Pinnacle Export Tool#

Export DICOM objects from raw Pinnacle data.

usage: pymedphys experimental pinnacle [-h] {export} ...

Positional Arguments#


Possible choices: export



Export a raw file to DICOM

pymedphys experimental pinnacle export [-h] [-o OUTPUT_DIRECTORY] [-v] [--mrn]
                                       [-l] [-m MODALITY] [-p PLAN] [-t TRIAL]
                                       [-i IMAGE] [-u UID_PREFIX] [-r ROISKIP]

Positional Arguments#


Root Patient directory of raw Pinnacle data (directory containing the ‘Patient’ file). Alternatively a TAR archive can be supplied.

Named Arguments#

-o, --output-directory

Directory in which to generate DICOM objects.

-v, --verbose

Flag to output debug information.

Default: False


Append the Patient ID/MRN to the end of the name of the export folder

Default: False

-l, --list

List all plans and trials available.

Default: False

-m, --modality

Modalities to export (CT exports the plans primary planning CT).

Default: []

-p, --plan

The name of the plan to export (first plan will be exported by default).

-t, --trial

The name of the trial to export (first trial will be exported by default).

-i, --image

The UID of an image series you would like to export (or ‘all’ to export all images).

-u, --uid-prefix

Prefix to use for generated UIDs.

-r, --roiskip

Regular expression defining which ROIs to skip. Note that you will probably need to enclose your regular expression in single-quotes. For example ‘Skin|.*_obj|RadCalc’ .