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Add support for Imaging Data Commons #1450

Merged
merged 6 commits into from
Feb 15, 2024
Merged

Add support for Imaging Data Commons #1450

merged 6 commits into from
Feb 15, 2024

Commits on Feb 13, 2024

  1. Do not filter by SOPClassUID 

    Google Healthcare API, used by Imaging Data Commons, does not allow
filtering by SOPClassUID. So we cannot use that in the search filter.
We should think of alternatives so that we can include only WSI results.

These changes were needed alongside [this wsidicom PR](imi-bigpicture/wsidicom#149)
in order to view an example dataset.

The following were used for testing:

url = 'https://proxy.imaging.datacommons.cancer.gov/current/viewer-only-no-downloads-see-tinyurl-dot-com-slash-3j3d9jyp/dicomWeb'
study_uid = '2.25.25644321580420796312527343668921514374'
series_uid = '1.3.6.1.4.1.5962.99.1.3205815762.381594633.1639588388306.2.0'

Signed-off-by: Patrick Avery <[email protected]>
    @psavery
    psavery committed Feb 13, 2024
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  2. Change defaults for importing 

    These work well for importing examples from the Imaging Data Commons.

It takes a while to import, so a limit of 10 series seems reasonable
for now.

Also, it's good to have a default filter of "Modality": "SM", because
otherwise, we would mostly receive non-WSI series.

Signed-off-by: Patrick Avery <[email protected]>
    @psavery
    psavery committed Feb 13, 2024
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  3. Apply limit and filters to studies, not series 

    We were previously just performing a `search_for_series()` and applying
the limit and filters to that search.

However, it is probably more intuitive for users to be searching for
studies, rather than series. So we are now performing a `search_for_studies()`
first, applying the limit and filters to this, and then locating all
series within those studies, and proceeding from there.

Signed-off-by: Patrick Avery <[email protected]>
    @psavery
    psavery committed Feb 13, 2024
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  4. Fix tests to take into account search by studies 

    We are now searching by studies, not series. The tests need to be
fixed to take this into account.

Signed-off-by: Patrick Avery <[email protected]>
    @psavery
    psavery committed Feb 13, 2024
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  5. Fix indentation in assetstoreImport template 

    Signed-off-by: Patrick Avery <[email protected]>
    @psavery
    psavery committed Feb 13, 2024
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  6. Don't infer file size right away 

    Importing the first 10 studies on IDC has been taking around 20 minutes.
About 65% of that time has been spent on inferring file sizes.

Even though we don't stream the file data, the request from which we get
the content length must be taking some time on the server. Skip doing
this for now. We can add it back in if we figure out a way to make it much
faster.

Signed-off-by: Patrick Avery <[email protected]>
    @psavery
    psavery committed Feb 13, 2024
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