fits reader is lazy
The fits reader is now lazy, and reads out whole tiles when it can. Previously it read a scanline at a time, and used WIO. We read in planes and combine with a set of im_bandjoin(). Use an im_flipver() at the end to get rows in the right order.
This commit is contained in:
John Cupitt
parent
c19a6d90be
commit
663c3c15fd
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@ -14,6 +14,7 @@
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- removed ancient balance stuff from im_lr/tbmosaic()
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- gtk-doc for mosaicing
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- add im_fits2vips() to the operation database
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- im_fits2vips() is lazy and much faster
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30/11/10 started 7.24.0
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- bump for new stable
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@ -9,6 +9,9 @@
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* - allow up to 10 dimensions as long as they are empty
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* 27/1/11
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* - lazy read
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* 31/1/11
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* - read in planes and combine with im_bandjoin()
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* - read whole tiles with fits_read_subset() when we can
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*/
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/*
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@ -38,9 +41,8 @@
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*/
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/*
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*/
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#define DEBUG
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#define VIPS_DEBUG
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*/
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#ifdef HAVE_CONFIG_H
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#include <config.h>
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@ -68,23 +70,13 @@
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TODO
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- test colour read with valgrind
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- ask Doug for a test colour image
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found WFPC2u5780205r_c0fx.fits on the fits samples page,
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though we don't read it correctly, argh
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when we read a line of a tile out, y and z seem to be swapped
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- read whole tiles, if the alignment is right
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actually, this is hard, we'd need to flip y somehow
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but it's tiny
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- test performance
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- remove the old scanline reader?
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*/
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/* vips only supports 3 dimensions, but we allow up to MAX_DIMENSIONS as long
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@ -105,6 +97,11 @@ typedef struct {
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long long int naxes[MAX_DIMENSIONS];
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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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*/
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int band_select;
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} Read;
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static void
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@ -136,7 +133,7 @@ read_destroy( Read *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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read_new( const char *filename, IMAGE *out, int band_select )
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{
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Read *read;
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int status;
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@ -148,6 +145,7 @@ read_new( const char *filename, IMAGE *out )
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read->out = out;
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read->fptr = NULL;
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read->lock = NULL;
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read->band_select = band_select;
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if( im_add_close_callback( out,
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(im_callback_fn) read_destroy, read, NULL ) ) {
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@ -197,11 +195,11 @@ fits2vips_get_header( Read *read, IMAGE *out )
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return( -1 );
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}
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#ifdef DEBUG
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#ifdef VIPS_DEBUG
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VIPS_DEBUG_MSG( "naxis = %d\n", read->naxis );
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for( i = 0; i < read->naxis; i++ )
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VIPS_DEBUG_MSG( "%d) %lld\n", i, read->naxes[i] );
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#endif /*DEBUG*/
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#endif /*VIPS_DEBUG*/
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width = 1;
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height = 1;
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@ -239,6 +237,11 @@ fits2vips_get_header( Read *read, IMAGE *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( read->band_select != -1 )
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bands = 1;
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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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@ -315,182 +318,124 @@ fits2vips_header( const char *filename, IMAGE *out )
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VIPS_DEBUG_MSG( "fits2vips_header: reading \"%s\"\n", filename );
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if( !(read = read_new( filename, out )) ||
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if( !(read = read_new( filename, out, -1 )) ||
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fits2vips_get_header( read, out ) )
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return( -1 );
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return( 0 );
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}
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/* Read the whole image in scanlines.
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kept for reference ... this works for colour fits images
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*/
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static int
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fits2vips_get_data_scanlinewise( 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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long fpixel[MAX_DIMENSIONS];
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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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/* Start of scanline. We have to read top-to-bottom.
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*/
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for( b = 0; b < MAX_DIMENSIONS; b++ )
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fpixel[b] = 1;
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fpixel[1] = im->Ysize - y;
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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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/* Allocate a line buffer. Have one of these for each thread so we can unpack
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* to vips in parallel.
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*/
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static void *
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fits2vips_start( IMAGE *out, void *a, void *b )
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{
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Read *read = (Read *) a;
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IMAGE *out = read->out;
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const int es = IM_IMAGE_SIZEOF_ELEMENT( out );
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PEL *band_buffer;
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if( !(band_buffer = IM_ARRAY( out, es * out->Xsize, PEL )) )
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return( NULL );
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return( (void *) band_buffer );
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}
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static int
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fits2vips_stop( void *seq, void *a, void *b )
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{
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im_free( seq );
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return( 0 );
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}
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static int
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fits2vips_generate( REGION *out, void *seq, void *a, void *b )
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{
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PEL *band_buffer = (PEL *) seq;
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Read *read = (Read *) a;
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Rect *r = &out->valid;
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IMAGE *im = read->out;
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PEL *q;
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int y, z;
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int z;
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int status;
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status = 0;
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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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status = 0;
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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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for( y = r->top; y < IM_RECT_BOTTOM( r ); y ++ ) {
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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( IM_REGION_LSKIP( out ) == IM_REGION_SIZEOF_LINE( out ) ) {
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VIPS_DEBUG_MSG( "fits2vips_generate: block read\n" );
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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] = im->Ysize - y;
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fpixel[1] = r->top + 1;
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fpixel[2] = read->band_select + 1;
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for( z = 0; z < MAX_DIMENSIONS; z++ )
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lpixel[z] = 1;
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lpixel[0] = IM_RECT_RIGHT( r );
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lpixel[1] = im->Ysize - y;
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lpixel[1] = IM_RECT_BOTTOM( r );
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lpixel[2] = read->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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for( z = 0; z < im->Bands; z++ ) {
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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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fpixel[2] = z + 1;
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lpixel[2] = z + 1;
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q = (PEL *) IM_REGION_ADDR( out, r->left, r->top );
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/* Break on ffgsv() for this call.
