Picai-prep

Latest version: v2.1.10

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2.0.0

**Major updates:**
* Archives are now converted case-by-case, instead of performing each phase after the other (i.e. collecting metadata for all cases, then converting images).
* Logging has improved and now offers three levels of verbosity: 1) show full case log when something goes wrong (default), 2) show full log for all cases, and 0) off.
* Improved usability of command-line interface: both DICOM → MHA and MHA → nnU-Net conversions are now available, as well as the generation of the conversion settings.
* Conversion of dynamic contrast-enhanced (DCE) scans is now supported (but experimental, feedback is welcome).

**Updates that may require you to update your existing scripts:**
* Some parameter names have changed (e.g. `input_path` to `input_dir` in `MHA2nnUNetConverter`). Please refer to the README or source code for the new values.
* Conversion settings for DICOM → MHA now require the `patient_id` and `study_id` for each item.

**Minor updates:**
* Multiprocessing is now optional. Set `num_threads=1` to turn off.
* Improved creation of dataset.json for nnUNet raw data archive.
* Any DICOM tag can now be used to match cases to their target MHA file.
* The way values from DICOM tags are matched with the provided values is now configurable. See Dicom2MHAConverter's docstring for details.

**Improved testing:**
* Test DICOM → MHA conversion from both Python and the command line interface
* Test conversion of DCE scans

1.3.2

* Multiprocessing for dcm2mha and mha2nnunet (https://github.com/DIAGNijmegen/picai_prep/pull/3)
* Increase flexibility dcm2mha pipeline (https://github.com/DIAGNijmegen/picai_prep/pull/5)
* Allow centre crop to (maximal) physical space (https://github.com/DIAGNijmegen/picai_prep/pull/6)
* Improved resampling to original/reference scan (https://github.com/DIAGNijmegen/picai_prep/pull/6)

1.2

Implemented a new resampling strategy to harmonize the different sequences for mha2nnunet. This new resampling method is simpler and better, so the old convoluted way has been removed.

1.1.1

1.1

1.0

Public release

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