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fits reader is lazy

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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 2011-01-31 15:24:41 +00:00
parent c19a6d90be
commit 663c3c15fd
3 changed files with 136 additions and 159 deletions
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1
ChangeLog
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@ -14,6 +14,7 @@
- removed ancient balance stuff from im_lr/tbmosaic()
- gtk-doc for mosaicing
- add im_fits2vips() to the operation database
- im_fits2vips() is lazy and much faster
30/11/10 started 7.24.0
- bump for new stable

290
libvips/format/fits.c
View File

@ -9,6 +9,9 @@
* - allow up to 10 dimensions as long as they are empty
* 27/1/11
* - lazy read
* 31/1/11
* - read in planes and combine with im_bandjoin()
* - read whole tiles with fits_read_subset() when we can
*/
/*
@ -38,9 +41,8 @@
*/
/*
*/
#define DEBUG
#define VIPS_DEBUG
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
@ -68,23 +70,13 @@
TODO
- test colour read with valgrind
- ask Doug for a test colour image
found WFPC2u5780205r_c0fx.fits on the fits samples page,
though we don't read it correctly, argh
when we read a line of a tile out, y and z seem to be swapped
- read whole tiles, if the alignment is right
actually, this is hard, we'd need to flip y somehow
but it's tiny
- test performance
- remove the old scanline reader?
*/
/* vips only supports 3 dimensions, but we allow up to MAX_DIMENSIONS as long
@ -105,6 +97,11 @@ typedef struct {
long long int naxes[MAX_DIMENSIONS];
GMutex *lock; /* Lock fits_*() calls with this */
/* Set this to -1 to read all bands, or a +ve int to read a specific
* band.
*/
int band_select;
} Read;
static void
@ -136,7 +133,7 @@ read_destroy( Read *read )
}
static Read *
read_new( const char *filename, IMAGE *out )
read_new( const char *filename, IMAGE *out, int band_select )
{
Read *read;
int status;
@ -148,6 +145,7 @@ read_new( const char *filename, IMAGE *out )
read->out = out;
read->fptr = NULL;
read->lock = NULL;
read->band_select = band_select;
if( im_add_close_callback( out,
(im_callback_fn) read_destroy, read, NULL ) ) {
@ -197,11 +195,11 @@ fits2vips_get_header( Read *read, IMAGE *out )
return( -1 );
}
#ifdef DEBUG
#ifdef VIPS_DEBUG
VIPS_DEBUG_MSG( "naxis = %d\n", read->naxis );
for( i = 0; i < read->naxis; i++ )
VIPS_DEBUG_MSG( "%d) %lld\n", i, read->naxes[i] );
#endif /*DEBUG*/
#endif /*VIPS_DEBUG*/
width = 1;
height = 1;
@ -239,6 +237,11 @@ fits2vips_get_header( Read *read, IMAGE *out )
return( -1 );
}
/* Are we in one-band mode?
*/
if( read->band_select != -1 )
bands = 1;
/* Get image format. We want the 'raw' format of the image, our caller
* can convert using the meta info if they want.
*/
@ -315,182 +318,124 @@ fits2vips_header( const char *filename, IMAGE *out )
VIPS_DEBUG_MSG( "fits2vips_header: reading \"%s\"\n", filename );
if( !(read = read_new( filename, out )) ||
if( !(read = read_new( filename, out, -1 )) ||
fits2vips_get_header( read, out ) )
return( -1 );
return( 0 );
}
/* Read the whole image in scanlines.
kept for reference ... this works for colour fits images
*/
static int
fits2vips_get_data_scanlinewise( 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;
long fpixel[MAX_DIMENSIONS];
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++ ) {
/* Start of scanline. We have to read top-to-bottom.
*/
for( b = 0; b < MAX_DIMENSIONS; b++ )
fpixel[b] = 1;
fpixel[1] = im->Ysize - y;
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 );
}
/* Allocate a line buffer. Have one of these for each thread so we can unpack
* to vips in parallel.
*/
static void *
fits2vips_start( IMAGE *out, void *a, void *b )
{
Read *read = (Read *) a;
IMAGE *out = read->out;
const int es = IM_IMAGE_SIZEOF_ELEMENT( out );
PEL *band_buffer;
if( !(band_buffer = IM_ARRAY( out, es * out->Xsize, PEL )) )
return( NULL );
return( (void *) band_buffer );
}
static int
fits2vips_stop( void *seq, void *a, void *b )
{
im_free( seq );
return( 0 );
}
static int
fits2vips_generate( REGION *out, void *seq, void *a, void *b )
{
PEL *band_buffer = (PEL *) seq;
Read *read = (Read *) a;
Rect *r = &out->valid;
IMAGE *im = read->out;
PEL *q;
int y, z;
int z;
int status;
status = 0;
long fpixel[MAX_DIMENSIONS];
long lpixel[MAX_DIMENSIONS];
long inc[MAX_DIMENSIONS];
status = 0;
VIPS_DEBUG_MSG( "fits2vips_generate: "
"generating left = %d, top = %d, width = %d, height = %d\n",
r->left, r->top, r->width, r->height );
for( y = r->top; y < IM_RECT_BOTTOM( r ); y ++ ) {
