static bool check_for_empty_tile(struct _openslide_tiff_level *tiffl,
TIFF *tiff,
int64_t tile_col, int64_t tile_row,
bool *is_empty,
GError **err) {
// set directory
if (!_openslide_tiff_set_dir(tiff, tiffl->dir, err)) {
return false;
}
// get tile number
ttile_t tile_no = TIFFComputeTile(tiff,
tile_col * tiffl->tile_w,
tile_row * tiffl->tile_h,
0, 0);
//g_debug("check_for_empty_tile: tile %d", tile_no);
// get tile size
toff_t *sizes;
if (!TIFFGetField(tiff, TIFFTAG_TILEBYTECOUNTS, &sizes)) {
g_set_error(err, OPENSLIDE_ERROR, OPENSLIDE_ERROR_FAILED,
"Cannot get tile size");
return false;
}
tsize_t tile_size = sizes[tile_no];
// return result
*is_empty = tile_size == 0;
return true;
}
/*
* Read and decompress a tile of data. The
* tile is selected by the (x,y,z,s) coordinates.
*/
tmsize_t
TIFFReadTile(TIFF* tif, void* buf, uint32 x, uint32 y, uint32 z, uint16 s)
{
if (!TIFFCheckRead(tif, 1) || !TIFFCheckTile(tif, x, y, z, s))
return ((tmsize_t)(-1));
return (TIFFReadEncodedTile(tif,
TIFFComputeTile(tif, x, y, z, s), buf, (tmsize_t)(-1)));
}
/*
* Read and decompress a tile of data. The
* tile is selected by the (x,y,z,s) coordinates.
*/
tsize_t
TIFFReadTile(TIFF* tif,
tdata_t buf, uint32 x, uint32 y, uint32 z, tsample_t s)
{
if (!TIFFCheckRead(tif, 1) || !TIFFCheckTile(tif, x, y, z, s))
return (-1);
return (TIFFReadEncodedTile(tif,
TIFFComputeTile(tif, x, y, z, s), buf, (tsize_t) -1));
}
dimension_size_type
TileInfo::tileIndex(dimension_size_type x,
dimension_size_type y,
dimension_size_type s) const
{
Sentry sentry;
::TIFF *tiff = impl->getTIFF();
return TIFFComputeTile(tiff, x, y, 0, s);
}
/* Variant of TIFFReadTile() that does
* * if *buf == NULL, *buf = _TIFFmalloc(bufsizetoalloc) only after TIFFFillTile() has
* succeeded. This avoid excessive memory allocation in case of truncated
* file.
* * calls regular TIFFReadEncodedTile() if *buf != NULL
*/
tmsize_t
_TIFFReadTileAndAllocBuffer(TIFF* tif,
void **buf, tmsize_t bufsizetoalloc,
uint32 x, uint32 y, uint32 z, uint16 s)
{
if (!TIFFCheckRead(tif, 1) || !TIFFCheckTile(tif, x, y, z, s))
return ((tmsize_t)(-1));
return (_TIFFReadEncodedTileAndAllocBuffer(tif,
TIFFComputeTile(tif, x, y, z, s),
buf, bufsizetoalloc,
(tmsize_t)(-1)));
}
/*
* Write and compress a tile of data. The
* tile is selected by the (x,y,z,s) coordinates.
*/
tmsize_t
TIFFWriteTile(TIFF* tif, void* buf, uint32 x, uint32 y, uint32 z, uint16 s)
{
if (!TIFFCheckTile(tif, x, y, z, s))
return ((tmsize_t)(-1));
/*
* NB: A tile size of -1 is used instead of tif_tilesize knowing
* that TIFFWriteEncodedTile will clamp this to the tile size.
* This is done because the tile size may not be defined until
* after the output buffer is setup in TIFFWriteBufferSetup.
