pymedphys/pymedphys: v0.34.0

News around this release Stuart Swerdloff (@sjswerdloff) has agreed to come on board as a maintainer of PyMedPhys. Thank you Stuart! You have been a massive help and encouragement. Created an online PyMedPhys GUI. It is accessible from https://app.pymedphys.com. This is in its early stages and most parts of the online GUI are not optimised for use in this fashion. Of note, its main purpose is to demonstrate the GUI functionality. If you wish to begin using this GUI in your centre install PyMedPhys on your local machine and then start it by calling pymedphys gui within a terminal/command prompt. The online demo GUI should not have sensitive information submitted to it. @matthewdeancooper uploaded his Masters thesis on deep learning auto-segmentation to the docs. PyMedPhys was featured in a talk at the ACPSEM 2020 Summer School. Both the video and slides are available online. "Stable" API changes (Won't truly be stable until after a 1.0.0 release) Breaking changes The parameter fraction_number within pymedphys.Delivery.from_dicom and pymedphys.Delivery.to_dicom has been changed to fraction_group_number. The name of the first argument to pymedphys.Delivery.from_dicom has been changed from dicom_dataset to rtplan. It now also accepts either a pydicom.Dataset or a filepath. A range of files utilised by pymedphys.data_path and related functions that contained the words "mudensity", "mu-density", or "mu_density" have been replaced with "metersetmap". The exceptions that pymedphys.Delivery.from_mosaiq raises when either no entry in Mosaiq is found (NoMosaiqEntries) or multiple entries are found (MultipleMosaiqEntries) now both inherit from ValueError instead of the base Exception class. Deprecations All instances of mudensity have been replaced with metersetmap. The mudensity API is still currently available, but it will be removed in a future release. pymedphys.Delivery.from_logfile has been renamed as pymedphys.Delivery.from_trf. The previous name is still temporarily available but it will be removed in a future release. New features Added CLI pymedphys dicom listen #1161. This begins a DICOM listener which will store the DICOM files sent to it to disk. It accepts the arguments --port, --aetitle, and --storage_directory. Thanks @pchlap! Bug fixes Sometimes a range of DICOM API calls would require the downloading of a baseline DICOM dictionary. This is now distributed with the library. GUI changes Logistics changes pymedphys gui now boots up a multi application index. This index breaks applications up into five categories, mature, maturing, raw, beta, and experimental. Pseudonymise A new pseudonymise application has been created. This allows users to drag and drop DICOM files into the GUI and then download the resulting DICOM file in its pseudonymised form. Thanks @sjswerdloff! MetersetMap New Features The MetersetMap comparison application (which used to be MU density) is now able to work with a bare bones configuration file which can be used by just dragging and dropping TRF and DICOM files for comparison. See #1117 for details of the configuration file needed. Path configuration now supports expansion of ~ to the users home directory. Bug fixes In some cases a patient having a middle name would cause the DICOM file upload method to crash. Thanks @mchamberland for reporting in #1137 and thanks @sjswerdloff for the prompt fix in #1144! Experimental applications A new "anonymise monaco" application has been exposed. This allows the back-end Monaco filesystem to be anonymised in such a way that Monaco can still open and work with the contents. A new "dashboard" application has been exposed. This connects to multiple Mosaiq sites and displays the QCLs across each site. A new "electrons" application has been exposed. This reads Monaco back-end files, extract the electron insert shape and then predicts the corresponding insert output factor. A new "iviewdb" application has been exposed. This allows for exploration of the iView database. Work has begun on a new Winston Lutz Arc GUI. Configuration changes New keys ~/.pymedphys/config.toml should now include a version = 1 entry. This is to support undergoing breaking changes within config.toml but allowing PyMedPhys to still read in old configuration files without issue. For use within the up-coming Winston-Lutz Arc GUI a new key site.export-directories.iviewdb has been created. Beta API changes Nil Experimental API changes Breaking changes Removed pymedphys experimental gui. New Features Within pymedphys.experimental.pseudonymisation both pseudonymise and is_valid_strategy_for_keywords were added. pseudonymise provides a convenient simple API for pseudonymisation. See the API docs for more information. Credit to @sjswerdloff for all his work here. Developer facing API changes The pymedphys library directory has moved to lib/pymedphys. After this move you will need to rerun poetry install -E dev The development branch of pymedphys has moved from master to main Documentation is now stored within the library, moving from docs to lib/pymedphys/docs Docs can now be built, viewed, and updated with hot-reloading by running poetry run pymedphys dev docs --live. The output directory for the docs building can now be controlled by passing an --output flag to pymedphys dev docs. A new CLI utility that propagates a range of files that depend upon each other files within the repo are "propagated" by calling poetry run pymedphys dev propagate. The files created/updated by this command are lib/pymedphys/_version.py, requirements.txt and requirements-dev.txt, lib/pymedphys/.pylintrc, lib/pymedphys/docs/README.rst, lib/pymedphys/docs/CHANGELOG.md, and the 'extras' field within pyproject.toml. pymedphys dev tests includes simplified flags. --run-only-slow can be undergone with --slow, --run-only-yarn with --cypress, --run-only-pydicom with --pydicom, and --run-only-pylinac with --pylinac. Within cypress end to end testing the custom cy.start command now has a parameter app which refers to the URL app key of the application to be tested http://localhost:8501/?app=${app}