Worc

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Added
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- Major documentation update.

Changed
~~~~~~~
- PyRadiomics setup not dependent on pre-install of numpy anymore, so altered
travis, yml, setup, and documentation.
- PREDICT updated, change dependencies.
- Defaults are now a bit different: see argumentation in the documentation.
Main thing is that PyRadiomics and PREDICT both compute certain features,
so it's redundant to use both. Additionally, the wavelet features
from PyRadiomics add +1000 features, which did not seem to help in many
experiments while majorly slowing down the computation.

Fixed
~~~~~
- Catch error when PCA does not converge in fit and score function.

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Added
~~~~~~~
- Labelprocessing can now also handle having patient ID in the feature files.
Was required for ComBat.

Changed
~~~~~~~
- Output of plot_SVM function is better ordered.
- Several defaults, as we now have PyRadiomics fully embedded, resulting in
a large increase in features.
- No more overrides for the full config, as the default now is the full config.

Fixed
~~~~~
- Cardinality of decomposition tool was incorrect.
- ComBat integration in WORC network now works properly.
- Documentation didn't build due to C-extension dependencies of PyRadiomics,
and thus therefore also PREDICT. Fixed in setup.py and readthedocs files.
- Documentation building.
- Bugfix in segmentix test output url.
- Bugfix in SimpleWORC facade when using features.
- Warning when using Evaluation pipeline without images.

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Added
~~~~~~~
- Catch error if number of segmentations supplied does not match number of
images.
- Add support in SimpleWORC and BasicWORC for multiple segmentations per
patient.
- Chi2 test in statistical testing.
- fastr tool to make boxplots of all features, overall and per class.
- Added this boxplot tool to the evaluate workflow.
- Option in evaluation to overfit feature scaling to test set: should only
be used to assess differences between the training and test sets, not
in an actual model.
- Option to delete small objects in segmentation.
- Option to within the preprocessing, use a dilated ROI.
- Otsu thresholding as mask for preprocessing.
- Memory for each fastr node is now in a dictionary of the WORC object and can
be easily changed.
- PyRadiomics now fully embedded and configurable.
- ComBat harmonization: currently as separate tool on full dataset,
not in cross-validation.
- Computation of ICC, and thresholding object to use ICC for feature selection.
- Added groupwise feature selection per feature extraction toolbox.
- Feature converter tool, to convert features from a toolbox to WORC compatible
format.
- RobustScaler for feature scaling.
- Decomposition to evaluate network.
- Combat: in WORK workflow.

Changed
~~~~~~~
- Resampling of objects is now after feature selection.
- Made plot_SVM function more memory efficient.
- For PCA, Relief, VarianceThreshold, and SelectFromModel feature selection,
you can now simply supply a float to determine the percentage of times
this method is used in the created workflows.
- Moved load_features from trainclassifier to file_io.
- Matching of PID from labels from label file to other objects is now all
converted to lower case.
- Refactoring of WORC network building.
- Segmentix tool is cleaned up. Segmentix script is moved to processing.

Fixed
~~~~~
- Order of methods in preprocessing function of SearchCV did not correspond
with that in fitandscore.
- Replace spaces in uri conversion of sources in SimpleWORC.
- Check whether all fitandscore jobs succeeded, otherwise throw error.
- Bug in PCA when n_components > min(n_samples, n_features)
- Random seed is now set and passed to PCA, Relief and all classifiers
for reproducability of the results.
- Evaluate can now also accept multiple feature toolboxes.

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Added
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- Some options for the plot_images slicer function.
- Validators to check your inputs before executing experiment.
- Timer in classification log.
- Backwards compatibility in fastr config.
- Option for fixed seed in cross-validation.
- BasicWORC Facade.
- Support for computing confidence intervals on differences between models.
- Error when config file cannot be found.

Changed
~~~~~~~
- Preprocessor slows down progress and is not always neccesary. Made it optional.
- Moved the preprocessor to the SearchCV script to do once on the training set,
not in within the algorithm optimization.
- Ensembling during training is turned-of, as it takes to much time. Only
used when plotting the performance.
- Debug flag includes fixed seed in cross-validation.
- Joblib now uses by default only 1 core and threading backend.

Fixed
~~~~~
- Bug in patient naming of plotting function: if ensembling was done in training,
do not re-ensemble.

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Added
~~~~~~~
- Support for Oncoradiomics RadiomiX tool
- Groupwise Search includes GLDZM, Fractal, location, NGTDM, NGLDM, wavelet,
and rgrd features
- SimpleWORC now also accepts features instead of images and segs as input
- Preprocessor object to preprocess the features before any fitting algorithms
are ran. Mostly to detect possible faults/errors in the data.

Changed
~~~~~~~
- On runtime, copy config.d file if it does not exist yet.

Fixed
~~~~~
- KNN imputation gave an error if >80% of the feature values were missing.
Added preprocessing function to remove these features.

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Added
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- Travis continuous integration for Windows.
- Removed RT Struct Reader, as it was buggy and not used.

Changed
~~~~~~~
- SimpleWORC now properly uses the fastr FileSystem plugin, instead
of supplying the absolute filepaths.

Fixed
~~~~~
- Under Windows, creation of the fastr home folder if it did not exist
did not work when using pip for installing. We now use a new feature
of fastr to simply add the WORC folder to the fastr config
at WORC import time.
- When debugging, override manual tempdir setting and always use default. On
Windows, Travis gives errors if the tempdir is not in a vfs mount.
- Use shutil.move in the datadownloader, as os.rename could not overwrite files.