Mirp

Fixes

- Masks can now be plotted in images without causing an error when using `matplotlib` version 3.9.0 or later.

Minor changes

- Tables with feature values now contain extra columns. These columns specify the file name (for non-DICOM input),
the directory path of the image and masks and several DICOM tags for identifying the input.

- MIRP now checks whether there are potential problems between the frames of reference of image and mask files.

Fixes

- Fixed an error that occurs when attempting to create a deep copy `ImageITKFile` objects.

Minor changes

- `show` method of `GenericImage` and subclasses now indicate if a user-provided `slice_id` is out-of-volume and
select the nearest slice instead.

- Naming of branches in the settings `xml` file now matches that of their respective settings classes. `xml` files
with the previous branch names still function.

- Errors encountered during file import and handling are now more descriptive.
- `extract_mask_labels` and `extract_image_parameters` now export extra information from DICOM metadata, e.g. series
UID.

Documentation

- Added a new tutorial on applying image filters to images.
- Added documentation on the feature naming system.
- Added documentation on the design of MIRP.

Fixes

- Computing features related to the minimum volume enclosing ellipsoid no longer produces warnings due to the use of
deprecated `numpy.matrix` class.

Minor changes

- If mask-related parameters are not provided for computing features or processing of images for deep learning, a
mask is generated that covers the entire image.

- Add fall-back methods for missing installation of the `ray` package for parallel processing. This can happen when
a python version is not supported by the `ray` package. `ray` is now a conditional dependency, until that package
is released for python `3.12`.

- The default export format for `deep_learning_processing` and `deep_learning_processing_generator` is now `dict`,
because the sample name is important for matching against observed outcomes.

- `write_file` arguments of `extract_mask_labels` and `extract_image_parameters` were deprecated as these were
redundant.

Fixes

- Streamlined importing and reading DICOM files results in faster processing of DICOM-based imaging.

- Fixed an indexing issue when attempting to split masks into bulk and rim sections in a slice-wise fashion.

- Fixed an indexing issue in Rank's method for noise estimation.

- Fixed incorrectly named image parameters file export. Instead of `mask_labels.csv`, image parameters are now
correctly exported to `image_metadata.csv`.

Major changes

- Added support for intensity scaling using the `intensity_scaling` parameter. Intensity scaling multiplies
intensities by a scalar value. Intensity scaling occurs after intensity normalisation (if any) and prior to adding
noise (if any). For example, intensity scaling can be used after intensity normalisation to scale intensities to a
different range. `intensity_normalisation = "range"` with `intensity_scaling = 1000.0` maps image intensities to
[1000.0, 0.0] instead of [1.0, 0.0].

- Added support for intensity transformation filters: square root (`"pyradiomics_square_root"`), square
(`"pyradiomics_square"`), logarithm (`"pyradiomics_logarithm"`) and exponential (`"pyradiomics_exponential"`).
These implementations are based on the definitions in the `pyradiomics`
[documentation](https://pyradiomics.readthedocs.io/en/latest/radiomics.html#module-radiomics.imageoperations).
Since these filters do not currently have an IBSI reference standard, these are mostly intended for reproducing
and validating radiomics models based on features extracted from pyradiomics.

- Modules were renamed according to the PEP8 standard. This does not affect the documented public interface, but may
affect external extensions. Public and private parts of the API are now indicated.

Minor changes

- Added support for Python version 3.10 using `typing-extensions`.
- Several changes were made to ensure proper functioning of MIRP with future versions of `pandas`.
- Some changes were made prevent deprecation warnings in future version of `numpy`.

Fixes

- Fixed missing merge changes from version 2.1.0 to the main branch.
- Fixed reading of `mask_name` from data xml files.
- `image_name` and `mask_name` configuration parameters are now parsed as single strings if only one value is
specified to match argument-based configuration.
- Fixed and updated several exception messages.
- Filter kernel names, specified using `filter_kernels` in xml files, are now correctly parsed as strings instead of
floats.