*/
return (TIFFWriteEncodedTile(tif,
TIFFComputeTile(tif, x, y, z, s), buf, (tmsize_t)(-1)));
}
static int
cvt_by_tile( TIFF *in, TIFF *out )
{
uint32* raster; /* retrieve RGBA image */
uint32 width, height; /* image width & height */
uint32 tile_width, tile_height;
uint32 row, col;
uint32 *wrk_line;
int ok = 1;
TIFFGetField(in, TIFFTAG_IMAGEWIDTH, &width);
TIFFGetField(in, TIFFTAG_IMAGELENGTH, &height);
if( !TIFFGetField(in, TIFFTAG_TILEWIDTH, &tile_width)
|| !TIFFGetField(in, TIFFTAG_TILELENGTH, &tile_height) ) {
TIFFError(TIFFFileName(in), "Source image not tiled");
return (0);
}
TIFFSetField(out, TIFFTAG_TILEWIDTH, tile_width );
TIFFSetField(out, TIFFTAG_TILELENGTH, tile_height );
/*
* Allocate tile buffer
*/
raster = (uint32*)_TIFFmalloc(tile_width * tile_height * sizeof (uint32));
if (raster == 0) {
TIFFError(TIFFFileName(in), "No space for raster buffer");
return (0);
}
/*
* Allocate a scanline buffer for swapping during the vertical
* mirroring pass.
*/
wrk_line = (uint32*)_TIFFmalloc(tile_width * sizeof (uint32));
if (!wrk_line) {
TIFFError(TIFFFileName(in), "No space for raster scanline buffer");
ok = 0;
}
/*
* Loop over the tiles.
*/
for( row = 0; ok && row < height; row += tile_height )
{
for( col = 0; ok && col < width; col += tile_width )
{
uint32 i_row;
/* Read the tile into an RGBA array */
if (!TIFFReadRGBATile(in, col, row, raster)) {
ok = 0;
break;
}
/*
* For some reason the TIFFReadRGBATile() function chooses the
* lower left corner as the origin. Vertically mirror scanlines.
*/
for( i_row = 0; i_row < tile_height / 2; i_row++ )
{
uint32 *top_line, *bottom_line;
top_line = raster + tile_width * i_row;
bottom_line = raster + tile_width * (tile_height-i_row-1);
_TIFFmemcpy(wrk_line, top_line, 4*tile_width);
_TIFFmemcpy(top_line, bottom_line, 4*tile_width);
_TIFFmemcpy(bottom_line, wrk_line, 4*tile_width);
}
/*
* Write out the result in a tile.
*/
if( TIFFWriteEncodedTile( out,
TIFFComputeTile( out, col, row, 0, 0),
raster,
4 * tile_width * tile_height ) == -1 )
{
ok = 0;
break;
}
}
}
_TIFFfree( raster );
_TIFFfree( wrk_line );
return ok;
}
static void TIFFWriteOvrRow( TIFFOvrCache * psCache )
{
int nRet, iTileX, iTileY = psCache->nBlockOffset;
unsigned char *pabyData;
uint32 nBaseDirOffset;
uint32 RowsInStrip;
/* -------------------------------------------------------------------- */
/* If the output cache is multi-byte per sample, and the file */
/* being written to is of a different byte order than the current */
/* platform, we will need to byte swap the data. */
/* -------------------------------------------------------------------- */
if( TIFFIsByteSwapped(psCache->hTIFF) )
{
if( psCache->nBitsPerPixel == 16 )
TIFFSwabArrayOfShort( (uint16 *) psCache->pabyRow1Blocks,
(psCache->nBytesPerBlock * psCache->nSamples) / 2 );
else if( psCache->nBitsPerPixel == 32 )
TIFFSwabArrayOfLong( (uint32 *) psCache->pabyRow1Blocks,
(psCache->nBytesPerBlock * psCache->nSamples) / 4 );
else if( psCache->nBitsPerPixel == 64 )
TIFFSwabArrayOfDouble( (double *) psCache->pabyRow1Blocks,
(psCache->nBytesPerBlock * psCache->nSamples) / 8 );
}
/* -------------------------------------------------------------------- */
/* Record original directory position, so we can restore it at */
/* end. */
