DICOM Files

Provides a various set of tools for DICOM header manipulation.

usage: pymedphys dicom [-h]
                       {anonymise,merge-contours,adjust-machine-name,adjust-RED,adjust-RED-by-structure-name,listen,send}
                       ...

Positional Arguments

dicom

Possible choices: anonymise, merge-contours, adjust-machine-name, adjust-RED, adjust-RED-by-structure-name, listen, send

Sub-commands:

anonymise

Anonymise DICOM files.

pymedphys dicom anonymise [-h] [-o OUTPUT_PATH] [-d] [-f] [-c]
                          [-k [KEYWORD ...]] [-p] [-u | -i]
                          input_path

Positional Arguments

input_path

Input file or directory path. If a directory is supplied, all DICOM files within the directory and its subdirectories will be anonymised

Named Arguments

-o, --output_path

Output file or directory path.

-d, --delete_original_files

Use this flag to delete the original, non-anonymised files in the processed directory. Each original file will only be deleted if anonymisation completed successfully for that file.

Default: False

-f, --preserve_filenames

Use this flag to preserve the original filenames in the anonymised DICOM filenames. Note that ‘_Anonymised.dcm’ will still be appended. Use with caution, since DICOM filenames may contain identifying information

Default: False

-c, --clear_values

Use this flag to simply clear the values of all of the identifying elements in the anonymised DICOM files, as opposed to replacing them with ‘dummy’ values.

Default: False

-k, --keywords_to_leave_unchanged

A space-separated list of DICOM keywords (e.g. ‘PatientName’) to exclude from anonymisation and error checking.

-p, --keep_private_tags

Use this flag to preserve private tags in the anonymised DICOM files.

Default: False

-u, --delete_unknown_tags

Use this flag to delete any unrecognised tags from the anonymised DICOM files.

Default: False

-i, --ignore_unknown_tags

Use this flag to ignore any unrecognised tags in the anonymised DICOM files.

Default: False

merge-contours

Merge overlapping contours within a DICOM structure file

pymedphys dicom merge-contours [-h] [--structures STRUCTURES [STRUCTURES ...]]
                               input_file output_file

Positional Arguments

input_file
output_file

Named Arguments

--structures

The structures for which to run the merge on. If not provided, then all structures will be processed.

adjust-machine-name

Change the machine name in an RT plan DICOM file

pymedphys dicom adjust-machine-name [-h]
                                    input_file output_file new_machine_name

Positional Arguments

input_file
output_file
new_machine_name

adjust-RED

Adjust the RED of structures within an RT structure DICOM file

pymedphys dicom adjust-RED [-h] [-i]
                           input_file output_file adjustment_map
                           [adjustment_map ...]

Positional Arguments

input_file
output_file
adjustment_map

An alternating list of structure name and then its associated RED. For example, pymedphys dicom adjust-RED input.dcm output.dcm struct_name 1.5 another_struct_name 0.2

Named Arguments

-i, --ignore_missing_structure

Use this flag to no longer raise an error when a defined structure name doesn’t exist within the input DICOM file.

Default: False

adjust-RED-by-structure-name

Use structure naming conventions to automatically adjust the relative electron density of a structure within a DICOM RT Structure set. For example, naming a structure a_structure_name RED=1.15 will cause that structure to have an override of 1.15 applied.

pymedphys dicom adjust-RED-by-structure-name [-h] input_file output_file

Positional Arguments

input_file

input_file

output_file

output_file

listen

Start a DICOM listener on the specified port

pymedphys dicom listen [-h] [--host HOST] [-d STORAGE_DIRECTORY] [-a AETITLE]
                       port

Positional Arguments

port

The port on which to listen

Named Arguments

--host

The host/IP to bind to

Default: “0.0.0.0”

-d, --storage_directory

Default: “.”

-a, --aetitle

The AE Title of this listen service

Default: “PYMEDPHYS”

send

Send DICOM objects to a DICOM endpoint

pymedphys dicom send [-h] [-a AETITLE] host port [dcmfiles ...]

Positional Arguments

host

The host name/IP of the DICOM listener

port

The port of the DICOM listener

dcmfiles

Path to DICOM objects to send

Named Arguments

-a, --aetitle

The Called AE Title

Default: “PYMEDPHYS”