CZI: questions about openslide grids
bgilbert at cs.cmu.edu
Mon Dec 15 19:30:54 EST 2014
On 12/15/2014 11:08 AM, SOUEDET Nicolas 215310 wrote:
> In CZI format, it is possible to have different tile dimensions for a
> single pyramid level.
> That allows to manage scanned ROI accurately, but I do not know how to
> manage it using an existing openslide grid.
> Moreover, openslide is built around this prerequisite that tiles of a
> same pyramid level have the same dimensions.
The OpenSlide core doesn't require tiles to be a consistent size. The
tile_w and tile_h members of struct _openslide_level are only used to
provide performance hints to the application, and can be set to zero if
they do not apply.
As to grids: the simple grid will not work for you, but the tilemap grid
might. It doesn't require all the tiles to be the same size; you can
specify the tile sizes as arguments to
_openslide_grid_tilemap_add_tile(). What tilemap does require is that
each tile can be approximately placed on a grid, such that:
- there is no more than one tile per grid cell, and
- the actual pixel coordinates of a tile are "close to" the ideal pixel
coordinates of its grid cell.
Depending on how CZI lays out tiles, this may or may not be sufficient
- If smaller tiles are only used when the corresponding large tile has a
single region of interest, the small tile can simply be placed into the
grid cell where the large tile would go.
- If large tiles are broken into a consistent number of pieces (perhaps
2 or 4 to a side), which may not all be present, then the tilemap grid
should be configured with tile advances matching the size of a small
tile. When large tiles exist, they will span multiple grid cells, but
the tilemap grid can handle that.
- If it is impossible to overlay any regular grid on the tiles because
there is *no* consistent structure, the tilemap grid will not work. We
would need to add a new grid that looks up tiles by performing a range
search over the tile coordinates. I've previously suggested that that
could be implemented as a wrapper around the SQLite R*Tree module.
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