/* -------------------------------------------------------------------- */
nBaseDirOffset = TIFFCurrentDirOffset( psCache->hTIFF );
nRet = TIFFSetSubDirectory( psCache->hTIFF, psCache->nDirOffset );
assert( nRet == 1 );
/* -------------------------------------------------------------------- */
/* Write blocks to TIFF file. */
/* -------------------------------------------------------------------- */
for( iTileX = 0; iTileX < psCache->nBlocksPerRow; iTileX++ )
{
int nTileID;
if (psCache->nPlanarConfig == PLANARCONFIG_SEPARATE)
{
int iSample;
for( iSample = 0; iSample < psCache->nSamples; iSample++ )
{
pabyData = TIFFGetOvrBlock( psCache, iTileX, iTileY, iSample );
if( psCache->bTiled )
{
nTileID = TIFFComputeTile( psCache->hTIFF,
iTileX * psCache->nBlockXSize,
iTileY * psCache->nBlockYSize,
0, (tsample_t) iSample );
TIFFWriteEncodedTile( psCache->hTIFF, nTileID,
pabyData,
TIFFTileSize(psCache->hTIFF) );
}
else
{
nTileID = TIFFComputeStrip( psCache->hTIFF,
iTileY * psCache->nBlockYSize,
(tsample_t) iSample );
RowsInStrip=psCache->nBlockYSize;
if ((iTileY+1)*psCache->nBlockYSize>psCache->nYSize)
RowsInStrip=psCache->nYSize-iTileY*psCache->nBlockYSize;
TIFFWriteEncodedStrip( psCache->hTIFF, nTileID,
pabyData,
TIFFVStripSize(psCache->hTIFF,RowsInStrip) );
}
}
}
else
{
pabyData = TIFFGetOvrBlock( psCache, iTileX, iTileY, 0 );
if( psCache->bTiled )
{
nTileID = TIFFComputeTile( psCache->hTIFF,
iTileX * psCache->nBlockXSize,
iTileY * psCache->nBlockYSize,
0, 0 );
TIFFWriteEncodedTile( psCache->hTIFF, nTileID,
pabyData,
TIFFTileSize(psCache->hTIFF) );
}
else
{
nTileID = TIFFComputeStrip( psCache->hTIFF,
iTileY * psCache->nBlockYSize,
0 );
RowsInStrip=psCache->nBlockYSize;
if ((iTileY+1)*psCache->nBlockYSize>psCache->nYSize)
RowsInStrip=psCache->nYSize-iTileY*psCache->nBlockYSize;
TIFFWriteEncodedStrip( psCache->hTIFF, nTileID,
pabyData,
TIFFVStripSize(psCache->hTIFF,RowsInStrip) );
}
}
}
/* TODO: add checks on error status return of TIFFWriteEncodedTile and TIFFWriteEncodedStrip */
/* -------------------------------------------------------------------- */
/* Rotate buffers. */
/* -------------------------------------------------------------------- */
pabyData = psCache->pabyRow1Blocks;
psCache->pabyRow1Blocks = psCache->pabyRow2Blocks;
psCache->pabyRow2Blocks = pabyData;
_TIFFmemset( pabyData, 0, psCache->nBytesPerRow );
psCache->nBlockOffset++;
/* -------------------------------------------------------------------- */
/* Restore access to original directory. */
/* -------------------------------------------------------------------- */
TIFFFlush( psCache->hTIFF );
/* TODO: add checks on error status return of TIFFFlush */
TIFFSetSubDirectory( psCache->hTIFF, nBaseDirOffset );
/* TODO: add checks on error status return of TIFFSetSubDirectory */
}
void TIFF_ProcessFullResBlock( TIFF *hTIFF, int nPlanarConfig,
int nOverviews, int * panOvList,
int nBitsPerPixel,
int nSamples, TIFFOvrCache ** papoRawBIs,
int nSXOff, int nSYOff,
unsigned char *pabySrcTile,
int nBlockXSize, int nBlockYSize,
int nSampleFormat, const char * pszResampling )
{
int iOverview, iSample;
for( iSample = 0; iSample < nSamples; iSample++ )
{
/*
* We have to read a tile/strip for each sample for
* PLANARCONFIG_SEPARATE. Otherwise, we just read all the samples
* at once when handling the first sample.
