Worc

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Added
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- Thresholding option in plot_SVM.
- NPV (Negative Preditive Value) to classification metrics.
- Facade for easier interaction with WORC.
- Thresholding option in plot_SVM.
- Function to create fixed splits for cross validation.
- n_splits parameter for train-test cross validation.
- Added generalization score.
- Parameter to choose how many of the optimal settings to save (maxlen).
- Option to combine multiple onevsrest models in plot_SVM.
- StatsticalTestThreshold feature selection for multilabel problems.
- Support for test sets in which only one class is present in various
plotting functions and the metrics.
- Installation: create fastr home if it does not exist yet.
- Boostrapping as performance evaluation in plot_SVM.
- Confidence intervals for boostrapping based on percentile.
- Catch for if patient is in the test set, but not the overall label set.
- Downloader for downloading example datasets.
- ReadTheDocs.yml for configuration of documentation.
- Unit test included in Travis.
- Various detectors.

Changed
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- Plot_SVR is removed: it's now embedded in plot_SVM.
- Moved statistical feature selection to last step in fit and score.
- Also the minimum train and validation score are now saved.
- Put scaler at top of fitandscore function.
- Make link in file conversion if output is same format as input.
- Sort keys in performance output JSON.
- VarianceThreshold features selection on by default.
- Removed grid_scores from SearchCV as support is dropped in sklearn > 0.20
- Renamed IntermediateFacade to SimpleWORC
- Use inspect to find packagedir

Fixed
~~~~~
- Metric computation can now handle it when both the truth and the predicted
labels are from a single class.
- Plotting module now correctly initialized.
- Plot_SVM now also works properly for regression.
- Masks for ROI normalization now properly added.
- Preprocessing: mask needed to be cast to binary.
- Failed workflows now return nan instead of zero for performance.
- Several bugs in multilabel performance evaluation
- Ring in segmentix was in sagital instead of axial direction.
- Added replacenan in features before applying SMOTE.
- Metadata test was not passed to calcfeatures: bugfix.
- Bugfix: overide labels in facade when predict_labels is called.
- Several bugfixes in the overrides in the facade configbuilder.
- Various print commands converted to Python3: .format prints were still
left and sometimes buggy.
- StatisticalTestFeatures and PlotRankedScores tools only accepted cardinality
of 1.
- Bugfixes in many plotting functions: opening files with 'w' instead of 'wb'
due to python3 conversion, Compatibility issues with plot_SVM due to
conversion.
- Except error when Grahpviz is not installed.
- Symlinking in worccastcovert not supported by Windows, reverted to copying.
- Bugfix in create_ensemble in SearchCV when using ensemble = 1.

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Added
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- Now ported to Python3.6+ (Python 2 is no longer supported!). Thereby also
to fastr3.
- Compatibility for Windows. Some small changes in functions, as some packages
behaviour differently under Windows. Also, adjusted sink and source paths
to use OS file separator.
- Config is now also a sink.


Changed
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- PCE and DTI node removed, as they were not open source.
- Pinfo file can now also be a csv. Txt is still supported.
- Use fastr as default for hyperparameter search parallelization instead
of Joblib, as this is much more flexible.
- When the conffidence interval cannot be computed, just use the mean.


Fixed
~~~~~
- WORC_config.py was not correctly copied in Windows due to incorrect path separation.
- Source creation for the config was only for Linux.
- In numpy 1.15>, booleans cannot be subtracted. Fixed an error due to this in
segmentix by using bitwise_xor instead.
- Bug when using masks, but not for all images, and segmentix.
- Cardinality of classify node was incorrect.

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Changed
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- PREDICT was updated, so had to update the requirements. Changed it
to a minimum of PREDICT to prevent these issues in the future.

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Added
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- Dummy workflow in segmentix and calcfeatures PREDICT tools.
- Added several new PREDICT parameters.
- Slicer tool.


Changed
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- Memory for elastix tool is now larger.

Fixed
~~~~~
-Evaluate framework now correctly adopts the name you give it.

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Added
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- Several new PREDICT variables to the config.
- Multilabel classification workflow.
- New oversampling strategy.
- RankedSVM multilabel classification and Relief feature selection.


Changed
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- Major reduction in memory usage, especially due to PREDICT updates.
- Only use first configuration in the classify config.
- Outputs are now in multiple subfolders instead of one big folder.


Fixed
~~~~~
- Minor bug in test workflow: needed str of label in appending to classify.
- There was a bug in using a .ini file as a config.

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Added
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- Feature imputation settings in WORC config.
- PCA settings in WORC config.
- Dummy file, which can generally be accepted by WORC.
- Preprocessing is now a separate node before the calcfeatures node.
- Started working on a RTStructReader tool.
- Added EditElastixTransformFile node to set FinalBSplineInterpolationOrder to 0
in Elastix. Neccesary for transforming segmentations.
- Registred image is also saved as a sink.
- Tex, Zip and PNG Datatypes
- Plot ROC tool for PREDICT
- Plot SVM tool for PREDICT
- Plot Barchart tool for PREDICT
- Plot Ranked Scores tool for PREDICT
- Plot statistical test tool for PREDICT
- Tools: Evaluation network. Can currently be run only serparately: future
work includes the optional addition of the Evaluate network to the WORC network.
- Settings for PREDICT General, which contains the joblib Parallel settings and
whether a temporary save will be made after each cross validation.


Changed
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- Separate sinks for the output segmentations of the elastix and segmentix
nodes.
- Switched from using PXCastConvert to WORCCastConvert, hence ITK is not
anymore required as well as ITK tools.

Fixed
~~~~~
- Patientclass ID was used for both test and training. Now given separate names.
- When elastix is used but segmentix isn't, there was a bug.
- DataFile dataype is now a TypeGroup instead of an URLType.
- Last transformation output from elastix is passed further to the network.
- Set FinalBSplineInterpolationOrder to 0 before transforming segmentation with
transformix.
- Bug: when giving multiple feature sources, only the first was used.