Release Notes

All notable changes to this project will be documented in this file.

This project adheres to Semantic Versioning.


Breaking Changes

  • A large number of functions that were previously exposed have now been made private in preparation for eventually stabilising the API. No function that was within the documentation has been removed. If there is a function that you were using that you would like to be exposed via import again, please let us know by opening an issue on GitHub and we will happily re-expose it! However, please bear in mind that the entire API that is currently exposed will likely change before a 1.0.0 release.
  • anonymise_dicom_dataset() has been renamed to anonymise_dataset() to remove redundant labelling.
  • mu_density_from_delivery_data moved from the msq module to the mudensity module.
  • compare_mosaiq_fields moved from the msq module into the plancompare module.
  • pymedphys.dicom.get_structure_aligned_cube has had its x0 paremeter changed from required to optional. It is no longer the first parameter passed to the function. By default x0 is now determined using the min/max bounds of the structure.
  • The DICOM coordinate extraction functions - extract_dicom_patient_xyz(), extract_iec_patient_xyz() and extract_iec_fixed_xyz() - have been combined into a single function called xyz_from_dataset(). The x, y, z axes can still be returned in either the DICOM, IEC fixed or IEC patient coordinate systems by passing the following case-insensitive strings to the coord_system= parameter of xyz_from_dataset():
    • DICOM: 'd' or 'DICOM'
    • IEC fixed: 'f', 'fixed' or 'IEC fixed'
    • IEC patient: 'p', 'patient' or 'IEC patient'

New Features

  • A DICOM anonymsation CLI! See the DICOM Files CLI docs.
  • anonymise_file() and anonymise_directory():
    • two new DICOM anonymisation wrapper functions that take a DICOM file and a directory as respective arguments.
  • is_anonymised_dataset(), is_anonymised_file() and is_anonymised_directory():
    • three new functions that check whether a pydicom dataset, a DICOM file or all files within a directory have been anonymised, respectively.
  • coords_from_xyz_axes() is a previously internal function that has now been exposed in the API. It converts x, y, z axes returned by xyz_from_dataset() into a full grid of coordinate triplets that correspond to the original grid (pixel array or dose grid).

0.7.2 – 2019/04/05

Dependency changes

  • Removed numpy version upperlimit

0.7.1 – 2019/04/05

Performance Improvements

  • reduced PyPI package size by removing unnessesary development testing files.

0.7.0 – 2019/04/05

Breaking Changes

  • anonymise_dicom has been renamed to anonymise_dicom_dataset
  • The CLI interface trf2csv has been replaced with pymedphys trf to-csv. This has the same usage, just a changed name to come in line with the rest of the CLI interfaces exposed by PyMedPhys.

New Features

  • Implementing a suite of Dicom objects, currently a work in progress:
    • DicomBase, a base DICOM class that wraps pydicom’s Dataset object. This class includes additions such as an anonymisation method.
    • DicomImage, designed to hold a single DICOM image slice. Might someday contain methods such as resample and the like.
    • DicomSeries, a series of DicomImage objects creating a CT dataset.
    • DicomStructure, designed to house DICOM structure datasets.
    • DicomPlan, a class that holds RT plan DICOM datasets.
    • DicomDose, a class that to hold RT DICOM dose datasets. It has helper functions and parameters such as coordinate transforms built into it.
    • DicomStudy, a class designed to hold an interrelated set of DicomDose, DicomPlan, DicomStructure, and DicomSeries. Not every type is required to create a DicomStudy. Certain methods will be available on DicomStudy depending what is housed within it. For example having both DicomDose and DicomStructure should enable DVH based methods.
    • DicomCollection, a class that can hold multiple studies, interrelated or not. A common use case that will likely be implemented is DicomCollection.from_directory(directory_path) which would pull all DICOM files nested within a directory and sort them into DicomStudy objects based on their header UIDs.
  • Added CLI commands for a WIP docker server, logfile orchestration, and DICOM editor tools.
  • Added a range of xlwings tools that allow the use of PyMedPhys functions within Excel
  • Added rudimentary code to pull profiles from Mephysto files.
  • The previously separate decodetrf library is now distributed within PyMedPhys. You can now simply install PyMedPhys and run pymedphys trf to-csv within the command line to convert .trf files into .csv files.

0.6.0 – 2019/03/15

Breaking Changes

  • All uses of “dcm” in directory names, module names, function names, etc. have been converted to “dicom”. Anything that makes use of this code will need to be adjusted accordingly. Required changes include:
    • pymedphys.dcm –> pymedphys.dicom
    • coords_and_dose_from_dcm() –> coords_and_dose_from_dicom()
    • dcmfromdict() –> dicom_dataset_from_dict()
    • gamma_dcm() –> gamma_dicom()
  • MU Density related functions are no longer available under the pymedphys.coll package, instead they are found within pymedphys.mudensity package.
  • The DICOM coordinate extraction functions now return simple tuples rather than Coords namedtuples:
    • extract_dicom_patient_xyz()
    • extract_iec_patient_xyz()
    • extract_iec_fixed_xyz()

New Features

  • DICOM anonymisation now permits replacing deidentified values with suitable “dummy” values. This helps to maintain compatibility with DICOM software that includes checks (beyond those specified in the DICOM Standard) of valid DICOM tag values. Replacing tags with dummy values upon anonymisation is now the default behaviour.
  • A set of 3D coordinate transformation functions, including rotations (passive or active) and translations. Transformations may be applied to a single coordinate triplet (an ndarray) or a list of arbitrarily many coordinate triplets (a 3 x n ndarray). NB: Documentation forthcoming.

Code Refactoring

  • All uses of dcm as a variable name for instances of PyDicom Datasets have been converted to ds to match PyDicom convention.

0.5.1 – 2019/01/05

New Features

  • Began keeping record of changes in