*/
if( nPlanarConfig == PLANARCONFIG_SEPARATE || iSample == 0 )
{
if( TIFFIsTiled(hTIFF) )
{
TIFFReadEncodedTile( hTIFF,
TIFFComputeTile(hTIFF, nSXOff, nSYOff,
0, iSample ),
pabySrcTile,
TIFFTileSize(hTIFF));
}
else
{
TIFFReadEncodedStrip( hTIFF,
TIFFComputeStrip(hTIFF, nSYOff, iSample),
pabySrcTile,
TIFFStripSize(hTIFF) );
}
}
/*
* Loop over destination overview layers
*/
for( iOverview = 0; iOverview < nOverviews; iOverview++ )
{
TIFFOvrCache *poRBI = papoRawBIs[iOverview];
unsigned char *pabyOTile;
int nTXOff, nTYOff, nOXOff, nOYOff, nOMult;
int nOBlockXSize = poRBI->nBlockXSize;
int nOBlockYSize = poRBI->nBlockYSize;
int nSkewBits, nSampleByteOffset;
/*
* Fetch the destination overview tile
*/
nOMult = panOvList[iOverview];
nOXOff = (nSXOff/nOMult) / nOBlockXSize;
nOYOff = (nSYOff/nOMult) / nOBlockYSize;
pabyOTile = TIFFGetOvrBlock( poRBI, nOXOff, nOYOff, iSample );
/*
* Establish the offset into this tile at which we should
* start placing data.
*/
nTXOff = (nSXOff - nOXOff*nOMult*nOBlockXSize) / nOMult;
nTYOff = (nSYOff - nOYOff*nOMult*nOBlockYSize) / nOMult;
/*
* Figure out the skew (extra space between ``our samples'') and
* the byte offset to the first sample.
*/
assert( (nBitsPerPixel % 8) == 0 );
if( nPlanarConfig == PLANARCONFIG_SEPARATE )
{
nSkewBits = 0;
nSampleByteOffset = 0;
}
else
{
nSkewBits = nBitsPerPixel * (nSamples-1);
nSampleByteOffset = (nBitsPerPixel/8) * iSample;
}
/*
* Perform the downsampling.
*/
#ifdef DBMALLOC
malloc_chain_check( 1 );
#endif
TIFF_DownSample( pabySrcTile + nSampleByteOffset,
nBlockXSize, nBlockYSize,
nSkewBits, nBitsPerPixel, pabyOTile,
poRBI->nBlockXSize, poRBI->nBlockYSize,
nTXOff, nTYOff,
nOMult, nSampleFormat, pszResampling );
#ifdef DBMALLOC
malloc_chain_check( 1 );
#endif
}
}
}
static int
cvt_by_tile( TIFF *in, TIFF *out )
{
uint32* raster; /* retrieve RGBA image */
uint32 width, height; /* image width & height */
uint32 tile_width, tile_height;
uint32 row, col;
uint32 *wrk_line;
tsize_t raster_size;
int ok = 1;
TIFFGetField(in, TIFFTAG_IMAGEWIDTH, &width);
TIFFGetField(in, TIFFTAG_IMAGELENGTH, &height);
if( !TIFFGetField(in, TIFFTAG_TILEWIDTH, &tile_width)
|| !TIFFGetField(in, TIFFTAG_TILELENGTH, &tile_height) ) {
TIFFError(TIFFFileName(in), "Source image not tiled");
return (0);
}
TIFFSetField(out, TIFFTAG_TILEWIDTH, tile_width );
TIFFSetField(out, TIFFTAG_TILELENGTH, tile_height );
/*
* Allocate tile buffer
*/
raster_size = multiply(multiply(tile_width, tile_height), sizeof (uint32));
if (!raster_size) {
TIFFError(TIFFFileName(in),
"Can't allocate buffer for raster of size %lux%lu",
(unsigned long) tile_width, (unsigned long) tile_height);
return (0);
}
raster = (uint32*)_TIFFmalloc(raster_size);
if (raster == 0) {
TIFFError(TIFFFileName(in), "No space for raster buffer");
return (0);
}
/*
* Allocate a scanline buffer for swapping during the vertical
* mirroring pass. (Request can't overflow given prior checks.)
