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KitwareMedical / otm-server

Apache License 2.0
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Compress images #94

Closed ebrahimebrahim closed 2 years ago

ebrahimebrahim commented 2 years ago

I just realized by using the nii rather than nii.gz extension in the filename we pass to ants.image_write, we are saving 3D volumes in an uncompressed format. We can make the preprocessed image visualizations load a lot faster if the images that need to be downloaded are compressed. Similarly, the atlas really ought to be compressed so that it downloads more quickly for those visualizations.

ebrahimebrahim commented 2 years ago

(sorry it seems I accidentally failed to branch this off of master branch, so #91 should be merged before this is)

ebrahimebrahim commented 2 years ago

@AlmightyYakob Two concerns here that I could use your help looking into:

  1. the current changes that I made on this branch don't work for me when I run preprocessing locally. The visualization doesn't seem to ever load (even locally); I see errors in console indicating that maybe we need to adjust the command that is used to read the image, in otm-client.
  2. I'd like to replace the atlas nii files by compressed ones, but I am not clear on where to put all the changes. E.g. there's factories.py (a test?) which seems to contain references to the atlas files, then there's populate_db.py and tasks.py that also mention them. Some guidance/assistance would help in this area.