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linnarsson-lab / loom-viewer

Tool for sharing, browsing and visualizing single-cell data stored in the Loom file format
BSD 2-Clause "Simplified" License
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Let users know where precomputed heatmap tiles are stored #45

Closed JobLeonard closed 8 years ago

JobLeonard commented 8 years ago

When using loom tile <loomfile> the output is currently something like:

2016-08-23 11:05:01,536 - DEBUG - Computing tile at x=3 y=1 z=10
2016-08-23 11:05:01,536 - DEBUG - Computing tile at x=6 y=2 z=11
2016-08-23 11:05:01,536 - DEBUG - Computing tile at x=12 y=4 z=12
2016-08-23 11:05:01,536 - DEBUG - Computing tile at x=24 y=8 z=13
2016-08-23 11:05:01,537 - DEBUG - Computing tile at x=25 y=8 z=13
2016-08-23 11:05:01,537 - DEBUG - Computing tile at x=24 y=9 z=13
2016-08-23 11:05:01,537 - DEBUG - Computing tile at x=25 y=9 z=13
2016-08-23 11:05:01,539 - DEBUG - Computing tile at x=13 y=4 z=12
2016-08-23 11:05:01,540 - DEBUG - Computing tile at x=26 y=8 z=13
2016-08-23 11:05:01,540 - DEBUG - Computing tile at x=27 y=8 z=13
2016-08-23 11:05:01,540 - DEBUG - Computing tile at x=26 y=9 z=13
2016-08-23 11:05:01,540 - DEBUG - Computing tile at x=27 y=9 z=13
2016-08-23 11:05:01,542 - DEBUG - Computing tile at x=12 y=5 z=12
2016-08-23 11:05:01,543 - DEBUG - Computing tile at x=24 y=10 z=13
2016-08-23 11:05:01,543 - DEBUG - Computing tile at x=25 y=10 z=13
2016-08-23 11:05:01,543 - DEBUG - Computing tile at x=24 y=11 z=13
2016-08-23 11:05:01,543 - DEBUG - Computing tile at x=25 y=11 z=13
2016-08-23 11:05:01,545 - DEBUG - Computing tile at x=13 y=5 z=12

It does not reveal where these tiles are stored. I think it would be good to tell the users where to find these tiles in case they want to clear the cached tiles (or even build in a clean flag), or if something goes wrong and they need to do manual cleanup.

Maybe something like appending the following after all tiles are generated:

<n> heatmap tiles precomputed for <loomfile> and stored at <tile storage>

This only applies to the precompute tiles command, since this will just be noisy if added after every tile fetched when running a server.

slinnarsson commented 8 years ago

They are stored inside the file. Removing them doesn't really do anything, because HDF5 is not great at reclaiming unused space. If you redo the tile command, the previous tiles are removed and replaced with new ones, but this tends to grow the file.

There is a tool to reclaim lost space from an HDF5 file (h5repack), but honestly it seems better then to just write a new file from scratch.

I will clarify this in the output of loom tile.