/* Special case: the region we are writing to is exactly the width we
* need, ie. we can read a rectangular area into it.
*/
if( IM_REGION_LSKIP( out ) == IM_REGION_SIZEOF_LINE( out ) ) {
VIPS_DEBUG_MSG( "fits2vips_generate: block read\n" );
for( z = 0; z < MAX_DIMENSIONS; z++ )
fpixel[z] = 1;
fpixel[0] = r->left + 1;
fpixel[1] = im->Ysize - y;
fpixel[1] = r->top + 1;
fpixel[2] = read->band_select + 1;
for( z = 0; z < MAX_DIMENSIONS; z++ )
lpixel[z] = 1;
lpixel[0] = IM_RECT_RIGHT( r );
lpixel[1] = im->Ysize - y;
lpixel[1] = IM_RECT_BOTTOM( r );
lpixel[2] = read->band_select + 1;
for( z = 0; z < MAX_DIMENSIONS; z++ )
inc[z] = 1;
for( z = 0; z < im->Bands; z++ ) {
/* Read one band of one scanline, then scatter-write
* into the line buffer.
*/
fpixel[2] = z + 1;
lpixel[2] = z + 1;
q = (PEL *) IM_REGION_ADDR( out, r->left, r->top );
/* Break on ffgsv() for this call.
*/
g_mutex_lock( read->lock );
if( fits_read_subset( read->fptr, read->datatype,
fpixel, lpixel, inc,
NULL, q, NULL, &status ) ) {
read_error( status );
g_mutex_unlock( read->lock );
return( -1 );
}
g_mutex_unlock( read->lock );
}
else {
int y;
for( y = r->top; y < IM_RECT_BOTTOM( r ); y ++ ) {
for( z = 0; z < MAX_DIMENSIONS; z++ )
fpixel[z] = 1;
fpixel[0] = r->left + 1;
fpixel[1] = y + 1;
fpixel[2] = read->band_select + 1;
for( z = 0; z < MAX_DIMENSIONS; z++ )
lpixel[z] = 1;
lpixel[0] = IM_RECT_RIGHT( r );
lpixel[1] = y + 1;
lpixel[2] = read->band_select + 1;
for( z = 0; z < MAX_DIMENSIONS; z++ )
inc[z] = 1;
q = (PEL *) IM_REGION_ADDR( out, r->left, y );
/* Break on ffgsv() for this call.
*/
g_mutex_lock( read->lock );
if( fits_read_subset( read->fptr, read->datatype,
fpixel, lpixel, inc,
NULL, band_buffer, NULL, &status ) ) {
NULL, q, NULL, &status ) ) {
read_error( status );
g_mutex_unlock( read->lock );
return( -1 );
}
g_mutex_unlock( read->lock );
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;
}
}
q = (PEL *) IM_REGION_ADDR( out, r->left, y );
for( z = 0; z < im->Bands; z++ ) {
}
return( 0 );
}
static int
fits2vips( const char *filename, IMAGE *out, int band_select )
{
Read *read;
/* The -1 mode is just for reading the header.
*/
g_assert( band_select >= 0 );
if( !(read = read_new( filename, out, band_select )) ||
fits2vips_get_header( read, out ) ||
im_demand_hint( out, IM_SMALLTILE, NULL ) ||
im_generate( out, NULL, fits2vips_generate, NULL, read, NULL ) )
return( -1 );
return( 0 );
}
/**
* im_fits2vips:
* @filename: file to load
@ -505,23 +450,54 @@ fits2vips_generate( REGION *out, void *seq, void *a, void *b )
int
im_fits2vips( const char *filename, IMAGE *out )
{
const int tile_size = 128;
Read *read;
IMAGE *cache;
IMAGE *t;
int n_bands;
VIPS_DEBUG_MSG( "im_fits2vips: reading \"%s\"\n", filename );
if( !(cache = im_open_local( out, "cache", "p" )) ||
!(read = read_new( filename, out )) ||
fits2vips_get_header( read, cache ) ||
im_demand_hint( cache, IM_SMALLTILE, NULL ) ||
im_generate( cache,
fits2vips_start, fits2vips_generate, fits2vips_stop,
read, NULL ) ||
im_tile_cache( cache, out,
tile_size, tile_size,
2 * (1 + cache->Xsize / tile_size) ) )
/* 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.
*/
if( !(t = im_open_local( out, "im_fits2vips", "p" )) ||
fits2vips_header( filename, t ) )
return( -1 );
n_bands = t->Bands;
if( n_bands == 1 ) {
if( !(t = im_open_local( out, "im_fits2vips", "p" )) ||
fits2vips( filename, t, 0 ) )
return( -1 );
}
else {
IMAGE *acc;
int i;
acc = NULL;
for( i = 0; i < n_bands; i++ ) {
if( !(t = im_open_local( out, "im_fits2vips", "p" )) ||
fits2vips( filename, t, i ) )
return( -1 );
if( !acc )
acc = t;
else {
IMAGE *t2;
if( !(t2 = im_open_local( out, "x", "p" )) ||
im_bandjoin( acc, t, t2 ) )
return( -1 );
acc = t2;
}
}
t = acc;
}
/* fits has inverted y.
*/
if( im_flipver( t, out ) )
return( -1 );
return( 0 );
@ -539,9 +515,9 @@ isfits( const char *filename )
if( fits_open_image( &fptr, filename, READONLY, &status ) ) {
VIPS_DEBUG_MSG( "isfits: error reading \"%s\"\n", filename );
#ifdef DEBUG
#ifdef VIPS_DEBUG
read_error( status );
#endif /*DEBUG*/
#endif /*VIPS_DEBUG*/
return( 0 );
}

4
libvips/format/im_tiff2vips.c
View File

@ -1130,8 +1130,8 @@ tiff_fill_region( REGION *out, void *seq, void *a, void *b )
/* Sizeof a pel in the TIFF file. This won't work for formats which
* are <1 byte per pel, like onebit :-( Fortunately, it's only used
* to calculate addresses within a tile, and because we are wrapped in
* im_tile_cache(), we will never have to calculate positions within a
* tile.
* im_tile_cache(), we will never have to calculate positions not
* within a tile.
*/
int tps = tls / rtiff->twidth;