CZI: questions about openslide grids

[Mathieu Malaterre]

Nicolas,

Pay attention that `DimensionEntries` (§4.4.6 Directory Entry – Schema
DV [Directory Variable length]) may contains arbitrary positions. I've
looked at a couple of CZI samples posted previously on the list, and
there is a small jitter of 10/15% around the exact (perfect) position.

Just to clarify, I've uploaded the points extracted from a slide from
Niels Werner Mortensen here, you'll understand what I mean:

http://cs.stackexchange.com/questions/35314/computing-average-tile-size-grid

I am not sure there is a structure in openslide which map those points
(with jitter) back to a tile index (or vice versa).

Good luck anyway,

On Tue, Dec 16, 2014 at 9:20 AM, SOUEDET Nicolas 215310
<nicolas.souedet at cea.fr> wrote:
> Hi Benjamin,
>
> Many thanks for your reply, I did not know that it was possible to set tile_w and tile_h to 0.
> I hope this will be sufficient.
>
> Nicolas Souedet
>
> -----Message d'origine-----
> De : openslide-users-bounces+nicolas.souedet=cea.fr at lists.andrew.cmu.edu [mailto:openslide-users-bounces+nicolas.souedet=cea.fr at lists.andrew.cmu.edu] De la part de Benjamin Gilbert
> Envoyé : mardi 16 décembre 2014 01:31
> À : openslide-users at lists.andrew.cmu.edu
> Objet : Re: CZI: questions about openslide grids
>
> 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.
>
> Hi Nicolas,
>
> 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 for you.
>
> - 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.
>
> --Benjamin Gilbert
>
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-- 
Mathieu