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*/
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g_mutex_lock( read->lock );
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if( fits_read_subset( read->fptr, read->datatype,
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fpixel, lpixel, inc,
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NULL, q, NULL, &status ) ) {
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read_error( status );
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g_mutex_unlock( read->lock );
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return( -1 );
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}
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g_mutex_unlock( read->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 < IM_RECT_BOTTOM( r ); y ++ ) {
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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] = y + 1;
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fpixel[2] = read->band_select + 1;
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for( z = 0; z < MAX_DIMENSIONS; z++ )
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lpixel[z] = 1;
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lpixel[0] = IM_RECT_RIGHT( r );
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lpixel[1] = y + 1;
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lpixel[2] = read->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 = (PEL *) IM_REGION_ADDR( out, r->left, y );
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/* Break on ffgsv() for this call.
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*/
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g_mutex_lock( read->lock );
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if( fits_read_subset( read->fptr, read->datatype,
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fpixel, lpixel, inc,
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NULL, band_buffer, NULL, &status ) ) {
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NULL, q, NULL, &status ) ) {
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read_error( status );
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g_mutex_unlock( read->lock );
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return( -1 );
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}
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g_mutex_unlock( read->lock );
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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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q = (PEL *) IM_REGION_ADDR( out, r->left, y );
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for( z = 0; z < im->Bands; z++ ) {
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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, IMAGE *out, int band_select )
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{
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Read *read;
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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( !(read = read_new( filename, out, band_select )) ||
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fits2vips_get_header( read, out ) ||
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im_demand_hint( out, IM_SMALLTILE, NULL ) ||
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im_generate( out, NULL, fits2vips_generate, NULL, read, 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_fits2vips:
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* @filename: file to load
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@ -505,23 +450,54 @@ fits2vips_generate( REGION *out, void *seq, void *a, void *b )
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int
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im_fits2vips( const char *filename, IMAGE *out )
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{
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const int tile_size = 128;
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Read *read;
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IMAGE *cache;
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IMAGE *t;
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int n_bands;
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VIPS_DEBUG_MSG( "im_fits2vips: reading \"%s\"\n", filename );
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if( !(cache = im_open_local( out, "cache", "p" )) ||
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!(read = read_new( filename, out )) ||
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fits2vips_get_header( read, cache ) ||
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im_demand_hint( cache, IM_SMALLTILE, NULL ) ||
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im_generate( cache,
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fits2vips_start, fits2vips_generate, fits2vips_stop,
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read, NULL ) ||
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im_tile_cache( cache, out,
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tile_size, tile_size,
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2 * (1 + cache->Xsize / tile_size) ) )
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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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if( !(t = im_open_local( out, "im_fits2vips", "p" )) ||
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fits2vips_header( filename, t ) )
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return( -1 );
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n_bands = t->Bands;
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if( n_bands == 1 ) {
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if( !(t = im_open_local( out, "im_fits2vips", "p" )) ||
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fits2vips( filename, t, 0 ) )
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return( -1 );
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}
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else {
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IMAGE *acc;
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int i;
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acc = NULL;
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for( i = 0; i < n_bands; i++ ) {
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if( !(t = im_open_local( out, "im_fits2vips", "p" )) ||
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fits2vips( filename, t, i ) )
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return( -1 );
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if( !acc )
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acc = t;
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else {
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IMAGE *t2;
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if( !(t2 = im_open_local( out, "x", "p" )) ||
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im_bandjoin( acc, t, t2 ) )
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return( -1 );
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acc = t2;
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}
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}
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t = acc;
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}
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/* fits has inverted y.
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*/
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if( im_flipver( t, out ) )
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return( -1 );
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return( 0 );
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@ -539,9 +515,9 @@ isfits( const char *filename )
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if( fits_open_image( &fptr, filename, READONLY, &status ) ) {
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VIPS_DEBUG_MSG( "isfits: error reading \"%s\"\n", filename );
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#ifdef DEBUG
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#ifdef VIPS_DEBUG
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read_error( status );
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#endif /*DEBUG*/
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#endif /*VIPS_DEBUG*/
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return( 0 );
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}
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@ -1130,8 +1130,8 @@ tiff_fill_region( REGION *out, void *seq, void *a, void *b )
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/* Sizeof a pel in the TIFF file. This won't work for formats which
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* are <1 byte per pel, like onebit :-( Fortunately, it's only used
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* to calculate addresses within a tile, and because we are wrapped in
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* im_tile_cache(), we will never have to calculate positions within a
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* tile.
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* im_tile_cache(), we will never have to calculate positions not
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* within a tile.
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*/
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int tps = tls / rtiff->twidth;
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