DICOM Files

DICOM Files#

Provides a various set of tools for DICOM header manipulation.

The anonymise subcommand is a legacy interface. It prints a notice of its limitations on standard error when it runs. Read its limitations in DICOM de-identification before sharing output.

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#

Replace the values of a fixed list of identifying attributes in DICOM files. UIDs and most RT attributes are kept.

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, files matching *.dcm within the directory and its subdirectories are processed. Matching is case-insensitive on Windows. The output keeps the source folder structure.

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 keep the original file names, with ‘_Anonymised.dcm’ appended, instead of naming each file after its modality and original SOP Instance UID. Either way, the name can identify the source: original file names may contain patient details, and the default names contain the original SOP Instance UID.

Default: False

-c, --clear_values

Use this flag to empty the values of the listed identifying attributes, instead of 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; 0 assigns a free port reported at startup

Named Arguments#

--host

The host/IP to bind to

Default: '0.0.0.0'

-d, --storage_directory

The folder to store received objects in, by default the current folder. Each object is stored in a folder named after its Patient ID, then in folders named after its Study and Series Instance UIDs, in a file named after its SOP Instance UID. In these names, the characters % / : * ? “ < > | and control characters are written as % and their two-digit hexadecimal code, and the names . and .. as %2E and %2E%2E.

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'