Pinnacle Export Tool

Export DICOM objects from raw Pinnacle data.

Warning

Research use only. The Pinnacle Export Tool is intended for research purposes only. Do not use it clinically. Inclusion in the public Python API does not imply clinical suitability or clinical validation.

Some conversion values are hard-coded rather than taken from the source data. Conversion support and validation vary by DICOM object and Pinnacle version, and some objects may not be converted correctly. Before using the output in research, compare it with the corresponding DICOM objects exported directly by the same Pinnacle version.

See also

For the Python library interface, see Pinnacle Export Tool.

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

Positional Arguments

pinnacle

Possible choices: export

Sub-commands

export

Export a raw file to DICOM

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

Positional Arguments

input_path

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

--mrn

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’ .