TCIA Image and Adjunct Patient Data Dataset #2877
Description
Is your feature request related to a problem? Please describe.
This is part of #2212, as a follow-up of #2310
this ticket looks for a prototype of an "application-level" command such as
monai.apps.CsvTciaDataset("ISPY1_Combined.csv",["M","N","P"],["AM"],["AE"],"/tmp","training",transforms)to
- fetch metadata (this file is an curated example; as described in Proposal: Integrating Image and Adjunct Patient Data from TCIA via CSV files #2212 Section C step 2)
- fetch the image data according to the metadata (via the rest API; doc: https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+REST+API+Guides)
More info about downloading:
the downloading from TCIA via Python in this notebook is leveraging https://github.com/lescientifik/tcia_downloader which is using a version of our API that's about to be upgraded. In order to use the newer version of the REST API I think you'll need to update https://github.com/lescientifik/tcia_downloader/blob/master/src/tcia.py with a new "TCIA_ENDPOINT" in this line:
TCIA_ENDPOINT = (
"https://services.cancerimagingarchive.net/services/v3/TCIA/query/getImage")We're still finalizing the documentation updates on our site, but I believe that should now be "https://services.cancerimagingarchive.net/nbia-api/services/v1/getImage".
As a starting point, the implementation will be in the tutorial repo.