rsna-anonymizer 17.3.2

RSNA DICOM Anonymizer

RSNA DICOM Anonymizer V17

Installation

Select the correct binary download for your platform from the available releases

Windows

1. Download and extract zip to desired application directory.
2. Execute Anonymizer.exe and override User Account Control to allow the program to "Run anyway".
3. Logs will be written to ~/AppData/Local/Anonymizer

Mac OSX

1. Download and extract zip file to desired application directory.
2. Mount the disk by clicking the Anonymizer_17.*.dmg file where * is the relevant version.
3. In the finder window presented, drag the Anonymzier icon to Applications folder.
4. Wait for the Application to be decompressed and copied.
5. Open a terminal (/Applications/Utilities/Terminal)
6. To remove extended attributes, in the terminal, execute the command: xattr -rc /Applications/Anonymizer_17.*.app.
7. Double click the application icon to execute.
8. Logs will be written to ~/Library/Logs/Anonymizer/anonymizer.log

Linux

1. Download and extract zip file to desired application directory.
2. Open terminal cd to application directory
3. chmod +x Anonymizer_17.* where * is the relevant version
4. Execute ./Anonymizer_17.*
5. Logs will be written to ~/Logs/Anonymizer/anonymizer.log

Documentation

Help files

Sponsors

Free code signing on Windows provided by SignPath.io, certificate by SignPath Foundation

Development

Setup

1. Setup python enviroment (>3.10) which includes Tkinter, recommend using pyenv with MacOS & Linux
2. Ensure python is installed with Tkinter: python -m tkinter, a small GUI window should open
3. Install virtual environment & package manager: pip install pipenv
4. Clone repository
5. Setup virtual enviroment and install all dependencies listed in Pipfile: pipenv install --dev

Unit Testing

For model and controller with coverage

1. Create tests/controller/.env file with your AWS_USERNAME and AWS_PASSWORD
2. pipenv shell
3. coverage run -m pytest tests
4. coverage report --omit="tests/*"

Build executables

1. If building on OSX ensure create-dmg is installed: brew install create-dmg
2. pipenv shell
3. cd src
4. python build.py
5. Executable will be in src/dist

Github Actions CI/CD

1. See: .github/workflows/build.yml
2. Triggered by push and pull request on master branch
3. Includes executable build step using build.py

Code Metrics

Using radon

1. pipenv shell
2. radon raw -i "tests,docs,prototyping" . > radon_results.txt
3. python src/radon_raw_totals.py

Translations

Languages for 17.1: en_US, de, es, fr

Ensure gettext is installed:

1. Windows: Install instructions or choco install gettext
2. Mac OSX: brew install gettext
3. Linux: sudo apt-get install gettext

Extracting messages from source files:

cd src/anonymizer/assets/locales/ ./extract_translations.sh

Updating translations:

cd src/anonymizer/assets/locales/ ./update_translations.sh

Software Architecture

Full class diagram here

Model

Two python classes pickled to files in project directory:

1. ProjectModel

./ProjectModel.pkl when project settings change

2. AnonymizerModel

./private/AnonymizerModel.pkl every 30 secs if files were stored

classDiagram
    class DICOMNode {
        <<model.project>>
        + ip
        + port
        + aet
        + local
    }
    class NetworkTimeouts {
        <<model.project>>
        + tcp_connection
        + acse
        + dimse
        + network
    }
    class LoggingLevels {
        <<model.project>>
        + anonymizer
        + pynetdicom
        + pydicom
    }
    class AWSCognito {
        <<model.project>>
        + account_id
        + region_name
        + app_client_id
        + user_pool_id
        + identity_pool_id
        + s3_bucket
        + s3_prefix
        + username
        + password
    }
    class ProjectModel {
        <<model.project>>
        + MODEL_VERSION
        + PRIVATE_DIR
        + PUBLIC_DIR
        + PHI_EXPORT_DIR
        + QUARANTINE_DIR
        + RSNA_ROOT_ORG_UID
        + IMPLEMENTATION_CLASS_UID
        + IMPLEMENTATION_VERSION_NAME
        + site_id
        + project_name
        + uid_root
        + storage_dir
        + modalities
        + storage_classes
        + transfer_syntaxes
        + anonymizer_script_path
        + export_to_aws
    }
    ProjectModel --* "1" LoggingLevels: logging_levels
    ProjectModel --* "1" NetworkTimeouts: network_timeouts
    ProjectModel --* "1" AWSCognito: aws_cognito
    ProjectModel --* "1" DICOMNode: scu
    ProjectModel --* "1" DICOMNode: scp
    ProjectModel --* "*" DICOMNode: remote_scps
    class Series {
        <<model.anonymizer>>
        + series_uid
        + series_desc
        + modality
        + instance_count
    }
    class Study {
        <<model.anonymizer>>
        + source
        + study_uid
        + study_date
        + anon_date_delta
        + accession_number
        + study_desc
        + target_instance_count
    }
    Study "1" --* "*" Series: series
    class PHI{
        <<model.anonymizer>>
        + patient_name
        + patient_id
        + sex
        + dob
        + ethnic_group
    }
    PHI "1" --* "*" Study: studies
    class AnonymizerModel {
        <<model.anonymizer>>
        + MODEL_VERSION
        + MAX_PATIENTS
        + default_anon_pt_id
        - _version
        - _site_id
        - _uid_root
        - _uid_prefix
        - _tag_keep
        - _patient_id_lookup
        - _uid_lookup
        - _acc_no_lookup
        - _patients
        - _studies
        - _series
        - _instances
    }
    AnonymizerModel "1" --* "*" PHI: _phi_lookup

