Picai-prep

What's Changed
* Allow dataset.json creation without labels by joeranbosma in https://github.com/DIAGNijmegen/picai_prep/pull/50
* Documentation bugfix by joeranbosma in https://github.com/DIAGNijmegen/picai_prep/pull/52
* Update README.md with Lancet Onc bib by anindox8 in https://github.com/DIAGNijmegen/picai_prep/pull/53
* Preprocessing: add option to only pad and never crop by joeranbosma in https://github.com/DIAGNijmegen/picai_prep/pull/54

New Contributors
* anindox8 made their first contribution in https://github.com/DIAGNijmegen/picai_prep/pull/53

**Full Changelog**: https://github.com/DIAGNijmegen/picai_prep/compare/v2.1.6...v2.1.8

What's Changed
* Remove common prefixes from filenames when checking DICOM slice filenames by joeranbosma in https://github.com/DIAGNijmegen/picai_prep/pull/45
* dcm2mha type hinting and output filename by joeranbosma in https://github.com/DIAGNijmegen/picai_prep/pull/46


**Full Changelog**: https://github.com/DIAGNijmegen/picai_prep/compare/v2.1.4...v2.1.6

What's Changed
* dcm2mha: remove localizer slices, improve logging by joeranbosma in https://github.com/DIAGNijmegen/picai_prep/pull/39
* dcm2mha: reduce memory usage by joeranbosma in https://github.com/DIAGNijmegen/picai_prep/pull/42
* Update README with dcm2mha options by snorthman in https://github.com/DIAGNijmegen/picai_prep/pull/43
* mha2nnunet: reduce logging about skipping cases by joeranbosma in https://github.com/DIAGNijmegen/picai_prep/pull/44


**Full Changelog**: https://github.com/DIAGNijmegen/picai_prep/compare/v2.1.3...v2.1.4

- Logging mha2nnunet (https://github.com/DIAGNijmegen/picai_prep/pull/32): Write the traceback to the log when an error occurs, instead of silently
continuing.
- mha2nnunet: skip converted cases (https://github.com/DIAGNijmegen/picai_prep/pull/35)

* Verify DICOM filenames bugfix (https://github.com/DIAGNijmegen/picai_prep/pull/31)
* Improve robustness (https://github.com/DIAGNijmegen/picai_prep/pull/29)
- Read metadata more reliably
- Cleanup terminal output, by prioritizing dicom.zip
- Cleanup spacing naming & ensure in-plane resolution

**Read dicom zip**
Implemented new `DICOMImageReader` to organise DICOM reading:
- Read DICOM data from a folder or dicom.zip.
- Improve support with `pydicom`: image origin and direction are now set correctly.
- Fix metadata reading with `pydicom`: metadata is now read in the same way as `SimpleITK`.
- Cleanup: split image reading with `SimpleITK`/`pydicom` to separate functions. Move `pydicom`-specific function `get_pydicom_value` to `dcm2mha.py`.
- Update slice from which metadata is read to align with `pydicom` (now orientation etc. is read from the same slice as the metadata, which is better consistency anyway).
- Added unit tests to verify image reading with `SimpleITK` and `pydicom`.

Add metadata reading to `DICOMImageReader`:
- metadata can now be read without extracting anything from the dicom.zip.
- bring the responsibility for checking DICOM filenames to `DICOMImageReader`.
- added tests for reading from dicom.zip.