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ImagingDataCommons / idc-slim

Interoperable slide microscopy viewer for thin clients (CORE REPO)
Apache License 2.0
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Unable to load HTAN image for specific case #84

Closed fedorov closed 1 year ago

fedorov commented 1 year ago

@dclunie @cgorman any thoughts?

https://viewer.imaging.datacommons.cancer.gov/slim/studies/2.25.174442227011591161839224535127252003551/series/1.3.6.1.4.1.5962.99.1.2352175091.700331458.1655914616819.4.0

image
fedorov commented 1 year ago

Curiously, that is the only study from the HTAN-HMS collection that does not have the PR series!

rodrigobasilio2022 commented 1 year ago

The dicom-microscopy-viewer package that slim uses expects that an image pyramid metadata should have in the attributes extent and resolutions a matrix 2d, but in the image in question they are 1d array attributes. Is that correct or i can assume they should be 1D arrays as in the file? Also there is a divergence in the pixelsSpacing in one of the pyramids of more than 1e-6, the accepted difference in the package. The divergence is less than 1e-5, so we could update the package, if the case.

rodrigobasilio2022 commented 1 year ago

Studying more the code it seems that issue is a bug in the code of the dicom-microscopy-viewer package: the two calculated attributes are in fact 1d arrays. @fedorov , can you make me an collaborator in https://github.com/ImagingDataCommons/dicom-microscopy-viewer so i can create a PR to solve the problem?

rodrigobasilio2022 commented 1 year ago

PR opened and tested.

fedorov commented 1 year ago

Confirmed this is now fixed in IDC test tier!