Controller

1. ProjectController

Main control class, descendent of pynetdicom.ApplicationEntity handling all DICOM file and network i/o.

2. AnonymizerController

Provides API & worker threads to anonymize queued DICOM files incoming from network or file system.

classDiagram
    class ProjectModel {
        <<model.project>>
    }
    class AnonymizerModel {
        <<model.anonymizer>>
    }
    class ApplicationEntity {
        <<pynetdicom.ae>>    
    }
    class Dataset {
        <<pydicom.Dataset>>
    }
    class PresentationContext {
        <<pynetdicom.presentation>>
    }
    class Event {
        <<pynetdicom.events>>
    }
    Event "1" ..> "1" Dataset
    class Association {
        <<pynetdicom.association>>
    }
    Association "1" ..> "*" Dataset
    class AnonymizerController {
        <<controller.anonymizer>>
    }
    AnonymizerController --* AnonymizerModel
    AnonymizerController --> ProjectModel
    AnonymizerController "1" ..> "*" Dataset
    class InstanceUIDHierarchy {
        <<controller.project>>
        + uid
        + number
    }
    class SeriesUIDHierarchy {
        <<controller.project>>
    }
    SeriesUIDHierarchy "1" --* "*" InstanceUIDHierarchy: instances
    class StudyUIDHierarchy {
        <<controller.project>>
    }
    StudyUIDHierarchy "1" --* "*" SeriesUIDHierarchy: series
    class EchoRequest {
        <<controller.project>>
    }
    class EchoResponse {
        <<controller.project>>
    }
    class FindStudyRequest {
        <<controller.project>>
    }
    class FindStudyResponse {
        <<controller.project>>
    }
    FindStudyResponse "1" --* "1" Dataset: status
    FindStudyResponse "1" --* "1" Dataset: study_result
    class MoveStudiesRequest {
        <<controller.project>>
    }
    MoveStudiesRequest "1" --* "*" StudyUIDHierarchy: studies
    class ExportPatientsRequest {
        <<controller.project>>
    }
    class ExportPatientsResponse {
        <<controller.project>>
    }
    class ProjectController {
        <<controller.project>>       
    }
    ApplicationEntity <|-- ProjectController
    ProjectController "1" --* "1" ProjectModel
    ProjectController "1" --* "1" AnonymizerController
    ProjectController "1" ..> "*" Dataset
    ProjectController "1" ..> "*" PresentationContext
    ProjectController "1" ..> "*" Event
    ProjectController "1" ..> "*" Association
    ProjectController "1" ..> "1" EchoRequest
    ProjectController "1" ..> "1" EchoResponse
    ProjectController "1" ..> "*" StudyUIDHierarchy
    ProjectController "1" ..> "1" FindStudyRequest
    ProjectController "1" ..> "*" FindStudyResponse
    ProjectController "1" ..> "1" MoveStudiesRequest
    ProjectController "1" ..> "1" ExportPatientsRequest
    ProjectController "1" ..> "*" ExportPatientsResponse

View

Python standard library for GUI: Tkinter (interface to Tk toolkit written in C) enhanced using UI library CustomTkinter. UI colors and fonts are set by ctk.ThemeManager from assets/themes/rsna_theme.json which handles appearance modes: System, Light & Dark.

