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chaichontat / samui

A performant scientific image visualization system.
https://samuibrowser.com/
GNU General Public License v3.0
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failing to convert TIFF to COG (from Gb to few Kb) for Vizgen MERFISH data #79

Closed IrinaVKuznetsova closed 1 year ago

IrinaVKuznetsova commented 1 year ago

Dear developers,

I'd like to test Samui on our Vizgen MERFISH data, so I tried to convert TIFF to COG. Each TIFF file is around 2.5Gb. Unfortunately, no matter what scale I choose in the loop image command TIFF file remains large (~40k Kb). This size is too large for Samui, which returns the error “Maximum call stack size exceeded”. I also tried to use –quality parameter, but the command failed to generate the output if this parameter is set to 20, anything above 20 generates a file of ~10,000Kb size, which is again too big for Samui. Would you be able to help me with this issue? Please see below the command I used to compress tiff file:

FILE=path_to_Tiff
loopy image $FILE --scale 0.497e-6       ### generates a tiff file ~40k Kb

OR,

FILE=path_to_Tiff
loopy image $FILE --scale 0.497e-6 –quality 20    #### doesn’t generate result

OR,

FILE=path_to_Tiff
loopy image $FILE --scale 0.497e-6 –quality 40    ### generates a tiff file ~10k Kb

Thank you so much for your time, looking forward to hearing from you. Regards, Irina

chaichontat commented 1 year ago

The issue was with our command line tool. We didn't update the logic in the command line tool to match the update in our Python API. It's now fixed with the latest commit. Please git pull and try the command again.