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Description:

idcindex 0.7.0

idc-index

[!WARNING]
This package is in its early development stages. Its functionality and API
will change.
Stay tuned for the updates and documentation, and please share your feedback
about it by opening issues in this repository, or by starting a discussion in
IDC User forum.

About
idc-index is a Python package that enables basic operations for working with
NCI Imaging Data Commons (IDC):

subsetting of the IDC data using selected metadata attributes
download of the files corresponding to selection
generation of the viewer URLs for the selected data

Getting started
Install the latest version of the package.
$ pip install --upgrade idc-index

Instantiate IDCClient, which provides the interface for main operations.
from idc_index import IDCClient

client = IDCClient.client()

You can use IDC Portal to
browse collections, cases, studies and series, copy their identifiers and
download the corresponding files using idc-index helper functions.
You can try this out with the rider_pilot collection, which is just 10.5 GB in
size:
client.download_from_selection(collection_id="rider_pilot", downloadDir=".")

... or run queries against the "mini" index of Imaging Data Commons data, and
download images that match your selection criteria! The following will select
all Magnetic Resonance (MR) series, and will download the first 10.
from idc_index import index

client = index.IDCClient()

query = """
SELECT
SeriesInstanceUID
FROM
index
WHERE
Modality = 'MR'
"""

selection_df = client.sql_query(query)

client.download_from_selection(
seriesInstanceUID=list(selection_df["SeriesInstanceUID"].values[:10]),
downloadDir=".",
)

Tutorial
Please check out
this tutorial notebook
for the introduction into using idc-index.
Resources

Imaging Data Commons Portal can be
used to explore the content of IDC from the web browser
s5cmd is a highly efficient, open source,
multi-platform S3 client that we use for downloading IDC data, which is hosted
in public AWS and GCS buckets. Distributed on PyPI as
s5cmd.
SlicerIDCBrowser 3D
Slicer extension that relies on idc-index for search and download of IDC
data

Acknowledgment
This software is maintained by the IDC team, which has been funded in whole or
in part with Federal funds from the NCI, NIH, under task order no. HHSN26110071
under contract no. HHSN261201500003l.
If this package helped your research, we would appreciate if you could cite IDC
paper below.

Fedorov, A., Longabaugh, W. J. R., Pot, D., Clunie, D. A., Pieper, S. D.,
Gibbs, D. L., Bridge, C., Herrmann, M. D., Homeyer, A., Lewis, R., Aerts, H.
J. W., Krishnaswamy, D., Thiriveedhi, V. K., Ciausu, C., Schacherer, D. P.,
Bontempi, D., Pihl, T., Wagner, U., Farahani, K., Kim, E. & Kikinis, R.
National Cancer Institute Imaging Data Commons: Toward Transparency,
Reproducibility, and Scalability in Imaging Artificial Intelligence.
RadioGraphics (2023). https://doi.org/10.1148/rg.230180