*/
wrk_line = (uint32*)_TIFFmalloc(tile_width * sizeof (uint32));
if (!wrk_line) {
TIFFError(TIFFFileName(in), "No space for raster scanline buffer");
ok = 0;
}
/*
* Loop over the tiles.
*/
for( row = 0; ok && row < height; row += tile_height )
{
for( col = 0; ok && col < width; col += tile_width )
{
uint32 i_row;
/* Read the tile into an RGBA array */
if (!TIFFReadRGBATile(in, col, row, raster)) {
ok = 0;
break;
}
/*
* XXX: raster array has 4-byte unsigned integer type, that is why
* we should rearrange it here.
*/
#if HOST_BIGENDIAN
TIFFSwabArrayOfLong(raster, tile_width * tile_height);
#endif
/*
* For some reason the TIFFReadRGBATile() function chooses the
* lower left corner as the origin. Vertically mirror scanlines.
*/
for( i_row = 0; i_row < tile_height / 2; i_row++ )
{
uint32 *top_line, *bottom_line;
top_line = raster + tile_width * i_row;
bottom_line = raster + tile_width * (tile_height-i_row-1);
_TIFFmemcpy(wrk_line, top_line, 4*tile_width);
_TIFFmemcpy(top_line, bottom_line, 4*tile_width);
_TIFFmemcpy(bottom_line, wrk_line, 4*tile_width);
}
/*
* Write out the result in a tile.
*/
if( TIFFWriteEncodedTile( out,
TIFFComputeTile( out, col, row, 0, 0),
raster,
4 * tile_width * tile_height ) == -1 )
{
ok = 0;
break;
}
}
}
_TIFFfree( raster );
_TIFFfree( wrk_line );
return ok;
}
static void aperio_tiff_tilereader(openslide_t *osr,
TIFF *tiff,
uint32_t *dest,
int64_t x, int64_t y,
int32_t w, int32_t h) {
// which compression?
uint16_t compression_mode;
TIFFGetField(tiff, TIFFTAG_COMPRESSION, &compression_mode);
// not for us? fallback
if ((compression_mode != APERIO_COMPRESSION_JP2K_YCBCR) &&
(compression_mode != APERIO_COMPRESSION_JP2K_RGB)) {
_openslide_generic_tiff_tilereader(osr, tiff, dest, x, y, w, h);
return;
}
// else, JPEG 2000!
opj_cio_t *stream = NULL;
opj_dinfo_t *dinfo = NULL;
opj_image_t *image = NULL;
opj_image_comp_t *comps = NULL;
// note: don't use info_handler, it outputs lots of junk
opj_event_mgr_t event_callbacks = {
.error_handler = error_callback,
.warning_handler = warning_callback,
};
// get tile number
ttile_t tile_no = TIFFComputeTile(tiff, x, y, 0, 0);
// g_debug("aperio reading tile_no: %d", tile_no);
// get tile size
toff_t *sizes;
if (TIFFGetField(tiff, TIFFTAG_TILEBYTECOUNTS, &sizes) == 0) {
_openslide_set_error(osr, "Cannot get tile size");
return; // ok, haven't allocated anything yet
}
tsize_t tile_size = sizes[tile_no];
// a slide with zero-length tiles has been seen in the wild
if (!tile_size) {
// fill with transparent
memset(dest, 0, w * h * 4);
//g_debug("skipping tile %d", tile_no);
return; // ok, haven't allocated anything yet
}
// get raw tile
tdata_t buf = g_slice_alloc(tile_size);
tsize_t size = TIFFReadRawTile(tiff, tile_no, buf, tile_size);
if (size == -1) {
_openslide_set_error(osr, "Cannot get raw tile");
goto DONE;
}
// init decompressor
opj_dparameters_t parameters;
dinfo = opj_create_decompress(CODEC_J2K);
opj_set_default_decoder_parameters(¶meters);
opj_setup_decoder(dinfo, ¶meters);
stream = opj_cio_open((opj_common_ptr) dinfo, buf, size);
opj_set_event_mgr((opj_common_ptr) dinfo, &event_callbacks, osr);
// decode
image = opj_decode(dinfo, stream);
// check error
if (openslide_get_error(osr)) {
goto DONE;
}
comps = image->comps;
// sanity check
if (image->numcomps != 3) {
_openslide_set_error(osr, "image->numcomps != 3");
goto DONE;
}
// TODO more checks?