1. Anonymizer

Main application class (ctk.CTk) with context sensitive menu (project open or closed)

2. WelcomeDialog

First view on fresh program start when no project open

3. HTMLView

Render html help files with simplified tag set using tkhtmlview library

4. SettingsDialog

Configures ProjectModel => DICOMNodeDialog, AWSCognitoDialog, NetworkTimeoutsDialog, ModalitiesDialog, SOPClassesDialog, TransferSyntaxesDialog, LoggingLevelsDialog

5. Dashboard

Displays project metrics and provides buttons for QueryView & ExportView

6. QueryView

Query remote scp and import studies using C-MOVE at specified level

7. ImportStudiesDialog

Display status of current C-MOVE import operation triggered from QueryView

8. ImportFilesDialog

Display status of file import operation triggered from menu File/Import Files or File/Import Directory

9. ExportView

Export anonymized studies to remote scp or AWS

classDiagram
    class ProjectController {
        <<controller.project>>       
    }
    class AnonymizerController {
        <<controller.anonymizer>>
    }
    class Tk {
        <<tkinter>>
    }
    class CTk {
        <<customtkinter>>
    }
    class WelcomeView {
        <<view.welcome>>
    }
    class HTMLScrolledText {
        <<tkhtmlview>>
    }
    class RenderHTML {
        <<tkhtmlview>>
    }
    class HTMLView {
    }
    HTMLView "1" --* "1" HTMLScrolledText
    HTMLView "1" --* "1" RenderHTML
    class DICOMNodeDialog {
        <<view.dicom_node_dialog>>
    }
    class AWSCognitoDialog {
        <<aws_cognito_dialog>>
    }
    class NetworkTimeoutsDialog {
        <<view.settings.network_timeouts.dialog>>
    }
    class ModalitiesDialog {
        <<view.settings.modalities_dialog>>
    } 
    class SOPClassesDialog {
        <<view.settings.sop_classes_dialog>>
    } 
    class TransferSyntaxesDialog {
        <<view.settings.transfer_syntaxes_dialog>>
    } 
    class LoggingLevelsDialog {
        <<view.settings.logging_levels_dialog>>
    }
    class SettingsDialog {
        <<view.settings.settings_dialog>>
    }
    SettingsDialog "1" ..> "*" JavaAnonymizerExportedStudy
    SettingsDialog "1" --* "1" DICOMNodeDialog: local_server
    SettingsDialog "1" --* "1" DICOMNodeDialog: query_server
    SettingsDialog "1" --* "1" DICOMNodeDialog: export_server
    SettingsDialog "1" --* "1" AWSCognitoDialog: aws_cognito
    SettingsDialog "1" --* "1" ModalitiesDialog: modalities
    SettingsDialog "1" --* "1" NetworkTimeoutsDialog: network_timeouts
    SettingsDialog "1" --* "1" SOPClassesDialog: sop_classes
    SettingsDialog "1" --* "1" TransferSyntaxesDialog: transfer_syntaxes
    SettingsDialog "1" --* "1" LoggingLevelsDialog: logging_levels
    class Dashboard {
        <<view.dashboard>>
    }
    Dashboard "1" --> "1" ProjectController
    class QueryView {
        <<view.query_retrieve_import>>
    }
    QueryView "1" --> "1" ProjectController
    QueryView "1" --> "1" Dashboard
    class ImportStudiesDialog {
        <<import_studies_dialog>>
    }
    ImportStudiesDialog "1" --> "1" ProjectController
    class ImportFilesDialog {
        <<view.import_files_dialog>>
    }
    ImportFilesDialog "1" --> "1" AnonymizerController
    class ExportView {
        <<view.export>>
    }
    ExportView "1" --> "1" ProjectController
    ExportView "1" --> "1" Dashboard
    Tk <|-- CTk
    class Anonymizer {
        <<anonymizer>> 
    }
    CTk <|-- Anonymizer
    Anonymizer "1" --* "1" ProjectController: controller
    Anonymizer "1" --* "1" WelcomeView: welcome_view
    Anonymizer "1" --* "1" QueryView: query_view
    Anonymizer "1" --* "1" ExportView: export_view
    Anonymizer "1" --* "1" Dashboard: dashboard
    Anonymizer "1" --* "*" HTMLView: help_views
    Anonymizer "1" --* "1" SettingsDialog
    Anonymizer "1" --* "1" ImportStudiesDialog
    Anonymizer "1" --* "1" ImportFilesDialog