kheops-client 0.3.1

Utility for querying and downloading data from a Kheops DICOM database

kheops-client

Utility for querying data from a Kheops DICOM database via the DICOMWeb API.

Setup

Install the Python package and command line utility using pip:

python -m pip install kheops-client

Alternatively, the package can be built and installed from source:

git clone https://github.com/hirsch-lab/kheops-client.git
cd kheops-client
python setup.py sdist
python -m pip install dist/kheops-client*.tar.gz

Usage

To access a Kheops database, one requires a URL to the DICOMWeb API and an access token. The examples below make use of the following variables:

URL="https://demo.kheops.online/api"
ACCESS_TOKEN="B18jTXCzTrQzj1ZednqHUY"
OUT_DIR="./downloads"

The tool offers two commands: list and download.

kheops-client --help
kheops-client list --help
kheops-client download --help

Query available studies and series

Query a list of available DICOM studies. A table with some information about the studies will be saved in the output directory.

kheops-client list studies \
    --url "$URL" \
    --token "$ACCESS_TOKEN" \
    --out-dir "$OUT_DIR"

Query a list of available DICOM series. Again, a table with some information about the series will be saved in the output directory.

kheops-client list series \
    --url "$URL" \
    --token "$ACCESS_TOKEN" \
    --out-dir "$OUT_DIR"

List the available series for a particular study by providing the --study-uid argument.

kheops-client list series \
    --url "$URL" \
    --token "$ACCESS_TOKEN" \
    --out-dir "$OUT_DIR" \
    --study-uid "2.16.840.1.113669.632.20.1211.10000098591"

It is possible to constrain the query by specifying search filters. The following query requests a list of all available series with modality CT.

kheops-client list series \
    --url "$URL" \
    --token "$ACCESS_TOKEN" \
    --search-filter "Modality" "CT" \
    --out-dir "$OUT_DIR"

Note that the search filters can be combined.

kheops-client list series \
    --url "$URL" \
    --token "$ACCESS_TOKEN" \
    --search-filter "Modality" "CT" \
    --search-filter "PatientID" "FrxHK8" \
    --out-dir "$OUT_DIR"

On some DICOMWeb servers, the retrieved lists may be truncated due to resource limitations (a warning will be issued in that case). In that case, arguments --limit and --offset can be of help.

kheops-client list series \
    --url "$URL" \
    --token "$ACCESS_TOKEN" \
    --out-dir "$OUT_DIR" \
    --limit 5 \
    --offset 10

Download DICOM data

It is possible to download single or multiple studies/series by using the download command.

For example, download a specific series by providing the arguments --study-uid and --series-uid. Use option --forced to override the data if it already exists in the output folder.

kheops-client download series \
    --url "$URL" \
    --token "$ACCESS_TOKEN" \
    --out-dir "$OUT_DIR" \
    --study-uid "2.16.840.1.113669.632.20.1211.10000098591" \
    --series-uid "1.2.840.113704.1.111.5692.1127829280.6" \
    --forced

To download all series in a study, just omit the argument --series-uid.

kheops-client download series \
    --url "$URL" \
    --token "$ACCESS_TOKEN" \
    --out-dir "$OUT_DIR" \
    --study-uid "2.16.840.1.113669.632.20.1211.10000098591" \
    --forced

Detail: This is pretty much equivalent to

kheops-client download studies \
    --url "$URL" \
    --token "$ACCESS_TOKEN" \
    --out-dir "$OUT_DIR" \
    --study-uid "2.16.840.1.113669.632.20.1211.10000098591" \
    --forced

It is possible to download a list of previously selected studies/series by passing a .csv file. The table must contain a named column "StudyInstanceUID" for the "studies" mode, and additionally a column "SeriesInstanceUID" for the "series" mode.

kheops-client download studies \
    --url "$URL" \
    --token "$ACCESS_TOKEN" \
    --out-dir "$OUT_DIR" \
    --in-file "path/to/file/patients_oldest_cta.csv"

Further arguments/options

• For testing, it may be useful to limit the maximum number of studies and to specify an offset: --limit and --offset
• Option --dry-run runs the commands without writing any output data
• Option --meta-only permits to download only the DICOM data structure without any bulk data.
• Control the verbosity level by using the flag --verbosity multiple times. Or by using the short form: -v, -vv, -vvv.

Python API

The above functionality is implemented in KheopsClient.

from kheops_client import KheopsClient
client = KheopsClient(url="URL", access_token="ACCESS_TOKEN")
client.list_studies(...)
client.list_series(...)
client.download_study(...)
client.download_series(...)
client.search_and_download_studies(...)
client.search_and_download_series(...)

Further reading

DICOM standard
DICOM dictionary browser
DICOMWeb standard
Pydicom (docs, api docs, github)
DICOMWeb client for python (github)