copy_aperio_tile(compression_mode, comps, dest,
w, h,
w / comps[0].w, h / comps[0].h,
w / comps[1].w, h / comps[1].h,
w / comps[2].w, h / comps[2].h);
DONE:
// erase
g_slice_free1(tile_size, buf);
if (image) opj_image_destroy(image);
if (stream) opj_cio_close(stream);
if (dinfo) opj_destroy_decompress(dinfo);
}
static
void TIFF_WriteOverview( TIFF *hTIFF, int nSamples, RawBlockedImage **papoRBI,
int bTiled, int nCompressFlag, int nPhotometric,
unsigned short *panRed,
unsigned short *panGreen,
unsigned short *panBlue,
int bUseSubIFDs )
{
int iSample;
RawBlockedImage *poRBI = papoRBI[0];
/* -------------------------------------------------------------------- */
/* Setup TIFF fields. */
/* -------------------------------------------------------------------- */
TIFFSetField( hTIFF, TIFFTAG_IMAGEWIDTH, poRBI->GetXSize() );
TIFFSetField( hTIFF, TIFFTAG_IMAGELENGTH, poRBI->GetYSize() );
TIFFSetField( hTIFF, TIFFTAG_PLANARCONFIG,
PLANARCONFIG_SEPARATE );
TIFFSetField( hTIFF, TIFFTAG_BITSPERSAMPLE, poRBI->GetBitsPerPixel() );
TIFFSetField( hTIFF, TIFFTAG_SAMPLESPERPIXEL, nSamples );
TIFFSetField( hTIFF, TIFFTAG_COMPRESSION, nCompressFlag );
TIFFSetField( hTIFF, TIFFTAG_PHOTOMETRIC, nPhotometric );
if( bTiled )
{
TIFFSetField( hTIFF, TIFFTAG_TILEWIDTH, poRBI->GetBlockXSize() );
TIFFSetField( hTIFF, TIFFTAG_TILELENGTH, poRBI->GetBlockYSize() );
}
else
TIFFSetField( hTIFF, TIFFTAG_ROWSPERSTRIP, poRBI->GetBlockYSize() );
TIFFSetField( hTIFF, TIFFTAG_SUBFILETYPE, FILETYPE_REDUCEDIMAGE );
/* -------------------------------------------------------------------- */
/* Write color table if one is present. */
/* -------------------------------------------------------------------- */
if( panRed != NULL )
{
TIFFSetField( hTIFF, TIFFTAG_COLORMAP, panRed, panGreen, panBlue );
}
/* -------------------------------------------------------------------- */
/* Write blocks to TIFF file. */
/* -------------------------------------------------------------------- */
for( iSample = 0; iSample < nSamples; iSample++ )
{
int iTileX, iTileY;
poRBI = papoRBI[iSample];
for( iTileY = 0;
iTileY*poRBI->GetBlockYSize() < poRBI->GetYSize();
iTileY++ )
{
for( iTileX = 0;
iTileX*poRBI->GetBlockXSize() < poRBI->GetXSize();
iTileX++ )
{
unsigned char *pabyData = poRBI->GetTile( iTileX, iTileY );
int nTileID;
if( bTiled )
{
nTileID =
TIFFComputeTile(hTIFF,
iTileX * poRBI->GetBlockXSize(),
iTileY * poRBI->GetBlockYSize(),
0, iSample );
TIFFWriteEncodedTile( hTIFF, nTileID,
pabyData, TIFFTileSize(hTIFF) );
}
else
{
nTileID =
TIFFComputeStrip(hTIFF, iTileY*poRBI->GetBlockYSize(),
iSample);
TIFFWriteEncodedStrip( hTIFF, nTileID,
pabyData, TIFFStripSize( hTIFF ) );
}
}
}
}
TIFFWriteDirectory( hTIFF );
}
