imaging/ml Switch to using our hosted CBIS-DDSM dataset instead of downloading it from TCIA about healthcare HOT 9 CLOSED

gcloud beta healthcare dicom-stores export instead of api call

@sadeel
gcloud and api call to export does not support filtering or export of single object, so we have two options:

• export whole store and try to filter jpegs on gcs
• requesting download each dicom separately by api calls to https://healthcare.googleapis.com/v1beta1/projects/chc-tcia/locations/us-central1/datasets/cbis-ddsm/dicomStores/cbis-ddsm/dicomWeb/studies/XYZ with specifying 'Accept': 'multipart/related; type="image/jpeg"; transfer-syntax=1.2.840.10008.1.2.4.50'

from healthcare.

I prefer first option, we want clients to use bulk operations such as ExportDicomData in such cases.

I think you might run into issues mapping the jpegs on gcs to the TCIA provided CSV...if you do feel free to store the mapping somewhere in the repo...perhaps as a static CSV

from healthcare.

I think you might run into issues mapping the jpegs on gcs to the TCIA provided CSV...if you do feel free to store the mapping somewhere in the repo...perhaps as a static CSV

since export generates folder structure by ids of dcms: /1.3.6.1.4.1.9590.100.1.2.100052171312354035019149694722933145864/1.3.6.1.4.1.9590.100.1.2.122021886313853636738943991213171853079/1.3.6.1.4.1.9590.100.1.2.143025478211711725141987429563024371610.jpg i think it will be possible to filter them without additional data

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@sadeel
i've faced problem with managing access to https://healthcare.googleapis.com/v1beta1/projects/chc-tcia/locations/us-central1/datasets/cbis-ddsm/dicomStores/cbis-ddsm
old service account may trigger export command, this account was created before our project got access to chc-tcia
but if i create new service account(with same permissions) and try to run export command i'll get permission error.
So access seems to be managed by CHC-API team, or i haven't found settings for this.

question: should README says that user should communicate with CHC-API team to grant permissions to service account or we have any additional way to get such permissions for service account?

from healthcare.

Yes, the readme should ask the user to request access for their service account using the form here:
https://cloud.google.com/healthcare/docs/resources/public-datasets/tcia#cloud-healthcare-api

We don't have good support for service accounts right now, I have filed a request internally to handle this. In the mean time, can we ask the user to request access using their email? Then, in the codelab, have the client authenticate using their email before doing ExportDicomData?

from healthcare.

Then, in the codelab, have the client authenticate using their email before doing ExportDicomData?

seems like gcloud init --console-only have only interactive mode for personal accounts so i'll have to put it into README, is it ok?

from healthcare.

That sounds fine. This should be a intermediate thing, we'll fix service account access eventually...

from healthcare.

That sounds fine. This should be a intermediate thing, we'll fix service account access eventually...

readme has been updated

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fixed in latest commit

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