read out. For many bands we read each band out
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* separately then join them.
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*/
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t = vips_image_new();
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if( vips__fits_read_header( filename, t ) ) {
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g_object_unref( t );
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if( !(fits = vips_fits_new_read( filename, out )) )
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return( -1 );
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if( vips_fits_get_header( fits, out ) ||
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vips_image_generate( out,
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NULL, vips_fits_generate, NULL, fits, NULL ) ) {
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vips_fits_close( fits );
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return( -1 );
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}
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bands = t->Bands;
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interpretation = t->Type;
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g_object_unref( t );
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if( bands == 1 ) {
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if( fits2vips( filename, out, 0 ) )
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return( -1 );
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}
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else {
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VipsImage **x;
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VipsImage **y;
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int i;
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t = vips_image_new();
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x = (VipsImage **) vips_object_local_array( VIPS_OBJECT( t ),
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bands );
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y = (VipsImage **) vips_object_local_array( VIPS_OBJECT( t ),
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3 );
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for( i = 0; i < bands; i++ ) {
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x[i] = vips_image_new();
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if( fits2vips( filename, x[i], i ) ) {
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g_object_unref( t );
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return( -1 );
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}
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}
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if( vips_bandjoin( x, &y[0], bands, NULL ) ||
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vips_copy( y[0], &y[1],
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"interpretation", interpretation,
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NULL ) ||
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vips_image_write( y[1], out ) ) {
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g_object_unref( t );
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return( -1 );
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}
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g_object_unref( t );
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}
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return( 0 );
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@ -619,8 +566,7 @@ vips_fits_new_write( VipsImage *in, const char *filename )
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fits->image = in;
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fits->fptr = NULL;
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fits->lock = NULL;
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fits->band_select = -1;
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fits->buffer = NULL;
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fits->line = NULL;
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g_signal_connect( in, "close",
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G_CALLBACK( vips_fits_close_cb ), fits );
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@ -629,7 +575,7 @@ vips_fits_new_write( VipsImage *in, const char *filename )
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/* We need to be able to hold one scanline of one band.
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*/
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if( !(fits->buffer = VIPS_ARRAY( NULL,
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if( !(fits->line = VIPS_ARRAY( NULL,
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VIPS_IMAGE_SIZEOF_ELEMENT( in ) * in->Xsize, VipsPel )) )
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return( NULL );
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@ -651,6 +597,20 @@ vips_fits_new_write( VipsImage *in, const char *filename )
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return( fits );
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}
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/* Header fields which cfitsio 4.1 writes for us start like this.
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*/
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const char *vips_fits_basic[] = {
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"SIMPLE ",
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"BITPIX ",
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"NAXIS ",
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"NAXIS1 ",
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"NAXIS2 ",
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"NAXIS3 ",
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"EXTEND ",
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"COMMENT FITS (Fl",
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"COMMENT and Astro",
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};
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static void *
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vips_fits_write_meta( VipsImage *image,
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const char *field, GValue *value, void *a )
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@ -672,6 +632,12 @@ vips_fits_write_meta( VipsImage *image,
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*/
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value_str = vips_value_get_ref_string( value, NULL );
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/* We don't want fields which cfitsio will have already written for us.
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*/
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for( int i = 0; i < VIPS_NUMBER( vips_fits_basic ); i++ )
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if( vips_isprefix( vips_fits_basic[i], value_str ) )
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return( NULL );
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VIPS_DEBUG_MSG( "vips_fits_write_meta: setting meta on fits image:\n" );
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VIPS_DEBUG_MSG( " value == \"%s\"\n", value_str );
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@ -758,7 +724,7 @@ vips_fits_write( VipsRegion *region, VipsRect *area, void *a )
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long fpixel[3];
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p1 = p + b * es;
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q = fits->buffer;
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q = fits->line;
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for( x = 0; x < area->width; x++ ) {
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for( k = 0; k < es; k++ )
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@ -776,7 +742,7 @@ vips_fits_write( VipsRegion *region, VipsRect *area, void *a )
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*/
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if( fits_write_pix( fits->fptr, fits->datatype,
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fpixel, area->width, fits->buffer,
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fpixel, area->width, fits->line,
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&status ) ) {
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vips_fits_error( status );
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return( -1 );
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